Characterization of the genomic organization of the region bordering the centromere of chromosome V of Podospora anserina by direct sequencing.

PubMed

Silar, Philippe; Barreau, Christian; Debuchy, Robert; Kicka, Sébastien; Turcq, Béatrice; Sainsard-Chanet, Annie; Sellem, Carole H; Billault, Alain; Cattolico, Laurence; Duprat, Simone; Weissenbach, Jean

2003-08-01

A Podospora anserina BAC library of 4800 clones has been constructed in the vector pBHYG allowing direct selection in fungi. Screening of the BAC collection for centromeric sequences of chromosome V allowed the recovery of clones localized on either sides of the centromere, but no BAC clone was found to contain the centromere. Seven BAC clones containing 322,195 and 156,244bp from either sides of the centromeric region were sequenced and annotated. One 5S rRNA gene, 5 tRNA genes, and 163 putative coding sequences (CDS) were identified. Among these, only six CDS seem specific to P. anserina. The gene density in the centromeric region is approximately one gene every 2.8kb. Extrapolation of this gene density to the whole genome of P. anserina suggests that the genome contains about 11,000 genes. Synteny analyses between P. anserina and Neurospora crassa show that co-linearity extends at the most to a few genes, suggesting rapid genome rearrangements between these two species.

Bacterial genomes lacking long-range correlations may not be modeled by low-order Markov chains: the role of mixing statistics and frame shift of neighboring genes.

PubMed

Cocho, Germinal; Miramontes, Pedro; Mansilla, Ricardo; Li, Wentian

2014-12-01

We examine the relationship between exponential correlation functions and Markov models in a bacterial genome in detail. Despite the well known fact that Markov models generate sequences with correlation function that decays exponentially, simply constructed Markov models based on nearest-neighbor dimer (first-order), trimer (second-order), up to hexamer (fifth-order), and treating the DNA sequence as being homogeneous all fail to predict the value of exponential decay rate. Even reading-frame-specific Markov models (both first- and fifth-order) could not explain the fact that the exponential decay is very slow. Starting with the in-phase coding-DNA-sequence (CDS), we investigated correlation within a fixed-codon-position subsequence, and in artificially constructed sequences by packing CDSs with out-of-phase spacers, as well as altering CDS length distribution by imposing an upper limit. From these targeted analyses, we conclude that the correlation in the bacterial genomic sequence is mainly due to a mixing of heterogeneous statistics at different codon positions, and the decay of correlation is due to the possible out-of-phase between neighboring CDSs. There are also small contributions to the correlation from bases at the same codon position, as well as by non-coding sequences. These show that the seemingly simple exponential correlation functions in bacterial genome hide a complexity in correlation structure which is not suitable for a modeling by Markov chain in a homogeneous sequence. Other results include: use of the (absolute value) second largest eigenvalue to represent the 16 correlation functions and the prediction of a 10-11 base periodicity from the hexamer frequencies. Copyright © 2014 Elsevier Ltd. All rights reserved.

A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina

PubMed Central

2010-01-01

Background The development of new microarray technologies makes custom long oligonucleotide arrays affordable for many experimental applications, notably gene expression analyses. Reliable results depend on probe design quality and selection. Probe design strategy should cope with the limited accuracy of de novo gene prediction programs, and annotation up-dating. We present a novel in silico procedure which addresses these issues and includes experimental screening, as an empirical approach is the best strategy to identify optimal probes in the in silico outcome. Findings We used four criteria for in silico probe selection: cross-hybridization, hairpin stability, probe location relative to coding sequence end and intron position. This latter criterion is critical when exon-intron gene structure predictions for intron-rich genes are inaccurate. For each coding sequence (CDS), we selected a sub-set of four probes. These probes were included in a test microarray, which was used to evaluate the hybridization behavior of each probe. The best probe for each CDS was selected according to three experimental criteria: signal-to-noise ratio, signal reproducibility, and representative signal intensities. This procedure was applied for the development of a gene expression Agilent platform for the filamentous fungus Podospora anserina and the selection of a single 60-mer probe for each of the 10,556 P. anserina CDS. Conclusions A reliable gene expression microarray version based on the Agilent 44K platform was developed with four spot replicates of each probe to increase statistical significance of analysis. PMID:20565839

A novel flavivirus detected in two Aedes spp. collected near the demilitarized zone of the Republic of Korea.

PubMed

Korkusol, Achareeya; Takhampunya, Ratree; Hang, Jun; Jarman, Richard G; Tippayachai, Bousaraporn; Kim, Heung-Chul; Chong, Sung-Tae; Davidson, Silas A; Klein, Terry A

2017-05-01

Flaviviruses comprise a large and diverse group of positive-stranded RNA viruses, including tick-, mosquito- and unknown-vector-borne flaviviruses. A novel flavivirus was detected in pools of Aedes vexans nipponii (n=1) and Aedes esoensis (n=3) collected in 2012 and 2013 near the demilitarized zone (DMZ), Republic of Korea (ROK). Phylogenetic analyses of the NS5, E gene and complete polyprotein coding sequence (CDS) showed that the novel virus fell within the Aedes-borne flaviviruses (ABFVs), with nucleotide identity ranging from 57.8-75.1 %, 46.1-74.2 % and 51.1-76.2 %, respectively. While the novel ABFV was distant from other flaviviruses within the group, it formed a clade with Ilomantsi virus (ILOV). Sequence alignments of the partial NS5 gene, full-length E gene and polyprotein CDS between the novel virus and ILOV showed approximately 76.2 % nucleotide identity and 90 % amino acid identity, respectively. The ABFV identified in Aedes mosquitoes from the ROK is a novel ABFV based on the sequence analyses and is designated as Panmunjeom flavivirus (PANFV).

Transcriptome Analysis and Comparison of Marmota monax and Marmota himalayana.

PubMed

Liu, Yanan; Wang, Baoju; Wang, Lu; Vikash, Vikash; Wang, Qin; Roggendorf, Michael; Lu, Mengji; Yang, Dongliang; Liu, Jia

2016-01-01

The Eastern woodchuck (Marmota monax) is a classical animal model for studying hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC) in humans. Recently, we found that Marmota himalayana, an Asian animal species closely related to Marmota monax, is susceptible to woodchuck hepatitis virus (WHV) infection and can be used as a new mammalian model for HBV infection. However, the lack of genomic sequence information of both Marmota models strongly limited their application breadth and depth. To address this major obstacle of the Marmota models, we utilized Illumina RNA-Seq technology to sequence the cDNA libraries of liver and spleen samples of two Marmota monax and four Marmota himalayana. In total, over 13 billion nucleotide bases were sequenced and approximately 1.5 billion clean reads were obtained. Following assembly, 106,496 consensus sequences of Marmota monax and 78,483 consensus sequences of Marmota himalayana were detected. For functional annotation, in total 73,603 Unigenes of Marmota monax and 78,483 Unigenes of Marmota himalayana were identified using different databases (NR, NT, Swiss-Prot, KEGG, COG, GO). The Unigenes were aligned by blastx to protein databases to decide the coding DNA sequences (CDS) and in total 41,247 CDS of Marmota monax and 34,033 CDS of Marmota himalayana were predicted. The single nucleotide polymorphisms (SNPs) and the simple sequence repeats (SSRs) were also analyzed for all Unigenes obtained. Moreover, a large-scale transcriptome comparison was performed and revealed a high similarity in transcriptome sequences between the two marmota species. Our study provides an extensive amount of novel sequence information for Marmota monax and Marmota himalayana. This information may serve as a valuable genomics resource for further molecular, developmental and comparative evolutionary studies, as well as for the identification and characterization of functional genes that are involved in WHV infection and HCC development in the woodchuck model.

Transcriptome Analysis and Comparison of Marmota monax and Marmota himalayana

PubMed Central

Wang, Lu; Vikash, Vikash; Wang, Qin; Roggendorf, Michael; Lu, Mengji; Yang, Dongliang; Liu, Jia

2016-01-01

The Eastern woodchuck (Marmota monax) is a classical animal model for studying hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC) in humans. Recently, we found that Marmota himalayana, an Asian animal species closely related to Marmota monax, is susceptible to woodchuck hepatitis virus (WHV) infection and can be used as a new mammalian model for HBV infection. However, the lack of genomic sequence information of both Marmota models strongly limited their application breadth and depth. To address this major obstacle of the Marmota models, we utilized Illumina RNA-Seq technology to sequence the cDNA libraries of liver and spleen samples of two Marmota monax and four Marmota himalayana. In total, over 13 billion nucleotide bases were sequenced and approximately 1.5 billion clean reads were obtained. Following assembly, 106,496 consensus sequences of Marmota monax and 78,483 consensus sequences of Marmota himalayana were detected. For functional annotation, in total 73,603 Unigenes of Marmota monax and 78,483 Unigenes of Marmota himalayana were identified using different databases (NR, NT, Swiss-Prot, KEGG, COG, GO). The Unigenes were aligned by blastx to protein databases to decide the coding DNA sequences (CDS) and in total 41,247 CDS of Marmota monax and 34,033 CDS of Marmota himalayana were predicted. The single nucleotide polymorphisms (SNPs) and the simple sequence repeats (SSRs) were also analyzed for all Unigenes obtained. Moreover, a large-scale transcriptome comparison was performed and revealed a high similarity in transcriptome sequences between the two marmota species. Our study provides an extensive amount of novel sequence information for Marmota monax and Marmota himalayana. This information may serve as a valuable genomics resource for further molecular, developmental and comparative evolutionary studies, as well as for the identification and characterization of functional genes that are involved in WHV infection and HCC development in the woodchuck model. PMID:27806133

Sequencing and Characterization of Novel PII Signaling Protein Gene in Microalga Haematococcus pluvialis.

PubMed

Ma, Ruijuan; Li, Yan; Lu, Yinghua

2017-10-11

The PII signaling protein is a key protein for controlling nitrogen assimilatory reactions in most organisms, but little information is reported on PII proteins of green microalga Haematococcus pluvialis . Since H. pluvialis cells can produce a large amount of astaxanthin upon nitrogen starvation, its PII protein may represent an important factor on elevated production of Haematococcus astaxanthin. This study identified and isolated the coding gene (Hp GLB1 ) from this microalga. The full-length of Hp GLB1 was 1222 bp, including 621 bp coding sequence (CDS), 103 bp 5' untranslated region (5' UTR), and 498 bp 3' untranslated region (3' UTR). The CDS could encode a protein with 206 amino acids (HpPII). Its calculated molecular weight (Mw) was 22.4 kDa and the theoretical isoelectric point was 9.53. When H. pluvialis cells were exposed to nitrogen starvation, the Hp GLB1 expression was increased 2.46 times in 48 h, concomitant with the raise of astaxanthin content. This study also used phylogenetic analysis to prove that HpPII was homogeneous to the PII proteins of other green microalgae. The results formed a fundamental basis for the future study on HpPII, for its potential physiological function in Haematococcus astaxanthin biosysthesis.

Staufen1 senses overall transcript secondary structure to regulate translation

PubMed Central

Ricci, Emiliano P; Kucukural, Alper; Cenik, Can; Mercier, Blandine C; Singh, Guramrit; Heyer, Erin E; Ashar-Patel, Ami; Peng, Lingtao; Moore, Melissa J

2015-01-01

Human Staufen1 (Stau1) is a double-stranded RNA (dsRNA)-binding protein implicated in multiple post-transcriptional gene-regulatory processes. Here we combined RNA immunoprecipitation in tandem (RIPiT) with RNase footprinting, formaldehyde cross-linking, sonication-mediated RNA fragmentation and deep sequencing to map Staufen1-binding sites transcriptome wide. We find that Stau1 binds complex secondary structures containing multiple short helices, many of which are formed by inverted Alu elements in annotated 3′ untranslated regions (UTRs) or in ‘strongly distal’ 3′ UTRs. Stau1 also interacts with actively translating ribosomes and with mRNA coding sequences (CDSs) and 3′ UTRs in proportion to their GC content and propensity to form internal secondary structure. On mRNAs with high CDS GC content, higher Stau1 levels lead to greater ribosome densities, thus suggesting a general role for Stau1 in modulating translation elongation through structured CDS regions. Our results also indicate that Stau1 regulates translation of transcription-regulatory proteins. PMID:24336223

Transcriptome-Derived Tetranucleotide Microsatellites and Their Associated Genes from the Giant Panda (Ailuropoda melanoleuca).

PubMed

Song, Xuhao; Shen, Fujun; Huang, Jie; Huang, Yan; Du, Lianming; Wang, Chengdong; Fan, Zhenxin; Hou, Rong; Yue, Bisong; Zhang, Xiuyue

2016-09-01

Recently, an increasing number of microsatellites or simple sequence repeats (SSRs) have been found and characterized from transcriptomes. Such SSRs can be employed as putative functional markers to easily tag corresponding genes, which play an important role in biomedical studies and genetic analysis. However, the transcriptome-derived SSRs for giant panda (Ailuropoda melanoleuca) are not yet available. In this work, we identified and characterized 20 tetranucleotide microsatellite loci from a transcript database generated from the blood of giant panda. Furthermore, we assigned their predicted transcriptome locations: 16 loci were assigned to untranslated regions (UTRs) and 4 loci were assigned to coding regions (CDSs). Gene identities of 14 transcripts contained corresponding microsatellites were determined, which provide useful information to study the potential contribution of SSRs to gene regulation in giant panda. The polymorphic information content (PIC) values ranged from 0.293 to 0.789 with an average of 0.603 for the 16 UTRs-derived SSRs. Interestingly, 4 CDS-derived microsatellites developed in our study were also polymorphic, and the instability of these 4 CDS-derived SSRs was further validated by re-genotyping and sequencing. The genes containing these 4 CDS-derived SSRs were embedded with various types of repeat motifs. The interaction of all the length-changing SSRs might provide a way against coding region frameshift caused by microsatellite instability. We hope these newly gene-associated biomarkers will pave the way for genetic and biomedical studies for giant panda in the future. In sum, this set of transcriptome-derived markers complements the genetic resources available for giant panda. © The American Genetic Association. 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Impact of the HIV-1 genetic background and HIV-1 population size on the evolution of raltegravir resistance.

PubMed

Fun, Axel; Leitner, Thomas; Vandekerckhove, Linos; Däumer, Martin; Thielen, Alexander; Buchholz, Bernd; Hoepelman, Andy I M; Gisolf, Elizabeth H; Schipper, Pauline J; Wensing, Annemarie M J; Nijhuis, Monique

2018-01-05

Emergence of resistance against integrase inhibitor raltegravir in human immunodeficiency virus type 1 (HIV-1) patients is generally associated with selection of one of three signature mutations: Y143C/R, Q148K/H/R or N155H, representing three distinct resistance pathways. The mechanisms that drive selection of a specific pathway are still poorly understood. We investigated the impact of the HIV-1 genetic background and population dynamics on the emergence of raltegravir resistance. Using deep sequencing we analyzed the integrase coding sequence (CDS) in longitudinal samples from five patients who initiated raltegravir plus optimized background therapy at viral loads > 5000 copies/ml. To investigate the role of the HIV-1 genetic background we created recombinant viruses containing the viral integrase coding region from pre-raltegravir samples from two patients in whom raltegravir resistance developed through different pathways. The in vitro selections performed with these recombinant viruses were designed to mimic natural population bottlenecks. Deep sequencing analysis of the viral integrase CDS revealed that the virological response to raltegravir containing therapy inversely correlated with the relative amount of unique sequence variants that emerged suggesting diversifying selection during drug pressure. In 4/5 patients multiple signature mutations representing different resistance pathways were observed. Interestingly, the resistant population can consist of a single resistant variant that completely dominates the population but also of multiple variants from different resistance pathways that coexist in the viral population. We also found evidence for increased diversification after stronger bottlenecks. In vitro selections with low viral titers, mimicking population bottlenecks, revealed that both recombinant viruses and HXB2 reference virus were able to select mutations from different resistance pathways, although typically only one resistance pathway emerged in each individual culture. The generation of a specific raltegravir resistant variant is not predisposed in the genetic background of the viral integrase CDS. Typically, in the early phases of therapy failure the sequence space is explored and multiple resistance pathways emerge and then compete for dominance which frequently results in a switch of the dominant population over time towards the fittest variant or even multiple variants of similar fitness that can coexist in the viral population.

Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes

PubMed Central

Yasui, Yasuo; Hirakawa, Hideki; Ueno, Mariko; Matsui, Katsuhiro; Katsube-Tanaka, Tomoyuki; Yang, Soo Jung; Aii, Jotaro; Sato, Shingo; Mori, Masashi

2016-01-01

Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits. PMID:27037832

MicroRNA-128 targets myostatin at coding domain sequence to regulate myoblasts in skeletal muscle development.

PubMed

Shi, Lei; Zhou, Bo; Li, Pinghua; Schinckel, Allan P; Liang, Tingting; Wang, Han; Li, Huizhi; Fu, Lingling; Chu, Qingpo; Huang, Ruihua

2015-09-01

MicroRNAs (miRNAs or miRs) play a critical role in skeletal muscle development. In a previous study we observed that miR-128 was highly expressed in skeletal muscle. However, its function in regulating skeletal muscle development is not clear. Our hypothesis was that miR-128 is involved in the regulation of the proliferation and differentiation of skeletal myoblasts. In this study, through bioinformatics analyses, we demonstrate that miR-128 specifically targeted mRNA of myostatin (MSTN), a critical inhibitor of skeletal myogenesis, at coding domain sequence (CDS) region, resulting in down-regulating of myostatin post-transcription. Overexpression of miR-128 inhibited proliferation of mouse C2C12 myoblast cells but promoted myotube formation; whereas knockdown of miR-128 had completely opposite effects. In addition, ectopic miR-128 regulated the expression of myogenic factor 5 (Myf5), myogenin (MyoG), paired box (Pax) 3 and 7. Furthermore, an inverse relationship was found between the expression of miR-128 and MSTN protein expression in vivo and in vitro. Taken together, these results reveal that there is a novel pathway in skeletal muscle development in which miR-128 regulates myostatin at CDS region to inhibit proliferation but promote differentiation of myoblast cells. Copyright © 2015 Elsevier Inc. All rights reserved.

OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals.

PubMed

Douzery, Emmanuel J P; Scornavacca, Celine; Romiguier, Jonathan; Belkhir, Khalid; Galtier, Nicolas; Delsuc, Frédéric; Ranwez, Vincent

2014-07-01

Comparative genomic studies extensively rely on alignments of orthologous sequences. Yet, selecting, gathering, and aligning orthologous exons and protein-coding sequences (CDS) that are relevant for a given evolutionary analysis can be a difficult and time-consuming task. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of orthologous genes in mammalian genomes using a phylogenetic framework. Since its first release in 2007, OrthoMaM has regularly evolved, not only to include newly available genomes but also to incorporate up-to-date software in its analytic pipeline. This eighth release integrates the 40 complete mammalian genomes available in Ensembl v73 and provides alignments, phylogenies, evolutionary descriptor information, and functional annotations for 13,404 single-copy orthologous CDS and 6,953 long exons. The graphical interface allows to easily explore OrthoMaM to identify markers with specific characteristics (e.g., taxa availability, alignment size, %G+C, evolutionary rate, chromosome location). It hence provides an efficient solution to sample preprocessed markers adapted to user-specific needs. OrthoMaM has proven to be a valuable resource for researchers interested in mammalian phylogenomics, evolutionary genomics, and has served as a source of benchmark empirical data sets in several methodological studies. OrthoMaM is available for browsing, query and complete or filtered downloads at http://www.orthomam.univ-montp2.fr/. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A combined paging alert and web-based instrument alters clinician behavior and shortens hospital length of stay in acute pancreatitis.

PubMed

Dimagno, Matthew J; Wamsteker, Erik-Jan; Rizk, Rafat S; Spaete, Joshua P; Gupta, Suraj; Sahay, Tanya; Costanzo, Jeffrey; Inadomi, John M; Napolitano, Lena M; Hyzy, Robert C; Desmond, Jeff S

2014-03-01

There are many published clinical guidelines for acute pancreatitis (AP). Implementation of these recommendations is variable. We hypothesized that a clinical decision support (CDS) tool would change clinician behavior and shorten hospital length of stay (LOS). Observational study, entitled, The AP Early Response (TAPER) Project. Tertiary center emergency department (ED) and hospital. Two consecutive samplings of patients having ICD-9 code (577.0) for AP were generated from the emergency department (ED) or hospital admissions. Diagnosis of AP was based on conventional Atlanta criteria. The Pre-TAPER-CDS-Tool group (5/30/06-6/22/07) had 110 patients presenting to the ED with AP per 976 ICD-9 (577.0) codes and the Post-TAPER-CDS-Tool group (5/30/06-6/22/07) had 113 per 907 ICD-9 codes (7/14/10-5/5/11). The TAPER-CDS-Tool, developed 12/2008-7/14/2010, is a combined early, automated paging-alert system, which text pages ED clinicians about a patient with AP and an intuitive web-based point-of-care instrument, consisting of seven early management recommendations. The pre- vs. post-TAPER-CDS-Tool groups had similar baseline characteristics. The post-TAPER-CDS-Tool group met two management goals more frequently than the pre-TAPER-CDS-Tool group: risk stratification (P<0.0001) and intravenous fluids >6L/1st 0-24 h (P=0.0003). Mean (s.d.) hospital LOS was significantly shorter in the post-TAPER-CDS-Tool group (4.6 (3.1) vs. 6.7 (7.0) days, P=0.0126). Multivariate analysis identified four independent variables for hospital LOS: the TAPER-CDS-Tool associated with shorter LOS (P=0.0049) and three variables associated with longer LOS: Japanese severity score (P=0.0361), persistent organ failure (P=0.0088), and local pancreatic complications (<0.0001). The TAPER-CDS-Tool is associated with changed clinician behavior and shortened hospital LOS, which has significant financial implications.

Sequence characterization of S100A8 gene reveals structural differences of protein and transcriptional factor binding sites in water buffalo and yak.

PubMed

Kathiravan, P; Goyal, S; Kataria, R S; Mishra, B P; Jayakumar, S; Joshi, B K

2011-01-01

The present study was undertaken to characterize the structure of S100A8 gene and its promoter in water buffalo and yak. Sequence data of 2.067 kb, 2.071 kb, and 2.052 kb with respect to complete S100A8 gene including 5' flanking region was generated in river buffalo, swamp buffalo, and yak, respectively. BLAST analysis of coding DNA sequences (CDS) of S100A8 gene revealed 95% homology of buffalo sequence with cattle, 85% with pig and horse, 83% with dog, 72-73% with murines, and around 79% with primates and humans. Phylogenetic analysis of predicted CDS revealed distinct clustering of murines, primates, and domestic animals with bovines and bubalines forming a subcluster among farm animals. In silico translation of predicted CDS revealed a sequence of 89 amino acids with 7 amino acid changes between cattle and buffalo and 2 changes between cattle and yak. The search for Pfam family revealed the N-terminal calcium binding domain and the noncanonical EF hand domain in the carboxy terminus, with more variations being observed in the N-terminal domain among different species. Two amino acid changes observed in carboxy terminal EF hand domain resulted in altered secondary structure of yak S100A8 protein. Analysis of S100A8 gene promoter revealed 14 putative motifs for transcriptional factor binding sites. Two putative motifs viz. C/EBP and v-Myb were found to be absent in swamp buffalo as compared to river buffalo and cattle. Differences in the structure of S100A8 protein and the transcriptional factor binding sites identified in the present study need to be analyzed further for their functional significance in yak and swamp buffalo respectively. Copyright © Taylor & Francis Group, LLC

The complete CDS of the prion protein (PRNP) gene of African lion (Panthera leo).

PubMed

Maj, Andrzej; Spellman, Garth M; Sarver, Shane K

2008-04-01

We provide the complete PRNP CDS sequence for the African lion, which is different from the previously published sequence and more similar to other carnivore sequences. The newly obtained prion protein sequence differs from the domestic cat sequence at three amino acid positions and contains only four octapeptide repeats. We recommend that this sequence be used as the reference sequence for future studies of the PRNP gene for this species.

GC-rich coding sequences reduce transposon-like, small RNA-mediated transgene silencing.

PubMed

Sidorenko, Lyudmila V; Lee, Tzuu-Fen; Woosley, Aaron; Moskal, William A; Bevan, Scott A; Merlo, P Ann Owens; Walsh, Terence A; Wang, Xiujuan; Weaver, Staci; Glancy, Todd P; Wang, PoHao; Yang, Xiaozeng; Sriram, Shreedharan; Meyers, Blake C

2017-11-01

The molecular basis of transgene susceptibility to silencing is poorly characterized in plants; thus, we evaluated several transgene design parameters as means to reduce heritable transgene silencing. Analyses of Arabidopsis plants with transgenes encoding a microalgal polyunsaturated fatty acid (PUFA) synthase revealed that small RNA (sRNA)-mediated silencing, combined with the use of repetitive regulatory elements, led to aggressive transposon-like silencing of canola-biased PUFA synthase transgenes. Diversifying regulatory sequences and using native microalgal coding sequences (CDSs) with higher GC content improved transgene expression and resulted in a remarkable trans-generational stability via reduced accumulation of sRNAs and DNA methylation. Further experiments in maize with transgenes individually expressing three crystal (Cry) proteins from Bacillus thuringiensis (Bt) tested the impact of CDS recoding using different codon bias tables. Transgenes with higher GC content exhibited increased transcript and protein accumulation. These results demonstrate that the sequence composition of transgene CDSs can directly impact silencing, providing design strategies for increasing transgene expression levels and reducing risks of heritable loss of transgene expression.

Analysis of alterative cleavage and polyadenylation by 3′ region extraction and deep sequencing

PubMed Central

Hoque, Mainul; Ji, Zhe; Zheng, Dinghai; Luo, Wenting; Li, Wencheng; You, Bei; Park, Ji Yeon; Yehia, Ghassan; Tian, Bin

2012-01-01

Alternative cleavage and polyadenylation (APA) leads to mRNA isoforms with different coding sequences (CDS) and/or 3′ untranslated regions (3′UTRs). Using 3′ Region Extraction And Deep Sequencing (3′READS), a method which addresses the internal priming and oligo(A) tail issues that commonly plague polyA site (pA) identification, we comprehensively mapped pAs in the mouse genome, thoroughly annotating 3′ ends of genes and revealing over five thousand pAs (~8% of total) flanked by A-rich sequences, which have hitherto been overlooked. About 79% of mRNA genes and 66% of long non-coding RNA (lncRNA) genes have APA; but these two gene types have distinct usage patterns for pAs in introns and upstream exons. Promoter-distal pAs become relatively more abundant during embryonic development and cell differentiation, a trend affecting pAs in both 3′-most exons and upstream regions. Upregulated isoforms generally have stronger pAs, suggesting global modulation of the 3′ end processing activity in development and differentiation. PMID:23241633

Recombinant yeast as a functional tool for understanding bitterness and cucurbitacin biosynthesis in watermelon (Citrullus spp.).

PubMed

Davidovich-Rikanati, Rachel; Shalev, Lior; Baranes, Nadine; Meir, Ayala; Itkin, Maxim; Cohen, Shahar; Zimbler, Kobi; Portnoy, Vitaly; Ebizuka, Yutaka; Shibuya, Masaaki; Burger, Yosef; Katzir, Nurit; Schaffer, Arthur A; Lewinsohn, Efraim; Tadmor, Ya'akov

2015-01-01

Cucurbitacins are a group of bitter-tasting oxygenated tetracyclic triterpenes that are produced in the family Cucurbitaceae and other plant families. The natural roles of cucurbitacins in plants are probably related to defence against pathogens and pests. Cucurbitadienol, a triterpene synthesized from oxidosqualene, is the first committed precursor to cucurbitacins produced by a specialized oxidosqualene cyclase termed cucurbitadienol synthase. We explored cucurbitacin accumulation in watermelon in relation to bitterness. Our findings show that cucurbitacins are accumulated in bitter-tasting watermelon, Citrullus lanatus var. citroides, as well as in their wild ancestor, C. colocynthis, but not in non-bitter commercial cultivars of sweet watermelon (C. lanatus var. lanatus). Molecular analysis of genes expressed in the roots of several watermelon accessions led to the isolation of three sequences (CcCDS1, CcCDS2 and ClCDS1), all displaying high similarity to the pumpkin CpCPQ, encoding a protein previously shown to possess cucurbitadienol synthase activity. We utilized the Saccharomyces cerevisiae strain BY4743, heterozygous for lanosterol synthase, to probe for possible encoded cucurbitadienol synthase activity of the expressed watermelon sequences. Functional expression of the two sequences isolated from C. colocynthis (CcCDS1 and CcCDS2) in yeast revealed that only CcCDS2 possessed cucurbitadienol synthase activity, while CcCDS1 did not display cucurbitadienol synthase activity in recombinant yeast. ClCDS1 isolated from C. lanatus var. lanatus is almost identical to CcCDS1. Our results imply that CcCDS2 plays a role in imparting bitterness to watermelon. Yeast has been an excellent diagnostic tool to determine the first committed step of cucurbitacin biosynthesis in watermelon. Copyright © 2014 John Wiley & Sons, Ltd.

Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes.

PubMed

Yasui, Yasuo; Hirakawa, Hideki; Ueno, Mariko; Matsui, Katsuhiro; Katsube-Tanaka, Tomoyuki; Yang, Soo Jung; Aii, Jotaro; Sato, Shingo; Mori, Masashi

2016-06-01

Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

PubMed

Damkliang, Kasikrit; Tandayya, Pichaya; Sangket, Unitsa; Pasomsub, Ekawat

2016-11-28

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. All local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.

PubMed

Damkliang, Kasikrit; Tandayya, Pichaya; Sangket, Unitsa; Pasomsub, Ekawat

2016-03-01

At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. The workflow supports 1,000 to 20,000 numbers in bootstrapping replication. The workflow performs the tree inferring such as Parsimony (PARS), Distance Matrix - Neighbor Joining (DIST-NJ), and Maximum Likelihood (ML) algorithms of EMBOSS PHYLIPNEW package based on our proposed Multiple Sequence Alignment (MSA) similarity score. The local web services are implemented and deployed into two types using the Soaplab2 and Apache Axis2 deployment. There are SOAP and Java Web Service (JWS) providing WSDL endpoints to Taverna Workbench, a workflow manager. The workflow has been validated, the performance has been measured, and its results have been verified. Our workflow's execution time is less than ten minutes for inferring a tree with 10,000 replicates of the bootstrapping numbers. This paper proposes a new integrated automatic workflow which will be beneficial to the bioinformaticians with an intermediate level of knowledge and experiences. The all local services have been deployed at our portal http://bioservices.sci.psu.ac.th.

Anopheles gambiae genome reannotation through synthesis of ab initio and comparative gene prediction algorithms

PubMed Central

Li, Jun; Riehle, Michelle M; Zhang, Yan; Xu, Jiannong; Oduol, Frederick; Gomez, Shawn M; Eiglmeier, Karin; Ueberheide, Beatrix M; Shabanowitz, Jeffrey; Hunt, Donald F; Ribeiro, José MC; Vernick, Kenneth D

2006-01-01

Background Complete genome annotation is a necessary tool as Anopheles gambiae researchers probe the biology of this potent malaria vector. Results We reannotate the A. gambiae genome by synthesizing comparative and ab initio sets of predicted coding sequences (CDSs) into a single set using an exon-gene-union algorithm followed by an open-reading-frame-selection algorithm. The reannotation predicts 20,970 CDSs supported by at least two lines of evidence, and it lowers the proportion of CDSs lacking start and/or stop codons to only approximately 4%. The reannotated CDS set includes a set of 4,681 novel CDSs not represented in the Ensembl annotation but with EST support, and another set of 4,031 Ensembl-supported genes that undergo major structural and, therefore, probably functional changes in the reannotated set. The quality and accuracy of the reannotation was assessed by comparison with end sequences from 20,249 full-length cDNA clones, and evaluation of mass spectrometry peptide hit rates from an A. gambiae shotgun proteomic dataset confirms that the reannotated CDSs offer a high quality protein database for proteomics. We provide a functional proteomics annotation, ReAnoXcel, obtained by analysis of the new CDSs through the AnoXcel pipeline, which allows functional comparisons of the CDS sets within the same bioinformatic platform. CDS data are available for download. Conclusion Comprehensive A. gambiae genome reannotation is achieved through a combination of comparative and ab initio gene prediction algorithms. PMID:16569258

Front air bag nondeployments in frontal crashes fatal to drivers or right-front passengers.

PubMed

Braver, Elisa R; McCartt, Anne T; Sherwood, Christopher P; Zuby, David S; Blanar, Laura; Scerbo, Marge

2010-04-01

Public concern has arisen about the reliability of front air bags because Fatality Analysis Reporting System (FARS) data indicate many nondeployed air bags in fatal frontal crashes. However, the accuracy of air bag deployment, the variable in question, is uncertain. This study aimed to provide more certain estimates of nondeployment incidence in fatal frontal crashes. Fatally injured passenger vehicle drivers and right-front passengers in frontal crashes were identified in two U.S. databases for calendar years 1998-2006 and model years 1994-2006: FARS, a census of police-reported fatal crashes on public roads, and National Automotive Sampling System/Crashworthiness Data System (NASS/CDS), a probability sample of tow-away crashes. NASS/CDS contains subsets of fatal crashes in FARS and collects detailed data using crash investigators. Front air bag deployment coding for front-seat occupant fatalities was compared in FARS and NASS/CDS, and case reviews were conducted. Among FARS frontal deaths with available deployment status (N = 43,169), front air bags were coded as not deployed for 18 percent of front occupants. In comparison, NASS/CDS (N = 628) reported 9 percent (weighted estimate) nondeployment among front occupants killed. Among crashes common to both databases, NASS/CDS reported deployments for 45 percent of front occupant deaths for which FARS had coded nondeployments. Detailed case reviews of NASS/CDS crashes indicated highly accurate coding for deployment status. Based on this case review, 8 percent (weighted estimate) of front occupant deaths in frontal crashes appeared to involve air bag nondeployments; 1-2 percent of front occupant deaths represented potential system failures where deployments would have been expected. Air bag deployments appeared unwarranted in most nondeployments based on crash characteristics. FARS data overstate the magnitude of the problem of air bag deployment failures; steps should be taken to improve coding. There are inherent uncertainties in judgments about whether or not air bags would be expected to deploy in some crashes. Continued monitoring of air bag performance is warranted.

Xuhuai goat H-FABP gene clone, subcellular localization of expression products and the preparation of transgenic mice.

PubMed

Yin, Yan-hui; Li, Bi-chun; Wei, Guang-hui; Zhu, Cai-ye; Li, Wei; Zhang, Ya-ni; Du, Li-xin; Cao, Wen-guang

2012-05-01

The aim of this study was to clone the heart-type fatty acid binding protein (H-FABP) gene of Xuhuai goat, to explore it bioinformatically, and analyze the subcellular localization using enhanced green fluorescent protein (EGFP). The results showed that the coding sequence (CDS) length of Xuhuai goat H-FABP gene was 402 bp, encoding 133 amino acids (GenBank accession number AY466498.1). The H-FABP cDNA coding sequence was compared with the corresponding region of human, chicken, brown rat, cow, wild boar, donkey, and zebrafish. The similarity were 89%, 76%, 85%, 84%, 93%, 91%, 70%, respectively. For the corresponding amino acid sequences, the similarity were 90%, 79%, 88%, 97%, 95%, 94%, 72%, respectively. This study did not find the signal peptide region in the H-FABP protein; it revealed that H-FABP protein might be a nonsecreted protein. H-FABP expression was detected in vitro by reverse transcription-polymerase chain reaction (RT-PCR), and the EGFP-H-FABP fusion protein was localized to the cytoplasm. The gene could also be transiently and permanently expressed in mice.

Clinical decision support for whole genome sequence information leveraging a service-oriented architecture: a prototype.

