Cotransduction with MGMT and Ubiquitous or Erythroid-Specific GFP Lentiviruses Allows Enrichment of Dual-Positive Hematopoietic Progenitor Cells In Vivo

PubMed Central

Roth, Justin C.; Ismail, Mourad; Reese, Jane S.; Lingas, Karen T.; Ferrari, Giuliana; Gerson, Stanton L.

2012-01-01

The P140K point mutant of MGMT allows robust hematopoietic stem cell (HSC) enrichment in vivo. Thus, dual-gene vectors that couple MGMT and therapeutic gene expression have allowed enrichment of gene-corrected HSCs in animal models. However, expression levels from dual-gene vectors are often reduced for one or both genes. Further, it may be desirable to express selection and therapeutic genes at distinct stages of cell differentiation. In this regard, we evaluated whether hematopoietic cells could be efficiently cotransduced using low MOIs of two separate single-gene lentiviruses, including MGMT for dual-positive cell enrichment. Cotransduction efficiencies were evaluated using a range of MGMT : GFP virus ratios, MOIs, and selection stringencies in vitro. Cotransduction was optimal when equal proportions of each virus were used, but low MGMT : GFP virus ratios resulted in the highest proportion of dual-positive cells after selection. This strategy was then evaluated in murine models for in vivo selection of HSCs cotransduced with a ubiquitous MGMT expression vector and an erythroid-specific GFP vector. Although the MGMT and GFP expression percentages were variable among engrafted recipients, drug selection enriched MGMT-positive leukocyte and GFP-positive erythroid cell populations. These data demonstrate cotransduction as a mean to rapidly enrich and evaluate therapeutic lentivectors in vivo. PMID:22888445

Evaluation of Phage Display Discovered Peptides as Ligands for Prostate-Specific Membrane Antigen (PSMA)

PubMed Central

Edwards, W. Barry

2013-01-01

The aim of this study was to identify potential ligands of PSMA suitable for further development as novel PSMA-targeted peptides using phage display technology. The human PSMA protein was immobilized as a target followed by incubation with a 15-mer phage display random peptide library. After one round of prescreening and two rounds of screening, high-stringency screening at the third round of panning was performed to identify the highest affinity binders. Phages which had a specific binding activity to PSMA in human prostate cancer cells were isolated and the DNA corresponding to the 15-mers were sequenced to provide three consensus sequences: GDHSPFT, SHFSVGS and EVPRLSLLAVFL as well as other sequences that did not display consensus. Two of the peptide sequences deduced from DNA sequencing of binding phages, SHSFSVGSGDHSPFT and GRFLTGGTGRLLRIS were labeled with 5-carboxyfluorescein and shown to bind and co-internalize with PSMA on human prostate cancer cells by fluorescence microscopy. The high stringency requirements yielded peptides with affinities KD∼1 µM or greater which are suitable starting points for affinity maturation. While these values were less than anticipated, the high stringency did yield peptide sequences that apparently bound to different surfaces on PSMA. These peptide sequences could be the basis for further development of peptides for prostate cancer tumor imaging and therapy. PMID:23935860

Secondary structure prediction and structure-specific sequence analysis of single-stranded DNA.

PubMed

Dong, F; Allawi, H T; Anderson, T; Neri, B P; Lyamichev, V I

2001-08-01

DNA sequence analysis by oligonucleotide binding is often affected by interference with the secondary structure of the target DNA. Here we describe an approach that improves DNA secondary structure prediction by combining enzymatic probing of DNA by structure-specific 5'-nucleases with an energy minimization algorithm that utilizes the 5'-nuclease cleavage sites as constraints. The method can identify structural differences between two DNA molecules caused by minor sequence variations such as a single nucleotide mutation. It also demonstrates the existence of long-range interactions between DNA regions separated by >300 nt and the formation of multiple alternative structures by a 244 nt DNA molecule. The differences in the secondary structure of DNA molecules revealed by 5'-nuclease probing were used to design structure-specific probes for mutation discrimination that target the regions of structural, rather than sequence, differences. We also demonstrate the performance of structure-specific 'bridge' probes complementary to non-contiguous regions of the target molecule. The structure-specific probes do not require the high stringency binding conditions necessary for methods based on mismatch formation and permit mutation detection at temperatures from 4 to 37 degrees C. Structure-specific sequence analysis is applied for mutation detection in the Mycobacterium tuberculosis katG gene and for genotyping of the hepatitis C virus.

Stringency and relaxation among the halobacteria.

PubMed Central

Cimmino, C; Scoarughi, G L; Donini, P

1993-01-01

Accumulation of stable RNA and production of guanosine polyphosphates (ppGpp and pppGpp) were studied during amino acid starvation in four species of halobacteria. In two of the four species, stable RNA was under stringent control, whereas one of the remaining two species was relaxed and the other gave an intermediate phenotype. The stringent reaction was reversed by anisomycin, an effect analogous to the chloroamphenicol-induced reversal of stringency in the eubacteria. During the stringent response, neither ppGpp nor pppGpp accumulation took place during starvation. In both growing and starved cells a very low basal level of the two polyphosphates appeared to be present. In the stringent species the intracellular concentration of GTP did not diminish but actually increased during the course of the stringent response. These data demonstrate that (i) wild-type halobacteria can have either the stringent or the relaxed phenotype (all wild-type eubacteria tested have been shown to be stringent); (ii) stringency in the halobacteria is dependent on the deaminoacylation of tRNA, as in the eubacteria; and (iii) in the halobacteria, ppGpp is not an effector of stringent control over stable-RNA synthesis. Images PMID:7691798

Improved Efficiency and Robustness in qPCR and Multiplex End-Point PCR by Twisted Intercalating Nucleic Acid Modified Primers

PubMed Central

Schneider, Uffe Vest; Mikkelsen, Nikolaj Dam; Lindqvist, Anja; Okkels, Limei Meng; Jøhnk, Nina; Lisby, Gorm

2012-01-01

We introduce quantitative polymerase chain reaction (qPCR) primers and multiplex end-point PCR primers modified by the addition of a single ortho-Twisted Intercalating Nucleic Acid (o-TINA) molecule at the 5′-end. In qPCR, the 5′-o-TINA modified primers allow for a qPCR efficiency of 100% at significantly stressed reaction conditions, increasing the robustness of qPCR assays compared to unmodified primers. In samples spiked with genomic DNA, 5′-o-TINA modified primers improve the robustness by increased sensitivity and specificity compared to unmodified DNA primers. In unspiked samples, replacement of unmodified DNA primers with 5′-o-TINA modified primers permits an increased qPCR stringency. Compared to unmodified DNA primers, this allows for a qPCR efficiency of 100% at lowered primer concentrations and at increased annealing temperatures with unaltered cross-reactivity for primers with single nucleobase mismatches. In a previously published octaplex end-point PCR targeting diarrheagenic Escherichia coli, application of 5′-o-TINA modified primers allows for a further reduction (>45% or approximately one hour) in overall PCR program length, while sustaining the amplification and analytical sensitivity for all targets in crude bacterial lysates. For all crude bacterial lysates, 5′-o-TINA modified primers permit a substantial increase in PCR stringency in terms of lower primer concentrations and higher annealing temperatures for all eight targets. Additionally, crude bacterial lysates spiked with human genomic DNA show lesser formation of non-target amplicons implying increased robustness. Thus, 5′-o-TINA modified primers are advantageous in PCR assays, where one or more primer pairs are required to perform at stressed reaction conditions. PMID:22701644

Degenerative encephalopathy in a coastal mountain kingsnake (Lampropeltis zonata multifasciata) due to adenoviral-like infection.

PubMed

Raymond, James T; Lamm, Marnie; Nordhausen, Robert; Latimer, Ken; Garner, Michael M

2003-04-01

In March 2000, an approximately 30-yr-old, male coastal mountain kingsnake (Lampropeltis zonata multifasciata) presented with disequilibrium and unresponsiveness to stimuli that ultimately lead to euthanasia. Histologically, there were foci of gliosis primarily within the caudal cerebrum, brainstem, and cervical spinal cord. Several glial cells and endothelial cells contained magenta, intranuclear inclusion bodies. Electron microscopy of the inclusions revealed paracrystalline arrays of 79-82 nm, viral-like particles. DNA in situ hybridization of sections of formalin-fixed brain using a mixture of two digoxigenin-end-labeled, adenovirus specific, oligonucleotide probes at low and high stringency was positive for adenovirus.

An RNA Domain Imparts Specificity and Selectivity to a Viral DNA Packaging Motor

PubMed Central

Zhao, Wei; Jardine, Paul J.

2015-01-01

ABSTRACT During assembly, double-stranded DNA viruses, including bacteriophages and herpesviruses, utilize a powerful molecular motor to package their genomic DNA into a preformed viral capsid. An integral component of the packaging motor in the Bacillus subtilis bacteriophage ϕ29 is a viral genome-encoded pentameric ring of RNA (prohead RNA [pRNA]). pRNA is a 174-base transcript comprised of two domains, domains I and II. Early studies initially isolated a 120-base form (domain I only) that retains high biological activity in vitro; hence, no function could be assigned to domain II. Here we define a role for this domain in the packaging process. DNA packaging using restriction digests of ϕ29 DNA showed that motors with the 174-base pRNA supported the correct polarity of DNA packaging, selectively packaging the DNA left end. In contrast, motors containing the 120-base pRNA had compromised specificity, packaging both left- and right-end fragments. The presence of domain II also provides selectivity in competition assays with genomes from related phages. Furthermore, motors with the 174-base pRNA were restrictive, in that they packaged only one DNA fragment into the head, whereas motors with the 120-base pRNA packaged several fragments into the head, indicating multiple initiation events. These results show that domain II imparts specificity and stringency to the motor during the packaging initiation events that precede DNA translocation. Heteromeric rings of pRNA demonstrated that one or two copies of domain II were sufficient to impart this selectivity/stringency. Although ϕ29 differs from other double-stranded DNA phages in having an RNA motor component, the function provided by pRNA is carried on the motor protein components in other phages. IMPORTANCE During virus assembly, genome packaging involves the delivery of newly synthesized viral nucleic acid into a protein shell. In the double-stranded DNA phages and herpesviruses, this is accomplished by a powerful molecular motor that translocates the viral DNA into a preformed viral shell. A key event in DNA packaging is recognition of the viral DNA among other nucleic acids in the host cell. Commonly, a DNA-binding protein mediates the interaction of viral DNA with the motor/head shell. Here we show that for the bacteriophage ϕ29, this essential step of genome recognition is mediated by a viral genome-encoded RNA rather than a protein. A domain of the prohead RNA (pRNA) imparts specificity and stringency to the motor by ensuring the correct orientation of DNA packaging and restricting initiation to a single event. Since this assembly step is unique to the virus, DNA packaging is a novel target for the development of antiviral drugs. PMID:26423956

An RNA Domain Imparts Specificity and Selectivity to a Viral DNA Packaging Motor.

PubMed

Zhao, Wei; Jardine, Paul J; Grimes, Shelley

2015-12-01

During assembly, double-stranded DNA viruses, including bacteriophages and herpesviruses, utilize a powerful molecular motor to package their genomic DNA into a preformed viral capsid. An integral component of the packaging motor in the Bacillus subtilis bacteriophage ϕ29 is a viral genome-encoded pentameric ring of RNA (prohead RNA [pRNA]). pRNA is a 174-base transcript comprised of two domains, domains I and II. Early studies initially isolated a 120-base form (domain I only) that retains high biological activity in vitro; hence, no function could be assigned to domain II. Here we define a role for this domain in the packaging process. DNA packaging using restriction digests of ϕ29 DNA showed that motors with the 174-base pRNA supported the correct polarity of DNA packaging, selectively packaging the DNA left end. In contrast, motors containing the 120-base pRNA had compromised specificity, packaging both left- and right-end fragments. The presence of domain II also provides selectivity in competition assays with genomes from related phages. Furthermore, motors with the 174-base pRNA were restrictive, in that they packaged only one DNA fragment into the head, whereas motors with the 120-base pRNA packaged several fragments into the head, indicating multiple initiation events. These results show that domain II imparts specificity and stringency to the motor during the packaging initiation events that precede DNA translocation. Heteromeric rings of pRNA demonstrated that one or two copies of domain II were sufficient to impart this selectivity/stringency. Although ϕ29 differs from other double-stranded DNA phages in having an RNA motor component, the function provided by pRNA is carried on the motor protein components in other phages. During virus assembly, genome packaging involves the delivery of newly synthesized viral nucleic acid into a protein shell. In the double-stranded DNA phages and herpesviruses, this is accomplished by a powerful molecular motor that translocates the viral DNA into a preformed viral shell. A key event in DNA packaging is recognition of the viral DNA among other nucleic acids in the host cell. Commonly, a DNA-binding protein mediates the interaction of viral DNA with the motor/head shell. Here we show that for the bacteriophage ϕ29, this essential step of genome recognition is mediated by a viral genome-encoded RNA rather than a protein. A domain of the prohead RNA (pRNA) imparts specificity and stringency to the motor by ensuring the correct orientation of DNA packaging and restricting initiation to a single event. Since this assembly step is unique to the virus, DNA packaging is a novel target for the development of antiviral drugs. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Conservation of the fourth gene among rotaviruses recovered from asymptomatic newborn infants and its possible role in attenuation.

PubMed Central

Flores, J; Midthun, K; Hoshino, Y; Green, K; Gorziglia, M; Kapikian, A Z; Chanock, R M

1986-01-01

RNA-RNA hybridization was performed to assess the extent of genetic relatedness among human rotaviruses isolated from children with gastroenteritis and from asymptomatic newborn infants. 32P-labeled single-stranded RNAs produced by in vitro transcription from viral cores of the different strains tested were used as probes in two different hybridization assays: undenatured genomic RNAs were resolved by polyacrylamide gel electrophoresis, denatured in situ, electrophoretically transferred to diazobenzyloxymethyl-paper (Northern blots), and then hybridized to the probes under two different conditions of stringency; and denatured genomic double-stranded RNAs were hybridized to the probes in solution and the hybrids which formed were identified by polyacrylamide gel electrophoresis. When analyzed by Northern blot hybridization at a low level of stringency, all genes from the strains tested cross-hybridized, providing evidence for some sequence homology in each of the corresponding genes. However, when hybridization stringency was increased, a difference in gene 4 sequence was detected between strains recovered from asymptomatic newborn infants ("nursery strains") and strains recovered from infants and young children with diarrhea. Although the nursery strains exhibited serotypic diversity (i.e., each of the four strains tested belonged to a different serotype), the fourth gene appeared to be highly conserved. Similarly, each of the virulent strains tested belonged to a different serotype; nonetheless, there was significant conservation of sequence among the fourth genes of three of these viruses. Significantly, the conserved fourth genes of the nursery strains were distinct from the fourth gene of each of the virulent viruses. These results were confirmed and extended during experiments in which the RNA-RNA hybridization was carried out in solution and the resulting hybrids were analyzed by polyacrylamide gel electrophoresis. Under these conditions, the fourth genes of the nursery strains were closely related to each other but not to the fourth genes of the virulent viruses. Full-length hybrids did not form between the fourth genes from the nursery strains and the corresponding genes from the strains recovered from symptomatic infants and young children. Images PMID:3023685

Distribution of endogenous type B and type D sheep retrovirus sequences in ungulates and other mammals.

PubMed Central

Hecht, S J; Stedman, K E; Carlson, J O; DeMartini, J C

1996-01-01

The jaagsiekte sheep retrovirus (JSRV), which appears to be a type B/D retrovirus chimera, has been incriminated as the cause of ovine pulmonary carcinoma. Recent studies suggest that the sequences related to this virus are found in the genomes of normal sheep and goats. To learn whether there are breeds of sheep that lack the endogenous viral sequences and to study their distribution among other groups of mammals, we surveyed several domestic sheep and goat breeds, other ungulates, and various mammal groups for sequences related to JSRV. Probes prepared from the envelope (SU) region of JSRV and the capsid (CA) region of a Peruvian type D virus related to JSRV were used in Southern blot hybridization with genomic DNA followed by low- and high-stringency washes. Fifteen to 20 CA and SU bands were found in all members of the 13 breeds of domestic sheep and 6 breeds of goats tested. There were similar findings in 6 wild Ovis and Capra genera. Within 22 other genera of Bovidae including domestic cattle, and 7 other families of Artiodactyla including Cervidae, there were usually a few CA or SU bands at low stringency and rare bands at high stringency. Among 16 phylogenetically distant genera, there were generally fewer bands hybridizing with either probe. These results reveal wide-spread phylogenetic distribution of endogenous type B and type D retroviral sequences related to JSRV among mammals and argue for further investigation of their potential role in disease. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:8622932

Risk of breast cancer with CXCR4-using HIV defined by V3 loop sequencing.

PubMed

Goedert, James J; Swenson, Luke C; Napolitano, Laura A; Haddad, Mojgan; Anastos, Kathryn; Minkoff, Howard; Young, Mary; Levine, Alexandra; Adeyemi, Oluwatoyin; Seaberg, Eric C; Aouizerat, Bradley; Rabkin, Charles S; Harrigan, P Richard; Hessol, Nancy A

2015-01-01

Evaluate the risk of female breast cancer associated with HIV-CXCR4 (X4) tropism as determined by various genotypic measures. A breast cancer case-control study, with pairwise comparisons of tropism determination methods, was conducted. From the Women's Interagency HIV Study repository, one stored plasma specimen was selected from 25 HIV-infected cases near the breast cancer diagnosis date and 75 HIV-infected control women matched for age and calendar date. HIV-gp120 V3 sequences were derived by Sanger population sequencing (PS) and 454-pyro deep sequencing (DS). Sequencing-based HIV-X4 tropism was defined using the geno2pheno algorithm, with both high-stringency DS [false-positive rate (3.5) and 2% X4 cutoff], and lower stringency DS (false-positive rate, 5.75 and 15% X4 cutoff). Concordance of tropism results by PS, DS, and previously performed phenotyping was assessed with kappa (κ) statistics. Case-control comparisons used exact P values and conditional logistic regression. In 74 women (19 cases, 55 controls) with complete results, prevalence of HIV-X4 by PS was 5% in cases vs 29% in controls (P = 0.06; odds ratio, 0.14; confidence interval: 0.003 to 1.03). Smaller case-control prevalence differences were found with high-stringency DS (21% vs 36%, P = 0.32), lower stringency DS (16% vs 35%, P = 0.18), and phenotyping (11% vs 31%, P = 0.10). HIV-X4 tropism concordance was best between PS and lower stringency DS (93%, κ = 0.83). Other pairwise concordances were 82%-92% (κ = 0.56-0.81). Concordance was similar among cases and controls. HIV-X4 defined by population sequencing (PS) had good agreement with lower stringency DS and was significantly associated with lower odds of breast cancer.

Development of a DNA-Based Method for Distinguishing the Malaria Vectors, Anopheles gambiae From Anopheles arabiensis.

DTIC Science & Technology

1986-06-01

our preliminary studies hybridization with the Droso- phila actin probe required such low stringency conditions that the signal to noise ratio made...Balabacensis complex of Southeast Asia (Diptera: Culicidae). Genetica 57:81-86. (14) Mahon RJ and PM Miethke. 1982. Anopheles farauti No. 3, a hitherto un

Human papillomavirus type 16 DNA in periungual squamous cell carcinomas

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

Moy, R.L.; Eliezri, Y.D.; Bennett, R.G.

1989-05-12

Ten squamous cell carcinomas (in situ or invasive) of the fingernail region were analyzed for the presence of DNA sequences homologous to human papilloma-virus (HPV) by dot blot hybridization. In most patients, the lesions were verrucae of long-term duration that were refractory to conventional treatment methods. Eight of the lesions contained HPV DNA sequences, and in six of these the sequences were related to HPV 16 as deduced from low-stringency nucleic acid hybridization followed by low- and high-stringency washes. Furthermore, the restriction endonuclease digestion pattern of DNA isolated from four of these lesions was diagnostic of episomal HPV 16. Themore » high-frequency association of HPV 16 with periungual squamous cell carcinoma is similar to that reported for HPV 16 with squamous cell carcinomas on mucous membranes at other sites, notably the genital tract. The findings suggest that HPV 16 may play an important role in the development of squamous cell carcinomas of the finger, most notably those lesions that are chronic and located in the periungual area.« less

Assessing the potential additionality of certification by the Round table on Responsible Soybeans and the Roundtable on Sustainable Palm Oil

NASA Astrophysics Data System (ADS)

Garrett, Rachael D.; Carlson, Kimberly M.; Rueda, Ximena; Noojipady, Praveen

2016-04-01

Multi-stakeholder roundtables offering certification programs are promising voluntary governance mechanisms to address sustainability issues associated with international agricultural supply chains. Yet, little is known about whether roundtable certifications confer additionality, the benefits of certification beyond what would be expected from policies and practices currently in place. Here, we examine the potential additionality of the Round table on Responsible Soybeans (RTRS) and the Roundtable on Sustainable Palm Oil (RSPO) in mitigating conversion of native vegetation to cropland. We develop a metric of additionality based on business as usual land cover change dynamics and roundtable standard stringency relative to existing policies. We apply this metric to all countries with RTRS (n = 8) and RSPO (n = 12) certified production in 2013-2014, as well as countries that have no certified production but are among the top ten global producers in terms of soy (n = 2) and oil palm (n = 2). We find RSPO and RTRS both have substantially higher levels of stringency than existing national policies except in Brazil and Uruguay. In regions where these certification standards are adopted, the mean estimated rate of tree cover conversion to the target crop is similar for both standards. RTRS has higher mean relative stringency than the RSPO, yet RSPO countries have slightly higher enforcement levels. Therefore, mean potential additionality of RTRS and RSPO is similar across regions. Notably, countries with the highest levels of additionality have some adoption. However, with extremely low adoption rates (0.41% of 2014 global harvested area), RTRS likely has lower impact than RSPO (14%). Like most certification programs, neither roundtable is effectively targeting smallholder producers. To improve natural ecosystem protection, roundtables could target adoption to regions with low levels of environmental governance and high rates of forest-to-cropland conversion.

78 FR 66648 - Approval and Promulgation of Implementation Plans; Texas; Procedures for Stringency...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-06

... ENVIRONMENTAL PROTECTION AGENCY 40 CFR Part 52 [EPA-R06-OAR-2010-0335; FRL-9902-50-Region 6] Approval and Promulgation of Implementation Plans; Texas; Procedures for Stringency Determinations and Minor Permit Revisions for Federal Operating Permits AGENCY: Environmental Protection Agency (EPA...

78 FR 55234 - Approval and Promulgation of Implementation Plans; Texas; Procedures for Stringency...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-10

... ENVIRONMENTAL PROTECTION AGENCY 40 CFR Part 52 [EPA-R06-OAR-2010-0335; FRL-9900-81-Region6] Approval and Promulgation of Implementation Plans; Texas; Procedures for Stringency Determinations and Minor Permit Revisions for Federal Operating Permits AGENCY: Environmental Protection Agency (EPA...

Practical and Theoretical Requirements for Controlling Rater Stringency in Peer Review.

ERIC Educational Resources Information Center

Cason, Gerald J.; Cason, Carolyn L.

This study describes a computer based, performance rating information processing system, performance rating theory, and programs for the application of the theory to obtain ratings free from the effects of reviewer stringency in reviewing abstracts of conference papers. Originally, the Performance Rating (PR) System was used to evaluate the…

Are More Stringent NCLB State Accountability Systems Associated with Better Student Outcomes? An Analysis of NAEP Results across States

ERIC Educational Resources Information Center

Wei, Xin

2012-01-01

This study developed a comprehensive measure of the stringency level of NCLB states' accountability systems, including the strength of their annual measurable objectives, confidence intervals, performance indexing, retesting, minimum subgroup size, and the difficulty levels of proficiency standards. This study related accountability stringency in…

Support for PhD Students: The Impact of Institutional Dynamics on the Pedagogy of Learning Development

ERIC Educational Resources Information Center

Peelo, Moira

2013-01-01

This paper explores one practitioner's learning development work with PhD students in a changing university context in which managerialism and financial stringency have combined. It questions how learning development practitioners can maintain their professional goals while negotiating issues arising from managerialism, financial stringency,…

Risk of Breast Cancer with CXCR4-using HIV Defined by V3-Loop Sequencing

PubMed Central

Goedert, James J.; Swenson, Luke C.; Napolitano, Laura A.; Haddad, Mojgan; Anastos, Kathryn; Minkoff, Howard; Young, Mary; Levine, Alexandra; Adeyemi, Oluwatoyin; Seaberg, Eric C.; Aouizerat, Bradley; Rabkin, Charles S.; Harrigan, P. Richard; Hessol, Nancy A.

2014-01-01

Objective Evaluate the risk of female breast cancer associated with HIV-CXCR4 (X4) tropism as determined by various genotypic measures. Methods A breast cancer case-control study, with pairwise comparisons of tropism determination methods, was conducted. From the Women's Interagency HIV Study repository, one stored plasma specimen was selected from 25 HIV-infected cases near the breast cancer diagnosis date and 75 HIV-infected control women matched for age and calendar date. HIVgp120-V3 sequences were derived by Sanger population sequencing (PS) and 454-pyro deep sequencing (DS). Sequencing-based HIV-X4 tropism was defined using the geno2pheno algorithm, with both high-stringency DS [False-Positive-Rate (FPR 3.5) and 2% X4 cutoff], and lower stringency DS (FPR 5.75, 15% X4 cut-off). Concordance of tropism results by PS, DS, and previously performed phenotyping was assessed with kappa (κ) statistics. Case-control comparisons used exact P-values and conditional logistic regression. Results In 74 women (19 cases, 55 controls) with complete results, prevalence of HIV-X4 by PS was 5% in cases vs 29% in controls (P=0.06, odds ratio 0.14, confidence interval 0.003-1.03). Smaller case-control prevalence differences were found with high-stringency DS (21% vs 36%, P=0.32), lower-stringency DS (16% vs 35%, P=0.18), and phenotyping (11% vs 31%, P=0.10). HIV-X4-tropism concordance was best between PS and lower-stringency DS (93%, κ=0.83). Other pairwise concordances were 82%-92% (κ=0.56-0.81). Concordance was similar among cases and controls. Conclusions HIV-X4 defined by population sequencing (PS) had good agreement with lower stringency deep sequencing and was significantly associated with lower odds of breast cancer. PMID:25321183

Evaluation of LSSP-PCR for identification of Leptospira spp. in urine samples of cattle with clinical suspicion of leptospirosis.

PubMed

Bomfim, Maria Rosa Quaresma; Koury, Matilde Cota

2006-12-20

We evaluated the use of low-stringency single specific primer PCR (LSSP-PCR) for genetically typing Leptospira directly from urine samples of cattle with clinical suspicion of leptospirosis. Urine samples obtained from 40 cattle with clinical suspicion of leptospirosis were amplified by specific PCR using the following primers: Internal 1/Internal 2 and G1/G2. The internal primers were designed from the gene sequence of the outer membrane lipoprotein Lip32 from Leptospira kirschneri, strain RM52. The PCR products were amplified with these two pairs of primers, which had approximately 497 and 285bp, respectively, and were subsequently used as a template for LSSP-PCR analysis. The genetic signatures from the leptospires which were present in the urine samples allowed us to make a preliminary identification of the leptospires by comparing the LSSP-PCR profiles obtained directly from urine samples with those from reference leptospires. The LSSP-PCR profiles obtained with the Internal 1 primer or with the G1 primer allowed the grouping of the leptospires into serogroups. LSSP-PCR was found to be a useful and sensitive approach capable of identifying leptospires directly from biological samples without the need for prior bacterial isolation. In conclusion, the LSSP-PCR technique may still be helpful in discriminating serogroups of Leptospira from different animal reservoirs, since the early identification of carrier animals and information on the shedding state are crucial to prevent the spread of leptospiral infection to other animals and humans.

40 CFR 51.351 - Enhanced I/M performance standard.

Code of Federal Regulations, 2011 CFR

2011-07-01

... vehicles. (10) Stringency. A 20% emission test failure rate among pre-1981 model year vehicles. (11) Waiver... 2001 and newer vehicles. (10) Stringency. A 20% emission test failure rate among pre-1981 model year... which will be achieved by the I/M program design in the SIP to those of the model program described in...

40 CFR 51.351 - Enhanced I/M performance standard.

Code of Federal Regulations, 2012 CFR

2012-07-01

... vehicles. (10) Stringency. A 20% emission test failure rate among pre-1981 model year vehicles. (11) Waiver... 2001 and newer vehicles. (10) Stringency. A 20% emission test failure rate among pre-1981 model year... which will be achieved by the I/M program design in the SIP to those of the model program described in...

40 CFR 51.351 - Enhanced I/M performance standard.

Code of Federal Regulations, 2010 CFR

2010-07-01

... vehicles. (10) Stringency. A 20% emission test failure rate among pre-1981 model year vehicles. (11) Waiver... 2001 and newer vehicles. (10) Stringency. A 20% emission test failure rate among pre-1981 model year... which will be achieved by the I/M program design in the SIP to those of the model program described in...

40 CFR 51.351 - Enhanced I/M performance standard.

Code of Federal Regulations, 2014 CFR

2014-07-01

... vehicles. (10) Stringency. A 20% emission test failure rate among pre-1981 model year vehicles. (11) Waiver... 2001 and newer vehicles. (10) Stringency. A 20% emission test failure rate among pre-1981 model year... which will be achieved by the I/M program design in the SIP to those of the model program described in...

40 CFR 51.351 - Enhanced I/M performance standard.

Code of Federal Regulations, 2013 CFR

2013-07-01

... vehicles. (10) Stringency. A 20% emission test failure rate among pre-1981 model year vehicles. (11) Waiver... 2001 and newer vehicles. (10) Stringency. A 20% emission test failure rate among pre-1981 model year... which will be achieved by the I/M program design in the SIP to those of the model program described in...

Identification of Vibrio splendidus as a Member of the Planktonic Luminous Bacteria from the Persian Gulf and Kuwait Region with luxA Probes

PubMed Central

Nealson, K. H.; Wimpee, B.; Wimpee, C.

1993-01-01

Hybridization probes specific for the luxA genes of four groups of luminous bacteria were used to screen luminous isolates obtained from the Persian Gulf, near Al Khiran, Kuwait Nine of these isolates were identified as Vibrio harveyi, a commonly encountered planktonic isolate, while three others showed no hybridization to any of the four probes (V. harveyi, Vibrio fischeri, Photobacterium phosphoreum, or Photobacterium leiognathi) under high-stringency conditions. Polymerase chain reaction amplification was used to prepare a luxA probe against one of these isolates, K-1, and this probe was screened under high-stringency conditions against a collection of DNAs from luminous bacteria; it was found to hybridize specifically to the DNA of the species Vibrio splendidus. A probe prepared against the type strain of V. splendidus (ATCC 33369) was tested against the collection of luminous bacterial DNA preparations and against the Kuwait isolates and was found to hybridize only against the type strain and the three unidentified Kuwait isolates. Extensive taxonomic analysis by standard methods confirmed the identification of the 13 isolates. Images PMID:16349023

Comprehensive characterization of glutamine synthetase-mediated selection for the establishment of recombinant CHO cells producing monoclonal antibodies.

PubMed

Noh, Soo Min; Shin, Seunghyeon; Lee, Gyun Min

2018-03-29

To characterize a glutamine synthetase (GS)-based selection system, monoclonal antibody (mAb) producing recombinant CHO cell clones were generated by a single round of selection at various methionine sulfoximine (MSX) concentrations (0, 25, and 50 μM) using two different host cell lines (CHO-K1 and GS-knockout CHO). Regardless of the host cell lines used, the clones selected at 50 μM MSX had the lowest average specific growth rate and the highest average specific production rates of toxic metabolic wastes, lactate and ammonia. Unlike CHO-K1, high producing clones could be generated in the absence of MSX using GS-knockout CHO with an improved selection stringency. Regardless of the host cell lines used, the clones selected at various MSX concentrations showed no significant difference in the GS, heavy chain, and light chain gene copies (P > 0.05). Furthermore, there was no correlation between the specific mAb productivity and these three gene copies (R 2  ≤ 0.012). Taken together, GS-mediated gene amplification does not occur in a single round of selection at a MSX concentration up to 50 μM. The use of the GS-knockout CHO host cell line facilitates the rapid generation of high producing clones with reduced production of lactate and ammonia in the absence of MSX.

Use of Molecular Methods for the Rapid Mass Detection of Schistosoma mansoni (Platyhelminthes: Trematoda) in Biomphalaria spp. (Gastropoda: Planorbidae)

PubMed Central

Jannotti-Passos, Liana Konovaloffi; Dos Santos Carvalho, Omar

2017-01-01

The low stringency-polymerase chain reaction (LS-PCR) and loop-mediated isothermal amplification (LAMP) assays were used to detect the presence of S. mansoni DNA in (1) Brazilian intermediate hosts (Biomphalaria glabrata, B. straminea, and B. tenagophila) with patent S. mansoni infections, (2) B. glabrata snails with prepatent S. mansoni infections, (3) various mixtures of infected and noninfected snails; and (4) snails infected with other trematode species. The assays showed high sensitivity and specificity and could detect S. mansoni DNA when one positive snail was included in a pool of 1,000 negative specimens of Biomphalaria. These molecular approaches can provide a low-cost, effective, and rapid method for detecting the presence of S. mansoni in pooled samples of field-collected Biomphalaria. These assays should aid mapping of transmission sites in endemic areas, especially in low prevalence regions and improve schistosomiasis surveillance. It will be a useful tool to monitor low infection rates of snails in areas where control interventions are leading towards the elimination of schistosomiasis. PMID:28246533

A microscopy-based screen employing multiplex genome sequencing identifies cargo-specific requirements for dynein velocity

PubMed Central

Tan, Kaeling; Roberts, Anthony J.; Chonofsky, Mark; Egan, Martin J.; Reck-Peterson, Samara L.

2014-01-01

The timely delivery of membranous organelles and macromolecules to specific locations within the majority of eukaryotic cells depends on microtubule-based transport. Here we describe a screening method to identify mutations that have a critical effect on intracellular transport and its regulation using mutagenesis, multicolor-fluorescence microscopy, and multiplex genome sequencing. This screen exploits the filamentous fungus Aspergillus nidulans, which has many of the advantages of yeast molecular genetics but uses long-range microtubule-based transport in a manner more similar to metazoan cells. Using this method, we identified seven mutants that represent novel alleles of components of the intracellular transport machinery: specifically, kinesin-1, cytoplasmic dynein, and the dynein regulators Lis1 and dynactin. The two dynein mutations identified in our screen map to dynein's AAA+ catalytic core. Single-molecule studies reveal that both mutations reduce dynein's velocity in vitro. In vivo these mutants severely impair the distribution and velocity of endosomes, a known dynein cargo. In contrast, another dynein cargo, the nucleus, is positioned normally in these mutants. These results reveal that different dynein functions have distinct stringencies for motor performance. PMID:24403603

Primary structure and functional characterization of a Drosophila dopamine receptor with high homology to human D1/5 receptors.

PubMed

Gotzes, F; Balfanz, S; Baumann, A

1994-01-01

Members of the superfamily of G-protein coupled receptors share significant similarities in sequence and transmembrane architecture. We have isolated a Drosophila homologue of the mammalian dopamine receptor family using a low stringency hybridization approach. The deduced amino acid sequence is approximately 70% homologous to the human D1/D5 receptors. When expressed in HEK 293 cells, the Drosophila receptor stimulates cAMP production in response to dopamine application. This effect was mimicked by SKF 38393, a specific D1 receptor agonist, but inhibited by dopaminergic antagonists such as butaclamol and flupentixol. In situ hybridization revealed that the Drosophila dopamine receptor is highly expressed in the somata of the optic lobes. This suggests that the receptor might be involved in the processing of visual information and/or visual learning in invertebrates.

The Effect of State Regulatory Stringency on Nursing Home Quality

PubMed Central

Mukamel, Dana B; Weimer, David L; Harrington, Charlene; Spector, William D; Ladd, Heather; Li, Yue

2012-01-01

Objective To test the hypothesis that more stringent quality regulations contribute to better quality nursing home care and to assess their cost-effectiveness. Data Sources/Setting Primary and secondary data from all states and U.S. nursing homes between 2005 and 2006. Study Design We estimated seven models, regressing quality measures on the Harrington Regulation Stringency Index and control variables. To account for endogeneity between regulation and quality, we used instrumental variables techniques. Quality was measured by staffing hours by type per case-mix adjusted day, hotel expenditures, and risk-adjusted decline in activities of daily living, high-risk pressure sores, and urinary incontinence. Data Collection All states' licensing and certification offices were surveyed to obtain data about deficiencies. Secondary data included the Minimum Data Set, Medicare Cost Reports, and the Economic Freedom Index. Principal Findings Regulatory stringency was significantly associated with better quality for four of the seven measures studied. The cost-effectiveness for the activities-of-daily-living measure was estimated at about 72,000 in 2011/ Quality Adjusted Life Year. Conclusions Quality regulations lead to better quality in nursing homes along some dimensions, but not all. Our estimates of cost-effectiveness suggest that increased regulatory stringency is in the ballpark of other acceptable cost-effective practices. PMID:22946859

Specificity Re-evaluation of Oligonucleotide Probes for the Detection of Marine Picoplankton by Tyramide Signal Amplification-Fluorescent In Situ Hybridization.

PubMed

Riou, Virginie; Périot, Marine; Biegala, Isabelle C

2017-01-01

Oligonucleotide probes are increasingly being used to characterize natural microbial assemblages by Tyramide Signal Amplification-Fluorescent in situ Hybridization (TSA-FISH, or CAtalysed Reporter Deposition CARD-FISH). In view of the fast-growing rRNA databases, we re-evaluated the in silico specificity of eleven bacterial and eukaryotic probes and competitor frequently used for the quantification of marine picoplankton. We performed tests on cell cultures to decrease the risk for non-specific hybridization, before they are used on environmental samples. The probes were confronted to recent databases and hybridization conditions were tested against target strains matching perfectly with the probes, and against the closest non-target strains presenting one to four mismatches. We increased the hybridization stringency from 55 to 65% formamide for the Eub338+EubII+EubIII probe mix to be specific to the Eubacteria domain. In addition, we found that recent changes in the Gammaproteobacteria classification decreased the specificity of Gam42a probe, and that the Roseo536R and Ros537 probes were not specific to, and missed part of the Roseobacter clade. Changes in stringency conditions were important for bacterial probes; these induced, respectively, a significant increase, in Eubacteria and Roseobacter and no significant changes in Gammaproteobacteria concentrations from the investigated natural environment. We confirmed the eukaryotic probes original conditions, and propose the Euk1209+NChlo01+Chlo02 probe mix to target the largest picoeukaryotic diversity. Experiences acquired through these investigations leads us to propose the use of seven steps protocol for complete FISH probe specificity check-up to improve data quality in environmental studies.

The recA gene from the thermophile Thermus aquaticus YT-1: cloning, expression, and characterization.

PubMed Central

Angov, E; Camerini-Otero, R D

1994-01-01

We have cloned, expressed, and purified the RecA analog from the thermophilic eubacterium Thermus aquaticus YT-1. Analysis of the deduced amino acid sequence indicates that the T. aquaticus RecA is structurally similar to the Escherichia coli RecA and suggests that RecA-like function has been conserved in thermophilic organisms. Preliminary biochemical analysis indicates that the protein has an ATP-dependent single-stranded DNA binding activity and can pair and carry out strand exchange to form a heteroduplex DNA under reaction conditions previously described for E. coli RecA, but at 55 to 65 degrees C. Further characterization of a thermophilically derived RecA protein should yield important information concerning DNA-protein interactions at high temperatures. In addition, a thermostable RecA protein may have some general applicability in stabilizing DNA-protein interactions in reactions which occur at high temperatures by increasing the specificity (stringency) of annealing reactions. Images PMID:8113181

Does variation among provincial drug formulary antimicrobial listings in Canada influence prescribing rates?

PubMed

Glass-Kaastra, Shiona K; Finley, Rita; Hutchinson, Jim; Patrick, David M; Weiss, Karl; Conly, John

2014-01-01

The financial accessibility of antimicrobial drugs to the outpatient community in Canada is governed at the provincial level through formularies. Each province may choose to list particular drugs or impose restriction criteria on products in order to guide prescribing and/or curtail costs. Although changes to formularies have been shown to change patterns in the use of individual products and alter costs, no comparison has been made among the provincial antimicrobial formularies with regards to flexibility/stringency, or an assessment of how these formularies impact overall antimicrobial use in the provinces. To summarize provincial antimicrobial formularies and assess whether their relative flexibility/stringency had a statistical impact upon provincial prescription volume during a one year period. Provincial drug plan formularies were accessed and summarized for all prescribed antimicrobials in Canada during 2010. The number of general and restricted benefits for each plan was compiled by antimicrobial classification. Population-adjusted prescription rates for all individual antimicrobials and by antimicrobial class were obtained from the Canadian Integrated Program for Antimicrobial Resistance Surveillance. Correlations between the number of general benefits, restricted benefits, and total benefits with the prescription rate in the provinces were assessed by Spearman rank correlation coefficients. Formularies varied considerably among the Canadian provinces. Quebec had the most flexible formulary, offering the greatest number of general benefits and fewest restrictions. In contrast, Saskatchewan's formulary displayed the lowest number of general benefits and most restrictions. Correlation analyses detected a single significant result; macrolide prescription rates decreased as the number of general macrolide benefits increased. All other rates of provincial antimicrobial prescribing and measures of flexibility/stringency revealed no significant correlations. Although antimicrobial formulary listings are used to guide prescribing rates within a province, our analysis of one year's data of the impact of the antimicrobial formulary structure did not correlate with antimicrobial prescribing rates, and other factors are likely to be at play.

A process for the quantification of aircraft noise and emissions interdependencies

NASA Astrophysics Data System (ADS)

de Luis, Jorge

The main purpose of this dissertation is to develop a process to improve actual policy-making procedures in terms of aviation environmental effects. This research work expands current practices with physics based publicly available models. The current method uses solely information provided by industry members, and this information is usually proprietary, and not physically intuitive. The process herein proposed provides information regarding the interdependencies between the environmental effects of aircraft. These interdependencies are also tied to the actual physical parameters of the aircraft and the engine, making it more intuitive for decision-makers to understand the impacts to the vehicle due to different policy scenarios. These scenarios involve the use of fleet analysis tools in which the existing aircraft are used to predict the environmental effects of imposing new stringency levels. The aircraft used are reduced to a series of coefficients that represent their performance, in terms of flight characteristics, fuel burn, noise, and emissions. These coefficients are then utilized to model flight operations and calculate what the environmental impacts of those aircraft are. If a particular aircraft does not meet the stringency to be analyzed, a technology response is applied to it, in order to meet that stringency. Depending on the level of reduction needed, this technology response can have an effect on the fuel burn characteristic of the aircraft. Another important point of the current stringency analysis process is that it does not take into account both noise and emissions concurrently, but instead, it considers them separately, one at a time. This assumes that the interdependencies between the two do not exists, which is not realistic. The latest stringency process delineated in 2004 imposed a 2% fuel burn penalty for any required improvements on NOx, no matter the type of aircraft or engine, assuming that no company had the ability to produce a vehicle with similar characteristics. This left all the performance characteristics of the aircraft untouched, except for the fuel burn, including the noise performance. The proposed alternative is to create a fleet of replacement aircraft to the current fleet that does not meet stringency. These replacement aircraft represent the achievable physical limits for state of the art systems. In this research work, the interdependencies between NOx, noise, and fuel burn are not neglected, and it is in fact necessary to take all three into account, simultaneously, to capture the physical limits that can be attained during a stringency analysis. In addition, the replacement aircraft show the linkage between environmental effects and fundamental aircraft and engine characteristics, something that has been neglected in previous policy making procedures. Another aspect that has been ignored is the creation of the coefficients used for the fleet analyses. In current literature, a defined process for the creation of those coefficients does not exist, but this research work develops a process to do so and demonstrates that the characteristics of the aircraft can be propagated to the coefficients and to the fleet analysis tools. The implementation of the process proposed shows that, first, the environmental metrics can be linked to the physical attributes of the aircraft using non-proprietary, physics based tools, second, those interdependencies can be propagated to fleet level tools, and third, this propagation provides an improvement in the policy making process, by showing what needs to change in an aircraft to meet different stringency levels.

Bio-Inspired Engineering of Protein-Based Heat Sensors

DTIC Science & Technology

2004-01-01

of Thermosensitive Proteins. 23 3.1 Introduction 23 3.2 Low Stringency PCR Identification of TRPV1 Homologues from Pit Viper Trigeminal Ganglion...Methods and Results. 24 3.3 Directed Evolution of TRPV1 Protein. 25 3.4 Methods and Results 25 3.5 References 27 Pappas, TC F49620-01-1-0552 3 1. Unique...cation channel TRPV1 . Thermal nociceptive neurons are fairly plentiful, and thus benefited studies linking TRPVI to thermal responses. The snake pit

KDNA Genetic Signatures Obtained by LSSP-PCR Analysis of Leishmania (Leishmania) infantum Isolated from the New and the Old World

PubMed Central

Alvarenga, Janaína Sousa Campos; Ligeiro, Carla Maia; Gontijo, Célia Maria Ferreira; Cortes, Sofia; Campino, Lenea; Vago, Annamaria Ravara; Melo, Maria Norma

2012-01-01

Background Visceral Leishmaniasis (VL) caused by species from the Leishmania donovani complex is the most severe form of the disease, lethal if untreated. VL caused by Leishmania infantum is a zoonosis with an increasing number of human cases and millions of dogs infected in the Old and the New World. In this study, L. infantum (syn. L.chagasi) strains were isolated from human and canine VL cases. The strains were obtained from endemic areas from Brazil and Portugal and their genetic polymorphism was ascertained using the LSSP-PCR (Low-Stringency Single Specific Primer PCR) technique for analyzing the kinetoplastid DNA (kDNA) minicircles hypervariable region. Principal Findings KDNA genetic signatures obtained by minicircle LSSP-PCR analysis of forty L. infantum strains allowed the grouping of strains in several clades. Furthermore, LSSP-PCR profiles of L. infantum subpopulations were closely related to the host origin (human or canine). To our knowledge this is the first study which used this technique to compare genetic polymorphisms among strains of L. infantum originated from both the Old and the New World. Conclusions LSSP-PCR profiles obtained by analysis of L. infantum kDNA hypervariable region of parasites isolated from human cases and infected dogs from Brazil and Portugal exhibited a genetic correlation among isolates originated from the same reservoir, human or canine. However, no association has been detected among the kDNA signatures and the geographical origin of L. infantum strains. PMID:22912862

Isolation of genes negatively or positively co-expressed with human recombination activating gene 1 (RAG1) by differential display PCR (DD RT-PCR).

PubMed

Verkoczy, L K; Berinstein, N L

1998-10-01

Differential display PCR (DD RT-PCR) has been extensively used for analysis of differential gene expression, but continues to be hampered by technical limitations that impair its effectiveness. In order to isolate novel genes co-expressing with human RAG1, we have developed an effective, multi-tiered screening/purification approach which effectively complements the standard DD RT-PCR methodology. In 'primary' screens, standard DD RT-PCR was used, detecting 22 reproducible differentially expressed amplicons between clonally related cell variants with differential constitutive expression of RAG mRNAs. 'Secondary' screens used differential display (DD) amplicons as probes in low and high stringency northern blotting. Eight of 22 independent DD amplicons detected nine independent differentially expressed transcripts. 'Tertiary' screens used reconfirmed amplicons as probes in northern analysis of multiple RAG-and RAG+sources. Reconfirmed DD amplicons detected six independent RAG co-expressing transcripts. All DD amplicons reconfirmed by northern blot were a heterogeneous mixture of cDNAs, necessitating further purification to isolate single cDNAs prior to subcloning and sequencing. To effectively select the appropriate cDNAs from DD amplicons, we excised and eluted the cDNA(s) directly from regions of prior northern blots in which differentially expressed transcripts were detected. Sequences of six purified cDNA clones specifically detecting RAG co-expressing transcripts included matches to portions of the human RAG2 and BSAP regions and to four novel partial cDNAs (three with homologies to human ESTs). Overall, our results also suggest that even when using clonally related variants from the same cell line in addition to all appropriate internal controls previously reported, further screening and purification steps are still required in order to efficiently and specifically isolate differentially expressed genes by DD RT-PCR.

Underage alcohol policies across 50 California cities: an assessment of best practices

PubMed Central

2012-01-01

Background We pursue two primary goals in this article: (1) to test a methodology and develop a dataset on U.S. local-level alcohol policy ordinances, and (2) to evaluate the presence, comprehensiveness, and stringency of eight local alcohol policies in 50 diverse California cities in relationship to recommended best practices in both public health literature and governmental recommendations to reduce underage drinking. Methods Following best practice recommendations from a wide array of authoritative sources, we selected eight local alcohol policy topics (e.g., conditional use permits, responsible beverage service training, social host ordinances, window/billboard advertising ordinances), and determined the presence or absence as well as the stringency (restrictiveness) and comprehensiveness (number of provisions) of each ordinance in each of the 50 cities in 2009. Following the alcohol policy literature, we created scores for each city on each type of ordinance and its associated components. We used these data to evaluate the extent to which recommendations for best practices to reduce underage alcohol use are being followed. Results (1) Compiling datasets of local-level alcohol policy laws and their comprehensiveness and stringency is achievable, even absent comprehensive, on-line, or other legal research tools. (2) We find that, with some exceptions, most of the 50 cities do not have high scores for presence, comprehensiveness, or stringency across the eight key policies. Critical policies such as responsible beverage service and deemed approved ordinances are uncommon, and, when present, they are generally neither comprehensive nor stringent. Even within policies that have higher adoption rates, central elements are missing across many or most cities’ ordinances. Conclusion This study demonstrates the viability of original legal data collection in the U.S. pertaining to local ordinances and of creating quantitative scores for each policy type to reflect comprehensiveness and stringency. Analysis of the resulting dataset reveals that, although the 50 cities have taken important steps to improve public health with regard to underage alcohol use and abuse, there is a great deal more that needs to be done to bring these cities into compliance with best practice recommendations. PMID:22734468

Single genome retrieval of context-dependent variability in mutation rates for human germline.

PubMed

Sahakyan, Aleksandr B; Balasubramanian, Shankar

2017-01-13

Accurate knowledge of the core components of substitution rates is of vital importance to understand genome evolution and dynamics. By performing a single-genome and direct analysis of 39,894 retrotransposon remnants, we reveal sequence context-dependent germline nucleotide substitution rates for the human genome. The rates are characterised through rate constants in a time-domain, and are made available through a dedicated program (Trek) and a stand-alone database. Due to the nature of the method design and the imposed stringency criteria, we expect our rate constants to be good estimates for the rates of spontaneous mutations. Benefiting from such data, we study the short-range nucleotide (up to 7-mer) organisation and the germline basal substitution propensity (BSP) profile of the human genome; characterise novel, CpG-independent, substitution prone and resistant motifs; confirm a decreased tendency of moieties with low BSP to undergo somatic mutations in a number of cancer types; and, produce a Trek-based estimate of the overall mutation rate in human. The extended set of rate constants we report may enrich our resources and help advance our understanding of genome dynamics and evolution, with possible implications for the role of spontaneous mutations in the emergence of pathological genotypes and neutral evolution of proteomes.

Granulocyte-Macrophage Colony-Stimulating Factor Priming plus Papillomavirus E6 DNA Vaccination: Effects on Papilloma Formation and Regression in the Cottontail Rabbit Papillomavirus-Rabbit Model

PubMed Central

Leachman, Sancy A.; Tigelaar, Robert E.; Shlyankevich, Mark; Slade, Martin D.; Irwin, Michele; Chang, Ed; Wu, T. C.; Xiao, Wei; Pazhani, Sundaram; Zelterman, Daniel; Brandsma, Janet L.

2000-01-01

A cottontail rabbit papillomavirus (CRPV) E6 DNA vaccine that induces significant protection against CRPV challenge was used in a superior vaccination regimen in which the cutaneous sites of vaccination were primed with an expression vector encoding granulocyte-macrophage colony-stimulating factor (GM-CSF), a cytokine that induces differentiation and local recruitment of professional antigen-presenting cells. This treatment induced a massive influx of major histocompatibility complex class II-positive cells. In a vaccination-challenge experiment, rabbit groups were treated by E6 DNA vaccination, GM-CSF DNA inoculation, or a combination of both treatments. After two immunizations, rabbits were challenged with CRPV at low, moderate, and high stringencies and monitored for papilloma formation. As expected, all clinical outcomes were monotonically related to the stringency of the viral challenge. The results demonstrate that GM-CSF priming greatly augmented the effects of CRPV E6 vaccination. First, challenge sites in control rabbits (at the moderate challenge stringency) had a 0% probability of remaining disease free, versus a 50% probability in E6-vaccinated rabbits, and whereas GM-CSF alone had no effect, the interaction between GM-CSF priming and E6 vaccination increased disease-free survival to 67%. Second, the incubation period before papilloma onset was lengthened by E6 DNA vaccination alone or to some extent by GM-CSF DNA inoculation alone, and the combination of treatments induced additive effects. Third, the rate of papilloma growth was reduced by E6 vaccination and, to a lesser extent, by GM-CSF treatment. In addition, the interaction between the E6 and GM-CSF treatments was synergistic and yielded more than a 99% reduction in papilloma volume. Finally, regression occurred among the papillomas that formed in rabbits treated with the E6 vaccine and/or with GM-CSF, with the highest regression frequency occurring in rabbits that received the combination treatment. PMID:10954571

High-stringency screening of target-binding partners using a microfluidic device

DOEpatents

Soh, Hyongsok; Lou, Xinhui; Lagally, Eric

2015-12-01

The invention provides a method of screening a library of candidate agents by contacting the library with a target in a reaction mixture under a condition of high stringency, wherein the target includes a tag that responds to a controllable force applied to the tag, and passing the members of the library through a microfluidic device in a manner that exposes the library members to the controllable force, thereby displacing members of the library that are bound to the target relative to their unbound counterparts. Kits and systems for use with the methods of the invention are also provided.

The origin and evolution of vertebrate sex chromosomes and dosage compensation

PubMed Central

Livernois, A M; Graves, J A M; Waters, P D

2012-01-01

In mammals, birds, snakes and many lizards and fish, sex is determined genetically (either male XY heterogamy or female ZW heterogamy), whereas in alligators, and in many reptiles and turtles, the temperature at which eggs are incubated determines sex. Evidently, different sex-determining systems (and sex chromosome pairs) have evolved independently in different vertebrate lineages. Homology shared by Xs and Ys (and Zs and Ws) within species demonstrates that differentiated sex chromosomes were once homologous, and that the sex-specific non-recombining Y (or W) was progressively degraded. Consequently, genes are left in single copy in the heterogametic sex, which results in an imbalance of the dosage of genes on the sex chromosomes between the sexes, and also relative to the autosomes. Dosage compensation has evolved in diverse species to compensate for these dose differences, with the stringency of compensation apparently differing greatly between lineages, perhaps reflecting the concentration of genes on the original autosome pair that required dosage compensation. We discuss the organization and evolution of amniote sex chromosomes, and hypothesize that dosage insensitivity might predispose an autosome to evolving function as a sex chromosome. PMID:22086077

Materials Selection Criteria for Nuclear Power Applications: A Decision Algorithm

NASA Astrophysics Data System (ADS)

Rodríguez-Prieto, Álvaro; Camacho, Ana María; Sebastián, Miguel Ángel

2016-02-01

An innovative methodology based on stringency levels is proposed in this paper and improves the current selection method for structural materials used in demanding industrial applications. This paper describes a new approach for quantifying the stringency of materials requirements based on a novel deterministic algorithm to prevent potential failures. We have applied the new methodology to different standardized specifications used in pressure vessels design, such as SA-533 Grade B Cl.1, SA-508 Cl.3 (issued by the American Society of Mechanical Engineers), DIN 20MnMoNi55 (issued by the German Institute of Standardization) and 16MND5 (issued by the French Nuclear Commission) specifications and determine the influence of design code selection. This study is based on key scientific publications on the influence of chemical composition on the mechanical behavior of materials, which were not considered when the technological requirements were established in the aforementioned specifications. For this purpose, a new method to quantify the efficacy of each standard has been developed using a deterministic algorithm. The process of assigning relative weights was performed by consulting a panel of experts in materials selection for reactor pressure vessels to provide a more objective methodology; thus, the resulting mathematical calculations for quantitative analysis are greatly simplified. The final results show that steel DIN 20MnMoNi55 is the best material option. Additionally, more recently developed materials such as DIN 20MnMoNi55, 16MND5 and SA-508 Cl.3 exhibit mechanical requirements more stringent than SA-533 Grade B Cl.1. The methodology presented in this paper can be used as a decision tool in selection of materials for a wide range of applications.

[Optimization and assessment of a reverse hybridization system for the detection of HBV drug-resistant mutations].

PubMed

Liu, Yan-chen; Huang, Ai-long; Hu, Yuan; Hu, Jie-li; Lai, Guo-qi; Zhang, Wen-lu

2011-12-01

To establish a detection method for HBV drug-resistant mutations related to lamivudine, adefovir and entecavir by optimization and assessment of reverse hybridization system. 26 degenerated probes covering 10 drug-resistant hotspots of 3 drugs were synthesized and immobilized on the same positively charged nylon membrane. PCR products labeled with digoxigenin were hybridized with corresponding probes. To improve the sensitivity and specificity, 4 reaction steps of reverse hybridization were optimized including the number of labeled digoxigenin, the energy intensity of UV cross-linking, hybridization and stringency wash conditions. To prove the feasibility, the specificity, sensitivity and accuracy of this system were assessed respectively. Sensitive and specific results are obtained by the optimization of the following 4 reaction steps: the primers labeled with 3 digoxigenin, energy intensity of UV cross-linking for 1500 x 0.1 mJ/cm², hybridization at 42 degrees C and stringency wash with 0.5 x SSC and 0.1% SDS solution at 44 degrees C for 30 min. In the assessment of system, the majority of probes have high specificity. The quantity of PCR product with a concentration of 10 ng/μl or above can be detected by this method. The concordant rate between reverse hybridization and direct sequencing is 93.9% in the clinical sample test. Though the specificity of several probes needs to be improved further, it is a simple, rapid and sensitive method which can detect HBV resistant mutations related to lamivudine, adefovir and entecavir simultaneously. Due to the short distance between 180 and 181, likewise 202 and 204, the sequence of the same probe covers two codon positions, and hybridization will be interfered by each other. To avoid such interference, the possible solution is that probes are designed by arranging and combining various forms of two near codons.

Chagas disease reactivation in a heart transplant patient infected by domestic Trypanosoma cruzi discrete typing unit I (TcIDOM).

PubMed

Costales, Jaime A; Kotton, Camille N; Zurita-Leal, Andrea C; Garcia-Perez, Josselyn; Llewellyn, Martin S; Messenger, Louisa A; Bhattacharyya, Tapan; Burleigh, Barbara A

2015-08-25

Trypanosoma cruzi, causative agent of Chagas disease, displays high intraspecific genetic diversity: six genetic lineages or discrete typing units (DTUs) are currently recognized, termed TcI through TcVI. Each DTU presents a particular distribution pattern across the Americas, and is loosely associated with different transmission cycles and hosts. Several DTUs are known to circulate in Central America. It has been previously suggested that TcI infection is benign and does not lead to chronic chagasic cardiomyopathy (CCC). In this study, we genotyped T. cruzi parasites circulating in the blood and from explanted cardiac tissue of an El Salvadorian patient who developed reactivation Chagas disease while on immunosuppressive medications after undergoing heart transplant in the U.S. as treatment for end-stage CCC. Parasite typing was performed through molecular methods (restriction fragment length polymorphism of polymerase reaction chain amplified products, microsatellite typing, maxicircle sequence typing and low-stringency single primer PCR, [LSSP-PCR]) as well as lineage-specific serology. We show that the parasites infecting the patient belong to the TcI DTU exclusively. Our data indicate that the parasites isolated from the patient belong to a genotype frequently associated with human infection throughout the Americas (TcIDOM). Our results constitute compelling evidence in support of TcI DTU's ability to cause end-stage CCC and help dispel any residual bias that infection with this lineage is benign, pointing to the need for increased surveillance for dissemination of this genotype in endemic regions, the USA and globally.

DR-78, a novel Drosophila melanogaster genomic DNA fragment highly homologous to the DNA-binding domain of thyroid hormone-retinoic acid-vitamin D receptor subfamily.

PubMed

Martín-Blanco, E; Kornberg, T B

1993-11-16

Degenerate oligodeoxyribonucleotides were designed for both ends of the DNA-binding domain of members of the nuclear receptor superfamily. PCR amplified Drosophila melanogaster DNA was purified and cloned (DR plasmids). Genomic lambda DASH clones were identified at high stringency with an amplified DR-78 plasmid DNA and isolated. The partial sequence shows a very probable open reading frame which would encode a peptide highly homologous to members of the thyroid hormone-retinoic acid-vitamin D receptor subfamily. The fragment corresponds to a single copy gene and was mapped at position 78D of chromosome three by in situ hybridization.

Roles of the amino group of purine bases in the thermodynamic stability of DNA base pairing.

PubMed

Nakano, Shu-ichi; Sugimoto, Naoki

2014-08-05

The energetic aspects of hydrogen-bonded base-pair interactions are important for the design of functional nucleotide analogs and for practical applications of oligonucleotides. The present study investigated the contribution of the 2-amino group of DNA purine bases to the thermodynamic stability of oligonucleotide duplexes under different salt and solvent conditions, using 2'-deoxyriboinosine (I) and 2'-deoxyribo-2,6-diaminopurine (D) as non-canonical nucleotides. The stability of DNA duplexes was changed by substitution of a single base pair in the following order: G • C > D • T ≈ I • C > A • T > G • T > I • T. The apparent stabilization energy due to the presence of the 2-amino group of G and D varied depending on the salt concentration, and decreased in the water-ethanol mixed solvent. The effects of salt concentration on the thermodynamics of DNA duplexes were found to be partially sequence-dependent, and the 2-amino group of the purine bases might have an influence on the binding of ions to DNA through the formation of a stable base-paired structure. Our results also showed that physiological salt conditions were energetically favorable for complementary base recognition, and conversely, low salt concentration media and ethanol-containing solvents were effective for low stringency oligonucleotide hybridization, in the context of conditions employed in this study.

Ribosomal DNA, tri- and bi-partite pericentromeres in the permanent translocation heterozygote Rhoeo spathacea.

PubMed

Golczyk, Hieronim; Hasterok, Robert; Szklarczyk, Marek

2010-12-01

High- and low-stringency FISH and base-specific fluorescence were performed on the permanent translocation heterozygote Rhoeo spathacea (2n = 12). Our results indicate that 45S rDNA arrays, rDNA-related sequences and other GC-rich DNA fraction(s) are located within the pericentromeric regions of all twelve chromosomes, usually colocalizing with the chromomycin A(3)-positive bands. Homogenization of the pericentromeric regions appears to result from the concerted spread of GC-rich sequences, with differential amplification likely. We found new 5S rDNA patterns, which suggest a variability in the breakpoints and in the consequent chromosome reorganizations. It was found that the large 5S rDNA locus residing on each of the 8E and 9E arms consisted of two smaller loci. On each of the two chromosome arms 3b and 4b, in addition to the major subtelomeric 5S rDNA locus, a new minor locus was found interstitially about 40% along the arm length. The arrangement of cytotogenetic landmarks and chromosome arm measurements are discussed with regard to genome repatterning in Rhoeo.

A randomized and blinded comparison of qPCR and NGS-based detection of aneuploidy in a cell line mixture model of blastocyst biopsy mosaicism.

PubMed

Goodrich, David; Tao, Xin; Bohrer, Chelsea; Lonczak, Agnieszka; Xing, Tongji; Zimmerman, Rebekah; Zhan, Yiping; Scott, Richard T; Treff, Nathan R

2016-11-01

A subset of preimplantation stage embryos may possess mosaicism of chromosomal constitution, representing a possible limitation to the clinical predictive value of comprehensive chromosome screening (CCS) from a single biopsy. However, contemporary methods of CCS may be capable of predicting mosaicism in the blastocyst by detecting intermediate levels of aneuploidy within a trophectoderm biopsy. This study evaluates the sensitivity and specificity of aneuploidy detection by two CCS platforms using a cell line mixture model of a mosaic trophectoderm biopsy. Four cell lines with known karyotypes were obtained and mixed together at specific ratios of six total cells (0:6, 1:5, 2:4, 3:3, 4:2, 5:1, and 6:0). A female euploid and a male trisomy 18 cell line were used for one set, and a male trisomy 13 and a male trisomy 15 cell line were used for another. Replicates of each mixture were prepared, randomized, and blinded for analysis by one of two CCS platforms (quantitative polymerase chain reaction (qPCR) or VeriSeq next-generation sequencing (NGS)). Sensitivity and specificity of aneuploidy detection at each level of mosaicism was determined and compared between platforms. With the default settings for each platform, the sensitivity of qPCR and NGS were not statistically different, and 100 % specificity was observed (no false positives) at all levels of mosaicism. However, the use of previously published custom criteria for NGS increased sensitivity but also significantly decreased specificity (33 % false-positive prediction of aneuploidy). By demonstrating increased false-positive diagnoses when reducing the stringency of predicting an abnormality, these data illustrate the importance of preclinical evaluation of new testing paradigms before clinical implementation.

SNP discovery by high-throughput sequencing in soybean

PubMed Central

2010-01-01

Background With the advance of new massively parallel genotyping technologies, quantitative trait loci (QTL) fine mapping and map-based cloning become more achievable in identifying genes for important and complex traits. Development of high-density genetic markers in the QTL regions of specific mapping populations is essential for fine-mapping and map-based cloning of economically important genes. Single nucleotide polymorphisms (SNPs) are the most abundant form of genetic variation existing between any diverse genotypes that are usually used for QTL mapping studies. The massively parallel sequencing technologies (Roche GS/454, Illumina GA/Solexa, and ABI/SOLiD), have been widely applied to identify genome-wide sequence variations. However, it is still remains unclear whether sequence data at a low sequencing depth are enough to detect the variations existing in any QTL regions of interest in a crop genome, and how to prepare sequencing samples for a complex genome such as soybean. Therefore, with the aims of identifying SNP markers in a cost effective way for fine-mapping several QTL regions, and testing the validation rate of the putative SNPs predicted with Solexa short sequence reads at a low sequencing depth, we evaluated a pooled DNA fragment reduced representation library and SNP detection methods applied to short read sequences generated by Solexa high-throughput sequencing technology. Results A total of 39,022 putative SNPs were identified by the Illumina/Solexa sequencing system using a reduced representation DNA library of two parental lines of a mapping population. The validation rates of these putative SNPs predicted with low and high stringency were 72% and 85%, respectively. One hundred sixty four SNP markers resulted from the validation of putative SNPs and have been selectively chosen to target a known QTL, thereby increasing the marker density of the targeted region to one marker per 42 K bp. Conclusions We have demonstrated how to quickly identify large numbers of SNPs for fine mapping of QTL regions by applying massively parallel sequencing combined with genome complexity reduction techniques. This SNP discovery approach is more efficient for targeting multiple QTL regions in a same genetic population, which can be applied to other crops. PMID:20701770

Comparing climate policy co-benefits in the United States and China

NASA Astrophysics Data System (ADS)

Selin, N. E.; Li, M.; Saari, R.; Zhang, D.; Karplus, V. J.; Li, C. T.; Thompson, T. M.; Mulvaney, K. M.; Rausch, S.

2016-12-01

We use modeling approaches that integrate atmospheric chemistry, economic analysis, and health impacts calculations to evaluate and compare the co-benefits of greenhouse gas reduction policies for the U.S. and China. Climate policies can have a variety of co-benefits for air quality, in particular on the concentrations of health-damaging pollutants O3 and PM2.5 as well as toxic pollutants such as mercury. Co-benefits. Controlling CO2 sources such as power plants and vehicles can lead to concomitant reductions in other pollutants such as SO2, NOx, and Hg. Here, we present and discuss our evaluations of co-benefits in the U.S. and China, at both national and regional (state/provincial) scales. In particular, we assess how policy design, stringency, and energy system characteristics affect projected co-benefits and their valuation for human health. We find that at the national scale in both the U.S. and China, monetized co-benefits can offset the costs of carbon policies. U.S. co-benefits exhibit diminishing returns to projected increases in policy stringency, while Chinese co-benefits show different behavior. The magnitude of health-related co-benefits is sensitive to the economic valuation methodology, and to the choice of health impact function, with China-specific functions yielding substantially less co-benefit than those typically used in the U.S. In both cases, we see overall national-scale co-benefits but substantial regional variation at sub-national scales, illustrating the benefits of coupled atmospheric-economic analysis.

Stringency of workplace air contaminant exposure limits: a case study of OSHA risk management.

PubMed

Hakes, J K

1999-12-01

Political context may play a large role in influencing the efficiency of environmental and health regulations. This case study uses data from a 1989 update of the Occupational Safety and Health Administration (OSHA) Permissible Exposure Limits (PELs) program to determine the relative effects of legislative mandates, costly acquisition of information by the agency, and pressure applied by special interest groups upon exposure standards. The empirical analysis suggests that federal agencies successfully thwart legislative attempts to limit agency discretion, and that agencies exercise bounded rationality by placing greater emphasis on more easily obtained information. The 1989 PELs were less significantly related to more costly information, contained "safety factors" for chemicals presenting relatively more ambiguous risks, and the proposed standard stringencies showed evidence of being influenced by vying industry and labor interests.

[THE FEATURES OF PREVALENCE OF SKIN DISEASE AS AN INDEX OF ECOLOGICALLY RELATED MORBIDITY OF POPULATION IN BIOCLIMATIC ZONES OF PRIMORYE KRAI].

PubMed

Yarygina, M V; Kiku, P F; Gorborukova, T V

2015-01-01

There are presented results of the socio-hygienic analysis of ecologically related skin pathology ofthe population of Primorsky Krai. The aim of the work is to establish the patterns of distribution of ecologically related skin diseases in various ecological bioclimatic zones of Primorsky Krai. There was performed an analysis of skin diseases ofform 12 according to ICD-10 main demographic groups (children, adolescents and adults) of the population of Primorsky Krai, residing in various bioclimatic zones of Krai with different levels of environmental stringency in rural and urban areas for the period of 2000-2013. There were established causal-effect relationships of the prevalence of skin diseases, as ecologically related pathology. The level of the prevalence of skin diseases among the population in the Primorye region depends on bioclimatic zones, the degree of the stringency of the environmental situation and combinations of environmental factors. The prevalence of skin diseases in adults, adolescents and children, as the organism's response to the impact ofthe parameters ofthe environment is affected by the complex offactors, the main of them are hygienic: the sanitary--hygienic level of ambient air pollution, the specification of chemical pollution and adverse physical factors in urban and rural settlements, the characteristics of the state of the soil. The medical-sociological research of the lifestyle of the population was performed on the basis of a specially designed questionnaire. The questionnaire included three arrays of issues: environmental, hygienic and social. On the basis of medical and sociological research with the use of multivariate analysis, method of correlation pleiades advanced by P. V. Terentiev, lifestyle and psycho-emotional factors, socio-hygienic, bioclimatic factors were found to play an important role in the prevalence of ecologically related pathology of skin in residents of Primorsky Krai. Differences in responses between urban and rural residents living in areas with various environmental stringency, confirm the preposition about the ambiguity of the approach to the solution of social, hygienic and environmental problems in areas with different socio-economic situation. The obtained results of the study allow us to determine the main directions of treatment and prevention and to develop targeted prevention programs.

Environmental Regulation, Foreign Direct Investment and Green Technological Progress-Evidence from Chinese Manufacturing Industries.

PubMed

Hu, Jiangfeng; Wang, Zhao; Lian, Yuehan; Huang, Qinghua

2018-01-29

This study examines the spillover effects of foreign direct investment (FDI) on green technology progress rate (as measured by the green total factor productivity). The analysis utilizes two measures of FDI, labor-based FDI and capital-based FDI, and separately investigates four sets of industry classifications-high/low discharge regulation and high/low emission standard regulation. The results indicate that in the low discharge regulation and low emission standard regulation industry, labor-based FDI has a significant negative spillover effect, and capital-based FDI has a significant positive spillover effect. However, in the high-intensity environmental regulation industry, the negative influence of labor-based FDI is completely restrained, and capital-based FDI continues to play a significant positive green technological spillover effects. These findings have clear policy implications: the government should be gradually reducing the labor-based FDI inflow or increasing stringency of environmental regulation in order to reduce or eliminate the negative spillover effect of the labor-based FDI.

