Sol-gel type synthesis of Bi.sub.2 (Sr,Ta.sub.2)O.sub.9 using an acetate based system

DOEpatents

Boyle, Timothy J.

1997-01-01

A method of forming a layered-perovskite bismuth-strontium-tantalum oxide (SBT) ferroelectric material is performed by dissolving a bismuth compound in a first solvent to form a first solution, mixing a strontium compound and a tantalum compound to form a binary mixture, dissolving the binary mixture in a second solvent to form a second solution, mixing the first solution with the second solution to form a SBT precursor solution, evaporating the first and second solvents to form a SBT precursor material and subsequently sintering said SBT precursor material in the presence of oxygen.

Sol-gel type synthesis of Bi{sub 2}(Sr,Ta{sub 2})O{sub 9} using an acetate based system

DOEpatents

Boyle, T.J.

1997-11-04

A method of forming a layered-perovskite bismuth-strontium-tantalum oxide (SBT) ferroelectric material is performed by dissolving a bismuth compound in a first solvent to form a first solution, mixing a strontium compound and a tantalum compound to form a binary mixture, dissolving the binary mixture in a second solvent to form a second solution, mixing the first solution with the second solution to form a SBT precursor solution, evaporating the first and second solvents to form a SBT precursor material and subsequently sintering said SBT precursor material in the presence of oxygen. 6 figs.

Use of PCR with Sequence-specific Primers for High-Resolution Human Leukocyte Antigen Typing of Patients with Narcolepsy

PubMed Central

Woo, Hye In; Joo, Eun Yeon; Lee, Kyung Wha

2012-01-01

Background Narcolepsy is a neurologic disorder characterized by excessive daytime sleepiness, symptoms of abnormal rapid eye movement (REM) sleep, and a strong association with HLA-DRB1*1501, -DQA1*0102, and -DQB1*0602. Here, we investigated the clinico-physical characteristics of Korean patients with narcolepsy, their HLA types, and the clinical utility of high-resolution PCR with sequence-specific primers (PCR-SSP) as a simple typing method for identifying DRB1*15/16, DQA1, and DQB1 alleles. Methods The study population consisted of 67 consecutively enrolled patients having unexplained daytime sleepiness and diagnosed narcolepsy based on clinical and neurological findings. Clinical data and the results of the multiple sleep latency test and polysomnography were reviewed, and HLA typing was performed using both high-resolution PCR-SSP and sequence-based typing (SBT). Results The 44 narcolepsy patients with cataplexy displayed significantly higher frequencies of DRB1*1501 (Pc= 0.003), DQA1*0102 (Pc=0.001), and DQB1*0602 (Pc=0.014) than the patients without cataplexy. Among patients carrying DRB1*1501-DQB1*0602 or DQA1*0102, the frequencies of a mean REM sleep latency of less than 20 min in nocturnal polysomnography and clinical findings, including sleep paralysis and hypnagogic hallucination were significantly higher. SBT and PCR-SSP showed 100% concordance for high-resolution typing of DRB1*15/16 alleles and DQA1 and DQB1 loci. Conclusions The clinical characteristics and somnographic findings of narcolepsy patients were associated with specific HLA alleles, including DRB1*1501, DQA1*0102, and DQB1*0602. Application of high-resolution PCR-SSP, a reliable and simple method, for both allele- and locus-specific HLA typing of DRB1*15/16, DQA1, and DQB1 would be useful for characterizing clinical status among subjects with narcolepsy. PMID:22259780

The great diversity of major histocompatibility complex class II genes in Philippine native cattle

PubMed Central

Takeshima, S.N.; Miyasaka, T.; Polat, M.; Kikuya, M.; Matsumoto, Y.; Mingala, C.N.; Villanueva, M.A.; Salces, A.J.; Onuma, M.; Aida, Y.

2014-01-01

Bovine leukocyte antigens (BoLA) are extensively used as markers for bovine disease and immunological traits. However, none of the BoLA genes in Southeast Asian breeds have been characterized by polymerase chain reaction (PCR)-sequence-based typing (SBT). Therefore, we sequenced exon 2 of the BoLA class II DRB3 gene from 1120 individual cows belonging to the Holstein, Sahiwal, Simbrah, Jersey, Brahman, and Philippine native breeds using PCR-SBT. Several cross-breeds were also examined. BoLA-DRB3 PCR-SBT identified 78 previously reported alleles and five novel alleles. The number of BoLA-DRB3 alleles identified in each breed from the Philippines was higher (71 in Philippine native cattle, 58 in Brahman, 46 in Holstein × Sahiwal, and 57 in Philippine native × Brahman) than that identified in breeds from other countries (e.g., 23 alleles in Japanese Black and 35 in Bolivian Yacumeño cattle). A phylogenetic tree based on the DA distance calculated from the BoLA-DRB3 allele frequency showed that Philippine native cattle from different Philippine islands are closely related, and all of them are closely similar to Philippine Brahman cattle but not to native Japanese and Latin American breeds. Furthermore, the BoLA-DRB3 allele frequency in Philippine native cattle from Luzon Island, located in the Northern Philippines was different from that in cattle from Iloilo, Bohol, and Leyte Islands, which are located in the Southern Philippines. Therefore, we conclude that Philippine native cattle can be divided into two populations, North and South areas. Moreover, a neutrality test revealed that Philippine native cattle from Leyte showed significantly greater genetic diversity, which may be maintained by balancing selection. This study shows that Asian breeds have high levels of BoLA-DRB3 polymorphism. This finding, especially the identification of five novel BoLA-DRB3 alleles, will be helpful for future SBT studies of BoLA-DRB3 alleles in East Asian cattle. PMID:25606401

Model-based classification of CPT data and automated lithostratigraphic mapping for high-resolution characterization of a heterogeneous sedimentary aquifer

PubMed Central

Mallants, Dirk; Batelaan, Okke; Gedeon, Matej; Huysmans, Marijke; Dassargues, Alain

2017-01-01

Cone penetration testing (CPT) is one of the most efficient and versatile methods currently available for geotechnical, lithostratigraphic and hydrogeological site characterization. Currently available methods for soil behaviour type classification (SBT) of CPT data however have severe limitations, often restricting their application to a local scale. For parameterization of regional groundwater flow or geotechnical models, and delineation of regional hydro- or lithostratigraphy, regional SBT classification would be very useful. This paper investigates the use of model-based clustering for SBT classification, and the influence of different clustering approaches on the properties and spatial distribution of the obtained soil classes. We additionally propose a methodology for automated lithostratigraphic mapping of regionally occurring sedimentary units using SBT classification. The methodology is applied to a large CPT dataset, covering a groundwater basin of ~60 km2 with predominantly unconsolidated sandy sediments in northern Belgium. Results show that the model-based approach is superior in detecting the true lithological classes when compared to more frequently applied unsupervised classification approaches or literature classification diagrams. We demonstrate that automated mapping of lithostratigraphic units using advanced SBT classification techniques can provide a large gain in efficiency, compared to more time-consuming manual approaches and yields at least equally accurate results. PMID:28467468

Model-based classification of CPT data and automated lithostratigraphic mapping for high-resolution characterization of a heterogeneous sedimentary aquifer.

PubMed

Rogiers, Bart; Mallants, Dirk; Batelaan, Okke; Gedeon, Matej; Huysmans, Marijke; Dassargues, Alain

2017-01-01

Cone penetration testing (CPT) is one of the most efficient and versatile methods currently available for geotechnical, lithostratigraphic and hydrogeological site characterization. Currently available methods for soil behaviour type classification (SBT) of CPT data however have severe limitations, often restricting their application to a local scale. For parameterization of regional groundwater flow or geotechnical models, and delineation of regional hydro- or lithostratigraphy, regional SBT classification would be very useful. This paper investigates the use of model-based clustering for SBT classification, and the influence of different clustering approaches on the properties and spatial distribution of the obtained soil classes. We additionally propose a methodology for automated lithostratigraphic mapping of regionally occurring sedimentary units using SBT classification. The methodology is applied to a large CPT dataset, covering a groundwater basin of ~60 km2 with predominantly unconsolidated sandy sediments in northern Belgium. Results show that the model-based approach is superior in detecting the true lithological classes when compared to more frequently applied unsupervised classification approaches or literature classification diagrams. We demonstrate that automated mapping of lithostratigraphic units using advanced SBT classification techniques can provide a large gain in efficiency, compared to more time-consuming manual approaches and yields at least equally accurate results.

Measuring Ambiguity in HLA Typing Methods

PubMed Central

Madbouly, Abeer; Freeman, John; Maiers, Martin

2012-01-01

In hematopoietic stem cell transplantation, donor selection is based primarily on matching donor and patient HLA genes. These genes are highly polymorphic and their typing can result in exact allele assignment at each gene (the resolution at which patients and donors are matched), but it can also result in a set of ambiguous assignments, depending on the typing methodology used. To facilitate rapid identification of matched donors, registries employ statistical algorithms to infer HLA alleles from ambiguous genotypes. Linkage disequilibrium information encapsulated in haplotype frequencies is used to facilitate prediction of the most likely haplotype assignment. An HLA typing with less ambiguity produces fewer high-probability haplotypes and a more reliable prediction. We estimated ambiguity for several HLA typing methods across four continental populations using an information theory-based measure, Shannon's entropy. We used allele and haplotype frequencies to calculate entropy for different sets of 1,000 subjects with simulated HLA typing. Using allele frequencies we calculated an average entropy in Caucasians of 1.65 for serology, 1.06 for allele family level, 0.49 for a 2002-era SSO kit, and 0.076 for single-pass SBT. When using haplotype frequencies in entropy calculations, we found average entropies of 0.72 for serology, 0.73 for allele family level, 0.05 for SSO, and 0.002 for single-pass SBT. Application of haplotype frequencies further reduces HLA typing ambiguity. We also estimated expected confirmatory typing mismatch rates for simulated subjects. In a hypothetical registry with all donors typed using the same method, the entropy values based on haplotype frequencies correspond to confirmatory typing mismatch rates of 1.31% for SSO versus only 0.08% for SBT. Intermediate-resolution single-pass SBT contains the least ambiguity of the methods we evaluated and therefore the most certainty in allele prediction. The presented measure objectively evaluates HLA typing methods and can help define acceptable HLA typing for donor recruitment. PMID:22952712

High Prevalence, Genetic Diversity and Intracellular Growth Ability of Legionella in Hot Spring Environments

PubMed Central

Zhou, Haijian; Wang, Huanxin; Xu, Ying; Zhao, Mingqiang; Guan, Hong; Li, Machao; Shao, Zhujun

2013-01-01

Background Legionella is the causative agent of Legionnaires' disease, and hot springs are a major source of outbreaks of this disease. It is important from a public health perspective to survey hot spring environments for the presence of Legionella. Methods Prospective surveillance of the extent of Legionella pollution was conducted at three hot spring recreational areas in Beijing, China in 2011. Pulsed-field gel electrophoresis (PFGE) and sequence-based typing (SBT) were used to describe the genetic polymorphism of isolates. The intracellular growth ability of the isolates was determined by interacting with J774 cells and plating the dilutions onto BCYE agar plates. Results Overall, 51.9% of spring water samples showed Legionella-positive, and their concentrations ranged from 1 CFU/liter to 2,218 CFU/liter. The positive rates of Legionella were significantly associated with a free chlorine concentration of ≥0.2 mg/L, urea concentration of ≥0.05 mg/L, total microbial counts of ≥400 CFU/ml and total coliform of ≥3 MPN/L (p<0.01). The Legionella concentrations were significantly associated with sample temperature, pH, total microbial counts and total coliform (p<0.01). Legionella pneumophila was the most frequently isolated species (98.9%), and the isolated serogroups included serogroups 3 (25.3%), 6 (23.4%), 5 (19.2%), 1 (18.5%), 2 (10.2%), 8 (0.4%), 10 (0.8%), 9 (1.9%) and 12 (0.4%). Two hundred and twenty-eight isolates were analyzed by PFGE and 62 different patterns were obtained. Fifty-seven L. pneumophila isolates were selected for SBT analysis and divided into 35 different sequence types with 5 main clonal groups. All the 57 isolates had high intracellular growth ability. Conclusions Our results demonstrated high prevalence and genetic polymorphism of Legionella in springs in Beijing, China, and the SBT and intracellular growth assay results suggested that the Legionella isolates of hot spring environments were pathogenic. Improved control and prevention strategies are urgently needed. PMID:23527075

Mucosal Proliferations in Completely Examined Fallopian Tubes Accompanying Ovarian Low-grade Serous Tumors: Neoplastic Precursor Lesions or Normal Variants of Benign Mucosa?

PubMed

Wolsky, Rebecca J; Price, Matt A; Zaloudek, Charles J; Rabban, Joseph T

2018-05-01

Malignant transformation of the fallopian tube mucosa, followed by exfoliation of malignant cells onto ovarian and/or peritoneal surfaces, has been implicated as the origin of most pelvic high-grade serous carcinoma. Whether a parallel pathway exists for pelvic low-grade serous tumors [ovarian serous borderline tumor (SBT) and low-grade serous carcinoma (LGSC)] remains to be fully elucidated. The literature is challenging to interpret due to variation in the diagnostic criteria and terminology for cytologically low-grade proliferations of the fallopian tube mucosa, as well as variation in fallopian tube specimen sampling. Recently, a candidate fallopian tube precursor to ovarian SBT, so-called papillary tubal hyperplasia, was described in advanced stage patients. The current study was designed to identify fallopian tube mucosal proliferations unique to patients with low-grade serous ovarian tumors (serous cystadenoma, SBT, LGSC) and to determine if they may represent precursors to the ovarian tumors. Fallopian tubes were thinly sliced and entirely examined microscopically, including all of the fimbriated and nonfimbriated portions of the tubes, from patients with ovarian serous cystadenoma (35), SBT (61), and LGSC (11) and from a control population of patients with ovarian mucinous cystadenoma (28), mature cystic teratoma (18) or uterine leiomyoma (14). The slides of the fallopian tubes were examined in randomized order, without knowledge of the clinical history or findings in the ovaries or other organs. Alterations of the mucosa of the fallopian tube were classified as type 1: nonpapillary proliferation of cytologically bland tubal epithelium exhibiting crowding, stratification, and/or tufting without papillary fibrovascular cores or as type 2: papillary alterations consisting of a fibrovascular core lined by a cytologically bland layer of tubal epithelium. A third abnormality, type 3, consisted of detached intraluminal papillae, buds, or nests of epithelium that cytologically resembled the epithelial component of SBT or LGSC. Mucosal proliferations were identified in subsets of all populations, including the control populations. Overall, type 1 proliferations were in 28% to 61% of all patients and type 2 alterations in 4% to 16%. There was no statistically significant difference in the incidence of type 1 or type 2 proliferations between the class of ovarian serous tumors (benign, SBT, LGSC), between early and advanced stage SBT, or between patients with any ovarian serous tumor and the control population of nonserous diagnoses. Type 3 alterations were only identified in patients with advanced stage SBT/LGSC and not in any early stage SBT or cystadenoma. These findings suggest that type 3 alterations floating in the fallopian tube lumen represent exfoliation of tumor cells from ovarian and/or peritoneal origin. Our study did not identify a mucosal-based proliferation of the fallopian tubes that was specific to ovarian low-grade serous tumors. Cytologically bland mucosal proliferations appear to be common in fallopian tubes from patients of all ages and unrelated to ovarian tumorigenesis. A consensus on diagnostic criteria and terminology for these types of proliferations is needed, as well as further study into their etiology, including possible association with hormonal environment.

A novel subtilase inhibitor in plants shows structural and functional similarities to protease propeptides.

PubMed

Hohl, Mathias; Stintzi, Annick; Schaller, Andreas

2017-04-14

The propeptides of subtilisin-like serine proteinases (subtilases, SBTs) serve dual functions as intramolecular chaperones that are required for enzyme folding and as inhibitors of the mature proteases. SBT propeptides are homologous to the I9 family of protease inhibitors that have only been described in fungi. Here we report the identification and characterization of subtilisin propeptide-like inhibitor 1 (SPI-1) from Arabidopsis thaliana Sequence similarity and the shared β-α-β-β-α-β core structure identified SPI-1 as a member of the I9 inhibitor family and as the first independent I9 inhibitor in higher eukaryotes. SPI-1 was characterized as a high-affinity, tight-binding inhibitor of Arabidopsis subtilase SBT4.13 with K d and K i values in the picomolar range. SPI-1 acted as a stable inhibitor of SBT4.13 over the physiologically relevant range of pH, and its inhibitory profile included many other SBTs from plants but not bovine chymotrypsin or bacterial subtilisin A. Upon binding to SBT4.13, the C-terminal extension of SPI-1 was proteolytically cleaved. The last four amino acids at the newly formed C terminus of SPI-1 matched both the cleavage specificity of SBT4.13 and the consensus sequence of Arabidopsis SBTs at the junction of the propeptide with the catalytic domain. The data suggest that the C terminus of SPI-1 acts as a competitive inhibitor of target proteases as it remains bound to the active site in a product-like manner. SPI-1 thus resembles SBT propeptides with respect to its mode of protease inhibition. However, in contrast to SBT propeptides, SPI-1 could not substitute as a folding assistant for SBT4.13. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Distribution of monoclonal antibody subgroups and sequence-based types among Legionella pneumophila serogroup 1 isolates derived from cooling tower water, bathwater, and soil in Japan.

PubMed

Amemura-Maekawa, Junko; Kikukawa, Kiyomi; Helbig, Jürgen H; Kaneko, Satoko; Suzuki-Hashimoto, Atsuko; Furuhata, Katsunori; Chang, Bin; Murai, Miyo; Ichinose, Masayuki; Ohnishi, Makoto; Kura, Fumiaki

2012-06-01

Legionella pneumophila serogroup (SG) 1 is the most frequent cause of legionellosis. This study analyzed environmental isolates of L. pneumophila SG 1 in Japan using monoclonal antibody (MAb) typing and sequence-based typing (SBT). Samples were analyzed from bathwater (BW; n = 50), cooling tower water (CT; n = 50), and soil (SO; n = 35). The distribution of MAb types varied by source, with the most prevalent types being Bellingham (42%), Oxford (72%), and OLDA (51%) in BW, CT, and SO, respectively. The ratios of MAb 3/1 positive isolates were 26, 2, and 14% from BW, CT, and SO, respectively. The environmental isolates from BW, CT, and SO were divided into 34 sequence types (STs; index of discrimination [IOD] = 0.973), 8 STs (IOD = 0.448), and 11 STs (IOD = 0.879), respectively. Genetic variation among CT isolates was smaller than seen in BW and SO. ST1 accounted for 74% of the CT isolates. The only common STs between (i) BW and CT, (ii) BW and SO, and (iii) CT and SO were ST1, ST129, and ST48, respectively, suggesting that each environment constitutes an independent habitat.

Culturable microbiota of ranched southern bluefin tuna (Thunnus maccoyii Castelnau).

PubMed

Valdenegro-Vega, V; Naeem, S; Carson, J; Bowman, J P; Tejedor del Real, J L; Nowak, B

2013-10-01

The Australian tuna industry is based on the ranching of wild southern bluefin tuna (SBT, Thunnus maccoyii). Within this industry, only opportunistic pathogens have been reported infecting external wounds of fish. This study aimed to identify different culturable bacteria present in three cohorts of SBT and to determine normal bacteria and potential pathogens in isolates from harvest fish and moribund/dead fish. Post-mortem changes in the microbiota were also studied. Moribund/dead showed a greater proportion of members from the family Vibrionaceae than harvested fish; the latter presented mainly non-Vibrio species. In harvested fish spleens, Vibrio splendidus I complex was the most commonly identified group among Vibrio isolates, while most groups from the family Vibrionaceae were isolated from gills. For moribund/dead, Vibrio chagasii and Photobacterium damselae subsp. damselae were common in gill, spleen and kidney samples. Non-Vibrio isolates from gills were characterized using 16S rRNA sequencing as Flavobacteriaceae and classes Gammaproteobacteria and Alphaproteobacteria, mainly from the genera Winogradskyella and Tenacibaculum. Post-mortem changes showed dynamic shifts in bacterial dominance in gills, with Vibrionaceae and non-Vibrio spp. found in similar proportions initially and types related to Pseudoalteromonas ruthenica prevailing after 27 h. Spleen samples showed little bacterial growth until 5 h post-mortem, while various Vibrio-associated species were isolated 27 h post-mortem. Bacterial isolates found include a range of potentially pathogenic bacteria that should be monitored though most of them have yet to be associated with disease in tuna. This study forms a foundation for future research into the bacterial population dynamics under different culture conditions of SBT. An understanding of the bacterial compositions in SBT is necessary to evaluate the effects of some bacterial species on their health. © 2013 The Society for Applied Microbiology.

Phase transition sequence in ferroelectric Aurivillius compounds investigated by single crystal X-ray diffraction

NASA Astrophysics Data System (ADS)

Boullay, P.; Tellier, J.; Mercurio, D.; Manier, M.; Zuñiga, F. J.; Perez-Mato, J. M.

2012-09-01

The investigation of the phase transition sequence in SrBi2Ta2O9 (SBT) and SrBi2Nb2O9 (SBN) is reported using single-crystal X-ray diffraction. By monitoring specific reflections as a function of temperature, sensitive either to the superstructure formation or to polar displacements, it was possible to check the existence or not of an intermediate phase. This latter was confirmed in SBT, but within experimental accuracy could not be detected in SBN.

High prevalence of the PER-1 gene among carbapenem-resistant Acinetobacter baumannii in Riyadh, Saudi Arabia.

PubMed

Aly, M M; Abu Alsoud, N M; Elrobh, M S; Al Johani, S M; Balkhy, H H

2016-11-01

The prevalence of carbapenem-resistant Acinetobacter baumannii in Saudi Arabia and their resistance genetic mechanisms are yet to be identified. We studied the prevalence and genetic diversity of extended-spectrum beta-lactamase genes, particularly the PER-1 gene, among carbapenem-resistant A. baumannii strains from patients at a tertiary care hospital in Riyadh, Saudi Arabia between 2006 and 2014. Fresh subcultured samples were tested for antimicrobial susceptibility minimum inhibitory concentration (MIC). Total genomic DNA was extracted from each isolate and further used for polymerase chain reaction (PCR) genotyping, sequence-based typing (SBT) of PER-1 and OXA-51-like gene, and multilocus sequence typing (MLST) of positive isolates. Randomly selected clinical isolates (n = 100) were subjected to MLST. A total of 503 isolates were characterized as multidrug-resistant (MDR) using the MIC. Isolates were further PCR tested for bla -TEM and bla -PER-1 resistance genes (n = 503). The genotyping results showed that 68/503 (14 %) isolates were positive to bla TEM. The genotyping results of PER-1-like genes showed that 384/503 (76.3 %) were positive among MDR Acinetobacter isolates. Based on SBT, the majority of these isolates were clustered into three main groups including isolates harboring PER-1: AB11 (bla -PER-1 ), isolate AB16 (bla -PER-1 ), and, finally, the plasmid pAB154 (bla -PER-7 ). Remarkably, many isolates were concealing the PER-1 gene and harboring the TEM resistance genes as well. MLST results for selected isolates (n = 100) identified four main sequence types (STs: 2, 19, 20, and 25) and four novel isolates (ST 486-489). We report 76.3 % prevalence of the PER-1 resistance gene among Acinetobacter clinical isolates from Riyadh, Saudi Arabia. Further work is needed to explore the clinical risks and patient outcome with such resistance related to healthcare-associated infections and investigate the genetic and molecular mechanisms that confer the MDR phenotype.

Smart device-based testing for medical students in Korea: satisfaction, convenience, and advantages.

PubMed

Lim, Eun Young; Yim, Mi Kyoung; Huh, Sun

2017-01-01

The aim of this study was to investigate respondents' satisfaction with smart device-based testing (SBT), as well as its convenience and advantages, in order to improve its implementation. The survey was conducted among 108 junior medical students at Kyungpook National University School of Medicine, Korea, who took a practice licensing examination using SBT in September 2015. The survey contained 28 items scored using a 5-point Likert scale. The items were divided into the following three categories: satisfaction with SBT administration, convenience of SBT features, and advantages of SBT compared to paper-and-pencil testing or computer-based testing. The reliability of the survey was 0.95. Of the three categories, the convenience of the SBT features received the highest mean (M) score (M= 3.75, standard deviation [SD]= 0.69), while the category of satisfaction with SBT received the lowest (M= 3.13, SD= 1.07). No statistically significant differences across these categories with respect to sex, age, or experience were observed. These results indicate that SBT was practical and effective to take and to administer.

Distribution of Monoclonal Antibody Subgroups and Sequence-Based Types among Legionella pneumophila Serogroup 1 Isolates Derived from Cooling Tower Water, Bathwater, and Soil in Japan

PubMed Central

Kikukawa, Kiyomi; Helbig, Jürgen H.; Kaneko, Satoko; Suzuki-Hashimoto, Atsuko; Furuhata, Katsunori; Chang, Bin; Murai, Miyo; Ichinose, Masayuki; Ohnishi, Makoto; Kura, Fumiaki

2012-01-01

Legionella pneumophila serogroup (SG) 1 is the most frequent cause of legionellosis. This study analyzed environmental isolates of L. pneumophila SG 1 in Japan using monoclonal antibody (MAb) typing and sequence-based typing (SBT). Samples were analyzed from bathwater (BW; n = 50), cooling tower water (CT; n = 50), and soil (SO; n = 35). The distribution of MAb types varied by source, with the most prevalent types being Bellingham (42%), Oxford (72%), and OLDA (51%) in BW, CT, and SO, respectively. The ratios of MAb 3/1 positive isolates were 26, 2, and 14% from BW, CT, and SO, respectively. The environmental isolates from BW, CT, and SO were divided into 34 sequence types (STs; index of discrimination [IOD] = 0.973), 8 STs (IOD = 0.448), and 11 STs (IOD = 0.879), respectively. Genetic variation among CT isolates was smaller than seen in BW and SO. ST1 accounted for 74% of the CT isolates. The only common STs between (i) BW and CT, (ii) BW and SO, and (iii) CT and SO were ST1, ST129, and ST48, respectively, suggesting that each environment constitutes an independent habitat. PMID:22492442

HLA genes in Madeira Island (Portugal) inferred from sequence-based typing: footprints from different origins.

PubMed

Spínola, Hélder; Bruges-Armas, Jácome; Mora, Marian Gantes; Middleton, Derek; Brehm, António

2006-04-01

Human leukocyte antigen (HLA)-A, HLA-B, and HLA-DRB1 polymorphisms were examined in Madeira Island populations. The data was obtained at high-resolution level, using sequence-based typing (SBT). The most frequent alleles at each loci were: A*020101 (24.6%), B*5101 (9.7%), B*440201 (9.2%), and DRB1*070101 (15.7%). The predominant three-loci haplotypes in Madeira were A*020101-B*510101-DRB1*130101 (2.7%) and A*010101-B*0801-DRB1*030101 (2.4%), previously found in north and central Portugal. The present study corroborates historical sources and other genetic studies that say Madeira were populated not only by Europeans, mostly Portuguese, but also sub-Saharan Africans due to slave trade. Comparison with other populations shows that Madeira experienced a stronger African influence due to slave trade than Portugal mainland and even the Azores archipelago. Despite this African genetic input, haplotype and allele frequencies were predominantly from European origin, mostly common to mainland Portugal.

Prevalence and Molecular Characteristics of Waterborne Pathogen Legionella in Industrial Cooling Tower Environments

PubMed Central

Li, Lijie; Qin, Tian; Li, Yun; Zhou, Haijian; Song, Hongmei; Ren, Hongyu; Li, Liping; Li, Yongguang; Zhao, Dong

2015-01-01

Cooling towers are a source of Legionnaires’ disease. It is important from a public health perspective to survey industrial cooling towers for the presence of Legionella. Prospective surveillance of the extent of Legionella pollution was conducted at factories in Shijiazhuang, China between March 2011 and September 2012. Overall, 35.7% of 255 industrial cooling tower water samples showed Legionella-positive, and their concentrations ranged from 100 Colony-Forming Units (CFU)/liter to 88,000 CFU/liter, with an average concentration of 9100 CFU/liter. A total of 121 isolates were obtained. All isolates were L. pneumophila, and the isolated serogroups included serogroups 1 (68 isolates, 56.2%), 6 (25, 20.7%), 5 (12, 9.9%), 8 (8, 6.6%), 3 (6, 5.0%) and 9 (2, 1.6%). All 121 isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and 64 different patterns were obtained. All 121 isolates were analyzed sequence-based typing (SBT), a full 7-allele profile was obtained from 117 isolates. One hundred and seventeen isolates were divided into 49 sequence types. Two virulence genes, lvh and rtxA, are analyzed by polymerase chain reaction (PCR). 92.6% (112/121) and 98.3% (119/121) isolates carried lvh and rtxA respectively and 90.9% (110/121) of tested isolates carried both genes. Our results demonstrated high prevalence and genetic polymorphism of L. pneumophila in industrial cooling tower environments in Shijiazhang, China, and the SBT and virulence gene PCR results suggested that the isolates were pathogenic. Improved control and prevention strategies are urgently needed. PMID:26473896

Prevalence and Molecular Characteristics of Waterborne Pathogen Legionella in Industrial Cooling Tower Environments.

PubMed

Li, Lijie; Qin, Tian; Li, Yun; Zhou, Haijian; Song, Hongmei; Ren, Hongyu; Li, Liping; Li, Yongguang; Zhao, Dong

2015-10-12

Cooling towers are a source of Legionnaires' disease. It is important from a public health perspective to survey industrial cooling towers for the presence of Legionella. Prospective surveillance of the extent of Legionella pollution was conducted at factories in Shijiazhuang, China between March 2011 and September 2012. Overall, 35.7% of 255 industrial cooling tower water samples showed Legionella-positive, and their concentrations ranged from 100 Colony-Forming Units (CFU)/liter to 88,000 CFU/liter, with an average concentration of 9100 CFU/liter. A total of 121 isolates were obtained. All isolates were L. pneumophila, and the isolated serogroups included serogroups 1 (68 isolates, 56.2%), 6 (25, 20.7%), 5 (12, 9.9%), 8 (8, 6.6%), 3 (6, 5.0%) and 9 (2, 1.6%). All 121 isolates were analyzed by pulsed-field gel electrophoresis (PFGE) and 64 different patterns were obtained. All 121 isolates were analyzed sequence-based typing (SBT), a full 7-allele profile was obtained from 117 isolates. One hundred and seventeen isolates were divided into 49 sequence types. Two virulence genes, lvh and rtxA, are analyzed by polymerase chain reaction (PCR). 92.6% (112/121) and 98.3% (119/121) isolates carried lvh and rtxA respectively and 90.9% (110/121) of tested isolates carried both genes. Our results demonstrated high prevalence and genetic polymorphism of L. pneumophila in industrial cooling tower environments in Shijiazhang, China, and the SBT and virulence gene PCR results suggested that the isolates were pathogenic. Improved control and prevention strategies are urgently needed.

A case of pneumonia caused by Legionella pneumophila serogroup 12 and treated successfully with imipenem.

PubMed

Nishizuka, Midori; Suzuki, Hiroki; Ara, Tomoka; Watanabe, Mari; Morita, Mami; Sato, Chisa; Tsuchida, Fumihiro; Seto, Junji; Amemura-Maekawa, Junko; Kura, Fumiaki; Takeda, Hiroaki

2014-06-01

The patient was an 83-year-old man hospitalized for Haemophilus influenzae pneumonia, who developed recurrent pneumonia after improvement of the initial episode. Legionella pneumophila serogroup 12 was isolated from the sputum, accompanied by increased serum antibody titers to L. pneumophila serogroup 12. Therefore, the patient was diagnosed as having Legionella pneumonia caused by L. pneumophila serogroup 12. Case reports of pneumonia caused by L. pneumophila serogroup 12 are rare, and the case described herein is the first report of clinical isolation of this organism in Japan. When the genotype was determined by the protocol of The European Working Group for Legionella Infections (Sequence-Based Typing [SBT] for epidemiological typing of L. pneumophila, Version 3.1), the sequence type was ST68. Imipenem/cilastatin therapy was found to be effective for the treatment of Legionella pneumonia in this patient. Copyright © 2014 Japanese Society of Chemotherapy and The Japanese Association for Infection Disease. Published by Elsevier Ltd. All rights reserved.

An Extracellular Subtilase Switch for Immune Priming in Arabidopsis

PubMed Central

Mauch-Mani, Brigitte; Gil, Ma José; Vera, Pablo

2013-01-01

In higher eukaryotes, induced resistance associates with acquisition of a priming state of the cells for a more effective activation of innate immunity; however, the nature of the components for mounting this type of immunological memory is not well known. We identified an extracellular subtilase from Arabidopsis, SBT3.3, the overexpression of which enhances innate immune responses while the loss of function compromises them. SBT3.3 expression initiates a durable autoinduction mechanism that promotes chromatin remodeling and activates a salicylic acid(SA)-dependent mechanism of priming of defense genes for amplified response. Moreover, SBT3.3 expression-sensitized plants for enhanced expression of the OXI1 kinase gene and activation of MAP kinases following pathogen attack, providing additional clues for the regulation of immune priming by SBT3.3. Conversely, in sbt3.3 mutant plants pathogen-mediated induction of SA-related defense gene expression is drastically reduced and activation of MAP kinases inhibited. Moreover, chromatin remodeling of defense-related genes normally associated with activation of an immune priming response appear inhibited in sbt3.3 plants, further indicating the importance of the extracellular SBT3.3 subtilase in the establishment of immune priming. Our results also point to an epigenetic control in the regulation of plant immunity, since SBT3.3 is up-regulated and priming activated when epigenetic control is impeded. SBT3.3 represents a new regulator of primed immunity. PMID:23818851

An extracellular subtilase switch for immune priming in Arabidopsis.

PubMed

Ramírez, Vicente; López, Ana; Mauch-Mani, Brigitte; Gil, Ma José; Vera, Pablo

2013-01-01

In higher eukaryotes, induced resistance associates with acquisition of a priming state of the cells for a more effective activation of innate immunity; however, the nature of the components for mounting this type of immunological memory is not well known. We identified an extracellular subtilase from Arabidopsis, SBT3.3, the overexpression of which enhances innate immune responses while the loss of function compromises them. SBT3.3 expression initiates a durable autoinduction mechanism that promotes chromatin remodeling and activates a salicylic acid(SA)-dependent mechanism of priming of defense genes for amplified response. Moreover, SBT3.3 expression-sensitized plants for enhanced expression of the OXI1 kinase gene and activation of MAP kinases following pathogen attack, providing additional clues for the regulation of immune priming by SBT3.3. Conversely, in sbt3.3 mutant plants pathogen-mediated induction of SA-related defense gene expression is drastically reduced and activation of MAP kinases inhibited. Moreover, chromatin remodeling of defense-related genes normally associated with activation of an immune priming response appear inhibited in sbt3.3 plants, further indicating the importance of the extracellular SBT3.3 subtilase in the establishment of immune priming. Our results also point to an epigenetic control in the regulation of plant immunity, since SBT3.3 is up-regulated and priming activated when epigenetic control is impeded. SBT3.3 represents a new regulator of primed immunity.

Small Bowel Transit and Altered Gut Microbiota in Patients With Liver Cirrhosis.

PubMed

Liu, Yang; Jin, Ye; Li, Jun; Zhao, Lei; Li, Zhengtian; Xu, Jun; Zhao, Fuya; Feng, Jing; Chen, Huinan; Fang, Chengyuan; Shilpakar, Rojina; Wei, Yunwei

2018-01-01

Disturbance of the gut microbiota is common in liver cirrhosis (LC) patients, the underlying mechanisms of which are yet to be unfolded. This study aims to explore the relationship between small bowel transit (SBT) and gut microbiota in LC patients. Cross-sectional design was applied with 36 LC patients and 20 healthy controls (HCs). The gut microbiota was characterized by 16S rRNA gene sequencing. The Firmicutes/Bacteroidetes (F/B) ratio and the Microbial Dysbiosis index (MDI) were used to evaluate the severity of microbiota dysbiosis. The scintigraphy method was performed in patients to describe the objective values of SBT. Patients were then subdivided according to the Child-Pugh score (threshold = 5) or SBT value (threshold = 0.6) for microbiota analysis. LC patients were characterized by an altered gut microbiota; F/B ratios and MDI were higher than HC in both Child_5 (14.00 ± 14.69 vs. 2.86 ± 0.99, p < 0.01; 0.49 ± 0.80 vs. -0.47 ± 0.69, p < 0.01) and Child_5+ (15.81 ± 15.11 vs. 2.86±0.99, p < 0.01; 1.11 ± 1.05 vs. -0.47 ± 0.69, p < 0.01) sub-groups in patients. Difference in the gut microbiota between Child_ 5 and Child_5+ patients was inappreciable, but the SBT was relatively slower in Child_5+ patients (43 ± 26% vs. 80 ± 15%, p < 0.05). Compared with the Child-Pugh score indicators, SBT showed stronger associations with bacterial genera. A clear difference in the gut microbiota was observed between SBT_0.6- and SBT_0.6+ patients [Pr(> F ) = 0.0068, pMANOVA], with higher F/B ratios and MDI in SBT_0.6- patients (19.71 ± 16.62 vs. 7.33 ± 6.65, p < 0.01; 1.02 ± 0.97 vs. 0.20 ± 0.58, p < 0.01). Similar results were observed between the SBT_0.6- and SBT_0.6+ sub-groups of patients with normal liver function and a Child-Pugh score of 5. SBT was negatively correlated with both the F/B ratio and MDI ( r = -0.34, p < 0.05; r = -0.38, p < 0.05). Interestingly, an increased capacity for the inferred pathway "bacterial invasion of epithelial cells" in patients, was highly negatively correlated with SBT ( r = -0.57, p < 0.01). The severity of microbiota dysbiosis in LC patients depends on SBT rather than Child-Pugh score. SBT per se might be significantly related to the gut microbiota abnormalities observed in patients with LC.

A glow of HLA typing in organ transplantation

PubMed Central

2013-01-01

The transplant of organs and tissues is one of the greatest curative achievements of this century. In organ transplantation, the adaptive immunity is considered the main response exerted to the transplanted tissue, since the main goal of the immune response is the MHC (major histocompatibility complex) molecules expressed on the surface of donor cells. Cell surface molecules that induce an antigenic stimulus cause the rejection immune response to grafted tissue or organ. A wide variety of transplantation antigens have been described, including the major histocompatibility molecules, minor histocompatibility antigens, ABO blood group antigens and endothelial cell antigens. The sensitization to MHC antigens may be caused by transfusions, pregnancy, or failed previous grafts leading to development of anti-human leukocyte antigen (HLA) antibodies that are important factor responsible for graft rejection in solid organ transplantation and play a role in post-transfusion complication Anti-HLA Abs may be present in healthy individuals. Methods for HLA typing are described, including serological methods, molecular techniques of sequence-specific priming (SSP), sequence-specific oligonucleotide probing (SSOP), Sequence based typing (SBT) and reference strand-based conformation analysis (RSCA) method. Problems with organ transplantation are reservoir of organs and immune suppressive treatments that used to decrease rate of rejection with less side effect and complications. PMID:23432791

Dog leucocyte antigen class II diversity and relationships among indigenous dogs of the island nations of Indonesia (Bali), Australia and New Guinea.

PubMed

Runstadler, J A; Angles, J M; Pedersen, N C

2006-11-01

The genetic polymorphism at the dog leucocyte antigen (DLA) class II loci DQA1, DQB1 and DRB1 was studied in a large genetically diverse population of feral and wild-type dogs from the large island nations of Indonesia (Bali), Australia and New Guinea (Bali street dog, dingo and New Guinea singing dog, respectively). Sequence-based typing (SBT) of the hypervariable region of DLA-DRB1, -DQA1 and -DQB1 alleles was used to determine genetic diversity. No new DQA1 alleles were recognized among the three dog populations, but five novel DLA-DRB1 and 2 novel DLA-DQB1 allele sequences were detected. Additional unknown alleles were postulated to exist in Bali street dogs, as indicated by the large percentage of individuals (15%-33%) that had indeterminate DRB1, DQA1 and DQB1 alleles by SBT. All three groups of dogs possessed alleles that were relatively uncommon in conventional purebreds. The New Guinea singing dog and dingo shared alleles that were not present in the Bali street dogs. These findings suggested that the dingo was more closely related to indigenous dogs from New Guinea. Feral dog populations, in particular large ones such as that of Bali, show genetic diversity that existed prior to phenotypic selection for breeds originating from their respective regions. This diversity needs to be identified and maintained in the face of progressive Westernization. These populations deserve further study as potential model populations for the evolution of major histocompatibility complex alleles, for the study of canine genetic diversity, for the development of dog breeds and for studies on the comigration of ancestral human and dog populations.

Thinking it through: mental rehearsal and performance on 2 types of laparoscopic cholecystectomy simulators.

PubMed

Paige, John T; Yu, Qingzhao; Hunt, John P; Marr, Alan B; Stuke, Lance E

2015-01-01

Simulation-based training (SBT) in laparoscopic cholecystectomy (LCCY) provides an opportunity for junior residents to learn the procedure in a safe, nonthreatening environment. Mental rehearsal (MR) has the potential of augmenting skill acquisition. This project investigated the correlation between MR of LCCY with performance on 2 different types of simulators: a procedural task (PT) training model and virtual reality (VR) machine. Prospective, quasi-experimental design with purposeful sampling. Postgraduate years (PGYs) 1 through 3 general surgical residents underwent standardized, distributed SBT in LCCY on either a PT trainer or a VR machine with group-based MR undertaken before 2 SBT sessions. Participants completed a pre-MR and post-MR session mental imagery questionnaire (MIQ) containing 8-items using a 7-point Likert-type scale. Data related to VR objective measures and PT video-based performances were also collected. Total scale mean scores were calculated for the first MR session and the second MR session and were compared using the t test. Pearson correlation analysis of MIQ scores with performance scores was determined. Louisiana State University Health New Orleans Health Sciences Center in New Orleans, Louisiana. This health sciences center is a tertiary care, academic state institution located in the Southeastern United States. A total of 21 PGYs 1 through 3 general surgery residents participated. They were purposefully divided into the PT and VR training groups to allow for even PGY distribution. Of the 21 participants, 19 completed both training sessions (n = 10 for PT [PGY1 = 4, PGY2 = 4, PGY3 = 2] and n = 9 for VR [PGY1 = 4, PGY2 = 3, PGY3 = 2]). After the Bonferroni adjustment, significant gains in the MIQ items related to confidence, visual imagery, and knowledge of the procedure were found. VR performance data demonstrated some statistically significant improvements. A significant negative correlation was present between the two-handed clip-and-cut VR task and MIQ gains. Group MR in LCCY before SBT on a VR machine is related to improved performance time for the VR two-handed clip-and-cut task. MR may be a useful adjunct to SBT LCCY. Future work will look at the translation of these skills to clinical practice. Copyright © 2015 Association of Program Directors in Surgery. Published by Elsevier Inc. All rights reserved.

Surgical simulation: Current practices and future perspectives for technical skills training.

PubMed

Bjerrum, Flemming; Thomsen, Ann Sofia Skou; Nayahangan, Leizl Joy; Konge, Lars

2018-06-17

Simulation-based training (SBT) has become a standard component of modern surgical education, yet successful implementation of evidence-based training programs remains challenging. In this narrative review, we use Kern's framework for curriculum development to describe where we are now and what lies ahead for SBT within surgery with a focus on technical skills in operative procedures. Despite principles for optimal SBT (proficiency-based, distributed, and deliberate practice) having been identified, massed training with fixed time intervals or a fixed number of repetitions is still being extensively used, and simulators are generally underutilized. SBT should be part of surgical training curricula, including theoretical, technical, and non-technical skills, and be based on relevant needs assessments. Furthermore, training should follow evidence-based theoretical principles for optimal training, and the effect of training needs to be evaluated using relevant outcomes. There is a larger, still unrealized potential of surgical SBT, which may be realized in the near future as simulator technologies evolve, more evidence-based training programs are implemented, and cost-effectiveness and impact on patient safety is clearly demonstrated.

Sorting genomes by reciprocal translocations, insertions, and deletions.

PubMed

Qi, Xingqin; Li, Guojun; Li, Shuguang; Xu, Ying

2010-01-01

The problem of sorting by reciprocal translocations (abbreviated as SBT) arises from the field of comparative genomics, which is to find a shortest sequence of reciprocal translocations that transforms one genome Pi into another genome Gamma, with the restriction that Pi and Gamma contain the same genes. SBT has been proved to be polynomial-time solvable, and several polynomial algorithms have been developed. In this paper, we show how to extend Bergeron's SBT algorithm to include insertions and deletions, allowing to compare genomes containing different genes. In particular, if the gene set of Pi is a subset (or superset, respectively) of the gene set of Gamma, we present an approximation algorithm for transforming Pi into Gamma by reciprocal translocations and deletions (insertions, respectively), providing a sorting sequence with length at most OPT + 2, where OPT is the minimum number of translocations and deletions (insertions, respectively) needed to transform Pi into Gamma; if Pi and Gamma have different genes but not containing each other, we give a heuristic to transform Pi into Gamma by a shortest sequence of reciprocal translocations, insertions, and deletions, with bounds for the length of the sorting sequence it outputs. At a conceptual level, there is some similarity between our algorithm and the algorithm developed by El Mabrouk which is used to sort two chromosomes with different gene contents by reversals, insertions, and deletions.

Phase-Transformation-Induced Extra Thermal Expansion Behavior of (SrxBa1-x)TiO3/Cu Composite.

PubMed

Sheng, Jie; Wang, Lidong; Li, Shouwei; Yin, Benke; Liu, Xiangli; Fei, Wei-Dong

2016-06-03

The properties of metal matrix composites (MMCs) can be optimized effectively through adjusting the type or the volume fraction of reinforcement. Generally, the coefficient of thermal expansion (CTE) of MMCs can be reduced by increasing the volume fraction of the reinforcement with lower CTE than metal matrix. However, it is great challenge to fabricate low CTE MMCs with low reinforcement volume fraction because of the limitation of reinforcement CTEs. SrxBa1-xTiO3 (SBT) powder presents negative thermal expansion behavior during the phase transformation from tetragonal to cubic phase. Here, we demonstrate that the phase transformation of SBT can be utilized to reduce and design the thermal expansion properties of SBT particle-reinforced Cu (SBT/Cu) composite, and ultralow CTE can be obtained in SBT/Cu composite. The X-ray diffraction analysis on heating indicates that the temperature range of phase transformation is extended greatly, therefore, the low CTE can be achieved within wide temperature range. Landau-Devonshire theory study on the phase transformation behaviors of SBT particles in the composite indicates that thermal mismatch stress significantly affects the Curie temperature of SBT particles and the CTE of the composite. The results given in the present study provide a new approach to design the MMCs with low CTE.

Collision partner selection schemes in DSMC: From micro/nano flows to hypersonic flows

NASA Astrophysics Data System (ADS)

Roohi, Ehsan; Stefanov, Stefan

2016-10-01

The motivation of this review paper is to present a detailed summary of different collision models developed in the framework of the direct simulation Monte Carlo (DSMC) method. The emphasis is put on a newly developed collision model, i.e., the Simplified Bernoulli trial (SBT), which permits efficient low-memory simulation of rarefied gas flows. The paper starts with a brief review of the governing equations of the rarefied gas dynamics including Boltzmann and Kac master equations and reiterates that the linear Kac equation reduces to a non-linear Boltzmann equation under the assumption of molecular chaos. An introduction to the DSMC method is provided, and principles of collision algorithms in the DSMC are discussed. A distinction is made between those collision models that are based on classical kinetic theory (time counter, no time counter (NTC), and nearest neighbor (NN)) and the other class that could be derived mathematically from the Kac master equation (pseudo-Poisson process, ballot box, majorant frequency, null collision, Bernoulli trials scheme and its variants). To provide a deeper insight, the derivation of both collision models, either from the principles of the kinetic theory or the Kac master equation, is provided with sufficient details. Some discussions on the importance of subcells in the DSMC collision procedure are also provided and different types of subcells are presented. The paper then focuses on the simplified version of the Bernoulli trials algorithm (SBT) and presents a detailed summary of validation of the SBT family collision schemes (SBT on transient adaptive subcells: SBT-TAS, and intelligent SBT: ISBT) in a broad spectrum of rarefied gas-flow test cases, ranging from low speed, internal micro and nano flows to external hypersonic flow, emphasizing first the accuracy of these new collision models and second, demonstrating that the SBT family scheme, if compared to other conventional and recent collision models, requires smaller number of particles per cell to obtain sufficiently accurate solutions.

Benefits of simulation based training for neonatal resuscitation education: a systematic review.

PubMed

Rakshasbhuvankar, A A; Patole, S K

2014-10-01

Simulation-based training (SBT) is being more frequently recommended for neonatal resuscitation education (NRE). It is important to assess if SBT improves clinical outcomes as neonatal resuscitation aims to improve survival without long-term neurodevelopmental impairment. We aimed to assess the evidence supporting benefits of SBT in NRE. A systematic review was conducted using the Cochrane methodology. PubMed, Embase, PsycInfo and Cochrane databases were searched. Related abstracts were scanned and full texts of the potentially relevant articles were studied. Randomised controlled trials (RCT) and quasi-experimental studies with controls (non-RCT) assessing SBT for NRE were eligible for inclusion in the review. Four small studies [three RCT (n=126) and one non-RCT (n=60)] evaluated SBT for NRE. Participants included medical students (one RCT and one non-RCT), residents (one RCT) and nursing staff (one RCT). Outcomes included performance in a simulation scenario, theoretical knowledge, and confidence in leading a resuscitation scenario. One RCT favoured simulation [improved resuscitation score (p=0.016), 2.31 more number of critical actions (p=0.017) and decreased time to achieve resuscitation steps (p=<0.001)]. The remaining two RCTs and the non-RCT did not find any difference between SBT and alternate methods of instruction. None of the four studies reported clinical outcomes. Evidence regarding benefits of SBT for NRE is limited. There are no data on clinical outcomes following SBT for NRE. Large RCTs assessing clinically important outcomes are required before SBT can be recommended widely for NRE. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Eight critical factors in creating and implementing a successful simulation program.

PubMed

Lazzara, Elizabeth H; Benishek, Lauren E; Dietz, Aaron S; Salas, Eduardo; Adriansen, David J

2014-01-01

Recognizing the need to minimize human error and adverse events, clinicians, researchers, administrators, and educators have strived to enhance clinicians' knowledge, skills, and attitudes through training. Given the risks inherent in learning new skills or advancing underdeveloped skills on actual patients, simulation-based training (SBT) has become an invaluable tool across the medical education spectrum. The large simulation, training, and learning literature was used to provide a synthesized yet innovative and "memorable" heuristic of the important facets of simulation program creation and implementation, as represented by eight critical "S" factors-science, staff, supplies, space, support, systems, success, and sustainability. These critical factors advance earlier work that primarily focused on the science of SBT success, to also include more practical, perhaps even seemingly obvious but significantly challenging components of SBT, such as resources, space, and supplies. SYSTEMS: One of the eight critical factors-systems-refers to the need to match fidelity requirements to training needs and ensure that technological infrastructure is in place. The type of learning objectives that the training is intended to address should determine these requirements. For example, some simulators emphasize physical fidelity to enable clinicians to practice technical and nontechnical skills in a safe environment that mirrors real-world conditions. Such simulators are most appropriate when trainees are learning how to use specific equipment or conduct specific procedures. The eight factors-science, staff, supplies, space, support, systems, success, and sustainability-represent a synthesis of the most critical elements necessary for successful simulation programs. The order of the factors does not represent a deliberate prioritization or sequence, and the factors' relative importance may change as the program evolves.

76 FR 33794 - Self-Regulatory Organizations; Chicago Stock Exchange, Incorporated; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-09

... types and indications that are eligible for entry to and accepted by the Matching System. The Exchange... Exchange with the ability to determine on an order type by order type basis which orders and indications... Rule 43.2 relating to the types of orders handled on the CBOE's Screen Based Trading System (``SBT...

Phase-Transformation-Induced Extra Thermal Expansion Behavior of (SrxBa1–x)TiO3/Cu Composite

PubMed Central

Sheng, Jie; Wang, Lidong; Li, Shouwei; Yin, Benke; Liu, Xiangli; Fei, Wei-Dong

2016-01-01

The properties of metal matrix composites (MMCs) can be optimized effectively through adjusting the type or the volume fraction of reinforcement. Generally, the coefficient of thermal expansion (CTE) of MMCs can be reduced by increasing the volume fraction of the reinforcement with lower CTE than metal matrix. However, it is great challenge to fabricate low CTE MMCs with low reinforcement volume fraction because of the limitation of reinforcement CTEs. SrxBa1−xTiO3 (SBT) powder presents negative thermal expansion behavior during the phase transformation from tetragonal to cubic phase. Here, we demonstrate that the phase transformation of SBT can be utilized to reduce and design the thermal expansion properties of SBT particle-reinforced Cu (SBT/Cu) composite, and ultralow CTE can be obtained in SBT/Cu composite. The X-ray diffraction analysis on heating indicates that the temperature range of phase transformation is extended greatly, therefore, the low CTE can be achieved within wide temperature range. Landau-Devonshire theory study on the phase transformation behaviors of SBT particles in the composite indicates that thermal mismatch stress significantly affects the Curie temperature of SBT particles and the CTE of the composite. The results given in the present study provide a new approach to design the MMCs with low CTE. PMID:27255420

Restaurant outbreak of Legionnaires' disease associated with a decorative fountain: an environmental and case-control study

PubMed Central

O'Loughlin, Rosalyn E; Kightlinger, Lon; Werpy, Matthew C; Brown, Ellen; Stevens, Valerie; Hepper, Clark; Keane, Tim; Benson, Robert F; Fields, Barry S; Moore, Matthew R

2007-01-01

Background From June to November 2005, 18 cases of community-acquired Legionnaires' disease (LD) were reported in Rapid City South Dakota. We conducted epidemiologic and environmental investigations to identify the source of the outbreak. Methods We conducted a case-control study that included the first 13 cases and 52 controls randomly selected from emergency department records and matched on underlying illness. We collected information about activities of case-patients and controls during the 14 days before symptom onset. Environmental samples (n = 291) were cultured for Legionella. Clinical and environmental isolates were compared using monoclonal antibody subtyping and sequence based typing (SBT). Results Case-patients were significantly more likely than controls to have passed through several city areas that contained or were adjacent to areas with cooling towers positive for Legionella. Six of 11 case-patients (matched odds ratio (mOR) 32.7, 95% CI 4.7-∞) reported eating in Restaurant A versus 0 controls. Legionella pneumophila serogroup 1 was isolated from four clinical specimens: 3 were Benidorm type strains and 1 was a Denver type strain. Legionella were identified from several environmental sites including 24 (56%) of 43 cooling towers tested, but only one site, a small decorative fountain in Restaurant A, contained Benidorm, the outbreak strain. Clinical and environmental Benidorm isolates had identical SBT patterns. Conclusion This is the first time that small fountain without obvious aerosol-generating capability has been implicated as the source of a LD outbreak. Removal of the fountain halted transmission. PMID:17688692

Epidemiological investigation of Candida species causing bloodstream infection in paediatric small bowel transplant recipients.

PubMed

Suhr, Mallory J; Gomes-Neto, João Carlos; Banjara, Nabaraj; Florescu, Diana F; Mercer, David F; Iwen, Peter C; Hallen-Adams, Heather E

2017-06-01

Small bowel transplantation (SBT) can be a life-saving medical procedure. However, these recipients experience high risk of bloodstream infections caused by Candida. This research aims to characterise the SBT recipient gut microbiota over time following transplantation and investigate the epidemiology of candidaemia in seven paediatric patients. Candida species from the recipients' ileum and bloodstream were identified by internal transcribed spacer sequence and distinguished to strain by multilocus sequence typing and randomly amplified polymorphic DNA. Antifungal susceptibility of bloodstream isolates was determined against nine antifungals. Twenty-two ileostomy samples harboured at least one Candida species. Fungaemia were caused by Candida parapsilosis, Candida albicans, Candida glabrata, Candida orthopsilosis and Candida pelliculosa. All but three bloodstream isolates showed susceptibility to all the antifungals tested. One C. glabrata isolate showed multidrug resistance to itraconazole, amphotericin B and posaconazole and intermediate resistance to caspofungin. Results are congruent with both endogenous (C. albicans, C. glabrata) and exogenous (C. parapsilosis) infections; results also suggest two patients were infected by the same strain of C. parapsilosis. Continuing to work towards a better understanding of sources of infection-particularly the exogenous sources-would lead to targeted prevention strategies. © 2017 Blackwell Verlag GmbH.

Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii).

PubMed

Bar, Ido; Cummins, Scott; Elizur, Abigail

2016-03-10

Controlling and managing the breeding of bluefin tuna (Thunnus spp.) in captivity is an imperative step towards obtaining a sustainable supply of these fish in aquaculture production systems. Germ cell transplantation (GCT) is an innovative technology for the production of inter-species surrogates, by transplanting undifferentiated germ cells derived from a donor species into larvae of a host species. The transplanted surrogates will then grow and mature to produce donor-derived seed, thus providing a simpler alternative to maintaining large-bodied broodstock such as the bluefin tuna. Implementation of GCT for new species requires the development of molecular tools to follow the fate of the transplanted germ cells. These tools are based on key reproductive and germ cell-specific genes. RNA-Sequencing (RNA-Seq) provides a rapid, cost-effective method for high throughput gene identification in non-model species. This study utilized RNA-Seq to identify key genes expressed in the gonads of Southern bluefin tuna (Thunnus maccoyii, SBT) and their specific expression patterns in male and female gonad cells. Key genes involved in the reproductive molecular pathway and specifically, germ cell development in gonads, were identified using analysis of RNA-Seq transcriptomes of male and female SBT gonad cells. Expression profiles of transcripts from ovary and testis cells were compared, as well as testis germ cell-enriched fraction prepared with Percoll gradient, as used in GCT studies. Ovary cells demonstrated over-expression of genes related to stem cell maintenance, while in testis cells, transcripts encoding for reproduction-associated receptors, sex steroids and hormone synthesis and signaling genes were over-expressed. Within the testis cells, the Percoll-enriched fraction showed over-expression of genes that are related to post-meiosis germ cell populations. Gonad development and germ cell related genes were identified from SBT gonads and their expression patterns in ovary and testis cells were determined. These expression patterns correlate with the reproductive developmental stage of the sampled fish. The majority of the genes described in this study were sequenced for the first time in T. maccoyii. The wealth of SBT gonadal and germ cell-related gene sequences made publicly available by this study provides an extensive resource for further GCT and reproductive molecular biology studies of this commercially valuable fish.

Sharing simulation-based training courses between institutions: opportunities and challenges.

PubMed

Laack, Torrey A; Lones, Ellen A; Schumacher, Donna R; Todd, Frances M; Cook, David A

2017-01-01

Sharing simulation-based training (SBT) courses between institutions could reduce time to develop new content but also presents challenges. We evaluate the process of sharing SBT courses across institutions in a mixed method study estimating the time required and identifying barriers and potential solutions. Two US academic medical institutions explored instructor experiences with the process of sharing four courses (two at each site) using personal interviews and a written survey and estimated the time needed to develop new content vs implement existing SBT courses. The project team spent approximately 618 h creating a collaboration infrastructure to support course sharing. Sharing two SBT courses was estimated to save 391 h compared with developing two new courses. In the qualitative analysis, participants noted the primary benefit of course sharing was time savings. Barriers included difficulty finding information and understanding overall course flow. Suggestions for improvement included establishing a standardized template, clearly identifying the target audience, providing a course overview, communicating with someone familiar with the original SBT course, employing an intuitive file-sharing platform, and considering local culture, context, and needs. Sharing SBT courses between institutions is feasible but not without challenges. An initial investment in a sharing infrastructure may facilitate downstream time savings compared with developing content de novo.

Distinctive proteolytic activity of cell envelope proteinase of Lactobacillus helveticus isolated from airag, a traditional Mongolian fermented mare's milk.

PubMed

Miyamoto, Mari; Ueno, Hiroshi M; Watanabe, Masayuki; Tatsuma, Yumi; Seto, Yasuyuki; Miyamoto, Taku; Nakajima, Hadjime

2015-03-16

Airag is a traditional fermented milk of Mongolia that is usually made from raw mare's milk. Lactobacillus helveticus is one of the lactic acid bacteria most frequently isolated from airag. In this study, we investigated the genetic and physiological characteristics of L. helveticus strains isolated from airag and clarified their significance in airag by comparing them with strains from different sources. Six strains of L. helveticus were isolated from five home-made airag samples collected from different regions of Mongolia. The optimal temperature for acidification in skim milk was 30 to 35°C for all the Mongolian strains, which is lower than those for the reference strains (JCM 1554 and JCM 1120(T)) isolated from European cheeses. All of the strains had a prtH1-like gene encoding a variant type of cell envelope proteinase (CEP). The CEP amino acid sequence in Snow Brand Typeculture (SBT) 11087 isolated from airag shared 71% identity with PrtH of L. helveticus CNRZ32 (AAD50643.1) but 98% identity with PrtH of Lactobacillus kefiranofaciens ZW3 (AEG40278.1) isolated from a traditional fermented milk in Tibet. The proteolytic activities of the CEP from SBT11087 on artificial substrate (N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide) and pure casein were measured using an intact-cell degradation assay. The activity of the CEP from SBT11087 was observed to be weak and exhibited a lower optimal temperature (40°C) than those from the reference strains (45-50°C). The specificity of the SBT11087 CEP for αS1-casein was typical of the CEPs previously reported in L. helveticus, as determined through the degradation profiles obtained through gel electrophoresis and mass spectrometry analyses. In contrast, the degradation profile of β-casein revealed that the CEP of SBT11087 primarily hydrolyzes its C-terminal domain and hydrolyzed nine of the 16 cleavage sites shared among the CEPs of other L. helveticus strains. Thus, the CEP of SBT11087 is distinct from those from previously reported L. helveticus strains in terms of its optimal temperature and its degradation of β-casein. Therefore, the Mongolian L. helveticus strains differ from other strains of the species in different collections and are specifically suited for the natural lactic acid bacterial population in airag. Copyright © 2014 Elsevier B.V. All rights reserved.

[Simulation-based training and OR apprenticeship for medical students : A prospective, randomized, single-blind study of clinical skills].

PubMed

Ott, T; Schmidtmann, I; Limbach, T; Gottschling, P F; Buggenhagen, H; Kurz, S; Pestel, G

2016-11-01

Simulation-based training (SBT) has developed into an established method of medical training. Studies focusing on the education of medical students have used simulation as an evaluation tool for defined skills. A small number of studies provide evidence that SBT improves medical students' skills in the clinical setting. Moreover, they were strictly limited to a few areas, such as the diagnosis of heart murmurs or the correct application of cricoid pressure. Other studies could not prove adequate transferability from the skills gained in SBT to the patient site. Whether SBT has an effect on medical students' skills in anesthesiology in the clinical setting is controversial. To explore this issue, we designed a prospective, randomized, single-blind trial that was integrated into the undergraduate anesthesiology curriculum of our department during the second year of the clinical phase of medical school. This study intended to explore the effect of SBT on medical students within the mandatory undergraduate anesthesiology curriculum of our department in the operating room with respect to basic skills in anesthesiology. After obtaining ethical approval, the participating students of the third clinical semester were randomized into two groups: the SIM-OR group was trained by a 225 min long SBT in basic skills in anesthesiology before attending the operating room (OR) apprenticeship. The OR-SIM group was trained after the operating room apprenticeship by SBT. During SBT the students were trained in five clinical skills detailed below. Further, two clinical scenarios were simulated using a full-scale simulator. The students had to prepare the patient and perform induction of anesthesia, including bag-mask ventilation after induction in scenario 1 and rapid sequence induction in scenario 2. Using the five-point Likert scale, five defined skills were evaluated at defined time points during the study period. 1) application of the safety checklist, 2) application of basic patient monitoring, 3) establishment of intravenous access, 4) bag-and-mask ventilation, and 5) adjustment of ventilatory parameters after the patients' airways were secured. A cumulative score of 5 points was defined as the best and a cumulative score of 25 as the worst rating for a defined time point. The primary endpoint was the cumulative score after day 1 in the operating room apprenticeship and the difference in cumulative scores from days 1 to 4. Our hypothesis was that the SIM-OR group would achieve a better score after day 1 in the operating room apprenticeship and would gain a larger increase in score from day 1 to day 4 than the OR-SIM group. 73 students were allocated to the OR-SIM group and 70 students to the SIM-OR group. There was no significant difference between the two groups after day 1 of the operating room apprenticeship and no difference in increase of the cumulative score from day 1 to day 4 (median of cumulative score on day 1: 'SIM-OR' 11.2 points vs. 'OR-SIM' 14.6 points; p = 0.067; median of difference from day 1 to day 4: 'SIM-OR' -3.7 vs. 'OR-SIM' -6.4; p = 0.110). With the methods applied, this study could not prove that 225 min of SBT before the operating room apprenticeship increased the medical students' clinical skills as evaluated in the operating room. Secondary endpoints indicate that medical students have better clinical skills at the end of the entire curriculum when they have been trained through SBT before the operating room apprenticeship. However, the authors believe that simulator training has a positive impact on students' acquisition of procedural and patient safety skills, even if the methods applied in this study may not mirror this aspect sufficiently.

Legionella detection and subgrouping in water air-conditioning cooling tower systems in Kuwait.

PubMed

Al-Matawah, Qadreyah; Al-Zenki, Sameer; Al-Azmi, Ahmad; Al-Waalan, Tahani; Al-Salameen, Fadila; Hejji, Ahmad Ben

2015-07-01

The main aim of the study was to test for the presence of Legionnaires' disease-causing microorganisms in air-conditioned buildings in Kuwait using molecular technologies. For this purpose, 547 samples were collected from 38 cooling towers for the analysis of Legionella pneumophila. These samples included those from water (n = 178), air (n = 231), and swabs (n = 138). Out of the 547 samples, 226 (41%) samples were presumptive positive for L. pneumophila, with L. pneumophila viable counts in the positive water samples ranging from 1 to 88 CFU/ml. Of the Legionella culture-positive samples, 204 isolates were examined by latex agglutination. These isolates were predominately identified as L. pneumophila serogroup (sg) 2-14. Using the Dresden panel of monoclonal antibodies, 74 representatives isolates were further serogrouped. Results showed that 51% of the isolates belonged to serogroup 7 followed by 1 (18%) and 3 (18%). Serogroups 4 (4%) and 10 (7%) were isolated at a lower frequency, and two isolates could not be assigned to a serogroup. These results indicate the wide prevalence of L. pneumophila serogroup 7 as the predominant serogroup at the selected sampling sites. Furthermore, the 74 L. pneumophila (sg1 = 13; sg3 = 13; sg4 = 3; sg7 = 38; sg10 = 5; sgX = 2) isolates were genotyped using the seven gene protocol sequence-based typing (SBT) scheme developed by the European Working Group for Legionella Infections (EWGLI). The results show that Legionella isolates were discriminated into nine distinct sequence typing (ST) profiles, five of which were new to the SBT database of EWGLI. Additionally, all of the ST1 serogroup 1 isolates were of the OLDA/Oxford subgroup. These baseline data will form the basis for the development of a Legionella environmental surveillance program and used for future epidemiological investigations.

A soil biotechnology system for wastewater treatment: technical, hygiene, environmental LCA and economic aspects.

PubMed

Kamble, Sheetal Jaisingh; Chakravarthy, Yogita; Singh, Anju; Chubilleau, Caroline; Starkl, Markus; Bawa, Itee

2017-05-01

Soil biotechnology (SBT) is a green engineering approach for wastewater treatment and recycling. Five SBT units located in the Mumbai region were under consideration of which holistic assessment of two SBT plants was carried out considering its technical, environmental and economic aspects and was compared with published research of other three. LCA has been done to evaluate the environmental impacts of construction and operation phase of SBT. Chemical oxygen demand (COD) and biochemical oxygen demand (BOD) removal of more than 90% can be achieved using this technology. Also, the nutrient removal proficiency (nitrate, nitrite, ammoniacal nitrogen, TKN, total nitrogen and phosphates) of this technique is good. On the other hand, SBT has low annual operation and maintenance cost, comparable to land-based systems and lower than conventional or advanced technologies. From the life cycle impact assessment, the main contributors for overall impact from the plant were identified as electricity consumption, discharges of COD, P-PO 4 3- and N-NH 4 + and disposal of sludge. The construction phase was found to have significantly more impact than the operation phase of the plant. This study suggests plant I is not relatively as efficient enough regarding sanitation. SBT provides several benefits over other conventional technologies for wastewater treatment. It is based on a bio-conversion process and is practically maintenance free. It does not produce any odorous bio-sludge and consumes the least energy.

Simulation-Based Medical Education Is No Better than Problem-Based Discussions and Induces Misjudgment in Self-Assessment

ERIC Educational Resources Information Center

Wenk, Manuel; Waurick, Rene; Schotes, David; Wenk, Melanie; Gerdes, Christina; Van Aken, Hugo K.; Popping, Daniel M.

2009-01-01

Simulation-based teaching (SBT) is increasingly used in medical education. As an alternative to other teaching methods there is a lack of evidence concerning its efficacy. The aim of this study was to evaluate the potency of SBT in anesthesia in comparison to problem-based discussion (PBD) with students in a randomized controlled setting.…

Epithelial borderline ovarian tumor: Diagnosis and treatment strategy.

PubMed

Ushijima, Kimio; Kawano, Kouichiro; Tsuda, Naotake; Nishio, Shin; Terada, Atsumu; Kato, Hiroyuki; Tasaki, Kazuto; Matsukuma, Ken

2015-05-01

Epithelial borderline ovarian tumors (BOT) are distinctive from benign tumors and carcinoma. They occur in younger women more often than carcinoma, and there is some difficulty making correct diagnosis of BOT. Two subtypes of BOT, serous and mucinous borderline tumor have different characteristics and very different clinical behavior. Serous borderline tumor (SBT) with micropapillary pattern shows more incidence of extra ovarian disease and often coexists with invasive implant. SBT with micropapillary pattern in advanced stage has showed a worse prognosis than typical SBT. Huge mucinous borderline tumors have histologic heterogeneity, and the accuracy of frozen section diagnosis is relatively low. Extensive sampling is required to reach a correct pathological diagnosis. Mucinous adenoma (intestinal type) also runs the risk of recurrence after cystectomy, or intraoperative rupture of cyst. Laparoscopic procedure for BOT has not increased the risk of recurrence. Fertility preserving procedures are generally accepted, except in advanced stage SBT with invasive implants. Only cystectomy shows a significant risk of recurrence. Re-staging surgery and full staging surgery is not necessary for all BOT. We should not attempt to treat them uniformly, by the single diagnosis of "borderline tumor". It depends on histologic type. Close communication with the pathologist is necessary to gain more detail and ask more pathological samples in order to make the optimal treatment strategy for each individual patients.

Rapid genotyping of Legionella pneumophila serogroup 1 strains by a novel DNA microarray-based assay during the outbreak investigation in Warstein, Germany 2013.

PubMed

Petzold, Markus; Ehricht, Ralf; Slickers, Peter; Pleischl, Stefan; Brockmann, Ansgar; Exner, Martin; Monecke, Stefan; Lück, Christian

2017-06-01

Between 1 August and 6 September 2013, an outbreak of Legionnaires' disease (LD) with 78 cases confirmed by positive urinary antigen tests occurred in Warstein, North Rhine-Westphalia, Germany. Legionella (L.) pneumophila, serogroup (Sg) 1, monoclonal antibody (mAb) subgroup Knoxville, sequence type (ST) 345, was identified as the epidemic strain. This strain was isolated from seven patients. To detect the source of the infection, epidemiological typing of clinical and environmental strains was performed in two consecutive steps. First, strains were typed by monoclonal antibodies. Indistinguishable strains were further subtyped by sequence-based typing (SBT) which is the internationally recognized standard method for epidemiological genotyping of L. pneumophila. In an early stage of the outbreak investigation, many environmental isolates were found to belong to the mAb subgroup Knoxville, but to two different STs, namely to ST 345, the epidemic strain, and to ST 600. A majority of environmental isolates belonged to ST 600 whereas the epidemic ST 345 strain was less common in environmental samples. To rapidly distinguish both Knoxville strains, we applied a novel typing method based on DNA-hybridization on glass chips. The new assay can easily and rapidly discriminate L. pneumophila Sg 1 strains. Thus, we were able to quickly identify the sources harboring the epidemic strain, i.e., two cooling towers of different companies, the waste water treatment plants (WWTP) of the city and one company as well as water samples of the river Wester and its branches. Copyright © 2016 Elsevier GmbH. All rights reserved.

The subtilisin-like protease SBT3 contributes to insect resistance in tomato

PubMed Central

Meyer, Michael; Huttenlocher, Franziska; Cedzich, Anna; Procopio, Susanne; Stroeder, Jasper; Pau-Roblot, Corinne; Lequart-Pillon, Michelle; Pelloux, Jérôme; Stintzi, Annick; Schaller, Andreas

2016-01-01

Subtilisin-like proteases (SBTs) constitute a large family of extracellular plant proteases, the function of which is still largely unknown. In tomato plants, the expression of SBT3 was found to be induced in response to wounding and insect attack in injured leaves but not in healthy systemic tissues. The time course of SBT3 induction resembled that of proteinase inhibitor II and other late wound response genes suggesting a role for SBT3 in herbivore defense. Consistent with such a role, larvae of the specialist herbivore Manduca sexta performed better on transgenic plants silenced for SBT3 expression (SBT3-SI). Supporting a contribution of SBT3 to systemic wound signaling, systemic induction of late wound response genes was attenuated in SBT3-SI plants. The partial loss of insect resistance may thus be explained by a reduction in systemic defense gene expression. Alternatively, SBT3 may play a post-ingestive role in plant defense. Similar to other anti-nutritive proteins, SBT3 was found to be stable and active in the insect’s digestive system, where it may act on unidentified proteins of insect or plant origin. Finally, a reduction in the level of pectin methylesterification that was observed in transgenic plants with altered levels of SBT3 expression suggested an involvement of SBT3 in the regulation of pectin methylesterases (PMEs). While such a role has been described in other systems, PME activity and the degree of pectin methylesterification did not correlate with the level of insect resistance in SBT3-SI and SBT3 overexpressing plants and are thus unrelated to the observed resistance phenotype. PMID:27259555

Epidemiological Investigation of Legionella pneumophila Serogroup 2 to 14 Isolates from Water Samples by Amplified Fragment Length Polymorphism and Sequence-Based Typing and Detection of Virulence Traits

PubMed Central

Katsiaflaka, Anna; Pournaras, Spyros; Kristo, Ioulia; Mouchtouri, Varvara A.; Kyritsi, Maria; Velonakis, Emmanuel; Vatopoulos, Alkiviadis C.

2016-01-01

ABSTRACT The aim of this study is to explore the dispersion, clonality, and virulence of Legionella pneumophila serogroups 2 to 14 in the Greek environment. Eighty L. pneumophila serogroup 2 to 14 strains isolated from water distribution systems of hotels, hospitals, athletic venues, and ferries in Greece were tested by monoclonal antibodies (MAbs) for serogroup discrimination and molecularly by amplified fragment length polymorphism (AFLP) for genetic diversity. Fifty-six of 80 strains were also typed by the sequence-based typing (SBT) method. Αll strains were further analyzed for detection of two pathogenicity loci: Legionella vir homologue (lvh) and repeats in structural toxin (rtxA). Thirty-seven strains (46.2%) belonged to serogroup 6, 26 strains (32.5%) to serogroup 3, and 7 (8.8%) to other serogroups (4, 5, 8, and 10). Ten strains (12.5%) were nontypeable (NT) into the known serogroups. Thirty-nine different AFLP types were found among the 80 L. pneumophila serogroup 2 to 14 strains, and 24 different SBT types were found among the 56 strains tested. Among the 80 strains, the lvh locus was present in 75 (93.8%), the rtxA locus was found in 76 (95%), and both loci were found in 73 (91.3%) strains. This study showed that there is genetic variability of L. pneumophila serogroups 2 to 14 in the Greek environment as well as a high percentage of the pathogenicity loci. Ιntroducing an effective diagnostic test for L. pneumophila serogroups 2 to 14 in urine and promoting the examination of respiratory specimens from patients hospitalized for pneumonia in Greek hospitals are essential. IMPORTANCE In this study, the dispersion, clonality, and virulence of environmental isolates of Legionella pneumophila serogroups 2 to 14 (Lp2–14) in Greece were investigated. Genetic variability of Lp2–14 in the Greek environment was identified together with the presence of the pathogenicity loci in a high percentage of the isolates. Despite the high prevalence of Lp2–14 in the Greek environment, no clinical cases were reported, which may be due to underdiagnosis of the disease. Almost all the legionellosis cases are diagnosed in Greece by using the urine antigen test, which is specific for Lp1. There is an urgent need to improve the clinical diagnosis of legionellosis by introducing an effective diagnostic test for Lp2–14 in urine and by promoting the PCR examination of respiratory specimens from patients with compatible clinical symptoms. PMID:27496776

Follow-up of coeliac disease with the novel one-hour 13C-sorbitol breath test versus the H2-sorbitol breath test.

PubMed

Tveito, Kari; Hetta, Anne Kristine; Askedal, Mia; Brunborg, Cathrine; Sandvik, Leiv; Løberg, Else Marit; Skar, Viggo

2011-07-01

We recently developed a (13)C-sorbitol breath test ((13)C-SBT) as an alternative to the H(2)-sorbitol breath test (H(2)-SBT) for coeliac disease. In this study we compared the diagnostic properties of the H(2)-SBT and the (13)C-SBT in follow-up of coeliac disease. Twenty-seven coeliac patients on a gluten-free diet (GFD) performed the breath tests. All had been tested before treatment in the initial study of the (13)C-SBT, in which 39 untreated coeliac patients, 40 patient controls, and 26 healthy volunteers participated. Five gram sorbitol and 100 mg (13)C-sorbitol were dissolved in 250 ml tap water and given orally. H(2), CH(4) and (13)CO(2) were measured in end-expiratory breath samples every 30 min for 4 h. Increased H(2) concentration ≥20 ppm from basal values was used as cut-off for the H(2)-SBT. Sixty minutes values were used as diagnostic index in the (13)C-SBT. (13)CO(2) levels at 60 min increased in 20/26 treated coeliac patients (77%) after GFD, but were significantly lower than in control groups. Out of 20 patients who had a positive H(2)-SBT before GFD, 12 had a negative H(2)-SBT after GFD. Peak H(2) concentrations were not correlated with (13)C-SBT results. The study confirms the sensitivity of a one-hour (13)C-SBT for small intestinal malabsorption. The (13)C-SBT has superior diagnostic properties compared with the H(2)-SBT in follow-up of coeliac disease.

Genetic diversity and structure of a rare endemic cactus and an assessment of its genetic relationship with a more common congener.

PubMed

Rayamajhi, Niraj; Sharma, Jyotsna

2018-06-01

Endemic, obligate outcrossing plant species with narrow geographic distributions and disjunct populations are prone to loss of genetic diversity. Simultaneously, delineating clear species boundaries is important for targeted conservation efforts. The rare and endemic cactus, Sclerocactus brevihamatus subsp. tobuschii (SBT), has a parapatric relationship with Sclerocactus brevihamatus subsp. brevihamatus (SBB) but genetic distance between the two taxa is unknown. We: (1) developed taxon-specific polymorphic microsatellites, (2) assessed genetic diversity within and among nine populations of SBT, and within one population of SBB, and (3) estimated the genetic relationship between the two subspecies. Within-population genetic diversity of SBT was moderate to high (mean H o  = 0.37; mean H e  = 0.59). Indirect estimate of inbreeding corrected for null alleles (F is-INEst ) was low for SBT, ranging from 0.03 to 0.14 (mean F is-INEst  = 0.07). Genetic differentiation among populations of SBT was low based on F st (0.08) and AMOVA (Ф PT  = 0.10). Lack of genetic and spatial correlation in SBT populations coupled with the presence of private alleles and bottleneck events in several populations suggests that reproductive isolation is occurring but that sufficient time may not have yet passed to manifest strong differentiation. Cluster analyses segregated the 10 populations into three distinct groups, and separated SBB genotypes clearly. Results suggest that while hybridization between the two subspecies may occur, SBT is clearly differentiated genetically from SBB to retain its current taxonomic status.

Boron Tolerance in Aspergillus nidulans Is Sustained by the SltA Pathway Through the SLC-Family Transporters SbtA and SbtB

PubMed Central

Villarino, María; Mendizabal, Gorka; Garzia, Aitor; Ugalde, Unai

2017-01-01

Microbial cells interact with the environment by adapting to external changes. Signal transduction pathways participate in both sensing and responding in the form of modification of gene expression patterns, enabling cell survival. The filamentous fungal-specific SltA pathway regulates tolerance to alkalinity, elevated cation concentrations and, as shown in this work, also stress conditions induced by borates. Growth of sltA− mutants is inhibited by increasing millimolar concentrations of boric acid or borax (sodium tetraborate). In an attempt to identify genes required for boron-stress response, we determined the boric acid or borax-dependent expression of sbtA and sbtB, orthologs of Saccharomyces cerevisiae bor1, and a reduction in their transcript levels in a ΔsltA mutant. Deletion of sbtA, but mainly that of sbtB, decreased the tolerance to boric acid or borax. In contrast, null mutants of genes coding for additional transporters of the Solute Carrier (SLC) family, sB, sbtD or sbtE, showed an unaltered growth pattern under the same stress conditions. Taken together, our results suggest that the SltA pathway induces, through SbtA and SbtB, the export of toxic concentrations of borates, which have largely recognized antimicrobial properties. PMID:28753996

Spontaneous Breathing Trials and Conservative Sedation Practices Reduce Mechanical Ventilation Duration in Subjects With ARDS.

PubMed

Kallet, Richard H; Zhuo, Hanjing; Yip, Vivian; Gomez, Antonio; Lipnick, Michael S

2018-01-01

Spontaneous breathing trials (SBTs) and daily sedation interruptions (DSIs) reduce both the duration of mechanical ventilation and ICU length of stay (LOS). The impact of these practices in patients with ARDS has not previously been reported. We examined whether implementation of SBT/DSI protocols reduce duration of mechanical ventilation and ICU LOS in a retrospective group of subjects with ARDS at a large, urban, level-1 trauma center. All ARDS survivors from 2002 to 2016 ( N = 1,053) were partitioned into 2 groups: 397 in the pre-SBT/DSI group (June 2002-December 2007) and 656 in the post-SBT/DSI group (January 2009-April 2016). Patients from 2008, during the protocol implementation period, were excluded. An additional SBT protocol database (2008-2010) was used to assess the efficacy of SBT in transitioning subjects with ARDS to unassisted breathing. Comparisons were assessed by either unpaired t tests or Mann-Whitney tests. Multiple comparisons were made using either one-way analysis of variance or Kruskal-Wallis and Dunn's tests. Linear regression modeling was used to determine variables independently associated with mechanical ventilation duration and ICU LOS; differences were considered statistically significant when P < .05. Compared to the pre-protocol group, subjects with ARDS managed with SBT/DSI protocols experienced pronounced reductions both in median (IQR) mechanical ventilation duration (14 [6-29] vs 9 [4-17] d, respectively, P < .001) and median ICU LOS (18 [8-33] vs 13 [7-22] d, respectively P < .001). In the final model, only treatment in the SBT/DSI period and higher baseline respiratory system compliance were independently associated with reduced mechanical ventilation duration and ICU LOS. Among subjects with ARDS in the SBT performance database, most achieved unassisted breathing with a median of 2 SBTs. Evidenced-based protocols governing weaning and sedation practices were associated with both reduced mechanical ventilation duration and ICU LOS in subjects with ARDS. However, higher respiratory system compliance in the SBT/DSI cohort also contributed to these improved outcomes. Copyright © 2018 by Daedalus Enterprises.

Usefulness of radiological signs of pulmonary congestion in predicting failed spontaneous breathing trials

PubMed Central

Antonio, Ana Carolina Peçanha; Teixeira, Cassiano; Castro, Priscylla Souza; Zanardo, Ana Paula; Gazzana, Marcelo Basso; Knorst, Marli

2017-01-01

ABSTRACT Objective: Inspiratory fall in intrathoracic pressure during a spontaneous breathing trial (SBT) may precipitate cardiac dysfunction and acute pulmonary edema. We aimed to determine the relationship between radiological signs of pulmonary congestion prior to an SBT and weaning outcomes. Methods: This was a post hoc analysis of a prospective cohort study involving patients in an adult medical-surgical ICU. All enrolled individuals met the eligibility criteria for liberation from mechanical ventilation. Tracheostomized subjects were excluded. The primary endpoint was SBT failure, defined as the inability to tolerate a T-piece trial for 30-120 min. An attending radiologist applied a radiological score on interpretation of digital chest X-rays performed before the SBT. Results: A total of 170 T-piece trials were carried out; SBT failure occurred in 28 trials (16.4%), and 133 subjects (78.3%) were extubated at first attempt. Radiological scores were similar between SBT-failure and SBT-success groups (median [interquartile range] = 3 [2-4] points vs. 3 [2-4] points; p = 0.15), which, according to the score criteria, represented interstitial lung congestion. The analysis of ROC curves demonstrated poor accuracy (area under the curve = 0.58) of chest x-rays findings of congestion prior to the SBT for discriminating between SBT failure and SBT success. No correlation was found between fluid balance in the 48 h preceding the SBT and radiological score results (ρ = −0.13). Conclusions: Radiological findings of pulmonary congestion should not delay SBT indication, given that they did not predict weaning failure in the medical-surgical critically ill population. (ClinicalTrials.gov identifier: NCT02022839 [http://www.clinicaltrials.gov/]) PMID:29364998

Three new HLA-C alleles (HLA-C*14:02:13, HLA-C*15:72 and HLA-C*15:74) in Saudi bone marrow donors.

PubMed

Fakhoury, H A; Jawdat, D; Alaskar, A S; Al Jumah, M; Cereb, N; Hajeer, A H

2015-10-01

Three new HLA-C alleles were identified by sequence-based typing method (SBT) in donors for the Saudi Bone Marrow Donor Registry (SBMDR). HLA-C*14:02:13 differs from HLA-C*14:02:01 by a silent G to A substitution at nucleotide position 400 in exon 2, where lysine at position 66 remains unchanged. HLA-C*15:72 differs from HLA-C*15:22 by a nonsynonymous C to A substitution at nucleotide position 796 in exon 3, resulting in an amino acid change from phenylalanine to leucine at position 116. HLA-C*15:74 differs from HLA-C*15:08 by a nonsynonymous C to T substitution at nucleotide position 914 in exon 3, resulting in an amino acid change from arginine to tryptophan at position 156. © 2015 John Wiley & Sons Ltd.

Funding quality pre-kindergarten slots with Philadelphia's new 'sugary drink tax': simulating effects of using an excise tax to address a social determinant of health.

PubMed

Langellier, Brent A; Lê-Scherban, Félice; Purtle, Jonathan

2017-09-01

Philadelphia passed a 1·5-cent-per-ounce sweetened beverage tax (SBT). Revenue will fund 10 000 quality pre-kindergarten slots for poor children. It is imperative to understand how revenue from SBT can be used to fund programmes to address education and other social determinants of health. The objective of the present study was to simulate quality pre-kindergarten attendance, educational achievement and sugar-sweetened beverage (SSB) consumption among Philadelphia children and adolescents under six intervention scenarios: (i) no intervention; (ii) 10 000 additional quality pre-kindergarten slots; (iii) a 1·5-cent-per-ounce SBT; (iv) expanded pre-kindergarten and 1·5-cent-per-ounce SBT; (v) a 3-cent-per-ounce SBT; and (vi) expanded pre-kindergarten and 3-cent-per-ounce SBT. We used an agent-based model to estimate pre-kindergarten enrolment, educational achievement and SSB consumption under the six policy scenarios. We identified key parameters in the model from the published literature and secondary analyses of the Panel Study of Income Dynamics - Child Development Supplement. Philadelphia, Pennsylvania, USA. Philadelphia children and adolescents aged 4-18 years. A 1·5-cents-per-ounce tax would reduce SSB consumption by 1·3 drinks/week among Philadelphia children and adolescents relative to no intervention, with larger effects among children below the poverty level. Quality pre-kindergarten expansion magnifies the effect of the SBT by 8 %, but has the largest effect on moderate-income children just above the poverty level. The SBT and quality pre-kindergarten programme each reduce SSB consumption, but primarily benefit different children and adolescents. Pairing an excise tax with a complementary programme to improve a social determinant of health represents a progressive strategy to combat obesity, a disease regressive in its social patterning.

Evaluation of Endotracheal Tube Scraping on Airway Resistance.