PubMed

Welch, Brandon M; Rodriguez-Loya, Salvador; Eilbeck, Karen; Kawamoto, Kensaku

2014-01-01

Whole genome sequence (WGS) information could soon be routinely available to clinicians to support the personalized care of their patients. At such time, clinical decision support (CDS) integrated into the clinical workflow will likely be necessary to support genome-guided clinical care. Nevertheless, developing CDS capabilities for WGS information presents many unique challenges that need to be overcome for such approaches to be effective. In this manuscript, we describe the development of a prototype CDS system that is capable of providing genome-guided CDS at the point of care and within the clinical workflow. To demonstrate the functionality of this prototype, we implemented a clinical scenario of a hypothetical patient at high risk for Lynch Syndrome based on his genomic information. We demonstrate that this system can effectively use service-oriented architecture principles and standards-based components to deliver point of care CDS for WGS information in real-time.

A proposed clinical decision support architecture capable of supporting whole genome sequence information.

PubMed

Welch, Brandon M; Loya, Salvador Rodriguez; Eilbeck, Karen; Kawamoto, Kensaku

2014-04-04

Whole genome sequence (WGS) information may soon be widely available to help clinicians personalize the care and treatment of patients. However, considerable barriers exist, which may hinder the effective utilization of WGS information in a routine clinical care setting. Clinical decision support (CDS) offers a potential solution to overcome such barriers and to facilitate the effective use of WGS information in the clinic. However, genomic information is complex and will require significant considerations when developing CDS capabilities. As such, this manuscript lays out a conceptual framework for a CDS architecture designed to deliver WGS-guided CDS within the clinical workflow. To handle the complexity and breadth of WGS information, the proposed CDS framework leverages service-oriented capabilities and orchestrates the interaction of several independently-managed components. These independently-managed components include the genome variant knowledge base, the genome database, the CDS knowledge base, a CDS controller and the electronic health record (EHR). A key design feature is that genome data can be stored separately from the EHR. This paper describes in detail: (1) each component of the architecture; (2) the interaction of the components; and (3) how the architecture attempts to overcome the challenges associated with WGS information. We believe that service-oriented CDS capabilities will be essential to using WGS information for personalized medicine.

A Proposed Clinical Decision Support Architecture Capable of Supporting Whole Genome Sequence Information

PubMed Central

Welch, Brandon M.; Rodriguez Loya, Salvador; Eilbeck, Karen; Kawamoto, Kensaku

2014-01-01

Whole genome sequence (WGS) information may soon be widely available to help clinicians personalize the care and treatment of patients. However, considerable barriers exist, which may hinder the effective utilization of WGS information in a routine clinical care setting. Clinical decision support (CDS) offers a potential solution to overcome such barriers and to facilitate the effective use of WGS information in the clinic. However, genomic information is complex and will require significant considerations when developing CDS capabilities. As such, this manuscript lays out a conceptual framework for a CDS architecture designed to deliver WGS-guided CDS within the clinical workflow. To handle the complexity and breadth of WGS information, the proposed CDS framework leverages service-oriented capabilities and orchestrates the interaction of several independently-managed components. These independently-managed components include the genome variant knowledge base, the genome database, the CDS knowledge base, a CDS controller and the electronic health record (EHR). A key design feature is that genome data can be stored separately from the EHR. This paper describes in detail: (1) each component of the architecture; (2) the interaction of the components; and (3) how the architecture attempts to overcome the challenges associated with WGS information. We believe that service-oriented CDS capabilities will be essential to using WGS information for personalized medicine. PMID:25411644

De novo RNA-seq and functional annotation of Ornithonyssus bacoti.

PubMed

Niu, DongLing; Wang, RuiLing; Zhao, YaE; Yang, Rui; Hu, Li

2018-06-01

Ornithonyssus bacoti (Hirst) (Acari: Macronyssidae) is a vector and reservoir of pathogens causing serious infectious diseases, such as epidemic hemorrhagic fever, endemic typhus, tularemia, and leptospirosis. Its genome and transcriptome data are lacking in public databases. In this study, total RNA was extracted from live O. bacoti to conduct RNA-seq, functional annotation, coding domain sequence (CDS) prediction and simple sequence repeats (SSRs) detection. The results showed that 65.8 million clean reads were generated and assembled into 72,185 unigenes, of which 49.4% were annotated by seven functional databases. 23,121 unigenes were annotated and assigned to 457 species by non-redundant protein sequence database. The BLAST top-two hit species were Metaseiulus occidentalis and Ixodes scapularis. The procedure detected 12,426 SSRs, of which tri- and di-nucleotides were the most abundant types and the representative motifs were AAT/ATT and AC/GT. 26,936 CDS were predicted with a mean length of 711 bp. 87 unigenes of 30 functional genes, which are usually involved in stress responses, drug resistance, movement, metabolism and allergy, were further identified by bioinformatics methods. The unigenes putatively encoding cytochrome P450 proteins were further analyzed phylogenetically. In conclusion, this study completed the RNA-seq and functional annotation of O. bacoti successfully, which provides reliable molecular data for its future studies of gene function and molecular markers.

Comparative Genomic Hybridization Analysis of Two Predominant Nordic Group I (Proteolytic) Clostridium botulinum Type B Clusters▿ †

PubMed Central

Lindström, Miia; Hinderink, Katja; Somervuo, Panu; Kiviniemi, Katri; Nevas, Mari; Chen, Ying; Auvinen, Petri; Carter, Andrew T.; Mason, David R.; Peck, Michael W.; Korkeala, Hannu

2009-01-01

Comparative genomic hybridization analysis of 32 Nordic group I Clostridium botulinum type B strains isolated from various sources revealed two homogeneous clusters, clusters BI and BII. The type B strains differed from reference strain ATCC 3502 by 413 coding sequence (CDS) probes, sharing 88% of all the ATCC 3502 genes represented on the microarray. The two Nordic type B clusters differed from each other by their response to 145 CDS probes related mainly to transport and binding, adaptive mechanisms, fatty acid biosynthesis, the cell membranes, bacteriophages, and transposon-related elements. The most prominent differences between the two clusters were related to resistance to toxic compounds frequently found in the environment, such as arsenic and cadmium, reflecting different adaptive responses in the evolution of the two clusters. Other relatively variable CDS groups were related to surface structures and the gram-positive cell wall, suggesting that the two clusters possess different antigenic properties. All the type B strains carried CDSs putatively related to capsule formation, which may play a role in adaptation to different environmental and clinical niches. Sequencing showed that representative strains of the two type B clusters both carried subtype B2 neurotoxin genes. As many of the type B strains studied have been isolated from foods or associated with botulism, it is expected that the two group I C. botulinum type B clusters present a public health hazard in Nordic countries. Knowing the genetic and physiological markers of these clusters will assist in targeting control measures against these pathogens. PMID:19270141

Caudal dysplasia sequence with penile enlargement: case report and a potential pathogenic hypothesis.

PubMed

Makhoul, I R; Aviram-Goldring, A; Paperna, T; Sujov, P; Rienstein, S; Smolkin, T; Epelman, M; Gershoni-Baruch, R

2001-02-15

The clinical spectrum of caudal dysplasia sequence (CDS) is noted for its diversity. The origin of CDS remains unknown, though poorly controlled gestational diabetes has been implicated in some cases. Here we describe the case of a newborn with CDS associated with penile enlargement (PE). The main anomalies included anal atresia, agenesis of the kidneys and of the sacrococcygeal vertebrae, dysgenesis of lumbar vertebrae, and bilateral cryptorchidism. Penile enlargement (7 cm), a rather unusual finding, has so far not been reported in association with CDS. Chromosomal analysis failed, and the neonate died 30 min after birth. Comparative genomic hybridization analysis using stored DNA showed a balanced normal male DNA content, which negates chromosomal losses or gains as a cause of CDS and/or PE. PE due to virilizing-type adrenal hyperplasia, caused by common mutations in the genes encoding for the adrenal enzymes 21-hydroxylase and 11-hydroxylase, was ruled out. We report on a previously unpublished case of the coexistence of PE and severe CDS and propose a possible pathogenetic hypothesis of this association. Copyright Wiley-Liss. Inc.

Using hidden Markov models and observed evolution to annotate viral genomes.

PubMed

McCauley, Stephen; Hein, Jotun

2006-06-01

ssRNA (single stranded) viral genomes are generally constrained in length and utilize overlapping reading frames to maximally exploit the coding potential within the genome length restrictions. This overlapping coding phenomenon leads to complex evolutionary constraints operating on the genome. In regions which code for more than one protein, silent mutations in one reading frame generally have a protein coding effect in another. To maximize coding flexibility in all reading frames, overlapping regions are often compositionally biased towards amino acids which are 6-fold degenerate with respect to the 64 codon alphabet. Previous methodologies have used this fact in an ad hoc manner to look for overlapping genes by motif matching. In this paper differentiated nucleotide compositional patterns in overlapping regions are incorporated into a probabilistic hidden Markov model (HMM) framework which is used to annotate ssRNA viral genomes. This work focuses on single sequence annotation and applies an HMM framework to ssRNA viral annotation. A description of how the HMM is parameterized, whilst annotating within a missing data framework is given. A Phylogenetic HMM (Phylo-HMM) extension, as applied to 14 aligned HIV2 sequences is also presented. This evolutionary extension serves as an illustration of the potential of the Phylo-HMM framework for ssRNA viral genomic annotation. The single sequence annotation procedure (SSA) is applied to 14 different strains of the HIV2 virus. Further results on alternative ssRNA viral genomes are presented to illustrate more generally the performance of the method. The results of the SSA method are encouraging however there is still room for improvement, and since there is overwhelming evidence to indicate that comparative methods can improve coding sequence (CDS) annotation, the SSA method is extended to a Phylo-HMM to incorporate evolutionary information. The Phylo-HMM extension is applied to the same set of 14 HIV2 sequences which are pre-aligned. The performance improvement that results from including the evolutionary information in the analysis is illustrated.

Simulation of MeV electron energy deposition in CdS quantum dots absorbed in silicate glass for radiation dosimetry

NASA Astrophysics Data System (ADS)

Baharin, R.; Hobson, P. R.; Smith, D. R.

2010-09-01

We are currently developing 2D dosimeters with optical readout based on CdS or CdS/CdSe core-shell quantum-dots using commercially available materials. In order to understand the limitations on the measurement of a 2D radiation profile the 3D deposited energy profile of MeV energy electrons in CdS quantum-dot-doped silica glass have been studied by Monte Carlo simulation using the CASINO and PENELOPE codes. Profiles for silica glass and CdS quantum-dot-doped silica glass were then compared.

Enhanced Gene Expression Rather than Natural Polymorphism in Coding Sequence of the OsbZIP23 Determines Drought Tolerance and Yield Improvement in Rice Genotypes

PubMed Central

Dey, Avishek; Samanta, Milan Kumar; Gayen, Srimonta; Sen, Soumitra K.; Maiti, Mrinal K.

2016-01-01

Drought is one of the major limiting factors for productivity of crops including rice (Oryza sativa L.). Understanding the role of allelic variations of key regulatory genes involved in stress-tolerance is essential for developing an effective strategy to combat drought. The bZIP transcription factors play a crucial role in abiotic-stress adaptation in plants via abscisic acid (ABA) signaling pathway. The present study aimed to search for allelic polymorphism in the OsbZIP23 gene across selected drought-tolerant and drought-sensitive rice genotypes, and to characterize the new allele through overexpression (OE) and gene-silencing (RNAi). Analyses of the coding DNA sequence (CDS) of the cloned OsbZIP23 gene revealed single nucleotide polymorphism at four places and a 15-nucleotide deletion at one place. The single-copy OsbZIP23 gene is expressed at relatively higher level in leaf tissues of drought-tolerant genotypes, and its abundance is more in reproductive stage. Cloning and sequence analyses of the OsbZIP23-promoter from drought-tolerant O. rufipogon and drought-sensitive IR20 cultivar showed variation in the number of stress-responsive cis-elements and a 35-nucleotide deletion at 5’-UTR in IR20. Analysis of the GFP reporter gene function revealed that the promoter activity of O. rufipogon is comparatively higher than that of IR20. The overexpression of any of the two polymorphic forms (1083 bp and 1068 bp CDS) of OsbZIP23 improved drought tolerance and yield-related traits significantly by retaining higher content of cellular water, soluble sugar and proline; and exhibited decrease in membrane lipid peroxidation in comparison to RNAi lines and non-transgenic plants. The OE lines showed higher expression of target genes-OsRab16B, OsRab21 and OsLEA3-1 and increased ABA sensitivity; indicating that OsbZIP23 is a positive transcriptional-regulator of the ABA-signaling pathway. Taken together, the present study concludes that the enhanced gene expression rather than natural polymorphism in coding sequence of OsbZIP23 is accountable for improved drought tolerance and yield performance in rice genotypes. PMID:26959651

Diversity in VP3, NSP3, and NSP4 of rotavirus B detected from Japanese cattle.

PubMed

Hayashi-Miyamoto, Michiko; Murakami, Toshiaki; Minami-Fukuda, Fujiko; Tsuchiaka, Shinobu; Kishimoto, Mai; Sano, Kaori; Naoi, Yuki; Asano, Keigo; Ichimaru, Toru; Haga, Kei; Omatsu, Tsutomu; Katayama, Yukie; Oba, Mami; Aoki, Hiroshi; Shirai, Junsuke; Ishida, Motohiko; Katayama, Kazuhiko; Mizutani, Tetsuya; Nagai, Makoto

2017-04-01

Bovine rotavirus B (RVB) is an etiological agent of diarrhea mostly in adult cattle. Currently, a few sequences of viral protein (VP)1, 2, 4, 6, and 7 and nonstructural protein (NSP)1, 2, and 5 of bovine RVB are available in the DDBJ/EMBL/GenBank databases, and none have been reported for VP3, NSP3, and NSP4. In order to fill this gap in the genetic characterization of bovine RVB strains, we used a metagenomics approach and sequenced and analyzed the complete coding sequences (CDS) of VP3, NSP3, and NSP4 genes, as well as the partial or complete CDS of other genes of RVBs detected from Japanese cattle. VP3, NSP3, and NSP4 of bovine RVBs shared low nucleotide sequence identities (63.3-64.9% for VP3, 65.9-68.2% for NSP3, and 52.6-56.2% for NSP4) with those of murine, human, and porcine RVBs, suggesting that bovine RVBs belong to a novel genotype. Furthermore, significantly low amino acid sequence identities were observed for NSP4 (36.1-39.3%) between bovine RVBs and the RVBs of other species. In contrast, hydrophobic plot analysis of NSP4 revealed profiles similar to those of RVBs of other species and rotavirus A (RVA) strains. Phylogenetic analyses of all gene segments revealed that bovine RVB strains formed a cluster that branched distantly from other RVBs. These results suggest that bovine RVBs have evolved independently from other RVBs but in a similar manner to other rotaviruses. These findings provide insights into the evolution and diversity of RVB strains. Copyright © 2017 Elsevier B.V. All rights reserved.

Plasmid AZOBR_p1-borne fabG gene for putative 3-oxoacyl-[acyl-carrier protein] reductase is essential for proper assembly and work of the dual flagellar system in the alphaproteobacterium Azospirillum brasilense Sp245.

PubMed

Filip'echeva, Yulia A; Shelud'ko, Andrei V; Prilipov, Alexei G; Burygin, Gennady L; Telesheva, Elizaveta M; Yevstigneyeva, Stella S; Chernyshova, Marina P; Petrova, Lilia P; Katsy, Elena I

2018-02-01

Azospirillum brasilense can swim and swarm owing to the activity of a constitutive polar flagellum (Fla) and inducible lateral flagella (Laf), respectively. Experimental data on the regulation of the Fla and Laf assembly in azospirilla are scarce. Here, the coding sequence (CDS) AZOBR_p1160043 (fabG1) for a putative 3-oxoacyl-[acyl-carrier protein (ACP)] reductase was found essential for the construction of both types of flagella. In an immotile leaky Fla - Laf - fabG1::Omegon-Km mutant, Sp245.1610, defects in flagellation and motility were fully complemented by expressing the CDS AZOBR_p1160043 from plasmid pRK415. When pRK415 with the cloned CDS AZOBR_p1160045 (fliC) for a putative 65.2 kDa Sp245 Fla flagellin was transferred into the Sp245.1610 cells, the bacteria also became able to assemble a motile single flagellum. Some cells, however, had unusual swimming behavior, probably because of the side location of the organelle. Although the assembly of Laf was not restored in Sp245.1610 (pRK415-p1160045), this strain was somewhat capable of swarming motility. We propose that the putative 3-oxoacyl-[ACP] reductase encoded by the CDS AZOBR_p1160043 plays a role in correct flagellar location in the cell envelope and (or) in flagellar modification(s), which are also required for the inducible construction of Laf and for proper swimming and swarming motility of A. brasilense Sp245.

Streptococcus iniae SF1: Complete Genome Sequence, Proteomic Profile, and Immunoprotective Antigens

PubMed Central

Zhang, Bao-cun; Zhang, Jian; Sun, Li

2014-01-01

Streptococcus iniae is a Gram-positive bacterium that is reckoned one of the most severe aquaculture pathogens. It has a broad host range among farmed marine and freshwater fish and can also cause zoonotic infection in humans. Here we report for the first time the complete genome sequence as well as the host factor-induced proteomic profile of a pathogenic S. iniae strain, SF1, a serotype I isolate from diseased fish. SF1 possesses a single chromosome of 2,149,844 base pairs, which contains 2,125 predicted protein coding sequences (CDS), 12 rRNA genes, and 45 tRNA genes. Among the protein-encoding CDS are genes involved in resource acquisition and utilization, signal sensing and transduction, carbohydrate metabolism, and defense against host immune response. Potential virulence genes include those encoding adhesins, autolysins, toxins, exoenzymes, and proteases. In addition, two putative prophages and a CRISPR-Cas system were found in the genome, the latter containing a CRISPR locus and four cas genes. Proteomic analysis detected 21 secreted proteins whose expressions were induced by host serum. Five of the serum-responsive proteins were subjected to immunoprotective analysis, which revealed that two of the proteins were highly protective against lethal S. iniae challenge when used as purified recombinant subunit vaccines. Taken together, these results provide an important molecular basis for future study of S. iniae in various aspects, in particular those related to pathogenesis and disease control. PMID:24621602

Production of Transgenic Pigs with an Introduced Missense Mutation of the Bone Morphogenetic Protein Receptor Type IB Gene Related to Prolificacy.