Environmental Regulation, Foreign Direct Investment and Green Technological Progress—Evidence from Chinese Manufacturing Industries

PubMed Central

Hu, Jiangfeng; Wang, Zhao; Lian, Yuehan; Huang, Qinghua

2018-01-01

This study examines the spillover effects of foreign direct investment (FDI) on green technology progress rate (as measured by the green total factor productivity). The analysis utilizes two measures of FDI, labor-based FDI and capital-based FDI, and separately investigates four sets of industry classifications—high/low discharge regulation and high/low emission standard regulation. The results indicate that in the low discharge regulation and low emission standard regulation industry, labor-based FDI has a significant negative spillover effect, and capital-based FDI has a significant positive spillover effect. However, in the high-intensity environmental regulation industry, the negative influence of labor-based FDI is completely restrained, and capital-based FDI continues to play a significant positive green technological spillover effects. These findings have clear policy implications: the government should be gradually reducing the labor-based FDI inflow or increasing stringency of environmental regulation in order to reduce or eliminate the negative spillover effect of the labor-based FDI. PMID:29382112

Implementing the undergraduate mini-CEX: a tailored approach at Southampton University.

PubMed

Hill, Faith; Kendall, Kathleen; Galbraith, Kevin; Crossley, Jim

2009-04-01

The mini-clinical evaluation exercise (mini-CEX) is widely used in the UK to assess clinical competence, but there is little evidence regarding its implementation in the undergraduate setting. This study aimed to estimate the validity and reliability of the undergraduate mini-CEX and discuss the challenges involved in its implementation. A total of 3499 mini-CEX forms were completed. Validity was assessed by estimating associations between mini-CEX score and a number of external variables, examining the internal structure of the instrument, checking competency domain response rates and profiles against expectations, and by qualitative evaluation of stakeholder interviews. Reliability was evaluated by overall reliability coefficient (R), estimation of the standard error of measurement (SEM), and from stakeholders' perceptions. Variance component analysis examined the contribution of relevant factors to students' scores. Validity was threatened by various confounding variables, including: examiner status; case complexity; attachment specialty; patient gender, and case focus. Factor analysis suggested that competency domains reflect a single latent variable. Maximum reliability can be achieved by aggregating scores over 15 encounters (R = 0.73; 95% confidence interval [CI] +/- 0.28 based on a 6-point assessment scale). Examiner stringency contributed 29% of score variation and student attachment aptitude 13%. Stakeholder interviews revealed staff development needs but the majority perceived the mini-CEX as more reliable and valid than the previous long case. The mini-CEX has good overall utility for assessing aspects of the clinical encounter in an undergraduate setting. Strengths include fidelity, wide sampling, perceived validity, and formative observation and feedback. Reliability is limited by variable examiner stringency, and validity by confounding variables, but these should be viewed within the context of overall assessment strategies.

Isolation of a species-specific mitochondrial DNA sequence for identification of Tilletia indica, the Karnal bunt of wheat fungus.

PubMed Central

Ferreira, M A; Tooley, P W; Hatziloukas, E; Castro, C; Schaad, N W

1996-01-01

Mitochondrial DNA (mtDNA) from five isolates of Tilletia indica was isolated and digested with several restriction enzymes. A 2.3-kb EcoRI fragment was chosen, cloned, and shown to hybridize with total DNA restricted with EcoRI from T. indica and not from a morphologically similar smut fungus, Tilletia barclayana. The clone was partially sequenced, and primers were designed and tested under high-stringency conditions in PCR assays. The primer pair Ti1/Ti4 amplified a 2.3-kb fragment from total DNA of 17 T. indica isolates from India, Pakistan, and Mexico. DNA from 25 isolates of other smut fungi (T. barclayana, Tilletia foetida, Tilletia caries, Tilletia fusca, and Tilletia controversa) did not produce any bands, as detected by ethidium bromide-stained agarose gels and Southern hybridizations. The sensitivity of the assay was determined and increased by using a single nested primer in a second round of amplification, so that 1 pg of total mycelial DNA could be detected. The results indicated that the primers which originated from a cloned mtDNA sequence can be used to differentiate T. indica from other Tilletia species and have the potential to identify teliospores contaminating wheat seeds. PMID:8572716

Expanding probe repertoire and improving reproducibility in human genomic hybridization

PubMed Central

Dorman, Stephanie N.; Shirley, Ben C.; Knoll, Joan H. M.; Rogan, Peter K.

2013-01-01

Diagnostic DNA hybridization relies on probes composed of single copy (sc) genomic sequences. Sc sequences in probe design ensure high specificity and avoid cross-hybridization to other regions of the genome, which could lead to ambiguous results that are difficult to interpret. We examine how the distribution and composition of repetitive sequences in the genome affects sc probe performance. A divide and conquer algorithm was implemented to design sc probes. With this approach, sc probes can include divergent repetitive elements, which hybridize to unique genomic targets under higher stringency experimental conditions. Genome-wide custom probe sets were created for fluorescent in situ hybridization (FISH) and microarray genomic hybridization. The scFISH probes were developed for detection of copy number changes within small tumour suppressor genes and oncogenes. The microarrays demonstrated increased reproducibility by eliminating cross-hybridization to repetitive sequences adjacent to probe targets. The genome-wide microarrays exhibited lower median coefficients of variation (17.8%) for two HapMap family trios. The coefficients of variations of commercial probes within 300 nt of a repetitive element were 48.3% higher than the nearest custom probe. Furthermore, the custom microarray called a chromosome 15q11.2q13 deletion more consistently. This method for sc probe design increases probe coverage for FISH and lowers variability in genomic microarrays. PMID:23376933

Acoustic flight test of the Piper Lance

DOT National Transportation Integrated Search

1986-12-01

Research is being conducted to refine current noise regulation of propeller-driven small airplanes. Studies are examining the prospect of a substituting a takeoff procedure of equal stringency for the level flyover certification test presently requir...

Towards Fluorescence In Vivo Hybridization (FIVH) Detection of H. pylori in Gastric Mucosa Using Advanced LNA Probes

PubMed Central

Fontenete, Sílvia; Leite, Marina; Guimarães, Nuno; Madureira, Pedro; Ferreira, Rui Manuel; Figueiredo, Céu; Wengel, Jesper; Azevedo, Nuno Filipe

2015-01-01

In recent years, there have been several attempts to improve the diagnosis of infection caused by Helicobacter pylori. Fluorescence in situ hybridization (FISH) is a commonly used technique to detect H. pylori infection but it requires biopsies from the stomach. Thus, the development of an in vivo FISH-based method (FIVH) that directly detects and allows the visualization of the bacterium within the human body would significantly reduce the time of analysis, allowing the diagnosis to be performed during endoscopy. In a previous study we designed and synthesized a phosphorothioate locked nucleic acid (LNA)/ 2’ O-methyl RNA (2’OMe) probe using standard phosphoramidite chemistry and FISH hybridization was then successfully performed both on adhered and suspended bacteria at 37°C. In this work we simplified, shortened and adapted FISH to work at gastric pH values, meaning that the hybridization step now takes only 30 minutes and, in addition to the buffer, uses only urea and probe at non-toxic concentrations. Importantly, the sensitivity and specificity of the FISH method was maintained in the range of conditions tested, even at low stringency conditions (e.g., low pH). In conclusion, this methodology is a promising approach that might be used in vivo in the future in combination with a confocal laser endomicroscope for H. pylori visualization. PMID:25915865

Expression of small cytoplasmic transcripts of the rat identifier element in vivo and in cultured cells.

PubMed Central

McKinnon, R D; Danielson, P; Brow, M A; Bloom, F E; Sutcliffe, J G

1987-01-01

We examined the level of expression of small RNA transcripts hybridizing to a rodent repetitive DNA element, the identifier (ID) sequence, in a variety of cell types in vivo and in cultured mammalian cells. A 160-nucleotide (160n) cytoplasmic poly(A)+ RNA (BC1) appeared in late embryonic and early postnatal rat brain development, was enriched in the cerebral cortex, and appeared to be restricted to neural tissue and the anterior pituitary gland. A 110n RNA (BC2) was specifically enriched in brain, especially the postnatal cortex, but was detectable at low levels in peripheral tissues. A third, related 75n poly(A)- RNA (T3) was found in rat brain and at lower levels in peripheral tissues but was very abundant in the testes. The BC RNAs were found in a variety of rat cell lines, and their level of expression was dependent upon cell culture conditions. A rat ID probe detected BC-like RNAs in mouse brain but not liver and detected a 200n RNA in monkey brain but not liver at lower hybridization stringencies. These RNAs were expressed by mouse and primate cell lines. Thus, tissue-specific expression of small ID-sequence-related transcripts is conserved among mammals, but the tight regulation found in vivo is lost by cells in culture. Images PMID:2439903

A predictive analysis of CO2 emissions, environmental policy stringency, and economic growth in China.

PubMed

Ahmed, Khalid; Ahmed, Sidrah

2018-03-28

This study takes environmental policy stringency and economic activity as the controlling variables and forecasts the CO 2 emissions in China up to 2022. In doing so, an application of corrected grey model with convolution is used over the annual time series data between 1990 and 2012. The simulation results show that (1) between 2012 and 2022, CO 2 emissions in China is expected to increase at an average rate of 17.46% annually, raising the emissions intensity from 7.04 in 2012 to 25.461 metric tons per capita by 2022; (2) stringent environmental policies reduce CO 2 emissions-whereas, GDP tends to increase the emissions intensity in China; (3) stringent environmental policies are found to have a negative impact on GDP in China. Based on the empirical findings, the study also provides some policy suggestions to reduce emissions intensity in China.

Accurate RNA consensus sequencing for high-fidelity detection of transcriptional mutagenesis-induced epimutations.

PubMed

Reid-Bayliss, Kate S; Loeb, Lawrence A

2017-08-29

Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing. The stringency of ARC-seq can be scaled to accommodate the quality of input RNAs. We apply ARC-seq to directly assess transcriptome-wide epimutations resulting from RNA polymerase mutants and oxidative stress.

Mapping neurofibromatosis 1 homologous loci by fluorescence in situ hybridization

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

Viskochil, D.; Breidenbach, H.H.; Cawthon, R.

Neurofibromatosis 1 maps to chromosome band 17q11.2 and the NF1 gene is comprised of 59 exons that span approximately 335 kb of genomic DNA. In order to further analyze the structure of NF1 from exons 2 through 27b, we isolated a number of cosmid and bacteriophage P-1 genomic clones using NF1-exon probes under high-stringency hybridization conditions. Using tagged, intron-based primers and DNA from various clones as a template, we PCR-amplified and sequenced individual NF1 exons. The exon sequences in PCR products from several genomic clones differed from the exon sequence derived from cloned NF1 cDNAs. Clones with variant sequences weremore » mapped by fluorescence in situ hybridization under high-stringency conditions. Three clones mapped to chromosome band 15q11.2, one mapped to 14q11.2, one mapped to both 2q14.1-14.3 and 14q11.2, one mapped to 2q33-34, and one mapped to both 18q11.2 and 21q21. Even though some PCR-product sequences retained proper splice junctions and open reading frames, we have yet to identify cDNAs that correspond to the variant exon sequences. We are now sequencing clones that map to NF1-homologous loci in order to develop discriminating primer pairs for the exclusive amplification of NF1-specific sequences in our efforts to develop a comprehensive NF1 mutation screen using genomic DNA as template. The role of NF1-homologous sequences may play in neurofibromatosis 1 is not clear.« less

Comparison of CpG island methylator phenotype (CIMP) frequency in colon cancer using different probe- and gene-specific scoring alternatives on recommended multi-gene panels.

PubMed

Berg, Marianne; Hagland, Hanne R; Søreide, Kjetil

2014-01-01

In colorectal cancer a distinct subgroup of tumours demonstrate the CpG island methylator phenotype (CIMP). However, a consensus of how to score CIMP is not reached, and variation in definition may influence the reported CIMP prevalence in tumours. Thus, we sought to compare currently suggested definitions and cut-offs for methylation markers and how they influence CIMP classification in colon cancer. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), with subsequent fragment analysis, was used to investigate methylation of tumour samples. In total, 31 CpG sites, located in 8 different genes (RUNX3, MLH1, NEUROG1, CDKN2A, IGF2, CRABP1, SOCS1 and CACNA1G) were investigated in 64 distinct colon cancers and 2 colon cancer cell lines. The Ogino gene panel includes all 8 genes, in addition to the Weisenberger panel of which only 5 of the 8 genes included were investigated. In total, 18 alternative combinations of scoring of CIMP positivity on probe-, gene-, and panel-level were analysed and compared. For 47 samples (71%), the CIMP status was constant and independent of criteria used for scoring; 34 samples were constantly scored as CIMP negative, and 13 (20%) consistently scored as CIMP positive. Only four of 31 probes (13%) investigated showed no difference in the numbers of positive samples using the different cut-offs. Within the panels a trend was observed that increasing the gene-level stringency resulted in a larger difference in CIMP positive samples than increasing the probe-level stringency. A significant difference between positive samples using 'the most stringent' as compared to 'the least stringent' criteria (20% vs 46%, respectively; p<0.005) was demonstrated. A statistical significant variation in the frequency of CIMP depending on the cut-offs and genes included in a panel was found, with twice as many positives samples by least compared to most stringent definition used.

Of Publishers and Pirates: License Agreements Promote Unethical Behavior, But That's Only the Beginning.

ERIC Educational Resources Information Center

Pournelle, Jerry

1984-01-01

Discussion of software license agreements implies that they actually contribute to software piracy because of their stringency and indicates that competition in the software publishing field will eventually eliminate the piracy problem. (MBR)

The Political Economy of Part-Time Academic Work in Canada.

ERIC Educational Resources Information Center

Rajagopal, Indhu; Farr, William D.

1989-01-01

Under continuing financial stringency, the university administration negotiates concessions with full-time faculty to satisfy their interests and maintain the stability of the system. Part-timers, excluded from the collegium, remain peripheral to these arrangements. (Author/MLW)

Towards Flexibility in Academic Labour Markets?

ERIC Educational Resources Information Center

Nieuwenhuysen, John

1985-01-01

It is argued that Australia's relatively uniform and consistent academic salary structure and personnel policies should be more flexible and competitive in order to alleviate current problems of academic labor market stagnation, uneven faculty distribution, and other results of financial stringency. (MSE)

Intelligent neuroprocessors for in-situ launch vehicle propulsion systems health management

NASA Technical Reports Server (NTRS)

Gulati, S.; Tawel, R.; Thakoor, A. P.

1993-01-01

Efficacy of existing on-board propulsion systems health management systems (HMS) are severely impacted by computational limitations (e.g., low sampling rates); paradigmatic limitations (e.g., low-fidelity logic/parameter redlining only, false alarms due to noisy/corrupted sensor signatures, preprogrammed diagnostics only); and telemetry bandwidth limitations on space/ground interactions. Ultra-compact/light, adaptive neural networks with massively parallel, asynchronous, fast reconfigurable and fault-tolerant information processing properties have already demonstrated significant potential for inflight diagnostic analyses and resource allocation with reduced ground dependence. In particular, they can automatically exploit correlation effects across multiple sensor streams (plume analyzer, flow meters, vibration detectors, etc.) so as to detect anomaly signatures that cannot be determined from the exploitation of single sensor. Furthermore, neural networks have already demonstrated the potential for impacting real-time fault recovery in vehicle subsystems by adaptively regulating combustion mixture/power subsystems and optimizing resource utilization under degraded conditions. A class of high-performance neuroprocessors, developed at JPL, that have demonstrated potential for next-generation HMS for a family of space transportation vehicles envisioned for the next few decades, including HLLV, NLS, and space shuttle is presented. Of fundamental interest are intelligent neuroprocessors for real-time plume analysis, optimizing combustion mixture-ratio, and feedback to hydraulic, pneumatic control systems. This class includes concurrently asynchronous reprogrammable, nonvolatile, analog neural processors with high speed, high bandwidth electronic/optical I/O interfaced, with special emphasis on NASA's unique requirements in terms of performance, reliability, ultra-high density ultra-compactness, ultra-light weight devices, radiation hardened devices, power stringency, and long life terms.

Specific 16S ribosomal RNA targeted oligonucleotide probe against Clavibacter michiganensis subsp. sepedonicus.

PubMed

Mirza, M S; Rademaker, J L; Janse, J D; Akkermans, A D

1993-11-01

In this article we report on the polymerase chain reaction amplification of a partial 16S rRNA gene from the plant pathogenic bacterium Clavibacter michiganensis subsp. sepedonicus. A partial sequence (about 400 base pairs) of the gene was determined that covered two variable regions important for oligonucleotide probe development. A specific 24mer oligonucleotide probe targeted against the V6 region of 16S rRNA was designed. Specificity of the probe was determined using dot blot hybridization. Under stringent conditions (60 degrees C), the probe hybridized with all 16 Cl. michiganensis subsp. sepedonicus strains tested. Hybridization did not occur with 32 plant pathogenic and saprophytic bacteria used as controls under the same conditions. Under less stringent conditions (55 degrees C) the related Clavibacter michiganensis subsp. insidiosus, Clavibacter michiganensis subsp. nebraskensis, and Clavibacter michiganensis subsp. tesselarius also showed hybridization. At even lower stringency (40 degrees C), all Cl. michiganensis subspecies tested including Clavibacter michiganensis subsp. michiganensis showed hybridization signal, suggesting that under these conditions the probe may be used as a species-specific probe for Cl. michiganensis.

Undesired variance due to examiner stringency/leniency effect in communication skill scores assessed in OSCEs.

PubMed

Harasym, Peter H; Woloschuk, Wayne; Cunning, Leslie

2008-12-01

Physician-patient communication is a clinical skill that can be learned and has a positive impact on patient satisfaction and health outcomes. A concerted effort at all medical schools is now directed at teaching and evaluating this core skill. Student communication skills are often assessed by an Objective Structure Clinical Examination (OSCE). However, it is unknown what sources of error variance are introduced into examinee communication scores by various OSCE components. This study primarily examined the effect different examiners had on the evaluation of students' communication skills assessed at the end of a family medicine clerkship rotation. The communication performance of clinical clerks from Classes 2005 and 2006 were assessed using six OSCE stations. Performance was rated at each station using the 28-item Calgary-Cambridge guide. Item Response Theory analysis using a Multifaceted Rasch model was used to partition the various sources of error variance and generate a "true" communication score where the effects of examiner, case, and items are removed. Variance and reliability of scores were as follows: communication scores (.20 and .87), examiner stringency/leniency (.86 and .91), case (.03 and .96), and item (.86 and .99), respectively. All facet scores were reliable (.87-.99). Examiner variance (.86) was more than four times the examinee variance (.20). About 11% of the clerks' outcome status shifted using "true" rather than observed/raw scores. There was large variability in examinee scores due to variation in examiner stringency/leniency behaviors that may impact pass-fail decisions. Exploring the benefits of examiner training and employing "true" scores generated using Item Response Theory analyses prior to making pass/fail decisions are recommended.

Genetic variability and molecular identification of Brazilian Biomphalaria species (Mollusca: Planorbidae).

PubMed

Carvalho, S; Caldeira, R L; Simpson, A J; Vidigal, T H

2001-01-01

Freshwater snails belonging to the genus Biomphalaria are intermediate hosts of the trematode Schistosoma mansoni in the Neotropical region and Africa. In Brazil, one subspecies and ten species of Biomphalaria have been identified: B. glabrata, B. tenagophila, B. straminea, B. occidentalis, B. peregrina, B. kuhniana, B. schrammi, B. amazonica, B. oligoza, B. intermedia and B.t. guaibensis. However, only the first three species are found naturally infected with S. mansoni. The classical identification of these planorbids is based on comparison of morphological characteristics of the shell and male and female reproductive organs, which is greatly complicated by the extensive intra-specific variation. Several molecular techniques have been used in studies on the identification, genetic structure as well as phylogenetic relationships between these groups of organisms. Using the randomly amplified polymorphic DNAs (RAPD) analysis we demonstrated that B. glabrata exhibits a remarkable degree of intra-specific polymorphism. Thus, the genetics of the snail host may be more important to the epidemiology of schistosomiasis than those of the parasite itself. Using the simple sequence repeat anchored polymerase chain reaction (SSR-PCR) in intra-populational and intra-specific studies we have demonstrated that snails belonging to the B. straminea complex (B. straminea, B. kuhniana and B. intermedia) clearly presented higher heterogeneity. Using the low stringency polymerase chain reaction (LS-PCR) technique we were able to separate B. glabrata from B. tenagophila and B. tenagophila from B. occidentalis. To separate all Brazilian Biomphalaria species we used the restriction fragment length polymorphism (PCR-RFLP) of the internal transcribed spacer region (ITS) of the DNA gene. The method also proved to be efficient for the specific identification of DNA extracted from snail eggs. Recently we have sequenced the ITS2 region for phylogenetic studies of all Biomphalaria snails from Brazil.

Seasonal variability of microbial biomass phosphorus in urban soils.

PubMed

Halecki, W; Gąsiorek, M

2015-01-01

Urban soils have been formed through human activities. Seasonal evaluation with time-control procedure are essential for plant, and activity of microorganisms. Therefore, these processes are crucial in the urban area due to geochemical changes in the past years. The purpose of this study was to investigate the changes of content of microbial biomass phosphorus (P) in the top layer of soils throughout the season. In this research, the concentration of microbial biomass P ranged from 0.01 to 6.29 mg·kg(-1). We used single-factor repeated-measure analysis of variance to test the effect of season on microbial biomass P content of selected urban soils. We found no statistically significant differences between the concentration of microbial biomass P in the investigated urban and sub-urban soils during the growing season. This analysis explicitly recognised that environmental urban conditions are steady. Specifically, we have studied how vegetation seasonality and ability of microbial biomass P are useful for detecting quality deviations, which affect the equilibrium of urban soil. In conclusion, seasonal variability of the stringency of assurance across the different compounds of soil reveals, as expected, the stable condition of the urban soils. Seasonal responses in microbial biomass P under urban soil use should establish a framework as a reference to the activity of the microorganisms. Copyright © 2014 Elsevier B.V. All rights reserved.

Genomic clones for human cholinesterase

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

Kott, M.; Venta, P.J.; Larsen, J.

1987-05-01

A human genomic library was prepared from peripheral white blood cells from a single donor by inserting an MboI partial digest into BamHI poly-linker sites of EMBL3. This library was screened using an oligolabeled human cholinesterase cDNA probe over 700 bp long. The latter probe was obtained from a human basal ganglia cDNA library. Of approximately 2 million clones screened with high stringency conditions several positive clones were identified; two have been plaque purified. One of these clones has been partially mapped using restriction enzymes known to cut within the coded region of the cDNA for human serum cholinesterase. Hybridizationmore » of the fragments and their sizes are as expected if the genomic clone is cholinesterase. Sequencing of the DNA fragments in M13 is in progress to verify the identify of the clone and the location of introns.« less

Spanning the genomics era: the vital role of a single institution biorepository for childhood cancer research over a decade

PubMed Central

Zhou, Li

2015-01-01

The ‘genomics era’ is considered to have begun with the commencement of the Human Genome Project. As translational genomic studies can only be established when human tissue samples are available for analysis, biospecimens are now proven to be an essential element for their success. During the genomics era the necessity for more extensive biobanking infrastructure has been highlighted. With the increased number of genomic studies into cancer, it is considered that the availability of biospecimens will become the rate limiting step. Despite the efforts in international biobanking, translational genomics is hampered when there low numbers of biospecimens for a particular rare diseases and is most apparent for paediatric cancer. As there is a call for biobanking practice to be responsive to the current experimental needs of the time and for more expansive systems of tissue procurement to be established we have asked the question what role does a single institution biorepository play in the current highly networked world of translational genomics. Here we describe such a case. The Tumour Bank at The Children’s Hospital at Westmead (TB-CHW) in the western suburbs of Sydney was formally established in 1998 as a key resource for translational paediatric cancer research. During the genomics era, we show that the TB-CHW has developed into a key biospecimen repository for the cancer research community, during which time it has increasingly found itself having a vital role in the establishment of translational genomics for paediatric cancer. Here we detail metrics that demonstrate how as a single institution biorepository, the TB-CHW has been a strong participant in the advancement of translational genomics throughout the genomics era. This paper describes the significant contribution of a single institutional hospital embedded tumour biobank to the genomic research community. Despite the increased stringencies placed on biobanking practice, the TB-CHW has shown that a single institution biorespository can have a consistent and effective contribution to translational research into rare paediatric malignancy demonstrating its long term benefit throughout the genomics era. PMID:26835365

FUEL ECONOMY AND CO2 EMISSIONS STANDARDS, MANUFACTURER PRICING STRATEGIES, AND FEEBATES

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

Liu, Changzheng; Greene, David L; Bunch, Dr David S.

2012-01-01

Corporate Average Fuel Economy (CAFE) standards and CO2 emissions standards for 2012 to 2016 have significantly increased the stringency of requirements for new light-duty vehicle fuel efficiency. This study investigates the role of technology adoption and pricing strategies in meeting new standards, as well as the impact of feebate policies. The analysis is carried out by means of a dynamic optimization model that simulates manufacturer decisions with the objective of maximizing social surplus while simultaneously considering consumer response and meeting CAFE and emissions standards. The results indicate that technology adoption plays the major role and that the provision of compliancemore » flexibility and the availability of cost-effective advanced technologies help manufacturers reduce the need for pricing to induce changes in the mix of vehicles sold. Feebates, when implemented along with fuel economy and emissions standards, can bring additional fuel economy improvement and emissions reduction, but the benefit diminishes with the increasing stringency of the standards.« less

A novel method for detection of H9N2 influenza viruses by an aptamer-real time-PCR.

PubMed

Hmila, Issam; Wongphatcharachai, Manoosak; Laamiri, Nacira; Aouini, Rim; Marnissi, Boutheina; Arbi, Marwa; Sreevatsan, Srinand; Ghram, Abdeljelil

2017-05-01

H9N2 Influenza subtype has emerged in Tunisia causing epidemics in poultry and resulting in major economic losses. New mutations in their hemagglutinin and neuraminidase proteins were acquired, suggesting their potential to directly infect humans. Effective surveillance tools should be implemented to help prevent potential spillover of the virus across species. We have developed a highly sensitive real time immuno-polymerase chain reaction (RT-I-PCR) method for detecting H9N2 virus. The assay applies aptamers as ligands to capture and detect the virus. First, a panel of specific ssDNA aptamers was selected via a one step high stringency protocol. Next, the panel of selected aptamers was characterized for their affinities and their specificity to H9N2 virus. The aptamer showing the highest binding affinity to the virus was used as ligand to develop a highly sensitive sandwich Aptamer I-PCR. A 3-log increase in analytical sensitivity was achieved as compared to a routinely used ELISA antigen test, highlighting the potential of this approach to detect very low levels of virus particles. The test was validated using clinical samples and constitutes a rapid and a label-free platform, opening a new venue for the development of aptamer -based viability sensing for a variety of microorganisms of economic importance in Tunisia and surrounding regions. Copyright © 2017 Elsevier B.V. All rights reserved.

Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout.

PubMed

Al-Tobasei, Rafet; Paneru, Bam; Salem, Mohamed

2016-01-01

The ENCODE project revealed that ~70% of the human genome is transcribed. While only 1-2% of the RNAs encode for proteins, the rest are non-coding RNAs. Long non-coding RNAs (lncRNAs) form a diverse class of non-coding RNAs that are longer than 200 nt. Emerging evidence indicates that lncRNAs play critical roles in various cellular processes including regulation of gene expression. LncRNAs show low levels of gene expression and sequence conservation, which make their computational identification in genomes difficult. In this study, more than two billion Illumina sequence reads were mapped to the genome reference using the TopHat and Cufflinks software. Transcripts shorter than 200 nt, with more than 83-100 amino acids ORF, or with significant homologies to the NCBI nr-protein database were removed. In addition, a computational pipeline was used to filter the remaining transcripts based on a protein-coding-score test. Depending on the filtering stringency conditions, between 31,195 and 54,503 lncRNAs were identified, with only 421 matching known lncRNAs in other species. A digital gene expression atlas revealed 2,935 tissue-specific and 3,269 ubiquitously-expressed lncRNAs. This study annotates the lncRNA rainbow trout genome and provides a valuable resource for functional genomics research in salmonids.

Relationship between microbial community dynamics and process performance during thermophilic sludge bioleaching.

PubMed

Chen, Shen-Yi; Chou, Li-Chieh

2016-08-01

Heavy metals can be removed from the sludge using bioleaching technologies at thermophilic condition, thereby providing an option for biotreatment of wasted sludge generated from wastewater treatment. The purposes of this study were to establish a molecular biology technique, real-time PCR, for the detection and enumeration of the sulfur-oxidizing bacteria during the thermophilic sludge bioleaching. The 16S rRNA gene for real-time PCR quantification targeted the bioleaching bacteria: Sulfobacillus thermosulfidooxidans, Sulfobacillus acidophilus, and Acidithiobacillus caldus. The specificity and stringency for thermophilic sulfur-oxidizing bacteria were tested before the experiments of monitoring the bacterial community, bacterial number during the thermophilic sludge bioleaching and the future application on testing various environmental samples. The results showed that S. acidophilus was identified as the dominant sulfur-oxidizing bacteria, while A. caldus and S. thermosulfidooxidans occurred in relatively low numbers. The total number of the sulfur-oxidizing bacteria increased during the thermophilic bioleaching process. Meanwhile, the decrease of pH, production of sulfate, degradation of SS/VSS, and solubilization of heavy metal were found to correlate well with the population of thermophilic sulfur-oxidizing bacteria during the bioleaching process. The real-time PCR used in this study is a suitable method to monitor numbers of thermophilic sulfur-oxidizing bacteria during the bioleaching process.

[Structure, organization and capacity problems in emergency medical services, emergency admission and intensive care units].

PubMed

Dick, W

1994-01-01

Emergency medicine is subjected worldwide to financial stringencies and organizational evaluations of cost-effectiveness. The various links in the chain of survival are affected differently. Bystander assistance or bystander CPR is available in only 30% of the emergencies, response intervals--if at all required by legislation--are observed to only a limited degree or are too extended for survival in cardiac arrest. A single emergency telephone number is lacking. Too many different phone numbers for emergency reporting result in confusion and delays. Organizational realities are not fully overcome and impair efficiency. The position of the emergency physician in the EMS System is inadequately defined, the qualification of too many emergency physicians are unsatisfactory. In spite of this, emergency physicians are frequently forced to answer out-of-hospital emergency calls. Conflicts between emergency physicians and EMTs may be overcome by providing both groups with comparable qualifications as well as by providing an explicit definition of emergency competence. A further source of conflict occurs at the juncture of prehospital and inhospital emergency care in the emergency department. Deficiencies on either side play a decisive role. At least in principle there are solutions to the deficiencies in the EMSS and in intensive care medicine. They are among others: Adequate financial compensation of emergency personnel, availability of sufficient numbers of highly qualified personnel, availability of a central receiving area with an adjacent emergency ward, constant information flow to the dispatch center on the number of available emergency beds, maintaining 5% of all beds as emergency beds, establishing intermediate care facilities. Efficiency of emergency physician activities can be demonstrated in polytraumatized patients or in patients with ventricular fibrillation or acute myocardial infarction, in patients with acute myocardial insufficiency and other emergency clinical pictures. Cost effectiveness is clearly in favor of emergency medicine. Future developments will be characterized by the consequences of new health care legislation and by effects of financial stringencies on the emergency medical services.

Yeast and bacterial diversity along a transect in an acidic, As-Fe rich environment revealed by cultural approaches.

PubMed

Delavat, François; Lett, Marie-Claire; Lièvremont, Didier

2013-10-01

Acid mine drainages (AMDs) are often thought to harbour low biodiversity, yet little is known about the diversity distribution along the drainages. Using culture-dependent approaches, the microbial diversity from the Carnoulès AMD sediment was investigated for the first time along a transect showing progressive environmental stringency decrease. In total, 20 bacterial genera were detected, highlighting a higher bacterial diversity than previously thought. Moreover, this approach led to the discovery of 16 yeast species, demonstrating for the first time the presence of this important phylogenetic group in this AMD. All in all, the location of the microbes along the transect helps to better understand their distribution in a pollution gradient. Copyright © 2013 Elsevier B.V. All rights reserved.

Detection of Human Papillomavirus Type 2 Related Sequence in Oral Papilloma

PubMed Central

Yamaguchi, Taihei; Shindoh, Masanobu; Amemiya, Akira; Inoue, Nobuo; Kawamura, Masaaki; Sakaoka, Hiroshi; Inoue, Masakazu; Fujinaga, Kei

1998-01-01

Oral papilloma is a benign tumourous lesion. Part of this lesion is associated with human papillomavirus (HPV) infection. We analysed the genetical and histopathological evidence for HPV type 2 infection in three oral papillomas. Southern blot hybridization showed HPV 2a sequence in one lesion. Cells of the positive specimen appeared to contain high copy numbers of the viral DNA in an episomal state. In situ staining demonstrated virus capsid antigen in koilocytotic cells and surrounding cells in the hyperplastic epithelial layer. Two other specimens contained no HPV sequences by labeled probe of full length linear HPVs 2a, 6b, 11, 16, 18, 31 and 33 DNA under low stringency hybridization conditions. These results showed the possibility that HPV 2 plays a role in oral papilloma. PMID:9699941

Identification of human rotavirus serotype by hybridization to polymerase chain reaction-generated probes derived from a hyperdivergent region of the gene encoding outer capsid protein VP7

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

Flores, J.; Sears, J.; Schael, I.P.

1990-08-01

We have synthesized {sup 32}P-labeled hybridization probes from a hyperdivergent region (nucleotides 51 to 392) of the rotavirus gene encoding the VP7 glycoprotein by using the polymerase chain reaction method. Both RNA (after an initial reverse transcription step) and cloned cDNA from human rotavirus serotypes 1 through 4 could be used as templates to amplify this region. High-stringency hybridization of each of the four probes to rotavirus RNAs dotted on nylon membranes allowed the specific detection of corresponding sequences and thus permitted identification of the serotype of the strains dotted. The procedure was useful when applied to rotaviruses isolated frommore » field studies.« less

Selection of stable scFv antibodies by phage display.

PubMed

Brockmann, Eeva-Christine

2012-01-01

ScFv fragments are popular recombinant antibody formats but often suffer from limited stability. Phage display is a powerful tool in antibody engineering and applicable also for stability selection. ScFv variants with improved stability can be selected from large randomly mutated phage displayed libraries with a specific antigen after the unstable variants have been inactivated by heat or GdmCl. Irreversible scFv denaturation, which is a prerequisite for efficient selection, is achieved by combining denaturation with reduction of the intradomain disulfide bonds. Repeated selection cycles of increasing stringency result in enrichment of stabilized scFv fragments. Procedures for constructing a randomly mutated scFv library by error-prone PCR and phage display selection for enrichment of stable scFv antibodies from the library are described here.

Off-Setting Differences in Reviewer Stringency.

ERIC Educational Resources Information Center

Cason, Carolyn L.; And Others

A total of 1,071 rating sheets were completed by individual reviewers evaluating abstracts submitted to Sigma Theta Tau International Honor Society for the International Research Congress in Edinburgh, Scotland. Only 972 sheets contained usable data. Reviewers indicated a total of 12 ratings with possible comments for each abstract on machine…

The effects of climate sensitivity and carbon cycle interactions on mitigation policy stringency

EPA Science Inventory

Climate sensitivity and climate-carbon cycle feedbacks interact to determine how global carbon and energy cycles will change in the future. While the science of these connections is well documented, their economic implications are not well understood. Here we examine the effect o...

12 CFR 1204.8 - How are records secured?

Code of Federal Regulations, 2010 CFR

2010-01-01

... § 1204.8 How are records secured? (a) What controls must FHFA have in place? Each FHFA office must establish administrative and physical controls to prevent unauthorized access to its systems of records... stringency of these controls should correspond to the sensitivity of the records that the controls protect...

Achieving More, Spending Less in Schools, Districts, and States

ERIC Educational Resources Information Center

Walberg, Herbert J.

2011-01-01

In an era of financial stringency and demands for better school performance, it is useful to think about several means of raising school productivity: (1) increase learning effectiveness without increasing costs; (2) reduce costs without diminishing effectiveness; or (3) both, that is, increase effectiveness and simultaneously reduce costs. The…

A quick and simple FISH protocol with hybridization-sensitive fluorescent linear oligodeoxynucleotide probes

PubMed Central

Wang, Dan Ohtan; Matsuno, Hitomi; Ikeda, Shuji; Nakamura, Akiko; Yanagisawa, Hiroyuki; Hayashi, Yasunori; Okamoto, Akimitsu

2012-01-01

Fluorescence in situ hybridization (FISH) is a powerful tool used in karyotyping, cytogenotyping, cancer diagnosis, species specification, and gene-expression analysis. Although widely used, conventional FISH protocols are cumbersome and time consuming. We have now developed a FISH method using exciton-controlled hybridization-sensitive fluorescent oligodeoxynucleotide (ECHO) probes. ECHO–FISH uses a 25-min protocol from fixation to mounting that includes no stringency washing steps. We use ECHO–FISH to detect both specific DNA and RNA sequences with multicolor probes. ECHO–FISH is highly reproducible, stringent, and compatible with other fluorescent cellular labeling techniques. The resolution allows detection of intranuclear speckles of poly(A) RNA in HeLa cells and dissociated hippocampal primary cultures, and mRNAs in the distal dendrites of hippocampal neurons. We also demonstrate detection of telomeric and centromeric DNA on metaphase mouse chromosomes. The simplicity of the ECHO–FISH method will likely accelerate cytogenetic and gene-expression analysis with high resolution. PMID:22101241

Northern blots: capillary transfer of RNA from agarose gels and filter hybridization using standard stringency conditions.

PubMed

Rio, Donald C

2015-03-02

In this protocol, an RNA sample, fractionated by gel electrophoresis, is transferred from the gel onto a membrane by capillary transfer. Short-wave UV light is used to fix the transferred RNA to the membrane. The membrane is then pretreated to block nonspecific probe-binding sites, and hybridization of the immobilized RNA to a (32)P-labeled DNA or RNA probe specific for the mRNA of interest is performed. Finally, the membrane is washed and subjected to autoradiography or phosphorimaging. Because exposure to UV cross-links the RNA to the membrane, the membrane can be stripped and hybridized with other probes. The procedure is suitable for detecting poly(A)(+)-selected mRNA or mRNA in total cellular RNA if the target transcript is relatively abundant. Using DNA or RNA probes labeled to 1 × 10(8)-10 × 10(8) cpm/µg, it should be possible to detect ∼5 pg of a specific RNA. © 2015 Cold Spring Harbor Laboratory Press.

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome.

PubMed

Ribeiro, Antonio; Golicz, Agnieszka; Hackett, Christine Anne; Milne, Iain; Stephen, Gordon; Marshall, David; Flavell, Andrew J; Bayer, Micha

2015-11-11

Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of large numbers of SNPs at low cost. However, both NGS data and their analysis are error-prone, which can lead to the generation of false positive (FP) SNPs. We explored the relationship between FP SNPs and seven factors involved in mapping-based variant calling - quality of the reference sequence, read length, choice of mapper and variant caller, mapping stringency and filtering of SNPs by read mapping quality and read depth. This resulted in 576 possible factor level combinations. We used error- and variant-free simulated reads to ensure that every SNP found was indeed a false positive. The variation in the number of FP SNPs generated ranged from 0 to 36,621 for the 120 million base pairs (Mbp) genome. All of the experimental factors tested had statistically significant effects on the number of FP SNPs generated and there was a considerable amount of interaction between the different factors. Using a fragmented reference sequence led to a dramatic increase in the number of FP SNPs generated, as did relaxed read mapping and a lack of SNP filtering. The choice of reference assembler, mapper and variant caller also significantly affected the outcome. The effect of read length was more complex and suggests a possible interaction between mapping specificity and the potential for contributing more false positives as read length increases. The choice of tools and parameters involved in variant calling can have a dramatic effect on the number of FP SNPs produced, with particularly poor combinations of software and/or parameter settings yielding tens of thousands in this experiment. Between-factor interactions make simple recommendations difficult for a SNP discovery pipeline but the quality of the reference sequence is clearly of paramount importance. Our findings are also a stark reminder that it can be unwise to use the relaxed mismatch settings provided as defaults by some read mappers when reads are being mapped to a relatively unfinished reference sequence from e.g. a non-model organism in its early stages of genomic exploration.

Biotype-specific tcpA genes in Vibrio cholerae.

PubMed

Iredell, J R; Manning, P A

1994-08-01

The tcpA gene, encoding the structural subunit of the toxin-coregulated pilus, has been isolated from a variety of clinical isolates of Vibrio cholerae, and the nucleotide sequence determined. Strict biotype-specific conservation within both the coding and putative regulatory regions was observed, with important differences between the El Tor and classical biotypes. V. cholerae O139 Bengal strains appear to have El Tor-type tcpA genes. Environmental O1 and non-O1 isolates have sequences that bind an El Tor-specific tcpA DNA probe and that are weakly and variably amplified by tcpA-specific polymerase chain reaction primers, under conditions of reduced stringency. The data presented allow the selection of primer pairs to help distinguish between clinical and environmental isolates, and to distinguish El Tor (and Bengal) biotypes from classical biotypes of V. cholerae. While the role of TcpA in cholera vaccine preparations remains unclear, the data strongly suggest that TcpA-containing vaccines directed at O1 strains need include only the two forms of TcpA, and that such vaccines directed at (O139) Bengal strains should include the TcpA of El Tor biotype.

Effects of Mastery Criterion on the Emergence of Derived Equivalence Relations

ERIC Educational Resources Information Center

Fienup, Daniel M.; Brodsky, Julia

2017-01-01

In this study, we manipulated mastery criterion form (rolling or block) and stringency (across 6 or 12 trials) and measured the emergence of derived relations. College students learned neuroanatomy equivalence classes and experienced one of two rolling mastery criteria (6 or 12 consecutive correct responses) or a block mastery criterion (12 trials…

Harvard and Money; A Memorandum on Issues and Choices.

ERIC Educational Resources Information Center

Harvard Univ., Cambridge , MA. Univ. Committee on Governance.

This report discusses some of the financial issues and choices with which Harvard University will have to cope in an environment of increased stringency: issues of money-allocation, money raising, and money management. Part I presents highlights of Harvard's recent financial history and its prospects in quantitative terms. Part II presents some…

76 FR 59338 - Approval and Promulgation of Air Quality Implementation Plans; Montana; Revisions to the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-26

....) Since for asphalt concrete plants and mineral crushers this revision (ARM 17.8.743(1)(b)) reduces the... plants and mineral crushers reduces the stringency of the current SIP approved regulations. We commented... of Subjects in 40 CFR Part 52 Environmental protection, Air pollution control, Carbon monoxide...

78 FR 719 - California State Motor Vehicle Pollution Control Standards; Urban Buses; Request for Waiver of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-04

.... Collectively, the five rulemakings elevated the stringency of exhaust emission standards and test procedures... Act for the emission standards and related test procedures contained in its urban bus regulations, as... Standards; Urban Buses; Request for Waiver of Preemption; Opportunity for Public Hearing and Comment AGENCY...

Making Decisions in a Time of Fiscal Stringency: The Longer-Term Implications.

ERIC Educational Resources Information Center

Bowen, Frank M.

The concept of traditional planning, programming, and budgeting systems (PPBS) is defined and compared with imperative planning, a term used to refer to whatever procedures higher education officials use to integrate program planning and budgeting. The University of Wisconsin system is described as an example of emerging budgetary practice in…

ASSESSMENT OF THE SWINE PROTEIN-ANNOTATED OLIGONUCLEOTIDE MICROARRAY AND UTILITY OF THE ARRAYS FOR EQTL AND TRANSCRIPTIONAL PROFILING STUDIES

USDA-ARS?s Scientific Manuscript database

We have evaluated the new Swine Protein-Annotated Oligonucleotide Microarray (http://www.pigoligoarray.org) by analyzing transcriptional profiles for longissimus dorsi muscle (LD), Bronchial lymph node (BLN) and Lung. Four LD samples were used to assess the stringency of hybridization conditions com...

Pharmacogenetic Selection of Volunteers Increases Stringency of Bioequivalence Studies; The Case of Clopidogrel

PubMed Central

Garcés-Eisele, J.; Ruiz-Argüelles, A.; Estrada-Marín, Larisa; Reyes-Núñez, Virginia; Vázquez-Pérez, R.; Guzmán-García, Olga; Coutiño-Medina, R.; Acosta-Sandria, Leticia; Cedillo-Carvallo, Beatriz

2014-01-01

Clinical response to clopidogrel varies widely due to under-dosing, drug interactions and intrinsic interindividual differences resulting from genetic polymorphisms. Cytochrome P450-2C19 is the principal enzyme involved in the activation of the prodrug and loss-of-function alleles have been described. Upon expiration of the pharmaceutical patent of clopidogrel, generic manufacturers have started to subject interchangeable formulations to bioequivalence studies. The purpose of the current investigation was to study the effect of selection of volunteers homozygous for the CYP2C19*1 haplotype on the bioavailability of clopidogrel. A regular 2×2 bioequivalence study between two formulations of clopidogrel was performed in volunteers selected and unselected for relevant CYP2C19 haplotypes for the Mexican population. It was found that selection of volunteers homozygous for the CYP2C19*1 haplotype, increased the stringency of bioequivalence statistics and resulted in bioinequivalence of a generic clopidogrel compound that otherwise proved equivalent when tested in an open unselected population. Augmentation of bioequivalence strictness is expected to result from pharmacogenetic selection of volunteers. PMID:25284925

Neutral evolution of proteins: The superfunnel in sequence space and its relation to mutational robustness

NASA Astrophysics Data System (ADS)

Noirel, Josselin; Simonson, Thomas

2008-11-01

Following Kimura's neutral theory of molecular evolution [M. Kimura, The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, 1983) (reprinted in 1986)], it has become common to assume that the vast majority of viable mutations of a gene confer little or no functional advantage. Yet, in silico models of protein evolution have shown that mutational robustness of sequences could be selected for, even in the context of neutral evolution. The evolution of a biological population can be seen as a diffusion on the network of viable sequences. This network is called a "neutral network." Depending on the mutation rate μ and the population size N, the biological population can evolve purely randomly (μN ≪1) or it can evolve in such a way as to select for sequences of higher mutational robustness (μN ≫1). The stringency of the selection depends not only on the product μN but also on the exact topology of the neutral network, the special arrangement of which was named "superfunnel." Even though the relation between mutation rate, population size, and selection was thoroughly investigated, a study of the salient topological features of the superfunnel that could affect the strength of the selection was wanting. This question is addressed in this study. We use two different models of proteins: on lattice and off lattice. We compare neutral networks computed using these models to random networks. From this, we identify two important factors of the topology that determine the stringency of the selection for mutationally robust sequences. First, the presence of highly connected nodes ("hubs") in the network increases the selection for mutationally robust sequences. Second, the stringency of the selection increases when the correlation between a sequence's mutational robustness and its neighbors' increases. The latter finding relates a global characteristic of the neutral network to a local one, which is attainable through experiments or molecular modeling.

Neutral evolution of proteins: The superfunnel in sequence space and its relation to mutational robustness.

PubMed

Noirel, Josselin; Simonson, Thomas

2008-11-14

Following Kimura's neutral theory of molecular evolution [M. Kimura, The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge, 1983) (reprinted in 1986)], it has become common to assume that the vast majority of viable mutations of a gene confer little or no functional advantage. Yet, in silico models of protein evolution have shown that mutational robustness of sequences could be selected for, even in the context of neutral evolution. The evolution of a biological population can be seen as a diffusion on the network of viable sequences. This network is called a "neutral network." Depending on the mutation rate mu and the population size N, the biological population can evolve purely randomly (muN<1) or it can evolve in such a way as to select for sequences of higher mutational robustness (muN>1). The stringency of the selection depends not only on the product muN but also on the exact topology of the neutral network, the special arrangement of which was named "superfunnel." Even though the relation between mutation rate, population size, and selection was thoroughly investigated, a study of the salient topological features of the superfunnel that could affect the strength of the selection was wanting. This question is addressed in this study. We use two different models of proteins: on lattice and off lattice. We compare neutral networks computed using these models to random networks. From this, we identify two important factors of the topology that determine the stringency of the selection for mutationally robust sequences. First, the presence of highly connected nodes ("hubs") in the network increases the selection for mutationally robust sequences. Second, the stringency of the selection increases when the correlation between a sequence's mutational robustness and its neighbors' increases. The latter finding relates a global characteristic of the neutral network to a local one, which is attainable through experiments or molecular modeling.

Development of species-specific rDNA probes for Giardia by multiple fluorescent in situ hybridization combined with immunocytochemical identification of cyst wall antigens.

PubMed

Erlandsen, Stanley L; Jarroll, Edward; Wallis, Peter; van Keulen, Harry

2005-08-01

In this study, we describe the development of fluorescent oligonucleotide probes to variable regions in the small subunit of 16S rRNA in three distinct Giardia species. Sense and antisense probes (17-22 mer) to variable regions 1, 3, and 8 were labeled with digoxygenin or selected fluorochomes (FluorX, Cy3, or Cy5). Optimal results were obtained with fluorochome-labeled oligonucleotides for detection of rRNA in Giardia cysts. Specificity of fluorescent in situ hybridization (FISH) was shown using RNase digestion and high stringency to diminish the hybridization signal, and oligonucleotide probes for rRNA in Giardia lamblia, Giardia muris, and Giardia ardeae were shown to specifically stain rRNA only within cysts or trophozoites of those species. The fluorescent oligonucleotide specific for rRNA in human isolates of Giardia was positive for ten different strains. A method for simultaneous FISH detection of cysts using fluorescent antibody (genotype marker) and two oligonucleotide probes (species marker) permitted visualization of G. lamblia and G. muris cysts in the same preparation. Testing of an environmental water sample revealed the presence of FISH-positive G. lamblia cysts with a specific rDNA probe for rRNA, while negative cysts were presumed to be of animal or bird origin.

78 FR 55221 - Approval and Promulgation of Implementation Plans; Texas; Procedures for Stringency...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-10

..., including those pertaining to the minor permit revisions. TCEQ subsequently adopted amendments to 30 TAC 122... were adopted or submitted to the Texas SIP in this rule package. 1. Minor permit revisions at 30 TAC... approaches only to the extent that such minor permit revision procedures are explicitly provided for in the...

Relationships and Values among Students and Staff in British and German Higher Education

ERIC Educational Resources Information Center

Pritchard, Rosalind

2005-01-01

Financial stringency and neo-liberal influences in higher education are impacting upon relationships and academic values in higher education. The aim of the present paper was to analyse how these forces operate differentially in the UK and Germany. The British students were significantly more satisfied than were their German counterparts with the…

78 FR 5303 - Approval and Promulgation of Implementation Plans; State of Missouri; Control of Sulfur Emissions...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-25

... Promulgation of Implementation Plans; State of Missouri; Control of Sulfur Emissions From Stationary Boilers.... Louis nonattainment area by limiting sulfur dioxide (SO 2 ) emissions (a precursor pollutant to PM 2.5... stringency of the SIP. Missouri's revision adds 10 CSR 10- 5.570 Control of Sulfur Emissions from Stationary...

Effects of a rater training on rating accuracy in a physical examination skills assessment

PubMed Central

Weitz, Gunther; Vinzentius, Christian; Twesten, Christoph; Lehnert, Hendrik; Bonnemeier, Hendrik; König, Inke R.

2014-01-01

Background: The accuracy and reproducibility of medical skills assessment is generally low. Rater training has little or no effect. Our knowledge in this field, however, relies on studies involving video ratings of overall clinical performances. We hypothesised that a rater training focussing on the frame of reference could improve accuracy in grading the curricular assessment of a highly standardised physical head-to-toe examination. Methods: Twenty-one raters assessed the performance of 242 third-year medical students. Eleven raters had been randomly assigned to undergo a brief frame-of-reference training a few days before the assessment. 218 encounters were successfully recorded on video and re-assessed independently by three additional observers. Accuracy was defined as the concordance between the raters' grade and the median of the observers' grade. After the assessment, both students and raters filled in a questionnaire about their views on the assessment. Results: Rater training did not have a measurable influence on accuracy. However, trained raters rated significantly more stringently than untrained raters, and their overall stringency was closer to the stringency of the observers. The questionnaire indicated a higher awareness of the halo effect in the trained raters group. Although the self-assessment of the students mirrored the assessment of the raters in both groups, the students assessed by trained raters felt more discontent with their grade. Conclusions: While training had some marginal effects, it failed to have an impact on the individual accuracy. These results in real-life encounters are consistent with previous studies on rater training using video assessments of clinical performances. The high degree of standardisation in this study was not suitable to harmonize the trained raters’ grading. The data support the notion that the process of appraising medical performance is highly individual. A frame-of-reference training as applied does not effectively adjust the physicians' judgement on medical students in real-live assessments. PMID:25489341

Effects of a rater training on rating accuracy in a physical examination skills assessment.

PubMed

Weitz, Gunther; Vinzentius, Christian; Twesten, Christoph; Lehnert, Hendrik; Bonnemeier, Hendrik; König, Inke R

2014-01-01

The accuracy and reproducibility of medical skills assessment is generally low. Rater training has little or no effect. Our knowledge in this field, however, relies on studies involving video ratings of overall clinical performances. We hypothesised that a rater training focussing on the frame of reference could improve accuracy in grading the curricular assessment of a highly standardised physical head-to-toe examination. Twenty-one raters assessed the performance of 242 third-year medical students. Eleven raters had been randomly assigned to undergo a brief frame-of-reference training a few days before the assessment. 218 encounters were successfully recorded on video and re-assessed independently by three additional observers. Accuracy was defined as the concordance between the raters' grade and the median of the observers' grade. After the assessment, both students and raters filled in a questionnaire about their views on the assessment. Rater training did not have a measurable influence on accuracy. However, trained raters rated significantly more stringently than untrained raters, and their overall stringency was closer to the stringency of the observers. The questionnaire indicated a higher awareness of the halo effect in the trained raters group. Although the self-assessment of the students mirrored the assessment of the raters in both groups, the students assessed by trained raters felt more discontent with their grade. While training had some marginal effects, it failed to have an impact on the individual accuracy. These results in real-life encounters are consistent with previous studies on rater training using video assessments of clinical performances. The high degree of standardisation in this study was not suitable to harmonize the trained raters' grading. The data support the notion that the process of appraising medical performance is highly individual. A frame-of-reference training as applied does not effectively adjust the physicians' judgement on medical students in real-live assessments.

Isoform specificity of progesterone receptor antibodies.

PubMed

Fabris, Victoria; Abascal, María F; Giulianelli, Sebastián; May, María; Sequeira, Gonzalo R; Jacobsen, Britta; Lombès, Marc; Han, Julie; Tran, Luan; Molinolo, Alfredo; Lanari, Claudia

2017-10-01

Progesterone receptors (PR) are prognostic and predictive biomarkers in hormone-dependent cancers. Two main PR isoforms have been described, PRB and PRA, that differ only in that PRB has 164 extra N-terminal amino acids. It has been reported that several antibodies empirically exclusively recognize PRA in formalin-fixed paraffin-embedded (FFPE) tissues. To confirm these findings, we used human breast cancer xenograft models, T47D-YA and -YB cells expressing PRA or PRB, respectively, MDA-MB-231 cells modified to synthesize PRB, and MDA-MB-231/iPRAB cells which can bi-inducibly express either PRA or PRB. Cells were injected into immunocompromised mice to generate tumours exclusively expressing PRA or PRB. PR isoform expression was verified using immunoblots. FFPE samples from the same tumours were studied by immunohistochemistry using H-190, clone 636, clone 16, and Ab-6 anti-PR antibodies, the latter exclusively recognizing PRB. Except for Ab-6, all antibodies displayed a similar staining pattern. Our results indicate that clones 16, 636, and the H-190 antibody recognize both PR isoforms. They point to the need for more stringency in evaluating the true specificity of purported PRA-specific antibodies as the PRA/PRB ratio may have prognostic and predictive value in breast cancer.

Southern Higher Education and the 1977 State Legislatures. Regional Spotlight Vol. XXI, No. 1.

ERIC Educational Resources Information Center

Anderson, Laura

While 1977 was hardly a banner year for southern higher education in terms of legislative appropriations, it was an improvement over the most recent years. Financial stringency in recent years has given way to modest revenue gains in most southern states, with many reporting small but larger than expected surpluses. Budget increases ranged from 6…

The Impact of the Economy on Libraries and the Impact of Libraries on the Economy of New York State.

ERIC Educational Resources Information Center

Johnson, Shirley B.

New York's library system, which helps to attract desirable information related industries, is endangered by inflation and budget stringency. Library costs have increased more rapidly than the general price level. Technological improvements, cost-saving in the long run, require initial capital outlays. The growth of book collections must keep pace…

SIP Shear Walls: Cyclic Performance of High-Aspect-Ratio Segments and Perforated Walls

Treesearch

Vladimir Kochkin; Douglas R. Rammer; Kevin Kauffman; Thomas Wiliamson; Robert J. Ross

2015-01-01

Increasing stringency of energy codes and the growing market demand for more energy efficient buildings gives structural insulated panel (SIP) construction an opportunity to increase its use in commercial and residential buildings. However, shear wall aspect ratio limitations and lack of knowledge on how to design SIPs with window and door openings are barriers to the...

Undesired Variance Due to Examiner Stringency/Leniency Effect in Communication Skill Scores Assessed in OSCEs

ERIC Educational Resources Information Center

Harasym, Peter H.; Woloschuk, Wayne; Cunning, Leslie

2008-01-01

Physician-patient communication is a clinical skill that can be learned and has a positive impact on patient satisfaction and health outcomes. A concerted effort at all medical schools is now directed at teaching and evaluating this core skill. Student communication skills are often assessed by an Objective Structure Clinical Examination (OSCE).…

Social Spending in Latin America: The Story of the 1980s. World Bank Discussion Papers No. 106.

ERIC Educational Resources Information Center

Grosh, Margaret E.

This study traces public sector expenditures for nine Latin American countries in the 1980s in order to determine how social services and social well-being fared during the economic stringencies of the decade. The countries included are Argentina, Bolivia, Brazil, Chile, Costa Rica, the Dominican Republic, El Salvador, Jamaica, and Venezuela. The…

EAPhy: A Flexible Tool for High-throughput Quality Filtering of Exon-alignments and Data Processing for Phylogenetic Methods.

PubMed

Blom, Mozes P K

2015-08-05

Recently developed molecular methods enable geneticists to target and sequence thousands of orthologous loci and infer evolutionary relationships across the tree of life. Large numbers of genetic markers benefit species tree inference but visual inspection of alignment quality, as traditionally conducted, is challenging with thousands of loci. Furthermore, due to the impracticality of repeated visual inspection with alternative filtering criteria, the potential consequences of using datasets with different degrees of missing data remain nominally explored in most empirical phylogenomic studies. In this short communication, I describe a flexible high-throughput pipeline designed to assess alignment quality and filter exonic sequence data for subsequent inference. The stringency criteria for alignment quality and missing data can be adapted based on the expected level of sequence divergence. Each alignment is automatically evaluated based on the stringency criteria specified, significantly reducing the number of alignments that require visual inspection. By developing a rapid method for alignment filtering and quality assessment, the consistency of phylogenetic estimation based on exonic sequence alignments can be further explored across distinct inference methods, while accounting for different degrees of missing data.

Hybridization parameters revisited: solutions containing SDS.

PubMed

Rose, Ken; Mason, John O; Lathe, Richard

2002-07-01

Salt concentration governs nucleic acid hybridization according to the Schildkraut-Lifson equation. High concentrations of SDS are used in some common protocols, but the effects of SDS on hybridization stringency have not been reported. We investigated hybridization parameters in solutions containing SDS. With targets immobilized on nylon membranes and PCR- or transcription-generated probes, we report that the 50% dissociation temperature (Tm*) in the absence of SDS was 15 degrees C-17degrees C lower than the calculated Tm. SDS had only modest effects on Tm* [1% (w/v) equating to 8 mM NaCl]. RNA/DNA hybrids were approximately 11 degrees C more stable than DNA/DNA hybrids. Incomplete homology (69%) significantly reduced the Tm* for DNA/DNA hybrids (approximately /4degrees C; 0.45 degrees C/% nonhomology) but far less so for RNA/DNA hybrids (approximately 2.3 degrees C; approximately 0.07 degrees C/% non-homology); incomplete homology also markedly reduced the extent of hybridization. On these nylonfilters, SDS had a major effect on nonspecific binding. Buffers lacking SDS, or with low salt concentration, gave high hybridization backgrounds; buffers containing SDS, or high-salt buffers, gave reproducibly low backgrounds.

Specific features of low-frequency vibrational dynamics and low-temperature heat capacity of double-walled carbon nanotubes

NASA Astrophysics Data System (ADS)

Avramenko, M. V.; Roshal, S. B.

2016-05-01

A continuous model has been constructed for low-frequency dynamics of a double-walled carbon nanotube. The formation of the low-frequency part of the phonon spectrum of a double-walled nanotube from phonon spectra of its constituent single-walled nanotubes has been considered in the framework of the proposed approach. The influence of the environment on the phonon spectrum of a single double-walled carbon nanotube has been analyzed. A combined method has been proposed for estimating the coefficients of the van der Waals interaction between the walls of the nanotube from the spectroscopic data and the known values of the elastic moduli of graphite. The low-temperature specific heat has been calculated for doublewalled carbon nanotubes, which in the field of applicability of the model ( T < 35 K) is substantially less than the sum of specific heats of two individual single-walled nanotubes forming it.

The human homolog of S. cerevisiae CDC27, CDC27 Hs, is encoded by a highly conserved intronless gene present in multiple copies in the human genome

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

Devor, E.J.; Dill-Devor, R.M.

1994-09-01

We have obtained a number of unique sequences via PCR amplification of human genomic DNA using degenerate primers under low stringency (42{degrees}C). One of these, an 853 bp product, has been identified as a partial genomic sequence of the human homolog of the S. cerevisiae CDC27 gene, CDC27Hs (GenBank No. U00001). This gene, reported by Turgendreich et al. is also designated EST00556 from Adams et al. We have undertaken a more detailed examination of our sequence, MCP34N, and have found that: 1. the genomic sequence is nearly identical to CDC27Hs over its entire 853 bp length; 2. an MCP34N-specific PCRmore » assay of several non-human primate species reveals amplification products in chimpanzee and gorilla genomes having greater than 90% sequence identity with CDC27Hs; and 3. an MCP34N-specific PCR assay of the BIOS hybrid cell line panel gives a discordancy pattern suggesting multiple loci. Based upon these data, we present the following initial characterization: 1. the complete MCP34N sequence identity with CDC27Hs indicates that the latter is encoded by an intronless gene; 2. CDC27Hs is highly conserved among higher primates; and 3. CDC27Hs is present in multiple copies in the human genome. These characteristics, taken together with those initially reported for CDC27Hs, suggest that this is an old gene that carries out an important but, as yet, unknown function in the human brain.« less

Bayesian Redshift Classification of Emission-line Galaxies with Photometric Equivalent Widths

NASA Astrophysics Data System (ADS)

Leung, Andrew S.; Acquaviva, Viviana; Gawiser, Eric; Ciardullo, Robin; Komatsu, Eiichiro; Malz, A. I.; Zeimann, Gregory R.; Bridge, Joanna S.; Drory, Niv; Feldmeier, John J.; Finkelstein, Steven L.; Gebhardt, Karl; Gronwall, Caryl; Hagen, Alex; Hill, Gary J.; Schneider, Donald P.

2017-07-01

We present a Bayesian approach to the redshift classification of emission-line galaxies when only a single emission line is detected spectroscopically. We consider the case of surveys for high-redshift Lyα-emitting galaxies (LAEs), which have traditionally been classified via an inferred rest-frame equivalent width (EW {W}{Lyα }) greater than 20 Å. Our Bayesian method relies on known prior probabilities in measured emission-line luminosity functions and EW distributions for the galaxy populations, and returns the probability that an object in question is an LAE given the characteristics observed. This approach will be directly relevant for the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX), which seeks to classify ˜106 emission-line galaxies into LAEs and low-redshift [{{O}} {{II}}] emitters. For a simulated HETDEX catalog with realistic measurement noise, our Bayesian method recovers 86% of LAEs missed by the traditional {W}{Lyα } > 20 Å cutoff over 2 < z < 3, outperforming the EW cut in both contamination and incompleteness. This is due to the method’s ability to trade off between the two types of binary classification error by adjusting the stringency of the probability requirement for classifying an observed object as an LAE. In our simulations of HETDEX, this method reduces the uncertainty in cosmological distance measurements by 14% with respect to the EW cut, equivalent to recovering 29% more cosmological information. Rather than using binary object labels, this method enables the use of classification probabilities in large-scale structure analyses. It can be applied to narrowband emission-line surveys as well as upcoming large spectroscopic surveys including Euclid and WFIRST.

Pseudosynapsis and Decreased Stringency of Meiotic Repair Pathway Choice on the Hemizygous Sex Chromosome of Caenorhabditis elegans Males

PubMed Central

Checchi, Paula M.; Lawrence, Katherine S.; Van, Mike V.; Larson, Braden J.; Engebrecht, JoAnne

2014-01-01

During meiosis, accurate chromosome segregation relies on homology to mediate chromosome pairing, synapsis, and crossover recombination. Crossovers are dependent upon formation and repair of double-strand breaks (DSBs) by homologous recombination (HR). In males of many species, sex chromosomes are largely hemizygous, yet DSBs are induced along nonhomologous regions. Here we analyzed the genetic requirements for meiotic DSB repair on the completely hemizygous X chromosome of Caenorhabditis elegans males. Our data reveal that the kinetics of DSB formation, chromosome pairing, and synapsis are tightly linked in the male germ line. Moreover, DSB induction on the X is concomitant with a brief period of pseudosynapsis that may allow X sister chromatids to masquerade as homologs. Consistent with this, neither meiotic kleisins nor the SMC-5/6 complex are essential for DSB repair on the X. Furthermore, early processing of X DSBs is dependent on the CtIP/Sae2 homolog COM-1, suggesting that as with paired chromosomes, HR is the preferred pathway. In contrast, the X chromosome is refractory to feedback mechanisms that ensure crossover formation on autosomes. Surprisingly, neither RAD-54 nor BRC-2 are essential for DSB repair on the X, suggesting that unlike autosomes, the X is competent for repair in the absence of HR. When both RAD-54 and the structure-specific nuclease XPF-1 are abrogated, X DSBs persist, suggesting that single-strand annealing is engaged in the absence of HR. Our findings indicate that alteration in sister chromatid interactions and flexibility in DSB repair pathway choice accommodate hemizygosity on sex chromosomes. PMID:24939994

Mapping ‘hydroscapes’ along the iso- to anisohydric continuum of stomatal regulation of plant water status

Treesearch

Frederick C. Meinzer; David R. Woodruff; Danielle E. Marias; Duncan D. Smith; Katherine A. McCulloh; Ava R. Howard; Alicia L. Magedman; Josep Penuelas

2016-01-01

The concept of iso- vs. anisohydry has been used to describe the stringency of stomatal regulation of plant water potential (ψ). However, metrics that accurately and consistently quantify species’ operating ranges along a continuum of iso- to anisohydry have been elusive. Additionally, most approaches to quantifying iso/anisohydry require labour-intensive measurements...

Inactive Wells: Economic and Policy Issues

NASA Astrophysics Data System (ADS)

Krupnick, A.

2016-12-01

This paper examines the economic and policy issues associated with various types of inactive oil and gas wells. It covers the costs of decommissioning wells, and compares them to the bonding requirements on these wells, looking at a large number of states. It also reviews the detailed regulations governing treatment of inactive wells by states and the federal government and compares them according to their completeness and stringency.

Proceedings of Conference on: Economics of Higher Education: A Comparative Perspective of Policy and Dilemma (New York, New York, March 30, 1978).

ERIC Educational Resources Information Center

Wasser, Henry, Ed.

Proceedings from a conference on the economics of higher education are presented. Following an introduction by Henry Wasser and opening remarks by Mina Rees, a paper by Gareth Williams is presented. In "The Buffer Under Pressure: An Examination of the British System of Financing Higher Education in Periods of Affluence and Stringency,"…

Stomatal kinetics and photosynthetic gas exchange along a continuum of isohydric to anisohydric regulation of plant water status

Treesearch

Frederick C. Meinzer; Duncan D. Smith; David R. Woodruff; Danielle E. Marias; Katherine A. McCulloh; Ava R. Howard; Alicia L. Magedman

2017-01-01

Species’ differences in the stringency of stomatal control of plant water potential represent a continuum of isohydric to anisohydric behaviours. However, little is known about how quasi-steady-state stomatal regulation of water potential may relate to dynamic behaviour of stomata and photosynthetic gas exchange in species operating at different positions along this...

Did States Use Implementation Discretion to Reduce the Stringency of NCLB? Evidence from a Database of State Regulations

ERIC Educational Resources Information Center

Wong, Vivian C.; Wing, Coady; Martin, David; Krishnamachari, Anandita

2018-01-01

When No Child Left Behind (NCLB) became law in 2002, it was viewed as an effort to create uniform standards for students and schools across the country. More than a decade later, we know surprisingly little about how states actually implemented NCLB and the extent to which state implementation decisions managed to undo the centralizing objectives…

Accumulation of Polyphosphate in Lactobacillus spp. and Its Involvement in Stress Resistance

PubMed Central

Alcántara, Cristina; Blasco, Amalia; Zúñiga, Manuel

2014-01-01

Polyphosphate (poly-P) is a polymer of phosphate residues synthesized and in some cases accumulated by microorganisms, where it plays crucial physiological roles such as the participation in the response to nutritional stringencies and environmental stresses. Poly-P metabolism has received little attention in Lactobacillus, a genus of lactic acid bacteria of relevance for food production and health of humans and animals. We show that among 34 strains of Lactobacillus, 18 of them accumulated intracellular poly-P granules, as revealed by specific staining and electron microscopy. Poly-P accumulation was generally dependent on the presence of elevated phosphate concentrations in the culture medium, and it correlated with the presence of polyphosphate kinase (ppk) genes in the genomes. The ppk gene from Lactobacillus displayed a genetic arrangement in which it was flanked by two genes encoding exopolyphosphatases of the Ppx-GppA family. The ppk functionality was corroborated by its disruption (LCABL_27820 gene) in Lactobacillus casei BL23 strain. The constructed ppk mutant showed a lack of intracellular poly-P granules and a drastic reduction in poly-P synthesis. Resistance to several stresses was tested in the ppk-disrupted strain, showing that it presented a diminished growth under high-salt or low-pH conditions and an increased sensitivity to oxidative stress. These results show that poly-P accumulation is a characteristic of some strains of lactobacilli and may thus play important roles in the physiology of these microorganisms. PMID:24375133

Evasion of affinity-based selection in germinal centers by Epstein-Barr virus LMP2A.

PubMed

Minamitani, Takeharu; Yasui, Teruhito; Ma, Yijie; Zhou, Hufeng; Okuzaki, Daisuke; Tsai, Chiau-Yuang; Sakakibara, Shuhei; Gewurz, Benjamin E; Kieff, Elliott; Kikutani, Hitoshi

2015-09-15

Epstein-Barr virus (EBV) infects germinal center (GC) B cells and establishes persistent infection in memory B cells. EBV-infected B cells can cause B-cell malignancies in humans with T- or natural killer-cell deficiency. We now find that EBV-encoded latent membrane protein 2A (LMP2A) mimics B-cell antigen receptor (BCR) signaling in murine GC B cells, causing altered humoral immune responses and autoimmune diseases. Investigation of the impact of LMP2A on B-cell differentiation in mice that conditionally express LMP2A in GC B cells or all B-lineage cells found LMP2A expression enhanced not only BCR signals but also plasma cell differentiation in vitro and in vivo. Conditional LMP2A expression in GC B cells resulted in preferential selection of low-affinity antibody-producing B cells despite apparently normal GC formation. GC B-cell-specific LMP2A expression led to systemic lupus erythematosus-like autoimmune phenotypes in an age-dependent manner. Epigenetic profiling of LMP2A B cells found increased H3K27ac and H3K4me1 signals at the zinc finger and bric-a-brac, tramtrack domain-containing protein 20 locus. We conclude that LMP2A reduces the stringency of GC B-cell selection and may contribute to persistent EBV infection and pathogenesis by providing GC B cells with excessive prosurvival effects.