PubMed

Scott, J Brady; Dubosky, Meagan N; Vines, David L; Sulaiman, Adewunmi S; Jendral, Kyle R; Singh, Gagan; Patel, Ankeet; Kaplan, Carl A; Gurka, David P; Balk, Robert A

2017-11-01

Spontaneous breathing trials (SBTs) are used to assess the readiness for discontinuation of mechanical ventilation. When airway resistance (R aw ) is elevated, the imposed work of breathing can lead to prolongation of mechanical ventilation. Biofilm and mucus build-up within the endotracheal tube (ETT) can increase R aw . Scraping the ETT can remove the biofilm build-up and decrease mechanical R aw . The primary aim of this study was to evaluate the impact of ETT scraping on R aw . The secondary aim was to determine whether decreasing R aw would impact subsequent SBT success. Intubated, mechanically ventilated subjects were enrolled if they failed an SBT and had an R aw of > 10 cm H 2 O/L/s. SBT failure was based on institutional guidelines, and R aw was calculated by subtracting the difference between the measured peak and plateau pressures using a square flow waveform with an inspiratory flow set at 60 L/min. The endOclear device was inserted into the ETT and withdrawn per manufacturer's guidelines. Scraping was repeated until the ETT was cleared. Change in R aw was compared pre- and post-ETT scraping using a paired t test. A Mann-Whitney U test evaluated the difference in percentage change in R aw between SBT groups. Twenty-nine subjects completed the study. The mean pre- and post-ETT scraping R aw values were 15.17 ± 3.83 and 12.05 ± 3.19 cm H 2 O/L/s, respectively ( P < .001). Subsequent SBT success was 48%; however, there was no difference in percentage change in R aw between subsequent passed SBT (18.61% [interquartile range 8.90-33.93%]) and failed SBT (23.88% [interquartile range 0.00-34.80%]), U = 78.5, z = -0.284, P = .78. No adverse events were noted with ETT scraping. This study demonstrated that ETT scraping can reduce R aw . The decrease in R aw post-ETT scraping did not affect subsequent SBT success. Copyright © 2017 by Daedalus Enterprises.

Evaluation of Legionella Air Contamination in Healthcare Facilities by Different Sampling Methods: An Italian Multicenter Study.

PubMed

Montagna, Maria Teresa; De Giglio, Osvalda; Cristina, Maria Luisa; Napoli, Christian; Pacifico, Claudia; Agodi, Antonella; Baldovin, Tatjana; Casini, Beatrice; Coniglio, Maria Anna; D'Errico, Marcello Mario; Delia, Santi Antonino; Deriu, Maria Grazia; Guida, Marco; Laganà, Pasqualina; Liguori, Giorgio; Moro, Matteo; Mura, Ida; Pennino, Francesca; Privitera, Gaetano; Romano Spica, Vincenzo; Sembeni, Silvia; Spagnolo, Anna Maria; Tardivo, Stefano; Torre, Ida; Valeriani, Federica; Albertini, Roberto; Pasquarella, Cesira

2017-06-22

Healthcare facilities (HF) represent an at-risk environment for legionellosis transmission occurring after inhalation of contaminated aerosols. In general, the control of water is preferred to that of air because, to date, there are no standardized sampling protocols. Legionella air contamination was investigated in the bathrooms of 11 HF by active sampling (Surface Air System and Coriolis ® μ) and passive sampling using settling plates. During the 8-hour sampling, hot tap water was sampled three times. All air samples were evaluated using culture-based methods, whereas liquid samples collected using the Coriolis ® μ were also analyzed by real-time PCR. Legionella presence in the air and water was then compared by sequence-based typing (SBT) methods. Air contamination was found in four HF (36.4%) by at least one of the culturable methods. The culturable investigation by Coriolis ® μ did not yield Legionella in any enrolled HF. However, molecular investigation using Coriolis ® μ resulted in eight HF testing positive for Legionella in the air. Comparison of Legionella air and water contamination indicated that Legionella water concentration could be predictive of its presence in the air. Furthermore, a molecular study of 12 L. pneumophila strains confirmed a match between the Legionella strains from air and water samples by SBT for three out of four HF that tested positive for Legionella by at least one of the culturable methods. Overall, our study shows that Legionella air detection cannot replace water sampling because the absence of microorganisms from the air does not necessarily represent their absence from water; nevertheless, air sampling may provide useful information for risk assessment. The liquid impingement technique appears to have the greatest capacity for collecting airborne Legionella if combined with molecular investigations.

Evaluation of Legionella Air Contamination in Healthcare Facilities by Different Sampling Methods: An Italian Multicenter Study

PubMed Central

Montagna, Maria Teresa; De Giglio, Osvalda; Cristina, Maria Luisa; Napoli, Christian; Pacifico, Claudia; Agodi, Antonella; Baldovin, Tatjana; Casini, Beatrice; Coniglio, Maria Anna; D’Errico, Marcello Mario; Delia, Santi Antonino; Deriu, Maria Grazia; Guida, Marco; Laganà, Pasqualina; Liguori, Giorgio; Moro, Matteo; Mura, Ida; Pennino, Francesca; Privitera, Gaetano; Romano Spica, Vincenzo; Sembeni, Silvia; Spagnolo, Anna Maria; Tardivo, Stefano; Torre, Ida; Valeriani, Federica; Albertini, Roberto; Pasquarella, Cesira

2017-01-01

Healthcare facilities (HF) represent an at-risk environment for legionellosis transmission occurring after inhalation of contaminated aerosols. In general, the control of water is preferred to that of air because, to date, there are no standardized sampling protocols. Legionella air contamination was investigated in the bathrooms of 11 HF by active sampling (Surface Air System and Coriolis®μ) and passive sampling using settling plates. During the 8-hour sampling, hot tap water was sampled three times. All air samples were evaluated using culture-based methods, whereas liquid samples collected using the Coriolis®μ were also analyzed by real-time PCR. Legionella presence in the air and water was then compared by sequence-based typing (SBT) methods. Air contamination was found in four HF (36.4%) by at least one of the culturable methods. The culturable investigation by Coriolis®μ did not yield Legionella in any enrolled HF. However, molecular investigation using Coriolis®μ resulted in eight HF testing positive for Legionella in the air. Comparison of Legionella air and water contamination indicated that Legionella water concentration could be predictive of its presence in the air. Furthermore, a molecular study of 12 L. pneumophila strains confirmed a match between the Legionella strains from air and water samples by SBT for three out of four HF that tested positive for Legionella by at least one of the culturable methods. Overall, our study shows that Legionella air detection cannot replace water sampling because the absence of microorganisms from the air does not necessarily represent their absence from water; nevertheless, air sampling may provide useful information for risk assessment. The liquid impingement technique appears to have the greatest capacity for collecting airborne Legionella if combined with molecular investigations. PMID:28640202

The Evolving Role of Simulation in Teaching Surgery in Undergraduate Medical Education.

PubMed

Acton, Robert D

2015-08-01

Simulation-based training (SBT) over the last 10 years has become a mainstay for surgical education at the graduate medical education (GME) level. More recently, however, the technique has rapidly become the standard for early efficient teaching of surgical skills and decision making at the undergraduate medical education (UME) level. The described benefits of SBT include its ability to compartmentalize education, to combine immediate assessment and feedback, and to accelerate knowledge and skill acquisition for the young learner. Consequently, SBT is now being adopted in multiple national medical student surgical educational initiatives. Copyright © 2015 Elsevier Inc. All rights reserved.

Association between HLA-A and -B polymorphisms and susceptibility to Henoch-Schönlein purpura in Han and Mongolian children from Inner Mongolia.

PubMed

Ren, S M; Yang, G L; Liu, C Z; Zhang, C X; Shou, Q H; Yu, S F; Li, W C; Su, X L

2012-02-03

We examined a possible association between HLA-A and -B polymorphisms and susceptibility to Henoch-Schönlein purpura (HSP) in Han and Mongolian children in Inner Mongolia, through a case-control study. Two hundred and sixty-eight unrelated children were enrolled, including 56 Mongolian and 50 Han children with HSP, 66 healthy Mongolian and 96 healthy Han children as a control group. HLA-A and -B alleles were indentified by PCR-sequence-specific oligonucleotide analysis and were further analyzed by PCR-sequencing-based typing (SBT). Frequencies of HLA-A*11, HLA-B*15 in Mongolian patients and HLA-A*26, HLA-B*35, HLA-B*52 in Han patients were higher than those in the corresponding control group (P < 0.05), while frequencies of HLA-B*07 and -B*40 in Mongolian HSP patients were lower than those in the control group (P < 0.05). Further analysis using PCR-SBT showed that all HLA-A*11 were HLA-A*1101, and most HLA-B*15 were HLA-B*1501 in Mongolian HSP patients. All HLA-A*26 were HLA-A*2601 and HLA-B*35 were mostly HLA-B*3503 in Han patients. There were more Han patients with severe manifestations than Mongolian patients (P < 0.05). Frequencies of HLA-A*26, HLA-B*35 and HLA-B*52 in Han patients were higher than in Mongolian patients (P < 0.05). We conclude that HLA-A*11(*1101) and -B*15(*1501) are associated with susceptibility to HSP in Mongolian children and HLA-A*26(*2601), HLA-B*35(*3503) and HLA-B*52 are associated with susceptibility to HSP in Han children. HLA-B*07 and -B*40 may be protective genes in Mongolian children. The different frequencies of HLA-A and -B in Mongolian and Han children may be responsible for the different manifestations in these two ethnic groups.

The STarT Back Screening Tool and Individual Psychological Measures: Evaluation of Prognostic Capabilities for Low Back Pain Clinical Outcomes in Outpatient Physical Therapy Settings

PubMed Central

Bishop, Mark D.; Fritz, Julie M.; Robinson, Michael E.; Asal, Nabih R.; Nisenzon, Anne N.

2013-01-01

Background Psychologically informed practice emphasizes routine identification of modifiable psychological risk factors being highlighted. Objective The purpose of this study was to test the predictive validity of the STarT Back Screening Tool (SBT) in comparison with single-construct psychological measures for 6-month clinical outcomes. Design This was an observational, prospective cohort study. Methods Patients (n=146) receiving physical therapy for low back pain were administered the SBT and a battery of psychological measures (Fear-Avoidance Beliefs Questionnaire physical activity scale and work scale [FABQ-PA and FABQ-W, respectively], Pain Catastrophizing Scale [PCS], 11-item version of the Tampa Scale of Kinesiophobia [TSK-11], and 9-item Patient Health Questionnaire [PHQ-9]) at initial evaluation and 4 weeks later. Treatment was at the physical therapist's discretion. Clinical outcomes consisted of pain intensity and self-reported disability. Prediction of 6-month clinical outcomes was assessed for intake SBT and psychological measure scores using multiple regression models while controlling for other prognostic variables. In addition, the predictive capabilities of intake to 4-week changes in SBT and psychological measure scores for 6-month clinical outcomes were assessed. Results Intake pain intensity scores (β=.39 to .45) and disability scores (β=.47 to .60) were the strongest predictors in all final regression models, explaining 22% and 24% and 43% and 48% of the variance for the respective clinical outcome at 6 months. Neither SBT nor psychological measure scores improved prediction of 6-month pain intensity. The SBT overall scores (β=.22) and SBT psychosocial scores (β=.25) added to the prediction of disability at 6 months. Four-week changes in TSK-11 scores (β=−.18) were predictive of pain intensity at 6 months. Four-week changes in FABQ-PA scores (β=−.21), TSK-11 scores (β=−.20) and SBT overall scores (β=−.18) were predictive of disability at 6 months. Limitations Physical therapy treatment was not standardized or accounted for in the analysis. Conclusions Prediction of clinical outcomes by psychology-based measures was dependent upon the clinical outcome domain of interest. Similar to studies from the primary care setting, initial screening with the SBT provided additional prognostic information for 6-month disability and changes in SBT overall scores may provide important clinical decision-making information for treatment monitoring. PMID:23125279

Interdisciplinary simulation-based training to improve delivery room communication.

PubMed

Dadiz, Rita; Weinschreider, Joanne; Schriefer, Jan; Arnold, Christine; Greves, Cole D; Crosby, Erin C; Wang, Hongyue; Pressman, Eva K; Guillet, Ronnie

2013-10-01

Poor communication among obstetric and pediatric professionals is associated with adverse perinatal events leading to severe disability and neonatal mortality. This study evaluated the effectiveness of an interdisciplinary simulation-based training (SBT) program to improve delivery room communication between obstetric and pediatric teams. Obstetric and pediatric teams participated in an SBT annually during 3 academic years, 2008-2011 (Y1-Y3), in a prospective, observational study. Eligible participants (n = 228) included attendings, fellows, house staff, midlevel providers, and nurses involved in delivery room care. Simulations were videotaped and evaluated using a validated 20-item checklist of best communication practices. Checklist scores were compared across years with the Kruskal-Wallis test. Providers were also surveyed annually regarding communication during actual deliveries using a standardized questionnaire. Ratings were analyzed using two-way analysis of covariance. At least 60% of eligible providers participated in 1 or more SBT sessions and completed surveys annually. Checklist scores on communication during SBT improved from Y1 (median, 6; interquartile range, 4) to Y3 (median, 11; interquartile range, 6) (P < 0.001). Survey results showed the perception of improvement over time in interteam communication during actual deliveries by obstetric (P < 0.005) and pediatric (P < 0.0001) providers. The obstetric team also perceived improved provider communication with the family (P < 0.05). Communication during SBT as well as the perception of communication during actual deliveries improved across the study period. The potential of a checklist to standardize delivery room communication and improve patient outcomes merits further investigation.

High Prevalence and Genetic Polymorphisms of Legionella in Natural and Man-Made Aquatic Environments in Wenzhou, China.

PubMed

Zhang, Leyi; Li, Yi; Wang, Xin; Shangguan, Zhihui; Zhou, Haijian; Wu, Yuejin; Wang, Lianghuai; Ren, Hongyu; Hu, Yun; Lin, Meifen; Qin, Tian

2017-02-24

Natural and engineered water systems are the main sources of Legionnaires' disease. It is essential from a public health perspective to survey water environments for the existence of Legionella . To analyze the main serogroups, genotypes and pathogenicity of the pathogen, a stratified sampling method was adopted to collect water samples randomly from shower water, cooling tower water, and local public hot springs in Wenzhou, China. Suspected strains were isolated from concentrated water samples. Serum agglutination assay and real-time PCR (Polymerase chain reaction) were used to identify L. pneumophila . Sequence-based typing (SBT) and pulsed-field gel electrophoresis (PFGE) were used to elucidate the genetic polymorphisms in the collected isolates. The intracellular growth ability of the isolates was determined through their interaction with J774 cells and plating them onto BCYE (Buffered Charcoal Yeast Extract) agar plates. Overall, 25.56% (46/180) of water samples were Legionella -positive; fifty-two strains were isolated and two kinds of serogroups were co-detected from six water samples from 2015 to 2016. Bacterial concentrations ranged from 20 CFU/100 mL to 10,720 CFU/100 mL. In detail, the Legionella -positive rates of shower water, cooling tower water and hot springs water were 15.45%, 13.33%, and 62.5%, respectively. The main serogroups were LP1 (30.69%) and LP3 (28.85%) and all strains carried the dot gene. Among them, 52 isolates and another 10 former isolates were analyzed by PFGE. Nineteen distinct patterns were observed in 52 strains isolated from 2015 to 2016 with three patterns being observed in 10 strains isolated from 2009 to 2014. Seventy-three strains containing 52 from this study and 21 former isolates were selected for SBT analysis and divided into 25 different sequence types in 4 main clonal groups belonging to 4 homomorphic types. Ten strains were chosen to show their abilities to grow and multiply in J744 cells. Taken together, our results demonstrate a high prevalence and genetic polymorphism of Legionella in Wenzhou's environmental water system. The investigated environmental water sources pose a potential threat to the public where intervention could help to prevent the occurrence of Legionnaires' disease.

High Prevalence and Genetic Polymorphisms of Legionella in Natural and Man-Made Aquatic Environments in Wenzhou, China

PubMed Central

Zhang, Leyi; Li, Yi; Wang, Xin; Shangguan, Zhihui; Zhou, Haijian; Wu, Yuejin; Wang, Lianghuai; Ren, Hongyu; Hu, Yun; Lin, Meifen; Qin, Tian

2017-01-01

Natural and engineered water systems are the main sources of Legionnaires’ disease. It is essential from a public health perspective to survey water environments for the existence of Legionella. To analyze the main serogroups, genotypes and pathogenicity of the pathogen, a stratified sampling method was adopted to collect water samples randomly from shower water, cooling tower water, and local public hot springs in Wenzhou, China. Suspected strains were isolated from concentrated water samples. Serum agglutination assay and real-time PCR (Polymerase chain reaction) were used to identify L. pneumophila. Sequence-based typing (SBT) and pulsed-field gel electrophoresis (PFGE) were used to elucidate the genetic polymorphisms in the collected isolates. The intracellular growth ability of the isolates was determined through their interaction with J774 cells and plating them onto BCYE (Buffered Charcoal Yeast Extract) agar plates. Overall, 25.56% (46/180) of water samples were Legionella-positive; fifty-two strains were isolated and two kinds of serogroups were co-detected from six water samples from 2015 to 2016. Bacterial concentrations ranged from 20 CFU/100 mL to 10,720 CFU/100 mL. In detail, the Legionella-positive rates of shower water, cooling tower water and hot springs water were 15.45%, 13.33%, and 62.5%, respectively. The main serogroups were LP1 (30.69%) and LP3 (28.85%) and all strains carried the dot gene. Among them, 52 isolates and another 10 former isolates were analyzed by PFGE. Nineteen distinct patterns were observed in 52 strains isolated from 2015 to 2016 with three patterns being observed in 10 strains isolated from 2009 to 2014. Seventy-three strains containing 52 from this study and 21 former isolates were selected for SBT analysis and divided into 25 different sequence types in 4 main clonal groups belonging to 4 homomorphic types. Ten strains were chosen to show their abilities to grow and multiply in J744 cells. Taken together, our results demonstrate a high prevalence and genetic polymorphism of Legionella in Wenzhou’s environmental water system. The investigated environmental water sources pose a potential threat to the public where intervention could help to prevent the occurrence of Legionnaires’ disease. PMID:28245548

Mutational analysis of BRAF and KRAS in ovarian serous borderline (atypical proliferative) tumours and associated peritoneal implants

PubMed Central

Ardighieri, Laura; Zeppernick, Felix; Hannibal, Charlotte G; Vang, Russell; Cope, Leslie; Junge, Jette; Kjaer, Susanne K; Kurman, Robert J; Shih, Ie-Ming

2014-01-01

There is debate as to whether peritoneal implants associated with serous borderline tumours/atypical proliferative serous tumours (SBT/APSTs) of the ovary are derived from the primary ovarian tumour or arise independently in the peritoneum. We analysed 57 SBT/APSTs from 45 patients with advanced-stage disease identified from a nation-wide tumour registry in Denmark. Mutational analysis for hotspots in KRAS and BRAF was successful in 55 APSTs and demonstrated KRAS mutations in 34 (61.8%) and BRAF mutations in eight (14.5%). Mutational analysis was successful in 56 peritoneal implants and revealed KRAS mutations in 34 (60.7%) and BRAF mutations in seven (12.5%). Mutational analysis could not be performed in two primary tumours and in nine implants, either because DNA amplification failed or because there was insufficient tissue for mutational analysis. For these specimens we performed VE1 immunohistochemistry, which was shown to be a specific and sensitive surrogate marker for a V600E BRAF mutation. VE1 staining was positive in one of two APSTs and seven of nine implants. Thus, among 63 implants for which mutation status was known (either by direct mutational analysis or by VE1 immunohistochemistry), 34 (53.9%) had KRAS mutations and 14 (22%) had BRAF mutations, of which identical KRAS mutations were found in 34 (91%) of 37 SBT/APST–implant pairs and identical BRAF mutations in 14 (100%) of 14 SBT/APST–implant pairs. Wild-type KRAS and BRAF (at the loci investigated) were found in 11 (100%) of 11 SBT/APST–implant pairs. Overall concordance of KRAS and BRAF mutations was 95% in 59 of 62 SBT/APST–implant (non-invasive and invasive) pairs (p < 0.00001). This study provides cogent evidence that the vast majority of peritoneal implants, non-invasive and invasive, harbour the identical KRAS or BRAF mutations that are present in the associated SBT/APST, supporting the view that peritoneal implants are derived from the primary ovarian tumour. PMID:24307542

Sea Buckthorn Leaf Extract Inhibits Glioma Cell Growth by Reducing Reactive Oxygen Species and Promoting Apoptosis.

PubMed

Kim, Sung-Jo; Hwang, Eunmi; Yi, Sun Shin; Song, Ki Duk; Lee, Hak-Kyo; Heo, Tae-Hwe; Park, Sang-Kyu; Jung, Yun Joo; Jun, Hyun Sik

2017-08-01

Hippophae rhamnoides L., also known as sea buckthorn (SBT), possesses a wide range of biological and pharmacological activities. However, the underlying mechanism is largely unknown. The present study examined whether SBT leaf extract could inhibit proliferation and promote apoptosis of rat glioma C6 cells. The results revealed that the treatment with SBT leaf extract inhibited proliferation of rat C6 glioma cells in a dose-dependent manner. SBT-induced reduction of C6 glioma cell proliferation and viability was accompanied by a decrease in production of reactive oxygen species (ROS), which are critical for the proliferation of tumor cells. SBT treatment not only significantly upregulated the expression of the pro-apoptotic protein Bcl-2-associated X (Bax) but also promoted its localization in the nucleus. Although increased expression and nuclear translocation of Bax were observed in SBT-treated C6 glioma cells, the induced nuclear morphological change was distinct from that of typical apoptotic cells in that most of SBT-treated cells were characterized by convoluted nuclei with cavitations and clumps of chromatin. All of these results suggest that SBT leaf extract could inhibit the rapid proliferation of rat C6 glioma cells, possibly by inducing the early events of apoptosis. Thus, SBT may serve as a potential therapeutic candidate for the treatment of glioma.

Serum Tryptase Monitoring in Indolent Systemic Mastocytosis: Association with Disease Features and Patient Outcome

PubMed Central

Matito, Almudena; Morgado, José Mario; Álvarez-Twose, Iván; Laura Sánchez-Muñoz; Pedreira, Carlos Eduardo; Jara-Acevedo, María; Teodosio, Cristina; Sánchez-López, Paula; Fernández-Núñez, Elisa; Moreno-Borque, Ricardo; García-Montero, Andrés; Orfao, Alberto; Escribano, Luis

2013-01-01

Background Serum baseline tryptase (sBT) is a minor diagnostic criterion for systemic mastocytosis (SM) of undetermined prognostic impact. We monitored sBT levels in indolent SM (ISM) patients and investigated its utility for predicting disease behaviour and outcome. Methods In total 74 adult ISM patients who were followed for ≥48 months and received no cytoreductive therapy were retrospectively studied. Patients were classified according to the pattern of evolution of sBT observed. Results Overall 16/74 (22%) cases had decreasing sBT levels, 48 (65%) patients showed increasing sBT levels and 10 (13%) patients showed a fluctuating pattern. Patients with significantly increasing sBT (sBT slope ≥0.15) after 48 months of follow-up showed a slightly greater rate of development of diffuse bone sclerosis (13% vs. 2%) and hepatomegaly plus splenomegaly (16% vs. 5%), as well as a significantly greater frequency of multilineage vs. mast cells (MC)-restricted KIT mutation (p = 0.01) together with a greater frequency of cases with progression of ISM to smouldering and aggressive SM (p = 0.03), and a shorter progression-free survival (p = 0.03). Conclusions Monitoring of sBT in ISM patients is closely associated with poor prognosis disease features as well as with disease progression, pointing out the need for a closer follow-up in ISM patients with progressively increasing sBT values. PMID:24155887

Serum tryptase monitoring in indolent systemic mastocytosis: association with disease features and patient outcome.

PubMed

Matito, Almudena; Morgado, José Mario; Álvarez-Twose, Iván; Sánchez-Muñoz, Laura; Pedreira, Carlos Eduardo; Jara-Acevedo, María; Teodosio, Cristina; Sánchez-López, Paula; Fernández-Núñez, Elisa; Moreno-Borque, Ricardo; García-Montero, Andrés; Orfao, Alberto; Escribano, Luis

2013-01-01

Serum baseline tryptase (sBT) is a minor diagnostic criterion for systemic mastocytosis (SM) of undetermined prognostic impact. We monitored sBT levels in indolent SM (ISM) patients and investigated its utility for predicting disease behaviour and outcome. In total 74 adult ISM patients who were followed for ≥48 months and received no cytoreductive therapy were retrospectively studied. Patients were classified according to the pattern of evolution of sBT observed. Overall 16/74 (22%) cases had decreasing sBT levels, 48 (65%) patients showed increasing sBT levels and 10 (13%) patients showed a fluctuating pattern. Patients with significantly increasing sBT (sBT slope ≥0.15) after 48 months of follow-up showed a slightly greater rate of development of diffuse bone sclerosis (13% vs. 2%) and hepatomegaly plus splenomegaly (16% vs. 5%), as well as a significantly greater frequency of multilineage vs. mast cells (MC)-restricted KIT mutation (p = 0.01) together with a greater frequency of cases with progression of ISM to smouldering and aggressive SM (p = 0.03), and a shorter progression-free survival (p = 0.03). Monitoring of sBT in ISM patients is closely associated with poor prognosis disease features as well as with disease progression, pointing out the need for a closer follow-up in ISM patients with progressively increasing sBT values.

Associations between polymorphisms of HLA-B gene and postmenopausal osteoporosis in Chinese Han population.

PubMed

Li, S-M; Zhou, D-X; Liu, M-Y

2014-08-01

Osteoporosis is a systemic skeletal disease, which is more prevalent in postmenopausal women. Osteoporosis likely develops beginning with genetic risk. This study explored the relationships between polymorphisms of HLA-B gene and postmenopausal osteoporosis in a Chinese Han population. Polymerase chain reaction sequence-based typing (PCR-SBT) method was used for DNA typing at HLA-B locus in 70 patients with postmenopausal osteoporosis and 73 healthy controls in female Han population of Shaanxi Province, situated in north-western China. We found that 40 HLA-B alleles in postmenopausal osteoporosis patients and control subjects, respectively. Furthermore, the frequency of HLA-B* 3501 allele was significantly higher in postmenopausal osteoporosis patients than in the control group (P = 0.033), and the relative risk was 7.632 (95% CI: 0.927-62.850). Our results suggest that HLA-B* 3501 was likely an important risk factor for postmenopausal osteoporosis. As different populations have different HLA polymorphisms, further investigation of the relationship of various HLA genes and osteoporosis with larger sample size is still necessary in the future. © 2014 John Wiley & Sons Ltd.

Role of VIP and substance P in NANC innervation in the longitudinal smooth muscle of the rat jejunum - influence of extrinsic denervation.

PubMed

Kasparek, Michael S; Fatima, Javairiah; Iqbal, Corey W; Duenes, Judith A; Sarr, Michael G

2007-07-01

This study was designed to determine changes in nonadrenergic, noncholinergic (NANC) neurotransmission mediated by Vasoactive Intestinal Polypeptide (VIP) and Substance P after small bowel transplantation (SBT). Six groups of rats (n > or = 6 per group) were studied: naïve controls (NC); 1 wk after anesthesia/sham celiotomy (SC-1); 1 or 8 wk after jejunal and ileal transection/reanastomosis (TA-1, TA-8), or syngeneic, orthotopic SBT (SBT-1, SBT-8). Jejunal longitudinal muscle strips were studied under NANC-conditions for spontaneous contractile activity, response to exogenous VIP and Substance P, and electrical field stimulation (EFS). Spontaneous activity did not differ between the six groups. VIP inhibited contractile activity in all groups 1 wk postoperatively (P < 0.05), which was prevented by the NO synthase inhibitor L-N(G)-nitro arginine (L-NNA). In contrast, VIP had no effect in the other groups. Precontraction with Substance P exposed an inhibitory effect of VIP in all groups (P < 0.05 each). Substance P increased contractile activity in all groups, but to a lesser extent in SBT-8 compared with NC, TA-8, and SBT-1 (P < 0.05). The inhibitory effect of EFS at 6 Hz was prevented by L-NNA in NC and TA-8; addition of the VIP antagonist ([D-p-Cl-Phe(6), Leu(17)]-VIP) increased contractile activity in NC, but not in TA-8 and SBT-8. The Substance P antagonist ([D-Pro(2), D-Trp(7,9)]-Substance P) decreased contractile activity during EFS at 50 Hz in NC and SBT-8. SBT decreased response to exogenous Substance P, although release of endogenous Substance P (EFS) is preserved. Changes in VIP signaling are acute and reversible and not caused by effects of SBT.

Managing simulation-based training: A framework for optimizing learning, cost, and time

NASA Astrophysics Data System (ADS)

Richmond, Noah Joseph

This study provides a management framework for optimizing training programs for learning, cost, and time when using simulation based training (SBT) and reality based training (RBT) as resources. Simulation is shown to be an effective means for implementing activity substitution as a way to reduce risk. The risk profile of 22 US Air Force vehicles are calculated, and the potential risk reduction is calculated under the assumption of perfect substitutability of RBT and SBT. Methods are subsequently developed to relax the assumption of perfect substitutability. The transfer effectiveness ratio (TER) concept is defined and modeled as a function of the quality of the simulator used, and the requirements of the activity trained. The Navy F/A-18 is then analyzed in a case study illustrating how learning can be maximized subject to constraints in cost and time, and also subject to the decision maker's preferences for the proportional and absolute use of simulation. Solution methods for optimizing multiple activities across shared resources are next provided. Finally, a simulation strategy including an operations planning program (OPP), an implementation program (IP), an acquisition program (AP), and a pedagogical research program (PRP) is detailed. The study provides the theoretical tools to understand how to leverage SBT, a case study demonstrating these tools' efficacy, and a set of policy recommendations to enable the US military to better utilize SBT in the future.

Acceptance-Based versus Standard Behavioral Treatment for Obesity: Results from the Mind Your Health Randomized Controlled Trial

PubMed Central

Forman, Evan M.; Butryn, Meghan L.; Manasse, Stephanie M.; Crosby, Ross D.; Goldstein, Stephanie P.; Wyckoff, Emily P.; Thomas, J. Graham

2016-01-01

Objective To evaluate the efficacy, as well as potential moderators and mediators, of a revised acceptance-based behavioral treatment (ABT) for obesity, relative to standard behavioral treatment (SBT). Design and Methods Participants with overweight and obesity (n=190) were randomized to 25 sessions of ABT or SBT over 1 year. Primary outcome (weight), mediator and moderator measurements were taken at baseline, 6 months and/or 12 months, and weight was also measured every session. Results Participants assigned to ABT attained a significantly greater 12-month weight loss (13.3% ± 0.83) than did those assigned to SBT (9.8% ± 0.87; p=.005). A condition by quadratic time effect on session-by-session weights (p=.01) indicated that SBT had a shallower trajectory of weight loss followed by an upward deflection. ABT participants were also more likely to maintain a 10% weight loss at 12 months (64.0% vs 48.9%; p=.04). No evidence of moderation was found. Results supported the mediating role of autonomous motivation and psychological acceptance of food-related urges. Conclusion Behavioral weight loss outcomes can be improved by integrating self-regulation skills that are reflected in acceptance-based treatment, i.e., tolerating discomfort and reduction in pleasure, enacting commitment to valued behavior, and being mindfully aware during moments of decision making. PMID:27670400

Acceptance-based versus standard behavioral treatment for obesity: Results from the mind your health randomized controlled trial.

PubMed

Forman, Evan M; Butryn, Meghan L; Manasse, Stephanie M; Crosby, Ross D; Goldstein, Stephanie P; Wyckoff, Emily P; Thomas, J Graham

2016-10-01

To evaluate the efficacy, as well as potential moderators and mediators, of a revised acceptance-based behavioral treatment (ABT) for obesity, relative to standard behavioral treatment (SBT). Participants with overweight and obesity (n = 190) were randomized to 25 sessions of ABT or SBT over 1 year. Primary outcome (weight), mediator, and moderator measurements were taken at baseline, 6 months, and/or 12 months, and weight was also measured every session. Participants assigned to ABT attained a significantly greater 12-month weight loss (13.3% ± 0.83%) than did those assigned to SBT (9.8% ± 0.87%; P = 0.005). A condition by quadratic time effect on session-by-session weights (P = 0.01) indicated that SBT had a shallower trajectory of weight loss followed by an upward deflection. ABT participants were also more likely to maintain a 10% weight loss at 12 months (64.0% vs. 48.9%; P = 0.04). No evidence of moderation was found. Results supported the mediating role of autonomous motivation and psychological acceptance of food-related urges. Behavioral weight loss outcomes can be improved by integrating self-regulation skills that are reflected in acceptance-based treatment, i.e., tolerating discomfort and reduction in pleasure, enacting commitment to valued behavior, and being mindfully aware during moments of decision-making. © 2016 The Obesity Society.

Obstetric skills drills: evaluation of teaching methods.

PubMed

Birch, L; Jones, N; Doyle, P M; Green, P; McLaughlin, A; Champney, C; Williams, D; Gibbon, K; Taylor, K

2007-11-01

To determine the most effective method of delivering training to staff on the management of an obstetric emergency. The research was conducted in a District General Hospital in the UK, delivering approximately 3500 women per year. Thirty-six staff, comprising of junior and senior medical and midwifery staff were included as research subjects. Each of the staff members were put into one of six multi-professional teams. Effectively, this gave six teams, each comprising of six members. Three teaching methods were employed. Lecture based teaching (LBT), simulation based teaching (SBT) or a combination of these two (LAS). Each team of staff were randomly allocated to undertake a full day of training in the management of Post Partum Haemorrhage utilising one of these three teaching methods. Team knowledge and performance were assessed pre-training, post training and at three months later. In addition to this assessment of knowledge and performance, qualitative semi-structured interviews were carried out with 50% of the original cohort one year after the training, to explore anxiety, confidence, communication, knowledge retention, enjoyment and transferable skills. All teams improved in their performance and knowledge. The teams taught using simulation only (SBT) were the only group to demonstrate sustained improvement in clinical management of the case, confidence, communication skills and knowledge. However, the study did not have enough power to reach statistical significance. The SBT group reported transferable skills and less anxiety in subsequent emergencies. SBT and LAS reported improved multidisciplinary communication. Although tiring, the SBT was enjoyed the most. Obstetrics is a high risk speciality, in which emergencies are to some extent, inevitable. Training staff to manage these emergencies is a fundamental principal of risk management. Traditional risk management strategies based on incident reporting and event analysis are reactive and not always effective. Simulation based training is an appropriate proactive approach to reducing errors and risk in obstetrics, improving teamwork and communication, whilst giving the student a multiplicity of transferable skills to improve their performance.

Prevalence of mip virulence gene and PCR-base sequence typing of Legionella pneumophila from cooling water systems of two cities in Iran.

PubMed

Ahmadrajabi, Roya; Shakibaie, Mohammad Reza; Iranmanesh, Zahra; Mollaei, Hamid Reza; Sobhanipoor, Mohammad Hossein

2016-07-03

Legionella pneumophila is the primary respiratory pathogen and mostly transmitted to human through water cooling systems and cause mild to severe pneumonia with high mortality rate especially in elderly both in hospitals and community. However, current Legionella risk assessments may be compromised by uncertainties in Legionella detection methods. Here, we investigated the presence of L. pneumophila mip gene in water samples collected from different hospitals cooling towers, nursing homes and building/hotels water coolants from two geographical locations of Iran (Kerman and Bam cities) during summer season of 2015 by both nested and real-time PCR methods. Analysis of the 128 water samples for presence of the mip gene by nested-PCR revealed, 18 (23%) positive cases in Kerman and 7(14%) in Bam. However, when samples were tested by real-time PCR, we identified 4 more new cases of L. pneumophila in the hospitals as well as nursing homes water systems that were missed by nested-PCR. The highest rate of contamination was detected in water obtained from hospitals cooling towers in both the cities (p≤0.05). Dendrogram analysis and clonal relationship by PCR-base sequence typing (SBT) of the L. pneumophila genomic DNAs in Kerman water samples showed close clonal similarities among the isolates, in contrast, isolates identified from Bam city demonstrated two fingerprint patterns. The clones from hospital water samples were more related to the L. pneumophila serogroup- 1.

Prevalence of mip virulence gene and PCR-base sequence typing of Legionella pneumophila from cooling water systems of two cities in Iran

PubMed Central

Ahmadrajabi, Roya; Shakibaie, Mohammad Reza; Iranmanesh, Zahra; Mollaei, Hamid Reza; Sobhanipoor, Mohammad Hossein

2016-01-01

ABSTRACT Legionella pneumophila is the primary respiratory pathogen and mostly transmitted to human through water cooling systems and cause mild to severe pneumonia with high mortality rate especially in elderly both in hospitals and community. However, current Legionella risk assessments may be compromised by uncertainties in Legionella detection methods. Here, we investigated the presence of L. pneumophila mip gene in water samples collected from different hospitals cooling towers, nursing homes and building/hotels water coolants from two geographical locations of Iran (Kerman and Bam cities) during summer season of 2015 by both nested and real-time PCR methods. Analysis of the 128 water samples for presence of the mip gene by nested-PCR revealed, 18 (23%) positive cases in Kerman and 7(14%) in Bam. However, when samples were tested by real-time PCR, we identified 4 more new cases of L. pneumophila in the hospitals as well as nursing homes water systems that were missed by nested-PCR. The highest rate of contamination was detected in water obtained from hospitals cooling towers in both the cities (p≤0.05). Dendrogram analysis and clonal relationship by PCR-base sequence typing (SBT) of the L. pneumophila genomic DNAs in Kerman water samples showed close clonal similarities among the isolates, in contrast, isolates identified from Bam city demonstrated two fingerprint patterns. The clones from hospital water samples were more related to the L. pneumophila serogroup- 1. PMID:27028760

Studying the Power of the Integrative Weaning Index in Predicting the Success Rate of the Spontaneous Breathing Trial in Patients under Mechanical Ventilation.

PubMed

Ebrahimabadi, Sahar; Moghadam, Ahmad Bagheri; Vakili, Mohammadali; Modanloo, Mahnaz; Khoddam, Homeira

2017-08-01

The use of weaning predictive indicators can avoid early extubation and wrongful prolonged mechanical ventilation. This study aimed to determine the power of the integrative weaning index (IWI) in predicting the success rate of the spontaneous breathing trial (SBT) in patients under mechanical ventilation. In this prospective study, 105 patients undergoing mechanical ventilation for over 48 h were enrolled. Before weaning initiation, the IWI was calculated and based on the defined cutoff point (≥25), the success rate of the SBT was predicted. In case of weaning from the device, 2-h SBT was performed and the physiologic and respiratory indices were continuously studied while being intubated. If they were in the normal range besides the patient's tolerance, the test was considered as a success. The result was then compared with the IWI and further analyzed. The SBT was successful in 90 (85.7%) and unsuccessful in 15 (14.3%) cases. The difference between the true patient outcome after SBT, and the IWI prediction was 0.143 according to the Kappa agreement coefficient ( P < 0.001). Moreover, regarding the predictive power, IWI had high sensitivity (95.6%), specificity (40%), positive and negative predictive values (90.5% and 60), positive and negative likelihood ratios (1.59 and 0.11), and accuracy (86.7%). The IWI as a more objective indicator has acceptable accuracy and power for predicting the 2-h SBT result. Therefore, in addition to the reliable prediction of the final weaning outcome, it has favorable power to predict if the patient is ready to breathe spontaneously as the first step to weaning.

Studying the Power of the Integrative Weaning Index in Predicting the Success Rate of the Spontaneous Breathing Trial in Patients under Mechanical Ventilation

PubMed Central

Ebrahimabadi, Sahar; Moghadam, Ahmad Bagheri; Vakili, Mohammadali; Modanloo, Mahnaz; Khoddam, Homeira

2017-01-01

Background and Aims: The use of weaning predictive indicators can avoid early extubation and wrongful prolonged mechanical ventilation. This study aimed to determine the power of the integrative weaning index (IWI) in predicting the success rate of the spontaneous breathing trial (SBT) in patients under mechanical ventilation. Materials and Methods: In this prospective study, 105 patients undergoing mechanical ventilation for over 48 h were enrolled. Before weaning initiation, the IWI was calculated and based on the defined cutoff point (≥25), the success rate of the SBT was predicted. In case of weaning from the device, 2-h SBT was performed and the physiologic and respiratory indices were continuously studied while being intubated. If they were in the normal range besides the patient's tolerance, the test was considered as a success. The result was then compared with the IWI and further analyzed. Results: The SBT was successful in 90 (85.7%) and unsuccessful in 15 (14.3%) cases. The difference between the true patient outcome after SBT, and the IWI prediction was 0.143 according to the Kappa agreement coefficient (P < 0.001). Moreover, regarding the predictive power, IWI had high sensitivity (95.6%), specificity (40%), positive and negative predictive values (90.5% and 60), positive and negative likelihood ratios (1.59 and 0.11), and accuracy (86.7%). Conclusion: The IWI as a more objective indicator has acceptable accuracy and power for predicting the 2-h SBT result. Therefore, in addition to the reliable prediction of the final weaning outcome, it has favorable power to predict if the patient is ready to breathe spontaneously as the first step to weaning. PMID:28904477

Stellar Population Synthesis of Star-forming Clumps in Galaxy Pairs and Non-interacting Spiral Galaxies

NASA Astrophysics Data System (ADS)

Zaragoza-Cardiel, Javier; Smith, Beverly J.; Rosado, Margarita; Beckman, John E.; Bitsakis, Theodoros; Camps-Fariña, Artemi; Font, Joan; Cox, Isaiah S.

2018-02-01

We have identified 1027 star-forming complexes in a sample of 46 galaxies from the Spirals, Bridges, and Tails (SB&T) sample of interacting galaxies, and 693 star-forming complexes in a sample of 38 non-interacting spiral (NIS) galaxies in 8 μm observations from the Spitzer Infrared Array Camera. We have used archival multi-wavelength UV-to IR observations to fit the observed spectral energy distribution of our clumps with the Code Investigating GALaxy Emission using a double exponentially declined star formation history. We derive the star formation rates (SFRs), stellar masses, ages and fractions of the most recent burst, dust attenuation, and fractional emission due to an active galactic nucleus for these clumps. The resolved star formation main sequence holds on 2.5 kpc scales, although it does not hold on 1 kpc scales. We analyzed the relation between SFR, stellar mass, and age of the recent burst in the SB&T and NIS samples, and we found that the SFR per stellar mass is higher in the SB&T galaxies, and the clumps are younger in the galaxy pairs. We analyzed the SFR radial profile and found that the SFR is enhanced through the disk and in the tidal features relative to normal spirals.

Automated pipeline to analyze non-contact infrared images of the paraventricular nucleus specific leptin receptor knock-out mouse model

NASA Astrophysics Data System (ADS)

Diaz Martinez, Myriam; Ghamari-Langroudi, Masoud; Gifford, Aliya; Cone, Roger; Welch, E. B.

2015-03-01

Evidence of leptin resistance is indicated by elevated leptin levels together with other hallmarks of obesity such as a defect in energy homeostasis.1 As obesity is an increasing epidemic in the US, the investigation of mechanisms by which leptin resistance has a pathophysiological impact on energy is an intensive field of research.2 However, the manner in which leptin resistance contributes to the dysregulation of energy, specifically thermoregulation,3 is not known. The aim of this study was to investigate whether the leptin receptor expressed in paraventricular nucleus (PVN) neurons plays a role in thermoregulation at different temperatures. Non-contact infrared (NCIR) thermometry was employed to measure surface body temperature (SBT) of nonanesthetized mice with a specific deletion of the leptin receptor in the PVN after exposure to room (25 °C) and cold (4 °C) temperature. Dorsal side infrared images of wild type (LepRwtwt/sim1-Cre), heterozygous (LepRfloxwt/sim1-Cre) and knock-out (LepRfloxflox/sim1-Cre) mice were collected. Images were input to an automated post-processing pipeline developed in MATLAB to calculate average and maximum SBTs. Linear regression was used to evaluate the relationship between sex, cold exposure and leptin genotype with SBT measurements. Findings indicate that average SBT has a negative relationship to the LepRfloxflox/sim1-Cre genotype, the female sex and cold exposure. However, max SBT is affected by the LepRfloxflox/sim1-Cre genotype and the female sex. In conclusion this data suggests that leptin within the PVN may have a neuroendocrine role in thermoregulation and that NCIR thermometry combined with an automated imaging-processing pipeline is a promising approach to determine SBT in non-anesthetized mice.

Diversity changes of microbial communities into hospital surface environments.

PubMed

Yano, Rika; Shimoda, Tomoko; Watanabe, Reina; Kuroki, Yasutoshi; Okubo, Torahiko; Nakamura, Shinji; Matsuo, Junji; Yoshimura, Sadako; Yamaguchi, Hiroyuki

2017-07-01

Previous works have demonstrated considerable variability in hospital cleanliness in Japan, suggesting that contamination is driven by factors that are currently poorly controlled. We undertook 16S rRNA sequence analysis to study population structures of hospital environmental microbiomes to see which factor(s) impacted contamination. One hundred forty-four samples were collected from surfaces of three hospitals with distinct sizes ("A": >500 beds, "B": 100-500 beds, "C": <100 beds). Sample locations of two ward types (Surgical and Internal) included patient room bed table (multiple) (4BT), patient overbed table (multiple) (4OT), patient room sink (multiple) (4S), patient room bed table (single) (SBT), patient overbed table (single) (SOT), patient room sink (single) (SS), nurse desk (ND), and nurse wagon (NW). Total DNA was extracted from each sample, and the 50 samples that yielded sufficient DNA were used for further 16S rRNA sequencing of hospital microbiome populations with cluster analysis. The number of assigned bacterial OTU populations was significantly decreased in hospital "C" compared to the other hospitals. Cluster analysis of sampling locations revealed that the population structure in almost all locations of hospital "C" and some locations in the other hospitals was very similar and unusually skewed with a family, Enterobacteriaceae. Interestingly, locations included patient area (4OT, 4BT, SBT) and nurse area (ND), with a device (NW) bridging the two and a place (4S and SS) shared between patients or visitors. We demonstrated diversity changes of hospital environmental microbiomes with a skewed population, presumably by medical staff pushing NWs or sinks shared by patients or visitors. Copyright © 2017 Japanese Society of Chemotherapy and The Japanese Association for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

The effects of active (hot-seat) versus observer roles during simulation-based training on stress levels and non-technical performance: a randomized trial.

PubMed

Bong, Choon Looi; Lee, Sumin; Ng, Agnes Suah Bwee; Allen, John Carson; Lim, Evangeline Hua Ling; Vidyarthi, Arpana

2017-01-01

Active 'hands-on' participation in the 'hot-seat' during immersive simulation-based training (SBT) induces stress for participants, which is believed to be necessary to improve performance. We hypothesized that observers of SBT can subsequently achieve an equivalent level of non-technical performance as 'hot-seat' participants despite experiencing lower stress. We randomized 37 anaesthesia trainees into two groups to undergo three consecutive SBT scenarios. Eighteen 'hot-seat' trainees actively participated in all three scenarios, and 19 'observer' trainees were directed to observe the first two scenarios and participated in the 'hot-seat' only in scenario 3. Salivary cortisol (SC) was measured at four time points during each scenario. Primary endpoint for stress response was the change in SC (ΔSC) from baseline. Performance was measured using the Anaesthetist's Non-Technical Skills (ANTS) Score. Mean SC increased in all participants whenever they were in the 'hot-seat' role, but not when in the observer role. Hot-seat ΔSC (mcg/dL) for scenarios 1, 2, and 3 were 0.122 ( p  = 0.001), 0.074 ( p  = 0.047), and 0.085 ( p  = 0.023), respectively. Observers ΔSC (mcg/dL) for scenarios 1, 2, and 3 were -0.062 ( p  = 0.091), 0.010 ( p  = 0.780), and 0.144 ( p  = 0.001), respectively. Mean ANTS scores were equivalent between the 'hot-seat' (40.0) and 'observer' (39.4) groups in scenario 3 ( p  = 0.733). Observers of SBT achieved an equivalent level of non-technical performance, while experiencing lower stress than trainees repeatedly trained in the 'hot-seat'. Our findings suggest that directed observers may benefit from immersive SBT even without repeated 'hands-on' experience and stress in the hot-seat. The directed observer role may offer a less stressful, practical alternative to the traditional 'hot-seat' role, potentially rendering SBT accessible to a wider audience. ClinicalTrials.gov Identifier NCT02211378, registered August 5, 2014, retrospectively registered.

Sedentary Behaviour in Swiss Children and Adolescents: Disentangling Associations with the Perceived and Objectively Measured Environment.

PubMed

Bringolf-Isler, Bettina; de Hoogh, Kees; Schindler, Christian; Kayser, Bengt; Suggs, L Suzanne; Dössegger, Alain; Probst-Hensch, Nicole

2018-05-04

Identifying correlates of sedentary behaviour across all levels of the ecological model and understanding their interrelations is a promising method to plan effective interventions. The present study examined whether the objectively assessed and the perceived neighbourhood are associated with children’s sedentary behaviour time (SBT). A comprehensive set of factors at different levels of influence across the ecological model were taken into account and analysed for mediating and modifying effects. Analyses were based on 1306 children and adolescents (6⁻16 years) participating in the population-based SOPHYA-study. Accelerometers were used to assess SBT, the perceived environment was examined by a validated parental questionnaire, and objective environmental data were allocated using GIS (ArcMap 10.2, Esri, Redlands, CA, USA) for each family’s residential address. A high perceived safety was associated with less SBT. Boys, those whose residential neighbourhood was characterized by dead ends in urban areas, a low main street density in the neighbourhood of children and greenness were less likely to exhibit SBT. The association of the objective environment with the respective parental perceptions was low and no significant mediating effect was found for the perceived environment. We conclude for land-use planning to reduce sedentary behaviour objective environments should be complemented with efforts to increase parental sense of security.

A generalized form of the Bernoulli Trial collision scheme in DSMC: Derivation and evaluation

NASA Astrophysics Data System (ADS)

Roohi, Ehsan; Stefanov, Stefan; Shoja-Sani, Ahmad; Ejraei, Hossein

2018-02-01

The impetus of this research is to present a generalized Bernoulli Trial collision scheme in the context of the direct simulation Monte Carlo (DSMC) method. Previously, a subsequent of several collision schemes have been put forward, which were mathematically based on the Kac stochastic model. These include Bernoulli Trial (BT), Ballot Box (BB), Simplified Bernoulli Trial (SBT) and Intelligent Simplified Bernoulli Trial (ISBT) schemes. The number of considered pairs for a possible collision in the above-mentioned schemes varies between N (l) (N (l) - 1) / 2 in BT, 1 in BB, and (N (l) - 1) in SBT or ISBT, where N (l) is the instantaneous number of particles in the lth cell. Here, we derive a generalized form of the Bernoulli Trial collision scheme (GBT) where the number of selected pairs is any desired value smaller than (N (l) - 1), i.e., Nsel < (N (l) - 1), keeping the same the collision frequency and accuracy of the solution as the original SBT and BT models. We derive two distinct formulas for the GBT scheme, where both formula recover BB and SBT limits if Nsel is set as 1 and N (l) - 1, respectively, and provide accurate solutions for a wide set of test cases. The present generalization further improves the computational efficiency of the BT-based collision models compared to the standard no time counter (NTC) and nearest neighbor (NN) collision models.

Microbiological diagnosis and molecular typing of Legionella strains during an outbreak of legionellosis in Southern Germany.

PubMed

Essig, Andreas; von Baum, Heike; Gonser, Theodor; Haerter, Georg; Lück, Christian

2016-02-01

An explosive outbreak of Legionnaires' disease with 64 reported cases occurred in Ulm/Neu-Ulm in the South of Germany in December 2009/January 2010 caused by Legionella (L.) pneumophila serogroup 1, monoclonal (mAb) subtype Knoxville, sequence type (ST) 62. Here we present the clinical microbiological results from 51 patients who were diagnosed at the University hospital of Ulm, the results of the environmental investigations and of molecular typing of patients and environmental strains. All 50 patients from whom urine specimens were available were positive for L. pneumophila antigen when an enzyme-linked immunosorbent assay (EIA) was used following concentration of those urine samples that tested initially negative. The sensitivity of the BinaxNow rapid immunographic assay (ICA), after 15 min reading and after 60 min reading were 70% and 84%, respectively. Direct typing confirmed the monoclonal subtype Knoxville in 5 out of 8 concentrated urine samples. Real time PCR testing of respiratory tract specimens for L. pneumophila was positive in 15 out of 25 (60%) patients. Direct nested sequence based typing (nSBT) in some of these samples allowed partial confirmation of ST62. L. pneumophila serogroup 1, monoclonal subtype Knoxville ST62, defined as the epidemic strain was isolated from 8 out of 31 outbreak patients (26%) and from one cooling tower confirming it as the most likely source of the outbreak. While rapid detection of Legionella antigenuria was crucial for the recognition and management of the outbreak, culture and molecular typing of the strains from patients and environmental specimens was the clue for the rapid identification of the source of infection. Copyright © 2016 Elsevier GmbH. All rights reserved.

Using Simulation in Interprofessional Education.

PubMed

Paige, John T; Garbee, Deborah D; Brown, Kimberly M; Rojas, Jose D

2015-08-01

Simulation-based training (SBT) is a powerful educational tool permitting the acquisition of surgical knowledge, skills, and attitudes at both the individual- and team-based level in a safe, nonthreatening learning environment at no risk to a patient. Interprofessional education (IPE), in which participants from 2 or more health or social care professions learn interactively, can help improve patient care through the promotion of efficient coordination, dissemination of advances in care across specialties and professions, and optimization of individual- and team-based function. Nonetheless, conducting SBT IPE sessions poses several tactical and strategic challenges that must be effectively overcome to reap IPE's benefits. Copyright © 2015 Elsevier Inc. All rights reserved.

Evaluation of LABType® SSO HLA Typing using the Luminex Platform: Cord Blood Registry Typing for the Korean Population.

PubMed

Roh, Eun-Youn; Song, Eun-Young; Chang, Jee-Young; Yoon, Jong-Hyun; Shin, Sue

2016-08-01

The performance of a new intermediate-resolution method using a PCR-Luminex platform and LABType® SSO A, B DRB1 kits as an HLA typing method for the cord blood (CB) registry of the Korean population was investigated. A total of 1,413 cord blood units (CBUs) were enrolled - 1,382 from Koreans and 31 from non-Koreans or mixed-ancestry individuals. HLA-A, -B, and -DRB1 typing was performed using the LABType® SSO typing kits. HLA typing with the DNA method and 2-digit results are mandatory for the public CB bank in Korea according to the "CB Act." The proportions of ambiguous results in the 2-digit assignment were 14.6% (206/1,413) and 14.8% (205/ 1,382) among the total subjects and the Korean donors, respectively. In the 2-digit resolution, 3 different HLA-A types (69 CBUs), 31 HLA-B types (124 CBUs), and 3 HLA-DRB1 types (13 CBUs) showed ambiguous results. The 'most probable type' to the ambiguous results based on the reported Korean HLA allele frequencies were able to be assigned. The most probable results were 100% consistent with the confirmed types as determined by the HD kits (DRB1) and additional PCR-SBT or PCR-SSP tests (A and B). Luminex technology is more automated and less labor intensive than the conventional SSO typing method, and the results are less affected by differences between inspectors. Although it is not satisfactory as a sole confirmation test and cannot be used as a replacement for the PCR-SBT test, the combination of Luminex technology with LABType® SSO kits and population frequency data provides a proper typing platform that can be used as a qualifying test for CB registries.

Enhancement of fatigue endurance in ferroelectric PZT ceramic by the addition of bismuth layered SBT

NASA Astrophysics Data System (ADS)

Namsar, O.; Pojprapai, S.; Watcharapasorn, A.; Jiansirisomboon, S.

2014-10-01

Electrical fatigue properties of (1-x)PZT-xSBT ceramics (x = 0-1.0 weight fraction) were characterized. It was found that pure PZT ceramic had severe polarization fatigue. This was mainly attributed to an occurrence of the macroscopic cracks at near-electrode regions. On the contrary, pure SBT ceramic exhibited excellent fatigue resistance, which was attributed primarily to weak domain wall pinning. As small amount of SBT (0.1 ≤ x ≤ 0.3) was added into PZT, a small reduction of remanent polarization after fatigue process was observed. This demonstrated that these ceramics had high stability during the repeated domain switching due to their low oxygen vacancy concentration. Therefore, these results suggested that this new ceramic PZT-SBT system seemed to be an alternative material for replacing pure PZT in ferroelectric memory applications.

SB-T-121205, a next-generation taxane, enhances apoptosis and inhibits migration/invasion in MCF-7/PTX cells

PubMed Central

Zheng, Xiaowei; Wang, Changwei; Xing, Yuanming; Chen, Siying; Meng, Ti; You, Haisheng; Ojima, Iwao; Dong, Yalin

2017-01-01

Breast cancer is the leading cause of cancer death among women. Paclitaxel, a mitotic inhibitor, is highly effective in the treatment of breast cancer. However, development of resistance to paclitaxel limits its clinical use. Identifying new compounds and new strategies that are effective against breast cancer, in particular drug-resistant cancer, is of great importance. The aim of the present study was to explore the potential of a next-generation taxoid, SB-T-121205, in modulating the proliferation, migration and invasion of paclitaxel-resistant human breast cancer cells (MCF-7/PTX) and further evaluate the underlying molecular mechanisms. The results of MTT assay showed that SB-T-121205 has much higher potency to human breast cancer cells (MCF-7/S, MCF-7/PTX and MDA-MB-453 cells) than paclitaxel, while that the non-tumorigenic human bronchial epithelial cells (BEAS-2B) were slightly less sensitive to SB-T-121205 than paclitaxel. Flow cytometry and western blot methods revealed that SB-T-121205 induced cell cycle arrest at the G2/M phase and apoptosis in MCF-7/PTX cells through accelerating mitochondrial apoptotic pathway, resulting in reduction of Bcl-2/Bax ratio, as well as elevation of caspase-3, caspase-9, and poly(ADP-ribose) polymerase (PARP) levels. Moreover, SB-T-121205 changed epithelial-mesenchymal transition (EMT) property, and suppressed migration and invasion abilities of MCF-7/PTX cells. Additionally, SB-T-121205 exerted antitumor activity by inhibiting the transgelin 2 and PI3K/Akt pathway. These findings indicate that SB-T-121205 is a potent antitumor agent that promotes apoptosis and also recedes migration/invasion abilities of MCF-7/PTX cells by restraining the activity of transgelin 2 and PI3K/Akt, as well as mitochondrial apoptotic pathway. Such results suggest a potential clinical value of SB-T-121205 in breast cancer treatment. PMID:28197640

Subgrouping For Patients With Low Back Pain: A Multidimensional Approach Incorporating Cluster Analysis & The STarT Back Screening Tool

PubMed Central

Beneciuk, Jason M.; Robinson, Michael E.; George, Steven Z.

2014-01-01

Early screening for psychological distress has been suggested to improve patient management for individuals experiencing low back pain. This study compared two approaches to psychological screening (i.e., multidimensional and unidimensional) so that preliminary recommendations on which approach may be appropriate for use in clinical settings other than primary care could be provided. Specifically, this study investigated STarT Back Screening Tool (SBT): 1) discriminant validity by evaluating its relationship with unidimensional psychological measures and 2) construct validity by evaluating how SBT risk categories compared to empirically derived subgroups using unidimensional psychological and disability measures. Patients (n = 146) receiving physical therapy for LBP were administered the SBT and a battery of unidimensional psychological measures at initial evaluation. Clinical measures consisted of pain intensity and self-reported disability. Several SBT risk dependent relationships (i.e., SBT low < medium < high risk) were identified for unidimensional psychological measure scores with depressive symptom scores associated with the strongest influence on SBT risk categorization. Empirically derived subgroups indicated that there was no evidence of distinctive patterns amongst psychological or disability measures other than high or low profiles, therefore two groups may provide a more clear representation of the level of pain associated psychological distress, maladaptive coping and disability in this setting, as compared to three groups which have been suggested when using the SBT in primary care settings. PMID:25451622

Sea buckthorn (Hippophae rhamnoides L.) oil protects against chronic stress-induced inhibitory function of natural killer cells in rats.

PubMed

Diandong, Hou; Feng, Gu; Zaifu, Liang; Helland, Timothy; Weixin, Fu; Liping, Cai

2016-03-01

Chronic stress can suppress natural killer (NK) cell activity; this may also be related to the effect of stress on the neuroendocrine-immune network. Sea buckthorn (SBT) (Hippophae rhamnoides L.) is a thorny nitrogen fixing deciduous shrub, native to both Europe and Asia. It has been used as a medicinal plant in Tibetan and Mongolian traditional medicines. SBT has multifarious medical properties, including anti-fatigue as well as immunoregulatory effects. This study reports the effects of SBT oil with regard to the cytotoxicity and quantity of NK cells in the blood of a chronic-stress rat model, in addition to its mechanisms on the neuroendocrine-immune network. These results show that SBT oil, given by gavage to rats with chronic stress, could increase the following: body weight, NK cell quantities, and cytotoxicity, as well as the expression of perforin and granzyme B. The results also show that SBT oil in rats with chronic stress could suppress cortisol, ACTH, IL-1β and TNF-α levels, in addition to increasing 5-HT and IFN-γ serum levels. This leads to suggest that SBT oil, in rats with chronic stress, can increase NK cell cytotoxicity by upregulating the expression of perforin and granzyme B, thus causing associated effects of SBT oil on the neuroendocrine-immune network. © The Author(s) 2015.

Sea buckthorn (Hippophae rhamnoides L.) oil protects against chronic stress-induced inhibitory function of natural killer cells in rats

PubMed Central

Diandong, Hou; Feng, Gu; Zaifu, Liang; Helland, Timothy; Weixin, Fu; Liping, Cai

2015-01-01

Chronic stress can suppress natural killer (NK) cell activity; this may also be related to the effect of stress on the neuroendocrine–immune network. Sea buckthorn (SBT) (Hippophae rhamnoides L.) is a thorny nitrogen fixing deciduous shrub, native to both Europe and Asia. It has been used as a medicinal plant in Tibetan and Mongolian traditional medicines. SBT has multifarious medical properties, including anti-fatigue as well as immunoregulatory effects. This study reports the effects of SBT oil with regard to the cytotoxicity and quantity of NK cells in the blood of a chronic-stress rat model, in addition to its mechanisms on the neuroendocrine–immune network. These results show that SBT oil, given by gavage to rats with chronic stress, could increase the following: body weight, NK cell quantities, and cytotoxicity, as well as the expression of perforin and granzyme B. The results also show that SBT oil in rats with chronic stress could suppress cortisol, ACTH, IL-1β and TNF-α levels, in addition to increasing 5-HT and IFN-γ serum levels. This leads to suggest that SBT oil, in rats with chronic stress, can increase NK cell cytotoxicity by upregulating the expression of perforin and granzyme B, thus causing associated effects of SBT oil on the neuroendocrine–immune network. PMID:26684638

Pathology of ochratoxin A-induced nephrotoxicity in Japanese quail and its protection by sea buckthorn (Hippophae rhamnoides L.).

PubMed

Patial, V; Asrani, R K; Patil, R D; Ledoux, D R; Rottinghaus, G E

2013-12-01

The present study was designed to study the protective effect of sea buckthorn (SBT) against renal damage induced by ochratoxin A (OTA) in Japanese quail. Day-old quail chicks were divided into six groups and fed a basal quail chick mash containing 2% SBT leaf powder (group SX), OTA at a dietary level of 3 ppm (group OX), 25 ppm L-beta-phenylalanine (Phe) plus 3 ppm OTA (group OP), 2% dietary level of SBT leaf powder plus 3 ppm OTA (group OS), SBT leaf extract at a level of 10%/L of drinking water plus 3 ppm OTA (group OSS), and a standard toxin-free feed (group CX, control) for 21 days. OTA at 3 ppm level in diet grossly revealed mild to moderate renal swelling in OX birds, and the severity was less in the case of OS, OSS, and OP birds. Microscopically, degenerative, necrotic, and inflammatory changes were observed in OX birds, but the changes were less severe in OS, OSS, and OP birds. Ultrastructural studies revealed remarkable and consistent changes in the proximal convoluted tubules (PCTs), with severe damage of mitochondria and endoplasmic reticulum in OX birds, whereas SBT-treated birds (groups OS, OSS) had mild changes in mitochondria. A moderate to marked increase in number of peroxisomes in the cytoplasm of PCTs was a consistent finding in the Phe- and SBT-treated groups kept on OTA in comparison to the group fed OTA alone. In conclusion, the inclusion of 2% SBT leaf powder in feed and SBT leaf extract in water provided partial protection against OTA-induced nephropathy in Japanese quail.

Section 1: Interfacial reactions and grain growth in ferroelectric SrBi{sub 2}Ta{sub 2}O (SBT) thin films on Si substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dickerson, B.D.; Zhang, X.; Desu, S.B.

1997-04-01

Much of the cost of traditional infrared cameras based on narrow-bandgap photoelectric semiconductors comes from the cryogenic cooling systems required to achieve high detectivity. Detectivity is inversely proportional to noise. Generation-recombination noise in photoelectric detectors increases roughly exponentially with temperature, but thermal noise in photoelectric detectors increases only linearly with temperature. Therefore `thermal detectors perform far better at room temperature than 8-14 {mu}m photon detectors.` Although potentially more affordable, uncooled pyroelectric cameras are less sensitive than cryogenic photoelectric cameras. One way to improve the sensitivity to cost ratio is to deposit ferroelectric pixels with good electrical properties directly on mass-produced,more » image-processing chips. `Good` properties include a strong temperature dependence of the remanent polarization, P{sub r}, or the relative dielectric constant, {epsilon}{sub r}, for sensitive operation in pyroelectric or dielectric mode, respectively, below or above the Curie temperature, which is 320 C for SBT. When incident infrared radiation is chopped, small oscillations in pixel temperature produce pyroelectric or dielectric alternating currents. The sensitivity of ferroelectric thermal detectors depends strongly on pixel microstructure, since P{sub r} and {epsilon}{sub r} increase with grain size during annealing. To manufacture SBT pixels on Si chips, acceptable SBT grain growth must be achieved at the lowest possible oxygen annealing temperature, to avoid damaging the Si chip below. Therefore current technical progress describes how grain size, reaction layer thickness, and electrical properties develop during the annealing of SBT pixels deposited on Si.« less

Inventory of File nam.t00z.goes24300.tm00.grib2

Science.gov Websites

of Records: 4 Number Level/Layer Parameter Forecast Valid Description 001 top of atmosphere SBT122 analysis Simulated Brightness Temperature for GOES 12, Channel 2 [K] 002 top of atmosphere SBT123 analysis Simulated Brightness Temperature for GOES 12, Channel 3 [K] 003 top of atmosphere SBT124 analysis Simulated

Inventory of File nam.t00z.goes21800.tm00.grib2

Science.gov Websites

of Records: 4 Number Level/Layer Parameter Forecast Valid Description 001 top of atmosphere SBT122 analysis Simulated Brightness Temperature for GOES 12, Channel 2 [K] 002 top of atmosphere SBT123 analysis Simulated Brightness Temperature for GOES 12, Channel 3 [K] 003 top of atmosphere SBT124 analysis Simulated

Inventory of File nam.t00z.goes22100.tm00.grib2

Science.gov Websites

of Records: 4 Number Level/Layer Parameter Forecast Valid Description 001 top of atmosphere SBT122 analysis Simulated Brightness Temperature for GOES 12, Channel 2 [K] 002 top of atmosphere SBT123 analysis Simulated Brightness Temperature for GOES 12, Channel 3 [K] 003 top of atmosphere SBT124 analysis Simulated

Antibacterial effect evaluation of moxalactam against extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae with in vitro pharmacokinetics/pharmacodynamics simulation

PubMed Central

Yu, Wei; Niu, Tianshui; Xiao, Tingting; Zhang, Jing; Xiao, Yonghong

2018-01-01

Objectives The aim of this study was to evaluate the bactericidal effects of moxalactam (MOX), cefotaxime (CTX), and cefoperazone/sulbactam (CFZ/SBT) against extended-spectrum β-lactamase (ESBL) producing Escherichia coli and Klebsiella pneumoniae, using an in vitro pharmacokinetics (PK)/pharmacodynamics model. Methods Two clinical ESBL-producing strains (blaCTX-M-15 positive E. coli 3376 and blaCTX-M-14 positive K. pneumoniae 2689) and E. coli American Type Culture Collection (ATCC)25922 were used in the study. The PK Auto Simulation System 400 was used to simulate the human PK procedures after intravenous administration of different doses of MOX, CTX, and CFZ/SBT. Bacterial growth recovery time (RT) and the area between the control growth curve and bactericidal curves (IE) were employed to assess the antibacterial efficacies of all the agents. Results The minimum inhibitory concentrations of MOX, CTX, and CFZ/SBT against E. coli ATCC25922, 3376, and 2689 strains were 0.5, 0.5, 0.25; 0.06, >256, 256; and 0.5/0.5, 16/16, 32/32 mg/L. All the agents demonstrated outstanding bactericidal effects against E. coli ATCC25922 (RT >24 h and IE >120 log10 CFU/mL·h−1) with simulating PK procedures, especially in the multiple dose administration models. Against ESBL producers, CTX and CFZ/SBT displayed only weak bactericidal effects, and subsequent regrowth was evident. MOX exhibited potent antibacterial activity against all the strains tested. The values of effective parameters of MOX were much higher than those of CTX and CFZ/SBT (the bacterial RTs with the 3 agents were >24, <4, and <13 h, and the IEs were >110, <10, and <60 log10 CFU/mL·h−1, respectively). Conclusion MOX demonstrated excellent bactericidal effect, which is worthy of further exploration to serve as an alternative therapeutic agent against ESBL-producing Enterobacteriaceae. PMID:29391816

Analog Testing of Operations Concepts for Mitigation of Communication Latency During Human Space Exploration

NASA Technical Reports Server (NTRS)

Chappell, Steven P.; Abercromby, Andrew F.; Miller, Matthew J.; Halcon, Christopher; Gernhardt, Michael L.

2016-01-01

OBJECTIVES: NASA Extreme Environment Mission Operations (NEEMO) is an underwater spaceflight analog that allows a true mission-like operational environment and uses buoyancy effects and added weight to simulate different gravity levels. Three missions were undertaken from 2014-2015, NEEMO's 18-20. All missions were performed at the Aquarius undersea research habitat. During each mission, the effects of varying operations concepts and tasks type and complexity on representative communication latencies associated with Mars missions were studied. METHODS: 12 subjects (4 per mission) were weighed out to simulate near-zero or partial gravity extravehicular activity (EVA) and evaluated different operations concepts for integration and management of a simulated Earth-based science backroom team (SBT) to provide input and direction during exploration activities. Exploration traverses were planned in advance based on precursor data collected. Subjects completed science-related tasks including presampling surveys, geologic-based sampling, and marine-based sampling as a portion of their tasks on saturation dives up to 4 hours in duration that were to simulate extravehicular activity (EVA) on Mars or the moons of Mars. One-way communication latencies, 5 and 10 minutes between space and mission control, were simulated throughout the missions. Objective data included task completion times, total EVA times, crew idle time, translation time, SBT assimilation time (defined as time available for SBT to discuss data/imagery after it has been collected, in addition to the time taken to watch imagery streaming over latency). Subjective data included acceptability, simulation quality, capability assessment ratings, and comments. RESULTS: Precursor data can be used effectively to plan and execute exploration traverse EVAs (plans included detailed location of science sites, high-fidelity imagery of the sites, and directions to landmarks of interest within a site). Operations concepts that allow for presampling surveys enable efficient traverse execution and meaningful Mission Control Center (MCC) interaction across long communication latencies and can be done with minimal crew idle time. Imagery and information from the EVA crew that is transmitted real-time to the intravehicular (IV) crewmember(s) can be used to verify that exploration traverse plans are being executed correctly. That same data can be effectively used by MCC (across comm latency) to provide further instructions to the crew from a SBT on sampling priorities, additional tasks, and changes to the plan. Text / data capabilities are preferred over voice capabilities between MCC and IV when executing exploration traverse plans over communication latency. Autonomous crew planning tools can be effective at modifying existing plans if the objectives and constraints are clearly defined.

Training on an inexpensive tablet-based device is equally effective as on a standard laparoscopic box trainer

PubMed Central

Montanari, Eliana; Schwameis, Richard; Louridas, Marisa; Göbl, Christian; Kuessel, Lorenz; Polterauer, Stephan; Husslein, Heinrich

2016-01-01

Abstract Background: The aim of the study was to assess whether an inexpensive tablet-based box trainer (TBT) is at least equally effective compared with a standard box trainer (SBT) to learn basic laparoscopic skills (BLS). BLS training outside the operating room has been shown to be beneficial for surgical residency. However, simulation trainers are expensive and are not consistently available in all training centers. Therefore, TBT and other homemade box trainers were developed. Methods: Medical students were randomized to either a TBT or an SBT and trained 4 fundamentals of laparoscopic surgery (FLS) tasks for 1 hour twice a week for 4 weeks. A baseline test before the training period and a posttraining test were performed. All students then completed a questionnaire to assess their assigned box trainer. The primary outcome measure was the improvement in total test scores. Improvement in the scores for the 4 individual FLS tasks was chosen as a secondary outcome measure. Results: Thirty-two medical students were recruited. Baseline test scores did not differ significantly between the groups. BLS improved significantly in both groups for the total score and for all 4 tasks separately. Participants in the TBT group showed a greater improvement of total scores than those in the SBT group, although this did not reach statistical significance; noninferiority of the TBT compared with the SBT concerning the improvement of total scores could be demonstrated. Regarding the individual FLS tasks, noninferiority of the TBT could be shown for the pattern cutting and the suturing with intracorporeal knot-tying task. The acceptance of the TBT by the trainees was very good. Conclusion: Learning BLS on a homemade TBT is at least equally effective as on an SBT, with the advantage of being very cost saving. Therefore, this readily available box trainer may be used as an effective, flexible training device outside the operating room to improve accessibility to simulation training. PMID:27684813

[Combined effect of sulbactam/cefoperazone and other antibiotics against clinical isolates of multi-resistant strains. II. In vitro combined effects of sulbactam/cefoperazone with imipenem/cilastatin, cefuzonam, flomoxef, amikacin or tobramycin].

PubMed

Kouda, M; Kumagai, I; Kobayashi, J; Sugai, R; Matsuzaki, H

1991-02-01

We evaluated combined effects of sulbactam/cefoperazone (SBT/CPZ) with each of imipenem/cilastatin (IPM), cefuzonam, flomoxef, amikacin (AMK) and tobramycin (TOB) against 324 clinical strains. Through this study, we obtained the following results. 1. Against Serratia marcescens and Enterobacter cloacae, good synergism was obtained by combining SBT/CPZ with IPM, AMK, or TOB. 2. Against Pseudomonas aeruginosa, good synergism was obtained by combining SBT/CPZ with AMK or TOB. 3. When SBT/CPZ was used in combination with IPM, antagonism was observed among about 45% of strains of P. aeruginosa.

Remedial Prospective of Hippophae rhamnoides Linn. (Sea Buckthorn)

PubMed Central

Patel, Chirag A.; Divakar, Kalyani; Santani, Devdas; Solanki, Himanshu K.; Thakkar, Jalaram H.

2012-01-01

Sea buckthorn (Hippophae rhamnoides L.) constitutes thorny nitrogen fixing deciduous shrub. Sea buckthorn(SBT) is primarily valued for its very rich vitamins A, B1, B12, C, E, K, and P; flavonoids, lycopene, carotenoids, and phytosterols. and therapeutically important since it is rich with potent antioxidants. Scientifically evaluated pharmacological actions of SBT are like inflammation inhibited by reduced permeability, loss of follicular aggregation of lymphocytes from the inflamed synovium and suppress lymphocyte proliferation. SBT-reduced recurrence of angina, ischemic electrocardiogram which might be due to decreased myocardial oxygen consumption and inhibition of platelet aggregation induced by collagen. SBT can kill both cancer cells of S180, P388, SGC7901 and lymphatic leukemia (L1200). The antiulcer activity may be related to reduce gastric empty time, inhibiting proteolytic activity and promoting wound reparation processes of mucosa. SBT exerts antihypertensive effect in part by blocking angiotensin-2 receptor on cell surface. SBT decreased the level of stress hormones and enhanced hypoxic tolerance in animals indicating its anti-stress, adaptogenic activity. A lot of research work is still needed to find cellular and molecular mechanisms of these activities and also yet to be explored for its activity in osteoporosis, hemorrhage, cataract, urinary stone, acne, psoriasis, polyneuritis, cheilosis, glossities, baldness, anti-obesity, gout, and chronic prostitis. PMID:22530142

HLA-F polymorphisms in a Euro-Brazilian population from Southern Brazil.

PubMed

Manvailer, L F S; Wowk, P F; Mattar, S B; da Siva, J S; da Graça Bicalho, M; Roxo, V M M S

2014-12-01

HLA-F is a non-classical major histocompatibility complex (MHC) gene. It codes class Ib MHC molecules with restricted distribution and less nucleotide variations than MHC class Ia genes. Of the 22 alleles registered on the IMGT database only four alleles encode for proteins that differ in their primary structure. To estimate genotype and allele frequencies, this study targeted on known protein coding regions of the HLA-F gene. Genotyping was performed by Sequence Base Typing (SBT). The sample was composed by 199-unrelated bone marrow donors from the Brazilian Bone Marrow Donor Registry (REDOME), Euro-Brazilians, from Southern Brazil. About 1673 bp were analyzed. The most frequent allele was HLA-F*01:01 (87.19%), followed by HLA-F*01:03 (12.31%), HLA-F*01:02 (0.25%) and HLA-F*01:04 (0.25%). Significant linkage disequilibrium (LD) was verified between HLA-F and HLA classes I and II alleles. This is the first study regarding HLA-F polymorphisms in a Euro-Brazilian population contributing to the Southern Brazilian genetic characterization. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Reliability and screening ability of the StarT Back screening tool in patients with low back pain in physiotherapy practice, a cohort study.

PubMed

Robinson, Hilde Stendal; Dagfinrud, Hanne

2017-05-31

Low back pain (LBP) is the most common reported musculoskeletal disorder, with large prevalence numbers and high costs. Focus on early identification of patients at risk of developing chronic LBP has increased. The Keele Start Back Tool (SBT) is a questionnaire aiming at screening prognostic indicators in LBP patients, categorizing patients into risk-groups and guide treatment. The aim of this study was to explore the Norwegian version of the SBT with regard to reliability of the SBT-scoring and the screening ability in LBP patients in primary care physiotherapy. LBP patients answered a package of questionnaires twice, with 1-3 days in between, containing SBT, Hannover functional ability questionnaire, pain intensity questions and demographics. The relative and absolute reliability of SBT was calculated using intraclass correlation coefficient (ICC) and the smallest detectable change respectively. Independent sample t-tests were used for group comparisons. Fifty-two patients with LBP. Mean age (SD) was 45 (12) years and 62% were female. The ICC (95% CI) for SBT total score and psychosocial subscore was 0.89 (0.82, 0.94) and 0.82 (0.70, 0.90) respectively. None of the participants were allocated to the high risk group. The medium risk group reported significantly more pain last week and more activity limitations than the low risk group at both test and retest (0.001 ≤ p ≤ 0.003), whereas no significant difference between the groups was found on pain now (0.05 ≤ p ≤ 0.16). The Norwegian version of the SBT was reliable and the screening ability was good as the subgrouping of patients into risk-groups reflected the severity of their back problems. The SBT may be an applicable and useful tool in physiotherapy practice.

A double-blind randomized pilot trial comparing computerized cognitive exercises to Tetris in adolescents with attention-deficit/hyperactivity disorder.

PubMed

Bikic, Aida; Christensen, Torben Østergaard; Leckman, James F; Bilenberg, Niels; Dalsgaard, Søren

2017-08-01

The purpose of this trial was to examine the feasibility and efficacy of computerized cognitive exercises from Scientific Brain Training (SBT), compared to the computer game Tetris as an active placebo, in a pilot study of adolescents with attention-deficit/hyperactivity disorder (ADHD). Eighteen adolescents with ADHD were randomized to treatment or control intervention for 7 weeks. Outcome measures were cognitive test, symptom, and motivation questionnaires. SBT and Tetris were feasible as home-based interventions, and participants' compliance was high, but participants perceived both interventions as not very interesting or helpful. There were no significant group differences on cognitive and ADHD-symptom measures after intervention. Pre-post intra-group measurement showed that the SBT had a significant beneficial effect on sustained attention, while the active placebo had significant beneficial effects on working memory, both with large effect sizes. Although no significant differences were found between groups on any measure, there were significant intra-group changes for each group.

Subgrouping low back pain: A comparison of the STarT Back Tool with the Örebro Musculoskeletal Pain Screening Questionnaire

PubMed Central

Hill, Jonathan C.; Dunn, Kate M.; Main, Chris J.; Hay, Elaine M.

2010-01-01

Introduction Clinicians require brief, practical tools to help identify low back pain (LBP) subgroups requiring early, targeted secondary prevention. The STarT Back Tool (SBT) was recently validated to subgroup LBP patients into early treatment pathways. Aim To test the SBT’s concurrent validity against an existing, popular LBP subgrouping tool, the Örebro Musculoskeletal Pain Screening Questionnaire (ÖMPSQ), and to compare the clinical characteristics of subgroups identified by each tool. Methods Two hundred and forty-four consecutive ‘non-specific’ LBP consulters at 8 UK GP practices aged 18–59 years were invited to complete a questionnaire. Measures included the ÖMPSQ and SBT, disability, fear, catastrophising, pain intensity, episode duration and demographics. Instruments were compared using Spearman’s correlations, tests for subgroup agreement and discriminant analysis of subgroup characteristics according to reference standards. Results Completed SBT (9-items) and ÖMPSQ (24-items) data was available for 130/244 patients (53%). The correlation of SBT and ÖMPSQ scores was ‘excellent (rs = 0.80). Subgroup characteristics were similar across the low, medium and high subgroups, but, the proportions allocated to ‘low’, ‘medium’ and ‘high’ risk groups were different, with fewer patients in the SBT’s high risk group. Both instruments similarly discriminated for reference standards such as disability, catastrophising, fear, comorbid pain and time off work. The ÖMPSQ was better at discriminating pain intensity, while the SBT was better for discriminating bothersomeness of back pain and referred leg pain. Conclusions The SBT baseline psychometrics performed similarly to the ÖMPSQ, but the SBT is shorter and easier to score and is an appropriate alternative for identifying high risk LBP patients in primary care. PMID:19223271

Importance of serum basal tryptase levels in children with insect venom allergy.

PubMed

Yavuz, S T; Sackesen, C; Sahiner, U M; Buyuktiryaki, B; Arik Yilmaz, E; Sekerel, B E; Soyer, O U; Tuncer, A

2013-03-01

The importance of serum basal tryptase (sBT) levels on patients with venom allergy is highlighted in recent adulthood studies. The aim of this study was to evaluate the sBT levels of venom-allergic children with varying severity of clinical reactions. We also aimed to document the association between sBT levels and severe systemic reactions (SR). Serum basal tryptase levels were estimated by UniCAP (Pharmacia & Upjohn, Uppsala, Sweden). Children who suffered from large local reaction (LLR) or SR after insect stings were included along with healthy control subjects without a history of any local or SR after insect stings. A total of 128 children (55 with SR, 18 with LLR, and 55 age and sex-matched control subjects) with a median age of 8.9 years (range 3.2-17.4) were enrolled. Severe SR was encountered in 24 (44%) patients with SRs. The median level of sBT in children with SRs (median, interquartile range) [4.2 μg/l (3.6-4.9)] was significantly higher than in children with LLRs [3.1 μg/l (2.5-4.0)] and healthy control subjects [2.9 μg/l (2.3-3.4)] (P < 0.001). Logistic regression analysis revealed sBT ≥ 4.8 μg/l as a significant risk factor for severe SR (5.7 [1.5-21.4]; P = 0.01) in children with venom allergy. Our results indicate that sBT levels are associated with a higher risk of severe SR in children with insect venom hypersensitivity. Determination of sBT levels may help clinicians to identify patients under risk of severe SRs and optimal and timely use of therapeutic interventions in children with venom allergy. © 2013 John Wiley & Sons A/S. Published by Blackwell Publishing Ltd.

Topology mapping to characterize cyanobacterial bicarbonate transporters: BicA (SulP/SLC26 family) and SbtA.

PubMed

Price, G Dean; Howitt, Susan M

2014-09-01

This mini-review addresses advances in understanding the transmembrane topologies of two unrelated, single-subunit bicarbonate transporters from cyanobacteria, namely BicA and SbtA. BicA is a Na(+)-dependent bicarbonate transporter that belongs to the SulP/SLC26 family that is widespread in both eukaryotes and prokaryotes. Topology mapping of BicA via the phoA/lacZ fusion reporter method identified 12 transmembrane helices with an unresolved hydrophobic region just beyond helix 8. Re-interpreting this data in the light of a recent topology study on rat prestin leads to a consensus topology of 14 transmembrane domains with a 7+7 inverted repeat structure. SbtA is also a Na(+)-dependent bicarbonate transporter, but of considerably higher affinity (Km 2-5 μM versus >100 μM for BicA). Whilst SbtA is widespread in cyanobacteria and a few bacteria, it appears to be absent from eukaryotes. Topology mapping of SbtA via the phoA/lacZ fusion reporter method identified 10 transmembrane helices. The topology consists of a 5+5 inverted repeat, with the two repeats separated by a large intracellular loop. The unusual location of the N and C-termini outside the cell raises the possibility that SbtA forms a novel fold, not so far identified by structural and topological studies on transport proteins.

[Establishment of a novel HLA genotyping method for preimplantation genetic diagnonis using multiple displacement amplification-polymerase chain reaction-sequencing based technique].

PubMed

Zhang, Yinfeng; Luo, Haining; Zhang, Yunshan

2015-12-01

To establish a novel HLA genotyping method for preimplantation genetic diagnonis (PGD) using multiple displacement amplification-polymerase chain reaction-sequencing based technique (MDA-PCR-SBT). Peripheral blood samples and 76 1PN, 2PN, 3PN discarded embryos from 9 couples were collected. The alleles of HLA-A, B, DR loci were detected from the MDA product with the PCR-SBT method. The HLA genotypes of the parental peripheral blood samples were analyzed with the same protocol. The genotypes of specific HLA region were evaluated for distinguishing the segregation of haplotypes among the family members, and primary HLA matching was performed between the embryos. The 76 embryos were subjected to MDA and 74 (97.4%) were successfully amplified. For the 34 embryos from the single blastomere group, the amplification rate was 94.1%, and for the 40 embryos in the two blastomeres group, the rate was 100%. The dropout rates for DQ allele and DR allele were 1.3% and 0, respectively. The positive rate for MDA in the single blastomere group was 100%, with the dropout rates for DQ allele and DR allele being 1.5% and 0, respectively. The positive rate of MDA for the two blastomere group was 100%, with the dropout rates for both DQ and DR alleles being 0. The recombination rate of fetal HLA was 20.2% (30/148). Due to the improper classification and abnormal fertilized embryos, the proportion of matched embryos HLA was 20.3% (15/74),which was lower than the theoretical value of 25%. PGD with HLA matching can facilitate creation of a HLA-identical donor (saviour child) for umbilical cord blood or bone marrow stem cells for its affected sibling with a genetic disease. Therefore, preimplantation HLA matching may provide a tool for couples desiring to conceive a potential donor progeny for transplantation for its sibling with a life-threatening disorder.

Adolescent Weight Control: An Intervention Targeting Parent Communication and Modeling Compared With Minimal Parental Involvement

PubMed Central

Hadley, Wendy; Sato, Amy; Kuhl, Elizabeth; Rancourt, Diana; Oster, Danielle; Lloyd-Richardson, Elizabeth

2015-01-01

Objective Adolescent weight control interventions demonstrate variable findings, with inconsistent data regarding the appropriate role for parents. The current study examined the efficacy of a standard adolescent behavioral weight control (BWC) intervention that also targeted parent–adolescent communication and parental modeling of healthy behaviors (Standard Behavioral Treatment + Enhanced Parenting; SBT + EP) compared with a standard BWC intervention (SBT). Methods 49 obese adolescents (M age = 15.10; SD = 1.33; 76% female; 67.3% non-Hispanic White) and a caregiver were randomly assigned to SBT or SBT + EP. Adolescent and caregiver weight and height, parental modeling, and weight-related communication were obtained at baseline and end of the 16-week intervention. Results Significant decreases in adolescent weight and increases in parental self-monitoring were observed across both conditions. Analyses of covariance revealed a trend for greater reduction in weight and negative maternal commentary among SBT condition participants. Conclusions Contrary to hypotheses, targeting parent–adolescent communication and parental modeling did not lead to better outcomes in adolescent weight control. PMID:25294840

The design of scenario-based training from the resilience engineering perspective: a study with grid electricians.