PubMed

Zhao, Xueyan; Yang, Qiang; Zhao, Kewei; Jiang, Chao; Ren, Dongren; Xu, Pan; He, Xiaofang; Liao, Rongrong; Jiang, Kai; Ma, Junwu; Xiao, Shijun; Ren, Jun; Xing, Yuyun

2016-07-01

In the last few decades, transgenic animal technology has witnessed an increasingly wide application in animal breeding. Reproductive traits are economically important to the pig industry. It has been shown that the bone morphogenetic protein receptor type IB (BMPR1B) A746G polymorphism is responsible for the fertility in sheep. However, this causal mutation exits exclusively in sheep and goat. In this study, we attempted to create transgenic pigs by introducing this mutation with the aim to improve reproductive traits in pigs. We successfully constructed a vector containing porcine BMPR1B coding sequence (CDS) with the mutant G allele of A746G mutation. In total, we obtained 24 cloned male piglets using handmade cloning (HMC) technique, and 12 individuals survived till maturation. A set of polymerase chain reactions indicated that 11 of 12 matured boars were transgene-positive individuals, and that the transgenic vector was most likely disrupted during cloning. Of 11 positive pigs, one (No. 11) lost a part of the terminator region but had the intact promoter and the CDS regions. cDNA sequencing showed that the introduced allele (746G) was expressed in multiple tissues of transgene-positive offspring of No.11. Western blot analysis revealed that BMPR1B protein expression in multiple tissues of transgene-positive F1 piglets was 0.5 to 2-fold higher than that in the transgene-negative siblings. The No. 11 boar showed normal litter size performance as normal pigs from the same breed. Transgene-positive F1 boars produced by No. 11 had higher semen volume, sperm concentration and total sperm per ejaculate than the negative siblings, although the differences did not reached statistical significance. Transgene-positive F1 sows had similar litter size performance to the negative siblings, and more data are needed to adequately assess the litter size performance. In conclusion, we obtained 24 cloned transgenic pigs with the modified porcine BMPR1B CDS using HMC. cDNA sequencing and western blot indicated that the exogenous BMPR1B CDS was successfully expressed in host pigs. The transgenic pigs showed normal litter size performance. However, no significant differences in litter size were found between transgene-positive and negative sows. Our study provides new insight into producing cloned transgenic livestock related to reproductive traits.

RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression.

PubMed

Na, Dokyun; Lee, Doheon

2010-10-15

RBSDesigner predicts the translation efficiency of existing mRNA sequences and designs synthetic ribosome binding sites (RBSs) for a given coding sequence (CDS) to yield a desired level of protein expression. The program implements the mathematical model for translation initiation described in Na et al. (Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with a desired expression level in prokaryotes. BMC Syst. Biol., 4, 71). The program additionally incorporates the effect on translation efficiency of the spacer length between a Shine-Dalgarno (SD) sequence and an AUG codon, which is crucial for the incorporation of fMet-tRNA into the ribosome. RBSDesigner provides a graphical user interface (GUI) for the convenient design of synthetic RBSs. RBSDesigner is written in Python and Microsoft Visual Basic 6.0 and is publicly available as precompiled stand-alone software on the web (http://rbs.kaist.ac.kr). dhlee@kaist.ac.kr

A method for the further assembly of targeted unigenes in a transcriptome after assembly by Trinity

PubMed Central

Xiao, Xinlong; Ma, Jinbiao; Sun, Yufang; Yao, Yinan

2015-01-01

RNA-sequencing has been widely used to obtain high throughput transcriptome sequences in various species, but the assembly of a full set of complete transcripts is still a significant challenge. Judging by the number of expected transcripts and assembled unigenes in a transcriptome library, we believe that some unigenes could be reassembled. In this study, using the nitrate transporter (NRT) gene family and phosphate transporter (PHT) gene family in Salicornia europaea as examples, we introduced an approach to further assemble unigenes found in transcriptome libraries which had been previously generated by Trinity. To find the unigenes of a particular transcript that contained gaps, we respectively selected 16 NRT candidate unigene pairs and 12 PHT candidate unigene pairs for which the two unigenes had the same annotations, the same expression patterns among various RNA-seq samples, and different positions of the proteins coded as mapped to a reference protein. To fill a gap between the two unigenes, PCR was performed using primers that mapped to the two unigenes and the PCR products were sequenced, which demonstrated that 5 unigene pairs of NRT and 3 unigene pairs of PHT could be reassembled when the gaps were filled using the corresponding PCR product sequences. This fast and simple method will reduce the redundancy of targeted unigenes and allow acquisition of complete coding sequences (CDS). PMID:26528307

De novo characterization of Lentinula edodes C(91-3) transcriptome by deep Solexa sequencing.

PubMed

Zhong, Mintao; Liu, Ben; Wang, Xiaoli; Liu, Lei; Lun, Yongzhi; Li, Xingyun; Ning, Anhong; Cao, Jing; Huang, Min

2013-02-01

Lentinula edodes, has been utilized as food, as well as, in popular medicine, moreover, its extract isolated from its mycelium and fruiting body have shown several therapeutic properties. Yet little is understood about its genes involved in these properties, and the absence of L.edodes genomes has been a barrier to the development of functional genomics research. However, high throughput sequencing technologies are now being widely applied to non-model species. To facilitate research on L.edodes, we leveraged Solexa sequencing technology in de novo assembly of L.edodes C(91-3) transcriptome. In a single run, we produced more than 57 million sequencing reads. These reads were assembled into 28,923 unigene sequences (mean size=689bp) including 18,120 unigenes with coding sequence (CDS). Based on similarity search with known proteins, assembled unigene sequences were annotated with gene descriptions, gene ontology (GO) and clusters of orthologous group (COG) terms. Our data provides the first comprehensive sequence resource available for functional genomics studies in L.edodes, and demonstrates the utility of Illumina/Solexa sequencing for de novo transcriptome characterization and gene discovery in a non-model mushroom. Copyright © 2012 Elsevier Inc. All rights reserved.

Cadmium sulfide nanocluster-based electrochemical stripping detection of DNA hybridization.

PubMed

Zhu, Ningning; Zhang, Aiping; He, Pingang; Fang, Yuzhi

2003-03-01

A novel, sensitive electrochemical DNA hybridization detection assay, using cadmium sulfide (CdS) nanoclusters as the oligonucleotide labeling tag, is described. The assay relies on the hybridization of the target DNA with the CdS nanocluster oligonucleotide DNA probe, followed by the dissolution of the CdS nanoclusters anchored on the hybrids and the indirect determination of the dissolved cadmium ions by sensitive anodic stripping voltammetry (ASV) at a mercury-coated glassy carbon electrode (GCE). The results showed that only a complementary sequence could form a double-stranded dsDNA-CdS with the DNA probe and give an obvious electrochemical response. A three-base mismatch sequence and non-complementary sequence had negligible response. The combination of the large number of cadmium ions released from each dsDNA hybrid with the remarkable sensitivity of the electrochemical stripping analysis for cadmium at mercury-film GCE allows detection at levels as low as 0.2 pmol L(-1) of the complementary sequence of DNA.

Novel genes related to nodulation, secretion systems, and surface structures revealed by a genome draft of Rhizobium tropici strain PRF 81.

PubMed

Pinto, Fabiana G S; Chueire, Ligia M O; Vasconcelos, Ana Tereza R; Nicolás, Marisa F; Almeida, Luiz G P; Souza, Rangel C; Menna, Pâmela; Barcellos, Fernando G; Megías, Manuel; Hungria, Mariangela

2009-05-01

Rhizobium tropici is representative of the diversity of tropical rhizobia, besides comprising strains very effective in fixing N(2) in symbiosis with the common bean (Phaseolus vulgaris L.). The genome of a Brazilian commercial inoculant R. tropici strain (PRF 81, =SEMIA 4088), estimated at 7.85 Mb, was analyzed through a total of 9,026 shotgun reads, assembled in 1,668 phrap contigs, and covering approximately 30% of the genome. Annotation identified 2,135 coding DNA sequences (CDS), and only 57.2% have possible functions. The genome comprises a mosaic of genes, with CDS showing the highest similarities with 134 microorganisms, none of which represents more than 19% of the CDS with putative known functions. The high saprophytic capacity of PRF 81 may reside in a variety of genes related to transport, biodegradation of xenobiotics, defense, and secretion proteins, many of which were reported for the first time in the present study. Novelty was also found in nodulation (nodG, a double nodIJ system, nodT, nolF, nolG) and capsular polysaccharide genes, showing stronger similarities with Sinorhizobium (=Ensifer) than with the main symbionts of the common bean -- R. etli and R. leguminosarum -- suggesting that the original host of R. tropici might be another tropical legume or emphasizing the highly promiscuous nature of this rhizobial species.

Transforming user needs into functional requirements for an antibiotic clinical decision support system: explicating content analysis for system design.

PubMed

Bright, T J

2013-01-01

Many informatics studies use content analysis to generate functional requirements for system development. Explication of this translational process from qualitative data to functional requirements can strengthen the understanding and scientific rigor when applying content analysis in informatics studies. To describe a user-centered approach transforming emergent themes derived from focus group data into functional requirements for informatics solutions and to illustrate these methods to the development of an antibiotic clinical decision support system (CDS). THE APPROACH CONSISTED OF FIVE STEPS: 1) identify unmet therapeutic planning information needs via Focus Group Study-I, 2) develop a coding framework of therapeutic planning themes to refine the domain scope to antibiotic therapeutic planning, 3) identify functional requirements of an antibiotic CDS system via Focus Group Study-II, 4) discover informatics solutions and functional requirements from coded data, and 5) determine the types of information needed to support the antibiotic CDS system and link with the identified informatics solutions and functional requirements. The coding framework for Focus Group Study-I revealed unmet therapeutic planning needs. Twelve subthemes emerged and were clustered into four themes; analysis indicated a need for an antibiotic CDS intervention. Focus Group Study-II included five types of information needs. Comments from the Barrier/Challenge to information access and Function/Feature themes produced three informatics solutions and 13 functional requirements of an antibiotic CDS system. Comments from the Patient, Institution, and Domain themes generated required data elements for each informatics solution. This study presents one example explicating content analysis of focus group data and the analysis process to functional requirements from narrative data. Illustration of this 5-step method was used to develop an antibiotic CDS system, resolving unmet antibiotic prescribing needs. As a reusable approach, these techniques can be refined and applied to resolve unmet information needs with informatics interventions in additional domains.

Transforming User Needs into Functional Requirements for an Antibiotic Clinical Decision Support System

PubMed Central

Bright, T.J.

2013-01-01

Summary Background Many informatics studies use content analysis to generate functional requirements for system development. Explication of this translational process from qualitative data to functional requirements can strengthen the understanding and scientific rigor when applying content analysis in informatics studies. Objective To describe a user-centered approach transforming emergent themes derived from focus group data into functional requirements for informatics solutions and to illustrate these methods to the development of an antibiotic clinical decision support system (CDS). Methods The approach consisted of five steps: 1) identify unmet therapeutic planning information needs via Focus Group Study-I, 2) develop a coding framework of therapeutic planning themes to refine the domain scope to antibiotic therapeutic planning, 3) identify functional requirements of an antibiotic CDS system via Focus Group Study-II, 4) discover informatics solutions and functional requirements from coded data, and 5) determine the types of information needed to support the antibiotic CDS system and link with the identified informatics solutions and functional requirements. Results The coding framework for Focus Group Study-I revealed unmet therapeutic planning needs. Twelve subthemes emerged and were clustered into four themes; analysis indicated a need for an antibiotic CDS intervention. Focus Group Study-II included five types of information needs. Comments from the Barrier/Challenge to information access and Function/Feature themes produced three informatics solutions and 13 functional requirements of an antibiotic CDS system. Comments from the Patient, Institution, and Domain themes generated required data elements for each informatics solution. Conclusion This study presents one example explicating content analysis of focus group data and the analysis process to functional requirements from narrative data. Illustration of this 5-step method was used to develop an antibiotic CDS system, resolving unmet antibiotic prescribing needs. As a reusable approach, these techniques can be refined and applied to resolve unmet information needs with informatics interventions in additional domains. PMID:24454586

Detailed transcriptome description of the neglected cestode Taenia multiceps.

PubMed

Wu, Xuhang; Fu, Yan; Yang, Deying; Zhang, Runhui; Zheng, Wanpeng; Nie, Huaming; Xie, Yue; Yan, Ning; Hao, Guiying; Gu, Xiaobin; Wang, Shuxian; Peng, Xuerong; Yang, Guangyou

2012-01-01

The larval stage of Taenia multiceps, a global cestode, encysts in the central nervous system (CNS) of sheep and other livestock. This frequently leads to their death and huge socioeconomic losses, especially in developing countries. This parasite can also cause zoonotic infections in humans, but has been largely neglected due to a lack of diagnostic techniques and studies. Recent developments in next-generation sequencing provide an opportunity to explore the transcriptome of T. multiceps. We obtained a total of 31,282 unigenes (mean length 920 bp) using Illumina paired-end sequencing technology and a new Trinity de novo assembler without a referenced genome. Individual transcription molecules were determined by sequence-based annotations and/or domain-based annotations against public databases (Nr, UniprotKB/Swiss-Prot, COG, KEGG, UniProtKB/TrEMBL, InterPro and Pfam). We identified 26,110 (83.47%) unigenes and inferred 20,896 (66.8%) coding sequences (CDS). Further comparative transcripts analysis with other cestodes (Taenia pisiformis, Taenia solium, Echincoccus granulosus and Echincoccus multilocularis) and intestinal parasites (Trichinella spiralis, Ancylostoma caninum and Ascaris suum) showed that 5,100 common genes were shared among three Taenia tapeworms, 261 conserved genes were detected among five Taeniidae cestodes, and 109 common genes were found in four zoonotic intestinal parasites. Some of the common genes were genes required for parasite survival, involved in parasite-host interactions. In addition, we amplified two full-length CDS of unigenes from the common genes using RT-PCR. This study provides an extensive transcriptome of the adult stage of T. multiceps, and demonstrates that comparative transcriptomic investigations deserve to be further studied. This transcriptome dataset forms a substantial public information platform to achieve a fundamental understanding of the biology of T. multiceps, and helps in the identification of drug targets and parasite-host interaction studies.

Variations in endothelin receptor B subtype 2 (EDNRB2) coding sequences and mRNA expression levels in 4 Muscovy duck plumage colour phenotypes.

PubMed

Wu, N; Qin, H; Wang, M; Bian, Y; Dong, B; Sun, G; Zhao, W; Chang, G; Xu, Q; Chen, G

2017-04-01

1. Endothelin receptor B subtype 2 (EDNRB2) is a paralog of EDNRB, which encodes a 7-transmembrane G-protein coupled receptor. Previous studies reported that EDNRB was essential for melanoblast migration in mammals and ducks. 2. Muscovy ducks have different plumage colour phenotypes. Variations in EDNRB2 coding sequences (CDSs) and mRNA expression levels were investigated in 4 different Muscovy duck plumage colour phenotypes, including black, black mutant, silver and white head. 3. The EDNRB2 gene from Muscovy duck was cloned; it had a length of 6435 bp and encoded 437 amino acids. The coding region was screened and potential single nucleotide polymorphisms were identified. Eight mutations were obtained, including one missense variant (c.64C > T) and 7 synonymous substitutions. The substitutions were associated with plumage colour phenotypes. 4. The EDNRB2 mRNA expression levels were compared between feather pulp from black birds and black mutant birds. The results indicated that EDNRB2 transcripts in feather pulp were significantly higher in black feathers than in white feathers. 5. The results determined the variation of EDNRB2 CDS and mRNA expression in Muscovy ducks of various plumage colours.

Clinical decision support alert malfunctions: analysis and empirically derived taxonomy.

PubMed

Wright, Adam; Ai, Angela; Ash, Joan; Wiesen, Jane F; Hickman, Thu-Trang T; Aaron, Skye; McEvoy, Dustin; Borkowsky, Shane; Dissanayake, Pavithra I; Embi, Peter; Galanter, William; Harper, Jeremy; Kassakian, Steve Z; Ramoni, Rachel; Schreiber, Richard; Sirajuddin, Anwar; Bates, David W; Sittig, Dean F

2018-05-01

To develop an empirically derived taxonomy of clinical decision support (CDS) alert malfunctions. We identified CDS alert malfunctions using a mix of qualitative and quantitative methods: (1) site visits with interviews of chief medical informatics officers, CDS developers, clinical leaders, and CDS end users; (2) surveys of chief medical informatics officers; (3) analysis of CDS firing rates; and (4) analysis of CDS overrides. We used a multi-round, manual, iterative card sort to develop a multi-axial, empirically derived taxonomy of CDS malfunctions. We analyzed 68 CDS alert malfunction cases from 14 sites across the United States with diverse electronic health record systems. Four primary axes emerged: the cause of the malfunction, its mode of discovery, when it began, and how it affected rule firing. Build errors, conceptualization errors, and the introduction of new concepts or terms were the most frequent causes. User reports were the predominant mode of discovery. Many malfunctions within our database caused rules to fire for patients for whom they should not have (false positives), but the reverse (false negatives) was also common. Across organizations and electronic health record systems, similar malfunction patterns recurred. Challenges included updates to code sets and values, software issues at the time of system upgrades, difficulties with migration of CDS content between computing environments, and the challenge of correctly conceptualizing and building CDS. CDS alert malfunctions are frequent. The empirically derived taxonomy formalizes the common recurring issues that cause these malfunctions, helping CDS developers anticipate and prevent CDS malfunctions before they occur or detect and resolve them expediently.

Molecular cloning, mRNA expression and tissue distribution analysis of Slc7a11 gene in alpaca (Lama paco) skins associated with different coat colors.