Long-Term Impact of Valid Case Criterion on Capturing Population-Level Growth under Item Response Theory Equating. Research Report. ETS RR-17-17

ERIC Educational Resources Information Center

Deng, Weiling; Monfils, Lora

2017-01-01

Using simulated data, this study examined the impact of different levels of stringency of the valid case inclusion criterion on item response theory (IRT)-based true score equating over 5 years in the context of K-12 assessment when growth in student achievement is expected. Findings indicate that the use of the most stringent inclusion criterion…

A Comparative Study of the Employee Skills/Training Acceptable to Employers Under Varying Degrees of Labor Market Stringencies. Final Report.

ERIC Educational Resources Information Center

Fisher, W. Halder; And Others

The purposes of this stud y were to test the dependability of stated employee selection criteria, to ascertain the degree of congruence between stated and actual selection criteria, and to determine the degree of change in criteria due to "looseness" or "tightness" of the local labor market. Seven test labor market areas representing a variety of…

CombiROC: an interactive web tool for selecting accurate marker combinations of omics data.

PubMed

Mazzara, Saveria; Rossi, Riccardo L; Grifantini, Renata; Donizetti, Simone; Abrignani, Sergio; Bombaci, Mauro

2017-03-30

Diagnostic accuracy can be improved considerably by combining multiple markers, whose performance in identifying diseased subjects is usually assessed via receiver operating characteristic (ROC) curves. The selection of multimarker signatures is a complicated process that requires integration of data signatures with sophisticated statistical methods. We developed a user-friendly tool, called CombiROC, to help researchers accurately determine optimal markers combinations from diverse omics methods. With CombiROC data from different domains, such as proteomics and transcriptomics, can be analyzed using sensitivity/specificity filters: the number of candidate marker panels rising from combinatorial analysis is easily optimized bypassing limitations imposed by the nature of different experimental approaches. Leaving to the user full control on initial selection stringency, CombiROC computes sensitivity and specificity for all markers combinations, performances of best combinations and ROC curves for automatic comparisons, all visualized in a graphic interface. CombiROC was designed without hard-coded thresholds, allowing a custom fit to each specific data: this dramatically reduces the computational burden and lowers the false negative rates given by fixed thresholds. The application was validated with published data, confirming the marker combination already originally described or even finding new ones. CombiROC is a novel tool for the scientific community freely available at http://CombiROC.eu.

Isoform specificity of progesterone receptor antibodies

PubMed Central

Fabris, Victoria; Abascal, María F; Giulianelli, Sebastián; May, María; Sequeira, Gonzalo R; Jacobsen, Britta; Lombès, Marc; Han, Julie; Tran, Luan; Molinolo, Alfredo

2017-01-01

Abstract Progesterone receptors (PR) are prognostic and predictive biomarkers in hormone‐dependent cancers. Two main PR isoforms have been described, PRB and PRA, that differ only in that PRB has 164 extra N‐terminal amino acids. It has been reported that several antibodies empirically exclusively recognize PRA in formalin‐fixed paraffin‐embedded (FFPE) tissues. To confirm these findings, we used human breast cancer xenograft models, T47D‐YA and ‐YB cells expressing PRA or PRB, respectively, MDA‐MB‐231 cells modified to synthesize PRB, and MDA‐MB‐231/iPRAB cells which can bi‐inducibly express either PRA or PRB. Cells were injected into immunocompromised mice to generate tumours exclusively expressing PRA or PRB. PR isoform expression was verified using immunoblots. FFPE samples from the same tumours were studied by immunohistochemistry using H‐190, clone 636, clone 16, and Ab‐6 anti‐PR antibodies, the latter exclusively recognizing PRB. Except for Ab‐6, all antibodies displayed a similar staining pattern. Our results indicate that clones 16, 636, and the H‐190 antibody recognize both PR isoforms. They point to the need for more stringency in evaluating the true specificity of purported PRA‐specific antibodies as the PRA/PRB ratio may have prognostic and predictive value in breast cancer. PMID:29085663

Baseline characteristics of different strata of astronaut corps

NASA Technical Reports Server (NTRS)

Hamm, Peggy B.; Pepper, L. J.

1993-01-01

The Longitudinal Study of Astronaut Health (LSAH) is an epidemiological study designed to study the effects of the occupational exposures incurred by astronauts in health outcomes and changes in physiological variables. Between 1959 and 1991, 195 individuals were selected for the program. The medical standards for selection have remained essentially unchanged since the Mercury Program, but the range and stringency of these criteria have been modified. Demographic and physiological variables identified during the selection year are examined for various strata of the Astronaut Corps. Specifically, age, sex, race, education, usual occupation, military affiliation, medical history, family medical history, visual and hearing measurements, physical exam variables, and specific laboratory values are investigated. Differences are examined in astronauts for the following criteria: (1) were selected prior to 1970 (n = 73) versus those selected after 1970 (n = 122); (2) have flown multiple missions versus those who have flown less than two missions; (3) have walked in space versus all others; (4) have more than 500 hours of mission time versus all others; and (5) have gone to the Moon versus all others. Length of time served in the Astronaut Corps is examined for each of these strata.

A Review of ETS Differential Item Functioning Assessment Procedures: Flagging Rules, Minimum Sample Size Requirements, and Criterion Refinement. Research Report. ETS RR-12-08

ERIC Educational Resources Information Center

Zwick, Rebecca

2012-01-01

Differential item functioning (DIF) analysis is a key component in the evaluation of the fairness and validity of educational tests. The goal of this project was to review the status of ETS DIF analysis procedures, focusing on three aspects: (a) the nature and stringency of the statistical rules used to flag items, (b) the minimum sample size…

Correlation between Mitochondrial Reactive Oxygen and Severity of Atherosclerosis.

PubMed

Dorighello, Gabriel G; Paim, Bruno A; Kiihl, Samara F; Ferreira, Mônica S; Catharino, Rodrigo R; Vercesi, Anibal E; Oliveira, Helena C F

2016-01-01

Atherosclerosis has been associated with mitochondria dysfunction and damage. Our group demonstrated previously that hypercholesterolemic mice present increased mitochondrial reactive oxygen (mtROS) generation in several tissues and low NADPH/NADP+ ratio. Here, we investigated whether spontaneous atherosclerosis in these mice could be modulated by treatments that replenish or spare mitochondrial NADPH, named citrate supplementation, cholesterol synthesis inhibition, or both treatments simultaneously. Robust statistical analyses in pooled group data were performed in order to explain the variation of atherosclerosis lesion areas as related to the classic atherosclerosis risk factors such as plasma lipids, obesity, and oxidative stress, including liver mtROS. Using three distinct statistical tools (univariate correlation, adjusted correlation, and multiple regression) with increasing levels of stringency, we identified a novel significant association and a model that reliably predicts the extent of atherosclerosis due to variations in mtROS. Thus, results show that atherosclerosis lesion area is positively and independently correlated with liver mtROS production rates. Based on these findings, we propose that modulation of mitochondrial redox state influences the atherosclerosis extent.

Occurrence of H2-Uptake Hydrogenases in Bradyrhizobium sp. (Lupinus) and Their Expression in Nodules of Lupinus spp. and Ornithopus compressus1

PubMed Central

Murillo, Jesús; Villa, Ana; Chamber, Manuel; Ruiz-Argüeso, Tomás

1989-01-01

Fifty-four strains of Bradyrhizobium sp. (Lupinus) from worldwide collections were screened by a colony hybridization method for the presence of DNA sequences homologous to the structural genes of the Bradyrhizobium japonicum hydrogenase. Twelve strains exhibited strong colony hybridization signals, and subsequent Southern blot hybridization experiments showed that they fell into two different groups on the basis of the pattern of EcoRI fragments containing the homology to the hup probe. All strains in the first group (UPM860, UPM861, and 750) expressed uptake hydrogenase activity in symbiosis with Lupinus albus, Lupinus angustifolius, Lupinus luteus, and Ornithopus compressus, but both the rate of H2 uptake by bacteroids and the relative efficiency of N2 fixation (RE = 1 - [H2 evolved in air/acetylene reduced]) by nodules were markedly affected by the legume host. L. angustifolius was the less permissive host for hydrogenase expression in symbiosis with the three strains (average RE = 0.76), and O. compressus was the more permissive (average RE = 1.0). None of the strains in the second group expressed hydrogenase activity in lupine nodules, and only one exhibited low H2-uptake activity in symbiosis with O. compressus. The inability of these putative Hup+ strains to induce hydrogenase activity in lupine nodules is discussed on the basis of the legume host effect. Among the 42 strains showing no homology to the B. japonicum hup-specific probe in the colony hybridization assay, 10 were examined in symbiosis with L. angustifolius. The average RE for these strains was 0.51. However, one strain, IM43B, exhibited high RE values (higher than 0.80) and high levels of hydrogenase activity in symbiosis with L. angustifolius, L. albus, and L. luteus. In Southern blot hybridization experiments, no homology was detected between the B. japonicum hup-specific DNA probe and total DNA from vegetative cells or bacteroids from strain IM43B even under low stringency hybridization conditions. We conclude from these results that strain IM43B contains hup DNA sequences different from those in B. japonicum and in other lupine rhizobia strains. Images Figure 1 Figure 2 PMID:16666550

Stringency of the 2-His–1-Asp Active-Site Motif in Prolyl 4-Hydroxylase

PubMed Central

Gorres, Kelly L.; Pua, Khian Hong; Raines, Ronald T.

2009-01-01

The non-heme iron(II) dioxygenase family of enzymes contain a common 2-His–1-carboxylate iron-binding motif. These enzymes catalyze a wide variety of oxidative reactions, such as the hydroxylation of aliphatic C–H bonds. Prolyl 4-hydroxylase (P4H) is an α-ketoglutarate-dependent iron(II) dioxygenase that catalyzes the post-translational hydroxylation of proline residues in protocollagen strands, stabilizing the ensuing triple helix. Human P4H residues His412, Asp414, and His483 have been identified as an iron-coordinating 2-His–1-carboxylate motif. Enzymes that catalyze oxidative halogenation do so by a mechanism similar to that of P4H. These halogenases retain the active-site histidine residues, but the carboxylate ligand is replaced with a halide ion. We replaced Asp414 of P4H with alanine (to mimic the active site of a halogenase) and with glycine. These substitutions do not, however, convert P4H into a halogenase. Moreover, the hydroxylase activity of D414A P4H cannot be rescued with small molecules. In addition, rearranging the two His and one Asp residues in the active site eliminates hydroxylase activity. Our results demonstrate a high stringency for the iron-binding residues in the P4H active site. We conclude that P4H, which catalyzes an especially demanding chemical transformation, is recalcitrant to change. PMID:19890397

Developing an alcohol policy assessment toolkit: application in the western Pacific.

PubMed

Carragher, Natacha; Byrnes, Joshua; Doran, Christopher M; Shakeshaft, Anthony

2014-10-01

To demonstrate the development and feasibility of a tool to assess the adequacy of national policies aimed at reducing alcohol consumption and related problems. We developed a quantitative tool - the Toolkit for Evaluating Alcohol policy Stringency and Enforcement (TEASE-16) - to assess the level of stringency and enforcement of 16 alcohol control policies. TEASE-16 was applied to policy data from nine study areas in the western Pacific: Australia, China excluding Hong Kong Special Administrative Region (SAR), Hong Kong SAR, Japan, Malaysia, New Zealand, the Philippines, Singapore and Viet Nam. Correlation and regression analyses were then used to examine the relationship between alcohol policy scores and income-adjusted levels of alcohol consumption per capita. Vast differences exist in how alcohol control policies are implemented in the western Pacific. Out of a possible 100 points, the nine study areas achieved TEASE-16 scores that ranged from 24.1 points for the Philippines to 67.5 points for Australia. Study areas with high policy scores - indicating relatively strong alcohol policy frameworks - had lower alcohol consumption per capita. Sensitivity analyses indicated scores and rankings for each study area remained relatively stable across different weighting schemes, indicating that TEASE-16 was robust. TEASE-16 could be used by international and national regulatory bodies and policy-makers to guide the design, implementation, evaluation and refinement of effective policies to reduce alcohol consumption and related problems.

miR-MaGiC improves quantification accuracy for small RNA-seq.

PubMed

Russell, Pamela H; Vestal, Brian; Shi, Wen; Rudra, Pratyaydipta D; Dowell, Robin; Radcliffe, Richard; Saba, Laura; Kechris, Katerina

2018-05-15

Many tools have been developed to profile microRNA (miRNA) expression from small RNA-seq data. These tools must contend with several issues: the small size of miRNAs, the small number of unique miRNAs, the fact that similar miRNAs can be transcribed from multiple loci, and the presence of miRNA isoforms known as isomiRs. Methods failing to address these issues can return misleading information. We propose a novel quantification method designed to address these concerns. We present miR-MaGiC, a novel miRNA quantification method, implemented as a cross-platform tool in Java. miR-MaGiC performs stringent mapping to a core region of each miRNA and defines a meaningful set of target miRNA sequences by collapsing the miRNA space to "functional groups". We hypothesize that these two features, mapping stringency and collapsing, provide more optimal quantification to a more meaningful unit (i.e., miRNA family). We test miR-MaGiC and several published methods on 210 small RNA-seq libraries, evaluating each method's ability to accurately reflect global miRNA expression profiles. We define accuracy as total counts close to the total number of input reads originating from miRNAs. We find that miR-MaGiC, which incorporates both stringency and collapsing, provides the most accurate counts.

Low-temperature specific heat of single-crystal Bi2CaSr2Cu2O8 and Tl2Ca2Ba2Cu3O10

NASA Astrophysics Data System (ADS)

Urbach, J. S.; Mitzi, D. B.; Kapitulnik, A.; Wei, J. Y. T.; Morris, D. E.

1989-06-01

We report specific-heat measurements from 2 to 15 K on single crystals of Bi2CaSr2Cu2O8 and Tl2Ca2Ba2Cu3O10 We find low-temperature deviations from the Debye law that can be attributed to spin-glass behavior of a small concentration of isolated impurity copper moments. At higher temperatures, we observe contributions to the specific heat that can be attributed to a soft-phonon mode, possibly associated with the superstructure in the Bi-O and Tl-O layers. From our single-crystal data, we conclude that the thallium- and bismuth-based copper oxide superconductors show no measurable linear term in the specific heat [γ(0)<=1 mJ/mole K2].

CRISPR-Cas Adaptive Immune Systems of the Sulfolobales: Unravelling Their Complexity and Diversity

PubMed Central

Garrett, Roger A.; Shah, Shiraz A.; Erdmann, Susanne; Liu, Guannan; Mousaei, Marzieh; León-Sobrino, Carlos; Peng, Wenfang; Gudbergsdottir, Soley; Deng, Ling; Vestergaard, Gisle; Peng, Xu; She, Qunxin

2015-01-01

The Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed. PMID:25764276

Moderate relationships between NAA and cognitive ability in healthy adults: implications for cognitive spectroscopy.

PubMed

Patel, Tulpesh; Blyth, Jacqueline C; Griffiths, Gareth; Kelly, Deirdre; Talcott, Joel B

2014-01-01

Proton Magnetic Resonance Spectroscopy ((1)H-MRS) is a non-invasive imaging technique that enables quantification of neurochemistry in vivo and thereby facilitates investigation of the biochemical underpinnings of human cognitive variability. Studies in the field of cognitive spectroscopy have commonly focused on relationships between measures of N-acetyl aspartate (NAA), a surrogate marker of neuronal health and function, and broad measures of cognitive performance, such as IQ. In this study, we used (1)H-MRS to interrogate single-voxels in occipitoparietal and frontal cortex, in parallel with assessments of psychometric intelligence, in a sample of 40 healthy adult participants. We found correlations between NAA and IQ that were within the range reported in previous studies. However, the magnitude of these effects was significantly modulated by the stringency of data screening and the extent to which outlying values contributed to statistical analyses. (1)H-MRS offers a sensitive tool for assessing neurochemistry non-invasively, yet the relationships between brain metabolites and broad aspects of human behavior such as IQ are subtle. We highlight the need to develop an increasingly rigorous analytical and interpretive framework for collecting and reporting data obtained from cognitive spectroscopy studies of this kind.

How children with special health care needs affect the employment decisions of low-income parents.

PubMed

Loprest, Pamela; Davidoff, Amy

2004-09-01

To better understand the impact of having a child with special health care needs (CSHCN), on low-income parents' employment decisions. Using data from the 1999 and 2000 National Health Interview Survey (NHIS), we estimate multivariate statistical regressions (logit and tobit models) to estimate the relationship between having a CSHCN and the likelihood of employment and hours of employment for a sample-of low-income single parents. Controlling for differences in demographic and family characteristics, we find no significant association between having a CSHCN and the probability of work or the number of hours worked among low-income single-parent families. Separate analysis of different dimensions of special health care needs shows that parents of children with activity limitations are significantly less likely to work and work fewer hours. This result does not hold true for the group of children defined based on elevated or special service use, or for the group of children with specific chronic conditions. These results indicate that only a specific subset of children with special needs present difficulties for low-income parents' work. This suggests that policies to help low-income single parents of children with disabilities move into work should target this specific subset of children with special health care needs.

Infection control practices and zoonotic disease risks among veterinarians in the United States.

PubMed

Wright, Jennifer G; Jung, Sherry; Holman, Robert C; Marano, Nina N; McQuiston, Jennifer H

2008-06-15

OBJECTIVE-To assess the knowledge and use of infection control practices (ICPs) among US veterinarians. DESIGN-Anonymous mail-out population survey. PROCEDURES-In 2005 a questionnaire was mailed to US small animal, large animal, and equine veterinarians who were randomly selected from the AVMA membership to assess precaution awareness (PA) and veterinarians' perceptions of zoonotic disease risks. Respondents were assigned a PA score (0 to 4) on the basis of their responses (higher scores representing higher stringency of ICPs); within a practice type, respondents' scores were categorized as being within the upper 25% or lower 75% of scores (high and low PA ranking, respectively). Characteristics associated with low PA rankings were assessed. RESULTS-Generally, respondents did not engage in protective behaviors or use personal protective equipment considered appropriate to protect against zoonotic disease transmission. Small animal and equine veterinarians employed in practices that had no written infection control policy were significantly more likely to have low PA ranking. Male gender was associated with low PA ranking among small animal and large animal veterinarians; equine practitioners not working in a teaching or referral hospital were more likely to have low PA ranking than equine practitioners working in such institutions. CONCLUSIONS AND CLINICAL RELEVANCE-Results indicated that most US veterinarians are not aware of appropriate personal protective equipment use and do not engage in practices that may help reduce zoonotic disease transmission. Gender differences may influence personal choices for ICPs. Provision of information and training on ICPs and establishment of written infection control policies could be effective means of improving ICPs in veterinary practices.

Gene Trapping Using Gal4 in Zebrafish

PubMed Central

Balciuniene, Jorune; Balciunas, Darius

2013-01-01

Large clutch size and external development of optically transparent embryos make zebrafish an exceptional vertebrate model system for in vivo insertional mutagenesis using fluorescent reporters to tag expression of mutated genes. Several laboratories have constructed and tested enhancer- and gene-trap vectors in zebrafish, using fluorescent proteins, Gal4- and lexA- based transcriptional activators as reporters 1-7. These vectors had two potential drawbacks: suboptimal stringency (e.g. lack of ability to differentiate between enhancer- and gene-trap events) and low mutagenicity (e.g. integrations into genes rarely produced null alleles). Gene Breaking Transposon (GBTs) were developed to address these drawbacks 8-10. We have modified one of the first GBT vectors, GBT-R15, for use with Gal4-VP16 as the primary gene trap reporter and added UAS:eGFP as the secondary reporter for direct detection of gene trap events. Application of Gal4-VP16 as the primary gene trap reporter provides two main advantages. First, it increases sensitivity for genes expressed at low expression levels. Second, it enables researchers to use gene trap lines as Gal4 drivers to direct expression of other transgenes in very specific tissues. This is especially pertinent for genes with non-essential or redundant functions, where gene trap integration may not result in overt phenotypes. The disadvantage of using Gal4-VP16 as the primary gene trap reporter is that genes coding for proteins with N-terminal signal sequences are not amenable to trapping, as the resulting Gal4-VP16 fusion proteins are unlikely to be able to enter the nucleus and activate transcription. Importantly, the use of Gal4-VP16 does not pre-select for nuclear proteins: we recovered gene trap mutations in genes encoding proteins which function in the nucleus, the cytoplasm and the plasma membrane. PMID:24121167

Development and Validation of Sandwich ELISA Microarrays with Minimal Assay Interference

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

Gonzalez, Rachel M.; Servoss, Shannon; Crowley, Sheila A.

Sandwich enzyme-linked immunosorbent assay (ELISA) microarrays are emerging as a strong candidate platform for multiplex biomarker analysis because of the ELISA’s ability to quantitatively measure rare proteins in complex biological fluids. Advantages of this platform are high-throughput potential, assay sensitivity and stringency, and the similarity to the standard ELISA test, which facilitates assay transfer from a research setting to a clinical laboratory. However, a major concern with the multiplexing of ELISAs is maintaining high assay specificity. In this study, we systematically determine the amount of assay interference and noise contributed by individual components of the multiplexed 24-assay system. We findmore » that non-specific reagent cross-reactivity problems are relatively rare. We did identify the presence of contaminant antigens in a “purified antigen”. We tested the validated ELISA microarray chip using paired serum samples that had been collected from four women at a 6-month interval. This analysis demonstrated that protein levels typically vary much more between individuals then within an individual over time, a result which suggests that longitudinal studies may be useful in controlling for biomarker variability across a population. Overall, this research demonstrates the importance of a stringent screening protocol and the value of optimizing the antibody and antigen concentrations when designing chips for ELISA microarrays.« less

Capital investment requirements for greenhouse gas emissions mitigation in power generation on near term to century time scales and global to regional spatial scales

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

Chaturvedi, Vaibhav; Clarke, Leon E.; Edmonds, James A.

Electrification plays a crucial role in cost-effective greenhouse gas emissions mitigation strategies. Such strategies in turn carry implications for financial capital markets. This paper explores the implication of climate mitigation policy for capital investment demands by the electric power sector on decade to century time scales. We go further to explore the implications of technology performance and the stringency of climate policy for capital investment demands by the power sector. Finally, we discuss the regional distribution of investment demands. We find that stabilizing GHG emissions will require additional investment in the electricity generation sector over and above investments that wouldmore » be need in the absence of climate policy, in the range of 16 to 29 Trillion US$ (60-110%) depending on the stringency of climate policy during the period 2015 to 2095 under default technology assumptions. This increase reflects the higher capital intensity of power systems that control emissions. Limits on the penetration of nuclear and carbon capture and storage technology could increase costs substantially. Energy efficiency improvements can reduce the investment requirement by 8 to21 Trillion US$ (default technology assumptions), depending on climate policy scenario with higher savings being obtained under the most stringent climate policy. The heaviest investments in power generation were observed in the China, India, SE Asia and Africa regions with the latter three regions dominating in the second half of the 21st century.« less

Lack of production of (p)ppGpp in Halobacterium volcanii under conditions that are effective in the eubacteria.

PubMed Central

Scoarughi, G L; Cimmino, C; Donini, P

1995-01-01

The stringent halobacterial strain Haloferax volcanii was subjected to a set of physiological conditions different from amino acid starvation that are known to cause production of guanosine polyphosphates [(p)pp Gpp] in eubacteria via the relA-independent (spoT) pathway. The conditions used were temperature upshift, treatment with cyanide, and total starvation. Under none of these conditions were detectable levels of (p)ppGpp observed. This result, in conjunction with our previous finding that (p)ppGpp synthesis does not occur under amino acid starvation, leads to the conclusion that in halobacteria both growth rate control and stringency are probably governed by mechanisms that operate in the absence of ppGpp. During exponential growth, a low level of phosphorylated compounds with electrophoretic mobilities similar, but not identical, to that of (p)ppGpp were observed. The intracellular concentration of these compounds increased considerably during the stationary phase of growth and with all of the treatments used. The compounds were identified as short-chain polyphosphates identical to those found under similar conditions in Saccharomyces cerevisiae. PMID:7798153

The effect of environmental regulation on firms' competitive performance: the case of the building & construction sector in some EU regions.

PubMed

Testa, Francesco; Iraldo, Fabio; Frey, Marco

2011-09-01

There is a considerable debate on the effects of environmental regulation on competitive performance. Based on survey data, this paper analyzes the two main research questions, derived from literature, on the links between environmental regulation and competitiveness, by focusing on firms operating in the building and construction sector, i.e.: 1) whether environmental policy stringency affects the competitive performance of firms in the building and construction sector 2) and how a specific form of environmental regulation (direct regulation, economic instruments and soft instruments) affects this performance? By applying a regression analysis, we find that a more stringent environmental regulation, measured by inspection frequency, provides a positive impulse for increasing investments in advanced technological equipment and innovative products and on business performance. Moreover, a well-designed "direct regulation" appears to be the most effective policy instrument for prompting the positive impact of environmental policies on innovation and intangible performance while economic instruments do negatively affect business performance. Copyright © 2011 Elsevier Ltd. All rights reserved.

Studying the Interface between Nanomaterials and Biomolecules

NASA Astrophysics Data System (ADS)

Torelli, Marco Diego

As engineered nanomaterials become ubiquitous among society, their inevitable entrance into the environment invites questions as to potential implications. As the field of nanotechnology progresses, responsible development of nanomaterials requires a broad availability of useful tools. To this aim, this work seeks to improve analytical abilities to address fundamental molecular interactions of nanomaterials with biological systems that can be expanded broadly, divided into the following: (1) A model applicable to X-ray photoelectron spectroscopy was developed and validated to correct the over-estimated signal for core:shell nanomaterials that can occur at small particle sizes approaching the electron attenuation length of the material being investigated. (2) To understand the role of underlying substrate in particle interactions, diamond and gold functionalized with a protein resisting molecule (hexaethylene glycol) were compared to test the ability of each to resist adsorption of charged proteins. It was demonstrated that the underlying substrate can have an effect on the ability of to properly resist proteins, with charged proteins adsorbing to gold, believed to be due to the ability of gold to form an image dipole. (3) To advance the use of nanodiamond in biological settings, methods to create robust chemical linkages at single digit sizes were developed. Alkene based oligo(ethylene glycol) molecules were successfully photochemically grafted to fully disaggregated detonation nanodiamond. Because the scalability of such methods currently limits such functionalization broadly, polyelectrolytic wrapping of nanodiamond was developed as a useful and scalable method to produce diamond nanoparticles with varying amine based functionalities. (4) Phage display was adapted as a method to determine chemical functionalities that interact with anatase titanium dioxide below 20 nm. In contrast to finding specific, individual inorganic binding sequences, we lowered the selection stringency to allow for a broader number of peptides to be samples. While no statistical size dependent differences were observed in the amino acid chemistries that interact with anatase TiO2, chemical functionalities and motifs that appear to be important for interaction with nano-anatase were identified. Specifically, positively charged and aromatic motifs working in concert were found to be important.

A model of binding on DNA microarrays: understanding the combined effect of probe synthesis failure, cross-hybridization, DNA fragmentation and other experimental details of affymetrix arrays

PubMed Central

2012-01-01

Background DNA microarrays are used both for research and for diagnostics. In research, Affymetrix arrays are commonly used for genome wide association studies, resequencing, and for gene expression analysis. These arrays provide large amounts of data. This data is analyzed using statistical methods that quite often discard a large portion of the information. Most of the information that is lost comes from probes that systematically fail across chips and from batch effects. The aim of this study was to develop a comprehensive model for hybridization that predicts probe intensities for Affymetrix arrays and that could provide a basis for improved microarray analysis and probe development. The first part of the model calculates probe binding affinities to all the possible targets in the hybridization solution using the Langmuir isotherm. In the second part of the model we integrate details that are specific to each experiment and contribute to the differences between hybridization in solution and on the microarray. These details include fragmentation, wash stringency, temperature, salt concentration, and scanner settings. Furthermore, the model fits probe synthesis efficiency and target concentration parameters directly to the data. All the parameters used in the model have a well-established physical origin. Results For the 302 chips that were analyzed the mean correlation between expected and observed probe intensities was 0.701 with a range of 0.88 to 0.55. All available chips were included in the analysis regardless of the data quality. Our results show that batch effects arise from differences in probe synthesis, scanner settings, wash strength, and target fragmentation. We also show that probe synthesis efficiencies for different nucleotides are not uniform. Conclusions To date this is the most complete model for binding on microarrays. This is the first model that includes both probe synthesis efficiency and hybridization kinetics/cross-hybridization. These two factors are sequence dependent and have a large impact on probe intensity. The results presented here provide novel insight into the effect of probe synthesis errors on Affymetrix microarrays; furthermore, the algorithms developed in this work provide useful tools for the analysis of cross-hybridization, probe synthesis efficiency, fragmentation, wash stringency, temperature, and salt concentration on microarray intensities. PMID:23270536

A Two-Stream Plasma Electron Microwave Source for High-Power Millimeter Wave Generation. Phase 1

DTIC Science & Technology

1989-03-29

MIT Press, Cambridge, MA, 1963). these findings that strong amplification is possible for repre- ’See, for example, G. E. Guest and D. J. Sigmar , Nucl...stringency of the stability criteria for electrostatic and whistler modes, as fl(z=O, 6, t=O) = -i/2u,(e/m) discussed by Guest and Sigmar [22], and...therein. Function. Academic Press, New York (1961). 1221 GUEST, G.E., SIGMAR , D.J., Nuci. Fusion It1(1971) [271 ABRAMOWITZ, M., STEGUN. I.A. (Eds

Molecular detection of native and invasive marine invertebrate larvae present in ballast and open water environmental samples collected in Puget Sound

USGS Publications Warehouse

Harvey, J.B.J.; Hoy, M.S.; Rodriguez, R.J.

2009-01-01

Non-native marine species have been and continue to be introduced into Puget Sound via several vectors including ship's ballast water. Some non-native species become invasive and negatively impact native species or near shore habitats. We present a new methodology for the development and testing of taxon specific PCR primers designed to assess environmental samples of ocean water for the presence of native and non-native bivalves, crustaceans and algae. The intergenic spacer regions (IGS; ITS1, ITS2 and 5.8S) of the ribosomal DNA were sequenced for adult samples of each taxon studied. We used these data along with those available in Genbank to design taxon and group specific primers and tested their stringency against artificial populations of plasmid constructs containing the entire IGS region for each of the 25 taxa in our study, respectively. Taxon and group specific primer sets were then used to detect the presence or absence of native and non-native planktonic life-history stages (propagules) from environmental samples of ballast water and plankton tow net samples collected in Puget Sound. This methodology provides an inexpensive and efficient way to test the discriminatory ability of taxon specific oligonucleotides (PCR primers) before creating molecular probes or beacons for use in molecular ecological applications such as probe hybridizations or microarray analyses. This work addresses the current need to develop molecular tools capable of diagnosing the presence of planktonic life-history stages from non-native marine species (potential invaders) in ballast water and other environmental samples. ?? 2008 Elsevier B.V.

DNA sequence divergence among derivatives of Escherichia coli K-12 detected by arbitrary primer PCR (random amplified polymorphic DNA) fingerprinting.

PubMed Central

Brikun, I; Suziedelis, K; Berg, D E

1994-01-01

Derivatives of Escherichia coli K-12 of known ancestry were characterized by random amplified polymorphic DNA (RAPD) fingerprinting to better understand genome evolution in this family of closely related strains. This sensitive method entails PCR amplification with arbitrary primers at low stringency and yields arrays of anonymous DNA fragments that are strain specific. Among 150 fragments scored, eight were polymorphic in that they were produced from some but not all strains. Seven polymorphic bands were chromosomal, and one was from the F-factor plasmid. Five of the six mapped polymorphic chromosomal bands came from just 7% of the genome, a 340-kb segment that includes the terminus of replication. Two of these were from the cryptic Rac prophage, and the inability to amplify them from strains was attributable to deletion (excision) or to rearrangement of Rac. Two other terminus-region segments that resulted in polymorphic bands appeared to have sustained point mutations that affected the ability to amplify them. Control experiments showed that RAPD bands from the 340-kb terminus-region segment and also from two plasmids (P1 and F) were represented in approximate proportion to their size. Optimization experiments showed that the concentration of thermostable polymerase strongly affected the arrays of RAPD products obtained. Comparison of RAPD polymorphisms and positions of strains exhibiting them in the pedigree suggests that many sequence changes occurred in these historic E. coli strains during their storage. We propose that the clustering of such mutations near the terminus reflects errors during completion of chromosome replication, possibly during slow growth in the stab cultures that were often used to store E. coli strains in the early years of bacterial genetics. Images PMID:8132463

Human ESP1/CRP2, a member of the LIM domain protein family: Characterization of the cDNA and assignment of the gene locus to chromosome 14q32.3

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

Karim, Mohammad Azharul; Ohta, Kohji; Matsuda, Ichiro

1996-01-15

The LIM domain is present in a wide variety of proteins with diverse functions and exhibits characteristic arrangements of Cys and His residues with a novel zinc-binding motif. LIM domain proteins have been implicated in development, cell regulation, and cell structure. A LIM domain protein was identified by screening a human cDNA library with rat cysteine-rich intestinal protein (CRIP) as a probe, under conditions of low stringency. Comparison of the predicted amino acid sequence with several LIM domain proteins revealed 93% of the residues to be identical to rat LIM domain protein, termed ESP1 or CRP2. Thus, the protein ismore » hereafter referred to as human ESP1/CRP2. The cDNA encompasses a 1171-base region, including 26, 624, and 521 bases in the 5{prime}-noncoding region, coding region, and 3{prime}-noncoding regions, respectively, and encodes the entire ESP1/CRP2 protein has two LIM domains, and each shares 35.1% and 77 or 79% identical residues with human cysteine-rich protein (CRP) and rat CRIP, respectively. Northern blot analysis of ESP1/CRP2 in various human tissues showed distinct tissue distributions compared with CRP and CRIP, suggesting that each might serve related but specific roles in tissue organization or function. Using a panel of human-rodent somatic cell hybrids, the ESP1/CRP2 locus was assigned to chromosome 14. Fluorescence in situ hybridization, using cDNA and a genome DNA fragment of the ESP1/CRP2 as probes, confirms this assignment and relegates regional localization to band 14q32.3 47 refs., 7 figs.« less

2,4-Dichlorophenoxyacetic acid-degrading bacteria contain mosaics of catabolic genes.

PubMed Central

Fulthorpe, R R; McGowan, C; Maltseva, O V; Holben, W E; Tiedje, J M

1995-01-01

DNA from 32 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria from diverse locations was probed with the first three genes of the well-known 2,4-D degradation pathway found in Alcaligenes eutrophus JMP134(pJP4). The majority of strains did not show high levels of homology to the first three genes of the 2,4-D degradation pathway, tfdA, -B, and -C. Most strains showed combinations of tfdA-, B-, and C-like elements that exhibited various degrees of homology to the gene probes. Strains having the same genomic fingerprints (as determined by repetitive extragenic palindromic PCR) exhibited the same hybridization pattern regardless of the geographic origin of the strain, with the exception of a strain isolated from Puerto Rico. This strain had the same genomic fingerprint as that of numerous other strains in the collection but differed in its hybridization against the tfdA gene probe. Members of the beta subdivision of the Proteobacteria class, specifically Alcaligenes, Burkholderia, and Rhodoferax species, carried DNA fragments with 60% or more sequence similarity to tfdA of pJP4, and most carried fragments showing at least 60% homology to tfdB. However, many strains did not hybridize with tfdC, although they exhibited chlorocatechol dioxygenase activity. Members of the alpha subdivision of the Proteobacteria class, mostly of the genus Sphingomonas, did not hybridize to either tfdA or tfdC, but some hybridized at low stringency to tfdB. The data suggest that extensive interspecies transfer of a variety of homologous degradative genes has been involved in the evolution of 2,4-D-degrading bacteria. PMID:7574638

Assessment of single-item literacy questions, age, and education level in the prediction of low health numeracy.

PubMed

Johnson, Tim V; Abbasi, Ammara; Kleris, Renee S; Ehrlich, Samantha S; Barthwaite, Echo; DeLong, Jennifer; Master, Viraj A

2013-08-01

Determining a patient's health literacy is important to optimum patient care. Single-item questions exist for screening written health literacy. We sought to assess the predictive potential of three common screening questions, along with patient age and education level, in the prediction of low health numerical literacy (numeracy). After demographic and educational information was obtained, 441 patients were administered three health literacy screening questions. The three-item Schwartz-Woloshin Numeracy Scale was then administered to assess for low health numeracy (score of 0 out of 3). This score served as the reference standard for Receiver Operating Characteristics (ROC) curve analysis. ROC curves were constructed and used to determine the area under the curve (AUC); a higher AUC suggests increased statistical significance. None of the three screening questions were significant predictors of low health numeracy. However, education level was a significant predictor of low health numeracy, with an AUC (95% CI) of 0.811 (0.720-0.902). This measure had a specificity of 95.3% at the cutoff of 12 years of education (<12 versus > or = 12 years of education) but was non-sensitive. Common single-item questions used to screen for written health literacy are ineffective screening tools for health numeracy. However, low education level is a specific predictor of low health numeracy.

Moderate relationships between NAA and cognitive ability in healthy adults: implications for cognitive spectroscopy

PubMed Central

Patel, Tulpesh; Blyth, Jacqueline C.; Griffiths, Gareth; Kelly, Deirdre; Talcott, Joel B.

2014-01-01

Background: Proton Magnetic Resonance Spectroscopy (1H-MRS) is a non-invasive imaging technique that enables quantification of neurochemistry in vivo and thereby facilitates investigation of the biochemical underpinnings of human cognitive variability. Studies in the field of cognitive spectroscopy have commonly focused on relationships between measures of N-acetyl aspartate (NAA), a surrogate marker of neuronal health and function, and broad measures of cognitive performance, such as IQ. Methodology/Principal Findings: In this study, we used 1H-MRS to interrogate single-voxels in occipitoparietal and frontal cortex, in parallel with assessments of psychometric intelligence, in a sample of 40 healthy adult participants. We found correlations between NAA and IQ that were within the range reported in previous studies. However, the magnitude of these effects was significantly modulated by the stringency of data screening and the extent to which outlying values contributed to statistical analyses. Conclusions/Significance: 1H-MRS offers a sensitive tool for assessing neurochemistry non-invasively, yet the relationships between brain metabolites and broad aspects of human behavior such as IQ are subtle. We highlight the need to develop an increasingly rigorous analytical and interpretive framework for collecting and reporting data obtained from cognitive spectroscopy studies of this kind. PMID:24592224

A Platform for Combined DNA and Protein Microarrays Based on Total Internal Reflection Fluorescence

PubMed Central

Asanov, Alexander; Zepeda, Angélica; Vaca, Luis

2012-01-01

We have developed a novel microarray technology based on total internal reflection fluorescence (TIRF) in combination with DNA and protein bioassays immobilized at the TIRF surface. Unlike conventional microarrays that exhibit reduced signal-to-background ratio, require several stages of incubation, rinsing and stringency control, and measure only end-point results, our TIRF microarray technology provides several orders of magnitude better signal-to-background ratio, performs analysis rapidly in one step, and measures the entire course of association and dissociation kinetics between target DNA and protein molecules and the bioassays. In many practical cases detection of only DNA or protein markers alone does not provide the necessary accuracy for diagnosing a disease or detecting a pathogen. Here we describe TIRF microarrays that detect DNA and protein markers simultaneously, which reduces the probabilities of false responses. Supersensitive and multiplexed TIRF DNA and protein microarray technology may provide a platform for accurate diagnosis or enhanced research studies. Our TIRF microarray system can be mounted on upright or inverted microscopes or interfaced directly with CCD cameras equipped with a single objective, facilitating the development of portable devices. As proof-of-concept we applied TIRF microarrays for detecting molecular markers from Bacillus anthracis, the pathogen responsible for anthrax. PMID:22438738

Molecular architecture of classical cytological landmarks: Centromeres and telomeres

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

Meyne, J.

1994-11-01

Both the human telomere repeat and the pericentromeric repeat sequence (GGAAT)n were isolated based on evolutionary conservation. Their isolation was based on the premise that chromosomal features as structurally and functionally important as telomeres and centromeres should be highly conserved. Both sequences were isolated by high stringency screening of a human repetitive DNA library with rodent repetitive DNA. The pHuR library (plasmid Human Repeat) used for this project was enriched for repetitive DNA by using a modification of the standard DNA library preparation method. Usually DNA for a library is cut with restriction enzymes, packaged, infected, and the library ismore » screened. A problem with this approach is that many tandem repeats don`t have any (or many) common restriction sites. Therefore, many of the repeat sequences will not be represented in the library because they are not restricted to a viable length for the vector used. To prepare the pHuR library, human DNA was mechanically sheared to a small size. These relatively short DNA fragments were denatured and then renatured to C{sub o}t 50. Theoretically only repetitive DNA sequences should renature under C{sub o}t 50 conditions. The single-stranded regions were digested using S1 nuclease, leaving the double-stranded, renatured repeat sequences.« less

Are 2 Questions Enough to Screen for Depression and Anxiety in Patients With Chronic Low Back Pain?

PubMed Central

Lie, Stein Atle; Eriksen, Hege R.

2014-01-01

Study Design. Cross-sectional study. Objective. To examine the sensitivity of 2 single-item questions compared with 2 longer questionnaires for screening depression and anxiety among patients with chronic low back pain (CLBP). Summary of Background Data. Psychosocial factors are frequently identified as risk factors for developing CLBP and as predictors for treatment, and questionnaires are often used to screen for this. Shorter instruments may be easier to use in clinical practice settings. Methods. A total of 564 patients with 2 to 10 months of at least 50% sickness absence due to nonspecific low back pain were assessed for depression and anxiety with the Mini-International Neuropsychiatric Interview (MINI). Single-item questions for depression and anxiety from the Subjective Health Complaint Inventory and 2 longer questionnaires, the Hospital Anxiety and Depression Scale and Hopkins Symptom Checklist–25, were compared with MINI results, considered the “gold standard” in this study. Sensitivity and specificity of single-item and longer questionnaires and receiver operating characteristic curves were compared. Results. According to MINI, the prevalence of anxiety disorders was 12% whereas that of depressive disorders was 4%. The screening questions showed 95% sensitivity and 56% specificity for depressive disorders and 68% sensitivity and 85% specificity for anxiety disorders. The longer questionnaire, Hospital Anxiety and Depression Scale, showed 91% sensitivity and 85% specificity for depressive disorders and 58% sensitivity and 83% specificity for anxiety disorders. Hopkins Symptom Checklist–25 showed 86% sensitivity and 74% specificity for depressive disorders and 67% sensitivity and 87% specificity for anxiety disorders. For 3 of the anxiety disorders and 2 of the depressive disorders, a perfect sensitivity was found between the screening questions and MINI. Conclusions. A single-item screening question was sensitive for depression but less sensitive for anxiety. The screening questions further performed equal to 2 widely used questionnaires. Validation of these results in other populations and compared with other short-item screeners is needed. Level of Evidence: 3 PMID:24480946

MRMaid, the web-based tool for designing multiple reaction monitoring (MRM) transitions.

PubMed

Mead, Jennifer A; Bianco, Luca; Ottone, Vanessa; Barton, Chris; Kay, Richard G; Lilley, Kathryn S; Bond, Nicholas J; Bessant, Conrad

2009-04-01

Multiple reaction monitoring (MRM) of peptides uses tandem mass spectrometry to quantify selected proteins of interest, such as those previously identified in differential studies. Using this technique, the specificity of precursor to product transitions is harnessed for quantitative analysis of multiple proteins in a single sample. The design of transitions is critical for the success of MRM experiments, but predicting signal intensity of peptides and fragmentation patterns ab initio is challenging given existing methods. The tool presented here, MRMaid (pronounced "mermaid") offers a novel alternative for rapid design of MRM transitions for the proteomics researcher. The program uses a combination of knowledge of the properties of optimal MRM transitions taken from expert practitioners and literature with MS/MS evidence derived from interrogation of a database of peptide identifications and their associated mass spectra. The tool also predicts retention time using a published model, allowing ordering of transition candidates. By exploiting available knowledge and resources to generate the most reliable transitions, this approach negates the need for theoretical prediction of fragmentation and the need to undertake prior "discovery" MS studies. MRMaid is a modular tool built around the Genome Annotating Proteomic Pipeline framework, providing a web-based solution with both descriptive and graphical visualizations of transitions. Predicted transition candidates are ranked based on a novel transition scoring system, and users may filter the results by selecting optional stringency criteria, such as omitting frequently modified residues, constraining the length of peptides, or omitting missed cleavages. Comparison with published transitions showed that MRMaid successfully predicted the peptide and product ion pairs in the majority of cases with appropriate retention time estimates. As the data content of the Genome Annotating Proteomic Pipeline repository increases, the coverage and reliability of MRMaid are set to increase further. MRMaid is freely available over the internet as an executable web-based service at www.mrmaid.info.

MRMaid, the Web-based Tool for Designing Multiple Reaction Monitoring (MRM) Transitions*

PubMed Central

Mead, Jennifer A.; Bianco, Luca; Ottone, Vanessa; Barton, Chris; Kay, Richard G.; Lilley, Kathryn S.; Bond, Nicholas J.; Bessant, Conrad

2009-01-01

Multiple reaction monitoring (MRM) of peptides uses tandem mass spectrometry to quantify selected proteins of interest, such as those previously identified in differential studies. Using this technique, the specificity of precursor to product transitions is harnessed for quantitative analysis of multiple proteins in a single sample. The design of transitions is critical for the success of MRM experiments, but predicting signal intensity of peptides and fragmentation patterns ab initio is challenging given existing methods. The tool presented here, MRMaid (pronounced “mermaid”) offers a novel alternative for rapid design of MRM transitions for the proteomics researcher. The program uses a combination of knowledge of the properties of optimal MRM transitions taken from expert practitioners and literature with MS/MS evidence derived from interrogation of a database of peptide identifications and their associated mass spectra. The tool also predicts retention time using a published model, allowing ordering of transition candidates. By exploiting available knowledge and resources to generate the most reliable transitions, this approach negates the need for theoretical prediction of fragmentation and the need to undertake prior “discovery” MS studies. MRMaid is a modular tool built around the Genome Annotating Proteomic Pipeline framework, providing a web-based solution with both descriptive and graphical visualizations of transitions. Predicted transition candidates are ranked based on a novel transition scoring system, and users may filter the results by selecting optional stringency criteria, such as omitting frequently modified residues, constraining the length of peptides, or omitting missed cleavages. Comparison with published transitions showed that MRMaid successfully predicted the peptide and product ion pairs in the majority of cases with appropriate retention time estimates. As the data content of the Genome Annotating Proteomic Pipeline repository increases, the coverage and reliability of MRMaid are set to increase further. MRMaid is freely available over the internet as an executable web-based service at www.mrmaid.info. PMID:19011259

Identifying Military and Combat-Specific Risk Factors for Child Adjustment: Comparing High and Low Risk Military Families and Civilian Families

DTIC Science & Technology

2016-08-01

Award Number: W81XWH-12-2-0034 TITLE: Identifying Military and Combat-Specific Risk Factors for Child Adjustment: Comparing High and Low Risk...2. REPORT TYPE Final 3. DATES COVERED (From - To) 15May2012 - 31Aug2016 Identifying Military and Combat-Specific Risk Factors for Child Adjustment...deployment and has a child between the age of 3 and 7 and comparison groups of civilain single parent families (N=200) and civilian dual parent

Coal fired air turbine cogeneration

NASA Astrophysics Data System (ADS)

Foster-Pegg, R. W.

Fuel options and generator configurations for installation of cogenerator equipment are reviewed, noting that the use of oil or gas may be precluded by cost or legislation within the lifetime of any cogeneration equipment yet to be installed. A coal fueled air turbine cogenerator plant is described, which uses external combustion in a limestone bed at atmospheric pressure and in which air tubes are sunk to gain heat for a gas turbine. The limestone in the 26 MW unit absorbs sulfur from the coal, and can be replaced by other sorbents depending on types of coal available and stringency of local environmental regulations. Low temperature combustion reduces NOx formation and release of alkali salts and corrosion. The air heat is exhausted through a heat recovery boiler to produce process steam, then can be refed into the combustion chamber to satisfy preheat requirements. All parts of the cogenerator are designed to withstand full combustion temperature (1500 F) in the event of air flow stoppage. Costs are compared with those of a coal fired boiler and purchased power, and it is shown that the increased capital requirements for cogenerator apparatus will yield a 2.8 year payback. Detailed flow charts, diagrams and costs schedules are included.

U.S. Air Quality and Health Benefits from Avoided Climate Change under Greenhouse Gas Mitigation.

PubMed

Garcia-Menendez, Fernando; Saari, Rebecca K; Monier, Erwan; Selin, Noelle E

2015-07-07

We evaluate the impact of climate change on U.S. air quality and health in 2050 and 2100 using a global modeling framework and integrated economic, climate, and air pollution projections. Three internally consistent socioeconomic scenarios are used to value health benefits of greenhouse gas mitigation policies specifically derived from slowing climate change. Our projections suggest that climate change, exclusive of changes in air pollutant emissions, can significantly impact ozone (O3) and fine particulate matter (PM2.5) pollution across the U.S. and increase associated health effects. Climate policy can substantially reduce these impacts, and climate-related air pollution health benefits alone can offset a significant fraction of mitigation costs. We find that in contrast to cobenefits from reductions to coemitted pollutants, the climate-induced air quality benefits of policy increase with time and are largest between 2050 and 2100. Our projections also suggest that increasing climate policy stringency beyond a certain degree may lead to diminishing returns relative to its cost. However, our results indicate that the air quality impacts of climate change are substantial and should be considered by cost-benefit climate policy analyses.

Intra-Platform Repeatability and Inter-Platform Comparability of MicroRNA Microarray Technology

PubMed Central

Sato, Fumiaki; Tsuchiya, Soken; Terasawa, Kazuya; Tsujimoto, Gozoh

2009-01-01

Over the last decade, DNA microarray technology has provided a great contribution to the life sciences. The MicroArray Quality Control (MAQC) project demonstrated the way to analyze the expression microarray. Recently, microarray technology has been utilized to analyze a comprehensive microRNA expression profiling. Currently, several platforms of microRNA microarray chips are commercially available. Thus, we compared repeatability and comparability of five different microRNA microarray platforms (Agilent, Ambion, Exiqon, Invitrogen and Toray) using 309 microRNAs probes, and the Taqman microRNA system using 142 microRNA probes. This study demonstrated that microRNA microarray has high intra-platform repeatability and comparability to quantitative RT-PCR of microRNA. Among the five platforms, Agilent and Toray array showed relatively better performances than the others. However, the current lineup of commercially available microRNA microarray systems fails to show good inter-platform concordance, probably because of lack of an adequate normalization method and severe divergence in stringency of detection call criteria between different platforms. This study provided the basic information about the performance and the problems specific to the current microRNA microarray systems. PMID:19436744

Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs.

PubMed

Powell, Bradford C; Hutchison, Clyde A

2006-01-19

Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs) of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs). We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins. "Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not) are attractive targets when seeking errors of gene prediction. Examination of mixed COGs reveals some situations in which genes appear to have been missed in current annotations and a smaller number of regions that appear to have been annotated as gene loci erroneously. This technique can also be used to detect potential pseudogenes or sequencing errors. Our method uses an adjustable parameter for degree of conservation among the studied genomes (stringency). We detail results for one level of stringency at which we found 83 potential genes which had not previously been identified, 60 potential pseudogenes, and 7 sequences with existing gene annotations that are probably incorrect. Systematic study of sequence conservation offers a way to improve existing annotations by identifying potentially homologous regions where the annotation of the presence or absence of a gene is inconsistent among genomes.

Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs

PubMed Central

Powell, Bradford C; Hutchison, Clyde A

2006-01-01

Background Experimental verification of gene products has not kept pace with the rapid growth of microbial sequence information. However, existing annotations of gene locations contain sufficient information to screen for probable errors. Furthermore, comparisons among genomes become more informative as more genomes are examined. We studied all open reading frames (ORFs) of at least 30 codons from the genomes of 27 sequenced bacterial strains. We grouped the potential peptide sequences encoded from the ORFs by forming Clusters of Orthologous Groups (COGs). We used this grouping in order to find homologous relationships that would not be distinguishable from noise when using simple BLAST searches. Although COG analysis was initially developed to group annotated genes, we applied it to the task of grouping anonymous DNA sequences that may encode proteins. Results "Mixed COGs" of ORFs (clusters in which some sequences correspond to annotated genes and some do not) are attractive targets when seeking errors of gene predicion. Examination of mixed COGs reveals some situations in which genes appear to have been missed in current annotations and a smaller number of regions that appear to have been annotated as gene loci erroneously. This technique can also be used to detect potential pseudogenes or sequencing errors. Our method uses an adjustable parameter for degree of conservation among the studied genomes (stringency). We detail results for one level of stringency at which we found 83 potential genes which had not previously been identified, 60 potential pseudogenes, and 7 sequences with existing gene annotations that are probably incorrect. Conclusion Systematic study of sequence conservation offers a way to improve existing annotations by identifying potentially homologous regions where the annotation of the presence or absence of a gene is inconsistent among genomes. PMID:16423288

Integrated assessment of global water scarcity over the 21st century - Part 2: Climate change mitigation policies

NASA Astrophysics Data System (ADS)

Hejazi, M. I.; Edmonds, J.; Clarke, L.; Kyle, P.; Davies, E.; Chaturvedi, V.; Eom, J.; Wise, M.; Patel, P.; Calvin, K.

2013-03-01

We investigate the effects of emission mitigation policies on water scarcity both globally and regionally using the Global Change Assessment Model (GCAM), a leading community integrated assessment model of energy, agriculture, climate, and water. Three climate policy scenarios with increasing mitigation stringency of 7.7, 5.5, and 4.2 W m-2 in year 2095 (equivalent to the SRES A2, B2, and B1 emission scenarios, respectively), under two carbon tax regimes (a universal carbon tax (UCT) which includes land use change emissions, and a fossil fuel and industrial emissions carbon tax (FFICT) which excludes land use change emissions) are analyzed. The results are compared to a baseline scenario (i.e. no climate change mitigation policy) with radiative forcing reaching 8.8 W m-2 (equivalent to the SRES A1Fi emission scenario) by 2095. When compared to the baseline scenario and maintaining the same baseline socioeconomic assumptions, water scarcity declines under a UCT mitigation policy but increases with a FFICT mitigation scenario by the year 2095 particularly with more stringent climate mitigation targets. The decreasing trend with UCT policy stringency is due to substitution from more water-intensive to less water-intensive choices in food and energy production, and in land use. Under the FFICT scenario, water scarcity is projected to increase driven by higher water demands for bio-energy crops. This study implies an increasingly prominent role for water availability in future human decisions, and highlights the importance of including water in integrated assessment of global change. Future research will be directed at incorporating water shortage feedbacks in GCAM to better understand how such stresses will propagate across the various human and natural systems in GCAM.

Eighty routes to a ribonucleotide world; dispersion and stringency in the decisive selection.

PubMed

Yarus, Michael

2018-05-21

We examine the initial emergence of genetics; that is, of an inherited chemical capability. The crucial actors are ribonucleotides, occasionally meeting in a prebiotic landscape. Previous work identified six influential variables during such random ribonucleotide pooling. Geochemical pools can be in periodic danger (e.g., from tides) or constant danger (e.g., from unfavorable weather). Such pools receive Gaussian nucleotide amounts sporadically, at random times, or get varying substrates simultaneously. Pools use cross-templated RNA synthesis (5'-5' product from 5'-3' template) or para-templated (5'-5' product from 5'-5' template) synthesis. Pools can undergo mild or strong selection, and be recently initiated (early) or late in age. Considering > 80 combinations of these variables, selection calculations identify a superior route. Most likely, an early, sporadically fed, cross-templating pool in constant danger, receiving ≥ 1 mM nucleotides while under strong selection for a coenzyme-like product will host selection of the first encoded biochemical functions. Predominantly templated products emerge from a critical event, the starting bloc selection, which exploits inevitable differences among early pools. Favorable selection has a simple rationale; it is increased by product dispersion (sd/mean), by selection intensity (mild or strong), or by combining these factors as stringency, reciprocal fraction of pools selected (1/sfsel). To summarize: chance utility, acting via a preference for disperse, templated coenzyme-like dinucleotides, uses stringent starting bloc selection to quickly establish majority encoded/genetic expression. Despite its computational origin, starting bloc selection is largely independent of specialized assumptions. This ribodinucleotide route to inheritance may also have facilitated 5'-3' chemical RNA replication. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Performance of Crohn's disease Clinical Trial Endpoints based upon Different Cutoffs for Patient Reported Outcomes or Endoscopic Activity: Analysis of EXTEND Data.

PubMed

Feagan, Brian; Sandborn, William J; Rutgeerts, Paul; Levesque, Barrett G; Khanna, Reena; Huang, Bidan; Zhou, Qian; Maa, Jen-Fue; Wallace, Kori; Lacerda, Ana; Thakkar, Roopal B; Robinson, Anne M

2018-04-23

Clinical trial endpoints for Crohn's disease (CD) activity correlate poorly with mucosal inflammation; to assess treatment efficacy, patient-reported outcomes and endoscopic assessments are preferred. This study assessed the impact on treatment efficacy estimations of using different definitions of clinical and endoscopic remission and endoscopic response, and of using site- or central-based endoscopy evaluation. This post hoc analysis of data fromEXTEND (extend the safety and efficacy of adalimumab through endoscopic healing), a placebo (PBO)-controlled, randomized trial of adalimumab (ADA) for mucosal healing, included adults with moderate-to-severe CD. Subsets of patients meeting specified Simplified Endoscopic Score for CD (SES-CD) inclusion criteria, according to site or central reading, and baseline stool frequency (SF) and/or abdominal pain score (AP) thresholds were evaluated. Various endpoint definitions based on the Crohn's Disease Activity Index (CDAI), its SF and AP components, SES-CD, and composite endpoints were compared between treatment groups. Increased stringency of Week 12 clinical endpoints compared to CDAI<150 to SF≤3.0/1.5&AP≤1.0 reduced PBO response rates by ≥12% and increased treatment effects by ≤10%. Amending the SES-CD endpoint from ≤4 to ≤2 reduced the treatment effect from 24% to 8%. Composite endpoints further diminished response rates and effect sizes. Site-based evaluation was associated with lower remission rates versus central reading in the PBO group and, thus, greater ADA-related treatment effects. This analysis is the first to demonstrate that increasing the stringency of clinical and endoscopic endpoint definitions in CD trials, especially lowering SF or SES-CD definitions, reduces the ability to detect treatment-related change in CD activity; focus on endpoints that reflect clinical change is warranted.

Integrated assessment of global water scarcity over the 21st century - Part 2: Climate change mitigation policies

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

Hejazi, Mohamad I.; Edmonds, James A.; Clarke, Leon E.

2013-01-01

We investigate the effects of emission mitigation policies on water scarcity both globally and regionally using the Global Change Assessment Model (GCAM), a leading community integrated assessment model of energy, agriculture, climate, and water. Three climate policy scenarios with increasing mitigation stringency of 7.7, 5.5, and 4.2 W/m2 in year 2095 (equivalent to the SRES A2, B2, and B1 emission scenarios, respectively), under two carbon tax regimes (a universal carbon tax (UCT) which includes land use change emissions, and a fossil fuel and industrial emissions carbon tax (FFICT) which excludes land use change emissions) are analyzed. The results are comparedmore » to a baseline scenario (i.e., no climate change mitigation policy) with radiative forcing reaching 8.8 W/m2 (equivalent to the SRES A1Fi emission scenario) by 2095. When compared to the baseline scenario and maintaining the same baseline underlying socioeconomic assumptions, water scarcity declines under a UCT mitigation policy while increases with a FFICT mitigation scenario by the year 2095 with more stringent climate mitigation targets. The decreasing trend with UCT policy stringency is due to substitution from more water-intensive to less water-intensive choices in food, energy, and land use. Under the FFICT scenario, water scarcity is projected to increase driven by higher water demands for bio-energy crops. This study implies an increasingly prominent role for water availability in future human decisions, and highlights the importance of including water in integrated assessment of global change. Future research will be directed at incorporating water shortage feedbacks in GCAM to better understand how such stresses will propagate across the various human and natural systems in GCAM.« less

An optimized method for extraction and detection of Coconut cadang-cadang viroid(CCCVd) from oil palm.

PubMed

Mohammadi, M R; Vadamalai, G; Joseph, H

2010-01-01

Coconut cadong-cadong viroid (CCCVd) causes the Lethal cadang-cadang disease of coconut palms in the Philippines and it is recently reported to be associated with the orange spotting disease on oil palm in Malaysia. The low concentration of the viroid RNA in oil palm as well as the high content of polyphenols and polysaccharides in this plant which interfere with the purification steps makes it difficult to extract and detect this viroid from oil palm. A previously described method was modified and optimized for extraction and detection of CCCVd from infected oil palms. Briefly, 7 g of leaf material was homogenized in a mortar or a blender using liquid nitrogen. 10 ml of extraction buffer (100 mM Tris-HCl pH 7.5, 100 mM NaCl, 10 mM EDTA) along with 100 mM 2-mercaptoethanol and 10 ml water saturated phenol was added to the frozen powder. After centrifuging at 4 degrees C, 4000 g for 30 min, the aqueous phase was extracted once more with phenol then once with chloroform-isoamyl alcohol (24:1). After adding sodium acetate, pH 5.6 to 200 mM, the mixture was precipitated with 2.5 vol ethanol overnight in -20 freezer and then the pellet was washed with 70% ethanol and air-dried. One milliliter of 8 M LiCl was added to the dried pellet and after shaking overnight at 4 degrees C and another centrifugation step the supernatant was collected and precipitated again with ethanol and then the resulting pellet was washed and air-dried. To carry out northern blotting, samples equivalent to 40 g of plant tissue were mixed with formamide buffer and loaded onto a 12% polyacrylamide gel containing 7 M urea and after separation by electrophoresis, were electroblotted onto membrane and fixed by UV cross-linking. Pre-hybridization and hybridization using hybridization buffer (50% formamide, 25%SSPE, 0.1% Ficol and PVP, 0.1 % SDS, 0.02 % DNA (5mg/ml)) was carried out at 45 degrees C for 90 min and 16 h, respectively followed by two low stringency washes (0.5 X SSC, 0.1% SDS, at room temperature for 5 min) and one high stringency wash (0.1X SSC, 0.1% SDS at 60 degrees C for 1 hour). In vitro synthesized DIG-labeled full-length CCCVd(-) RNA probe was used in hybridization step. DIG Nucleic Acid Detection Kit (Roche) instructions were followed for detection procedure and as a result the blue bands corresponding to the position of the viroid were appeared on the membrane. The result of this study showed the ability of DIG labeled probe in detection of the viroid and also provided a suitable extraction and hybridization method for the detection of CCCVd from oil palm.

Stringency of substrate specificity of Escherichia coli malate dehydrogenase.

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

Boernke, W. E.; Millard, C. S.; Stevens, P. W.

1995-09-10

Malate dehydrogenase and lactate dehydrogenase are members of the structurally and functionally homologous family of 2-ketoacid dehydrogenases. Both enzymes display high specificity for their respective keto substrates, oxaloacetate and pyruvate. Closer analysis of their specificity, however, reveals that the specificity of malate dehydrogenase is much stricter and less malleable than that of lactate dehydrogenase. Site-specific mutagenesis of the two enzymes in an attempt to reverse their specificity has met with contrary results. Conversion of a specific active-site glutamine to arginine in lactate dehydrogenase from Bacillus stearothermophilus generated an enzyme that displayed activity toward oxaloacetate equal to that of the nativemore » enzyme toward pyruvate (H. M. Wilks et al. (1988) Science 242, 1541-1544). We have constructed a series of mutants in the mobile, active site loop of the Escherichia coli malate dehydrogenase that incorporate the complementary change, conversion of arginine 81 to glutamine, to evaluate the role of charge distribution and conformational flexibility within this loop in defining the substrate specificity of these enzymes. Mutants incorporating the change R81Q all had reversed specificity, displaying much higher activity toward pyruvate than to the natural substrate, oxaloacetate. In contrast to the mutated lactate dehydrogenase, these reversed-specificity mutants were much less active than the native enzyme. Secondary mutations within the loop of the E. coli enzyme (A80N, A80P, A80P/M85E/D86T) had either no or only moderately beneficial effects on the activity of the mutant enzyme toward pyruvate. The mutation A80P, which can be expected to reduce the overall flexibility of the loop, modestly improved activity toward pyruvate. The possible physiological relevance of the stringent specificity of malate dehydrogenase was investigated. In normal strains of E. coli, fermentative metabolism was not affected by expression of the mutant malate dehydrogenase. However, when expressed in a strain of E. coli unable to ferment glucose, the mutant enzyme restored growth and produced lactic acid as the sole fermentation product.« less

Musite, a tool for global prediction of general and kinase-specific phosphorylation sites.

PubMed

Gao, Jianjiong; Thelen, Jay J; Dunker, A Keith; Xu, Dong

2010-12-01

Reversible protein phosphorylation is one of the most pervasive post-translational modifications, regulating diverse cellular processes in various organisms. High throughput experimental studies using mass spectrometry have identified many phosphorylation sites, primarily from eukaryotes. However, the vast majority of phosphorylation sites remain undiscovered, even in well studied systems. Because mass spectrometry-based experimental approaches for identifying phosphorylation events are costly, time-consuming, and biased toward abundant proteins and proteotypic peptides, in silico prediction of phosphorylation sites is potentially a useful alternative strategy for whole proteome annotation. Because of various limitations, current phosphorylation site prediction tools were not well designed for comprehensive assessment of proteomes. Here, we present a novel software tool, Musite, specifically designed for large scale predictions of both general and kinase-specific phosphorylation sites. We collected phosphoproteomics data in multiple organisms from several reliable sources and used them to train prediction models by a comprehensive machine-learning approach that integrates local sequence similarities to known phosphorylation sites, protein disorder scores, and amino acid frequencies. Application of Musite on several proteomes yielded tens of thousands of phosphorylation site predictions at a high stringency level. Cross-validation tests show that Musite achieves some improvement over existing tools in predicting general phosphorylation sites, and it is at least comparable with those for predicting kinase-specific phosphorylation sites. In Musite V1.0, we have trained general prediction models for six organisms and kinase-specific prediction models for 13 kinases or kinase families. Although the current pretrained models were not correlated with any particular cellular conditions, Musite provides a unique functionality for training customized prediction models (including condition-specific models) from users' own data. In addition, with its easily extensible open source application programming interface, Musite is aimed at being an open platform for community-based development of machine learning-based phosphorylation site prediction applications. Musite is available at http://musite.sourceforge.net/.

Heating efficiency dependency on size and morphology of magnetite nanoparticles

NASA Astrophysics Data System (ADS)

Parekh, Kinnari; Parmar, Harshida; Sharma, Vinay; Ramanujan, R. V.

2018-04-01

Different size magnetite nanoparticles ranging from superparamagnetic (9 nm) to single domain (27 nm) and multi domain (53 nm) were synthesized using chemical route. Morphology of these particles as seen from TEM images indicates shape change from spherical to cubic with the growth of particles. The saturation magnetization (σs) and Specific Loss Power (SLP) showed maximum for single domain size, 72 emu/g and 102 W/g, respectively then those of multi domain size particles. These samples show higher SLP at relatively low concentration, low frequency and low amplitude compared to samples prepared by other routes.

Pandemic Influenza Preparedness and Response Among Public-Housing Residents, Single-Parent Families, and Low-Income Populations

PubMed Central

Truman, Benedict I.; Hutchins, Sonja; Richard, Roland; Brown, Clive; Guillory, Joyce A.; Rashid, Jamila

2009-01-01

During the early stages of an influenza pandemic, a pandemic vaccine likely will not be available. Therefore, interventions to mitigate pandemic influenza transmission in communities will be an important component of the response to a pandemic. Public-housing residents, single-parent families, and low-income populations may have difficulty complying with community-wide interventions. To enable compliance with community interventions, stakeholders recommended the following: (1) community mobilization and partnerships, (2) culturally specific emergency communications planning, (3) culturally specific education and training programs, (4) evidence-based measurement and evaluation efforts, (5) strategic planning policies, (6) inclusion of community members as partners, and (7) policy and program changes to minimize morbidity and mortality. PMID:19797740

Temporally-Controlled Site-Specific Recombination in Zebrafish

PubMed Central

Hans, Stefan; Kaslin, Jan; Freudenreich, Dorian; Brand, Michael

2009-01-01

Conventional use of the site-specific recombinase Cre is a powerful technology in mouse, but almost absent in other vertebrate model organisms. In zebrafish, Cre-mediated recombination efficiency was previously very low. Here we show that using transposon-mediated transgenesis, Cre is in fact highly efficient in this organism. Furthermore, temporal control of recombination can be achieved by using the ligand-inducible CreERT2. Site-specific recombination only occurs upon administration of the drug tamoxifen (TAM) or its active metabolite, 4-hydroxy-tamoxifen (4-OHT). Cre-mediated recombination is detectable already 4 or 2 hours after administration of TAM or 4-OHT, demonstrating fast recombination kinetics. In addition, low doses of TAM allow mosaic labeling of single cells. Combined, our results show that conditional Cre/lox will be a valuable tool for both, embryonic and adult zebrafish studies. Furthermore, single copy insertion transgenesis of Cre/lox constructs suggest a strategy suitable also for other organisms. PMID:19247481

M13 phage-functionalized single-walled carbon nanotubes as nanoprobes for second near-infrared window fluorescence imaging of targeted tumors.

PubMed

Yi, Hyunjung; Ghosh, Debadyuti; Ham, Moon-Ho; Qi, Jifa; Barone, Paul W; Strano, Michael S; Belcher, Angela M

2012-03-14

Second near-infrared (NIR) window light (950-1400 nm) is attractive for in vivo fluorescence imaging due to its deep penetration depth in tissues and low tissue autofluorescence. Here we show genetically engineered multifunctional M13 phage can assemble fluorescent single-walled carbon nanotubes (SWNTs) and ligands for targeted fluorescence imaging of tumors. M13-SWNT probe is detectable in deep tissues even at a low dosage of 2 μg/mL and up to 2.5 cm in tissue-like phantoms. Moreover, targeted probes show specific and up to 4-fold improved uptake in prostate specific membrane antigen positive prostate tumors compared to control nontargeted probes. This M13 phage-based second NIR window fluorescence imaging probe has great potential for specific detection and therapy monitoring of hard-to-detect areas. © 2012 American Chemical Society

M13 phage-functionalized single-walled carbon nanotubes as nanoprobes for second near-infrared window fluorescence imaging of targeted tumors

PubMed Central

HAM, MOON-HO; QI, JIFA; BARONE, PAUL W.; STRANO, MICHAEL S.; BELCHER, ANGELA M.

2014-01-01

Second near-infrared (NIR) window light (950-1,400 nm) is attractive for in vivo fluorescence imaging due to its deep penetration depth in tissues and low tissue autofluorescence. Here we show genetically engineered multifunctional M13 phage can assemble fluorescent single-walled carbon nanotubes (SWNTs) and ligands for targeted fluorescence imaging of tumors. M13-SWNT probe is detectable in deep tissues even at a low dosage of 2 μg/mL and up to 2.5 cm in tissue-like phantoms. Moreover, targeted probes show specific and up to four-fold improved uptake in prostate specific membrane antigen positive prostate tumors compared to control non-targeted probes. This M13 phage-based second NIR window fluorescence imaging probe has great potential for specific detection and therapy monitoring of hard-to-detect areas. PMID:22268625

Spinal cord stimulation for axial low back pain: a prospective, controlled trial comparing dual with single percutaneous electrodes.