PubMed

Saurin, Tarcisio Abreu; Wachs, Priscila; Righi, Angela Weber; Henriqson, Eder

2014-07-01

Although scenario-based training (SBT) can be an effective means to help workers develop resilience skills, it has not yet been analyzed from the resilience engineering (RE) perspective. This study introduces a five-stage method for designing SBT from the RE view: (a) identification of resilience skills, work constraints and actions for re-designing the socio-technical system; (b) design of template scenarios, allowing the simulation of the work constraints and the use of resilience skills; (c) design of the simulation protocol, which includes briefing, simulation and debriefing; (d) implementation of both scenarios and simulation protocol; and (e) evaluation of the scenarios and simulation protocol. It is reported how the method was applied in an electricity distribution company, in order to train grid electricians. The study was framed as an application of design science research, and five research outputs are discussed: method, constructs, model of the relationships among constructs, instantiations of the method, and theory building. Concerning the last output, the operationalization of the RE perspective on three elements of SBT is presented: identification of training objectives; scenario design; and debriefing. Copyright © 2013 Elsevier Ltd. All rights reserved.

Motor learning in a complex balance task and associated neuroplasticity: a comparison between endurance athletes and nonathletes.

PubMed

Seidel, Oliver; Carius, Daniel; Kenville, Rouven; Ragert, Patrick

2017-09-01

Studies suggested that motor expertise is associated with functional and structural brain alterations, which positively affect sensorimotor performance and learning capabilities. The purpose of the present study was to unravel differences in motor skill learning and associated functional neuroplasticity between endurance athletes (EA) and nonathletes (NA). For this purpose, participants had to perform a multimodal balance task (MBT) training on 2 sessions, which were separated by 1 wk. Before and after MBT training, a static balance task (SBT) had to be performed. MBT-induced functional neuroplasticity and neuromuscular alterations were assessed by means of functional near-infrared spectroscopy (fNIRS) and electromyography (EMG) during SBT performance. We hypothesized that EA would showed superior initial SBT performance and stronger MBT-induced improvements in SBT learning rates compared with NA. On a cortical level, we hypothesized that MBT training would lead to differential learning-dependent functional changes in motor-related brain regions [such as primary motor cortex (M1)] during SBT performance. In fact, EA showed superior initial SBT performance, whereas learning rates did not differ between groups. On a cortical level, fNIRS recordings (time × group interaction) revealed a stronger MBT-induced decrease in left M1 and inferior parietal lobe (IPL) for deoxygenated hemoglobin in EA. Even more interesting, learning rates were correlated with fNIRS changes in right M1/IPL. On the basis of these findings, we provide novel evidence for superior MBT training-induced functional neuroplasticity in highly trained athletes. Future studies should investigate these effects in different sports disciplines to strengthen previous work on experience-dependent neuroplasticity. NEW & NOTEWORTHY Motor expertise is associated with functional/structural brain plasticity. How such neuroplastic reorganization translates into altered motor learning processes remains elusive. We investigated endurance athletes (EA) and nonathletes (NA) in a multimodal balance task (MBT). EA showed superior static balance performance (SBT), whereas MBT-induced SBT improvements did not differ between groups. Functional near-infrared spectroscopy recordings revealed a differential MBT training-induced decrease of deoxygenated hemoglobin in left primary motor cortex and inferior parietal lobe between groups. Copyright © 2017 the American Physiological Society.

Internet provision of tailored advice on falls prevention activities for older people: a randomized controlled evaluation.

PubMed

Yardley, Lucy; Nyman, Samuel R

2007-06-01

Falls are very common in older persons and can result in substantial disability and distress. By undertaking strength and balance training (SBT) exercises, older people can reduce their risk of falling. The Internet offers a potentially cost-effective means of disseminating information about SBT to older people and their carers. A particular advantage of using the Internet for this purpose is that the advice given can be 'tailored' to the needs of the individual. This study used a randomized controlled design to evaluate an interactive web-based program that tailored advice about undertaking SBT activities. The participants were 280 people with an age range of 65-97 years recruited by advertising the website by email and the Internet. Those randomized to the tailored advice were presented with advice tailored to their personal self-rated balance capabilities, health problems and activity preferences. Those in the control group were presented with all the advice from which the tailored advice was selected. After reading the advice, those in the tailored advice group (n = 144) had more positive attitudes (p < 0.01) than those in the control group (n = 136), reporting greater perceived relevance of the SBT activities, greater confidence in the ability to carry them out, and hence stronger intentions to undertake the activities. This study provides an initial indication that an interactive website might offer a cost-effective way to provide personalized advice to some older people. Further research is required to determine whether website-based advice on falls prevention changes behavior as well as intentions and whether the advice needs to be supplemented by other forms of support.

Effect of chronic, extrinsic denervation on functional NANC innervation with vasoactive intestinal polypeptide and substance P in longitudinal muscle of rat jejunum.

PubMed

Kasparek, M S; Fatima, J; Iqbal, C W; Duenes, J A; Sarr, M G

2008-03-01

Intestinal denervation contributes to enteric motor dysfunction after intestinal transplantation [small bowel transplantation (SBT)]. Our aim was to determine long-term effects of extrinsic denervation on functional non-adrenergic, non-cholinergic innervation with vasoactive intestinal polypeptide (VIP) and substance P. Contractile activity of jejunal longitudinal muscle from six age-matched, naïve control rats (NC) and eight rats 1 year after syngeneic SBT were studied in tissue chambers. Spontaneous contractile activity did not differ between groups. Exogenous VIP inhibited contractile activity dose-dependently in both groups, greater in NC than in SBT. The VIP antagonist ([D-p-Cl-Phe(6),Leu(17)]-VIP) and the nitric oxide synthase inhibitor l-N(G)-nitro arginine prevented inhibition by exogenous VIP and electrical field stimulation (EFS) in both groups. Exogenous substance P increased contractile activity dose-dependently, greater in NC than in SBT. The substance P antagonist ([D-Pro(2),D-Trp(7,9)]-substance P) inhibited effects of exogenous substance P and increased the EFS-induced inhibitory response. Immunohistofluorescence showed staining for tyrosine hydroxylase in the jejunoileum 1 year after SBT suggesting sympathetic reinnervation. In rat jejunal longitudinal muscle after chronic denervation, response to exogenous VIP and substance P is decreased, while endogenous release of both neurotransmitters is preserved. These alterations in excitatory and inhibitory pathways occur despite extrinsic reinnervation and might contribute to enteric motor dysfunction after SBT.

Effect of chronic, extrinsic denervation on functional NANC innervation with vasoactive intestinal polypeptide and substance P in longitudinal muscle of rat jejunum1

PubMed Central

KASPAREK, M. S.; FATIMA, J.; IQBAL, C. W.; DUENES, J. A.; SARR, M. G.

2008-01-01

Intestinal denervation contributes to enteric motor dysfunction after intestinal transplantation [small bowel transplantation (SBT)]. Our aim was to determine long-term effects of extrinsic denervation on functional non-adrenergic, non-cholinergic innervation with vasoactive intestinal polypeptide (VIP) and substance P. Contractile activity of jejunal longitudinal muscle from six age-matched, naïve control rats (NC) and eight rats 1 year after syngeneic SBT were studied in tissue chambers. Spontaneous contractile activity did not differ between groups. Exogenous VIP inhibited contractile activity dose-dependently in both groups, greater in NC than in SBT. The VIP antagonist ([D-p-Cl-Phe6,Leu17]-VIP) and the nitric oxide synthase inhibitor L-NG-nitro arginine prevented inhibition by exogenous VIP and electrical field stimulation (EFS) in both groups. Exogenous substance P increased contractile activity dose-dependently, greater in NC than in SBT. The substance P antagonist ([D-Pro2,D-Trp7,9]-substance P) inhibited effects of exogenous substance P and increased the EFS-induced inhibitory response. Immunohistofluorescence showed staining for tyrosine hydroxylase in the jejunoileum 1 year after SBT suggesting sympathetic reinnervation. In rat jejunal longitudinal muscle after chronic denervation, response to exogenous VIP and substance P is decreased, while endogenous release of both neurotransmitters is preserved. These alterations in excitatory and inhibitory pathways occur despite extrinsic reinnervation and might contribute to enteric motor dysfunction after SBT. PMID:17971029

The predictive ability of the STarT Back Tool was limited in people with chronic low back pain: a prospective cohort study.

PubMed

Kendell, Michelle; Beales, Darren; O'Sullivan, Peter; Rabey, Martin; Hill, Jonathan; Smith, Anne

2018-04-01

In people with chronic non-specific low back pain (LBP), what is the predictive and discriminative validity of the STarT Back Tool (SBT) for pain intensity, self-reported LBP-related disability, and global self-perceived change at 1-year follow-up? What is the profile of the SBT risk subgroups with respect to demographic variables, pain intensity, self-reported LBP-related disability, and psychological measures? Prospective cohort study. A total of 290 adults with dominant axial LBP of≥3months' duration recruited from the general community, and private physiotherapy, psychology, and pain-management clinics in Western Australia. The 1-year follow-up measures were pain intensity, LBP-related disability, and global self-perceived change. Outcomes were collected on 264 participants. The SBT categorised 82 participants (28%) as low risk, 116 (40%) as medium risk, and 92 (32%) as high risk. The risk subgroups differed significantly (p<0.05) on baseline pain, disability, and psychological scores. The SBT's predictive ability was strongest for disability: RR was 2.30 (95% CI 1.28 to 4.10) in the medium-risk group and 2.86 (95% CI 1.60 to 5.11) in the high-risk group. The SBT's predictive ability was weaker for pain: RR was 1.25 (95% CI 1.04 to 1.51) in the medium-risk group and 1.26 (95% CI 1.03 to 1.52) in the high-risk group. For the SBT total score, the AUC was 0.71 (95% CI 0.64 to 0.77) for disability and 0.63 (95% CI 0.55 to 0.71) for pain. This was the first large study to investigate the SBT in a population exclusively with chronic LBP. The SBT provided an acceptable indication of 1-year disability, had poor predictive and discriminative ability for future pain, and was unable to predict or discriminate global perceived change. In this cohort with chronic non-specific LBP, the SBT's predictive and discriminative abilities were restricted to disability at 1year. [Kendell M, Beales D, O'Sullivan P, Rabey M, Hill J, Smith A (2018) The predictive ability of the STarT Back Tool was limited in people with chronic low back pain: a prospective cohort study. Journal of Physiotherapy 64: 107-113]. Copyright © 2018 Australian Physiotherapy Association. Published by Elsevier B.V. All rights reserved.

Shaking up the system: the role of change in maternal-adolescent communication quality and adolescent weight loss.

PubMed

Hadley, Wendy; McCullough, Mary Beth; Rancourt, Diana; Barker, David; Jelalian, Elissa

2015-01-01

The association between directly observed mother-adolescent weight-related communication quality and adolescent percent overweight within the context of an adolescent weight control study was examined. As part of a larger study examining the impact of a behavioral weight control intervention that included attention to parent-adolescent communication (Standard Behavioral Treatment + Enhanced Parenting, SBT + EP) compared with an efficacious Standard Behavioral Treatment (SBT), 38 mother-adolescent dyads participated in a weight-related videotaped discussion. Discussions were taped and collected pre- and postintervention. No significant differences emerged in the quality of mother-adolescent communication between SBT (n = 19) and SBT + EP (n = 19) participants, nor was baseline mother-adolescent communication quality associated with adolescents' weight loss in either condition. However, a decline in communication quality was associated with better outcomes for adolescents participating in the SBT group. This study provides preliminary evidence that a change in mother-adolescent communication is associated with successful weight loss among adolescents. © The Author 2014. Published by Oxford University Press on behalf of the Society of Pediatric Psychology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The cost-effectiveness of shopping to a predetermined grocery list to reduce overweight and obesity

PubMed Central

Au, N; Marsden, G; Mortimer, D; Lorgelly, P K

2013-01-01

Background: Pre-commitment strategies can encourage participants to commit to a healthy food plan and have been suggested as a potential strategy for weight loss. However, it is unclear whether such strategies are cost-effective. Objective: To analyse whether pre-commitment interventions that facilitate healthier diets are a cost-effective approach to tackle obesity. Methods: Effectiveness evidence was obtained from a systematic review of the literature. For interventions demonstrating a clinically significant change in weight, a Markov model was employed to simulate the long-term health and economic consequences. The review supported modelling just one intervention: grocery shopping to a predetermined list combined with standard behavioural therapy (SBT). SBT alone and do nothing were used as comparators. The target population was overweight or obese adult women. A lifetime horizon for health effects (expressed as quality-adjusted life years (QALYs)) and costs from the perspective of the UK health sector were used to calculate incremental cost-effectiveness ratios (ICERs). Results: In the base case analysis, the pre-commitment strategy of shopping to a list was found to be more effective and cost saving when compared against SBT, and cost-effective when compared against ‘do nothing' (ICER=£166 per QALY gained). A sensitivity analysis indicated that shopping to a list remained dominant or cost-effective under various scenarios. Conclusion: Our findings suggest grocery shopping to a predetermined list combined with SBT is a cost-effective means for reducing obesity and its related health conditions. PMID:23797384

Sea Buckthorn (Hippophaë rhamnoides L.) Oil Improves Atopic Dermatitis-Like Skin Lesions via Inhibition of NF-κB and STAT1 Activation.

PubMed

Hou, Dian-Dong; Di, Zheng-Hong; Qi, Rui-Qun; Wang, He-Xiao; Zheng, Song; Hong, Yu-Xiao; Guo, Hao; Chen, Hong-Duo; Gao, Xing-Hua

2017-01-01

The objective of this study was to evaluate the topical effects of sea buckthorn (SBT) oil on atopic dermatitis (AD)-like lesions in a mouse model generated by repeated topical administration of DNCB in BALB/c mice. DNCB was applied repeatedly on the dorsal skin of mice to induce AD-like lesions. Following AD induction, SBT oil was applied daily on the dorsal skin for 4 weeks. The severity of skin lesions was examined macroscopically and histologically. We further measured the production of MDC/CCL22 and TARC/CCL17 in IFN-γ/TNF-α activated HaCaT cells. Topically applied SBT oil in DNCB-treated mice ameliorated the severity score of dermatitis, decreased epidermal thickness, reduced spleen and lymph node weights, and prevented mast cell infiltration. In addition, SBT oil suppressed the Th2 chemokines TARC and MDC via dose-dependent inhibition of NF-κB, JAK2/STAT1, and p38-MAPK signaling pathways in IFN-γ/TNF-α-activated HaCaT cells. These results suggest that SBT oil had a beneficial effect on AD-like skin lesions, partially via inhibition of the Th2 chemokines TARC and MDC in inflamed skin. © 2017 S. Karger AG, Basel.

Surviving Sengstaken.

PubMed

Jayakumar, S; Odulaja, A; Patel, S; Davenport, M; Ade-Ajayi, N

2015-07-01

To report the outcomes of children who underwent Sengstaken-Blakemore tube (SBT) insertion for life-threatening haemetemesis. Single institution retrospective review (1997-2012) of children managed with SBT insertion. Patient demographics, diagnosis and outcomes were noted. Data are expressed as median (range). 19 children [10 male, age 1 (0.4-16) yr] were identified; 18 had gastro-oesophageal varices and 1 aorto-oesophageal fistula. Varices were secondary to: biliary atresia (n=8), portal vein thrombosis (n=5), alpha-1-anti-trypsin deficiency (n=1), cystic fibrosis (n=1), intrahepatic cholestasis (n=1), sclerosing cholangitis (n=1) and nodular hyperplasia with arterio-portal shunt (n=1). Three children deteriorated rapidly and did not survive to have post-SBT endoscopy. The child with an aortooesophageal fistula underwent aortic stent insertion and subsequently oesophageal replacement. Complications included gastric mucosal ulceration (n=3, 16%), pressure necrosis at lips and cheeks (n=6, 31%) and SBT dislodgment (n=1, 6%). Six (31%) children died. The remaining 13 have been followed up for 62 (2-165) months; five required liver transplantation, two underwent a mesocaval shunt procedure and 6 have completed endoscopic variceal obliteration and are under surveillance. SBT can be an effective, albeit temporary, life-saving manoeuvre in children with catastrophic haematemesis. Copyright © 2015 Elsevier Inc. All rights reserved.

Simulation fails to replicate stress in trainees performing a technical procedure in the clinical environment.

PubMed

Baker, B G; Bhalla, A; Doleman, B; Yarnold, E; Simons, S; Lund, J N; Williams, J P

2017-01-01

Simulation-based training (SBT) has become an increasingly important method by which doctors learn. Stress has an impact upon learning, performance, technical, and non-technical skills. However, there are currently no studies that compare stress in the clinical and simulated environment. We aimed to compare objective (heart rate variability, HRV) and subjective (state trait anxiety inventory, STAI) measures of stress theatre with a simulated environment. HRV recordings were obtained from eight anesthetic trainees performing an uncomplicated rapid sequence induction at pre-determined procedural steps using a wireless Polar RS800CX monitor © in an emergency theatre setting. This was repeated in the simulated environment. Participants completed an STAI before and after the procedure. Eight trainees completed the study. The theatre environment caused an increase in objective stress vs baseline (p = .004). There was no significant difference between average objective stress levels across all time points (p = .20) between environments. However, there was a significant interaction between the variables of objective stress and environment (p = .045). There was no significant difference in subjective stress (p = .27) between environments. Simulation was unable to accurately replicate the stress of the technical procedure. This is the first study that compares the stress during SBT with the theatre environment and has implications for the assessment of simulated environments for use in examinations, rating of technical and non-technical skills, and stress management training.

Lower extremity sagittal joint moment production during split-belt treadmill walking

PubMed Central

Roemmich, Ryan T.; Stegemöller, Elizabeth L.; Hass, Chris J.

2012-01-01

The split-belt treadmill (SBT) has recently been used to rehabilitate locomotor asymmetries in clinical populations. However, the joint mechanics produced while walking on a SBT are not well-understood. The purpose of this study was to investigate the lower extremity sagittal joint moments produced by each limb during SBT walking and provide insight as to how these joint moment patterns may be useful in rehabilitating unilateral gait deficits. Thirteen healthy young volunteers walked on the SBT with the belts tied and in a “SPLIT” session in which one belt moved twice as fast as the other. Sagittal lower extremity joint moment and ground reaction force impulses were then calculated over the braking and propulsive phases of the gait cycle. Paired t-tests were performed to analyze magnitude differences between conditions (i.e. the fast and slow limbs during SPLIT vs. the same limb during tied-belt walking) and between the fast and slow limbs during SPLIT. During the SPLIT session, the fast limb produced higher ground reaction force and ankle moment impulses during the propulsive and braking phases, and lower knee moment impulses during the propulsive phase when compared to the slow limb. The knee moment impulse was also significantly higher during braking in the slow limb than in the fast limb. The mechanics of each limb during the SPLIT session also differed from the mechanics observed when the belt speeds were tied. Based on these findings, we suggest that each belt may have intrinsic value in rehabilitating specific unilateral locomotor deficits. PMID:22985473

A nationwide study of serous "borderline" ovarian tumors in Denmark 1978-2002: centralized pathology review and overall survival compared with the general population.

PubMed

Hannibal, Charlotte Gerd; Vang, Russell; Junge, Jette; Frederiksen, Kirsten; Kjaerbye-Thygesen, Anette; Andersen, Klaus Kaae; Tabor, Ann; Kurman, Robert J; Kjaer, Susanne K

2014-08-01

To describe the study population and estimate overall survival of women with a serous "borderline" ovarian tumor (SBT) in Denmark over 25 years relative to the general population. The Danish Pathology Data Bank and the Danish Cancer Registry were used to identify 1487 women diagnosed with SBTs from 1978 to 2002. The histologic slides were collected from Danish pathology departments and reviewed by expert pathologists and classified as SBT/atypical proliferative serous tumor (APST) or noninvasive low-grade serous carcinoma (LGSC). Associated implants were classified as noninvasive or invasive. Medical records were collected from hospital departments and reviewed. Data were analyzed using Kaplan-Meier and relative survival was estimated with follow-up through September 2, 2013. A cohort of 1042 women with a confirmed SBT diagnosis was identified. Women with stage I had an overall survival similar to the overall survival expected from the general population (p=0.3), whereas women with advanced stage disease had a poorer one (p<0.0001). This was evident both in women with noninvasive (p<0.0001) and invasive implants (p<0.0001). Only among women with advanced stage, overall survival of women with SBT/APST (p<0.0001) and noninvasive LGSC (p<0.0001) was poorer than expected from the general population. To date this is the largest nationwide cohort of SBTs where all tumors have been verified by expert pathologists. Only in women with advanced stage SBT, overall survival is poorer than in the general population which applies both to women with noninvasive and invasive implants as well as to women with SBT/APST and noninvasive LGSC. Copyright © 2014. Published by Elsevier Inc.

Parity, infertility, oral contraceptives, and hormone replacement therapy and the risk of ovarian serous borderline tumors: A nationwide case-control study.

PubMed

Rasmussen, Emma L Kaderly; Hannibal, Charlotte Gerd; Dehlendorff, Christian; Baandrup, Louise; Junge, Jette; Vang, Russell; Kurman, Robert J; Kjaer, Susanne K

2017-03-01

Few studies have examined the risk of an ovarian serous borderline tumor (SBT) associated with parity, infertility, oral contraceptives (OCs), or hormone replacement therapy (HRT), which was the study aim. This nationwide case-control study included all women with an SBT diagnosis in Denmark, 1978-2002. SBTs were confirmed by centralized expert pathology review. For each case, 15 age-matched female controls were randomly selected using risk-set sampling. Cases and controls with previous cancer (except for non-melanoma skin cancer) and controls with bilateral oophorectomy or salpingo-oophorectomy were excluded. Conditional logistic regression was used to estimate adjusted odds ratios (ORs) and 95% confidence intervals (CIs). We found a strongly decreased risk of SBTs among parous women which decreased with increasing number of children (p<0.01). Older age at first birth also decreased the SBT risk (p=0.03). An increased SBT risk was associated with infertility (OR=3.31; 95% CI: 2.44-4.49), which was present both among parous and nulliparous women. HRT use increased the SBT risk (OR=1.32; 95% CI: 1.02-1.72), whereas OC use decreased the risk (OR=0.40; 95% CI: 0.26-0.62). Our nationwide study with expert histopathologic review of all SBTs showed that parity, infertility, use of HRT, and use of OCs, respectively, were strongly associated with the risk of SBTs. This is the first study to report a strong and significantly decreased SBT risk associated with OC use and a significantly increased risk with infertility, and HRT use. This supports that SBTs and serous ovarian cancer share similar risk factors. Copyright © 2017 Elsevier Inc. All rights reserved.

FMRFamide-like peptides expand the behavioral repertoire of a densely connected nervous system

PubMed Central

Schaedel, Oren N.; Rogers, Alicia K.

2017-01-01

Animals, including humans, can adapt to environmental stress through phenotypic plasticity. The free-living nematode Caenorhabditis elegans can adapt to harsh environments by undergoing a whole-animal change, involving exiting reproductive development and entering the stress-resistant dauer larval stage. The dauer is a dispersal stage with dauer-specific behaviors for finding and stowing onto carrier animals, but how dauers acquire these behaviors, despite having a physically limited nervous system of 302 neurons, is poorly understood. We compared dauer and reproductive development using whole-animal RNA sequencing at fine time points and at sufficient depth to measure transcriptional changes within single cells. We detected 8,042 genes differentially expressed during dauer and reproductive development and observed striking up-regulation of neuropeptide genes during dauer entry. We knocked down neuropeptide processing using sbt-1 mutants and demonstrate that neuropeptide signaling promotes the decision to enter dauer rather than reproductive development. We also demonstrate that during dauer neuropeptides modulate the dauer-specific nictation behavior (carrier animal-hitchhiking) and are necessary for switching from repulsion to CO2 (a carrier animal cue) in nondauers to CO2 attraction in dauers. We tested individual neuropeptides using CRISPR knockouts and existing strains and demonstrate that the combined effects of flp-10 and flp-17 mimic the effects of sbt-1 on nictation and CO2 attraction. Through meta-analysis, we discovered similar up-regulation of neuropeptides in the dauer-like infective juveniles of diverse parasitic nematodes, suggesting the antiparasitic target potential of SBT-1. Our findings reveal that, under stress, increased neuropeptide signaling in C. elegans enhances their decision-making accuracy and expands their behavioral repertoire. PMID:29167374

Effect of sea buckthorn berries and pulp in a liquid emulsion on gastric ulcer scores and gastric juice pH in horses.

PubMed

Huff, N K; Auer, A D; Garza, F; Keowen, M L; Kearney, M T; McMullin, R B; Andrews, F M

2012-01-01

Sea buckthorn berries (Hippophae rhamnoides) are rich in vitamin C and E, carotenoids, flavonoids, fatty acids, plant sterols, lignans, and minerals. A feed supplement containing sea buckthorn berries might have efficacy in treatment and prevention of gastric ulcers in horses. To test the efficacy of a commercially available formulation of sea buckthorn berries and pulp (SeaBuck SBT Gastro-Plus) for treatment and prevention of gastric ulcers in stall-confined horses. Eight Thoroughbred and Thoroughbred-cross horses (3-10 years of age, 5 geldings and 3 mares, 380-600 kg body weight). This study was a 2-period crossover in which all horses received no treatment (untreated controls; n = 8) and treatment (SeaBuckSBT Gastro-Plus, 4 ounces [35.6 g berries and pulp], twice daily; n = 8) mixed with a pelleted complete feed (18% crude fiber; 9% starch; 14% crude protein). Horses were treated for 4 weeks followed by a 1-week (d28-d35) alternating feed-deprivation period to induce or worsen existing ulcers. Gastroscopic examinations were performed on days 0, 28, and 35. Gastric juice pH was measured and gastric ulcer number and severity scores were assigned by a masked investigator. Mean nonglandular gastric ulcer scores significantly (P < .05) increased in all horses after day 28, as a result of intermittent feed deprivation. Mean nonglandular gastric ulcer number (P = .84) and severity (P = .51) were not significantly different between SBT-treated and untreated control horses. However, mean glandular ulcer number (P = .02) and glandular ulcer severity (P = .02) were significantly lower in the SBT-treated horses compared with the untreated control at week 5. SeaBuck SBT Gastro-Plus liquid fed to horses did not show efficacy in treatment or prevention of naturally occurring nonglandular ulcers in horses; however, glandular ulcer scores were significantly lower in SBT-treated horses after feed deprivation. Thus, SBT might have efficacy in prevention of glandular ulcers in horses housed in stalls and undergoing intermittent feeding. Copyright © 2012 by the American College of Veterinary Internal Medicine.

Long-term effects of extrinsic denervation on VIP and substance P innervation in circular muscle of rat jejunum.

PubMed

Kasparek, Michael S; Fatima, Javairiah; Iqbal, Corey W; Duenes, Judith A; Sarr, Michael G

2007-10-01

Intestinal denervation contributes to enteric motor dysfunction after small bowel transplantation (SBT). Our aim was to determine long-term effects of extrinsic denervation on function of nonadrenergic, noncholinergic innervation with substance P and vasoactive intestinal polypeptide (VIP). Contractile activity of jejunal circular muscle strips from six age-matched, naive control rats (NC) and eight rats 1 year after syngeneic SBT was studied in tissue chambers. Spontaneous contractile activity did not differ between groups. Exogenous VIP inhibited contractile activity dose-dependently to a comparable degree in both groups. The VIP antagonist ([D-p-Cl-Phe(6),Leu(17)]-VIP) and the nitric oxide synthase inhibitor L-NG-nitro-arginine did not affect VIP-induced inhibition but increased contractile activity during electrical field stimulation (EFS) in both groups. Exogenous substance P increased contractile activity dose-dependently, greater in NC than SBT. The substance P antagonist ([D-Pro(2),D-Trp(7,9)]-substance P) inhibited effects of exogenous substance P and decreased the excitatory EFS response. Immunohistofluorescence showed tyrosine hydroxylase staining after SBT indicating sympathetic reinnervation. In jejunal circular muscle after chronic denervation, response to exogenous substance P, but not VIP, is decreased, whereas endogenous release of both neurotransmitters is preserved. Alterations in balance of excitatory and inhibitory pathways occur despite extrinsic reinnervation and might contribute to enteric motor dysfunction after SBT.

Climatic significance of the ostracode fauna from the Pliocene Kap Kobenhavn Formation, north Greenland

USGS Publications Warehouse

Brouwers, E.M.; Jorgensen, N.O.; Cronin, T. M.

1991-01-01

The Kap Kobenhavn Formation crops out in Greenland at 80??N latitude and marks the most northerly onshore Pliocene locality known. The sands and silts that comprise the formation were deposited in marginal marine and shallow marine environments. An abundant and diverse vertebrate and invertebrate fauna and plant megafossil flora provide age and paleoclimatic constraints. The age estimated for the Kap Kobenhavn ranges from 2.0 to 3.0 million years old. Winter and summer bottom water paleotemperatures were estimated on the basis of the ostracode assemblages. The marine ostracode fauna in units B1 and B2 indicate a subfrigid to frigid marine climate, with estimated minimum sea bottom temperatures (SBT) of -2??C and estimated maximum SBT of 6-8??C. Sediments assigned to unit B2 at locality 72 contain a higher proportion of warm water genera, and the maximum SBT is estimated at 9-10??C. The marginal marine fauna in the uppermost unit B3 (locality 68) indicates a cold temperate to subfrigid marine climate, with an estimated minimum SBT of -2??C and an estimated maximum SBT ranging as high as 12-14??C. These temperatures indicated that, on the average, the Kap Kobenhavn winters in the late Pliocene were similar to or perhaps 1-2??C warmer than winters today and that summer temperatures were 7-8??C warmer than today. -from Authors

Morbid obesity and pregnancy outcomes after single blastocyst transfer: a retrospective, North American study.

PubMed

Russo, Miguel; Ates, Senem; Shaulov, Talya; Dahan, Michael H

2017-04-01

Maternal obesity has been shown to affect reproductive function and pregnancy outcomes following in vitro fertilization. More recently, studies have demonstrated lower live birth rates after single blastocyst transfer (SBT) in patients who are overweight or obese. However, the impact of morbid obesity on pregnancy outcomes after SBT has not been well elucidated. The present study aimed to determine whether morbid obesity has a detrimental impact on pregnancy outcomes after SBT in a North American population. A retrospective, cohort study including 520 nulliparous and multiparous women undergoing top-quality SBT between August 2010 and March 2014 at a University Health Centre in North America was conducted. Primary outcomes included: miscarriage rate, clinical pregnancy rate, and live birth rate. Subjects were divided into different BMI categories (kg/m 2 ), including <20, 20-24.9, 25.0-29.9, 30-40, and 40 or more. The miscarriage rate per pregnancy for each group, respectively, was 36, 64, 59, 61, and 50% (p = 0.16); the clinical pregnancy (per patient) rate per group was 36, 52, 38, 26, and 10% (p = 0.009); and the live birth rate (per patient) per group was 35, 50, 38, 26 and 10% (p = 0.03). Morbid obesity is a strong and independent predictor of poor pregnancy outcomes in patients undergoing top-quality SBT.

[Association of HLA-DPA1 and -DPB1 polymorphisms with Posner-Schlossman syndrome among southern Chinese Han population].

PubMed

Zhao, Jun; Zhu, Tianhui; He, Liumei; Shen, Xiaoli; Wang, Yanjun; Deng, Zhihui

2015-04-01

To assess the association of HLA-DPA1 and -DPB1 polymorphisms with Posner-Schlossman syndrome (PSS) in southern Chinese Han population. A total of 100 randomly selected PSS patients of southern Chinese Han origin were served as the experimental group, while 128 unrelated healthy blood donors of the same origin were served as the control group. All samples were subjected to sequencing-based typing (SBT) for exon 2 of HLA-DPA1 and -DPB1 loci in both directions. HLA genotype was assigned using an Assign 3.5 HLA SBT software. The allele frequencies and haplotype frequencies of HLA-DPA1 and -DPB1 of the two groups were compared. x² test, P value and odds ratio (OR) value were calculated. Six HLA-DPA1 alleles in the experimental group and 4 HLA-DPA1 alleles in the healthy control group were identified. The allelic frequency for HLA-DPA1*02:01 in the experimental group was significantly lower than the control group (4.50% vs. 12.109%; x²=8.124, P=0.004). Sixteen HLA-DPB1 alleles were identified in both the experimental and control groups. The allelic frequencies for HLA-DPB1*14:01 and - DPB1*17:01 in the experimental group were significantly lower than those of the control group ( DPB1*14:01: 1.00% vs. 4.688%, x²=5.130, P=0.024; DPB1*17:01: 0% vs. 2.344%, x²=3.897, P=0.048). The DPA1-DPB1 haplotypes for the experimental and control groups were 23 and 25, respectively. The haplotype frequencies for both DPA1*02:01- DPB1*14:01 and DPA1*02:01- DPB1*17:01 were significantly lower than those of the control group. DPA1*02:01- DPB1*14:01 and DPA1*02:01- DPB1*17:01 haplotypes may provide considerable protection effect against PSS in the southern Chinese Han population.

Effect of modified atmosphere packaging (map) on the quality of sea buckthorn berry fruits during postharvest storage

USDA-ARS?s Scientific Manuscript database

The effect of modified atmosphere packaging (MAP) on the quality of the berry fruits of sea buckthorn (SBT) during refrigerated storage was investigated. SBT berries were packaged in 160 and 525 oxygen transmission rate (OTR) films or in vented clamshell containers (air control) and stored at 10C fo...

Protective effects of aqueous fruit extract from Sea Buckthorn (Hippophae rhamnoides L. Spp. Turkestanica) on haloperidol-induced orofacial dyskinesia and neuronal alterations in the striatum.

PubMed

Batool, Farhat; Shah, Asad Hussain; Ahmed, Syed Dilnawaz; Saify, Zafar Saeid; Haleem, Darakhshan Jabeen

2010-08-01

Long-term treatment of haloperidol, a neuroleptic, induces neurodegeneration specifically in the striatum (caudate and putamen), which plays an important role in the development of orofacial dyskinesia, a putative model of tardive dyskinesia (TD). This study investigated the protective effects of a concomitant treatment of aqueous fruit extract of Sea buckthorn (Hippophae rhamnoides L. spp. Turkestanica) (SBT-FE) (40 mg/kg, orally) plus haloperidol (3.0 mg/kg, ip) administration on an animal model of TD and on striatal neuronal alterations. Rats received daily haloperidol (3.0 mg/kg ip) and saline injections for 15 days. Seven-day posttreatment, aqueous SBT-FE (40 mg/kg) was administered daily via a feeding tube. Hypolocomotive effects (home cage activity, exploratory activity, catalepsy, and vacuous chewing movements) were monitored consecutively in each group. On the last day of the experiments, changes in extracellular levels of striatal dopamine (DA), dihydroxyphenyl acetic acid (DOPAC) and homovanillic acid (HVA) were determined by HPLC-EC. Aqueous SBT-FE attenuated haloperidol-induced VCMs after second week of treatment and locomotor activity was greater in rats treated with SBT-FE compared with the controls. The results indicate that DA and HVA levels in the striatum were significantly (P <.01) altered in rats given SBT-FE before injections of haloperidol. Hippophae rhamnoides fruit extract has a protective role against haloperidol-induced orofacial dyskinesia. Consequently, use of Hippophae rhamnoides as a possible therapeutic agent for the treatment of tardive dyskinesia should be considered.

"K"-Balance Partitioning: An Exact Method with Applications to Generalized Structural Balance and Other Psychological Contexts

ERIC Educational Resources Information Center

Brusco, Michael; Steinley, Douglas

2010-01-01

Structural balance theory (SBT) has maintained a venerable status in the psychological literature for more than 5 decades. One important problem pertaining to SBT is the approximation of structural or generalized balance via the partitioning of the vertices of a signed graph into "K" clusters. This "K"-balance partitioning problem also has more…

Praziquantel coverage in schools and communities targeted for the elimination of urogenital schistosomiasis in Zanzibar: a cross-sectional survey.

PubMed

Knopp, Stefanie; Person, Bobbie; Ame, Shaali M; Ali, Said M; Muhsin, Juma; Juma, Saleh; Khamis, Iddi S; Rabone, Muriel; Blair, Lynsey; Fenwick, Alan; Mohammed, Khalfan A; Rollinson, David

2016-01-04

Biannual mass drug administration (MDA) with praziquantel and additional interventions to eliminate urogenital schistosomiasis has been implemented on the Zanzibar islands, United Republic of Tanzania, since 2012. We aimed to assess the coverage of school-based treatment (SBT) and community-wide treatment (CWT), to validate the coverage reported by the Zanzibar Ministry of Health (MoH) and to identify reasons for non-compliance. We conducted a post-MDA cross-sectional survey in 93 schools and 92 communities on Pemba and Unguja islands in early 2014, 3-5 months after the last MDA round. Pupils and adults were asked whether they had received and taken the praziquantel treatment provided in the last SBT or CWT, respectively, and the observed and reported coverage were compared. Reasons for non-compliance were recorded in a pretested questionnaire and assessed in qualitative interviews. Urine samples of participants were examined for Schistosoma haematobium eggs with a single urine filtration. Around 8000 pupils and 4000 adults were included in the analysis. Our survey revealed a SBT coverage of 85.2% in Pemba and of 86.9% in Unguja, which was in line with MoH reports from Pemba (84.3%) and higher than reports from Unguja (63.9%). However, 15 among the 48 schools surveyed in Unguja had not received SBT. Among the interviewed adults, 53.6% in Pemba and 64.9% in Unguja had received praziquantel during CWT, which was less than the 59.0% and 67.7%, respectively, indicated by MoH reports. Moreover, only 43.8% and 54.0% of adults in Pemba and Unguja, respectively, had taken all the tablets as recommended. The main reasons for not receiving or taking praziquantel were absence during CWT, no drug distributor coming, being busy, fear of adverse events, pregnancy, breastfeeding or feeling healthy. To increase coverage and compliance in Zanzibar, SBT should target all schools and mobilization, sensitization and implementation of the CWT need to be improved. To reach elimination of urogenital schistosomiasis transmission in Zanzibar and elsewhere, a very high treatment coverage and compliance at national and local level is key and additional control measures such as snail control and behaviour change interventions will need to be implemented area wide. ISRCTN48837681.

Progressive learning in endoscopy simulation training improves clinical performance: a blinded randomized trial.

PubMed

Grover, Samir C; Scaffidi, Michael A; Khan, Rishad; Garg, Ankit; Al-Mazroui, Ahmed; Alomani, Tareq; Yu, Jeffrey J; Plener, Ian S; Al-Awamy, Mohamed; Yong, Elaine L; Cino, Maria; Ravindran, Nikila C; Zasowski, Mark; Grantcharov, Teodor P; Walsh, Catharine M

2017-11-01

A structured comprehensive curriculum (SCC) that uses simulation-based training (SBT) can improve clinical colonoscopy performance. This curriculum may be enhanced through the application of progressive learning, a training strategy centered on incrementally challenging learners. We aimed to determine whether a progressive learning-based curriculum (PLC) would lead to superior clinical performance compared with an SCC. This was a single-blinded randomized controlled trial conducted at a single academic center. Thirty-seven novice endoscopists were recruited and randomized to either a PLC (n = 18) or to an SCC (n = 19). The PLC comprised 6 hours of SBT, which progressed in complexity and difficulty. The SCC included 6 hours of SBT, with cases of random order of difficulty. Both groups received expert feedback and 4 hours of didactic teaching. Participants were assessed at baseline, immediately after training, and 4 to 6 weeks after training. The primary outcome was participants' performance during their first 2 clinical colonoscopies, as assessed by using the Joint Advisory Group Direct Observation of Procedural Skills assessment tool (JAG DOPS). Secondary outcomes were differences in endoscopic knowledge, technical and communication skills, and global performance in the simulated setting. The PLC group outperformed the SCC group during first and second clinical colonoscopies, measured by JAG DOPS (P < .001). Additionally, the PLC group had superior technical and communication skills and global performance in the simulated setting (P < .05). There were no differences between groups in endoscopic knowledge (P > .05). Our findings demonstrate the superiority of a PLC for endoscopic simulation, compared with an SCC. Challenging trainees progressively is a simple, theory-based approach to simulation whereby the performance of clinical colonoscopies can be improved. (Clinical trial registration number: NCT02000180.). Copyright © 2017 American Society for Gastrointestinal Endoscopy. Published by Elsevier Inc. All rights reserved.

Variation in diurnal sedation in mechanically ventilated patients who are managed with a sedation protocol alone or a sedation protocol and daily interruption.

PubMed

Mehta, Sangeeta; Meade, Maureen; Burry, Lisa; Mallick, Ranjeeta; Katsios, Christina; Fergusson, Dean; Dodek, Peter; Burns, Karen; Herridge, Margaret; Devlin, John W; Tanios, Maged; Fowler, Robert; Jacka, Michael; Skrobik, Yoanna; Olafson, Kendiss; Cook, Deborah

2016-08-01

Mechanically ventilated patients may receive more sedation during the night than during the day, potentially delaying extubation. We compared nighttime and daytime benzodiazepine and opioid administration in adult patients enrolled in a multicenter sedation trial comparing protocolized sedation alone or protocolized sedation combined with daily sedation interruption; and we evaluated whether nighttime and daytime doses were associated with liberation from mechanical ventilation. This is a secondary analysis of a randomized trial which was conducted in 16 North American medical-surgical ICUs. In all 423 patients, nurses applied a validated sedation scale hourly to titrate benzodiazepine and opioid infusions to achieve a light level of sedation. Using fentanyl equivalents and midazolam equivalents, we compared dosages administered during night (19:00 to 07:00) and day (07:00 to 19:00) shifts. Using multivariable logistic regression we evaluated the association between nighttime and daytime opioid and sedative doses, and spontaneous breathing trial (SBT) conduct, SBT success, and extubation. Nighttime benzodiazepine and opioid doses were significantly higher than daytime doses (mean difference midazolam equivalents 23.3 mg, 95 % CI 12.9, 33.8, p < 0.0001; mean difference fentanyl equivalents 356 mcg, 95 % CI 130, 582, p = 0.0021). Mean Sedation Agitation Scale score was similar between night and day, and was at target (3.2 vs 3.3, 95 % CI -0.05, 0.02, p = 0.35). Self-reported nurse workload was similar during the night and day. Patients were more often restrained during day shifts (76.3 % vs 73.7 %, p < 0.0001), and there were more unintentional device removals during the day compared with night (15.9 % vs 9.1 %, p < 0.0001). Increases in nighttime drug doses were independently associated with failure to meet SBT screening criteria, SBT failure, and the decision not to extubate the patient despite successful SBT. Patients received higher doses of opioids and benzodiazepines at night. Higher nighttime doses were associated with SBT failure and delayed extubation. ClinicalTrials.gov NCT00675363 . Registered 7 May 2008.

Sea buckthorn bud extract displays activity against cell-cultured Influenza virus.

PubMed

Torelli, A; Gianchecchi, E; Piccirella, S; Manenti, A; Piccini, G; Llorente Pastor, E; Canovi, B; Montomoli, E

2015-08-05

Vaccines and antiviral drugs are the most widely used methods of preventing or treating Influenza virus infection. The role of sea buckthorn (SBT) bud dry extract as a natural antiviral drug against Influenza was investigated. Influenza virus was cultured in the MDCK cell line, with or without SBT bud extract, and virus growth was assessed by HA and TCID50 virus titration in terms of cytopathic effect on cells. Several concentrations of extract were tested, the virus titer being measured on day 4 after infection. After infection, the virus titer in the control sample was calculated to be 2.5 TCID50/ml; treatment with SBT bud extract reduced the virus titer to 2.0 TCID50/ml at 50 μg/ml, while the HA titer was reduced from 1431 (control) to 178. Concentrations lower than 50μg/ml displayed an inhibitory effect in the HA assay, but not in the TCID50 virus titration; however, observation of the viral cultures confirmed a slowdown of viral growth at all concentrations. Natural dietary supplements and phytotherapy are a growing market and offer new opportunities for the treatment of several diseases and disorders. These preliminary experiments are the first to show that SBT bud extract is able to reduce the growth of the Influenza A H1N1 virus in vitro at a concentration of 50 μg/ml. This discovery opens up the possibility of using SBT bud extract as a valid weapon against Influenza and, in addition, as the starting-point for the discovery of new drugs. © Copyright by Pacini Editore SpA, Pisa, Italy.

Are triage questions sufficient to assign fall risk precautions in the ED?

PubMed

Southerland, Lauren T; Slattery, Lauren; Rosenthal, Joseph A; Kegelmeyer, Deborah; Kloos, Anne

2017-02-01

The American College of Emergency Physicians Geriatric Emergency Department (ED) Guidelines and the Center for Disease Control recommend that older adults be assessed for risk of falls. The standard ED assessment is a verbal query of fall risk factors, which may be inadequate. We hypothesized that the addition of a functional balance test endorsed by the Center for Disease Control Stop Elderly Accidents, Deaths, and Injuries Falls Prevention Guidelines, the 4-Stage Balance Test (4SBT), would improve the detection of patients at risk for falls. Prospective pilot study of a convenience sample of ambulatory adults 65 years and older in the ED. All participants received the standard nursing triage fall risk assessment. After patients were stabilized in their ED room, the 4SBT was administered. The 58 participants had an average age of 74.1 years (range, 65-94), 40.0% were women, and 98% were community dwelling. Five (8.6%) presented to the ED for a fall-related chief complaint. The nursing triage screen identified 39.7% (n=23) as at risk for falls, whereas the 4SBT identified 43% (n=25). Combining triage questions with the 4SBT identified 60.3% (n=35) as at high risk for falls, as compared with 39.7% (n=23) with triage questions alone (P<.01). Ten (17%) of the patients at high risk by 4SBT and missed by triage questions were inpatients unaware that they were at risk for falls (new diagnoses). Incorporating a quick functional test of balance into the ED assessment for fall risk is feasible and significantly increases the detection of older adults at risk for falls. Copyright © 2016 Elsevier Inc. All rights reserved.

Space cryogenics at CEA-SBT

NASA Astrophysics Data System (ADS)

Duband, Lionel; Charles, Ivan; Duval, Jean-Marc; Ercolani, Eric; Gully, Philippe; Luchier, Nicolas; Prouve, Thomas; Thibault, Pierre

2017-11-01

The "Service des Basses Températures" (SBT) of CEA Grenoble has been involved in space cryogenics for over 20 years now. In fact a dedicated laboratory was created within SBT to carry out these developments, the "Cryocoolers and Space Cryogenics" group, which comprises about 20 persons as of today. Various cryocoolers have been developed in the past and our fields of activity focus now on four main technologies: sorption coolers, multistage pulse tubes, adiabatic demagnetization refrigerators (ADR), and cryogenic loop heat pipes. In addition work on two new concepts for ground based dilution refrigerators is also ongoing. Finally developments on various key technologies such as the heat switches, the suspension or structural systems are also carried out. These developments are mainly funded by the European Space Agency (ESA) or by the Centre National d'Etudes Spatiales (CNES). For most of these systems the common feature is the absence of any moving parts or any friction, which guarantees a very good reliability and make them very good candidates for space borne instruments requiring cryogenic temperatures. In this paper we give an overview of these developments with a particular focus on the sub Kelvin coolers. Based on the HERSCHEL heritage for which we developed the flight sorption coolers, we are now proposing an original concept featuring the association of a 300 mK sorption unit with a miniature adiabatic demagnetization refrigerator. This combination will allow to provide temperature as low as 50 mK with a system weighting less than 5 kg. This development may have direct application for the XEUS and SPICA missions.

[Identifying and sequence analysis of HLA-B*2736].

PubMed

Li, Zhen; Zou, Hong-Yan; Shao, Chao-Peng; Tang, Si; Wang, Da-Ming; Cheng, Liang-Hong

2007-11-01

An unknown HLA-B allele which was similar to HLA-B*270401 was detected by FLOW-SSOPCR-SSP and heterozygous sequence-based typing (SBT) in Chinese Han individual. Its anomalous patterns suggested the possible presence of new allele. Amplifying exon 2-5(include intron 2-4) of the HLA-B*27 allele separately by using allele-specific primers and sequencing in both directions. Identifying the difference between the novel B*27 allele and B*270401. The sequence of novel B*27 from exon 2 to partial exon 5 is 1 815 bp. There are 10 nt changes from B*270401 in exon 3-4, at nt634where A-->C(codon130 AGC-->CGC, 130 S-->R); nt670 where A-->T (codon142 ACC-->TCC, 142 T-->S); nt683 where G-->T (codon146 TGG-->TTG, 146 W-->L); nt698 where A-->T (codon151 GAG-->GTG, 151 E-->V); nt774 where G-->C (codon176 GAG-->GAC, 176 E-->D); nt776 where C-->A (codon177 ACG-->AAG, 177 T-->K); nt781 where C-->G (codon179 CAG-->GAG, 179Q-->E); nt789 where G-->T (codon181 GCG-->GCT) resulting no coding change; nt1438 where C-->T (codon206 GGC-->GGT) resulting no coding change; nt1449 where G-->C (codon210 GGG-->GCG, 210G-->A). In IMGT/HLA database, only three alleles (B*270502/2706/2732) have sequences of introns. The same sequence in intron 2 showed homology between the novel HLA-B*27 allele and B*2706, but their homology could not be supported in intron 3-4. Comparing the sequence of the novel B*27 allele in intron 3 and 4 with B*27 group, it showed there are three mutations at nt106 C-->G, nt179 G-->A, nt536 G-->A and one deletion at nt168 in intron 3 and one mutations at nt82 T-->C in intron 4, but the sequence of the novel B*27 allele in intron 3 and 4 was all the same to B*070201. The sequence was submitted to Gen-Bank and the accession number was DQ915176. The allele has been confirmed as an extension of B*2736 by the WHO Nomenclature committee in November 2006.

Multilayer Lead-Free Ceramic Capacitors with Ultrahigh Energy Density and Efficiency.

PubMed

Li, Jinglei; Li, Fei; Xu, Zhuo; Zhang, Shujun

2018-06-26

The utilization of antiferroelectric (AFE) materials is thought to be an effective approach to enhance the energy density of dielectric capacitors. However, the high energy dissipation and inferior reliability that are associated with the antiferroelectric-ferroelectric phase transition are the main issues that restrict the applications of antiferroelectric ceramics. Here, simultaneously achieving high energy density and efficiency in a dielectric ceramic is proposed by combining antiferroelectric and relaxor features. Based on this concept, a lead-free dielectric (Na 0.5 Bi 0.5 )TiO 3 -x(Sr 0.7 Bi 0.2 )TiO 3 (NBT-xSBT) system is investigated and the corresponding multilayer ceramic capacitors (MLCCs) are fabricated. A record-high energy density of 9.5 J cm -3 , together with a high energy efficiency of 92%, is achieved in NBT-0.45SBT multilayer ceramic capacitors, which consist of ten dielectric layers with the single-layer thickness of 20 µm and the internal electrode area of 6.25 mm 2 . Furthermore, the newly developed capacitor exhibits a wide temperature usage range of -60 to 120 °C, with an energy-density variation of less than 10%, and satisfactory cycling reliability, with degradation of less than 8% over 10 6 cycles. These characteristics demonstrate that the NBT-0.45SBT multilayer ceramic is a promising candidate for high-power energy storage applications. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Automatic Tube Compensation versus Pressure Support Ventilation and Extubation Outcome in Children: A Randomized Controlled Study

PubMed Central

El-beleidy, Ahmed Saad El-din; Khattab, Asser Abd EL-Hamied; El-Sherbini, Seham Awad; Al-gebaly, Hebatalla Fadel

2013-01-01

Background. Automatic tube compensation (ATC) has been developed to overcome the imposed work of breathing due to artificial airways during spontaneous breathing trials (SBTs). Objectives. This study aimed to assess extubation outcome after an SBT (spontaneous breathing trial) with ATC compared with pressure support ventilation (PSV) and to determine the risk factors for extubation failure. Methods. Patients ready for extubation were randomly assigned to two-hour spontaneous breathing trial with either ATC or pressure support ventilation. Results. In the ATC group (n = 17), 11 (65%) patients passed the SBT with subsequent extubation failure (9%). While in PSV group (n = 19), 10 (53%) patients passed the SBT with subsequent extubation failure (10%). This represented a positive predictive value for ATC of 91% and PSV of 90% (P = 0.52). Five (83%) of the patients who failed the SBT in ATC group were reintubated. This represented a higher negative predictive value for ATC of 83% than for PSV which was 56%. None of the assessed risk factors were independently associated with extubation failure including failed trial. Conclusion. ATC was equivalent to PSV in predicting patients with successful extubation. A trial failure in ATC group is associated with but does not definitely predict extubation failure. PMID:23533800

Moving Cages Further Offshore: Effects on Southern Bluefin Tuna, T. maccoyii, Parasites, Health and Performance

PubMed Central

Kirchhoff, Nicole T.; Rough, Kirsty M.; Nowak, Barbara F.

2011-01-01

The effects of offshore aquaculture on SBT health (particularly parasitic infections and haematology) and performance were the main aim of this study. Two cohorts of ranched Southern Bluefin tuna (SBT) (Thunnus maccoyii) were monitored throughout the commercial season, one maintained in the traditional near shore tuna farming zone and one maintained further offshore. SBT maintained offshore had reduced mortality, increased condition index at week 6 post transfer, reduced blood fluke and sealice loads, and haematological variables such as haemoglobin or lysozyme equal to or exceeding near shore maintained fish. The offshore cohort had no Cardicola forsteri and a 5% prevalence of Caligus spp., compared to a prevalence of 85% for Cardicola forsteri and 55% prevalence for Caligus spp. near shore at 6 weeks post transfer. This study is the first of its kind to examine the effects of commercial offshore sites on farmed fish parasites, health and performance. PMID:21901129

Characterization of bovine MHC DRB3 diversity in Latin American Creole cattle breeds.

PubMed

Giovambattista, Guillermo; Takeshima, Shin-nosuke; Ripoli, Maria Veronica; Matsumoto, Yuki; Franco, Luz Angela Alvarez; Saito, Hideki; Onuma, Misao; Aida, Yoko

2013-04-25

In cattle, bovine leukocyte antigens (BoLAs) have been extensively used as markers for diseases and immunological traits. However, none of the highly adapted Latin American Creole breeds have been characterized for BoLA gene polymorphism by high resolution typing methods. In this work, we sequenced exon 2 of the BoLA class II DRB3 gene from 179 cattle (113 Bolivian Yacumeño cattle and 66 Colombian Hartón del Valle cattle breeds) using a polymerase chain reaction sequence-based typing (PCR-SBT) method. We identified 36 previously reported alleles and three novel alleles. Thirty-five (32 reported and three new) and 24 alleles (22 reported and two new) were detected in Yacumeño and Hartón del Valle breeds, respectively. Interestingly, Latin American Creole cattle showed a high degree of gene diversity despite their small population sizes, and 10 alleles including three new alleles were found only in these two Creole breeds. We next compared the degree of genetic variability at the population and sequence levels and the genetic distance in the two breeds with those previously reported in five other breeds: Holstein, Japanese Shorthorn, Japanese Black, Jersey, and Hanwoo. Both Creole breeds presented gene diversity higher than 0.90, a nucleotide diversity higher than 0.07, and mean number of pairwise differences higher than 19, indicating that Creole cattle had similar genetic diversity at BoLA-DRB3 to the other breeds. A neutrality test showed that the high degree of genetic variability may be maintained by balancing selection. The FST index and the exact G test showed significant differences across all cattle populations (FST=0.0478; p<0.001). Results from the principal components analysis and the phylogenetic tree showed that Yacumeño and Hartón del Valle breeds were closely related to each other. Collectively, our results suggest that the high level of genetic diversity could be explained by the multiple origins of the Creole germplasm (European, African and Indicus), and this diversity might be maintained by balancing selection. Copyright © 2013 Elsevier B.V. All rights reserved.

Prostate Cancer Stem Cell-Targeted Efficacy of a New-Generation Taxoid, SBT-1214 and Novel Polyenolic Zinc-Binding Curcuminoid, CMC2.24

PubMed Central

Botchkina, Galina I.; Zuniga, Edison S.; Rowehl, Rebecca H.; Park, Rosa; Bhalla, Rahuldev; Bialkowska, Agnieszka B.; Johnson, Francis; Golub, Lorne M.; Zhang, Yu; Ojima, Iwao; Shroyer, Kenneth R.

2013-01-01

Background Prostate cancer is the second leading cause of cancer death among men. Multiple evidence suggests that a population of tumor-initiating, or cancer stem cells (CSCs) is responsible for cancer development and exceptional drug resistance, representing a highly important therapeutic target. The present study evaluated CSC-specific alterations induced by new-generation taxoid SBT-1214 and a novel polyenolic zinc-binding curcuminoid, CMC2.24, in prostate CSCs. Principal Findings The CD133high/CD44high phenotype was isolated from spontaneously immortalized patient-derived PPT2 cells and highly metastatic PC3MM2 cells. Weekly treatment of the NOD/SCID mice bearing PPT2- and PC3MM3-induced tumors with the SBT-1214 led to dramatic suppression of tumor growth. Four of six PPT2 and 3 of 6 PC3MM2 tumors have shown the absence of viable cells in residual tumors. In vitro, SBT-1214 (100nM-1µM; for 72 hr) induced about 60% cell death in CD133high/CD44+/high cells cultured on collagen I in stem cell medium (in contrast, the same doses of paclitaxel increased proliferation of these cells). The cytotoxic effects were increased when SBT-1214 was combined with the CMC2.24. A stem cell-specific PCR array assay revealed that this drug combination mediated massive inhibition of multiple constitutively up-regulated stem cell-related genes, including key pluripotency transcription factors. Importantly, this drug combination induced expression of p21 and p53, which were absent in CD133high/CD44high cells. Viable cells that survived this treatment regimen were no longer able to induce secondary spheroids, exhibited significant morphological abnormalities and died in 2-5 days. Conclusions We report here that the SBT-1214 alone, or in combination with CMC2.24, possesses significant activity against prostate CD133high/CD44+/high tumor-initiating cells. This drug combination efficiently inhibits expression of the majority of stem cell-related genes and pluripotency transcription factors. In addition, it induces a previously absent expression of p21 and p53 (“gene wake-up”), which can potentially reverse drug resistance by increasing sensitivity to anti-cancer drugs. PMID:24086245

A direct comparison of U.S. Environmental Protection Agency's method 304B and batch tests for determining activated-sludge biodegradation rate constants for volatile organic compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cano, M.L.; Wilcox, M.E.; Compernolle, R. van

Biodegradation rate constants for volatile organic compounds (VOCs) in activated-sludge systems are needed to quantify emissions. One current US environmental Protection Agency method for determining a biodegradation rate constant is Method 304B. In this approach, a specific activated-sludge unit is simulated by a continuous biological treatment system with a sealed headspace. Batch experiments, however, can be alternatives to Method 304B. Two of these batch methods are the batch test that uses oxygen addition (BOX) and the serum bottle test (SBT). In this study, Method 304B was directly compared to BOX and SBT experiments. A pilot-scale laboratory reactor was constructed tomore » serve as the Method 304B unit. Biomass from the unit was also used to conduct BOX and modified SBT experiments (modification involved use of a sealed draft-tube reactor with a headspace recirculation pump instead of a serum bottle) for 1,2-dichloroethane, diisopropyl ether, methyl tertiary butyl ether, and toluene. Three experimental runs--each consisting of one Method 304B experiment, one BOX experiment, and one modified SBT experiment--were completed. The BOX and SBT data for each run were analyzed using a Monod model, and best-fit biodegradation kinetic parameters were determined for each experiment, including a first-order biodegradation rate constant (K{sub 1}). Experimental results suggest that for readily biodegradable VOCs the two batch techniques can provide improved means of determining biodegradation rate constants compared with Method 304B. In particular, these batch techniques avoid the Method 304B problem associated with steady-state effluent concentrations below analytical detection limits. However, experimental results also suggest that the two batch techniques should not be used to determine biodegradation rate constants for slowly degraded VOCs (i.e., K{sub 1} {lt} 0.1 L/g VSS-h).« less

Role of the heat capacity change in understanding and modeling melting thermodynamics of complementary duplexes containing standard and nucleobase-modified LNA.

PubMed

Hughesman, Curtis B; Turner, Robin F B; Haynes, Charles A

2011-06-14

Melting thermodynamic data obtained by differential scanning calorimetry (DSC) are reported for 43 duplexed oligonucleotides containing one or more locked nucleic acid (LNA) substitutions. The measured heat capacity change (ΔC(p)) for the helix-to-coil transition is used to compute the changes in enthalpy and entropy for melting of an LNA-bearing duplex at the T(m) of its corresponding isosequential unmodified DNA duplex to allow rigorous thermodynamic analysis of the stability enhancements provided by LNA substitutions. Contrary to previous studies, our analysis shows that the origin of the improved stability is almost exclusively a net reduction (ΔΔS° < 0) in the entropy gain accompanying the helix-to-coil transition, with the magnitude of the reduction dependent on the type of nucleobase and its base pairing properties. This knowledge and our average measured value for ΔC(p) of 42 ± 11 cal mol(-1) K(-1) bp(-1) are then used to derive a new model that accurately predicts melting thermodynamics and the increased melting temperature (ΔT(m)) of heteroduplexes formed between an unmodified DNA strand and a complementary strand containing any number and configuration of standard LNA nucleotides A, T, C, and G. This single-base thermodynamic (SBT) model requires only four entropy-related parameters in addition to ΔC(p). Finally, DSC data for 20 duplexes containing the nucleobase-modified LNAs 2-aminoadenine (D) and 2-thiothymine (H) are reported and used to determine SBT model parameters for D and H. The data and model suggest that along with the greater stability enhancement provided by D and H bases relative to their corresponding A and T analogues, the unique pseudocomplementary properties of D-H base pairs may make their use appealing for in vitro and in vivo applications.

Elevated methane levels in small intestinal bacterial overgrowth suggests delayed small bowel and colonic transit.

PubMed

Suri, Jaspreet; Kataria, Rahul; Malik, Zubair; Parkman, Henry P; Schey, Ron

2018-05-01

Limited research exists regarding the relationship between small intestinal bacterial overgrowth (SIBO), small bowel transit (SBT), and colonic transit (CT). Furthermore, symptom analysis is limited between the subtypes of SIBO: hydrogen producing (H-SIBO) and methane producing (M-SIBO). The primary aims of this study are to: compare the SBT and CT in patients with a positive lactulose breath test (LBT) to those with a normal study; compare the SBT and CT among patients with H-SIBO or M-SIBO; compare the severity of symptoms in patients with a positive LBT to those with a normal study; compare the severity of symptoms among patients with H-SIBO or M-SIBO.A retrospective review was performed for 89 patients who underwent a LBT and whole gut transit scintigraphy (WGTS) between 2014 and 2016. Seventy-eight patients were included. WGTS evaluated gastric emptying, SBT (normal ≥40% radiotracer bolus accumulated at the ileocecal valve at 6 hours), and CT (normal geometric center of colonic activity = 1.6-7.0 at 24 hours, 4.0-7.0 at 48 hours, 6.2-7.0 at 72 hours; elevated geometric center indicates increased transit). We also had patients complete a pretest symptom survey to evaluate nausea, bloating, constipation, diarrhea, belching, and flatulence.A total of 78 patients (69 females, 9 males, mean age of 48 years, mean BMI of 25.9) were evaluated. Forty-seven patients had a positive LBT (H-SIBO 66%, M-SIBO 34%). Comparison of SBT among patients with a positive LBT to normal LBT revealed no significant difference (62.1% vs 58.6%, P = .63). The mean accumulated radiotracer was higher for H-SIBO compared to M-SIBO (71.5% vs 44.1%; P < .05). For CT, all SIBO patients had no significant difference in geometric centers of colonic activity at 24, 48, and 72 hours when compared to the normal group. When subtyping, H-SIBO had significantly higher geometric centers compared to the M-SIBO group at 24 hours (4.4 vs 3.1, P < .001), 48 hours (5.2 vs 3.8, P = .002), and at 72 hours (5.6 vs 4.3, P = .006). The symptom severity scores did not differ between the positive and normal LBT groups. A higher level of nausea was present in the H-SIBO group when compared to the M-SIBO group.Overall, the presence of SIBO does not affect SBT or CT at 24, 48, and 72 hours. However, when analyzing the subtypes, M-SIBO has significantly more delayed SBT and CT when compared to H-SIBO. These results suggest the presence of delayed motility in patients with high methane levels on LBT.

Have “new” methods in medical education reached German-speaking Central Europe: a survey

PubMed Central

2014-01-01

Background Simulation-based-training (SBT) in the education of health professionals is discussed as an effective alternative for knowledge and skills enhancement as well as for the establishment of a secure learning environment, for learners and patients. In the Anglo-American region, SBT and simulation and training centers (STC) are numbered as standard for medical training. In German-speaking Central Europe, priority is still given to the establishment of SBT and STC. The purpose of this study was (i) to survey the status quo relating to the existence and facilities of simulation and training centers at medical universities in German-speaking Central Europe and (ii) the evaluation of training methods, especially in the area of emergency medicine skills. Methods All public and private medical universities or medical faculties in Germany (36), Austria (4) and German-speaking Switzerland (3) were interviewed. In the survey, information regarding the existence and facilities of STCs and information with regards to the use of SBT in the area of emergency medicine was requested. The questions were partly posed in a closed-ended-, in an open-ended- and in a multiple choice format (with the possibility of selecting more than one answer). Results Of a total of 43 contacted medical universities/medical faculties, 40 ultimately participated in the survey. As decisive for the establishment of a STC the potential to improve the clinical-practical training and the demand by students were listed. Obligatory training in a STC during the first and sixth academic year was confirmed only by 12 institutions, before the first invasive procedure on patients by 17 institutions. 13 institutions confirmed the use of the STC for the further training of physicians and care-staff. Training for the acute care and emergency medicine skills in the field of pediatrics, for the most part, occurs decentralized. Conclusions New methods in medical training have reached German-speaking Central Europe, but the simulation and training centers vary in size, equipment or regarding their integration into the obligatory curriculum as much as the number and variety of the offering to be trained voluntarily or on an obligatory basis. PMID:25129398

Have "new" methods in medical education reached German-speaking Central Europe: a survey.

PubMed

Fandler, Martin; Habersack, Marion; Dimai, Hans P

2014-08-16

Simulation-based-training (SBT) in the education of health professionals is discussed as an effective alternative for knowledge and skills enhancement as well as for the establishment of a secure learning environment, for learners and patients. In the Anglo-American region, SBT and simulation and training centers (STC) are numbered as standard for medical training. In German-speaking Central Europe, priority is still given to the establishment of SBT and STC. The purpose of this study was (i) to survey the status quo relating to the existence and facilities of simulation and training centers at medical universities in German-speaking Central Europe and (ii) the evaluation of training methods, especially in the area of emergency medicine skills. All public and private medical universities or medical faculties in Germany (36), Austria (4) and German-speaking Switzerland (3) were interviewed. In the survey, information regarding the existence and facilities of STCs and information with regards to the use of SBT in the area of emergency medicine was requested. The questions were partly posed in a closed-ended-, in an open-ended- and in a multiple choice format (with the possibility of selecting more than one answer). Of a total of 43 contacted medical universities/medical faculties, 40 ultimately participated in the survey. As decisive for the establishment of a STC the potential to improve the clinical-practical training and the demand by students were listed. Obligatory training in a STC during the first and sixth academic year was confirmed only by 12 institutions, before the first invasive procedure on patients by 17 institutions. 13 institutions confirmed the use of the STC for the further training of physicians and care-staff. Training for the acute care and emergency medicine skills in the field of pediatrics, for the most part, occurs decentralized. New methods in medical training have reached German-speaking Central Europe, but the simulation and training centers vary in size, equipment or regarding their integration into the obligatory curriculum as much as the number and variety of the offering to be trained voluntarily or on an obligatory basis.

A Standardised Abundance Index from Commercial Spotting Data of Southern Bluefin Tuna (Thunnus maccoyii): Random Effects to the Rescue

PubMed Central

Basson, Marinelle; Farley, Jessica H.

2014-01-01

Commercial aerial spotting of surface schools of juvenile southern bluefin tuna (SBT), Thunnus maccoyii, is conducted as part of fishing operations in the Great Australian Bight in summer. This provides the opportunity to efficiently collect large amounts of data on sightings of SBT. The data can potentially be used to construct a time-series index of relative abundance by standardising the data for issues such as weather, spotter ability and ocean conditions. Unlike a statistically designed survey, the commercial spotting is governed by business considerations and fishing operations. The SBT dataset is therefore highly unbalanced with regard to spotters operating in each season. This complicates the standardisation of the data, particularly with regard to interactions between covariates. We show how a generalized additive model with random effects can simplify both the fitting of the model and the construction of an index, while also avoiding the need to leave out strata or interaction terms that are important. The approach is applicable to standardisation of more traditional catch and effort data. PMID:25541730

A standardised abundance index from commercial spotting data of southern bluefin tuna (Thunnus maccoyii): random effects to the rescue.

PubMed

Basson, Marinelle; Farley, Jessica H

2014-01-01

Commercial aerial spotting of surface schools of juvenile southern bluefin tuna (SBT), Thunnus maccoyii, is conducted as part of fishing operations in the Great Australian Bight in summer. This provides the opportunity to efficiently collect large amounts of data on sightings of SBT. The data can potentially be used to construct a time-series index of relative abundance by standardising the data for issues such as weather, spotter ability and ocean conditions. Unlike a statistically designed survey, the commercial spotting is governed by business considerations and fishing operations. The SBT dataset is therefore highly unbalanced with regard to spotters operating in each season. This complicates the standardisation of the data, particularly with regard to interactions between covariates. We show how a generalized additive model with random effects can simplify both the fitting of the model and the construction of an index, while also avoiding the need to leave out strata or interaction terms that are important. The approach is applicable to standardisation of more traditional catch and effort data.

Effect of dietary supplementation of sea buckthorn and giloe leaf meal on the body weight gain, feed conversion ratio, biochemical attributes, and meat composition of turkey poults

PubMed Central

Sharma, Aditya; Shukla, Pankaj Kumar; Bhattacharyya, Amitav; Kumar, Upendra; Roy, Debashis; Yadav, Brijesh; Prakash, Atul

2018-01-01

Aim: In the recent past, few studies have been carried out about sea buckthorn (SBT) and giloe in chicken as a part of the quest for suitable alternatives to antibiotics. However, studies in turkeys are lacking. Hence, the present study was conducted to evaluate the effects of SBT and giloe leaf meal by dietary feed supplementation in turkey poults. Materials and Methods: A total of 1-day-old turkey poults (n=84) of small white variety were distributed into four dietary treatments having three replicates each with seven birds. The study was conducted in turkey poults during 0-8 weeks of age. During the experiment, the poults were fed basal ration (28% crude protein [CP], 2800 Kcal/kg ME) T1, T2-basal ration was supplemented with SBT leaf meal powder at 0.5%, T3-basal ration was supplemented with giloe leaf meal powder at 0.5%, and T4-basal ration was fed along with supplementation of both SBT at 0.5% and giloe leaf meal powder at 0.5%. Results: T2 turkey poults had a significantly higher (p<0.01) body weight gain than T3 and T4 at 7th week of age. Weekly body weight gain was significantly higher (p<0.05) in T2 than T3 during 5th-8th week and 0-8th week of the growth phase. Feed conversion ratio (FCR) was significantly better (p<0.01) in T2 than other treatment groups during 4th-8th week phase of growth (2.09 vs. 2.36, 2.29 and 2.31). Further, FCR was significantly better (p<0.01) in T2 group as compared to other treatment groups during 0-8th week of growth phase (1.95 vs. 2.21, 2.21 and 2.12). Plasma uric acid was found significantly increased (p<0.05) in T1 than T3 and T4, and alkaline phosphatase value was significantly higher (p<0.05) in T1 and T3 than T2. Zinc content of breast (pectoralis major) muscles was significantly higher (p<0.05) in T2 and T4 as compared to T1, while ether extract (EE) in thigh (ilio tibialis) muscles was significantly higher (p<0.05) in T2 as compared to the other treatment groups. Conclusion: It may be concluded that supplementation of SBT leaf meal at 0.5% may improve production performance of turkey poults. Supplementation of 0.5% SBT leaf meal may result in higher levels of zinc and EE in the breast and thigh cuts of turkey poults. PMID:29479163

Effect of dietary supplementation of sea buckthorn and giloe leaf meal on the body weight gain, feed conversion ratio, biochemical attributes, and meat composition of turkey poults.

PubMed

Sharma, Aditya; Shukla, Pankaj Kumar; Bhattacharyya, Amitav; Kumar, Upendra; Roy, Debashis; Yadav, Brijesh; Prakash, Atul

2018-01-01

In the recent past, few studies have been carried out about sea buckthorn (SBT) and giloe in chicken as a part of the quest for suitable alternatives to antibiotics. However, studies in turkeys are lacking. Hence, the present study was conducted to evaluate the effects of SBT and giloe leaf meal by dietary feed supplementation in turkey poults. A total of 1-day-old turkey poults (n=84) of small white variety were distributed into four dietary treatments having three replicates each with seven birds. The study was conducted in turkey poults during 0-8 weeks of age. During the experiment, the poults were fed basal ration (28% crude protein [CP], 2800 Kcal/kg ME) T1, T2-basal ration was supplemented with SBT leaf meal powder at 0.5%, T3-basal ration was supplemented with giloe leaf meal powder at 0.5%, and T4-basal ration was fed along with supplementation of both SBT at 0.5% and giloe leaf meal powder at 0.5%. T2 turkey poults had a significantly higher (p<0.01) body weight gain than T3 and T4 at 7 th week of age. Weekly body weight gain was significantly higher (p<0.05) in T2 than T3 during 5 th -8 th week and 0-8 th week of the growth phase. Feed conversion ratio (FCR) was significantly better (p<0.01) in T2 than other treatment groups during 4 th -8 th week phase of growth (2.09 vs. 2.36, 2.29 and 2.31). Further, FCR was significantly better (p<0.01) in T2 group as compared to other treatment groups during 0-8 th week of growth phase (1.95 vs. 2.21, 2.21 and 2.12). Plasma uric acid was found significantly increased (p<0.05) in T1 than T3 and T4, and alkaline phosphatase value was significantly higher (p<0.05) in T1 and T3 than T2. Zinc content of breast (pectoralis major) muscles was significantly higher (p<0.05) in T2 and T4 as compared to T1, while ether extract (EE) in thigh (ilio tibialis) muscles was significantly higher (p<0.05) in T2 as compared to the other treatment groups. It may be concluded that supplementation of SBT leaf meal at 0.5% may improve production performance of turkey poults. Supplementation of 0.5% SBT leaf meal may result in higher levels of zinc and EE in the breast and thigh cuts of turkey poults.

Do heart and respiratory rate variability improve prediction of extubation outcomes in critically ill patients?

PubMed Central

2014-01-01

Introduction Prolonged ventilation and failed extubation are associated with increased harm and cost. The added value of heart and respiratory rate variability (HRV and RRV) during spontaneous breathing trials (SBTs) to predict extubation failure remains unknown. Methods We enrolled 721 patients in a multicenter (12 sites), prospective, observational study, evaluating clinical estimates of risk of extubation failure, physiologic measures recorded during SBTs, HRV and RRV recorded before and during the last SBT prior to extubation, and extubation outcomes. We excluded 287 patients because of protocol or technical violations, or poor data quality. Measures of variability (97 HRV, 82 RRV) were calculated from electrocardiogram and capnography waveforms followed by automated cleaning and variability analysis using Continuous Individualized Multiorgan Variability Analysis (CIMVA™) software. Repeated randomized subsampling with training, validation, and testing were used to derive and compare predictive models. Results Of 434 patients with high-quality data, 51 (12%) failed extubation. Two HRV and eight RRV measures showed statistically significant association with extubation failure (P <0.0041, 5% false discovery rate). An ensemble average of five univariate logistic regression models using RRV during SBT, yielding a probability of extubation failure (called WAVE score), demonstrated optimal predictive capacity. With repeated random subsampling and testing, the model showed mean receiver operating characteristic area under the curve (ROC AUC) of 0.69, higher than heart rate (0.51), rapid shallow breathing index (RBSI; 0.61) and respiratory rate (0.63). After deriving a WAVE model based on all data, training-set performance demonstrated that the model increased its predictive power when applied to patients conventionally considered high risk: a WAVE score >0.5 in patients with RSBI >105 and perceived high risk of failure yielded a fold increase in risk of extubation failure of 3.0 (95% confidence interval (CI) 1.2 to 5.2) and 3.5 (95% CI 1.9 to 5.4), respectively. Conclusions Altered HRV and RRV (during the SBT prior to extubation) are significantly associated with extubation failure. A predictive model using RRV during the last SBT provided optimal accuracy of prediction in all patients, with improved accuracy when combined with clinical impression or RSBI. This model requires a validation cohort to evaluate accuracy and generalizability. Trial registration ClinicalTrials.gov NCT01237886. Registered 13 October 2010. PMID:24713049

Molecular characterization of swine leukocyte antigen gene diversity in purebred Pietrain pigs.

PubMed

Essler, Sabine E; Ertl, Werner; Deutsch, Julia; Ruetgen, Barbara C; Groiss, Sandra; Stadler, Maria; Wysoudil, Bhuma; Gerner, Wilhelm; Ho, Chak-Sum; Saalmueller, Armin

2013-04-01

The porcine major histocompatibility complex (MHC) harbors the highly polymorphic swine leukocyte antigen (SLA) class I and II gene clusters encoding glycoproteins that present antigenic peptides to T cells in the adaptive immune response. In Austria, the majority of commercial pigs are F 2 descendants of F 1 Large White/Landrace hybrids paired with Pietrain boars. Therefore, the repertoire of SLA alleles and haplotypes present in Pietrain pigs has an important influence on that of their descendants. In this study, we characterized the SLA class I ( SLA-1 , SLA-2 , SLA-3 ) and class II ( SLA-DRB1 , SLA-DQB1 , SLA-DQA ) genes of 27 purebred Pietrain pigs using a combination of the high-resolution sequence-based typing (SBT) method and a low-resolution (Lr) PCR-based method using allele-group, sequence-specific primers (PCR-SSP). A total of 15 class I and 13 class II haplotypes were identified in the studied cohort. The most common SLA class I haplotype Lr-43.0 ( SLA-1 *11XX- SLA-3 *04XX- SLA-2 *04XX) was identified in 11 animals with a frequency of 20%. For SLA class II, the most prevalent haplotype, Lr-0.14 [ SLA-DRB1 *0901- SLA-DQB1 *0801- SLA-DQA *03XX], was found in 14 animals with a frequency of 26%. Two class II haplotypes, tentatively designated as Lr-Pie-0.1 [ SLA-DRB1 *01XX/be01/ha04- SLA-DQB1 *05XX- SLA - DQA*blank] and Lr-Pie-0.2 [ SLA-DRB1 *06XX- SLA-DQB1 *03XX- SLA-DQA *03XX], appeared to be novel and have never been reported so far in other pig populations. We showed that SLA genotyping using PCR-SSP-based assays represents a rapid and cost-effective way to study SLA diversity in outbred commercial pigs and may facilitate the development of more effective vaccines or identification of disease-resistant pigs in the context of SLA antigens to improve overall swine health. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

Novel properties of Hippophae rhamnoides L. twig and leaf extracts - anti-virulence action and synergy with antifungals studied in vitro on Candida spp. model.

PubMed

Sadowska, Beata; Budzyńska, Aleksandra; Stochmal, Anna; Żuchowski, Jerzy; Różalska, Barbara

2017-06-01

Original, chemically characterized Sea buckthorn (SBT) twig and leaf extracts were in vitro studied in terms of anti-Candida activity. Minimum inhibitory concentrations (MICs) of the extracts against C. albicans ATCC 10231 ranged: 250 μg/ml (twig), 31.5 μg/ml (leaf), and against C. glabrata G1 (clinical isolate) - 15.6 μg/ml (twig), 3.9 μg/ml (leaf). Next the extracts have been used at their subMIC. Both extracts significantly enhanced activity of fluconazole (FLC) and caspofungin (CAS) against C. albicans and increased their efficacy against C. glabrata, measured by an agar dilution assay combined with the E-test. The extracts inhibited C. albicans morphogenesis such as germ tube and hyphae formation as well as invasion to the "Spider" Agar. Antiadhesive and anti-biofilm activities of the extracts were evaluated by Alamar Blue reduction assay. It showed not significant reduction in the degree of cell adhesion (by 10-15%) but noticeable decrease of biofilm formation (by 80% in the case of SBT-twig extract). In conclusion, this study provided the evidence that SBT extracts, used at non-cytotoxic concentrations for the fibroblasts (IC 50 from 664.8 μg/ml to 1060.4 μg/ml), targeted some of Candida spp. virulence factors essential for the establishment of the infection. SBT twigs, previously regarded as waste material, were shown to be also a valuable source of the substances with promising antimicrobial activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Increased serum baseline tryptase levels and extensive skin involvement are predictors for the severity of mast cell activation episodes in children with mastocytosis

PubMed Central

Alvarez-Twose, I.; Vañó-Galván, S.; Sánchez-Muñoz, L.; Morgado, J. M.; Matito, A.; Torrelo, A.; Jaén, P.; Schwartz, L. B.; Orfao, A.; Escribano, L

2012-01-01

Background Despite the good prognosis of pediatric mastocytosis, some patients suffer from severe mast cell (MC) mediator-associated symptoms. The aim of this study was to identify predictors for severe MC mediator release symptoms in children with mastocytosis in the skin (MIS). Methods Serum baseline total tryptase (sbT) levels in 111 children with MIS – 80 maculopapular cutaneous mastocytosis/plaque mastocytosis, 22 nodular mastocytosis, and nine diffuse cutaneous mastocytosis – were investigated as a predictive biomarker for the occurrence of MC mediator-related signs and symptoms within the first 18 months after disease onset. Results Twelve children (11%) who showed extensive cutaneous disease involving >90% of body surface area (BSA) suffered from severe symptoms requiring hospitalization, with (n = 5) or without (n = 6) management in the intensive care unit (ICU) owing to life-threatening complications. The median sbT was significantly (P < 0.001) higher in patients with extensive cutaneous disease vs those with <90% of BSA involved (45.5 vs 5.2 µg/l, respectively), as well as in children with grade 4 (severe mastocytosis-related symptoms requiring emergency therapy and hospitalization) vs those with grade <4 (46.2 vs 5.2 µg/l, respectively). Receiver operating characteristics curve analyses showed that the optimal cutoff s for sbT to predict the need for daily antimediator therapy, hospitalization, and the management in an ICU were 6.6, 15.5, and 30.8 µg/l, respectively (sensitivity and specificity of 77% and 79%, 100% and 95%, and 100% and 96%, respectively). Conclusions Increased sbT in association with extensive cutaneous involvement identifies patients at risk for severe MC activation events in pediatric mastocytosis. PMID:22458675

Validation of the REMA score for predicting mast cell clonality and systemic mastocytosis in patients with systemic mast cell activation symptoms.

PubMed

Alvarez-Twose, I; González-de-Olano, D; Sánchez-Muñoz, L; Matito, A; Jara-Acevedo, M; Teodosio, C; García-Montero, A; Morgado, J M; Orfao, A; Escribano, L

2012-01-01

A variable percentage of patients with systemic mast cell (MC) activation symptoms meet criteria for systemic mastocytosis (SM). We prospectively evaluated the clinical utility of the REMA score versus serum baseline tryptase (sBt) levels for predicting MC clonality and SM in 158 patients with systemic MC activation symptoms in the absence of mastocytosis in the skin (MIS). World Health Organization criteria for SM were applied in all cases. MC clonality was defined as the presence of KIT-mutated MC or by a clonal HUMARA test. The REMA score consisted of the assignment of positive or negative points as follows: male (+1), female (-1), sBt <15 μg/l (-1) or >25 μg/l (+2), presence (-2) or absence (+1) of pruritus, hives or angioedema and presence (+3) of presyncope or syncope. Efficiency of the REMA score for predicting MC clonality and SM was assessed by receiver operating characteristic (ROC) curve analyses and compared to those obtained by means of sBt levels alone. Molecular studies revealed the presence of clonal MC in 68/80 SM cases and in 11/78 patients who did not meet the criteria for SM. ROC curve analyses confirmed the greater sensitivity and a similar specificity of the REMA score versus sBt levels (84 vs. 59% and 74 vs. 70% for MC clonality and 87 vs. 62% and 73 vs. 71% for SM, respectively). Our results confirm the clinical utility of the REMA score to predict MC clonality and SM in patients suffering from systemic MC activation symptoms without MIS. Copyright © 2011 S. Karger AG, Basel.

Increased serum baseline tryptase levels and extensive skin involvement are predictors for the severity of mast cell activation episodes in children with mastocytosis.

PubMed

Alvarez-Twose, I; Vañó-Galván, S; Sánchez-Muñoz, L; Morgado, J M; Matito, A; Torrelo, A; Jaén, P; Schwartz, L B; Orfao, A; Escribano, L

2012-06-01

Despite the good prognosis of pediatric mastocytosis, some patients suffer from severe mast cell (MC) mediator-associated symptoms. The aim of this study was to identify predictors for severe MC mediator release symptoms in children with mastocytosis in the skin (MIS). Serum baseline total tryptase (sbT) levels in 111 children with MIS - 80 maculopapular cutaneous mastocytosis/plaque mastocytosis, 22 nodular mastocytosis, and nine diffuse cutaneous mastocytosis - were investigated as a predictive biomarker for the occurrence of MC mediator-related signs and symptoms within the first 18 months after disease onset. Twelve children (11%) who showed extensive cutaneous disease involving >90% of body surface area (BSA) suffered from severe symptoms requiring hospitalization, with (n = 5) or without (n = 6) management in the intensive care unit (ICU) owing to life-threatening complications. The median sbT was significantly (P < 0.001) higher in patients with extensive cutaneous disease vs those with <90% of BSA involved (45.5 vs 5.2 μg/l, respectively), as well as in children with grade 4 (severe mastocytosis-related symptoms requiring emergency therapy and hospitalization) vs those with grade <4 (46.2 vs 5.2 μg/l, respectively). Receiver operating characteristics curve analyses showed that the optimal cutoff s for sbT to predict the need for daily antimediator therapy, hospitalization, and the management in an ICU were 6.6, 15.5, and 30.8 μg/l, respectively (sensitivity and specificity of 77% and 79%, 100% and 95%, and 100% and 96%, respectively). Increased sbT in association with extensive cutaneous involvement identifies patients at risk for severe MC activation events in pediatric mastocytosis. © 2012 John Wiley & Sons A/S.

Demographic Structure, Sex Ratio and Growth Rates of Southern Bluefin Tuna (Thunnus maccoyii) on the Spawning Ground

PubMed Central

Farley, Jessica H.; Eveson, J. Paige; Davis, Tim L. O.; Andamari, Retno; Proctor, Craig H.; Nugraha, Budi; Davies, Campbell R.

2014-01-01

The demographics of the southern bluefin tuna (SBT) Thunnus maccoyii spawning stock were examined through a large-scale monitoring program of the Indonesian longline catch on the spawning ground between 1995 and 2012. The size and age structure of the spawning population has undergone significant changes since monitoring began. There has been a reduction in the relative abundance of larger/older SBT in the catch since the early 2000s, and a corresponding decrease in mean length and age, but there was no evidence of a significant truncation of the age distribution. Pulses of young SBT appear in the catches in the early- and mid-2000s and may be the first evidence of increased recruitment into the spawning stock since 1995. Fish in these two recruitment pulses were spawned around 1991 and 1997. Size-related variations in sex ratio were also observed with female bias for fish less than 170 cm FL and male bias for fish greater than 170 cm FL. This trend of increasing proportion of males with size above 170 cm FL is likely to be related to sexual dimorphism in growth rates as male length-at-age is greater than that for females after age 10 years. Mean length-at-age of fish aged 8–10 years was greater for both males and females on the spawning ground than off the spawning ground, suggesting that size may be the dominant factor determining timing of maturation in SBT. In addition to these direct results, the data and samples from this program have been central to the assessment and management of this internationally harvested stock. PMID:24797529

Loneliness, Social Integration and Consumption of Sugar-Containing Beverages: Testing the Social Baseline Theory

PubMed Central

Henriksen, Roger Ekeberg; Torsheim, Torbjørn; Thuen, Frode

2014-01-01

Objective Social Baseline Theory (SBT) proposes that close relationships aid in metabolic resource management and that individuals without significant relationships may experience more demands on their own neural metabolic resources on a daily basis when solving problems, remaining vigilant against potential threats and regulating emotional responses. This study tests a hypothesised consequence derived from SBT: relative social isolation leads to increased levels of sugar intake. Methods Based on cross-sectional, self-reported data from the Norwegian Mother and Child Cohort Study (N = 90 084), information on social integration and the consumption of both sugar-sweetened and artificially sweetened sodas and juices was obtained from a large number of women in early pregnancy. Multiple regression analyses were conducted to assess whether loneliness, marital status, relationship satisfaction, advice from others than partner, and cohesion at work is associated with consumption of sodas and juices. Results Perceived loneliness was associated with elevated intake of all sugary beverages, while relationship satisfaction was negatively associated with all sugary beverages. Being married or cohabitating, having supportive friends, and having a sense of togetherness at work were associated with lower intake of two out of three sugar-containing beverages. These associations were significant, even after controlling for factors such as body mass index, weight related self-image, depression, physical activity, educational level, age and income. In comparison, a statistically significant relationship emerged between relationship satisfaction and artificially sweetened cola. No other predictor variables were significantly associated with any type of artificially sweetened beverage. Conclusions This study indicates that loneliness and social integration influence the level of consumption of sugary beverages. The results support the hypothesis derived from the Social Baseline Theory that relative social isolation leads to increased levels of sugar intake. PMID:25105408

Prediction of HR/BP response to the spontaneous breathing trial by fluctuation dissipation theory

NASA Astrophysics Data System (ADS)

Chen, Man

2014-03-01

We applied the non-equilibrium fluctuation dissipation theorem to predict how critically-ill patients respond to treatment, based on both heart rate data and blood pressure data collected by standard hospital monitoring devices. The non-equilibrium fluctuation dissipation theorem relates the response of a system to a perturbation to the fluctuations in the stationary state of the system. It is shown that the response of patients to a standard procedure performed on patients, the spontaneous breathing trial (SBT), can be predicted by the non-equilibrium fluctuation dissipation approach. We classify patients into different groups according to the patients' characteristics. For each patient group, we extend the fluctuation dissipation theorem to predict interactions between blood pressure and beat-to-beat dynamics of heart rate in response to a perturbation (SBT), We also extract the form of the perturbation function directly from the physiological data, which may help to reduce the prediction error. We note this method is not limited to the analysis of the heart rate dynamics, but also can be applied to analyze the response of other physiological signals to other clinical interventions.