PubMed

Tian, Xue; Meng, Xiaolin; Wang, Liangyan; Song, Yunfei; Zhang, Danli; Ji, Yuankai; Li, Xuejun; Dong, Changsheng

2015-01-25

Slc7a11 encoding solute carrier family 7 member 11 (amionic amino acid transporter light chain, xCT), has been identified to be a critical genetic regulator of pheomelanin synthesis in hair and melanocytes. To better understand the molecular characterization of Slc7a11 and the expression patterns in skin of white versus brown alpaca (lama paco), we cloned the full length coding sequence (CDS) of alpaca Slc7a11 gene and analyzed the expression patterns using Real Time PCR, Western blotting and immunohistochemistry. The full length CDS of 1512bp encodes a 503 amino acid polypeptide. Sequence analysis showed that alpaca xCT contains 12 transmembrane regions consistent with the highly conserved amino acid permease (AA_permease_2) domain similar to other vertebrates. Sequence alignment and phylogenetic analysis revealed that alpaca xCT had the highest identity and shared the same branch with Camelus ferus. Real Time PCR and Western blotting suggested that xCT was expressed at significantly high levels in brown alpaca skin, and transcripts and protein possessed the same expression pattern in white and brown alpaca skins. Additionally, immunohistochemical analysis further demonstrated that xCT staining was robustly increased in the matrix and root sheath of brown alpaca skin compared with that of white. These results suggest that Slc7a11 functions in alpaca coat color regulation and offer essential information for further exploration on the role of Slc7a11 in melanogenesis. Copyright © 2014 Elsevier B.V. All rights reserved.

Cable Discharge System for fundamental detonator studies

NASA Technical Reports Server (NTRS)

Peevy, Gregg R.; Barnhart, Steven G.; Brigham, William P.

1994-01-01

Sandia National Laboratories has recently completed the modification and installation of a cable discharge system (CDS) which will be used to study the physics of exploding bridgewire (EBW) detonators and exploding foil initiators (EFI or slapper). Of primary interest are the burst characteristics of these devices when subjected to the constant current pulse delivered by this system. The burst process involves the heating of the bridge material to a conductive plasma and is essential in describing the electrical properties of the bridgewire foil for use in diagnostics or computer models. The CDS described herein is capable of delivering up to an 8000 A pulse of 3 micron duration. Experiments conducted with the CDS to characterize the EBW and EFI burst behavior are also described. In addition, the CDS simultaneous VISAR capability permits updating the EFI electrical Gurney analysis parameters used in our computer simulation codes. Examples of CDS generated data for a typical EFI and EBW detonator are provided.

Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet

PubMed Central

Tett, Adrian; Spiers, Andrew J; Crossman, Lisa C; Ager, Duane; Ciric, Lena; Dow, J Maxwell; Fry, John C; Harris, David; Lilley, Andrew; Oliver, Anna; Parkhill, Julian; Quail, Michael A; Rainey, Paul B; Saunders, Nigel J; Seeger, Kathy; Snyder, Lori AS; Squares, Rob; Thomas, Christopher M; Turner, Sarah L; Zhang, Xue-Xian; Field, Dawn; Bailey, Mark J

2009-01-01

The plasmid pQBR103 was found within Pseudomonas populations colonizing the leaf and root surfaces of sugar beet plants growing at Wytham, Oxfordshire, UK. At 425 kb it is the largest self-transmissible plasmid yet sequenced from the phytosphere. It is known to enhance the competitive fitness of its host, and parts of the plasmid are known to be actively transcribed in the plant environment. Analysis of the complete sequence of this plasmid predicts a coding sequence (CDS)-rich genome containing 478 CDSs and an exceptional degree of genetic novelty; 80% of predicted coding sequences cannot be ascribed a function and 60% are orphans. Of those to which function could be assigned, 40% bore greatest similarity to sequences from Pseudomonas spp, and the majority of the remainder showed similarity to other c-proteobacterial genera and plasmids. pQBR103 has identifiable regions presumed responsible for replication and partitioning, but despite being tra+ lacks the full complement of any previously described conjugal transfer functions. The DNA sequence provided few insights into the functional significance of plant-induced transcriptional regions, but suggests that 14% of CDSs may be expressed (11 CDSs with functional annotation and 54 without), further highlighting the ecological importance of these novel CDSs. Comparative analysis indicates that pQBR103 shares significant regions of sequence with other plasmids isolated from sugar beet plants grown at the same geographic location. These plasmid sequences indicate there is more novelty in the mobile DNA pool accessible to phytosphere pseudomonas than is currently appreciated or understood. PMID:18043644

Blood transcriptomics of captive forest musk deer (Moschus berezovskii) and possible associations with the immune response to abscesses.

PubMed

Sun, Xiaoning; Cai, Ruibo; Jin, Xuelin; Shafer, Aaron B A; Hu, Xiaolong; Yang, Shuang; Li, Yimeng; Qi, Lei; Liu, Shuqiang; Hu, Defu

2018-01-12

Forest musk deer (Moschus berezovskii; FMD) are both economically valuable and highly endangered. A problem for FMD captive breeding programs has been the susceptibility of FMD to abscesses. To investigate the mechanisms of abscess development in FMD, the blood transcriptomes of three purulent and three healthy individuals were generated. A total of ~39.68 Gb bases were generated using Illumina HiSeq 4000 sequencing technology and 77,752 unigenes were identified after assembling. All the unigenes were annotated, with 63,531 (81.71%) mapping to at least one database. Based on these functional annotations, 45,798 coding sequences (CDS) were detected, along with 12,697 simple sequence repeats (SSRs) and 65,536 single nucleotide polymorphisms (SNPs). A total of 113 unigenes were found to be differentially expressed between healthy and purulent individuals. Functional annotation indicated that most of these differentially expressed genes were involved in the regulation of immune system processes, particularly those associated with parasitic and bacterial infection pathways.

Cell Nucleus-Targeting Zwitterionic Carbon Dots.

PubMed

Jung, Yun Kyung; Shin, Eeseul; Kim, Byeong-Su

2015-12-22

An innovative nucleus-targeting zwitterionic carbon dot (CD) vehicle has been developed for anticancer drug delivery and optical monitoring. The zwitterionic functional groups of the CDs introduced by a simple one-step synthesis using β-alanine as a passivating and zwitterionic ligand allow cytoplasmic uptake and subsequent nuclear translocation of the CDs. Moreover, multicolor fluorescence improves the accuracy of the CDs as an optical code. The CD-based drug delivery system constructed by non-covalent grafting of doxorubicin, exhibits superior antitumor efficacy owing to enhanced nuclear delivery in vitro and tumor accumulation in vivo, resulting in highly effective tumor growth inhibition. Since the zwitterionic CDs are highly biocompatible and effectively translocated into the nucleus, it provides a compelling solution to a multifunctional nanoparticle for substantially enhanced nuclear uptake of drugs and optical monitoring of translocation.

Cell Nucleus-Targeting Zwitterionic Carbon Dots

PubMed Central

Jung, Yun Kyung; Shin, Eeseul; Kim, Byeong-Su

2015-01-01

An innovative nucleus-targeting zwitterionic carbon dot (CD) vehicle has been developed for anticancer drug delivery and optical monitoring. The zwitterionic functional groups of the CDs introduced by a simple one-step synthesis using β-alanine as a passivating and zwitterionic ligand allow cytoplasmic uptake and subsequent nuclear translocation of the CDs. Moreover, multicolor fluorescence improves the accuracy of the CDs as an optical code. The CD-based drug delivery system constructed by non-covalent grafting of doxorubicin, exhibits superior antitumor efficacy owing to enhanced nuclear delivery in vitro and tumor accumulation in vivo, resulting in highly effective tumor growth inhibition. Since the zwitterionic CDs are highly biocompatible and effectively translocated into the nucleus, it provides a compelling solution to a multifunctional nanoparticle for substantially enhanced nuclear uptake of drugs and optical monitoring of translocation. PMID:26689549

Preemptive genotyping for personalized medicine: design of the right drug, right dose, right time-using genomic data to individualize treatment protocol.

PubMed

Bielinski, Suzette J; Olson, Janet E; Pathak, Jyotishman; Weinshilboum, Richard M; Wang, Liewei; Lyke, Kelly J; Ryu, Euijung; Targonski, Paul V; Van Norstrand, Michael D; Hathcock, Matthew A; Takahashi, Paul Y; McCormick, Jennifer B; Johnson, Kiley J; Maschke, Karen J; Rohrer Vitek, Carolyn R; Ellingson, Marissa S; Wieben, Eric D; Farrugia, Gianrico; Morrisette, Jody A; Kruckeberg, Keri J; Bruflat, Jamie K; Peterson, Lisa M; Blommel, Joseph H; Skierka, Jennifer M; Ferber, Matthew J; Black, John L; Baudhuin, Linnea M; Klee, Eric W; Ross, Jason L; Veldhuizen, Tamra L; Schultz, Cloann G; Caraballo, Pedro J; Freimuth, Robert R; Chute, Christopher G; Kullo, Iftikhar J

2014-01-01

To report the design and implementation of the Right Drug, Right Dose, Right Time-Using Genomic Data to Individualize Treatment protocol that was developed to test the concept that prescribers can deliver genome-guided therapy at the point of care by using preemptive pharmacogenomics (PGx) data and clinical decision support (CDS) integrated into the electronic medical record (EMR). We used a multivariate prediction model to identify patients with a high risk of initiating statin therapy within 3 years. The model was used to target a study cohort most likely to benefit from preemptive PGx testing among the Mayo Clinic Biobank participants, with a recruitment goal of 1000 patients. We used a Cox proportional hazards model with variables selected through the Lasso shrinkage method. An operational CDS model was adapted to implement PGx rules within the EMR. The prediction model included age, sex, race, and 6 chronic diseases categorized by the Clinical Classifications Software for International Classification of Diseases, Ninth Revision codes (dyslipidemia, diabetes, peripheral atherosclerosis, disease of the blood-forming organs, coronary atherosclerosis and other heart diseases, and hypertension). Of the 2000 Biobank participants invited, 1013 (51%) provided blood samples, 256 (13%) declined participation, 555 (28%) did not respond, and 176 (9%) consented but did not provide a blood sample within the recruitment window (October 4, 2012, through March 20, 2013). Preemptive PGx testing included CYP2D6 genotyping and targeted sequencing of 84 PGx genes. Synchronous real-time CDS was integrated into the EMR and flagged potential patient-specific drug-gene interactions and provided therapeutic guidance. This translational project provides an opportunity to begin to evaluate the impact of preemptive sequencing and EMR-driven genome-guided therapy. These interventions will improve understanding and implementation of genomic data in clinical practice. Copyright © 2014 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

Transterm—extended search facilities and improved integration with other databases

PubMed Central

Jacobs, Grant H.; Stockwell, Peter A.; Tate, Warren P.; Brown, Chris M.

2006-01-01

Transterm has now been publicly available for >10 years. Major changes have been made since its last description in this database issue in 2002. The current database provides data for key regions of mRNA sequences, a curated database of mRNA motifs and tools to allow users to investigate their own motifs or mRNA sequences. The key mRNA regions database is derived computationally from Genbank. It contains 3′ and 5′ flanking regions, the initiation and termination signal context and coding sequence for annotated CDS features from Genbank and RefSeq. The database is non-redundant, enabling summary files and statistics to be prepared for each species. Advances include providing extended search facilities, the database may now be searched by BLAST in addition to regular expressions (patterns) allowing users to search for motifs such as known miRNA sequences, and the inclusion of RefSeq data. The database contains >40 motifs or structural patterns important for translational control. In this release, patterns from UTRsite and Rfam are also incorporated with cross-referencing. Users may search their sequence data with Transterm or user-defined patterns. The system is accessible at . PMID:16381889

The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs

PubMed Central

Garzia, Aitor; Jafarnejad, Seyed Mehdi; Meyer, Cindy; Chapat, Clément; Gogakos, Tasos; Morozov, Pavel; Amiri, Mehdi; Shapiro, Maayan; Molina, Henrik; Tuschl, Thomas; Sonenberg, Nahum

2017-01-01

Cryptic polyadenylation within coding sequences (CDS) triggers ribosome-associated quality control (RQC), followed by degradation of the aberrant mRNA and polypeptide, ribosome disassembly and recycling. Although ribosomal subunit dissociation and nascent peptide degradation are well-understood, the molecular sensors of aberrant mRNAs and their mechanism of action remain unknown. We studied the Zinc Finger Protein 598 (ZNF598) using PAR-CLIP and revealed that it cross-links to tRNAs, mRNAs and rRNAs, thereby placing the protein on translating ribosomes. Cross-linked reads originating from AAA-decoding tRNALys(UUU) were 10-fold enriched over its cellular abundance, and poly-lysine encoded by poly(AAA) induced RQC in a ZNF598-dependent manner. Encounter with translated polyA segments by ZNF598 triggered ubiquitination of several ribosomal proteins, requiring the E2 ubiquitin ligase UBE2D3 to initiate RQC. Considering that human CDS are devoid of >4 consecutive AAA codons, sensing of prematurely placed polyA tails by a specialized RNA-binding protein is a novel nucleic-acid-based surveillance mechanism of RQC. PMID:28685749

The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs.

PubMed

Garzia, Aitor; Jafarnejad, Seyed Mehdi; Meyer, Cindy; Chapat, Clément; Gogakos, Tasos; Morozov, Pavel; Amiri, Mehdi; Shapiro, Maayan; Molina, Henrik; Tuschl, Thomas; Sonenberg, Nahum

2017-07-07

Cryptic polyadenylation within coding sequences (CDS) triggers ribosome-associated quality control (RQC), followed by degradation of the aberrant mRNA and polypeptide, ribosome disassembly and recycling. Although ribosomal subunit dissociation and nascent peptide degradation are well-understood, the molecular sensors of aberrant mRNAs and their mechanism of action remain unknown. We studied the Zinc Finger Protein 598 (ZNF598) using PAR-CLIP and revealed that it cross-links to tRNAs, mRNAs and rRNAs, thereby placing the protein on translating ribosomes. Cross-linked reads originating from AAA-decoding tRNA Lys (UUU) were 10-fold enriched over its cellular abundance, and poly-lysine encoded by poly(AAA) induced RQC in a ZNF598-dependent manner. Encounter with translated polyA segments by ZNF598 triggered ubiquitination of several ribosomal proteins, requiring the E2 ubiquitin ligase UBE2D3 to initiate RQC. Considering that human CDS are devoid of >4 consecutive AAA codons, sensing of prematurely placed polyA tails by a specialized RNA-binding protein is a novel nucleic-acid-based surveillance mechanism of RQC.

Ag nanoclusters could efficiently quench the photoresponse of CdS quantum dots for novel energy transfer-based photoelectrochemical bioanalysis.

PubMed

Zhang, Ling; Sun, Yue; Liang, Yan-Yu; He, Jian-Ping; Zhao, Wei-Wei; Xu, Jing-Juan; Chen, Hong-Yuan

2016-11-15

Herein the influence of ultrasmall Ag nanoclusters (Ag NCs) against CdS quantum dots (QDs) in a photoelectrochemical (PEC) nanosystem was exploited for the first time, based on which a novel PEC bioanalysis was successfully developed via the efficient quenching effect of Ag NCs against the CdS QDs. In a model system, DNA assay was achieved by using molecular beacon (MB) probes anchored on a CdS QDs modified electrode, and the MB probes contain two segments that can hybridize with both target DNA sequence and the label of DNA encapsulated Ag NCs. After the MB probe was unfolded by the target DNA sequence, the labels of oligonucleotide encapsulated Ag NCs would be brought in close proximity to the CdS QDs electrode surface, and efficient photocurrent quenching of QDs could be resulted from an energy transfer process that originated from NCs. Thus, by monitoring the attenuation in the photocurrent signal, an elegant and sensitive PEC DNA bioanalysis could be accomplished. The developed biosensor displayed a linear range from 1.0pM to 10nM and the detection limit was experimentally found to be of 0.3pM. This work presents a feasible signaling principle that could act as a common basis for general PEC bioanalysis development. Copyright © 2016 Elsevier B.V. All rights reserved.