PubMed

North, Richard B; Kidd, David H; Olin, John; Sieracki, Jeffrey M; Farrokhi, Farrokh; Petrucci, Loredana; Cutchis, Protagoras N

2005-06-15

A prospective, controlled, clinical trial comparing single and dual percutaneous electrodes in the treatment of axial low back pain from failed back surgery syndrome. To clarify technical requirements and test the hypothesis that placing two linear arrays in parallel, thereby doubling the number of contacts, improves outcome. Technical improvements have enhanced outcomes of spinal cord stimulation for chronic axial low back pain. Dual, parallel electrodes reportedly improve these outcomes. Acting as their own controls, 20 patients who passed screening with single, 4-contact electrodes received permanent dual, 4-contact electrodes with 7- or 10-mm intercontact distances at the same vertebral level(s). We quantified and compared the technical and clinical results of the single and dual electrodes, adjusting stimulation parameters to specific psychophysical thresholds. Single electrodes provided significant (P < 0.01) advantages in patient- and computer-calculated ratings of pain coverage by paresthesias and in the scaled amplitude necessary to cover the low back, compared with dual 7-mm electrodes. Slight advantages without statistical significance were observed for the single over the dual 10-mm electrodes. Amplitude requirements were significantly lower for the single electrode than for either dual electrode. At long-term follow-up, 53% of patients met the criteria for clinical success. While we observed disadvantages for dual electrodes in treating axial low back pain, we achieved technical success with single or dual electrodes in most patients and maintained this success clinically with dual electrodes in 53%.

Self consistency grouping: a stringent clustering method

PubMed Central

2012-01-01

Background Numerous types of clustering like single linkage and K-means have been widely studied and applied to a variety of scientific problems. However, the existing methods are not readily applicable for the problems that demand high stringency. Methods Our method, self consistency grouping, i.e. SCG, yields clusters whose members are closer in rank to each other than to any member outside the cluster. We do not define a distance metric; we use the best known distance metric and presume that it measures the correct distance. SCG does not impose any restriction on the size or the number of the clusters that it finds. The boundaries of clusters are determined by the inconsistencies in the ranks. In addition to the direct implementation that finds the complete structure of the (sub)clusters we implemented two faster versions. The fastest version is guaranteed to find only the clusters that are not subclusters of any other clusters and the other version yields the same output as the direct implementation but does so more efficiently. Results Our tests have demonstrated that SCG yields very few false positives. This was accomplished by introducing errors in the distance measurement. Clustering of protein domain representatives by structural similarity showed that SCG could recover homologous groups with high precision. Conclusions SCG has potential for finding biological relationships under stringent conditions. PMID:23320864

Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms

PubMed Central

Clouse, Ronald M.; Linchangco, Gregorio V.; Kerr, Alexander M.; Reid, Robert W.; Janies, Daniel A.

2015-01-01

Tissue inhibitors of metalloproteinases (TIMPs) help regulate the extracellular matrix (ECM) in animals, mostly by inhibiting matrix metalloproteinases (MMPs). They are important activators of mutable collagenous tissue (MCT), which have been extensively studied in echinoderms, and the four TIMP copies in humans have been studied for their role in cancer. To understand the evolution of TIMPs, we combined 405 TIMPs from an echinoderm transcriptome dataset built from 41 specimens representing all five classes of echinoderms with variants from protostomes and chordates. We used multiple sequence alignment with various stringencies of alignment quality to cull highly divergent sequences and then conducted phylogenetic analyses using both nucleotide and amino acid sequences. Phylogenetic hypotheses consistently recovered TIMPs as diversifying in the ancestral deuterostome and these early lineages continuing to diversify in echinoderms. The four vertebrate TIMPs diversified from a single copy in the ancestral chordate, all other copies being lost. Consistent with greater MCT needs owing to body wall liquefaction, evisceration, autotomy and reproduction by fission, holothuroids had significantly more TIMPs and higher read depths per contig. Ten cysteine residues, an HPQ binding site and several other residues were conserved in at least 70% of all TIMPs. The conservation of binding sites and the placement of echinoderm TIMPs involved in MCT modification suggest that ECM regulation remains the primary function of TIMP genes, although within this role there are a large number of specialized copies. PMID:27017967

Location analysis for the estrogen receptor-α reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements

PubMed Central

Mason, Christopher E.; Shu, Feng-Jue; Wang, Cheng; Session, Ryan M.; Kallen, Roland G.; Sidell, Neil; Yu, Tianwei; Liu, Mei Hui; Cheung, Edwin; Kallen, Caleb B.

2010-01-01

Location analysis for estrogen receptor-α (ERα)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERα-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: <10% and 10–20% nucleotide deviation from the canonical ERE sequence. We demonstrate that ∼50% of all ERα-bound loci do not have a discernable ERE and show that most ERα-bound EREs are not perfect consensus EREs. Approximately one-third of all ERα-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERα-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptor-bound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogen-dependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERα binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers. PMID:20047966

Location analysis for the estrogen receptor-alpha reveals binding to diverse ERE sequences and widespread binding within repetitive DNA elements.

PubMed

Mason, Christopher E; Shu, Feng-Jue; Wang, Cheng; Session, Ryan M; Kallen, Roland G; Sidell, Neil; Yu, Tianwei; Liu, Mei Hui; Cheung, Edwin; Kallen, Caleb B

2010-04-01

Location analysis for estrogen receptor-alpha (ERalpha)-bound cis-regulatory elements was determined in MCF7 cells using chromatin immunoprecipitation (ChIP)-on-chip. Here, we present the estrogen response element (ERE) sequences that were identified at ERalpha-bound loci and quantify the incidence of ERE sequences under two stringencies of detection: <10% and 10-20% nucleotide deviation from the canonical ERE sequence. We demonstrate that approximately 50% of all ERalpha-bound loci do not have a discernable ERE and show that most ERalpha-bound EREs are not perfect consensus EREs. Approximately one-third of all ERalpha-bound ERE sequences reside within repetitive DNA sequences, most commonly of the AluS family. In addition, the 3-bp spacer between the inverted ERE half-sites, rather than being random nucleotides, is C(A/T)G-enriched at bona fide receptor targets. Diverse ERalpha-bound loci were validated using electrophoretic mobility shift assay and ChIP-polymerase chain reaction (PCR). The functional significance of receptor-bound loci was demonstrated using luciferase reporter assays which proved that repetitive element ERE sequences contribute to enhancer function. ChIP-PCR demonstrated estrogen-dependent recruitment of the coactivator SRC3 to these loci in vivo. Our data demonstrate that ERalpha binds to widely variant EREs with less sequence specificity than had previously been suspected and that binding at repetitive and nonrepetitive genomic targets is favored by specific trinucleotide spacers.

Economic impacts of bio-refinery and resource cascading systems: an applied general equilibrium analysis for Poland.

PubMed

Ignaciuk, Adriana M; Sanders, Johan

2007-12-01

Due to more stringent energy and climate policies, it is expected that many traditional chemicals will be replaced by their biomass-based substitutes, bio-chemicals. These innovations, however, can influence land allocation since the demand for land dedicated to specific crops might increase. Moreover, it can have an influence on traditional agricultural production. In this paper, we use an applied general equilibrium framework, in which we include two different bio-refinery processes and incorporate so-called cascading mechanisms. The bio-refinery processes use grass, as one of the major inputs, to produce bio-nylon and propane-diol (1,3PDO) to substitute currently produced fossil fuel-based nylon and ethane-diol. We examine the impact of specific climate policies on the bioelectricity share in total electricity production, land allocation, and production quantities and prices of selected commodities. The novel technologies become competitive, with an increased stringency of climate policies. This switch, however, does not induce a higher share of bioelectricity. The cascade does stimulate the production of bioelectricity, but it induces more of a shift in inputs in the bioelectricity sector (from biomass to the cascaded bio-nylon and 1, 3PDO) than an increase in production level of bioelectricity. We conclude that dedicated biomass crops will remain the main option for bioelectricity production: the contribution of the biomass systems remains limited. Moreover, the bioelectricity sector looses a competition for land for biomass production with bio-refineries.

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

Andersen, G.L.; He, Z.; DeSantis, T.Z.

Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogeneticmore » microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer oligonucleotide probes and covers more than 10,000 gene sequences in 150 gene categories involved in carbon, nitrogen, sulfur, and phosphorus cycling, metal resistance and reduction, and organic contaminant degradation. GeoChip can be used as a generic tool for microbial community analysis, and also link microbial community structure to ecosystem functioning. Examples of the application of both arrays in different environmental samples will be described in the two subsequent sections.« less

Highly macroscopically degenerated single-point ground states as source of specific heat capacity anomalies in magnetic frustrated systems

NASA Astrophysics Data System (ADS)

Jurčišinová, E.; Jurčišin, M.

2018-04-01

Anomalies of the specific heat capacity are investigated in the framework of the exactly solvable antiferromagnetic spin- 1 / 2 Ising model in the external magnetic field on the geometrically frustrated tetrahedron recursive lattice. It is shown that the Schottky-type anomaly in the behavior of the specific heat capacity is related to the existence of unique highly macroscopically degenerated single-point ground states which are formed on the borders between neighboring plateau-like ground states. It is also shown that the very existence of these single-point ground states with large residual entropies predicts the appearance of another anomaly in the behavior of the specific heat capacity for low temperatures, namely, the field-induced double-peak structure, which exists, and should be observed experimentally, along with the Schottky-type anomaly in various frustrated magnetic system.

Diagnostic Accuracy of the Veteran Affairs' Traumatic Brain Injury Screen.

PubMed

Louise Bender Pape, Theresa; Smith, Bridget; Babcock-Parziale, Judith; Evans, Charlesnika T; Herrold, Amy A; Phipps Maieritsch, Kelly; High, Walter M

2018-01-31

To comprehensively estimate the diagnostic accuracy and reliability of the Department of Veterans Affairs (VA) Traumatic Brain Injury (TBI) Clinical Reminder Screen (TCRS). Cross-sectional, prospective, observational study using the Standards for Reporting of Diagnostic Accuracy criteria. Three VA Polytrauma Network Sites. Operation Iraqi Freedom, Operation Enduring Freedom veterans (N=433). TCRS, Comprehensive TBI Evaluation, Structured TBI Diagnostic Interview, Symptom Attribution and Classification Algorithm, and Clinician-Administered Posttraumatic Stress Disorder (PTSD) Scale. Forty-five percent of veterans screened positive on the TCRS for TBI. For detecting occurrence of historical TBI, the TCRS had a sensitivity of .56 to .74, a specificity of .63 to .93, a positive predictive value (PPV) of 25% to 45%, a negative predictive value (NPV) of 91% to 94%, and a diagnostic odds ratio (DOR) of 4 to 13. For accuracy of attributing active symptoms to the TBI, the TCRS had a sensitivity of .64 to .87, a specificity of .59 to .89, a PPV of 26% to 32%, an NPV of 92% to 95%, and a DOR of 6 to 9. The sensitivity was higher for veterans with PTSD (.80-.86) relative to veterans without PTSD (.57-.82). The specificity, however, was higher among veterans without PTSD (.75-.81) relative to veterans with PTSD (.36-.49). All indices of diagnostic accuracy changed when participants with questionably valid (QV) test profiles were eliminated from analyses. The utility of the TCRS to screen for mild TBI (mTBI) depends on the stringency of the diagnostic reference standard to which it is being compared, the presence/absence of PTSD, and QV test profiles. Further development, validation, and use of reproducible diagnostic algorithms for symptom attribution after possible mTBI would improve diagnostic accuracy. Published by Elsevier Inc.

The effect of genome-wide association scan quality control on imputation outcome for common variants.

PubMed

Southam, Lorraine; Panoutsopoulou, Kalliope; Rayner, N William; Chapman, Kay; Durrant, Caroline; Ferreira, Teresa; Arden, Nigel; Carr, Andrew; Deloukas, Panos; Doherty, Michael; Loughlin, John; McCaskie, Andrew; Ollier, William E R; Ralston, Stuart; Spector, Timothy D; Valdes, Ana M; Wallis, Gillian A; Wilkinson, J Mark; Marchini, Jonathan; Zeggini, Eleftheria

2011-05-01

Imputation is an extremely valuable tool in conducting and synthesising genome-wide association studies (GWASs). Directly typed SNP quality control (QC) is thought to affect imputation quality. It is, therefore, common practise to use quality-controlled (QCed) data as an input for imputing genotypes. This study aims to determine the effect of commonly applied QC steps on imputation outcomes. We performed several iterations of imputing SNPs across chromosome 22 in a dataset consisting of 3177 samples with Illumina 610 k (Illumina, San Diego, CA, USA) GWAS data, applying different QC steps each time. The imputed genotypes were compared with the directly typed genotypes. In addition, we investigated the correlation between alternatively QCed data. We also applied a series of post-imputation QC steps balancing elimination of poorly imputed SNPs and information loss. We found that the difference between the unQCed data and the fully QCed data on imputation outcome was minimal. Our study shows that imputation of common variants is generally very accurate and robust to GWAS QC, which is not a major factor affecting imputation outcome. A minority of common-frequency SNPs with particular properties cannot be accurately imputed regardless of QC stringency. These findings may not generalise to the imputation of low frequency and rare variants.

Cynefin as Reference Framework to Facilitate Insight and Decision-Making in Complex Contexts of Biomedical Research.

PubMed

Kempermann, Gerd

2017-01-01

The Cynefin scheme is a concept of knowledge management, originally devised to support decision making in management, but more generally applicable to situations, in which complexity challenges the quality of insight, prediction, and decision. Despite the fact that life itself, and especially the brain and its diseases, are complex to the extent that complexity could be considered their cardinal feature, complex problems in biomedicine are often treated as if they were actually not more than the complicated sum of solvable sub-problems. Because of the emergent properties of complex contexts this is not correct. With a set of clear criteria Cynefin helps to set apart complex problems from "simple/obvious," "complicated," "chaotic," and "disordered" contexts in order to avoid misinterpreting the relevant causality structures. The distinction comes with the insight, which specific kind of knowledge is possible in each of these categories and what are the consequences for resulting decisions and actions. From student's theses over the publication and grant writing process to research politics, misinterpretation of complexity can have problematic or even dangerous consequences, especially in clinical contexts. Conceptualization of problems within a straightforward reference language like Cynefin improves clarity and stringency within projects and facilitates communication and decision-making about them.

A Single-Case Study of Distributed Leadership in a Successful School Serving Low-Socioeconomic Students

ERIC Educational Resources Information Center

Muhovich, Phyllis

2018-01-01

Educational leaders struggle to improve and maintain student achievement while at the same time reduce the achievement gap between students from low socioeconomic backgrounds and their peers educated in higher socioeconomic communities. The practice of distributed leadership has shown promise in improving school achievement. The specific problem…

Impacts of Hospital Budget Limits in Rochester, New York

PubMed Central

Friedman, Bernard; Wong, Herbert S.

1995-01-01

During 1980-87, eight hospitals in the Rochester, New York area participated in an experimental program to limit total revenue. This article analyzes: increase of costs for Rochester hospitals; trends for inputs and compensation; and cash flow margins. Real expense per case grew annually by about 3 percent less in Rochester. However, after 1984, Medicare prospective payment had an effect of similar size outside Rochester. Some capital inputs to hospital care were restrained, as were wages and particularly benefits. The program did not generally raise or stabilize hospital revenue margins, while the ratio of cash flow to debt trended down. Financial stringency of this program relative to alternatives may have contributed to its end. PMID:10151889

Impacts of hospital budget limits in Rochester, New York.

PubMed

Friedman, B; Wong, H S

1995-01-01

During 1980-87, eight hospitals in the Rochester, New York area participated in an experimental program to limit total revenue. This article analyzes: increase of costs for Rochester hospitals; trends for inputs and compensation; and cash flow margins. Real expense per case grew annually by about 3 percent less in Rochester. However, after 1984, Medicare prospective payment had an effect of similar size outside Rochester. Some capital inputs to hospital care were restrained, as were wages and particularly benefits. The program did not generally raise or stabilize hospital revenue margins, while the ratio of cash flow to debt trended down. Financial stringency of this program relative to alternatives may have contributed to its end.

A rapid low-cost high-density DNA-based multi-detection test for routine inspection of meat species.

PubMed

Lin, Chun Chi; Fung, Lai Ling; Chan, Po Kwok; Lee, Cheuk Man; Chow, Kwok Fai; Cheng, Shuk Han

2014-02-01

The increasing occurrence of food frauds suggests that species identification should be part of food authentication. Current molecular-based species identification methods have their own limitations or drawbacks, such as relatively time-consuming experimental steps, expensive equipment and, in particular, these methods cannot identify mixed species in a single experiment. This project proposes an improved method involving PCR amplification of the COI gene and detection of species-specific sequences by hybridisation. Major innovative breakthrough lies in the detection of multiple species, including pork, beef, lamb, horse, cat, dog and mouse, from a mixed sample within a single experiment. The probes used are species-specific either in sole or mixed species samples. As little as 5 pg of DNA template in the PCR is detectable in the proposed method. By designing species-specific probes and adopting reverse dot blot hybridisation and flow-through hybridisation, a low-cost high-density DNA-based multi-detection test suitable for routine inspection of meat species was developed. © 2013.

[Nonpharmacological correction of low back pain by single or integrated means of medical rehabilitation and the evaluation of their effectiveness].

PubMed

Sakalauskiene, Giedre

2009-01-01

Low back pain is a global worldwide problem. A great attention is given to correction of this health status by a wide range of rehabilitation specialists. Some single or integrated physical factors, physiotherapy, specific and nonspecific physical exercises, alternative methods of treatment, also the complex of multidisciplinary rehabilitation means are applied in the management of low back pain. The evidence-based data are analyzed in order to identify which nonpharmacological means are effective in pain correction; in addition, the effectiveness of various methods and models of low back pain management are compared in this article. Research data evaluating the impact effectiveness of single or integrated means of rehabilitation are very controversial. There are no evidence-based specific recommendations for the correction of this health status objectively assessing advantages of physiotherapy or physical factors and referring the definite indications of their prescription. It is thought that multidisciplinary rehabilitation is most effective in management of chronic low back pain. The positive results depend on the experience of a physician and other rehabilitation specialists. A patient's motivation to participate in the process of pain control is very important. It is recommended to inform a patient about the effectiveness of administered methods. There is a lack of evidence-based trials evaluating the effectiveness of nonpharmacological methods of pain control in Lithuania. Therefore, the greater attention of researchers and administrative structures of health care should be given to this problem in order to develop the evidence-based guidelines for an effective correction of low back pain.

Single quantum dot analysis enables multiplexed point mutation detection by gap ligase chain reaction.

PubMed

Song, Yunke; Zhang, Yi; Wang, Tza-Huei

2013-04-08

Gene point mutations present important biomarkers for genetic diseases. However, existing point mutation detection methods suffer from low sensitivity, specificity, and a tedious assay processes. In this report, an assay technology is proposed which combines the outstanding specificity of gap ligase chain reaction (Gap-LCR), the high sensitivity of single-molecule coincidence detection, and the superior optical properties of quantum dots (QDs) for multiplexed detection of point mutations in genomic DNA. Mutant-specific ligation products are generated by Gap-LCR and subsequently captured by QDs to form DNA-QD nanocomplexes that are detected by single-molecule spectroscopy (SMS) through multi-color fluorescence burst coincidence analysis, allowing for multiplexed mutation detection in a separation-free format. The proposed assay is capable of detecting zeptomoles of KRAS codon 12 mutation variants with near 100% specificity. Its high sensitivity allows direct detection of KRAS mutation in crude genomic DNA without PCR pre-amplification. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Low thrust vehicle concept study

NASA Technical Reports Server (NTRS)

1980-01-01

Low thrust chemical (hydrogen-oxygen) propulsion systems configured specifically for low acceleration orbit transfer of large space systems were defined. Results indicate that it is cost effective and least risk to combine the OTV and stowed spacecraft in a single 65 K Shuttle. The study shows that the engine for an optimized low thrust stage (1) does not require very low thrust; (2) 1-3 K thrust range appears optimum; (3) thrust transient is not a concern; (4) throttling probably not worthwhile; and (5) multiple thrusters complicate OTV/LSS design and aggravate LSS loads. Regarding the optimum vehicle for low acceleration missions, the single shuttle launch (LSS and expendable OTV) is most cost effective and least risky. Multiple shuttles increase diameter 20%. The space based radar structure short OTV (which maximizes space available for packaged LSS) favors use of torus tank. Propellant tank pressures/vapor residuals are little affected by engine thrust level or number of burns.

Low-Radiation Cellular Inductive Powering of Rodent Wireless Brain Interfaces: Methodology and Design Guide.

PubMed

Soltani, Nima; Aliroteh, Miaad S; Salam, M Tariqus; Perez Velazquez, Jose Luis; Genov, Roman

2016-08-01

This paper presents a general methodology of inductive power delivery in wireless chronic rodent electrophysiology applications. The focus is on such systems design considerations under the following key constraints: maximum power delivery under the allowable specific absorption rate (SAR), low cost and spatial scalability. The methodology includes inductive coil design considerations within a low-frequency ferrite-core-free power transfer link which includes a scalable coil-array power transmitter floor and a single-coil implanted or worn power receiver. A specific design example is presented that includes the concept of low-SAR cellular single-transmitter-coil powering through dynamic tracking of a magnet-less receiver spatial location. The transmitter coil instantaneous supply current is monitored using a small number of low-cost electronic components. A drop in its value indicates the proximity of the receiver due to the reflected impedance of the latter. Only the transmitter coil nearest to the receiver is activated. Operating at the low frequency of 1.5 MHz, the inductive powering floor delivers a maximum of 15.9 W below the IEEE C95 SAR limit, which is over three times greater than that in other recently reported designs. The power transfer efficiency of 39% and 13% at the nominal and maximum distances of 8 cm and 11 cm, respectively, is maintained.

Spintronic microfluidic platform for biomedical and environmental applications

NASA Astrophysics Data System (ADS)

Cardoso, F. A.; Martins, V. C.; Fonseca, L. P.; Germano, J.; Sousa, L. A.; Piedade, M. S.; Freitas, P. P.

2010-09-01

Faster, more sensitive and easy to operate biosensing devices still are a need at important areas such as biomedical diagnostics, food control and environmental monitoring. Recently, spintronic-devices have emerged as a promising alternative to the existent technologies [1-3]. A number of advantages, namely high sensitivity, easy integration, miniaturization, scalability, robustness and low cost make these devices potentially capable of responding to the existent technological need. In parallel, the field of microfluidics has shown great advances [4]. Microfluidic systems allow the analysis of small sample volumes (from micro- down to pico-liters), often by automate sample processing with the ability to integrate several steps into a single device (analyte amplification, concentration, separation and/or labeling), all in a reduced assay time (minutes to hours) and affordable cost. The merging of these two technologies, magnetoresistive biochips and microfluidics, will enable the development of highly competitive devices. This work reports the integration of a magnetoresistive biochip with a microfluidic system inside a portable and autonomous electronic platform aiming for a fully integrated device. A microfluidic structure fabricated in polydimethylsiloxane with dimensions of W: 0.5mm, H: 0.1mm, L: 10mm, associated to a mechanical system to align and seal the channel by pressure is presented (Fig. 1) [5]. The goal is to perform sample loading and transportation over the chip and simultaneously control the stringency and uniformity of the wash-out process. The biochip output is acquired by an electronic microsystem incorporating the circuitry to control, address and read-out the 30 spin-valve sensors sequentially (Fig. 1) [2]. This platform is being applied to the detection of water-borne microbial pathogens (e.g. Salmonella and Escherichia coli) and genetic diseases diagnosis (e.g. cystic fibrosis) through DNA hybridization assays. Open chamber measurements were performed as described elsewhere [2]. Briefly, a 20 μl sample droplet is manually dispensed over the chip, limited by a polymeric frame. When using the microfluidic system for sample loading, a known volume of sample is introduced into the fluidic system through the help of a syringe pump at a controlled velocity.

Spin-State Transition in La1-xSrxCoO3 Single Crystals

NASA Astrophysics Data System (ADS)

Bhardwaj, S.; Prabhakaran, D.; Awasthi, A. M.

2011-07-01

We present a study of the thermal conductivity (κ), specific heat (Cp) and Raman spectra of La1-xSrxCoO3 (x = 0,0.1) single crystals. Both the specimens have low thermal conductivity and board Raman peaks, arising from strong scattering of phonons by lattice disorder, produced by (and doping-enhanced) spin-states admixture of the Co3+ ions. The thermal conductivity anomalously deviates from ˜1/T behaviour at high (room) temperatures, expected of an insulator. High-temperature specific heat reveals large decrease in the metal-insulator (M-I) transition temperature with Sr-doping.

Influence of Salinity on Bacterioplankton Communities from the Brazilian Rain Forest to the Coastal Atlantic Ocean

PubMed Central

Silveira, Cynthia B.; Vieira, Ricardo P.; Cardoso, Alexander M.; Paranhos, Rodolfo; Albano, Rodolpho M.; Martins, Orlando B.

2011-01-01

Background Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean. Methodology/Principal Findings We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent. Conclusions/Significance Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean. PMID:21408023

Influence of salinity on bacterioplankton communities from the Brazilian rain forest to the coastal Atlantic Ocean.

PubMed

Silveira, Cynthia B; Vieira, Ricardo P; Cardoso, Alexander M; Paranhos, Rodolfo; Albano, Rodolpho M; Martins, Orlando B

2011-03-09

Planktonic bacteria are recognized as important drivers of biogeochemical processes in all aquatic ecosystems, however, the taxa that make up these communities are poorly known. The aim of this study was to investigate bacterial communities in aquatic ecosystems at Ilha Grande, Rio de Janeiro, Brazil, a preserved insular environment of the Atlantic rain forest and how they correlate with a salinity gradient going from terrestrial aquatic habitats to the coastal Atlantic Ocean. We analyzed chemical and microbiological parameters of water samples and constructed 16S rRNA gene libraries of free living bacteria obtained at three marine (two coastal and one offshore) and three freshwater (water spring, river, and mangrove) environments. A total of 836 sequences were analyzed by MOTHUR, yielding 269 freshwater and 219 marine operational taxonomic units (OTUs) grouped at 97% stringency. Richness and diversity indexes indicated that freshwater environments were the most diverse, especially the water spring. The main bacterial group in freshwater environments was Betaproteobacteria (43.5%), whereas Cyanobacteria (30.5%), Alphaproteobacteria (25.5%), and Gammaproteobacteria (26.3%) dominated the marine ones. Venn diagram showed no overlap between marine and freshwater OTUs at 97% stringency. LIBSHUFF statistics and PCA analysis revealed marked differences between the freshwater and marine libraries suggesting the importance of salinity as a driver of community composition in this habitat. The phylogenetic analysis of marine and freshwater libraries showed that the differences in community composition are consistent. Our data supports the notion that a divergent evolutionary scenario is driving community composition in the studied habitats. This work also improves the comprehension of microbial community dynamics in tropical waters and how they are structured in relation to physicochemical parameters. Furthermore, this paper reveals for the first time the pristine bacterioplankton communities in a tropical island at the South Atlantic Ocean.

Low host specificity and abundance of frugivorous lepidoptera in the lowland rain forests of Papua New Guinea

PubMed Central

Ctvrtecka, Richard; Miller, Scott E.; Rosati, Margaret E.; Molem, Kenneth; Damas, Kipiro; Gewa, Bradley; Novotny, Vojtech

2017-01-01

We studied a community of frugivorous Lepidoptera in the lowland rainforest of Papua New Guinea. Rearing revealed 122 species represented by 1,720 individuals from 326 woody plant species. Only fruits from 52% (171) of the plant species sampled were attacked. On average, Lepidoptera were reared from 1 in 89 fruits and a kilogram of fruit was attacked by 1.01 individuals. Host specificity of Lepidoptera was notably low: 69% (33) of species attacked plants from >1 family, 8% (4) fed on single family, 6% (3) on single genus and 17% (8) were monophagous. The average kilogram of fruits was infested by 0.81 individual from generalist species (defined here as feeding on >1 plant genus) and 0.07 individual from specialist species (feeding on a single host or congeneric hosts). Lepidoptera preferred smaller fruits with both smaller mesocarp and seeds. Large-seeded fruits with thin mesocarp tended to host specialist species whereas those with thick, fleshy mesocarp were often infested with both specialist and generalist species. The very low incidence of seed damage suggests that pre-dispersal seed predation by Lepidoptera does not play a major role in regulating plant populations via density-dependent mortality processes outlined by the Janzen-Connell hypothesis. PMID:28231249

Low host specificity and abundance of frugivorous lepidoptera in the lowland rain forests of Papua New Guinea.

PubMed

Sam, Katerina; Ctvrtecka, Richard; Miller, Scott E; Rosati, Margaret E; Molem, Kenneth; Damas, Kipiro; Gewa, Bradley; Novotny, Vojtech

2017-01-01

We studied a community of frugivorous Lepidoptera in the lowland rainforest of Papua New Guinea. Rearing revealed 122 species represented by 1,720 individuals from 326 woody plant species. Only fruits from 52% (171) of the plant species sampled were attacked. On average, Lepidoptera were reared from 1 in 89 fruits and a kilogram of fruit was attacked by 1.01 individuals. Host specificity of Lepidoptera was notably low: 69% (33) of species attacked plants from >1 family, 8% (4) fed on single family, 6% (3) on single genus and 17% (8) were monophagous. The average kilogram of fruits was infested by 0.81 individual from generalist species (defined here as feeding on >1 plant genus) and 0.07 individual from specialist species (feeding on a single host or congeneric hosts). Lepidoptera preferred smaller fruits with both smaller mesocarp and seeds. Large-seeded fruits with thin mesocarp tended to host specialist species whereas those with thick, fleshy mesocarp were often infested with both specialist and generalist species. The very low incidence of seed damage suggests that pre-dispersal seed predation by Lepidoptera does not play a major role in regulating plant populations via density-dependent mortality processes outlined by the Janzen-Connell hypothesis.

Crystal structure and low-energy Einstein mode in ErV{sub 2}Al{sub 20} intermetallic cage compound

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

Winiarski, Michał J., E-mail: mwiniarski@mif.pg.gda.pl; Klimczuk, Tomasz

Single crystals of a new ternary aluminide ErV{sub 2}Al{sub 20} were grown using a self-flux method. The crystal structure was determined by powder X-ray diffraction measurements and Rietveld refinement, and physical properties were studied by means of electrical resistivity, magnetic susceptibility and specific heat measurements. These measurements reveal that ErV{sub 2}Al{sub 20} is a Curie-Weiss paramagnet down to 1.95 K with an effective magnetic moment μ{sub eff} =9.27(1) μ{sub B} and Curie-Weiss temperature Θ{sub CW} =−0.55(4) K. The heat capacity measurements show a broad anomaly at low temperatures that is attributed to the presence of a low-energy Einstein mode withmore » characteristic temperature Θ{sub E} =44 K, approximately twice as high as in the isostructural ‘Einstein solid’ VAl{sub 10.1}. - Graphical abstract: A low-energy Einstein mode is observed in a novel intermetallic cage compound ErV{sub 2}Al{sub 20} by specific heat and resistivity measurements. - Highlights: • Single crystals of a new compound ErV{sub 2}Al{sub 20} were grown by self-flux method. • Crystal structure is reported, based on powder x-ray diffraction. • ErV{sub 2}Al{sub 20} is a Curie-Weiss paramagnet. • Low-energy ‘rattling’ phonon mode (Θ{sub E}=44 K) is found in specific heat measurements.« less

Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms.

PubMed

Zhang, Qiang; Wang, Tingting; Zhou, Qian; Zhang, Peng; Gong, Yanhai; Gou, Honglei; Xu, Jian; Ma, Bo

2017-01-23

Wider application of single-cell analysis has been limited by the lack of an easy-to-use and low-cost strategy for single-cell isolation that can be directly coupled to single-cell sequencing and single-cell cultivation, especially for small-size microbes. Herein, a facile droplet microfluidic platform was developed to dispense individual microbial cells into conventional standard containers for downstream analysis. Functional parts for cell encapsulation, droplet inspection and sorting, as well as a chip-to-tube capillary interface were integrated on one single chip with simple architecture, and control of the droplet sorting was achieved by a low-cost solenoid microvalve. Using microalgal and yeast cells as models, single-cell isolation success rate of over 90% and single-cell cultivation success rate of 80% were demonstrated. We further showed that the individual cells isolated can be used in high-quality DNA and RNA analyses at both gene-specific and whole-genome levels (i.e. real-time quantitative PCR and genome sequencing). The simplicity and reliability of the method should improve accessibility of single-cell analysis and facilitate its wider application in microbiology researches.

Development of a facile droplet-based single-cell isolation platform for cultivation and genomic analysis in microorganisms

PubMed Central

Zhang, Qiang; Wang, Tingting; Zhou, Qian; Zhang, Peng; Gong, Yanhai; Gou, Honglei; Xu, Jian; Ma, Bo

2017-01-01

Wider application of single-cell analysis has been limited by the lack of an easy-to-use and low-cost strategy for single-cell isolation that can be directly coupled to single-cell sequencing and single-cell cultivation, especially for small-size microbes. Herein, a facile droplet microfluidic platform was developed to dispense individual microbial cells into conventional standard containers for downstream analysis. Functional parts for cell encapsulation, droplet inspection and sorting, as well as a chip-to-tube capillary interface were integrated on one single chip with simple architecture, and control of the droplet sorting was achieved by a low-cost solenoid microvalve. Using microalgal and yeast cells as models, single-cell isolation success rate of over 90% and single-cell cultivation success rate of 80% were demonstrated. We further showed that the individual cells isolated can be used in high-quality DNA and RNA analyses at both gene-specific and whole-genome levels (i.e. real-time quantitative PCR and genome sequencing). The simplicity and reliability of the method should improve accessibility of single-cell analysis and facilitate its wider application in microbiology researches. PMID:28112223

DNA origami-based shape IDs for single-molecule nanomechanical genotyping

NASA Astrophysics Data System (ADS)

Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

2017-04-01

Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ~10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level.

DNA origami-based shape IDs for single-molecule nanomechanical genotyping

PubMed Central

Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

2017-01-01

Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ∼10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level. PMID:28382928

Comparing Student Achievement in Single-Gender and Coeducational Classrooms Using the Tennessee Comprehensive Achievement Program

ERIC Educational Resources Information Center

Young, La Sandra M.

2016-01-01

Schools across the nation are faced with an increased urgency to seek innovative strategies to improve low academic performance of students as mandated by No Child Left Behind Legislation (Friend, 2006). Specifically, in the state of Tennessee in schools such as those located in the Shelby County Schools District who have experienced low student…

Gene expression profiling of single cells on large-scale oligonucleotide arrays

PubMed Central

Hartmann, Claudia H.; Klein, Christoph A.

2006-01-01

Over the last decade, important insights into the regulation of cellular responses to various stimuli were gained by global gene expression analyses of cell populations. More recently, specific cell functions and underlying regulatory networks of rare cells isolated from their natural environment moved to the center of attention. However, low cell numbers still hinder gene expression profiling of rare ex vivo material in biomedical research. Therefore, we developed a robust method for gene expression profiling of single cells on high-density oligonucleotide arrays with excellent coverage of low abundance transcripts. The protocol was extensively tested with freshly isolated single cells of very low mRNA content including single epithelial, mature and immature dendritic cells and hematopoietic stem cells. Quantitative PCR confirmed that the PCR-based global amplification method did not change the relative ratios of transcript abundance and unsupervised hierarchical cluster analysis revealed that the histogenetic origin of an individual cell is correctly reflected by the gene expression profile. Moreover, the gene expression data from dendritic cells demonstrate that cellular differentiation and pathway activation can be monitored in individual cells. PMID:17071717

Improving the efficiency of CHO cell line generation using glutamine synthetase gene knockout cells.

PubMed

Fan, Lianchun; Kadura, Ibrahim; Krebs, Lara E; Hatfield, Christopher C; Shaw, Margaret M; Frye, Christopher C

2012-04-01

Although Chinese hamster ovary (CHO) cells, with their unique characteristics, have become a major workhorse for the manufacture of therapeutic recombinant proteins, one of the major challenges in CHO cell line generation (CLG) is how to efficiently identify those rare, high-producing clones among a large population of low- and non-productive clones. It is not unusual that several hundred individual clones need to be screened for the identification of a commercial clonal cell line with acceptable productivity and growth profile making the cell line appropriate for commercial application. This inefficiency makes the process of CLG both time consuming and laborious. Currently, there are two main CHO expression systems, dihydrofolate reductase (DHFR)-based methotrexate (MTX) selection and glutamine synthetase (GS)-based methionine sulfoximine (MSX) selection, that have been in wide industrial use. Since selection of recombinant cell lines in the GS-CHO system is based on the balance between the expression of the GS gene introduced by the expression plasmid and the addition of the GS inhibitor, L-MSX, the expression of GS from the endogenous GS gene in parental CHOK1SV cells will likely interfere with the selection process. To study endogenous GS expression's potential impact on selection efficiency, GS-knockout CHOK1SV cell lines were generated using the zinc finger nuclease (ZFN) technology designed to specifically target the endogenous CHO GS gene. The high efficiency (∼2%) of bi-allelic modification on the CHO GS gene supports the unique advantages of the ZFN technology, especially in CHO cells. GS enzyme function disruption was confirmed by the observation of glutamine-dependent growth of all GS-knockout cell lines. Full evaluation of the GS-knockout cell lines in a standard industrial cell culture process was performed. Bulk culture productivity improved two- to three-fold through the use of GS-knockout cells as parent cells. The selection stringency was significantly increased, as indicated by the large reduction of non-producing and low-producing cells after 25 µM L-MSX selection, and resulted in a six-fold efficiency improvement in identifying similar numbers of high-productive cell lines for a given recombinant monoclonal antibody. The potential impact of GS-knockout cells on recombinant protein quality is also discussed. Copyright © 2011 Wiley Periodicals, Inc.

Challenges facing general internal medicine in the 99th Congress.

PubMed

Prout, D M

1986-01-01

Since 1976, federal support for training in general internal medicine has been provided through the primary care residency programs under Title VII of the Public Health Service Act. Continuation of these programs is now in jeopardy because of severe fiscal pressures and the response of Congress to the resulting budgetary stringency. General internal medicine faces immediate problems in the budgetary, authorization, and appropriations arenas. However, Congressional proposals for changing the method by which Medicare pays for all graduate medical education may provide an important opportunity. Under a revised method of financing graduate medical education, general internal medicine could eliminate its historical dependence on increasingly unstable federal grant funds and could contribute to the development of new federal incentives for training in the primary care specialties.

Intellectual Disability, Mild Cognitive Impairment, and Risk for Dementia

PubMed Central

Silverman, Wayne P.; Zigman, Warren B.; Krinsky-McHale, Sharon J.; Ryan, Robert; Schupf, Nicole

2013-01-01

People with intellectual disability (ID) are living longer than ever before, raising concerns about old-age associated disorders. Dementia is among the most serious of these disorders, and theories relating cognitive reserve to risk predict that older adults with ID should be particularly vulnerable. Previous estimates of relative risk for dementia associated with ID have been inconsistent, and the present analyses examined the possible influence of variation in diagnostic criteria on findings. As expected, relaxation in the stringency of case definition for adults with ID increased relative risk, underscoring the importance of developing valid criteria for defining mild cognitive impairment, early dementia, and distinguishing between the two in adults with ID. Once available, these standards will contribute to more effective evidence-based planning. PMID:24273589

Solid-phase supports for the in situ assembly of quantum dot-FRET hybridization assays in channel microfluidics.

PubMed

Tavares, Anthony J; Noor, M Omair; Uddayasankar, Uvaraj; Krull, Ulrich J; Vannoy, Charles H

2014-01-01

Semiconductor quantum dots (QDs) have long served as integral components in signal transduction modalities such as Förster resonance energy transfer (FRET). The majority of bioanalytical methods using QDs for FRET-based techniques simply monitor binding-induced conformational changes. In more recent work, QDs have been incorporated into solid-phase support systems, such as microfluidic chips, to serve as physical platforms in the development of functional biosensors and bioprobes. Herein, we describe a simple strategy for the transduction of nucleic acid hybridization that combines a novel design method based on FRET with an electrokinetically controlled microfluidic technology, and that offers further potential for amelioration of sample-handling issues and for simplification of dynamic stringency control.

Effect of the stringency of conditions on caloric test results in healthy subjects.

PubMed

Krstulovic, Claudio; Tulsidas Mahtani, Bharti; Atrache Al Attrache, Nabil; Pérez-Garrigues, Herminio

The caloric test is widely used to assess vestibular function, but the conditions in which it is performed can vary. Caloric nystagmus obtained in 57 healthy subjects were compared: 24 subjects studied in ideal conditions and 33 subjects in non-ideal conditions. A statistically significant decrease in the slow phase velocity of the 4 irrigations performed on the subjects in non-ideal conditions was observed. This must be considered, especially in subjects with suspected bilateral involvement. Stringent conditions reduce the risk of misdiagnosis with bilateral deficit. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Otorrinolaringología y Cirugía de Cabeza y Cuello. All rights reserved.

Low-cost and highly efficient DNA biosensor for heavy metal ion using specific DNAzyme-modified microplate and portable glucometer-based detection mode.

PubMed

Zhang, Jin; Tang, Ying; Teng, Liumei; Lu, Minghua; Tang, Dianping

2015-06-15

A simple and low-cost DNA sensing platform based on Pb(2+)-specific DNAzyme-modified microplate was successfully developed for highly sensitive monitoring of lead ion (Pb(2+), one kind of toxic heavy metal ion) in the environmental samples coupling with a portable personal glucometer (PGM)-based detection mode. The detection cell was first prepared simply by means of immobilizing the DNAzyme on the streptavidin-modified microplate. Gold nanoparticle labeled with single-stranded DNA and invertase (Enz-AuNP-DNA) was utilized as the signal-transduction tag to produce PGM substrate (glucose). Upon addition of lead ion into the microplate, the substrate strand of the immobilized DNAzyme was catalytically cleaved by target Pb(2+), and the newly generated single-strand DNA in the microplate could hybridize again with the single-stranded DNA on the Enz-AuNP-DNA. Accompanying with the Enz-AuNP-DNA, the carried invertase could convert sucrose into glucose. The as-produced glucose could be monitored by using a widely accessible PGM for in situ amplified digital readout. Based on Enz-AuNP-DNA amplification strategy, as low as 1.0 pM Pb(2+) could be detected under the optimal conditions. Moreover, the methodology also showed good reproducibility and high selectivity toward target Pb(2+) against other metal ions because of highly specific Pb(2+)-dependent DNAzyme, and was applicable for monitoring Pb(2+) in the naturally contaminated sewage and spiked drinking water samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Compendium of Single Event Effects, Total Ionizing Dose, and Displacement Damage for Candidate Spacecraft Electronics for NASA

NASA Technical Reports Server (NTRS)

LaBel, Kenneth A.; OBryan, Martha V.; Chen, Dakai; Campola, Michael J.; Casey, Megan C.; Pellish, Jonathan A.; Lauenstein, Jean-Marie; Wilcox, Edward P.; Topper, Alyson D.; Ladbury, Raymond L.;

Low-speed single-element airfoil synthesis

NASA Technical Reports Server (NTRS)

Mcmasters, J. H.; Henderson, M. L.

1979-01-01

The use of recently developed airfoil analysis/design computational tools to clarify, enrich and extend the existing experimental data base on low-speed, single element airfoils is demonstrated. A discussion of the problem of tailoring an airfoil for a specific application at its appropriate Reynolds number is presented. This problem is approached by use of inverse (or synthesis) techniques, wherein a desirable set of boundary layer characteristics, performance objectives, and constraints are specified, which then leads to derivation of a corresponding viscous flow pressure distribution. Examples are presented which demonstrate the synthesis approach, following presentation of some historical information and background data which motivate the basic synthesis process.

Surface Passivation and Junction Formation Using Low Energy Hydrogen Implants

NASA Technical Reports Server (NTRS)

Fonash, S. J.

1985-01-01

New applications for high current, low energy hydrogen ion implants on single crystal and polycrystal silicon grain boundaries are discussed. The effects of low energy hydrogen ion beams on crystalline Si surfaces are considered. The effect of these beams on bulk defects in crystalline Si is addressed. Specific applications of H+ implants to crystalline Si processing are discussed. In all of the situations reported on, the hydrogen beams were produced using a high current Kaufman ion source.

Chagas' disease in Aboriginal and Creole communities from the Gran Chaco Region of Argentina: Seroprevalence and molecular parasitological characterization.

PubMed

Lucero, R H; Brusés, B L; Cura, C I; Formichelli, L B; Juiz, N; Fernández, G J; Bisio, M; Deluca, G D; Besuschio, S; Hernández, D O; Schijman, A G

2016-07-01

Most indigenous ethnias from Northern Argentina live in rural areas of "the Gran Chaco" region, where Trypanosoma cruzi is endemic. Serological and parasitological features have been poorly characterized in Aboriginal populations and scarce information exist regarding relevant T. cruzi discrete typing units (DTU) and parasitic loads. This study was focused to characterize T. cruzi infection in Qom, Mocoit, Pit'laxá and Wichi ethnias (N=604) and Creole communities (N=257) inhabiting rural villages from two highly endemic provinces of the Argentinean Gran Chaco. DNA extracted using Hexadecyltrimethyl Ammonium Bromide reagent from peripheral blood samples was used for conventional PCR targeted to parasite kinetoplastid DNA (kDNA) and identification of DTUs using nuclear genomic markers. In kDNA-PCR positive samples from three rural Aboriginal communities of "Monte Impenetrable Chaqueño", minicircle signatures were characterized by Low stringency single primer-PCR and parasitic loads calculated using Real-Time PCR. Seroprevalence was higher in Aboriginal (47.98%) than in Creole (27.23%) rural communities (Chi square, p=4.e(-8)). A low seroprevalence (4.3%) was detected in a Qom settlement at the suburbs of Resistencia city (Fisher Exact test, p=2.e(-21)).The kDNA-PCR positivity was 42.15% in Aboriginal communities and 65.71% in Creole populations (Chi square, p=5.e(-4)). Among Aboriginal communities kDNA-PCR positivity was heterogeneous (Chi square, p=1.e(-4)). Highest kDNA-PCR positivity (79%) was detected in the Qom community of Colonia Aborigen and the lowest PCR positivity in two different surveys at the Wichi community of Misión Nueva Pompeya (33.3% in 2010 and 20.8% in 2014). TcV (or TcII/V/VI) was predominant in both Aboriginal and Creole communities, in agreement with DTU distribution reported for the region. Besides, two subjects were infected with TcVI, one with TcI and four presented mixed infections of TcV plus TcII/VI. Most minicircle signatures clustered according to their original localities, but in a few cases, signatures from one locality clustered with signatures from other village, suggesting circulation of the same strains in the area. Parasitic loads ranged from undetectable to around 50 parasite equivalents/mL, showing higher values than those generally observed in chronic Chagas disease patients living in urban centers of Argentina. Our findings reveal the persistence of high levels of infection in these neglected populations. Copyright © 2016. Published by Elsevier B.V.

Contribution of low-temperature single-molecule techniques to structural issues of pigment–protein complexes from photosynthetic purple bacteria

PubMed Central

Löhner, Alexander; Cogdell, Richard

2018-01-01

As the electronic energies of the chromophores in a pigment–protein complex are imposed by the geometrical structure of the protein, this allows the spectral information obtained to be compared with predictions derived from structural models. Thereby, the single-molecule approach is particularly suited for the elucidation of specific, distinctive spectral features that are key for a particular model structure, and that would not be observable in ensemble-averaged spectra due to the heterogeneity of the biological objects. In this concise review, we illustrate with the example of the light-harvesting complexes from photosynthetic purple bacteria how results from low-temperature single-molecule spectroscopy can be used to discriminate between different structural models. Thereby the low-temperature approach provides two advantages: (i) owing to the negligible photobleaching, very long observation times become possible, and more importantly, (ii) at cryogenic temperatures, vibrational degrees of freedom are frozen out, leading to sharper spectral features and in turn to better resolved spectra. PMID:29321265

On the applicability of low-dimensional models for convective flow reversals at extreme Prandtl numbers

NASA Astrophysics Data System (ADS)

Mannattil, Manu; Pandey, Ambrish; Verma, Mahendra K.; Chakraborty, Sagar

2017-12-01

Constructing simpler models, either stochastic or deterministic, for exploring the phenomenon of flow reversals in fluid systems is in vogue across disciplines. Using direct numerical simulations and nonlinear time series analysis, we illustrate that the basic nature of flow reversals in convecting fluids can depend on the dimensionless parameters describing the system. Specifically, we find evidence of low-dimensional behavior in flow reversals occurring at zero Prandtl number, whereas we fail to find such signatures for reversals at infinite Prandtl number. Thus, even in a single system, as one varies the system parameters, one can encounter reversals that are fundamentally different in nature. Consequently, we conclude that a single general low-dimensional deterministic model cannot faithfully characterize flow reversals for every set of parameter values.

Isolation and Identification of Genes Activating Uas2-Dependent Adh2 Expression in Saccharomyces Cerevisiae

PubMed Central

Donoviel, M. S.; Young, E. T.

1996-01-01

Two cis-acting elements have been identified that act synergistically to regulate expression of the glucose-repressed alcohol dehydrogenase 2 (ADH2) gene. UAS1 is bound by the trans-activator Adr1p. UAS2 is thought to be the binding site for an unidentified regulatory protein. A genetic selection based on a UAS2-dependent ADH2 reporter was devised to isolate genes capable of activating UAS2-dependent transcription. One set of UAS2-dependent genes contained SPT6/CRE2/SSN20. Multicopy SPT6 caused improper expression of chromosomal ADH2. A second set of UAS2-dependent clones contained a previously uncharacterized open reading frame designated MEU1 (Multicopy Enhancer of UAS2). A frame shift mutation in MEU1 abolished its ability to activate UAS2-dependent gene expression. Multicopy MEU1 expression suppressed the constitutive ADH2 expression caused by cre2-1. Disruption of MEU1 reduced endogenous ADH2 expression about twofold but had no effect on cell viability or growth. No homologues of MEU1 were identified by low-stringency Southern hybridization of yeast genomic DNA, and no significant homologues were found in the sequence data bases. A MEU1/β-gal fusion protein was not localized to a particular region of the cell. MEU1 is linked to PPR1 on chromosome XII. PMID:8807288

PlantTribes: a gene and gene family resource for comparative genomics in plants

PubMed Central

Wall, P. Kerr; Leebens-Mack, Jim; Müller, Kai F.; Field, Dawn; Altman, Naomi S.; dePamphilis, Claude W.

2008-01-01

The PlantTribes database (http://fgp.huck.psu.edu/tribe.html) is a plant gene family database based on the inferred proteomes of five sequenced plant species: Arabidopsis thaliana, Carica papaya, Medicago truncatula, Oryza sativa and Populus trichocarpa. We used the graph-based clustering algorithm MCL [Van Dongen (Technical Report INS-R0010 2000) and Enright et al. (Nucleic Acids Res. 2002; 30: 1575–1584)] to classify all of these species’ protein-coding genes into putative gene families, called tribes, using three clustering stringencies (low, medium and high). For all tribes, we have generated protein and DNA alignments and maximum-likelihood phylogenetic trees. A parallel database of microarray experimental results is linked to the genes, which lets researchers identify groups of related genes and their expression patterns. Unified nomenclatures were developed, and tribes can be related to traditional gene families and conserved domain identifiers. SuperTribes, constructed through a second iteration of MCL clustering, connect distant, but potentially related gene clusters. The global classification of nearly 200 000 plant proteins was used as a scaffold for sorting ∼4 million additional cDNA sequences from over 200 plant species. All data and analyses are accessible through a flexible interface allowing users to explore the classification, to place query sequences within the classification, and to download results for further study. PMID:18073194

3'-terminal sequence of a small round structured virus (SRSV) in Japan.

PubMed

Utagawa, E T; Takeda, N; Inouye, S; Kasuga, K; Yamazaki, S

1994-01-01

We determined the nucleotide sequence of about 1,000 bases from the 3'-terminus of a small round structured virus (SRSV), which caused a gastroenteritis outbreak in Chiba Prefecture, Japan, in 1987. The sequence was compared with the corresponding sequence region of Norwalk virus; it consisted of a part of the open reading frame 2 (ORF2), whole ORF3, and 3'-noncoding region (NCR). The 624-base-long ORF3 had sequence homology of 68% with the corresponding region of Norwalk virus. (The amino acid sequence homology was 74%.) The 94-base-long NCR had 65% homology with Norwalk virus. We then selected two consensus-sequence portions in the above sequence between Chiba and Norwalk viruses for primers in the reverse transcriptase-polymerase chain reaction (RT-PCR). Using this primer set, we detected 669-bp bands in agarose gel electrophoresis of RT-PCR products from feces containing Chiba or Norwalk viruses. Furthermore, in Southern hybridization with Chiba probes which were labeled with digoxigenin-dUTP in PCR, the bands of the two viruses were clearly stained under a low stringency condition. Since both Chiba and Norwalk viruses were detected by the above primer set although they are geographically and chronologically different viruses, our primer-pair may be useful for detection of a broad range of SRSVs which cause gastroenteritis in different areas.

Guanine nucleotide-binding regulatory proteins in retinal pigment epithelial cells

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

Jiang, Meisheng; Tran, V.T.; Fong, H.K.W.

1991-05-01

The expression of GTP-binding regulatory proteins (G proteins) in retinal pigment epithelial (RPE) cells was analyzed by RNA blot hybridization and cDNA amplification. Both adult and fetal human RPE cells contain mRNA for multiple G protein {alpha} subunits (G{alpha}) including G{sub s}{alpha}, G{sub i-1}{alpha}, G{sub i-2}{alpha}, G{sub i-3}{alpha}, and G{sub z}{alpha} (or G{sub x}{alpha}), where G{sub s} and G{sub i} are proteins that stimulate or inhibit adenylyl cyclase, respectively, and G{sub z} is a protein that may mediate pertussis toxin-insensitive events. Other G{alpha}-related mRNA transcripts were detected in fetal RPE cells by low-stringency hybridization to G{sub i-2}{alpha} and G{sub s}{alpha}more » protein-coding cDNA probes. The diversity of G proteins in RPE cells was further studied by cDNA amplification with reverse transcriptase and the polymerase chain reaction. This approach revealed that, besides the above mentioned members of the G{alpha} gene family, at least two other G{alpha} subunits are expressed in RPE cells. Human retinal cDNA clones that encode one of the additional G{alpha} subunits were isolated and characterized. The results indicate that this G{alpha} subunit belongs to a separate subfamily of G proteins that may be insensitive to inhibition by pertussis toxin.« less

Identification of a GTP-binding protein. cap alpha. subunit that lacks an apparent ADP-ribosylation site for pertussis toxin

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

Fong, H.K.W.; Yoshimoto, K.K.; Eversole-Cire, P.

1988-05-01

Recent molecular cloning of cDNA for the ..cap alpha.. subunit of bovine transducin (a guanine nucleotide-binding regulatory protein, or G protein) has revealed the presence of two retinal-specific transducins, called T/sub r/ and T/sub c/, which are expressed in rod or cone photoreceptor cells. In a further study of G-protein diversity and signal transduction in the retina, the authors have identified a G-protein ..cap alpha.. subunit, which they refer to as G/sub z/..cap alpha.., by isolating a human retinal cDNA clone that cross-hybridizes at reduced stringency with bovine T/sub r/ ..cap alpha..-subunit cDNA. The deduced amino acid sequence of G/submore » z/..cap alpha.. is 41-67% identical with those of other known G-protein ..cap alpha.. subunits. However, the 355-residue G/sub z/..cap alpha.. lacks a consensus site for ADP-ribosylation by pertussis toxin, and its amino acid sequence varies within a number of regions that are strongly conserved among all of the other G-protein ..cap alpha.. subunits. They suggest that G/sub z/..cap alpha.., which appears to be highly expressed in neural tissues, represents a member of a subfamily of G proteins that mediate signal transduction in pertussis toxin-insensitive systems.« less

Progress toward thin-film GaAs solar cells using a single-crystal Si substrate with a Ge interlayer

NASA Technical Reports Server (NTRS)

Yeh, Y. C. M.; Wang, K. L.; Zwerdling, S.

1982-01-01

Development of a technology for fabricating light-weight, high-efficiency, radiation-resistant solar cells for space applications is reported. The approaches currently adopted are to fabricate shallow homojunction n(+)/p as well as p/n AlGaAs-heteroface GaAs solar cells by organometallic chemical vapor deposition (OM-CVD) on single-crystal Si substrates using in each case, a thin Ge epi-interlayer first grown by CVD. This approach maintains the advantages of the low specific gravity of Si as well as the high efficiency and radiation-resistant properties of the GaAs solar cell which can lead to greatly improved specific power for a solar array. The growth of single-crystal GaAs epilayers on Ge epi-interlayers on Si substrates is investigated. Related solar cell fabrication is reviewed.

Energy-Specific Optimization of Attenuation Thresholds for Low-Energy Virtual Monoenergetic Images in Renal Lesion Evaluation.

PubMed

Patel, Bhavik N; Farjat, Alfredo; Schabel, Christoph; Duvnjak, Petar; Mileto, Achille; Ramirez-Giraldo, Juan Carlos; Marin, Daniele

2018-05-01

The purpose of this study was to determine in vitro and in vivo the optimal threshold for renal lesion vascularity at low-energy (40-60 keV) virtual monoenergetic imaging. A rod simulating unenhanced renal parenchymal attenuation (35 HU) was fitted with a syringe containing water. Three iodinated solutions (0.38, 0.57, and 0.76 mg I/mL) were inserted into another rod that simulated enhanced renal parenchyma (180 HU). Rods were inserted into cylindric phantoms of three different body sizes and scanned with single- and dual-energy MDCT. In addition, 102 patients (32 men, 70 women; mean age, 66.8 ± 12.9 [SD] years) with 112 renal lesions (67 nonvascular, 45 vascular) measuring 1.1-8.9 cm underwent single-energy unenhanced and contrast-enhanced dual-energy CT. Optimal threshold attenuation values that differentiated vascular from nonvascular lesions at 40-60 keV were determined. Mean optimal threshold values were 30.2 ± 3.6 (standard error), 20.9 ± 1.3, and 16.1 ± 1.0 HU in the phantom, and 35.9 ± 3.6, 25.4 ± 1.8, and 17.8 ± 1.8 HU in the patients at 40, 50, and 60 keV. Sensitivity and specificity for the thresholds did not change significantly between low-energy and 70-keV virtual monoenergetic imaging (sensitivity, 87-98%; specificity, 90-91%). The AUC from 40 to 70 keV was 0.96 (95% CI, 0.93-0.99) to 0.98 (95% CI, 0.95-1.00). Low-energy virtual monoenergetic imaging at energy-specific optimized attenuation thresholds can be used for reliable characterization of renal lesions.

Deep proteomic profiling of vasopressin-sensitive collecting duct cells. I. Virtual Western blots and molecular weight distributions.

PubMed

Yang, Chin-Rang; Tongyoo, Pumipat; Emamian, Milad; Sandoval, Pablo C; Raghuram, Viswanathan; Knepper, Mark A

2015-12-15

The mouse mpkCCD cell line is a continuous cultured epithelial cell line with characteristics of renal collecting duct principal cells. This line is widely used to study epithelial transport and its regulation. To provide a data resource useful for experimental design and interpretation in studies using mpkCCD cells, we have carried out "deep" proteomic profiling of these cells using three levels of fractionation (differential centrifugation, SDS-PAGE, and HPLC) followed by tandem mass spectrometry to identify and quantify proteins. The analysis of all resulting samples generated 34.6 gigabytes of spectral data. As a result, we identified 6,766 proteins in mpkCCD cells at a high level of stringency. These proteins are expressed over eight orders of magnitude of protein abundance. The data are provided to users as a public data base (https://helixweb.nih.gov/ESBL/Database/mpkFractions/). The mass spectrometry data were mapped back to their gel slices to generate "virtual Western blots" for each protein. For most of the 6,766 proteins, the apparent molecular weight from SDS-PAGE agreed closely with the calculated molecular weight. However, a substantial fraction (>15%) of proteins was found to run aberrantly, with much higher or much lower mobilities than predicted. These proteins were analyzed to identify mechanisms responsible for altered mobility on SDS-PAGE, including high or low isoelectric point, high or low hydrophobicity, physiological cleavage, residence in the lysosome, posttranslational modifications, and expression of alternative isoforms due to alternative exon usage. Additionally, this analysis identified a previously unrecognized isoform of aquaporin-2 with apparent molecular mass <20 kDa. Copyright © 2015 the American Physiological Society.

Deep proteomic profiling of vasopressin-sensitive collecting duct cells. I. Virtual Western blots and molecular weight distributions

PubMed Central

Yang, Chin-Rang; Tongyoo, Pumipat; Emamian, Milad; Sandoval, Pablo C.; Raghuram, Viswanathan

2015-01-01

The mouse mpkCCD cell line is a continuous cultured epithelial cell line with characteristics of renal collecting duct principal cells. This line is widely used to study epithelial transport and its regulation. To provide a data resource useful for experimental design and interpretation in studies using mpkCCD cells, we have carried out “deep” proteomic profiling of these cells using three levels of fractionation (differential centrifugation, SDS-PAGE, and HPLC) followed by tandem mass spectrometry to identify and quantify proteins. The analysis of all resulting samples generated 34.6 gigabytes of spectral data. As a result, we identified 6,766 proteins in mpkCCD cells at a high level of stringency. These proteins are expressed over eight orders of magnitude of protein abundance. The data are provided to users as a public data base (https://helixweb.nih.gov/ESBL/Database/mpkFractions/). The mass spectrometry data were mapped back to their gel slices to generate “virtual Western blots” for each protein. For most of the 6,766 proteins, the apparent molecular weight from SDS-PAGE agreed closely with the calculated molecular weight. However, a substantial fraction (>15%) of proteins was found to run aberrantly, with much higher or much lower mobilities than predicted. These proteins were analyzed to identify mechanisms responsible for altered mobility on SDS-PAGE, including high or low isoelectric point, high or low hydrophobicity, physiological cleavage, residence in the lysosome, posttranslational modifications, and expression of alternative isoforms due to alternative exon usage. Additionally, this analysis identified a previously unrecognized isoform of aquaporin-2 with apparent molecular mass <20 kDa. PMID:26310816

Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies.

PubMed

Damiati, E; Borsani, G; Giacopuzzi, Edoardo

2016-05-01

The Ion Proton platform allows to perform whole exome sequencing (WES) at low cost, providing rapid turnaround time and great flexibility. Products for WES on Ion Proton system include the AmpliSeq Exome kit and the recently introduced HiQ sequencing chemistry. Here, we used gold standard variants from GIAB consortium to assess the performances in variants identification, characterize the erroneous calls and develop a filtering strategy to reduce false positives. The AmpliSeq Exome kit captures a large fraction of bases (>94 %) in human CDS, ClinVar genes and ACMG genes, but with 2,041 (7 %), 449 (13 %) and 11 (19 %) genes not fully represented, respectively. Overall, 515 protein coding genes contain hard-to-sequence regions, including 90 genes from ClinVar. Performance in variants detection was maximum at mean coverage >120×, while at 90× and 70× we measured a loss of variants of 3.2 and 4.5 %, respectively. WES using HiQ chemistry showed ~71/97.5 % sensitivity, ~37/2 % FDR and ~0.66/0.98 F1 score for indels and SNPs, respectively. The proposed low, medium or high-stringency filters reduced the amount of false positives by 10.2, 21.2 and 40.4 % for indels and 21.2, 41.9 and 68.2 % for SNP, respectively. Amplicon-based WES on Ion Proton platform using HiQ chemistry emerged as a competitive approach, with improved accuracy in variants identification. False-positive variants remain an issue for the Ion Torrent technology, but our filtering strategy can be applied to reduce erroneous variants.

Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth*

PubMed Central

Mertz, Joseph; Tan, Haiyan; Pagala, Vishwajeeth; Bai, Bing; Chen, Ping-Chung; Li, Yuxin; Cho, Ji-Hoon; Shaw, Timothy; Wang, Xusheng; Peng, Junmin

2015-01-01

The mind bomb 1 (Mib1) ubiquitin ligase is essential for controlling metazoan development by Notch signaling and possibly the Wnt pathway. It is also expressed in postmitotic neurons and regulates neuronal morphogenesis and synaptic activity by mechanisms that are largely unknown. We sought to comprehensively characterize the Mib1 interactome and study its potential function in neuron development utilizing a novel sequential elution strategy for affinity purification, in which Mib1 binding proteins were eluted under different stringency and then quantified by the isobaric labeling method. The strategy identified the Mib1 interactome with both deep coverage and the ability to distinguish high-affinity partners from low-affinity partners. A total of 817 proteins were identified during the Mib1 affinity purification, including 56 high-affinity partners and 335 low-affinity partners, whereas the remaining 426 proteins are likely copurified contaminants or extremely weak binding proteins. The analysis detected all previously known Mib1-interacting proteins and revealed a large number of novel components involved in Notch and Wnt pathways, endocytosis and vesicle transport, the ubiquitin-proteasome system, cellular morphogenesis, and synaptic activities. Immunofluorescence studies further showed colocalization of Mib1 with five selected proteins: the Usp9x (FAM) deubiquitinating enzyme, alpha-, beta-, and delta-catenins, and CDKL5. Mutations of CDKL5 are associated with early infantile epileptic encephalopathy-2 (EIEE2), a severe form of mental retardation. We found that the expression of Mib1 down-regulated the protein level of CDKL5 by ubiquitination, and antagonized CDKL5 function during the formation of dendritic spines. Thus, the sequential elution strategy enables biochemical characterization of protein interactomes; and Mib1 analysis provides a comprehensive interactome for investigating its role in signaling networks and neuronal development. PMID:25931508

Low temperature Schottky anomalies in the specific heat of LaCoO3: Defect-stabilized finite spin states

NASA Astrophysics Data System (ADS)

He, C.; Zheng, H.; Mitchell, J. F.; Foo, M. L.; Cava, R. J.; Leighton, C.

2009-03-01

Measurement of the low temperature specific heat of LaCoO3 single crystals reveals a previously unobserved Schottky anomaly with an energy level splitting, 0.5 meV, that is associated with the first excited spin state of the Co3+ ion. These states persist well below 2 K and have a g-factor around 3.5, consistent with the high-spin spin-orbit triplet, implying the existence of a low density (approximately 0.1% of the sites) of finite-spin Co ions even in the T =0 limit. We propose that these states are trapped at defects and are consistent with the magnetic excitons observed in earlier work.

Impact experiments into multiple-mesh targets: Concept development of a lightweight collisional bumper

NASA Technical Reports Server (NTRS)

Hoerz, Friedrich; Cintala, Mark J.; Bernhard, Ronald P.; Cardenas, Frank; Davidson, William; Haynes, Gerald; See, Thomas H.; Winkler, Jerry; Gray, Barry

1993-01-01

The utility of multiple-mesh targets as potential lightweight shields to protect spacecraft in low-Earth orbit against collisional damage is explored. Earlier studies revealed that single meshes comminute hypervelocity impactors with efficiencies comparable to contiguous targets. Multiple interaction of projectile fragments with any number of meshes should lead to increased comminution, deceleration, and dispersion of the projectile, such that all debris exiting the mesh stack possesses low specific energies (ergs/sq cm) that would readily be tolerated by many flight systems. The study is conceptually exploring the sensitivity of major variables such as impact velocity, the specific areal mass (g/sq cm) of the total mesh stack (SM), and the separation distance (S) between individual meshes. Most experiments employed five or ten meshes with total SM typically less than 0.5 the specific mass of the impactor, and silicate glass impactors rather than metal projectiles. While projectile comminution increases with increasing impact velocity due to progressively higher shock stresses, encounters with multiple-meshes at low velocity (1-2 km/s) already lead to significant disruption of the glass impactors, with the resulting fragments being additionally decelerated and dispersed by subsequent meshes, and, unlike most contiguous single-plate bumpers, leading to respectable performance at low velocity. Total specific bumper mass must be the subject of careful trade-off studies; relatively massive bumpers will generate too much debris being dislodged from the bumper itself, while exceptionally lightweight designs will not cause sufficient comminution, deceleration, or dispersion of the impactor. Separation distance was found to be a crucial design parameter, as it controls the dispersion of the fragment cloud. Substantial mass savings could result if maximum separation distances were employed. The total mass of debris dislodged by multiple-mesh stacks is modestly smaller than that of single, contiguous-membrane shields. The cumulative surface area of all penetration holes in multiple mesh stacks is an order of magnitude smaller than that in analog multiple-foil shields, suggesting good long-term performance of the mesh designs. Due to different experimental conditions, direct and quantitative comparison with other lightweight shields is not possible at present.

Similarities in the chromosomal distribution of AG and AC repeats within and between Drosophila, human and barley chromosomes.

PubMed

Cuadrado, A; Jouve, N

2007-01-01

Two simple sequence repeats (SSRs), AG and AC, were mapped directly in the metaphase chromosomes of man and barley (Hordeum vulgare L.), and in the metaphase and polytene chromosomes of Drosophila melanogaster. To this end, synthetic oligonucleotides corresponding to (AG)(12) and (AC)(8) were labelled by the random primer technique and used as probes in fluorescent in situ hybridisation (FISH) under high stringency and strict washing conditions. The distribution and intensity of the signals for the repeat sequences were found to be characteristic of the chromosomes and genomes of the three species analysed. The AC repeat sites were uniformly dispersed along the euchromatic segments of all three genomes; in fact, they were largely excluded from the heterochromatin. The Drosophila genome showed a high density of AC sequences on the X chromosome in both mitotic and polytene nuclei. In contrast, the AG repeats were associated with the euchromatic regions of the polytene chromosomes (and in high density on the X chromosome), but were only seen in specific heterochromatic regions in the mitotic chromosomes of all three species. In Drosophila, the AG repeats were exclusively distributed on the tips of the Y chromosome and near the centromere on both arms of chromosome 2. In barley and man, AG repeats were associated with the centromeres (of all chromosomes) and nucleolar organizer regions, respectively. The conserved chromosome distribution of AC within and between these three phylogenetically distant species, and the association of AG in specific chromosome regions with structural or functional properties, suggests that long clusters of these repeats may have some, as yet unknown, role. Copyright (c) 2007 S. Karger AG, Basel.

Nutritional management of cow's milk allergy in children: An update.