Multistate storage nonvolatile memory device based on ferroelectricity and resistive switching effects of SrBi2Ta2O9 films

NASA Astrophysics Data System (ADS)

Song, Zhiwei; Li, Gang; Xiong, Ying; Cheng, Chuanpin; Zhang, Wanli; Tang, Minghua; Li, Zheng; He, Jiangheng

2018-05-01

A memory device with a Pt/SrBi2Ta2O9(SBT)/Pt(111) structure was shown to have excellent combined ferroelectricity and resistive switching properties, leading to higher multistate storage memory capacity in contrast to ferroelectric memory devices. In this device, SBT polycrystalline thin films with significant (115) orientation were fabricated on Pt(111)/Ti/SiO2/Si(100) substrates using CVD (chemical vapor deposition) method. Measurement results of the electric properties exhibit reproducible and reliable ferroelectricity switching behavior and bipolar resistive switching effects (BRS) without an electroforming process. The ON/OFF ratio of the resistive switching was found to be about 103. Switching mechanisms for the low resistance state (LRS) and high resistance state (HRS) currents are likely attributed to the Ohmic and space charge-limited current (SCLC) behavior, respectively. Moreover, the ferroelectricity and resistive switching effects were found to be mutually independent, and the four logic states were obtained by controlling the periodic sweeping voltage. This work holds great promise for nonvolatile multistate memory devices with high capacity and low cost.

Impact of bubble size on growth and CO2 uptake of Arthrospira (Spirulina) platensis KMMCC CY-007.

PubMed

Kim, Kisok; Choi, Jaeho; Ji, Yosep; Park, Soyoung; Do, Hyungki; Hwang, Cherwon; Lee, Bongju; Holzapfel, Wilhelm

2014-10-01

Optimisation of cyanobacterial cell productivity should consider the key factors light cycle and carbon source. We studied the influence of CO2 bubble size on carbon uptake and fixation, on basis of mRNA expression levels in Arthrospira platensis KMMCC CY-007 at 30°C (light intensity: 40μmolm(-2)s(-1); 1% CO2). Growth rate, carbon fixation and lipid accumulation were examined over 7days under fine bubble (FB) (100μm Ø) bulk bubble (BB) (5000μm Ø) and non-CO2 (NB) aeration. The low affinity CO2 uptake mRNA (NDH-I4 complex) was stronger expressed than the high affinity NDH-I3 complex (bicA and sbtA) under 1% CO2 and FB conditions, with no expression of bicA1 and sbtA1 after 4days. The high affinity CO2 uptake mRNA levels corresponded to biomass, carbon content and lipid accumulation, and increase in NDH-I3 complex (9.72-fold), bicA (5.69-fold), and sbtA (10.61-fold), compared to NB, or BB conditions. Copyright © 2014 Elsevier Ltd. All rights reserved.

MICA genetic polymorphism and HLA-A,C,B,MICA and DRB1 haplotypic variation in a southern Chinese Han population: identification of two new MICA alleles, MICA*060 and MICA*062.

PubMed

Tian, Wei; Cai, JinHong; Liu, XueXiang

2011-06-01

In this study, 201 healthy, unrelated Han subjects in Hunan province, southern China, were investigated by sequence-based typing (SBT) for the allelic variation of the human major histocompatibility complex (MHC) class I chain-related gene A (MICA). Nineteen MICA alleles were observed, among which MICA*008:01 predominated with gene frequency of 30.35%. There was significant linkage disequilibrium (LD) of MICA*012:01 with HLA-B*54 and HLA-B*55, which was not observed in a northern Chinese Han population. Haplotype HLA-A*11-C*07-B60-MICA*008:01 (9.16%) was highly specific to this southern Chinese Han population. The most common five-locus haplotype in this population was HLA-A*02-C*01-B*46-MICA*010-DRB1*09 (8.73%). A new MICA allele, MICA*060, was identified on an HLA-A*02-C*01-B*55:02-DRB1*14 haplotype through extended family analysis. MICA*060 has probably arisen from MICA*012:01. Another new MICA allele, MICA*062, was identified by screening 1432 subjects using polymerase chain reaction-sequence-specific priming technology. MICA*062 has probably derived from MICA*010. Of particular interest is that MICA*062 was carried on an HLA-C*08-B*48:01-DRB1*14 haplotypic segment, as HLA-B*48 has been consistently shown to be primarily linked to MICA gene deletion in east Asian populations. Our results provide new insight into MICA genetic polymorphism in human populations. The findings reported here are of importance for future studies on the potential role of MICA in allogeneic organ transplantation and disease association in populations of Chinese ancestry. Copyright © 2011 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Social Baseline Theory: The Social Regulation of Risk and Effort

PubMed Central

Coan, James A.; Sbarra, David A.

2015-01-01

We describe Social Baseline Theory (SBT), a perspective that integrates the study of social relationships with principles of attachment, behavioral ecology, cognitive neuroscience, and perception science. SBT suggests the human brain expects access to social relationships that mitigate risk and diminish the level of effort needed to meet a variety of goals. This is accomplished in part by incorporating relational partners into neural representations of the self. By contrast, decreased access to relational partners increases cognitive and physiological effort. Relationship disruptions entail re-defining the self as independent, which implies greater risk, increased effort, and diminished well being. The ungrafting of the self and other may mediate recovery from relationship loss. PMID:25825706

Influence of styryl dyes on blood erythrocytes

NASA Astrophysics Data System (ADS)

Nizomov, Negmat; Barakaeva, Mubaro; Kurtaliev, Eldar N.; Rahimov, Sherzod I.; Khakimova, Dilorom P.; Khodjayev, Gayrat; Yashchuk, Valeriy N.

2008-08-01

It was studied the influence of F, Sbt, Sil, Sbo monomer and homodimer Dst-5, Dst-10, Dbt-5, Dbt-10, Dil-10, Dbo-10 styryl dyes on blood erythrocytes of white rats. It was shown that the homodimer styryl dyes Dst-5, Dbt-5 and Dbo-10 decrease the erythrocytes quantity by 1.5-2 times more as compared with monomer dyes Sbt and Sbo. The main cause of dyes different action is the different oxidation degree of intracellular hemoglobin evoked by these dyes. It was established that the observed effects was connected with different penetration of these dyes through membrane of erythrocytes and with interaction of these dyes with albumin localized in membranes of cells.

The frequency of HLA-B(∗)57:01 and the risk of abacavir hypersensitivity reactions in the majority population of Costa Rica.

PubMed

Arrieta-Bolaños, Esteban; Madrigal, J Alejandro; Marsh, Steven G E; Shaw, Bronwen E; Salazar-Sánchez, Lizbeth

2014-11-01

HLA-B(∗)57:01 is a well-known and cost-effective pharmacogenetic marker for abacavir hypersensitivity. As with other HLA alleles, there is widespread variation in its frequency across populations. The Costa Rica Central Valley Population (CCVP) is the major population in this country. The frequency of HLA-B(∗)57:01 in this population has not been described yet. Thus, our aim was to determine the frequency of this allele in the CCVP. 200 unrelated healthy volunteer donors born in the CCVP were typed. HLA-B(∗)57-positive samples identified by HLA intermediate resolution typing methods were further typed by SBT to high resolution. An HLA-B(∗)57:01 carrier frequency of 5.00% was determined in this sample. This frequency is relatively high in comparison to reports from other populations in Latin America. These results suggest that there is a considerable frequency of HLA-B(∗)57:01 in the CCVP and that pharmacogenetic testing for HIV+ patients who are going to receive abacavir-based treatment should be considered in this country. Copyright © 2014 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

90° switching of polarization in La3+-doped SrBi2Ta2O9 thin films

NASA Astrophysics Data System (ADS)

Liu, J. S.; Zhang, S. R.; Zeng, H. Z.; Fei, W. D.; Du, S. Y.

2006-05-01

The crystal structure and polarization switching behavior of SrBi1.4La0.6Ta2O9 (SBLT) thin films have been studied by x-ray diffraction and piezoresponse force microscopy (PFM), respectively. Compared with SrBi2Ta2O9 (SBT), SBLT thin films show a reduced orthorhombic distortion. The polarization rotation of SBLT thin film, which is driven by negative and positive direct current (dc) biases, has been investigated by a combination of vertical and lateral PFM (VPFM and LPFM, respectively). After dc bias applications, the VPFM image is hardly changed, whereas the LPFM image experiences an obvious variation. It is believed that such difference is caused by 90° polarization switching. However, this kind of switching can be only realized by the exchange of a axis and b axis. By virtue of the reduced orthorhombic distortion, the a-b exchange in SBLT is easier than that in SBT. Unfortunately, stress is created due to the 90° polarization switching in SBLT thin films. The internal stress is found to increase with the repeated switching cycles, and so the polarization reorientation in SBLT is constrained. Thus, the fatigue resistance of SBLT thin films is not thought to be as good as that of SBT.

Characterization of zinc alloy by sheet bulging test with analytical models and digital image correlation

NASA Astrophysics Data System (ADS)

Vitu, L.; Laforge, N.; Malécot, P.; Boudeau, N.; Manov, S.; Milesi, M.

2018-05-01

Zinc alloys are used in a wide range of application such as electronics, automotive and building construction. Their various shapes are generally obtained by metal forming operation such as stamping. Therefore, it is important to characterize the material with adequate characterization tests. Sheet Bulging Test (SBT) is well recognized in the metal forming community. Different theoretical models of the literature for the evaluation of thickness and radius of the deformed sheet in SBT have been studied in order to get the hardening curve of different materials. These theoretical models present the advantage that the experimental procedure is very simple. But Koç et al. showed their limitation, since the combination of thickness and radius evaluations depend on the material. As Zinc alloys are strongly anisotropic with a special crystalline structure, a procedure is adopted for characterizing the hardening curve of a Zinc alloy. The anisotropy is first studied with tensile test, and SBT with elliptical dies is also investigated. Parallel to this, Digital Image Correlation (DIC) measures are carried out. The results obtained from theoretical models and DIC measures are compared. Measures done on post-mortem specimens complete the comparisons. Finally, DIC measures give better results and the resulting hardening curve of the studied zinc alloy is provided.

Marine Sponge-Derived Streptomyces sp. SBT343 Extract Inhibits Staphylococcal Biofilm Formation

PubMed Central

Balasubramanian, Srikkanth; Othman, Eman M.; Kampik, Daniel; Stopper, Helga; Hentschel, Ute; Ziebuhr, Wilma; Oelschlaeger, Tobias A.; Abdelmohsen, Usama R.

2017-01-01

Staphylococcus epidermidis and Staphylococcus aureus are opportunistic pathogens that cause nosocomial and chronic biofilm-associated infections. Indwelling medical devices and contact lenses are ideal ecological niches for formation of staphylococcal biofilms. Bacteria within biofilms are known to display reduced susceptibilities to antimicrobials and are protected from the host immune system. High rates of acquired antibiotic resistances in staphylococci and other biofilm-forming bacteria further hamper treatment options and highlight the need for new anti-biofilm strategies. Here, we aimed to evaluate the potential of marine sponge-derived actinomycetes in inhibiting biofilm formation of several strains of S. epidermidis, S. aureus, and Pseudomonas aeruginosa. Results from in vitro biofilm-formation assays, as well as scanning electron and confocal microscopy, revealed that an organic extract derived from the marine sponge-associated bacterium Streptomyces sp. SBT343 significantly inhibited staphylococcal biofilm formation on polystyrene, glass and contact lens surfaces, without affecting bacterial growth. The extract also displayed similar antagonistic effects towards the biofilm formation of other S. epidermidis and S. aureus strains tested but had no inhibitory effects towards Pseudomonas biofilms. Interestingly the extract, at lower effective concentrations, did not exhibit cytotoxic effects on mouse fibroblast, macrophage and human corneal epithelial cell lines. Chemical analysis by High Resolution Fourier Transform Mass Spectrometry (HRMS) of the Streptomyces sp. SBT343 extract proportion revealed its chemical richness and complexity. Preliminary physico-chemical characterization of the extract highlighted the heat-stable and non-proteinaceous nature of the active component(s). The combined data suggest that the Streptomyces sp. SBT343 extract selectively inhibits staphylococcal biofilm formation without interfering with bacterial cell viability. Due to absence of cell toxicity, the extract might represent a good starting material to develop a future remedy to block staphylococcal biofilm formation on contact lenses and thereby to prevent intractable contact lens-mediated ocular infections. PMID:28261188

Alzheimer’s and Cognitive Reserve

PubMed Central

Roe, Catherine M.; Mintun, Mark A.; D’Angelo, Gina; Xiong, Chengjie; Grant, Elizabeth A.; Morris, John C.

2009-01-01

Objective To evaluate the cognitive reserve hypothesis by examining whether individuals of greater educational attainment have better cognitive function than individuals with less education in the presence of elevated fibrillar brain amyloid. Design, Setting, and Participants Uptake of N-methyl-[11C]2-(4′-methylaminophenyl)-6-hydroybenzothiazole, or [11C]PIB for “Pittsburgh Compound-B,” was measured for participants assessed between August 15, 2003 and January 8, 2008 at the Washington University Alzheimer’s Disease Research Center and diagnosed either as nondemented (N=161) or with dementia of the Alzheimer type (N=37). Multiple regression was used to determine whether [11C]PIB uptake interacted with level of educational attainment to predict cognitive function. Main Outcome Measures Scores on the Clinical Dementia Rating - Sum of Boxes (CDR-SB), Mini-Mental State Exam (MMSE), and Short Blessed Test (SBT), and individual measures from a psychometric battery. Results [11C]PIB uptake interacted with years of education in predicting scores on the CDR-SB (p=.003), the MMSE (p<.001), the SBT (p=.03) and a measure of verbal abstract reasoning and conceptualization (p=.02), such that performance on these measures increased with increasing education for participants with elevated PIB uptake. Education was unrelated to global cognitive functioning scores among those with lower PIB uptake. Conclusions These results support the hypothesis that cognitive reserve influences the association between Alzheimer disease pathology and cognition. PMID:19001165

Clinical, biological, and molecular characteristics of clonal mast cell disorders presenting with systemic mast cell activation symptoms.

PubMed

Alvarez-Twose, Iván; González de Olano, David; Sánchez-Muñoz, Laura; Matito, Almudena; Esteban-López, Maria I; Vega, Arantza; Mateo, Maria Belén; Alonso Díaz de Durana, Maria D; de la Hoz, Belén; Del Pozo Gil, Maria D; Caballero, Teresa; Rosado, Ana; Sánchez Matas, Isabel; Teodósio, Cristina; Jara-Acevedo, María; Mollejo, Manuela; García-Montero, Andrés; Orfao, Alberto; Escribano, Luis

2010-06-01

Systemic mast cell activation disorders (MCADs) are characterized by severe and systemic mast cell (MC) mediators-related symptoms frequently associated with increased serum baseline tryptase (sBt). To analyze the clinical, biological, and molecular characteristics of adult patients presenting with systemic MC activation symptoms/anaphylaxis in the absence of skin mastocytosis who showed clonal (c) versus nonclonal (nc) MCs and to provide indication criteria for bone marrow (BM) studies. Eighty-three patients were studied. Patients showing clonal BM MCs were grouped into indolent systemic mastocytosis without skin lesions (ISMs(-); n = 48) and other c-MCADs (n = 3)-both with CD25(++) BM MCs and either positive mast/stem cell growth factor receptor gene (KIT) mutation or clonal human androgen receptor assay (HUMARA) tests-and nc-MCAD (CD25-negative BM MCs in the absence of KIT mutation; n = 32) and compared for their clinical, biological, and molecular characteristics. Most clonal patients (48/51; 94%) met the World Health Organization criteria for systemic mastocytosis and were classified as ISMs(-), whereas the other 3 c-MCAD and all nc-MCAD patients did not. In addition, although both patients with ISMs(-) and patients with nc-MCAD presented with idiopathic and allergen-induced anaphylaxis, the former showed a higher frequency of men, cardiovascular symptoms, and insect bite as a trigger, together with greater sBt. Based on a multivariate analysis, a highly efficient model to predict clonality before BM sampling was built that includes male sex (P = .01), presyncopal and/or syncopal episodes (P = .009) in the absence of urticaria and angioedema (P = .003), and sBt >25 microg/L (P = .006) as independent predictive factors. Patients with c-MCAD and ISMs(-) display unique clinical and laboratory features different from nc-MCAD patients. A significant percentage of c-MCAD patients can be considered as true ISMs(-) diagnosed at early phases of the disease. Copyright (c) 2010 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

A Smartphone Application Suite for Assessing Mobility.

PubMed

Madhushri, Priyanka; Dzhagaryan, Armen A; Jovanov, Emil; Milenkovic, Aleksandar

2016-08-01

Modern smartphones integrate a growing number of inertial and environmental sensors that can enable the development of new mobile health applications. In this paper we introduce a suite of smartphone applications for assessing mobility in elderly population. The suite currently includes applications that automate and quantify the following standardized medical tests for assessing mobility: Timed-Up-and-Go (TUG), 30 Seconds Chair Stand Test (30SCS), and a 4-stage Balance Test (4SBT). For each smartphone application we describe its functionality and a list of parameters extracted by processing signals from smartphone's inertial sensors. The paper shows the results from studies conducted on geriatric patients for TUG tests and from studies conducted in the laboratory on healthy subjects for 30SCS and 4SBT tests.

Gut microbiota and its implications in small bowel transplantation.

PubMed

Wang, Chenyang; Li, Qiurong; Li, Jieshou

2018-06-01

The gut microbiota is mainly composed of a diverse population of commensal bacterial species and plays a pivotal role in the maintenance of intestinal homeostasis, immune modulation and metabolism. The influence of the gut microbiota on solid organ transplantation has recently been recognized. In fact, several studies indicated that acute and chronic allograft rejection in small bowel transplantation (SBT) is closely associated with the alterations in microbial patterns in the gut. In this review, we focused on the recent findings regarding alterations in the microbiota following SBTand the potential roles of these alterations in the development of acute and chronic allograft rejection. We also reviewed important advances with respect to the interplays between the microbiota and host immune systems in SBT. Furthermore, we explored the potential of the gut microbiota as a microbial marker and/or therapeutic target for the predication and intervention of allograft rejection and chronic dysfunction. Given that current research on the gut microbiota has become increasingly sophisticated and comprehensive, large cohort studies employing metagenomic analysis and multivariate linkage should be designed for the characterization of host-microbe interaction and causality between microbiota alterations and clinical outcomes in SBT. The findings are expected to provide valuable insights into the role of gut microbiota in the development of allograft rejection and other transplant-related complications and introduce novel therapeutic targets and treatment approaches in clinical practice.

Are MUPs a Toxic Waste Disposal System?

PubMed

Kwak, Jae; Strasser, Eva; Luzynski, Ken; Thoß, Michaela; Penn, Dustin J

2016-01-01

Male house mice produce large quantities of major urinary proteins (MUPs), which function to bind and transport volatile pheromones, though they may also function as scavengers that bind and excrete toxic compounds ('toxic waste hypothesis'). In this study, we demonstrate the presence of an industrial chemical, 2,4-di-tert-butylphenol (DTBP), in the urine of wild-derived house mice (Mus musculus musculus). Addition of guanidine hydrochloride to male and female urine resulted in an increased release of DTBP. This increase was only observed in the high molecular weight fractions (HMWF; > 3 kDa) separated from male or female urine, suggesting that the increased release of DTBP was likely due to the denaturation of MUPs and the subsequent release of MUP-bound DTBP. Furthermore, when DTBP was added to a HMWF isolated from male urine, an increase in 2-sec-butyl-4,5-dihydrothiazole (SBT), the major ligand of MUPs and a male-specific pheromone, was observed, indicating that DTBP was bound to MUPs and displaced SBT. These results suggest that DTBP is a MUP ligand. Moreover, we found evidence for competitive ligand binding between DTBP and SBT, suggesting that males potentially face a tradeoff between eliminating toxic wastes versus transporting pheromones. Our findings support the hypothesis that MUPs bind and eliminate toxic wastes, which may provide the most important fitness benefits of excreting large quantities of these proteins.

Clonal mast cell disorders in patients with severe Hymenoptera venom allergy and normal serum tryptase levels.

PubMed

Zanotti, Roberta; Lombardo, Carla; Passalacqua, Giovanni; Caimmi, Cristian; Bonifacio, Massimiliano; De Matteis, Giovanna; Perbellini, Omar; Rossini, Maurizio; Schena, Donatella; Busa, Moira; Marcotulli, Maria Cinzia; Bilò, Maria Beatrice; Franchini, Maurizio; Marchi, Giovanni; Simioni, Livio; Bonadonna, Patrizia

2015-07-01

Systemic mastocytosis is a clonal mast cell (MC) disease that can lead to potentially fatal anaphylactic reactions caused by excessive MC mediator release. The prevalence of mastocytosis in patients with Hymenoptera venom allergy is high, and thus the disease should be suspected in patients with severe reactions caused by Hymenoptera stings and increased serum basal tryptase (SBT) levels. We sought to evaluate the presence of clonal MC disorders in patients seen at our mastocytosis center with Hymenoptera sting-induced anaphylaxis, documented hypotension, absence of urticaria pigmentosa, and normal SBT levels. Twenty-two patients with Hymenoptera sting-induced anaphylaxis, without skin lesions, and with tryptase levels of less than 11.4 ng/mL underwent bone marrow evaluation. Bone mineral density was assessed in those patients with ascertained mastocytosis. In 16 of 22 patients, a diagnosis of indolent mastocytosis could be established, and 1 patient had a monoclonal MC activation syndrome. Patients with mastocytosis had higher SBT levels (P = .03) but only rarely had angioedema/urticaria associated with hypotension (P = .004). The absence of urticaria or angioedema in severe reactions to Hymenoptera stings with hypotension might represent the most relevant factor in identifying patients with mastocytosis, regardless of their serum tryptase levels. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Frequencies of immune hypersensitivity reaction-associated HLA class I alleles in healthy South African Indian and mixed ancestry populations determined by a novel real-time PCR assay.

PubMed

Loubser, S; Paximadis, M; Gentle, N; Puren, A; Gray, C M; Tiemessen, C T

2014-10-01

We have determined the frequencies of human leucocyte antigen (HLA)-B*57:01, HLA-B*35:05, HLA-C*04 and HLA-C*08 in healthy individuals of South African Indian (SAI) ethnicity (n = 50) and South African mixed (SAM) ancestry (n = 50) using real-time allele-specific polymerase chain reaction (AS-PCR) assay. HLA-B*57:01 associates with immune hypersensitivity reaction (IHR) in individuals exposed to abacavir (ABC), while nevirapine (NVP) IHR associates with HLA-B*35:05, HLA-C*04 and HLA-C*08. Real-time AS-PCR assays typically use less DNA, are more cost-effective and rapid compared with conventional genotyping methods, such as sequence-based typing (SBT). The assay was developed using samples of known HLA class I genotype and subsequently applied to the SAI and SAM samples. HLA-B*57:01 was detected in SAM and SAI populations at frequencies of 8.0% and 12.0%, respectively, while HLA-B*35:05 was not found in SAI individuals, but was present in 6.0% of SAM individuals. HLA-C*04 was detected in 22.0% and 24.0% of SAM and SAI individuals, respectively, while 10.0% and 8.0% of SAM and SAI individuals, respectively, were HLA-C*08 positive. This study reports the development of a novel real-time AS-PCR assay to identify HLA class I alleles associated with ABC and NVP IHR and has established the frequencies of these alleles present in healthy SAI and SAM populations. Using South African demographic data, our hypothetical analysis suggests that a substantial number of individuals would benefit from the assay. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Polymorphisms of HLA-DRB1, -DQA1 and -DQB1 in inhabitants of Astana, the capital city of Kazakhstan.

PubMed

Kuranov, Alexandr B; Vavilov, Mikhail N; Abildinova, Gulshara Zh; Akilzhanova, Ainur R; Iskakova, Aisha N; Zholdybayeva, Elena V; Boldyreva, Margarita N; Müller, Claudia A; Momynaliev, Kuvat T

2014-01-01

Kazakhstan has been inhabited by different populations, such as the Kazakh, Kyrgyz, Uzbek and others. Here we investigate allelic and haplotypic polymorphisms of human leukocyte antigen (HLA) genes at DRB1, DQA1 and DQB1 loci in the Kazakh ethnic group, and their genetic relationship between world populations. A total of 157 unrelated Kazakh ethnic individuals from Astana were genotyped using sequence based typing (SBT-Method) for HLA-DRB1, -DQA1 and -DQB1 loci. Allele frequencies, neighbor-joining method, and multidimensional scaling analysis have been obtained for comparison with other world populations. Statistical analyses were performed using Arlequin v3.11. Applying the software PAST v. 2.17 the resulting genetic distance matrix was used for a multidimensional scaling analysis (MDS). Respectively 37, 17 and 19 alleles were observed at HLA-DRB1, -DQA1 and -DQB1 loci. The most frequent alleles were HLA-DRB1*07:01 (13.1%), HLA-DQA1*03:01 (13.1%) and HLA-DQB1*03:01 (17.6%). In the observed group of Kazakhs DRB1*07:01-DQA1*02:01-DQB1*02:01 (8.0%) was the most common three loci haplotype. DRB1*10:01-DQB1*05:01 showed the strongest linkage disequilibrium. The Kazakh population shows genetic kinship with the Kazakhs from China, Uyghurs, Mongolians, Todzhinians, Tuvinians and as well as with other Siberians and Asians. The HLA-DRB1, -DQA1 and -DQB1 loci are highly polymorphic in the Kazakh population, and this population has the closest relationship with other Asian and Siberian populations.

Estimation of tracheal pressure and imposed expiratory work of breathing by the endotracheal tube, heat and moisture exchanger, and ventilator during mechanical ventilation.

PubMed

Uchiyama, Akinori; Yoshida, Takeshi; Yamanaka, Hidenori; Fujino, Yuji

2013-07-01

The resistance of the endotracheal tube (ETT), the heat and moisture exchanger (HME), and the ventilator may affect the patient's respiratory status. Although previous studies examined the inspiratory work of breathing (WOB), investigation of WOB in the expiratory phase is rare. We estimated tracheal pressure at the tip of the ETT (Ptrach) and calculated expiratory WOB imposed by the ETT, the HME, and the expiratory valve. We examined imposed expiratory WOB in patients under a continuous mandatory ventilation (CMV) mode and during spontaneous breathing trials (SBTs). We hypothesized that imposed expiratory WOB would increase with heightened ventilatory demand. We measured airway pressure (Paw) and respiratory flow (V). We estimated Ptrach using the equation Ptrach = Paw - K1 × V(K2) - 2.70 × V(L/s)(1.42). K1 and K2 were determined by the inner diameter (ID) of the ETT. Imposed expiratory WOB was calculated from the area of Ptrach above PEEP versus lung volume. We examined imposed expiratory WOB and imposed expiratory resistance in relation to mean expiratory flow. We examined 28 patients under CMV mode, and 29 during SBT. During both CMV and SBT, as mean expiratory flow increased, imposed expiratory WOB increased. The regression curves between mean expiratory flow (x) (L/s) and imposed expiratory WOB (y) (J/L) were y = 1.35x(0.83) (R(2) = 0.79) for 7 mm ID ETT under CMV, y = 1.12x(0.82) (R(2) = 0.73) for 8 mm ID ETT under CMV, y = 1.07x(1.04) (R(2) = 0.85) for 7 mm ID ETT during SBT, and y = 0.84x(0.93) (R(2) = 0.75) for 8 mm ID ETT during SBT. Levels of imposed expiratory WOB were affected by ETT diameter and ventilator mode. The reason for increasing imposed expiratory WOB was an increase in expiratory resistance imposed by the ETT and HME. Under mechanical ventilation, imposed expiratory WOB should be considered in patients with higher minute ventilation.

Association between physiological falls risk and physical performance tests among community-dwelling older adults.

PubMed

Singh, Devinder K A; Pillai, Sharmila G K; Tan, Sin Thien; Tai, Chu Chiau; Shahar, Suzana

2015-01-01

Physical performance and balance declines with aging and may lead to increased risk of falls. Physical performance tests may be useful for initial fall-risk screening test among community-dwelling older adults. Physiological profile assessment (PPA), a composite falls risk assessment tool is reported to have 75% accuracy to screen for physiological falls risk. PPA correlates with Timed Up and Go (TUG) test. However, the association between many other commonly used physical performance tests and PPA is not known. The aim of the present study was to examine the association between physiological falls risk measured using PPA and a battery of physical performance tests. One hundred and forty older adults from a senior citizens club in Kuala Lumpur, Malaysia (94 females, 46 males), aged 60 years and above (65.77±4.61), participated in this cross-sectional study. Participants were screened for falls risk using PPA. A battery of physical performance tests that include ten-step test (TST), short physical performance battery (SPPB), functional reach test (FRT), static balance test (SBT), TUG, dominant hand-grip strength (DHGS), and gait speed test (GST) were also performed. Spearman's rank correlation and binomial logistic regression were performed to examine the significantly associated independent variables (physical performance tests) with falls risk (dependent variable). Approximately 13% older adults were at high risk of falls categorized using PPA. Significant differences (P<0.05) were demonstrated for age, TST, SPPB, FRT, SBT, TUG between high and low falls risk group. A significant (P<0.01) weak correlation was found between PPA and TST (r=0.25), TUG (r=0.27), SBT (r=0.23), SPPB (r=-0.33), and FRT (r=-0.23). Binary logistic regression results demonstrated that SBT measuring postural sways objectively using a balance board was the only significant predictor of physiological falls risk (P<0.05, odds ratio of 2.12). The reference values of physical performance tests in our study may be used as a guide for initial falls screening to categorize high and low physiological falls risk among community-dwelling older adults. A more comprehensive assessment of falls risk can be performed thereafter for more specific intervention of underlying impairments.

Simulation-Based Training of Non-Technical Skills in Colonoscopy: Protocol for a Randomized Controlled Trial.

PubMed

Khan, Rishad; Scaffidi, Michael A; Walsh, Catharine M; Lin, Peter; Al-Mazroui, Ahmed; Chana, Barinder; Kalaichandran, Ruben; Lee, Woojin; Grantcharov, Teodor P; Grover, Samir C

2017-08-04

Non-technical skills (NTS), such as communication and professionalism, contribute to the safe and effective completion of procedures. NTS training has previously been shown to improve surgical performance. Moreover, increases in NTS have been associated with improved clinical endoscopic performance. Despite this evidence, NTS training has not been tested as an intervention in endoscopy. The aim of this study is to evaluate the effectiveness of a simulation-based training (SBT) curriculum of NTS on novice endoscopists' performance of clinical colonoscopy. Novice endoscopists were randomized to 2 groups. The control group received 4 hours of interactive didactic sessions on colonoscopy theory and 6 hours of SBT. Hours 5 and 6 of the SBT were integrated scenarios, wherein participants interacted with a standardized patient and nurse, while performing a colonoscopy on the virtual reality (VR) simulator. The NTS (intervention) group received the same teaching sessions but the last hour was focused on NTS teaching. The NTS group also reviewed a checklist of tasks relevant to NTS concepts prior to each integrated scenario case and was provided with dedicated feedback on their NTS performance during the integrated scenario practice. All participants were assessed at baseline, immediately after training, and 4 to 6 weeks post-training. The primary outcome measure is colonoscopy-specific performance in the clinical setting. In total, 42 novice endoscopists completed the study. Data collection and analysis is ongoing. We anticipate completion of all assessments by August 2017. Data analysis, manuscript writing, and subsequent submission for publication is expected to be completed by December 2017. Results from this study may inform the implementation of NTS training into postgraduate gastrointestinal curricula. NTS curricula may improve attitudes towards patient safety and self-reflection among trainees. Moreover, enhanced NTS may lead to superior clinical performance and outcomes in colonoscopy. Clinicaltrial.gov NCT02877420; https://www.clinicaltrials.gov/ct2/show/NCT02877420 (Archived by WebCite at http://www.webcitation.org/6rw94ubXX NCT02877420). ©Rishad Khan, Michael A Scaffidi, Catharine M Walsh, Peter Lin, Ahmed Al-Mazroui, Barinder Chana, Ruben Kalaichandran, Woojin Lee, Teodor P Grantcharov, Samir C Grover. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 04.08.2017.

Augmentation of humoral and cellular immunity in response to Tetanus and Diphtheria toxoids by supercritical carbon dioxide extracts of Hippophae rhamnoides L. leaves.

PubMed

Jayashankar, Bindhya; Singh, Divya; Tanwar, Himanshi; Mishra, K P; Murthy, Swetha; Chanda, Sudipta; Mishra, Jigni; Tulswani, R; Misra, K; Singh, S B; Ganju, Lilly

2017-03-01

Hippophae rhamnoides L. commonly known as Seabuckthorn (SBT), a wild shrub of family Elaegnacea, has extensively used for treating various ailments like skin diseases, jaundice, asthma, lung troubles. SBT leaves have been reported to possess several pharmacological properties including immunomodulatory, antioxidant, anti-inflammatory, antimicrobial and tissue regeneration etc. The present study was undertaken to evaluate the adjuvant property of supercritical carbon dioxide extracts (SCEs 300ET and 350ET) of SBT leaves in balb/c mice immunized with Tetanus and Diphtheria toxoids. The dynamic changes in the immune response were measured in terms of humoral and cell-mediated immune responses. We have seen the effect of SCEs on immunoglobulin subtypes and secondary immune response generation. In addition, the effect of SCEs on antigen specific cellular immunity was evaluated. Our results show that SCEs 300ET and 350ET significantly enhanced antibody titers in response to both TT and DT antigens. The secondary immune response generated was significantly increased in case of TT immunized animals. SCEs also enhanced cytokine levels (IFN-γ, IL-4, TNF-α and IL-1β) and increased lymphoproliferation. Besides, both SCEs did not show any toxic effects. Therefore, the study suggests that SCEs are safe and have potent immunostimulatory activity and hence, seems to be a promising balanced Th1 and Th2 directing immunological adjuvant for various veterinary as well as human vaccines. Copyright © 2017. Published by Elsevier B.V.

Healing efficacy of sea buckthorn (Hippophae rhamnoides L.) seed oil in an ovine burn wound model.

PubMed

Ito, Hiroshi; Asmussen, Sven; Traber, Daniel L; Cox, Robert A; Hawkins, Hal K; Connelly, Rhykka; Traber, Lillian D; Walker, Timothy W; Malgerud, Erik; Sakurai, Hiroyuki; Enkhbaatar, Perenlei

2014-05-01

To investigate the efficacy of sea buckthorn (SBT) seed oil - a rich source of substances known to have anti-atherogenic and cardioprotective activity, and to promote skin and mucosa epithelization - on burn wound healing, five adult sheep were subjected to 3rd degree flame burns. Two burn sites were made on the dorsum of the sheep and the eschar was excised down to the fascia. Split-thickness skin grafts were harvested, meshed, and fitted to the wounds. The autograft was placed on the fascia and SBT seed oil was topically applied to one recipient and one donor site, respectively, with the remaining sites treated with vehicle. The wound blood flow (LASER Doppler), and epithelization (ultrasound) were determined at 6, 14, and 21 days after injury. 14 days after grafting, the percentage of epithelization in the treated sites was greater (95 ± 2.2% vs. 83 ± 2.9%, p<0.05) than in the untreated sites. Complete epithelization time was shorter in both treated recipient and donor sites (14.20 ± 0.48 vs. 19.60 ± 0.40 days, p<0.05 and 13.40 ± 1.02 vs. 19.60 ± 0.50 days, p<0.05, respectively) than in the untreated sites, confirmed by ultrasound. In conclusion, SBT seed oil has significant wound healing activity in full-thickness burns and split-thickness harvested wounds. Copyright © 2013 Elsevier Ltd and ISBI. All rights reserved.

HLA-DRB1 Alleles Are Associated with the Susceptibility to Sporadic Parkinson’s Disease in Chinese Han Population

PubMed Central

Sun, Congcong; Wei, Lei; Luo, Feifei; Li, Yi; Li, Jiaobiao; Zhu, Feiqi; Kang, Ping; Xu, Rensi; Xiao, LuLu; Liu, Zhuolin; Xu, Pingyi

2012-01-01

Immune disorders may play an important role in the pathogenesis of Parkinson's disease (PD). Recently, polymorphisms in the HLA-DR region have been found to be associated with sporadic PD in European ancestry populations. However, polymorphisms in the HLA complex are highly variable with ethnic and geographic origin. To explore the relationships between polymorphisms of the HLA-DR region and sporadic PD in Chinese Han population, we genotyped 567 sporadic PD patients and 746 healthy controls in two independent series for the HLA-DRB1 locus with Polymerase chain reaction-sequence based typing(PCR-SBT). The χ2 test was used to evaluate the distribution of allele frequencies between the patients and healthy controls. The impact of HLA-DRB1 alleles on PD risk was estimated by unconditional logistic regression. We found a significant higher frequency of HLA-DRB1*0301 in sporadic PD patients than in healthy controls and a positive association, which was independent of onset age, between HLA-DRB1*0301 and PD risk. Conversely, a lower frequency of HLA-DRB1*0406 was found in sporadic PD patients than in healthy controls, with a negative association between HLA-DRB1*0406 and PD risk. Furthermore, a meta-analysis involving 195205 individuals was conducted to summarize the frequencies of these two alleles in populations from various ethnic regions, we found a higher frequency of HLA-DRB1*0301, but a lower frequency of HLA-DRB1*0406 in European ancestry populations than that in Asians, this was consistent with the higher prevalence of sporadic PD in European ancestry populations. Based on these results, we speculate that HLA-DRB1 alleles are associated with the susceptibility to sporadic PD in Chinese Han population, among them HLA-DRB1*0301 is a risk allele while the effect of HLA-DRB1*0406 deserves debate. PMID:23139797

Micro-power dissipation device described

NASA Astrophysics Data System (ADS)

Mao, X.; Zhou, L.; Zhou, J.

1985-11-01

The common-emitter current gain beta of a common two-pole transistor is generally below 250. They are referred to as high-beta or high gain transistors when the beta of such transistors exceeds 300. When the beta of a transistor is higher than 1,000, it is called a super-beta transistor (SBT) or supergain transistor. The micropower dissipation type has the widest applications among the high-beta. Micropower dissipation high-beta means that there is a high gain or a superhigh gain under a microcurrent. The device is widely used in small signal-detection systems and stereo audio equipment because of their characteristics of high gain, low frequency and low noise under small signals.

Functional Genome Mining for Metabolites Encoded by Large Gene Clusters through Heterologous Expression of a Whole-Genome Bacterial Artificial Chromosome Library in Streptomyces spp.

PubMed Central

Xu, Min; Wang, Yemin; Zhao, Zhilong; Gao, Guixi; Huang, Sheng-Xiong; Kang, Qianjin; He, Xinyi; Lin, Shuangjun; Pang, Xiuhua; Deng, Zixin

2016-01-01

ABSTRACT Genome sequencing projects in the last decade revealed numerous cryptic biosynthetic pathways for unknown secondary metabolites in microbes, revitalizing drug discovery from microbial metabolites by approaches called genome mining. In this work, we developed a heterologous expression and functional screening approach for genome mining from genomic bacterial artificial chromosome (BAC) libraries in Streptomyces spp. We demonstrate mining from a strain of Streptomyces rochei, which is known to produce streptothricins and borrelidin, by expressing its BAC library in the surrogate host Streptomyces lividans SBT5, and screening for antimicrobial activity. In addition to the successful capture of the streptothricin and borrelidin biosynthetic gene clusters, we discovered two novel linear lipopeptides and their corresponding biosynthetic gene cluster, as well as a novel cryptic gene cluster for an unknown antibiotic from S. rochei. This high-throughput functional genome mining approach can be easily applied to other streptomycetes, and it is very suitable for the large-scale screening of genomic BAC libraries for bioactive natural products and the corresponding biosynthetic pathways. IMPORTANCE Microbial genomes encode numerous cryptic biosynthetic gene clusters for unknown small metabolites with potential biological activities. Several genome mining approaches have been developed to activate and bring these cryptic metabolites to biological tests for future drug discovery. Previous sequence-guided procedures relied on bioinformatic analysis to predict potentially interesting biosynthetic gene clusters. In this study, we describe an efficient approach based on heterologous expression and functional screening of a whole-genome library for the mining of bioactive metabolites from Streptomyces. The usefulness of this function-driven approach was demonstrated by the capture of four large biosynthetic gene clusters for metabolites of various chemical types, including streptothricins, borrelidin, two novel lipopeptides, and one unknown antibiotic from Streptomyces rochei Sal35. The transfer, expression, and screening of the library were all performed in a high-throughput way, so that this approach is scalable and adaptable to industrial automation for next-generation antibiotic discovery. PMID:27451447

Study of A-site doping of SrBi4Ti4O15 Bi-layered compounds using micro-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Hao, H.; Liu, H. X.; Cao, M. H.; Min, X. M.; Ouyang, S. X.

2006-10-01

The temperature-dependent Raman spectra of Mg- and La-doped SrBi4Ti4O15 (SBT) were studied in the range 40 590 °C. A quantum chemistry calculation was employed to estimate these two substitution states. It was found that A-site doping in this study not only caused multiplicative substitution states, but also the Raman spectra changed with the substitution amount. In a La-doped perovskite-like layer, La would occupy the Bi site when x>0.10 and the 314 and 550 cm-1 modes related to the rotating and tilting of the TiO6 octahedron firstly became wide and then became sharp. With the increase of the substitution amount, both substitution states of Mg-doped SBT lead to the widening of 270 and 520 cm-1 peaks.

Health condition and physical function as predictors of adherence in long-term strength and balance training among community-dwelling older adults.

PubMed

Aartolahti, Eeva; Tolppanen, Anna-Maija; Lönnroos, Eija; Hartikainen, Sirpa; Häkkinen, Arja

2015-01-01

Strength and balance training (SBT) has remarkable health benefits, but little is known regarding exercise adherence in older adults. We examined the adherence to strength and balance training and determinants of adherence among ≥75 year old adults. 182 community-dwelling individuals (aged 75-98 years, 71% female) began group-based SBT as part of a population-based Geriatric Multidisciplinary Strategy for the Good Care of the Elderly study. Training was offered once a week for 2.3 years. Adherence was defined as the proportion of attended sessions relative to offered sessions. Participants were classified based on their adherence level into low (≤33.3%), moderate (33.4-66.5%) and high (≥66.6%) adherers. The mean length of training was 19 ± 9 months, and 68% continued participation for at least two years. The mean training adherence was 55 ± 29% for all participants and 18%, 53% and 82% for low, moderate and high adherers, respectively. High adherence was predicted by female sex; younger age; better cognition; independence in Instrumental Activities of Daily Living; higher knee extension strength; faster walking speed; and better performance on the Berg Balance Scale and Timed Up and Go tests. Poorer self-perceived health and the use of a walking aid were related to low adherence. Long-term continuation of training is possible for older community-dwelling adults, although poorer health and functional limitations affect training adherence. Our findings have implications for tailoring interventions and support for older adults to optimize their exercise adherence. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

DNA typing of HLA-A, -C, -B, AND -DRB1 in the children with autism in the Republic of Macedonia.

PubMed

Trajkovski, V; Spiroski, M

2015-01-01

In the present study, we report the first DNA analysis of HLA class I and class II alleles in Macedonian autistic subjects. We have analyzed the HLA-A, -C, -B, DRB1 genotypes of 35 autistic patients, and 98 healthy unrelated Macedonians (control group). HLA DNA typing of class I genes was performed using a Reverse Line Strip method (RLS), and the Sequencing Based Typing method (SBT) was used for typing of class II genes. In the autistic subjects for HLA-A locus 14 alleles have been identified with 2 being predominant *02 (25.7 %), and *24 (18.6 %). Among the 11 identified HLA-C alleles, 3 were predominant such as *12 (20.0 %), *07 (17.1 %), and *03 (12.9 %). Among the 18 identified HLA-B alleles, 2 were predominant: *51 (18.6 %), and *18 (11.4 %). For HLA-DRB1 locus, 10 alleles have been identified with 2 of them predominant such as: *11 (21.4 %), and *01 (14.3 %). The allele and haplotype frequencies in the patients group were compared to those of 98 control subjects. Our results showed significantly increased frequencies of HLA-C*03 (OR = 2.74*; χ2 = 4.68; p = 0.03), and HLA-DRB1*01 (OR = 3.10*; χ2 = 6.26; p = 0.012) alleles in autistic patients when compared to the controls. The most frequent haplotype frequencies in autistic sample were A*11-C*12-B*52-DRB1*15 (2.9 %), A*24-C*03-B*55-DRB1*16 (2.9 %), and A*24-C*03-B*55-DRB1*16 (2.9 %), but they were not statistically significant when compared to the control group. None of our patients carried allele or haplotype, which were protective in our population. Hardy-Weinberg equilibrium in autistic group showed that HLA-A (p < 0.03), HLA-C (p < 0.04), and HLA-DRB1 (p < 0.002) loci were in linkage disequilibria. In the control group, we found only for the HLA-DRB1 locus linkage disequilibrium (p < 0.002). Our results demonstrated the association of HLA-C*03 and HLA-DRB1*01 alleles with Macedonian autistic patients (Tab. 7, Ref. 37).

Evaluation of cough peak expiratory flow as a predictor of successful mechanical ventilation discontinuation: a narrative review of the literature.

PubMed

Jiang, Chuan; Esquinas, Antonio; Mina, Bushra

2017-01-01

A crucial step in the transition from mechanical ventilation to extubation is the successful performance of a spontaneous breathing trial (SBT). The American College of Chest Physicians (ACCP) Guidelines recommend removal of the endotracheal tube upon successful completion of a SBT. However, this does not guarantee successful extubation as there remains a risk of re-intubation. Guidelines have outlined ventilator liberation protocols, selected use of non-invasive ventilation on extubation, early mobilization, and dynamic ventilator metrics to prevent and better predict extubation failure. However, a significant percentage of patients still fail mechanical ventilation discontinuation. A common reason for re-intubation is having a weak cough strength, which reflects the inability to protect the airway. Evaluation of cough strength via objective measures using peak expiratory flow rate is a non-invasive and easily reproducible assessment which can predict extubation failure. We conducted a narrative review of the literature regarding use of cough strength as a predictive index for extubation failure risk. Results of our review show that cough strength, quantified objectively with a cough peak expiratory flow measurement (CPEF), is strongly associated with extubation success. Furthermore, various cutoff thresholds have been identified and can provide reasonable diagnostic accuracy and predictive power for extubation failure. These results demonstrate that measurement of the CPEF can be a useful tool to predict extubation failure in patients on MV who have passed a SBT. In addition, the data suggest that this diagnostic modality may reduce ICU length of stay, ICU expenditures, and morbidity and mortality.

Prolonged weaning: from the intensive care unit to home.

PubMed

Navalesi, P; Frigerio, P; Patzlaff, A; Häußermann, S; Henseke, P; Kubitschek, M

2014-01-01

Weaning is the process of withdrawing mechanical ventilation which starts with the first spontaneous breathing trial (SBT). Based on the degree of difficulty and duration, weaning is classified as simple, difficult and prolonged. Prolonged weaning, which includes patients who fail 3 SBTs or are still on mechanical ventilation 7 days after the first SBT, affects a relatively small fraction of mechanically ventilated ICU patients but these, however, requires disproportionate resources. There are several potential causes which can lead to prolonged weaning. It is nonetheless important to understand the problem from the point of view of each individual patient in order to adopt appropriate treatment and define precise prognosis. An otherwise stable patient who remains on mechanical ventilation will be considered for transfer to a specialized weaning unit (SWU). Though there is not a precise definition, SWU can be considered as highly specialized and protected environments for patients requiring mechanical ventilation despite resolution of the acute disorder. Proper staffing, well defined short-term and long-term goals, attention to psychological and social problems represent key determinants of SWU success. Some patients cannot be weaned, either partly or entirely, and may require long-term home mechanical ventilation. In these cases the logistics relating to caregivers and the equipment must be carefully considered and addressed. Copyright © 2014 Sociedade Portuguesa de Pneumologia. Published by Elsevier España. All rights reserved.

Association between physiological falls risk and physical performance tests among community-dwelling older adults

PubMed Central

Singh, Devinder KA; Pillai, Sharmila GK; Tan, Sin Thien; Tai, Chu Chiau; Shahar, Suzana

2015-01-01

Background Physical performance and balance declines with aging and may lead to increased risk of falls. Physical performance tests may be useful for initial fall-risk screening test among community-dwelling older adults. Physiological profile assessment (PPA), a composite falls risk assessment tool is reported to have 75% accuracy to screen for physiological falls risk. PPA correlates with Timed Up and Go (TUG) test. However, the association between many other commonly used physical performance tests and PPA is not known. The aim of the present study was to examine the association between physiological falls risk measured using PPA and a battery of physical performance tests. Methods One hundred and forty older adults from a senior citizens club in Kuala Lumpur, Malaysia (94 females, 46 males), aged 60 years and above (65.77±4.61), participated in this cross-sectional study. Participants were screened for falls risk using PPA. A battery of physical performance tests that include ten-step test (TST), short physical performance battery (SPPB), functional reach test (FRT), static balance test (SBT), TUG, dominant hand-grip strength (DHGS), and gait speed test (GST) were also performed. Spearman’s rank correlation and binomial logistic regression were performed to examine the significantly associated independent variables (physical performance tests) with falls risk (dependent variable). Results Approximately 13% older adults were at high risk of falls categorized using PPA. Significant differences (P<0.05) were demonstrated for age, TST, SPPB, FRT, SBT, TUG between high and low falls risk group. A significant (P<0.01) weak correlation was found between PPA and TST (r=0.25), TUG (r=0.27), SBT (r=0.23), SPPB (r=−0.33), and FRT (r=−0.23). Binary logistic regression results demonstrated that SBT measuring postural sways objectively using a balance board was the only significant predictor of physiological falls risk (P<0.05, odds ratio of 2.12). Conclusion The reference values of physical performance tests in our study may be used as a guide for initial falls screening to categorize high and low physiological falls risk among community-dwelling older adults. A more comprehensive assessment of falls risk can be performed thereafter for more specific intervention of underlying impairments. PMID:26316727

High-Resolution Analyses of Human Leukocyte Antigens Allele and Haplotype Frequencies Based on 169,995 Volunteers from the China Bone Marrow Donor Registry Program

PubMed Central

Zhou, Xiao-Yang; Zhu, Fa-Ming; Li, Jian-Ping; Mao, Wei; Zhang, De-Mei; Liu, Meng-Li; Hei, Ai-Lian; Dai, Da-Peng; Jiang, Ping; Shan, Xiao-Yan; Zhang, Bo-Wei; Zhu, Chuan-Fu; Shen, Jie; Deng, Zhi-Hui; Wang, Zheng-Lei; Yu, Wei-Jian; Chen, Qiang; Qiao, Yan-Hui; Zhu, Xiang-Ming; Lv, Rong; Li, Guo-Ying; Li, Guo-Liang; Li, Heng-Cong; Zhang, Xu; Pei, Bin; Jiao, Li-Xin; Shen, Gang; Liu, Ying; Feng, Zhi-Hui; Su, Yu-Ping; Xu, Zhao-Xia; Di, Wen-Ying; Jiang, Yao-Qin; Fu, Hong-Lei; Liu, Xiang-Jun; Liu, Xiang; Zhou, Mei-Zhen; Du, Dan; Liu, Qi; Han, Ying; Zhang, Zhi-Xin; Cai, Jian-Ping

2015-01-01

Allogeneic hematopoietic stem cell transplantation is a widely used and effective therapy for hematopoietic malignant diseases and numerous other disorders. High-resolution human leukocyte antigen (HLA) haplotype frequency distributions not only facilitate individual donor searches but also determine the probability with which a particular patient can find HLA-matched donors in a registry. The frequencies of the HLA-A, -B, -C, -DRB1, and -DQB1 alleles and haplotypes were estimated among 169,995 Chinese volunteers using the sequencing-based typing (SBT) method. Totals of 191 HLA-A, 244 HLA-B, 146 HLA-C, 143 HLA-DRB1 and 47 HLA-DQB1 alleles were observed, which accounted for 6.98%, 7.06%, 6.46%, 9.11% and 7.91%, respectively, of the alleles in each locus in the world (IMGT 3.16 Release, Apr. 2014). Among the 100 most common haplotypes from the 169,995 individuals, nine distinct haplotypes displayed significant regionally specific distributions. Among these, three were predominant in the South China region (i.e., the 20th, 31st, and 81sthaplotypes), another three were predominant in the Southwest China region (i.e., the 68th, 79th, and 95th haplotypes), one was predominant in the South and Southwest China regions (the 18th haplotype), one was relatively common in the Northeast and North China regions (the 94th haplotype), and one was common in the Northeast, North and Northwest China (the 40th haplotype). In conclusion, this is the first to analyze high-resolution HLA diversities across the entire country of China, based on a detailed and complete data set that covered 31 provinces, autonomous regions, and municipalities. Specifically, we also evaluated the HLA matching probabilities within and between geographic regions and analyzed the regional differences in the HLA diversities in China. We believe that the data presented in this study might be useful for unrelated HLA-matched donor searches, donor registry planning, population genetic studies, and anthropogenesis studies. PMID:26421847

Perpendicular transport in superlattice bipolar transistors (SBT)

NASA Astrophysics Data System (ADS)

Sibille, A.; Palmier, J. F.; Minot, C.; Harmand, J. C.; Dubon-Chevallier, C.

Diffusion-limited electron transport in superlattices is studied by gain measurements on heterojunction bipolar transistors with a {GaAs}/{GaAlAs} superlattice base. In the case of thin barriers, Bloch conduction is observed, while hopping between localized levels prevails for large barriers. A transition occurs between these two regimes, localization being achieved when the energy broadening induced by the electron-phonon coupling added to the disorder due to imperfect growth is of the order of the miniband width. This interpretation is supported by temperature dependence measurements of the perpendicular mobilities in relation with theoretical calculations of these mobilities.

Redirecting the Cyanobacterial Bicarbonate Transporters BicA and SbtA to the Chloroplast Envelope: Soluble and Membrane Cargos Need Different Chloroplast Targeting Signals in Plants

PubMed Central

Rolland, Vivien; Badger, Murray R.; Price, G. Dean

2016-01-01

Most major crops used for human consumption are C3 plants, which yields are limited by photosynthetic inefficiency. To circumvent this, it has been proposed to implement the cyanobacterial CO2-concentrating mechanism (CCM), principally consisting of bicarbonate transporters and carboxysomes, into plant chloroplasts. As it is currently not possible to recover homoplasmic transplastomic monocots, foreign genes must be introduced in these plants via nuclear transformation. Consequently, it is paramount to ensure that resulting proteins reach the appropriate sub-cellular compartment, which for cyanobacterial transporters BicA and SbtA, is the chloroplast inner-envelope membrane (IEM). At present, targeting signals to redirect large transmembrane proteins from non-chloroplastic organisms to plant chloroplast envelopes are unknown. The goal of this study was to identify such signals, using agrobacteria-mediated transient expression and confocal microscopy to determine the sub-cellular localization of ∼37 GFP-tagged chimeras. Initially, fragments of chloroplast proteins known to target soluble cargos to the stroma were tested for their ability to redirect BicA, but they proved ineffective. Next, different N-terminal regions from Arabidopsis IEM transporters were tested. We demonstrated that the N-terminus of AtHP59, AtPLGG1 or AtNTT1 (92–115 amino acids), containing a cleavable chloroplast transit peptide (cTP) and a membrane protein leader (MPL), was sufficient to redirect BicA or SbtA to the chloroplast envelope. This constitutes the first evidence that nuclear-encoded transmembrane proteins from non-chloroplastic organisms can be targeted to the envelope of plant chloroplasts; a finding which represents an important advance in chloroplast engineering by opening up the door to further manipulation of the chloroplastic envelope. PMID:26973659

Lactobacillus gasseri SBT2055 reduces postprandial and fasting serum non-esterified fatty acid levels in Japanese hypertriacylglycerolemic subjects.

PubMed

Ogawa, Akihiro; Kadooka, Yukio; Kato, Ken; Shirouchi, Bungo; Sato, Masao

2014-02-19

Lactobacillus gasseri SBT2055 (LG2055) inhibits dietary fat absorption in rats and exerts preventive effects on abdominal adiposity in rats and humans. The present study aimed to evaluate the effects of LG2055 on postprandial serum lipid responses in Japanese subjects with hypertriacylglycerolemia after the intake of oral fat-loading test (OFLT) meals. We conducted a single-blind, placebo-controlled, within-subject, repeated-measure intervention trial. Twenty subjects initially ingested the fermented milk (FM) without LG2055 for 4 weeks (control FM period), followed by a 4-week washout period, and then consumed FM containing LG2055 for 4 weeks (active FM period). The subjects were asked to consume FM at 200 g/day. At the end of each 4-week period, an 8-h OFLT was conducted. Blood samples were collected at fasting and every hour for 8 h after OFLT meal intake. Thereafter, postprandial serum non-esterified fatty acid (NEFA) and triacylglycerol (TAG) levels and fasting blood parameters were measured. The OFLT showed that the postprandial serum NEFA levels from 120 to 480 min and the postprandial serum TAG level at 120 min in the active FM period were significantly (P < 0.05) lower than those in the control FM period. The fasting serum NEFA level in the active FM period significantly (P < 0.001) decreased at week 4 from the initial period compared with the control FM period. The consumption of probiotic LG2055 reduced postprandial and fasting serum NEFA levels, suggesting its possible contribution to the reduction of the risk for obesity and type 2 diabetes mellitus. UMIN000011605.

Trematode infections in farm animals and their vector snails in Saint Martin’s Island, the southeastern offshore area of Bangladesh in the Bay of Bengal

PubMed Central

YASIN, M. Golam; ALIM, Md. Abdul; Anisuzzaman; AHASAN, Syed Ali; MUNSI, Md. Nuruzzaman; CHOWDHURY, Emdadul Haque; HATTA, Takeshi; TSUJI, Naotoshi; MONDAL, Md. Motahar Hussain

2018-01-01

The prevalence of snail-borne trematode (SBT) infections in farm animals on the offshore Saint (St.) Martin’s Island of Bangladesh were 68.9% for cattle, 76.7% for buffaloes, 56.3% for goats, respectively. Examination of fecal samples showed that paramphistomes infection was the most common at 50.5% followed by schistosomes at 23.7% and Fasciola at 2.3%. Fasciola infection was found in cattle (1.9%) and buffaloes (16.7%) but not in goats. Schistosome infection in cattle, buffaloes and goats were 31.1, 6.7 and 17.5%, respectively. Prevalence of SBTs was higher in older animals. Thiara tuberculata (Melanoides tuberculata) were found to serve as vector for paramphistomes and Indoplanorbis exustus for schistosomes and paramphistomes, respectively. Our results suggest that SBT and their vector snails are highly endemic on St. Martin’s Island of Bangladesh, and proper attention is needed to control these infections. PMID:29503348

Severe impacts of brown tides caused by Sargassum spp. on near-shore Caribbean seagrass communities.

PubMed

van Tussenbroek, Brigitta I; Hernández Arana, Héctor A; Rodríguez-Martínez, Rosa E; Espinoza-Avalos, Julio; Canizales-Flores, Hazel M; González-Godoy, Carlos E; Barba-Santos, M Guadalupe; Vega-Zepeda, Alejandro; Collado-Vides, Ligia

2017-09-15

From mid-2014 until the end of 2015, the Mexican Caribbean coast experienced a massive influx of drifting Sargassum spp. that accumulated on the shores, resulting in build-up of decaying beach-cast material and near-shore murky brown waters (Sargassum-brown-tides, Sbt). The effects of Sbt on four near-shore waters included reduction in light, oxygen (hypoxia or anoxia) and pH. The monthly influx of nitrogen, and phosphorus by drifting Sargassum spp. was estimated at 6150 and 61kgkm -1 respectively, resulting in eutrophication. Near-shore seagrass meadows dominated by Thalassia testudinum were replaced by a community dominated by calcareous rhizophytic algae and drifting algae and/or epiphytes, resulting in 61.6-99.5% loss of below-ground biomass. Near-shore corals suffered total or partial mortality. Recovery of affected seagrass meadows may take years or even decades, or changes could be permanent if massive influxes of Sargassum spp. recur. Copyright © 2017. Published by Elsevier Ltd.

Sustaining Control of Schistosomiasis Mansoni in Western Côte d’Ivoire: Results from a SCORE Study, One Year after Initial Praziquantel Administration

PubMed Central

Assaré, Rufin K.; Tian-Bi, Yves-Nathan T.; Yao, Patrick K.; N’Guessan, Nicaise A.; Ouattara, Mamadou; Yapi, Ahoua; Coulibaly, Jean T.; Meïté, Aboulaye; Hürlimann, Eveline; Knopp, Stefanie; Utzinger, Jürg; N’Goran, Eliézer K.

2016-01-01

Background The Schistosomiasis Consortium for Operational Research and Evaluation (SCORE) has launched several large-scale trials to determine the best strategies for gaining and sustaining control of schistosomiasis and transitioning toward elimination. In Côte d’Ivoire, a 5-year cluster-randomized trial is being implemented in 75 schools to sustain the control of schistosomiasis mansoni. We report Schistosoma mansoni infection levels in children one year after the initial school-based treatment (SBT) with praziquantel and compare with baseline results to determine the effect of the intervention. Methodology The baseline cross-sectional survey was conducted in late 2011/early 2012 and the first follow-up in May 2013. Three consecutive stool samples were collected from 9- to 12-year-old children in 75 schools at baseline and 50 schools at follow-up. Stool samples were subjected to duplicate Kato-Katz thick smears. Directly observed treatment (DOT) coverage of the SBT was assessed and the prevalence and intensity of S. mansoni infection compared between baseline and follow-up. Principal Findings The S. mansoni prevalence in the 75 schools surveyed at baseline was 22.1% (95% confidence interval (CI): 19.5–24.4%). The DOT coverage was 84.2%. In the 50 schools surveyed at baseline and one year after treatment, the overall prevalence of S. mansoni infection decreased significantly from 19.7% (95% CI: 18.5–20.8%) to 12.8% (95% CI: 11.9–13.8%), while the arithmetic mean S. mansoni eggs per gram of stool (EPG) among infected children slightly increased from 92.2 EPG (95% CI: 79.2–105.3 EPG) to 109.3 EPG (95% CI: 82.7–135.9 EPG). In two of the 50 schools, the prevalence increased significantly, despite a DOT coverage of >75%. Conclusions/Significance One year after the initial SBT, the S. mansoni prevalence had decreased. Despite this positive trend, an increase was observed in some schools. Moreover, the infection intensity among S. mansoni-infected children was slightly higher at the 1-year follow-up compared to the baseline situation. Our results emphasize the heterogeneity of transmission dynamics and provide a benchmark for the future yearly follow-up surveys of this multi-year SCORE intervention study. PMID:26789749

Integration of SrBi2Ta2O9 thin films for high density ferroelectric random access memory

NASA Astrophysics Data System (ADS)

Wouters, D. J.; Maes, D.; Goux, L.; Lisoni, J. G.; Paraschiv, V.; Johnson, J. A.; Schwitters, M.; Everaert, J.-L.; Boullart, W.; Schaekers, M.; Willegems, M.; Vander Meeren, H.; Haspeslagh, L.; Artoni, C.; Caputa, C.; Casella, P.; Corallo, G.; Russo, G.; Zambrano, R.; Monchoix, H.; Vecchio, G.; Van Autryve, L.

2006-09-01

Ferroelectric random access memory (FeRAM) is an attractive candidate technology for embedded nonvolatile memory, especially in applications where low power and high program speed are important. Market introduction of high-density FeRAM is, however, lagging behind standard complementary metal-oxide semiconductor (CMOS) because of the difficult integration technology. This paper discusses the major integration issues for high-density FeRAM, based on SrBi2Ta2O9 (strontium bismuth tantalate or SBT), in relation to the fabrication of our stacked cell structure. We have worked in the previous years on the development of SBT-FeRAM integration technology, based on a so-called pseudo-three-dimensional (3D) cell, with a capacitor that can be scaled from quasi two-dimensional towards a true three-dimensional capacitor where the sidewalls will importantly contribute to the signal. In the first phase of our integration development, we integrated our FeRAM cell in a 0.35μm CMOS technology. In a second phase, then, possibility of scaling of our cell is demonstrated in 0.18μm technology. The excellent electrical and reliability properties of the small integrated ferroelectric capacitors prove the feasibility of the technology, while the verification of the potential 3D effect confirms the basic scaling potential of our concept beyond that of the single-mask capacitor. The paper outlines the different material and technological challenges, and working solutions are demonstrated. While some issues are specific to our own cell, many are applicable to different stacked FeRAM cell concepts, or will become more general concerns when more developments are moving into 3D structures.

Characterization of the effective electrostriction coefficients in ferroelectric thin films

NASA Astrophysics Data System (ADS)

Kholkin, A. L.; Akdogan, E. K.; Safari, A.; Chauvy, P.-F.; Setter, N.

2001-06-01

Electromechanical properties of a number of ferroelectric films including PbZrxTi1-xO3(PZT), 0.9PbMg1/3Nb2/3O3-0.1PbTiO3(PMN-PT), and SrBi2Ta2O9(SBT) are investigated using laser interferometry combined with conventional dielectric measurements. Effective electrostriction coefficients of the films, Qeff, are determined using a linearized electrostriction equation that couples longitudinal piezoelectric coefficient, d33, with the polarization and dielectric constant. It is shown that, in PZT films, electrostriction coefficients slightly increase with applied electric field, reflecting the weak contribution of non-180° domains to piezoelectric properties. In contrast, in PMN-PT and SBT films electrostriction coefficients are field independent, indicating the intrinsic nature of the piezoelectric response. The experimental values of Qeff are significantly smaller than those of corresponding bulk materials due to substrate clamping and possible size effects. Electrostriction coefficients of PZT layers are shown to depend strongly on the composition and preferred orientation of the grains. In particular, Qeff of (100) textured rhombohedral films (x=0.7) is significantly greater than that of (111) layers. Thus large anisotropy of the electrostrictive coefficients is responsible for recently observed large piezoelectric coefficients of (100) textured PZT films. Effective electrostriction coefficients obtained by laser interferometry allow evaluation of the electromechanical properties of ferroelectric films based solely on the dielectric parameters and thus are very useful in the design and fabrication of microsensors and microactuators.

Development of Mycoplasma synoviae (MS) core genome multilocus sequence typing (cgMLST) scheme.

PubMed

Ghanem, Mostafa; El-Gazzar, Mohamed

2018-05-01

Mycoplasma synoviae (MS) is a poultry pathogen with reported increased prevalence and virulence in recent years. MS strain identification is essential for prevention, control efforts and epidemiological outbreak investigations. Multiple multilocus based sequence typing schemes have been developed for MS, yet the resolution of these schemes could be limited for outbreak investigation. The cost of whole genome sequencing became close to that of sequencing the seven MLST targets; however, there is no standardized method for typing MS strains based on whole genome sequences. In this paper, we propose a core genome multilocus sequence typing (cgMLST) scheme as a standardized and reproducible method for typing MS based whole genome sequences. A diverse set of 25 MS whole genome sequences were used to identify 302 core genome genes as cgMLST targets (35.5% of MS genome) and 44 whole genome sequences of MS isolates from six countries in four continents were used for typing applying this scheme. cgMLST based phylogenetic trees displayed a high degree of agreement with core genome SNP based analysis and available epidemiological information. cgMLST allowed evaluation of two conventional MLST schemes of MS. The high discriminatory power of cgMLST allowed differentiation between samples of the same conventional MLST type. cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation between MS isolates. Like conventional MLST, it provides stable and expandable nomenclature, allowing for comparing and sharing the typing results between different laboratories worldwide. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Typing of canine parvovirus isolates using mini-sequencing based single nucleotide polymorphism analysis.

PubMed

Naidu, Hariprasad; Subramanian, B Mohana; Chinchkar, Shankar Ramchandra; Sriraman, Rajan; Rana, Samir Kumar; Srinivasan, V A

2012-05-01

The antigenic types of canine parvovirus (CPV) are defined based on differences in the amino acids of the major capsid protein VP2. Type specificity is conferred by a limited number of amino acid changes and in particular by few nucleotide substitutions. PCR based methods are not particularly suitable for typing circulating variants which differ in a few specific nucleotide substitutions. Assays for determining SNPs can detect efficiently nucleotide substitutions and can thus be adapted to identify CPV types. In the present study, CPV typing was performed by single nucleotide extension using the mini-sequencing technique. A mini-sequencing signature was established for all the four CPV types (CPV2, 2a, 2b and 2c) and feline panleukopenia virus. The CPV typing using the mini-sequencing reaction was performed for 13 CPV field isolates and the two vaccine strains available in our repository. All the isolates had been typed earlier by full-length sequencing of the VP2 gene. The typing results obtained from mini-sequencing matched completely with that of sequencing. Typing could be achieved with less than 100 copies of standard plasmid DNA constructs or ≤10¹ FAID₅₀ of virus by mini-sequencing technique. The technique was also efficient for detecting multiple types in mixed infections. Copyright © 2012 Elsevier B.V. All rights reserved.

Reads2Type: a web application for rapid microbial taxonomy identification.

PubMed

Saputra, Dhany; Rasmussen, Simon; Larsen, Mette V; Haddad, Nizar; Sperotto, Maria Maddalena; Aarestrup, Frank M; Lund, Ole; Sicheritz-Pontén, Thomas

2015-11-25

Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing. In the near future, healthcare institutions and routine diagnostic microbiology laboratories may need to sequence the entire genome of microbial isolates. Therefore we have developed Reads2Type, a web-based tool for taxonomy identification based on whole bacterial genome sequence data. Raw sequencing data provided by the user are mapped against a set of marker probes that are derived from currently available bacteria complete genomes. Using a dataset of 1003 whole genome sequenced bacteria from various sequencing platforms, Reads2Type was able to identify the species with 99.5 % accuracy and on the minutes time scale. In comparison with other tools, Reads2Type offers the advantage of not needing to transfer sequencing files, as the entire computational analysis is done on the computer of whom utilizes the web application. This also prevents data privacy issues to arise. The Reads2Type tool is available at http://www.cbs.dtu.dk/~dhany/reads2type.html.

78 FR 42589 - Additional Designations, Foreign Narcotics Kingpin Designation Act

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-16

...) [SDNTK] (Linked To: ISSA EMPRESA UNIPERSONAL; Linked To: INVERSIONES GILFE S.A.; Linked To: INDUITEX LTDA...: INDUITEX LTDA.; Linked To: INVERSIONES GILFE S.A.; Linked To: ORBITAL HORIZONS CORP.; Linked To: FUNDACION... INVESTMENT INC.; Linked To: SBT S.A.; Linked To: ISSA EMPRESA UNIPERSONAL; Linked To: INVERSIONES GILFE S.A...

Impact of seabird activity on nitrous oxide and methane fluxes from High Arctic tundra in Svalbard, Norway

NASA Astrophysics Data System (ADS)

Zhu, Renbin; Chen, Qingqing; Ding, Wei; Xu, Hua

2012-12-01

In this study, tundra N2O and CH4 fluxes were measured from one seabird sanctuary (SBT) and two non-seabird colonies (NST-I and NST-II) in Ny-Ålesund (79°55'N, 11°56'E), Svalbard during the summers of 2008 and 2009. N2O and CH4 fluxes from SBT showed large temporal and spatial variations depending on the intensity of seabird activity. High seabird activity sites showed large N2O and CH4 emissions while low N2O and CH4 emissions, even CH4 uptake occurred at medium and low seabird activity sites. Overall the mean fluxes were 18.3 ± 3.6 μg N2O m-2 h-1 and 53.5 ± 20.3 μg CH4 m-2 h-1 from tundra SBT whereas tundra NST-I and NST-II represented a relatively weak N2O source (8.3 ± 13.2 μg N2O m-2 h-1) and strong CH4 sink (-82.8 ± 22.3 μg CH4 m-2 h-1). Seabird activity was the strongest control of N2O and CH4 fluxes compared with soil temperature and moisture, and high N2O and CH4 emissions were created by soil physical and chemical processes (the sufficient supply of nutrients NH4+-N, NO3--N, total nitrogen, total phosphorus and total carbon from seabird guano, seabird tramp and appropriate water content) related to the seabird activity. Our work suggests that tundra ecosystems impacted by seabird activity are the potential "hotspots" for N2O and CH4 emissions although these sources have been largely neglected at present. Furthermore the combination of seabird activity and warming climate will likely further enhance N2O and CH4 emissions from the High Arctic tundra.

Physical Therapists' Ability to Identify Psychological Factors and Their Self-Reported Competence to Manage Chronic Low Back Pain.

PubMed

Brunner, Emanuel; Dankaerts, Wim; Meichtry, André; O'Sullivan, Kieran; Probst, Michel

2018-06-01

In the management of chronic low back pain (LBP), identifying and managing more patients who are at high risk and who have psychological barriers to recovery is important yet difficult. The objective of this study was to test physical therapists' ability to allocate patients into risk stratification groups, test correlations between therapists' assessments of psychological factors and patient questionnaires, and explore relationships between psychological factors and therapists' self-reported competence to manage patients with chronic LBP. This was a pragmatic, observational study. Patients completed the STarT Back Tool (SBT, for risk stratification), the Four-Dimensional Symptom Questionnaire (distress, depression, anxiety), and the Tampa Scale of Kinesiophobia (kinesiophobia) prior to the intake session. After this session, physical therapists estimated patient prognostic risk using the 3 SBT categories and rated patient psychological factors using a 0-to-10 scale. Finally, therapists reported their self-reported competence to manage the patient. Intraclass and Spearman rank correlations tested correlations between therapists' intuitive assessments and patient questionnaires. A linear-mixed model explored relationships between psychological factors and therapists' self-reported competence. Forty-nine patients were managed by 20 therapists. Therapists accurately estimated SBT risk allocation in only 41% of patients. Correlations between therapist perceptions and patient questionnaires were moderate for distress (r = 0.602) and fair for depression (r = 0.304) and anxiety (r = 0.327). There was no correlation for kinesiophobia (r = -0.007). Patient distress was identified as a negative predictor of therapists' self-reported competence. This was a cross-sectional study, conducted in only 1 center. Physical therapists were not very accurate at allocating patients into risk stratification groups or identifying psychological factors. Therapists' self-reported competence in managing patients was lowest when patients reported higher distress.

Temperature tracking by North Sea benthic invertebrates in response to climate change.

PubMed

Hiddink, Jan G; Burrows, Michael T; García Molinos, Jorge

2015-01-01

Climate change is a major threat to biodiversity and distributions shifts are one of the most significant threats to global warming, but the extent to which these shifts keep pace with a changing climate is yet uncertain. Understanding the factors governing range shifts is crucial for conservation management to anticipate patterns of biodiversity distribution under future anthropogenic climate change. Soft-sediment invertebrates are a key faunal group because of their role in marine biogeochemistry and as a food source for commercial fish species. However, little information exists on their response to climate change. Here, we evaluate changes in the distribution of 65 North Sea benthic invertebrate species between 1986 and 2000 by examining their geographic, bathymetric and thermal niche shifts and test whether species are tracking their thermal niche as defined by minimum, mean or maximum sea bottom (SBT) and surface (SST) temperatures. Temperatures increased in the whole North Sea with many benthic invertebrates showing north-westerly range shifts (leading/trailing edges as well as distribution centroids) and deepening. Nevertheless, distribution shifts for most species (3.8-7.3 km yr(-1) interquantile range) lagged behind shifts in both SBT and SST (mean 8.1 km yr(-1)), resulting in many species experiencing increasing temperatures. The velocity of climate change (VoCC) of mean SST accurately predicted both the direction and magnitude of distribution centroid shifts, while maximum SST did the same for contraction of the trailing edge. The VoCC of SBT was not a good predictor of range shifts. No good predictor of expansions of the leading edge was found. Our results show that invertebrates need to shift at different rates and directions to track the climate velocities of different temperature measures, and are therefore lagging behind most temperature measures. If these species cannot withstand a change in thermal habitat, this could ultimately lead to a drop in benthic biodiversity. © 2014 John Wiley & Sons Ltd.

Multilocus sequence typing of total-genome-sequenced bacteria.

PubMed

Larsen, Mette V; Cosentino, Salvatore; Rasmussen, Simon; Friis, Carsten; Hasman, Henrik; Marvig, Rasmus Lykke; Jelsbak, Lars; Sicheritz-Pontén, Thomas; Ussery, David W; Aarestrup, Frank M; Lund, Ole

2012-04-01

Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from the MLST databases are downloaded monthly, and the best-matching MLST alleles of the specified MLST scheme are found using a BLAST-based ranking method. The sequence type is then determined by the combination of alleles identified. The method was tested on preassembled genomes from 336 isolates covering 56 MLST schemes, on short sequence reads from 387 isolates covering 10 schemes, and on a small test set of short sequence reads from 29 isolates for which the sequence type had been determined by traditional methods. The method presented here enables investigators to determine the sequence types of their isolates on the basis of WGS data. This method is publicly available at www.cbs.dtu.dk/services/MLST.

Assessing the benefits of five years of different approaches to treatment of urogenital schistosomiasis: A SCORE project in Northern Mozambique.

PubMed

Phillips, Anna E; Gazzinelli-Guimaraes, Pedro H; Aurelio, Herminio O; Ferro, Josefo; Nala, Rassul; Clements, Michelle; King, Charles H; Fenwick, Alan; Fleming, Fiona M; Dhanani, Neerav

2017-12-01

In Mozambique, schistosomiasis is highly endemic across the whole country. The Schistosomiasis Consortium for Operational Research and Evaluation (SCORE) coordinates a five-year study that has been implemented in various African countries, including Mozambique. The overall goal of SCORE was to better understand how to best apply preventive chemotherapy with praziquantel (PZQ) for schistosomiasis control by evaluating the impact of alternative treatment approaches. This was a cluster-randomised trial that compared the impact of different treatment strategies in study areas with prevalence among school children of ≥21% S. haematobium infection by urine dipstick. Each village was randomly allocated to one of six possible combinations of community-wide treatment (CWT), school-based treatment (SBT), and/or drug holidays over a period of four years, followed by final data collection in the fifth year. The most intense intervention arm involved four years of CWT, while the least intensive arm involved two years of SBT followed by two consecutive years of PZQ holiday. Each study arm included 25 villages randomly assigned to one of the six treatment arms. The primary outcome of interest was change in prevalence and intensity of S. haematobium among 100 children aged 9-to-12-years that were sampled each year in every village. In addition to children aged 9-to-12 years, 100 children aged 5-8 years in their first-year of school and 50 adults (aged 20-55 years) were tested in the first and final fifth year of the study. Prevalence and intensity of S. haematobium infection was evaluated by two filtrations, each of 10mL, from a single urine specimen. In total, data was collected from 81,167 individuals across 149 villages in ten districts of Cabo Delgado province, Northern Mozambique. Overall PZQ treatment resulted in a significant reduction in the prevalence of S. haematobium infection from Year 1 to Year 5, where the average prevalence went from 60.5% to 38.8%, across all age groups and treatment arms. The proportion of those heavily infected also reduced from 17.6% to 11.9% over five years. There was a significantly higher likelihood of males being infected than females at baseline, but no significant difference between the sexes in their response to treatment. The only significant response based on a study arm was seen in both the 9-to-12-year-old and first-year cross sections, where two consecutive treatment holidays resulted in a significantly higher final prevalence of S. haematobium than no treatment holidays. When the arms were grouped together, four rounds of treatment (regardless of whether it was CWT or SBT), however, did result in a significantly greater reduction in S. haematobium prevalence than two rounds of treatment (i.e. with two intermittent or consecutive holiday years) over a five-year period. Although PC was successful in reducing the burden of active infection, even among those heavily infected, annual CWT did not have a significantly greater impact on disease prevalence or intensity than less intense treatment arms. This may be due to extremely high starting prevalence and intensity in the study area, with frequent exposure to reinfection, or related to challenges in achieving high treatment coverage More frequent treatment had a greater impact on prevalence and intensity of infection when arms were grouped by number of treatments, however, cost efficiency was greater in arms only receiving two treatments. Finally, a significant reduction in prevalence of S. haematobium was seen in adults even in the SBT arms implying the rate of transmission in the community had been decreased, even where only school children have been treated, which has significant logistical and cost-saving implications for a national control programme in justifying CWT.

Assessing the benefits of five years of different approaches to treatment of urogenital schistosomiasis: A SCORE project in Northern Mozambique

PubMed Central

Gazzinelli-Guimaraes, Pedro H.; Aurelio, Herminio O.; Ferro, Josefo; Nala, Rassul; Clements, Michelle; King, Charles H.; Fenwick, Alan; Fleming, Fiona M.; Dhanani, Neerav

2017-01-01

Background In Mozambique, schistosomiasis is highly endemic across the whole country. The Schistosomiasis Consortium for Operational Research and Evaluation (SCORE) coordinates a five-year study that has been implemented in various African countries, including Mozambique. The overall goal of SCORE was to better understand how to best apply preventive chemotherapy with praziquantel (PZQ) for schistosomiasis control by evaluating the impact of alternative treatment approaches. Methods This was a cluster-randomised trial that compared the impact of different treatment strategies in study areas with prevalence among school children of ≥21% S. haematobium infection by urine dipstick. Each village was randomly allocated to one of six possible combinations of community-wide treatment (CWT), school-based treatment (SBT), and/or drug holidays over a period of four years, followed by final data collection in the fifth year. The most intense intervention arm involved four years of CWT, while the least intensive arm involved two years of SBT followed by two consecutive years of PZQ holiday. Each study arm included 25 villages randomly assigned to one of the six treatment arms. The primary outcome of interest was change in prevalence and intensity of S. haematobium among 100 children aged 9-to-12-years that were sampled each year in every village. In addition to children aged 9-to-12 years, 100 children aged 5–8 years in their first-year of school and 50 adults (aged 20–55 years) were tested in the first and final fifth year of the study. Prevalence and intensity of S. haematobium infection was evaluated by two filtrations, each of 10mL, from a single urine specimen. Principal findings In total, data was collected from 81,167 individuals across 149 villages in ten districts of Cabo Delgado province, Northern Mozambique. Overall PZQ treatment resulted in a significant reduction in the prevalence of S. haematobium infection from Year 1 to Year 5, where the average prevalence went from 60.5% to 38.8%, across all age groups and treatment arms. The proportion of those heavily infected also reduced from 17.6% to 11.9% over five years. There was a significantly higher likelihood of males being infected than females at baseline, but no significant difference between the sexes in their response to treatment. The only significant response based on a study arm was seen in both the 9-to-12-year-old and first-year cross sections, where two consecutive treatment holidays resulted in a significantly higher final prevalence of S. haematobium than no treatment holidays. When the arms were grouped together, four rounds of treatment (regardless of whether it was CWT or SBT), however, did result in a significantly greater reduction in S. haematobium prevalence than two rounds of treatment (i.e. with two intermittent or consecutive holiday years) over a five-year period. Conclusions Although PC was successful in reducing the burden of active infection, even among those heavily infected, annual CWT did not have a significantly greater impact on disease prevalence or intensity than less intense treatment arms. This may be due to extremely high starting prevalence and intensity in the study area, with frequent exposure to reinfection, or related to challenges in achieving high treatment coverage More frequent treatment had a greater impact on prevalence and intensity of infection when arms were grouped by number of treatments, however, cost efficiency was greater in arms only receiving two treatments. Finally, a significant reduction in prevalence of S. haematobium was seen in adults even in the SBT arms implying the rate of transmission in the community had been decreased, even where only school children have been treated, which has significant logistical and cost-saving implications for a national control programme in justifying CWT. PMID:29220347

Typing Clostridium difficile strains based on tandem repeat sequences

PubMed Central

2009-01-01

Background Genotyping of epidemic Clostridium difficile strains is necessary to track their emergence and spread. Portability of genotyping data is desirable to facilitate inter-laboratory comparisons and epidemiological studies. Results This report presents results from a systematic screen for variation in repetitive DNA in the genome of C. difficile. We describe two tandem repeat loci, designated 'TR6' and 'TR10', which display extensive sequence variation that may be useful for sequence-based strain typing. Based on an investigation of 154 C. difficile isolates comprising 75 ribotypes, tandem repeat sequencing demonstrated excellent concordance with widely used PCR ribotyping and equal discriminatory power. Moreover, tandem repeat sequences enabled the reconstruction of the isolates' largely clonal population structure and evolutionary history. Conclusion We conclude that sequence analysis of the two repetitive loci introduced here may be highly useful for routine typing of C. difficile. Tandem repeat sequence typing resolves phylogenetic diversity to a level equivalent to PCR ribotypes. DNA sequences may be stored in databases accessible over the internet, obviating the need for the exchange of reference strains. PMID:19133124

78 FR 65759 - Notice of Receipt of Petition for Decision That Nonconforming 2012 Ahlm SBT 16-25 Trailers Are...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-01

... electrical system during manufacture. Conforming conspicuity tape and lights were installed during... Than Passenger Cars: The vehicle is equipped with tires conforming to the requirements of the standard. Standard No. 120 Tire Selection and Rims for Motor Vehicles Other Than Passenger Cars: The vehicle will...

Mechanism-Based Tumor-Targeting Drug Delivery System. Validation of Efficient Vitamin Receptor-Mediated Endocytosis and Drug Release

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, S.; Wong, S.; Zhao, X.

An efficient mechanism-based tumor-targeting drug delivery system, based on tumor-specific vitamin-receptor mediated endocytosis, has been developed. The tumor-targeting drug delivery system is a conjugate of a tumor-targeting molecule (biotin: vitamin H or vitamin B-7), a mechanism-based self-immolative linker and a second-generation taxoid (SB-T-1214) as the cytotoxic agent. This conjugate (1) is designed to be (i) specific to the vitamin receptors overexpressed on tumor cell surface and (ii) internalized efficiently through receptor-mediated endocytosis, followed by smooth drug release via glutathione-triggered self-immolation of the linker. In order to monitor and validate the sequence of events hypothesized, i.e., receptor-mediated endocytosis of the conjugate,more » drug release, and drug-binding to the target protein (microtubules), three fluorescent/fluorogenic molecular probes (2, 3, and 4) were designed and synthesized. The actual occurrence of these processes was unambiguously confirmed by means of confocal fluorescence microscopy (CFM) and flow cytometry using L1210FR leukemia cells, overexpressing biotin receptors. The molecular probe 4, bearing the taxoid linked to fluorescein, was also used to examine the cell specificity (i.e., efficacy of receptor-based cell targeting) for three cell lines, L1210FR (biotin receptors overexpressed), L1210 (biotin receptors not overexpressed), and WI38 (normal human lung fibroblast, biotin receptor negative). As anticipated, the molecular probe 4 exhibited high specificity only to L1210FR. To confirm the direct correlation between the cell-specific drug delivery and anticancer activity of the probe 4, its cytotoxicity against these three cell lines was also examined. The results clearly showed a good correlation between the two methods. In the same manner, excellent cell-specific cytotoxicity of the conjugate 1 (without fluorescein attachment to the taxoid) against the same three cell lines was confirmed. This mechanism-based tumor-targeting drug delivery system will find a range of applications.« less

An automated genotyping tool for enteroviruses and noroviruses.