Detailed Transcriptome Description of the Neglected Cestode Taenia multiceps

PubMed Central

Wu, Xuhang; Fu, Yan; Yang, Deying; Zhang, Runhui; Zheng, Wanpeng; Nie, Huaming; Xie, Yue; Yan, Ning; Hao, Guiying; Gu, Xiaobin; Wang, Shuxian; Peng, Xuerong; Yang, Guangyou

2012-01-01

Background The larval stage of Taenia multiceps, a global cestode, encysts in the central nervous system (CNS) of sheep and other livestock. This frequently leads to their death and huge socioeconomic losses, especially in developing countries. This parasite can also cause zoonotic infections in humans, but has been largely neglected due to a lack of diagnostic techniques and studies. Recent developments in next-generation sequencing provide an opportunity to explore the transcriptome of T. multiceps. Methodology/Principal Findings We obtained a total of 31,282 unigenes (mean length 920 bp) using Illumina paired-end sequencing technology and a new Trinity de novo assembler without a referenced genome. Individual transcription molecules were determined by sequence-based annotations and/or domain-based annotations against public databases (Nr, UniprotKB/Swiss-Prot, COG, KEGG, UniProtKB/TrEMBL, InterPro and Pfam). We identified 26,110 (83.47%) unigenes and inferred 20,896 (66.8%) coding sequences (CDS). Further comparative transcripts analysis with other cestodes (Taenia pisiformis, Taenia solium, Echincoccus granulosus and Echincoccus multilocularis) and intestinal parasites (Trichinella spiralis, Ancylostoma caninum and Ascaris suum) showed that 5,100 common genes were shared among three Taenia tapeworms, 261 conserved genes were detected among five Taeniidae cestodes, and 109 common genes were found in four zoonotic intestinal parasites. Some of the common genes were genes required for parasite survival, involved in parasite-host interactions. In addition, we amplified two full-length CDS of unigenes from the common genes using RT-PCR. Conclusions/Significance This study provides an extensive transcriptome of the adult stage of T. multiceps, and demonstrates that comparative transcriptomic investigations deserve to be further studied. This transcriptome dataset forms a substantial public information platform to achieve a fundamental understanding of the biology of T. multiceps, and helps in the identification of drug targets and parasite-host interaction studies. PMID:23049872

Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene

PubMed Central

Firth, Andrew E

2008-01-01

Background The genus Orbivirus includes several species that infect livestock – including Bluetongue virus (BTV) and African horse sickness virus (AHSV). These viruses have linear dsRNA genomes divided into ten segments, all of which have previously been assumed to be monocistronic. Results Bioinformatic evidence is presented for a short overlapping coding sequence (CDS) in the Orbivirus genome segment 9, overlapping the VP6 cistron in the +1 reading frame. In BTV, a 77–79 codon AUG-initiated open reading frame (hereafter ORFX) is present in all 48 segment 9 sequences analysed. The pattern of base variations across the 48-sequence alignment indicates that ORFX is subject to functional constraints at the amino acid level (even when the constraints due to coding in the overlapping VP6 reading frame are taken into account; MLOGD software). In fact the translated ORFX shows greater amino acid conservation than the overlapping region of VP6. The ORFX AUG codon has a strong Kozak context in all 48 sequences. Each has only one or two upstream AUG codons, always in the VP6 reading frame, and (with a single exception) always with weak or medium Kozak context. Thus, in BTV, ORFX may be translated via leaky scanning. A long (83–169 codon) ORF is present in a corresponding location and reading frame in all other Orbivirus species analysed except Saint Croix River virus (SCRV; the most divergent). Again, the pattern of base variations across sequence alignments indicates multiple coding in the VP6 and ORFX reading frames. Conclusion At ~9.5 kDa, the putative ORFX product in BTV is too small to appear on most published protein gels. Nonetheless, a review of past literature reveals a number of possible detections. We hope that presentation of this bioinformatic analysis will stimulate an attempt to experimentally verify the expression and functional role of ORFX, and hence lead to a greater understanding of the molecular biology of these important pathogens. PMID:18489030

Optical characterization of CdS nanoparticles embedded into the comb-type amphiphilic graft copolymer

NASA Astrophysics Data System (ADS)

Kalaycı, Özlem A.; Duygulu, Özgür; Hazer, Baki

2013-01-01

This study refers to the synthesis and characterization of a novel organic/inorganic hybrid nanocomposite material containing cadmium sulfide (CdS) nanoparticles. For this purpose, a series of polypropylene (PP)-g-polyethylene glycol (PEG), PP-g-PEG comb-type amphiphilic graft copolymers were synthesized. PEGs with Mn = 400, 2000, 3350, and 8000 Da were used and the graft copolymers obtained were coded as PPEG400, PPEG2000, PPEG3350, and PPEG8000. CdS nanoparticles were formed in tetrahydrofuran solution of PP-g-PEG amphiphilic comb-type copolymer by the reaction between aqueous solutions of Na2S and Cd(CH3COO)2 simultaneously. Micelle formation of PPEG2000 comb-type amphiphilic graft copolymer in both solvent/non-solvent (petroleum ether-THF) by transmission electron microscopy (TEM). The optical characteristics, size morphology, phase analysis, and dispersion of CdS nanoparticles embedded in PPEG400, PPEG2000, PPEG3350, and PPEG8000 comb-type amphiphilic graft copolymer micelles were determined by high resolution TEM (HRTEM), energy dispersive spectroscopy, UV-vis spectroscopy, and fluorescence emission spectroscopy techniques. The aggregate size of PPEG2000-CdS is between 10 and 50 nm; however, in the case of PPEG400-CdS, PPEG3350-CdS, and PPEG8000-CdS samples, it is up to approximately 100 nm. The size of CdS quantum dots in the aggregates for PPEG2000 and PPEG8000 samples was observed as 5 nm by HRTEM analysis, and this result was also supported by UV-vis absorbance spectra and fluorescence emission spectra.

Agile Acceptance Test–Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software

PubMed Central

Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-01-01

Background Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test–driven development and automated regression testing promotes reliability. Test–driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a “safety net” for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and “living” design documentation. Rapid-cycle development or “agile” methods are being successfully applied to CDS development. The agile practice of automated test–driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as “executable requirements.” Objective We aimed to establish feasibility of acceptance test–driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Methods Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory’s expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. Results We used test–driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the “executable requirements” are shown prior to building the CDS alert, during build, and after successful build. Conclusions Automated acceptance test–driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test–driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. PMID:29653922

Agile Acceptance Test-Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software.

PubMed

Basit, Mujeeb A; Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-04-13

Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test-driven development and automated regression testing promotes reliability. Test-driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a "safety net" for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and "living" design documentation. Rapid-cycle development or "agile" methods are being successfully applied to CDS development. The agile practice of automated test-driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as "executable requirements." We aimed to establish feasibility of acceptance test-driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory's expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. We used test-driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the "executable requirements" are shown prior to building the CDS alert, during build, and after successful build. Automated acceptance test-driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test-driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. ©Mujeeb A Basit, Krystal L Baldwin, Vaishnavi Kannan, Emily L Flahaven, Cassandra J Parks, Jason M Ott, Duwayne L Willett. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 13.04.2018.

Identification of a Novel De Novo Heterozygous Deletion in the SOX10 Gene in Waardenburg Syndrome Type II Using Next-Generation Sequencing.

PubMed

Li, Haonan; Jin, Peng; Hao, Qian; Zhu, Wei; Chen, Xia; Wang, Ping

2017-11-01

Waardenburg syndrome (WS) is a rare autosomal dominant disorder associated with pigmentation abnormalities and sensorineural hearing loss. In this study, we investigated the genetic cause of WSII in a patient and evaluated the reliability of the targeted next-generation exome sequencing method for the genetic diagnosis of WS. Clinical evaluations were conducted on the patient and targeted next-generation sequencing (NGS) was used to identify the candidate genes responsible for WSII. Multiplex ligation-dependent probe amplification (MLPA) and real-time quantitative polymerase chain reaction (qPCR) were performed to confirm the targeted NGS results. Targeted NGS detected the entire deletion of the coding sequence (CDS) of the SOX10 gene in the WSII patient. MLPA results indicated that all exons of the SOX10 heterozygous deletion were detected; no aberrant copy number in the PAX3 and microphthalmia-associated transcription factor (MITF) genes was found. Real-time qPCR results identified the mutation as a de novo heterozygous deletion. This is the first report of using a targeted NGS method for WS candidate gene sequencing; its accuracy was verified by using the MLPA and qPCR methods. Our research provides a valuable method for the genetic diagnosis of WS.

Next Generation Sequencing and Transcriptome Analysis Predicts Biosynthetic Pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a Non-Model Plant with Potent Laxative Properties.

PubMed

Rama Reddy, Nagaraja Reddy; Mehta, Rucha Harishbhai; Soni, Palak Harendrabhai; Makasana, Jayanti; Gajbhiye, Narendra Athamaram; Ponnuchamy, Manivel; Kumar, Jitendra

2015-01-01

Senna (Cassia angustifolia Vahl.) is a world's natural laxative medicinal plant. Laxative properties are due to sennosides (anthraquinone glycosides) natural products. However, little genetic information is available for this species, especially concerning the biosynthetic pathways of sennosides. We present here the transcriptome sequencing of young and mature leaf tissue of Cassia angustifolia using Illumina MiSeq platform that resulted in a total of 6.34 Gb of raw nucleotide sequence. The sequence assembly resulted in 42230 and 37174 transcripts with an average length of 1119 bp and 1467 bp for young and mature leaf, respectively. The transcripts were annotated using NCBI BLAST with 'green plant database (txid 33090)', Swiss Prot, Kyoto Encylcopedia of Genes & Genomes (KEGG), Cluster of Orthologous Gene (COG) and Gene Ontology (GO). Out of the total transcripts, 40138 (95.0%) and 36349 (97.7%) from young and mature leaf, respectively, were annotated by BLASTX against green plant database of NCBI. We used InterProscan to see protein similarity at domain level, a total of 34031 (young leaf) and 32077 (mature leaf) transcripts were annotated against the Pfam domains. All transcripts from young and mature leaf were assigned to 191 KEGG pathways. There were 166 and 159 CDS, respectively, from young and mature leaf involved in metabolism of terpenoids and polyketides. Many CDS encoding enzymes leading to biosynthesis of sennosides were identified. A total of 10,763 CDS differentially expressing in both young and mature leaf libraries of which 2,343 (21.7%) CDS were up-regulated in young compared to mature leaf. Several differentially expressed genes found functionally associated with sennoside biosynthesis. CDS encoding for many CYPs and TF families were identified having probable roles in metabolism of primary as well as secondary metabolites. We developed SSR markers for molecular breeding of senna. We have identified a set of putative genes involved in various secondary metabolite pathways, especially those related to the synthesis of sennosides which will serve as an important platform for public information about gene expression, genomics, and functional genomics in senna.

Next Generation Sequencing and Transcriptome Analysis Predicts Biosynthetic Pathway of Sennosides from Senna (Cassia angustifolia Vahl.), a Non-Model Plant with Potent Laxative Properties

PubMed Central

Rama Reddy, Nagaraja Reddy; Mehta, Rucha Harishbhai; Soni, Palak Harendrabhai; Makasana, Jayanti; Gajbhiye, Narendra Athamaram; Ponnuchamy, Manivel; Kumar, Jitendra

2015-01-01

Senna (Cassia angustifolia Vahl.) is a world’s natural laxative medicinal plant. Laxative properties are due to sennosides (anthraquinone glycosides) natural products. However, little genetic information is available for this species, especially concerning the biosynthetic pathways of sennosides. We present here the transcriptome sequencing of young and mature leaf tissue of Cassia angustifolia using Illumina MiSeq platform that resulted in a total of 6.34 Gb of raw nucleotide sequence. The sequence assembly resulted in 42230 and 37174 transcripts with an average length of 1119 bp and 1467 bp for young and mature leaf, respectively. The transcripts were annotated using NCBI BLAST with ‘green plant database (txid 33090)’, Swiss Prot, Kyoto Encylcopedia of Genes & Genomes (KEGG), Cluster of Orthologous Gene (COG) and Gene Ontology (GO). Out of the total transcripts, 40138 (95.0%) and 36349 (97.7%) from young and mature leaf, respectively, were annotated by BLASTX against green plant database of NCBI. We used InterProscan to see protein similarity at domain level, a total of 34031 (young leaf) and 32077 (mature leaf) transcripts were annotated against the Pfam domains. All transcripts from young and mature leaf were assigned to 191 KEGG pathways. There were 166 and 159 CDS, respectively, from young and mature leaf involved in metabolism of terpenoids and polyketides. Many CDS encoding enzymes leading to biosynthesis of sennosides were identified. A total of 10,763 CDS differentially expressing in both young and mature leaf libraries of which 2,343 (21.7%) CDS were up-regulated in young compared to mature leaf. Several differentially expressed genes found functionally associated with sennoside biosynthesis. CDS encoding for many CYPs and TF families were identified having probable roles in metabolism of primary as well as secondary metabolites. We developed SSR markers for molecular breeding of senna. We have identified a set of putative genes involved in various secondary metabolite pathways, especially those related to the synthesis of sennosides which will serve as an important platform for public information about gene expression, genomics, and functional genomics in senna. PMID:26098898

Genome Analysis of the Domestic Dog (Korean Jindo) by Massively Parallel Sequencing

PubMed Central

Kim, Ryong Nam; Kim, Dae-Soo; Choi, Sang-Haeng; Yoon, Byoung-Ha; Kang, Aram; Nam, Seong-Hyeuk; Kim, Dong-Wook; Kim, Jong-Joo; Ha, Ji-Hong; Toyoda, Atsushi; Fujiyama, Asao; Kim, Aeri; Kim, Min-Young; Park, Kun-Hyang; Lee, Kang Seon; Park, Hong-Seog

2012-01-01

Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the TCOF1 locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics. PMID:22474061

Model documentation, Coal Market Module of the National Energy Modeling System

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

NONE

This report documents the objectives and the conceptual and methodological approach used in the development of the National Energy Modeling System`s (NEMS) Coal Market Module (CMM) used to develop the Annual Energy Outlook 1998 (AEO98). This report catalogues and describes the assumptions, methodology, estimation techniques, and source code of CMM`s two submodules. These are the Coal Production Submodule (CPS) and the Coal Distribution Submodule (CDS). CMM provides annual forecasts of prices, production, and consumption of coal for NEMS. In general, the CDS integrates the supply inputs from the CPS to satisfy demands for coal from exogenous demand models. The internationalmore » area of the CDS forecasts annual world coal trade flows from major supply to major demand regions and provides annual forecasts of US coal exports for input to NEMS. Specifically, the CDS receives minemouth prices produced by the CPS, demand and other exogenous inputs from other NEMS components, and provides delivered coal prices and quantities to the NEMS economic sectors and regions.« less

Preemptive Genotyping for Personalized Medicine: Design of the Right Drug, Right Dose, Right Time – Using Genomic Data to Individualize Treatment Protocol

PubMed Central

Bielinski, Suzette J.; Olson, Janet E.; Pathak, Jyotishman; Weinshilboum, Richard M.; Wang, Liewei; Lyke, Kelly J.; Ryu, Euijung; Targonski, Paul V.; Van Norstrand, Michael D.; Hathcock, Matthew A.; Takahashi, Paul Y.; McCormick, Jennifer B.; Johnson, Kiley J.; Maschke, Karen J.; Rohrer Vitek, Carolyn R.; Ellingson, Marissa S.; Wieben, Eric D.; Farrugia, Gianrico; Morrisette, Jody A.; Kruckeberg, Keri J.; Bruflat, Jamie K.; Peterson, Lisa M.; Blommel, Joseph H.; Skierka, Jennifer M.; Ferber, Matthew J.; Black, John L.; Baudhuin, Linnea M.; Klee, Eric W.; Ross, Jason L.; Veldhuizen, Tamra L.; Schultz, Cloann G.; Caraballo, Pedro J.; Freimuth, Robert R.; Chute, Christopher G.; Kullo, Iftikhar J.

2014-01-01

Objective To report the design and implementation of the Right Drug, Right Dose, Right Time: Using Genomic Data to Individualize Treatment Protocol that was developed to test the concept that prescribers can deliver genome guided therapy at the point-of-care by using preemptive pharmacogenomics (PGx) data and clinical decision support (CDS) integrated in the electronic medical record (EMR). Patients and Methods We used a multivariable prediction model to identify patients with a high risk of initiating statin therapy within 3 years. The model was used to target a study cohort most likely to benefit from preemptive PGx testing among Mayo Clinic Biobank participants with a recruitment goal of 1000 patients. Cox proportional hazards model was utilized using the variables selected through the Lasso shrinkage method. An operational CDS model was adapted to implement PGx rules within the EMR. Results The prediction model included age, sex, race, and 6 chronic diseases categorized by the Clinical Classifications Software for ICD-9 codes (dyslipidemia, diabetes, peripheral atherosclerosis, disease of the blood-forming organs, coronary atherosclerosis and other heart diseases, and hypertension). Of the 2000 Biobank participants invited, 50% provided blood samples, 13% refused, 28% did not respond, and 9% consented but did not provide a blood sample within the recruitment window (October 4, 2012 – March 20, 2013). Preemptive PGx testing included CYP2D6 genotyping and targeted sequencing of 84 PGx genes. Synchronous real-time CDS is integrated in the EMR and flags potential patient-specific drug-gene interactions and provides therapeutic guidance. Conclusion These interventions will improve understanding and implementation of genomic data in clinical practice. PMID:24388019

Molecular cloning, expression profile, polymorphism and the genetic effects of the dopamine D1 receptor gene on duck reproductive traits.

PubMed

Wang, Cui; Li, Shijun; Li, Chuang; Feng, Yanping; Peng, Xiuli; Gong, Yanzhang

2012-09-01

The dopamine D1 receptor (DRD1), a member of the dopamine receptor (DR) gene family, participates in the regulation of reproductive behaviors in birds. In this study, a 1,390 bp fragment covering the complete coding region (CDS) of duck DRD1 gene was obtained. The cDNA (GenBank: JQ346726) contains a 1,353 bp CDS and a 37 bp 3'- UTR including a TGA termination codon (nucleotides 1,354-1,356 bp). The duck DRD1 shares about 76-96 % nucleic acid identity and 82-98 % amino acid identity with their counterparts in other species. A phylogenetic tree based on amino acid sequences displays that duck DRD1 protein is closely related with those of chicken and zebra finch. The quantitative real-time PCR analysis indicates that the DRD1 mRNA is widely expressed in all examined tissues. Five single nucleotide polymorphisms (SNPs) (c.189A > T, c.507C > T, c.681C > T, c.765A > T, c.1044A > G) in the CDS of duck DRD1 gene were indentified, c.681C > T and c.765A > T were genotyped and analyzed in a two generations duck population by using of PCR-RFLP. Association analysis demonstrated that the c.681C > T genotypes were significantly associated with body weight at sexual maturity (when laying their first egg) (P < 0.01), egg production within 360 days (P < 0.05) and 420 days (P < 0.01); the c.765A > T genotypes were significantly associated with egg shape index and egg shell strength (P < 0.05). Those results suggest that the DRD1 gene may be a potential genetic marker to improve some reproductive traits in ducks.

Characterization of the Biosynthetic Operon for the Antibacterial Peptide Herbicolin in Pantoea vagans Biocontrol Strain C9-1 and Incidence in Pantoea Species

PubMed Central

Kamber, Tim; Lansdell, Theresa A.; Stockwell, Virginia O.; Ishimaru, Carol A.; Smits, Theo H. M.