PubMed

Dupont, C; Chouraqui, J-P; Linglart, A; Bocquet, A; Darmaun, D; Feillet, F; Frelut, M-L; Girardet, J-P; Hankard, R; Rozé, J-C; Simeoni, U; Briend, A

2018-04-01

Cow's milk is one of the most common foods responsible for allergic reactions in children. Cow's milk allergy (CMA) involves immunoglobulin E (IgE)- and non-IgE-mediated reactions, the latter being both variable and nonspecific. Guidelines thus emphasize the need for physicians to recognize the specific syndromes of CMA and to respect strict diagnostic modalities. Whatever the clinical pattern of CMA, the mainstay of treatment is the elimination from the diet of cow's milk proteins. The challenge is that both the disease and the elimination diet may result in insufficient height and weight gain and bone mineralization. If, during CMA, the mother is not able or willing to breastfeed, the child must be fed a formula adapted to CMA dietary management, during infancy and later, if the disease persists. This type of formula must be adequate in terms of allergic efficacy and nutritional safety. In older children, when CMA persists, the use of cow's milk baked or heated at a sufficient temperature, frequently tolerated by children with CMA, may help alleviate the stringency of the elimination diet. Guidance on the implementation of the elimination diet by qualified healthcare professionals is always necessary. This guidance should also include advice to ensure adequate bone growth, especially relating to calcium intake. Specific attention should be given to children presenting with several risk factors for weak bone mineral density, i.e., multiple food allergies, vitamin D deficiency, poor sun exposure, steroid use, or severe eczema. When CMA is outgrown, a prolonged elimination diet may negatively impact the quality of the diet over the long term. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Optimized Probe Masking for Comparative Transcriptomics of Closely Related Species

PubMed Central

Poeschl, Yvonne; Delker, Carolin; Trenner, Jana; Ullrich, Kristian Karsten; Quint, Marcel; Grosse, Ivo

2013-01-01

Microarrays are commonly applied to study the transcriptome of specific species. However, many available microarrays are restricted to model organisms, and the design of custom microarrays for other species is often not feasible. Hence, transcriptomics approaches of non-model organisms as well as comparative transcriptomics studies among two or more species often make use of cost-intensive RNAseq studies or, alternatively, by hybridizing transcripts of a query species to a microarray of a closely related species. When analyzing these cross-species microarray expression data, differences in the transcriptome of the query species can cause problems, such as the following: (i) lower hybridization accuracy of probes due to mismatches or deletions, (ii) probes binding multiple transcripts of different genes, and (iii) probes binding transcripts of non-orthologous genes. So far, methods for (i) exist, but these neglect (ii) and (iii). Here, we propose an approach for comparative transcriptomics addressing problems (i) to (iii), which retains only transcript-specific probes binding transcripts of orthologous genes. We apply this approach to an Arabidopsis lyrata expression data set measured on a microarray designed for Arabidopsis thaliana, and compare it to two alternative approaches, a sequence-based approach and a genomic DNA hybridization-based approach. We investigate the number of retained probe sets, and we validate the resulting expression responses by qRT-PCR. We find that the proposed approach combines the benefit of sequence-based stringency and accuracy while allowing the expression analysis of much more genes than the alternative sequence-based approach. As an added benefit, the proposed approach requires probes to detect transcripts of orthologous genes only, which provides a superior base for biological interpretation of the measured expression responses. PMID:24260119

Timing resolution and time walk in super low K factor single-photon avalanche diode-measurement and optimization

NASA Astrophysics Data System (ADS)

Fong, Bernicy S.; Davies, Murray; Deschamps, Pierre

2018-01-01

Timing resolution (or timing jitter) and time walk are separate parameters associated with a detector's response time. Studies have been done mostly on the time resolution of various single-photon detectors. As the designer and manufacturer of the ultra-low noise (ƙ-factor) silicon avalanche photodiode the super low K factor (SLiK) single-photon avalanche diode (SPAD), which is used in many single-photon counting applications, we often get inquiries from customers to better understand how this detector behaves under different operating conditions. Hence, here, we will be focusing on the study of these time-related parameters specifically for the SLiK SPAD, as a way to provide the most direct information for users of this detector to help with its use more efficiently and effectively. We will be providing the study data on how these parameters can be affected by temperature (both intrinsic to the detector chip and environmental input based on operating conditions), operating voltage, photon wavelength, as well as light spot size. How these parameters can be optimized and the trade-offs from optimization from the desired performance will be presented?

Optical trapping and Raman spectroscopy of single nanostructures using standing-wave Raman tweezers

NASA Astrophysics Data System (ADS)

Wu, Mu-ying; He, Lin; Chen, Gui-hua; Yang, Guang; Li, Yong-qing

2017-08-01

Optical tweezers integrated with Raman spectroscopy allows analyzing a single trapped micro-particle, but is generally less effective for individual nano-sized objects in the 10-100 nm range. The main challenge is the weak gradient force on nanoparticles that is insufficient to overcome the destabilizing effect of scattering force and Brownian motion. Here, we present standing-wave Raman tweezers for stable trapping and sensitive characterization of single isolated nanostructures with a low laser power by combining a standing-wave optical trap (SWOT) with confocal Raman spectroscopy. This scheme has stronger intensity gradients and balanced scattering forces, and thus is more stable and sensitive in measuring nanoparticles in liquid with 4-8 fold increase in the Raman signals. It can be used to analyze many nanoparticles that cannot be measured with single-beam Raman tweezers, including individual single-walled carbon nanotubes (SWCNT), graphene flakes, biological particles, polystyrene beads (100 nm), SERS-active metal nanoparticles, and high-refractive semiconductor nanoparticles with a low laser power of a few milliwatts. This would enable sorting and characterization of specific SWCNTs and other nanoparticles based on their increased Raman fingerprints.

Strategic parenting, birth order, and school performance.

PubMed

Hotz, V Joseph; Pantano, Juan

2015-10-01

Fueled by new evidence, there has been renewed interest about the effects of birth order on human capital accumulation. The underlying causal mechanisms for such effects remain unsettled. We consider a model in which parents impose more stringent disciplinary environments in response to their earlier-born children's poor performance in school in order to deter such outcomes for their later-born offspring. We provide robust empirical evidence that school performance of children in the National Longitudinal Study Children (NLSY-C) declines with birth order as does the stringency of their parents' disciplinary restrictions. When asked how they will respond if a child brought home bad grades, parents state that they would be less likely to punish their later-born children. Taken together, these patterns are consistent with a reputation model of strategic parenting.

Methodological guidelines for developing accident modification functions.

PubMed

Elvik, Rune

2015-07-01

This paper proposes methodological guidelines for developing accident modification functions. An accident modification function is a mathematical function describing systematic variation in the effects of road safety measures. The paper describes ten guidelines. An example is given of how to use the guidelines. The importance of exploratory analysis and an iterative approach in developing accident modification functions is stressed. The example shows that strict compliance with all the guidelines may be difficult, but represents a level of stringency that should be strived for. Currently the main limitations in developing accident modification functions are the small number of good evaluation studies and the often huge variation in estimates of effect. It is therefore still not possible to develop accident modification functions for very many road safety measures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Open-Air Biowarfare Testing and the Evolution of Values

PubMed Central

2016-01-01

The United States and the United Kingdom ended outdoor biological warfare testing in populated areas nearly half a century ago. Yet, the conduct, health effects, and propriety of those tests remain controversial. The varied views reflect the limits of currently available test information and evolving societal values on research involving human subjects. Western political culture has changed since the early days of the American and British testing programs. People have become less reluctant to question authority, and institutional review boards must now pre-approve research involving human subjects. Further, the heightened stringency of laboratory containment has accentuated the safety gap between a confined test space and one without physical boundaries. All this makes it less likely that masses of people would again be unwittingly subjected to secret open-air biological warfare tests. PMID:27564984

Strategic parenting, birth order, and school performance

PubMed Central

Pantano, Juan

2015-01-01

Fueled by new evidence, there has been renewed interest about the effects of birth order on human capital accumulation. The underlying causal mechanisms for such effects remain unsettled. We consider a model in which parents impose more stringent disciplinary environments in response to their earlier-born children’s poor performance in school in order to deter such outcomes for their later-born offspring. We provide robust empirical evidence that school performance of children in the National Longitudinal Study Children (NLSY-C) declines with birth order as does the stringency of their parents’ disciplinary restrictions. When asked how they will respond if a child brought home bad grades, parents state that they would be less likely to punish their later-born children. Taken together, these patterns are consistent with a reputation model of strategic parenting. PMID:26366045

Specific features of a single-pulse sliding discharge in neon near the threshold for spark breakdown

NASA Astrophysics Data System (ADS)

Trusov, K. K.

2017-08-01

Experimental data on the spatial structure of a single-pulse sliding discharge in neon at voltages below, equal to, and above the threshold for spark breakdown are discussed. The experiments were carried at gas pressures of 30 and 100 kPa and different polarities of the discharge voltage. Photographs of the plasma structure in two discharge chambers with different dimensions of the discharge zone and different thicknesses of an alumina dielectric plate on the surface of which the discharge develops are inspected. Common features of the prebreakdown discharge and its specific features depending on the voltage polarity and gas pressure are analyzed. It is shown that, at voltages below the threshold for spark breakdown, a low-current glow discharge with cathode and anode spots develops in the electrode gap. Above the breakdown threshold, regardless of the voltage polarity, spark channels directed from the cathode to the anode develop against the background of a low-current discharge.

Use of allele scores as instrumental variables for Mendelian randomization

PubMed Central

Burgess, Stephen; Thompson, Simon G

2013-01-01

Background An allele score is a single variable summarizing multiple genetic variants associated with a risk factor. It is calculated as the total number of risk factor-increasing alleles for an individual (unweighted score), or the sum of weights for each allele corresponding to estimated genetic effect sizes (weighted score). An allele score can be used in a Mendelian randomization analysis to estimate the causal effect of the risk factor on an outcome. Methods Data were simulated to investigate the use of allele scores in Mendelian randomization where conventional instrumental variable techniques using multiple genetic variants demonstrate ‘weak instrument’ bias. The robustness of estimates using the allele score to misspecification (for example non-linearity, effect modification) and to violations of the instrumental variable assumptions was assessed. Results Causal estimates using a correctly specified allele score were unbiased with appropriate coverage levels. The estimates were generally robust to misspecification of the allele score, but not to instrumental variable violations, even if the majority of variants in the allele score were valid instruments. Using a weighted rather than an unweighted allele score increased power, but the increase was small when genetic variants had similar effect sizes. Naive use of the data under analysis to choose which variants to include in an allele score, or for deriving weights, resulted in substantial biases. Conclusions Allele scores enable valid causal estimates with large numbers of genetic variants. The stringency of criteria for genetic variants in Mendelian randomization should be maintained for all variants in an allele score. PMID:24062299

Accessing the Soil Metagenome for Studies of Microbial Diversity▿ †

PubMed Central

Delmont, Tom O.; Robe, Patrick; Cecillon, Sébastien; Clark, Ian M.; Constancias, Florentin; Simonet, Pascal; Hirsch, Penny R.; Vogel, Timothy M.

2011-01-01

Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome. PMID:21183646

A High Power Density Single-Phase PWM Rectifier With Active Ripple Energy Storage

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

Wang, Ruxi; Wang, Fei; Boroyevich, Dushan

It is well known that single-phase pulse width modulation rectifiers have second-order harmonic currents and corresponding ripple voltages on the dc bus. The low-frequency harmonic current is normally filtered using a bulk capacitor in the bus, which results in low power density. However, pursuing high power density in converter design is a very important goal in the aerospace applications. This paper studies methods for reducing the energy storage capacitor for single-phase rectifiers. The minimum ripple energy storage requirement is derived independently of a specific topology. Based on theminimum ripple energy requirement, the feasibility of the active capacitor s reduction schemesmore » is verified. Then, we propose a bidirectional buck boost converter as the ripple energy storage circuit, which can effectively reduce the energy storage capacitance. The analysis and design are validated by simulation and experimental results.« less

Membrane filtration immobilization technique-a simple and novel method for primary isolation and enrichment of bacteriophages.

PubMed

Ghugare, G S; Nair, A; Nimkande, V; Sarode, P; Rangari, P; Khairnar, K

2017-02-01

To develop a method for the isolation and enrichment of bacteriophages selectively against specific bacteria coupled with a membrane filtration technique. Rapid isolation and concentration of host-specific bacteriophages was achieved by exposure of the sample suspected to contain bacteriophages to a specific host immobilized on a 0·45 μm membrane in a membrane filtration unit. The principle behind this method is the exploitation of host-specific interaction of bacteriophages with their host and maximizing this interaction using a classic membrane filtration method. This provides a chance for each bacteriophage in the sample to interact with the specific host on the membrane filter fitted with a vacuum pump. Specific bacteriophages of the host are retained on the membrane along with its host cells due to the effect of adsorption and these adsorbed bacteriophages (along with their hosts) on the filter disc are then amplified and enriched in regular nutritive broth tryptose soya broth by incubation. With the help of the plaque assay method, host-specific phages of various bacterial species were isolated, segregated and enriched. The phage concentration method coupled with membrane filtration immobilization of host bacteria was able to isolate and enrich the host-specific bacteriophages by several fold using a lower quantity of an environmental water sample, or other phage suspensions. Enrichment of phages from single plaques was also achieved. The isolation and detection of host-specific bacteriophages from a low density bacteriophage water sample in a single step by the use of a simple and basic microbiological technique can be achieved. Enrichment of phages from low phage titre suspensions is also achieved very effectively. © 2016 The Society for Applied Microbiology.

INVESTIGATING UNCERTAINTY AND SENSITIVITY IN INTEGRATED MULTIMEDIA ENVIRONMENTAL MODELS: TOOLS FOR 3MRA

EPA Science Inventory

Sufficiently elucidating uncertainty and sensitivity structures in environmental models can be a difficult task, even for low-order, single-media constructs driven by a unique set of site-specific data. The ensuing challenge of examining ever more complex, integrated, higher-ord...

INVESTIGATING UNCERTAINTY AND SENSITIVITY IN INTEGRATED, MULTIMEDIA ENVIRONMENTAL MODELS: TOOLS FOR FRAMES-3MRA

EPA Science Inventory

Elucidating uncertainty and sensitivity structures in environmental models can be a difficult task, even for low-order, single-medium constructs driven by a unique set of site-specific data. Quantitative assessment of integrated, multimedia models that simulate hundreds of sites...

Plasmonic Nanobubbles Rapidly Detect and Destroy Drug-Resistant Tumors

PubMed Central

Lukianova-Hleb, Ekaterina Y.; Ren, Xiaoyang; Townley, Debra; Wu, Xiangwei; Kupferman, Michael E.; Lapotko, Dmitri O.

2012-01-01

The resistance of residual cancer cells after oncological resection to adjuvant chemoradiotherapies results in both high recurrence rates and high non-specific tissue toxicity, thus preventing the successful treatment of such cancers as head and neck squamous cell carcinoma (HNSCC). The patients' survival rate and quality of life therefore depend upon the efficacy, selectivity and low non-specific toxicity of the adjuvant treatment. We report a novel, theranostic in vivo technology that unites both the acoustic diagnostics and guided intracellular delivery of anti-tumor drug (liposome-encapsulated doxorubicin, Doxil) in one rapid process, namely a pulsed laser-activated plasmonic nanobubble (PNB). HNSCC-bearing mice were treated with gold nanoparticle conjugates, Doxil, and single near-infrared laser pulses of low energy. Tumor-specific clusters of gold nanoparticles (solid gold spheres) converted the optical pulses into localized PNBs. The acoustic signals of the PNB detected the tumor with high specificity and sensitivity. The mechanical impact of the PNB, co-localized with Doxil liposomes, selectively ejected the drug into the cytoplasm of cancer cells. Cancer cell-specific generation of PNBs and their intracellular co-localization with Doxil improved the in vivo therapeutic efficacy from 5-7% for administration of only Doxil or PNBs alone to 90% thus demonstrating the synergistic therapeutic effect of the PNB-based intracellular drug release. This mechanism also reduced the non-specific toxicity of Doxil below a detectable level and the treatment time to less than one minute. Thus PNBs combine highly sensitive diagnosis, overcome drug resistance and minimize non-specific toxicity in a single rapid theranostic procedure for intra-operative treatment. PMID:23139725

High/variable mixture ratio O2/H2 engine

NASA Technical Reports Server (NTRS)

Adams, A.; Parsley, R. C.

1988-01-01

Vehicle/engine analysis studies have identified the High/Dual Mixture Ratio O2/H2 Engine cycle as a leading candidate for an advanced Single Stage to Orbit (SSTO) propulsion system. This cycle is designed to allow operation at a higher than normal O/F ratio of 12 during liftoff and then transition to a more optimum O/F ratio of 6 at altitude. While operation at high mixture ratios lowers specific impulse, the resultant high propellant bulk density and high power density combine to minimize the influence of atmospheric drag and low altitude gravitational forces. Transition to a lower mixture ratio at altitude then provides improved specific impulse relative to a single mixture ratio engine that must select a mixture ratio that is balanced for both low and high altitude operation. This combination of increased altitude specific impulse and high propellant bulk density more than offsets the compromised low altitude performance and results in an overall mission benefit. Two areas of technical concern relative to the execution of this dual mixture ratio cycle concept are addressed. First, actions required to transition from high to low mixture ratio are examined, including an assessment of the main chamber environment as the main chamber mixture ratio passes through stoichiometric. Secondly, two approaches to meet a requirement for high turbine power at high mixture ratio condition are examined. One approach uses high turbine temperature to produce the power and requires cooled turbines. The other approach incorporates an oxidizer-rich preburner to increase turbine work capability via increased turbine mass flow.

Technological change, depletion and environmental policy in the offshore oil and gas industry

NASA Astrophysics Data System (ADS)

Managi, Shunsuke

Technological change is central to maintaining standards of living in modern economies with finite resources and increasingly stringent environmental goals. Successful environmental policies can contribute to efficiency by encouraging, rather than inhibiting, technological innovation. However, little research to date has focused on the design and implementation of environmental regulations that encourage technological progress, or in insuring productivity improvements in the face of depletion of natural resources and increasing stringency of environmental regulations. This study models and measures productivity change, with an application to offshore oil and gas production in the Gulf of Mexico using Data Envelopment Analysis. This is an important application because energy resources are central to sustaining our economy. The net effects of technological progress and depletion on productivity of offshore oil and gas production are measured using a unique field-level set of data of production from all wells in the Gulf of Mexico over the time period from 1946--1998. Results are consistent with the hypothesis that technological progress has mitigated depletion effects over the study period, but the pattern differs from the conventional wisdom for nonrenewable resource industries. The Porter Hypothesis was recast, and revised version was tested. The Porter Hypothesis states that well designed environmental regulations can potentially contribute to productive efficiency in the long run by encouraging innovation. The Porter Hypothesis was recast to include market and nonmarket outputs. Our results support the recast version of Porter hypothesis, which examine productivity of joint production of market and environmental outputs. But we find no evidence for the standard formulation of the Porter hypothesis, that increased stringency of environmental regulation lead to increased productivity of market outputs and therefore increased industry profits. The model is used to forecast market and environmental outputs under alternative policy scenarios. Reliable baseline forecast and response to different policy actions of production and pollution are critical to the formation of sound energy and environmental policy. Forecast of production and pollution until year 2050 are generated from the model. Detailed policy scenarios provide quantitative assessments of potential benefits that indicate the significance of potential benefits of technological change and well-designed environmental policy.

Global Scenarios of Air Pollution until 2030: Combining Air Quality, Climate Change and Energy Access Policies

NASA Astrophysics Data System (ADS)

Rao, S.; Dentener, F. J.; Klimont, Z.; Riahi, K.

2011-12-01

Outdoor air pollution is increasingly recognized as a significant contributor to global health outcomes. This has led to the implementation of a number of air quality policies worldwide, with total air pollution control costs in 2005 estimated at US$195 billion. More than 80% of the world's population is still found to be exposed to PM2.5 concentrations exceeding WHO air quality guidelines and health impacts resulting from these exposures estimated at around 2-5% of the global disease burden. Key questions to answer are 1) How will pollutant emissions evolve in the future given developments in the energy system and how will energy and environmental policies influence such emission trends. 2) What implications will this have for resulting exposures and related health outcomes. In order to answer these questions, varying levels of stringency of air quality legislation are analyzed in combination with policies on universal access to clean cooking fuels and limiting global temperature change to 2°C in 2100. Bottom-up methodologies using energy emissions modeling are used to derive sector-based pollutant emission trajectories until 2030. Emissions are spatially downscaled and used in combination with a global transport chemistry model to derive ambient concentrations of PM2.5. Health impacts of these exposures are further estimated consistent with WHO data and methodology. The results indicate that currently planned air quality legislation combined with rising energy demand will be insufficient in controlling future emissions growth in developing countries. In order to achieve significant reductions in pollutant emissions of the order of more than 50% from 2005 levels and reduce exposures to levels consistent with WHO standards, it will be necessary to increase the stringency of such legislations and combine them with policies on energy access and climate change. Combined policies also result in reductions in air pollution control costs as compared to those associated with current legislations. Health related co-benefits of combined policies are also found to be large, especially in developing countries- a reduction of more than 50% in terms of pollution related mortality impacts as compared to today.

MiniDSS: a low-power and high-precision miniaturized digital sun sensor

NASA Astrophysics Data System (ADS)

de Boer, B. M.; Durkut, M.; Laan, E.; Hakkesteegt, H.; Theuwissen, A.; Xie, N.; Leijtens, J. L.; Urquijo, E.; Bruins, P.

2017-11-01

A high-precision and low-power miniaturized digital sun sensor has been developed at TNO. The single-chip sun sensor comprises an application specific integrated circuit (ASIC) on which an active pixel sensor (APS), read-out and processing circuitry as well as communication circuitry are combined. The design was optimized for low recurrent cost. The sensor is albedo insensitive and the prototype combines an accuracy in the order of 0.03° with a mass of just 72 g and a power consumption of only 65 mW.

A cognitive dual task affects gait variability in patients suffering from chronic low back pain.

PubMed

Hamacher, Dennis; Hamacher, Daniel; Schega, Lutz

2014-11-01

Chronic pain and gait variability in a dual-task situation are both associated with higher risk of falling. Executive functions regulate (dual-task) gait variability. A possible cause explaining why chronic pain increases risk of falling in an everyday dual-task situation might be that pain interferes with executive functions and results in a diminished dual-task capability with performance decrements on the secondary task. The main goal of this experiment was to evaluate the specific effects of a cognitive dual task on gait variability in chronic low back pain (CLBP) patients. Twelve healthy participants and twelve patients suffering from CLBP were included. The subjects were asked to perform a cognitive single task, a walking single task and a motor-cognitive dual task. Stride variability of trunk movements was calculated. A two-way ANOVA was performed to compare single-task walking with dual-task walking and the single cognitive task performance with the motor-cognitive dual-task performance. We did not find any differences in both of the single-task performances between groups. However, regarding single-task walking and dual-task walking, we observed an interaction effect indicating that low back pain patients show significantly higher gait variability in the dual-task condition as compared to controls. Our data suggest that chronic pain reduces motor-cognitive dual-task performance capability. We postulate that the detrimental effects are caused by central mechanisms where pain interferes with executive functions which, in turn, might contribute to increased risk of falling.

Root yield and quality of sugarbeet hybrids with pollinators selected for sodium, potassium, or amino-nitrogen concentration

USDA-ARS?s Scientific Manuscript database

Sodium, potassium, and amino-nitrogen, collectively referred to as impurities, are natural constituents of sugarbeet that impede sucrose extraction during factory operations. Lines selected specifically for low or high concentration of a single impurity component were crossed as pollinators with a ...

SODIUM BICARBONATE FACILITATES LOW-DOSE ORAL TOLERANCE TO PEANUT IN MICE

EPA Science Inventory

Rationale: Oral tolerance specifically inhibits production of allergic IgE antibody and is therefore a potential method for suppressing food allergy. We have previously demonstrated that a single oral dose of one mg is sufficient to induce oral tolerance to egg white but not pean...

Imaging proteins at the single-molecule level.

PubMed

Longchamp, Jean-Nicolas; Rauschenbach, Stephan; Abb, Sabine; Escher, Conrad; Latychevskaia, Tatiana; Kern, Klaus; Fink, Hans-Werner

2017-02-14

Imaging single proteins has been a long-standing ambition for advancing various fields in natural science, as for instance structural biology, biophysics, and molecular nanotechnology. In particular, revealing the distinct conformations of an individual protein is of utmost importance. Here, we show the imaging of individual proteins and protein complexes by low-energy electron holography. Samples of individual proteins and protein complexes on ultraclean freestanding graphene were prepared by soft-landing electrospray ion beam deposition, which allows chemical- and conformational-specific selection and gentle deposition. Low-energy electrons do not induce radiation damage, which enables acquiring subnanometer resolution images of individual proteins (cytochrome C and BSA) as well as of protein complexes (hemoglobin), which are not the result of an averaging process.

Imaging proteins at the single-molecule level

PubMed Central

Longchamp, Jean-Nicolas; Rauschenbach, Stephan; Abb, Sabine; Escher, Conrad; Latychevskaia, Tatiana; Kern, Klaus; Fink, Hans-Werner

2017-01-01

Imaging single proteins has been a long-standing ambition for advancing various fields in natural science, as for instance structural biology, biophysics, and molecular nanotechnology. In particular, revealing the distinct conformations of an individual protein is of utmost importance. Here, we show the imaging of individual proteins and protein complexes by low-energy electron holography. Samples of individual proteins and protein complexes on ultraclean freestanding graphene were prepared by soft-landing electrospray ion beam deposition, which allows chemical- and conformational-specific selection and gentle deposition. Low-energy electrons do not induce radiation damage, which enables acquiring subnanometer resolution images of individual proteins (cytochrome C and BSA) as well as of protein complexes (hemoglobin), which are not the result of an averaging process. PMID:28087691

Real-time Molecular Study of Bystander Effects of Low dose Low LET radiation Using Living Cell Imaging and Nanoparticale Optics

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

Natarajan, Mohan; Xu, Nancy R; Mohan, Sumathy

2013-06-03

In this study two novel approaches are proposed to investigate precisely the low dose low LET radiation damage and its effect on bystander cells in real time. First, a flow shear model system, which would provide us a near in vivo situation where endothelial cells in the presence of extra cellular matrix experiencing continuous flow shear stress, will be used. Endothelial cells on matri-gel (simulated extra cellular matrix) will be subjected to physiological flow shear (that occurs in normal blood vessels). Second, a unique tool (Single nano particle/single live cell/single molecule microscopy and spectroscopy; Figure A) will be used tomore » track the molecular trafficking by single live cell imaging. Single molecule chemical microscopy allows one to single out and study rare events that otherwise might be lost in assembled average measurement, and monitor many target single molecules simultaneously in real-time. Multi color single novel metal nanoparticle probes allow one to prepare multicolor probes (Figure B) to monitor many single components (events) simultaneously and perform multi-complex analysis in real-time. These nano-particles resist to photo bleaching and hence serve as probes for unlimited timeframe of analysis. Single live cell microscopy allows one to image many single cells simultaneously in real-time. With the combination of these unique tools, we will be able to study under near-physiological conditions the cellular and sub-cellular responses (even subtle changes at one molecule level) to low and very low doses of low LET radiation in real time (milli-second or nano-second) at sub-10 nanometer spatial resolution. This would allow us to precisely identify, at least in part, the molecular mediators that are responsible of radiation damage in the irradiated cells and the mediators that are responsible for initiating the signaling in the neighboring cells. Endothelial cells subjected to flow shear (2 dynes/cm2 or 16 dynes/cm2) and exposed to 0.1, 1 and 10 cGy on coverslips will be examined for (a) low LET radiation-induced alterations of cellular function and its physiological relevance in real time; and (b) radiation damage triggered bystander effect on the neighboring unirradiated cells. First, to determine the low LET radiation induced alteration of cellular function we will examine: (i) the real time transformation of single membrane transporters in single living cells; (ii) the pump efficiency of membrane efflux pump of live cells in real time at the molecular level; (iii) the kinetics of single-ligand receptor interaction on single live cell surface (Figure C); and (iv) alteration in chromosome replication in living cell. Second, to study the radiation triggered bystander responses, we will examine one of the key signaling pathway i.e. TNF- alpha/NF-kappa B mediated signaling. TNF-alpha specific nano particle sensors (green) will be developed to detect the releasing dynamics, transport mechanisms and ligand-receptor binding on live cell surface in real time. A second sensor (blue) will be developed to simultaneously monitor the track of NF-kB inside the cell. The proposed nano-particle optics approach would complement our DOE funded study on biochemical mechanisms of TNF-alpha- NF-kappa B-mediated bystander effect.« less

Functionalized nanopipettes: toward label-free, single cell biosensors.

PubMed

Actis, Paolo; Mak, Andy C; Pourmand, Nader

2010-08-01

Nanopipette technology has been proven to be a label-free biosensor capable of identifying DNA and proteins. The nanopipette can include specific recognition elements for analyte discrimination based on size, shape, and charge density. The fully electrical read-out and the ease and low-cost fabrication are unique features that give this technology an enormous potential. Unlike other biosensing platforms, nanopipettes can be precisely manipulated with submicron accuracy and used to study single cell dynamics. This review is focused on creative applications of nanopipette technology for biosensing. We highlight the potential of this technology with a particular attention to integration of this biosensor with single cell manipulation platforms.

Functionalized nanopipettes: toward label-free, single cell biosensors

PubMed Central

Actis, Paolo; Mak, Andy C.

2010-01-01

Nanopipette technology has been proven to be a label-free biosensor capable of identifying DNA and proteins. The nanopipette can include specific recognition elements for analyte discrimination based on size, shape, and charge density. The fully electrical read-out and the ease and low-cost fabrication are unique features that give this technology an enormous potential. Unlike other biosensing platforms, nanopipettes can be precisely manipulated with submicron accuracy and used to study single cell dynamics. This review is focused on creative applications of nanopipette technology for biosensing. We highlight the potential of this technology with a particular attention to integration of this biosensor with single cell manipulation platforms. PMID:20730113

In-Line Fiber Optic Interferometric Sensors in Single-Mode Fibers

PubMed Central

Zhu, Tao; Wu, Di; Liu, Min; Duan, De-Wen

2012-01-01

In-line fiber optic interferometers have attracted intensive attention for their potential sensing applications in refractive index, temperature, pressure and strain measurement, etc. Typical in-line fiber-optic interferometers are of two types: Fabry-Perot interferometers and core-cladding-mode interferometers. It's known that the in-line fiber optic interferometers based on single-mode fibers can exhibit compact structures, easy fabrication and low cost. In this paper, we review two kinds of typical in-line fiber optic interferometers formed in single-mode fibers fabricated with different post-processing techniques. Also, some recently reported specific technologies for fabricating such fiber optic interferometers are presented. PMID:23112608

Compartmentalization of HIV-1 within the female genital tract is due to monotypic and low-diversity variants not distinct viral populations.

PubMed

Bull, Marta; Learn, Gerald; Genowati, Indira; McKernan, Jennifer; Hitti, Jane; Lockhart, David; Tapia, Kenneth; Holte, Sarah; Dragavon, Joan; Coombs, Robert; Mullins, James; Frenkel, Lisa

2009-09-22

Compartmentalization of HIV-1 between the genital tract and blood was noted in half of 57 women included in 12 studies primarily using cell-free virus. To further understand differences between genital tract and blood viruses of women with chronic HIV-1 infection cell-free and cell-associated virus populations were sequenced from these tissues, reasoning that integrated viral DNA includes variants archived from earlier in infection, and provides a greater array of genotypes for comparisons. Multiple sequences from single-genome-amplification of HIV-1 RNA and DNA from the genital tract and blood of each woman were compared in a cross-sectional study. Maximum likelihood phylogenies were evaluated for evidence of compartmentalization using four statistical tests. Genital tract and blood HIV-1 appears compartmentalized in 7/13 women by >/=2 statistical analyses. These subjects' phylograms were characterized by low diversity genital-specific viral clades interspersed between clades containing both genital and blood sequences. Many of the genital-specific clades contained monotypic HIV-1 sequences. In 2/7 women, HIV-1 populations were significantly compartmentalized across all four statistical tests; both had low diversity genital tract-only clades. Collapsing monotypic variants into a single sequence diminished the prevalence and extent of compartmentalization. Viral sequences did not demonstrate tissue-specific signature amino acid residues, differential immune selection, or co-receptor usage. In women with chronic HIV-1 infection multiple identical sequences suggest proliferation of HIV-1-infected cells, and low diversity tissue-specific phylogenetic clades are consistent with bursts of viral replication. These monotypic and tissue-specific viruses provide statistical support for compartmentalization of HIV-1 between the female genital tract and blood. However, the intermingling of these clades with clades comprised of both genital and blood sequences and the absence of tissue-specific genetic features suggests compartmentalization between blood and genital tract may be due to viral replication and proliferation of infected cells, and questions whether HIV-1 in the female genital tract is distinct from blood.

Controlling the surface termination of NdGaO3 (110): the role of the gas atmosphere.

PubMed

Cavallaro, Andrea; Harrington, George F; Skinner, Stephen J; Kilner, John A

2014-07-07

In this work the effect of gas atmosphere on the surface termination reconstruction of single crystal NdGaO3 (110) (NGO) during thermal annealing was analyzed. Using Low Energy Ion Scattering (LEIS) it has been possible to study the chemical composition of the first atomic layer of treated NGO single crystal samples. NGO has been analyzed both as-received and after a specific thermal treatment at 1000 °C under different gas fluxes (argon, nitrogen, static air, synthetic air, nitrogen plus 5% hydrogen and wet synthetic air respectively). Thermal annealing of perovskite single crystals, as already reported in the literature, is used to obtain a fully A-cation surface termination. Nevertheless the effect of the gas-atmosphere on this process has not been previously reported. By the use of sequential low energy Ar(+) sputtering combined with the primary ion LEIS analysis, the reconstruction of the outermost atomic layers has allowed the clarification of the mechanism of NGO neodymium surface enrichment. It is proposed that the gallium at the surface is submitted to a reduction/evaporation mechanism caused by low oxygen partial pressure and/or high water pressure in the vector gas. Below the first surface atomic layers of an as-received NGO single-crystal a gallium-rich phase has also been observed.

Single tube genotyping of sickle cell anaemia using PCR-based SNP analysis

PubMed Central

Waterfall, Christy M.; Cobb, Benjamin D.

2001-01-01

Allele-specific amplification (ASA) is a generally applicable technique for the detection of known single nucleotide polymorphisms (SNPs), deletions, insertions and other sequence variations. Conventionally, two reactions are required to determine the zygosity of DNA in a two-allele system, along with significant upstream optimisation to define the specific test conditions. Here, we combine single tube bi-directional ASA with a ‘matrix-based’ optimisation strategy, speeding up the whole process in a reduced reaction set. We use sickle cell anaemia as our model SNP system, a genetic disease that is currently screened using ASA methods. Discriminatory conditions were rapidly optimised enabling the unambiguous identification of DNA from homozygous sickle cell patients (HbS/S), heterozygous carriers (HbA/S) or normal DNA in a single tube. Simple downstream mathematical analyses based on product yield across the optimisation set allow an insight into the important aspects of priming competition and component interactions in this competitive PCR. This strategy can be applied to any polymorphism, defining specific conditions using a multifactorial approach. The inherent simplicity and low cost of this PCR-based method validates bi-directional ASA as an effective tool in future clinical screening and pharmacogenomic research where more expensive fluorescence-based approaches may not be desirable. PMID:11726702

Single tube genotyping of sickle cell anaemia using PCR-based SNP analysis.

PubMed

Waterfall, C M; Cobb, B D

2001-12-01

Allele-specific amplification (ASA) is a generally applicable technique for the detection of known single nucleotide polymorphisms (SNPs), deletions, insertions and other sequence variations. Conventionally, two reactions are required to determine the zygosity of DNA in a two-allele system, along with significant upstream optimisation to define the specific test conditions. Here, we combine single tube bi-directional ASA with a 'matrix-based' optimisation strategy, speeding up the whole process in a reduced reaction set. We use sickle cell anaemia as our model SNP system, a genetic disease that is currently screened using ASA methods. Discriminatory conditions were rapidly optimised enabling the unambiguous identification of DNA from homozygous sickle cell patients (HbS/S), heterozygous carriers (HbA/S) or normal DNA in a single tube. Simple downstream mathematical analyses based on product yield across the optimisation set allow an insight into the important aspects of priming competition and component interactions in this competitive PCR. This strategy can be applied to any polymorphism, defining specific conditions using a multifactorial approach. The inherent simplicity and low cost of this PCR-based method validates bi-directional ASA as an effective tool in future clinical screening and pharmacogenomic research where more expensive fluorescence-based approaches may not be desirable.

Air quality co-benefits of carbon pricing in China

NASA Astrophysics Data System (ADS)

Li, Mingwei; Zhang, Da; Li, Chiao-Ting; Mulvaney, Kathleen M.; Selin, Noelle E.; Karplus, Valerie J.

2018-05-01

Climate policies targeting energy-related CO2 emissions, which act on a global scale over long time horizons, can result in localized, near-term reductions in both air pollution and adverse human health impacts. Focusing on China, the largest energy-using and CO2-emitting nation, we develop a cross-scale modelling approach to quantify these air quality co-benefits, and compare them to the economic costs of climate policy. We simulate the effects of an illustrative climate policy, a price on CO2 emissions. In a policy scenario consistent with China's recent pledge to reach a peak in CO2 emissions by 2030, we project that national health co-benefits from improved air quality would partially or fully offset policy costs depending on chosen health valuation. Net health co-benefits are found to rise with increasing policy stringency.

Low-thrust Isp sensitivity study

NASA Technical Reports Server (NTRS)

Schoenman, L.

1982-01-01

A comparison of the cooling requirements and attainable specific impulse performance of engines in the 445 to 4448N thrust class utilizing LOX/RP-1, LOX/Hydrogen and LOX/Methane propellants is presented. The unique design requirements for the regenerative cooling of low-thrust engines operating at high pressures (up to 6894 kPa) were explored analytically by comparing single cooling with the fuel and the oxidizer, and dual cooling with both the fuel and the oxidizer. The effects of coolant channel geometry, chamber length, and contraction ratio on the ability to provide proper cooling were evaluated, as was the resulting specific impulse. The results show that larger contraction ratios and smaller channels are highly desirable for certain propellant combinations.

A Review of Single Source Precursors for the Deposition of Ternary Chalcopyrite Materials

NASA Technical Reports Server (NTRS)

Banger, K. K.; Cowen, J.; Harris, J.; McClarnon, R.; Hehemann, D. G.; Duraj, S. A.; Scheiman, D.; Hepp, A. F.

2002-01-01

The development of thin-film solar cells on flexible, lightweight, space-qualified durable substrates (i.e. Kapton) provides an attractive solution to fabricating solar arrays with high specific power, (W/kg). The syntheses and thermal modulation of ternary single source precursors, based on the [{LR}2Cu(SR')2In(SR')2] architecture in good yields are described. Thermogravimetric analyses (TGA) and Low temperature Differential Scanning Caloriometry, (DSC) demonstrate that controlled manipulation of the steric and electronic properties of either the group five-donor and/or chalcogenide moiety permits directed adjustment of the thermal stability and physical properties of the precursors. TGA-Evolved Gas Analysis, confirms that single precursors decompose by the initial extrusion of the sulphide moiety, followed by the loss of the neutral donor group, (L) to release the ternary chalcopyrite matrix. X-ray diffraction studies, EDS and SEM on the non-volatile pyrolized material demonstrate that these derivatives afford single-phase CuInS2/CuInSe2 materials at low temperature. Thin-film fabrication studies demonstrate that these single source precursors can be used in a spray chemical vapor deposition process, for depositing CuInS2 onto flexible polymer substrates at temperatures less than 400 C.

LCR testing for gonorrhoea and chlamydia in population surveys and other screenings of low prevalence populations: coping with decreased positive predictive value.

PubMed

Zenilman, J M; Miller, W C; Gaydos, C; Rogers, S M; Turner, C F

2003-04-01

Nucleic acid amplification tests have facilitated field based STD studies and increased screening activities. However, even with highly specific tests, the positive predictive value (PPV) of such tests may be lower than desirable in low prevalence populations. We estimated PPVs for a single LCR test in a population survey in which positive specimens were retested. The Baltimore STD and Behavior Survey (BSBS) was a population based behavioural survey of adults which included collecting urine specimens to assess the prevalence of gonorrhoea and chlamydial infection. Gonorrhoea and chlamydial infection were diagnosed by ligase chain reaction (LCR). Nearly all positive results were retested by LCR. Because of cost considerations, negative results were not confirmed. Predicted curves for the PPV were calculated for a single testing assuming an LCR test sensitivity of 95%, and test specificities in the range 95.0%-99.9%, for disease prevalences between 1% and 10%. Positive specimens were retested to derive empirical estimates of the PPV of a positive result on a single LCR test. 579 participants age 18-35 provided urine specimens. 20 (3.5%) subjects initially tested positive for chlamydial infection, and 39 (6.7%) tested positive for gonococcal infection. If positive results on the repeat LCR are taken as confirmation of a "true" infection, the observed PPV for the first LCR testing was 89.5% for chlamydial infection and 83.3% for gonorrhoea. This is within the range of theoretical PPVs calculated from the assumed sensitivities and specificities of the LCR assays. Empirical performance of a single LCR testing approximated the theoretically predicted PPV in this field study. This result demonstrates the need to take account of the lower PPVs obtained when such tests are used in field studies or clinical screening of low prevalence populations. Repeat testing of specimens, preferably with a different assay (for example, polymerase chain reaction), and disclosure of the non-trivial potential for false positive test results would seem appropriate in all such studies.

Severe community-acquired pneumonia. Assessment of severity criteria.

PubMed

Ewig, S; Ruiz, M; Mensa, J; Marcos, M A; Martinez, J A; Arancibia, F; Niederman, M S; Torres, A

1998-10-01

The purpose of the study was to validate the criteria used in the guidelines of the American Thoracic Society (ATS) for severe community-acquired pneumonia (CAP). Severe pneumonia was defined as admission to the intensive care unit (ICU). Overall 331 nonsevere (84%) and 64 severe cases (16%) of CAP were prospectively studied. Mortality was 19 of 395 (5%) and 19 of 64 (30%), respectively. Single severity criteria as well as the ATS definition of severe pneumonia were assessed calculating the operative indices. A modified prediction rule including minor (baseline) and major (baseline or evolutionary) criteria was derived. Single minor criteria at admission had a low sensitivity and positive predictive value. Defining severe pneumonia according to the ATS guidelines had a high sensitivity (98%). However, specificity and positive predictive value were low (32% and 24%, respectively). A modified prediction rule (presence of two or three minor criteria [systolic blood pressure < 90 mm Hg, multilobar involvement, PaO2/FIO2 < 250] or one of two major criteria [requirement of mechanical ventilation, presence of septic shock]) had a sensitivity of 78%, a specificity of 94%, a positive predictive value of 75%, and a negative predictive value of 95%. The ATS definition of severe pneumonia was highly sensitive but insufficiently specific and had a low positive predictive value. Our suggested modified rule had a more balanced performance and, if validated in an independent population, may represent a more accurate definition of severe CAP.

Purification and characterization of a GH43 β-xylosidase from Enterobacter sp. identified and cloned from forest soil bacteria.

PubMed

Campos, Eleonora; Negro Alvarez, María José; Sabarís di Lorenzo, Gonzalo; Gonzalez, Sergio; Rorig, Marcela; Talia, Paola; Grasso, Daniel H; Sáez, Felicia; Manzanares Secades, Paloma; Ballesteros Perdices, Mercedes; Cataldi, Angel A

2014-01-01

The use of lignocellulosic biomass for second generation biofuels requires optimization of enzymatic breakdown of plant cell walls. In this work, cellulolytic bacteria were isolated from a native and two cultivated forest soil samples. Amplification of glycosyl hydrolases was attempted by using a low stringency-degenerate primer PCR strategy, using total soil DNA and bulk DNA pooled from positive colonies as template. A set of primers was designed based on Acidothermus cellulolyticus genome, by search of conserved domains of glycosyl hydrolases (GH) families of interest. Using this approach, a fragment containing an open reading frame (ORF) with 98% identity to a putative GH43 beta-xylosidase coding gene from Enterobacter cloacae was amplified and cloned. The full protein was expressed in Escherichia coli as N-terminal or C-terminal His-tagged fusions and purified under native conditions. Only N-terminal fusion protein, His-Xyl43, presented beta-xylosidase activity. On pNPX, optimal activity was achieved at pH 6 and 40 °C and Km and Kcat values were 2.92 mM and 1.32 seg(-1), respectively. Activity was also demonstrated on xylobiose (X2), with Km 17.8 mM and Kcat 380 s(-1). These results demonstrated that Xyl43 is a functional beta-xylosidase and it is the first evidence of this activity for Enterobacter sp. Copyright © 2013 Elsevier GmbH. All rights reserved.

[Invasive fungal infections in children with cancer, neutropenia and fever, in Chile].

PubMed

Lucero, Yalda; Brücher, Roberto; Alvarez, Ana María; Becker, Ana; Cofré, José; Enríquez, Nancy; Payá, Ernesto; Salgado, Carmen; Santolaya, María Elena; Tordecilla, Juan; Varas, Mónica; Villarroel, Milena; Viviani, Tamara; Zubieta, Marcela; O'Ryan, Miguel

2002-10-01

Invasive fungal infections (IFI) cause prolonged hospitalizations and increase the possibility of death among patients with cancer and febrile neutropenia (FN). Up to 10% of febrile neutropenic episodes may be caused by IFI. To estimate the incidence of IFI among a large group of Chilean children with cancer and FN. Clinical and laboratory information was collected from a data base provided by the "Programa Infantil Nacional de Drogas Antineoplásicas" (PINDA) that included 445 FN episodes occurring in five hospitals in Santiago, Chile. This information was used to identify children that presented with signs and symptoms compatible with an IFI. According to predefined criteria based on a literature review, IFI episodes were categorized as "proven", "probable" or "possible". A total of 41/445 episodes (9.2%) were compatible with an IFI of which 4 (0.9%) were proven, 23 (5.2%) probable, and 14 (3.1%) possible. Hospitalization was longer (27 vs 8 days, p < .01), new infectious foci appeared with higher frequency (71 vs 38%, p < .01), and mortality was higher (10 vs 1.6%, p < .001) in children with IFI compatible episodes, when compared to children who did not have an IFI. The estimated incidence of IFI in Chilean children with cancer and FN ranged between 6-9% depending on the stringency of criteria selection used for classification. This estimate is similar to that reported by other studies. The low detection yield of clinically compatible IFI underscores the need of improved diagnosis of fungal infections in this population.

Detecting single-abasic residues within a DNA strand immobilized in a biological nanopore using an integrated CMOS sensor.

PubMed

Kim, Jungsuk; Maitra, Raj D; Pedrotti, Ken; Dunbar, William B

2013-02-01

In this paper, we demonstrate the application of a novel current-measuring sensor (CMS) customized for nanopore applications. The low-noise CMS is fabricated in a 0.35μm CMOS process and is implemented in experiments involving DNA captured in an α-hemolysin (α-HL) nanopore. Specifically, the CMS is used to build a current amplitude map as a function of varying positions of a single-abasic residue within a homopolymer cytosine single-stranded DNA (ssDNA) that is captured and held in the pore. Each ssDNA is immobilized using a biotin-streptavidin linkage. Five different DNA templates are measured and compared: one all-cytosine ssDNA, and four with a single-abasic residue substitution that resides in or near the ~1.5nm aperture of the α-HL channel when the strand is immobilized. The CMOS CMS is shown to resolves the ~5Å displacements of the abasic residue within the varying templates. The demonstration represents an advance in application-specific circuitry that is optimized for small-footprint nanopore applications, including genomic sequencing.

Marek's disease is a natural model for lymphomas overexpressing Hodgkin's disease antigen (CD30)

PubMed Central

Burgess, S. C.; Young, J. R.; Baaten, B. J. G.; Hunt, L.; Ross, L. N. J.; Parcells, M. S.; Kumar, P. M.; Tregaskes, C. A.; Lee, L. F.; Davison, T. F.

2004-01-01

Animal models are essential for elucidating the molecular mechanisms of carcinogenesis. Hodgkin's and many diverse non-Hodgkin's lymphomas overexpress the Hodgkin's disease antigen CD30 (CD30hi), a tumor necrosis factor receptor II family member. Here we show that chicken Marek's disease (MD) lymphoma cells are also CD30hi and are a unique natural model for CD30hi lymphoma. Chicken CD30 resembles an ancestral form, and we identify a previously undescribed potential cytoplasmic signaling domain conserved in chicken, human, and mouse CD30. Our phylogeneic analysis defines a relationship between the structures of human and mouse CD30 and confirms that mouse CD30 represents the ancestral mammalian gene structure. CD30 expression by MD virus (MDV)-transformed lymphocytes correlates with expression of the MDV Meq putative oncogene (a c-Jun homologue) in vivo. The chicken CD30 promoter has 15 predicted high-stringency Meq-binding transcription factor recognition motifs, and Meq enhances transcription from the CD30 promoter in vitro. Plasma proteomics identified a soluble form of CD30. CD30 overexpression is evolutionarily conserved and defines one class of neoplastic transformation events, regardless of etiology. We propose that CD30 is a component of a critical intracellular signaling pathway perturbed in neoplastic transformation. Specific anti-CD30 Igs occurred after infection of genetically MD-resistant chickens with oncogenic MDV, suggesting immunity to CD30 could play a role in MD lymphoma regression. PMID:15356338

Correlation of Periodontal Disease With Inflammatory Arthritis in the Time Before Modern Medical Intervention.

PubMed

Rothschild, Bruce

2017-03-01

Controversy exists regarding possible correlation of periodontal disease with rheumatoid arthritis (RA) and ankylosing spondylitis (AS). Confounding factors may relate to stringency of inflammatory disease diagnosis and the effect of therapeutic intervention for RA on periodontal disease. These factors are investigated in this study. Forty-five individuals with documented RA (n = 15), spondyloarthropathy (n = 15), and calcium pyrophosphate deposition disease (CPPD) (n = 15), from the Hamann-Todd collection of human skeletons compiled from 1912 to 1938, and 15 individuals contemporarily incorporated in the collection were examined for tooth loss, cavity occurrence, average and maximum lingual and buccal depth of space between tooth and bone, periosteal reaction, serpentine bone resorption, abscess formation, and root penetration of the bone surface and analyzed by analysis of variance. Tooth loss was common, but actual number of teeth lost, cavity occurrence, average and maximum lingual and buccal depth of space between tooth and bone, periosteal reaction, serpentine grooving surrounding teeth (considered a sign of inflammation), abscess formation, and root exposure (penetration of bone surface) were indistinguishable among controls and individuals with RA, spondyloarthropathy, and CPPD. Although many factors can affect periodontal disease, presence of inflammatory arthritis does not appear to be one of them. The implication is that dental disease was common in the general population and not necessarily associated with arthritis, at least before the advent of modern rheumatologic medications. As specific diagnosis did not affect prevalence, perhaps current prevalence controversy may relate to current intervention, a subject for further study.

Validation of the use of self-reported hearing loss and the Hearing Handicap Inventory for elderly among rural Indian elderly population.

PubMed

Deepthi, R; Kasthuri, Arvind

2012-01-01

Hearing loss is a potentially disabling problem among elderly leading to physical and social dysfunction. Though audiometric assessment of hearing loss is considered as gold standard, it is not feasible in community settings. Several questionnaires measuring hearing handicap have been developed. Knowledge regarding applicability of these questionnaires among rural elderly is limited, hence a study was planned to validate single question and Shortened Hearing Handicap Inventory for Elderly (HHIE-S) in detecting hearing loss against pure tone-audiometry among rural Indian elderly. A single question 'do you feel you have a hearing loss?' and the HHIE-S was administered to 175 elderly in two rural areas. Hearing ability was assessed using pure tone audiometry. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of both screening tools were compared with pure tone averages (PTAs) greater than 25, 40 and 55 dB hearing level (mild, moderate and severe hearing loss, respectively). The single question yielded low sensitivity (30.9%) and high specificity (93.9%) for mild hearing loss. Similarly HHIE-S yielded a sensitivity of 26.2% and specificity of 95.9%. Sensitivity with single question increased to 76.2% and specificity decreased to 83.1% with severe hearing loss. Sensitivity with HHIE-S also increased to 76.2% and specificity decreased to 87.7% with severe hearing loss. These hearing screening questionnaires will be useful in identifying more disabling hearing losses among rural elderly which helps in rehabilitation services planning. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Constraints to estimating the prevalence of trypanosome infections in East African zebu cattle.

PubMed

Cox, Andrew P; Tosas, Olga; Tilley, Aimee; Picozzi, Kim; Coleman, Paul; Hide, Geoff; Welburn, Susan C

2010-09-06

In East Africa, animal trypanosomiasis is caused by many tsetse transmitted protozoan parasites including Trypanosoma vivax, T. congolense and subspecies of T. brucei s.l. (T. b. brucei and zoonotic human infective T. b. rhodesiense) that may co-circulate in domestic and wild animals. Accurate species-specific prevalence measurements of these parasites in animal populations are complicated by mixed infections of trypanosomes within individual hosts, low parasite densities and difficulties in conducting field studies. Many Polymerase Chain Reaction (PCR) based diagnostic tools are available to characterise and quantify infection in animals. These are important for assessing the contribution of infections in animal reservoirs and the risk posed to humans from zoonotic trypanosome species. New matrices for DNA capture have simplified large scale field PCR analyses but few studies have examined the impact of these techniques on prevalence estimations. The Whatman FTA matrix has been evaluated using a random sample of 35 village zebu cattle from a population naturally exposed to trypanosome infection. Using a generic trypanosome-specific PCR, prevalence was systematically evaluated. Multiple PCR samples taken from single FTA cards demonstrated that a single punch from an FTA card is not sufficient to confirm the infectivity status of an individual animal as parasite DNA is unevenly distributed across the card. At low parasite densities in the host, this stochastic sampling effect results in underestimation of prevalence based on single punch PCR testing. Repeated testing increased the estimated prevalence of all Trypanosoma spp. from 9.7% to 86%. Using repeat testing, a very high prevalence of pathogenic trypanosomes was detected in these local village cattle: T. brucei (34.3%), T. congolense (42.9%) and T. vivax (22.9%). These results show that, despite the convenience of Whatman FTA cards and specific PCR based detection tools, the chronically low parasitaemias in indigenous African zebu cattle make it difficult to establish true prevalence. Although this study specifically applies to FTA cards, a similar effect would be experienced with other approaches using blood samples containing low parasite densities. For example, using blood film microscopy or PCR detection from liquid samples where the probability of detecting a parasite or DNA molecule, in the required number of fields of view or PCR reaction, is less than one.

Constraints to estimating the prevalence of trypanosome infections in East African zebu cattle

PubMed Central

2010-01-01

Background In East Africa, animal trypanosomiasis is caused by many tsetse transmitted protozoan parasites including Trypanosoma vivax, T. congolense and subspecies of T. brucei s.l. (T. b. brucei and zoonotic human infective T. b. rhodesiense) that may co-circulate in domestic and wild animals. Accurate species-specific prevalence measurements of these parasites in animal populations are complicated by mixed infections of trypanosomes within individual hosts, low parasite densities and difficulties in conducting field studies. Many Polymerase Chain Reaction (PCR) based diagnostic tools are available to characterise and quantify infection in animals. These are important for assessing the contribution of infections in animal reservoirs and the risk posed to humans from zoonotic trypanosome species. New matrices for DNA capture have simplified large scale field PCR analyses but few studies have examined the impact of these techniques on prevalence estimations. Results The Whatman FTA matrix has been evaluated using a random sample of 35 village zebu cattle from a population naturally exposed to trypanosome infection. Using a generic trypanosome-specific PCR, prevalence was systematically evaluated. Multiple PCR samples taken from single FTA cards demonstrated that a single punch from an FTA card is not sufficient to confirm the infectivity status of an individual animal as parasite DNA is unevenly distributed across the card. At low parasite densities in the host, this stochastic sampling effect results in underestimation of prevalence based on single punch PCR testing. Repeated testing increased the estimated prevalence of all Trypanosoma spp. from 9.7% to 86%. Using repeat testing, a very high prevalence of pathogenic trypanosomes was detected in these local village cattle: T. brucei (34.3%), T. congolense (42.9%) and T. vivax (22.9%). Conclusions These results show that, despite the convenience of Whatman FTA cards and specific PCR based detection tools, the chronically low parasitaemias in indigenous African zebu cattle make it difficult to establish true prevalence. Although this study specifically applies to FTA cards, a similar effect would be experienced with other approaches using blood samples containing low parasite densities. For example, using blood film microscopy or PCR detection from liquid samples where the probability of detecting a parasite or DNA molecule, in the required number of fields of view or PCR reaction, is less than one. PMID:20815940

Receiver operating characteristic analysis of prediction for gastric cancer development using serum pepsinogen and Helicobacter pylori antibody tests.

PubMed

Hamashima, Chisato; Sasazuki, Shizuka; Inoue, Manami; Tsugane, Shoichiro

2017-03-09

Chronic Helicobacter pylori infection plays a central role in the development of gastric cancer as shown by biological and epidemiological studies. The H. pylori antibody and serum pepsinogen (PG) tests have been anticipated to predict gastric cancer development. We determined the predictive sensitivity and specificity of gastric cancer development using these tests. Receiver operating characteristic analysis was performed, and areas under the curve were estimated. The predictive sensitivity and specificity of gastric cancer development were compared among single tests and combined methods using serum pepsinogen and H. pylori antibody tests. From a large-scale population-based cohort of over 100,000 subjects followed between 1990 and 2004, 497 gastric cancer subjects and 497 matched healthy controls were chosen. The predictive sensitivity and specificity were low in all single tests and combination methods. The highest predictive sensitivity and specificity were obtained for the serum PG I/II ratio. The optimal PG I/II cut-off values were 2.5 and 3.0. At a PG I/II cut-off value of 3.0, the sensitivity was 86.9% and the specificity was 39.8%. Even if three biomarkers were combined, the sensitivity was 97.2% and the specificity was 21.1% when the cut-off values were 3.0 for PG I/II, 70 ng/mL for PG I, and 10.0 U/mL for H. pylori antibody. The predictive accuracy of gastric cancer development was low with the serum pepsinogen and H. pylori antibody tests even if these tests were combined. To adopt these biomarkers for gastric cancer screening, a high specificity is required. When these tests are adopted for gastric cancer screening, they should be carefully interpreted with a clear understanding of their limitations.

High-throughput microfluidic single-cell digital polymerase chain reaction.

PubMed

White, A K; Heyries, K A; Doolin, C; Vaninsberghe, M; Hansen, C L

2013-08-06

Here we present an integrated microfluidic device for the high-throughput digital polymerase chain reaction (dPCR) analysis of single cells. This device allows for the parallel processing of single cells and executes all steps of analysis, including cell capture, washing, lysis, reverse transcription, and dPCR analysis. The cDNA from each single cell is distributed into a dedicated dPCR array consisting of 1020 chambers, each having a volume of 25 pL, using surface-tension-based sample partitioning. The high density of this dPCR format (118,900 chambers/cm(2)) allows the analysis of 200 single cells per run, for a total of 204,000 PCR reactions using a device footprint of 10 cm(2). Experiments using RNA dilutions show this device achieves shot-noise-limited performance in quantifying single molecules, with a dynamic range of 10(4). We performed over 1200 single-cell measurements, demonstrating the use of this platform in the absolute quantification of both high- and low-abundance mRNA transcripts, as well as micro-RNAs that are not easily measured using alternative hybridization methods. We further apply the specificity and sensitivity of single-cell dPCR to performing measurements of RNA editing events in single cells. High-throughput dPCR provides a new tool in the arsenal of single-cell analysis methods, with a unique combination of speed, precision, sensitivity, and specificity. We anticipate this approach will enable new studies where high-performance single-cell measurements are essential, including the analysis of transcriptional noise, allelic imbalance, and RNA processing.

Patterns of interaction specificity of fungus-growing termites and Termitomyces symbionts in South Africa

PubMed Central

Aanen, Duur K; Ros, Vera ID; de Fine Licht, Henrik H; Mitchell, Jannette; de Beer, Z Wilhelm; Slippers, Bernard; Rouland-LeFèvre, Corinne; Boomsma, Jacobus J

2007-01-01

Background Termites of the subfamily Macrotermitinae live in a mutualistic symbiosis with basidiomycete fungi of the genus Termitomyces. Here, we explored interaction specificity in fungus-growing termites using samples from 101 colonies in South-Africa and Senegal, belonging to eight species divided over three genera. Knowledge of interaction specificity is important to test the hypothesis that inhabitants (symbionts) are taxonomically less diverse than 'exhabitants' (hosts) and to test the hypothesis that transmission mode is an important determinant for interaction specificity. Results Analysis of Molecular Variance among symbiont ITS sequences across termite hosts at three hierarchical levels showed that 47 % of the variation occurred between genera, 18 % between species, and the remaining 35 % between colonies within species. Different patterns of specificity were evident. High mutual specificity was found for the single Macrotermes species studied, as M. natalensis was associated with a single unique fungal haplotype. The three species of the genus Odontotermes showed low symbiont specificity: they were all associated with a genetically diverse set of fungal symbionts, but their fungal symbionts showed some host specificity, as none of the fungal haplotypes were shared between the studied Odontotermes species. Finally, bilaterally low specificity was found for the four tentatively recognized species of the genus Microtermes, which shared and apparently freely exchanged a common pool of divergent fungal symbionts. Conclusion Interaction specificity was high at the genus level and generally much lower at the species level. A comparison of the observed diversity among fungal symbionts with the diversity among termite hosts, indicated that the fungal symbiont does not follow the general pattern of an endosymbiont, as we found either similar diversity at both sides or higher diversity in the symbiont. Our results further challenge the hypothesis that transmission-mode is a general key-determinant of interaction specificity in fungus-growing termites. PMID:17629911

Efficacy of Web-Based Personalized Normative Feedback: A Two-Year Randomized Controlled Trial

ERIC Educational Resources Information Center

Neighbors, Clayton; Lewis, Melissa A.; Atkins, David C.; Jensen, Megan M.; Walter, Theresa; Fossos, Nicole; Lee, Christine M.; Larimer, Mary E.

2010-01-01

Objective: Web-based brief alcohol interventions have the potential to reach a large number of individuals at low cost; however, few controlled evaluations have been conducted to date. The present study was designed to evaluate the efficacy of gender-specific versus gender-nonspecific personalized normative feedback (PNF) with single versus…

Single and Double Deficits in Early Readers in Rural, Low-Wealth Communities

ERIC Educational Resources Information Center

Fedora, Pledger M.

2016-01-01

This study used secondary data to test the double-deficit hypothesis that rapid automatized naming (RAN) deficits and phonological awareness (PA) deficits are 2 core reading-related deficits and that students exhibiting deficits in both areas would be the most severely impaired in entry-level reading ability. Specifically, this study investigated…

West Virginia Women Business Owners: Current Study and Trends Report.

ERIC Educational Resources Information Center

Holup, Linda L.; FitzGerald, Kathleen M.

This report profiles current West Virginia women business owners and notes significant trends in the last eight years. It highlights a subgroup of women business owners, specifically low income, single women with children. These survey areas are discussed: industry sector, type of ownership, reasons for going/not going into business, planning…

Amplified electrochemical detection of nucleic acid hybridization via selective preconcentration of unmodified gold nanoparticles.

PubMed

Li, Yuan; Tian, Rui; Zheng, Xingwang; Huang, Rongfu

2016-08-31

The common drawback of optical methods for rapid detection of nucleic acid by exploiting the differential affinity of single-/double-stranded nucleic acids for unmodified gold nanoparticles (AuNPs) is its relatively low sensitivity. In this article, on the basis of selective preconcentration of AuNPs unprotected by single-stranded DNA (ssDNA) binding, a novel electrochemical strategy for nucleic acid sequence identification assay has been developed. Through detecting the redox signal mediated by AuNPs on 1, 6-hexanedithiol blocked gold electrode, the proposed method is able to ensure substantial signal amplification and a low background current. This strategy is demonstrated for quantitative analysis of the target microRNA (let-7a) in human breast adenocarcinoma cells, and a detection limit of 16 fM is readily achieved with desirable specificity and sensitivity. These results indicate that the selective preconcentration of AuNPs for electrochemical signal readout can offer a promising platform for the detection of specific nucleic acid sequence. Copyright © 2016 Elsevier B.V. All rights reserved.

Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences

PubMed Central

Sevy, Alexander M.; Jacobs, Tim M.; Crowe, James E.; Meiler, Jens

2015-01-01

Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a ‘single state’ design (SSD) paradigm. Multi-specificity design (MSD), on the other hand, involves considering the stability of multiple protein states simultaneously. We have developed a novel MSD algorithm, which we refer to as REstrained CONvergence in multi-specificity design (RECON). The algorithm allows each state to adopt its own sequence throughout the design process rather than enforcing a single sequence on all states. Convergence to a single sequence is encouraged through an incrementally increasing convergence restraint for corresponding positions. Compared to MSD algorithms that enforce (constrain) an identical sequence on all states the energy landscape is simplified, which accelerates the search drastically. As a result, RECON can readily be used in simulations with a flexible protein backbone. We have benchmarked RECON on two design tasks. First, we designed antibodies derived from a common germline gene against their diverse targets to assess recovery of the germline, polyspecific sequence. Second, we design “promiscuous”, polyspecific proteins against all binding partners and measure recovery of the native sequence. We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes. PMID:26147100

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

Xu, Q; Han, H; Xing, L

Purpose: Dictionary learning based method has attracted more and more attentions in low-dose CT due to the superior performance on suppressing noise and preserving structural details. Considering the structures and noise vary from region to region in one imaging object, we propose a region-specific dictionary learning method to improve the low-dose CT reconstruction. Methods: A set of normal-dose images was used for dictionary learning. Segmentations were performed on these images, so that the training patch sets corresponding to different regions can be extracted out. After that, region-specific dictionaries were learned from these training sets. For the low-dose CT reconstruction, amore » conventional reconstruction, such as filtered back-projection (FBP), was performed firstly, and then segmentation was followed to segment the image into different regions. Sparsity constraints of each region based on its dictionary were used as regularization terms. The regularization parameters were selected adaptively according to different regions. A low-dose human thorax dataset was used to evaluate the proposed method. The single dictionary based method was performed for comparison. Results: Since the lung region is very different from the other part of thorax, two dictionaries corresponding to lung region and the rest part of thorax respectively were learned to better express the structural details and avoid artifacts. With only one dictionary some artifact appeared in the body region caused by the spot atoms corresponding to the structures in the lung region. And also some structure in the lung regions cannot be recovered well by only one dictionary. The quantitative indices of the result by the proposed method were also improved a little compared to the single dictionary based method. Conclusion: Region-specific dictionary can make the dictionary more adaptive to different region characteristics, which is much desirable for enhancing the performance of dictionary learning based method.« less

Mild neurotrauma indicates a range-specific pressure response to low level shock wave exposure.

PubMed

Vandevord, Pamela J; Bolander, Richard; Sajja, Venkata Siva Sai Sujith; Hay, Kathryn; Bir, Cynthia A

2012-01-01

Identifying the level of overpressure required to create physiological deficits is vital to advance prevention, diagnostic, and treatment strategies for individuals exposed to blasts. In this study, a rodent model of primary blast neurotrauma was employed to determine the pressure at which acute neurological alterations occurred. Rats were exposed to a single low intensity shock wave at a pressure of 0, 97, 117, or 153 kPa. Following exposure, rats were assessed for acute cognitive alterations using the Morris water maze and motor dysfunction using the horizontal ladder test. Subsequently, histological analyses of three brain regions (primary motor cortex, the hippocampal dentate gyrus region, and the posteromedial cortical amygdala) were conducted. Histological parameters included measuring the levels of glial fibrillary acidic protein (GFAP) to identify astrocyte activation, cleaved caspase-3 for early apoptosis identification and Fluoro-Jade B (FJB) which labels degenerating neurons within the brain tissue. The results demonstrated that an exposure to a single 117 kPa shock wave revealed a significant change in overall neurological deficits when compared to controls and the other pressures. The animals showed significant alterations in water maze parameters and a histological increase in the number of GFAP, caspase-3, and FJB-positive cells. It is suggested that when exposed to a low level shock wave, there may be a biomechanical response elicited by a specific pressure range which can cause low level neurological deficits within the rat. These data indicate that neurotrauma induced from a shock wave may lead to cognitive deficits in short-term learning and memory of rats. Additional histological evidence supports significant and diffuse glial activation and cellular damage. Further investigation into the biomechanical aspects of shock wave exposure is required to elucidate this pressure range-specific phenomenon.

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells.

PubMed

Kim, Kyu-Tae; Lee, Hye Won; Lee, Hae-Ock; Kim, Sang Cheol; Seo, Yun Jee; Chung, Woosung; Eum, Hye Hyeon; Nam, Do-Hyun; Kim, Junhyong; Joo, Kyeung Min; Park, Woong-Yang

2015-06-19

Intra-tumoral genetic and functional heterogeneity correlates with cancer clinical prognoses. However, the mechanisms by which intra-tumoral heterogeneity impacts therapeutic outcome remain poorly understood. RNA sequencing (RNA-seq) of single tumor cells can provide comprehensive information about gene expression and single-nucleotide variations in individual tumor cells, which may allow for the translation of heterogeneous tumor cell functional responses into customized anti-cancer treatments. We isolated 34 patient-derived xenograft (PDX) tumor cells from a lung adenocarcinoma patient tumor xenograft. Individual tumor cells were subjected to single cell RNA-seq for gene expression profiling and expressed mutation profiling. Fifty tumor-specific single-nucleotide variations, including KRAS(G12D), were observed to be heterogeneous in individual PDX cells. Semi-supervised clustering, based on KRAS(G12D) mutant expression and a risk score representing expression of 69 lung adenocarcinoma-prognostic genes, classified PDX cells into four groups. PDX cells that survived in vitro anti-cancer drug treatment displayed transcriptome signatures consistent with the group characterized by KRAS(G12D) and low risk score. Single-cell RNA-seq on viable PDX cells identified a candidate tumor cell subgroup associated with anti-cancer drug resistance. Thus, single-cell RNA-seq is a powerful approach for identifying unique tumor cell-specific gene expression profiles which could facilitate the development of optimized clinical anti-cancer strategies.

New nucleic acid testing devices to diagnose infectious diseases in resource-limited settings.

PubMed

Maffert, P; Reverchon, S; Nasser, W; Rozand, C; Abaibou, H

2017-10-01

Point-of-care diagnosis based on nucleic acid testing aims to incorporate all the analytical steps, from sample preparation to nucleic acid amplification and detection, in a single device. This device needs to provide a low-cost, robust, sensitive, specific, and easily readable analysis. Microfluidics has great potential for handling small volumes of fluids on a single platform. Microfluidic technology has recently been applied to paper, which is already used in low-cost lateral flow tests. Nucleic acid extraction from a biological specimen usually requires cell filtration and lysis on specific membranes, while affinity matrices, such as chitosan or polydiacetylene, are well suited to concentrating nucleic acids for subsequent amplification. Access to electricity is often difficult in resource-limited areas, so the amplification step needs to be equipment-free. Consequently, the reaction has to be isothermal to alleviate the need for a thermocycler. LAMP, NASBA, HDA, and RPA are examples of the technologies available. Nucleic acid detection techniques are currently based on fluorescence, colorimetry, or chemiluminescence. For point-of-care diagnostics, the results should be readable with the naked eye. Nowadays, interpretation and communication of results to health professionals could rely on a smartphone, used as a telemedicine device. The major challenge of creating an "all-in-one" diagnostic test involves the design of an optimal solution and a sequence for each analytical step, as well as combining the execution of all these steps on a single device. This review provides an overview of available materials and technologies which seem to be adapted to point-of-care nucleic acid-based diagnosis, in low-resource areas.

Ultrasensitive Detection of Single-Walled Carbon Nanotubes Using Surface Plasmon Resonance.

PubMed

Jang, Daeho; Na, Wonhwi; Kang, Minwook; Kim, Namjoon; Shin, Sehyun

2016-01-05

Because single-walled carbon nanotubes (SWNTs) are known to be a potentially dangerous material, inducing cancers and other diseases, any possible leakage of SWNTs through an aquatic medium such as drinking water will result in a major public threat. To solve this problem, for the present study, a highly sensitive, quantitative detection method of SWNTs in an aqueous solution was developed using surface plasmon resonance (SPR) spectroscopy. For a highly sensitive and specific detection, a strong affinity conjugation with biotin-streptavidin was adopted on an SPR sensing mechanism. During the pretreatment process, the SWNT surface was functionalized and hydrophilized using a thymine-chain based biotinylated single-strand DNA linker (B-ssDNA) and bovine serum albumin (BSA). The pretreated SWNTs were captured on a sensing film, the surface of which was immobilized with streptavidin on biotinylated gold film. The captured SWNTs were measured in real-time using SPR spectroscopy. Specific binding with SWNTs was verified through several validation experiments. The present method using an SPR sensor is capable of detecting SWNTs of as low as 100 fg/mL, which is the lowest level reported thus far for carbon-nanotube detection. In addition, the SPR sensor showed a linear characteristic within the range of 100 pg/mL to 200 ng/mL. These findings imply that the present SPR sensing method can detect an extremely low level of SWNTs in an aquatic environment with high sensitivity and high specificity, and thus any potential leakage of SWNTs into an aquatic environment can be precisely monitored within a couple of hours.