PubMed

Kroneman, A; Vennema, H; Deforche, K; v d Avoort, H; Peñaranda, S; Oberste, M S; Vinjé, J; Koopmans, M

2011-06-01

Molecular techniques are established as routine in virological laboratories and virus typing through (partial) sequence analysis is increasingly common. Quality assurance for the use of typing data requires harmonization of genotype nomenclature, and agreement on target genes, depending on the level of resolution required, and robustness of methods. To develop and validate web-based open-access typing-tools for enteroviruses and noroviruses. An automated web-based typing algorithm was developed, starting with BLAST analysis of the query sequence against a reference set of sequences from viruses in the family Picornaviridae or Caliciviridae. The second step is phylogenetic analysis of the query sequence and a sub-set of the reference sequences, to assign the enterovirus type or norovirus genotype and/or variant, with profile alignment, construction of phylogenetic trees and bootstrap validation. Typing is performed on VP1 sequences of Human enterovirus A to D, and ORF1 and ORF2 sequences of genogroup I and II noroviruses. For validation, we used the tools to automatically type sequences in the RIVM and CDC enterovirus databases and the FBVE norovirus database. Using the typing-tools, 785(99%) of 795 Enterovirus VP1 sequences, and 8154(98.5%) of 8342 norovirus sequences were typed in accordance with previously used methods. Subtyping into variants was achieved for 4439(78.4%) of 5838 NoV GII.4 sequences. The online typing-tools reliably assign genotypes for enteroviruses and noroviruses. The use of phylogenetic methods makes these tools robust to ongoing evolution. This should facilitate standardized genotyping and nomenclature in clinical and public health laboratories, thus supporting inter-laboratory comparisons. Copyright © 2011 Elsevier B.V. All rights reserved.

Simulation-based training for cardiology procedures: Are we any further forward in evidencing real-world benefits?

PubMed

Harrison, Christopher M; Gosai, Jivendra N

2017-04-01

Simulation-based training as an educational tool for healthcare professionals continues to grow in sophistication, scope, and usage. There have been a number of studies demonstrating the utility of the technique, and it is gaining traction as part of the training curricula for the next generation of cardiologists. In this review, we focus on the recent literature for the efficacy of simulation for practical procedures specific to cardiology, focusing on transesophageal echocardiography, cardiac catheterization, coronary angioplasty, and electrophysiology. A number of studies demonstrated improved performance by those trained using SBT when compared to other methods, although evidence of this leading to an improvement in patient outcomes remains scarce. We discuss this evidence, and the implications for practice for training in cardiology. Copyright © 2017 Elsevier Inc. All rights reserved.

Update on Pneumocystis carinii f. sp. hominis Typing Based on Nucleotide Sequence Variations in Internal Transcribed Spacer Regions of rRNA Genes

PubMed Central

Lee, Chao-Hung; Helweg-Larsen, Jannik; Tang, Xing; Jin, Shaoling; Li, Baozheng; Bartlett, Marilyn S.; Lu, Jang-Jih; Lundgren, Bettina; Lundgren, Jens D.; Olsson, Mats; Lucas, Sebastian B.; Roux, Patricia; Cargnel, Antonietta; Atzori, Chiara; Matos, Olga; Smith, James W.

1998-01-01

Pneumocystis carinii f. sp. hominis isolates from 207 clinical specimens from nine countries were typed based on nucleotide sequence variations in the internal transcribed spacer regions I and II (ITS1 and ITS2, respectively) of rRNA genes. The number of ITS1 nucleotides has been revised from the previously reported 157 bp to 161 bp. Likewise, the number of ITS2 nucleotides has been changed from 177 to 192 bp. The number of ITS1 sequence types has increased from 2 to 15, and that of ITS2 has increased from 3 to 14. The 15 ITS1 sequence types are designated types A through O, and the 14 ITS2 types are named types a through n. A total of 59 types of P. carinii f. sp. hominis were found in this study. PMID:9508304

Oxygen-vacancy-related dielectric relaxation in SrBi2Ta1.8V0.2O9 ferroelectrics

NASA Astrophysics Data System (ADS)

Wu, Yun; Forbess, Mike J.; Seraji, Seana; Limmer, Steven J.; Chou, Tammy P.; Cao, Guozhong

2001-05-01

The strontium bismuth tantalate vanadate, SrBi2Ta1.8V0.2O9, (SBTV) layered perovskite ferroelectrics were made by solid state powder sintering. It was found that the SBTV ferroelectrics had the same crystal structure as that of strontium bismuth tantalate, SrBi2Ta2O9 (SBT), but an increased paraferroelectric transition temperature at ˜360 °C as compared to 305 °C for SBT. In addition, SBTV ferroelectrics showed a frequency dispersion at low frequencies and broadened dielectric peaks at the paraferroelectric transition temperature that shifted to a higher temperature with a reduced frequency. However, after a postsintering annealing at 850 °C in air for 60 h, SBTV ferroelectrics showed reduced dielectric constants and tangent loss, particularly at high temperatures. In addition, no frequency dependence of paraferroelectric transition was found in the annealed SBTV ferroelectrics. Furthermore, there was a significant reduction in dc conductivity with annealing. The prior results implied that the dielectric relaxation in the as-sintered SBTV ferroelectrics was most likely due to the oxygen-vacancy-related dielectric relaxation instead of relaxor ferroelectric behavior.

A binary histologic grading system for ovarian serous carcinoma is an independent prognostic factor: a population-based study of 4317 women diagnosed in Denmark 1978-2006.

PubMed

Hannibal, Charlotte Gerd; Vang, Russell; Junge, Jette; Kjaerbye-Thygesen, Anette; Kurman, Robert J; Kjaer, Susanne K

2012-06-01

To evaluate the prognostic significance of histologic grade on survival of ovarian serous cancer in Denmark during nearly 30 years. Using the nationwide Danish Pathology Data Bank, we evaluated 4317 women with ovarian serous carcinoma in 1978-2006. All pathology reports were scrutinized and tumors classified as either low-grade serous carcinomas (LGSC) or high-grade serous carcinomas (HGSC). Tumors in which the original pathology reports were described as well-differentiated were classified as LGSC, and those that were described as moderately or poorly differentiated were classified as HGSC. We obtained histologic slides from the pathology departments for women with a diagnosis of well-differentiated serous carcinoma during 1997-2006, which were then reviewed by expert gynecologic pathologists. Data were analyzed using Kaplan-Meier methods and Cox proportional hazards regression analysis with follow-up through June 2009. Women with HGSC had a significantly increased risk of dying (HR=1.9; 95% CI: 1.6-2.3) compared with women with LGSC while adjusting for age and stage. Expert review of 171 women originally classified as well-differentiated in 1997-2006 were interpreted as LGSC in 30% of cases, whereas 12% were interpreted as HGSC and 50% as serous borderline ovarian tumors (SBT). Compared with women with confirmed LGSC, women with SBT at review had a significantly lower risk of dying (HR=0.5; 95% CI: 0.22-0.99), and women with HGSC at review had a non-significantly increased risk of dying (HR=1.6; 95% CI: 0.7-3.4). A binary grading system is a significant predictor of survival for ovarian serous carcinoma. Copyright © 2012 Elsevier Inc. All rights reserved.

Cryogenic system for the ArTeMiS large sub millimeter camera

NASA Astrophysics Data System (ADS)

Ercolani, E.; Relland, J.; Clerc, L.; Duband, L.; Jourdan, T.; Talvard, M.; Le Pennec, J.; Martignac, J.; Visticot, F.

2014-07-01

A new photonic camera has been developed in the framework of the ArTéMis project (Bolometers architecture for large field of view ground based telescopes in the sub-millimeter). This camera scans the sky in the sub-millimeter range at simultaneously three different wavelengths, namely 200 μm, 350 μm, 450 μm, and is installed inside the APEX telescope located at 5100m above sea level in Chile. Bolometric detectors cooled to 300 mK are used in the camera, which is integrated in an original cryostat developed at the low temperature laboratory (SBT) of the INAC institut. This cryostat contains filters, optics, mirrors and detectors which have to be implemented according to mass, size and stiffness requirements. As a result the cryostat exhibits an unusual geometry. The inner structure of the cryostat is a 40 K plate which acts as an optical bench and is bound to the external vessel through two hexapods, one fixed and the other one mobile thanks to a ball bearing. Once the cryostat is cold, this characteristic enabled all the different elements to be aligned with the optical axis. The cryogenic chain is built around a pulse tube cooler (40 K and 4 K) coupled to a double stage helium sorption cooler (300 mK). The cryogenic and vacuum processes are managed by a Siemens PLC and all the data are showed and stored on a CEA SCADA system. This paper describes the mechanical and thermal design of the cryostat, its command control, and the first thermal laboratory tests. This work was carried out in collaboration with the Astrophysics laboratory SAp of the IRFU institut. SAp and SBT have installed the camera in July 2013 inside the Cassegrain cabin of APEX.

Classification of community types, successional sequences, and landscapes of the Copper River Delta, Alaska.

Treesearch

Keith. Boggs

2000-01-01

A classification of community types, successional sequences, and landscapes is presented for the piedmont of the Copper River Delta. The classification was based on a sampling of 471 sites. A total of 75 community types, 42 successional sequences, and 6 landscapes are described. The classification of community types reflects the existing vegetation communities on the...

Gut microbiota and allogeneic transplantation.

PubMed

Wang, Weilin; Xu, Shaoyan; Ren, Zhigang; Jiang, Jianwen; Zheng, Shusen

2015-08-23

The latest high-throughput sequencing technologies show that there are more than 1000 types of microbiota in the human gut. These microbes are not only important to maintain human health, but also closely related to the occurrence and development of various diseases. With the development of transplantation technologies, allogeneic transplantation has become an effective therapy for a variety of end-stage diseases. However, complications after transplantation still restrict its further development. Post-transplantation complications are closely associated with a host's immune system. There is also an interaction between a person's gut microbiota and immune system. Recently, animal and human studies have shown that gut microbial populations and diversity are altered after allogeneic transplantations, such as liver transplantation (LT), small bowel transplantation (SBT), kidney transplantation (KT) and hematopoietic stem cell transplantation (HTCT). Moreover, when complications, such as infection, rejection and graft versus host disease (GVHD) occur, gut microbial populations and diversity present a significant dysbiosis. Several animal and clinical studies have demonstrated that taking probiotics and prebiotics can effectively regulate gut microbiota and reduce the incidence of complications after transplantation. However, the role of intestinal decontamination in allogeneic transplantation is controversial. This paper reviews gut microbial status after transplantation and its relationship with complications. The role of intervention methods, including antibiotics, probiotics and prebiotics, in complications after transplantation are also discussed. Further research in this new field needs to determine the definite relationship between gut microbial dysbiosis and complications after transplantation. Additionally, further research examining gut microbial intervention methods to ameliorate complications after transplantation is warranted. A better understanding of the relationship between gut microbiota and complications after allogeneic transplantation may make gut microbiota as a therapeutic target in the future.

Molecular Strain Typing of Mycobacterium tuberculosis: a Review of Frequently Used Methods

PubMed Central

2016-01-01

Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, remains one of the most serious global health problems. Molecular typing of M. tuberculosis has been used for various epidemiologic purposes as well as for clinical management. Currently, many techniques are available to type M. tuberculosis. Choosing the most appropriate technique in accordance with the existing laboratory conditions and the specific features of the geographic region is important. Insertion sequence IS6110-based restriction fragment length polymorphism (RFLP) analysis is considered the gold standard for the molecular epidemiologic investigations of tuberculosis. However, other polymerase chain reaction-based methods such as spacer oligonucleotide typing (spoligotyping), which detects 43 spacer sequence-interspersing direct repeats (DRs) in the genomic DR region; mycobacterial interspersed repetitive units–variable number tandem repeats, (MIRU-VNTR), which determines the number and size of tandem repetitive DNA sequences; repetitive-sequence-based PCR (rep-PCR), which provides high-throughput genotypic fingerprinting of multiple Mycobacterium species; and the recently developed genome-based whole genome sequencing methods demonstrate similar discriminatory power and greater convenience. This review focuses on techniques frequently used for the molecular typing of M. tuberculosis and discusses their general aspects and applications. PMID:27709842

Molecular Strain Typing of Mycobacterium tuberculosis: a Review of Frequently Used Methods.

PubMed

Ei, Phyu Win; Aung, Wah Wah; Lee, Jong Seok; Choi, Go Eun; Chang, Chulhun L

2016-11-01

Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, remains one of the most serious global health problems. Molecular typing of M. tuberculosis has been used for various epidemiologic purposes as well as for clinical management. Currently, many techniques are available to type M. tuberculosis. Choosing the most appropriate technique in accordance with the existing laboratory conditions and the specific features of the geographic region is important. Insertion sequence IS6110-based restriction fragment length polymorphism (RFLP) analysis is considered the gold standard for the molecular epidemiologic investigations of tuberculosis. However, other polymerase chain reaction-based methods such as spacer oligonucleotide typing (spoligotyping), which detects 43 spacer sequence-interspersing direct repeats (DRs) in the genomic DR region; mycobacterial interspersed repetitive units-variable number tandem repeats, (MIRU-VNTR), which determines the number and size of tandem repetitive DNA sequences; repetitive-sequence-based PCR (rep-PCR), which provides high-throughput genotypic fingerprinting of multiple Mycobacterium species; and the recently developed genome-based whole genome sequencing methods demonstrate similar discriminatory power and greater convenience. This review focuses on techniques frequently used for the molecular typing of M. tuberculosis and discusses their general aspects and applications.

Direct typing of Canine parvovirus (CPV) from infected dog faeces by rapid mini sequencing technique.

PubMed

V, Pavana Jyothi; S, Akila; Selvan, Malini K; Naidu, Hariprasad; Raghunathan, Shwethaa; Kota, Sathish; Sundaram, R C Raja; Rana, Samir Kumar; Raj, G Dhinakar; Srinivasan, V A; Mohana Subramanian, B

2016-12-01

Canine parvovirus (CPV) is a non-enveloped single stranded DNA virus with an icosahedral capsid. Mini-sequencing based CPV typing was developed earlier to detect and differentiate all the CPV types and FPV in a single reaction. This technique was further evaluated in the present study by performing the mini-sequencing directly from fecal samples which avoided tedious virus isolation steps by cell culture system. Fecal swab samples were collected from 84 dogs with enteritis symptoms, suggestive of parvoviral infection from different locations across India. Seventy six of these samples were positive by PCR; the subsequent mini-sequencing reaction typed 74 of them as type 2a virus, and 2 samples as type 2b. Additionally, 25 of the positive samples were typed by cycle sequencing of PCR products. Direct CPV typing from fecal samples using mini-sequencing showed 100% correlation with CPV typing by cycle sequencing. Moreover, CPV typing was achieved by mini-sequencing even with faintly positive PCR amplicons which was not possible by cycle sequencing. Therefore, the mini-sequencing technique is recommended for regular epidemiological follow up of CPV types, since the technique is rapid, highly sensitive and high capacity method for CPV typing. Copyright © 2016. Published by Elsevier B.V.

Measuring Stability and Security in Iraq

DTIC Science & Technology

2009-12-01

tackle the country’s corruption problem. The KRG recently issued a white paper outlining elements of a new strategy for good gover - nance, in part to...Iraq. The State Board of Tourism (SBT) hosted several tourist groups during this reporting 16 January 29, 2010 period. This year Iraq will...coordi- nated tours for the first American tourism company, Advantage Travel and Tours. Additionally, 27 signed investment licenses totaling $2

Storage and utilization of HLA genomic data--new approaches to HLA typing.

PubMed

Helmberg, W

2000-01-01

Currently available DNA-based HLA typing assays can provide detailed information about sequence motifs of a tested sample. It is still a common practice, however, for information acquired by high-resolution sequence specific oligonucleotide probe (SSOP) typing or sequence specific priming (SSP) to be presented in a low-resolution serological format. Unfortunately, this representation can lead to significant loss of useful data in many cases. An alternative to assigning allele equivalents to suchDNA typing results is simply to store the observed typing pattern and utilize the information with the help of Virtual DNA Analysis (VDA). Interpretation of the stored typing patterns can then be updated based on newly defined alleles, assuming the sequence motifs detected by the typing reagents are known. Rather than updating reagent specificities in individual laboratories, such updates should be performed in a central, publicly available sequence database. By referring to this database, HLA genomic data can then be stored and transferred between laboratories without loss of information. The 13th International Histocompatibility Workshop offers an ideal opportunity to begin building this common database for the entire human MHC.

Phenotypic H-Antigen Typing by Mass Spectrometry Combined with Genetic Typing of H Antigens, O Antigens, and Toxins by Whole-Genome Sequencing Enhances Identification of Escherichia coli Isolates.

PubMed

Cheng, Keding; Chui, Huixia; Domish, Larissa; Sloan, Angela; Hernandez, Drexler; McCorrister, Stuart; Robinson, Alyssia; Walker, Matthew; Peterson, Lorea A M; Majcher, Miles; Ratnam, Sam; Haldane, David J M; Bekal, Sadjia; Wylie, John; Chui, Linda; Tyler, Shaun; Xu, Bianli; Reimer, Aleisha; Nadon, Celine; Knox, J David; Wang, Gehua

2016-08-01

Mass spectrometry-based phenotypic H-antigen typing (MS-H) combined with whole-genome-sequencing-based genetic identification of H antigens, O antigens, and toxins (WGS-HOT) was used to type 60 clinical Escherichia coli isolates, 43 of which were previously identified as nonmotile, H type undetermined, or O rough by serotyping or having shown discordant MS-H and serotyping results. Whole-genome sequencing confirmed that MS-H was able to provide more accurate data regarding H antigen expression than serotyping. Further, enhanced and more confident O antigen identification resulted from gene cluster based typing in combination with conventional typing based on the gene pair comprising wzx and wzy and that comprising wzm and wzt The O antigen was identified in 94.6% of the isolates when the two genetic O typing approaches (gene pair and gene cluster) were used in conjunction, in comparison to 78.6% when the gene pair database was used alone. In addition, 98.2% of the isolates showed the existence of genes for various toxins and/or virulence factors, among which verotoxins (Shiga toxin 1 and/or Shiga toxin 2) were 100% concordant with conventional PCR based testing results. With more applications of mass spectrometry and whole-genome sequencing in clinical microbiology laboratories, this combined phenotypic and genetic typing platform (MS-H plus WGS-HOT) should be ideal for pathogenic E. coli typing. Copyright © 2016 Cheng et al.

Sequence analysis of chloroplast chlB gene of medicinal Ephedra species and its application to authentication of Ephedra Herb.

PubMed

Guo, Yahong; Tsuruga, Ayako; Yamaguchi, Shigeharu; Oba, Koji; Iwai, Kasumi; Sekita, Setsuko; Mizukami, Hajime

2006-06-01

Chloroplast chlB gene encoding subunit B of light-independent protochlorophyllide reductase was amplified from herbarium and crude drug specimens of Ephedra sinica, E. intermedia, E. equisetina, and E. przewalskii. Sequence comparison of the chlB gene indicated that all the E. sinica specimens have the same sequence type (Type S) distinctive from other species, while there are two sequence types (Type E1 and Type E2) in E. equisetina. E. intermedia and E. prezewalskii revealed an identical sequence type (Type IP). E. sinica was also identified by digesting the chlB fragment with Bcl I. A novel method for DNA authentication of Ephedra Herb based on the sequences of the chloroplast chlB gene and internal transcribed spacer of nuclear rRNA genes was developed and successfully applied for identification of the crude drugs obtained in the Chinese market.

Effectiveness of the standard and an alternative set of Streptococcus pneumoniae multi locus sequence typing primers.

PubMed

Adamiak, Paul; Vanderkooi, Otto G; Kellner, James D; Schryvers, Anthony B; Bettinger, Julie A; Alcantara, Joenel

2014-06-03

Multi-locus sequence typing (MLST) is a portable, broadly applicable method for classifying bacterial isolates at an intra-species level. This methodology provides clinical and scientific investigators with a standardized means of monitoring evolution within bacterial populations. MLST uses the DNA sequences from a set of genes such that each unique combination of sequences defines an isolate's sequence type. In order to reliably determine the sequence of a typing gene, matching sequence reads for both strands of the gene must be obtained. This study assesses the ability of both the standard, and an alternative set of, Streptococcus pneumoniae MLST primers to completely sequence, in both directions, the required typing alleles. The results demonstrated that for five (aroE, recP, spi, xpt, ddl) of the seven S. pneumoniae typing alleles, the standard primers were unable to obtain the complete forward and reverse sequences. This is due to the standard primers annealing too closely to the target regions, and current sequencing technology failing to sequence the bases that are too close to the primer. The alternative primer set described here, which includes a combination of primers proposed by the CDC and several designed as part of this study, addresses this limitation by annealing to highly conserved segments further from the target region. This primer set was subsequently employed to sequence type 105 S. pneumoniae isolates collected by the Canadian Immunization Monitoring Program ACTive (IMPACT) over a period of 18 years. The inability of several of the standard S. pneumoniae MLST primers to fully sequence the required region was consistently observed and is the result of a shift in sequencing technology occurring after the original primers were designed. The results presented here introduce clear documentation describing this phenomenon into the literature, and provide additional guidance, through the introduction of a widely validated set of alternative primers, to research groups seeking to undertake S. pneumoniae MLST based studies.

Unraveling systematic inventory of Echinops (Asteraceae) with special reference to nrDNA ITS sequence-based molecular typing of Echinops abuzinadianus.

PubMed

Ali, M A; Al-Hemaid, F M; Lee, J; Hatamleh, A A; Gyulai, G; Rahman, M O

2015-10-02

The present study explored the systematic inventory of Echinops L. (Asteraceae) of Saudi Arabia, with special reference to the molecular typing of Echinops abuzinadianus Chaudhary, an endemic species to Saudi Arabia, based on the internal transcribed spacer (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA. A sequence similarity search using BLAST and a phylogenetic analysis of the ITS sequence of E. abuzinadianus revealed a high level of sequence similarity with E. glaberrimus DC. (section Ritropsis). The novel primary sequence and the secondary structure of ITS2 of E. abuzinadianus could potentially be used for molecular genotyping.

Novel fabrication method for zirconia restorations: bonding strength of machinable ceramic to zirconia with resin cements.

PubMed

Kuriyama, Soichi; Terui, Yuichi; Higuchi, Daisuke; Goto, Daisuke; Hotta, Yasuhiro; Manabe, Atsufumi; Miyazaki, Takashi

2011-01-01

A novel method was developed to fabricate all-ceramic restorations which comprised CAD/CAM-fabricated machinable ceramic bonded to CAD/CAM-fabricated zirconia framework using resin cement. The feasibility of this fabrication method was assessed in this study by investigating the bonding strength of a machinable ceramic to zirconia. A machinable ceramic was bonded to a zirconia plate using three kinds of resin cements: ResiCem (RE), Panavia (PA), and Multilink (ML). Conventional porcelain-fused-to-zirconia specimens were also prepared to serve as control. Shear bond strength test (SBT) and Schwickerath crack initiation test (SCT) were carried out. SBT revealed that PA (40.42 MPa) yielded a significantly higher bonding strength than RE (28.01 MPa) and ML (18.89 MPa). SCT revealed that the bonding strengths of test groups using resin cement were significantly higher than those of Control. Notably, the bonding strengths of RE and ML were above 25 MPa even after 10,000 times of thermal cycling -adequately meeting the ISO 9693 standard for metal-ceramic restorations. These results affirmed the feasibility of the novel fabrication method, in that a CAD/CAM-fabricated machinable ceramic is bonded to a CAD/CAM-fabricated zirconia framework using a resin cement.

[The combination effects of antibacterial agents against clinical isolated multiple-drug resistant Pseudomonas aeruginosa].

PubMed

Maesaki, Shigefumi; Yamaguchi, Toshiyuki; Sasaki, Kazumasa; Hashikita, Giichi; Shibuya, Shunsuke; Watanabe, Masaharu; Takayama, Sadao; Kawakami, Sayoko; Nagasawa, Mitsuaki; Suzuki, Noriyasu; Uchida, Takashi; Okabe, Tadashi; Kobayashi, Sugako

2006-02-01

The effectiveness of antibacterial agents against 70 strains of clinically isolated multiple-drug resistant Pseudomonas aeruginosa (MDRP) was measured by the micro dilution method. Fifty of all strains (71%) produced metallo-beta-lactamase and the IMP-1 gene was detected by polymerase chain reaction (PCR). The MIC90 (the minimum inhibitory concentration of an antibiotic necessary to inhibit the growth of 90% of bacterial strains) values of biapenem (BIPM), meropenem (MEPM), tazobactam/piperacillin (TAZ/PIPC), sulbactam/ cefoperazone (SBT/CPZ), cefepime (CFPM), ciprofloxacin (CPFX), pazufloxacin (PZFX), amikacin (AMK) and aztreonam (AZT) were found to be 265, 512, 256, 512, 512, 64, 128, 128 and 128 microg/mL, respectively. The in vitro combination effects of antibacterial agents were examined against 62 strains of MDRP and the synergy or additive effects were evaluated by fractional inhibitory concentration (FIC) index calculated by the checkerboard method. The combination of AMK and AZT showed synergy effects on 15/59 (25.4%) strains of MDRP. The synergy and additive effects on the MDRP strains were also found by the other antibacterial agents combination such as TAZ/PIPC and AMK, CFPM and AMK, and SBT/CPZ and AZT. These results suggested the necessity of further investigation of clinical usefulness.

Recent progress of Spectrolab high-efficiency space solar cells

NASA Astrophysics Data System (ADS)

Law, Daniel C.; Boisvert, J. C.; Rehder, E. M.; Chiu, P. T.; Mesropian, S.; Woo, R. L.; Liu, X. Q.; Hong, W. D.; Fetzer, C. M.; Singer, S. B.; Bhusari, D. M.; Edmondson, K. M.; Zakaria, A.; Jun, B.; Krut, D. D.; King, R. R.; Sharma, S. K.; Karam, N. H.

2013-09-01

Recent progress in III-V multijunction space solar cell has led to Spectrolab's GaInP/GaAs/Ge triple-junction, XTJ, cells with average 1-sun efficiency of 29% (AM0, 28°C) for cell size ranging from 59 to 72-cm2. High-efficiency inverted metamorphic (IMM) multijunction cells are developed as the next space solar cell architecture. Spectrolab's large-area IMM3J and IMM4J cells have achieved 33% and 34% 1-sun, AM0 efficiencies, respectively. The IMM3J and the IMM4J cells have both demonstrated normalized power retention of 0.86 at 5x1014 e-/cm2 fluence and 0.83 and 0.82 at 1x1015 e-/cm2 fluence post 1-MeV electron radiation, respectively. The IMM cells were further assembled into coverglass-interconnect-cell (CIC) strings and affixed to typical rigid aluminum honeycomb panels for thermal cycling characterization. Preliminary temperature cycling data of two coupons populated with IMM cell strings showed no performance degradation. Spectrolab has also developed semiconductor bonded technology (SBT) where highperformance component subcells were grown on GaAs and InP substrates separately then bonded directly to form the final multijunction cells. Large-area SBT 5-junction cells have achieved a 35.1% efficiency under 1-sun, AM0 condition.

Sequence of Child Care Type and Child Development: What Role Does Peer Exposure Play?

ERIC Educational Resources Information Center

Morrissey, Taryn W.

2010-01-01

Child care arrangements change as children age; in general, hours in home-based child care decrease as hours in center-based settings increase. This sequence of child care type may correspond with children's developmental needs; the small peer groups and low child-adult ratios typical of home-based care may allow for more individual child-adult…

How Social Communications Influence Advertising Perception and Response in Online Communities?

PubMed Central

Zeng, Fue; Tao, Ran; Yang, Yanwu; Xie, Tingting

2017-01-01

This research aims to explore how social communications of online communities affect users’ perception and responses toward social media advertising. We developed a conceptual model based on the SBT, encapsulating 9 constructs and 10 hypothesis extracted from the extant social media advertising literature. Our research outcome proves that social communications can effectively boost users’ behaviors to be in accordance with an online social community, thus facilitate their acceptance and responses toward social media advertising, with users’ group intention as an intervening factor. From an operational standpoint, it’s an effective way to build and maintain social bonds between users and the community by boosting social communications, supporting fluent interpersonal communications. In addition, managers of an online community should elaborate on users’ group intentions to increase users’ advertising acceptance and response. PMID:28855879

How Social Communications Influence Advertising Perception and Response in Online Communities?

PubMed

Zeng, Fue; Tao, Ran; Yang, Yanwu; Xie, Tingting

2017-01-01

This research aims to explore how social communications of online communities affect users' perception and responses toward social media advertising. We developed a conceptual model based on the SBT, encapsulating 9 constructs and 10 hypothesis extracted from the extant social media advertising literature. Our research outcome proves that social communications can effectively boost users' behaviors to be in accordance with an online social community, thus facilitate their acceptance and responses toward social media advertising, with users' group intention as an intervening factor. From an operational standpoint, it's an effective way to build and maintain social bonds between users and the community by boosting social communications, supporting fluent interpersonal communications. In addition, managers of an online community should elaborate on users' group intentions to increase users' advertising acceptance and response.

Small Bowel Transplant

PubMed Central

2003-01-01

EXECUTIVE SUMMARY Objective The Medical Advisory Secretariat undertook a review of the evidence on the effectiveness and cost-effectiveness of small bowel transplant in the treatment of intestinal failure. Small Bowel Transplantation Intestinal failure is the loss of absorptive capacity of the small intestine that results in an inability to meet the nutrient and fluid requirements of the body via the enteral route. Patients with intestinal failure usually receive nutrients intravenously, a procedure known as parenteral nutrition. However, long-term parenteral nutrition is associated with complications including liver failure and loss of venous access due to recurrent infections. Small bowel transplant is the transplantation of a cadaveric intestinal allograft for the purpose of restoring intestinal function in patients with irreversible intestinal failure. The transplant may involve the small intestine alone (isolated small bowel ISB), the small intestine and the liver (SB-L) when there is irreversible liver failure, or multiple organs including the small bowel (multivisceral MV or cluster). Although living related donor transplant is being investigated at a limited number of centres, cadaveric donors have been used in most small bowel transplants. The actual transplant procedure takes approximately 12-18 hours. After intestinal transplant, the patient is generally placed on prophylactic antibiotic medication and immunosuppressive regimen that, in the majority of cases, would include tacrolimus, corticosteroids and an induction agent. Close monitoring for infection and rejection are essential for early treatment. Medical Advisory Secretariat Review The Medical Advisory Secretariat undertook a review of 35 reports from 9 case series and 1 international registry. Sample size of the individual studies ranged from 9 to 155. As of May 2001, 651 patients had received small bowel transplant procedures worldwide. According to information from the Canadian Organ Replacement Register, a total of 27 small bowel transplants were performed in Canada from 1988 to 2002. Patient Outcomes The experience in small bowel transplant is still limited. International data showed that during the last decade, patient survival and graft survival rates from SBT have improved, mainly because of improved immunosuppression therapy and earlier detection and treatment of infection and rejection. The Intestinal Transplant Registry reported 1-year actuarial patient survival rates of 69% for isolated small bowel transplant, 66% for small bowel-liver transplant, and 63% for multivisceral transplant, and a graft survival rate of 55% for ISB and 63% for SB-L and MV. The range of 1-year patient survival rates reported ranged from 33%-87%. Reported 1-year graft survival rates ranged from 46-71%. Regression analysis performed by the International Transplant Registry in 1997 indicated that centres that have performed at least 10 small bowel transplants had better patient and graft survival rates than centres that performed less than 10 transplants. However, analysis of the data up to May 2001 suggests that the critical mass of 10 transplants no longer holds true for transplants after 1995, and that good results can be achieved at any multiorgan transplant program with moderate patient volumes. The largest Centre reported an overall 1-year patient and graft survival rate of 72% and 64% respectively, and 5-year patient and graft survival of 48% and 40% respectively. The overall 1-year patient survival rate reported for Ontario pediatric small bowel transplants was 61% with the highest survival rate of 83% for ISB. The majority (70% or higher) of surviving small bowel transplant recipients was able to wean from parenteral nutrition and meet all caloric needs enterally. Some may need enteral or parenteral supplementation during periods of illness. Growth and weight gain in children after ISB were reported by two studies while two other studies reported a decrease in growth velocity with no catch-up growth. The quality of life after SBT was reported to be comparable to that of patients on home enteral nutrition. A study found that while the parents of pediatric SBT recipients reported significant limitations in the physical and psychological well being of the children compared with normal school children, the pediatric SBT recipients themselves reported a quality of life similar to other school children. Survival was found to be better in transplants performed since 1991. Patient survival was associated with the type of organ transplanted with better survival in isolated small bowel recipients. Adverse Events Despite improvement in patient and graft survival rates, small bowel transplant is still associated with significant mortality and morbidity. Infection with subsequent sepsis is the leading cause of death (51.3%). Bacterial, fungal and viral infections have all been reported. The most common viral infections are cytomegalorvirus (18-40%) and Epstein-Barr virus. The latter often led to ß-cell post-transplant lymphoproliferative disease. Graft rejection is the second leading cause of death after SBT (10.4%) and is responsible for 57% of graft removal. Acute rejection rates ranged from 51% to 83% in the major programs. Most of the acute rejection episodes were mild and responded to steroids and OKT3. Antilymphocyte therapy was needed in up to 27% of patients. Isolated small bowel allograft and positive lymphocytotoxic cross-match were found to be risk factors for acute rejection. Post-transplant lymphoproliferative disease occurred in 21% of SBT recipients and accounted for 7% of post-transplant mortality. The frequency was higher in pediatric recipients (31%) and in adults receiving composite visceral allografts (25%). The allograft itself is often involved in post-transplant lymphoproliferative disease. The reported incidence of host versus graft disease varied widely among centers (0% - 14%). Surgical complications were reported to occur in 85% of SB-L transplants and 25% of ISB transplants. Reoperations were required in 45% - 66% of patients in a large series and the most common reason for reoperation was intra-abdominal abscess. The median cost of intestinal transplant in the US was reported to be approximately $275,000US (approximately CDN$429,000) per case. A US study concluded that based on the US cost of home parenteral nutrition, small bowel transplant could be cost-effective by the second year after the transplant. Conclusion There is evidence that small bowel transplant can prolong the life of some patients with irreversible intestinal failure who can no longer continue to be managed by parenteral nutrition therapy. Both patient survival and graft survival rates have improved with time. However, small bowel transplant is still associated with significant mortality and morbidity. The outcomes are inferior to those of total parenteral nutrition. Evidence suggests that this procedure should only be used when total parenteral nutrition is no longer feasible. PMID:23074441

Genetic analysis of Fasciola isolates from cattle in Korea based on second internal transcribed spacer (ITS-2) sequence of nuclear ribosomal DNA.

PubMed

Choe, Se-Eun; Nguyen, Thuy Thi-Dieu; Kang, Tae-Gyu; Kweon, Chang-Hee; Kang, Seung-Won

2011-09-01

Nuclear ribosomal DNA sequence of the second internal transcribed spacer (ITS-2) has been used efficiently to identify the liver fluke species collected from different hosts and various geographic regions. ITS-2 sequences of 19 Fasciola samples collected from Korean native cattle were determined and compared. Sequence comparison including ITS-2 sequences of isolates from this study and reference sequences from Fasciola hepatica and Fasciola gigantica and intermediate Fasciola in Genbank revealed seven identical variable sites of investigated isolates. Among 19 samples, 12 individuals had ITS-2 sequences completely identical to that of pure F. hepatica, five possessed the sequences identical to F. gigantica type, whereas two shared the sequence of both F. hepatica and F. gigantica. No variations in length and nucleotide composition of ITS-2 sequence were observed within isolates that belonged to F. hepatica or F. gigantica. At the position of 218, five Fasciola containing a single-base substitution (C>T) formed a distinct branch inside the F. gigantica-type group which was similar to those of Asian-origin isolates. The phylogenetic tree of the Fasciola spp. based on complete ITS-2 sequences from this study and other representative isolates in different locations clearly showed that pure F. hepatica, F. gigantica type and intermediate Fasciola were observed. The result also provided additional genetic evidence for the existence of three forms of Fasciola isolated from native cattle in Korea by genetic approach using ITS-2 sequence.

A PCR technique based on the Hip1 interspersed repetitive sequence distinguishes cyanobacterial species and strains.

PubMed

Smith, J K; Parry, J D; Day, J G; Smith, R J

1998-10-01

The use of primers based on the Hip1 sequence as a typing technique for cyanobacteria has been investigated. The discovery of short repetitive sequence structures in bacterial DNA during the last decade has led to the development of PCR-based methods for typing, i.e., distinguishing and identifying, bacterial species and strains. An octameric palindromic sequence known as Hip1 has been shown to be present in the chromosomal DNA of many species of cyanobacteria as a highly repetitious interspersed sequence. PCR primers were constructed that extended the Hip1 sequence at the 3' end by two bases. Five of the 16 possible extended primers were tested. Each of the five primers produced a different set of products when used to prime PCR from cyanobacterial genomic DNA. Each primer produced a distinct set of products for each of the 15 cyanobacterial species tested. The ability of Hip1-based PCR to resolve taxonomic differences was assessed by analysis of independent isolates of Anabaena flos-aquae and Nostoc ellipsosporum obtained from the CCAP (Culture Collection of Algae and Protozoa, IFE, Cumbria, UK). A PCR-based RFLP analysis of products amplified from the 23S-16S rDNA intergenic region was used to characterize the isolates and to compare with the Hip1 typing data. The RFLP and Hip1 typing yielded similar results and both techniques were able to distinguish different strains. On the basis of these results it is suggested that the Hip1 PCR technique may assist in distinguishing cyanobacterial species and strains.

Computer Program for Vibration Prediction of Fighter Aircraft Equipments

DTIC Science & Technology

1977-11-01

scribing a useful variety of flight vibration phases . Notice that identical variations can be reflected into the high frequency rolloff curve (equation 13...flight attitudes ranging from straight and level states to a variety of significant flight maneuvers and phases . Pro- gram outputs, digital and...R (f) adjusted value of R(f) due to c (g 2/Hz) SBT (f) special function for the buffet turn flight phase PBT (f) pressure spectral density speqtrum

Impact of fiber-optic laryngoscopy on the weaning process from mechanical ventilation in high-risk patients for postextubation stridor.

PubMed

Lemyze, Malcolm; Durville, Emmanuelle; Meddour, Mehdi; Jonard, Marie; Temime, Johanna; Barailler, Stéphanie; Thevenin, Didier; Mallat, Jihad

2017-02-01

The objective of this study was to assess the impact of fiber-optic laryngoscopy (FOL) on the weaning process from mechanical ventilation in critically ill patients with a positive cuff leak test (CLT) as compared with the current recommended strategy based on corticosteroids.In this prospective observational pilot study conducted over a 1-year period in a 15-bed ICU, CLT was systematically performed before extubation in all intubated patients having passed a spontaneous breathing trial (SBT). After the endotracheal tube cuff was deflated, cuff leak volume (CLVol) was assessed during assisted controlled ventilation. When CLT was positive (CLVol < 110 mL), patients either were evaluated using FOL by our half-time FOL-practitioner when present, or received corticosteroids.Among the 233 patients included, 34 (14.6%) had a positive CLT that hampered extubation. Seventeen were treated by corticosteroids and 17 were evaluated by FOL. In the corticosteroids group, the CLVol was still <110 mL at 24 hours in 9 patients (53%). Corticosteroids strategy merely prolonged the total duration of mechanical ventilation (7 [4-11] vs 4 [2-6] days, P = 0.01) by increasing the time between successful SBT and the moment when extubation was effectively achieved (30 [24-60] vs 1.5 [1-2] hours, P < 0.001). This resulted in 2 self-extubations (12%) and 9 FOL-guided extubations (53%) in the corticosteroids group. Massive swelling of the arytenoids was the most common feature shown by FOL. The patients evaluated by FOL who exhibited the thin anterior V-shaped opening of the vocal cords-the V sign-(n = 26, 100%) were immediately extubated without any stridor or respiratory failure afterward.In this pilot study, a FOL-based extubation strategy was feasible and reliable, and significantly reduced the duration of mechanical ventilation in patients with a positive CLT. We describe the "V sign" of FOL that safely allows a successful prompt extubation in patients considered at high risk for postextubation stridor.

Creation of a type IIS restriction endonuclease with a long recognition sequence

PubMed Central

Lippow, Shaun M.; Aha, Patti M.; Parker, Matthew H.; Blake, William J.; Baynes, Brian M.; Lipovšek, Daša

2009-01-01

Type IIS restriction endonucleases cleave DNA outside their recognition sequences, and are therefore particularly useful in the assembly of DNA from smaller fragments. A limitation of type IIS restriction endonucleases in assembly of long DNA sequences is the relative abundance of their target sites. To facilitate ligation-based assembly of extremely long pieces of DNA, we have engineered a new type IIS restriction endonuclease that combines the specificity of the homing endonuclease I-SceI with the type IIS cleavage pattern of FokI. We linked a non-cleaving mutant of I-SceI, which conveys to the chimeric enzyme its specificity for an 18-bp DNA sequence, to the catalytic domain of FokI, which cuts DNA at a defined site outside the target site. Whereas previously described chimeric endonucleases do not produce type IIS-like precise DNA overhangs suitable for ligation, our chimeric endonuclease cleaves double-stranded DNA exactly 2 and 6 nt from the target site to generate homogeneous, 5′, four-base overhangs, which can be ligated with 90% fidelity. We anticipate that these enzymes will be particularly useful in manipulation of DNA fragments larger than a thousand bases, which are very likely to contain target sites for all natural type IIS restriction endonucleases. PMID:19304757

Automated typing of red blood cell and platelet antigens: a whole-genome sequencing study.

PubMed

Lane, William J; Westhoff, Connie M; Gleadall, Nicholas S; Aguad, Maria; Smeland-Wagman, Robin; Vege, Sunitha; Simmons, Daimon P; Mah, Helen H; Lebo, Matthew S; Walter, Klaudia; Soranzo, Nicole; Di Angelantonio, Emanuele; Danesh, John; Roberts, David J; Watkins, Nick A; Ouwehand, Willem H; Butterworth, Adam S; Kaufman, Richard M; Rehm, Heidi L; Silberstein, Leslie E; Green, Robert C

2018-06-01

There are more than 300 known red blood cell (RBC) antigens and 33 platelet antigens that differ between individuals. Sensitisation to antigens is a serious complication that can occur in prenatal medicine and after blood transfusion, particularly for patients who require multiple transfusions. Although pre-transfusion compatibility testing largely relies on serological methods, reagents are not available for many antigens. Methods based on single-nucleotide polymorphism (SNP) arrays have been used, but typing for ABO and Rh-the most important blood groups-cannot be done with SNP typing alone. We aimed to develop a novel method based on whole-genome sequencing to identify RBC and platelet antigens. This whole-genome sequencing study is a subanalysis of data from patients in the whole-genome sequencing arm of the MedSeq Project randomised controlled trial (NCT01736566) with no measured patient outcomes. We created a database of molecular changes in RBC and platelet antigens and developed an automated antigen-typing algorithm based on whole-genome sequencing (bloodTyper). This algorithm was iteratively improved to address cis-trans haplotype ambiguities and homologous gene alignments. Whole-genome sequencing data from 110 MedSeq participants (30 × depth) were used to initially validate bloodTyper through comparison with conventional serology and SNP methods for typing of 38 RBC antigens in 12 blood-group systems and 22 human platelet antigens. bloodTyper was further validated with whole-genome sequencing data from 200 INTERVAL trial participants (15 × depth) with serological comparisons. We iteratively improved bloodTyper by comparing its typing results with conventional serological and SNP typing in three rounds of testing. The initial whole-genome sequencing typing algorithm was 99·5% concordant across the first 20 MedSeq genomes. Addressing discordances led to development of an improved algorithm that was 99·8% concordant for the remaining 90 MedSeq genomes. Additional modifications led to the final algorithm, which was 99·2% concordant across 200 INTERVAL genomes (or 99·9% after adjustment for the lower depth of coverage). By enabling more precise antigen-matching of patients with blood donors, antigen typing based on whole-genome sequencing provides a novel approach to improve transfusion outcomes with the potential to transform the practice of transfusion medicine. National Human Genome Research Institute, Doris Duke Charitable Foundation, National Health Service Blood and Transplant, National Institute for Health Research, and Wellcome Trust. Copyright © 2018 Elsevier Ltd. All rights reserved.

Molecular epidemiologic analysis of a Pneumocystis pneumonia outbreak among renal transplant patients.

PubMed

Urabe, N; Ishii, Y; Hyodo, Y; Aoki, K; Yoshizawa, S; Saga, T; Murayama, S Y; Sakai, K; Homma, S; Tateda, K

2016-04-01

Between 18 November and 3 December 2011, five renal transplant patients at the Department of Nephrology, Toho University Omori Medical Centre, Tokyo, were diagnosed with Pneumocystis pneumonia (PCP). We used molecular epidemiologic methods to determine whether the patients were infected with the same strain of Pneumocystis jirovecii. DNA extracted from the residual bronchoalveolar lavage fluid from the five outbreak cases and from another 20 cases of PCP between 2007 and 2014 were used for multilocus sequence typing to compare the genetic similarity of the P. jirovecii. DNA base sequencing by the Sanger method showed some regions where two bases overlapped and could not be defined. A next-generation sequencer was used to analyse the types and ratios of these overlapping bases. DNA base sequences of P. jirovecii in the bronchoalveolar lavage fluid from four of the five PCP patients in the 2011 outbreak and from another two renal transplant patients who developed PCP in 2013 were highly homologous. The Sanger method revealed 14 genomic regions where two differing DNA bases overlapped and could not be identified. Analyses of the overlapping bases by a next-generation sequencer revealed that the differing types of base were present in almost identical ratios. There is a strong possibility that the PCP outbreak at the Toho University Omori Medical Centre was caused by the same strain of P. jirovecii. Two different types of base present in some regions may be due to P. jirovecii's being a diploid species. Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

DNA-based differentiation of the Ecuadorian cocoa types CCN-51 and Arriba based on sequence differences in the chloroplast genome.

PubMed

Herrmann, Luise; Haase, Ilka; Blauhut, Maike; Barz, Nadine; Fischer, Markus

2014-12-17

Two cocoa types, Arriba and CCN-51, are being cultivated in Ecuador. With regard to the unique aroma, Arriba is considered a fine cocoa type, while CCN-51 is a bulk cocoa because of its weaker aroma. Because it is being assumed that Arriba is mixed with CCN-51, there is an interest in the analytical differentiation of the two types. Two methods to identify CCN-51 adulterations in Arriba cocoa were developed on the basis of differences in the chloroplast DNA. On the one hand, a different repeat of the sequence TAAAG in the inverted repeat region results in a different length of amplicons for the two cocoa types, which can be detected by agarose gel electrophoresis, capillary gel electrophoresis, and denaturing high-performance liquid chromatography. On the other hand, single nucleotide polymorphisms (SNPs) between the CCN-51 and Arriba sequences represent restriction sites, which can be used for restriction fragment length polymorphism analysis. A semi-quantitative analysis based on these SNPs is feasible. A method for an exact quantitation based on these results is not realizable. These sequence variations were confirmed for a comprehensive cultivar collection of Arriba and CCN-51, for both bean and leaf samples.

Effects of yogurt starter cultures on the survival of Lactobacillus acidophilus.

PubMed

Ng, Elizabeth W; Yeung, Marie; Tong, Phillip S

2011-01-31

Recognized to confer health benefits to consumers, probiotics such as Lactobacillus acidophilus are commonly incorporated into fermented dairy products worldwide; among which yogurt is a popular delivery vehicle. To materialize most of the putative health benefits associated with probiotics, an adequate amount of viable cells must be delivered at the time of consumption. However, the loss in their viabilities during refrigerated storage has been demonstrated previously. This study focused on the effects of yogurt starter cultures on the survival of five strains of L. acidophilus, with emphases on low pH and acid production. Differential survival behavior between L. acidophilus strains was further analyzed. To this end, viable cell counts of L. acidophilus were determined weekly during 4°C storage in various types of yogurts made with Streptococcus thermophilus alone, L. delbrueckii ssp. bulgaricus alone, both species of the starter cultures, or glucono-delta-lactone (GDL). All yogurt types, except for pasteurized yogurts, were co-fermented with L. acidophilus. Yogurt filtrate was analyzed for the presence of any inhibitory substance and for the amount of hydrogen peroxide. Multiplication of L. acidophilus was not affected by the starter cultures as all strains reached high level on day 0 of the storage period. Throughout the 28-day storage period, cell counts of L. acidophilus PIM703 and SBT2062 remained steady (~6 × 10(7)CFU/g) in yogurts made with both starter cultures, whereas those of ATCC 700396 and NCFM were reduced by a maximum of 3 and 4.6 logs, respectively. When starter cultures were replaced by GDL, all strains survived well, suggesting that a low pH was not a critical factor dictating their survival. In addition, the filtrate collected from yogurts made with starter cultures appeared to have higher inhibitory activities against L. acidophilus than that made with GDL. The presence of viable starter cultures was necessary to adversely affect the survival of some strains, as pasteurized yogurts had no effect on their survival. In particular, the inhibitory effect exerted by L. delbrueckii ssp. bulgaricus on L. acidophilus NCFM was highly pronounced than by S. thermophilus, nevertheless, the same effect was not observed on SBT2062. The inhibition against stationary-phase NCFM cells might be caused by the elevated level of hydrogen peroxide produced by L. delbrueckii ssp. bulgaricus. Delineating factors driving the differences in survival trait among probiotic strains will lead to a more efficacious delivery of health benefits in fermented dairy products through targeted technological interventions. Copyright © 2010 Elsevier B.V. All rights reserved.

The Effects of CBI Lesson Sequence Type and Field Dependence on Learning from Computer-Based Cooperative Instruction in Web

ERIC Educational Resources Information Center

Ipek, Ismail

2010-01-01

The purpose of this study was to investigate the effects of CBI lesson sequence type and cognitive style of field dependence on learning from Computer-Based Cooperative Instruction (CBCI) in WEB on the dependent measures, achievement, reading comprehension and reading rate. Eighty-seven college undergraduate students were randomly assigned to…

Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies.

PubMed

Chen, Hui; Luthra, Rajyalakshmi; Goswami, Rashmi S; Singh, Rajesh R; Roy-Chowdhuri, Sinchita

2015-08-28

Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects.

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods

PubMed Central

2012-01-01

Background With the decrease of DNA sequencing costs, sequence-based typing methods are rapidly becoming the gold standard for epidemiological surveillance. These methods provide reproducible and comparable results needed for a global scale bacterial population analysis, while retaining their usefulness for local epidemiological surveys. Online databases that collect the generated allelic profiles and associated epidemiological data are available but this wealth of data remains underused and are frequently poorly annotated since no user-friendly tool exists to analyze and explore it. Results PHYLOViZ is platform independent Java software that allows the integrated analysis of sequence-based typing methods, including SNP data generated from whole genome sequence approaches, and associated epidemiological data. goeBURST and its Minimum Spanning Tree expansion are used for visualizing the possible evolutionary relationships between isolates. The results can be displayed as an annotated graph overlaying the query results of any other epidemiological data available. Conclusions PHYLOViZ is a user-friendly software that allows the combined analysis of multiple data sources for microbial epidemiological and population studies. It is freely available at http://www.phyloviz.net. PMID:22568821

Lower Interbreath Interval Complexity Is Associated With Extubation Failure in Mechanically Ventilated Patients During Spontaneous Breathing Trials

DTIC Science & Technology

2010-06-01

patient tolerated the SBT, then measurement of respiratory rate (RR), rapid shallow breathing index (RSBI), and negative inspiratory force ( NIF ) were...no deaths in either cohort during the study period. The characteristics of the two groups, along with RR, duration of IBI, NIF , and RSBI calculated... NIF , and RSBI did not differ between groups, and that all subjects who were extubated had weaning parameters predictive of success. To explore the

Evidence of separate subgroups of juvenile southern bluefin tuna.

PubMed

Chambers, Mark S; Sidhu, Leesa A; O'Neill, Ben; Sibanda, Nokuthaba

2017-11-01

Archival tagging studies of southern bluefin tuna (SBT , Thunnus maccoyii ) have revealed that juveniles residing in the Great Australian Bight (GAB) over the austral summer undertake seasonal cyclic migrations to the southeast Indian Ocean and the Tasman Sea during winter. However, there remains disagreement about the extent of mixing between juvenile SBT regularly caught by longline fleets south of Africa and those observed in the GAB. Some researchers have argued that archival tag recoveries indicate most juveniles reside in the GAB over the austral summer. Others have suggested that recoveries of conventional and archival tags are better explained by a juvenile population consisting of separate groups on the eastern and western sides of the Indian Ocean with limited intermixing. We present analyses of catch and tag recovery data and re-examine archival tagging studies. The evidence provided strongly favors the hypothesis of separate juvenile subgroups, or contingents, with limited intermixing. We draw some tentative conclusions about the nature of the putative contingents and discuss some implications of these findings for the interpretation of existing datasets and future research priorities. We also provide the first evidence that the migration choices of juveniles that summer in the GAB are influenced by fidelity to winter feeding grounds and suggest this helps explain the collapse of the surface fishery off New South Wales in the 1980s.

Exploring the "Obesity Paradox" as a Correlate of Cognitive and Physical Function in Community-dwelling Black and White Older Adults.

PubMed

Skinner, Jeannine S; Abel, Willie Mae; McCoy, Katryna; Wilkins, Consuelo H

2017-01-01

The obesity paradox has been documented in aged populations, yet it remains unclear if this paradox persists for physical and cognitive outcomes in community-dwelling older adult populations. Our study examines associations between body mass index (BMI) classification, cognitive function, and physical function. We also investigate whether these associations are modified by race or age. Cross-sectional study. Senior residential sites and community centers in Saint Louis, Missouri. Study participants included 331 adults, aged >55 years. Age was stratified into young-old (aged 55-74 years) and older (aged ≥75 years). Physical function was measured using the mini-Physical Performance Test (mini-PPT) and grip strength. Cognitive function was assessed with the Short Blessed Test (SBT) and the Trail Making Tests (TMT-A and TMT-B) performance. Older adults who were obese had significantly better cognitive flexibility (TMT-B) performance than normal weight older adults (P=.02), and this association was not influenced by age or race. Adiposity was not associated with psychomotor speed (TMT-A), general cognition (SBT), or measures of physical function (Ps>.05). In a diverse sample of community-dwelling older adults, we found partial support for the controversial obesity paradox. Our results suggest excess adiposity may be protective for executive function processes. Future research is needed to examine the underlying physiological processes linking adiposity to executive function in older adults.

From structure to function - a family portrait of plant subtilases.

PubMed

Schaller, Andreas; Stintzi, Annick; Rivas, Susana; Serrano, Irene; Chichkova, Nina V; Vartapetian, Andrey B; Martínez, Dana; Guiamét, Juan J; Sueldo, Daniela J; van der Hoorn, Renier A L; Ramírez, Vicente; Vera, Pablo

2018-05-01

Contents Summary 901 I. Introduction 901 II. Biochemistry and structure of plant SBTs 902 III. Phylogeny of plant SBTs and family organization 903 IV. Physiological roles of plant SBTs 905 V. Conclusions and outlook 911 Acknowledgements 912 References 912 SUMMARY: Subtilases (SBTs) are serine peptidases that are found in all three domains of life. As compared with homologs in other Eucarya, plant SBTs are more closely related to archaeal and bacterial SBTs, with which they share many biochemical and structural features. However, in the course of evolution, functional diversification led to the acquisition of novel, plant-specific functions, resulting in the present-day complexity of the plant SBT family. SBTs are much more numerous in plants than in any other organism, and include enzymes involved in general proteolysis as well as highly specific processing proteases. Most SBTs are targeted to the cell wall, where they contribute to the control of growth and development by regulating the properties of the cell wall and the activity of extracellular signaling molecules. Plant SBTs affect all stages of the life cycle as they contribute to embryogenesis, seed development and germination, cuticle formation and epidermal patterning, vascular development, programmed cell death, organ abscission, senescence, and plant responses to their biotic and abiotic environments. In this article we provide a comprehensive picture of SBT structure and function in plants. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perez-Miller, Samantha; Zou, Qin; Novotny, Milos V.

In mice, the major urinary proteins (MUP) play a key role in pheromonal communication by binding and transporting semiochemicals. MUP-IV is the only isoform known to be expressed in the vomeronasal mucosa. In comparison with the MUP isoforms that are abundantly excreted in the urine, MUP-IV is highly specific for the male mouse pheromone 2-sec-butyl-4,5-dihydrothiazole (SBT). To examine the structural basis of this ligand preference, we determined the X-ray crystal structure of MUP-IV bound to three mouse pheromones: SBT, 2,5-dimethylpyrazine, and 2-heptanone. We also obtained the structure of MUP-IV with 2-ethylhexanol bound in the cavity. These four structures show thatmore » relative to the major excreted MUP isoforms, three amino acid substitutions within the binding calyx impact ligand coordination. The F103 for A along with F54 for L result in a smaller cavity, potentially creating a more closely packed environment for the ligand. The E118 for G substitution introduces a charged group into a hydrophobic environment. The sidechain of E118 is observed to hydrogen bond to polar groups on all four ligands with nearly the same geometry as seen for the water-mediated hydrogen bond network in the MUP-I and MUP-II crystal structures. These differences in cavity size and interactions between the protein and ligand are likely to contribute to the observed specificity of MUP-IV.« less

Real-Time PCR Typing of Escherichia coli Based on Multiple Single Nucleotide Polymorphisms--a Convenient and Rapid Method.

PubMed

Lager, Malin; Mernelius, Sara; Löfgren, Sture; Söderman, Jan

2016-01-01

Healthcare-associated infections caused by Escherichia coli and antibiotic resistance due to extended-spectrum beta-lactamase (ESBL) production constitute a threat against patient safety. To identify, track, and control outbreaks and to detect emerging virulent clones, typing tools of sufficient discriminatory power that generate reproducible and unambiguous data are needed. A probe based real-time PCR method targeting multiple single nucleotide polymorphisms (SNP) was developed. The method was based on the multi locus sequence typing scheme of Institute Pasteur and by adaptation of previously described typing assays. An 8 SNP-panel that reached a Simpson's diversity index of 0.95 was established, based on analysis of sporadic E. coli cases (ESBL n = 27 and non-ESBL n = 53). This multi-SNP assay was used to identify the sequence type 131 (ST131) complex according to the Achtman's multi locus sequence typing scheme. However, it did not fully discriminate within the complex but provided a diagnostic signature that outperformed a previously described detection assay. Pulsed-field gel electrophoresis typing of isolates from a presumed outbreak (n = 22) identified two outbreaks (ST127 and ST131) and three different non-outbreak-related isolates. Multi-SNP typing generated congruent data except for one non-outbreak-related ST131 isolate. We consider multi-SNP real-time PCR typing an accessible primary generic E. coli typing tool for rapid and uniform type identification.

Subtyping Salmonella enterica serovar enteritidis isolates from different sources by using sequence typing based on virulence genes and clustered regularly interspaced short palindromic repeats (CRISPRs).

PubMed

Liu, Fenyun; Kariyawasam, Subhashinie; Jayarao, Bhushan M; Barrangou, Rodolphe; Gerner-Smidt, Peter; Ribot, Efrain M; Knabel, Stephen J; Dudley, Edward G

2011-07-01

Salmonella enterica subsp. enterica serovar Enteritidis is a major cause of food-borne salmonellosis in the United States. Two major food vehicles for S. Enteritidis are contaminated eggs and chicken meat. Improved subtyping methods are needed to accurately track specific strains of S. Enteritidis related to human salmonellosis throughout the chicken and egg food system. A sequence typing scheme based on virulence genes (fimH and sseL) and clustered regularly interspaced short palindromic repeats (CRISPRs)-CRISPR-including multi-virulence-locus sequence typing (designated CRISPR-MVLST)-was used to characterize 35 human clinical isolates, 46 chicken isolates, 24 egg isolates, and 63 hen house environment isolates of S. Enteritidis. A total of 27 sequence types (STs) were identified among the 167 isolates. CRISPR-MVLST identified three persistent and predominate STs circulating among U.S. human clinical isolates and chicken, egg, and hen house environmental isolates in Pennsylvania, and an ST that was found only in eggs and humans. It also identified a potential environment-specific sequence type. Moreover, cluster analysis based on fimH and sseL identified a number of clusters, of which several were found in more than one outbreak, as well as 11 singletons. Further research is needed to determine if CRISPR-MVLST might help identify the ecological origins of S. Enteritidis strains that contaminate chickens and eggs.

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.

PubMed

Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

2015-05-01

Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. ivan.borozan@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

PubMed Central

Borozan, Ivan; Watt, Stuart; Ferretti, Vincent

2015-01-01

Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized. Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences. Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html. Contact: ivan.borozan@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25573913

Ribosomal DNA intergenic spacer sequence in foxtail millet, Setaria italica (L.) P. Beauv. and its characterization and application to typing of foxtail millet landraces.

PubMed

Fukunaga, Kenji; Ichitani, Katsuyuki; Taura, Satoru; Sato, Muneharu; Kawase, Makoto

2005-02-01

We determined the sequence of ribosomal DNA (rDNA) intergenic spacer (IGS) of foxtail millet isolated in our previous study, and identified subrepeats in the polymorphic region. We also developed a PCR-based method for identifying rDNA types based on sequence information and assessed 153 accessions of foxtail millet. Results were congruent with our previous works. This study provides new findings regarding the geographical distribution of rDNA variants. This new method facilitates analyses of numerous foxtail millet accessions. It is helpful for typing of foxtail millet germplasms and elucidating the evolution of this millet.

Polymorphic amplified typing sequences (PATS) and pulsed-field gel electrophoresis (PFGE) yield comparable results in the strain typing of a diverse set of bovine Escherichia coli O157 isolates

USDA-ARS?s Scientific Manuscript database

The PCR-based Escherichia coli O157 (O157) strain typing system, Polymorphic Amplified Typing Sequences (PATS), targets insertions-deletions (Indels) and single nucleotide polymorphisms (SNPs) at the XbaI and AvrII(BlnI) restriction enzyme sites, respectively, besides amplifying four known virulenc...

Comparison of Three Different Hepatitis C Virus Genotyping Methods: 5'NCR PCR-RFLP, Core Type-Specific PCR, and NS5b Sequencing in a Tertiary Care Hospital in South India.

PubMed

Daniel, Hubert D-J; David, Joel; Raghuraman, Sukanya; Gnanamony, Manu; Chandy, George M; Sridharan, Gopalan; Abraham, Priya

2017-05-01

Based on genetic heterogeneity, hepatitis C virus (HCV) is classified into seven major genotypes and 64 subtypes. In spite of the sequence heterogeneity, all genotypes share an identical complement of colinear genes within the large open reading frame. The genetic interrelationships between these genes are consistent among genotypes. Due to this property, complete sequencing of the HCV genome is not required. HCV genotypes along with subtypes are critical for planning antiviral therapy. Certain genotypes are also associated with higher progression to liver cirrhosis. In this study, 100 blood samples were collected from individuals who came for routine HCV genotype identification. These samples were used for the comparison of two different genotyping methods (5'NCR PCR-RFLP and HCV core type-specific PCR) with NS5b sequencing. Of the 100 samples genotyped using 5'NCR PCR-RFLP and HCV core type-specific PCR, 90% (κ = 0.913, P < 0.00) and 96% (κ = 0.794, P < 0.00) correlated with NS5b sequencing, respectively. Sixty percent and 75% of discordant samples by 5'NCR PCR-RFLP and HCV core type-specific PCR, respectively, belonged to genotype 6. All the HCV genotype 1 subtypes were classified accurately by both the methods. This study shows that the 5'NCR-based PCR-RFLP and the HCV core type-specific PCR-based assays correctly identified HCV genotypes except genotype 6 from this region. Direct sequencing of the HCV core region was able to identify all the genotype 6 from this region and serves as an alternative to NS5b sequencing. © 2016 Wiley Periodicals, Inc.

Expression profile analysis of genes involved in horizontal gravitropism bending growth in the creeping shoots of ground-cover chrysanthemum by suppression subtractive hybridization.

PubMed

Xia, Shengjun; Chen, Yu; Jiang, Jiafu; Chen, Sumei; Guan, Zhiyong; Fang, Weimin; Chen, Fadi

2013-01-01

The molecular mechanisms underlying gravitropic bending of shoots are poorly understood and how genes related with this growing progress is still unclear. To identify genes related to asymmetric growth in the creeping shoots of chrysanthemum, suppression subtractive hybridization was used to visualize differential gene expression in the upper and lower halves of creeping shoots of ground-cover chrysanthemum under gravistimulation. Sequencing of 43 selected clones produced 41 unigenes (40 singletons and 1 unigenes), which were classifiable into 9 functional categories. A notable frequency of genes involve in cell wall biosynthesis up-regulated during gravistimulation in the upper side or lower side were found, such as beta tubulin (TUB), subtilisin-like protease (SBT), Glutathione S-transferase (GST), and expensing-like protein (EXP), lipid transfer proteins (LTPs), glycine-rich protein (GRP) and membrane proteins. Our findings also highlighted the function of some metal transporter during asymmetric growth, including the boron transporter (BT) and ZIP transporter (ZT), which were thought primarily for maintaining the integrity of cell walls and played important roles in cellulose biosynthesis. CmTUB (beta tubulin) was cloned, and the expression profile and phylogeny was examined, because the cytoskeleton of plant cells involved in the plant gravitropic bending growth is well known.

Noninvasive Prenatal Paternity Testing (NIPAT) through Maternal Plasma DNA Sequencing: A Pilot Study.

PubMed

Jiang, Haojun; Xie, Yifan; Li, Xuchao; Ge, Huijuan; Deng, Yongqiang; Mu, Haofang; Feng, Xiaoli; Yin, Lu; Du, Zhou; Chen, Fang; He, Nongyue

2016-01-01

Short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) have been already used to perform noninvasive prenatal paternity testing from maternal plasma DNA. The frequently used technologies were PCR followed by capillary electrophoresis and SNP typing array, respectively. Here, we developed a noninvasive prenatal paternity testing (NIPAT) based on SNP typing with maternal plasma DNA sequencing. We evaluated the influence factors (minor allele frequency (MAF), the number of total SNP, fetal fraction and effective sequencing depth) and designed three different selective SNP panels in order to verify the performance in clinical cases. Combining targeted deep sequencing of selective SNP and informative bioinformatics pipeline, we calculated the combined paternity index (CPI) of 17 cases to determine paternity. Sequencing-based NIPAT results fully agreed with invasive prenatal paternity test using STR multiplex system. Our study here proved that the maternal plasma DNA sequencing-based technology is feasible and accurate in determining paternity, which may provide an alternative in forensic application in the future.

Use of the LUS in sequence allele designations to facilitate probabilistic genotyping of NGS-based STR typing results.

PubMed

Just, Rebecca S; Irwin, Jodi A

2018-05-01

Some of the expected advantages of next generation sequencing (NGS) for short tandem repeat (STR) typing include enhanced mixture detection and genotype resolution via sequence variation among non-homologous alleles of the same length. However, at the same time that NGS methods for forensic DNA typing have advanced in recent years, many caseworking laboratories have implemented or are transitioning to probabilistic genotyping to assist the interpretation of complex autosomal STR typing results. Current probabilistic software programs are designed for length-based data, and were not intended to accommodate sequence strings as the product input. Yet to leverage the benefits of NGS for enhanced genotyping and mixture deconvolution, the sequence variation among same-length products must be utilized in some form. Here, we propose use of the longest uninterrupted stretch (LUS) in allele designations as a simple method to represent sequence variation within the STR repeat regions and facilitate - in the nearterm - probabilistic interpretation of NGS-based typing results. An examination of published population data indicated that a reference LUS region is straightforward to define for most autosomal STR loci, and that using repeat unit plus LUS length as the allele designator can represent greater than 80% of the alleles detected by sequencing. A proof of concept study performed using a freely available probabilistic software demonstrated that the LUS length can be used in allele designations when a program does not require alleles to be integers, and that utilizing sequence information improves interpretation of both single-source and mixed contributor STR typing results as compared to using repeat unit information alone. The LUS concept for allele designation maintains the repeat-based allele nomenclature that will permit backward compatibility to extant STR databases, and the LUS lengths themselves will be concordant regardless of the NGS assay or analysis tools employed. Further, these biologically based, easy-to-derive designations uphold clear relationships between parent alleles and their stutter products, enabling analysis in fully continuous probabilistic programs that model stutter while avoiding the algorithmic complexities that come with string based searches. Though using repeat unit plus LUS length as the allele designator does not capture variation that occurs outside of the core repeat regions, this straightforward approach would permit the large majority of known STR sequence variation to be used for mixture deconvolution and, in turn, result in more informative mixture statistics in the near term. Ultimately, the method could bridge the gap from current length-based probabilistic systems to facilitate broader adoption of NGS by forensic DNA testing laboratories. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Review and International Recommendation of Methods for Typing Neisseria gonorrhoeae Isolates and Their Implications for Improved Knowledge of Gonococcal Epidemiology, Treatment, and Biology

PubMed Central

Unemo, Magnus; Dillon, Jo-Anne R.

2011-01-01

Summary: Gonorrhea, which may become untreatable due to multiple resistance to available antibiotics, remains a public health problem worldwide. Precise methods for typing Neisseria gonorrhoeae, together with epidemiological information, are crucial for an enhanced understanding regarding issues involving epidemiology, test of cure and contact tracing, identifying core groups and risk behaviors, and recommending effective antimicrobial treatment, control, and preventive measures. This review evaluates methods for typing N. gonorrhoeae isolates and recommends various methods for different situations. Phenotypic typing methods, as well as some now-outdated DNA-based methods, have limited usefulness in differentiating between strains of N. gonorrhoeae. Genotypic methods based on DNA sequencing are preferred, and the selection of the appropriate genotypic method should be guided by its performance characteristics and whether short-term epidemiology (microepidemiology) or long-term and/or global epidemiology (macroepidemiology) matters are being investigated. Currently, for microepidemiological questions, the best methods for fast, objective, portable, highly discriminatory, reproducible, typeable, and high-throughput characterization are N. gonorrhoeae multiantigen sequence typing (NG-MAST) or full- or extended-length porB gene sequencing. However, pulsed-field gel electrophoresis (PFGE) and Opa typing can be valuable in specific situations, i.e., extreme microepidemiology, despite their limitations. For macroepidemiological studies and phylogenetic studies, DNA sequencing of chromosomal housekeeping genes, such as multilocus sequence typing (MLST), provides a more nuanced understanding. PMID:21734242

Enantiospecific recognition of DNA sequences by a proflavine Tröger base.

PubMed

Bailly, C; Laine, W; Demeunynck, M; Lhomme, J

2000-07-05

The DNA interaction of a chiral Tröger base derived from proflavine was investigated by DNA melting temperature measurements and complementary biochemical assays. DNase I footprinting experiments demonstrate that the binding of the proflavine-based Tröger base is both enantio- and sequence-specific. The (+)-isomer poorly interacts with DNA in a non-sequence-selective fashion. In sharp contrast, the corresponding (-)-isomer recognizes preferentially certain DNA sequences containing both A. T and G. C base pairs, such as the motifs 5'-GTT. AAC and 5'-ATGA. TCAT. This is the first experimental demonstration that acridine-type Tröger bases can be used for enantiospecific recognition of DNA sequences. Copyright 2000 Academic Press.

spa typing for epidemiological surveillance of Staphylococcus aureus.

PubMed

Hallin, Marie; Friedrich, Alexander W; Struelens, Marc J

2009-01-01

The spa typing method is based on sequencing of the polymorphic X region of the protein A gene (spa), present in all strains of Staphylococcus aureus. The X region is constituted of a variable number of 24-bp repeats flanked by well-conserved regions. This single-locus sequence-based typing method combines a number of technical advantages, such as rapidity, reproducibility, and portability. Moreover, due to its repeat structure, the spa locus simultaneously indexes micro- and macrovariations, enabling the use of spa typing in both local and global epidemiological studies. These studies are facilitated by the establishment of standardized spa type nomenclature and Internet shared databases.

Amplicon Sequencing of the slpH Locus Permits Culture-Independent Strain Typing of Lactobacillus helveticus in Dairy Products

PubMed Central

Moser, Aline; Wüthrich, Daniel; Bruggmann, Rémy; Eugster-Meier, Elisabeth; Meile, Leo; Irmler, Stefan

2017-01-01

The advent of massive parallel sequencing technologies has opened up possibilities for the study of the bacterial diversity of ecosystems without the need for enrichment or single strain isolation. By exploiting 78 genome data-sets from Lactobacillus helveticus strains, we found that the slpH locus that encodes a putative surface layer protein displays sufficient genetic heterogeneity to be a suitable target for strain typing. Based on high-throughput slpH gene sequencing and the detection of single-base DNA sequence variations, we established a culture-independent method to assess the biodiversity of the L. helveticus strains present in fermented dairy food. When we applied the method to study the L. helveticus strain composition in 15 natural whey cultures (NWCs) that were collected at different Gruyère, a protected designation of origin (PDO) production facilities, we detected a total of 10 sequence types (STs). In addition, we monitored the development of a three-strain mix in raclette cheese for 17 weeks. PMID:28775722

Molecular and phylogenetic characterizations of an Eimeria krijgsmanni Yakimoff & Gouseff, 1938 (Apicomplexa: Eimeriidae) mouse intestinal protozoan parasite by partial 18S ribosomal RNA gene sequence analysis.

PubMed

Takeo, Toshinori; Tanaka, Tetsuya; Matsubayashi, Makoto; Maeda, Hiroki; Kusakisako, Kodai; Matsui, Toshihiro; Mochizuki, Masami; Matsuo, Tomohide

2014-08-01

Previously, we characterized an undocumented strain of Eimeria krijgsmanni by morphological and biological features. Here, we present a detailed molecular phylogenetic analysis of this organism. Namely, 18S ribosomal RNA gene (rDNA) sequences of E. krijgsmanni were analyzed to incorporate this species into a comprehensive Eimeria phylogeny. As a result, partial 18S rDNA sequence from E. krijgsmanni was successfully determined, and two different types, Type A and Type B, that differed by 1 base pair were identified. E. krijgsmanni was originally isolated from a single oocyst, and thus the result show that the two types might have allelic sequence heterogeneity in the 18S rDNA. Based on phylogenetic analyses, the two types of E. krijgsmanni 18S rDNA formed one of two clades among murine Eimeria spp.; these Eimeria clades reflected morphological similarity among the Eimeria spp. This is the third molecular phylogenetic characterization of a murine Eimeria spp. in addition to E. falciformis and E. papillata. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Metal Organic Chemical Vapor Deposition of Oxide Films for Advanced Applications

DTIC Science & Technology

2000-06-01

coatings , photovoltaics, touch sensitive controls, electromagnetic shielding (as found on microwave ovens and stealth fighters), static dissipaters, and so...depositing high quality films. The methods are physical vapor deposition ( PVD ), spin/mist deposition, (CVD), and alternating layer (AL) CVD. PVD ...PZT & SBT, YBa2Cu3O, CeO, InO, TCOs, Varistors Ta2O5 , ZrO, MnO, HfO, CeO, MnO, MgO SAW/microwave Silicon/: Si, SiGe, SiGeC, �. Opto-electronics

High-Resolution Melting Analysis for Rapid Detection of Sequence Type 131 Escherichia coli.

PubMed

Harrison, Lucas B; Hanson, Nancy D

2017-06-01

Escherichia coli isolates belonging to the sequence type 131 (ST131) clonal complex have been associated with the global distribution of fluoroquinolone and β-lactam resistance. Whole-genome sequencing and multilocus sequence typing identify sequence type but are expensive when evaluating large numbers of samples. This study was designed to develop a cost-effective screening tool using high-resolution melting (HRM) analysis to differentiate ST131 from non-ST131 E. coli in large sample populations in the absence of sequence analysis. The method was optimized using DNA from 12 E. coli isolates. Singleplex PCR was performed using 10 ng of DNA, Type-it HRM buffer, and multilocus sequence typing primers and was followed by multiplex PCR. The amplicon sizes ranged from 630 to 737 bp. Melt temperature peaks were determined by performing HRM analysis at 0.1°C resolution from 50 to 95°C on a Rotor-Gene Q 5-plex HRM system. Derivative melt curves were compared between sequence types and analyzed by principal component analysis. A blinded study of 191 E. coli isolates of ST131 and unknown sequence types validated this methodology. This methodology returned 99.2% specificity (124 true negatives and 1 false positive) and 100% sensitivity (66 true positives and 0 false negatives). This HRM methodology distinguishes ST131 from non-ST131 E. coli without sequence analysis. The analysis can be accomplished in about 3 h in any laboratory with an HRM-capable instrument and principal component analysis software. Therefore, this assay is a fast and cost-effective alternative to sequencing-based ST131 identification. Copyright © 2017 Harrison and Hanson.

The repeating nucleotide sequence in the repetitive mitochondrial DNA from a "low-density" petite mutant of yeast.

PubMed Central

Van Kreijl, C F; Bos, J L

1977-01-01

The repeating nucleotide sequence of 68 base pairs in the mtDNA from an ethidium-induced cytoplasmic petite mutant of yeast has been determined. For sequence analysis specifically primed and terminated RNA copies, obtained by in vitro transcription of the separated strands, were use. The sequence consists of 66 consecutive AT base pairs flanked by two GC pairs and comprises nearly all of the mutant mitochondrial genome. The sequence, moreover, also represents the first part of wild-type mtDNA sequence so far. Images PMID:198740

A novel HLA-B allele, B*5214, detected in a Taiwanese volunteer bone marrow donor using a sequence-based typing method.

PubMed

Chen, M J; Chu, C C; Shyr, M H; Lin, C L; Lin, P Y; Yang, K L

2010-02-01

HLA-B*5214, a novel rare allele of HLA-B*52 variant, was found in a Taiwanese volunteer bone marrow donor by sequence-based typing method. The sequence of B*5214 is identical to that of B*520101 in exon 2 but differs from B*520101 in exon 3 at nucleotide positions 419 A-->T and 435 A-->G. Alteration of these two nucleotides resulted an amino acid substitution at amino acid residue 116 Y-->F ( TAC-->TTC) and a silent exchange at residue 121 K-->K (AAA-->AAG).

Transcriptomic analysis of Siberian ginseng (Eleutherococcus senticosus) to discover genes involved in saponin biosynthesis.

PubMed

Hwang, Hwan-Su; Lee, Hyoshin; Choi, Yong Eui

2015-03-14

Eleutherococcus senticosus, Siberian ginseng, is a highly valued woody medicinal plant belonging to the family Araliaceae. E. senticosus produces a rich variety of saponins such as oleanane-type, noroleanane-type, 29-hydroxyoleanan-type, and lupane-type saponins. Genomic or transcriptomic approaches have not been used to investigate the saponin biosynthetic pathway in this plant. In this study, de novo sequencing was performed to select candidate genes involved in the saponin biosynthetic pathway. A half-plate 454 pyrosequencing run produced 627,923 high-quality reads with an average sequence length of 422 bases. De novo assembly generated 72,811 unique sequences, including 15,217 contigs and 57,594 singletons. Approximately 48,300 (66.3%) unique sequences were annotated using BLAST similarity searches. All of the mevalonate pathway genes for saponin biosynthesis starting from acetyl-CoA were isolated. Moreover, 206 reads of cytochrome P450 (CYP) and 145 reads of uridine diphosphate glycosyltransferase (UGT) sequences were isolated. Based on methyl jasmonate (MeJA) treatment and real-time PCR (qPCR) analysis, 3 CYPs and 3 UGTs were finally selected as candidate genes involved in the saponin biosynthetic pathway. The identified sequences associated with saponin biosynthesis will facilitate the study of the functional genomics of saponin biosynthesis and genetic engineering of E. senticosus.

Influence of laminate sequence and fabric type on the inherent acoustic nonlinearity in carbon fiber reinforced composites.

PubMed

Chakrapani, Sunil Kishore; Barnard, Daniel J; Dayal, Vinay

2016-05-01

This paper presents the study of influence of laminate sequence and fabric type on the baseline acoustic nonlinearity of fiber-reinforced composites. Nonlinear elastic wave techniques are increasingly becoming popular in detecting damage in composite materials. It was earlier observed by the authors that the non-classical nonlinear response of fiber-reinforced composite is influenced by the fiber orientation [Chakrapani, Barnard, and Dayal, J. Acoust. Soc. Am. 137(2), 617-624 (2015)]. The current study expands this effort to investigate the effect of laminate sequence and fabric type on the non-classical nonlinear response. Two hypotheses were developed using the previous results, and the theory of interlaminar stresses to investigate the influence of laminate sequence and fabric type. Each hypothesis was tested by capturing the nonlinear response by performing nonlinear resonance spectroscopy and measuring frequency shifts, loss factors, and higher harmonics. It was observed that the laminate sequence can either increase or decrease the nonlinear response based on the stacking sequence. Similarly, tests were performed to compare unidirectional fabric and woven fabric and it was observed that woven fabric exhibited a lower nonlinear response compared to the unidirectional fabric. Conjectures based on the matrix properties and interlaminar stresses were used in an attempt to explain the observed nonlinear responses for different configurations.

Transforming BIM to BEM: Generation of Building Geometry for the NASA Ames Sustainability Base BIM

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Donnell, James T.; Maile, Tobias; Rose, Cody

Typical processes of whole Building Energy simulation Model (BEM) generation are subjective, labor intensive, time intensive and error prone. Essentially, these typical processes reproduce already existing data, i.e. building models already created by the architect. Accordingly, Lawrence Berkeley National Laboratory (LBNL) developed a semi-automated process that enables reproducible conversions of Building Information Model (BIM) representations of building geometry into a format required by building energy modeling (BEM) tools. This is a generic process that may be applied to all building energy modeling tools but to date has only been used for EnergyPlus. This report describes and demonstrates each stage inmore » the semi-automated process for building geometry using the recently constructed NASA Ames Sustainability Base throughout. This example uses ArchiCAD (Graphisoft, 2012) as the originating CAD tool and EnergyPlus as the concluding whole building energy simulation tool. It is important to note that the process is also applicable for professionals that use other CAD tools such as Revit (“Revit Architecture,” 2012) and DProfiler (Beck Technology, 2012) and can be extended to provide geometry definitions for BEM tools other than EnergyPlus. Geometry Simplification Tool (GST) was used during the NASA Ames project and was the enabling software that facilitated semi-automated data transformations. GST has now been superseded by Space Boundary Tool (SBT-1) and will be referred to as SBT-1 throughout this report. The benefits of this semi-automated process are fourfold: 1) reduce the amount of time and cost required to develop a whole building energy simulation model, 2) enable rapid generation of design alternatives, 3) improve the accuracy of BEMs and 4) result in significantly better performing buildings with significantly lower energy consumption than those created using the traditional design process, especially if the simulation model was used as a predictive benchmark during operation. Developing BIM based criteria to support the semi-automated process should result in significant reliable improvements and time savings in the development of BEMs. In order to define successful BIMS, CAD export of IFC based BIMs for BEM must adhere to a standard Model View Definition (MVD) for simulation as provided by the concept design BIM MVD (buildingSMART, 2011). In order to ensure wide scale adoption, companies would also need to develop their own material libraries to support automated activities and undertake a pilot project to improve understanding of modeling conventions and design tool features and limitations.« less

SeqRate: sequence-based protein folding type classification and rates prediction

PubMed Central

2010-01-01

Background Protein folding rate is an important property of a protein. Predicting protein folding rate is useful for understanding protein folding process and guiding protein design. Most previous methods of predicting protein folding rate require the tertiary structure of a protein as an input. And most methods do not distinguish the different kinetic nature (two-state folding or multi-state folding) of the proteins. Here we developed a method, SeqRate, to predict both protein folding kinetic type (two-state versus multi-state) and real-value folding rate using sequence length, amino acid composition, contact order, contact number, and secondary structure information predicted from only protein sequence with support vector machines. Results We systematically studied the contributions of individual features to folding rate prediction. On a standard benchmark dataset, the accuracy of folding kinetic type classification is 80%. The Pearson correlation coefficient and the mean absolute difference between predicted and experimental folding rates (sec-1) in the base-10 logarithmic scale are 0.81 and 0.79 for two-state protein folders, and 0.80 and 0.68 for three-state protein folders. SeqRate is the first sequence-based method for protein folding type classification and its accuracy of fold rate prediction is improved over previous sequence-based methods. Its performance can be further enhanced with additional information, such as structure-based geometric contacts, as inputs. Conclusions Both the web server and software of predicting folding rate are publicly available at http://casp.rnet.missouri.edu/fold_rate/index.html. PMID:20438647

Multilocus sequence typing reveals a novel subspeciation of Lactobacillus delbrueckii.

PubMed

Tanigawa, Kana; Watanabe, Koichi

2011-03-01

Currently, the species Lactobacillus delbrueckii is divided into four subspecies, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. indicus and L. delbrueckii subsp. lactis. These classifications were based mainly on phenotypic identification methods and few studies have used genotypic identification methods. As a result, these subspecies have not yet been reliably delineated. In this study, the four subspecies of L. delbrueckii were discriminated by phenotype and by genotypic identification [amplified-fragment length polymorphism (AFLP) and multilocus sequence typing (MLST)] methods. The MLST method developed here was based on the analysis of seven housekeeping genes (fusA, gyrB, hsp60, ileS, pyrG, recA and recG). The MLST method had good discriminatory ability: the 41 strains of L. delbrueckii examined were divided into 34 sequence types, with 29 sequence types represented by only a single strain. The sequence types were divided into eight groups. These groups could be discriminated as representing different subspecies. The results of the AFLP and MLST analyses were consistent. The type strain of L. delbrueckii subsp. delbrueckii, YIT 0080(T), was clearly discriminated from the other strains currently classified as members of this subspecies, which were located close to strains of L. delbrueckii subsp. lactis. The MLST scheme developed in this study should be a useful tool for the identification of strains of L. delbrueckii to the subspecies level.

Type III restriction-modification enzymes: a historical perspective.

PubMed

Rao, Desirazu N; Dryden, David T F; Bheemanaik, Shivakumara

2014-01-01

Restriction endonucleases interact with DNA at specific sites leading to cleavage of DNA. Bacterial DNA is protected from restriction endonuclease cleavage by modifying the DNA using a DNA methyltransferase. Based on their molecular structure, sequence recognition, cleavage position and cofactor requirements, restriction-modification (R-M) systems are classified into four groups. Type III R-M enzymes need to interact with two separate unmethylated DNA sequences in inversely repeated head-to-head orientations for efficient cleavage to occur at a defined location (25-27 bp downstream of one of the recognition sites). Like the Type I R-M enzymes, Type III R-M enzymes possess a sequence-specific ATPase activity for DNA cleavage. ATP hydrolysis is required for the long-distance communication between the sites before cleavage. Different models, based on 1D diffusion and/or 3D-DNA looping, exist to explain how the long-distance interaction between the two recognition sites takes place. Type III R-M systems are found in most sequenced bacteria. Genome sequencing of many pathogenic bacteria also shows the presence of a number of phase-variable Type III R-M systems, which play a role in virulence. A growing number of these enzymes are being subjected to biochemical and genetic studies, which, when combined with ongoing structural analyses, promise to provide details for mechanisms of DNA recognition and catalysis.

The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies.

PubMed

Yoshida, Catherine E; Kruczkiewicz, Peter; Laing, Chad R; Lingohr, Erika J; Gannon, Victor P J; Nash, John H E; Taboada, Eduardo N

2016-01-01

For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub-typing allows for continuity with historical serotyping data as we transition towards the increasing adoption of genomic analyses in epidemiology. The SISTR platform is freely available on the web at https://lfz.corefacility.ca/sistr-app/.

Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types

PubMed Central

McIntyre, Chloe L.; Knowles, Nick J.

2013-01-01

Human rhinoviruses (HRVs) frequently cause mild upper respiratory tract infections and more severe disease manifestations such as bronchiolitis and asthma exacerbations. HRV is classified into three species within the genus Enterovirus of the family Picornaviridae. HRV species A and B contain 75 and 25 serotypes identified by cross-neutralization assays, although the use of such assays for routine HRV typing is hampered by the large number of serotypes, replacement of virus isolation by molecular methods in HRV diagnosis and the poor or absent replication of HRV species C in cell culture. To address these problems, we propose an alternative, genotypic classification of HRV-based genetic relatedness analogous to that used for enteroviruses. Nucleotide distances between 384 complete VP1 sequences of currently assigned HRV (sero)types identified divergence thresholds of 13, 12 and 13 % for species A, B and C, respectively, that divided inter- and intra-type comparisons. These were paralleled by 10, 9.5 and 10 % thresholds in the larger dataset of >3800 VP4 region sequences. Assignments based on VP1 sequences led to minor revisions of existing type designations (such as the reclassification of serotype pairs, e.g. A8/A95 and A29/A44, as single serotypes) and the designation of new HRV types A101–106, B101–103 and C34–C51. A protocol for assignment and numbering of new HRV types using VP1 sequences and the restriction of VP4 sequence comparisons to type identification and provisional type assignments is proposed. Genotypic assignment and identification of HRV types will be of considerable value in the future investigation of type-associated differences in disease outcomes, transmission and epidemiology. PMID:23677786

Experimental Characterisation of a Pulse Tube Cryocooler for Ground Applications

NASA Astrophysics Data System (ADS)

Charles, I.; Duband, L.; Martin, J.-Y.; Mullié, J. C.; Bruins, P. C.