2012-01-01

Pantoea vagans C9-1 is a biocontrol strain that produces at least two antibiotics inhibiting the growth of Erwinia amylovora, the causal agent of fire blight disease of pear and apple. One antibiotic, herbicolin I, was purified from culture filtrates of P. vagans C9-1 and determined to be 2-amino-3-(oxirane-2,3-dicarboxamido)-propanoyl-valine, also known as Nß-epoxysuccinamoyl-DAP-valine. A plasposon library was screened for mutants that had lost the ability to produce herbicolin I. It was shown that mutants had reduced biocontrol efficacy in immature pear assays. The biosynthetic gene cluster in P. vagans C9-1 was identified by sequencing the flanking regions of the plasposon insertion sites. The herbicolin I biosynthetic gene cluster consists of 10 coding sequences (CDS) and is located on the 166-kb plasmid pPag2. Sequence comparisons identified orthologous gene clusters in Pantoea agglomerans CU0119 and Serratia proteamaculans 568. A low incidence of detection of the biosynthetic cluster in a collection of 45 Pantoea spp. from biocontrol, environmental, and clinical origins showed that this is a rare trait among the tested strains. PMID:22504810

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

PubMed Central

Takeda, Jun-ichi; Suzuki, Yutaka; Nakao, Mitsuteru; Barrero, Roberto A.; Koyanagi, Kanako O.; Jin, Lihua; Motono, Chie; Hata, Hiroko; Isogai, Takao; Nagai, Keiichi; Otsuki, Tetsuji; Kuryshev, Vladimir; Shionyu, Masafumi; Yura, Kei; Go, Mitiko; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Wiemann, Stefan; Nomura, Nobuo; Sugano, Sumio; Gojobori, Takashi; Imanishi, Tadashi

2006-01-01

We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56 419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37 670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. We also identified interesting patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or having overlapping protein coding sequences (CDSs) of different reading frames (multiple CDS). In these cases, completely unrelated proteins are encoded by a single locus. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function, which is mediated by the fast expanding universe of alternative splicing variants. PMID:16914452

Variability of Creatine Metabolism Genes in Children with Autism Spectrum Disorder.

PubMed

Cameron, Jessie M; Levandovskiy, Valeriy; Roberts, Wendy; Anagnostou, Evdokia; Scherer, Stephen; Loh, Alvin; Schulze, Andreas

2017-07-31

Creatine deficiency syndrome (CDS) comprises three separate enzyme deficiencies with overlapping clinical presentations: arginine:glycine amidinotransferase ( GATM gene, glycine amidinotransferase), guanidinoacetate methyltransferase ( GAMT gene), and creatine transporter deficiency ( SLC6A8 gene, solute carrier family 6 member 8). CDS presents with developmental delays/regression, intellectual disability, speech and language impairment, autistic behaviour, epileptic seizures, treatment-refractory epilepsy, and extrapyramidal movement disorders; symptoms that are also evident in children with autism. The objective of the study was to test the hypothesis that genetic variability in creatine metabolism genes is associated with autism. We sequenced GATM , GAMT and SLC6A8 genes in 166 patients with autism (coding sequence, introns and adjacent untranslated regions). A total of 29, 16 and 25 variants were identified in each gene, respectively. Four variants were novel in GATM , and 5 in SLC6A8 (not present in the 1000 Genomes, Exome Sequencing Project (ESP) or Exome Aggregation Consortium (ExAC) databases). A single variant in each gene was identified as non-synonymous, and computationally predicted to be potentially damaging. Nine variants in GATM were shown to have a lower minor allele frequency (MAF) in the autism population than in the 1000 Genomes database, specifically in the East Asian population (Fisher's exact test). Two variants also had lower MAFs in the European population. In summary, there were no apparent associations of variants in GAMT and SLC6A8 genes with autism. The data implying there could be a lower association of some specific GATM gene variants with autism is an observation that would need to be corroborated in a larger group of autism patients, and with sub-populations of Asian ethnicities. Overall, our findings suggest that the genetic variability of creatine synthesis/transport is unlikely to play a part in the pathogenesis of autism spectrum disorder (ASD) in children.

Comparative analysis of the complete genome of an epidemic hospital sequence type 203 clone of vancomycin-resistant Enterococcus faecium

PubMed Central

2013-01-01

Background In this report we have explored the genomic and microbiological basis for a sustained increase in bloodstream infections at a major Australian hospital caused by Enterococcus faecium multi-locus sequence type (ST) 203, an outbreak strain that has largely replaced a predecessor ST17 sequence type. Results To establish a ST203 reference sequence we fully assembled and annotated the genome of Aus0085, a 2009 vancomycin-resistant Enterococcus faecium (VREfm) bloodstream isolate, and the first example of a completed ST203 genome. Aus0085 has a 3.2 Mb genome, comprising a 2.9 Mb circular chromosome and six circular plasmids (2 kb–130 kb). Twelve percent of the 3222 coding sequences (CDS) in Aus0085 are not present in ST17 E. faecium Aus0004 and ST18 E. faecium TX16. Extending this comparison to an additional 12 ST17 and 14 ST203 E. faecium hospital isolate genomes revealed only six genomic regions spanning 41 kb that were present in all ST203 and absent from all ST17 genomes. The 40 CDS have predicted functions that include ion transport, riboflavin metabolism and two phosphotransferase systems. Comparison of the vancomycin resistance-conferring Tn1549 transposon between Aus0004 and Aus0085 revealed differences in transposon length and insertion site, and van locus sequence variation that correlated with a higher vancomycin MIC in Aus0085. Additional phenotype comparisons between ST17 and ST203 isolates showed that while there were no differences in biofilm-formation and killing of Galleria mellonella, ST203 isolates grew significantly faster and out-competed ST17 isolates in growth assays. Conclusions Here we have fully assembled and annotated the first ST203 genome, and then characterized the genomic differences between ST17 and ST203 E. faecium. We also show that ST203 E. faecium are faster growing and can out-compete ST17 E. faecium. While a causal genetic basis for these phenotype differences is not provided here, this study revealed conserved genetic differences between the two clones, differences that can now be tested to explain the molecular basis for the success and emergence of ST203 E. faecium. PMID:24004955

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

PubMed Central

Leroy, Philippe; Guilhot, Nicolas; Sakai, Hiroaki; Bernard, Aurélien; Choulet, Frédéric; Theil, Sébastien; Reboux, Sébastien; Amano, Naoki; Flutre, Timothée; Pelegrin, Céline; Ohyanagi, Hajime; Seidel, Michael; Giacomoni, Franck; Reichstadt, Mathieu; Alaux, Michael; Gicquello, Emmanuelle; Legeai, Fabrice; Cerutti, Lorenzo; Numa, Hisataka; Tanaka, Tsuyoshi; Mayer, Klaus; Itoh, Takeshi; Quesneville, Hadi; Feuillet, Catherine

2012-01-01

In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future. PMID:22645565

Seqping: gene prediction pipeline for plant genomes using self-training gene models and transcriptomic data.

PubMed

Chan, Kuang-Lim; Rosli, Rozana; Tatarinova, Tatiana V; Hogan, Michael; Firdaus-Raih, Mohd; Low, Eng-Ti Leslie

2017-01-27

Gene prediction is one of the most important steps in the genome annotation process. A large number of software tools and pipelines developed by various computing techniques are available for gene prediction. However, these systems have yet to accurately predict all or even most of the protein-coding regions. Furthermore, none of the currently available gene-finders has a universal Hidden Markov Model (HMM) that can perform gene prediction for all organisms equally well in an automatic fashion. We present an automated gene prediction pipeline, Seqping that uses self-training HMM models and transcriptomic data. The pipeline processes the genome and transcriptome sequences of the target species using GlimmerHMM, SNAP, and AUGUSTUS pipelines, followed by MAKER2 program to combine predictions from the three tools in association with the transcriptomic evidence. Seqping generates species-specific HMMs that are able to offer unbiased gene predictions. The pipeline was evaluated using the Oryza sativa and Arabidopsis thaliana genomes. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis showed that the pipeline was able to identify at least 95% of BUSCO's plantae dataset. Our evaluation shows that Seqping was able to generate better gene predictions compared to three HMM-based programs (MAKER2, GlimmerHMM and AUGUSTUS) using their respective available HMMs. Seqping had the highest accuracy in rice (0.5648 for CDS, 0.4468 for exon, and 0.6695 nucleotide structure) and A. thaliana (0.5808 for CDS, 0.5955 for exon, and 0.8839 nucleotide structure). Seqping provides researchers a seamless pipeline to train species-specific HMMs and predict genes in newly sequenced or less-studied genomes. We conclude that the Seqping pipeline predictions are more accurate than gene predictions using the other three approaches with the default or available HMMs.

Rapid Evolution of Ovarian-Biased Genes in the Yellow Fever Mosquito (Aedes aegypti).

PubMed

Whittle, Carrie A; Extavour, Cassandra G

2017-08-01

Males and females exhibit highly dimorphic phenotypes, particularly in their gonads, which is believed to be driven largely by differential gene expression. Typically, the protein sequences of genes upregulated in males, or male-biased genes, evolve rapidly as compared to female-biased and unbiased genes. To date, the specific study of gonad-biased genes remains uncommon in metazoans. Here, we identified and studied a total of 2927, 2013, and 4449 coding sequences (CDS) with ovary-biased, testis-biased, and unbiased expression, respectively, in the yellow fever mosquito Aedes aegypti The results showed that ovary-biased and unbiased CDS had higher nonsynonymous to synonymous substitution rates (dN/dS) and lower optimal codon usage (those codons that promote efficient translation) than testis-biased genes. Further, we observed higher dN/dS in ovary-biased genes than in testis-biased genes, even for genes coexpressed in nonsexual (embryo) tissues. Ovary-specific genes evolved exceptionally fast, as compared to testis- or embryo-specific genes, and exhibited higher frequency of positive selection. Genes with ovary expression were preferentially involved in olfactory binding and reception. We hypothesize that at least two potential mechanisms could explain rapid evolution of ovary-biased genes in this mosquito: (1) the evolutionary rate of ovary-biased genes may be accelerated by sexual selection (including female-female competition or male-mate choice) affecting olfactory genes during female swarming by males, and/or by adaptive evolution of olfactory signaling within the female reproductive system ( e.g. , sperm-ovary signaling); and/or (2) testis-biased genes may exhibit decelerated evolutionary rates due to the formation of mating plugs in the female after copulation, which limits male-male sperm competition. Copyright © 2017 by the Genetics Society of America.

Influence of intron length on interaction characters between post-spliced intron and its CDS in ribosomal protein genes

NASA Astrophysics Data System (ADS)

Zhao, Xiaoqing; Li, Hong; Bao, Tonglaga; Ying, Zhiqiang

2012-09-01

Many experiment evidences showed that sequence structures of introns and intron loss/gain can influence gene expression, but current mechanisms did not refer to the functions of post-spliced introns directly. We propose that postspliced introns play their functions in gene expression by interacting with their mRNA sequences and the interaction is characterized by the matched segments between introns and their CDS. In this study, we investigated the interaction characters with length series by improved Smith-Waterman local alignment software for the ribosomal protein genes in C. elegans and D. melanogaster. Our results showed that RF values of five intron groups are significantly high in the central non-conserved region and very low in 5'-end and 3'-end splicing region. It is interesting that the number of the optimal matched regions gradually increases with intron length. Distributions of the optimal matched regions are different for five intron groups. Our study revealed that there are more interaction regions between longer introns and their CDS than shorter, and it provides a positive pattern for regulating the gene expression.

Complete genome sequences of two novel autographiviruses infecting a bacterium from the Pseudomonas fluorescens group.

PubMed

Nowicki, Grzegorz; Walkowiak-Nowicka, Karolina; Zemleduch-Barylska, Agata; Mleczko, Anna; Frąckowiak, Patryk; Nowaczyk, Natalia; Kozdrowska, Emilia; Barylski, Jakub

2017-09-01

In this paper, we describe two independent isolates of a new member of the subfamily Autographivirinae, Pseudomonas phage KNP. The type strain (KNP) has a linear, 40,491-bp-long genome with GC content of 57.3%, and 50 coding DNA sequences (CDSs). The genome of the second strain (WRT) contains one CDS less, encodes a significantly different tail fiber protein and is shorter (40,214 bp; GC content, 57.4%). Phylogenetic analysis indicates that both KNP and WRT belong to the genus T7virus. Together with genetically similar Pseudomonas phages (gh-1, phiPSA2, phiPsa17, PPPL-1, shl2, phi15, PPpW-4, UNO-SLW4, phiIBB-PF7A, Pf-10, and Phi-S1), they form a divergent yet coherent group that stands apart from the T7-like viruses (sensu lato). Analysis of the diversity of this group and its relatedness to other members of the subfamily Autographivirinae led us to the conclusion that this group might be considered as a candidate for a new genus.

Pathogenic mutations of TGFBI and CHST6 genes in Chinese patients with Avellino, lattice, and macular corneal dystrophies.

PubMed

Huo, Ya-nan; Yao, Yu-feng; Yu, Ping

2011-09-01

To investigate gene mutations associated with three different types of corneal dystrophies (CDs), and to establish a phenotype-genotype correlation. Two patients with Avellino corneal dystrophy (ACD), four patients with lattice corneal dystrophy type I (LCD I) from one family, and three patients with macular corneal dystrophy type I (MCD I) were subjected to both clinical and genetic examinations. Slit lamp examination was performed for all the subjects to assess their corneal phenotypes. Genomic DNA was extracted from peripheral blood leukocytes. The coding regions of the human transforming growth factor β-induced (TGFBI) gene and carbohydrate sulfotransferase 6 (CHST6) gene were amplified by polymerase chain reaction (PCR) and subjected to direct sequencing. DNA samples from 50 healthy volunteers were used as controls. Clinical examination showed three different phenotypes of CDs. Genetic examination identified that two ACD subjects were associated with homozygous R124H mutation of TGFBI, and four LCD I subjects were all associated with R124C heterozygous mutation. One MCD I subject was associated with a novel S51X homozygous mutation in CHST6, while the other two MCD I subjects harbored a previously reported W232X homozygous mutation. Our study highlights the prevalence of codon 124 mutations in the TGFBI gene among the Chinese ACD and LCD I patients. Moreover, we found a novel mutation among MCD I patients.

Cognitive dimensions of talim: evaluating weaving notation through cognitive dimensions (CDs) framework.

PubMed

Kaur, Gagan Deep

2017-05-01

The design process in Kashmiri carpet weaving is distributed over a number of actors and artifacts and is mediated by a weaving notation called talim. The script encodes entire design in practice-specific symbols. This encoded script is decoded and interpreted via design-specific conventions by weavers to weave the design embedded in it. The cognitive properties of this notational system are described in the paper employing cognitive dimensions (CDs) framework of Green (People and computers, Cambridge University Press, Cambridge, 1989) and Blackwell et al. (Cognitive technology: instruments of mind-CT 2001, LNAI 2117, Springer, Berlin, 2001). After introduction to the practice, the design process is described in 'The design process' section which includes coding and decoding of talim. In 'Cognitive dimensions of talim' section, after briefly discussing CDs framework, the specific cognitive dimensions possessed by talim are described in detail.

Variations in 5S rDNAs in diploid and tetraploid offspring of red crucian carp × common carp.

PubMed

Ye, Lihai; Zhang, Chun; Tang, Xiaojun; Chen, Yiyi; Liu, Shaojun

2017-08-08

The allotetraploid hybrid fish (4nAT) that was created in a previous study through an intergeneric cross between red crucian carp (Carassius auratus red var., ♀) and common carp (Cyprinus carpio L., ♂) provided an excellent platform to investigate the effect of hybridization and polyploidization on the evolution of 5S rDNA. The 5S rDNAs of paternal common carp were made up of a coding sequence (CDS) and a non-transcribed spacer (NTS) unit, and while the 5S rDNAs of maternal red crucian carp contained a CDS and a NTS unit, they also contained a variable number of interposed regions (IPRs). The CDSs of the 5S rDNAs in both parental fishes were conserved, while their NTS units seemed to have been subjected to rapid evolution. The diploid hybrid 2nF 1 inherited all the types of 5S rDNAs in both progenitors and there were no signs of homeologous recombination in the 5S rDNAs of 2nF 1 by sequencing of PCR products. We obtained two segments of 5S rDNA with a total length of 16,457 bp from allotetraploid offspring 4nAT through bacterial artificial chromosome (BAC) sequencing. Using this sequence together with the 5S rDNA sequences amplified from the genomic DNA of 4nAT, we deduced that the 5S rDNAs of 4nAT might be inherited from the maternal progenitor red crucian carp. Additionally, the IPRs in the 5S rDNAs of 4nAT contained A-repeats and TA-repeats, which was not the case for the IPRs in the 5S rDNAs of 2nF 1 . We also detected two signals of a 200-bp fragment of 5S rDNA in the chromosomes of parental progenitors and hybrid progenies by fluorescence in situ hybridization (FISH). We deduced that during the evolution of 5S rDNAs in different ploidy hybrid fishes, interlocus gene conversion events and tandem repeat insertion events might occurred in the process of polyploidization. This study provided new insights into the relationship among the evolution of 5S rDNAs, hybridization and polyploidization, which were significant in clarifying the genome evolution of polyploid fish.