Constitutive Model for Anisotropic Creep Behaviors of Single-Crystal Ni-Base Superalloys in the Low-Temperature, High-Stress Regime (Postprint)

DTIC Science & Technology

2012-01-19

specific dislocation reactions. Rae et al .[4,5,7] proposed micromechanisms for primary creep caused by SF shearing of c0 precipitates by ah112i...near the [0 0 1] was done by Matan et al .[3] They proposed a phenomenological creep model, which was adopted from Gilman’s dislocation density model...the original loading orientation). MacLachlan et al .[18 21] proposed a series of creep models for anisotropic creep of single-crystal superalloys. Their

Reliability, validity, sensitivity and specificity of Guajarati version of the Roland-Morris Disability Questionnaire.

PubMed

Nambi, S Gopal

2013-01-01

The most common instruments developed to assess the functional status of patients with Non specific low back pain is the Roland-Morris Disability Questionnaire (RMDQ). Clinical and epidemiological research related to low back pain in the Gujarati population would be facilitated by the availability of well-established outcome measures. To find the reliability, validity, sensitivity and specificity of the Gujarati version of the RMDQ for use in Non Specific Chronic low back pain. A reliability, validity, sensitivity and specificity study of Gujarati version of the Roland-Morris Disability Questionnaire (RMDQ). Thirty out patients with Non Specific Chronic low back pain were assessed by the RMDQ. Reliability is assessed by using internal consistency and the intra-class correlation coefficient (ICC). Internal construct validity is assessed by RASCH Analysis and external construct validity is assessed by association with pain and spinal movement. Clinical calculator was used to determine the sensitivity and specificity. Internal consistency of the RMDQ is found to be adequate (> 0.65) at both times, with high ICC's also at both time points. Internal construct validity of the scale is good, indicating a single underlying construct. Expected associations with pain and spinal movement confirm external construct validity. The Sensitivity and Specificity at cut off point of 0.5 was 80% and 84% with respectively positive predictive value (PPV) of 83.33% and negative predictive value (NPV) of 80.76%. The Questionnaire is at the ordinal level. The RMDQ is a one-dimensional, ordinal measure, which works well in the Gujarati population.

Geologic setting of the low-level burial grounds

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

Lindsey, K.A.; Jaeger, G.K.; Slate, J.L.

1994-10-13

This report describes the regional and site specific geology of the Hanford Sites low-level burial grounds in the 200 East and West Areas. The report incorporates data from boreholes across the entire 200 Areas, integrating the geology of this area into a single framework. Geologic cross-sections, isopach maps, and structure contour maps of all major geological units from the top of the Columbia River Basalt Group to the surface are included. The physical properties and characteristics of the major suprabasalt sedimentary units also are discussed.

Identification of Single- and Multiple-Class Specific Signature Genes from Gene Expression Profiles by Group Marker Index

PubMed Central

Tsai, Yu-Shuen; Aguan, Kripamoy; Pal, Nikhil R.; Chung, I-Fang

2011-01-01

Informative genes from microarray data can be used to construct prediction model and investigate biological mechanisms. Differentially expressed genes, the main targets of most gene selection methods, can be classified as single- and multiple-class specific signature genes. Here, we present a novel gene selection algorithm based on a Group Marker Index (GMI), which is intuitive, of low-computational complexity, and efficient in identification of both types of genes. Most gene selection methods identify only single-class specific signature genes and cannot identify multiple-class specific signature genes easily. Our algorithm can detect de novo certain conditions of multiple-class specificity of a gene and makes use of a novel non-parametric indicator to assess the discrimination ability between classes. Our method is effective even when the sample size is small as well as when the class sizes are significantly different. To compare the effectiveness and robustness we formulate an intuitive template-based method and use four well-known datasets. We demonstrate that our algorithm outperforms the template-based method in difficult cases with unbalanced distribution. Moreover, the multiple-class specific genes are good biomarkers and play important roles in biological pathways. Our literature survey supports that the proposed method identifies unique multiple-class specific marker genes (not reported earlier to be related to cancer) in the Central Nervous System data. It also discovers unique biomarkers indicating the intrinsic difference between subtypes of lung cancer. We also associate the pathway information with the multiple-class specific signature genes and cross-reference to published studies. We find that the identified genes participate in the pathways directly involved in cancer development in leukemia data. Our method gives a promising way to find genes that can involve in pathways of multiple diseases and hence opens up the possibility of using an existing drug on other diseases as well as designing a single drug for multiple diseases. PMID:21909426

Slow positrons in the study of surface and near-surface defects

NASA Astrophysics Data System (ADS)

Lynn, K. G.

A general theoretical model is presented which includes the probability of a positron diffusing back to the surface after implantation, and thermalization in samples containing various defects. This model incorporates surface state and thermal desorption from this state, as well as reflection back into the bulk. With this model vacancy formation enthalpies, activation energies of positrons from surface states, and specific trapping rates are deduced from the positronium fraction data. An amorphous Al/sub x/O/sub y/ overlayer on Al is discussed as an example of trapping in overlayers. In well-annealed single crystal samples, the positron is shown to be freely diffusing at low temperatures, whereas in a neutron-irradiatied Al single crystal sample the positron is localized at low positron binding energy defects presumably created during irradiation.

Studentized continuous wavelet transform (t-CWT) in the analysis of individual ERPs: real and simulated EEG data

PubMed Central

Real, Ruben G. L.; Kotchoubey, Boris; Kübler, Andrea

2014-01-01

This study aimed at evaluating the performance of the Studentized Continuous Wavelet Transform (t-CWT) as a method for the extraction and assessment of event-related brain potentials (ERP) in data from a single subject. Sensitivity, specificity, positive (PPV) and negative predictive values (NPV) of the t-CWT were assessed and compared to a variety of competing procedures using simulated EEG data at six low signal-to-noise ratios. Results show that the t-CWT combines high sensitivity and specificity with favorable PPV and NPV. Applying the t-CWT to authentic EEG data obtained from 14 healthy participants confirmed its high sensitivity. The t-CWT may thus be well suited for the assessment of weak ERPs in single-subject settings. PMID:25309308

Studentized continuous wavelet transform (t-CWT) in the analysis of individual ERPs: real and simulated EEG data.

PubMed

Real, Ruben G L; Kotchoubey, Boris; Kübler, Andrea

2014-01-01

This study aimed at evaluating the performance of the Studentized Continuous Wavelet Transform (t-CWT) as a method for the extraction and assessment of event-related brain potentials (ERP) in data from a single subject. Sensitivity, specificity, positive (PPV) and negative predictive values (NPV) of the t-CWT were assessed and compared to a variety of competing procedures using simulated EEG data at six low signal-to-noise ratios. Results show that the t-CWT combines high sensitivity and specificity with favorable PPV and NPV. Applying the t-CWT to authentic EEG data obtained from 14 healthy participants confirmed its high sensitivity. The t-CWT may thus be well suited for the assessment of weak ERPs in single-subject settings.

Low-Mass, Low-Power Hall Thruster System

NASA Technical Reports Server (NTRS)

Pote, Bruce

2015-01-01

NASA is developing an electric propulsion system capable of producing 20 mN thrust with input power up to 1,000 W and specific impulse ranging from 1,600 to 3,500 seconds. The key technical challenge is the target mass of 1 kg for the thruster and 2 kg for the power processing unit (PPU). In Phase I, Busek Company, Inc., developed an overall subsystem design for the thruster/cathode, PPU, and xenon feed system. This project demonstrated the feasibility of a low-mass power processing architecture that replaces four of the DC-DC converters of a typical PPU with a single multifunctional converter and a low-mass Hall thruster design employing permanent magnets. In Phase II, the team developed an engineering prototype model of its low-mass BHT-600 Hall thruster system, with the primary focus on the low-mass PPU and thruster. The goal was to develop an electric propulsion thruster with the appropriate specific impulse and propellant throughput to enable radioisotope electric propulsion (REP). This is important because REP offers the benefits of nuclear electric propulsion without the need for an excessively large spacecraft and power system.

PERSISTENCE OF HAPTEN-ANTIBODY COMPLEXES IN THE CIRCULATION OF IMMUNIZED ANIMALS AFTER A SINGLE INTRAVENOUS INJECTION OF HAPTEN

PubMed Central

Schmidt, Donald H.; Kaufman, Bette M.; Butler, Vincent P.

1974-01-01

To study the fate of a low molecular weight antigen (hapten) in the circulation of animals whose sera contain antibodies specific for that low molecular weight antigen, a single injection of digoxin-3H (0.4 mg/kg) was administered intravenously to 18 rabbits. Thirteen animals (nine nonimmunized and four immunized with bovine serum albumin) served as control animals. In five rabbits which had been immunized with a digoxin-bovine serum albumin conjugate and whose sera contained digoxin-specific antibodies, the mean 12-h serum digoxin concentration was 8,300 ng/ml (control: 92 ng/ml) and the mean serum concentration 12 mo after the single injection of digoxin-3H was 85 ng/ml. In digoxin-immunized rabbits, less than 10% of the digoxin-3H was excreted in the first 10 days (control: 77% recovered in urine and feces) and the mean biological half-life of digoxin, as calculated from serum digoxin-3H disappearance curves, was 72 days (control: 3.4 days). In sera of digoxin-immunized rabbits, more than 90% of the circulating digoxin-3H was immunoglobulin bound, as determined by the double-antibody and dextran-coated charcoal methods. The serum disappearance rate of 125I-antidigoxin antibodies was similar in nonimmunized and in immunized animals and in the presence or absence of digoxin. It is concluded that the biological half-life of a hapten may be markedly prolonged when the hapten is bound to specific antibody. The persistence of antibody-hapten complexes in the circulation suggests that these complexes may not be deposited in tissues and raises the possibility that low molecular weight determinants may be capable of preventing or reversing the deposition of immune complexes, containing macromolecular antigens, in the tissues of experimental animals and man. PMID:4129823

Critical Current Statistics of a Graphene-Based Josephson Junction Infrared Single Photon Detector

NASA Astrophysics Data System (ADS)

Walsh, Evan D.; Lee, Gil-Ho; Efetov, Dmitri K.; Heuck, Mikkel; Crossno, Jesse; Taniguchi, Takashi; Watanabe, Kenji; Ohki, Thomas A.; Kim, Philip; Englund, Dirk; Fong, Kin Chung

Graphene is a promising material for single photon detection due to its broadband absorption and exceptionally low specific heat. We present a photon detector using a graphene sheet as the weak link in a Josephson junction (JJ) to form a threshold detector for single infrared photons. Calculations show that such a device could experience temperature changes of a few hundred percent leading to sub-Hz dark count rates and internal efficiencies approaching unity. We have fabricated the graphene-based JJ (gJJ) detector and measure switching events that are consistent with single photon detection under illumination by an attenuated laser. We study the physical mechanism for these events through the critical current behavior of the gJJ as a function of incident photon flux.

Preferentially oriented, High temperature superconductors by seeding and a method for their preparation

DOEpatents

Lee, Dominic F.; Kroeger, Donald M.; Goyal, Amit

2001-01-01

A multi-domained bulk REBa.sub.2 Cu.sub.3 O.sub.x with low-angle domain boundaries which resembles a quasi-single domained material and a method for producing the same comprising arranging multiple seeds, which can be small single crystals, single domained melt-textured REBa.sub.2 Cu.sub.3 O.sub.x pieces, textured substrates comprised of grains with low misorientation angles, or thick film REBa.sub.2 Cu.sub.3 O.sub.x deposited on such textured substrate, such seeds being tailored for various REBa.sub.2 Cu.sub.3 O.sub.x compounds, in specific pattern and relative seed orientations on a superconductor precursor material which may be placed in contact with a porous substrate so as to reduce the amount of liquid phase in the melt. Because seeds can be arranged in virtually any pattern, high quality REBa.sub.2 Cu.sub.3 O.sub.x elements of virtually unlimited size and complex geometry can be fabricated.

Method for preparing preferentially oriented, high temperature superconductors using solution reagents

DOEpatents

Lee, Dominic F.; Kroeger, Donald M.; Goyal, Amit

2002-01-01

A multi-domained bulk REBa.sub.2 CU.sub.3 O.sub.x with low-angle domain boundaries which resemble a quasi-single domained material and a method for producing the same comprising arranging multiple seeds, which can be small single crystals, single domained melt-textured REBa.sub.2 CU.sub.3 O.sub.x pieces, textured substrates comprises of grains with low misorientation angles, or thick film REBa.sub.2 CU.sub.3 O.sub.x deposited on such textured substrate, such seeds being tailored for various REBa.sub.2 CU.sub.3 O.sub.x compounds, in specific pattern and relative seed orientations on a superconductor precursor material which may be placed in contact with a porous substrate so as to reduce the amount of liquid phase in the melt. Because seeds can be arranged in virtually any pattern, high quality REBa.sub.2 CU.sub.3 O.sub.x elements of virtually unlimited size and complex geometry can be fabricated.

Lanthanum-Based Metal-Organic Frameworks for Specific Detection of Sudan Virus RNA Conservative Sequences down to Single-Base Mismatch.

PubMed

Yang, Shui-Ping; Zhao, Wei; Hu, Pei-Pei; Wu, Ke-Yang; Jiang, Zhi-Hong; Bai, Li-Ping; Li, Min-Min; Chen, Jin-Xiang

2017-12-18

Reactions of La(NO 3 ) 3 ·6H 2 O with the polar, tritopic quaternized carboxylate ligands N-carboxymethyl-3,5-dicarboxylpyridinium bromide (H 3 CmdcpBr) and N-(4-carboxybenzyl)-3,5-dicarboxylpyridinium bromide (H 3 CbdcpBr) afford two water-stable metal-organic frameworks (MOFs) of {[La 4 (Cmdcp) 6 (H 2 O) 9 ]} n (1, 3D) and {[La 2 (Cbdcp) 3 (H 2 O) 10 ]} n (2, 2D). MOFs 1 and 2 absorb the carboxyfluorescein (FAM)-tagged probe DNA (P-DNA) and quench the fluorescence of FAM via a photoinduced electron transfer (PET) process. The nonemissive P-DNA@MOF hybrids thus formed in turn function as sensing platforms to distinguish conservative linear, single-stranded RNA sequences of Sudan virus with high selectivity and low detection limits of 112 and 67 pM, respectively (at a signal-to-noise ratio of 3). These hybrids also exhibit high specificity and discriminate down to single-base mismatch RNA sequences.

Single Cell Analysis: From Technology to Biology and Medicine.

PubMed

Pan, Xinghua

2014-01-01

Single-cell analysis heralds a new era that allows "omics" analysis, notably genomics, transcriptomics, epigenomics and proteomics at the single-cell level. It enables the identification of the minor subpopulations that may play a critical role in a biological process of a population of cells, which conventionally are regarded as homogeneous. It provides an ultra-sensitive tool to clarify specific molecular mechanisms and pathways and reveal the nature of cell heterogeneity. It also facilitates the clinical investigation of patients when a very low quantity or a single cell is available for analysis, such as noninvasive prenatal diagnosis and cancer screening, and genetic evaluation for in vitro fertilization. Within a few short years, single-cell analysis, especially whole genomic sequencing and transcriptomic sequencing, is becoming robust and broadly accessible, although not yet a routine practice. Here, with single cell RNA-seq emphasized, an overview of the discipline, progresses, and prospects of single-cell analysis and its applications in biology and medicine are given with a series of logic and theoretical considerations.

Development of HgCdTe single-element APDs based detectors for low flux short wave infrared applications

NASA Astrophysics Data System (ADS)

Foubert, K.; Lasfargues, G.; Mathieu, L.; Benahmed, S.; Vojetta, G.; Rothman, J.; Benoît à la Guillaume, Q.; Calvo, Vincent; Picot-Clemente, Jérémy; Le Mounier, Florent; Gibert, Fabien

2013-03-01

The remarkable properties (internal gain larger than 100 and close to unity excess noise factor) of Short Wave Infrared (SWIR) HgCdTe electron-initiated Avalanche Photodiodes (e-APDs) are put to good use to demanding applications, i.e. spectroscopy and LIDAR. Knowing the requirements of both situations, we have designed specific models based on highly sensitive single elements APDs and adapted proximity electronics. On one hand, we use the e-APDs low noise equivalent power (NEP) at 180K (few fW/Hz1/2). We simultaneously designed a specific Transimpedance Amplifier (TIA) which allows us to take advantage of the low APD NEP. The combination of both elements along with a dedicated cryostat enables direct LIDAR detection at moderate bandwidth (BW = 20 MHz) without the need for long time averaging, which is crucial in far field (>= 5 km) analysis. One the other hand, we have optimized a low-noise and low-frequency LN2 cooled prototype operating with an external commercial amplifier. It allows us to observe the photoluminescence of Ge nanostructures in the range 1.5-2.5 μm with a significantly increased SNR along with a reduce pump laser power. The possibility to use these detectors in the photon counting limit will be discussed in light of our recent results. In parallel, we present preliminary time response measurements performed on SWIR APD suggesting that a higher GHz BW could be reached with this type of detector. This is however subjected to optical optimization at the moment.

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding.

PubMed

Shahi, Payam; Kim, Samuel C; Haliburton, John R; Gartner, Zev J; Abate, Adam R

2017-03-14

Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing.

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

NASA Astrophysics Data System (ADS)

Shahi, Payam; Kim, Samuel C.; Haliburton, John R.; Gartner, Zev J.; Abate, Adam R.

2017-03-01

Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing.

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

PubMed Central

Shahi, Payam; Kim, Samuel C.; Haliburton, John R.; Gartner, Zev J.; Abate, Adam R.

2017-01-01

Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing. We demonstrate this novel approach by characterizing surface proteins of different cell types at the single-cell level and distinguishing between the cells by their protein expression profiles. DNA-tagged antibodies provide multiple advantages for profiling proteins in single cells, including the ability to amplify low-abundance tags to make them detectable with sequencing, to use molecular indices for quantitative results, and essentially limitless multiplexing. PMID:28290550

Wide variation of prostate-specific antigen doubling time of untreated, clinically localized, low-to-intermediate grade, prostate carcinoma.

PubMed

Choo, Richard; Klotz, Laurence; Deboer, Gerrit; Danjoux, Cyril; Morton, Gerard C

2004-08-01

To assess the prostate specific antigen (PSA) doubling time of untreated, clinically localized, low-to-intermediate grade prostate carcinoma. A prospective single-arm cohort study has been in progress since November 1995 to assess the feasibility of a watchful-observation protocol with selective delayed intervention for clinically localized, low-to-intermediate grade prostate adenocarcinoma. The PSA doubling time was estimated from a linear regression of ln(PSA) against time, assuming a simple exponential growth model. As of March 2003, 231 patients had at least 6 months of follow-up (median 45) and at least three PSA measurements (median 8, range 3-21). The distribution of the doubling time was: < 2 years, 26 patients; 2-5 years, 65; 5-10 years, 42; 10-20 years, 26; 20-50 years, 16; >50 years, 56. The median doubling time was 7.0 years; 42% of men had a doubling time of >10 years. The doubling time of untreated clinically localized, low-to-intermediate grade prostate cancer varies widely.

Heat-pump-centered integrated community energy systems: Systems development, Consolidated Natural Gas Service Company

NASA Astrophysics Data System (ADS)

Baker, N. R.; Donakowski, T. D.; Foster, R. B.; Sala, D. L.; Tison, R. R.; Whaley, T. P.; Yudow, B. D.; Swenson, P. F.

1980-01-01

The heat actuated heat pump centered integrated community energy system (HAHP-ICES) is described. The system utilizes a gas fired, engine-driven, heat pump and commercial buildings, and offers several advantages over the more conventional equipment it is intended to supplant. The general nonsite specific application assumes a hypothetical community of one 59,000 cu ft office building and five 24 unit, low rise apartment buildings located in a region with a climate similar to Chicago. Various sensitivity analyses are performed and through which the performance characteristics of the HAHP are explored. The results provided the selection criteria for the site specific application of the HAHP-ICES concept to a real world community. The site-specific community consists of: 42 town houses; five 120 unit, low rise apartment buildings; five 104 unit high rise apartment buildings; one 124,000 cu ft office building; and a single 135,000 cu ft retail building.

Ion sensing method

DOEpatents

Smith, Richard Harding; Martin, Glenn Brian

2004-05-18

The present invention allows the determination of trace levels of ionic substances in a sample solution (ions, metal ions, and other electrically charged molecules) by coupling a separation method, such as liquid chromatography, with ion selective electrodes (ISE) prepared so as to allow detection at activities below 10.sup.-6 M. The separation method distributes constituent molecules into fractions due to unique chemical and physical properties, such as charge, hydrophobicity, specific binding interactions, or movement in an electrical field. The separated fractions are detected by means of the ISE(s). These ISEs can be used singly or in an array. Accordingly, modifications in the ISEs are used to permit detection of low activities, specifically, below 10.sup.-6 M, by using low activities of the primary analyte (the molecular species which is specifically detected) in the inner filling solution of the ISE. Arrays constructed in various ways allow flow-through sensing for multiple ions.

Nano-enabled bioanalytical approaches to ultrasensitive detection of low abundance single nucleotide polymorphisms

PubMed Central

Lapitan Jr., Lorico D. S.; Guo, Yuan

2015-01-01

Single nucleotide polymorphisms (SNPs) constitute the most common types of genetic variations in the human genome. A number of SNPs have been linked to the development of life threatening diseases including cancer, cardiovascular diseases and neurodegenerative diseases. The ability for ultrasensitive and accurate detection of low abundant disease-related SNPs in bodily fluids (e.g. blood, serum, etc.) holds a significant value in the development of non-invasive future biodiagnostic tools. Over the past two decades, nanomaterials have been utilized in a myriad of biosensing applications due to their ability of detecting extremely low quantities of biologically important biomarkers with high sensitivity and accuracy. Of particular interest is the application of such technologies in the detection of SNPs. The use of various nanomaterials, coupled with different powerful signal amplification strategies, has paved the way for a new generation of ultrasensitive SNP biodiagnostic assays. Over the past few years, several ultrasensitive SNP biosensors capable of detecting specific targets down to the ultra-low regimes (ca. aM and below) and therefore holding great promises for early clinical diagnosis of diseases have been developed. This mini review will highlight some of the most recent, significant advances in nanomaterial-based ultrasensitive SNP sensing technologies capable of detecting specific targets on the attomolar (10–18 M) regime or below. In particular, the design of novel, powerful signal amplification strategies that hold the key to the ultrasensitivity is highlighted. PMID:25785914

THE RELATIVE IMPORTANCE OF THE VADOSE ZONE IN MULTIMEDIA RISK ASSESSMENT MODELING APPLIED AT A NATIONAL SCALE: AN ANALYSIS OF BENZENE USING 3MRA

EPA Science Inventory

Evaluating uncertainty and parameter sensitivity in environmental models can be a difficult task, even for low-order, single-media constructs driven by a unique set of site-specific data. The challenge of examining ever more complex, integrated, higher-order models is a formidab...

Mosquito Infectivity and Parasitemia after Controlled Human Malaria Infection.

PubMed

Walk, Jona; van Gemert, Geert-Jan; Graumans, Wouter; Sauerwein, Robert; Bijker, Else M

2018-04-30

Controlled Human Malaria Infection (CHMI) has become an increasingly important tool for the evaluation of drugs and vaccines. Controlled Human Malaria Infection has been demonstrated to be a reproducible model; however, there is some variability in time to onset of parasitemia between volunteers and studies. At our center, mosquitoes infected with Plasmodium falciparum by membrane feeding have variable and high salivary gland sporozoite load (mean 78,415; range 26,500-160,500). To determine whether this load influences parasitemia after CHMI, we analyzed data from 13 studies. We found no correlation between the sporozoite load of a mosquito batch and time to parasitemia or parasite density of first-wave parasitemia. These findings support the use of infected mosquito bite as a reproducible means of inducing P. falciparum infection and suggest that within this range, salivary gland sporozoite load does not influence the stringency of a CHMI.

[Traditional Chinese medicine pairs (III)--effect of extract of Ginseng Radix et Rhizoma and Puerariae Lobatae Radix on intestinal absorption in rats].

PubMed

Chen, Yi-hang; Li, Meng-xuan; Meng, Zhao-qing; Yang, Jiao-jiao; Huang, Wen-zhe; Wang, Zhen-zhong; Wang, Yue-sheng; Xiao, Wei

2015-08-01

This study focused on the intestinal absorption of traditional Chinese medicines (TCM) to reveal the scientific connotation of the compatibility of TCM pairs. The single pass intestinal perfusion (SPIP) was used in rats to compare the absorption of single extracts from Puerariae Lobatae Radix, single extracts from Ginseng Radix et Rhizoma, combined extracts from Puerariae Lobatae Radix and Ginseng Radix et Rhizoma and Puerariae Lobatae Radix and Ginseng Radix et Rhizoma mixture in rats. The content of puerarin, ginsenoside Rg1, ginsenoside Re and ginsenoside Rb1 in liquid were tested by HPLC. The speed constant (Ka) and apparent permeability coefficients (Papp) were calculated and compared. Specifically, the order of puerarin Ka and Papp values from high to low was Ginseng Radix et Rhizoma and Puerariae Lobatae Radix mixture > single extracts from Puerariae Lobatae Radix > combined extracts from Ginseng Radix et Rhizoma and Puerariae Lobatae Radix; the order of ginsenosides Ka and Papp values from high to low was Ginseng Radix et Rhizoma and Puerariae Lobatae Radix mixture > single extracts from Ginseng Radix et Rhizoma > combined extracts from Ginseng Radix et Rhizoma and Puerariae Lobatae Radix. The combined administration of Ginseng Radix et Rhizoma and Puerariae Lobatae Radix may improve the absorption in the intestinal tract.

Low temperature specific heat of charge ordered Pr_1-xCa_xMnO_3

NASA Astrophysics Data System (ADS)

Smolyaninova, V. N.; Biswas, Amlan; Zhang, X.; Greene, R. L.

2000-03-01

Mixed-valent perovskite manganese oxides at certain doping levels develope a real space ordering of Mn^3+ and Mn^4+ at low temperatures^1, which can be destroyed (``melted'') by the application of a modest magnetic field.^2 To better understand the low-temperature ground state and the physics of the ``melted'' charge-ordered state, the specific heat, resistivity and magnetization of charge-ordered Pr_1-xCa_xMnO3 were measured with and without magnetic field for single crystal and ceramic samples of different x. A large excess specific heat of nonmagnetic origin was found, similar to that found in La_0.5Ca_0.5MnO3 ^3. Significant changes in the specific heat associated with the ``melting'' of the charge ordering were observed in applied magnetic fields up to 9 T. Possible explanations for this anomalous specific heat and its magnetic field dependence will be discussed . ^*This work is supported in part by NSF MRSEC Grant at the University of Maryland. ^1S. Mori, C. H. Chen and S-W. Cheong, Nature 392, 473 (1998). ^2Y. Tomioka et al., Phys. Rev. Lett. 74, 5108 (1995). ^3V. N. Smolyaninova, K. Ghosh and R. L. Greene, Phys. Rev. B 58, R14 725 (1998).

smiFISH and FISH-quant - a flexible single RNA detection approach with super-resolution capability.

PubMed

Tsanov, Nikolay; Samacoits, Aubin; Chouaib, Racha; Traboulsi, Abdel-Meneem; Gostan, Thierry; Weber, Christian; Zimmer, Christophe; Zibara, Kazem; Walter, Thomas; Peter, Marion; Bertrand, Edouard; Mueller, Florian

2016-12-15

Single molecule FISH (smFISH) allows studying transcription and RNA localization by imaging individual mRNAs in single cells. We present smiFISH (single molecule inexpensive FISH), an easy to use and flexible RNA visualization and quantification approach that uses unlabelled primary probes and a fluorescently labelled secondary detector oligonucleotide. The gene-specific probes are unlabelled and can therefore be synthesized at low cost, thus allowing to use more probes per mRNA resulting in a substantial increase in detection efficiency. smiFISH is also flexible since differently labelled secondary detector probes can be used with the same primary probes. We demonstrate that this flexibility allows multicolor labelling without the need to synthesize new probe sets. We further demonstrate that the use of a specific acrydite detector oligonucleotide allows smiFISH to be combined with expansion microscopy, enabling the resolution of transcripts in 3D below the diffraction limit on a standard microscope. Lastly, we provide improved, fully automated software tools from probe-design to quantitative analysis of smFISH images. In short, we provide a complete workflow to obtain automatically counts of individual RNA molecules in single cells. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Clinical skills-related learning goals of senior medical students after performance feedback.

PubMed

Chang, Anna; Chou, Calvin L; Teherani, Arianne; Hauer, Karen E

2011-09-01

Lifelong learning is essential for doctors to maintain competence in clinical skills. With performance feedback, learners should be able to formulate specific and achievable learning goals in areas of need. We aimed to determine: (i) the type and specificity of medical student learning goals after a required clinical performance examination; (ii) differences in goal setting among low, average and high performers, and (iii) whether low performers articulate learning goals that are concordant with their learning needs. We conducted a single-site, multi-year, descriptive comparison study. Senior medical students were given performance benchmarks, individual feedback and guidelines on learning goals; each student was subsequently instructed to write two clinical skills learning goals. Investigators coded the learning goals for specificity, categorised the goals, and performed statistical analyses to determine their concordance with student performance level (low, average or high) in data gathering (history taking and physical examination) or communication skills. All 208 students each wrote two learning goals and most (n=200, 96%) wrote two specific learning goals. Nearly two-thirds of low performers in data gathering wrote at least one learning goal that referred to history taking or physical examination; one-third wrote learning goals pertaining to the organisation of the encounter. High performers in data gathering wrote significantly more patient education goals and significantly fewer history-taking goals than average or low performers. Only 50% of low performers in communication wrote learning goals related to communication skills. Low performers in communication were significantly more likely than average or high performers to identify learning goals related to improving performance in future examinations. The provision of performance benchmarking, individual feedback and brief written guidelines helped most senior medical students in our study to write specific clinical skills learning goals. Many low-performing students did not write learning goals concordant with their areas of weakness. Future work might focus on enhancing low performers' continued learning in areas of performance deficits. © Blackwell Publishing Ltd 2011.

Fine needle aspiration cytology of breast cancer in women aged 70 years and older.

PubMed

Tse, Gary M K; Somali, Anjali; Chan, Anthony W H; Chaiwun, Benjaporn; Lui, Philip C W; Moriya, Takuya; Hwang, Jacqueline S G; Chan, Norman H L; Tan, Puay Hoon

2008-10-01

Elderly breast cancers are associated with a more favourable biological marker profile and higher proportion of specific subtypes, some of which are of low histological grade. We reviewed the fine needle aspiration cytology (FNAC) to assess the cytological characteristics and any clues to assist in the diagnosis. The aspirates of 140 cancers of various histological types and grades and 39 benign lesions were evaluated for 13 cytological parameters including cellularity of the direct and cytospin smears, epithelial cell clusters, cellular atypism, cytoplasmic features, vacuoles, mitotic figures, presence of myoepithelial cells, single background epithelial cells, the presence of naked nuclei, stromal fragments and necrosis. We found that the presence of background single epithelial cells, atypism of such cells, absence of benign appearing epithelial fragments, nuclear atypism of the epithelial cells within the fragments, presence of moderate amount of cytoplasm of these cells, absence of myoepithelial cells within the cluster, and absence of bipolar nuclei in the background have a strong association with malignancy. Scoring only the presence of single cells in the background, single cell atypism and the absence of bipolar nuclei in a scoring system can differentiate between benign and malignant aspirates with high (>90%) sensitivity and specificity. Assessing the presence of single cells in the background, single cell atypism and the absence of bipolar nuclei facilitates identification of malignancy in the aspiration of breast lesions from elderly patients.

[Extension of cardiac monitoring function by used of ordinary ECG machine].

PubMed

Chen, Zhencheng; Jiang, Yong; Ni, Lili; Wang, Hongyan

2002-06-01

This paper deals with a portable monitor system on liquid crystal display (LCD) based on this available ordinary ECG machine, which is low power and suitable for China's specific condition. Apart from developing the overall scheme of the system, this paper also has completed the design of the hardware and the software. The 80c196 single chip microcomputer is taken as the central microprocessor and real time electrocardiac single is data treated and analyzed in the system. With the performance of ordinary monitor, this machine also possesses the following functions: five types of arrhythmia analysis, alarm, freeze, and record of automatic pappering, convenient in carrying, with alternate-current (AC) or direct-current (DC) powered. The hardware circuit is simplified and the software structure is optimized in this paper. Multiple low power designs and LCD unit design are adopted and completed in it. Popular in usage, low in cost price, the portable monitor system will have a valuable influence on China's monitor system field.

Probing the target search of DNA-binding proteins in mammalian cells using TetR as model searcher

NASA Astrophysics Data System (ADS)

Normanno, Davide; Boudarène, Lydia; Dugast-Darzacq, Claire; Chen, Jiji; Richter, Christian; Proux, Florence; Bénichou, Olivier; Voituriez, Raphaël; Darzacq, Xavier; Dahan, Maxime

2015-07-01

Many cellular functions rely on DNA-binding proteins finding and associating to specific sites in the genome. Yet the mechanisms underlying the target search remain poorly understood, especially in the case of the highly organized mammalian cell nucleus. Using as a model Tet repressors (TetRs) searching for a multi-array locus, we quantitatively analyse the search process in human cells with single-molecule tracking and single-cell protein-DNA association measurements. We find that TetRs explore the nucleus and reach their target by 3D diffusion interspersed with transient interactions with non-cognate sites, consistent with the facilitated diffusion model. Remarkably, nonspecific binding times are broadly distributed, underlining a lack of clear delimitation between specific and nonspecific interactions. However, the search kinetics is not determined by diffusive transport but by the low association rate to nonspecific sites. Altogether, our results provide a comprehensive view of the recruitment dynamics of proteins at specific loci in mammalian cells.

Superconducting gap symmetry in the superconductor BaFe1.9Ni0.1As2

NASA Astrophysics Data System (ADS)

Kuzmicheva, T. E.; Kuzmichev, S. A.; Sadakov, A. V.; Gavrilkin, S. Yu.; Tsvetkov, A. Yu.; Lu, X.; Luo, H.; Vasiliev, A. N.; Pudalov, V. M.; Chen, Xiao-Jia; Abdel-Hafiez, Mahmoud

2018-06-01

We report on the Andreev spectroscopy and specific heat of high-quality single crystals of BaFe1.9Ni0.1As2 . The intrinsic multiple Andreev reflection spectroscopy reveals two anisotropic superconducting gaps ΔL≈3.2 -4.5 meV , ΔS≈1.2 -1.6 meV (the ranges correspond to the minimum and maximum value of the coupling energy in the kxky plane). The 25 %-30 % anisotropy shows the absence of nodes in the superconducting gaps. Using a two-band model with s -wave-like gaps ΔL≈3.2 meV and ΔS≈1.6 meV , the temperature dependence of the electronic specific heat can be well described. A linear magnetic field dependence of the low-temperature specific heat offers further support of s -wave type of the order parameter. We find that a d -wave or single-gap BCS theory under the weak-coupling approach cannot describe our experiments.

Steepest Ascent Low/Non-Low-Frequency Ratio in Empirical Mode Decomposition to Separate Deterministic and Stochastic Velocities From a Single Lagrangian Drifter

NASA Astrophysics Data System (ADS)

Chu, Peter C.

2018-03-01

SOund Fixing And Ranging (RAFOS) floats deployed by the Naval Postgraduate School (NPS) in the California Current system from 1992 to 2001 at depth between 150 and 600 m (http://www.oc.nps.edu/npsRAFOS/) are used to study 2-D turbulent characteristics. Each drifter trajectory is adaptively decomposed using the empirical mode decomposition (EMD) into a series of intrinsic mode functions (IMFs) with corresponding specific scale for each IMF. A new steepest ascent low/non-low-frequency ratio is proposed in this paper to separate a Lagrangian trajectory into low-frequency (nondiffusive, i.e., deterministic) and high-frequency (diffusive, i.e., stochastic) components. The 2-D turbulent (or called eddy) diffusion coefficients are calculated on the base of the classical turbulent diffusion with mixing length theory from stochastic component of a single drifter. Statistical characteristics of the calculated 2-D turbulence length scale, strength, and diffusion coefficients from the NPS RAFOS data are presented with the mean values (over the whole drifters) of the 2-D diffusion coefficients comparable to the commonly used diffusivity tensor method.

The Single Habitat Module Concept for Exploration - Mission Planning and Mass Estimates

NASA Technical Reports Server (NTRS)

Chambliss, Joe; Studak, J. W.

2013-01-01

The Single Habitat Module (SHM) concept approach to the infrastructure and conduct of exploration missions combines many new promising technologies with a central concept of mission architectures that use a single habitat module for all phases of an exploration mission. Integrating mission elements near Earth and fully fueling them prior to departure of the vicinity of Earth provides the capability of using the single habitat both in transit to/from an exploration destination and while exploring the destination. The concept employs the capability to return the habitat and interplanetary propulsion system to Earth vicinity so that those elements can be reused on subsequent exploration missions. This paper provides an overview of the SHM concept and the advantages it provides. The paper also provides a summary of calculations of the mass of the Habitat Propulsion System (HPS) needed to get the habitat from low-Mars orbit (LMO) to the surface and back to LMO, and an overview of trajectory and mission mass assessments related to use of a high specific impulse space-based propulsion system. Those calculations led to the conclusion that the SHM concept results in low total mass required and streamlines mission operations to explore Mars (or other exploration destinations).

Ground Motion Uncertainty and Variability (single-station sigma): Insights from Euroseistest, Greece

NASA Astrophysics Data System (ADS)

Ktenidou, O. J.; Roumelioti, Z.; Abrahamson, N. A.; Cotton, F.; Pitilakis, K.

2014-12-01

Despite recent improvements in networks and data, the global aleatory uncertainty (sigma) in GMPEs is still large. One reason is the ergodic approach, where we combine data in space to make up for lack of data in time. By estimating the systematic site response, we can make site-specific GMPEs and use a lower, site-specific uncertainty: single-station sigma. In this study we use the EUROSEISTEST database (http://euroseisdb.civil.auth.gr), which has two distinct advantages: good existing knowledge of site conditions at all stations, and careful relocation of the recorded events. Constraining the site and source parameters as best we can, we minimise the within- and between-events components of the global, ergodic sigma. Following that, knowledge of the site response from empirical and theoretical approaches permits us to move on to single-station sigma. The variability per site is not clearly correlated to the site class. We show that in some cases knowledge of Vs30 is not sufficient, and that site-specific data are needed to capture the response, possibly due to 2D/3D effects from complex geometry. Our values of single-station sigma are low compared to the literature. This may be due to the good ray coverage we have in all directions for small, nearby records. Indeed, our single-station sigma values are similar to published single-path values, which means that they may correspond to a fully -rather than partially- non-ergodic approach. We find larger ground motion variability for short distances and small magnitudes. This may be related to the uncertainty in the depth affecting nearby records more, or to stress drop and causing trade-offs between the source and site terms for small magnitudes.

Evaluating low-resolution tomography neurofeedback by single dissociation of mental grotation task from stop signal task performance.

PubMed

Getter, Nir; Kaplan, Zeev; Todder, Doron

2015-10-01

Electroencephalography source localization neurofeedback, i.e Standardized low-resolution tomography (sLORETA) neurofeedback are non-invasive method for altering region specific brain activity. This is an improvement over traditional neurofeedback which were based on recordings from a single scalp-electrode. We proposed three criteria clusters as a methodological framework to evaluate electroencephalography source localization neurofeedback and present relevant data. Our objective was to evaluate standardized low resolution EEG tomography neurofeedback by examining how training one neuroanatomical area effects the mental rotation task (which is related to the activity of bilateral Parietal regions) and the stop-signal test (which is related to frontal structures). Twelve healthy participants were enrolled in a single session sLORETA neurofeedback protocol. The participants completed both the mental rotation task and the stop-signal test before and after one sLORETA neurofeedback session. During sLORETA neurofeedback sessions participants watched one sitcom episode while the picture quality co-varied with activity in the superior parietal lobule. Participants were rewarded for increasing activity in this region only. Results showed a significant reaction time decrease and an increase in accuracy after sLORETA neurofeedback on the mental rotation task but not after stop signal task. Together with behavioral changes a significant activity increase was found at the left parietal brain after sLORETA neurofeedback compared with baseline. We concluded that activity increase in the parietal region had a specific effect on the mental rotation task. Tasks unrelated to parietal brain activity were unaffected. Therefore, sLORETA neurofeedback could be used as a research, or clinical tool for cognitive disorders. Copyright © 2015 Elsevier B.V. All rights reserved.

Choosing MUSE: Validation of a Low-Cost, Portable EEG System for ERP Research

PubMed Central

Krigolson, Olave E.; Williams, Chad C.; Norton, Angela; Hassall, Cameron D.; Colino, Francisco L.

2017-01-01

In recent years there has been an increase in the number of portable low-cost electroencephalographic (EEG) systems available to researchers. However, to date the validation of the use of low-cost EEG systems has focused on continuous recording of EEG data and/or the replication of large system EEG setups reliant on event-markers to afford examination of event-related brain potentials (ERP). Here, we demonstrate that it is possible to conduct ERP research without being reliant on event markers using a portable MUSE EEG system and a single computer. Specifically, we report the results of two experiments using data collected with the MUSE EEG system—one using the well-known visual oddball paradigm and the other using a standard reward-learning task. Our results demonstrate that we could observe and quantify the N200 and P300 ERP components in the visual oddball task and the reward positivity (the mirror opposite component to the feedback-related negativity) in the reward-learning task. Specifically, single sample t-tests of component existence (all p's < 0.05), computation of Bayesian credible intervals, and 95% confidence intervals all statistically verified the existence of the N200, P300, and reward positivity in all analyses. We provide with this research paper an open source website with all the instructions, methods, and software to replicate our findings and to provide researchers with an easy way to use the MUSE EEG system for ERP research. Importantly, our work highlights that with a single computer and a portable EEG system such as the MUSE one can conduct ERP research with ease thus greatly extending the possible use of the ERP methodology to a variety of novel contexts. PMID:28344546

Choosing MUSE: Validation of a Low-Cost, Portable EEG System for ERP Research.

PubMed

Krigolson, Olave E; Williams, Chad C; Norton, Angela; Hassall, Cameron D; Colino, Francisco L

2017-01-01

In recent years there has been an increase in the number of portable low-cost electroencephalographic (EEG) systems available to researchers. However, to date the validation of the use of low-cost EEG systems has focused on continuous recording of EEG data and/or the replication of large system EEG setups reliant on event-markers to afford examination of event-related brain potentials (ERP). Here, we demonstrate that it is possible to conduct ERP research without being reliant on event markers using a portable MUSE EEG system and a single computer. Specifically, we report the results of two experiments using data collected with the MUSE EEG system-one using the well-known visual oddball paradigm and the other using a standard reward-learning task. Our results demonstrate that we could observe and quantify the N200 and P300 ERP components in the visual oddball task and the reward positivity (the mirror opposite component to the feedback-related negativity) in the reward-learning task. Specifically, single sample t -tests of component existence (all p 's < 0.05), computation of Bayesian credible intervals, and 95% confidence intervals all statistically verified the existence of the N200, P300, and reward positivity in all analyses. We provide with this research paper an open source website with all the instructions, methods, and software to replicate our findings and to provide researchers with an easy way to use the MUSE EEG system for ERP research. Importantly, our work highlights that with a single computer and a portable EEG system such as the MUSE one can conduct ERP research with ease thus greatly extending the possible use of the ERP methodology to a variety of novel contexts.

A low-dose, dual-phase cardiovascular CT protocol to assess left atrial appendage anatomy and exclude thrombus prior to left atrial intervention.

PubMed

Lazoura, Olga; Ismail, Tevfik F; Pavitt, Christopher; Lindsay, Alistair; Sriharan, Mona; Rubens, Michael; Padley, Simon; Duncan, Alison; Wong, Tom; Nicol, Edward

2016-02-01

Assessment of the left atrial appendage (LAA) for thrombus and anatomy is important prior to atrial fibrillation (AF) ablation and LAA exclusion. The use of cardiovascular CT (CCT) to detect LAA thrombus has been limited by the high incidence of pseudothrombus on single-pass studies. We evaluated the diagnostic accuracy of a two-phase protocol incorporating a limited low-dose delayed contrast-enhanced examination of the LAA, compared with a single-pass study for LAA morphological assessment, and transesophageal echocardiography (TEE) for the exclusion of thrombus. Consecutive patients (n = 122) undergoing left atrial interventions for AF were assessed. All had a two-phase CCT protocol (first-past scan plus a limited, 60-s delayed scan of the LAA) and TEE. Sensitivity, specificity, diagnostic accuracy, positive (PPV) and negative predictive values (NPV) were calculated for the detection of true thrombus on first-pass and delayed scans, using TEE as the gold standard. Overall, 20/122 (16.4 %) patients had filling defects on the first-pass study. All affected the full delineation of the LAA morphology; 17/20 (85 %) were confirmed as pseudo-filling defects. Three (15 %) were seen on late-pass and confirmed as true thrombi on TEE; a significant improvement in diagnostic performance relative to a single-pass scan (McNemar Chi-square 17, p < 0.001). The sensitivity, specificity, diagnostic accuracy, PPV and NPV was 100, 85.7, 86.1, 15.0 and 100 % respectively for first-pass scans, and 100 % for all parameters for the delayed scans. The median (range) additional radiation dose for the delayed scan was 0.4 (0.2-0.6) mSv. A low-dose delayed scan significantly improves the identification of true LAA anatomy and thrombus in patients undergoing LA intervention.

Potential applications of MMC and aluminum-lithium alloys in cameras for CRAF spacecraft. [Comet Rendezvous Asteroid Flyby Mission

NASA Technical Reports Server (NTRS)

Lane, Marc; Hsieh, Cheng; Adams, Lloyd

1989-01-01

In undertaking the design of a 2000-mm focal length camera for the Mariner Mark II series of spacecraft, JPL sought novel materials with the requisite dimensional and thermal stability, outgassing and corrosion resistance, low mass, high stiffness, and moderate cost. Metal-matrix composites and Al-Li alloys have, in addition to excellent mechanical properties and low density, a suitably low coefficient of thermal expansion, high specific stiffness, and good electrical conductivity. The greatest single obstacle to application of these materials to camera structure design is noted to have been the lack of information regarding long-term dimensional stability.

Diagnostic utility of a one-item question to screen for depressive disorders: results from the KORA F3 study.

PubMed

Blozik, Eva; Scherer, Martin; Lacruz, Maria E; Ladwig, Karl-Heinz

2013-12-23

Screening for depressive disorders in the general adult population is recommended, however, it is unclear which instruments combine user friendliness and diagnostic utility. We evaluated the test performance of a yes/no single item screener for depressive disorders ("Have you felt depressed or sad much of the time in the past year?") in comparison to the depressive disorder module of the Patient Health Questionnaire (PHQ-9). Data from 3184 participants of the population-based KORA F3 survey in Augsburg/ Germany were used to analyse sensitivity, specificity, ROC area, positive likelihood ratio (LR+), negative likelihood ratio (LR-), positive predictive value (PPV), and negative predictive value (NPV) of the single item screener in comparison with "depressive mood" and "major depressive disorder" defined according to PHQ-9 (both interviewer-administered versions). In comparison to PHQ-9 "depressive mood", sensitivity was low (46%) with an excellent specificity (94%), (PPV 76%; NPV 82%; LR + 8.04; LR- .572, ROC area .702). When using the more conservative definition for "major depressive disorder", sensitivity increased to 83% with a specificity of 88%. The PPV under the conservative definition was low (32%), but NPV was 99% (LR + 6.65; LR- .196; ROC area .852). Results varied across age groups and between males and females. The single item screener is able to moderately decrease post-test probability of major depressive disorders and to identify populations that should undergo additional, more detailed evaluation for depression. It may have limited utility in combination with additional screening tests or for selection of at-risk populations, but cannot be recommended for routine use as a screening tool in clinical practice.

Diagnostic utility of a one-item question to screen for depressive disorders: results from the KORA F3 study

PubMed Central

2013-01-01

Background Screening for depressive disorders in the general adult population is recommended, however, it is unclear which instruments combine user friendliness and diagnostic utility. We evaluated the test performance of a yes/no single item screener for depressive disorders (“Have you felt depressed or sad much of the time in the past year?”) in comparison to the depressive disorder module of the Patient Health Questionnaire (PHQ-9). Methods Data from 3184 participants of the population-based KORA F3 survey in Augsburg/ Germany were used to analyse sensitivity, specificity, ROC area, positive likelihood ratio (LR+), negative likelihood ratio (LR-), positive predictive value (PPV), and negative predictive value (NPV) of the single item screener in comparison with “depressive mood” and “major depressive disorder” defined according to PHQ-9 (both interviewer-administered versions). Results In comparison to PHQ-9 “depressive mood”, sensitivity was low (46%) with an excellent specificity (94%), (PPV 76%; NPV 82%; LR + 8.04; LR- .572, ROC area .702). When using the more conservative definition for “major depressive disorder”, sensitivity increased to 83% with a specificity of 88%. The PPV under the conservative definition was low (32%), but NPV was 99% (LR + 6.65; LR- .196; ROC area .852). Results varied across age groups and between males and females. Conclusions The single item screener is able to moderately decrease post-test probability of major depressive disorders and to identify populations that should undergo additional, more detailed evaluation for depression. It may have limited utility in combination with additional screening tests or for selection of at-risk populations, but cannot be recommended for routine use as a screening tool in clinical practice. PMID:24359193

A MPPT Algorithm Based PV System Connected to Single Phase Voltage Controlled Grid

NASA Astrophysics Data System (ADS)

Sreekanth, G.; Narender Reddy, N.; Durga Prasad, A.; Nagendrababu, V.

2012-10-01

Future ancillary services provided by photovoltaic (PV) systems could facilitate their penetration in power systems. In addition, low-power PV systems can be designed to improve the power quality. This paper presents a single-phase PV systemthat provides grid voltage support and compensation of harmonic distortion at the point of common coupling thanks to a repetitive controller. The power provided by the PV panels is controlled by a Maximum Power Point Tracking algorithm based on the incremental conductance method specifically modified to control the phase of the PV inverter voltage. Simulation and experimental results validate the presented solution.

An evaluation of composite propulsion for single-stage-to-orbit vehicles designed for horizontal take-off

NASA Technical Reports Server (NTRS)

Martin, J. A.

1977-01-01

Composite propulsion was analyzed for single-stage-to-orbit vehicles designed for horizontal take-off. Trajectory, geometric, and mass analyses were performed to establish the orbital payload capability of six engines. The results indicated that none of the engines performed adequately to deliver payloads to orbit as analyzed. The single-stage turbine and oxidizer-rich gas generator resulted in a low engine specific impulse, and the performance increment of the ejector subsystem was less than that of a separate rocket system with a high combustion pressure. There was a benefit from incorporating a fan into the engine, and removal of the fan from the airstream during the ramjet mode increased the orbital payload capability.

Low cost coherent demodulation for mobile satellite terminals

NASA Technical Reports Server (NTRS)

Dutta, Santanu; Henely, Steven J.

1993-01-01

This paper describes some low cost approaches to coherent BPSK demodulation for mobile satellite receivers. The specific application is an Inmarsat-C Land Mobile Earth Station (LMES), but the techniques are applicable to any PSK demodulator. The techniques discussed include combined sampling and quadrature downconversion with a single A/D and novel DSP algorithms for carrier acquisition offering both superior performance and economy of DSP resources. The DSP algorithms run at 5.7 MIPS, and the entire DSP subsystem, built with commercially available parts, costs under $60 at quantity-10,000.

Polarized-neutron study of spin dynamics in the Kondo insulator YbB12.

PubMed

Nemkovski, K S; Mignot, J-M; Alekseev, P A; Ivanov, A S; Nefeodova, E V; Rybina, A V; Regnault, L-P; Iga, F; Takabatake, T

2007-09-28

Inelastic neutron scattering experiments have been performed on the archetype compound YbB(12), using neutron polarization analysis to separate the magnetic signal from the phonon background. With decreasing temperature, components characteristic for a single-site spin-fluctuation dynamics are suppressed, giving place to specific, strongly Q-dependent, low-energy excitations near the spin-gap edge. This crossover is discussed in terms of a simple crystal-field description of the incoherent high-temperature state and a predominantly local mechanism for the formation of the low-temperature singlet ground state.

Nucleic acid detection system and method for detecting influenza

DOEpatents

Cai, Hong; Song, Jian

2015-03-17

The invention provides a rapid, sensitive and specific nucleic acid detection system which utilizes isothermal nucleic acid amplification in combination with a lateral flow chromatographic device, or DNA dipstick, for DNA-hybridization detection. The system of the invention requires no complex instrumentation or electronic hardware, and provides a low cost nucleic acid detection system suitable for highly sensitive pathogen detection. Hybridization to single-stranded DNA amplification products using the system of the invention provides a sensitive and specific means by which assays can be multiplexed for the detection of multiple target sequences.

Medication adherence among patients in a chronic disease clinic.

PubMed

Tourkmani, Ayla M; Al Khashan, Hisham I; Albabtain, Monirah A; Al Harbi, Turki J; Al Qahatani, Hala B; Bakhiet, Ahmed H

2012-12-01

To assess motivation and knowledge domains of medication adherence intention, and to determine their predictors in an ambulatory setting. We conducted a cross-sectional survey study among patients attending a chronic disease clinic at the Family and Community Medicine Department, Prince Sultan Military Medical City, Riyadh, Kingdom of Saudi Arabia between June and September 2010. Adherence intention was assessed using Modified Morisky Scale. Predictors of low motivation and/or knowledge were determined using logistic regression models. A total of 347 patients were interviewed during the study duration. Most patients (75.5%) had 2 or more chronic diseases with an average of 6.3 +/- 2.3 medications, and 6.5 +/- 2.9 pills per prescription. The frequency of adherence intention was low (4.6%), variable (37.2%), and high (58.2%). In multivariate logistic regression analysis, younger age and having asthma were significantly associated with low motivation, while male gender, single status, and not having hypertension were significantly associated with low knowledge. Single status was the only independent predictor of low adherence intention. In a population with multiple chronic diseases and high illiteracy rate, more than 40% had low/variable intention to adhere to prescribed medications. Identifying predictors of this group may help in providing group-specific interventional programs.

Variations in costs for the care of low-birth-weight infants among academic hospitals.

PubMed

Herrod, Henry G; Chang, Cyril F; Steinberg, Stephanie S

2010-05-01

To determine the relative role that academic hospitals (AHs) play in providing neonatal care for low-birth-weight infants within a single state and to determine if there are variations in inpatient costs for neonatal services among AHs. Retrospective analysis of hospital costs for low-birth-weight infants. Cases were identified using 2003-2005 data from the Tennessee Hospital Discharge Data System. A specific focus was discharge data from the 5 AHs that support obstetrical residencies and have a neonatal intensive care unit. Cases included all discharged infants with a birth weight of <2500 grams. The 5 AHs discharged 18% of the total normal-birth-weight infants and 30% of the low-birth-weight infants for the entire state. AHs had higher costs associated with these infants than did other hospitals, with a single exception The difference in costs at this hospital was consistent with the finding of lower utilization rates of hospital services, a shorter average length of stay, and lower costs for infants insured by the state Medicaid program. Academic obstetrical hospitals discharged a disproportionately high percentage of low-birth-weight infants compared with other Tennessee hospitals. The lower costs observed in the Shelby County hospital indicates that other hospitals could potentially lower their costs for the care of low-birth-weight infants.

A branch-migration based fluorescent probe for straightforward, sensitive and specific discrimination of DNA mutations

PubMed Central

Xiao, Xianjin; Wu, Tongbo; Xu, Lei; Chen, Wei

2017-01-01

Abstract Genetic mutations are important biomarkers for cancer diagnostics and surveillance. Preferably, the methods for mutation detection should be straightforward, highly specific and sensitive to low-level mutations within various sequence contexts, fast and applicable at room-temperature. Though some of the currently available methods have shown very encouraging results, their discrimination efficiency is still very low. Herein, we demonstrate a branch-migration based fluorescent probe (BM probe) which is able to identify the presence of known or unknown single-base variations at abundances down to 0.3%-1% within 5 min, even in highly GC-rich sequence regions. The discrimination factors between the perfect-match target and single-base mismatched target are determined to be 89–311 by measurement of their respective branch-migration products via polymerase elongation reactions. The BM probe not only enabled sensitive detection of two types of EGFR-associated point mutations located in GC-rich regions, but also successfully identified the BRAF V600E mutation in the serum from a thyroid cancer patient which could not be detected by the conventional sequencing method. The new method would be an ideal choice for high-throughput in vitro diagnostics and precise clinical treatment. PMID:28201758

The low-abundance transcriptome reveals novel biomarkers, specific intracellular pathways and targetable genes associated with advanced gastric cancer.

PubMed

Bizama, Carolina; Benavente, Felipe; Salvatierra, Edgardo; Gutiérrez-Moraga, Ana; Espinoza, Jaime A; Fernández, Elmer A; Roa, Iván; Mazzolini, Guillermo; Sagredo, Eduardo A; Gidekel, Manuel; Podhajcer, Osvaldo L

2014-02-15

Studies on the low-abundance transcriptome are of paramount importance for identifying the intimate mechanisms of tumor progression that can lead to novel therapies. The aim of the present study was to identify novel markers and targetable genes and pathways in advanced human gastric cancer through analyses of the low-abundance transcriptome. The procedure involved an initial subtractive hybridization step, followed by global gene expression analysis using microarrays. We observed profound differences, both at the single gene and gene ontology levels, between the low-abundance transcriptome and the whole transcriptome. Analysis of the low-abundance transcriptome led to the identification and validation by tissue microarrays of novel biomarkers, such as LAMA3 and TTN; moreover, we identified cancer type-specific intracellular pathways and targetable genes, such as IRS2, IL17, IFNγ, VEGF-C, WISP1, FZD5 and CTBP1 that were not detectable by whole transcriptome analyses. We also demonstrated that knocking down the expression of CTBP1 sensitized gastric cancer cells to mainstay chemotherapeutic drugs. We conclude that the analysis of the low-abundance transcriptome provides useful insights into the molecular basis and treatment of cancer. © 2013 UICC.

Slower postnatal motor development in infants of mothers with latent toxoplasmosis during the first 18 months of life.

PubMed

Kaňková, Sárka; Sulc, Jan; Křivohlavá, Romana; Kuběna, Aleš; Flegr, Jaroslav

2012-11-01

Toxoplasmosis, a zoonosis caused by a protozoan, Toxoplasma gondii, is probably the most widespread human parasitosis in developed countries. Pregnant women with latent toxoplasmosis have seemingly younger fetuses especially in the 16th week of gestation, which suggests that fetuses of Toxoplasma-infected mothers have slower rates of development in the first trimester of pregnancy. In the present retrospective cohort study, we analyzed data on postnatal motor development of infants from 331 questionnaire respondents including 53 Toxoplasma-infected mothers to search for signs of early postnatal development disorders. During the first year of life, a slower postnatal motor development was observed in infants of mothers with latent toxoplasmosis. These infants significantly later developed the ability to control the head position (p=0.039), to roll from supine to prone position (p=0.022) and were slightly later to begin crawling (p=0.059). Our results are compatible with the hypothesis that the difference in the rates of prenatal and early postnatal development between children of Toxoplasma-negative and Toxoplasma-positive mothers might be caused by a decreased stringency of embryo quality control in partly immunosuppressed Toxoplasma-positive mothers resulting in a higher proportion of infants with genetic or developmental disorders in offspring. However, because of relatively low return rate of questionnaires and an associated risk of a sieve effect, our results should be considered as preliminary and performing a large scale prospective study in the future is critically needed. Copyright © 2012 Elsevier Ltd. All rights reserved.

Funding health and social services for older people - a qualitative study of care recipients in the last year of life.

PubMed

Hanratty, Barbara; Lowson, Elizabeth; Holmes, Louise; Grande, Gunn; Addington-Hall, Julia; Payne, Sheila; Seymour, Jane

2012-05-01

This study explores the views of older adults who are receiving health and social care at the end of their lives, on how services should be funded, and describes their health-related expenditure. Qualitative interview study. North West England. 30 people aged 69-93 years, diagnosed with lung cancer, heart failure or stroke and judged by health professionals to be in their last year of life. Sixteen participants lived in disadvantaged areas. Views of older adults on funding of services. Participants expressed a belief in an earned entitlement to services funded from taxation, based on a broad sense of being a good citizen. Irrespective of social background, older people felt that those who could afford to pay for social care, should do so. Sale of assets and use of children's inheritance to fund care was widely perceived as an injustice. The costs of living with illness are a burden, and families are filling many of the gaps left by welfare provision. People who had worked in low-wage occupations were most concerned to justify their current acceptance of services, and distance themselves from what they described as welfare 'spongers' or 'layabouts.' There is a gap between the health and social care system that older adults expect and what may be provided by a reformed welfare state at a time of financial stringencies. The values that underpinned the views expressed--mutuality, care for the most needy, and the importance of working to contribute to society--are an important contribution to the debate on welfare funding.

Identification of an additional member of the protein-tyrosine-phosphatase family: evidence for alternative splicing in the tyrosine phosphatase domain.

PubMed Central

Matthews, R J; Cahir, E D; Thomas, M L

1990-01-01

Protein-tyrosine-phosphatases (protein-tyrosine-phosphate phosphohydrolase, EC 3.13.48) have been implicated in the regulation of cell growth; however, to date few tyrosine phosphatases have been characterized. To identify additional family members, the cDNA for the human tyrosine phosphatase leukocyte common antigen (LCA; CD45) was used to screen, under low stringency, a mouse pre-B-cell cDNA library. Two cDNA clones were isolated and sequence analysis predicts a protein sequence of 793 amino acids. We have named the molecule LRP (LCA-related phosphatase). RNA transfer analysis indicates that the cDNAs were derived from a 3.2-kilobase mRNA. The LRP mRNA is transcribed in a wide variety of tissues. The predicted protein structure can be divided into the following structural features: a short 19-amino acid leader sequence, an exterior domain of 123 amino acids that is predicted to be highly glycosylated, a 24-amino acid membrane-spanning region, and a 627-amino acid cytoplasmic region. The cytoplasmic region contains two approximately 260-amino acid domains, each with homology to the tyrosine phosphatase family. One of the cDNA clones differed in that it had a 108-base-pair insertion that, while preserving the reading frame, would disrupt the first protein-tyrosine-phosphatase domain. Analysis of genomic DNA indicates that the insertion is due to an alternatively spliced exon. LRP appears to be evolutionarily conserved as a putative homologue has been identified in the invertebrate Styela plicata. Images PMID:2162042

In Silico Analysis of Antibiotic Resistance Genes in the Gut Microflora of Individuals from Diverse Geographies and Age-Groups

PubMed Central

Ghosh, Tarini Shankar; Gupta, Sourav Sen; Nair, Gopinath Balakrish; Mande, Sharmila S.

2013-01-01

The spread of antibiotic resistance, originating from the rampant and unrestrictive use of antibiotics in humans and livestock over the past few decades has emerged as a global health problem. This problem has been further compounded by recent reports implicating the gut microbial communities to act as reservoirs of antibiotic resistance. We have profiled the presence of probable antibiotic resistance genes in the gut flora of 275 individuals from eight different nationalities. For this purpose, available metagenomic data sets corresponding to 275 gut microbiomes were analyzed. Sequence similarity searches of the genomic fragments constituting each of these metagenomes were performed against genes conferring resistance to around 240 antibiotics. Potential antibiotic resistance genes conferring resistance against 53 different antibiotics were detected in the human gut microflora analysed in this study. In addition to several geography/country-specific patterns, four distinct clusters of gut microbiomes, referred to as ‘Resistotypes’, exhibiting similarities in their antibiotic resistance profiles, were identified. Groups of antibiotics having similarities in their resistance patterns within each of these clusters were also detected. Apart from this, mobile multi-drug resistance gene operons were detected in certain gut microbiomes. The study highlighted an alarmingly high abundance of antibiotic resistance genes in two infant gut microbiomes. The results obtained in the present study presents a holistic ‘big picture’ on the spectra of antibiotic resistance within our gut microbiota across different geographies. Such insights may help in implementation of new regulations and stringency on the existing ones. PMID:24391833

Proteomic Identification of Monoclonal Antibodies from Serum

PubMed Central

2015-01-01

Characterizing the in vivo dynamics of the polyclonal antibody repertoire in serum, such as that which might arise in response to stimulation with an antigen, is difficult due to the presence of many highly similar immunoglobulin proteins, each specified by distinct B lymphocytes. These challenges have precluded the use of conventional mass spectrometry for antibody identification based on peptide mass spectral matches to a genomic reference database. Recently, progress has been made using bottom-up analysis of serum antibodies by nanoflow liquid chromatography/high-resolution tandem mass spectrometry combined with a sample-specific antibody sequence database generated by high-throughput sequencing of individual B cell immunoglobulin variable domains (V genes). Here, we describe how intrinsic features of antibody primary structure, most notably the interspersed segments of variable and conserved amino acid sequences, generate recurring patterns in the corresponding peptide mass spectra of V gene peptides, greatly complicating the assignment of correct sequences to mass spectral data. We show that the standard method of decoy-based error modeling fails to account for the error introduced by these highly similar sequences, leading to a significant underestimation of the false discovery rate. Because of these effects, antibody-derived peptide mass spectra require increased stringency in their interpretation. The use of filters based on the mean precursor ion mass accuracy of peptide-spectrum matches is shown to be particularly effective in distinguishing between “true” and “false” identifications. These findings highlight important caveats associated with the use of standard database search and error-modeling methods with nonstandard data sets and custom sequence databases. PMID:24684310

Rapid Magnetic Nanobiosensor for the detection of Serratia marcescen

NASA Astrophysics Data System (ADS)

Aljabali, Alaa A. A.; Hussein, Emad; Aljumaili, Omar; Zoubi, Mazhar Al; Altrad, Bahaa; Albatayneh, Khaled; Al-razaq, Mutaz A. Abd

2018-02-01

The development of rapid, sensitive, accurate and reliable bacterial detection methods are of keen interest to ensure food safety and hospital security. Therefore, the development of a fast, specific, low-cost and trusted methods is in high demand. Magnetic nanoparticles with their unique material properties have been utilized as a tool for pathogen detection. Here, we present a novel iron oxide nanoparticles labeled with specific targeting antibodies to improve specificity and extend the use of nanoparticles as nanosensors. The results indicated that antibody labeled iron oxide platform that binds specifically to Serriata marcescenst in a straightforward method is very specific and sensitive. The system is capable of rapid and specific detection of various clinically relevant bacterial species, with sensitivity down to single bacteria. The generic platform could be used to identify pathogens for a variety of applications rapidly.

Demonstration of single crystal growth via solid-solid transformation of a glass

DOE PAGES

Savytskii, Dmytro; Knorr, Brian; Dierolf, Volkmar; ...

2016-03-18

Many advanced technologies have relied on the availability of single crystals of appropriate material such as silicon for microelectronics or superalloys for turbine blades. Similarly, many promising materials could unleash their full potential if they were available in a single crystal form. However, the current methods are unsuitable for growing single crystals of these oftentimes incongruently melting, unstable or metastable materials. Here we demonstrate a strategy to overcome this hurdle by avoiding the gaseous or liquid phase, and directly converting glass into a single crystal. Specifically, Sb 2S 3 single crystals are grown in Sb-S-I glasses as an example ofmore » this approach. In this first unambiguous demonstration of an all-solid-state glass → crystal transformation, extraneous nucleation is avoided relative to crystal growth via spatially localized laser heating and inclusion of a suitable glass former in the composition. Lastly, the ability to fabricate patterned single-crystal architecture on a glass surface is demonstrated, providing a new class of micro-structured substrate for low cost epitaxial growth, active planar devices, etc.« less

Single-mode tunable laser emission in the single-exciton regime from colloidal nanocrystals

PubMed Central

Grivas, Christos; Li, Chunyong; Andreakou, Peristera; Wang, Pengfei; Ding, Ming; Brambilla, Gilberto; Manna, Liberato; Lagoudakis, Pavlos

2013-01-01

Whispering-gallery-mode resonators have been extensively used in conjunction with different materials for the development of a variety of photonic devices. Among the latter, hybrid structures, consisting of dielectric microspheres and colloidal core/shell semiconductor nanocrystals as gain media, have attracted interest for the development of microlasers and studies of cavity quantum electrodynamic effects. Here we demonstrate single-exciton, single-mode, spectrally tuned lasing from ensembles of optical antenna-designed, colloidal core/shell CdSe/CdS quantum rods deposited on silica microspheres. We obtain single-exciton emission by capitalizing on the band structure of the specific core/shell architecture that strongly localizes holes in the core, and the two-dimensional quantum confinement of electrons across the elongated shell. This creates a type-II conduction band alignment driven by coulombic repulsion that eliminates non-radiative multi-exciton Auger recombination processes, thereby inducing a large exciton–bi-exciton energy shift. Their ultra-low thresholds and single-mode, single-exciton emission make these hybrid lasers appealing for various applications, including quantum information processing. PMID:23974520

Reducing single-use plastic shopping bags in the USA.

PubMed

Wagner, Travis P

2017-12-01

In the USA, local governments have the primary responsibility to manage MSW. However, local governments lack the authority to explicitly shift costs or responsibility back onto the producer for specific problem wastes. A particularly problematic waste for local governments is the single-use plastic bag. In 2014, in the USA, 103.465 billion single-use plastic shopping bags were consumed. Because of their extremely low recyclability rate, plastic bags remain a significant source of land-based litter and marine debris and impair stormwater management systems. They also reduce the effectiveness of automated recycling systems. In response, local governments increasingly have adopted a variety of measures specifically intended to reduce the store-level consumption of single-use shopping bags in 5 major categories: bans, imposition of fees and taxes, establishing minimum product design of bags, requiring consumer education, and mandating retailer take-back programs. As of September 2017, there were 271 local governments in the USA with plastic bag ordinances covering 9.7% of the nation's population. The majority (95%) of the ordinances is a ban on single-use plastic bags; 56.9% of these bans also include a mandatory fee on paper and/or reusable bags. For the fee-based ordinances, the mode is $0.10 per bag; every tax/fee ordinance allows retailers to retain some or all the collected fee. As local governments continue to increase their actions on plastic bags, 11 states have enacted laws to prohibit local governments from regulating single-use plastic bags. Because of the success with single-use bags, local governments are also enacting similar ordinances on single-use expanded polystyrene consumer products and other single-use plastic products. Copyright © 2017 Elsevier Ltd. All rights reserved.

77 FR 19008 - Guidelines for Home Energy Professionals: Standard Work Specifications for Single Family Energy...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-29

... Professionals: Standard Work Specifications for Single Family Energy Upgrades AGENCY: Office of Energy...: Standard Work Specifications for Single Family Energy Upgrades. This document is a set of work specifications applicable to energy efficiency retrofits of single family homes. These specifications are...

Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells.

PubMed

Xin, Yurong; Kim, Jinrang; Ni, Min; Wei, Yi; Okamoto, Haruka; Lee, Joseph; Adler, Christina; Cavino, Katie; Murphy, Andrew J; Yancopoulos, George D; Lin, Hsin Chieh; Gromada, Jesper

2016-03-22

This study provides an assessment of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells. The system combines microfluidic technology and nanoliter-scale reactions. We sequenced 622 cells, allowing identification of 341 islet cells with high-quality gene expression profiles. The cells clustered into populations of α-cells (5%), β-cells (92%), δ-cells (1%), and pancreatic polypeptide cells (2%). We identified cell-type-specific transcription factors and pathways primarily involved in nutrient sensing and oxidation and cell signaling. Unexpectedly, 281 cells had to be removed from the analysis due to low viability, low sequencing quality, or contamination resulting in the detection of more than one islet hormone. Collectively, we provide a resource for identification of high-quality gene expression datasets to help expand insights into genes and pathways characterizing islet cell types. We reveal limitations in the C1 Fluidigm cell capture process resulting in contaminated cells with altered gene expression patterns. This calls for caution when interpreting single-cell transcriptomics data using the C1 Fluidigm system.