2004-06-01

Developments on high frequency high heat lift pulse tubes are carried out at CEA/SBT. Based on a previous study on an in line configuration, two new pulse tube cold fingers have been manufactured: a coaxial configuration and a U-shape configuration. Measurements performed with the coaxial configuration have demonstrated cooling power in excess of 6 W at 80 K with 140 W of mechanical input power. The results obtained with these two configurations are presented. The impact of the rejection temperature has also been studied and is discussed. In parallel, a new compressor with pistons supported by flexure bearings has been designed and manufactured. This compressor has been coupled with the pulse tube. Tests performed with the new developed flexure-bearing compressors and a conventional compressor are presented and compared. The pulse tube cold finger associated with the new compressor leads to a reliable and low vibration cooler.

Optimizing Decision Preparedness by Adapting Scenario Complexity and Automating Scenario Generation

NASA Technical Reports Server (NTRS)

Dunne, Rob; Schatz, Sae; Flore, Stephen M.; Nicholson, Denise

2011-01-01

Klein's recognition-primed decision (RPD) framework proposes that experts make decisions by recognizing similarities between current decision situations and previous decision experiences. Unfortunately, military personnel arQ often presented with situations that they have not experienced before. Scenario-based training (S8T) can help mitigate this gap. However, SBT remains a challenging and inefficient training approach. To address these limitations, the authors present an innovative formulation of scenario complexity that contributes to the larger research goal of developing an automated scenario generation system. This system will enable trainees to effectively advance through a variety of increasingly complex decision situations and experiences. By adapting scenario complexities and automating generation, trainees will be provided with a greater variety of appropriately calibrated training events, thus broadening their repositories of experience. Preliminary results from empirical testing (N=24) of the proof-of-concept formula are presented, and future avenues of scenario complexity research are also discussed.

Comparative performance of high-density oligonucleotide sequencing and dideoxynucleotide sequencing of HIV type 1 pol from clinical samples.

PubMed

Günthard, H F; Wong, J K; Ignacio, C C; Havlir, D V; Richman, D D

1998-07-01

The performance of the high-density oligonucleotide array methodology (GeneChip) in detecting drug resistance mutations in HIV-1 pol was compared with that of automated dideoxynucleotide sequencing (ABI) of clinical samples, viral stocks, and plasmid-derived NL4-3 clones. Sequences from 29 clinical samples (plasma RNA, n = 17; lymph node RNA, n = 5; lymph node DNA, n = 7) from 12 patients, from 6 viral stock RNA samples, and from 13 NL4-3 clones were generated by both methods. Editing was done independently by a different investigator for each method before comparing the sequences. In addition, NL4-3 wild type (WT) and mutants were mixed in varying concentrations and sequenced by both methods. Overall, a concordance of 99.1% was found for a total of 30,865 bases compared. The comparison of clinical samples (plasma RNA and lymph node RNA and DNA) showed a slightly lower match of base calls, 98.8% for 19,831 nucleotides compared (protease region, 99.5%, n = 8272; RT region, 98.3%, n = 11,316), than for viral stocks and NL4-3 clones (protease region, 99.8%; RT region, 99.5%). Artificial mixing experiments showed a bias toward calling wild-type bases by GeneChip. Discordant base calls are most likely due to differential detection of mixtures. The concordance between GeneChip and ABI was high and appeared dependent on the nature of the templates (directly amplified versus cloned) and the complexity of mixes.

Cost-effectiveness of targeted and tailored interventions on colorectal cancer screening use.

PubMed

Lairson, David R; DiCarlo, Melissa; Myers, Ronald E; Wolf, Thomas; Cocroft, James; Sifri, Randa; Rosenthal, Michael; Vernon, Sally W; Wender, Richard

2008-02-15

Colorectal cancer (CRC) screening is cost-effective but underused. The objective of this study was to determine the cost-effectiveness of targeted and tailored behavioral interventions to increase CRC screening use by conducting an economic analysis associated with a randomized trial among patients in a large, racially and ethnically diverse, urban family practice in Philadelphia. The incremental costs per unit increase were measured in individuals who were screened during the 24 months after intervention. Percent increase in screening was adjusted for baseline differences in the study groups. Each intervention arm received a targeted screening invitation letter, stool blood test (SBT) cards, informational booklet, and reminder letter. Tailored interventions incrementally added tailored messages and reminder telephone calls. Program costs of the targeted intervention were 42 dollars per participant. Additional costs of adding tailored print materials and of delivering a reminder telephone call were 150 dollars and 200 dollars per participant, respectively. The cost per additional individual screened was 319 dollars when comparing the no intervention group with the targeted intervention group. The targeted intervention was more effective and less costly than the tailored intervention. Although tailoring plus reminder telephone call was the most effective strategy, it was very costly per additional individual screened. Mailed SBT cards significantly boosted CRC screening use. However, going beyond the targeted intervention to include tailoring or tailoring plus reminder calls in the manner used in this study did not appear to be an economically attractive strategy. Cancer 2008. (c) 2007 American Cancer Society.

NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.

PubMed

Lee, Sejoon; Lee, Soohyun; Ouellette, Scott; Park, Woong-Yang; Lee, Eunjung A; Park, Peter J

2017-06-20

In many next-generation sequencing (NGS) studies, multiple samples or data types are profiled for each individual. An important quality control (QC) step in these studies is to ensure that datasets from the same subject are properly paired. Given the heterogeneity of data types, file types and sequencing depths in a multi-dimensional study, a robust program that provides a standardized metric for genotype comparisons would be useful. Here, we describe NGSCheckMate, a user-friendly software package for verifying sample identities from FASTQ, BAM or VCF files. This tool uses a model-based method to compare allele read fractions at known single-nucleotide polymorphisms, considering depth-dependent behavior of similarity metrics for identical and unrelated samples. Our evaluation shows that NGSCheckMate is effective for a variety of data types, including exome sequencing, whole-genome sequencing, RNA-seq, ChIP-seq, targeted sequencing and single-cell whole-genome sequencing, with a minimal requirement for sequencing depth (>0.5X). An alignment-free module can be run directly on FASTQ files for a quick initial check. We recommend using this software as a QC step in NGS studies. https://github.com/parklab/NGSCheckMate. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Multi-Virulence-Locus Sequence Typing of Staphylococcus lugdunensis Generates Results Consistent with a Clonal Population Structure and Is Reliable for Epidemiological Typing

PubMed Central

Didi, Jennifer; Lemée, Ludovic; Gibert, Laure; Pons, Jean-Louis

2014-01-01

Staphylococcus lugdunensis is an emergent virulent coagulase-negative staphylococcus responsible for severe infections similar to those caused by Staphylococcus aureus. To understand its potentially pathogenic capacity and have further detailed knowledge of the molecular traits of this organism, 93 isolates from various geographic origins were analyzed by multi-virulence-locus sequence typing (MVLST), targeting seven known or putative virulence-associated loci (atlLR2, atlLR3, hlb, isdJ, SLUG_09050, SLUG_16930, and vwbl). The polymorphisms of the putative virulence-associated loci were moderate and comparable to those of the housekeeping genes analyzed by multilocus sequence typing (MLST). However, the MVLST scheme generated 43 virulence types (VTs) compared to 20 sequence types (STs) based on MLST, indicating that MVLST was significantly more discriminating (Simpson's index [D], 0.943). No hypervirulent lineage or cluster specific to carriage strains was defined. The results of multilocus sequence analysis of known and putative virulence-associated loci are consistent with a clonal population structure for S. lugdunensis, suggesting a coevolution of these genes with housekeeping genes. Indeed, the nonsynonymous to synonymous evolutionary substitutions (dN/dS) ratio, the Tajima's D test, and Single-likelihood ancestor counting (SLAC) analysis suggest that all virulence-associated loci were under negative selection, even atlLR2 (AtlL protein) and SLUG_16930 (FbpA homologue), for which the dN/dS ratios were higher. In addition, this analysis of virulence-associated loci allowed us to propose a trilocus sequence typing scheme based on the intragenic regions of atlLR3, isdJ, and SLUG_16930, which is more discriminant than MLST for studying short-term epidemiology and further characterizing the lineages of the rare but highly pathogenic S. lugdunensis. PMID:25078912

The multilocus sequence typing network: mlst.net.

PubMed

Aanensen, David M; Spratt, Brian G

2005-07-01

The unambiguous characterization of strains of a pathogen is crucial for addressing questions relating to its epidemiology, population and evolutionary biology. Multilocus sequence typing (MLST), which defines strains from the sequences at seven house-keeping loci, has become the method of choice for molecular typing of many bacterial and fungal pathogens (and non-pathogens), and MLST schemes and strain databases are available for a growing number of prokaryotic and eukaryotic organisms. Sequence data are ideal for strain characterization as they are unambiguous, meaning strains can readily be compared between laboratories via the Internet. Laboratories undertaking MLST can quickly progress from sequencing the seven gene fragments to characterizing their strains and relating them to those submitted by others and to the population as a whole. We provide the gateway to a number of MLST schemes, each of which contain a set of tools for the initial characterization of strains, and methods for relating query strains to other strains of the species, including clustering based on differences in allelic profiles, phylogenetic trees based on concatenated sequences, and a recently developed method (eBURST) for identifying clonal complexes within a species and displaying the overall structure of the population. This network of MLST websites is available at http://www.mlst.net.

Structural and sequence features of two residue turns in beta-hairpins.

PubMed

Madan, Bharat; Seo, Sung Yong; Lee, Sun-Gu

2014-09-01

Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences. © 2014 Wiley Periodicals, Inc.

Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance, a Novel Antimicrobial Resistance Multilocus Typing Scheme for Tracking Global Dissemination of N. gonorrhoeae Strains.

PubMed

Demczuk, W; Sidhu, S; Unemo, M; Whiley, D M; Allen, V G; Dillon, J R; Cole, M; Seah, C; Trembizki, E; Trees, D L; Kersh, E N; Abrams, A J; de Vries, H J C; van Dam, A P; Medina, I; Bharat, A; Mulvey, M R; Van Domselaar, G; Martin, I

2017-05-01

A curated Web-based user-friendly sequence typing tool based on antimicrobial resistance determinants in Neisseria gonorrhoeae was developed and is publicly accessible (https://ngstar.canada.ca). The N. gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR) molecular typing scheme uses the DNA sequences of 7 genes ( penA , mtrR , porB , ponA , gyrA , parC , and 23S rRNA) associated with resistance to β-lactam antimicrobials, macrolides, or fluoroquinolones. NG-STAR uses the entire penA sequence, combining the historical nomenclature for penA types I to XXXVIII with novel nucleotide sequence designations; the full mtrR sequence and a portion of its promoter region; portions of ponA , porB , gyrA , and parC ; and 23S rRNA sequences. NG-STAR grouped 768 isolates into 139 sequence types (STs) ( n = 660) consisting of 29 clonal complexes (CCs) having a maximum of a single-locus variation, and 76 NG-STAR STs ( n = 109) were identified as unrelated singletons. NG-STAR had a high Simpson's diversity index value of 96.5% (95% confidence interval [CI] = 0.959 to 0.969). The most common STs were NG-STAR ST-90 ( n = 100; 13.0%), ST-42 and ST-91 ( n = 45; 5.9%), ST-64 ( n = 44; 5.72%), and ST-139 ( n = 42; 5.5%). Decreased susceptibility to azithromycin was associated with NG-STAR ST-58, ST-61, ST-64, ST-79, ST-91, and ST-139 ( n = 156; 92.3%); decreased susceptibility to cephalosporins was associated with NG-STAR ST-90, ST-91, and ST-97 ( n = 162; 94.2%); and ciprofloxacin resistance was associated with NG-STAR ST-26, ST-90, ST-91, ST-97, ST-150, and ST-158 ( n = 196; 98.0%). All isolates of NG-STAR ST-42, ST-43, ST-63, ST-81, and ST-160 ( n = 106) were susceptible to all four antimicrobials. The standardization of nomenclature associated with antimicrobial resistance determinants through an internationally available database will facilitate the monitoring of the global dissemination of antimicrobial-resistant N. gonorrhoeae strains. © Crown copyright 2017.

BrucellaBase: Genome information resource.

PubMed

Sankarasubramanian, Jagadesan; Vishnu, Udayakumar S; Khader, L K M Abdul; Sridhar, Jayavel; Gunasekaran, Paramasamy; Rajendhran, Jeyaprakash

2016-09-01

Brucella sp. causes a major zoonotic disease, brucellosis. Brucella belongs to the family Brucellaceae under the order Rhizobiales of Alphaproteobacteria. We present BrucellaBase, a web-based platform, providing features of a genome database together with unique analysis tools. We have developed a web version of the multilocus sequence typing (MLST) (Whatmore et al., 2007) and phylogenetic analysis of Brucella spp. BrucellaBase currently contains genome data of 510 Brucella strains along with the user interfaces for BLAST, VFDB, CARD, pairwise genome alignment and MLST typing. Availability of these tools will enable the researchers interested in Brucella to get meaningful information from Brucella genome sequences. BrucellaBase will regularly be updated with new genome sequences, new features along with improvements in genome annotations. BrucellaBase is available online at http://www.dbtbrucellosis.in/brucellabase.html or http://59.99.226.203/brucellabase/homepage.html. Copyright © 2016 Elsevier B.V. All rights reserved.

The spa typing of methicillin-resistant Staphylococcus aureus isolates by High Resolution Melting (HRM) analysis.

PubMed

Fasihi, Yasser; Fooladi, Saba; Mohammadi, Mohammad Ali; Emaneini, Mohammad; Kalantar-Neyestanaki, Davood

2017-09-06

Molecular typing is an important tool for control and prevention of infection. A suitable molecular typing method for epidemiological investigation must be easy to perform, highly reproducible, inexpensive, rapid and easy to interpret. In this study, two molecular typing methods including the conventional PCR-sequencing method and high resolution melting (HRM) analysis were used for staphylococcal protein A (spa) typing of 30 Methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered from clinical samples. Based on PCR-sequencing method results, 16 different spa types were identified among the 30 MRSA isolates. Among the 16 different spa types, 14 spa types separated by HRM method. Two spa types including t4718 and t2894 were not separated from each other. According to our results, spa typing based on HRM analysis method is very rapid, easy to perform and cost-effective, but this method must be standardized for different regions, spa types, and real-time machinery.

The complete genome sequence of human adenovirus 84, a highly recombinant new Human mastadenovirus D type with a unique fiber gene.

PubMed

Kaján, Győző L; Kajon, Adriana E; Pinto, Alexis Castillo; Bartha, Dániel; Arnberg, Niklas

2017-10-15

A novel human adenovirus was isolated from a pediatric case of acute respiratory disease in Panama City, Panama in 2011. The clinical isolate was initially identified as an intertypic recombinant based on hexon and fiber gene sequencing. Based on the analysis of its complete genome sequence, the novel complex recombinant Human mastadenovirus D (HAdV-D) strain was classified into a new HAdV type: HAdV-84, and it was designated Adenovirus D human/PAN/P309886/2011/84[P43H17F84]. HAdV-D types possess usually an ocular or gastrointestinal tropism, and respiratory association is scarcely reported. The virus has a novel fiber type, most closely related to, but still clearly distant from that of HAdV-36. The predicted fiber is hypothesised to bind sialic acid with lower affinity compared to HAdV-37. Bioinformatic analysis of the complete genomic sequence of HAdV-84 revealed multiple homologous recombination events and provided deeper insight into HAdV evolution. Copyright © 2017 Elsevier B.V. All rights reserved.

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

PubMed Central

Robins-Browne, Roy M.; Holt, Kathryn E.; Ingle, Danielle J.; Hocking, Dianna M.; Yang, Ji; Tauschek, Marija

2016-01-01

The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtype E.coli, including biotyping, serotyping, and pathotyping. These schemes have proved invaluable in identifying and tracking outbreaks, and for prognostication in individual cases of infection, but they are imprecise and potentially misleading due to the malleability and continuous evolution of E. coli. Whole genome sequencing can be used to accurately determine E. coli subtypes that are based on allelic variation or differences in gene content, such as serotyping and pathotyping. Whole genome sequencing also provides information about single nucleotide polymorphisms in the core genome of E. coli, which form the basis of sequence typing, and is more reliable than other systems for tracking the evolution and spread of individual strains. A typing scheme for E. coli based on genome sequences that includes elements of both the core and accessory genomes, should reduce typing anomalies and promote understanding of how different varieties of E. coli spread and cause disease. Such a scheme could also define pathotypes more precisely than current methods. PMID:27917373

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

PubMed

Robins-Browne, Roy M; Holt, Kathryn E; Ingle, Danielle J; Hocking, Dianna M; Yang, Ji; Tauschek, Marija

2016-01-01

The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtype E .coli, including biotyping, serotyping, and pathotyping. These schemes have proved invaluable in identifying and tracking outbreaks, and for prognostication in individual cases of infection, but they are imprecise and potentially misleading due to the malleability and continuous evolution of E. coli . Whole genome sequencing can be used to accurately determine E. coli subtypes that are based on allelic variation or differences in gene content, such as serotyping and pathotyping. Whole genome sequencing also provides information about single nucleotide polymorphisms in the core genome of E. coli , which form the basis of sequence typing, and is more reliable than other systems for tracking the evolution and spread of individual strains. A typing scheme for E. coli based on genome sequences that includes elements of both the core and accessory genomes, should reduce typing anomalies and promote understanding of how different varieties of E. coli spread and cause disease. Such a scheme could also define pathotypes more precisely than current methods.

Core genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis.

PubMed

Cavanagh, Jorunn Pauline; Klingenberg, Claus; Hanssen, Anne-Merethe; Fredheim, Elizabeth Aarag; Francois, Patrice; Schrenzel, Jacques; Flægstad, Trond; Sollid, Johanna Ericson

2012-06-01

The notoriously multi-resistant Staphylococcus haemolyticus is an emerging pathogen causing serious infections in immunocompromised patients. Defining the population structure is important to detect outbreaks and spread of antimicrobial resistant clones. Currently, the standard typing technique is pulsed-field gel electrophoresis (PFGE). In this study we describe novel molecular typing schemes for S. haemolyticus using multi locus sequence typing (MLST) and multi locus variable number of tandem repeats (VNTR) analysis. Seven housekeeping genes (MLST) and five VNTR loci (MLVF) were selected for the novel typing schemes. A panel of 45 human and veterinary S. haemolyticus isolates was investigated. The collection had diverse PFGE patterns (38 PFGE types) and was sampled over a 20 year-period from eight countries. MLST resolved 17 sequence types (Simpsons index of diversity [SID]=0.877) and MLVF resolved 14 repeat types (SID=0.831). We found a low sequence diversity. Phylogenetic analysis clustered the isolates in three (MLST) and one (MLVF) clonal complexes, respectively. Taken together, neither the MLST nor the MLVF scheme was suitable to resolve the population structure of this S. haemolyticus collection. Future MLVF and MLST schemes will benefit from addition of more variable core genome sequences identified by comparing different fully sequenced S. haemolyticus genomes. Copyright © 2012 Elsevier B.V. All rights reserved.

Detection of cystic fibrosis mutations in a GeneChip{trademark} assay format

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miyada, C.G.; Cronin, M.T.; Kim, S.M.

1994-09-01

We are developing assays for the detection of cystic fibrosis mutations based on DNA hybridization. A DNA sample is amplified by PCR, labeled by incorporating a fluorescein-tagged dNTP, enzymatically treated to produce smaller fragments and hybridized to a series of short (13-16 bases) oligonucleotides synthesized on a glass surface via photolithography. The hybrids are detected by eqifluorescence and mutations are identified by the specific pattern of hybridization. In a GeneChip assay, the chip surface is composed of a series of subarrays, each being specific for a particular mutation. Each subarray is further subdivided into a series of probes (40 total),more » half based on the mutant sequence and the remainder based on the wild-type sequence. For each of the subarrays, there is a redundancy in the number of probes that should hybridize to either a wild-type or a mutant target. The multiple probe strategy provides sequence information for a short five base region overlapping the mutation site. In addition, homozygous wild-type and mutant as well as heterozygous samples are each identified by a specific pattern of hybridization. The small size of each probe feature (250 x 250 {mu}m{sup 2}) permits the inclusion of additional probes required to generate sequence information by hybridization.« less

Salmon Supplementation Studies in Idaho Rivers, 1996-1998 Progress Report.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reighn, Christopher A.; Lewis, Bert; Taki, Doug

1999-06-01

Information contained in this report summarizes the work that has been done by the Shoshone-Bannock Tribes Fisheries Department under BPA Project No. 89-098-3, Contract Number 92-BI-49450. Relevant data generated by the Shoshone-Bannock Tribe will be collated with other ISS cooperator data collected from the Salmon and Clearwater rivers and tributary streams. A summary of data presented in this report and an initial project-wide level supplementation evaluation will be available in the ISS 5 year report that is currently in progress. The Shoshone-Bannock Tribal Fisheries Department is responsible for monitoring a variety of chinook salmon (Oncorhynchus tshawytscha) production parameters as partmore » of the Idaho Supplementation Studies (BPA Project No. 89-098-3, Contract Number 92-BI-49450). Parameters include parr abundance in tributaries to the upper Salmon River; adult chinook salmon spawner abundance, redd counts, and carcass collection. A rotary screw trap is operated on the East Fork Salmon River and West Fork Yankee Fork Salmon River to enumerate and PIT-tag chinook smolts. These traps are also used to monitor parr movement, and collect individuals for the State and Tribal chinook salmon captive rearing program. The SBT monitors fisheries parameters in the following six tributaries of the Salmon River: Bear Valley Creek, East Fork Salmon River, Herd Creek, South Fork Salmon River, Valley Creek, and West Fork Yankee Fork. Chinook populations in all SBT-ISS monitored streams continue to decline. The South Fork Salmon River and Bear Valley Creek have the strongest remaining populations. Snorkel survey methodology was used to obtain parr population estimates for ISS streams from 1992 to 1997. Confidence intervals for the parr population estimates were large, especially when the populations were low. In 1998, based on ISS cooperator agreement, snorkeling to obtain parr population estimates was ceased due to the large confidence intervals. A rotary screw trap was operated on the West Fork Yankee Fork during the spring, summer, and fall of 1998 to monitor juvenile chinook migration. A screw trap was also operated on the East Fork of the Salmon River during the spring and fall from 1993 to 1997. Supplementation treatments have occurred on the South Fork Salmon River (IDFG), the East Fork Salmon River (EFSR), and the West Fork Yankee Fork of the Salmon River (WFYF). The EFSR received supplementation treatments yearly through 1995. There have been no treatments since 1995, and no significant future treatments from local broodstock are planned due to extremely poor escapement. The WFYF received a single presmolt treatment in 1994. There was an egg and adult release treatment in 1998 from the captive rearing program, not part of the original ISS study. Similarly, no significant future treatments are planned for the West Fork Yankee Fork due to extremely poor escapement. However, small scale experimental captive rearing and broodstock techniques are currently being tested with populations from the EFSR and WFYF. Captive rearing/broodstock techniques could potentially provide feedback for evaluation of supplementation. The other three SBT-ISS streams are control streams and do not receive supplementation treatments.« less

Massively parallel pyrosequencing of the mitochondrial genome with the 454 methodology in forensic genetics.

PubMed

Mikkelsen, Martin; Frank-Hansen, Rune; Hansen, Anders J; Morling, Niels

2014-09-01

of sequencing of whole mitochondrial genome, HV1 and HV2 DNA with the second generation system (SGS) Roche 454 GS Junior were compared with results of Sanger sequencing and SNP typing with SNaPshot single base extension detected with MALDI-TOF and capillary electrophoresis. We investigated the performance of the software analysis of the data, reproducibility, ability to sequence homopolymeric regions, detection of mixtures and heteroplasmy as well as the implications of the depth of coverage. We found full reproducibility between samples sequenced twice with SGS. We found close to full concordance between the mtDNA sequences of 26 samples obtained with (1) the 454 SGS method using a depth of coverage above 100 and (2) Sanger sequencing and SNP typing. The discrepancies were primarily observed in homopolymeric regions. The 454 SGS method was able to sequence 95% of the reads correctly in homopolymers up to 4 bases, and up to 6 bases could be sequenced with similar success if the results were carefully, visually inspected. The 454 technology was able to detect mixtures or heteroplasmy of approximately 10%. We detected previously unreported heteroplasmy in the GM9947A component of the NIST human mitochondrial DNA SRM-2392 standard reference material. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Diversity of 16S rRNA genes of new Ehrlichia strains isolated from horses with clinical signs of Potomac horse fever.

PubMed

Wen, B; Rikihisa, Y; Fuerst, P A; Chaichanasiriwithaya, W

1995-04-01

Ehrlichia risticii is the causative agent of Potomac horse fever. Variations among the major antigens of different local E. risticii strains have been detected previously. To further assess genetic variability in this species or species complex, the sequences of the 16S rRNA genes of several isolates obtained from sick horses diagnosed as having Potomac horse fever were determined. The sequences of six isolates obtained from Ohio and three isolates obtained from Kentucky were amplified by PCR. Three groups of sequences were identified. The sequences of five of the Ohio isolates were identical to the sequence of the type strain of E. risticii, the Illinois strain. The sequence of one Ohio isolate, isolate 081, was unique; this sequence differed in 10 nucleotides from the sequence of the type strain (level of similarity, 99.3%). The sequences of the three Kentucky isolates were identical to each other, but differed by five bases from the sequence of the type strain (level of similarity, 99.6%). The levels of sequence similarity of isolate 081, the Kentucky isolates, and the type strain to the next most closely related Ehrlichia sp., Ehrlichia sennetsu, were 99.3, 99.2, and 99.2%, respectively. On the basis of the distinct antigenic profiles and the levels of 16S rRNA sequence divergence, isolate 081 is as divergent from the type strain of E. risticii as E. sennetsu is. Therefore, we suggest that strain 081 and the Kentucky isolates may represent two new distinct Ehrlichia species.

The evolution and population structure of Lactobacillus fermentum from different naturally fermented products as determined by multilocus sequence typing (MLST).

PubMed

Dan, Tong; Liu, Wenjun; Song, Yuqin; Xu, Haiyan; Menghe, Bilige; Zhang, Heping; Sun, Zhihong

2015-05-20

Lactobacillus fermentum is economically important in the production and preservation of fermented foods. A repeatable and discriminative typing method was devised to characterize L. fermentum at the molecular level. The multilocus sequence typing (MLST) scheme developed was based on analysis of the internal sequence of 11 housekeeping gene fragments (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). MLST analysis of 203 isolates of L. fermentum from Mongolia and seven provinces/ autonomous regions in China identified 57 sequence types (ST), 27 of which were represented by only a single isolate, indicating high genetic diversity. Phylogenetic analyses based on the sequence of the 11 housekeeping gene fragments indicated that the L. fermentum isolates analyzed belonged to two major groups. A standardized index of association (I A (S)) indicated a weak clonal population structure in L. fermentum. Split decomposition analysis indicated that recombination played an important role in generating the genetic diversity observed in L. fermentum. The results from the minimum spanning tree strongly suggested that evolution of L. fermentum STs was not correlated with geography or food-type. The MLST scheme developed will be valuable for further studies on the evolution and population structure of L. fermentum isolates used in food products.

Population-scale whole genome sequencing identifies 271 highly polymorphic short tandem repeats from Japanese population.

PubMed

Hirata, Satoshi; Kojima, Kaname; Misawa, Kazuharu; Gervais, Olivier; Kawai, Yosuke; Nagasaki, Masao

2018-05-01

Forensic DNA typing is widely used to identify missing persons and plays a central role in forensic profiling. DNA typing usually uses capillary electrophoresis fragment analysis of PCR amplification products to detect the length of short tandem repeat (STR) markers. Here, we analyzed whole genome data from 1,070 Japanese individuals generated using massively parallel short-read sequencing of 162 paired-end bases. We have analyzed 843,473 STR loci with two to six basepair repeat units and cataloged highly polymorphic STR loci in the Japanese population. To evaluate the performance of the cataloged STR loci, we compared 23 STR loci, widely used in forensic DNA typing, with capillary electrophoresis based STR genotyping results in the Japanese population. Seventeen loci had high correlations and high call rates. The other six loci had low call rates or low correlations due to either the limitations of short-read sequencing technology, the bioinformatics tool used, or the complexity of repeat patterns. With these analyses, we have also purified the suitable 218 STR loci with four basepair repeat units and 53 loci with five basepair repeat units both for short read sequencing and PCR based technologies, which would be candidates to the actual forensic DNA typing in Japanese population.

High-resolution melting genotyping of Enterococcus faecium based on multilocus sequence typing derived single nucleotide polymorphisms.

PubMed

Tong, Steven Y C; Xie, Shirley; Richardson, Leisha J; Ballard, Susan A; Dakh, Farshid; Grabsch, Elizabeth A; Grayson, M Lindsay; Howden, Benjamin P; Johnson, Paul D R; Giffard, Philip M

2011-01-01

We have developed a single nucleotide polymorphism (SNP) nucleated high-resolution melting (HRM) technique to genotype Enterococcus faecium. Eight SNPs were derived from the E. faecium multilocus sequence typing (MLST) database and amplified fragments containing these SNPs were interrogated by HRM. We tested the HRM genotyping scheme on 85 E. faecium bloodstream isolates and compared the results with MLST, pulsed-field gel electrophoresis (PFGE) and an allele specific real-time PCR (AS kinetic PCR) SNP typing method. In silico analysis based on predicted HRM curves according to the G+C content of each fragment for all 567 sequence types (STs) in the MLST database together with empiric data from the 85 isolates demonstrated that HRM analysis resolves E. faecium into 231 "melting types" (MelTs) and provides a Simpson's Index of Diversity (D) of 0.991 with respect to MLST. This is a significant improvement on the AS kinetic PCR SNP typing scheme that resolves 61 SNP types with D of 0.95. The MelTs were concordant with the known ST of the isolates. For the 85 isolates, there were 13 PFGE patterns, 17 STs, 14 MelTs and eight SNP types. There was excellent concordance between PFGE, MLST and MelTs with Adjusted Rand Indices of PFGE to MelT 0.936 and ST to MelT 0.973. In conclusion, this HRM based method appears rapid and reproducible. The results are concordant with MLST and the MLST based population structure.

Survey of local and global biological network alignment: the need to reconcile the two sides of the same coin.

PubMed

Guzzi, Pietro Hiram; Milenkovic, Tijana

2018-05-01

Analogous to genomic sequence alignment that allows for across-species transfer of biological knowledge between conserved sequence regions, biological network alignment can be used to guide the knowledge transfer between conserved regions of molecular networks of different species. Hence, biological network alignment can be used to redefine the traditional notion of a sequence-based homology to a new notion of network-based homology. Analogous to genomic sequence alignment, there exist local and global biological network alignments. Here, we survey prominent and recent computational approaches of each network alignment type and discuss their (dis)advantages. Then, as it was recently shown that the two approach types are complementary, in the sense that they capture different slices of cellular functioning, we discuss the need to reconcile the two network alignment types and present a recent first step in this direction. We conclude with some open research problems on this topic and comment on the usefulness of network alignment in other domains besides computational biology.

Ribosomal subunit protein typing using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification and discrimination of Aspergillus species.

PubMed

Nakamura, Sayaka; Sato, Hiroaki; Tanaka, Reiko; Kusuya, Yoko; Takahashi, Hiroki; Yaguchi, Takashi

2017-04-26

Accurate identification of Aspergillus species is a very important subject. Mass spectral fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is generally employed for the rapid identification of fungal isolates. However, the results are based on simple mass spectral pattern-matching, with no peak assignment and no taxonomic input. We propose here a ribosomal subunit protein (RSP) typing technique using MALDI-TOF MS for the identification and discrimination of Aspergillus species. The results are concluded to be phylogenetic in that they reflect the molecular evolution of housekeeping RSPs. The amino acid sequences of RSPs of genome-sequenced strains of Aspergillus species were first verified and compared to compile a reliable biomarker list for the identification of Aspergillus species. In this process, we revealed that many amino acid sequences of RSPs (about 10-60%, depending on strain) registered in the public protein databases needed to be corrected or newly added. The verified RSPs were allocated to RSP types based on their mass. Peak assignments of RSPs of each sample strain as observed by MALDI-TOF MS were then performed to set RSP type profiles, which were then further processed by means of cluster analysis. The resulting dendrogram based on RSP types showed a relatively good concordance with the tree based on β-tubulin gene sequences. RSP typing was able to further discriminate the strains belonging to Aspergillus section Fumigati. The RSP typing method could be applied to identify Aspergillus species, even for species within section Fumigati. The discrimination power of RSP typing appears to be comparable to conventional β-tubulin gene analysis. This method would therefore be suitable for species identification and discrimination at the strain to species level. Because RSP typing can characterize the strains within section Fumigati, this method has potential as a powerful and reliable tool in the field of clinical microbiology.

Routine HLA-B genotyping with PCR-sequence-specific oligonucleotides detects a B*52 variant (B*5206).

PubMed

Hoelsch, K; Lenggeler, I; Pfannes, W; Knabe, H; Klein, H-G; Woelpl, A

2005-05-01

A new human leukocyte antigen (HLA)-B allele was found during routine typing of samples for a German unrelated bone marrow donor registry, the "Aktion Knochenmarkspende Bayern". After first interpretation of data of two independent low-resolution sequence-specific oligonucleotide typing tests, a B*51 variant was suggested. Further analysis via sequence-based typing identified the sequence as new B*52 allele. This new allele officially assigned as B*5206 differs from HLA-B*520102 by one nucleotide exchange in exon 2. The mutation is located at nucleotide position 274, at which a cytosine is substituted by a thymine leading to an amino acid change at protein position 67 from serine (TCC) to phenylalanine (TTC).

Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites.

PubMed

Rogan, P K; Schneider, T D

1995-01-01

Predicting the effects of nucleotide substitutions in human splice sites has been based on analysis of consensus sequences. We used a graphic representation of sequence conservation and base frequency, the sequence logo, to demonstrate that a change in a splice acceptor of hMSH2 (a gene associated with familial nonpolyposis colon cancer) probably does not reduce splicing efficiency. This confirms a population genetic study that suggested that this substitution is a genetic polymorphism. The information theory-based sequence logo is quantitative and more sensitive than the corresponding splice acceptor consensus sequence for detection of true mutations. Information analysis may potentially be used to distinguish polymorphisms from mutations in other types of transcriptional, translational, or protein-coding motifs.

Development of chemiluminescent probe hybridization, RT-PCR and nucleic acid cycle sequencing assays of Sabin type 3 isolates to identify base pair 472 Sabin type 3 mutants associated with vaccine associated paralytic poliomyelitis.

PubMed

Old, M O; Logan, L H; Maldonado, Y A

1997-11-01

Sabin type 3 polio vaccine virus is the most common cause of poliovaccine associated paralytic poliomyelitis. Vaccine associated paralytic poliomyelitis cases have been associated with Sabin type 3 revertants containing a single U to C substitution at bp 472 of Sabin type 3. A rapid method of identification of Sabin type 3 bp 472 mutants is described. An enterovirus group-specific probe for use in a chemiluminescent dot blot hybridization assay was developed to identify enterovirus positive viral lysates. A reverse transcription-polymerase chain reaction (RT-PCR) assay producing a 319 bp PCR product containing the Sabin type 3 bp 472 mutation site was then employed to identify Sabin type 3 isolates. Chemiluminescent nucleic acid cycle sequencing of the purified 319 bp PCR product was then employed to identify nucleic acid sequences at bp 472. The enterovirus group probe hybridization procedure and isolation of the Sabin type 3 PCR product were highly sensitive and specific; nucleic acid cycle sequencing corresponded to the known sequence of stock Sabin type 3 isolates. These methods will be used to identify the Sabin type 3 reversion rate from sequential stool samples of infants obtained after the first and second doses of oral poliovirus vaccine.

DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification

PubMed Central

2013-01-01

Background Mitochondrial DNA (mtDNA) typing can be a useful aid for identifying people from compromised samples when nuclear DNA is too damaged, degraded or below detection thresholds for routine short tandem repeat (STR)-based analysis. Standard mtDNA typing, focused on PCR amplicon sequencing of the control region (HVS I and HVS II), is limited by the resolving power of this short sequence, which misses up to 70% of the variation present in the mtDNA genome. Methods We used in-solution hybridisation-based DNA capture (using DNA capture probes prepared from modern human mtDNA) to recover mtDNA from post-mortem human remains in which the majority of DNA is both highly fragmented (<100 base pairs in length) and chemically damaged. The method ‘immortalises’ the finite quantities of DNA in valuable extracts as DNA libraries, which is followed by the targeted enrichment of endogenous mtDNA sequences and characterisation by next-generation sequencing (NGS). Results We sequenced whole mitochondrial genomes for human identification from samples where standard nuclear STR typing produced only partial profiles or demonstrably failed and/or where standard mtDNA hypervariable region sequences lacked resolving power. Multiple rounds of enrichment can substantially improve coverage and sequencing depth of mtDNA genomes from highly degraded samples. The application of this method has led to the reliable mitochondrial sequencing of human skeletal remains from unidentified World War Two (WWII) casualties approximately 70 years old and from archaeological remains (up to 2,500 years old). Conclusions This approach has potential applications in forensic science, historical human identification cases, archived medical samples, kinship analysis and population studies. In particular the methodology can be applied to any case, involving human or non-human species, where whole mitochondrial genome sequences are required to provide the highest level of maternal lineage discrimination. Multiple rounds of in-solution hybridisation-based DNA capture can retrieve whole mitochondrial genome sequences from even the most challenging samples. PMID:24289217

HPV-QUEST: A highly customized system for automated HPV sequence analysis capable of processing Next Generation sequencing data set.

PubMed

Yin, Li; Yao, Jiqiang; Gardner, Brent P; Chang, Kaifen; Yu, Fahong; Goodenow, Maureen M

2012-01-01

Next Generation sequencing (NGS) applied to human papilloma viruses (HPV) can provide sensitive methods to investigate the molecular epidemiology of multiple type HPV infection. Currently a genotyping system with a comprehensive collection of updated HPV reference sequences and a capacity to handle NGS data sets is lacking. HPV-QUEST was developed as an automated and rapid HPV genotyping system. The web-based HPV-QUEST subtyping algorithm was developed using HTML, PHP, Perl scripting language, and MYSQL as the database backend. HPV-QUEST includes a database of annotated HPV reference sequences with updated nomenclature covering 5 genuses, 14 species and 150 mucosal and cutaneous types to genotype blasted query sequences. HPV-QUEST processes up to 10 megabases of sequences within 1 to 2 minutes. Results are reported in html, text and excel formats and display e-value, blast score, and local and coverage identities; provide genus, species, type, infection site and risk for the best matched reference HPV sequence; and produce results ready for additional analyses.

Epstein-Barr Virus Sequence Variation—Biology and Disease

PubMed Central

Tzellos, Stelios; Farrell, Paul J.

2012-01-01

Some key questions in Epstein-Barr virus (EBV) biology center on whether naturally occurring sequence differences in the virus affect infection or EBV associated diseases. Understanding the pattern of EBV sequence variation is also important for possible development of EBV vaccines. At present EBV isolates worldwide can be grouped into Type 1 and Type 2, a classification based on the EBNA2 gene sequence. Type 1 EBV is the most prevalent worldwide but Type 2 is common in parts of Africa. Type 1 transforms human B cells into lymphoblastoid cell lines much more efficiently than Type 2 EBV. Molecular mechanisms that may account for this difference in cell transformation are now becoming clearer. Advances in sequencing technology will greatly increase the amount of whole EBV genome data for EBV isolated from different parts of the world. Study of regional variation of EBV strains independent of the Type 1/Type 2 classification and systematic investigation of the relationship between viral strains, infection and disease will become possible. The recent discovery that specific mutation of the EBV EBNA3B gene may be linked to development of diffuse large B cell lymphoma illustrates the importance that mutations in the virus genome may have in infection and human disease. PMID:25436768

Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt?

PubMed Central

2017-01-01

The Gram-positive, anaerobic bacterium Propionibacterium acnes forms part of the normal microbiota on human skin and mucosal surfaces. While normally associated with skin health, P. acnes is also an opportunistic pathogen linked with a range of human infections and clinical conditions. Over the last decade, our knowledge of the intraspecies phylogenetics and taxonomy of this bacterium has increased tremendously due to the introduction of DNA typing schemes based on single and multiple gene loci, as well as whole genomes. Furthermore, this work has led to the identification of specific lineages associated with skin health and human disease. In this review we will look back at the introduction of DNA sequence typing of P. acnes based on recA and tly loci, and then describe how these methods provided a basic understanding of the population genetic structure of the bacterium, and even helped characterize the grapevine-associated lineage of P. acnes, known as P. acnes type Zappe, which appears to have undergone a host switch from humans-to-plants. Particular limitations of recA and tly sequence typing will also be presented, as well as a detailed discussion of more recent, higher resolution, DNA-based methods to type P. acnes and investigate its evolutionary history in greater detail. PMID:29267255

Evaluation of an automated repetitive sequence-based PCR system for subtyping Enterobacter sakazakii.

PubMed

Healy, B; Mullane, N; Collin, V; Mailler, S; Iversen, C; Chatellier, S; Storrs, M; Fanning, S

2008-07-01

Enterobacter sakazakii is regarded as a ubiquitous organism that can be isolated from a wide range of foods and environments. Infection in at-risk infants has been epidemiologically linked to the consumption of contaminated powdered infant formula. Preventing the dissemination of this pathogen in a powdered infant formula manufacturing facility is an important step in ensuring consumer confidence in a given brand together with the protection of the health status of a vulnerable population. In this study we report the application of a repetitive sequence-based PCR typing method to subtype a previously well-characterized collection of E. sakazakii isolates of diverse origin. While both methods successfully discriminated between the collection of isolates, repetitive sequence-based PCR identified 65 types, whereas pulsed-field gel electrophoresis identified 110 types showing > or =95% similarity. The method was quick and easy to perform, and our data demonstrated the utility and value of this approach to monitor in-process contamination, which could potentially contribute to a reduction in the transmission of E. sakazakii.

Collaborative Adaptation Planning for Water Security: Preliminary Lessons, Challenges, and the Way Forward for Maipo Basin Adaptation Plan, Chile

NASA Astrophysics Data System (ADS)

Vicuna, S.; Scott, C. A.; Bonelli, S.; Bustos, E.; Meza, F. J.

2014-12-01

The Maipo basin holds 40% of Chile's total population and almost half of the country's Gross Domestic Product. The basin is located in the semiarid central region of the country and, aside from the typical pressures of growth in developing country basins, the Maipo river faces climate change impacts associated with a reduction in total runoff and changes in its seasonality. Surface water is the main water source for human settlements and economic activities including agriculture. In 2012 we started a research project to create a climate variability and climate change adaptation plan for the basin. The pillars of the plan are co-produced by researchers and a Scenario Building Team (SBT) with membership of relevant water and land use stakeholders (including from civil society, public and private sectors) in the basin. Following similar experiences in other regions in the world that have faced the challenges of dealing with long term planning under uncertainty, the project has divided the task of developing the plan into a series of interconnected elements. A critical first component is to work on the desired vision(s) of the basin for the future. In this regards, the "water security" concept has been chosen as a framework that accommodates all objectives of the SBT members. Understanding and quantifying the uncertainties that could affect the future water security of the basin is another critical aspect of the plan. Near and long term climate scenarios are one dimension of these uncertainties that are combined with base development uncertainties such as urban growth scenarios. A third component constructs the models/tools that allows the assessment of impacts on water security that could arise under these scenarios. The final critical component relates to the development of the adaptation measures that could avoid the negative impacts and/or capture the potential opportunities. After two years in the development of the adaptation plan a series of results has been achieved in all critical components that are presented here. The success in the process now poses a series of new challenges, most importantly: how to implement and monitor the evolution of the adaptation process.

Genome-wide-analyses of Listeria monocytogenes from food-processing plants reveal clonal diversity and date the emergence of persisting sequence types.

PubMed

Knudsen, Gitte M; Nielsen, Jesper Boye; Marvig, Rasmus L; Ng, Yin; Worning, Peder; Westh, Henrik; Gram, Lone

2017-08-01

Whole genome sequencing is increasing used in epidemiology, e.g. for tracing outbreaks of food-borne diseases. This requires in-depth understanding of pathogen emergence, persistence and genomic diversity along the food production chain including in food processing plants. We sequenced the genomes of 80 isolates of Listeria monocytogenes sampled from Danish food processing plants over a time-period of 20 years, and analysed the sequences together with 10 public available reference genomes to advance our understanding of interplant and intraplant genomic diversity of L. monocytogenes. Except for three persisting sequence types (ST) based on Multi Locus Sequence Typing being ST7, ST8 and ST121, long-term persistence of clonal groups was limited, and new clones were introduced continuously, potentially from raw materials. No particular gene could be linked to the persistence phenotype. Using time-based phylogenetic analyses of the persistent STs, we estimate the L. monocytogenes evolutionary rate to be 0.18-0.35 single nucleotide polymorphisms/year, suggesting that the persistent STs emerged approximately 100 years ago, which correlates with the onset of industrialization and globalization of the food market. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Species-specific Typing of DNA Based on Palindrome Frequency Patterns

PubMed Central

Lamprea-Burgunder, Estelle; Ludin, Philipp; Mäser, Pascal

2011-01-01

DNA in its natural, double-stranded form may contain palindromes, sequences which read the same from either side because they are identical to their reverse complement on the sister strand. Short palindromes are underrepresented in all kinds of genomes. The frequency distribution of short palindromes exhibits more than twice the inter-species variance of non-palindromic sequences, which renders palindromes optimally suited for the typing of DNA. Here, we show that based on palindrome frequency, DNA sequences can be discriminated to the level of species of origin. By plotting the ratios of actual occurrence to expectancy, we generate palindrome frequency patterns that allow to cluster different sequences of the same genome and to assign plasmids, and in some cases even viruses to their respective host genomes. This finding will be of use in the growing field of metagenomics. PMID:21429991

[Analysis of 4 clustered high risk acute flaccid paralysis cases in Shanxi Province in 2006].

PubMed

Yan, Dong-mei; Zhang, Yong; Wang, Dong-yan

2010-04-01

Analysis of epidemiology of 4 clustered high risk acute flaccid paralysis(AFP) cases reported by Shanxi province in 2006 and VP1 gene characteristic for type III poliovirus isolated from the four AFP cases. Virus isolation and identification were conducted according to the 4th edition of WHO polio laboratory manual. The sequence of VP1 region were amplified and sequenced. The phylogenetic trees based on VP1 region were constructed. Three of four high risk AFP cases were suspected as vaccine associated paralysis poliomyelitis (VAPP), the onset date of them were close. VP1 sequencing of the four type III isolates revealed that the identity were 99.7%, 99.9%, 99.4% and 99.9% respectively compared with vaccine reference strain-BJOPV3. According to WHO criteria, the four isolates were identified as type III vaccine-related poliovirus. Phylogenetic analysis based on VP1 coding sequence showed that the four type III poliovirus were not related significantly. The type III poliovirus isolated from 3 suspected VAPP cases shared one nucleotide mutation at 2637 (C-->U), which result in the amino acid mutation from Val into Ala. The improvement of laboratory surveillance for clustered high risk AFP cases should be strengthened so as to detect and prevent poliovirus circulation timely.

Comparison and Evaluation of the Molecular Typing Methods for Toxigenic Vibrio cholerae in Southwest China.

PubMed

Liao, Feng; Mo, Zhishuo; Chen, Meiling; Pang, Bo; Fu, Xiaoqing; Xu, Wen; Jing, Huaiqi; Kan, Biao; Gu, Wenpeng

2018-01-01

Vibrio cholerae O1 strains taken from the repository of Yunnan province, southwest China, were abundant and special. We selected 70 typical toxigenic V. cholerae (69 O1 and one O139 serogroup strains) isolated from Yunnan province, performed the pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and MLST of virulence gene (V-MLST) methods, and evaluated the resolution abilities for typing methods. The ctxB subunit sequence analysis for all strains have shown that cholera between 1986 and 1995 was associated with mixed infections with El Tor and El Tor variants, while infections after 1996 were all caused by El Tor variant strains. Seventy V. cholerae obtained 50 PFGE patterns, with a high resolution. The strains could be divided into three groups with predominance of strains isolated during 1980s, 1990s, and 2000s, respectively, showing a good consistency with the epidemiological investigation. We also evaluated two MLST method for V. cholerae , one was used seven housekeeping genes ( adk , gyrB , metE , pntA , mdh , purM , and pyrC ), and all the isolates belonged to ST69; another was used nine housekeeping genes ( cat , chi , dnaE , gyrB , lap , pgm , recA , rstA , and gmd ). A total of seven sequence types (STs) were found by using this method for all the strains; among them, rstA gene had five alleles, recA and gmd have two alleles, and others had only one allele. The virulence gene sequence typing method ( ctxAB , tcpA , and toxR ) showed that 70 strains were divided into nine STs; among them, tcpA gene had six alleles, toxR had five alleles, while ctxAB was identical for all the strains. The latter two sequences based typing methods also had consistency with epidemiology of the strains. PFGE had a higher resolution ability compared with the sequence based typing method, and MLST used seven housekeeping genes showed the lower resolution power than nine housekeeping genes and virulence genes methods. These two sequence typing methods could distinguish some epidemiological special strains in local area.

Nucleotide sequences of the tet(M) genes from the American and Dutch type tetracycline resistance plasmids of Neisseria gonorrhoeae.

PubMed

Gascoyne-Binzi, D M; Heritage, J; Hawkey, P M

1993-11-01

High-level tetracycline-resistant Neisseria gonorrhoeae (TRNG) has been associated with the presence of a plasmid approximately 25.2 MDa in size which carries a Tet M tetracycline resistance determinant. Two different plasmid types, American and Dutch, have previously been described, based on the restriction endonuclease digestion pattern. In this study, the tet(M) genes from the two plasmid types have been amplified by the polymerase chain reaction (PCR) and then sequenced. The gene sequences from the two plasmids shared 96.8% identity, and showed similarities with different segments of the tet(M) gene sequences from Tn1545, Tn916 and Ureaplasma urealyticum. The data suggest that it is highly likely that the Tet M determinant found in the American type plasmid has a different origin from that present in the Dutch plasmid.

Cloning, sequencing, and expression of cDNA for human. beta. -glucuronidase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oshima, A.; Kyle, J.W.; Miller, R.D.

1987-02-01

The authors report here the cDNA sequence for human placental ..beta..-glucuronidase (..beta..-D-glucuronoside glucuronosohydrolase, EC 3.2.1.31) and demonstrate expression of the human enzyme in transfected COS cells. They also sequenced a partial cDNA clone from human fibroblasts that contained a 153-base-pair deletion within the coding sequence and found a second type of cDNA clone from placenta that contained the same deletion. Nuclease S1 mapping studies demonstrated two types of mRNAs in human placenta that corresponded to the two types of cDNA clones isolated. The NH/sub 2/-terminal amino acid sequence determined for human spleen ..beta..-glucuronidase agreed with that inferred from the DNAmore » sequence of the two placental clones, beginning at amino acid 23, suggesting a cleaved signal sequence of 22 amino acids. When transfected into COS cells, plasmids containing either placental clone expressed an immunoprecipitable protein that contained N-linked oligosaccharides as evidenced by sensitivity to endoglycosidase F. However, only transfection with the clone containing the 153-base-pair segment led to expression of human ..beta..-glucuronidase activity. These studies provide the sequence for the full-length cDNA for human ..beta..-glucuronidase, demonstrate the existence of two populations of mRNA for ..beta..-glucuronidase in human placenta, only one of which specifies a catalytically active enzyme, and illustrate the importance of expression studies in verifying that a cDNA is functionally full-length.« less

Development of an ELA-DRA gene typing method based on pyrosequencing technology.

PubMed

Díaz, S; Echeverría, M G; It, V; Posik, D M; Rogberg-Muñoz, A; Pena, N L; Peral-García, P; Vega-Pla, J L; Giovambattista, G

2008-11-01

The polymorphism of equine lymphocyte antigen (ELA) class II DRA gene had been detected by polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP) and reference strand-mediated conformation analysis. These methodologies allowed to identify 11 ELA-DRA exon 2 sequences, three of which are widely distributed among domestic horse breeds. Herein, we describe the development of a pyrosequencing-based method applicable to ELA-DRA typing, by screening samples from eight different horse breeds previously typed by PCR-SSCP. This sequence-based method would be useful in high-throughput genotyping of major histocompatibility complex genes in horses and other animal species, making this system interesting as a rapid screening method for animal genotyping of immune-related genes.

Genome Sequence of the Thermophile Bacillus coagulans Hammer, the Type Strain of the Species

PubMed Central

Su, Fei; Tao, Fei; Tang, Hongzhi

2012-01-01

Here we announce a 3.0-Mb assembly of the Bacillus coagulans Hammer strain, which is the type strain of the species within the genus Bacillus. Genomic analyses based on the sequence may provide insights into the phylogeny of the species and help to elucidate characteristics of the poorly studied strains of Bacillus coagulans. PMID:23105047

Genome sequence of the thermophile Bacillus coagulans Hammer, the type strain of the species.

PubMed

Su, Fei; Tao, Fei; Tang, Hongzhi; Xu, Ping

2012-11-01

Here we announce a 3.0-Mb assembly of the Bacillus coagulans Hammer strain, which is the type strain of the species within the genus Bacillus. Genomic analyses based on the sequence may provide insights into the phylogeny of the species and help to elucidate characteristics of the poorly studied strains of Bacillus coagulans.

Development of a Multiplex Single Base Extension Assay for Mitochondrial DNA Haplogroup Typing

PubMed Central

Nelson, Tahnee M.; Just, Rebecca S.; Loreille, Odile; Schanfield, Moses S.; Podini, Daniele

2007-01-01

Aim To provide a screening tool to reduce time and sample consumption when attempting mtDNA haplogroup typing. Methods A single base primer extension assay was developed to enable typing, in a single reaction, of twelve mtDNA haplogroup specific polymorphisms. For validation purposes a total of 147 samples were tested including 73 samples successfully haplogroup typed using mtDNA control region (CR) sequence data, 21 samples inconclusively haplogroup typed by CR data, 20 samples previously haplogroup typed using restriction fragment length polymorphism (RFLP) analysis, and 31 samples of known ancestral origin without previous haplogroup typing. Additionally, two highly degraded human bones embalmed and buried in the early 1950s were analyzed using the single nucleotide polymorphisms (SNP) multiplex. Results When the SNP multiplex was used to type the 96 previously CR sequenced specimens, an increase in haplogroup or macrohaplogroup assignment relative to conventional CR sequence analysis was observed. The single base extension assay was also successfully used to assign a haplogroup to decades-old, embalmed skeletal remains dating to World War II. Conclusion The SNP multiplex was successfully used to obtain haplogroup status of highly degraded human bones, and demonstrated the ability to eliminate possible contributors. The SNP multiplex provides a low-cost, high throughput method for typing of mtDNA haplogroups A, B, C, D, E, F, G, H, L1/L2, L3, M, and N that could be useful for screening purposes for human identification efforts and anthropological studies. PMID:17696300

Protein sequences clustering of herpes virus by using Tribe Markov clustering (Tribe-MCL)

NASA Astrophysics Data System (ADS)

Bustamam, A.; Siswantining, T.; Febriyani, N. L.; Novitasari, I. D.; Cahyaningrum, R. D.

2017-07-01

The herpes virus can be found anywhere and one of the important characteristics is its ability to cause acute and chronic infection at certain times so as a result of the infection allows severe complications occurred. The herpes virus is composed of DNA containing protein and wrapped by glycoproteins. In this work, the Herpes viruses family is classified and analyzed by clustering their protein-sequence using Tribe Markov Clustering (Tribe-MCL) algorithm. Tribe-MCL is an efficient clustering method based on the theory of Markov chains, to classify protein families from protein sequences using pre-computed sequence similarity information. We implement the Tribe-MCL algorithm using an open source program of R. We select 24 protein sequences of Herpes virus obtained from NCBI database. The dataset consists of three types of glycoprotein B, F, and H. Each type has eight herpes virus that infected humans. Based on our simulation using different inflation factor r=1.5, 2, 3 we find a various number of the clusters results. The greater the inflation factor the greater the number of their clusters. Each protein will grouped together in the same type of protein.

Variability of the protein sequences of lcrV between epidemic and atypical rhamnose-positive strains of Yersinia pestis.

PubMed

Anisimov, Andrey P; Panfertsev, Evgeniy A; Svetoch, Tat'yana E; Dentovskaya, Svetlana V

2007-01-01

Sequencing of lcrV genes and comparison of the deduced amino acid sequences from ten Y. pestis strains belonging mostly to the group of atypical rhamnose-positive isolates (non-pestis subspecies or pestoides group) showed that the LcrV proteins analyzed could be classified into five sequence types. This classification was based on major amino acid polymorphisms among LcrV proteins in the four "hot points" of the protein sequences. Some additional minor polymorphisms were found throughout these sequence types. The "hot points" corresponded to amino acids 18 (Lys --> Asn), 72 (Lys --> Arg), 273 (Cys --> Ser), and 324-326 (Ser-Gly-Lys --> Arg) in the LcrV sequence of the reference Y. pestis strain CO92. One possible explanation for polymorphism in amino acid sequences of LcrV among different strains is that strain-specific variation resulted from adaptation of the plague pathogen to different rodent and lagomorph hosts.

The nucleotide sequence of the intergenic region between the 5.8S and 26S rRNA genes of the yeast ribosomal RNA operon. Possible implications for the interaction between 5.8S and 26S rRNA and the processing of the primary transcript.

PubMed Central

Veldman, G M; Klootwijk, J; van Heerikhuizen, H; Planta, R J

1981-01-01

We have determined the nucleotide sequence of part of a cloned yeast ribosomal RNA operon extending from the 5.8S RNA gene downstream into the 5' -terminal region of the 26S RNA gene. We mapped the pertinent processing sites, viz. the 5' end of 26S rRNA and the 3'ends of 5.8S rRNA and its immediate precursor, 7S RNA. At the 3' end of 7S RNA we find the sequence UCGUUU which is very similar to the type I consensus sequence UCAUUA/U present at the 3' ends of 17S, 5.8S and 26S rRNA as well as 18S precursor rRNA in yeast. At the 5' end of the 26S RNA gene we find a sequence of thirteen nucleotides which is homologous to the type II sequence present at the 5' termini of both the 17S and the 5.8S RNA gene. These findings further support the suggestion put forward earlier (G.M. Veldman et al. (1980) Nucl. Acids Res. 8, 2907-2920) that both consensus sequences are involved in the recognition of precursor rRNA by the processing nuclease(s). We discuss a model for the processing of yeast rRNA in which a processing enzyme sequentially recognizes several combinations of a type I and a type II consensus sequence. We also describe the existence of a significant base complementarity between sequences in the 5' -terminal region of 26S rRNA and the 3' -terminal region of 5.8S rRNA. We suggest that base pairing between these sequences contributes to the binding between 5.8S and 26S rRNA. Images PMID:7312619

A RESTful application programming interface for the PubMLST molecular typing and genome databases

PubMed Central

Bray, James E.; Maiden, Martin C. J.

2017-01-01

Abstract Molecular typing is used to differentiate microorganisms at the subspecies or strain level for epidemiological investigations, infection control, public health and environmental sampling. DNA sequence-based typing methods require authoritative databases that link sequence variants to nomenclature in order to facilitate communication and comparison of identified types in national or global settings. The PubMLST website (https://pubmlst.org/) fulfils this role for over a hundred microorganisms for which it hosts curated molecular sequence typing data, providing sequence and allelic profile definitions for multi-locus sequence typing (MLST) and single-gene typing approaches. In recent years, these have expanded to cover the whole genome with schemes such as core genome MLST (cgMLST) and whole genome MLST (wgMLST) which catalogue the allelic diversity found in hundreds to thousands of genes. These approaches provide a common nomenclature for high-resolution strain characterization and comparison. Molecular typing information is linked to isolate provenance, phenotype, and increasingly genome assemblies, providing a resource for outbreak investigation and research in to population structure, gene association, global epidemiology and vaccine coverage. A Representational State Transfer (REST) Application Programming Interface (API) has been developed for the PubMLST website to make these large quantities of structured molecular typing and whole genome sequence data available for programmatic access by any third party application. The API is an integral component of the Bacterial Isolate Genome Sequence Database (BIGSdb) platform that is used to host PubMLST resources, and exposes all public data within the site. In addition to data browsing, searching and download, the API supports authentication and submission of new data to curator queues. Database URL: http://rest.pubmlst.org/ PMID:29220452

Epidemiological information is key when interpreting whole genome sequence data – lessons learned from a large Legionella pneumophila outbreak in Warstein, Germany, 2013

PubMed Central

Petzold, Markus; Prior, Karola; Moran-Gilad, Jacob; Harmsen, Dag; Lück, Christian

2017-01-01

Introduction Whole genome sequencing (WGS) is increasingly used in Legionnaires’ disease (LD) outbreak investigations, owing to its higher resolution than sequence-based typing, the gold standard typing method for Legionella pneumophila, in the analysis of endemic strains. Recently, a gene-by-gene typing approach based on 1,521 core genes called core genome multilocus sequence typing (cgMLST) was described that enables a robust and standardised typing of L. pneumophila. Methods: We applied this cgMLST scheme to isolates obtained during the largest outbreak of LD reported so far in Germany. In this outbreak, the epidemic clone ST345 had been isolated from patients and four different environmental sources. In total 42 clinical and environmental isolates were retrospectively typed. Results: Epidemiologically unrelated ST345 isolates were clearly distinguishable from the epidemic clone. Remarkably, epidemic isolates split up into two distinct clusters, ST345-A and ST345-B, each respectively containing a mix of clinical and epidemiologically-related environmental samples. Discussion/conclusion: The outbreak was therefore likely caused by both variants of the single sequence type, which pre-existed in the environmental reservoirs. The two clusters differed by 40 alleles located in two neighbouring genomic regions of ca 42 and 26 kb. Additional analysis supported horizontal gene transfer of the two regions as responsible for the difference between the variants. Both regions comprise virulence genes and have previously been reported to be involved in recombination events. This corroborates the notion that genomic outbreak investigations should always take epidemiological information into consideration when making inferences. Overall, cgMLST proved helpful in disentangling the complex genomic epidemiology of the outbreak. PMID:29162202

Epidemiological information is key when interpreting whole genome sequence data - lessons learned from a large Legionella pneumophila outbreak in Warstein, Germany, 2013.

PubMed

Petzold, Markus; Prior, Karola; Moran-Gilad, Jacob; Harmsen, Dag; Lück, Christian

2017-11-01

IntroductionWhole genome sequencing (WGS) is increasingly used in Legionnaires' disease (LD) outbreak investigations, owing to its higher resolution than sequence-based typing, the gold standard typing method for Legionella pneumophila, in the analysis of endemic strains. Recently, a gene-by-gene typing approach based on 1,521 core genes called core genome multilocus sequence typing (cgMLST) was described that enables a robust and standardised typing of L. pneumophila . Methods : We applied this cgMLST scheme to isolates obtained during the largest outbreak of LD reported so far in Germany. In this outbreak, the epidemic clone ST345 had been isolated from patients and four different environmental sources. In total 42 clinical and environmental isolates were retrospectively typed. Results : Epidemiologically unrelated ST345 isolates were clearly distinguishable from the epidemic clone. Remarkably, epidemic isolates split up into two distinct clusters, ST345-A and ST345-B, each respectively containing a mix of clinical and epidemiologically-related environmental samples. Discussion/conclusion : The outbreak was therefore likely caused by both variants of the single sequence type, which pre-existed in the environmental reservoirs. The two clusters differed by 40 alleles located in two neighbouring genomic regions of ca 42 and 26 kb. Additional analysis supported horizontal gene transfer of the two regions as responsible for the difference between the variants. Both regions comprise virulence genes and have previously been reported to be involved in recombination events. This corroborates the notion that genomic outbreak investigations should always take epidemiological information into consideration when making inferences. Overall, cgMLST proved helpful in disentangling the complex genomic epidemiology of the outbreak.

Weaning failure and respiratory muscle function: What has been done and what can be improved?

PubMed

Magalhães, Paulo A F; Camillo, Carlos A; Langer, Daniel; Andrade, Lívia B; Duarte, Maria do Carmo M B; Gosselink, Rik

2018-01-01

Respiratory muscle dysfunction, being a common cause of weaning failure, is strongly associated with prolonged mechanical ventilation (MV) and prolonged stay in intensive care units. Inspiratory muscle training (IMT) has been described as an important contributor to the treatment of respiratory muscle dysfunction in critically ill patients. Its effectiveness is however yet controversial. To discuss evidence for assessment of readiness and the effectiveness of interventions for liberation from MV, with special attention to the role of IMT. PubMed, LILACS, PEDro and Web of Science were searched for papers of assessment and treatment of patients who failed liberation from MV after at least one attempt published in English or Portuguese until June 2016. Weaning predictors are related to weaning success (86%-100% for sensitivity and 7%-69% for specificity) and work of breathing (73%-100% for sensitivity and 56%-100% for specificity). Spontaneous breathing trials (SBT), noninvasive MV and early mobilization have been reported to improve weaning outcomes. Two modalities of IMT were identified in five selected studies: 1) adjustment of ventilator trigger sensitivity 2) inspiratory threshold loading. Both IMT training modalities promoted significant increases in respiratory muscle strength. IMT with threshold loading showed positive effect on endurance compared to control. Methods to indentify respiratory muscle weakness in critically ill patients are feasible and described as indexes that show good accuracy. Individualized and supervised rehabilitation programs including IMT, SBT, noninvasive MV and early mobilization should be encouraged in patients with inspiratory muscle weakness. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gene sequence analyses and other DNA-based methods for yeast species recognition

USDA-ARS?s Scientific Manuscript database

DNA sequence analyses, as well as other DNA-based methodologies, have transformed the way in which yeasts are identified. The focus of this chapter will be on the resolution of species using various types of DNA comparisons. In other chapters in this book, Rozpedowska, Piškur and Wolfe discuss mul...

Introduction of the hybcell-based compact sequencing technology and comparison to state-of-the-art methodologies for KRAS mutation detection.

PubMed

Zopf, Agnes; Raim, Roman; Danzer, Martin; Niklas, Norbert; Spilka, Rita; Pröll, Johannes; Gabriel, Christian; Nechansky, Andreas; Roucka, Markus

2015-03-01

The detection of KRAS mutations in codons 12 and 13 is critical for anti-EGFR therapy strategies; however, only those methodologies with high sensitivity, specificity, and accuracy as well as the best cost and turnaround balance are suitable for routine daily testing. Here we compared the performance of compact sequencing using the novel hybcell technology with 454 next-generation sequencing (454-NGS), Sanger sequencing, and pyrosequencing, using an evaluation panel of 35 specimens. A total of 32 mutations and 10 wild-type cases were reported using 454-NGS as the reference method. Specificity ranged from 100% for Sanger sequencing to 80% for pyrosequencing. Sanger sequencing and hybcell-based compact sequencing achieved a sensitivity of 96%, whereas pyrosequencing had a sensitivity of 88%. Accuracy was 97% for Sanger sequencing, 85% for pyrosequencing, and 94% for hybcell-based compact sequencing. Quantitative results were obtained for 454-NGS and hybcell-based compact sequencing data, resulting in a significant correlation (r = 0.914). Whereas pyrosequencing and Sanger sequencing were not able to detect multiple mutated cell clones within one tumor specimen, 454-NGS and the hybcell-based compact sequencing detected multiple mutations in two specimens. Our comparison shows that the hybcell-based compact sequencing is a valuable alternative to state-of-the-art methodologies used for detection of clinically relevant point mutations.

Multi-virulence-locus sequence typing of Staphylococcus lugdunensis generates results consistent with a clonal population structure and is reliable for epidemiological typing.

PubMed

Didi, Jennifer; Lemée, Ludovic; Gibert, Laure; Pons, Jean-Louis; Pestel-Caron, Martine

2014-10-01

Staphylococcus lugdunensis is an emergent virulent coagulase-negative staphylococcus responsible for severe infections similar to those caused by Staphylococcus aureus. To understand its potentially pathogenic capacity and have further detailed knowledge of the molecular traits of this organism, 93 isolates from various geographic origins were analyzed by multi-virulence-locus sequence typing (MVLST), targeting seven known or putative virulence-associated loci (atlLR2, atlLR3, hlb, isdJ, SLUG_09050, SLUG_16930, and vwbl). The polymorphisms of the putative virulence-associated loci were moderate and comparable to those of the housekeeping genes analyzed by multilocus sequence typing (MLST). However, the MVLST scheme generated 43 virulence types (VTs) compared to 20 sequence types (STs) based on MLST, indicating that MVLST was significantly more discriminating (Simpson's index [D], 0.943). No hypervirulent lineage or cluster specific to carriage strains was defined. The results of multilocus sequence analysis of known and putative virulence-associated loci are consistent with a clonal population structure for S. lugdunensis, suggesting a coevolution of these genes with housekeeping genes. Indeed, the nonsynonymous to synonymous evolutionary substitutions (dN/dS) ratio, the Tajima's D test, and Single-likelihood ancestor counting (SLAC) analysis suggest that all virulence-associated loci were under negative selection, even atlLR2 (AtlL protein) and SLUG_16930 (FbpA homologue), for which the dN/dS ratios were higher. In addition, this analysis of virulence-associated loci allowed us to propose a trilocus sequence typing scheme based on the intragenic regions of atlLR3, isdJ, and SLUG_16930, which is more discriminant than MLST for studying short-term epidemiology and further characterizing the lineages of the rare but highly pathogenic S. lugdunensis. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Novel Single Nucleotide Polymorphism-Based Assay for Genotyping Mycobacterium avium subsp. paratuberculosis

PubMed Central

Goldstone, Robert J.; McLuckie, Joyce; Smith, David G. E.

2015-01-01

Typing of Mycobacterium avium subspecies paratuberculosis strains presents a challenge, since they are genetically monomorphic and traditional molecular techniques have limited discriminatory power. The recent advances and availability of whole-genome sequencing have extended possibilities for the characterization of Mycobacterium avium subspecies paratuberculosis, and whole-genome sequencing can provide a phylogenetic context to facilitate global epidemiology studies. In this study, we developed a single nucleotide polymorphism (SNP) assay based on PCR and restriction enzyme digestion or sequencing of the amplified product. The SNP analysis was performed using genome sequence data from 133 Mycobacterium avium subspecies paratuberculosis isolates with different genotypes from 8 different host species and 17 distinct geographic regions around the world. A total of 28,402 SNPs were identified among all of the isolates. The minimum number of SNPs required to distinguish between all of the 133 genomes was 93 and between only the type C isolates was 41. To reduce the number of SNPs and PCRs required, we adopted an approach based on sequential detection of SNPs and a decision tree. By the analysis of 14 SNPs Mycobacterium avium subspecies paratuberculosis isolates can be characterized within 14 phylogenetic groups with a higher discriminatory power than mycobacterial interspersed repetitive unit–variable number tandem repeat assay and other typing methods. Continuous updating of genome sequences is needed in order to better characterize new phylogenetic groups and SNP profiles. The novel SNP assay is a discriminative, simple, reproducible method and requires only basic laboratory equipment for the large-scale global typing of Mycobacterium avium subspecies paratuberculosis isolates. PMID:26677250

Improved detection of genetic markers of antimicrobial resistance by hybridization probe-based melting curve analysis using primers to mask proximal mutations: examples include the influenza H275Y substitution.

PubMed

Whiley, David M; Jacob, Kevin; Nakos, Jennifer; Bletchly, Cheryl; Nimmo, Graeme R; Nissen, Michael D; Sloots, Theo P

2012-06-01

Numerous real-time PCR assays have been described for detection of the influenza A H275Y alteration. However, the performance of these methods can be undermined by sequence variation in the regions flanking the codon of interest. This is a problem encountered more broadly in microbial diagnostics. In this study, we developed a modification of hybridization probe-based melting curve analysis, whereby primers are used to mask proximal mutations in the sequence targets of hybridization probes, so as to limit the potential for sequence variation to interfere with typing. The approach was applied to the H275Y alteration of the influenza A (H1N1) 2009 strain, as well as a Neisseria gonorrhoeae mutation associated with antimicrobial resistance. Assay performances were assessed using influenza A and N. gonorrhoeae strains characterized by DNA sequencing. The modified hybridization probe-based approach proved successful in limiting the effects of proximal mutations, with the results of melting curve analyses being 100% consistent with the results of DNA sequencing for all influenza A and N. gonorrhoeae strains tested. Notably, these included influenza A and N. gonorrhoeae strains exhibiting additional mutations in hybridization probe targets. Of particular interest was that the H275Y assay correctly typed influenza A strains harbouring a T822C nucleotide substitution, previously shown to interfere with H275Y typing methods. Overall our modified hybridization probe-based approach provides a simple means of circumventing problems caused by sequence variation, and offers improved detection of the influenza A H275Y alteration and potentially other resistance mechanisms.

Surveillance and laboratory detection for non-polio enteroviruses in the European Union/European Economic Area, 2016

PubMed Central

Harvala, Heli; Jasir, Aftab; Penttinen, Pasi; Pastore Celentano, Lucia; Greco, Donato; Broberg, Eeva

2017-01-01

Enteroviruses (EVs) cause severe outbreaks of respiratory and neurological disease as illustrated by EV-D68 and EV-A71 outbreaks, respectively. We have mapped European laboratory capacity for identification and characterisation of non-polio EVs to improve preparedness to respond to (re)-emerging EVs linked to severe disease. An online questionnaire on non-polio EV surveillance and laboratory detection was submitted to all 30 European Union (EU)/European Economic Area (EEA) countries. Twenty-nine countries responded; 26 conducted laboratory-based non-polio EV surveillance, and 24 included neurological infections in their surveillance. Eleven countries have established specific surveillance for EV-D68 via sentinel influenza surveillance (n = 7), typing EV-positive respiratory samples (n = 10) and/or acute flaccid paralysis surveillance (n = 5). Of 26 countries performing non-polio EV characterisation/typing, 10 further characterised culture-positive EV isolates, whereas the remainder typed PCR-positive but culture-negative samples. Although 19 countries have introduced sequence-based EV typing, seven still rely entirely on virus isolation. Based on 2015 data, six countries typed over 300 specimens mostly by sequencing, whereas 11 countries characterised under 50 EV-positive samples. EV surveillance activity varied between EU/EEA countries, and did not always specifically target patients with neurological and/or respiratory infections. Introduction of sequence-based typing methods is needed throughout the EU/EEA to enhance laboratory capacity for the detection of EVs. PMID:29162204

Surveillance and laboratory detection for non-polio enteroviruses in the European Union/European Economic Area, 2016.

PubMed

Harvala, Heli; Jasir, Aftab; Penttinen, Pasi; Pastore Celentano, Lucia; Greco, Donato; Broberg, Eeva

2017-11-01

Enteroviruses (EVs) cause severe outbreaks of respiratory and neurological disease as illustrated by EV-D68 and EV-A71 outbreaks, respectively. We have mapped European laboratory capacity for identification and characterisation of non-polio EVs to improve preparedness to respond to (re)-emerging EVs linked to severe disease. An online questionnaire on non-polio EV surveillance and laboratory detection was submitted to all 30 European Union (EU)/European Economic Area (EEA) countries. Twenty-nine countries responded; 26 conducted laboratory-based non-polio EV surveillance, and 24 included neurological infections in their surveillance. Eleven countries have established specific surveillance for EV-D68 via sentinel influenza surveillance (n = 7), typing EV-positive respiratory samples (n = 10) and/or acute flaccid paralysis surveillance (n = 5). Of 26 countries performing non-polio EV characterisation/typing, 10 further characterised culture-positive EV isolates, whereas the remainder typed PCR-positive but culture-negative samples. Although 19 countries have introduced sequence-based EV typing, seven still rely entirely on virus isolation. Based on 2015 data, six countries typed over 300 specimens mostly by sequencing, whereas 11 countries characterised under 50 EV-positive samples. EV surveillance activity varied between EU/EEA countries, and did not always specifically target patients with neurological and/or respiratory infections. Introduction of sequence-based typing methods is needed throughout the EU/EEA to enhance laboratory capacity for the detection of EVs.

Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks.

PubMed

Rusconi, Brigida; Sanjar, Fatemeh; Koenig, Sara S K; Mammel, Mark K; Tarr, Phillip I; Eppinger, Mark

2016-01-01

Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and long-term evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies.

Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks

PubMed Central

Rusconi, Brigida; Sanjar, Fatemeh; Koenig, Sara S. K.; Mammel, Mark K.; Tarr, Phillip I.; Eppinger, Mark

2016-01-01

Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and long-term evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies. PMID:27446025

AgdbNet – antigen sequence database software for bacterial typing

PubMed Central

Jolley, Keith A; Maiden, Martin CJ

2006-01-01

Background Bacterial typing schemes based on the sequences of genes encoding surface antigens require databases that provide a uniform, curated, and widely accepted nomenclature of the variants identified. Due to the differences in typing schemes, imposed by the diversity of genes targeted, creating these databases has typically required the writing of one-off code to link the database to a web interface. Here we describe agdbNet, widely applicable web database software that facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. Results Databases are described by XML files that are parsed by a Perl CGI script. Each database can have any number of loci, which may be defined by nucleotide and/or peptide sequences. The software is currently in use on at least five public databases for the typing of Neisseria meningitidis, Campylobacter jejuni and Streptococcus equi and can be set up to query internal isolate tables or suitably-configured external isolate databases, such as those used for multilocus sequence typing. The style of the resulting website can be fully configured by modifying stylesheets and through the use of customised header and footer files that surround the output of the script. Conclusion The software provides a rapid means of setting up customised Internet antigen sequence databases. The flexible configuration options enable typing schemes with differing requirements to be accommodated. PMID:16790057

Characteristics and molecular phylogeny of Fasciola flukes from Bangladesh, determined based on spermatogenesis and nuclear and mitochondrial DNA analyses.

PubMed

Mohanta, Uday Kumar; Ichikawa-Seki, Madoka; Shoriki, Takuya; Katakura, Ken; Itagaki, Tadashi

2014-07-01

This study aimed to precisely discriminate Fasciola spp. based on DNA sequences of nuclear internal transcribed spacer 1 (ITS1) and mitochondrial nicotinamide adenine dinucleotide (NADH) dehydrogenase subunit 1 (nad1) gene. We collected 150 adult flukes from the bile ducts of cattle, buffaloes, sheep, and goats from six different regions of Bangladesh. Spermatogenic status was determined by analyzing stained seminal vesicles. The ITS1 types were analyzed using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The nad1 haplotypes were identified based on PCR and direct sequencing and analyzed phylogenetically by comparing with nad1 haplotypes of Fasciola spp. from other Asian countries. Of the 127 aspermic flukes, 98 were identified as Fg type in ITS1, whereas 29 were identified as Fh/Fg type, indicating a combination of ITS1 sequences of Fasciola hepatica and Fasciola gigantica. All the 127 aspermic flukes showed Fsp-NDI-Bd11 in nad1 haplotype with nucleotide sequences identical to aspermic Fasciola sp. from Asian countries. Further, 20 spermic flukes were identified as F. gigantica based on their spermatogenic status and Fg type in ITS1. F. gigantica population was thought to be introduced into Bangladesh considerably earlier than the aspermic Fasciola sp. because 11 haplotypes with high haplotype diversity were detected from the F. gigantica population. However, three flukes from Bangladesh could not be precisely identified, because their spermatogenic status, ITS1 types, and nad1 haplotypes were ambiguous. Therefore, developing a robust method to distinguish aspermic Fasciola sp. from other Fasciola species is necessary in the future.

Population Based Assessment of MHC Class 1 Antigens Down Regulation as Marker in Increased Risk for Development and Progression of Breast Cancer From Benign Breast Lesions

DTIC Science & Technology

2006-01-01

isolated using a routine salting-out method (DNA E-Z Prepkit, Orchid Diagnostics Europe, St Katelijne Waver, Belgium). Sequence based typing In...electrophoresis using ethidiumbromide to show the single 2 KB band before sequencing. Next, sequencing reactions were performed separately for exons 2, 3...Multiplex reverse transcription-polymerase chain reaction for simultaneous screening of 29 translocations and chromosomal aberrations in acute

Non coding extremities of the seven influenza virus type C vRNA segments: effect on transcription and replication by the type C and type A polymerase complexes

PubMed Central

Crescenzo-Chaigne, Bernadette; Barbezange, Cyril; van der Werf, Sylvie

2008-01-01

Background The transcription/replication of the influenza viruses implicate the terminal nucleotide sequences of viral RNA, which comprise sequences at the extremities conserved among the genomic segments as well as variable 3' and 5' non-coding (NC) regions. The plasmid-based system for the in vivo reconstitution of functional ribonucleoproteins, upon expression of viral-like RNAs together with the nucleoprotein and polymerase proteins has been widely used to analyze transcription/replication of influenza viruses. It was thus shown that the type A polymerase could transcribe and replicate type A, B, or C vRNA templates whereas neither type B nor type C polymerases were able to transcribe and replicate type A templates efficiently. Here we studied the importance of the NC regions from the seven segments of type C influenza virus for efficient transcription/replication by the type A and C polymerases. Results The NC sequences of the seven genomic segments of the type C influenza virus C/Johannesburg/1/66 strain were found to be more variable in length than those of the type A and B viruses. The levels of transcription/replication of viral-like vRNAs harboring the NC sequences of the respective type C virus segments flanking the CAT reporter gene were comparable in the presence of either type C or type A polymerase complexes except for the NS and PB2-like vRNAs. For the NS-like vRNA, the transcription/replication level was higher after introduction of a U residue at position 6 in the 5' NC region as for all other segments. For the PB2-like vRNA the CAT expression level was particularly reduced with the type C polymerase. Analysis of mutants of the 5' NC sequence in the PB2-like vRNA, the shortest 5' NC sequence among the seven segments, showed that additional sequences within the PB2 ORF were essential for the efficiency of transcription but not replication by the type C polymerase complex. Conclusion In the context of a PB2-like reporter vRNA template, the sequence upstream the polyU stretch plays a role in the transcription/replication process by the type C polymerase complex. PMID:18973655

Study of mitochondria D-loop gene to detect the heterogeneity of gemak in Turnicidae family

NASA Astrophysics Data System (ADS)

Setiati, N.; Partaya

2018-03-01

As a part of life biodiversity, birds in Turnicidae family should be preserved from the extinction and its type heterogeneity decline. One effort for giving the strategic base of plasma nutfah conservation is through genetic heterogeneity study. The aim of the research is to analyze D-loop gen from DNA mitochondria of gemak bird in Turnicidae family molecularly. From the result of the analysis, it may be known the genetic heterogeneity of gemak bird based on the sequence of D-loop gen. The collection of both types of gemak of Turnicidae family is still easy since we can find them in ricefield area after harvest particularly for Gemakloreng (Turnix sylvatica), it means while gemak tegalan (Turnixsusciator) is getting difficult to find. Based on the above DNA quantification standard, the blood sample of Gemak in this research is mostly grouped into pure blood (ranges from 1,63 – 1,90), and it deserves to be used for PCR analysis. The sequencing analysis has not detected the sequence of nucleotide completely. However, it indicates sequence polymorphism of base as the arranger of D-loop gen. D-loop gen may identify genetic heterogeneity of gemak bird of Turnicidae family, but it is necessary to perform further sequencing analysis with PCR-RFLP technique. This complete nucleotide sequence is obtained and easy to detect after being cut restriction enzyme.

[Clustered regularly interspaced short palindromic repeats (CRISPR) site in Bacillus anthracis].

PubMed

Gao, Zhiqi; Wang, Dongshu; Feng, Erling; Wang, Bingxiang; Hui, Yiming; Han, Shaobo; Jiao, Lei; Liu, Xiankai; Wang, Hengliang

2014-11-04

To investigate the polymorphism of clustered regularly interspaced short palindromic repeats (CRISPR) in Bacillu santhracis and the application to molecular typing based on the polymorphism of CRISPR in B. anthracis. We downloaded the whole genome sequence of 6 B. anthracis strains and extracted the CRISPR sites. We designed the primers of CRISPR sites and amplified the CRISPR fragments in 193 B. anthracis strains by PCR and sequenced these fragments. In order to reveal the polymorphism of CRISPR in B. anthracis, wealigned all the extracted sequences and sequenced results by local blasting. At the same time, we also analyzed the CRISPR sites in B. cereus and B. thuringiensis. We did not find any polymorphism of CRISPR in B. anthracis. The molecular typing approach based on CRISPR polymorphism is not suitable for B. anthracis, but it is possible for us to distinguish B. anthracis from B. cereus and B. thuringiensis.

Classification of circulation type sequences applied to snow avalanches over the eastern Pyrenees (Andorra and Catalonia)

NASA Astrophysics Data System (ADS)

Esteban, Pere; Beck, Christoph; Philipp, Andreas

2010-05-01

Using data associated with accidents or damages caused by snow avalanches over the eastern Pyrenees (Andorra and Catalonia) several atmospheric circulation type catalogues have been obtained. For this purpose, different circulation type classification methods based on Principal Component Analysis (T-mode and S-mode using the extreme scores) and on optimization procedures (Improved K-means and SANDRA) were applied . Considering the characteristics of the phenomena studied, not only single day circulation patterns were taken into account but also sequences of circulation types of varying length. Thus different classifications with different numbers of types and for different sequence lengths were obtained using the different classification methods. Simple between type variability, within type variability, and outlier detection procedures have been applied for selecting the best result concerning snow avalanches type classifications. Furthermore, days without occurrence of the hazards were also related to the avalanche centroids using pattern-correlations, facilitating the calculation of the anomalies between hazardous and no hazardous days, and also frequencies of occurrence of hazardous events for each circulation type. Finally, the catalogues statistically considered the best results are evaluated using the avalanche forecaster expert knowledge. Consistent explanation of snow avalanches occurrence by means of circulation sequences is obtained, but always considering results from classifications with different sequence length. This work has been developed in the framework of the COST Action 733 (Harmonisation and Applications of Weather Type Classifications for European regions).

spa Typing and Multilocus Sequence Typing Show Comparable Performance in a Macroepidemiologic Study of Staphylococcus aureus in the United States

PubMed Central

O'Hara, F. Patrick; Suaya, Jose A.; Ray, G. Thomas; Baxter, Roger; Brown, Megan L.; Mera, Robertino M.; Close, Nicole M.; Thomas, Elizabeth

2016-01-01

A number of molecular typing methods have been developed for characterization of Staphylococcus aureus isolates. The utility of these systems depends on the nature of the investigation for which they are used. We compared two commonly used methods of molecular typing, multilocus sequence typing (MLST) (and its clustering algorithm, Based Upon Related Sequence Type [BURST]) with the staphylococcal protein A (spa) typing (and its clustering algorithm, Based Upon Repeat Pattern [BURP]), to assess the utility of these methods for macroepidemiology and evolutionary studies of S. aureus in the United States. We typed a total of 366 clinical isolates of S. aureus by these methods and evaluated indices of diversity and concordance values. Our results show that, when combined with the BURP clustering algorithm to delineate clonal lineages, spa typing produces results that are highly comparable with those produced by MLST/BURST. Therefore, spa typing is appropriate for use in macroepidemiology and evolutionary studies and, given its lower implementation cost, this method appears to be more efficient. The findings are robust and are consistent across different settings, patient ages, and specimen sources. Our results also support a model in which the methicillin-resistant S. aureus (MRSA) population in the United States comprises two major lineages (USA300 and USA100), which each consist of closely related variants. PMID:26669861

spa Typing and Multilocus Sequence Typing Show Comparable Performance in a Macroepidemiologic Study of Staphylococcus aureus in the United States.

PubMed

O'Hara, F Patrick; Suaya, Jose A; Ray, G Thomas; Baxter, Roger; Brown, Megan L; Mera, Robertino M; Close, Nicole M; Thomas, Elizabeth; Amrine-Madsen, Heather

2016-01-01

A number of molecular typing methods have been developed for characterization of Staphylococcus aureus isolates. The utility of these systems depends on the nature of the investigation for which they are used. We compared two commonly used methods of molecular typing, multilocus sequence typing (MLST) (and its clustering algorithm, Based Upon Related Sequence Type [BURST]) with the staphylococcal protein A (spa) typing (and its clustering algorithm, Based Upon Repeat Pattern [BURP]), to assess the utility of these methods for macroepidemiology and evolutionary studies of S. aureus in the United States. We typed a total of 366 clinical isolates of S. aureus by these methods and evaluated indices of diversity and concordance values. Our results show that, when combined with the BURP clustering algorithm to delineate clonal lineages, spa typing produces results that are highly comparable with those produced by MLST/BURST. Therefore, spa typing is appropriate for use in macroepidemiology and evolutionary studies and, given its lower implementation cost, this method appears to be more efficient. The findings are robust and are consistent across different settings, patient ages, and specimen sources. Our results also support a model in which the methicillin-resistant S. aureus (MRSA) population in the United States comprises two major lineages (USA300 and USA100), which each consist of closely related variants.