Site-specific PEGylation of an anti-CEA/CD3 bispecific antibody improves its antitumor efficacy

PubMed Central

Pan, Haitao; Liu, Jiayu; Deng, Wentong; Xing, Jieyu; Li, Qing; Wang, Zhong

2018-01-01

Introduction Bispecific antibodies that engage immune cells to kill cancer cells are actively pursued in cancer immunotherapy. Different types of bispecific antibodies, including single-chain fragments, Fab fragments, nanobodies, and immunoglobulin Gs (IgGs), have been studied. However, the low molecular weight of bispecific antibodies with single-chain or Fab fragments generally leads to their rapid clearance in vivo, which limits the therapeutic potential of these bispecific antibodies. Materials and methods In this study, we used a site-specific PEGylation strategy to modify the bispecific single-domain antibody-linked Fab (S-Fab), which was designed by linking an anticarcinoembryonic antigen (anti-CEA) nanobody with an anti-CD3 Fab. Results The half-life (t1/2) of PEGylated S-Fab (polyethylene glycol-S-Fab) was increased 12-fold in vivo with a slightly decreased tumor cell cytotoxicity in vitro as well as more potent tumor growth inhibition in vivo compared to S-Fab. Conclusion This study demonstrated that PEGylation is an effective approach to enhance the antitumor efficacy of bispecific antibodies. PMID:29881272

Naked-eye fingerprinting of single nucleotide polymorphisms on psoriasis patients

NASA Astrophysics Data System (ADS)

Valentini, Paola; Marsella, Alessandra; Tarantino, Paolo; Mauro, Salvatore; Baglietto, Silvia; Congedo, Maurizio; Paolo Pompa, Pier

2016-05-01

We report a low-cost test, based on gold nanoparticles, for the colorimetric (naked-eye) fingerprinting of a panel of single nucleotide polymorphisms (SNPs), relevant for the personalized therapy of psoriasis. Such pharmacogenomic tests are not routinely performed on psoriasis patients, due to the high cost of standard technologies. We demonstrated high sensitivity and specificity of our colorimetric test by validating it on a cohort of 30 patients, through a double-blind comparison with two state-of-the-art instrumental techniques, namely reverse dot blotting and sequencing, finding 100% agreement. This test offers high parallelization capabilities and can be easily generalized to other SNPs of clinical relevance, finding broad utility in diagnostics and pharmacogenomics.We report a low-cost test, based on gold nanoparticles, for the colorimetric (naked-eye) fingerprinting of a panel of single nucleotide polymorphisms (SNPs), relevant for the personalized therapy of psoriasis. Such pharmacogenomic tests are not routinely performed on psoriasis patients, due to the high cost of standard technologies. We demonstrated high sensitivity and specificity of our colorimetric test by validating it on a cohort of 30 patients, through a double-blind comparison with two state-of-the-art instrumental techniques, namely reverse dot blotting and sequencing, finding 100% agreement. This test offers high parallelization capabilities and can be easily generalized to other SNPs of clinical relevance, finding broad utility in diagnostics and pharmacogenomics. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr02200f

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

Not Available

This report, Evaluation of the Performance of Houses with and without Supplemental Dehumidification in a Hot-Humid Climate, describes a research study that that was conducted by the Building Science Corporation (BSC) Building America Research Team. BSC seeks to research and report on the field monitoring of the performance of in-situ supplemental dehumidification systems in low energy, high performance, homes in a Hot-Humid climate. The purpose of this research project was to observe and compare the humidity control performance of new, single family, low energy, and high performance, homes. Specifically, the study sought to compare the interior conditions and mechanical systemsmore » operation between two distinct groups of houses, homes with a supplemental dehumidifier installed in addition to HVAC system, and homes without any supplemental dehumidification. The subjects of the study were ten single-family new construction homes in New Orleans, LA. Data logging equipment was installed at each home in 2012. Interior conditions and various end-use loads were monitored for one year. In terms of averages, the homes with dehumidifiers are limiting elevated levels of humidity in the living space. However, there was significant variation in humidity control between individual houses. An analysis of the equipment operation did not show a clear correlation between energy use and humidity levels. In general, no single explanatory variable appears to provide a consistent understanding of the humidity control in each house. Indoor humidity is likely due to all of the factors we have examined, and the specifics of how they are used by each occupant.« less

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

Kerrigan, P.; Norton, P.

This report, Evaluation of the Performance of Houses with and without Supplemental Dehumidification in a Hot-Humid Climate, describes a research study that that was conducted by the Building Science Corporation (BSC) Building America Research Team. BSC seeks to research and report on the field monitoring of the performance of in-situ supplemental dehumidification systems in low energy, high performance, homes in a Hot-Humid climate. The purpose of this research project was to observe and compare the humidity control performance of new, single family, low energy, and high performance, homes. Specifically, the study sought to compare the interior conditions and mechanical systemsmore » operation between two distinct groups of houses, homes with a supplemental dehumidifier installed in addition to HVAC system, and homes without any supplemental dehumidification. The subjects of the study were ten single-family new construction homes in New Orleans, LA.Data logging equipment was installed at each home in 2012. Interior conditions and various end-use loads were monitored for one year. In terms of averages, the homes with dehumidifiers are limiting elevated levels of humidity in the living space. However, there was significant variation in humidity control between individual houses. An analysis of the equipment operation did not show a clear correlation between energy use and humidity levels. In general, no single explanatory variable appears to provide a consistent understanding of the humidity control in each house. Indoor humidity is likely due to all of the factors we have examined, and the specifics of how they are used by each occupant.« less

Enabling Low-Power, Multi-Modal Neural Interfaces Through a Common, Low-Bandwidth Feature Space.

PubMed

Irwin, Zachary T; Thompson, David E; Schroeder, Karen E; Tat, Derek M; Hassani, Ali; Bullard, Autumn J; Woo, Shoshana L; Urbanchek, Melanie G; Sachs, Adam J; Cederna, Paul S; Stacey, William C; Patil, Parag G; Chestek, Cynthia A

2016-05-01

Brain-Machine Interfaces (BMIs) have shown great potential for generating prosthetic control signals. Translating BMIs into the clinic requires fully implantable, wireless systems; however, current solutions have high power requirements which limit their usability. Lowering this power consumption typically limits the system to a single neural modality, or signal type, and thus to a relatively small clinical market. Here, we address both of these issues by investigating the use of signal power in a single narrow frequency band as a decoding feature for extracting information from electrocorticographic (ECoG), electromyographic (EMG), and intracortical neural data. We have designed and tested the Multi-modal Implantable Neural Interface (MINI), a wireless recording system which extracts and transmits signal power in a single, configurable frequency band. In prerecorded datasets, we used the MINI to explore low frequency signal features and any resulting tradeoff between power savings and decoding performance losses. When processing intracortical data, the MINI achieved a power consumption 89.7% less than a more typical system designed to extract action potential waveforms. When processing ECoG and EMG data, the MINI achieved similar power reductions of 62.7% and 78.8%. At the same time, using the single signal feature extracted by the MINI, we were able to decode all three modalities with less than a 9% drop in accuracy relative to using high-bandwidth, modality-specific signal features. We believe this system architecture can be used to produce a viable, cost-effective, clinical BMI.

Design considerations for eye-safe single-aperture laser radars

NASA Astrophysics Data System (ADS)

Starodubov, D.; McCormick, K.; Volfson, L.

2015-05-01

The design considerations for low cost, shock resistant, compact and efficient laser radars and ranging systems are discussed. The reviewed approach with single optical aperture allows reducing the size, weight and power of the system. Additional design benefits include improved stability, reliability and rigidity of the overall system. The proposed modular architecture provides simplified way of varying the performance parameters of the range finder product family by selecting the sets of specific illumination and detection modules. The performance operation challenges are presented. The implementation of non-reciprocal optical elements is considered. The cross talk between illumination and detection channels for single aperture design is reviewed. 3D imaging capability for the ranging applications is considered. The simplified assembly and testing process for single aperture range finders that allows to mass produce the design are discussed. The eye safety of the range finder operation is summarized.

Superconductivity in single crystalline YPd2Ge2

NASA Astrophysics Data System (ADS)

Chajewski, G.; Wiśniewski, P.; Hackemer, A.; Pikul, A. P.; Kaczorowski, D.

2018-05-01

Single crystals of the YPd2Ge2 compound, crystallizing in the body-centered tetragonal ThCr2Si2-type structure, were studied by means of low-temperature magnetization, specific heat and electrical resistivity measurements. The zero-field data confirmed bulk and intrinsic superconductivity of the compound with the critical temperature 1.14 K, while the experiments performed in magnetic fields revealed a non-trivial character of the superconducting state. In particular, low and close to each other critical fields μ0Hc1 and μ0Hc2 (of about 20-30 mT) and field-induced first-order phase transition occurring only in the field parallel to the ab plane suggest possible cross-over from the type-I to type-II/1 superconductivity. Moreover, YPd2Ge2 exhibits robust surface superconductivity with the critical field μ0Hc3 about 20 times larger than μ0Hc1 and μ0Hc2.

Label-free detection of DNA hybridization using carbon nanotube network field-effect transistors

NASA Astrophysics Data System (ADS)

Star, Alexander; Tu, Eugene; Niemann, Joseph; Gabriel, Jean-Christophe P.; Joiner, C. Steve; Valcke, Christian

2006-01-01

We report carbon nanotube network field-effect transistors (NTNFETs) that function as selective detectors of DNA immobilization and hybridization. NTNFETs with immobilized synthetic oligonucleotides have been shown to specifically recognize target DNA sequences, including H63D single-nucleotide polymorphism (SNP) discrimination in the HFE gene, responsible for hereditary hemochromatosis. The electronic responses of NTNFETs upon single-stranded DNA immobilization and subsequent DNA hybridization events were confirmed by using fluorescence-labeled oligonucleotides and then were further explored for label-free DNA detection at picomolar to micromolar concentrations. We have also observed a strong effect of DNA counterions on the electronic response, thus suggesting a charge-based mechanism of DNA detection using NTNFET devices. Implementation of label-free electronic detection assays using NTNFETs constitutes an important step toward low-cost, low-complexity, highly sensitive and accurate molecular diagnostics. hemochromatosis | SNP | biosensor

Unconventional Magnetic Domain Structure in the Ferromagnetic Phase of MnP Single Crystals

NASA Astrophysics Data System (ADS)

Koyama, Tsukasa; Yano, Shin-ichiro; Togawa, Yoshihiko; Kousaka, Yusuke; Mori, Shigeo; Inoue, Katsuya; Kishine, Jun-ichiro; Akimitsu, Jun

2012-04-01

We have studied ferromagnetic (FM) structures in the FM phase of MnP single crystals by low-temperature Lorentz transmission electron microscopy and small-angle electron diffraction analysis. In Lorentz Fresnel micrographs, striped FM domain structures were observed at an external magnetic field less than 10 Oe in specimens with the ab-plane in their plane. From real- and reciprocal-space analyses, it was clearly identified that striped FM domains oriented to the c-axis appear with Bloch-type domain walls in the b-direction and order regularly along the a-axis with a constant separation less than 100 nm. Moreover, the magnetic chirality reverses in alternate FM domain walls. These specific spin configuration of striped FM domains will affect the magnetic phase transition from the FM phase to the proper screw spiral phase at low temperature or to the FAN phase in magnetic fields in MnP.

Multiplexed Five-Color Molecular Imaging of Cancer Cells and Tumor Tissues with Carbon Nanotube Raman Tags in the Near-Infrared

PubMed Central

Liu, Zhuang; Tabakman, Scott; Sherlock, Sarah; Li, Xiaolin; Chen, Zhuo; Jiang, Kaili; Fan, Shoushan; Dai, Hongjie

2011-01-01

Single-walled carbon nanotubes (SWNTs) with five different C13/C12 isotope compositions and well-separated Raman peaks have been synthesized and conjugated to five targeting ligands in order to impart molecular specificity. Multiplexed Raman imaging of live cells has been carried out by highly specific staining of cells with a five-color mixture of SWNTs. Ex vivo multiplexed Raman imaging of tumor samples uncovers a surprising up-regulation of epidermal growth factor receptor (EGFR) on LS174T colon cancer cells from cell culture to in vivo tumor growth. This is the first time five-color multiplexed molecular imaging has been performed in the near-infrared (NIR) region under a single laser excitation. Near zero interfering background of imaging is achieved due to the sharp Raman peaks unique to nanotubes over the low, smooth autofluorescence background of biological species. PMID:21442006

Superconducting properties of Rh 9 In 4 S 4 single crystals

DOE PAGES

Kaluarachchi, Udhara S.; Lin, Qisheng; Xie, Weiwei; ...

2016-03-28

The synthesis and crystallographic, thermodynamic, and transport properties of single crystalline Rh 9In 4S 4 were studied. The resistivity, magnetization, and specific heat measurements all clearly indicate bulk superconductivity with a critical temperature, T c~2.25 K. The Sommerfeld coefficient γ and the Debye temperature (ΘD) were found to be 34 mJ mol –1 K –2 and 217 K, respectively. The observed specific heat jump, ΔC/γT c=1.66, is larger than the expected BCS weak coupling value of 1.43. Ginzburg-Landau (GL) ratio of the low-temperature GL-penetration depth, λ GL≈5750 Å, to the GL-coherence length, ξ GL≈94 Å, is large: κ ~60. However,more » we observed a peak effect in the resistivity measurement as a function of both temperature and magnetic field.« less

Surface-modified CMOS IC electrochemical sensor array targeting single chromaffin cells for highly parallel amperometry measurements.

PubMed

Huang, Meng; Delacruz, Joannalyn B; Ruelas, John C; Rathore, Shailendra S; Lindau, Manfred

2018-01-01

Amperometry is a powerful method to record quantal release events from chromaffin cells and is widely used to assess how specific drugs modify quantal size, kinetics of release, and early fusion pore properties. Surface-modified CMOS-based electrochemical sensor arrays allow simultaneous recordings from multiple cells. A reliable, low-cost technique is presented here for efficient targeting of single cells specifically to the electrode sites. An SU-8 microwell structure is patterned on the chip surface to provide insulation for the circuitry as well as cell trapping at the electrode sites. A shifted electrode design is also incorporated to increase the flexibility of the dimension and shape of the microwells. The sensitivity of the electrodes is validated by a dopamine injection experiment. Microwells with dimensions slightly larger than the cells to be trapped ensure excellent single-cell targeting efficiency, increasing the reliability and efficiency for on-chip single-cell amperometry measurements. The surface-modified device was validated with parallel recordings of live chromaffin cells trapped in the microwells. Rapid amperometric spikes with no diffusional broadening were observed, indicating that the trapped and recorded cells were in very close contact with the electrodes. The live cell recording confirms in a single experiment that spike parameters vary significantly from cell to cell but the large number of cells recorded simultaneously provides the statistical significance.

Favorable Preliminary Outcomes for Men With Low- and Intermediate-risk Prostate Cancer Treated With 19-Gy Single-fraction High-dose-rate Brachytherapy

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

Krauss, Daniel J., E-mail: dkrauss@beaumont.edu; Ye, Hong; Martinez, Alvaro A.

Purpose: To report the toxicity and preliminary clinical outcomes of a prospective trial evaluating 19-Gy, single-fraction high-dose-rate (HDR) brachytherapy for men with low- and intermediate-risk prostate cancer. Methods and Materials: A total of 63 patients were treated according to an institutional review board-approved prospective study of single-fraction HDR brachytherapy. Eligible patients had tumor stage ≤T2a, prostate-specific antigen level ≤15 ng/mL, and Gleason score ≤7. Patients with a prostate gland volume >50 cm{sup 3} and baseline American Urologic Association symptom score >12 were ineligible. Patients underwent transrectal ultrasound-guided transperineal implantation of the prostate, followed by single-fraction HDR brachytherapy. Treatment was delivered using {sup 192}Irmore » to a dose of 19 Gy prescribed to the prostate, with no additional margin applied. Results: Of the 63 patients, 58 had data available for analysis. Five patients had withdrawn consent during the follow-up period. The median follow-up period was 2.9 years (range 0.3-5.2). The median age was 61.4 years. The median gland volume at treatment was 34.8 cm{sup 3}. Of the 58 patients, 91% had T1 disease, 71% had Gleason score ≤6 (29% with Gleason score 7), and the median pretreatment prostate-specific antigen level was 5.1 ng/mL. The acute and chronic grade 2 genitourinary toxicity incidence was 12.1% and 10.3%, respectively. No grade 3 urinary toxicity occurred. No patients experienced acute rectal toxicity grade ≥2, and 2 experienced grade ≥2 chronic gastrointestinal toxicity. Three patients experienced biochemical failure, yielding a 3-year cumulative incidence estimate of 6.8%. Conclusions: Single-fraction HDR brachytherapy is well-tolerated, with favorable preliminary biochemical and clinical disease control rates.« less

Recombinant low-seroprevalent adenoviral vectors Ad26 and Ad35 expressing the respiratory syncytial virus (RSV) fusion protein induce protective immunity against RSV infection in cotton rats.

PubMed

Widjojoatmodjo, Myra N; Bogaert, Lies; Meek, Bob; Zahn, Roland; Vellinga, Jort; Custers, Jerome; Serroyen, Jan; Radošević, Katarina; Schuitemaker, Hanneke

2015-10-05

RSV is an important cause of lower respiratory tract infections in children, the elderly and in those with underlying medical conditions. Although the high disease burden indicates an urgent need for a vaccine against RSV, no licensed RSV vaccine is currently available. We developed an RSV vaccine candidate based on the low-seroprevalent human adenovirus serotypes 26 and 35 (Ad26 and Ad35) encoding the RSV fusion (F) gene. Single immunization of mice with either one of these vectors induced high titers of RSV neutralizing antibodies and high levels of F specific interferon-gamma-producing T cells. A Th1-type immune response was indicated by a high IgG2a/IgG1 ratio of RSV-specific antibodies, strong induction of RSV-specific interferon-gamma and tumor necrosis factor-alpha cytokine producing CD8 Tcells, and low RSV-specific CD4 T-cell induction. Both humoral and cellular responses were increased upon a boost with RSV-F expressing heterologous adenovirus vector (Ad35 boost after Ad26 prime or vice versa). Both single immunization and prime-boost immunization of cotton rats induced high and long-lasting RSV neutralizing antibody titers and protective immunity against lung and nasal RSV A2 virus load up to at least 30 weeks after immunization. Cotton rats were also completely protected against challenge with a RSV B strain (B15/97) after heterologous prime-boost immunization. Lungs from vaccinated animals showed minimal damage or inflammatory infiltrates post-challenge, in contrast to animals vaccinated with formalin-inactivated virus. Our results suggest that recombinant human adenoviral Ad26 and Ad35 vectors encoding the RSV F gene have the potential to provide broad and durable protection against RSV in humans, and appear safe to be investigated in infants. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

IgE to recombinant allergens Api m 1, Ves v 1, and Ves v 5 distinguish double sensitization from crossreaction in venom allergy.

PubMed

Müller, U; Schmid-Grendelmeier, P; Hausmann, O; Helbling, A

2012-08-01

Diagnostic tests in patients with Hymenoptera venom allergy are frequently positive to venoms of both honey bee and wasp (Vespula). Component-resolved analysis with recombinant species-specific major allergens (rSSMA) may help to distinguish true double sensitization from crossreactivity. Included were 121 patients with systemic allergic reactions to Hymenoptera stings, 76 with double positivity of serum-specific IgE (sIgE) to both venoms, 45 with single positivity to bee or wasp venom, and 32 controls without history of systemic reactions to Hymenoptera stings and no sIgE to whole venoms. In venom-allergic patients and controls, sIgE to rSSMA Api m 1 of bee venom and to Ves v 1 and Ves v 5 of wasp venom were tested by ImmunoCAP. Only 47% of 76 patients with double positivity to whole venoms reacted also to rSSMA of both species. Specificity of sIgE to the 3 rSSMA was very high, with no sIgE to rSSMA of the other species in single-positive venom-allergic patients and only one control with low sIgE to Ves v 1. All wasp-allergic single-positive patients had sIgE to Ves v 5 and/or Ves v 1, and 78.3% of single-positive bee venom-allergic patients had sIgE to Api m 1. Specificity of sIgE to rSSMA of both species is excellent. Sensitivity of sIgE to rSSMA was optimal for wasp venom. Sensitivity of bee venom Api m 1 could be increased by adding rSSMA of other important bee venom allergens. © 2012 John Wiley & Sons A/S.

The single-payer option: a reconsideration.

PubMed

Oliver, Adam

2009-08-01

This article discusses some of the merits and demerits of the single-payer model of health care financing, with particular reference to the English National Health Service (NHS). Specifically, it is argued that the main merits are that the model can directly provide universal health care coverage, thus eradicating or at least alleviating market failure and equity concerns, and that it can achieve this with relatively low total health care expenditure in general and -- as compared to the commercial multiple insurance model -- low administrative costs in particular. A perceived demerit of the single-payer model is that it can lead to excessive health care rationing, particularly in terms of waiting times, although it is argued here that long waits are probably caused by insufficient funding rather than by the single-payer model per se. Moreover, rationing of one form or another occurs in all health care systems, and single-payer models may be the best option if the aim is to incorporate structured rationing such that an entire population is subject to the same rules and is thus treated equitably. A further perceived disadvantage of the single-payer model is that it offers limited choice, which is necessarily true with respect to choice of insurer, but choice of provider can be, and increasingly is, a feature of centrally tax-financed health care systems. No model of health care funding is perfect; trade-offs are inevitable. Whether the merits of the single-payer model are judged to outweigh the demerits will typically vary both across countries at any point in time and within a country over time.

Single-Molecule Optical Spectroscopy and Imaging: From Early Steps to Recent Advances

NASA Astrophysics Data System (ADS)

Moerner, William E.

The initial steps toward optical detection and spectroscopy of single molecules arose out of the study of spectral hole-burning in inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989. In the early 1990s, many fascinating physical effects were observed for individual molecules such as spectral diffusion, optical switching, vibrational spectra, and magnetic resonance of a single molecular spin. Since the mid-1990s when experiments moved to room temperature, a wide variety of biophysical effects may be explored, and a number of physical phenomena from the low temperature studies have analogs at high temperature. Recent advances worldwide cover a huge range, from in vitro studies of enzymes, proteins, and oligonucleotides, to observations in real time of a single protein performing a specific function inside a living cell. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation of individual fluorophores leads naturally to localization beyond the optical diffraction limit. Combining this with active optical control of the number of emitting molecules leads to superresolution imaging, a new frontier for optical microscopy beyond the optical diffraction limit and for chemical design of photoswitchable fluorescent labels. Finally, to study one molecule in aqueous solution without surface perturbations, a new electrokinetic trap is described (the ABEL trap) which can trap single small biomolecules without the need for large dielectric beads.

Single crystal growth of Ga3Ni2 by the Czochralski method

NASA Astrophysics Data System (ADS)

Wencka, Magdalena; Pillaca, Mirtha; Gille, Peter

2016-09-01

Intermetallic compounds have proved to be interesting alternatives to heterogeneous catalysts prepared from pure noble metals or their alloys. As to study their intrinsic properties, to determine the crystalline structures of specific surfaces and finally to understand elementary processes of heterogeneous catalysis, single crystals of these intermetallics are needed. Inspired by the recent discovery of Ga-Ni catalysts for carbon dioxide reduction to methanol, we have grown for the first time cm3-size single crystals of trigonal Ga3Ni2. We report in detail on the synthesis and Czochralski growth from high-temperature solution using Ga as native solvent. Inclusion formation of Ga-rich fluid proved to be the most severe problem that was minimized by using an extremely low pulling rate down to 25 μm/h.

Chemical Vapor Detection using Single-walled Carbon Nanotubes

DTIC Science & Technology

2006-05-01

1 / f noise , and achieving chemical specificity. Recently, researchers have developed approaches to...nanoscale materials, exhibit a large component of 1 / f noise .11 Such 1 / f noise is a particular concern for chemical detection, because the sensors operate at...low frequencies. We discuss how SWNT networks can be designed to reduce the level of 1 / f noise to acceptable levels.12 Lastly, we discuss the issue

A k-nearest neighbor approach for estimation of single-tree biomass

Treesearch

Lutz Fehrmann; Christoph Kleinn

2007-01-01

Allometric biomass models are typically site and species specific. They are mostly based on a low number of independent variables such as diameter at breast height and tree height. Because of relatively small datasets, their validity is limited to the set of conditions of the study, such as site conditions and diameter range. One challenge in the context of the current...

Low Carbon Design Research on the Space Layout Types of Office Buildings

NASA Astrophysics Data System (ADS)

Xia, Bing

2018-01-01

It is beneficial to find out the relationship of the spatial layout and low-carbon design in order to reduce buildings’ carbon emissions in the conceptual design phase. This paper analyzes and compares shape coefficient values, annual energy consumption and lighting performance of office buildings of different space layout types in Shanghai. Based on morphological characteristics of different types, the study also analyzes and presents low-carbon design strategies for each single type. This study assumes that architects should conduct passive and active design according to the specific building space layout, so that to make best use of the advantages and bypassing the disadvantages, in order to maximally reduce buildings’ carbon emissions.

Prototyping Instruments for Chemical Laboratory Using Inexpensive Electronic Modules.

PubMed

Urban, Pawel L

2018-05-15

Open-source electronics and programming can augment chemical and biomedical research. Currently, chemists can choose from a broad range of low-cost universal electronic modules (microcontroller boards and single-board computers) and use them to assemble working prototypes of scientific tools to address specific experimental problems and to support daily research work. The learning time can be as short as a few hours, and the required budget is often as low as 50 USD. Prototyping instruments using low-cost electronic modules gives chemists enormous flexibility to design and construct customized instrumentation, which can reduce the delays caused by limited access to high-end commercial platforms. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[What is hidden behind the Baking Tray Task? Study of sensibility and specificity in right-hemispheric stroke patients].

PubMed

Garcia-Fernandez, Juan; Garcia-Molina, Alberto; Aparicio-Lopez, Celeste; Sanchez-Carrion, Rocío; Ensenat, Antònia; Pena-Casanova, Jordi; Roig-Rovira, Teresa

2015-12-16

Tham and Tegner proposed the Baking Tray Task (BTT) as a fast simple assessment test for detecting spatial negligence. However, very few studies have examined its validity as a diagnostic test. To analyse the diagnostic validity of the BTT by measuring its specificity and sensitivity in a sample of subjects with right hemisphere strokes. Forty-eight patients with right hemisphere vascular lesions were distributed in two groups (negligence group, n = 35; non-negligence group, n = 13) according to the scores obtained in a battery of visuospatial examination tests. The participants' performance on the BTT was compared with that of a healthy control group (n = 12). The results showed a high level of sensitivity of the BTT, but low specificity. The performance on the BTT of eight of the 13 members of the non-negligence group was suggestive of negligence. The BTT has proved to be a sensitive test for the detection of spatial negligence. Yet, based on its low specificity, its use alone as a single diagnostic test is not recommended.

Novel rolling circle amplification and DNA origami-based DNA belt-involved signal amplification assay for highly sensitive detection of prostate-specific antigen (PSA).

PubMed

Yan, Juan; Hu, Chongya; Wang, Ping; Liu, Rui; Zuo, Xiaolei; Liu, Xunwei; Song, Shiping; Fan, Chunhai; He, Dannong; Sun, Gang

2014-11-26

Prostate-specific antigen (PSA) is one of the most important biomarkers for the early diagnosis and prognosis of prostate cancer. Although many efforts have been made to achieve significant progress for the detection of PSA, challenges including relative low sensitivity, complicated operation, sophisticated instruments, and high cost remain unsolved. Here, we have developed a strategy combining rolling circle amplification (RCA)-based DNA belts and magnetic bead-based enzyme-linked immunosorbent assay (ELISA) for the highly sensitive and specific detection of PSA. At first, a 96-base circular DNA template was designed and prepared for the following RCA. Single stranded DNA (ssDNA) products from RCA were used as scaffold strand for DNA origami, which was hybridized with three staple strands of DNA. The resulting DNA belts were conjugated with multiple enzymes for signal amplification and then employed to magnetic bead based ELISA for PSA detection. Through our strategy, as low as 50 aM of PSA can be detected with excellent specificity.

The effects of prospective mate quality on investments in healthy body weight among single women.

PubMed

Harris, Matthew C; Cronin, Christopher J

2017-02-01

This paper examines how a single female's investment in healthy body weight is affected by the quality of single males in her marriage market. A principle concern in estimation is the presence of market-level unobserved heterogeneity that may be correlated with changes in single male quality, measured as earning potential. To address this concern, we employ a differencing strategy that normalizes the exercise behaviors of single women to those of their married counterparts. Our main results suggest that when potential mate quality in a marriage market decreases, single black women invest less in healthy body weight. For example, we find that a 10 percentage point increase in the proportion of low quality single black males leads to a 5-10% decrease in vigorous exercise taken by single black females. Results for single white women are qualitatively similar, but not consistent across specifications. These results highlight the relationship between male and female human capital acquisition that is driven by participation in the marriage market. Our results suggest that programs designed to improve the economic prospects of single males may yield positive externalities in the form of improved health behaviors, such as more exercise, particularly for single black females. Copyright © 2016 Elsevier B.V. All rights reserved.

Recent development in low-constraint fracture toughness testing for structural integrity assessment of pipelines

NASA Astrophysics Data System (ADS)

Kang, Jidong; Gianetto, James A.; Tyson, William R.

2018-03-01

Fracture toughness measurement is an integral part of structural integrity assessment of pipelines. Traditionally, a single-edge-notched bend (SE(B)) specimen with a deep crack is recommended in many existing pipeline structural integrity assessment procedures. Such a test provides high constraint and therefore conservative fracture toughness results. However, for girth welds in service, defects are usually subjected to primarily tensile loading where the constraint is usually much lower than in the three-point bend case. Moreover, there is increasing use of strain-based design of pipelines that allows applied strains above yield. Low-constraint toughness tests represent more realistic loading conditions for girth weld defects, and the corresponding increased toughness can minimize unnecessary conservatism in assessments. In this review, we present recent developments in low-constraint fracture toughness testing, specifically using single-edgenotched tension specimens, SENT or SE(T). We focus our review on the test procedure development and automation, round-robin test results and some common concerns such as the effect of crack tip, crack size monitoring techniques, and testing at low temperatures. Examples are also given of the integration of fracture toughness data from SE(T) tests into structural integrity assessment.

A low-cost three-dimensional laser surface scanning approach for defining body segment parameters.

PubMed

Pandis, Petros; Bull, Anthony Mj

2017-11-01

Body segment parameters are used in many different applications in ergonomics as well as in dynamic modelling of the musculoskeletal system. Body segment parameters can be defined using different methods, including techniques that involve time-consuming manual measurements of the human body, used in conjunction with models or equations. In this study, a scanning technique for measuring subject-specific body segment parameters in an easy, fast, accurate and low-cost way was developed and validated. The scanner can obtain the body segment parameters in a single scanning operation, which takes between 8 and 10 s. The results obtained with the system show a standard deviation of 2.5% in volumetric measurements of the upper limb of a mannequin and 3.1% difference between scanning volume and actual volume. Finally, the maximum mean error for the moment of inertia by scanning a standard-sized homogeneous object was 2.2%. This study shows that a low-cost system can provide quick and accurate subject-specific body segment parameter estimates.

Magnetic study of the low temperature anomalies in the magnetodielectric terbium iron garnet

NASA Astrophysics Data System (ADS)

Lahoubi, Mahieddine

2018-05-01

The anomalous magnetic properties at low temperatures of terbium iron garnet (TbIG) are analyzed and summarized using neutron powder diffraction (NPD) experiments together with high field magnetization, magnetostriction and specific heat measurements performed on single crystals. Reliable information at both microscopic and macroscopic levels is provided about the significant change of the double umbrella structure observed in the NPD results near 54 K. The positions of the observed maxima at 55-65 K in the paraprocess magnetic susceptibility along the three mean directions and paraprocess of the forced magnetostriction along the easy axis of magnetization 〈111〉 agree with the manifestations of the "low-temperature point" TB predicted by Belov at 58 K. However, the pronounced maximum at 57 K in the excess of specific heat in zero magnetic fields reveals that the Schottky effect causes anomaly at temperature close the TB point. The results are discussed and compared with previous magnetic, magneto-optical and magnetodielectric reports.

Low-temperature magnetic properties of GdCoIn5

NASA Astrophysics Data System (ADS)

Betancourth, D.; Facio, J. I.; Pedrazzini, P.; Jesus, C. B. R.; Pagliuso, P. G.; Vildosola, V.; Cornaglia, Pablo S.; García, D. J.; Correa, V. F.

2015-01-01

A comprehensive experimental and theoretical study of the low temperature properties of GdCoIn5 was performed. Specific heat, thermal expansion, magnetization and electrical resistivity were measured in good quality single crystals down to 4He temperatures. All the experiments show a second-order-like phase transition at 30 K probably associated with the onset of antiferromagnetic order. The magnetic susceptibility shows a pronounced anisotropy below TN with an easy magnetic axis perpendicular to the crystallographic ĉ-axis. Total energy GGA+U calculations indicate a ground state with magnetic moments localized at the Gd ions and allowed a determination of the Gd-Gd magnetic interactions. Band structure calculations of the electron and phonon contributions to the specific heat together with Quantum Monte Carlo calculations of the magnetic contributions show a very good agreement with the experimental data. Comparison between experiment and calculations suggests a significant anharmonic contribution to the specific heat at high temperature (T ≳ 100 K).

The effects of lumbar extensor strength on disability and mobility in patients with persistent low back pain.

PubMed

Helmhout, Pieter H; Witjes, Marloes; Nijhuis-VAN DER Sanden, Ria W; Bron, Carel; van Aalst, Michiel; Staal, J Bart

2017-04-01

It is assumed that low back pain patients who use pain-avoiding immobilizing strategies may benefit from specific back flexion and extension exercises aimed at reducing sagittal lumbar hypomobility. The aim of this study was to test this potential working mechanism in chronic low back pain patients undergoing lumbar extensor strengthening training. A single-group prospective cohort design was used in this study. Patients with persistent low back complaints for at least 2 years were recruited at a specialized physical therapy clinics center. They participated in a progressive 11-week lumbar extensor strength training program, once a week. At baseline, sagittal lumbar mobility in flexion and extension was measured with a computer-assisted inclinometer. Self-rated pain intensity was measured using a visual analogue scale, back-specific functional status was assessed with the Quebec Back Pain Disability Scale and the Patient Specific Complains questionnaire. Statistically significant improvements were found in pain (28% decrease) and functional disability (23% to 36% decrease). Most progress was seen in the first 5 treatment weeks. Lumbar mobility in flexion showed non-significant increases over time (+12%). Pre-post treatment changes in flexion and extension mobility did not contribute significantly to the models. The retained factors together explained 15% to 48% of the variation in outcome. Specific lumbar strengthening showed clinically relevant improvements in pain and disability in patients with persistent chronic low back pain. These improvements did not necessarily relate to improvements in lumbar mobility. Parameters representing other domains of adaptations to exercise may be needed to evaluate the effects of back pain management.

A Single Electrochemical Probe Used for Analysis of Multiple Nucleic Acid Sequences

PubMed Central

Mills, Dawn M.; Calvo-Marzal, Percy; Pinzon, Jeffer M.; Armas, Stephanie; Kolpashchikov, Dmitry M.; Chumbimuni-Torres, Karin Y.

2017-01-01

Electrochemical hybridization sensors have been explored extensively for analysis of specific nucleic acids. However, commercialization of the platform is hindered by the need for attachment of separate oligonucleotide probes complementary to a RNA or DNA target to an electrode’s surface. Here we demonstrate that a single probe can be used to analyze several nucleic acid targets with high selectivity and low cost. The universal electrochemical four-way junction (4J)-forming (UE4J) sensor consists of a universal DNA stem-loop (USL) probe attached to the electrode’s surface and two adaptor strands (m and f) which hybridize to the USL probe and the analyte to form a 4J associate. The m adaptor strand was conjugated with a methylene blue redox marker for signal ON sensing and monitored using square wave voltammetry. We demonstrated that a single sensor can be used for detection of several different DNA/RNA sequences and can be regenerated in 30 seconds by a simple water rinse. The UE4J sensor enables a high selectivity by recognition of a single base substitution, even at room temperature. The UE4J sensor opens a venue for a re-useable universal platform that can be adopted at low cost for the analysis of DNA or RNA targets. PMID:29371782

MALDI-typing of infectious algae of the genus Prototheca using SOM portraits.

PubMed

Wirth, Henry; von Bergen, Martin; Murugaiyan, Jayaseelan; Rösler, Uwe; Stokowy, Tomasz; Binder, Hans

2012-01-01

MALDI-typing has become a frequently used approach for the identification of microorganisms and recently also of invertebrates. Similarity-comparisons are usually based on single-spectral data. We apply self-organizing maps (SOM) to portray the MS-spectral data with individual resolution and to improve the typing of Prototheca algae by using meta-spectra representing prototypes of groups of similar-behaving single spectra. The MALDI-TOF peaklists of more than 300 algae extracts referring to five Prototheca species were transformed into colored mosaic images serving as molecular portraits of the individual samples. The portraits visualize the algae-specific distribution of high- and low-amplitude peaks in two dimensions. Species-specific pattern of MS intensities were readily discernable in terms of unique single spots of high amplitude MS-peaks which collect characteristic fingerprint spectra. The spot patterns allow the visual identification of groups of samples referring to different species, genotypes or isolates. The use of meta-peaks instead of single-peaks reduces the dimension of the data and leads to an increased discriminating power in downstream analysis. We expect that our SOM portray method improves MS-based classifications and feature selection in upcoming applications of MALDI-typing based species identifications especially of closely related species. Copyright © 2011. Published by Elsevier B.V.

Design and Construction of a Single-Tube, LATE-PCR, Multiplex Endpoint Assay with Lights-On/Lights-Off Probes for the Detection of Pathogens Associated with Sepsis

PubMed Central

Carver-Brown, Rachel K.; Reis, Arthur H.; Rice, Lisa M.; Czajka, John W.; Wangh, Lawrence J.

2012-01-01

Aims. The goal of this study was to construct a single tube molecular diagnostic multiplex assay for the detection of microbial pathogens commonly associated with septicemia, using LATE-PCR and Lights-On/Lights-Off probe technology. Methods and Results. The assay described here identified pathogens associated with sepsis by amplification and analysis of the 16S ribosomal DNA gene sequence for bacteria and specific gene sequences for fungi. A sequence from an unidentified gene in Lactococcus lactis subsp. cremoris served as a positive control for assay function. LATE-PCR was used to generate single-stranded amplicons that were then analyzed at endpoint over a wide temperature range in a specific fluorescent color. Each bacterial target was identified by its pattern of hybridization to Lights-On/Lights-Off probes derived from molecular beacons. Complex mixtures of targets were also detected. Conclusions. All microbial targets were identified in samples containing low starting copy numbers of pathogen genomic DNA, both as individual targets and in complex mixtures. Significance and Impact of the Study. This assay uses new technology to achieve an advance in the field of molecular diagnostics: a single-tube multiplex assay for identification of pathogens commonly associated with sepsis. PMID:23326668

Structural and magnetic transitions in spinel FeM n 2 O 4 single crystals

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

Nepal, Roshan; Zhang, Qiang; Dai, Samuel

Materials that form the spinel structure are known to exhibit geometric frustration, which can lead to magnetic frustration as well. Through magnetization and neutron diffraction measurements, we find that FeMn 2O 4 undergoes one structural and two magnetic transitions. The structural transition occurs at T s ~595K from cubic at high temperatures to tetragonal at low temperatures. Here, two magnetic transitions are ferrimagnetic at T FI–1 ~373K and T FI–2 ~50K, respectively. Further investigation of the specific heat, thermal conductivity, and Seebeck coefficient confirms both magnetic transitions. Of particular interest is that there is a significant magnetic contribution to themore » low-temperature specific heat and thermal conductivity, providing a unique system to study heat transport by magnetic excitations.« less

Structural and magnetic transitions in spinel FeM n 2 O 4 single crystals

DOE PAGES

Nepal, Roshan; Zhang, Qiang; Dai, Samuel; ...

2018-01-11

Materials that form the spinel structure are known to exhibit geometric frustration, which can lead to magnetic frustration as well. Through magnetization and neutron diffraction measurements, we find that FeMn 2O 4 undergoes one structural and two magnetic transitions. The structural transition occurs at T s ~595K from cubic at high temperatures to tetragonal at low temperatures. Here, two magnetic transitions are ferrimagnetic at T FI–1 ~373K and T FI–2 ~50K, respectively. Further investigation of the specific heat, thermal conductivity, and Seebeck coefficient confirms both magnetic transitions. Of particular interest is that there is a significant magnetic contribution to themore » low-temperature specific heat and thermal conductivity, providing a unique system to study heat transport by magnetic excitations.« less

Thermal Radiometer Signal Processing Using Radiation Hard CMOS Application Specific Integrated Circuits for Use in Harsh Planetary Environments

NASA Technical Reports Server (NTRS)

Quilligan, G.; DuMonthier, J.; Aslam, S.; Lakew, B.; Kleyner, I.; Katz, R.

2015-01-01

Thermal radiometers such as proposed for the Europa Clipper flyby mission require low noise signal processing for thermal imaging with immunity to Total Ionizing Dose (TID) and Single Event Latchup (SEL). Described is a second generation Multi- Channel Digitizer (MCD2G) Application Specific Integrated Circuit (ASIC) that accurately digitizes up to 40 thermopile pixels with greater than 50 Mrad (Si) immunity TID and 174 MeV-sq cm/mg SEL. The MCD2G ASIC uses Radiation Hardened By Design (RHBD) techniques with a 180 nm CMOS process node.

Thermal Radiometer Signal Processing using Radiation Hard CMOS Application Specific Integrated Circuits for use in Harsh Planetary Environments

NASA Astrophysics Data System (ADS)

Quilligan, G.; DuMonthier, J.; Aslam, S.; Lakew, B.; Kleyner, I.; Katz, R.

2015-10-01

Thermal radiometers such as proposed for the Europa Clipper flyby mission [1] require low noise signal processing for thermal imaging with immunity to Total Ionizing Dose (TID) and Single Event Latchup (SEL). Described is a second generation Multi- Channel Digitizer (MCD2G) Application Specific Integrated Circuit (ASIC) that accurately digitizes up to 40 thermopile pixels with greater than 50 Mrad (Si) immunity TID and 174 MeV-cm2/mg SEL. The MCD2G ASIC uses Radiation Hardened By Design (RHBD) techniques with a 180 nm CMOS process node.

78 FR 18576 - Guidelines for Home Energy Professionals: Standard Work Specifications for Single Family Energy...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-27

... Professionals: Standard Work Specifications for Single Family Energy Upgrades AGENCY: Office of Energy... Single Family Energy Upgrades (SWS). This content is a set of recommended work specifications applicable to energy efficiency retrofits of single family homes. These specifications are intended as a...

The Cyclic Stress-Strain Behavior of a Single Crystal Nickel-Base Superalloy. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Gabb, Timothy P.

1988-01-01

The cyclic stress-strain response and similar deformation structures of the single crystal nickel based superalloy was described under a specific set of conditions. The isothermal low cycle fatigue response and deformation structures were described at a typical intermediate temperature and at high temperature. Specimens oriented near the (001) and (111) crystallographic orientations were tested at 1050 C, where more moderate orientation effects were expected. This enabled the description of the deformation structures at each of the 2 temperatures and their relationship to the observed cyclic stress-strain behavior. The initial yield strength of all specimens tested at 650 C was controlled by the shearing of the gamma prime precipitates by dislocation pairs. Low cycle fatigue tests at 650 C had cyclic hardening, which was associated with dislocation interactions in the gamma matrix. The initial yield strength of specimens tested at 1050 C was associated with dislocation bypassing of the gamma prime precipitates. Low cycle fatigue tests at 1050 C had cyclic softening, associated with extensive dislocation recovery at the gamma-gamma prime interfaces along with some gamma prime precipitate coarsening.

System-on-chip-centric unattended embedded sensors in homeland security and defense applications

NASA Astrophysics Data System (ADS)

Jannson, Tomasz; Forrester, Thomas; Degrood, Kevin; Shih, Min-Yi; Walter, Kevin; Lee, Kang; Gans, Eric; Esterkin, Vladimir

2009-05-01

System-on-chip (SoC) single-die electronic integrated circuit (IC) integration has recently been attracting a great deal of attention, due to its high modularity, universality, and relatively low fabrication cost. The SoC also has low power consumption and it is naturally suited to being a base for integration of embedded sensors. Such sensors can run unattended, and can be either commercial off-the-shelf (COTS) electronic, COTS microelectromechanical systems (MEMS), or optical-COTS or produced in house (i.e., at Physical Optics Corporation, POC). In the version with the simplest electronic packaging, they can be integrated with low-power wireless RF that can communicate with a central processing unit (CPU) integrated in-house and installed on the specific platform of interest. Such a platform can be a human body (for e-clothing), unmanned aerial vehicle (UAV), unmanned ground vehicle (UGV), or many others. In this paper we discuss SoC-centric embedded unattended sensors in Homeland Security and military applications, including specific application scenarios (or CONOPS). In one specific example, we analyze an embedded polarization optical sensor produced in house, including generalized Lambertian light-emitting diode (LED) sources and secondary nonimaging optics (NIO).

Is physiotherapy integrated virtual walking effective on pain, function, and kinesiophobia in patients with non-specific low-back pain? Randomised controlled trial.

PubMed

Yilmaz Yelvar, Gul Deniz; Çırak, Yasemin; Dalkılınç, Murat; Parlak Demir, Yasemin; Guner, Zeynep; Boydak, Ayşenur

2017-02-01

According to literature, virtual reality was found to reduce pain and kinesiophobia in patients with chronic pain. The purpose of the study was to investigate short-term effect of the virtual reality on pain, function, and kinesiophobia in patients with subacute and chronic non-specific low-back pain METHODS: This randomised controlled study in which 44 patients were randomly assigned to the traditional physiotherapy (control group, 22 subjects) or virtual walking integrated physiotherapy (experimental group, 22 subjects). Before and after treatment, Visual Analog Scale (VAS), TAMPA Kinesiophobia Scale (TKS), Oswestry Disability Index (ODI), Nottingham Health Profile (NHP), Timed-up and go Test (TUG), 6-Minute Walk Test (6MWT), and Single-Leg Balance Test were assessed. The interaction effect between group and time was assessed by using repeated-measures analysis of covariance. After treatment, both groups showed improvement in all parameters. However, VAS, TKS, TUG, and 6MWT scores showed significant differences in favor of the experimental group. Virtual walking integrated physiotherapy reduces pain and kinesiophobia, and improved function in patients with subacute and chronic non-specific low-back pain in short term.

Language, reading, and math learning profiles in an epidemiological sample of school age children.

PubMed

Archibald, Lisa M D; Oram Cardy, Janis; Joanisse, Marc F; Ansari, Daniel

2013-01-01

Dyscalculia, dyslexia, and specific language impairment (SLI) are relatively specific developmental learning disabilities in math, reading, and oral language, respectively, that occur in the context of average intellectual capacity and adequate environmental opportunities. Past research has been dominated by studies focused on single impairments despite the widespread recognition that overlapping and comorbid deficits are common. The present study took an epidemiological approach to study the learning profiles of a large school age sample in language, reading, and math. Both general learning profiles reflecting good or poor performance across measures and specific learning profiles involving either weak language, weak reading, weak math, or weak math and reading were observed. These latter four profiles characterized 70% of children with some evidence of a learning disability. Low scores in phonological short-term memory characterized clusters with a language-based weakness whereas low or variable phonological awareness was associated with the reading (but not language-based) weaknesses. The low math only group did not show these phonological deficits. These findings may suggest different etiologies for language-based deficits in language, reading, and math, reading-related impairments in reading and math, and isolated math disabilities.

Language, Reading, and Math Learning Profiles in an Epidemiological Sample of School Age Children

PubMed Central

Archibald, Lisa M. D.; Oram Cardy, Janis; Joanisse, Marc F.; Ansari, Daniel

2013-01-01

Dyscalculia, dyslexia, and specific language impairment (SLI) are relatively specific developmental learning disabilities in math, reading, and oral language, respectively, that occur in the context of average intellectual capacity and adequate environmental opportunities. Past research has been dominated by studies focused on single impairments despite the widespread recognition that overlapping and comorbid deficits are common. The present study took an epidemiological approach to study the learning profiles of a large school age sample in language, reading, and math. Both general learning profiles reflecting good or poor performance across measures and specific learning profiles involving either weak language, weak reading, weak math, or weak math and reading were observed. These latter four profiles characterized 70% of children with some evidence of a learning disability. Low scores in phonological short-term memory characterized clusters with a language-based weakness whereas low or variable phonological awareness was associated with the reading (but not language-based) weaknesses. The low math only group did not show these phonological deficits. These findings may suggest different etiologies for language-based deficits in language, reading, and math, reading-related impairments in reading and math, and isolated math disabilities. PMID:24155959

Apolipoprotein E genotyping by multiplex tetra-primer amplification refractory mutation system PCR in single reaction tube.

PubMed

Yang, Young Geun; Kim, Jong Yeol; Park, Su Jeong; Kim, Suhng Wook; Jeon, Ok-Hee; Kim, Doo-Sik

2007-08-31

Apolipoprotein E (APOE) plays a critical role in lipoprotein metabolism by binding to both low-density lipoprotein and APOE receptors. The APOE gene has three allelic forms, epsilon2, epsilon3, and epsilon4, which encode different isoforms of the APOE protein. In this study, we have developed a new genotyping method for APOE. Our multiplex tetra-primer amplification refractory mutation system (multiplex T-ARMS) polymerase chain reaction (PCR) was performed in a single reaction tube with six primers consisting of two common primers and two specific primers for each of two single nucleotide polymorphism (SNP) sites. We obtained definitive electropherograms that showed three (epsilon2/epsilon2, epsilon3/epsilon3, and epsilon4/epsilon4), four (epsilon2/epsilon3 and epsilon3/epsilon4), and five (epsilon2/epsilon4) amplicons by multiplex T-ARMS PCR in a single reaction tube. Multiplex T-ARMS PCR for APOE genotyping is a simple and accurate method that requires only a single PCR reaction, without any another treatments or expensive instrumentation, to simultaneously identify two sites of single nucleotide polymorphisms.

Quantitative Aspects of Single Molecule Microscopy

PubMed Central

Ober, Raimund J.; Tahmasbi, Amir; Ram, Sripad; Lin, Zhiping; Ward, E. Sally

2015-01-01

Single molecule microscopy is a relatively new optical microscopy technique that allows the detection of individual molecules such as proteins in a cellular context. This technique has generated significant interest among biologists, biophysicists and biochemists, as it holds the promise to provide novel insights into subcellular processes and structures that otherwise cannot be gained through traditional experimental approaches. Single molecule experiments place stringent demands on experimental and algorithmic tools due to the low signal levels and the presence of significant extraneous noise sources. Consequently, this has necessitated the use of advanced statistical signal and image processing techniques for the design and analysis of single molecule experiments. In this tutorial paper, we provide an overview of single molecule microscopy from early works to current applications and challenges. Specific emphasis will be on the quantitative aspects of this imaging modality, in particular single molecule localization and resolvability, which will be discussed from an information theoretic perspective. We review the stochastic framework for image formation, different types of estimation techniques and expressions for the Fisher information matrix. We also discuss several open problems in the field that demand highly non-trivial signal processing algorithms. PMID:26167102

Low-income Renewable Energy Programs: Case Studies of State Policy in California and Massachusetts

NASA Astrophysics Data System (ADS)

Kelly, Kaitlin

Energy policies aimed at reducing the burden of monthly utility costs on low-income families have been established since the 1970s. Energy use impacts low-income families and organizations through housing specific costs, health and wellness, and opportunity costs. States have begun to run renewable energy installation programs aimed at reducing costs for low-income communities. This thesis examines two of these programs, the solar photovoltaic policies in California as part of the Single Family Affordable Solar Housing and Multi-family Affordable Solar Housing programs, and the Low-income Solar Housing program in Massachusetts. Lessons learned from reviewing these programs are that renewable energy programs are an effective strategy for reducing utility costs for low-income communities, but that the total effectiveness of the program is dependent on removing cost barriers, implementing energy efficiency improvements, and increasing consumer education through established community networks and relationships.

Results of a Pilates exercise program in patients with chronic non-specific low back pain: a randomized controlled trial.

PubMed

Valenza, M C; Rodríguez-Torres, J; Cabrera-Martos, I; Díaz-Pelegrina, A; Aguilar-Ferrándiz, M E; Castellote-Caballero, Y

2017-06-01

To investigate the effects of a Pilates exercise program on disability, pain, lumbar mobility, flexibility and balance in patients with chronic non-specific low back pain. Randomized controlled trial. University laboratory. A total of 54 patients with chronic non-specific low back pain. Patients were randomly allocated to an experimental group ( n=27) included in a Pilates exercise program or to a control group ( n=27) receiving information in a form of a leaflet. Disability (Roland-Morris Disability Questionnaire and Oswestry Disability Index), current, average and pain at it least and at its worst (Visual Analogue Scales), lumbar mobility (modified Shober test), flexibility (finger-to-floor test) and balance (single limb stance test) were measured at baseline and after the intervention. A between-group analysis showed significant differences in the intervention group compared to the control group for both disability scores, the Rolland-Morris questionnaire (mean change±standard deviation of 5.31±3.37 and 2.40±6.78 respectively and between-groups mean difference of 3.2 ± 4.12, p=0.003) and the Oswestry Disability Index ( p<0.001), current pain ( p=0.002) and pain at it least ( p=0.033), flexibility (0.032) and balance (0.043). An 8-week Pilates exercise program is effective in improving disability, pain, flexibility and balance in patients with chronic non-specific low back pain.

Quantitative Detection of Low-Abundance Transcripts at Single-Cell Level in Human Epidermal Keratinocytes by Digital Droplet Reverse Transcription-Polymerase Chain Reaction.

PubMed

Auvré, Frédéric; Coutier, Julien; Martin, Michèle T; Fortunel, Nicolas O

2018-05-08

Genetic and epigenetic characterization of the large cellular diversity observed within tissues is essential to understanding the molecular networks that ensure the regulation of homeostasis, repair, and regeneration, but also pathophysiological processes. Skin is composed of multiple cell lineages and is therefore fully concerned by this complexity. Even within one particular lineage, such as epidermal keratinocytes, different immaturity statuses or differentiation stages are represented, which are still incompletely characterized. Accordingly, there is presently great demand for methods and technologies enabling molecular investigation at single-cell level. Also, most current methods used to analyze gene expression at RNA level, such as RT-qPCR, do not directly provide quantitative data, but rather comparative ratios between two conditions. A second important need in skin biology is thus to determine the number of RNA molecules in a given cell sample. Here, we describe a workflow that we have set up to meet these specific needs, by means of transcript quantification in cellular micro-samples using flow cytometry sorting and reverse transcription-digital droplet polymerase chain reaction. As a proof-of-principle, the workflow was tested for the detection of transcription factor transcripts expressed at low levels in keratinocyte precursor cells. A linear correlation was found between quantification values and keratinocyte input numbers in a low quantity range from 40 cells to 1 cell. Interpretable signals were repeatedly obtained from single-cell samples corresponding to estimated expression levels as low as 10-20 transcript copies per keratinocyte or less. The present workflow may have broad applications for the detection and quantification of low-abundance nucleic acid species in single cells, opening up perspectives for the study of cell-to-cell genetic and molecular heterogeneity. Interestingly, the process described here does not require internal references such as house-keeping gene expression, as it is initiated with defined cell numbers, precisely sorted by flow cytometry.

Development of advanced Czochralski growth process to produce low cost 150 kg silicon ingots from a single crucible for technology readiness

NASA Technical Reports Server (NTRS)

1980-01-01

The design and development of an advanced Czochralski crystal grower are described. Several exhaust gas analysis system equipment specifications studied are discussed. Process control requirements were defined and design work began on the melt temperature, melt level, and continuous diameter control. Sensor development included assembly and testing of a bench prototype of a diameter scanner system.

Single photon laser altimeter simulator and statistical signal processing

NASA Astrophysics Data System (ADS)

Vacek, Michael; Prochazka, Ivan

2013-05-01

Spaceborne altimeters are common instruments onboard the deep space rendezvous spacecrafts. They provide range and topographic measurements critical in spacecraft navigation. Simultaneously, the receiver part may be utilized for Earth-to-satellite link, one way time transfer, and precise optical radiometry. The main advantage of single photon counting approach is the ability of processing signals with very low signal-to-noise ratio eliminating the need of large telescopes and high power laser source. Extremely small, rugged and compact microchip lasers can be employed. The major limiting factor, on the other hand, is the acquisition time needed to gather sufficient volume of data in repetitive measurements in order to process and evaluate the data appropriately. Statistical signal processing is adopted to detect signals with average strength much lower than one photon per measurement. A comprehensive simulator design and range signal processing algorithm are presented to identify a mission specific altimeter configuration. Typical mission scenarios (celestial body surface landing and topographical mapping) are simulated and evaluated. The high interest and promising single photon altimeter applications are low-orbit (˜10 km) and low-radial velocity (several m/s) topographical mapping (asteroids, Phobos and Deimos) and landing altimetry (˜10 km) where range evaluation repetition rates of ˜100 Hz and 0.1 m precision may be achieved. Moon landing and asteroid Itokawa topographical mapping scenario simulations are discussed in more detail.

Effect of government actions on technological innovation for SO2 control.

PubMed

Taylor, Margaret R; Rubin, Edward S; Hounshell, David A

2003-10-15

The relationship between government actions and innovation in environmental control technology is important for the design of cost-effective policies to achieve environmental goals. This paper examines such relationships for the case of sulfur dioxide control technology for U.S. coal-fired power plants. The study employs several complementary research methods, including analyses of key government actions, technology patenting activity, technology performance and cost trends, knowledge transfer activities, and expert elicitations. Our results indicate that government regulation appears to be a greater stimulus to inventive activity than government-sponsored research support alone, and that the anticipation of regulation also spurs inventive activity. Regulatory stringency focuses this activity along particular technical pathways and is a key factor in creating markets for environmental technologies. We also find that with greater technology adoption, both new and existing systems experience notable efficiency improvements and capital cost reductions. The important role of government in fostering knowledge transfer via technical conferences and other measures is also seen as an important factor in promoting environmental technology innovation.

Expression of the highly conserved vaccinia virus E6 protein is required for virion morphogenesis

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

Resch, Wolfgang; Weisberg, Andrea S.; Moss, Bernard, E-mail: bmoss@nih.go

2009-04-10

The vaccinia virus E6R gene (VACVWR062) is conserved in all members of the poxvirus family and encodes a protein associated with the mature virion. We confirmed this association and provided evidence for an internal location. An inducible mutant that conditionally expresses E6 was constructed. In the absence of inducer, plaque formation and virus production were severely inhibited in several cell lines, whereas some replication occurred in others. This difference could be due to variation in the stringency of repression, since we could not isolate a stable deletion mutant even in the more 'permissive' cells. Under non-permissive conditions, viral late proteinsmore » were synthesized but processing of core proteins was inefficient, indicative of an assembly block. Transmission electron microscopy of sections of cells infected with the mutant in the absence of inducer revealed morphogenetic defects with crescents and empty immature virions adjacent to dense inclusions of viroplasm. Mature virions were infrequent and cores appeared to have lucent centers.« less

Multiple components in restriction enzyme digests of mammalian (insectivore), avian and reptilian genomic DNA hybridize with murine immunoglobulin VH probes.

PubMed

Litman, G W; Berger, L; Jahn, C L

1982-06-11

High molecular weight genomic DNAs isolated from an insectivore, Tupaia, and a representative reptilian, Caiman, and avian, Gallus, were digested with restriction endonucleases transferred to nitrocellulose and hybridized with nick-translated probes of murine VH genes. The derivations of the probes designated S107V (1) and mu 107V (2,3) have been described previously. Under conditions of reduced stringency, multiple hybridizing components were observed with Tupaia and Caiman; only mu mu 107V exhibited significant hybridization with the separated fragments of Gallus DNA. The nick-translated S107V probe was digested with Fnu4H1 and subinserts corresponding to the 5' and 3' regions both detected multiple hybridizing components in Tupaia and Caiman DNA. A 5' probe lacking the leader sequence identified the same components as the intact 5' probe, suggesting that VH coding regions distant as the reptilians may possess multiple genetic components which exhibit significant homology with murine immunoglobulin in VH regions.

Multiple components in restriction enzyme digests of mammalian (insectivore), avian and reptilian genomic DNA hybridize with murine immunoglobulin VH probes.

PubMed Central

Litman, G W; Berger, L; Jahn, C L

1982-01-01

High molecular weight genomic DNAs isolated from an insectivore, Tupaia, and a representative reptilian, Caiman, and avian, Gallus, were digested with restriction endonucleases transferred to nitrocellulose and hybridized with nick-translated probes of murine VH genes. The derivations of the probes designated S107V (1) and mu 107V (2,3) have been described previously. Under conditions of reduced stringency, multiple hybridizing components were observed with Tupaia and Caiman; only mu mu 107V exhibited significant hybridization with the separated fragments of Gallus DNA. The nick-translated S107V probe was digested with Fnu4H1 and subinserts corresponding to the 5' and 3' regions both detected multiple hybridizing components in Tupaia and Caiman DNA. A 5' probe lacking the leader sequence identified the same components as the intact 5' probe, suggesting that VH coding regions distant as the reptilians may possess multiple genetic components which exhibit significant homology with murine immunoglobulin in VH regions. Images PMID:6285298

Reliability of Fault Tolerant Control Systems. Part 2

NASA Technical Reports Server (NTRS)

Wu, N. Eva

2000-01-01

This paper reports Part II of a two part effort that is intended to delineate the relationship between reliability and fault tolerant control in a quantitative manner. Reliability properties peculiar to fault-tolerant control systems are emphasized, such as the presence of analytic redundancy in high proportion, the dependence of failures on control performance, and high risks associated with decisions in redundancy management due to multiple sources of uncertainties and sometimes large processing requirements. As a consequence, coverage of failures through redundancy management can be severely limited. The paper proposes to formulate the fault tolerant control problem as an optimization problem that maximizes coverage of failures through redundancy management. Coverage modeling is attempted in a way that captures its dependence on the control performance and on the diagnostic resolution. Under the proposed redundancy management policy, it is shown that an enhanced overall system reliability can be achieved with a control law of a superior robustness, with an estimator of a higher resolution, and with a control performance requirement of a lesser stringency.

The Effects of Climate Sensitivity and Carbon Cycle Interactions on Mitigation Policy Stringency

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

Calvin, Katherine V.; Bond-Lamberty, Benjamin; Edmonds, James A.

2015-07-01

Climate sensitivity and climate-carbon cycle feedbacks interact to determine how global carbon and energy cycles will change in the future. While the science of these connections is well documented, their economic implications are not well understood. Here we examine the effect of climate change on the carbon cycle, the uncertainty in climate outcomes inherent in any given policy target, and the economic implications. We examine three policy scenarios—a no policy “Reference” (REF) scenario, and two policies that limit total radiative forcing—with four climate sensitivities using a coupled integrated assessment model. Like previous work, we find that, within a given scenario,more » there is a wide range of temperature change and sea level rise depending on the realized climate sensitivity. We expand on this previous work to show that temperature-related feedbacks on the carbon cycle result in more mitigation required as climate sensitivity increases. Thus, achieving a particular radiative forcing target becomes increasingly expensive as climate sensitivity increases.« less

Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus.

PubMed

Moncla, Louise H; Zhong, Gongxun; Nelson, Chase W; Dinis, Jorge M; Mutschler, James; Hughes, Austin L; Watanabe, Tokiko; Kawaoka, Yoshihiro; Friedrich, Thomas C

2016-02-10

Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed two polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a "loose" bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses. Copyright © 2016 Elsevier Inc. All rights reserved.

Counterterm counterexamples

NASA Astrophysics Data System (ADS)

Pope, C. N.; Sohnius, M. F.; Stelle, K. S.

We show that, contrary to previous conjectures, there exist acceptable counterterms for Ricci-flat N = 1 and N = 2 super-symmetric σ-models. In the N = 1 case we present infinite sequences of counterterms, starting from the 7-loop order, that do not vanish for general riemannian Ricci-flat metrics but do vanish when the metric is also Kähler. We then investigate the counterterms for theories with Ricci-flat Kähler metrics (i.e. N = 2 models). Acceptable counterterms must vanish for hyper-Kähler metrics (the N = 4 case), and must respect the principle of universality; i.e. that counterterms to the metric can be expressed without the use of complex structures or other special tensors, which do not exist for general riemannian spaces. We show that a recently proposed 4-loop counterterm for the N = 2 models does indeed satisfy these two conditions, despite the apparent stringency of the universality principle. Hence the finiteness of Ricci-flat N = 1 and N = 2 supersymmetric σ-models seems unlikely to persist beyond the 3-loop order.

Architecture of human translation initiation factor 3

PubMed Central

Querol-Audi, Jordi; Sun, Chaomin; Vogan, Jacob M.; Smith, Duane; Gu, Yu; Cate, Jamie; Nogales, Eva

2013-01-01

SUMMARY Eukaryotic translation initiation factor 3 (eIF3) plays a central role in protein synthesis by organizing the formation of the 43S preinitiation complex. Using genetic tag visualization by electron microscopy, we reveal the molecular organization of ten human eIF3 subunits, including an octameric core. The structure of eIF3 bears a close resemblance to that of the proteasome lid, with a conserved spatial organization of eight core subunits containing PCI and MPN domains that coordinate functional interactions in both complexes. We further show that eIF3 subunits a and c interact with initiation factors eIF1 and eIF1A, which control the stringency of start codon selection. Finally, we find that subunit j, which modulates messenger RNA interactions with the small ribosomal subunit, makes multiple independent interactions with the eIF3 octameric core. These results highlight the conserved architecture of eIF3 and how it scaffolds key factors that control translation initiation in higher eukaryotes, including humans. PMID:23623729

REGRES: A FORTRAN-77 program to calculate nonparametric and ``structural'' parametric solutions to bivariate regression equations

NASA Astrophysics Data System (ADS)

Rock, N. M. S.; Duffy, T. R.

REGRES allows a range of regression equations to be calculated for paired sets of data values in which both variables are subject to error (i.e. neither is the "independent" variable). Nonparametric regressions, based on medians of all possible pairwise slopes and intercepts, are treated in detail. Estimated slopes and intercepts are output, along with confidence limits, Spearman and Kendall rank correlation coefficients. Outliers can be rejected with user-determined stringency. Parametric regressions can be calculated for any value of λ (the ratio of the variances of the random errors for y and x)—including: (1) major axis ( λ = 1); (2) reduced major axis ( λ = variance of y/variance of x); (3) Y on Xλ = infinity; or (4) X on Y ( λ = 0) solutions. Pearson linear correlation coefficients also are output. REGRES provides an alternative to conventional isochron assessment techniques where bivariate normal errors cannot be assumed, or weighting methods are inappropriate.

Application of Fuzzy TOPSIS for evaluating machining techniques using sustainability metrics

NASA Astrophysics Data System (ADS)

Digalwar, Abhijeet K.

2018-04-01

Sustainable processes and techniques are getting increased attention over the last few decades due to rising concerns over the environment, improved focus on productivity and stringency in environmental as well as occupational health and safety norms. The present work analyzes the research on sustainable machining techniques and identifies techniques and parameters on which sustainability of a process is evaluated. Based on the analysis these parameters are then adopted as criteria’s to evaluate different sustainable machining techniques such as Cryogenic Machining, Dry Machining, Minimum Quantity Lubrication (MQL) and High Pressure Jet Assisted Machining (HPJAM) using a fuzzy TOPSIS framework. In order to facilitate easy arithmetic, the linguistic variables represented by fuzzy numbers are transformed into crisp numbers based on graded mean representation. Cryogenic machining was found to be the best alternative sustainable technique as per the fuzzy TOPSIS framework adopted. The paper provides a method to deal with multi criteria decision making problems in a complex and linguistic environment.

Daubert v. Merrell: Opening floodgates of scientific uncertainty?

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

Bibko, P.N.

1994-12-31

At last year`s plenary session on May 27, 1993, Col. John Glass, Deputy Director of the Army`s environmental program, acknowledged public pressure to expedite site restoration. A few days later, Gary Vest, Deputy Assistant Secretary for the Air Force told a Senate committee that clean-up levels should be relaxed depending upon intended land use. Soon after, EPA publicly announced support for relaxed clean-up levels depending upon use after restoration. Ironically, also on May 27, 1993, while EPA and the Department of Defense were considering the stringency of clean-up levels, the Environmental Defense Fund and Physicians for Social Responsibility were warningmore » the White House of the increasing health risks due to environmental contamination. The author emphasizes the need to set clean-up standards at levels that will assure protection of public health, and at the same time minimize the legal liability of those involved with the disposal or storage of hazardous waste.« less

Simulation Studies of Satellite Laser CO2 Mission Concepts

NASA Technical Reports Server (NTRS)

Kawa, Stephan Randy; Mao, J.; Abshire, J. B.; Collatz, G. J.; Sun X.; Weaver, C. J.

2011-01-01

Results of mission simulation studies are presented for a laser-based atmospheric CO2 sounder. The simulations are based on real-time carbon cycle process modeling and data analysis. The mission concept corresponds to ASCENDS as recommended by the US National Academy of Sciences Decadal Survey. Compared to passive sensors, active (lidar) sensing of CO2 from space has several potentially significant advantages that hold promise to advance CO2 measurement capability in the next decade. Although the precision and accuracy requirements remain at unprecedented levels of stringency, analysis of possible instrument technology indicates that such sensors are more than feasible. Radiative transfer model calculations, an instrument model with representative errors, and a simple retrieval approach complete the cycle from "nature" run to "pseudodata" CO2. Several mission and instrument configuration options are examined, and the sensitivity to key design variables is shown. Examples are also shown of how the resulting pseudo-measurements might be used to address key carbon cycle science questions.

Enantiomers of Single-Wall Carbon Nanotubes Show Distinct Coating Displacement Kinetics.

PubMed

Zheng, Yu; Bachilo, Sergei M; Weisman, R Bruce

2018-06-27

It is known that specific oligomers of single-stranded DNA (ssDNA) can show remarkable selectivity when coating different structural species of single-wall carbon nanotubes (SWCNTs). We report that (ATT) 4 ssDNA coatings strongly distinguish between the two optical isomers of (7,5) SWCNTs. This causes resolvable shifts in their fluorescence spectra and differences of 2 orders of magnitude in the room temperature rates of coating displacement, as monitored through changes in nanotube fluorescence wavelength and intensity on exposure to sodium deoxycholate. During coating displacement, the enantiomer with high affinity for the ssDNA oligomer is deduced to form an intermediate hybrid that is not observed for the low affinity enantiomer. These results reveal that enantiomeric differences in SWCNTs complexed with ssDNA are more diverse and dramatic than previously recognized.

Applications of particle microbeams in space radiation research.

PubMed

Durante, Marco

2009-03-01

Galactic cosmic radiation is acknowledged as one of the major barriers to human space exploration. In space, astronauts are exposed to charged particles from Z = 1 (H) up to Z = 28 (Ni), but the probability of a hit to a specific single cell in the human body is low. Particle microbeams can deliver single charged particles of different charge and energy to single cells from different tissues, and microbeam studies are therefore very useful for improving current risk estimates for long-term space travel. 2D in vitro cell cultures can be very useful for establishing basic molecular mechanisms, but they are not sufficient to extrapolate risk, given the substantial evidence proving tissue effects are key in determining the response to radiation insult. 3D tissue or animal systems represent a more promising target for space radiobiology using microbeams.

Improved prediction of biochemical recurrence after radical prostatectomy by genetic polymorphisms.

PubMed

Morote, Juan; Del Amo, Jokin; Borque, Angel; Ars, Elisabet; Hernández, Carlos; Herranz, Felipe; Arruza, Antonio; Llarena, Roberto; Planas, Jacques; Viso, María J; Palou, Joan; Raventós, Carles X; Tejedor, Diego; Artieda, Marta; Simón, Laureano; Martínez, Antonio; Rioja, Luis A

2010-08-01

Single nucleotide polymorphisms are inherited genetic variations that can predispose or protect individuals against clinical events. We hypothesized that single nucleotide polymorphism profiling may improve the prediction of biochemical recurrence after radical prostatectomy. We performed a retrospective, multi-institutional study of 703 patients treated with radical prostatectomy for clinically localized prostate cancer who had at least 5 years of followup after surgery. All patients were genotyped for 83 prostate cancer related single nucleotide polymorphisms using a low density oligonucleotide microarray. Baseline clinicopathological variables and single nucleotide polymorphisms were analyzed to predict biochemical recurrence within 5 years using stepwise logistic regression. Discrimination was measured by ROC curve AUC, specificity, sensitivity, predictive values, net reclassification improvement and integrated discrimination index. The overall biochemical recurrence rate was 35%. The model with the best fit combined 8 covariates, including the 5 clinicopathological variables prostate specific antigen, Gleason score, pathological stage, lymph node involvement and margin status, and 3 single nucleotide polymorphisms at the KLK2, SULT1A1 and TLR4 genes. Model predictive power was defined by 80% positive predictive value, 74% negative predictive value and an AUC of 0.78. The model based on clinicopathological variables plus single nucleotide polymorphisms showed significant improvement over the model without single nucleotide polymorphisms, as indicated by 23.3% net reclassification improvement (p = 0.003), integrated discrimination index (p <0.001) and likelihood ratio test (p <0.001). Internal validation proved model robustness (bootstrap corrected AUC 0.78, range 0.74 to 0.82). The calibration plot showed close agreement between biochemical recurrence observed and predicted probabilities. Predicting biochemical recurrence after radical prostatectomy based on clinicopathological data can be significantly improved by including patient genetic information. Copyright (c) 2010 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Accounting for substitution and spatial heterogeneity in a labelled choice experiment.

PubMed

Lizin, S; Brouwer, R; Liekens, I; Broeckx, S

2016-10-01

Many environmental valuation studies using stated preferences techniques are single-site studies that ignore essential spatial aspects, including possible substitution effects. In this paper substitution effects are captured explicitly in the design of a labelled choice experiment and the inclusion of different distance variables in the choice model specification. We test the effect of spatial heterogeneity on welfare estimates and transfer errors for minor and major river restoration works, and the transferability of river specific utility functions, accounting for key variables such as site visitation, spatial clustering and income. River specific utility functions appear to be transferable, resulting in low transfer errors. However, ignoring spatial heterogeneity increases transfer errors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Socioeconomic disparities in osteoporosis prevalence: different results in the overall Korean adult population and single-person households.

PubMed

Kim, Jungmee; Lee, Joongyub; Shin, Ju-Young; Park, Byung-Joo

2015-03-01

The present study was conducted in order to examine the association between socioeconomic status (SES) and osteoporosis prevalence in Korea and to assess whether different associations are found in single-person households. A cross-sectional population-based study was conducted using the Korea National Health and Nutrition Examination Survey, from 2008 to 2011. The study subjects were people aged ≥ 50 years with osteoporosis as defined by bone mineral density. Multivariate logistic models were used to estimate prevalence odds ratios (pORs) and 95% confidence intervals (CIs). Gender differences in the likelihood of osteoporosis were analyzed based on household income, education level, and residential area. There were 8221 osteoporosis patients aged ≥ 50 years, of whom 927 lived in single-person households. There was a gender-specific association between osteoporosis prevalence and all three SES factors that we analyzed: income, education, and residential area. After adjusting for age, SES, and health behaviors, including body mass index (BMI), low household income was only significantly associated with osteoporosis in men, whereas education level had an inverse relationship with osteoporosis only in women (p = 0.01, p < 0.001, respectively). However, after controlling for age and BMI, rural residency was only associated with osteoporosis in women living in single-person households (pOR, 1.59; 95% CI, 1.05 to 2.43). The Korean adult population showed a gender-specific relationship between SES and osteoporosis prevalence, with a different pattern found in single-person households.

Interferometric biosensing platform for multiplexed digital detection of viral pathogens and biomarkers

NASA Astrophysics Data System (ADS)

Daaboul, George

Label-free optical biosensors have been established as proven tools for monitoring specific biomolecular interactions. However, compact and robust embodiments of such instruments have yet to be introduced in order to provide sensitive, quantitative, and high-throughput biosensing for low-cost research and clinical applications. Here we present the interferometric reflectance-imaging sensor (IRIS). IRIS allows sensitive label free analysis using an inexpensive and durable multi-color LED illumination source on a silicon based surface. IRIS monitors biomolecular interaction through measurement of biomass addition to the sensor's surface. We demonstrate the capability of this system to dynamically monitor antigen---antibody interactions with a noise floor of 5.2 pg/mm 2 and DNA single mismatch detection under isothermal melting conditions in an array format. Ensemble detection of binding events using IRIS did not provide the sensitivity needed for detection of infectious disease and biomarkers at clinically relevant concentrations. Therefore, a new approach was adapted to the IRIS platform that allowed the detection and identification of individual nanoparticles on the sensor's surface. The new detection method was termed single-particle IRIS (SP-IRIS). We developed two detection modalities for SP-IRIS. The first modality is when the target is a nanoparticle such as a virus. We verified that SP-IRIS can accurately detect and size individual viral particles. Then we demonstrated that single nanoparticle counting and sizing methodology on SP-IRIS leads to a specific and sensitive virus sensor that can be multiplexed. Finally, we developed an assay for the detection of Ebola and Marburg. A detection limit of 3 x 103 PFU/ml was demonstrated for vesicular stomatitis virus (VSV) pseudotyped with Ebola or Marburg virus glycoprotein. We have demonstrated that virus detection can be done in human whole blood directly without the need for sample preparation. The second modality of SP-IRIS we developed was single molecule counting of biomarkers utilizing a sandwich assay with detection probes labeled with gold nanoparticles. We demonstrated the use of single molecule counting in a nucleic acid assay for melanoma biomarker detection. We showed that a single molecule counting assay can lead to detection limits in the attomolar range. The improved sensitivity of IRIS utilizing single nanoparticle detection holds promise for a simple and low-cost technology for rapid virus detection and multiplexed molecular screening for clinical applications.

Pediatric low-grade gliomas and the need for new options for therapy: why and how?

PubMed Central

Qaddoumi, Ibrahim; Sultan, Iyad; Broniscer, Alberto

2009-01-01

Pediatric low-grade gliomas are the most common tumors of the central nervous system in children, accounting for almost 50% of all childhood brain tumors. They are a heterogeneous group of tumors with different histologic subtypes. Most treatment studies address low-grade gliomas as a single entity, depriving us of histology-specific treatment outcomes. This is mostly due to a lack of understanding of tumor biology at the molecular level. Pediatric low-grade gliomas are not benign, and most incompletely resected tumors will progress and negatively affect quality of life. The advancements made in understanding sporadic pilocytic astrocytoma and neurofibromatosis 1-associated pilocytic astrocytoma in particular have paved the way for potential targeted therapy and biological stratification. Such progress in pilocytic astrocytoma needs to be consolidated and expanded to other histologic varieties of pediatric low-grade gliomas. PMID:19164945

Development of a high-specific-speed centrifugal compressor

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

Rodgers, C.

1997-07-01

This paper describes the development of a subscale single-stage centrifugal compressor with a dimensionless specific speed (Ns) of 1.8, originally designed for full-size application as a high volume flow, low pressure ratio, gas booster compressor. The specific stage is noteworthy in that it provides a benchmark representing the performance potential of very high-specific-speed compressors, of which limited information is found in the open literature. Stage and component test performance characteristics are presented together with traverse results at the impeller exit. Traverse test results were compared with recent CFD computational predictions for an exploratory analytical calibration of a very high-specific-speed impellermore » geometry. The tested subscale (0.583) compressor essentially satisfied design performance expectations with an overall stage efficiency of 74% including, excessive exit casing losses. It was estimated that stage efficiency could be increased to 81% with exit casing losses halved.« less

Inter-rater reliability of three standardized functional tests in patients with low back pain

PubMed Central

Tidstrand, Johan; Horneij, Eva

2009-01-01

Background Of all patients with low back pain, 85% are diagnosed as "non-specific lumbar pain". Lumbar instability has been described as one specific diagnosis which several authors have described as delayed muscular responses, impaired postural control as well as impaired muscular coordination among these patients. This has mostly been measured and evaluated in a laboratory setting. There are few standardized and evaluated functional tests, examining functional muscular coordination which are also applicable in the non-laboratory setting. In ordinary clinical work, tests of functional muscular coordination should be easy to apply. The aim of this present study was to therefore standardize and examine the inter-rater reliability of three functional tests of muscular functional coordination of the lumbar spine in patients with low back pain. Methods Nineteen consecutive individuals, ten men and nine women were included. (Mean age 42 years, SD ± 12 yrs). Two independent examiners assessed three tests: "single limb stance", "sitting on a Bobath ball with one leg lifted" and "unilateral pelvic lift" on the same occasion. The standardization procedure took altered positions of the spine or pelvis and compensatory movements of the free extremities into account. The inter-rater reliability was analyzed by Cohen's kappa coefficient (κ) and by percentage agreement. Results The inter-rater reliability for the right and the left leg respectively was: for the single limb stance very good (κ: 0.88–1.0), for sitting on a Bobath ball good (κ: 0.79) and very good (κ: 0.88) and for the unilateral pelvic lift: good (κ: 0.61) and moderate (κ: 0.47). Conclusion The present study showed good to very good inter-rater reliability for two standardized tests, that is, the single-limb stance and sitting on a Bobath-ball with one leg lifted. Inter-rater reliability for the unilateral pelvic lift test was moderate to good. Validation of the tests in their ability to evaluate lumbar stability is required. PMID:19490644

Characterization of rubella-specific humoral immunity following two doses of MMR vaccine using proteome microarray technology

PubMed Central

Haralambieva, Iana H.; Gibson, Michael J.; Kennedy, Richard B.; Ovsyannikova, Inna G.; Warner, Nathaniel D.; Grill, Diane E.

2017-01-01

Introduction//Background The lack of standardization of the currently used commercial anti-rubella IgG antibody assays leads to frequent misinterpretation of results for samples with low/equivocal antibody concentration. The use of alternative approaches in rubella serology could add new information leading to a fuller understanding of rubella protective immunity and neutralizing antibody response after vaccination. Methods We applied microarray technology to measure antibodies to all rubella virus proteins in 75 high and 75 low rubella virus-specific antibody responders after two MMR vaccine doses. These data were used in multivariate penalized logistic regression modeling of rubella-specific neutralizing antibody response after vaccination. Results We measured antibodies to all rubella virus structural proteins (i.e., the glycoproteins E1 and E2 and the capsid C protein) and to the non-structural protein P150. Antibody levels to each of these proteins were: correlated with the neutralizing antibody titer (p<0.006); demonstrated differences between the high and the low antibody responder groups (p<0.008); and were components of the model associated with/predictive of vaccine-induced rubella virus-specific neutralizing antibody titers (misclassification error = 0.2). Conclusion Our study supports the use of this new technology, as well as the use of antibody profiles/patterns (rather than single antibody measures) as biomarkers of neutralizing antibody response and correlates of protective immunity in rubella virus serology. PMID:29145521

Development of Thin Solar Cells for Space Applications at NASA Glenn Research Center

NASA Technical Reports Server (NTRS)

Dickman, John E.; Hepp, Aloysius; Banger, Kulbinder K.; Harris, Jerry D.; Jin, Michael H.

2003-01-01

NASA GRC Thin Film Solar Cell program is developing solar cell technologies for space applications which address two critical metrics: higher specific power (power per unit mass) and lower launch stowed volume. To be considered for space applications, an array using thin film solar cells must offer significantly higher specific power while reducing stowed volume compared to the present technologies being flown on space missions, namely crystalline solar cells. The NASA GRC program is developing single-source precursors and the requisite deposition hardware to grow high-efficiency, thin-film solar cells on polymer substrates at low deposition temperatures. Using low deposition temperatures enables the thin film solar cells to be grown on a variety of polymer substrates, many of which would not survive the high temperature processing currently used to fabricate thin film solar cells. The talk will present the latest results of this research program.

Optimization of simultaneous tritium–radiocarbon internal gas proportional counting

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

Bonicalzi, R. M.; Aalseth, C. E.; Day, A. R.

Specific environmental applications can benefit from dual tritium and radiocarbon measurements in a single compound. Assuming typical environmental levels, it is often the low tritium activity relative to the higher radiocarbon activity that limits the dual measurement. In this paper, we explore the parameter space for a combined tritium and radiocarbon measurement using a methane sample mixed with an argon fill gas in low-background proportional counters of a specific design. We present an optimized methane percentage, detector fill pressure, and analysis energy windows to maximize measurement sensitivity while minimizing count time. The final optimized method uses a 9-atm fill ofmore » P35 (35% methane, 65% argon), and a tritium analysis window from 1.5 to 10.3 keV, which stops short of the tritium beta decay endpoint energy of 18.6 keV. This method optimizes tritium counting efficiency while minimizing radiocarbon beta decay interference.« less

An Arabidopsis mutation in translation elongation factor 2 causes superinduction of CBF/DREB1 transcription factor genes but blocks the induction of their downstream targets under low temperatures.

PubMed

Guo, Yan; Xiong, Liming; Ishitani, Manabu; Zhu, Jian-Kang

2002-05-28

Low temperature regulates gene expression in bacteria, yeast, and animals as well as in plants. However, the signal transduction cascades mediating the low temperature responses are not well understood in any organism. To identify components in low temperature signaling genetically, we isolated Arabidopsis thaliana mutants in which cold-responsive genes are no longer induced by low temperatures. One of these mutations, los1-1, specifically blocks low temperature-induced transcription of cold-responsive genes. Surprisingly, cold-induced expression of the early response transcriptional activators, C-repeat/dehydration responsive element binding factors (CBF/DREB1s), is enhanced by the los1-1 mutation. The los1-1 mutation also reduces the capacity of plants to develop freezing tolerance but does not impair the vernalization response. Genetic analysis indicated that los1-1 is a recessive mutation in a single nuclear gene. The LOS1 gene encodes a translation elongation factor 2-like protein. Protein labeling studies show that new protein synthesis is blocked in los1-1 mutant plants specifically in the cold. These results reveal a critical role of new protein synthesis in the proper transduction of low temperature signals. Our results also suggest that cold-induced transcription of CBF/DREB1s is feedback inhibited by their gene products or by products of their downstream target genes.

Immediate effects of Pilates based therapeutic exercise on postural control of young individuals with non-specific low back pain: A randomized controlled trial.

PubMed

Lopes, Susana; Correia, Christophe; Félix, Gonçalo; Lopes, Mário; Cruz, Ana; Ribeiro, Fernando

2017-10-01

Low back pain affects the person's ability to keep balance, especially in challenging conditions. The purpose of this study was to determine the immediate effects of Pilates exercises on postural sway and dynamic balance of young individuals with non-specific low back pain. Controlled laboratory design. Forty-six participants with non-specific low back pain were randomized to a Pilates (n=23, 10 males; age: 21.8±3.2years) and a control group (n=23, 9 males; age: 22.8±3.6years). Postural sway was assessed with a force platform and dynamic balance with the Star Excursion Balance Test, before and after the intervention or rest period. To assess postural sway, participants stood still on an unstable surface set on the force plate for 90s, with eyes closed. The intervention lasted 20min and consisted on four Pilates exercises: single leg stretch (level 1), pelvic press (level 1), swimming (level 1) and kneeling opposite arm and leg reach. At baseline, no differences were found between groups. The Pilates group improved in all the postural sway values (area of CoP: 11.5±3.4 to 9.7±2.7cm 2 , p=0.002 and CoP velocity: 2.8±0.6 to 2.3±0.5cm/s, p<0.001) and in the Star Excursion Balance Test. Control group only improved in CoP velocity, however, this improvement was significantly inferior compared to the Pilates group. Pilates exercises immediately improved postural sway and dynamic balance in young adults with non-specific low back pain. Copyright © 2017 Elsevier Ltd. All rights reserved.

Prevalence of human papillomavirus among STD clinic attenders in Jamaica: association of younger age and increased sexual activity.

PubMed

Figueroa, J P; Ward, E; Luthi, T E; Vermund, S H; Brathwaite, A R; Burk, R D

1995-01-01

Human papillomavirus is the major etiologic agent of cervical cancer. Although the incidence of cancer of the cervix is high in Jamaica, the prevalence of human papillomavirus among Jamaican women has not been defined. To estimate the prevalence of human papillomavirus infection and associated risk factors in women attending an STD clinic in Kingston, Jamaica. A cross-sectional survey was done of 202 women attending an STD clinic in Kingston in 1990. Cervical and vaginal cells were collected by lavage, and human papillomavirus genomes were detected in extracted DNA using low-stringency Southern blot hybridization. Fifty-eight (28.7%) women were identified as HPV positive. Prevalence of HPV by age group was 39% in women 15-19 years old, 33% of women 20-24 years old, 31% in women 25-29 years old, and 17% in those 30 years or older. Increasing age was significantly associated with a lower prevalence of human papillomavirus infection (test for trend, P = 0.025). The effect of age was independent of years of sexual activity. Women reporting more than one sexual partner per month on average were found to have a significantly higher HPV prevalence (odds ratio 2.87, 95% confidence Interval 1.29-6.38), as were women who reported more frequent sex (test for trend, P = 0.006). Sexual behavior is associated with risk of human papillomavirus infection. The decrease of human papillomavirus prevalence in older women agrees with other studies that argue in favor of a biological effect, such as increased immunity to human papillomavirus with age. A better understanding of why immunity to human papillomavirus may develop in older women may provide the basis for developing an effective vaccine to prevent cancer of the cervix.

Evaluation of different methods used to assess disease activity in rheumatoid arthritis: analyses of abatacept clinical trial data

PubMed Central

Dougados, M; Schmidely, N; Le Bars, M; Lafosse, C; Schiff, M; Smolen, J S; Aletaha, D; van Riel, P; Wells, G

2009-01-01

Objectives: To evaluate different methods of reporting response to treatment or disease status for their ability to discriminate between active therapy and placebo, or to reflect structural progression or patient satisfaction with treatment using an exploratory analysis of the Abatacept in Inadequate Responders to Methotrexate (AIM) trial. Methods: 424 active (abatacept ∼10 mg/kg) and 214 placebo-treated patients with rheumatoid arthritis (RA) were evaluated. Methods of reporting included: (1) response (American College of Rheumatology (ACR) criteria) versus state (disease activity score in 28 joints (DAS28) criteria); (2) stringency (ACR20 vs 50 vs 70; moderate disease activity state (MDAS; DAS28 <5.1) vs low disease activity state (LDAS; DAS28 ⩽3.2) vs DAS28-defined remission (DAS28 <2.6)); (3) time to onset (time to first ACR50/LDAS) and (4) sustainability of ACR50/LDAS for consecutive visits. Methods were assessed according to: (1) discriminatory capacity (number of patients needed to study (NNS)); (2) structural progression (Genant-modified Sharp score) and (3) patient satisfaction with treatment. Positive likelihood ratios (LR) evaluated the ability of the above methods to reflect structural damage and patient satisfaction. Results: MDAS and ACR20 had the highest discriminatory capacity (NNS 49 and 69). Sustained LDAS best reflected no radiographic progression (positive LR ⩾2). More stringent criteria (at least ACR50/LDAS), faster onset (⩽3 months) and sustainability (>3 visits) of ACR50/LDAS best reflected patient satisfaction (positive LR >10). Conclusions: The optimal method for reporting a measure of disease activity may differ depending on the outcome of interest. Time to onset and sustainability can be important factors when evaluating treatment response and disease status in patients with RA. PMID:19074177

Funding health and social services for older people – a qualitative study of care recipients in the last year of life

PubMed Central

Hanratty, Barbara; Lowson, Elizabeth; Holmes, Louise; Grande, Gunn; Addington-Hall, Julia; Payne, Sheila; Seymour, Jane

2012-01-01

Objectives This study explores the views of older adults who are receiving health and social care at the end of their lives, on how services should be funded, and describes their health-related expenditure. Design Qualitative interview study Setting North West England Participants 30 people aged 69–93 years, diagnosed with lung cancer, heart failure or stroke and judged by health professionals to be in their last year of life. Sixteen participants lived in disadvantaged areas. Main outcome measures Views of older adults on funding of services. Results Participants expressed a belief in an earned entitlement to services funded from taxation, based on a broad sense of being a good citizen. Irrespective of social background, older people felt that those who could afford to pay for social care, should do so. Sale of assets and use of children's inheritance to fund care was widely perceived as an injustice. The costs of living with illness are a burden, and families are filling many of the gaps left by welfare provision. People who had worked in low-wage occupations were most concerned to justify their current acceptance of services, and distance themselves from what they described as welfare ‘spongers’ or ‘layabouts.’ Conclusions There is a gap between the health and social care system that older adults expect and what may be provided by a reformed welfare state at a time of financial stringencies. The values that underpinned the views expressed – mutuality, care for the most needy, and the importance of working to contribute to society – are an important contribution to the debate on welfare funding. PMID:22537882

Bone morphogenetic protein and Notch signalling crosstalk in poor-prognosis, mesenchymal-subtype colorectal cancer.

PubMed

Irshad, Shazia; Bansal, Mukesh; Guarnieri, Paolo; Davis, Hayley; Al Haj Zen, Ayman; Baran, Brygida; Pinna, Claudia Maria Assunta; Rahman, Haseeb; Biswas, Sujata; Bardella, Chiara; Jeffery, Rosemary; Wang, Lai Mun; East, James Edward; Tomlinson, Ian; Lewis, Annabelle; Leedham, Simon John

2017-06-01

The functional role of bone morphogenetic protein (BMP) signalling in colorectal cancer (CRC) is poorly defined, with contradictory results in cancer cell line models reflecting the inherent difficulties of assessing a signalling pathway that is context-dependent and subject to genetic constraints. By assessing the transcriptional response of a diploid human colonic epithelial cell line to BMP ligand stimulation, we generated a prognostic BMP signalling signature, which was applied to multiple CRC datasets to investigate BMP heterogeneity across CRC molecular subtypes. We linked BMP and Notch signalling pathway activity and function in human colonic epithelial cells, and normal and neoplastic tissue. BMP induced Notch through a γ-secretase-independent interaction, regulated by the SMAD proteins. In homeostasis, BMP/Notch co-localization was restricted to cells at the top of the intestinal crypt, with more widespread interaction in some human CRC samples. BMP signalling was downregulated in the majority of CRCs, but was conserved specifically in mesenchymal-subtype tumours, where it interacts with Notch to induce an epithelial-mesenchymal transition (EMT) phenotype. In intestinal homeostasis, BMP-Notch pathway crosstalk is restricted to differentiating cells through stringent pathway segregation. Conserved BMP activity and loss of signalling stringency in mesenchymal-subtype tumours promotes a synergistic BMP-Notch interaction, and this correlates with poor patient prognosis. BMP signalling heterogeneity across CRC subtypes and cell lines can account for previous experimental contradictions. Crosstalk between the BMP and Notch pathways will render mesenchymal-subtype CRC insensitive to γ-secretase inhibition unless BMP activation is concomitantly addressed. © 2017 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland. © 2017 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Sequence conservation on the Y chromosome

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

Gibson, L.H.; Yang-Feng, L.; Lau, C.

The Y chromosome is present in all mammals and is considered to be essential to sex determination. Despite intense genomic research, only a few genes have been identified and mapped to this chromosome in humans. Several of them, such as SRY and ZFY, have been demonstrated to be conserved and Y-located in other mammals. In order to address the issue of sequence conservation on the Y chromosome, we performed fluorescence in situ hybridization (FISH) with DNA from a human Y cosmid library as a probe to study the Y chromosomes from other mammalian species. Total DNA from 3,000-4,500 cosmid poolsmore » were labeled with biotinylated-dUTP and hybridized to metaphase chromosomes. For human and primate preparations, human cot1 DNA was included in the hybridization mixture to suppress the hybridization from repeat sequences. FISH signals were detected on the Y chromosomes of human, gorilla, orangutan and baboon (Old World monkey) and were absent on those of squirrel monkey (New World monkey), Indian munjac, wood lemming, Chinese hamster, rat and mouse. Since sequence analysis suggested that specific genes, e.g. SRY and ZFY, are conserved between these two groups, the lack of detectable hybridization in the latter group implies either that conservation of the human Y sequences is limited to the Y chromosomes of the great apes and Old World monkeys, or that the size of the syntenic segment is too small to be detected under the resolution of FISH, or that homologeous sequences have undergone considerable divergence. Further studies with reduced hybridization stringency are currently being conducted. Our results provide some clues as to Y-sequence conservation across species and demonstrate the limitations of FISH across species with total DNA sequences from a particular chromosome.« less

Applying the food safety objective and related standards to thermal inactivation of Salmonella in poultry meat.

PubMed

Membré, Jeanne-Marie; Bassett, John; Gorris, Leon G M

2007-09-01

The objective of this study was to investigate the practicality of designing a heat treatment process in a food manufacturing operation for a product governed by a Food Safety Objective (FSO). Salmonella in cooked poultry meat was taken as the working example. Although there is no FSO for this product in current legislation, this may change in the (near) future. Four different process design calculations were explored by means of deterministic and probabilistic approaches to mathematical data handling and modeling. It was found that the probabilistic approach was a more objective, transparent, and quantifiable approach to establish the stringency of food safety management systems. It also allowed the introduction of specific prevalence rates. The key input analyzed in this study was the minimum time required for the heat treatment at a fixed temperature to produce a product that complied with the criterion for product safety, i.e., the FSO. By means of the four alternative process design calculations, the minimum time requirement at 70 degrees C was established and ranged from 0.26 to 0.43 min. This is comparable to the U.S. regulation recommendations and significantly less than that of 2 min at 70 degrees C used, for instance, in the United Kingdom regulation concerning vegetative microorganisms in ready-to-eat foods. However, the objective of this study was not to challenge existing regulations but to provide an illustration of how an FSO established by a competent authority can guide decisions on safe product and process designs in practical operation; it hopefully contributes to the collaborative work between regulators, academia, and industries that need to continue learning and gaining experience from each other in order to translate risk-based concepts such as the FSO into everyday operational practice.

Generation and purification of highly-specific antibodies for detecting post-translationally modified proteins in vivo

PubMed Central

Arur, Swathi; Schedl, Tim

2014-01-01

Post-translational modifications alter protein structure, affecting activity, stability, localization and/or binding partners. Antibodies that specifically recognize post-translationally modified proteins have a number of uses including immuno-cytochemistry and immuno-precipitation of the modified protein to purify protein-protein and protein-nucleic acid complexes. However, antibodies directed at modified sites on individual proteins are often non-specific. Here we describe a protocol to purify polyclonal antibodies that specifically detect the modified protein of interest. The approach uses iterative rounds of subtraction and affinity purification, using stringent washes to remove antibodies that recognize the unmodified protein and low sequence complexity epitopes containing the modified amino acid. Dot and western blots assays are employed to assess antibody preparation specificity. The approach is designed to overcome the common occurrence that a single round of subtraction and affinity purification is not sufficient to obtain a modified protein specific antibody preparation. One full round of antibody purification and specificity testing takes 6 days of discontinuous time. PMID:24457330

Stable optical trapping and sensitive characterization of nanostructures using standing-wave Raman tweezers

PubMed Central

Wu, Mu-ying; Ling, Dong-xiong; Ling, Lin; Li, William; Li, Yong-qing

2017-01-01

Optical manipulation and label-free characterization of nanoscale structures open up new possibilities for assembly and control of nanodevices and biomolecules. Optical tweezers integrated with Raman spectroscopy allows analyzing a single trapped particle, but is generally less effective for individual nanoparticles. The main challenge is the weak gradient force on nanoparticles that is insufficient to overcome the destabilizing effect of scattering force and Brownian motion. Here, we present standing-wave Raman tweezers for stable trapping and sensitive characterization of single isolated nanostructures with a low laser power by combining a standing-wave optical trap with confocal Raman spectroscopy. This scheme has stronger intensity gradients and balanced scattering forces, and thus can be used to analyze many nanoparticles that cannot be measured with single-beam Raman tweezers, including individual single-walled carbon nanotubes (SWCNT), graphene flakes, biological particles, SERS-active metal nanoparticles, and high-refractive semiconductor nanoparticles. This would enable sorting and characterization of specific SWCNTs and other nanoparticles based on their increased Raman fingerprints. PMID:28211526

Pollution reduction technology program for class T4(JT8D) engines

NASA Technical Reports Server (NTRS)

Roberts, R.; Fiorentino, A. J.; Diehl, L. A.

1977-01-01

The technology required to develop commercial gas turbine engines with reduced exhaust emissions was demonstrated. Can-annular combustor systems for the JT8D engine family (EPA class T4) were investigated. The JT8D turbofan engine is an axial-flow, dual-spool, moderate-bypass-ratio design. It has a two-stage fan, a four-stage low-pressure compressor driven by a three-stage low-pressure turbine, and a seven-stage high-pressure compressor driven by a single-stage high-pressure turbine. A cross section of the JT8D-17 showing the mechanical configuration is given. Key specifications for this engine are listed.

Sulfide chemiluminescence detection

DOEpatents

Spurlin, Stanford R.; Yeung, Edward S.

1985-01-01

A method of chemiluminescently determining a sulfide which is either hydrogen sulfide or methyl mercaptan by reacting the sulfide with chlorine dioxide at low pressure and under conditions which allow a longer reaction time in emission of a single photon for every two sulfide containing species, and thereafter, chemiluminescently detecting and determining the sulfide. The invention also relates not only to the detection method, but the novel chemical reaction and a specifically designed chemiluminescence detection cell for the reaction.

The simultaneous ex vivo detection of low-frequency antigen-specific CD4+ and CD8+ T-cell responses using overlapping peptide pools.

PubMed

Singh, Satwinder Kaur; Meyering, Maaike; Ramwadhdoebe, Tamara H; Stynenbosch, Linda F M; Redeker, Anke; Kuppen, Peter J K; Melief, Cornelis J M; Welters, Marij J P; van der Burg, Sjoerd H

2012-11-01

The ability to measure antigen-specific T cells at the single-cell level by intracellular cytokine staining (ICS) is a promising immunomonitoring tool and is extensively applied in the evaluation of immunotherapy of cancer. The protocols used to detect antigen-specific CD8+ T-cell responses generally work for the detection of antigen-specific T cells in samples that have undergone at least one round of in vitro pre-stimulation. Application of a common protocol but now using long peptides as antigens was not suitable to simultaneously detect antigen-specific CD8+ and CD4+ T cells directly ex vivo in cryopreserved samples. CD8 T-cell reactivity to monocytes pulsed with long peptides as antigens ranged between 5 and 25 % of that observed against monocytes pulsed with a direct HLA class I fitting minimal CTL peptide epitope. Therefore, we adapted our ICS protocol and show that the use of tenfold higher concentration of long peptides to load APC, the use of IFN-α and poly(I:C) to promote antigen processing and improve T-cell stimulation, does allow for the ex vivo detection of low-frequency antigen-specific CD8+ and CD4+ T cells in an HLA-independent setting. While most of the improvements were related to increasing the ability to measure CD8+ T-cell reactivity following stimulation with long peptides to at least 50 % of the response detected when using a minimal peptide epitope, the final analysis of blood samples from vaccinated patients successfully showed that the adapted ICS protocol also increases the ability to ex vivo detect low-frequency p53-specific CD4+ T-cell responses in cryopreserved PBMC samples.

A new class of homogeneous nucleic acid probes based on specific displacement hybridization

PubMed Central

Li, Qingge; Luan, Guoyan; Guo, Qiuping; Liang, Jixuan

2002-01-01

We have developed a new class of probes for homogeneous nucleic acid detection based on the proposed displacement hybridization. Our probes consist of two complementary oligodeoxyribonucleotides of different length labeled with a fluorophore and a quencher in close proximity in the duplex. The probes on their own are quenched, but they become fluorescent upon displacement hybridization with the target. These probes display complete discrimination between a perfectly matched target and single nucleotide mismatch targets. A comparison of double-stranded probes with corresponding linear probes confirms that the presence of the complementary strand significantly enhances their specificity. Using four such probes labeled with different color fluorophores, each designed to recognize a different target, we have demonstrated that multiple targets can be distinguished in the same solution, even if they differ from one another by as little as a single nucleotide. Double-stranded probes were used in real-time nucleic acid amplifications as either probes or as primers. In addition to its extreme specificity and flexibility, the new class of probes is simple to design and synthesize, has low cost and high sensitivity and is accessible to a wide range of labels. This class of probes should find applications in a variety of areas wherever high specificity of nucleic acid hybridization is relevant. PMID:11788731

Effect of exposure to good vs poor medical trainee performance on attending physician ratings of subsequent performances.

PubMed

Yeates, Peter; O'Neill, Paul; Mann, Karen; Eva, Kevin W

2012-12-05

Competency-based models of education require assessments to be based on individuals' capacity to perform, yet the nature of human judgment may fundamentally limit the extent to which such assessment is accurately possible. To determine whether recent observations of the Mini Clinical Evaluation Exercise (Mini-CEX) performance of postgraduate year 1 physicians influence raters' scores of subsequent performances, consistent with either anchoring bias (scores biased similar to previous experience) or contrast bias (scores biased away from previous experience). Internet-based randomized, blinded experiment using videos of Mini-CEX assessments of postgraduate year 1 trainees interviewing new internal medicine patients. Participants were 41 attending physicians from England and Wales experienced with the Mini-CEX, with 20 watching and scoring 3 good trainee performances and 21 watching and scoring 3 poor performances. All then watched and scored the same 3 borderline video performances. The study was completed between July and November 2011. The primary outcome was scores assigned to the borderline videos, using a 6-point Likert scale (anchors included: 1, well below expectations; 3, borderline; 6, well above expectations). Associations were tested in a multivariable analysis that included participants' sex, years of practice, and the stringency index (within-group z score of initial 3 ratings). The mean rating scores assigned by physicians who viewed borderline video performances following exposure to good performances was 2.7 (95% CI, 2.4-3.0) vs 3.4 (95% CI, 3.1-3.7) following exposure to poor performances (difference of 0.67 [95% CI, 0.28-1.07]; P = .001). Borderline videos were categorized as consistent with failing scores in 33 of 60 assessments (55%) in those exposed to good performances and in 15 of 63 assessments (24%) in those exposed to poor performances (P < .001). They were categorized as consistent with passing scores in 5 of 60 assessments (8.3%) in those exposed to good performances compared with 25 of 63 assessments (39.5%) in those exposed to poor performances (P < .001). Sex and years of attending practice were not associated with scores. The priming condition (good vs poor performances) and the stringency index jointly accounted for 45% of the observed variation in raters' scores for the borderline videos (P < .001). In an experimental setting, attending physicians exposed to videos of good medical trainee performances rated subsequent borderline performances lower than those who had been exposed to poor performances, consistent with a contrast bias.

Low-cost embedded systems for democratizing ocean sensor technology in the coastal zone

NASA Astrophysics Data System (ADS)

Glazer, B. T.; Lio, H. I.

2017-12-01

Environmental sciences suffer from undersampling. Enabling sustained and unattended data collection in the coastal zone typically involves expensive instrumentation and infrastructure deployed as cabled observatories or moorings with little flexibility in deployment location following initial installation. High costs of commercially-available or custom instruments have limited the number of sensor sites that can be targeted by academic researchers, and have also limited engagement with the public. We have developed a novel, low-cost, open-source sensor and software platform to enable wireless data transfer of biogeochemical sensors in the coastal zone. The platform is centered upon widely available, low-cost, single board computers and microcontrollers. We have used a blend of on-hand research-grade sensors and low-cost open-source electronics that can be assembled by tech-savvy non-engineers. Robust, open-source code that remains customizable for specific miniNode configurations can match a specific site's measurement needs, depending on the scientific research priorities. We have demonstrated prototype capabilities and versatility through lab testing and field deployments of multiple sensor nodes with multiple sensor inputs, all of which are streaming near-real-time data from Kaneohe Bay over wireless RF links to a shore-based base station.

Low specificity of 2 tetanus rapid tests in Cambodia.

PubMed

Schlumberger, M; Yvonnet, B; Lesage, G; Tep, B

2015-01-01

Rapid testing for tetanus on serum or blood allows for an immediate evaluation of individual protection against tetanus in developed countries, using a "single step" immunochromatographic technique using tetanus toxoid. The specificity of these tests, compared to the reference method for tetanus, mouse serum neutralization testing, has however never been assessed in these countries, due to the difficulty to perform serum neutralization titration in mice, because of animal testing bioethical regulations. A collection of sera from adult volunteers in Cambodia, living in rural environment, was tested for tetanus antibodies by ELISA in France, and by mouse serum neutralization in Vietnam. This allowed estimating the sensitivity and specificity of 2 rapid tetanus tests, available on the market: TQS™ and Tetanotop™. The sensitivity of these tests was adequate, compared to mice serum neutralization test, for a test threshold of 0.01 IU/mL, (100% for TQS™, 91% for Tetanotop™), but their specificity was very low (1% for TQS™ and 13% for Tetanotop™). The results prove that these rapid tests for the assessment of individual protection against tetanus should not be used in the adult rural Cambodian population. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Biological auctions with multiple rewards

PubMed Central

Reiter, Johannes G.; Kanodia, Ayush; Gupta, Raghav; Nowak, Martin A.; Chatterjee, Krishnendu

2015-01-01

The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards. PMID:26180069

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

Karube, Masataka, E-mail: mstk117@gmail.com; Department of Radiology, The University of Tokyo Hospital, Tokyo; Yamamoto, Naoyoshi

Purpose: In an aging society, many senior citizens want less invasive treatment because of potential medical complications. The National Institute of Radiological Sciences has started to treat stage I lung cancer with single-fraction carbon-ion radiation therapy (CIRT) as a dose escalation prospective phase 1/2 trial. We evaluated the efficacy and safety of CIRT for patients 80 years of age and older, undergoing single-fraction CIRT. Methods and Materials: Peripheral non-small cell lung cancer patients who were treated with single-fraction CIRT were prospectively followed. We analyzed the data from among these patients 80 years of age and older. Results: There were 70 patients. Medianmore » age was 83 years (range: 80-89) and median follow-up period was 42.7 months (range: 12-128 months). Three-year local control, cause-specific survival, and overall survival rates were 88.0%, 81.6%, and 72.4%, respectively. Five-year local control, cause-specific survival, and overall survival rates were 85.8%, 64.9%, and 39.7%, respectively. There were no adverse effects higher than grade 2 either in the acute or late phase in terms of skin and lung. Analgesic agents were necessary for only 5 patients (7.1%), to relieve muscular or rib fracture pain caused by irradiation. Conclusions: Single-fraction CIRT was low-risk and effective, even for the elderly.« less

Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR.

PubMed

Shuga, Joe; Zeng, Yong; Novak, Richard; Lan, Qing; Tang, Xiaojiang; Rothman, Nathaniel; Vermeulen, Roel; Li, Laiyu; Hubbard, Alan; Zhang, Luoping; Mathies, Richard A; Smith, Martyn T

2013-09-01

Cancers are heterogeneous and genetically unstable. New methods are needed that provide the sensitivity and specificity to query single cells at the genetic loci that drive cancer progression, thereby enabling researchers to study the progression of individual tumors. Here, we report the development and application of a bead-based hemi-nested microfluidic droplet digital PCR (dPCR) technology to achieve 'quantitative' measurement and single-molecule sequencing of somatically acquired carcinogenic translocations at extremely low levels (<10(-6)) in healthy subjects. We use this technique in our healthy study population to determine the overall concentration of the t(14;18) translocation, which is strongly associated with follicular lymphoma. The nested dPCR approach improves the detection limit to 1×10(-7) or lower while maintaining the analysis efficiency and specificity. Further, the bead-based dPCR enabled us to isolate and quantify the relative amounts of the various clonal forms of t(14;18) translocation in these subjects, and the single-molecule sensitivity and resolution of dPCR led to the discovery of new clonal forms of t(14;18) that were otherwise masked by the conventional quantitative PCR measurements. In this manner, we created a quantitative map for this carcinogenic mutation in this healthy population and identified the positions on chromosomes 14 and 18 where the vast majority of these t(14;18) events occur.

Biomechanical comparison of single-row arthroscopic rotator cuff repair technique versus transosseous repair technique.

PubMed

Tocci, Stephen L; Tashjian, Robert Z; Leventhal, Evan; Spenciner, David B; Green, Andrew; Fleming, Braden C

2008-01-01

This study determined the effect of tear size on gap formation of single-row simple-suture arthroscopic rotator cuff repair (ARCR) vs transosseous Mason-Allen suture open RCR (ORCR) in 13 pairs of human cadaveric shoulders. A massive tear was created in 6 pairs and a large tear in 7. Repairs were cyclically tested in low-load and high-load conditions, with no significant difference in gap formation. Under low-load, gapping was greater in massive tears. Under high-load, there was a trend toward increased gap with ARCR for large tears. All repairs of massive tears failed in high-load. Gapping was greater posteriorly in massive tears for both techniques. Gap formation of a modeled RCR depends upon the tear size. ARCR of larger tears may have higher failure rates than ORCR, and the posterior aspect appears to be the site of maximum gapping. Specific attention should be directed toward maximizing initial fixation of larger rotator cuff tears, especially at the posterior aspect.

X-ray irradiation-induced structural changes on Single Wall Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Bardi, N.; Jurewicz, I.; King, A. K.; Alkhorayef, M. A.; Bradley, D.; Dalton, A. B.

2017-11-01

Dosimetry devices based on Carbon Nanotubes are a promising new technology. In particular using devices based on single wall Carbon Nanotubes may offer a tissue equivalent response with the possibility for device miniaturisation, high scale manufacturing and low cost. An important precursor to device fabrication requires a quantitative study of the effects of X-ray radiation on the physical and chemical properties of the individual nanotubes. In this study, we concentrate on the effects of relatively low doses, 20 cGy and 45 cGy , respectively. We use a range of characterization techniques including scanning electron microscopy, Raman spectroscopy and X-ray photoelectron spectroscopy to quantify the effects of the radiation dose on inherent properties of the nanotubes. Specifically we find that the radiation exposure results in a reduction in the sp2 nature of the nanotube bond structure. Moreover, our analysis indicates that the exposure results in nanotubes that have an increased defect density which ultimately effects the electrical properties of the nanotubes.

Vacancy and curvature effects on the phonon properties of single wall carbon nanotube

NASA Astrophysics Data System (ADS)

Hossain Howlader, Ashraful; Sherajul Islam, Md.; Tanaka, Satoru; Makino, Takayuki; Hashimoto, Akihiro

2018-02-01

Single wall carbon nanotube (SWCNT) is considered as an ideal candidate for next-generation nanoelectronics owing to its unusual properties. Here we have performed an in-depth theoretical analysis of the effect of vacancy defects and curvature on the phonon properties of (10,0) and (10,10) SWCNTs using the forced vibrational method. We report that Raman active E2g mode softens towards the low-frequency region with increasing vacancies and curvature in both types of CNTs. Vacancy induces some new peaks at low-frequency region of the phonon density of states. Phonon localization properties are also manifested. Our calculated mode pattern and localization length show that optical phonon at Raman D-band frequency is strongly localized in vacancy defected and large curved CNTs. Our findings will be helpful in explaining the thermal conductivity, specific heat capacity, and Raman spectra in vacancy type disordered CNTs, as well as electron transport properties of CNT-based nanoelectronic devices.

Low loss photonic components in high index bismuth borate glass by femtosecond laser direct writing.

PubMed

Yang, Weijia; Corbari, Costantino; Kazansky, Peter G; Sakaguchi, Koichi; Carvalho, Isabel C S

2008-09-29

Single mode, low loss waveguides were fabricated in high index bismuth borate glass by femtosecond laser direct writing. A specific set of writing parameters leading to waveguides perfectly mode matched to standard single-mode fibers at 1.55 microm with an overall insertion loss of approximately 1 dB and with propagation loss below 0.2 dB/cm was identified. Photonic components such as Y-splitters and directional couplers were also demonstrated. A close agreement between their performances and theoretical predictions based upon the characterization of the waveguide properties is shown. Finally, the nonlinear refractive index of the waveguides has been measured to be 6.6 x 10(-15) cm(2)/W by analyzing self-phase modulation of the propagating femtosecond laser pulse at the wavelength of 1.46 microm. Broadening of the transmitted light source as large as 500 nm was demonstrated through a waveguide with the length of 1.8 cm.

A microfluidic device for label-free, physical capture of circulating tumor cell-clusters

PubMed Central

Sarioglu, A. Fatih; Aceto, Nicola; Kojic, Nikola; Donaldson, Maria C.; Zeinali, Mahnaz; Hamza, Bashar; Engstrom, Amanda; Zhu, Huili; Sundaresan, Tilak K.; Miyamoto, David T.; Luo, Xi; Bardia, Aditya; Wittner, Ben S.; Ramaswamy, Sridhar; Shioda, Toshi; Ting, David T.; Stott, Shannon L.; Kapur, Ravi; Maheswaran, Shyamala; Haber, Daniel A.; Toner, Mehmet

2015-01-01

Cancer cells metastasize through the bloodstream either as single migratory circulating tumor cells (CTCs) or as multicellular groupings (CTC-clusters). Existing technologies for CTC enrichment are designed primarily to isolate single CTCs, and while CTC-clusters are detectable in some cases, their true prevalence and significance remain to be determined. Here, we developed a microchip technology (Cluster-Chip) specifically designed to capture CTC-clusters independent of tumor-specific markers from unprocessed blood. CTC-clusters are isolated through specialized bifurcating traps under low shear-stress conditions that preserve their integrity and even two-cell clusters are captured efficiently. Using the Cluster-Chip, we identify CTC-clusters in 30–40% of patients with metastatic cancers of the breast, prostate and melanoma. RNA sequencing of CTC-clusters confirms their tumor origin and identifies leukocytes within the clusters as tissue-derived macrophages. Together, the development of a device for efficient capture of CTC-clusters will enable detailed characterization of their biological properties and role in cancer metastasis. PMID:25984697

A New Versatile Microarray-based Method for High Throughput Screening of Carbohydrate-active Enzymes*

PubMed Central

Vidal-Melgosa, Silvia; Pedersen, Henriette L.; Schückel, Julia; Arnal, Grégory; Dumon, Claire; Amby, Daniel B.; Monrad, Rune Nygaard; Westereng, Bjørge; Willats, William G. T.

2015-01-01

Carbohydrate-active enzymes have multiple biological roles and industrial applications. Advances in genome and transcriptome sequencing together with associated bioinformatics tools have identified vast numbers of putative carbohydrate-degrading and -modifying enzymes including glycoside hydrolases and lytic polysaccharide monooxygenases. However, there is a paucity of methods for rapidly screening the activities of these enzymes. By combining the multiplexing capacity of carbohydrate microarrays with the specificity of molecular probes, we have developed a sensitive, high throughput, and versatile semiquantitative enzyme screening technique that requires low amounts of enzyme and substrate. The method can be used to assess the activities of single enzymes, enzyme mixtures, and crude culture broths against single substrates, substrate mixtures, and biomass samples. Moreover, we show that the technique can be used to analyze both endo-acting and exo-acting glycoside hydrolases, polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. We demonstrate the potential of the technique by identifying the substrate specificities of purified uncharacterized enzymes and by screening enzyme activities from fungal culture broths. PMID:25657012

Synchronous acquisition of multi-channel signals by single-channel ADC based on square wave modulation

NASA Astrophysics Data System (ADS)

Yi, Xiaoqing; Hao, Liling; Jiang, Fangfang; Xu, Lisheng; Song, Shaoxiu; Li, Gang; Lin, Ling

2017-08-01

Synchronous acquisition of multi-channel biopotential signals, such as electrocardiograph (ECG) and electroencephalograph, has vital significance in health care and clinical diagnosis. In this paper, we proposed a new method which is using single channel ADC to acquire multi-channel biopotential signals modulated by square waves synchronously. In this method, a specific modulate and demodulate method has been investigated without complex signal processing schemes. For each channel, the sampling rate would not decline with the increase of the number of signal channels. More specifically, the signal-to-noise ratio of each channel is n times of the time-division method or an improvement of 3.01 ×log2n dB, where n represents the number of the signal channels. A numerical simulation shows the feasibility and validity of this method. Besides, a newly developed 8-lead ECG based on the new method has been introduced. These experiments illustrate that the method is practicable and thus is potential for low-cost medical monitors.

Age-independent anti-Müllerian hormone (AMH) standard deviation scores to estimate ovarian function.

PubMed

Helden, Josef van; Weiskirchen, Ralf

2017-06-01

To determine single year age-specific anti-Müllerian hormone (AMH) standard deviation scores (SDS) for women associated to normal ovarian function and different ovarian disorders resulting in sub- or infertility. Determination of particular year median and mean AMH values with standard deviations (SD), calculation of age-independent cut off SDS for the discrimination between normal ovarian function and ovarian disorders. Single-year-specific median, mean, and SD values have been evaluated for the Beckman Access AMH immunoassay. While the decrease of both median and mean AMH values is strongly correlated with increasing age, calculated SDS values have been shown to be age independent with the differentiation between normal ovarian function measured as occurred ovulation with sufficient luteal activity compared with hyperandrogenemic cycle disorders or anovulation associated with high AMH values and reduced ovarian activity or insufficiency associated with low AMH, respectively. These results will be helpful for the treatment of patients and the ventilation of the different reproductive options. Copyright © 2017 Elsevier B.V. All rights reserved.

Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis

PubMed Central

Félix, Marie-Anne

2016-01-01

Patterning of C. elegans vulval cell fates relies on inductive signaling. In this induction event, a single cell, the gonadal anchor cell, secretes LIN-3/EGF and induces three out of six competent precursor cells to acquire a vulval fate. We previously showed that this developmental system is robust to a four-fold variation in lin-3/EGF genetic dose. Here using single-molecule FISH, we find that the mean level of expression of lin-3 in the anchor cell is remarkably conserved. No change in lin-3 expression level could be detected among C. elegans wild isolates and only a low level of change—less than 30%—in the Caenorhabditis genus and in Oscheius tipulae. In C. elegans, lin-3 expression in the anchor cell is known to require three transcription factor binding sites, specifically two E-boxes and a nuclear-hormone-receptor (NHR) binding site. Mutation of any of these three elements in C. elegans results in a dramatic decrease in lin-3 expression. Yet only a single E-box is found in the Drosophilae supergroup of Caenorhabditis species, including C. angaria, while the NHR-binding site likely only evolved at the base of the Elegans group. We find that a transgene from C. angaria bearing a single E-box is sufficient for normal expression in C. elegans. Even a short 58 bp cis-regulatory fragment from C. angaria with this single E-box is able to replace the three transcription factor binding sites at the endogenous C. elegans lin-3 locus, resulting in the wild-type expression level. Thus, regulatory evolution occurring in cis within a 58 bp lin-3 fragment, results in a strict requirement for the NHR binding site and a second E-box in C. elegans. This single-cell, single-molecule, quantitative and functional evo-devo study demonstrates that conserved expression levels can hide extensive change in cis-regulatory site requirements and highlights the evolution of new cis-regulatory elements required for cell-specific gene expression. PMID:27588814

The zinc fingers of YY1 bind single-stranded RNA with low sequence specificity.

PubMed

Wai, Dorothy C C; Shihab, Manar; Low, Jason K K; Mackay, Joel P

2016-11-02

Classical zinc fingers (ZFs) are traditionally considered to act as sequence-specific DNA-binding domains. More recently, classical ZFs have been recognised as potential RNA-binding modules, raising the intriguing possibility that classical-ZF transcription factors are involved in post-transcriptional gene regulation via direct RNA binding. To date, however, only one classical ZF-RNA complex, that involving TFIIIA, has been structurally characterised. Yin Yang-1 (YY1) is a multi-functional transcription factor involved in many regulatory processes, and binds DNA via four classical ZFs. Recent evidence suggests that YY1 also interacts with RNA, but the molecular nature of the interaction remains unknown. In the present work, we directly assess the ability of YY1 to bind RNA using in vitro assays. Systematic Evolution of Ligands by EXponential enrichment (SELEX) was used to identify preferred RNA sequences bound by the YY1 ZFs from a randomised library over multiple rounds of selection. However, a strong motif was not consistently recovered, suggesting that the RNA sequence selectivity of these domains is modest. YY1 ZF residues involved in binding to single-stranded RNA were identified by NMR spectroscopy and found to be largely distinct from the set of residues involved in DNA binding, suggesting that interactions between YY1 and ssRNA constitute a separate mode of nucleic acid binding. Our data are consistent with recent reports that YY1 can bind to RNA in a low-specificity, yet physiologically relevant manner. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Substitute CT generation from a single ultra short time echo MRI sequence: preliminary study

NASA Astrophysics Data System (ADS)

Ghose, Soumya; Dowling, Jason A.; Rai, Robba; Liney, Gary P.

2017-04-01

In MR guided radiation therapy planning both MR and CT images for a patient are acquired and co-registered to obtain a tissue specific HU map. Generation of the HU map directly from the MRI would eliminate the CT acquisition and may improve radiation therapy planning. In this preliminary study of substitute CT (sCT) generation, two porcine leg phantoms were scanned using a 3D ultrashort echo time (PETRA) sequence and co-registered to corresponding CT images to build tissue specific regression models. The model was created from one co-registered CT-PETRA pair to generate the sCT for the other PETRA image. An expectation maximization based clustering was performed on the co-registered PETRA image to identify the soft tissues, dense bone and air class membership probabilities. A tissue specific non linear regression model was built from one registered CT-PETRA pair dataset to predict the sCT of the second PETRA image in a two-fold cross validation schema. A complete substitute CT is generated in 3 min. The mean absolute HU error for air was 0.3 HU, bone was 95 HU, fat was 30 HU and for muscle it was 10 HU. The mean surface reconstruction error for the bone was 1.3 mm. The PETRA sequence enabled a low mean absolute surface distance for the bone and a low HU error for other classes. The sCT generated from a single PETRA sequence shows promise for the generation of fast sCT for MRI based radiation therapy planning.

Characterisation of false-positive observations in botanical surveys

PubMed Central

2017-01-01

Errors in botanical surveying are a common problem. The presence of a species is easily overlooked, leading to false-absences; while misidentifications and other mistakes lead to false-positive observations. While it is common knowledge that these errors occur, there are few data that can be used to quantify and describe these errors. Here we characterise false-positive errors for a controlled set of surveys conducted as part of a field identification test of botanical skill. Surveys were conducted at sites with a verified list of vascular plant species. The candidates were asked to list all the species they could identify in a defined botanically rich area. They were told beforehand that their final score would be the sum of the correct species they listed, but false-positive errors counted against their overall grade. The number of errors varied considerably between people, some people create a high proportion of false-positive errors, but these are scattered across all skill levels. Therefore, a person’s ability to correctly identify a large number of species is not a safeguard against the generation of false-positive errors. There was no phylogenetic pattern to falsely observed species; however, rare species are more likely to be false-positive as are species from species rich genera. Raising the threshold for the acceptance of an observation reduced false-positive observations dramatically, but at the expense of more false negative errors. False-positive errors are higher in field surveying of plants than many people may appreciate. Greater stringency is required before accepting species as present at a site, particularly for rare species. Combining multiple surveys resolves the problem, but requires a considerable increase in effort to achieve the same sensitivity as a single survey. Therefore, other methods should be used to raise the threshold for the acceptance of a species. For example, digital data input systems that can verify, feedback and inform the user are likely to reduce false-positive errors significantly. PMID:28533972

Characterization of the molecular basis of group II intron RNA recognition by CRS1-CRM domains.

PubMed

Keren, Ido; Klipcan, Liron; Bezawork-Geleta, Ayenachew; Kolton, Max; Shaya, Felix; Ostersetzer-Biran, Oren

2008-08-22

CRM (chloroplast RNA splicing and ribosome maturation) is a recently recognized RNA-binding domain of ancient origin that has been retained in eukaryotic genomes only within the plant lineage. Whereas in bacteria CRM domains exist as single domain proteins involved in ribosome maturation, in plants they are found in a family of proteins that contain between one and four repeats. Several members of this family with multiple CRM domains have been shown to be required for the splicing of specific plastidic group II introns. Detailed biochemical analysis of one of these factors in maize, CRS1, demonstrated its high affinity and specific binding to the single group II intron whose splicing it facilitates, the plastid-encoded atpF intron RNA. Through its association with two intronic regions, CRS1 guides the folding of atpF intron RNA into its predicted "catalytically active" form. To understand how multiple CRM domains cooperate to achieve high affinity sequence-specific binding to RNA, we analyzed the RNA binding affinity and specificity associated with each individual CRM domain in CRS1; whereas CRM3 bound tightly to the RNA, CRM1 associated specifically with a unique region found within atpF intron domain I. CRM2, which demonstrated only low binding affinity, also seems to form specific interactions with regions localized to domains I, III, and IV. We further show that CRM domains share structural similarities and RNA binding characteristics with the well known RNA recognition motif domain.

Recombinant human albumin supports single cell cloning of CHO cells in chemically defined media.

PubMed

Zhu, Jiang; Wooh, Jong Wei; Hou, Jeff Jia Cheng; Hughes, Benjamin S; Gray, Peter P; Munro, Trent P

2012-01-01

Biologic drugs, such as monoclonal antibodies, are commonly made using mammalian cells in culture. The cell lines used for manufacturing should ideally be clonal, meaning derived from a single cell, which represents a technically challenging process. Fetal bovine serum is often used to support low cell density cultures, however, from a regulatory perspective, it is preferable to avoid animal-derived components to increase process consistency and reduce the risk of contamination from adventitious agents. Chinese hamster ovary (CHO) cells are the most widely used cell line in industry and a large number of serum-free, protein-free, and fully chemically defined growth media are commercially available, although these media alone do not readily support efficient single cell cloning. In this work, we have developed a simple, fully defined, single-cell cloning media, specifically for CHO cells, using commercially available reagents. Our results show that a 1:1 mixture of CD-CHO™ and DMEM/F12 supplemented with 1.5 g/L of recombinant albumin (Albucult®) supports single cell cloning. This formulation can support recovery of single cells in 43% of cultures compared to 62% in the presence of serum. Copyright © 2012 American Institute of Chemical Engineers (AIChE).

Process of infection with bacteriophage phi chi 174. XL. Viral DNA replication of phi chi 174 mutants blocked in progeny single-stranded DNA synthesis.

PubMed Central

Fukuda, A; Sinsheimer, R L

1976-01-01

Mutation in several different cistrons of bacteriophage phi chi 174 blocks net progeny single-stranded DNA synthesis at the late period of infection (15). For the study of the functions of these cistrons in single-stranded DNA synthesis, asymmetric replication of replicative form DNA was examined at the late period of infection with amber mutants of these cistrons. While the normal, rapid process of asymmetric single-stranded viral DNA synthesis is blocked at the late period of these mutant infections, an asymmetric synthesis of the viral strand of replicative-form DNA is observed in this period, though at a reduced level, together with degradation of prelabeled viral strand. Some intermediate replicative-form molecules were also detected. Asymmetric synthesis of the viral strand of replicative-form DNA at the late period of phi chi infection is completely inhibited in the presence of a low concentration (35mug/ml) of chloramphenicol (which also blocks net single-stranded viral DNA synthesis). These results are discussed in terms of the possible role of the specific viral proteins for normal single-stranded DNA synthesis. PMID:1255871

Optimization and evaluation of single-cell whole-genome multiple displacement amplification.

PubMed

Spits, C; Le Caignec, C; De Rycke, M; Van Haute, L; Van Steirteghem, A; Liebaers, I; Sermon, K

2006-05-01

The scarcity of genomic DNA can be a limiting factor in some fields of genetic research. One of the methods developed to overcome this difficulty is whole genome amplification (WGA). Recently, multiple displacement amplification (MDA) has proved very efficient in the WGA of small DNA samples and pools of cells, the reaction being catalyzed by the phi29 or the Bst DNA polymerases. The aim of the present study was to develop a reliable, efficient, and fast protocol for MDA at the single-cell level. We first compared the efficiency of phi29 and Bst polymerases on DNA samples and single cells. The phi29 polymerase generated accurately, in a short time and from a single cell, sufficient DNA for a large set of tests, whereas the Bst enzyme showed a low efficiency and a high error rate. A single-cell protocol was optimized using the phi29 polymerase and was evaluated on 60 single cells; the DNA obtained DNA was assessed by 22 locus-specific PCRs. This new protocol can be useful for many applications involving minute quantities of starting material, such as forensic DNA analysis, prenatal and preimplantation genetic diagnosis, or cancer research. (c) 2006 Wiley-Liss, Inc.

Prediction of Adult Dyslipidemia Using Genetic and Childhood Clinical Risk Factors: The Cardiovascular Risk in Young Finns Study.

PubMed

Nuotio, Joel; Pitkänen, Niina; Magnussen, Costan G; Buscot, Marie-Jeanne; Venäläinen, Mikko S; Elo, Laura L; Jokinen, Eero; Laitinen, Tomi; Taittonen, Leena; Hutri-Kähönen, Nina; Lyytikäinen, Leo-Pekka; Lehtimäki, Terho; Viikari, Jorma S; Juonala, Markus; Raitakari, Olli T

2017-06-01

Dyslipidemia is a major modifiable risk factor for cardiovascular disease. We examined whether the addition of novel single-nucleotide polymorphisms for blood lipid levels enhances the prediction of adult dyslipidemia in comparison to childhood lipid measures. Two thousand four hundred and twenty-two participants of the Cardiovascular Risk in Young Finns Study who had participated in 2 surveys held during childhood (in 1980 when aged 3-18 years and in 1986) and at least once in a follow-up study in adulthood (2001, 2007, and 2011) were included. We examined whether inclusion of a lipid-specific weighted genetic risk score based on 58 single-nucleotide polymorphisms for low-density lipoprotein cholesterol, 71 single-nucleotide polymorphisms for high-density lipoprotein cholesterol, and 40 single-nucleotide polymorphisms for triglycerides improved the prediction of adult dyslipidemia compared with clinical childhood risk factors. Adjusting for age, sex, body mass index, physical activity, and smoking in childhood, childhood lipid levels, and weighted genetic risk scores were associated with an increased risk of adult dyslipidemia for all lipids. Risk assessment based on 2 childhood lipid measures and the lipid-specific weighted genetic risk scores improved the accuracy of predicting adult dyslipidemia compared with the approach using only childhood lipid measures for low-density lipoprotein cholesterol (area under the receiver-operating characteristic curve 0.806 versus 0.811; P =0.01) and triglycerides (area under the receiver-operating characteristic curve 0.740 versus area under the receiver-operating characteristic curve 0.758; P <0.01). The overall net reclassification improvement and integrated discrimination improvement were significant for all outcomes. The inclusion of weighted genetic risk scores to lipid-screening programs in childhood could modestly improve the identification of those at highest risk of dyslipidemia in adulthood. © 2017 American Heart Association, Inc.

Analgesic effects of treatments for non-specific low back pain: a meta-analysis of placebo-controlled randomized trials.

PubMed

Machado, L A C; Kamper, S J; Herbert, R D; Maher, C G; McAuley, J H

2009-05-01

Estimates of treatment effects reported in placebo-controlled randomized trials are less subject to bias than those estimates provided by other study designs. The objective of this meta-analysis was to estimate the analgesic effects of treatments for non-specific low back pain reported in placebo-controlled randomized trials. Medline, Embase, Cinahl, PsychInfo and Cochrane Central Register of Controlled Trials databases were searched for eligible trials from earliest records to November 2006. Continuous pain outcomes were converted to a common 0-100 scale and pooled using a random effects model. A total of 76 trials reporting on 34 treatments were included. Fifty percent of the investigated treatments had statistically significant effects, but for most the effects were small or moderate: 47% had point estimates of effects of <10 points on the 100-point scale, 38% had point estimates from 10 to 20 points and 15% had point estimates of >20 points. Treatments reported to have large effects (>20 points) had been investigated only in a single trial. This meta-analysis revealed that the analgesic effects of many treatments for non-specific low back pain are small and that they do not differ in populations with acute or chronic symptoms.

Manufacture of patient-specific vascular replicas for endovascular simulation using fast, low-cost method

NASA Astrophysics Data System (ADS)

Kaneko, Naoki; Mashiko, Toshihiro; Ohnishi, Taihei; Ohta, Makoto; Namba, Katsunari; Watanabe, Eiju; Kawai, Kensuke

2016-12-01

Patient-specific vascular replicas are essential to the simulation of endovascular treatment or for vascular research. The inside of silicone replica is required to be smooth for manipulating interventional devices without resistance. In this report, we demonstrate the fabrication of patient-specific silicone vessels with a low-cost desktop 3D printer. We show that the surface of an acrylonitrile butadiene styrene (ABS) model printed by the 3D printer can be smoothed by a single dipping in ABS solvent in a time-dependent manner, where a short dip has less effect on the shape of the model. The vascular mold is coated with transparent silicone and then the ABS mold is dissolved after the silicone is cured. Interventional devices can pass through the inside of the smoothed silicone vessel with lower pushing force compared to the vessel without smoothing. The material cost and time required to fabricate the silicone vessel is about USD $2 and 24 h, which is much lower than the current fabrication methods. This fast and low-cost method offers the possibility of testing strategies before attempting particularly difficult cases, while improving the training of endovascular therapy, enabling the trialing of new devices, and broadening the scope of vascular research.

Advanced aeroservoelastic stabilization techniques for hypersonic flight vehicles

NASA Technical Reports Server (NTRS)

Chan, Samuel Y.; Cheng, Peter Y.; Myers, Thomas T.; Klyde, David H.; Magdaleno, Raymond E.; Mcruer, Duane T.

1992-01-01

Advanced high performance vehicles, including Single-Stage-To-Orbit (SSTO) hypersonic flight vehicles, that are statically unstable, require higher bandwidth flight control systems to compensate for the instability resulting in interactions between the flight control system, the engine/propulsion dynamics, and the low frequency structural modes. Military specifications, such as MIL-F-9490D and MIL-F-87242, tend to limit treatment of structural modes to conventional gain stabilization techniques. The conventional gain stabilization techniques, however, introduce low frequency effective time delays which can be troublesome from a flying qualities standpoint. These time delays can be alleviated by appropriate blending of gain and phase stabilization techniques (referred to as Hybrid Phase Stabilization or HPS) for the low frequency structural modes. The potential of using HPS for compensating structural mode interaction was previously explored. It was shown that effective time delay was significantly reduced with the use of HPS; however, the HPS design was seen to have greater residual response than a conventional gain stablized design. Additional work performed to advance and refine the HPS design procedure, to further develop residual response metrics as a basis for alternative structural stability specifications, and to develop strategies for validating HPS design and specification concepts in manned simulation is presented. Stabilization design sensitivity to structural uncertainties and aircraft-centered requirements are also assessed.

Multiplexed Affinity-Based Separation of Proteins and Cells Using Inertial Microfluidics.

PubMed

Sarkar, Aniruddh; Hou, Han Wei; Mahan, Alison E; Han, Jongyoon; Alter, Galit

2016-03-30

Isolation of low abundance proteins or rare cells from complex mixtures, such as blood, is required for many diagnostic, therapeutic and research applications. Current affinity-based protein or cell separation methods use binary 'bind-elute' separations and are inefficient when applied to the isolation of multiple low-abundance proteins or cell types. We present a method for rapid and multiplexed, yet inexpensive, affinity-based isolation of both proteins and cells, using a size-coded mixture of multiple affinity-capture microbeads and an inertial microfluidic particle sorter device. In a single binding step, different targets-cells or proteins-bind to beads of different sizes, which are then sorted by flowing them through a spiral microfluidic channel. This technique performs continuous-flow, high throughput affinity-separation of milligram-scale protein samples or millions of cells in minutes after binding. We demonstrate the simultaneous isolation of multiple antibodies from serum and multiple cell types from peripheral blood mononuclear cells or whole blood. We use the technique to isolate low abundance antibodies specific to different HIV antigens and rare HIV-specific cells from blood obtained from HIV+ patients.

PCR detection of thermophilic spore-forming bacteria involved in canned food spoilage.

PubMed

Prevost, S; Andre, S; Remize, F

2010-12-01

Thermophilic bacteria that form highly heat-resistant spores constitute an important group of spoilage bacteria of low-acid canned food. A PCR assay was developed in order to rapidly trace these bacteria. Three PCR primer pairs were designed from rRNA gene sequences. These primers were evaluated for the specificity and the sensitivity of detection. Two primer pairs allowed detection at the species level of Geobacillus stearothermophilus and Moorella thermoacetica/thermoautrophica. The other pair allowed group-specific detection of anaerobic thermophilic bacteria of the genera Thermoanaerobacterium, Thermoanaerobacter, Caldanerobium and Caldanaerobacter. After a single enrichment step, these PCR assays allowed the detection of 28 thermophiles from 34 cans of spoiled low-acid food. In addition, 13 ingredients were screened for the presence of these bacteria. This PCR assay serves as a detection method for strains able to spoil low-acid canned food treated at 55°C. It will lead to better reactivity in the canning industry. Raw materials and ingredients might be qualified not only for quantitative spore contamination, but also for qualitative contamination by highly heat-resistant spores.

Quantum dash based single section mode locked lasers for photonic integrated circuits.

PubMed

Joshi, Siddharth; Calò, Cosimo; Chimot, Nicolas; Radziunas, Mindaugas; Arkhipov, Rostislav; Barbet, Sophie; Accard, Alain; Ramdane, Abderrahim; Lelarge, Francois

2014-05-05

We present the first demonstration of an InAs/InP Quantum Dash based single-section frequency comb generator designed for use in photonic integrated circuits (PICs). The laser cavity is closed using a specifically designed Bragg reflector without compromising the mode-locking performance of the self pulsating laser. This enables the integration of single-section mode-locked laser in photonic integrated circuits as on-chip frequency comb generators. We also investigate the relations between cavity modes in such a device and demonstrate how the dispersion of the complex mode frequencies induced by the Bragg grating implies a violation of the equi-distance between the adjacent mode frequencies and, therefore, forbids the locking of the modes in a classical Bragg Device. Finally we integrate such a Bragg Mirror based laser with Semiconductor Optical Amplifier (SOA) to demonstrate the monolithic integration of QDash based low phase noise sources in PICs.

Quantifying clustered DNA damage induction and repair by gel electrophoresis, electronic imaging and number average length analysis

NASA Technical Reports Server (NTRS)

Sutherland, Betsy M.; Georgakilas, Alexandros G.; Bennett, Paula V.; Laval, Jacques; Sutherland, John C.; Gewirtz, A. M. (Principal Investigator)

2003-01-01

Assessing DNA damage induction, repair and consequences of such damages requires measurement of specific DNA lesions by methods that are independent of biological responses to such lesions. Lesions affecting one DNA strand (altered bases, abasic sites, single strand breaks (SSB)) as well as damages affecting both strands (clustered damages, double strand breaks) can be quantified by direct measurement of DNA using gel electrophoresis, gel imaging and number average length analysis. Damage frequencies as low as a few sites per gigabase pair (10(9)bp) can be quantified by this approach in about 50ng of non-radioactive DNA, and single molecule methods may allow such measurements in DNA from single cells. This review presents the theoretical basis, biochemical requirements and practical aspects of this approach, and shows examples of their applications in identification and quantitation of complex clustered damages.

Adaptive Optics System with Deformable Composite Mirror and High Speed, Ultra-Compact Electronics

NASA Astrophysics Data System (ADS)

Chen, Peter C.; Knowles, G. J.; Shea, B. G.

2006-06-01

We report development of a novel adaptive optics system for optical astronomy. Key components are very thin Deformable Mirrors (DM) made of fiber reinforced polymer resins, subminiature PMN-PT actuators, and low power, high bandwidth electronics drive system with compact packaging and minimal wiring. By using specific formulations of fibers, resins, and laminate construction, we are able to fabricate mirror face sheets that are thin (< 2mm), have smooth surfaces and excellent optical shape. The mirrors are not astigmatic and do not develop surface irregularities when cooled. The actuators are small footprint multilayer PMN-PT ceramic devices with large stroke (2- 20 microns), high linearity, low hysteresis, low power, and flat frequency response to >2 KHz. By utilizing QorTek’s proprietary synthetic impendence power supply technology, all the power, control, and signal extraction for many hundreds to 1000s of actuators and sensors can be implemented on a single matrix controller printed circuit board co-mounted with the DM. The matrix controller, in turn requires only a single serial bus interface, thereby obviating the need for massive wiring harnesses. The technology can be scaled up to multi-meter aperture DMs with >100K actuators.