Whole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.

PubMed

Schürch, A C; Arredondo-Alonso, S; Willems, R J L; Goering, R V

2018-04-01

Whole genome sequence (WGS)-based strain typing finds increasing use in the epidemiologic analysis of bacterial pathogens in both public health as well as more localized infection control settings. This minireview describes methodologic approaches that have been explored for WGS-based epidemiologic analysis and considers the challenges and pitfalls of data interpretation. Personal collection of relevant publications. When applying WGS to study the molecular epidemiology of bacterial pathogens, genomic variability between strains is translated into measures of distance by determining single nucleotide polymorphisms in core genome alignments or by indexing allelic variation in hundreds to thousands of core genes, assigning types to unique allelic profiles. Interpreting isolate relatedness from these distances is highly organism specific, and attempts to establish species-specific cutoffs are unlikely to be generally applicable. In cases where single nucleotide polymorphism or core gene typing do not provide the resolution necessary for accurate assessment of the epidemiology of bacterial pathogens, inclusion of accessory gene or plasmid sequences may provide the additional required discrimination. As with all epidemiologic analysis, realizing the full potential of the revolutionary advances in WGS-based approaches requires understanding and dealing with issues related to the fundamental steps of data generation and interpretation. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Discovery of a bovine enterovirus in alpaca.

PubMed

McClenahan, Shasta D; Scherba, Gail; Borst, Luke; Fredrickson, Richard L; Krause, Philip R; Uhlenhaut, Christine

2013-01-01

A cytopathic virus was isolated using Madin-Darby bovine kidney (MDBK) cells from lung tissue of alpaca that died of a severe respiratory infection. To identify the virus, the infected cell culture supernatant was enriched for virus particles and a generic, PCR-based method was used to amplify potential viral sequences. Genomic sequence data of the alpaca isolate was obtained and compared with sequences of known viruses. The new alpaca virus sequence was most similar to recently designated Enterovirus species F, previously bovine enterovirus (BEVs), viruses that are globally prevalent in cattle, although they appear not to cause significant disease. Because bovine enteroviruses have not been previously reported in U.S. alpaca, we suspect that this type of infection is fairly rare, and in this case appeared not to spread beyond the original outbreak. The capsid sequence of the detected virus had greatest homology to Enterovirus F type 1 (indicating that the virus should be considered a member of serotype 1), but the virus had greater homology in 2A protease sequence to type 3, suggesting that it may have been a recombinant. Identifying pathogens that infect a new host species for the first time can be challenging. As the disease in a new host species may be quite different from that in the original or natural host, the pathogen may not be suspected based on the clinical presentation, delaying diagnosis. Although this virus replicated in MDBK cells, existing standard culture and molecular methods could not identify it. In this case, a highly sensitive generic PCR-based pathogen-detection method was used to identify this pathogen.

Discovery of a Bovine Enterovirus in Alpaca

PubMed Central

McClenahan, Shasta D.; Scherba, Gail; Borst, Luke; Fredrickson, Richard L.; Krause, Philip R.; Uhlenhaut, Christine

2013-01-01

A cytopathic virus was isolated using Madin-Darby bovine kidney (MDBK) cells from lung tissue of alpaca that died of a severe respiratory infection. To identify the virus, the infected cell culture supernatant was enriched for virus particles and a generic, PCR-based method was used to amplify potential viral sequences. Genomic sequence data of the alpaca isolate was obtained and compared with sequences of known viruses. The new alpaca virus sequence was most similar to recently designated Enterovirus species F, previously bovine enterovirus (BEVs), viruses that are globally prevalent in cattle, although they appear not to cause significant disease. Because bovine enteroviruses have not been previously reported in U.S. alpaca, we suspect that this type of infection is fairly rare, and in this case appeared not to spread beyond the original outbreak. The capsid sequence of the detected virus had greatest homology to Enterovirus F type 1 (indicating that the virus should be considered a member of serotype 1), but the virus had greater homology in 2A protease sequence to type 3, suggesting that it may have been a recombinant. Identifying pathogens that infect a new host species for the first time can be challenging. As the disease in a new host species may be quite different from that in the original or natural host, the pathogen may not be suspected based on the clinical presentation, delaying diagnosis. Although this virus replicated in MDBK cells, existing standard culture and molecular methods could not identify it. In this case, a highly sensitive generic PCR-based pathogen-detection method was used to identify this pathogen. PMID:23950875

A novel wavelet sequence based on deep bidirectional LSTM network model for ECG signal classification.

PubMed

Yildirim, Özal

2018-05-01

Long-short term memory networks (LSTMs), which have recently emerged in sequential data analysis, are the most widely used type of recurrent neural networks (RNNs) architecture. Progress on the topic of deep learning includes successful adaptations of deep versions of these architectures. In this study, a new model for deep bidirectional LSTM network-based wavelet sequences called DBLSTM-WS was proposed for classifying electrocardiogram (ECG) signals. For this purpose, a new wavelet-based layer is implemented to generate ECG signal sequences. The ECG signals were decomposed into frequency sub-bands at different scales in this layer. These sub-bands are used as sequences for the input of LSTM networks. New network models that include unidirectional (ULSTM) and bidirectional (BLSTM) structures are designed for performance comparisons. Experimental studies have been performed for five different types of heartbeats obtained from the MIT-BIH arrhythmia database. These five types are Normal Sinus Rhythm (NSR), Ventricular Premature Contraction (VPC), Paced Beat (PB), Left Bundle Branch Block (LBBB), and Right Bundle Branch Block (RBBB). The results show that the DBLSTM-WS model gives a high recognition performance of 99.39%. It has been observed that the wavelet-based layer proposed in the study significantly improves the recognition performance of conventional networks. This proposed network structure is an important approach that can be applied to similar signal processing problems. Copyright © 2018 Elsevier Ltd. All rights reserved.

Genotype-specific signal generation based on digestion of 3-way DNA junctions: application to KRAS variation detection.

PubMed

Amicarelli, Giulia; Adlerstein, Daniel; Shehi, Erlet; Wang, Fengfei; Makrigiorgos, G Mike

2006-10-01

Genotyping methods that reveal single-nucleotide differences are useful for a wide range of applications. We used digestion of 3-way DNA junctions in a novel technology, OneCutEventAmplificatioN (OCEAN) that allows sequence-specific signal generation and amplification. We combined OCEAN with peptide-nucleic-acid (PNA)-based variant enrichment to detect and simultaneously genotype v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) codon 12 sequence variants in human tissue specimens. We analyzed KRAS codon 12 sequence variants in 106 lung cancer surgical specimens. We conducted a PNA-PCR reaction that suppresses wild-type KRAS amplification and genotyped the product with a set of OCEAN reactions carried out in fluorescence microplate format. The isothermal OCEAN assay enabled a 3-way DNA junction to form between the specific target nucleic acid, a fluorescently labeled "amplifier", and an "anchor". The amplifier-anchor contact contains the recognition site for a restriction enzyme. Digestion produces a cleaved amplifier and generation of a fluorescent signal. The cleaved amplifier dissociates from the 3-way DNA junction, allowing a new amplifier to bind and propagate the reaction. The system detected and genotyped KRAS sequence variants down to approximately 0.3% variant-to-wild-type alleles. PNA-PCR/OCEAN had a concordance rate with PNA-PCR/sequencing of 93% to 98%, depending on the exact implementation. Concordance rate with restriction endonuclease-mediated selective-PCR/sequencing was 89%. OCEAN is a practical and low-cost novel technology for sequence-specific signal generation. Reliable analysis of KRAS sequence alterations in human specimens circumvents the requirement for sequencing. Application is expected in genotyping KRAS codon 12 sequence variants in surgical specimens or in bodily fluids, as well as single-base variations and sequence alterations in other genes.

Free energy determinants of secondary structure formation: III. beta-turns and their role in protein folding.

PubMed

Yang, A S; Hitz, B; Honig, B

1996-06-21

The stability of beta-turns is calculated as a function of sequence and turn type with a Monte Carlo sampling technique. The conformational energy of four internal hydrogen-bonded turn types, I, I', II and II', is obtained by evaluating their gas phase energy with the CHARMM force field and accounting for solvation effects with the Finite Difference Poisson-Boltzmann (FDPB) method. All four turn types are found to be less stable than the coil state, independent of the sequence in the turn. The free-energy penalties associated with turn formation vary between 1.6 kcal/mol and 7.7 kcal/mol, depending on the sequence and turn type. Differences in turn stability arise mainly from intraresidue interactions within the two central residues of the turn. For each combination of the two central residues, except for -Gly-Gly-, the most stable beta-turn type is always found to occur most commonly in native proteins. The fact that a model based on local interactions accounts for the observed preference of specific sequences suggests that long-range tertiary interactions tend to play a secondary role in determining turn conformation. In contrast, for beta-hairpins, long-range interactions appear to dominate. Specifically, due to the right-handed twist of beta-strands, type I' turns for -Gly-Gly- are found to occur with high frequency, even when local energetics would dictate otherwise. The fact that any combination of two residues is found able to adopt a relatively low-energy turn structure explains why the amino acid sequence in turns is highly variable. The calculated free-energy cost of turn formation, when combined with related numbers obtained for alpha-helices and beta-sheets, suggests a model for the initiation of protein folding based on metastable fragments of secondary structure.

Identification of Fasciola species based on mitochondrial and nuclear DNA reveals the co-existence of intermediate Fasciola and Fasciola gigantica in Thailand.

PubMed

Wannasan, Anchalee; Khositharattanakool, Pathamet; Chaiwong, Prasong; Piangjai, Somsak; Uparanukraw, Pichart; Morakote, Nimit

2014-11-01

Molecular techniques were used to identify Fasciola species collected from Chiang Mai Thailand. Morphometrically, 65 stained and 45 fresh worms collected from cattle suggested the possible occurrence of both F. gigantica and F. hepatica. Twenty-two worms comprising 15 from cattle and 7 from human patients, were identified subsequently based on three genetic markers: mitochondrial nicotinamide adenine dinucleotide dehydrogenase subunit 1 (nad1), mitochondrial cytochrome c oxidase subunit 1 (cox1) and nuclear ribosomal internal transcribed spacer 2 (ITS2). All of them presented the F. gigantica type in maternally inherited mitochondrial sequences (nad1 and cox1), with six types in each sequence (FgNDI-CM1 to FgNDI-CM6 and FgCOI-CM1 to FgCOI-CM6, respectively). Remarkably, the predominant nad1 type, FgNDI-CM6, was identical to that of aspermic Fasciola sp. formerly reported from Thailand, Japan, Korea, China, Vietnam, and Myanmar. ITS2 sequences were analyzed successfully in 20 worms. Fifteen worms showed the F. gigantica type and five (including one worm from a patient) had mixed ITS2 sequences of both F. gigantica and F. hepatica in the same worms, with additional heterogeneity within both ITS2 types. This study revealed the intermediate form of Fasciola coexisting with F. gigantica for the first time in Thailand.

The Fundamental Plane and the Surface Brightness Test for the Expansion of the Universe

NASA Astrophysics Data System (ADS)

Kjaergaard, Per; Jorgensen, Inger; Moles, Mariano

1993-12-01

We have determined the Petrosian radius, rη , and the enclosed mean surface brightness within the Petrosian radius, <μ>η, for 33 elliptical and S0 galaxies in the Coma cluster from new accurate CCD surface photometry. For the Petrosian parameter η = 1.39, rη and <μ>η are compared with the effective radius, re, and the effective mean surface brightness, <μ>e derived from fitting a de Vaucouleurs law. The fundamental plane (FP) expressed using rη and <μ>η is the same as the FP found by Jørgensen, Franx, & Kjaergaard (1993) using re and <μ>e. The FP can be used to predict the mean surface brightness within the effective radius or the corresponding Petrosian radius (η = 1.39) with an uncertainty of ±0.14 mag for Coma cluster ellipticals. Thus the FP, applied to clusters, appears to be a suitable tool for performing the surface brightness test (SBT) for the expansion of the universe. We suggest that instead of correcting individual galaxies to some standard conditions, e.g., the same metric radius, the fundamental plane itself should be considered the standard. It is argued that the metric size enclosing around 75% of the total light represents a reasonable compromise between resolution and faint level detection when performing the SBT. This radius could be derived as the Petrosian radius corresponding to η = 2.0 or from a global fit to that part of the observed profile which encompasses 75% of the total light. In case both small and large galaxies are well described by a de Vaucouleurs law the global fit can be performed on a smaller central part of the brightness profile. The use of the FP involves the time consuming determinations of velocity dispersions. We find that <μ>η (η = 1.39) can be predicted from the log rη alone with an accuracy of 0.3 mag for the Coma cluster ellipticals. Our discussion of the various error contributions to the predicted mean surface brightness for faint cluster ellipticals at redshifts z < 0.5 shows that the final error is probably dominated by extra scatter due to, e.g., environmental and evolutionary effects. Thus it might be possible that the use of velocity dispersions are not necessary. To get significant results for the SBT, clusters out to a redshift of approximately z = 0.3 have to be observed. For the most distant galaxies light levels down to about 25-26 mag arcsec-2 in the red and sizes as small as approximately 2" have to be accurately measured. We outline an observational program which will allow the control of the different sources of scatter, including cosmic evolution, producing conclusive results about the expansion of the universe.

Reconsideration of Protocrea (Hypocreales, Hypocreaceae)

USDA-ARS?s Scientific Manuscript database

The genus Protocrea is re-defined, based on holotype and fresh specimens of its type species P. farinosa, using morphology of teleomorph and anamorph and phylogenetic analyses of rpb2 sequences. Data based on currently available specimens suggest the existence of six species. Apart from the type, P....

Sequencing artifacts in the type A influenza databases and attempts to correct them.

PubMed

Suarez, David L; Chester, Nikki; Hatfield, Jason

2014-07-01

There are over 276 000 influenza gene sequences in public databases, with the quality of the sequences determined by the contributor. As part of a high school class project, influenza sequences with possible errors were identified in the public databases based on the size of the gene being longer than expected, with the hypothesis that these sequences would have an error. Students contacted sequence submitters alerting them of the possible sequence issue(s) and requested they the suspect sequence(s) be correct as appropriate. Type A influenza viruses were screened, and gene segments longer than the accepted size were identified for further analysis. Attention was placed on sequences with additional nucleotides upstream or downstream of the highly conserved non-coding ends of the viral segments. A total of 1081 sequences were identified that met this criterion. Three types of errors were commonly observed: non-influenza primer sequence wasn't removed from the sequence; PCR product was cloned and plasmid sequence was included in the sequence; and Taq polymerase added an adenine at the end of the PCR product. Internal insertions of nucleotide sequence were also commonly observed, but in many cases it was unclear if the sequence was correct or actually contained an error. A total of 215 sequences, or 22.8% of the suspect sequences, were corrected in the public databases in the first year of the student project. Unfortunately 138 additional sequences with possible errors were added to the databases in the second year. Additional awareness of the need for data integrity of sequences submitted to public databases is needed to fully reap the benefits of these large data sets. © 2014 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

Identification, Classification, and Phylogeny of the Pathogenic Species Exophiala jeanselmei and Related Species by Mitochondrial Cytochrome b Gene Analysis

PubMed Central

Wang, Li; Yokoyama, Koji; Miyaji, Makoto; Nishimura, Kazuko

2001-01-01

We analyzed a 402-bp sequence of the mitochondrial cytochrome b gene of 34 strains of Exophiala jeanselmei and 16 strains representing 12 related species. The strains of E. jeanselmei were classified into 20 DNA types and 17 amino acid types. The differences between these strains were found in 1 to 60 nucleotides and 1 to 17 amino acids. On the basis of the identities and similarities of nucleotide and amino acid sequences, some strains were reidentified: i.e., two strains of E. jeanselmei var. hetermorpha and one strain of E. castellanii as E. dermatitidis (including the type strain), three strains of E. jeanselmei as E. jeanselmei var. lecanii-corni (including the type strain), three strains of E. jeanselmei as E. bergeri (including the type strain), seven strains of E. jeanselmei as E. pisciphila (including the type strain), seven strains of E. jeanselmei as E. jeanselmei var. jeanselmei (including the type strain), one strain of E. jeanselmei as Fonsecaea pedrosoi (including the type strain), and one strain of E. jeanselmei as E. spinifera (including the type strain). Some E. jeanselmei strains showed distinct nucleotide and amino acid sequences. The amino-acid-based UPGMA (unweighted pair group method with the arithmetic mean) tree exhibited nearly the same topology as those of the DNA-based trees obtained by neighbor joining, maximum parsimony, and maximum likelihood methods. PMID:11724862

KpnBI is the prototype of a new family (IE) of bacterial type I restriction-modification system

PubMed Central

Chin, V.; Valinluck, V.; Magaki, S.; Ryu, J.

2004-01-01

KpnBI is a restriction-modification (R-M) system recognized in the GM236 strain of Klebsiella pneumoniae. Here, the KpnBI modification genes were cloned into a plasmid using a modification expression screening method. The modification genes that consist of both hsdM (2631 bp) and hsdS (1344 bp) genes were identified on an 8.2 kb EcoRI chromosomal fragment. These two genes overlap by one base and share the same promoter located upstream of the hsdM gene. Using recently developed plasmid R-M tests and a computer program RM Search, the DNA recognition sequence for the KpnBI enzymes was identified as a new 8 nt sequence containing one degenerate base with a 6 nt spacer, CAAANNNNNNRTCA. From Dam methylation and HindIII sensitivity tests, the methylation loci were predicted to be the italicized third adenine in the 5′ specific region and the adenine opposite the italicized thymine in the 3′ specific region. Combined with previous sequence data for hsdR, we concluded that the KpnBI system is a typical type I R-M system. The deduced amino acid sequences of the three subunits of the KpnBI system show only limited homologies (25 to 33% identity) at best, to the four previously categorized type I families (IA, IB, IC, and ID). Furthermore, their identity scores to other uncharacterized putative genome type I sequences were 53% at maximum. Therefore, we propose that KpnBI is the prototype of a new ‘type IE’ family. PMID:15475385

Mitochondrial sequence divergence among Antarctic killer whale ecotypes is consistent with multiple species.

PubMed

LeDuc, Richard G; Robertson, Kelly M; Pitman, Robert L

2008-08-23

Recently, three visually distinct forms of killer whales (Orcinus orca) were described from Antarctic waters and designated as types A, B and C. Based on consistent differences in prey selection and habitat preferences, morphological divergence and apparent lack of interbreeding among these broadly sympatric forms, it was suggested that they may represent separate species. To evaluate this hypothesis, we compared complete sequences of the mitochondrial control region from 81 Antarctic killer whale samples, including 9 type A, 18 type B, 47 type C and 7 type-undetermined individuals. We found three fixed differences that separated type A from B and C, and a single fixed difference that separated type C from A and B. These results are consistent with reproductive isolation among the different forms, although caution is needed in drawing further conclusions. Despite dramatic differences in morphology and ecology, the relatively low levels of sequence divergence in Antarctic killer whales indicate that these evolutionary changes occurred relatively rapidly and recently.

A Pedagogical Theory and Practice for College Writing Courses and Writing across the Curriculum Courses: A Social Constructionist Perspective on Learning through Argument.

ERIC Educational Resources Information Center

Soffree-Cady, Flore

To provide a writing pedagogy grounded in theory, a teaching method was developed which sequenced certain types of assignments. The classification of types and the organizational structure of the sequences were based on a teaching model that draws upon theories from various disciplines. Although the teaching activities are not new in themselves,…

A Bioinformatics-Based Alternative mRNA Splicing Code that May Explain Some Disease Mutations Is Conserved in Animals.

PubMed

Qu, Wen; Cingolani, Pablo; Zeeberg, Barry R; Ruden, Douglas M

2017-01-01

Deep sequencing of cDNAs made from spliced mRNAs indicates that most coding genes in many animals and plants have pre-mRNA transcripts that are alternatively spliced. In pre-mRNAs, in addition to invariant exons that are present in almost all mature mRNA products, there are at least 6 additional types of exons, such as exons from alternative promoters or with alternative polyA sites, mutually exclusive exons, skipped exons, or exons with alternative 5' or 3' splice sites. Our bioinformatics-based hypothesis is that, in analogy to the genetic code, there is an "alternative-splicing code" in introns and flanking exon sequences, analogous to the genetic code, that directs alternative splicing of many of the 36 types of introns. In humans, we identified 42 different consensus sequences that are each present in at least 100 human introns. 37 of the 42 top consensus sequences are significantly enriched or depleted in at least one of the 36 types of introns. We further supported our hypothesis by showing that 96 out of 96 analyzed human disease mutations that affect RNA splicing, and change alternative splicing from one class to another, can be partially explained by a mutation altering a consensus sequence from one type of intron to that of another type of intron. Some of the alternative splicing consensus sequences, and presumably their small-RNA or protein targets, are evolutionarily conserved from 50 plant to animal species. We also noticed the set of introns within a gene usually share the same splicing codes, thus arguing that one sub-type of splicesosome might process all (or most) of the introns in a given gene. Our work sheds new light on a possible mechanism for generating the tremendous diversity in protein structure by alternative splicing of pre-mRNAs.

Identification of Trypanosoma cruzi Discrete Typing Units (DTUs) in Latin-American migrants in Barcelona (Spain).

PubMed

Abras, Alba; Gállego, Montserrat; Muñoz, Carmen; Juiz, Natalia A; Ramírez, Juan Carlos; Cura, Carolina I; Tebar, Silvia; Fernández-Arévalo, Anna; Pinazo, María-Jesús; de la Torre, Leonardo; Posada, Elizabeth; Navarro, Ferran; Espinal, Paula; Ballart, Cristina; Portús, Montserrat; Gascón, Joaquim; Schijman, Alejandro G

2017-04-01

Trypanosoma cruzi, the causative agent of Chagas disease, is divided into six Discrete Typing Units (DTUs): TcI-TcVI. We aimed to identify T. cruzi DTUs in Latin-American migrants in the Barcelona area (Spain) and to assess different molecular typing approaches for the characterization of T. cruzi genotypes. Seventy-five peripheral blood samples were analyzed by two real-time PCR methods (qPCR) based on satellite DNA (SatDNA) and kinetoplastid DNA (kDNA). The 20 samples testing positive in both methods, all belonging to Bolivian individuals, were submitted to DTU characterization using two PCR-based flowcharts: multiplex qPCR using TaqMan probes (MTq-PCR), and conventional PCR. These samples were also studied by sequencing the SatDNA and classified as type I (TcI/III), type II (TcII/IV) and type I/II hybrid (TcV/VI). Ten out of the 20 samples gave positive results in the flowcharts: TcV (5 samples), TcII/V/VI (3) and mixed infections by TcV plus TcII (1) and TcV plus TcII/VI (1). By SatDNA sequencing, we classified the 20 samples, 19 as type I/II and one as type I. The most frequent DTU identified by both flowcharts, and suggested by SatDNA sequencing in the remaining samples with low parasitic loads, TcV, is common in Bolivia and predominant in peripheral blood. The mixed infection by TcV-TcII was detected for the first time simultaneously in Bolivian migrants. PCR-based flowcharts are very useful to characterize DTUs during acute infection. SatDNA sequence analysis cannot discriminate T. cruzi populations at the level of a single DTU but it enabled us to increase the number of characterized cases in chronically infected patients. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Several Families of Sequences with Low Correlation and Large Linear Span

NASA Astrophysics Data System (ADS)

Zeng, Fanxin; Zhang, Zhenyu

In DS-CDMA systems and DS-UWB radios, low correlation of spreading sequences can greatly help to minimize multiple access interference (MAI) and large linear span of spreading sequences can reduce their predictability. In this letter, new sequence sets with low correlation and large linear span are proposed. Based on the construction Trm1[Trnm(αbt+γiαdt)]r for generating p-ary sequences of period pn-1, where n=2m, d=upm±v, b=u±v, γi∈GF(pn), and p is an arbitrary prime number, several methods to choose the parameter d are provided. The obtained sequences with family size pn are of four-valued, five-valued, six-valued or seven-valued correlation and the maximum nontrivial correlation value is (u+v-1)pm-1. The simulation by a computer shows that the linear span of the new sequences is larger than that of the sequences with Niho-type and Welch-type decimations, and similar to that of [10].

On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy.

PubMed

Coulthart, Michael B; Posada, David; Crandall, Keith A; Dekaban, Gregory A

2006-03-01

Recently, the putative finding of ancient human T cell leukemia virus type 1 (HTLV-1) long terminal repeat (LTR) DNA sequences in association with a 1500-year-old Chilean mummy has stirred vigorous debate. The debate is based partly on the inherent uncertainties associated with phylogenetic reconstruction when only short sequences of closely related genotypes are available. However, a full analysis of what phylogenetic information is present in the mummy data has not previously been published, leaving open the question of what precisely is the range of admissible interpretation. To fulfill this need, we re-analyzed the mummy data in a new way. We first performed phylogenetic analysis of 188 published LTR DNA sequences from extant strains belonging to the HTLV-1 Cosmopolitan clade, using the method of statistical parsimony which is designed both to optimize phylogenetic resolution among sequences with little evolutionary divergence, and to permit precise mapping of individual sequence mutations onto branches of a divergence network. We then deduced possible phylogenetic positions for the two main categories of published Chilean mummy sequences, based on their published 157-nucleotide LTR sequences. The possible phylogenetic placements for one of the mummy sequence categories are consistent with a modern origin. However, one of these placements for the other mummy sequence category falls very close to the root of the Cosmopolitan clade, consistent with an ancient origin for both this mummy sequence and the Cosmopolitan clade.

Core Genome Multilocus Sequence Typing Scheme for High-Resolution Typing of Enterococcus faecium

PubMed Central

de Been, Mark; Pinholt, Mette; Top, Janetta; Bletz, Stefan; van Schaik, Willem; Brouwer, Ellen; Rogers, Malbert; Kraat, Yvette; Bonten, Marc; Corander, Jukka; Westh, Henrik; Harmsen, Dag

2015-01-01

Enterococcus faecium, a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium. However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium. cgMLST transfers genome-wide single nucleotide polymorphism (SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks. PMID:26400782

Core Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium.

PubMed

de Been, Mark; Pinholt, Mette; Top, Janetta; Bletz, Stefan; Mellmann, Alexander; van Schaik, Willem; Brouwer, Ellen; Rogers, Malbert; Kraat, Yvette; Bonten, Marc; Corander, Jukka; Westh, Henrik; Harmsen, Dag; Willems, Rob J L

2015-12-01

Enterococcus faecium, a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium. However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium. cgMLST transfers genome-wide single nucleotide polymorphism(SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks.

Microgravity

NASA Image and Video Library

1998-12-01

Type II restriction enzymes, such as Eco R1 endonulease, present a unique advantage for the study of sequence-specific recognition because they leave a record of where they have been in the form of the cleaved ends of the DNA sites where they were bound. The differential behavior of a sequence -specific protein at sites of differing base sequence is the essence of the sequence-specificity; the core question is how do these proteins discriminate between different DNA sequences especially when the two sequences are very similar. Principal Investigator: Dan Carter/New Century Pharmaceuticals

Protein Crystal Eco R1 Endonulease-DNA Complex

NASA Technical Reports Server (NTRS)

1998-01-01

Type II restriction enzymes, such as Eco R1 endonulease, present a unique advantage for the study of sequence-specific recognition because they leave a record of where they have been in the form of the cleaved ends of the DNA sites where they were bound. The differential behavior of a sequence -specific protein at sites of differing base sequence is the essence of the sequence-specificity; the core question is how do these proteins discriminate between different DNA sequences especially when the two sequences are very similar. Principal Investigator: Dan Carter/New Century Pharmaceuticals

Statistical theory for protein combinatorial libraries. Packing interactions, backbone flexibility, and the sequence variability of a main-chain structure.

PubMed

Kono, H; Saven, J G

2001-02-23

Combinatorial experiments provide new ways to probe the determinants of protein folding and to identify novel folding amino acid sequences. These types of experiments, however, are complicated both by enormous conformational complexity and by large numbers of possible sequences. Therefore, a quantitative computational theory would be helpful in designing and interpreting these types of experiment. Here, we present and apply a statistically based, computational approach for identifying the properties of sequences compatible with a given main-chain structure. Protein side-chain conformations are included in an atom-based fashion. Calculations are performed for a variety of similar backbone structures to identify sequence properties that are robust with respect to minor changes in main-chain structure. Rather than specific sequences, the method yields the likelihood of each of the amino acids at preselected positions in a given protein structure. The theory may be used to quantify the characteristics of sequence space for a chosen structure without explicitly tabulating sequences. To account for hydrophobic effects, we introduce an environmental energy that it is consistent with other simple hydrophobicity scales and show that it is effective for side-chain modeling. We apply the method to calculate the identity probabilities of selected positions of the immunoglobulin light chain-binding domain of protein L, for which many variant folding sequences are available. The calculations compare favorably with the experimentally observed identity probabilities.

Mapping Base Modifications in DNA by Transverse-Current Sequencing

NASA Astrophysics Data System (ADS)

Alvarez, Jose R.; Skachkov, Dmitry; Massey, Steven E.; Kalitsov, Alan; Velev, Julian P.

2018-02-01

Sequencing DNA modifications and lesions, such as methylation of cytosine and oxidation of guanine, is even more important and challenging than sequencing the genome itself. The traditional methods for detecting DNA modifications are either insensitive to these modifications or require additional processing steps to identify a particular type of modification. Transverse-current sequencing in nanopores can potentially identify the canonical bases and base modifications in the same run. In this work, we demonstrate that the most common DNA epigenetic modifications and lesions can be detected with any predefined accuracy based on their tunneling current signature. Our results are based on simulations of the nanopore tunneling current through DNA molecules, calculated using nonequilibrium electron-transport methodology within an effective multiorbital model derived from first-principles calculations, followed by a base-calling algorithm accounting for neighbor current-current correlations. This methodology can be integrated with existing experimental techniques to improve base-calling fidelity.

Single Assay for Simultaneous Detection and Differential Identification of Human and Avian Influenza Virus Types, Subtypes, and Emergent Variants

PubMed Central

Metzgar, David; Myers, Christopher A.; Russell, Kevin L.; Faix, Dennis; Blair, Patrick J.; Brown, Jason; Vo, Scott; Swayne, David E.; Thomas, Colleen; Stenger, David A.; Lin, Baochuan; Malanoski, Anthony P.; Wang, Zheng; Blaney, Kate M.; Long, Nina C.; Schnur, Joel M.; Saad, Magdi D.; Borsuk, Lisa A.; Lichanska, Agnieszka M.; Lorence, Matthew C.; Weslowski, Brian; Schafer, Klaus O.; Tibbetts, Clark

2010-01-01

For more than four decades the cause of most type A influenza virus infections of humans has been attributed to only two viral subtypes, A/H1N1 or A/H3N2. In contrast, avian and other vertebrate species are a reservoir of type A influenza virus genome diversity, hosting strains representing at least 120 of 144 combinations of 16 viral hemagglutinin and 9 viral neuraminidase subtypes. Viral genome segment reassortments and mutations emerging within this reservoir may spawn new influenza virus strains as imminent epidemic or pandemic threats to human health and poultry production. Traditional methods to detect and differentiate influenza virus subtypes are either time-consuming and labor-intensive (culture-based) or remarkably insensitive (antibody-based). Molecular diagnostic assays based upon reverse transcriptase-polymerase chain reaction (RT-PCR) have short assay cycle time, and high analytical sensitivity and specificity. However, none of these diagnostic tests determine viral gene nucleotide sequences to distinguish strains and variants of a detected pathogen from one specimen to the next. Decision-quality, strain- and variant-specific pathogen gene sequence information may be critical for public health, infection control, surveillance, epidemiology, or medical/veterinary treatment planning. The Resequencing Pathogen Microarray (RPM-Flu) is a robust, highly multiplexed and target gene sequencing-based alternative to both traditional culture- or biomarker-based diagnostic tests. RPM-Flu is a single, simultaneous differential diagnostic assay for all subtype combinations of type A influenza viruses and for 30 other viral and bacterial pathogens that may cause influenza-like illness. These other pathogen targets of RPM-Flu may co-infect and compound the morbidity and/or mortality of patients with influenza. The informative specificity of a single RPM-Flu test represents specimen-specific viral gene sequences as determinants of virus type, A/HN subtype, virulence, host-range, and resistance to antiviral agents. PMID:20140251

Single assay for simultaneous detection and differential identification of human and avian influenza virus types, subtypes, and emergent variants.

PubMed

Metzgar, David; Myers, Christopher A; Russell, Kevin L; Faix, Dennis; Blair, Patrick J; Brown, Jason; Vo, Scott; Swayne, David E; Thomas, Colleen; Stenger, David A; Lin, Baochuan; Malanoski, Anthony P; Wang, Zheng; Blaney, Kate M; Long, Nina C; Schnur, Joel M; Saad, Magdi D; Borsuk, Lisa A; Lichanska, Agnieszka M; Lorence, Matthew C; Weslowski, Brian; Schafer, Klaus O; Tibbetts, Clark

2010-02-03

For more than four decades the cause of most type A influenza virus infections of humans has been attributed to only two viral subtypes, A/H1N1 or A/H3N2. In contrast, avian and other vertebrate species are a reservoir of type A influenza virus genome diversity, hosting strains representing at least 120 of 144 combinations of 16 viral hemagglutinin and 9 viral neuraminidase subtypes. Viral genome segment reassortments and mutations emerging within this reservoir may spawn new influenza virus strains as imminent epidemic or pandemic threats to human health and poultry production. Traditional methods to detect and differentiate influenza virus subtypes are either time-consuming and labor-intensive (culture-based) or remarkably insensitive (antibody-based). Molecular diagnostic assays based upon reverse transcriptase-polymerase chain reaction (RT-PCR) have short assay cycle time, and high analytical sensitivity and specificity. However, none of these diagnostic tests determine viral gene nucleotide sequences to distinguish strains and variants of a detected pathogen from one specimen to the next. Decision-quality, strain- and variant-specific pathogen gene sequence information may be critical for public health, infection control, surveillance, epidemiology, or medical/veterinary treatment planning. The Resequencing Pathogen Microarray (RPM-Flu) is a robust, highly multiplexed and target gene sequencing-based alternative to both traditional culture- or biomarker-based diagnostic tests. RPM-Flu is a single, simultaneous differential diagnostic assay for all subtype combinations of type A influenza viruses and for 30 other viral and bacterial pathogens that may cause influenza-like illness. These other pathogen targets of RPM-Flu may co-infect and compound the morbidity and/or mortality of patients with influenza. The informative specificity of a single RPM-Flu test represents specimen-specific viral gene sequences as determinants of virus type, A/HN subtype, virulence, host-range, and resistance to antiviral agents.

Detection of cystic fibrosis transmembrane conductance regulator ΔF508 gene mutation using a paper-based nucleic acid hybridization assay and a smartphone camera.

PubMed

Malhotra, Karan; Noor, M Omair; Krull, Ulrich J

2018-05-29

Diagnostic technology that makes use of paper platforms in conjunction with the ubiquitous availability of digital cameras in cellular telephones and personal assistive devices offers opportunities for development of bioassays that are cost effective and widely distributed. Assays that operate effectively in aqueous solution require further development for implementation in paper substrates, overcoming issues associated with surface interactions on a matrix that offers a large surface-to-volume ratio and constraints on convective mixing. This report presents and compares two related methods for determination of oligonucleotides that serve as indicators of cystic fibrosis, differentiating between the normal wild-type sequence, and a mutant-type sequence that has a 3-base replacement. The transduction strategy operates by selective hybridization of oligonucleotide probes that are conjugated to fluorescent quantum dots, where hybridization of target sequences causes a molecular fluorophore to approach the quantum dot and become emissive through fluorescence resonance energy transfer. Detection can rely on hybridization of a target that is labelled with Cy3 fluorophore, or in the presence of an unlabelled target when a sandwich assay format is implemented with a labelled reporter oligonucleotide. Selectivity to determine the presence of mismatched sequences involves appropriate selection of nucleotide sequences to set melt temperatures, in conjunction with control of stringency conditions using formamide as a chaotrope. It was determined that both direct and sandwich assays on paper substrates are able to distinguish between wild-type and mutant-type samples.

Retrosynthetic Reaction Prediction Using Neural Sequence-to-Sequence Models

PubMed Central

2017-01-01

We describe a fully data driven model that learns to perform a retrosynthetic reaction prediction task, which is treated as a sequence-to-sequence mapping problem. The end-to-end trained model has an encoder–decoder architecture that consists of two recurrent neural networks, which has previously shown great success in solving other sequence-to-sequence prediction tasks such as machine translation. The model is trained on 50,000 experimental reaction examples from the United States patent literature, which span 10 broad reaction types that are commonly used by medicinal chemists. We find that our model performs comparably with a rule-based expert system baseline model, and also overcomes certain limitations associated with rule-based expert systems and with any machine learning approach that contains a rule-based expert system component. Our model provides an important first step toward solving the challenging problem of computational retrosynthetic analysis. PMID:29104927

A novel multi-locus sequence typing (MLST) protocol for Leuconostoc lactis isolates from traditional dairy products in China and Mongolia.

PubMed

Dan, Tong; Liu, Wenjun; Sun, Zhihong; Lv, Qiang; Xu, Haiyan; Song, Yuqin; Zhang, Heping

2014-06-09

Economically, Leuconostoc lactis is one of the most important species in the genus Leuconostoc. It plays an important role in the food industry including the production of dextrans and bacteriocins. Currently, traditional molecular typing approaches for characterisation of this species at the isolate level are either unavailable or are not sufficiently reliable for practical use. Multilocus sequence typing (MLST) is a robust and reliable method for characterising bacterial and fungal species at the molecular level. In this study, a novel MLST protocol was developed for 50 L. lactis isolates from Mongolia and China. Sequences from eight targeted genes (groEL, carB, recA, pheS, murC, pyrG, rpoB and uvrC) were obtained. Sequence analysis indicated 20 different sequence types (STs), with 13 of them being represented by a single isolate. Phylogenetic analysis based on the sequences of eight MLST loci indicated that the isolates belonged to two major groups, A (34 isolates) and B (16 isolates). Linkage disequilibrium analyses indicated that recombination occurred at a low frequency in L. lactis, indicating a clonal population structure. Split-decomposition analysis indicated that intraspecies recombination played a role in generating genotypic diversity amongst isolates. Our results indicated that MLST is a valuable tool for typing L. lactis isolates that can be used for further monitoring of evolutionary changes and population genetics.

Composition for nucleic acid sequencing

DOEpatents

Korlach, Jonas [Ithaca, NY; Webb, Watt W [Ithaca, NY; Levene, Michael [Ithaca, NY; Turner, Stephen [Ithaca, NY; Craighead, Harold G [Ithaca, NY; Foquet, Mathieu [Ithaca, NY

2008-08-26

The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

Method for sequencing nucleic acid molecules

DOEpatents

Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

2006-06-06

The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

Method for sequencing nucleic acid molecules

DOEpatents

Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

2006-05-30

The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

Evaluation of the Bacterial Diversity in the Human Tongue Coating Based on Genus-Specific Primers for 16S rRNA Sequencing.

PubMed

Sun, Beili; Zhou, Dongrui; Tu, Jing; Lu, Zuhong

2017-01-01

The characteristics of tongue coating are very important symbols for disease diagnosis in traditional Chinese medicine (TCM) theory. As a habitat of oral microbiota, bacteria on the tongue dorsum have been proved to be the cause of many oral diseases. The high-throughput next-generation sequencing (NGS) platforms have been widely applied in the analysis of bacterial 16S rRNA gene. We developed a methodology based on genus-specific multiprimer amplification and ligation-based sequencing for microbiota analysis. In order to validate the efficiency of the approach, we thoroughly analyzed six tongue coating samples from lung cancer patients with different TCM types, and more than 600 genera of bacteria were detected by this platform. The results showed that ligation-based parallel sequencing combined with enzyme digestion and multiamplification could expand the effective length of sequencing reads and could be applied in the microbiota analysis.

A seminested PCR assay for detection and typing of human papillomavirus based on E1 gene sequences.

PubMed

Cavalcante, Gustavo Henrique O; de Araújo, Josélio M G; Fernandes, José Veríssimo; Lanza, Daniel C F

2018-05-01

HPV infection is considered one of the leading causes of cervical cancer in the world. To date, more than 180 types of HPV have been described and viral typing is critical for defining the prognosis of cancer. In this work, a seminested PCR which allow fast and inexpensively detection and typing of HPV is presented. The system is based on the amplification of a variable length region within the viral gene E1, using three primers that potentially anneal in all HPV genomes. The amplicons produced in the first step can be identified by high resolution electrophoresis or direct sequencing. The seminested step includes nine specific primers which can be used in multiplex or individual reactions to discriminate the main types of HPV by amplicon size differentiation using agarose electrophoresis, reducing the time spent and cost per analysis. Copyright © 2017 Elsevier Inc. All rights reserved.

Kernel based machine learning algorithm for the efficient prediction of type III polyketide synthase family of proteins.

PubMed

Mallika, V; Sivakumar, K C; Jaichand, S; Soniya, E V

2010-07-13

Type III Polyketide synthases (PKS) are family of proteins considered to have significant roles in the biosynthesis of various polyketides in plants, fungi and bacteria. As these proteins shows positive effects to human health, more researches are going on regarding this particular protein. Developing a tool to identify the probability of sequence being a type III polyketide synthase will minimize the time consumption and manpower efforts. In this approach, we have designed and implemented PKSIIIpred, a high performance prediction server for type III PKS where the classifier is Support Vector Machines (SVMs). Based on the limited training dataset, the tool efficiently predicts the type III PKS superfamily of proteins with high sensitivity and specificity. The PKSIIIpred is available at http://type3pks.in/prediction/. We expect that this tool may serve as a useful resource for type III PKS researchers. Currently work is being progressed for further betterment of prediction accuracy by including more sequence features in the training dataset.

Redesigning the type II' β-turn in green fluorescent protein to type I': implications for folding kinetics and stability.

PubMed

Madan, Bharat; Sokalingam, Sriram; Raghunathan, Govindan; Lee, Sun-Gu

2014-10-01

Both Type I' and Type II' β-turns have the same sense of the β-turn twist that is compatible with the β-sheet twist. They occur predominantly in two residue β-hairpins, but the occurrence of Type I' β-turns is two times higher than Type II' β-turns. This suggests that Type I' β-turns may be more stable than Type II' β-turns, and Type I' β-turn sequence and structure can be more favorable for protein folding than Type II' β-turns. Here, we redesigned the native Type II' β-turn in GFP to Type I' β-turn, and investigated its effect on protein folding and stability. The Type I' β-turns were designed based on the statistical analysis of residues in natural Type I' β-turns. The substitution of the native "GD" sequence of i+1 and i+2 residues with Type I' preferred "(N/D)G" sequence motif increased the folding rate by 50% and slightly improved the thermodynamic stability. Despite the enhancement of in vitro refolding kinetics and stability of the redesigned mutants, they showed poor soluble expression level compared to wild type. To overcome this problem, i and i + 3 residues of the designed Type I' β-turn were further engineered. The mutation of Thr to Lys at i + 3 could restore the in vivo soluble expression of the Type I' mutant. This study indicates that Type II' β-turns in natural β-hairpins can be further optimized by converting the sequence to Type I'. © 2014 Wiley Periodicals, Inc.

Nucleotide sequence and proposed secondary structure of Columnea latent viroid: a natural mosaic of viroid sequences.

PubMed Central

Hammond, R; Smith, D R; Diener, T O

1989-01-01

The Columnea latent viroid (CLV) occurs latently in certain Columnea erythrophae plants grown commercially. In potato and tomato, CLV causes potato spindle tuber viroid (PSTV)-like symptoms. Its nucleotide sequence and proposed secondary structure reveal that CLV consists of a single-stranded circular RNA of 370 nucleotides which can assume a rod-like structure with extensive base-pairing characteristic of all known viroids. The electrophoretic mobility of circular CLV under nondenaturing conditions suggests a potential tertiary structure. CLV contains extensive sequence homologies to the PSTV group of viroids but contains a central conserved region identical to that of hop stunt viroid (HSV). CLV also shares some biological properties with each of the two types of viroids. Most probably, CLV is the result of intracellular RNA recombination between an HSV-type and one or more PSTV-type viroids replicating in the same plant. Images PMID:2602114

Reclassification of Actinobacillus muris as Muribacter muris gen. nov., comb. nov.

PubMed

Nicklas, Werner; Bisgaard, Magne; Aalbæk, Bent; Kuhnert, Peter; Christensen, Henrik

2015-10-01

To reinvestigate the taxonomy of [Actinobacillus] muris, 474 strains, mainly from mice and rats, were characterized by phenotype and 130 strains selected for genotypic characterization by 16S rRNA and partial rpoB gene sequencing. The type strain was further investigated by whole-genome sequencing. Phylogenetic analysis of the DNA sequences showed one monophyletic group with intragroup similarities of 96.7 and 97.2 % for the 16S rRNA and rpoB genes, respectively. The highest 16S rRNA gene sequence similarity to a taxon with a validly published name outside the group was 95.9 %, to the type strain of [Pasteurella] pneumotropica. The closest related taxon based on rpoB sequence comparison was 'Haemophilus influenzae-murium', with 88.4 % similarity. A new genus and a new combination, Muribacter muris gen. nov., comb. nov., are proposed based on a distinct phylogenetic position based on 16S rRNA and rpoB gene sequence comparisons, with major divergence from the existing genera of the family Pasteurellaceae. The new genus has the characteristics of [A.] muris with the emendation that acid formation from ( - )-d-mannitol and hydrolysis of aesculin are variable, while the α-glucosidase test is positive. There is no requirement for exogenously supplied NAD (V factor) for the majority of strains investigated; however, one strain was found to require NAD. The major fatty acids of the type strain of Muribacter muris were C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I, C16 : 1ω7c and C16 : 0, which is in line with most genera of the Pasteurellaceae. The type strain of Muribacter muris is CCUG 16938T ( = NCTC 12432T = ATCC 49577T).

Modeling and prediction of peptide drift times in ion mobility spectrometry using sequence-based and structure-based approaches.

PubMed

Zhang, Yiming; Jin, Quan; Wang, Shuting; Ren, Ren

2011-05-01

The mobile behavior of 1481 peptides in ion mobility spectrometry (IMS), which are generated by protease digestion of the Drosophila melanogaster proteome, is modeled and predicted based on two different types of characterization methods, i.e. sequence-based approach and structure-based approach. In this procedure, the sequence-based approach considers both the amino acid composition of a peptide and the local environment profile of each amino acid in the peptide; the structure-based approach is performed with the CODESSA protocol, which regards a peptide as a common organic compound and generates more than 200 statistically significant variables to characterize the whole structure profile of a peptide molecule. Subsequently, the nonlinear support vector machine (SVM) and Gaussian process (GP) as well as linear partial least squares (PLS) regression is employed to correlate the structural parameters of the characterizations with the IMS drift times of these peptides. The obtained quantitative structure-spectrum relationship (QSSR) models are evaluated rigorously and investigated systematically via both one-deep and two-deep cross-validations as well as the rigorous Monte Carlo cross-validation (MCCV). We also give a comprehensive comparison on the resulting statistics arising from the different combinations of variable types with modeling methods and find that the sequence-based approach can give the QSSR models with better fitting ability and predictive power but worse interpretability than the structure-based approach. In addition, though the QSSR modeling using sequence-based approach is not needed for the preparation of the minimization structures of peptides before the modeling, it would be considerably efficient as compared to that using structure-based approach. Copyright © 2011 Elsevier Ltd. All rights reserved.

Pressure support versus T-tube for weaning from mechanical ventilation in adults.

PubMed

Ladeira, Magdaline T; Vital, Flávia M R; Andriolo, Régis B; Andriolo, Brenda N G; Atallah, Alvaro N; Peccin, Maria S

2014-05-27

Mechanical ventilation is important in caring for patients with critical illness. Clinical complications, increased mortality, and high costs of health care are associated with prolonged ventilatory support or premature discontinuation of mechanical ventilation. Weaning refers to the process of gradually or abruptly withdrawing mechanical ventilation. The weaning process begins after partial or complete resolution of the underlying pathophysiology precipitating respiratory failure and ends with weaning success (successful extubation in intubated patients or permanent withdrawal of ventilatory support in tracheostomized patients). To evaluate the effectiveness and safety of two strategies, a T-tube and pressure support ventilation, for weaning adult patients with respiratory failure that required invasive mechanical ventilation for at least 24 hours, measuring weaning success and other clinically important outcomes. We searched the following electronic databases: Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library 2012, Issue 6); MEDLINE (via PubMed) (1966 to June 2012); EMBASE (January 1980 to June 2012); LILACS (1986 to June 2012); CINAHL (1982 to June 2012); SciELO (from 1997 to August 2012); thesis repository of CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) (http://capesdw.capes.gov.br/capesdw/) (August 2012); and Current Controlled Trials (August 2012).We reran the search in December 2013. We will deal with any studies of interest when we update the review. We included randomized controlled trials (RCTs) that compared a T-tube with pressure support (PS) for the conduct of spontaneous breathing trials and as methods of gradual weaning of adult patients with respiratory failure of various aetiologies who received invasive mechanical ventilation for at least 24 hours. Two authors extracted data and assessed the methodological quality of the included studies. Meta-analyses using the random-effects model were conducted for nine outcomes. Relative risk (RR) and mean difference (MD) or standardized mean difference (SMD) were used to estimate the treatment effect, with 95% confidence intervals (CI). We included nine RCTs with 1208 patients; 622 patients were randomized to a PS spontaneous breathing trial (SBT) and 586 to a T-tube SBT. The studies were classified into three categories of weaning: simple, difficult, and prolonged. Four studies placed patients in two categories of weaning. Pressure support ventilation (PSV) and a T-tube were used directly as SBTs in four studies (844 patients, 69.9% of the sample). In 186 patients (15.4%) both interventions were used along with gradual weaning from mechanical ventilation; the PS was gradually decreased, twice a day, until it was minimal and periods with a T-tube were gradually increased to two and eight hours for patients with difficult and prolonged weaning. In two studies (14.7% of patients) the PS was lowered to 2 to 4 cm H2O and 3 to 5 cm H2O based on ventilatory parameters until the minimal PS levels were reached. PS was then compared to the trial with the T-tube (TT).We identified 33 different reported outcomes in the included studies; we took 14 of them into consideration and performed meta-analyses on nine. With regard to the sequence of allocation generation, allocation concealment, selective reporting and attrition bias, no study presented a high risk of bias. We found no clear evidence of a difference between PS and TT for weaning success (RR 1.07, 95% CI 0.97 to 1.17, 9 studies, low quality of evidence), intensive care unit (ICU) mortality (RR 0.81, 95% CI 0.53 to 1.23, 5 studies, low quality of evidence), reintubation (RR 0.92, 95% CI 0.66 to 1.26, 7 studies, low quality evidence), ICU and long-term weaning unit (LWU) length of stay (MD -7.08 days, 95% CI -16.26 to 2.1, 2 studies, low quality of evidence) and pneumonia (RR 0.67, 95% CI 0.08 to 5.85, 2 studies, low quality of evidence). PS was significantly superior to the TT for successful SBTs (RR 1.09, 95% CI 1.02 to 1.17, 4 studies, moderate quality of evidence). Four studies reported on weaning duration, however we were unable to combined the study data because of differences in how the studies presented their data. One study was at high risk of other bias and four studies were at high risk for detection bias. Three studies reported that the weaning duration was shorter with PS, and in one study the duration was shorter in patients with a TT. To date, we have found evidence of generally low quality from studies comparing pressure support ventilation (PSV) and with a T-tube. The effects on weaning success, ICU mortality, reintubation, ICU and LWU length of stay, and pneumonia were imprecise. However, PSV was more effective than a T-tube for successful spontaneous breathing trials (SBTs) among patients with simple weaning. Based on the findings of single trials, three studies presented a shorter weaning duration in the group undergoing PS SBT, however a fourth study found a shorter weaning duration with a T-tube.

GeneChip{sup {trademark}} screening assay for cystic fibrosis mutations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cronn, M.T.; Miyada, C.G.; Fucini, R.V.

1994-09-01

GeneChip{sup {trademark}} assays are based on high density, carefully designed arrays of short oligonucleotide probes (13-16 bases) built directly on derivatized silica substrates. DNA target sequence analysis is achieved by hybridizing fluorescently labeled amplification products to these arrays. Fluorescent hybridization signals located within the probe array are translated into target sequence information using the known probe sequence at each array feature. The mutation screening assay for cystic fibrosis includes sets of oligonucleotide probes designed to detect numerous different mutations that have been described in 14 exons and one intron of the CFTR gene. Each mutation site is addressed by amore » sub-array of at least 40 probe sequences, half designed to detect the wild type gene sequence and half designed to detect the reported mutant sequence. Hybridization with homozygous mutant, homozygous wild type or heterozygous targets results in distinctive hybridization patterns within a sub-array, permitting specific discrimination of each mutation. The GeneChip probe arrays are very small (approximately 1 cm{sup 2}). There miniature size coupled with their high information content make GeneChip probe arrays a useful and practical means for providing CF mutation analysis in a clinical setting.« less

Identification of four novel HLA-B alleles, B*1590, B*1591, B*2726, and B*4705, from an East African population by high-resolution sequence-based typing.

PubMed

Luo, M; Mao, X; Plummer, F A

2005-02-01

We report here four novel HLA-B alleles, B*1590, B*1591, B*2726, and B*4705, identified from an East African population during sequence-based HLA-B typing. The novel alleles were confirmed by sequencing two separate polymerase chain reaction products, and by molecular cloning and sequencing multiple clones. B*1590 is identical to B*1510 at exon 2 and exon 3, except for a difference (GCCGTC) at codon 158. Sequence differences at codon 152 (GAGGTG) and codon 167 (TGGTCG) differentiate B*1591 from B*1503 at exon 3. B*2726 is identical to B*2708 at exon 2 and exon 3, except for a difference (AAGCAG) at codon 70. B*4705 was identified in three Kenyan women. The allele is identical to B*47010101/02 at exon 2 and exon 3, except for differences at codon 97 (AGGAAT) and codon 99 (TTTTAT). These new alleles have been named by the WHO Nomenclature Committee. Identification of these novel HLA-B alleles reflects the genetic diversity of this East African population.

Integrated massively parallel sequencing of 15 autosomal STRs and Amelogenin using a simplified library preparation approach.

PubMed

Xue, Jian; Wu, Riga; Pan, Yajiao; Wang, Shunxia; Qu, Baowang; Qin, Ying; Shi, Yuequn; Zhang, Chuchu; Li, Ran; Zhang, Liyan; Zhou, Cheng; Sun, Hongyu

2018-04-02

Massively parallel sequencing (MPS) technologies, also termed as next-generation sequencing (NGS), are becoming increasingly popular in study of short tandem repeats (STR). However, current library preparation methods are usually based on ligation or two-round PCR that requires more steps, making it time-consuming (about 2 days), laborious and expensive. In this study, a 16-plex STR typing system was designed with fusion primer strategy based on the Ion Torrent S5 XL platform which could effectively resolve the above challenges for forensic DNA database-type samples (bloodstains, saliva stains, etc.). The efficiency of this system was tested in 253 Han Chinese participants. The libraries were prepared without DNA isolation and adapter ligation, and the whole process only required approximately 5 h. The proportion of thoroughly genotyped samples in which all the 16 loci were successfully genotyped was 86% (220/256). Of the samples, 99.7% showed 100% concordance between NGS-based STR typing and capillary electrophoresis (CE)-based STR typing. The inconsistency might have been caused by off-ladder alleles and mutations in primer binding sites. Overall, this panel enabled the large-scale genotyping of the DNA samples with controlled quality and quantity because it is a simple, operation-friendly process flow that saves labor, time and costs. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crash sequence based risk matrix for motorcycle crashes.

PubMed

Wu, Kun-Feng; Sasidharan, Lekshmi; Thor, Craig P; Chen, Sheng-Yin

2018-04-05

Considerable research has been conducted related to motorcycle and other powered-two-wheeler (PTW) crashes; however, it always has been controversial among practitioners concerning with types of crashes should be first targeted and how to prioritize resources for the implementation of mitigating actions. Therefore, there is a need to identify types of motorcycle crashes that constitute the greatest safety risk to riders - most frequent and most severe crashes. This pilot study seeks exhibit the efficacy of a new approach for prioritizing PTW crash causation sequences as they relate to injury severity to better inform the application of mitigating countermeasures. To accomplish this, the present study constructed a crash sequence-based risk matrix to identify most frequent and most severe motorcycle crashes in an attempt to better connect causes and countermeasures of PTW crashes. Although the frequency of each crash sequence can be computed from crash data, a crash severity model is needed to compare the levels of crash severity among different crash sequences, while controlling for other factors that also have effects on crash severity such drivers' age, use of helmet, etc. The construction of risk matrix based on crash sequences involve two tasks: formulation of crash sequence and the estimation of a mixed-effects (ME) model to adjust the levels of severities for each crash sequence to account for other crash contributing factors that would have an effect on the maximum level of crash severity in a crash. Three data elements from the National Automotive Sampling System - General Estimating System (NASS-GES) data were utilized to form a crash sequence: critical event, crash types, and sequence of events. A mixed-effects model was constructed to model the severity levels for each crash sequence while accounting for the effects of those crash contributing factors on crash severity. A total of 8039 crashes involving 8208 motorcycles occurred during 2011 and 2013 were included in this study, weighted to represent 338,655 motorcyclists involved in traffic crashes in three years (2011-2013)(NHTSA, 2013). The top five most frequent and severe types of crash sequences were identified, accounting for 23 percent of all the motorcycle crashes included in the study, and they are (1) run-off-road crashes on the right, and hitting roadside objects, (2) cross-median crashes, and rollover, (3) left-turn oncoming crashes, and head-on, (4) crossing over (passing through) or turning into opposite direction at intersections, and (5) side-impacted. In addition to crash sequences, several other factors were also identified to have effects on crash severity: use of helmet, presence of horizontal curves, alcohol consumption, road surface condition, roadway functional class, and nighttime condition. Copyright © 2018 Elsevier Ltd. All rights reserved.

Molecular characterization and epidemiology of cefoxitin resistance among Enterobacteriaceae lacking inducible chromosomal ampC genes from hospitalized and non-hospitalized patients in Algeria: description of new sequence type in Klebsiella pneumoniae isolates.

PubMed

Gharout-Sait, Alima; Touati, Abdelaziz; Guillard, Thomas; Brasme, Lucien; de Champs, Christophe

2015-01-01

In this study, 922 consecutive non-duplicate clinical isolates of Enterobacteriaceae obtained from hospitalized and non-hospitalized patients at Bejaia, Algeria were analyzed for AmpC-type β-lactamases production. The ampC genes and their genetic environment were characterized using polymerase chain reaction (PCR) and sequencing. Plasmid incompatibility groups were determined by using PCR-based replicon typing. Phylogenetic grouping and multilocus sequence typing were determined for molecular typing of the plasmid-mediated AmpC (pAmpC) isolates. Of the isolates, 15 (1.6%) were identified as AmpC producers including 14 CMY-4-producing isolates and one DHA-1-producing Klebsiella pneumoniae. All AmpC-producing isolates co-expressed the broad-spectrum TEM-1 β-lactamase and three of them co-produced CTX-M and/or SHV-12 ESBL. Phylogenetic grouping and virulence genotyping of the E. coli isolates revealed that most of them belonged to groups D and B1. Multilocus sequence typing analysis of K. pneumoniae isolates identified four different sequence types (STs) with two new sequences: ST1617 and ST1618. Plasmid replicon typing indicates that blaCMY-4 gene was located on broad host range A/C plasmid, while LVPK replicon was associated with blaDHA-1. All isolates carrying blaCMY-4 displayed the transposon-like structures ISEcp1/ΔISEcp1-blaCMY-blc-sugE. Our study showed that CMY-4 was the main pAmpC in the Enterobacteriaceae isolates in Algeria. Copyright © 2015 Elsevier Editora Ltda. All rights reserved.

Sickle cell disease in Madhya Pradesh, Central India: A comparison of clinical profile of sickle cell homozygote vs. sickle-beta thalassaemia individuals.

PubMed

Yadav, Rajiv; Lazarus, Monica; Ghanghoria, Pawan; Singh, Mpss; Gupta, Rasik Behari; Kumar, Surendra; Sharma, Ravendra K; Shanmugam, Rajasubramaniam

2016-10-01

The clinical manifestation in sickle cell disease (SCD) patients varies from one individual to another due to factors like the presence of alpha-thalassaemia mutation, foetal haemoglobin, and β-globin gene haplotype. The present study enumerates the clinical profile of sickle cell anaemia patients from Central India. Seven hundred seventy-six SCD patients from Jabalpur and surrounding districts (Madhya Pradesh) in central India were registered with the sickle cell clinic of NIRTH, Jabalpur. The present study reveals recorded signs and symptoms of genetically confirmed sickle cell anaemia (404) and sickle beta thalassaemia (92) patients. Majority of the patients were from scheduled caste communities (47.9%) and Gond tribal community (13.8%). Splenomegaly was the most common clinical manifestation observed (71.4%). Overall, 63.5% patients had a history of blood transfusion. The most frequent signs and symptoms observed were Pallor, Icterus, Joint pain, Fever, and Fatigue. Majority of the patients revealed onset of disease prior to attaining the age of 3 years (sickle cell anaemia 44.3% and sickle beta thalassaemia 35.9%). Mean haemoglobin levels among SCA individuals were marginally higher than SBT patients. On the other hand, mean foetal haemoglobin levels among SBT individuals showed the reverse trend. Notably, the present study reports the first incidence of priapism recorded in Central India. The study revealed a high prevalence of SCD among scheduled caste, backward caste, and tribal communities. Dissemination of study findings, screening, pre-marriage counselling, and pre-natal diagnosis are fundamental to preventing or lowering of birth of sickle cell anaemia children in the affected populations.

Experimental high-frequency ultrasound can detect graft rejection after small bowel transplantation.

PubMed

Yang, R; Liu, Q; Wu, E X; Pescovitz, M D; Collins, M H; Kopecky, K K; Grosfeld, J L

1994-02-01

Early diagnosis of graft rejection after small bowel transplantation (SBT) can allow prompt institution of vigorous immunosuppressive therapy, with resultant reversal of the rejection process. The current method for graft monitoring is random mucosal biopsy from a stomal site or through an endoscope. However, because early rejection often has a patchy distribution, it could be missed by random biopsy. We hypothesized that the pathological process of rejection would alter acoustic impedance of the tissue and thus change the ultrasonic patterns of the graft intestinal wall. If this hypothesis is correct, then high-frequency endoscopic ultrasound (US) could be used to monitor the entire transplanted bowel and guide the biopsy, with improved yields. This hypothesis was tested in a rat orthotopic SBT model. Sixty-two intestinal specimens (9 isografts, 12 allografts treated with cyclosporine A [CsA], 22 untreated allografts, and 19 intestines from normal rats) were collected for in vitro transluminal US imaging (30 MHz) and histopathologic study. The echo pattern of normal rat intestinal wall consisted of five echo layers that correlated spatially with the histological layers: the innermost hyperechoic layer 1, plus hypoechoic layer 2, corresponded to the mucosa; hyperechoic layer 3, the submucosa; anechoic layer 4, the muscularis propria; and hyperechoic layer 5, the serosa. The isografts and CsA-treated allografts were identical histologically and ultrasonically to normal intestine. However, the echo patterns of the untreated allografts had progressive loss of architectural stratification, with worsening rejection. The change began with patchy indistinctness and disruption of hyperechoic layers 1, 3 and 5, and progressed to total obliteration of the layers, with the intestinal wall becoming a nonstratified hypoechoic structure.(ABSTRACT TRUNCATED AT 250 WORDS)

Gibberellins Interfere with Symbiosis Signaling and Gene Expression and Alter Colonization by Arbuscular Mycorrhizal Fungi in Lotus japonicus1

PubMed Central

Takeda, Naoya; Handa, Yoshihiro; Tsuzuki, Syusaku; Kojima, Mikiko; Sakakibara, Hitoshi; Kawaguchi, Masayoshi

2015-01-01

Arbuscular mycorrhiza is a mutualistic plant-fungus interaction that confers great advantages for plant growth. Arbuscular mycorrhizal (AM) fungi enter the host root and form symbiotic structures that facilitate nutrient supplies between the symbionts. The gibberellins (GAs) are phytohormones known to inhibit AM fungal infection. However, our transcriptome analysis and phytohormone quantification revealed GA accumulation in the roots of Lotus japonicus infected with AM fungi, suggesting that de novo GA synthesis plays a role in arbuscular mycorrhiza development. We found pleiotropic effects of GAs on the AM fungal infection. In particular, the morphology of AM fungal colonization was drastically altered by the status of GA signaling in the host root. Exogenous GA treatment inhibited AM hyphal entry into the host root and suppressed the expression of Reduced Arbuscular Mycorrhization1 (RAM1) and RAM2 homologs that function in hyphal entry and arbuscule formation. On the other hand, inhibition of GA biosynthesis or suppression of GA signaling also affected arbuscular mycorrhiza development in the host root. Low-GA conditions suppressed arbuscular mycorrhiza-induced subtilisin-like serine protease1 (SbtM1) expression that is required for AM fungal colonization and reduced hyphal branching in the host root. The reduced hyphal branching and SbtM1 expression caused by the inhibition of GA biosynthesis were recovered by GA treatment, supporting the theory that insufficient GA signaling causes the inhibitory effects on arbuscular mycorrhiza development. Most studies have focused on the negative role of GA signaling, whereas our study demonstrates that GA signaling also positively interacts with symbiotic responses and promotes AM colonization of the host root. PMID:25527715

Piezoelectric properties of nonstoichiometric Sr1-xBi2+2x/3Ta2O9 ceramics

NASA Astrophysics Data System (ADS)

Jain, Rajni; Chauhan, Arun Kumar Singh; Gupta, Vinay; Sreenivas, K.

2005-06-01

The effect of poling on the structural, dielectric, and piezoelectric properties has been investigated for sol-gel-derived strontium bismuth tantalate (SBT) [Sr1-xBi2+2x/3Ta2O9] ceramics with x =0.0,0.15,0.30,0.45. The dielectric and ferroelectric properties are found to improve with increase in x up to 0.3. Beyond x >0.3 the properties are found to degrade due to the limited solid solubility and the presence of a mixed phase of bismuth tantalate (BiTaO4) is detected with x =0.45. Poling treatment reduces the dielectric dispersion and dielectric loss in the frequency range (0.1-100kHz). The resonance and antiresonance frequencies increase with increase in x (x=0-0.30), and the corresponding minimum impedance decreases. The measured coupling coefficients (kp) are small (0.0967-0.1) for x =0-0.30, and the electromechanical quality factor (Qm=915) is a maximum for the Sr0.7Bi2.2Ta2O9 composition (x=0.30). The estimated piezoelectric charge coefficient (d31) and piezoelectric voltage coefficient (g31) are 5.2pC/N and 5.8×10-3Vm/N, respectively. The positive values of d31 and g31 and the low dielectric permittivity of SBT yield a high value for the hydrostatic coefficients, despite the low charge coefficient of d33=24pC/N. The maximum values of charge coefficient (dh=34pC/N) and voltage coefficient (gh=39×10-3Vm/N) are obtained for Sr0.7Bi2.2Ta2O9 composition, and the estimated hydrostatic figure of merit (dhgh×10-15=1215m2/N) is high.

Mouse Models for Assessing the Protective Efficacy of Lactobacillus gasseri SBT2055 against Helicobacter suis Infection Associated with the Development of Gastric Mucosa-Associated Lymphoid Tissue Lymphoma.

PubMed

Matsui, Hidenori; Takahashi, Tetsufumi; Øverby, Anders; Murayama, Somay Yamagata; Yoshida, Haruno; Yamamoto, Yuji; Nishiyama, Keita; Seto, Yasuyuki; Takahashi, Takashi; Mukai, Takao; Nakamura, Masahiko

2015-08-01

Helicobacter suis strain TKY infection has been strongly associated with the development of gastric mucosa-associated lymphoid tissue (MALT) lymphoma in a C57BL/6J mouse model. 1. C57BL/6J mice were intragastrically administered Lactobacillus strains once daily with 10(8)-10(9) colony-forming units (CFU), starting 2 days before intragastric infection with H. suis TKY (approximately 1 × 10(4) copies of 16S rRNA genes) or H. pylori Sydney strain 1 (SS1; 3 × 10(8) CFU) and continuing for 14 days after infection. 2. C57BL/6J mice were given powdered feed mixed with lyophilized L. gasseri SBT2055 (LG2055) cells (5 × 10(8) CFU/g), starting 2 weeks before intragastric infection with H. suis TKY and continuing 12 months after infection. 1. Among the 5 Lactobacillus strains that we examined, only LG2055 exhibited significantly preventive efficacy against both H. suis TKY and H. pylori SS1 at day 15 after infection. 2. Dietary supplementation with LG2055 protected mice from the formation of round protrusive lesions in the gastric fundus 12 months after infection with H. suis TKY, whereas such lesions had developed in the gastric fundus of nonsupplemented mice 12 months after infection. In addition, the formation of lymphoid follicles in gastric mucus layers was suppressed by dietary LG2055 at 3 months after infection. LG2055 administration is effective for suppressing the progression of gastric MALT lymphoma by reducing H. suis colonization. © 2015 John Wiley & Sons Ltd.

Gibberellins interfere with symbiosis signaling and gene expression and alter colonization by arbuscular mycorrhizal fungi in Lotus japonicus.

PubMed

Takeda, Naoya; Handa, Yoshihiro; Tsuzuki, Syusaku; Kojima, Mikiko; Sakakibara, Hitoshi; Kawaguchi, Masayoshi

2015-02-01

Arbuscular mycorrhiza is a mutualistic plant-fungus interaction that confers great advantages for plant growth. Arbuscular mycorrhizal (AM) fungi enter the host root and form symbiotic structures that facilitate nutrient supplies between the symbionts. The gibberellins (GAs) are phytohormones known to inhibit AM fungal infection. However, our transcriptome analysis and phytohormone quantification revealed GA accumulation in the roots of Lotus japonicus infected with AM fungi, suggesting that de novo GA synthesis plays a role in arbuscular mycorrhiza development. We found pleiotropic effects of GAs on the AM fungal infection. In particular, the morphology of AM fungal colonization was drastically altered by the status of GA signaling in the host root. Exogenous GA treatment inhibited AM hyphal entry into the host root and suppressed the expression of Reduced Arbuscular Mycorrhization1 (RAM1) and RAM2 homologs that function in hyphal entry and arbuscule formation. On the other hand, inhibition of GA biosynthesis or suppression of GA signaling also affected arbuscular mycorrhiza development in the host root. Low-GA conditions suppressed arbuscular mycorrhiza-induced subtilisin-like serine protease1 (SbtM1) expression that is required for AM fungal colonization and reduced hyphal branching in the host root. The reduced hyphal branching and SbtM1 expression caused by the inhibition of GA biosynthesis were recovered by GA treatment, supporting the theory that insufficient GA signaling causes the inhibitory effects on arbuscular mycorrhiza development. Most studies have focused on the negative role of GA signaling, whereas our study demonstrates that GA signaling also positively interacts with symbiotic responses and promotes AM colonization of the host root. © 2015 American Society of Plant Biologists. All Rights Reserved.

Typing of Panton-Valentine Leukocidin-Encoding Phages and lukSF-PV Gene Sequence Variation in Staphylococcus aureus from China.

PubMed

Zhao, Huanqiang; Hu, Fupin; Jin, Shu; Xu, Xiaogang; Zou, Yuhan; Ding, Baixing; He, Chunyan; Gong, Fang; Liu, Qingzhong

2016-01-01

Panton-Valentine leukocidin (PVL, encoded by lukSF-PV genes), a bi-component and pore-forming toxin, is carried by different staphylococcal bacteriophages. The prevalence of PVL in Staphylococcus aureus has been reported around the globe. However, the data on PVL-encoding phage types, lukSF-PV gene variation and chromosomal phage insertion sites for PVL-positive S. aureus are limited, especially in China. In order to obtain a more complete understanding of the molecular epidemiology of PVL-positive S. aureus, an integrated and modified PCR-based scheme was applied to detect the PVL-encoding phage types. Phage insertion locus and the lukSF-PV variant were determined by PCR and sequencing. Meanwhile, the genetic background was characterized by staphylococcal cassette chromosome mec (SCCmec) typing, staphylococcal protein A (spa) gene polymorphisms typing, pulsed-field gel electrophoresis (PFGE) typing, accessory gene regulator (agr) locus typing and multilocus sequence typing (MLST). Seventy eight (78/1175, 6.6%) isolates possessed the lukSF-PV genes and 59.0% (46/78) of PVL-positive strains belonged to CC59 lineage. Eight known different PVL-encoding phage types were detected, and Φ7247PVL/ΦST5967PVL (n = 13) and ΦPVL (n = 12) were the most prevalent among them. While 25 (25/78, 32.1%) isolates, belonging to ST30, and ST59 clones, were unable to be typed by the modified PCR-based scheme. Single nucleotide polymorphisms (SNPs) were identified at five locations in the lukSF-PV genes, two of which were non-synonymous. Maximum-likelihood tree analysis of attachment sites sequences detected six SNP profiles for attR and eight for attL, respectively. In conclusion, the PVL-positive S. aureus mainly harbored Φ7247PVL/ΦST5967PVL and ΦPVL in the regions studied. lukSF-PV gene sequences, PVL-encoding phages, and phage insertion locus generally varied with lineages. Moreover, PVL-positive clones that have emerged worldwide likely carry distinct phages.

Structural characterization of copia-type retrotransposons leads to insights into the marker development in a biofuel crop, Jatropha curcas L.

PubMed Central

2013-01-01

Background Recently, Jatropha curcas L. has attracted worldwide attention for its potential as a source of biodiesel. However, most DNA markers have demonstrated high levels of genetic similarity among and within jatropha populations around the globe. Despite promising features of copia-type retrotransposons as ideal genetic tools for gene tagging, mutagenesis, and marker-assisted selection, they have not been characterized in the jatropha genome yet. Here, we examined the diversity, evolution, and genome-wide organization of copia-type retrotransposons in the Asian, African, and Mesoamerican accessions of jatropha, then introduced a retrotransposon-based marker for this biofuel crop. Results In total, 157 PCR fragments that were amplified using the degenerate primers for the reverse transcriptase (RT) domain of copia-type retroelements were sequenced and aligned to construct the neighbor-joining tree. Phylogenetic analysis demonstrated that isolated copia RT sequences were classified into ten families, which were then grouped into three lineages. An in-depth study of the jatropha genome for the RT sequences of each family led to the characterization of full consensus sequences of the jatropha copia-type families. Estimated copy numbers of target sequences were largely different among families, as was presence of genes within 5 kb flanking regions for each family. Five copia-type families were as appealing candidates for the development of DNA marker systems. A candidate marker from family Jc7 was particularly capable of detecting genetic variation among different jatropha accessions. Fluorescence in situ hybridization (FISH) to metaphase chromosomes reveals that copia-type retrotransposons are scattered across chromosomes mainly located in the distal part regions. Conclusion This is the first report on genome-wide analysis and the cytogenetic mapping of copia-type retrotransposons of jatropha, leading to the discovery of families bearing high potential as DNA markers. Distinct dynamics of individual copia-type families, feasibility of a retrotransposon-based insertion polymorphism marker system in examining genetic variability, and approaches for the development of breeding strategies in jatropha using copia-type retrotransposons are discussed. PMID:24020916

Comparison of advanced whole genome sequence-based methods to distinguish strains of Salmonella enterica serovar Heidelberg involved in foodborne outbreaks in Québec.

PubMed

Vincent, Caroline; Usongo, Valentine; Berry, Chrystal; Tremblay, Denise M; Moineau, Sylvain; Yousfi, Khadidja; Doualla-Bell, Florence; Fournier, Eric; Nadon, Céline; Goodridge, Lawrence; Bekal, Sadjia

2018-08-01

Salmonella enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. This serovar ranks second and third among serovars that cause human infections in Québec and Canada, respectively, and has been associated with severe infections. Traditional typing methods such as PFGE do not display adequate discrimination required to resolve outbreak investigations due to the low level of genetic diversity of isolates belonging to this serovar. This study evaluates the ability of four whole genome sequence (WGS)-based typing methods to differentiate among 145 S. Heidelberg strains involved in four distinct outbreak events and sporadic cases of salmonellosis that occurred in Québec between 2007 and 2016. Isolates from all outbreaks were indistinguishable by PFGE. The core genome single nucleotide variant (SNV), core genome multilocus sequence typing (MLST) and whole genome MLST approaches were highly discriminatory and separated outbreak strains into four distinct phylogenetic clusters that were concordant with the epidemiological data. The clustered regularly interspaced short palindromic repeats (CRISPR) typing method was less discriminatory. However, CRISPR typing may be used as a secondary method to differentiate isolates of S. Heidelberg that are genetically similar but epidemiologically unrelated to outbreak events. WGS-based typing methods provide a highly discriminatory alternative to PFGE for the laboratory investigation of foodborne outbreaks. Copyright © 2018 Elsevier Ltd. All rights reserved.

Coupling detrended fluctuation analysis for multiple warehouse-out behavioral sequences

NASA Astrophysics Data System (ADS)

Yao, Can-Zhong; Lin, Ji-Nan; Zheng, Xu-Zhou

2017-01-01

Interaction patterns among different warehouses could make the warehouse-out behavioral sequences less predictable. We firstly take a coupling detrended fluctuation analysis on the warehouse-out quantity, and find that the multivariate sequences exhibit significant coupling multifractal characteristics regardless of the types of steel products. Secondly, we track the sources of multifractal warehouse-out sequences by shuffling and surrogating original ones, and we find that fat-tail distribution contributes more to multifractal features than the long-term memory, regardless of types of steel products. From perspective of warehouse contribution, some warehouses steadily contribute more to multifractal than other warehouses. Finally, based on multiscale multifractal analysis, we propose Hurst surface structure to investigate coupling multifractal, and show that multiple behavioral sequences exhibit significant coupling multifractal features that emerge and usually be restricted within relatively greater time scale interval.

Genetic diversity analysis of Leuconostoc mesenteroides from Korean vegetables and food products by multilocus sequence typing.

PubMed

Sharma, Anshul; Kaur, Jasmine; Lee, Sulhee; Park, Young-Seo

2018-06-01

In the present study, 35 Leuconostoc mesenteroides strains isolated from vegetables and food products from South Korea were studied by multilocus sequence typing (MLST) of seven housekeeping genes (atpA, groEL, gyrB, pheS, pyrG, rpoA, and uvrC). The fragment sizes of the seven amplified housekeeping genes ranged in length from 366 to 1414 bp. Sequence analysis indicated 27 different sequence types (STs) with 25 of them being represented by a single strain indicating high genetic diversity, whereas the remaining 2 were characterized by five strains each. In total, 220 polymorphic nucleotide sites were detected among seven housekeeping genes. The phylogenetic analysis based on the STs of the seven loci indicated that the 35 strains belonged to two major groups, A (28 strains) and B (7 strains). Split decomposition analysis showed that intraspecies recombination played a role in generating diversity among strains. The minimum spanning tree showed that the evolution of the STs was not correlated with food source. This study signifies that the multilocus sequence typing is a valuable tool to access the genetic diversity among L. mesenteroides strains from South Korea and can be used further to monitor the evolutionary changes.

Use of Whole-Genus Genome Sequence Data To Develop a Multilocus Sequence Typing Tool That Accurately Identifies Yersinia Isolates to the Species and Subspecies Levels

PubMed Central

Hall, Miquette; Chattaway, Marie A.; Reuter, Sandra; Savin, Cyril; Strauch, Eckhard; Carniel, Elisabeth; Connor, Thomas; Van Damme, Inge; Rajakaruna, Lakshani; Rajendram, Dunstan; Jenkins, Claire; Thomson, Nicholas R.

2014-01-01

The genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica. PMID:25339391

Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile.

PubMed

Bletz, Stefan; Janezic, Sandra; Harmsen, Dag; Rupnik, Maja; Mellmann, Alexander

2018-06-01

Clostridium difficile , recently renamed Clostridioides difficile , is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, highly discriminatory subtyping is necessary. Today, methods based on whole-genome sequencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature are missing. Here we report a core genome multilocus sequence typing (cgMLST) approach developed for C. difficile Initially, we determined the breadth of the C. difficile population based on all available MLST sequence types with Bayesian inference (BAPS). The resulting BAPS partitions were used in combination with C. difficile clade information to select representative isolates that were subsequently used to define cgMLST target genes. Finally, we evaluated the novel cgMLST scheme with genomes from 3,025 isolates. BAPS grouping ( n = 6 groups) together with the clade information led to a total of 11 representative isolates that were included for cgMLST definition and resulted in 2,270 cgMLST genes that were present in all isolates. Overall, 2,184 to 2,268 cgMLST targets were detected in the genome sequences of 70 outbreak-associated and reference strains, and on average 99.3% cgMLST targets (1,116 to 2,270 targets) were present in 2,954 genomes downloaded from the NCBI database, underlining the representativeness of the cgMLST scheme. Moreover, reanalyzing different cluster scenarios with cgMLST were concordant to published single nucleotide variant analyses. In conclusion, the novel cgMLST is representative for the whole C. difficile population, is highly discriminatory in outbreak situations, and provides a unique nomenclature facilitating interlaboratory exchange. Copyright © 2018 American Society for Microbiology.

Phylogenetic analysis of Mycobacterium massiliense strains having recombinant rpoB gene laterally transferred from Mycobacterium abscessus.

PubMed

Kim, Byoung-Jun; Kim, Ga-Na; Kim, Bo-Ram; Shim, Tae-Sun; Kook, Yoon-Hoh; Kim, Bum-Joon

2017-01-01

Recent multi locus sequence typing (MLST) and genome based studies indicate that lateral gene transfer (LGT) events in the rpoB gene are prevalent between Mycobacterium abscessus complex strains. To check the prevalence of the M. massiliense strains subject to rpoB LGT (Rec-mas), we applied rpoB typing (711 bp) to 106 Korean strains of M. massiliense infection that had already been identified by hsp65 sequence analysis (603 bp). The analysis indicated 6 smooth strains in M. massiliense Type I (10.0%, 6/60) genotypes but no strains in M. massiliense Type II genotypes (0%, 0/46), showing a discrepancy between the 2 typing methods. Further MLST analysis based on the partial sequencing of seven housekeeping genes, argH, cya, glpK, gnd, murC, pta and purH, as well as erm(41) PCR proved that these 6 Rec-mas strains consisted of two distinct genotypes belonging to M. massiliense and not M. abscessus. The complete rpoB sequencing analysis showed that these 6 Rec-mas strains have an identical hybrid rpoB gene, of which a 478 bp partial rpoB fragment may be laterally transferred from M. abscessus. Notably, five of the 6 Rec-mas strains showed complete identical sequences in a total of nine genes, including the seven MLST genes, hsp65, and rpoB, suggesting their clonal propagation in South Korea. In conclusion, we identified 6 M. massiliense smooth strains of 2 phylogenetically distinct genotypes with a specific hybrid rpoB gene laterally transferred from M. abscessus from Korean patients. Their clinical relevance and bacteriological traits remain to be elucidated.

Phylogenetic analysis of Mycobacterium massiliense strains having recombinant rpoB gene laterally transferred from Mycobacterium abscessus

PubMed Central

Kim, Byoung-Jun; Kim, Ga-Na; Kim, Bo-Ram; Shim, Tae-Sun; Kook, Yoon-Hoh

2017-01-01

Recent multi locus sequence typing (MLST) and genome based studies indicate that lateral gene transfer (LGT) events in the rpoB gene are prevalent between Mycobacterium abscessus complex strains. To check the prevalence of the M. massiliense strains subject to rpoB LGT (Rec-mas), we applied rpoB typing (711 bp) to 106 Korean strains of M. massiliense infection that had already been identified by hsp65 sequence analysis (603 bp). The analysis indicated 6 smooth strains in M. massiliense Type I (10.0%, 6/60) genotypes but no strains in M. massiliense Type II genotypes (0%, 0/46), showing a discrepancy between the 2 typing methods. Further MLST analysis based on the partial sequencing of seven housekeeping genes, argH, cya, glpK, gnd, murC, pta and purH, as well as erm(41) PCR proved that these 6 Rec-mas strains consisted of two distinct genotypes belonging to M. massiliense and not M. abscessus. The complete rpoB sequencing analysis showed that these 6 Rec-mas strains have an identical hybrid rpoB gene, of which a 478 bp partial rpoB fragment may be laterally transferred from M. abscessus. Notably, five of the 6 Rec-mas strains showed complete identical sequences in a total of nine genes, including the seven MLST genes, hsp65, and rpoB, suggesting their clonal propagation in South Korea. In conclusion, we identified 6 M. massiliense smooth strains of 2 phylogenetically distinct genotypes with a specific hybrid rpoB gene laterally transferred from M. abscessus from Korean patients. Their clinical relevance and bacteriological traits remain to be elucidated. PMID:28604829

Distribution of sequence-based types of legionella pneumophila serogroup 1 strains isolated from cooling towers, hot springs, and potable water systems in China.

PubMed

Qin, Tian; Zhou, Haijian; Ren, Hongyu; Guan, Hong; Li, Machao; Zhu, Bingqing; Shao, Zhujun

2014-04-01

Legionella pneumophila serogroup 1 causes Legionnaires' disease. Water systems contaminated with Legionella are the implicated sources of Legionnaires' disease. This study analyzed L. pneumophila serogroup 1 strains in China using sequence-based typing. Strains were isolated from cooling towers (n = 96), hot springs (n = 42), and potable water systems (n = 26). Isolates from cooling towers, hot springs, and potable water systems were divided into 25 sequence types (STs; index of discrimination [IOD], 0.711), 19 STs (IOD, 0.934), and 3 STs (IOD, 0.151), respectively. The genetic variation among the potable water isolates was lower than that among cooling tower and hot spring isolates. ST1 was the predominant type, accounting for 49.4% of analyzed strains (n = 81), followed by ST154. With the exception of two strains, all potable water isolates (92.3%) belonged to ST1. In contrast, 53.1% (51/96) and only 14.3% (6/42) of cooling tower and hot spring, respectively, isolates belonged to ST1. There were differences in the distributions of clone groups among the water sources. The comparisons among L. pneumophila strains isolated in China, Japan, and South Korea revealed that similar clones (ST1 complex and ST154 complex) exist in these countries. In conclusion, in China, STs had several unique allelic profiles, and ST1 was the most prevalent sequence type of environmental L. pneumophila serogroup 1 isolates, similar to its prevalence in Japan and South Korea.

A Wide Variety of Clostridium perfringens Type A Food-Borne Isolates That Carry a Chromosomal cpe Gene Belong to One Multilocus Sequence Typing Cluster

PubMed Central

Xiao, Yinghua; Wagendorp, Arjen; Moezelaar, Roy; Abee, Tjakko

2012-01-01

Of 98 suspected food-borne Clostridium perfringens isolates obtained from a nationwide survey by the Food and Consumer Product Safety Authority in The Netherlands, 59 strains were identified as C. perfringens type A. Using PCR-based techniques, the cpe gene encoding enterotoxin was detected in eight isolates, showing a chromosomal location for seven isolates and a plasmid location for one isolate. Further characterization of these strains by using (GTG)5 fingerprint repetitive sequence-based PCR analysis distinguished C. perfringens from other sulfite-reducing clostridia but did not allow for differentiation between various types of C. perfringens strains. To characterize the C. perfringens strains further, multilocus sequence typing (MLST) analysis was performed on eight housekeeping genes of both enterotoxic and non-cpe isolates, and the data were combined with a previous global survey covering strains associated with food poisoning, gas gangrene, and isolates from food or healthy individuals. This revealed that the chromosomal cpe strains (food strains and isolates from food poisoning cases) belong to a distinct cluster that is significantly distant from all the other cpe plasmid-carrying and cpe-negative strains. These results suggest that different groups of C. perfringens have undergone niche specialization and that a distinct group of food isolates has specific core genome sequences. Such findings have epidemiological and evolutionary significance. Better understanding of the origin and reservoir of enterotoxic C. perfringens may allow for improved control of this organism in foods. PMID:22865060

Pyrosequencing-based quantitative measurement of CALR mutation allele burdens and their clinical implications in patients with myeloproliferative neoplasms.

PubMed

Oh, Yejin; Song, Ik-Chan; Kim, Jimyung; Kwon, Gye Cheol; Koo, Sun Hoe; Kim, Seon Young

2018-05-01

We developed a pyrosequencing-based method for the quantification of CALR mutations and compared the results using Sanger sequencing, fragment length analysis (FLA), digital-droplet PCR (ddPCR), and next-generation sequencing (NGS). Method validation studies were performed using cloned plasmid controls. Samples from 24 patients with myeloproliferative neoplasms were evaluated. Among the 24 patients, 15 had CALR mutations (7 type 1, 2 type 2, and 6 other mutations). The type 1 or type 2 mutation-positive results from pyrosequencing exhibited 100% concordance with the Sanger sequencing results. One novel CALR mutation was not detected by pyrosequencing. The CALR mutation allele burdens measured by pyrosequencing were slightly lower than those measured by FLA but slightly higher than the results obtained using ddPCR. Pyrosequencing exhibited high correlations with both methods. The mutation allele burdens estimated by NGS were significantly lower than those measured by pyrosequencing. An increased CALR mutation allele burden was associated with overt primary myelofibrosis. Patients with >70% mutation allele burdens in myeloid cells had a significantly longer time from diagnosis (P = 0.007), more bone marrow fibrosis (P = 0.010), and lower hemoglobin (P = 0.007). Pyrosequencing was a useful rapid sequencing method to determine the burden of CALR mutations. Copyright © 2018 Elsevier B.V. All rights reserved.

Multilocus sequence typing and pulsed-field gel electrophoresis analysis of Oenococcus oeni from different wine-producing regions of China.

PubMed

Wang, Tao; Li, Hua; Wang, Hua; Su, Jing

2015-04-16

The present study established a typing method with NotI-based pulsed-field gel electrophoresis (PFGE) and stress response gene schemed multilocus sequence typing (MLST) for 55 Oenococcus oeni strains isolated from six individual regions in China and two model strains PSU-1 (CP000411) and ATCC BAA-1163 (AAUV00000000). Seven stress response genes, cfa, clpL, clpP, ctsR, mleA, mleP and omrA, were selected for MLST testing, and positive selective pressure was detected for these genes. Furthermore, both methods separated the strains into two clusters. The PFGE clusters are correlated with the region, whereas the sequence types (STs) formed by the MLST confirm the two clusters identified by PFGE. In addition, the population structure was a mixture of evolutionary pathways, and the strains exhibited both clonal and panmictic characteristics. Copyright © 2015 Elsevier B.V. All rights reserved.

CRISPRTarget

PubMed Central

Biswas, Ambarish; Gagnon, Joshua N.; Brouns, Stan J.J.; Fineran, Peter C.; Brown, Chris M.

2013-01-01

The bacterial and archaeal CRISPR/Cas adaptive immune system targets specific protospacer nucleotide sequences in invading organisms. This requires base pairing between processed CRISPR RNA and the target protospacer. For type I and II CRISPR/Cas systems, protospacer adjacent motifs (PAM) are essential for target recognition, and for type III, mismatches in the flanking sequences are important in the antiviral response. In this study, we examine the properties of each class of CRISPR. We use this information to provide a tool (CRISPRTarget) that predicts the most likely targets of CRISPR RNAs (http://bioanalysis.otago.ac.nz/CRISPRTarget). This can be used to discover targets in newly sequenced genomic or metagenomic data. To test its utility, we discover features and targets of well-characterized Streptococcus thermophilus and Sulfolobus solfataricus type II and III CRISPR/Cas systems. Finally, in Pectobacterium species, we identify new CRISPR targets and propose a model of temperate phage exposure and subsequent inhibition by the type I CRISPR/Cas systems. PMID:23492433

Genetic diversity of pneumococcal surface protein A in invasive pneumococcal isolates from Korean children, 1991-2016.

PubMed

Yun, Ki Wook; Choi, Eun Hwa; Lee, Hoan Jong

2017-01-01

Pneumococcal surface protein A (PspA) is an important virulence factor of pneumococci and has been investigated as a primary component of a capsular serotype-independent pneumococcal vaccine. Thus, we sought to determine the genetic diversity of PspA to explore its potential as a vaccine candidate. Among the 190 invasive pneumococcal isolates collected from Korean children between 1991 and 2016, two (1.1%) isolates were found to have no pspA by multiple polymerase chain reactions. The full length pspA genes from 185 pneumococcal isolates were sequenced. The length of pspA varied, ranging from 1,719 to 2,301 base pairs with 55.7-100% nucleotide identity. Based on the sequences of the clade-defining regions, 68.7% and 49.7% were in PspA family 2 and clade 3/family 2, respectively. PspA clade types were correlated with genotypes using multilocus sequence typing and divided into several subclades based on diversity analysis of the N-terminal α-helical regions, which showed nucleotide sequence identities of 45.7-100% and amino acid sequence identities of 23.1-100%. Putative antigenicity plots were also diverse among individual clades and subclades. The differences in antigenicity patterns were concentrated within the N-terminal 120 amino acids. In conclusion, the N-terminal α-helical domain, which is known to be the major immunogenic portion of PspA, is genetically variable and should be further evaluated for antigenic differences and cross-reactivity between various PspA types from pneumococcal isolates.

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

PubMed Central

Schadt, Eric E.; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H.; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A.; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

2013-01-01

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types. PMID:23093720

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.

PubMed

Schadt, Eric E; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

2013-01-01

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types.

Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity

PubMed Central

Li, Chang-Lin; Li, Kai-Cheng; Wu, Dan; Chen, Yan; Luo, Hao; Zhao, Jing-Rong; Wang, Sa-Shuang; Sun, Ming-Ming; Lu, Ying-Jin; Zhong, Yan-Qing; Hu, Xu-Ye; Hou, Rui; Zhou, Bei-Bei; Bao, Lan; Xiao, Hua-Sheng; Zhang, Xu

2016-01-01

Sensory neurons are distinguished by distinct signaling networks and receptive characteristics. Thus, sensory neuron types can be defined by linking transcriptome-based neuron typing with the sensory phenotypes. Here we classify somatosensory neurons of the mouse dorsal root ganglion (DRG) by high-coverage single-cell RNA-sequencing (10 950 ± 1 218 genes per neuron) and neuron size-based hierarchical clustering. Moreover, single DRG neurons responding to cutaneous stimuli are recorded using an in vivo whole-cell patch clamp technique and classified by neuron-type genetic markers. Small diameter DRG neurons are classified into one type of low-threshold mechanoreceptor and five types of mechanoheat nociceptors (MHNs). Each of the MHN types is further categorized into two subtypes. Large DRG neurons are categorized into four types, including neurexophilin 1-expressing MHNs and mechanical nociceptors (MNs) expressing BAI1-associated protein 2-like 1 (Baiap2l1). Mechanoreceptors expressing trafficking protein particle complex 3-like and Baiap2l1-marked MNs are subdivided into two subtypes each. These results provide a new system for cataloging somatosensory neurons and their transcriptome databases. PMID:26691752

mirVAFC: A Web Server for Prioritizations of Pathogenic Sequence Variants from Exome Sequencing Data via Classifications.

PubMed

Li, Zhongshan; Liu, Zhenwei; Jiang, Yi; Chen, Denghui; Ran, Xia; Sun, Zhong Sheng; Wu, Jinyu

2017-01-01

Exome sequencing has been widely used to identify the genetic variants underlying human genetic disorders for clinical diagnoses, but the identification of pathogenic sequence variants among the huge amounts of benign ones is complicated and challenging. Here, we describe a new Web server named mirVAFC for pathogenic sequence variants prioritizations from clinical exome sequencing (CES) variant data of single individual or family. The mirVAFC is able to comprehensively annotate sequence variants, filter out most irrelevant variants using custom criteria, classify variants into different categories as for estimated pathogenicity, and lastly provide pathogenic variants prioritizations based on classifications and mutation effects. Case studies using different types of datasets for different diseases from publication and our in-house data have revealed that mirVAFC can efficiently identify the right pathogenic candidates as in original work in each case. Overall, the Web server mirVAFC is specifically developed for pathogenic sequence variant identifications from family-based CES variants using classification-based prioritizations. The mirVAFC Web server is freely accessible at https://www.wzgenomics.cn/mirVAFC/. © 2016 WILEY PERIODICALS, INC.

High speed nucleic acid sequencing

DOEpatents

Korlach, Jonas [Ithaca, NY; Webb, Watt W [Ithaca, NY; Levene, Michael [Ithaca, NY; Turner, Stephen [Ithaca, NY; Craighead, Harold G [Ithaca, NY; Foquet, Mathieu [Ithaca, NY

2011-05-17

The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid. Each type of labeled nucleotide comprises an acceptor fluorophore attached to a phosphate portion of the nucleotide such that the fluorophore is removed upon incorporation into a growing strand. Fluorescent signal is emitted via fluorescent resonance energy transfer between the donor fluorophore and the acceptor fluorophore as each nucleotide is incorporated into the growing strand. The sequence is deduced by identifying which base is being incorporated into the growing strand.

Population structure of Lactobacillus helveticus isolates from naturally fermented dairy products based on multilocus sequence typing.

PubMed

Sun, Zhihong; Liu, Wenjun; Song, Yuqin; Xu, Haiyan; Yu, Jie; Bilige, Menghe; Zhang, Heping; Chen, Yongfu

2015-05-01

Lactobacillus helveticus is an economically important lactic acid bacterium used in industrial dairy fermentation. In the present study, the population structure of 245 isolates of L. helveticus from different naturally fermented dairy products in China and Mongolia were investigated using an multilocus sequence typing scheme with 11 housekeeping genes. A total of 108 sequence types were detected, which formed 8 clonal complexes and 27 singletons. Results from Structure, SplitsTree, and ClonalFrame software analyses demonstrated the presence of 3 subpopulations in the L. helveticus isolates used in our study, namely koumiss, kurut-tarag, and panmictic lineages. Most L. helveticus isolates from particular ecological origins had specific population structures. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

HLA-B*5808, a new HLA-B allele characterized by sequence based typing.

PubMed

Poli, F; Crespiatico, L; Frison, S; Longhi, E; Marlianici, E; Scalamogna, M

2003-12-01

This brief communication describes a new HLA-B allele (HLA-B*5808) detected in an Italian white volunteer bone marrow donor. With serology, this subject was typed as HLA-B15,17, whereas with molecular biology B*15, B*51, B*52 and/or B*58 could be assigned. In order to clarify the results, direct and cloning sequencing of exons 2, 3 and 4 were carried out. This new allele is identical to HLA-B*5801 in exon 2 except for a silent point mutation at nucleotide 141 where a C is substituted by a T; exons 3 and 4 are typical of HLA-B*51, B*52 and B*78. The peculiar sequence of B*5808 could explain the discrepancy between the serological and molecular typing results.

Evolution of EF-hand calcium-modulated proteins. IV. Exon shuffling did not determine the domain compositions of EF-hand proteins

NASA Technical Reports Server (NTRS)

Kretsinger, R. H.; Nakayama, S.

1993-01-01

In the previous three reports in this series we demonstrated that the EF-hand family of proteins evolved by a complex pattern of gene duplication, transposition, and splicing. The dendrograms based on exon sequences are nearly identical to those based on protein sequences for troponin C, the essential light chain myosin, the regulatory light chain, and calpain. This validates both the computational methods and the dendrograms for these subfamilies. The proposal of congruence for calmodulin, troponin C, essential light chain, and regulatory light chain was confirmed. There are, however, significant differences in the calmodulin dendrograms computed from DNA and from protein sequences. In this study we find that introns are distributed throughout the EF-hand domain and the interdomain regions. Further, dendrograms based on intron type and distribution bear little resemblance to those based on protein or on DNA sequences. We conclude that introns are inserted, and probably deleted, with relatively high frequency. Further, in the EF-hand family exons do not correspond to structural domains and exon shuffling played little if any role in the evolution of this widely distributed homolog family. Calmodulin has had a turbulent evolution. Its dendrograms based on protein sequence, exon sequence, 3'-tail sequence, intron sequences, and intron positions all show significant differences.

Clarification of the Concept of Ganoderma orbiforme with High Morphological Plasticity

PubMed Central

Wang, Dong-Mei; Wu, Sheng-Hua; Yao, Yi-Jian

2014-01-01

Ganoderma has been considered a very difficult genus among the polypores to classify and is currently in a state of taxonomic chaos. In a study of Ganoderma collections including numerous type specimens, we found that six species namely G. cupreum, G. densizonatum, G. limushanense, G. mastoporum, G. orbiforme, G. subtornatum, and records of G. fornicatum from Mainland China and Taiwan are very similar to one another in basidiocarp texture, pilear cuticle structure, context color, pore color and basidiospore characteristics. Further, we sequenced the nrDNA ITS region (ITS1 and ITS2) and partial mtDNA SSU region of the studied materials, and performed phylogenetic analyses based on these sequence data. The nrDNA ITS sequence analysis results show that the eight nrDNA ITS sequences derived from this study have single-nucleotide polymorphisms in ITS1 and/or ITS2 at inter- and intra-individual levels. In the nrDNA ITS phylogenetic trees, all the sequences from this study are grouped together with those of G. cupreum and G. mastoporum retrieved from GenBank to form a distinct clade. The mtDNA SSU sequence analysis results reveal that the five mtDNA SSU sequences derived from this study are clustered together with those of G. cupreum retrieved from GenBank and also form a distinct clade in the mtDNA SSU phylogenetic trees. Based on morphological and molecular data, we conclude that the studied taxa are conspecific. Among the names assigned to this species, G. fornicatum given to Asian collections has nomenclatural priority over the others. However, the type of G. fornicatum from Brazil is probably lost and a modern description based on the type lacks. The identification of the Asian collections to G. fornicatum therefore cannot be confirmed. To the best of our knowledge, G. orbiforme is the earliest valid name for use. PMID:24875218

A novel multi-locus sequence typing (MLST) protocol for Leuconostoc lactis isolates from traditional dairy products in China and Mongolia

PubMed Central

2014-01-01

Background Economically, Leuconostoc lactis is one of the most important species in the genus Leuconostoc. It plays an important role in the food industry including the production of dextrans and bacteriocins. Currently, traditional molecular typing approaches for characterisation of this species at the isolate level are either unavailable or are not sufficiently reliable for practical use. Multilocus sequence typing (MLST) is a robust and reliable method for characterising bacterial and fungal species at the molecular level. In this study, a novel MLST protocol was developed for 50 L. lactis isolates from Mongolia and China. Results Sequences from eight targeted genes (groEL, carB, recA, pheS, murC, pyrG, rpoB and uvrC) were obtained. Sequence analysis indicated 20 different sequence types (STs), with 13 of them being represented by a single isolate. Phylogenetic analysis based on the sequences of eight MLST loci indicated that the isolates belonged to two major groups, A (34 isolates) and B (16 isolates). Linkage disequilibrium analyses indicated that recombination occurred at a low frequency in L. lactis, indicating a clonal population structure. Split-decomposition analysis indicated that intraspecies recombination played a role in generating genotypic diversity amongst isolates. Conclusions Our results indicated that MLST is a valuable tool for typing L. lactis isolates that can be used for further monitoring of evolutionary changes and population genetics. PMID:24912963

Lactobacillus delbrueckii subsp. jakobsenii subsp. nov., isolated from dolo wort, an alcoholic fermented beverage in Burkina Faso.

PubMed

Adimpong, David B; Nielsen, Dennis S; Sørensen, Kim I; Vogensen, Finn K; Sawadogo-Lingani, Hagrétou; Derkx, Patrick M F; Jespersen, Lene

2013-10-01

Lactobacillus delbrueckii is divided into five subspecies based on phenotypic and genotypic differences. A novel isolate, designated ZN7a-9(T), was isolated from malted sorghum wort used for making an alcoholic beverage (dolo) in Burkina Faso. The results of 16S rRNA gene sequencing, DNA-DNA hybridization and peptidoglycan cell-wall structure type analyses indicated that it belongs to the species L. delbrueckii. The genome sequence of isolate ZN7a-9(T) was determined by Illumina-based sequencing. Multilocus sequence typing (MLST) and split-decomposition analyses were performed on seven concatenated housekeeping genes obtained from the genome sequence of strain ZN7a-9(T) together with 41 additional L. delbrueckii strains. The results of the MLST and split-decomposition analyses could not establish the exact subspecies of L. delbrueckii represented by strain ZN7a-9(T) as it clustered with L. delbrueckii strains unassigned to any of the recognized subspecies of L. delbrueckii. Strain ZN7a-9(T) additionally differed from the recognized type strains of the subspecies of L. delbrueckii with respect to its carbohydrate fermentation profile. In conclusion, the cumulative results indicate that strain ZN7a-9(T) represents a novel subspecies of L. delbrueckii closely related to Lactobacillus delbrueckii subsp. lactis and Lactobacillus delbrueckii subsp. delbrueckii for which the name Lactobacillus delbrueckii subsp. jakobsenii subsp. nov. is proposed. The type strain is ZN7a-9(T) = DSM 26046(T) = LMG 27067(T).

FlyBase: genes and gene models

PubMed Central

Drysdale, Rachel A.; Crosby, Madeline A.

2005-01-01

FlyBase (http://flybase.org) is the primary repository of genetic and molecular data of the insect family Drosophilidae. For the most extensively studied species, Drosophila melanogaster, a wide range of data are presented in integrated formats. Data types include mutant phenotypes, molecular characterization of mutant alleles and aberrations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions. There is a growing body of data for other Drosophila species; this is expected to increase dramatically over the next year, with the completion of draft-quality genomic sequences of an additional 11 Drosphila species. PMID:15608223

Influenza virus sequence feature variant type analysis: evidence of a role for NS1 in influenza virus host range restriction.

PubMed

Noronha, Jyothi M; Liu, Mengya; Squires, R Burke; Pickett, Brett E; Hale, Benjamin G; Air, Gillian M; Galloway, Summer E; Takimoto, Toru; Schmolke, Mirco; Hunt, Victoria; Klem, Edward; García-Sastre, Adolfo; McGee, Monnie; Scheuermann, Richard H

2012-05-01

Genetic drift of influenza virus genomic sequences occurs through the combined effects of sequence alterations introduced by a low-fidelity polymerase and the varying selective pressures experienced as the virus migrates through different host environments. While traditional phylogenetic analysis is useful in tracking the evolutionary heritage of these viruses, the specific genetic determinants that dictate important phenotypic characteristics are often difficult to discern within the complex genetic background arising through evolution. Here we describe a novel influenza virus sequence feature variant type (Flu-SFVT) approach, made available through the public Influenza Research Database resource (www.fludb.org), in which variant types (VTs) identified in defined influenza virus protein sequence features (SFs) are used for genotype-phenotype association studies. Since SFs have been defined for all influenza virus proteins based on known structural, functional, and immune epitope recognition properties, the Flu-SFVT approach allows the rapid identification of the molecular genetic determinants of important influenza virus characteristics and their connection to underlying biological functions. We demonstrate the use of the SFVT approach to obtain statistical evidence for effects of NS1 protein sequence variations in dictating influenza virus host range restriction.

Fuzzy logic based on-line fault detection and classification in transmission line.

PubMed

Adhikari, Shuma; Sinha, Nidul; Dorendrajit, Thingam

2016-01-01

This study presents fuzzy logic based online fault detection and classification of transmission line using Programmable Automation and Control technology based National Instrument Compact Reconfigurable i/o (CRIO) devices. The LabVIEW software combined with CRIO can perform real time data acquisition of transmission line. When fault occurs in the system current waveforms are distorted due to transients and their pattern changes according to the type of fault in the system. The three phase alternating current, zero sequence and positive sequence current data generated by LabVIEW through CRIO-9067 are processed directly for relaying. The result shows that proposed technique is capable of right tripping action and classification of type of fault at high speed therefore can be employed in practical application.

An asparagine residue at the N-terminus affects the maturation process of low molecular weight glutenin subunits of wheat endosperm

PubMed Central

2014-01-01

Background Wheat glutenin polymers are made up of two main subunit types, the high- (HMW-GS) and low- (LMW-GS) molecular weight subunits. These latter are represented by heterogeneous proteins. The most common, based on the first amino acid of the mature sequence, are known as LMW-m and LMW-s types. The mature sequences differ as a consequence of three extra amino acids (MET-) at the N-terminus of LMW-m types. The nucleotide sequences of their encoding genes are, however, nearly identical, so that the relationship between gene and protein sequences is difficult to ascertain. It has been hypothesized that the presence of an asparagine residue in position 23 of the complete coding sequence for the LMW-s type might account for the observed three-residue shortened sequence, as a consequence of cleavage at the asparagine by an asparaginyl endopeptidase. Results We performed site-directed mutagenesis of a LMW-s gene to replace asparagine at position 23 with threonine and thus convert it to a candidate LMW-m type gene. Similarly, a candidate LMW-m type gene was mutated at position 23 to replace threonine with asparagine. Next, we produced transgenic durum wheat (cultivar Svevo) lines by introducing the mutated versions of the LMW-m and LMW-s genes, along with the wild type counterpart of the LMW-m gene. Proteomic comparisons between the transgenic and null segregant plants enabled identification of transgenic proteins by mass spectrometry analyses and Edman N-terminal sequencing. Conclusions Our results show that the formation of LMW-s type relies on the presence of an asparagine residue close to the N-terminus generated by signal peptide cleavage, and that LMW-GS can be quantitatively processed most likely by vacuolar asparaginyl endoproteases, suggesting that those accumulated in the vacuole are not sequestered into stable aggregates that would hinder the action of proteolytic enzymes. Rather, whatever is the mechanism of glutenin polymer transport to the vacuole, the proteins remain available for proteolytic processing, and can be converted to the mature form by the removal of a short N-terminal sequence. PMID:24629124

Generation of a novel next-generation sequencing-based method for the isolation of new human papillomavirus types.

PubMed

Brancaccio, Rosario N; Robitaille, Alexis; Dutta, Sankhadeep; Cuenin, Cyrille; Santare, Daiga; Skenders, Girts; Leja, Marcis; Fischer, Nicole; Giuliano, Anna R; Rollison, Dana E; Grundhoff, Adam; Tommasino, Massimo; Gheit, Tarik

2018-05-07

With the advent of new molecular tools, the discovery of new papillomaviruses (PVs) has accelerated during the past decade, enabling the expansion of knowledge about the viral populations that inhabit the human body. Human PVs (HPVs) are etiologically linked to benign or malignant lesions of the skin and mucosa. The detection of HPV types can vary widely, depending mainly on the methodology and the quality of the biological sample. Next-generation sequencing is one of the most powerful tools, enabling the discovery of novel viruses in a wide range of biological material. Here, we report a novel protocol for the detection of known and unknown HPV types in human skin and oral gargle samples using improved PCR protocols combined with next-generation sequencing. We identified 105 putative new PV types in addition to 296 known types, thus providing important information about the viral distribution in the oral cavity and skin. Copyright © 2018. Published by Elsevier Inc.

Promoter Sequences Prediction Using Relational Association Rule Mining

PubMed Central

Czibula, Gabriela; Bocicor, Maria-Iuliana; Czibula, Istvan Gergely

2012-01-01

In this paper we are approaching, from a computational perspective, the problem of promoter sequences prediction, an important problem within the field of bioinformatics. As the conditions for a DNA sequence to function as a promoter are not known, machine learning based classification models are still developed to approach the problem of promoter identification in the DNA. We are proposing a classification model based on relational association rules mining. Relational association rules are a particular type of association rules and describe numerical orderings between attributes that commonly occur over a data set. Our classifier is based on the discovery of relational association rules for predicting if a DNA sequence contains or not a promoter region. An experimental evaluation of the proposed model and comparison with similar existing approaches is provided. The obtained results show that our classifier overperforms the existing techniques for identifying promoter sequences, confirming the potential of our proposal. PMID:22563233

Stellar model chromospheres. IX - Chromospheric activity in dwarf stars

NASA Technical Reports Server (NTRS)

Kelch, W. L.; Worden, S. P.; Linsky, J. L.

1979-01-01

High-resolution Ca II K line profiles are used to model the upper photospheres and lower chromospheres of eight main-sequence stars ranging in spectral type from F0 to M0 and exhibiting different degrees of chromospheric activity. The model chromospheres are studied as a function of spectral type and activity for stars of similar spectral type in order to obtain evidence of enhanced nonradiative heating in the upper-photospheric models and in the ratio of minimum temperature at the base of the chromosphere to effective temperature, a correlation between activity and temperature in the lower chromospheres, and a correlation of the width at the base of the K-line emission core and at the K2 features with activity. Chromospheric radiative losses are estimated for the modelled stars and other previously analyzed main-sequence stars. The results obtained strengthen the argument that dMe flare stars exhibit fundamentally solar-type activity but on an increased scale.

Labeled nucleotide phosphate (NP) probes

DOEpatents

Korlach, Jonas [Ithaca, NY; Webb, Watt W [Ithaca, NY; Levene, Michael [Ithaca, NY; Turner, Stephen [Ithaca, NY; Craighead, Harold G [Ithaca, NY; Foquet, Mathieu [Ithaca, NY

2009-02-03

The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

Evaluation of targeted exome sequencing for 28 protein-based blood group systems, including the homologous gene systems, for blood group genotyping.

PubMed

Schoeman, Elizna M; Lopez, Genghis H; McGowan, Eunike C; Millard, Glenda M; O'Brien, Helen; Roulis, Eileen V; Liew, Yew-Wah; Martin, Jacqueline R; McGrath, Kelli A; Powley, Tanya; Flower, Robert L; Hyland, Catherine A

2017-04-01

Blood group single nucleotide polymorphism genotyping probes for a limited range of polymorphisms. This study investigated whether massively parallel sequencing (also known as next-generation sequencing), with a targeted exome strategy, provides an extended blood group genotype and the extent to which massively parallel sequencing correctly genotypes in homologous gene systems, such as RH and MNS. Donor samples (n = 28) that were extensively phenotyped and genotyped using single nucleotide polymorphism typing, were analyzed using the TruSight One Sequencing Panel and MiSeq platform. Genes for 28 protein-based blood group systems, GATA1, and KLF1 were analyzed. Copy number variation analysis was used to characterize complex structural variants in the GYPC and RH systems. The average sequencing depth per target region was 66.2 ± 39.8. Each sample harbored on average 43 ± 9 variants, of which 10 ± 3 were used for genotyping. For the 28 samples, massively parallel sequencing variant sequences correctly matched expected sequences based on single nucleotide polymorphism genotyping data. Copy number variation analysis defined the Rh C/c alleles and complex RHD hybrids. Hybrid RHD*D-CE-D variants were correctly identified, but copy number variation analysis did not confidently distinguish between D and CE exon deletion versus rearrangement. The targeted exome sequencing strategy employed extended the range of blood group genotypes detected compared with single nucleotide polymorphism typing. This single-test format included detection of complex MNS hybrid cases and, with copy number variation analysis, defined RH hybrid genes along with the RHCE*C allele hitherto difficult to resolve by variant detection. The approach is economical compared with whole-genome sequencing and is suitable for a red blood cell reference laboratory setting. © 2017 AABB.

Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279 T), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia

DOE PAGES

Goker, Markus; Lu, Megan; Fiebig, Anne; ...

2014-06-15

Methanoplanus limicola Wildgruber et al. 1984 is a mesophilic methanogen that was isolated from a swamp composed of drilling waste near Naples, Italy, shortly after the Archaea were recognized as a separate domain of life. Methanoplanus is the type genus in the family Methanoplanaceae, a taxon that felt into disuse since modern 16S rRNA gene sequences-based taxonomy was established. Methanoplanus is now placed within the Methanomicrobiaceae, a family that is so far poorly characterized at the genome level. The only other type strain of the genus with a sequenced genome, Methanoplanus petrolearius SEBR 4847 T, turned out to be misclassifiedmore » and required reclassification to Methanolacinia. Both, Methanoplanus and Methanolacinia, needed taxonomic emendations due to a significant deviation of the G+C content of their genomes from previously published (pregenome-sequence era) values. Until now genome sequences were published for only four of the 33 species with validly published names in the Methanomicrobiaceae. Here we describe the features of M. limicola, together with the improved-high-quality draft genome sequence and an notation of the type strain, M3 T. The 3,200,946 bp long chromosome (permanent draft sequence) with its 3,064 protein-coding and 65 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

Laser mass spectrometry for DNA sequencing, disease diagnosis, and fingerprinting

NASA Astrophysics Data System (ADS)

Chen, C. H. Winston; Taranenko, N. I.; Zhu, Y. F.; Chung, C. N.; Allman, S. L.

1997-05-01

Since laser mass spectrometry has the potential for achieving very fast DNA analysis, we recently applied it to DNA sequencing, DNA typing for fingerprinting, and DNA screening for disease diagnosis. Two different approaches for sequencing DNA have been successfully demonstrated. One is to sequence DNA with DNA ladders produced from Sanger's enzymatic method. The other is to do direct sequencing without DNA ladders. The need for quick DNA typing for identification purposes is critical for forensic application. Our preliminary results indicate laser mass spectrometry can possible be used for rapid DNA fingerprinting applications at a much lower cost than gel electrophoresis. Population screening for certain genetic disease can be a very efficient step to reducing medical costs through prevention. Since laser mass spectrometry can provide very fast DNA analysis, we applied laser mass spectrometry to disease diagnosis. Clinical samples with both base deletion and point mutation have been tested with complete success.

Development of a new-type riboswitch using an aptazyme and an anti-RBS sequence.

PubMed

Ogawa, Atsushi; Maeda, Mizuo

2007-01-01

We constructed a new-type riboswitch, which functions in E. coli, using an aptazyme and an anti-RBS sequence. This riboswitch usually suppresses the gene expression with its anti-RBS sequence bound to the RBS of its own mRNA(OFF), while it activates the translation only when a cofactor of the aptazyme is added to release the anti-RBS sequence from itself as a result of cofactor-induced self-cleavage by the aptazyme (ON). Although this aptazyme-based riboswitch did not function at 37 degrees C in vivo in spite of its high activity at this temperature in vitro, it worked well at lower temperature (23 degrees C). We also improved the efficiency of this riboswitch by constructing a cascading system.

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

PubMed

Ochoa, David; García-Gutiérrez, Ponciano; Juan, David; Valencia, Alfonso; Pazos, Florencio

2013-01-27

A widespread family of methods for studying and predicting protein interactions using sequence information is based on co-evolution, quantified as similarity of phylogenetic trees. Part of the co-evolution observed between interacting proteins could be due to co-adaptation caused by inter-protein contacts. In this case, the co-evolution is expected to be more evident when evaluated on the surface of the proteins or the internal layers close to it. In this work we study the effect of incorporating information on predicted solvent accessibility to three methods for predicting protein interactions based on similarity of phylogenetic trees. We evaluate the performance of these methods in predicting different types of protein associations when trees based on positions with different characteristics of predicted accessibility are used as input. We found that predicted accessibility improves the results of two recent versions of the mirrortree methodology in predicting direct binary physical interactions, while it neither improves these methods, nor the original mirrortree method, in predicting other types of interactions. That improvement comes at no cost in terms of applicability since accessibility can be predicted for any sequence. We also found that predictions of protein-protein interactions are improved when multiple sequence alignments with a richer representation of sequences (including paralogs) are incorporated in the accessibility prediction.

Formation of (DNA)2-LNA triplet with recombinant base recognition: A quantum mechanical study

NASA Astrophysics Data System (ADS)

Mall, Vijaya Shri; Tiwari, Rakesh Kumar

2018-05-01

The formation of DNA triple helix offers the verity of new possibilities in molecular biology. However its applications are limited to purine and pyrimidine rich sequences recognized by forming Hoogsteen/Reverse Hoogsteen triplets in major groove sites of DNA duplex. To overcome this drawback modification in bases backbone and glucose of nucleotide unit of DNA have been proposed so that the third strand base recognized by both the bases of DNA duplex by forming Recombinant type(R-type) of bonding in mixed sequences. Here we performed Quanrum Mechanical (Hartree-Fock and DFT) methodology on natural DNA and Locked Nucleic Acids(LNA) triplets using 6-31G and some other new advance basis sets. Study suggests energetically stable conformation has been observed for recombinant triplets in order of G-C*G > A-T*A > G-C*C > T-A*T for both type of triplets. Interestingly LNA leads to more stable conformation in all set of triplets, clearly suggests an important biological tool to overcome above mentioned drawbacks.

Streptococcus caprae sp. nov., isolated from Iberian ibex (Capra pyrenaica hispanica).

PubMed

Vela, A I; Mentaberre, G; Lavín, S; Domínguez, L; Fernández-Garayzábal, J F

2016-01-01

Biochemical and molecular genetic studies were performed on a novel Gram-stain-positive, catalase-negative, coccus-shaped organism isolated from tonsil samples of two Iberian ibexes. The micro-organism was identified as a streptococcal species based on its cellular, morphological and biochemical characteristics. 16S rRNA gene sequence comparison studies confirmed its identification as a member of the genus Streptococcus, but the organism did not correspond to any species of this genus. The nearest phylogenetic relative of the unknown coccus from ibex was Streptococcus porci 2923-03T (96.6 % 16S rRNA gene sequence similarity). Analysis based on rpoB and sodA gene sequences revealed sequence similarity values lower than 86.0 and 83.8 %, respectively, from the type strains of recognized Streptococcus species. The novel bacterial isolate was distinguished from Streptococcus porci and other Streptococcus species using biochemical tests. Based on both phenotypic and phylogenetic findings, it is proposed that the unknown bacterium be classified as representing a novel species of the genus Streptococcus, for which the name Streptococcus caprae sp. nov. is proposed. The type strain is DICM07-02790-1CT ( = CECT 8872T = CCUG 67170T).

An Assessment of Cumulative Axial and Torsional Fatigue in a Cobalt-Base Superalloy

NASA Technical Reports Server (NTRS)

Kalluri, Sreeramesh; Bonacuse, Peter J.

2010-01-01

Cumulative fatigue under axial and torsional loading conditions can include both load-order (higMow and low/high) as well as load-type sequence (axial/torsional and torsional/axial) effects. Previously reported experimental studies on a cobalt-base superalloy, Haynes 188 at 538 C, addressed these effects. These studies characterized the cumulative axial and torsional fatigue behavior under high amplitude followed by low amplitude (Kalluri, S. and Bonacuse, P. J., "Cumulative Axial and Torsional Fatigue: An Investigation of Load-Type Sequance Effects," in Multiaxial Fatigue and Deformation: Testing and Prediction, ASTM STP 1387, S. Kalluri, and P. J. Bonacuse, Eds., American Society for Testing and Materials, West Conshohocken, PA, 2000, pp. 281-301) and low amplitude followed by high amplitude (Bonacuse, P. and Kalluri, S. "Sequenced Axial and Torsional Cumulative Fatigue: Low Amplitude Followed by High Amplitude Loading," Biaxial/Multiaxial Fatigue and Fracture, ESIS Publication 31, A. Carpinteri, M. De Freitas, and A. Spagnoli, Eds., Elsevier, New York, 2003, pp. 165-182) conditions. In both studies, experiments with the following four load-type sequences were performed: (a) axial/axial, (b) torsional/torsional, (c) axial/torsional, and (d) torsional/axial. In this paper, the cumulative axial and torsional fatigue data generated in the two previous studies are combined to generate a comprehensive cumulative fatigue database on both the load-order and load-type sequence effects. This comprehensive database is used to examine applicability of the Palmgren-langer-Miner linear damage rule and a nonlinear damage curve approach for Haynes 188 subjected to the load-order and load-type sequencing described above. Summations of life fractions from the experiments are compared to the predictions from both the linear and nonlinear cumulative fatigue damage approaches. The significance of load-order versus load-type sequence effects for axial and torsional loading conditions is discussed. Possible reasons for the observed differences between the computed and observed summations of cycle fractions are rationalized in terms of the observed ever lutions of cyclic axial and shear stress ranges in the cumulative fatigue tests.

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

PubMed

Schoch, Conrad L; Robbertse, Barbara; Robert, Vincent; Vu, Duong; Cardinali, Gianluigi; Irinyi, Laszlo; Meyer, Wieland; Nilsson, R Henrik; Hughes, Karen; Miller, Andrew N; Kirk, Paul M; Abarenkov, Kessy; Aime, M Catherine; Ariyawansa, Hiran A; Bidartondo, Martin; Boekhout, Teun; Buyck, Bart; Cai, Qing; Chen, Jie; Crespo, Ana; Crous, Pedro W; Damm, Ulrike; De Beer, Z Wilhelm; Dentinger, Bryn T M; Divakar, Pradeep K; Dueñas, Margarita; Feau, Nicolas; Fliegerova, Katerina; García, Miguel A; Ge, Zai-Wei; Griffith, Gareth W; Groenewald, Johannes Z; Groenewald, Marizeth; Grube, Martin; Gryzenhout, Marieka; Gueidan, Cécile; Guo, Liangdong; Hambleton, Sarah; Hamelin, Richard; Hansen, Karen; Hofstetter, Valérie; Hong, Seung-Beom; Houbraken, Jos; Hyde, Kevin D; Inderbitzin, Patrik; Johnston, Peter R; Karunarathna, Samantha C; Kõljalg, Urmas; Kovács, Gábor M; Kraichak, Ekaphan; Krizsan, Krisztina; Kurtzman, Cletus P; Larsson, Karl-Henrik; Leavitt, Steven; Letcher, Peter M; Liimatainen, Kare; Liu, Jian-Kui; Lodge, D Jean; Luangsa-ard, Janet Jennifer; Lumbsch, H Thorsten; Maharachchikumbura, Sajeewa S N; Manamgoda, Dimuthu; Martín, María P; Minnis, Andrew M; Moncalvo, Jean-Marc; Mulè, Giuseppina; Nakasone, Karen K; Niskanen, Tuula; Olariaga, Ibai; Papp, Tamás; Petkovits, Tamás; Pino-Bodas, Raquel; Powell, Martha J; Raja, Huzefa A; Redecker, Dirk; Sarmiento-Ramirez, J M; Seifert, Keith A; Shrestha, Bhushan; Stenroos, Soili; Stielow, Benjamin; Suh, Sung-Oui; Tanaka, Kazuaki; Tedersoo, Leho; Telleria, M Teresa; Udayanga, Dhanushka; Untereiner, Wendy A; Diéguez Uribeondo, Javier; Subbarao, Krishna V; Vágvölgyi, Csaba; Visagie, Cobus; Voigt, Kerstin; Walker, Donald M; Weir, Bevan S; Weiß, Michael; Wijayawardene, Nalin N; Wingfield, Michael J; Xu, J P; Yang, Zhu L; Zhang, Ning; Zhuang, Wen-Ying; Federhen, Scott

2014-01-01

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353. Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US.

Predicting membrane protein types by fusing composite protein sequence features into pseudo amino acid composition.

PubMed

Hayat, Maqsood; Khan, Asifullah

2011-02-21

Membrane proteins are vital type of proteins that serve as channels, receptors, and energy transducers in a cell. Prediction of membrane protein types is an important research area in bioinformatics. Knowledge of membrane protein types provides some valuable information for predicting novel example of the membrane protein types. However, classification of membrane protein types can be both time consuming and susceptible to errors due to the inherent similarity of membrane protein types. In this paper, neural networks based membrane protein type prediction system is proposed. Composite protein sequence representation (CPSR) is used to extract the features of a protein sequence, which includes seven feature sets; amino acid composition, sequence length, 2 gram exchange group frequency, hydrophobic group, electronic group, sum of hydrophobicity, and R-group. Principal component analysis is then employed to reduce the dimensionality of the feature vector. The probabilistic neural network (PNN), generalized regression neural network, and support vector machine (SVM) are used as classifiers. A high success rate of 86.01% is obtained using SVM for the jackknife test. In case of independent dataset test, PNN yields the highest accuracy of 95.73%. These classifiers exhibit improved performance using other performance measures such as sensitivity, specificity, Mathew's correlation coefficient, and F-measure. The experimental results show that the prediction performance of the proposed scheme for classifying membrane protein types is the best reported, so far. This performance improvement may largely be credited to the learning capabilities of neural networks and the composite feature extraction strategy, which exploits seven different properties of protein sequences. The proposed Mem-Predictor can be accessed at http://111.68.99.218/Mem-Predictor. Copyright © 2010 Elsevier Ltd. All rights reserved.

Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples

PubMed Central

Nguyen, David; Valenzuela, Nicole; Takemura, Ping; Bolon, Yung-Tsi; Springer, Brianna; Saito, Katsuyuki; Zheng, Ying; Hague, Tim; Pasztor, Agnes; Horvath, Gyorgy; Rigo, Krisztina; Reed, Elaine F.; Zhang, Qiuheng

2016-01-01

Background Unambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT), HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS) of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP) registry donors using long-range PCR by next generation sequencing (NGS) approach on buccal swab DNA. Methods Multiplex long-range PCR primers amplified the full-length of HLA class I genes (A, B, C) from promotor to 3’ UTR. Class II genes (DRB1, DQB1) were amplified from exon 2 through part of exon 4. PCR amplicons were pooled and sheared using Covaris fragmentation. Library preparation was performed using the Illumina TruSeq Nano kit on the Beckman FX automated platform. Each sample was tagged with a unique barcode, followed by 2×250 bp paired-end sequencing on the Illumina MiSeq. HLA typing was assigned using Omixon Twin software that combines two independent computational algorithms to ensure high confidence in allele calling. Consensus sequence and typing results were reported in Histoimmunogenetics Markup Language (HML) format. All homozygous alleles were confirmed by Luminex SSO typing and exon novelties were confirmed by Sanger sequencing. Results Using this automated workflow, over 10,063 NMDP registry donors were successfully typed under high-resolution by NGS. Despite known challenges of nucleic acid degradation and low DNA concentration commonly associated with buccal-based specimens, 97.8% of samples were successfully amplified using long-range PCR. Among these, 98.2% were successfully reported by NGS, with an accuracy rate of 99.84% in an independent blind Quality Control audit performed by the NDMP. In this study, NGS-HLA typing identified 23 null alleles (0.023%), 92 rare alleles (0.091%) and 42 exon novelties (0.042%). Conclusion Long-range, unambiguous HLA genotyping is achievable on clinical buccal swab-extracted DNA. Importantly, full-length gene sequencing and the ability to curate full sequence data will permit future interrogation of the impact of introns, expanded exons, and other gene regulatory sequences on clinical outcomes in transplantation. PMID:27798706

Application of High-Throughput Next-Generation Sequencing for HLA Typing on Buccal Extracted DNA: Results from over 10,000 Donor Recruitment Samples.

PubMed

Yin, Yuxin; Lan, James H; Nguyen, David; Valenzuela, Nicole; Takemura, Ping; Bolon, Yung-Tsi; Springer, Brianna; Saito, Katsuyuki; Zheng, Ying; Hague, Tim; Pasztor, Agnes; Horvath, Gyorgy; Rigo, Krisztina; Reed, Elaine F; Zhang, Qiuheng

2016-01-01

Unambiguous HLA typing is important in hematopoietic stem cell transplantation (HSCT), HLA disease association studies, and solid organ transplantation. However, current molecular typing methods only interrogate the antigen recognition site (ARS) of HLA genes, resulting in many cis-trans ambiguities that require additional typing methods to resolve. Here we report high-resolution HLA typing of 10,063 National Marrow Donor Program (NMDP) registry donors using long-range PCR by next generation sequencing (NGS) approach on buccal swab DNA. Multiplex long-range PCR primers amplified the full-length of HLA class I genes (A, B, C) from promotor to 3' UTR. Class II genes (DRB1, DQB1) were amplified from exon 2 through part of exon 4. PCR amplicons were pooled and sheared using Covaris fragmentation. Library preparation was performed using the Illumina TruSeq Nano kit on the Beckman FX automated platform. Each sample was tagged with a unique barcode, followed by 2×250 bp paired-end sequencing on the Illumina MiSeq. HLA typing was assigned using Omixon Twin software that combines two independent computational algorithms to ensure high confidence in allele calling. Consensus sequence and typing results were reported in Histoimmunogenetics Markup Language (HML) format. All homozygous alleles were confirmed by Luminex SSO typing and exon novelties were confirmed by Sanger sequencing. Using this automated workflow, over 10,063 NMDP registry donors were successfully typed under high-resolution by NGS. Despite known challenges of nucleic acid degradation and low DNA concentration commonly associated with buccal-based specimens, 97.8% of samples were successfully amplified using long-range PCR. Among these, 98.2% were successfully reported by NGS, with an accuracy rate of 99.84% in an independent blind Quality Control audit performed by the NDMP. In this study, NGS-HLA typing identified 23 null alleles (0.023%), 92 rare alleles (0.091%) and 42 exon novelties (0.042%). Long-range, unambiguous HLA genotyping is achievable on clinical buccal swab-extracted DNA. Importantly, full-length gene sequencing and the ability to curate full sequence data will permit future interrogation of the impact of introns, expanded exons, and other gene regulatory sequences on clinical outcomes in transplantation.

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.

PubMed

Xu, Weijia; Ozer, Stuart; Gutell, Robin R

2009-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure.

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA

PubMed Central

Xu, Weijia; Ozer, Stuart; Gutell, Robin R.

2010-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure. PMID:20502534

High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq).

PubMed

Jiao, Yang; Li, Ran; Wu, Chao; Ding, Yibin; Liu, Yanning; Jia, Danmei; Wang, Lifeng; Xu, Xiang; Zhu, Jing; Zheng, Min; Jia, Junling

2018-01-15

Highly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious diseases. Additionally, it is routinely performed for identifying matched donors in transplantation medicine. Although many HLA typing approaches have been developed, the complexity, low-efficiency and high-cost of current HLA-typing assays limit their application in population-based high-throughput HLA typing for donors, which is required for creating large-scale databases for transplantation and precision medicine. Here, we present a cost-efficient Saturated Tiling Capture Sequencing (STC-Seq) approach to capturing 14 HLA class I and II genes. The highly efficient capture (an approximately 23,000-fold enrichment) of these genes allows for simplified allele calling. Tests on five genes (HLA-A/B/C/DRB1/DQB1) from 31 human samples and 351 datasets using STC-Seq showed results that were 98% consistent with the known two sets of digitals (field1 and field2) genotypes. Additionally, STC can capture genomic DNA fragments longer than 3 kb from HLA loci, making the library compatible with the third-generation sequencing. STC-Seq is a highly accurate and cost-efficient method for HLA typing which can be used to facilitate the establishment of population-based HLA databases for the precision and transplantation medicine.

Systematic revision of the adeleid haemogregarines, with creation of Bartazoon n. g., reassignment of Hepatozoon argantis Garnham, 1954 to Hemolivia, and molecular data on Hemolivia stellata

PubMed Central

Karadjian, Grégory; Chavatte, Jean-Marc; Landau, Irène

2015-01-01

Life cycles and molecular data for terrestrial haemogregarines are reviewed in this article. Collection material was re-examined: Hepatozoon argantis Garnham, 1954 in Argas brumpti was reassigned to Hemolivia as Hemolivia argantis (Garnham, 1954) n. comb.; parasite DNA was extracted from a tick crush on smear of an archived slide of Hemolivia stellata in Amblyomma rotondatum, then the 18S ssrRNA gene was amplified by PCR. A systematic revision of the group is proposed, based on biological life cycles and phylogenetic reconstruction. Four types of life cycles, based on parasite vector, vertebrate host and the characteristics of their development, are defined. We propose combining species, based on their biology, into four groups (types I, II, III and IV). The characters of each type are defined and associated with a type genus and a type species. The biological characters of each type are associated with a different genus and a type species. The phylogenetic reconstruction with sequences deposited in the databases and our own new sequence of Hemolivia stellata is consistent with this classification. The classification is as follows: Type I, Hepatozoon Miller, 1908, type species H. perniciosum Miller, 1908; Type II, Karyolysus Labbé, 1894, type species K. lacertae (Danilewsky, 1886) Reichenow, 1913; Type III Hemolivia Petit et al., 1990, type species H. stellata, Petit et al., 1990; and Type IV: Bartazoon n. g., type species B. breinli (Mackerras, 1960). PMID:26551414

Sequence diversity within the reovirus S2 gene: reovirus genes reassort in nature, and their termini are predicted to form a panhandle motif.

PubMed Central

Chapell, J D; Goral, M I; Rodgers, S E; dePamphilis, C W; Dermody, T S

1994-01-01

To better understand genetic diversity within mammalian reoviruses, we determined S2 nucleotide and deduced sigma 2 amino acid sequences of nine reovirus strains and compared these sequences with those of prototype strains of the three reovirus serotypes. The S2 gene and sigma 2 protein are highly conserved among the four type 1, one type 2, and seven type 3 strains studied. Phylogenetic analyses based on S2 nucleotide sequences of the 12 reovirus strains indicate that diversity within the S2 gene is independent of viral serotype. Additionally, we found marked topological differences between phylogenetic trees generated from S1 and S2 gene nucleotide sequences of the seven type 3 strains. These results demonstrate that reovirus S1 and S2 genes have distinct evolutionary histories, thus providing phylogenetic evidence for lateral transfer of reovirus genes in nature. When variability among the 12 sigma 2-encoding S2 nucleotide sequences was analyzed at synonymous positions, we found that approximately 60 nucleotides at the 5' terminus and 30 nucleotides at the 3' terminus were markedly conserved in comparison with other sigma 2-encoding regions of S2. Predictions of RNA secondary structures indicate that the more conserved S2 sequences participate in the formation of an extended region of duplex RNA interrupted by a pair of stem-loops. Among the 12 deduced sigma 2 amino acid sequences examined, substitutions were observed at only 11% of amino acid positions. This finding suggests that constraints on the structure or function of sigma 2, perhaps in part because of its location in the virion core, have limited sequence diversity within this protein. PMID:8289378

Multiple Locus Variable-Number Tandem-Repeat and Single-Nucleotide Polymorphism-Based Brucella Typing Reveals Multiple Lineages in Brucella melitensis Currently Endemic in China.

PubMed

Sun, Mingjun; Jing, Zhigang; Di, Dongdong; Yan, Hao; Zhang, Zhicheng; Xu, Quangang; Zhang, Xiyue; Wang, Xun; Ni, Bo; Sun, Xiangxiang; Yan, Chengxu; Yang, Zhen; Tian, Lili; Li, Jinping; Fan, Weixing

2017-01-01

Brucellosis is a worldwide zoonotic disease caused by Brucella spp. In China, brucellosis is recognized as a reemerging disease mainly caused by Brucella melitensis specie. To better understand the currently endemic B. melitensis strains in China, three Brucella genotyping methods were applied to 110 B. melitensis strains obtained in past several years. By MLVA genotyping, five MLVA-8 genotypes were identified, among which genotypes 42 (1-5-3-13-2-2-3-2) was recognized as the predominant genotype, while genotype 63 (1-5-3-13-2-3-3-2) and a novel genotype of 1-5-3-13-2-4-3-2 were second frequently observed. MLVA-16 discerned a total of 57 MLVA-16 genotypes among these Brucella strains, with 41 genotypes being firstly detected and the other 16 genotypes being previously reported. By BruMLSA21 typing, six sequence types (STs) were identified, among them ST8 is the most frequently seen in China while the other five STs were firstly detected and designated as ST137, ST138, ST139, ST140, and ST141 by international multilocus sequence typing database. Whole-genome sequence (WGS)-single-nucleotide polymorphism (SNP)-based typing and phylogenetic analysis resolved Chinese B. melitensis strains into five clusters, reflecting the existence of multiple lineages among these Chinese B. melitensis strains. In phylogeny, Chinese lineages are more closely related to strains collected from East Mediterranean and Middle East countries, such as Turkey, Kuwait, and Iraq. In the next few years, MLVA typing will certainly remain an important epidemiological tool for Brucella infection analysis, as it displays a high discriminatory ability and achieves result largely in agreement with WGS-SNP-based typing. However, WGS-SNP-based typing is found to be the most powerful and reliable method in discerning Brucella strains and will be popular used in the future.

An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences.

PubMed

Ye, Kai; Kosters, Walter A; Ijzerman, Adriaan P

2007-03-15

Pattern discovery in protein sequences is often based on multiple sequence alignments (MSA). The procedure can be computationally intensive and often requires manual adjustment, which may be particularly difficult for a set of deviating sequences. In contrast, two algorithms, PRATT2 (http//www.ebi.ac.uk/pratt/) and TEIRESIAS (http://cbcsrv.watson.ibm.com/) are used to directly identify frequent patterns from unaligned biological sequences without an attempt to align them. Here we propose a new algorithm with more efficiency and more functionality than both PRATT2 and TEIRESIAS, and discuss some of its applications to G protein-coupled receptors, a protein family of important drug targets. In this study, we designed and implemented six algorithms to mine three different pattern types from either one or two datasets using a pattern growth approach. We compared our approach to PRATT2 and TEIRESIAS in efficiency, completeness and the diversity of pattern types. Compared to PRATT2, our approach is faster, capable of processing large datasets and able to identify the so-called type III patterns. Our approach is comparable to TEIRESIAS in the discovery of the so-called type I patterns but has additional functionality such as mining the so-called type II and type III patterns and finding discriminating patterns between two datasets. The source code for pattern growth algorithms and their pseudo-code are available at http://www.liacs.nl/home/kosters/pg/.

On the Sequence-Directed Nature of Human Gene Mutation: The Role of Genomic Architecture and the Local DNA Sequence Environment in Mediating Gene Mutations Underlying Human Inherited Disease

PubMed Central

Cooper, David N.; Bacolla, Albino; Férec, Claude; Vasquez, Karen M.; Kehrer-Sawatzki, Hildegard; Chen, Jian-Min

2011-01-01

Different types of human gene mutation may vary in size, from structural variants (SVs) to single base-pair substitutions, but what they all have in common is that their nature, size and location are often determined either by specific characteristics of the local DNA sequence environment or by higher-order features of the genomic architecture. The human genome is now recognized to contain ‘pervasive architectural flaws’ in that certain DNA sequences are inherently mutation-prone by virtue of their base composition, sequence repetitivity and/or epigenetic modification. Here we explore how the nature, location and frequency of different types of mutation causing inherited disease are shaped in large part, and often in remarkably predictable ways, by the local DNA sequence environment. The mutability of a given gene or genomic region may also be influenced indirectly by a variety of non-canonical (non-B) secondary structures whose formation is facilitated by the underlying DNA sequence. Since these non-B DNA structures can interfere with subsequent DNA replication and repair, and may serve to increase mutation frequencies in generalized fashion (i.e. both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease. PMID:21853507

Molecular and Cellular Mechanisms for the Interaction between Gold Nanoparticles and Neuroimmune Cells Based on Size, Shape, and Charge

DTIC Science & Technology

2014-04-25

IgG secretion. 2.3 Designing of Synthetic peptide The immunogenic peptides against the foot and mouth disease virus ( FMDV ) were designed and...synthesized based on viral protein 1 of type O FMDV . The amino acid sequence for pFMDV is NGSSKYGDTSTNNVRGDLQVLAQKAERTLC. An extra cysteine was added...peptides were synthesized based on the amino acid sequence of the VP1 coat protein of the FMDV (table 1). The peptide pFMDVD (19 amino acids in length

ProDeGe: A computational protocol for fully automated decontamination of genomes

DOE PAGES

Tennessen, Kristin; Andersen, Evan; Clingenpeel, Scott; ...

2015-06-09

Single amplified genomes and genomes assembled from metagenomes have enabled the exploration of uncultured microorganisms at an unprecedented scale. However, both these types of products are plagued by contamination. Since these genomes are now being generated in a high-throughput manner and sequences from them are propagating into public databases to drive novel scientific discoveries, rigorous quality controls and decontamination protocols are urgently needed. Here, we present ProDeGe (Protocol for fully automated Decontamination of Genomes), the first computational protocol for fully automated decontamination of draft genomes. ProDeGe classifies sequences into two classes—clean and contaminant—using a combination of homology and feature-based methodologies.more » On average, 84% of sequence from the non-target organism is removed from the data set (specificity) and 84% of the sequence from the target organism is retained (sensitivity). Lastly, the procedure operates successfully at a rate of ~0.30 CPU core hours per megabase of sequence and can be applied to any type of genome sequence.« less

ProDeGe: A computational protocol for fully automated decontamination of genomes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tennessen, Kristin; Andersen, Evan; Clingenpeel, Scott

Single amplified genomes and genomes assembled from metagenomes have enabled the exploration of uncultured microorganisms at an unprecedented scale. However, both these types of products are plagued by contamination. Since these genomes are now being generated in a high-throughput manner and sequences from them are propagating into public databases to drive novel scientific discoveries, rigorous quality controls and decontamination protocols are urgently needed. Here, we present ProDeGe (Protocol for fully automated Decontamination of Genomes), the first computational protocol for fully automated decontamination of draft genomes. ProDeGe classifies sequences into two classes—clean and contaminant—using a combination of homology and feature-based methodologies.more » On average, 84% of sequence from the non-target organism is removed from the data set (specificity) and 84% of the sequence from the target organism is retained (sensitivity). Lastly, the procedure operates successfully at a rate of ~0.30 CPU core hours per megabase of sequence and can be applied to any type of genome sequence.« less

Comparison of the nucleotide and amino acid sequences of the RsrI and EcoRI restriction endonucleases.

PubMed

Stephenson, F H; Ballard, B T; Boyer, H W; Rosenberg, J M; Greene, P J

1989-12-21

The RsrI endonuclease, a type-II restriction endonuclease (ENase) found in Rhodobacter sphaeroides, is an isoschizomer of the EcoRI ENase. A clone containing an 11-kb BamHI fragment was isolated from an R. sphaeroides genomic DNA library by hybridization with synthetic oligodeoxyribonucleotide probes based on the N-terminal amino acid (aa) sequence of RsrI. Extracts of E. coli containing a subclone of the 11-kb fragment display RsrI activity. Nucleotide sequence analysis reveals an 831-bp open reading frame encoding a polypeptide of 277 aa. A 50% identity exists within a 266-aa overlap between the deduced aa sequences of RsrI and EcoRI. Regions of 75-100% aa sequence identity correspond to key structural and functional regions of EcoRI. The type-II ENases have many common properties, and a common origin might have been expected. Nevertheless, this is the first demonstration of aa sequence similarity between ENases produced by different organisms.

16S-23S rRNA gene internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Porphyromonas.

PubMed

Conrads, Georg; Citron, Diane M; Tyrrell, Kerin L; Horz, Hans-Peter; Goldstein, Ellie J C

2005-03-01

The 16S-23S rRNA gene internal transcribed spacer (ITS) regions of 11 reference strains of Porphyromonas species, together with Bacteroides distasonis and Tannerella forsythensis, were analysed to examine interspecies relationships. Compared with the phylogenetic tree generated using 16S rRNA gene sequences, the resolution of the ITS sequence-based tree was higher, but species positioning and clustering were similar with both approaches. The recent separation of Porphyromonas gulae and Porphyromonas gingivalis into distinct species was confirmed by the ITS data. In addition, analysis of the ITS sequences of 24 clinical isolates of Porphyromonas asaccharolytica plus the type strain ATCC 25260(T) divided the sequences into two clusters, of which one was alpha-fucosidase-positive (like the type strain) while the other was alpha-fucosidase-negative. The latter resembled the previously studied unusual extra-oral isolates of 'Porphyromonas endodontalis-like organisms' (PELOs) which could therefore be called 'Porphyromonas asaccharolytica-like organisms' (PALOs), based on the genetic identification. Moreover, the proposal of alpha-fucosidase-negative P. asaccharolytica strains as a new species should also be considered.

Method for identifying and quantifying nucleic acid sequence aberrations

DOEpatents

Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

1998-01-01

A method for detecting nucleic acid sequence aberrations by detecting nucleic acid sequences having both a first and a second nucleic acid sequence type, the presence of the first and second sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. The method uses a first hybridization probe which includes a nucleic acid sequence that is complementary to a first sequence type and a first complexing agent capable of attaching to a second complexing agent and a second hybridization probe which includes a nucleic acid sequence that selectively hybridizes to the second nucleic acid sequence type over the first sequence type and includes a detectable marker for detecting the second hybridization probe.

Method for identifying and quantifying nucleic acid sequence aberrations

DOEpatents

Lucas, J.N.; Straume, T.; Bogen, K.T.

1998-07-21

A method is disclosed for detecting nucleic acid sequence aberrations by detecting nucleic acid sequences having both a first and a second nucleic acid sequence type, the presence of the first and second sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. The method uses a first hybridization probe which includes a nucleic acid sequence that is complementary to a first sequence type and a first complexing agent capable of attaching to a second complexing agent and a second hybridization probe which includes a nucleic acid sequence that selectively hybridizes to the second nucleic acid sequence type over the first sequence type and includes a detectable marker for detecting the second hybridization probe. 11 figs.

Recent progress in the research about Propionibacterium acnes strain diversity and acne: pathogen or bystander?

PubMed

Kwon, Hyuck Hoon; Suh, Dae Hun

2016-11-01

Recent progress has steadily reported the existence of the diverse strains of Propionibacterium acnes, and these studies have contributed to the elucidation of their contradictory roles between normal commensals and pathogens. In this review, the authors aimed to provide an update on the recent understanding of research about P. acnes strain diversity and acne, analyzing the potential implications for clinical applications. Before the era of genomic research, P. acnes was known to be distinguished based on serological agglutination tests, cell wall sugar analysis, or fermentation traits. Since the complete genome sequence of P. acnes was first deciphered, genetic studies based on sequence data have expanded with the introduction of more refined and precise DNA-based typing methods, including multilocus sequence typing and metagenomics. These sophisticated techniques have revealed that P. acnes consists of phylogenetically distinct cluster groups with various pathogenic traits, including elicitation of inflammation, protein secretome profile, and unique distribution patterns in various skin loci. In following large-scale studies from patients' acne samples have revealed that specific sequence types are included within the phylogenetic divisions and further suggested that particular P. acnes strains play an etiologic role in acne while others are associated with health, providing a firm platform for evidential-based research into the exact role of this organism in acne. We strongly believe that future research would provide fruitful results in not only clarifying the apparent controversy with respect to roles of P. acnes but also developing therapeutic drugs by pinpointing specific targets of the pathogenic strain only. © 2016 The International Society of Dermatology.

Single-Molecule Electrical Random Resequencing of DNA and RNA

NASA Astrophysics Data System (ADS)

Ohshiro, Takahito; Matsubara, Kazuki; Tsutsui, Makusu; Furuhashi, Masayuki; Taniguchi, Masateru; Kawai, Tomoji

2012-07-01

Two paradigm shifts in DNA sequencing technologies--from bulk to single molecules and from optical to electrical detection--are expected to realize label-free, low-cost DNA sequencing that does not require PCR amplification. It will lead to development of high-throughput third-generation sequencing technologies for personalized medicine. Although nanopore devices have been proposed as third-generation DNA-sequencing devices, a significant milestone in these technologies has been attained by demonstrating a novel technique for resequencing DNA using electrical signals. Here we report single-molecule electrical resequencing of DNA and RNA using a hybrid method of identifying single-base molecules via tunneling currents and random sequencing. Our method reads sequences of nine types of DNA oligomers. The complete sequence of 5'-UGAGGUA-3' from the let-7 microRNA family was also identified by creating a composite of overlapping fragment sequences, which was randomly determined using tunneling current conducted by single-base molecules as they passed between a pair of nanoelectrodes.

Dual signal amplification for highly sensitive electrochemical detection of uropathogens via enzyme-based catalytic target recycling.

PubMed

Su, Jiao; Zhang, Haijie; Jiang, Bingying; Zheng, Huzhi; Chai, Yaqin; Yuan, Ruo; Xiang, Yun

2011-11-15

We report an ultrasensitive electrochemical approach for the detection of uropathogen sequence-specific DNA target. The sensing strategy involves a dual signal amplification process, which combines the signal enhancement by the enzymatic target recycling technique with the sensitivity improvement by the quantum dot (QD) layer-by-layer (LBL) assembled labels. The enzyme-based catalytic target DNA recycling process results in the use of each target DNA sequence for multiple times and leads to direct amplification of the analytical signal. Moreover, the LBL assembled QD labels can further enhance the sensitivity of the sensing system. The coupling of these two effective signal amplification strategies thus leads to low femtomolar (5fM) detection of the target DNA sequences. The proposed strategy also shows excellent discrimination between the target DNA and the single-base mismatch sequences. The advantageous intrinsic sequence-independent property of exonuclease III over other sequence-dependent enzymes makes our new dual signal amplification system a general sensing platform for monitoring ultralow level of various types of target DNA sequences. Copyright © 2011 Elsevier B.V. All rights reserved.

Targeted therapy according to next generation sequencing-based panel sequencing.

PubMed

Saito, Motonobu; Momma, Tomoyuki; Kono, Koji

2018-04-17

Targeted therapy against actionable gene mutations shows a significantly higher response rate as well as longer survival compared to conventional chemotherapy, and has become a standard therapy for many cancers. Recent progress in next-generation sequencing (NGS) has enabled to identify huge number of genetic aberrations. Based on sequencing results, patients recommend to undergo targeted therapy or immunotherapy. In cases where there are no available approved drugs for the genetic mutations detected in the patients, it is recommended to be facilitate the registration for the clinical trials. For that purpose, a NGS-based sequencing panel that can simultaneously target multiple genes in a single investigation has been used in daily clinical practice. To date, various types of sequencing panels have been developed to investigate genetic aberrations with tumor somatic genome variants (gain-of-function or loss-of-function mutations, high-level copy number alterations, and gene fusions) through comprehensive bioinformatics. Because sequencing panels are efficient and cost-effective, they are quickly being adopted outside the lab, in hospitals and clinics, in order to identify personal targeted therapy for individual cancer patients.

'DNA Strider': a 'C' program for the fast analysis of DNA and protein sequences on the Apple Macintosh family of computers.

PubMed Central

Marck, C

1988-01-01

DNA Strider is a new integrated DNA and Protein sequence analysis program written with the C language for the Macintosh Plus, SE and II computers. It has been designed as an easy to learn and use program as well as a fast and efficient tool for the day-to-day sequence analysis work. The program consists of a multi-window sequence editor and of various DNA and Protein analysis functions. The editor may use 4 different types of sequences (DNA, degenerate DNA, RNA and one-letter coded protein) and can handle simultaneously 6 sequences of any type up to 32.5 kB each. Negative numbering of the bases is allowed for DNA sequences. All classical restriction and translation analysis functions are present and can be performed in any order on any open sequence or part of a sequence. The main feature of the program is that the same analysis function can be repeated several times on different sequences, thus generating multiple windows on the screen. Many graphic capabilities have been incorporated such as graphic restriction map, hydrophobicity profile and the CAI plot- codon adaptation index according to Sharp and Li. The restriction sites search uses a newly designed fast hexamer look-ahead algorithm. Typical runtime for the search of all sites with a library of 130 restriction endonucleases is 1 second per 10,000 bases. The circular graphic restriction map of the pBR322 plasmid can be therefore computed from its sequence and displayed on the Macintosh Plus screen within 2 seconds and its multiline restriction map obtained in a scrolling window within 5 seconds. PMID:2832831

Comparison of Sanger and next generation sequencing performance for genotyping Cryptosporidium isolates at the 18S rRNA and actin loci.

PubMed

Paparini, Andrea; Gofton, Alexander; Yang, Rongchang; White, Nicole; Bunce, Michael; Ryan, Una M

2015-01-01

Cryptosporidium is an important enteric pathogen that infects a wide range of humans and animals. Rapid and reliable detection and characterisation methods are essential for understanding the transmission dynamics of the parasite. Sanger sequencing, and high-throughput sequencing (HTS) on an Ion Torrent platform, were compared with each other for their sensitivity and accuracy in detecting and characterising 25 Cryptosporidium-positive human and animal faecal samples. Ion Torrent reads (n = 123,857) were obtained at both 18S rRNA and actin loci for 21 of the 25 samples. Of these, one isolate at the actin locus (Cattle 05) and three at the 18S rRNA locus (HTS 10, HTS 11 and HTS 12), suffered PCR drop-out (i.e. PCR failures) when using fusion-tagged PCR. Sanger sequences were obtained for both loci for 23 of the 25 samples and showed good agreement with Ion Torrent-based genotyping. Two samples both from pythons (SK 02 and SK 05) produced mixed 18S and actin chromatograms by Sanger sequencing but were clearly identified by Ion Torrent sequencing as C. muris. One isolate (SK 03) was typed as C. muris by Sanger sequencing but was identified as a mixed C. muris and C. tyzzeri infection by HTS. 18S rRNA Type B sequences were identified in 4/6 C. parvum isolates when deep sequenced but were undetected in Sanger sequencing. Sanger was cheaper than Ion Torrent when sequencing a small numbers of samples, but when larger numbers of samples are considered (n = 60), the costs were comparative. Fusion-tagged amplicon based approaches are a powerful way of approaching mixtures, the only draw-back being the loss of PCR efficiency on low-template samples when using primers coupled to MID tags and adaptors. Taken together these data show that HTS has excellent potential for revealing the "true" composition of species/types in a Cryptosporidium infection, but that HTS workflows need to be carefully developed to ensure sensitivity, accuracy and contamination are controlled. Copyright © 2015 Elsevier Inc. All rights reserved.

An Active RBSE Framework to Generate Optimal Stimulus Sequences in a BCI for Spelling

NASA Astrophysics Data System (ADS)

Moghadamfalahi, Mohammad; Akcakaya, Murat; Nezamfar, Hooman; Sourati, Jamshid; Erdogmus, Deniz

2017-10-01

A class of brain computer interfaces (BCIs) employs noninvasive recordings of electroencephalography (EEG) signals to enable users with severe speech and motor impairments to interact with their environment and social network. For example, EEG based BCIs for typing popularly utilize event related potentials (ERPs) for inference. Presentation paradigm design in current ERP-based letter by letter typing BCIs typically query the user with an arbitrary subset characters. However, the typing accuracy and also typing speed can potentially be enhanced with more informed subset selection and flash assignment. In this manuscript, we introduce the active recursive Bayesian state estimation (active-RBSE) framework for inference and sequence optimization. Prior to presentation in each iteration, rather than showing a subset of randomly selected characters, the developed framework optimally selects a subset based on a query function. Selected queries are made adaptively specialized for users during each intent detection. Through a simulation-based study, we assess the effect of active-RBSE on the performance of a language-model assisted typing BCI in terms of typing speed and accuracy. To provide a baseline for comparison, we also utilize standard presentation paradigms namely, row and column matrix presentation paradigm and also random rapid serial visual presentation paradigms. The results show that utilization of active-RBSE can enhance the online performance of the system, both in terms of typing accuracy and speed.

RNA interference inhibits herpes simplex virus type 1 isolated from saliva samples and mucocutaneous lesions.

PubMed

Silva, Amanda Perse da; Lopes, Juliana Freitas; Paula, Vanessa Salete de

2014-01-01

The aim of this study was to evaluate the use of RNA interference to inhibit herpes simplex virus type-1 replication in vitro. For herpes simplex virus type-1 gene silencing, three different small interfering RNAs (siRNAs) targeting the herpes simplex virus type-1 UL39 gene (sequence si-UL 39-1, si-UL 39-2, and si-UL 39-3) were used, which encode the large subunit of ribonucleotide reductase, an essential enzyme for DNA synthesis. Herpes simplex virus type-1 was isolated from saliva samples and mucocutaneous lesions from infected patients. All mucocutaneous lesions' samples were positive for herpes simplex virus type-1 by real-time PCR and by virus isolation; all herpes simplex virus type-1 from saliva samples were positive by real-time PCR and 50% were positive by virus isolation. The levels of herpes simplex virus type-1 DNA remaining after siRNA treatment were assessed by real-time PCR, whose results demonstrated that the effect of siRNAs on gene expression depends on siRNA concentration. The three siRNA sequences used were able to inhibit viral replication, assessed by real-time PCR and plaque assays and among them, the sequence si-UL 39-1 was the most effective. This sequence inhibited 99% of herpes simplex virus type-1 replication. The results demonstrate that silencing herpes simplex virus type-1 UL39 expression by siRNAs effectively inhibits herpes simplex virus type-1 replication, suggesting that siRNA based antiviral strategy may be a potential therapeutic alternative. Copyright © 2014. Published by Elsevier Editora Ltda.

Molecular and comparative analysis of Salmonella enterica Senftenberg from humans and animals using PFGE, MLST and NARMS.

PubMed

Stepan, Ryan M; Sherwood, Julie S; Petermann, Shana R; Logue, Catherine M

2011-06-27

Salmonella species are recognized worldwide as a significant cause of human and animal disease. In this study the molecular profiles and characteristics of Salmonella enterica Senftenberg isolated from human cases of illness and those recovered from healthy or diagnostic cases in animals were assessed. Included in the study was a comparison with our own sequenced strain of S. Senfteberg recovered from production turkeys in North Dakota. Isolates examined in this study were subjected to antimicrobial susceptibility profiling using the National Antimicrobial Resistance Monitoring System (NARMS) panel which tested susceptibility to 15 different antimicrobial agents. The molecular profiles of all isolates were determined using Pulsed Field Gel Electrophoresis (PFGE) and the sequence types of the strains were obtained using Multi-Locus Sequence Type (MLST) analysis based on amplification and sequence interrogation of seven housekeeping genes (aroC, dnaN, hemD, hisD, purE, sucA, and thrA). PFGE data was input into BioNumerics analysis software to generate a dendrogram of relatedness among the strains. The study found 93 profiles among 98 S. Senftenberg isolates tested and there were primarily two sequence types associated with humans and animals (ST185 and ST14) with overlap observed in all host types suggesting that the distribution of S. Senftenberg sequence types is not host dependent. Antimicrobial resistance was observed among the animal strains, however no resistance was detected in human isolates suggesting that animal husbandry has a significant influence on the selection and promotion of antimicrobial resistance. The data demonstrates the circulation of at least two strain types in both animal and human health suggesting that S. Senftenberg is relatively homogeneous in its distribution. The data generated in this study could be used towards defining a pathotype for this serovar.

Molecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Isolates in the Gulf Cooperation Council States: Dominance of OXA-23-Type Producers

PubMed Central

Sartor, Anna L.; Sidjabat, Hanna E.; Balkhy, Hanan H.; Walsh, Timothy R.; Al Johani, Sameera M.; AlJindan, Reem Y.; Alfaresi, Mubarak; Ibrahim, Emad; Al-Jardani, Amina; Al Salman, Jameela; Dashti, Ali A.; Johani, Khalid; Paterson, David L.

2015-01-01

The molecular epidemiology and mechanisms of resistance of carbapenem-resistant Acinetobacter baumannii (CRAB) were determined in hospitals in the states of the Cooperation Council for the Arab States of the Gulf (Gulf Cooperation Council [GCC]), namely, Saudi Arabia, United Arab Emirates, Oman, Qatar, Bahrain, and Kuwait. Isolates were subjected to PCR-based detection of antibiotic resistance genes and repetitive sequence-based PCR (rep-PCR) assessments of clonality. Selected isolates were subjected to multilocus sequence typing (MLST). We investigated 117 isolates resistant to carbapenem antibiotics (either imipenem or meropenem). All isolates were positive for OXA-51. The most common carbapenemases were the OXA-23-type, found in 107 isolates, followed by OXA-40-type (OXA-24-type), found in 5 isolates; 3 isolates carried the ISAba1 element upstream of blaOXA-51-type. No OXA-58-type, NDM-type, VIM-type, or IMP-type producers were detected. Multiple clones were detected with 16 clusters of clonally related CRAB. Some clusters involved hospitals in different states. MLST analysis of 15 representative isolates from different clusters identified seven different sequence types (ST195, ST208, ST229, ST436, ST450, ST452, and ST499), as well as three novel STs. The vast majority (84%) of the isolates in this study were associated with health care exposure. Awareness of multidrug-resistant organisms in GCC states has important implications for optimizing infection control practices; establishing antimicrobial stewardship programs within hospital, community, and agricultural settings; and emphasizing the need for establishing regional active surveillance systems. This will help to control the spread of CRAB in the Middle East and in hospitals accommodating transferred patients from this region. PMID:25568439

Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii isolates in the Gulf Cooperation Council States: dominance of OXA-23-type producers.

PubMed

Zowawi, Hosam M; Sartor, Anna L; Sidjabat, Hanna E; Balkhy, Hanan H; Walsh, Timothy R; Al Johani, Sameera M; AlJindan, Reem Y; Alfaresi, Mubarak; Ibrahim, Emad; Al-Jardani, Amina; Al Salman, Jameela; Dashti, Ali A; Johani, Khalid; Paterson, David L

2015-03-01

The molecular epidemiology and mechanisms of resistance of carbapenem-resistant Acinetobacter baumannii (CRAB) were determined in hospitals in the states of the Cooperation Council for the Arab States of the Gulf (Gulf Cooperation Council [GCC]), namely, Saudi Arabia, United Arab Emirates, Oman, Qatar, Bahrain, and Kuwait. Isolates were subjected to PCR-based detection of antibiotic resistance genes and repetitive sequence-based PCR (rep-PCR) assessments of clonality. Selected isolates were subjected to multilocus sequence typing (MLST). We investigated 117 isolates resistant to carbapenem antibiotics (either imipenem or meropenem). All isolates were positive for OXA-51. The most common carbapenemases were the OXA-23-type, found in 107 isolates, followed by OXA-40-type (OXA-24-type), found in 5 isolates; 3 isolates carried the ISAba1 element upstream of blaOXA-51-type. No OXA-58-type, NDM-type, VIM-type, or IMP-type producers were detected. Multiple clones were detected with 16 clusters of clonally related CRAB. Some clusters involved hospitals in different states. MLST analysis of 15 representative isolates from different clusters identified seven different sequence types (ST195, ST208, ST229, ST436, ST450, ST452, and ST499), as well as three novel STs. The vast majority (84%) of the isolates in this study were associated with health care exposure. Awareness of multidrug-resistant organisms in GCC states has important implications for optimizing infection control practices; establishing antimicrobial stewardship programs within hospital, community, and agricultural settings; and emphasizing the need for establishing regional active surveillance systems. This will help to control the spread of CRAB in the Middle East and in hospitals accommodating transferred patients from this region. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Genetic variation and DNA fingerprinting of durian types in Malaysia using simple sequence repeat (SSR) markers.

PubMed

Siew, Ging Yang; Ng, Wei Lun; Tan, Sheau Wei; Alitheen, Noorjahan Banu; Tan, Soon Guan; Yeap, Swee Keong

2018-01-01

Durian ( Durio zibethinus ) is one of the most popular tropical fruits in Asia. To date, 126 durian types have been registered with the Department of Agriculture in Malaysia based on phenotypic characteristics. Classification based on morphology is convenient, easy, and fast but it suffers from phenotypic plasticity as a direct result of environmental factors and age. To overcome the limitation of morphological classification, there is a need to carry out genetic characterization of the various durian types. Such data is important for the evaluation and management of durian genetic resources in producing countries. In this study, simple sequence repeat (SSR) markers were used to study the genetic variation in 27 durian types from the germplasm collection of Universiti Putra Malaysia. Based on DNA sequences deposited in Genbank, seven pairs of primers were successfully designed to amplify SSR regions in the durian DNA samples. High levels of variation among the 27 durian types were observed (expected heterozygosity, H E  = 0.35). The DNA fingerprinting power of SSR markers revealed by the combined probability of identity (PI) of all loci was 2.3×10 -3 . Unique DNA fingerprints were generated for 21 out of 27 durian types using five polymorphic SSR markers (the other two SSR markers were monomorphic). We further tested the utility of these markers by evaluating the clonal status of shared durian types from different germplasm collection sites, and found that some were not clones. The findings in this preliminary study not only shows the feasibility of using SSR markers for DNA fingerprinting of durian types, but also challenges the current classification of durian types, e.g., on whether the different types should be called "clones", "varieties", or "cultivars". Such matters have a direct impact on the regulation and management of durian genetic resources in the region.

Genetic variation and DNA fingerprinting of durian types in Malaysia using simple sequence repeat (SSR) markers

PubMed Central

Siew, Ging Yang; Tan, Sheau Wei; Tan, Soon Guan; Yeap, Swee Keong

2018-01-01

Durian (Durio zibethinus) is one of the most popular tropical fruits in Asia. To date, 126 durian types have been registered with the Department of Agriculture in Malaysia based on phenotypic characteristics. Classification based on morphology is convenient, easy, and fast but it suffers from phenotypic plasticity as a direct result of environmental factors and age. To overcome the limitation of morphological classification, there is a need to carry out genetic characterization of the various durian types. Such data is important for the evaluation and management of durian genetic resources in producing countries. In this study, simple sequence repeat (SSR) markers were used to study the genetic variation in 27 durian types from the germplasm collection of Universiti Putra Malaysia. Based on DNA sequences deposited in Genbank, seven pairs of primers were successfully designed to amplify SSR regions in the durian DNA samples. High levels of variation among the 27 durian types were observed (expected heterozygosity, HE = 0.35). The DNA fingerprinting power of SSR markers revealed by the combined probability of identity (PI) of all loci was 2.3×10−3. Unique DNA fingerprints were generated for 21 out of 27 durian types using five polymorphic SSR markers (the other two SSR markers were monomorphic). We further tested the utility of these markers by evaluating the clonal status of shared durian types from different germplasm collection sites, and found that some were not clones. The findings in this preliminary study not only shows the feasibility of using SSR markers for DNA fingerprinting of durian types, but also challenges the current classification of durian types, e.g., on whether the different types should be called “clones”, “varieties”, or “cultivars”. Such matters have a direct impact on the regulation and management of durian genetic resources in the region. PMID:29511604

BEAUTY: an enhanced BLAST-based search tool that integrates multiple biological information resources into sequence similarity search results.

PubMed

Worley, K C; Wiese, B A; Smith, R F

1995-09-01

BEAUTY (BLAST enhanced alignment utility) is an enhanced version of the NCBI's BLAST data base search tool that facilitates identification of the functions of matched sequences. We have created new data bases of conserved regions and functional domains for protein sequences in NCBI's Entrez data base, and BEAUTY allows this information to be incorporated directly into BLAST search results. A Conserved Regions Data Base, containing the locations of conserved regions within Entrez protein sequences, was constructed by (1) clustering the entire data base into families, (2) aligning each family using our PIMA multiple sequence alignment program, and (3) scanning the multiple alignments to locate the conserved regions within each aligned sequence. A separate Annotated Domains Data Base was constructed by extracting the locations of all annotated domains and sites from sequences represented in the Entrez, PROSITE, BLOCKS, and PRINTS data bases. BEAUTY performs a BLAST search of those Entrez sequences with conserved regions and/or annotated domains. BEAUTY then uses the information from the Conserved Regions and Annotated Domains data bases to generate, for each matched sequence, a schematic display that allows one to directly compare the relative locations of (1) the conserved regions, (2) annotated domains and sites, and (3) the locally aligned regions matched in the BLAST search. In addition, BEAUTY search results include World-Wide Web hypertext links to a number of external data bases that provide a variety of additional types of information on the function of matched sequences. This convenient integration of protein families, conserved regions, annotated domains, alignment displays, and World-Wide Web resources greatly enhances the biological informativeness of sequence similarity searches. BEAUTY searches can be performed remotely on our system using the "BCM Search Launcher" World-Wide Web pages (URL is < http:/ /gc.bcm.tmc.edu:8088/ search-launcher/launcher.html > ).

Longitudinal stability of MRI for mapping brain change using tensor-based morphometry.

PubMed

Leow, Alex D; Klunder, Andrea D; Jack, Clifford R; Toga, Arthur W; Dale, Anders M; Bernstein, Matt A; Britson, Paula J; Gunter, Jeffrey L; Ward, Chadwick P; Whitwell, Jennifer L; Borowski, Bret J; Fleisher, Adam S; Fox, Nick C; Harvey, Danielle; Kornak, John; Schuff, Norbert; Studholme, Colin; Alexander, Gene E; Weiner, Michael W; Thompson, Paul M

2006-06-01

Measures of brain change can be computed from sequential MRI scans, providing valuable information on disease progression, e.g., for patient monitoring and drug trials. Tensor-based morphometry (TBM) creates maps of these brain changes, visualizing the 3D profile and rates of tissue growth or atrophy, but its sensitivity depends on the contrast and geometric stability of the images. As part of the Alzheimer's Disease Neuroimaging Initiative (ADNI), 17 normal elderly subjects were scanned twice (at a 2-week interval) with several 3D 1.5 T MRI pulse sequences: high and low flip angle SPGR/FLASH (from which Synthetic T1 images were generated), MP-RAGE, IR-SPGR (N = 10) and MEDIC (N = 7) scans. For each subject and scan type, a 3D deformation map aligned baseline and follow-up scans, computed with a nonlinear, inverse-consistent elastic registration algorithm. Voxelwise statistics, in ICBM stereotaxic space, visualized the profile of mean absolute change and its cross-subject variance; these maps were then compared using permutation testing. Image stability depended on: (1) the pulse sequence; (2) the transmit/receive coil type (birdcage versus phased array); (3) spatial distortion corrections (using MEDIC sequence information); (4) B1-field intensity inhomogeneity correction (using N3). SPGR/FLASH images acquired using a birdcage coil had least overall deviation. N3 correction reduced coil type and pulse sequence differences and improved scan reproducibility, except for Synthetic T1 images (which were intrinsically corrected for B1-inhomogeneity). No strong evidence favored B0 correction. Although SPGR/FLASH images showed least deviation here, pulse sequence selection for the ADNI project was based on multiple additional image analyses, to be reported elsewhere.

Longitudinal stability of MRI for mapping brain change using tensor-based morphometry

PubMed Central

Leow, Alex D.; Klunder, Andrea D.; Jack, Clifford R.; Toga, Arthur W.; Dale, Anders M.; Bernstein, Matt A.; Britson, Paula J.; Gunter, Jeffrey L.; Ward, Chadwick P.; Whitwell, Jennifer L.; Borowski, Bret J.; Fleisher, Adam S.; Fox, Nick C.; Harvey, Danielle; Kornak, John; Schuff, Norbert; Studholme, Colin; Alexander, Gene E.; Weiner, Michael W.; Thompson, Paul M.

2007-01-01

Measures of brain change can be computed from sequential MRI scans, providing valuable information on disease progression, e.g., for patient monitoring and drug trials. Tensor-based morphometry (TBM) creates maps of these brain changes, visualizing the 3D profile and rates of tissue growth or atrophy, but its sensitivity depends on the contrast and geometric stability of the images. A s part of the Alzheimer’s Disease Neuroimaging Initiative (ADNI), 17 normal elderly subjects were scanned twice (at a 2-week interval) with several 3D 1.5 T MRI pulse sequences: high and low flip angle SPGR/FLASH (from which Synthetic T1 images were generated), MP-RAGE, IR-SPGR (N = 10) and MEDIC (N = 7) scans. For each subject and scan type, a 3D deformation map aligned baseline and follow-up scans, computed with a nonlinear, inverse-consistent elastic registration algorithm. Voxelwise statistics, in ICBM stereotaxic space, visualized the profile of mean absolute change and its cross-subject variance; these maps were then compared using permutation testing. Image stability depended on: (1) the pulse sequence; (2) the transmit/receive coil type (birdcage versus phased array); (3) spatial distortion corrections (using MEDIC sequence information); (4) B1-field intensity inhomogeneity correction (using N3). SPGR/FLASH images acquired using a birdcage coil had least overall deviation. N3 correction reduced coil type and pulse sequence differences and improved scan reproducibility, except for Synthetic T1 images (which were intrinsically corrected for B1-inhomogeneity). No strong evidence favored B0 correction. Although SPGR/FLASH images showed least deviation here, pulse sequence selection for the ADNI project was based on multiple additional image analyses, to be reported elsewhere. PMID:16480900

Diversity Analysis of Dairy and Nondairy Lactococcus lactis Isolates, Using a Novel Multilocus Sequence Analysis Scheme and (GTG)5-PCR Fingerprinting▿

PubMed Central

Rademaker, Jan L. W.; Herbet, Hélène; Starrenburg, Marjo J. C.; Naser, Sabri M.; Gevers, Dirk; Kelly, William J.; Hugenholtz, Jeroen; Swings, Jean; van Hylckama Vlieg, Johan E. T.

2007-01-01

The diversity of a collection of 102 lactococcus isolates including 91 Lactococcus lactis isolates of dairy and nondairy origin was explored using partial small subunit rRNA gene sequence analysis and limited phenotypic analyses. A subset of 89 strains of L. lactis subsp. cremoris and L. lactis subsp. lactis isolates was further analyzed by (GTG)5-PCR fingerprinting and a novel multilocus sequence analysis (MLSA) scheme. Two major genomic lineages within L. lactis were found. The L. lactis subsp. cremoris type-strain-like genotype lineage included both L. lactis subsp. cremoris and L. lactis subsp. lactis isolates. The other major lineage, with a L. lactis subsp. lactis type-strain-like genotype, comprised L. lactis subsp. lactis isolates only. A novel third genomic lineage represented two L. lactis subsp. lactis isolates of nondairy origin. The genomic lineages deviate from the subspecific classification of L. lactis that is based on a few phenotypic traits only. MLSA of six partial genes (atpA, encoding ATP synthase alpha subunit; pheS, encoding phenylalanine tRNA synthetase; rpoA, encoding RNA polymerase alpha chain; bcaT, encoding branched chain amino acid aminotransferase; pepN, encoding aminopeptidase N; and pepX, encoding X-prolyl dipeptidyl peptidase) revealed 363 polymorphic sites (total length, 1,970 bases) among 89 L. lactis subsp. cremoris and L. lactis subsp. lactis isolates with unique sequence types for most isolates. This allowed high-resolution cluster analysis in which dairy isolates form subclusters of limited diversity within the genomic lineages. The pheS DNA sequence analysis yielded two genetic groups dissimilar to the other genotyping analysis-based lineages, indicating a disparate acquisition route for this gene. PMID:17890345