An Efficient Approach for the Development of Locus Specific Primers in Bread Wheat (Triticum aestivum L.) and Its Application to Re-Sequencing of Genes Involved in Frost Tolerance

PubMed Central

Babben, Steve; Perovic, Dragan; Koch, Michael; Ordon, Frank

2015-01-01

Recent declines in costs accelerated sequencing of many species with large genomes, including hexaploid wheat (Triticum aestivum L.). Although the draft sequence of bread wheat is known, it is still one of the major challenges to developlocus specific primers suitable to be used in marker assisted selection procedures, due to the high homology of the three genomes. In this study we describe an efficient approach for the development of locus specific primers comprising four steps, i.e. (i) identification of genomic and coding sequences (CDS) of candidate genes, (ii) intron- and exon-structure reconstruction, (iii) identification of wheat A, B and D sub-genome sequences and primer development based on sequence differences between the three sub-genomes, and (iv); testing of primers for functionality, correct size and localisation. This approach was applied to single, low and high copy genes involved in frost tolerance in wheat. In summary for 27 of these genes for which sequences were derived from Triticum aestivum, Triticum monococcum and Hordeum vulgare, a set of 119 primer pairs was developed and after testing on Nulli-tetrasomic (NT) lines, a set of 65 primer pairs (54.6%), corresponding to 19 candidate genes, turned out to be specific. Out of these a set of 35 fragments was selected for validation via Sanger's amplicon re-sequencing. All fragments, with the exception of one, could be assigned to the original reference sequence. The approach presented here showed a much higher specificity in primer development in comparison to techniques used so far in bread wheat and can be applied to other polyploid species with a known draft sequence. PMID:26565976

Molecular Cloning, Bioinformatics Analysis and Expression of Insulin-Like Growth Factor 2 from Tianzhu White Yak, Bos grunniens

PubMed Central

Zhang, Quanwei; Gong, Jishang; Wang, Xueying; Wu, Xiaohu; Li, Yalan; Ma, Youji; Zhang, Yong; Zhao, Xingxu

2014-01-01

The IGF family is essential for normal embryonic and postnatal development and plays important roles in the immune system, myogenesis, bone metabolism and other physiological functions, which makes the study of its structure and biological characteristics important. Tianzhu white yak (Bos grunniens) domesticated under alpine hypoxia environments, is well adapted to survive and grow against severe hypoxia and cold temperatures for extended periods. In this study, a full coding sequence of the IGF2 gene of Tianzhu white yak was amplified by reverse transcription PCR and rapid-amplification of cDNA ends (RACE) for the first time. The cDNA sequence revealed an open reading frame of 450 nucleotides, encoding a protein with 179 amino acids. Its expression in different tissues was also studied by Real time PCR. Phylogenetic tree analysis indicated that yak IGF2 was similar to Bos taurus, and 3D structure showed high similarity with the human IGF2. The putative full CDS of yak IGF2 was amplified by PCR in five tissues, and cDNA sequence analysis showed high homology to bovine IGF2. Moreover the super secondary structure prediction showed a similar 3D structure with human IGF2. Its conservation in sequence and structure has facilitated research on IGF2 and its physiological function in yak. PMID:24394317

MiR-191 Regulates Primary Human Fibroblast Proliferation and Directly Targets Multiple Oncogenes

PubMed Central

Polioudakis, Damon; Abell, Nathan S.; Iyer, Vishwanath R.

2015-01-01

miRNAs play a central role in numerous pathologies including multiple cancer types. miR-191 has predominantly been studied as an oncogene, but the role of miR-191 in the proliferation of primary cells is not well characterized, and the miR-191 targetome has not been experimentally profiled. Here we utilized RNA induced silencing complex immunoprecipitations as well as gene expression profiling to construct a genome wide miR-191 target profile. We show that miR-191 represses proliferation in primary human fibroblasts, identify multiple proto-oncogenes as novel miR-191 targets, including CDK9, NOTCH2, and RPS6KA3, and present evidence that miR-191 extensively mediates target expression through coding sequence (CDS) pairing. Our results provide a comprehensive genome wide miR-191 target profile, and demonstrate miR-191’s regulation of primary human fibroblast proliferation. PMID:25992613

A Comprehensive Analysis of Transcript-Supported De Novo Genes in Saccharomyces sensu stricto Yeasts

PubMed Central

Lu, Tzu-Chiao; Leu, Jun-Yi; Lin, Wen-Chang

2017-01-01

Abstract Novel genes arising from random DNA sequences (de novo genes) have been suggested to be widespread in the genomes of different organisms. However, our knowledge about the origin and evolution of de novo genes is still limited. To systematically understand the general features of de novo genes, we established a robust pipeline to analyze >20,000 transcript-supported coding sequences (CDSs) from the budding yeast Saccharomyces cerevisiae. Our analysis pipeline combined phylogeny, synteny, and sequence alignment information to identify possible orthologs across 20 Saccharomycetaceae yeasts and discovered 4,340 S. cerevisiae-specific de novo genes and 8,871 S. sensu stricto-specific de novo genes. We further combine information on CDS positions and transcript structures to show that >65% of de novo genes arose from transcript isoforms of ancient genes, especially in the upstream and internal regions of ancient genes. Fourteen identified de novo genes with high transcript levels were chosen to verify their protein expressions. Ten of them, including eight transcript isoform-associated CDSs, showed translation signals and five proteins exhibited specific cytosolic localizations. Our results suggest that de novo genes frequently arise in the S. sensu stricto complex and have the potential to be quickly integrated into ancient cellular network. PMID:28981695

Head injuries (TBI) to adults and children in motor vehicle crashes.

PubMed

Viano, David C; Parenteau, Chantal S; Xu, Likang; Faul, Mark

2017-08-18

This is a descriptive study. It determined the annual, national incidence of head injuries (traumatic brain injury, TBI) to adults and children in motor vehicle crashes. It evaluated NASS-CDS for exposure and incidence of various head injuries in towaway crashes. It evaluated 3 health databases for emergency department (ED) visits, hospitalizations, and deaths due to TBI in motor vehicle occupants. Four databases were evaluated using 1997-2010 data on adult (15+ years old) and child (0-14 years old) occupants in motor vehicle crashes: (1) NASS-CDS estimated the annual incidence of various head injuries and outcomes in towaway crashes, (2) National Hospital Ambulatory Medical Care Survey (NHAMCS)-estimated ED visits for TBI, (3) National Hospital Discharge Survey (NHDS) estimated hospitalizations for TBI, and (4) National Vital Statistics System (NVSS) estimated TBI deaths. The 4 databases provide annual national totals for TBI related injury and death in motor vehicle crashes based on differing definitions with TBI coded by the Abbreviated Injury Scale (AIS) in NASS-CDS and by International Classification of Diseases (ICD) in the health data. Adults: NASS-CDS had 16,980 ± 2,411 (risk = 0.43 ± 0.06%) with severe head injury (AIS 4+) out of 3,930,543 exposed adults in towaway crashes annually. There were 49,881 ± 9,729 (risk = 1.27 ± 0.25%) hospitalized with AIS 2+ head injury, without death. There were 6,753 ± 882 (risk = 0.17 ± 0.02%) fatalities with a head injury cause. The public health data had 89,331 ± 6,870 ED visits, 33,598 ± 1,052 hospitalizations, and 6,682 ± 22 deaths with TBI. NASS-CDS estimated 48% more hospitalized with AIS 2+ head injury without death than NHDS occupants hospitalized with TBI. NASS-CDS estimated 29% more deaths with AIS 3+ head injury than NVSS occupant TBI deaths but only 1% more deaths with a head injury cause. Children: NASS-CDS had 1,453 ± 318 (risk = 0.32 ± 0.07%) with severe head injury (AIS 4+) out of 454,973 exposed children annually. There were 2,581 ± 683 (risk = 0.57 ± 0.15%) hospitalized with AIS 2+ head injury, without death. There were 466 ± 132 (risk = 0.10 ± 0.03%) fatalities with a head injury cause. The public health data had 19,251 ± 2,803 ED visits, 3,363 ± 255 hospitalizations, and 488 ± 6 deaths with TBI. NASS-CDS estimated 24% fewer hospitalized children with AIS 2+ head injury without death than NHDS hospitalization with TBI. NASS-CDS estimated 31% more deaths with AIS 3+ head injury than NVSS child deaths but 5% fewer deaths with a head injury cause. The annual national incidence of motor vehicle-related head injury (TBI) was estimated using 1997-2010 NASS-CDS from the Department of Transportation and NHAMCS (ED visits), NHDS (hospitalizations), and NVSS (deaths) from the Department of Health and Human Services. The transportation and health databases use different definitions and coding, which complicates direct comparisons. Future work is needed where ICD to AIS translators are used if comparisons of serious head injuries in NASS and health data sets are to be made.

Novel Mutations in pncA Gene of Pyrazinamide Resistant Clinical Isolates of Mycobacterium tuberculosis.

PubMed

Kahbazi, Manijeh; Sarmadian, Hossein; Ahmadi, Azam; Didgar, Farshideh; Sadrnia, Maryam; Poolad, Toktam; Arjomandzadegan, Mohammad

2018-04-16

In clinical isolates of Mycobacterium tuberculosis (MTB), resistance to pyrazinamide occurs by mutations in any positions of the pncA gene (NC_000962.3) especially in nucleotides 359 and 374. In this study we examined the pncA gene sequence in clinical isolates of MTB. Genomic DNA of 33 clinical isolates of MTB was extracted by the Chelex100 method. The polymerase chain reactions (PCR) were performed using specific primers for amplification of 744 bp amplicon comprising the coding sequences (CDS) of the pncA gene. PCR products were sequenced by an automated sequencing Bioscience system. Additionally, semi Nested-allele specific (sNASP) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods were carried out for verification of probable mutations in nucleotides 359 and 374. Sequencing results showed that from 33 MTB clinical isolates, nine pyrazinamide-resistant isolates have mutations. Furthermore, no mutation was detected in 24 susceptible strains in the entire 561 bp of the pncA gene. Moreover, new mutations of G→A at position 3 of the pncA gene were identified in some of the resistant isolates. Results showed that the sNASP method could detect mutations in nucleotide 359 and 374 of the pncA gene, but the PCR-RFLP method by the SacII enzyme could not detect these mutations. In conclusion, the identification of new mutations in the pncA gene confirmed the probable occurrence of mutations in any nucleotides of the pncA gene sequence in resistant isolates of MTB.

Characterization and functional analysis of hypoxia-inducible factor HIF1α and its inhibitor HIF1αn in tilapia.

PubMed

Li, Hong Lian; Gu, Xiao Hui; Li, Bi Jun; Chen, Xiao; Lin, Hao Ran; Xia, Jun Hong

2017-01-01

Hypoxia is a major cause of fish morbidity and mortality in the aquatic environment. Hypoxia-inducible factors are very important modulators in the transcriptional response to hypoxic stress. In this study, we characterized and conducted functional analysis of hypoxia-inducible factor HIF1α and its inhibitor HIF1αn in Nile tilapia (Oreochromis niloticus). By cloning and Sanger sequencing, we obtained the full length cDNA sequences for HIF1α (2686bp) and HIF1αn (1308bp), respectively. The CDS of HIF1α includes 15 exons encoding 768 amino acid residues and the CDS of HIF1αn contains 8 exons encoding 354 amino acid residues. The complete CDS sequences of HIF1α and HIF1αn cloned from tilapia shared very high homology with known genes from other fishes. HIF1α show differentiated expression in different tissues (brain, heart, gill, spleen, liver) and at different hypoxia exposure times (6h, 12h, 24h). HIF1αn expression level under hypoxia is generally increased (6h, 12h, 24h) and shows extremely highly upregulation in brain tissue under hypoxia. A functional determination site analysis in the protein sequences between fish and land animals identified 21 amino acid sites in HIF1α and 2 sites in HIF1αn as significantly associated sites (α = 0.05). Phylogenetic tree-based positive selection analysis suggested 22 sites in HIF1α as positively selected sites with a p-value of at least 95% for fish lineages compared to the land animals. Our study could be important for clarifying the mechanism of fish adaptation to aquatic hypoxia environment.

Characterization and functional analysis of hypoxia-inducible factor HIF1α and its inhibitor HIF1αn in tilapia

PubMed Central

Li, Hong Lian; Gu, Xiao Hui; Li, Bi Jun; Chen, Xiao; Lin, Hao Ran; Xia, Jun Hong

2017-01-01

Hypoxia is a major cause of fish morbidity and mortality in the aquatic environment. Hypoxia-inducible factors are very important modulators in the transcriptional response to hypoxic stress. In this study, we characterized and conducted functional analysis of hypoxia-inducible factor HIF1α and its inhibitor HIF1αn in Nile tilapia (Oreochromis niloticus). By cloning and Sanger sequencing, we obtained the full length cDNA sequences for HIF1α (2686bp) and HIF1αn (1308bp), respectively. The CDS of HIF1α includes 15 exons encoding 768 amino acid residues and the CDS of HIF1αn contains 8 exons encoding 354 amino acid residues. The complete CDS sequences of HIF1α and HIF1αn cloned from tilapia shared very high homology with known genes from other fishes. HIF1α show differentiated expression in different tissues (brain, heart, gill, spleen, liver) and at different hypoxia exposure times (6h, 12h, 24h). HIF1αn expression level under hypoxia is generally increased (6h, 12h, 24h) and shows extremely highly upregulation in brain tissue under hypoxia. A functional determination site analysis in the protein sequences between fish and land animals identified 21 amino acid sites in HIF1α and 2 sites in HIF1αn as significantly associated sites (α = 0.05). Phylogenetic tree-based positive selection analysis suggested 22 sites in HIF1α as positively selected sites with a p-value of at least 95% for fish lineages compared to the land animals. Our study could be important for clarifying the mechanism of fish adaptation to aquatic hypoxia environment. PMID:28278251

Assessment of Holocene soil erosion rates on the loess plateau in East Poland using sedimentary archives from closed depressions

NASA Astrophysics Data System (ADS)

Kołodyńska-Gawrysiak, Renata; Poesen, Jean; Gawrysiak, Leszek

2016-04-01

Closed depressions (CDs) are typical geomorphological features of the European loess belt. They are closed sedimentation basins that enable the estimation of long-term soil erosion rates for different land use environments. This study was conducted in eastern Poland (Nałęczów Plateau). In this region CDs are rather small landforms and the area of 70% of all CDs does not exceed 1500 m2. The study objective was to assess Holocene soil erosion rates in the loess plateau based on a quantitative analysis of colluvial sediments deposited in CDs. Two representative CDs were selected for this study: one CD is located in an old (long-term) forest and the other is situated in a long-term agricultural land. The maximum depth of the CD in the forest, the mean slope gradient and area of the corresponding catchment are 4.9 m, 3.410 and 7568 m² respectively. For the CD in agricultural land these values are 3.2 m, 2.760 and 5156 m² respectively. In both CDs several dozen of drillings and two trenches (2 m long, 1m wide, 2 m deep) were made in the deepest point of the CDs. Mean long-term soil erosion rates were calculated based on the stratigraphy of the soil-sediment sequence infilling the CDs. C-14 and OSL datings of soils and colluvial sediments within the CDs were obtained. For the long-term agricultural used catchment of the CD it was calculated that since 6.31 ± 0.35 ka BP the mean annual soil loss due to water and tillage erosion is 0.63-0.7 t/ha/year or 279.3 mm. In the prehistoric period since 6.31 ± 0.35 ka BP until 1026-1162 AD the mean annual soil erosion rate amounted to 0,10-0.11 t/ha/year or 41.5 mm. During the last ca. 1000 years mean soil erosion rates increased to 3.99-4.63 t/ha/year or 249.2 mm. Results of long-term soil erosion rates (calculated using colluvial sediment sequences in CDs) from agricultural catchments in the loess regions of eastern Poland (this study) and Central Belgium (Gillijns et al. 2005) are quite similar. For the forested catchment of the CD the mean annual soil erosion rate since at least ca. 1000 years is 0.073-0.086 t/ha/year or 41.9 mm. In this catchment soil erosion and correlative colluviation deposits occurred mainly in prehistoric times. CDs play an important role for archiving sediments which allow to reconstruct both natural and anthropogenic processes in the past. The study of these sediment archives allows a better understanding of human-environment interactions and its impact on long-term soil erosion rates. Acknowledgements: The research project was financially supported by the National Centre of Science - project PB-B-12-287-00-13: The origin and evolution of closed depressions in the loess area of the Lublin Upland and their importance for the reconstruction of postglacial morphogenesis of the loess covers. References: Gillijns K., Poesen J., Deckers J., 2005: On the characteristics and origin of closed depression in loess-derived soils in Europe- a case study from central Belgium. Catena 60, 43-58.

The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection

PubMed Central

Kong, Yimeng; Pan, Bohu; Chen, Longxian; Wang, Hongbing; Hao, Pei; Li, Xuan

2016-01-01

The hydrolytic deamination of adenosine to inosine (A-to-I editing) in precursor mRNA induces variable gene products at the post-transcription level. How and to what extent A-to-I RNA editing diversifies transcriptome is not fully characterized in the evolution, and very little is known about the selective constraints that drive the evolution of RNA editing events. Here we present a study on A-to-I RNA editing, by generating a global profile of A-to-I editing for a phylogeny of seven Drosophila species, a model system spanning an evolutionary timeframe of approximately 45 million years. Of totally 9281 editing events identified, 5150 (55.5%) are located in the coding sequences (CDS) of 2734 genes. Phylogenetic analysis places these genes into 1,526 homologous families, about 5% of total gene families in the fly lineages. Based on conservation of the editing sites, the editing events in CDS are categorized into three distinct types, representing events on singleton genes (type I), and events not conserved (type II) or conserved (type III) within multi-gene families. While both type I and II events are subject to purifying selection, notably type III events are positively selected, and highly enriched in the components and functions of the nervous system. The tissue profiles are documented for three editing types, and their critical roles are further implicated by their shifting patterns during holometabolous development and in post-mating response. In conclusion, three A-to-I RNA editing types are found to have distinct evolutionary dynamics. It appears that nervous system functions are mainly tested to determine if an A-to-I editing is beneficial for an organism. The coding plasticity enabled by A-to-I editing creates a new class of binary variations, which is a superior alternative to maintain heterozygosity of expressed genes in a diploid mating system. PMID:27467689

An engineered promoter driving expression of a microbial avirulence gene confers recognition of TAL effectors and reduces growth of diverse Xanthomonas strains in citrus.

PubMed

Shantharaj, Deepak; Römer, Patrick; Figueiredo, Jose F L; Minsavage, Gerald V; Krönauer, Christina; Stall, Robert E; Moore, Gloria A; Fisher, Latanya C; Hu, Yang; Horvath, Diana M; Lahaye, Thomas; Jones, Jeffrey B

2017-09-01

Xanthomonas citri ssp. citri (X. citri), causal agent of citrus canker, uses transcription activator-like effectors (TALEs) as major pathogenicity factors. TALEs, which are delivered into plant cells through the type III secretion system (T3SS), interact with effector binding elements (EBEs) in host genomes to activate the expression of downstream susceptibility genes to promote disease. Predictably, TALEs bind EBEs in host promoters via known combinations of TALE amino acids to DNA bases, known as the TALE code. We introduced 14 EBEs, matching distinct X. citri TALEs, into the promoter of the pepper Bs3 gene (ProBs3 1EBE ), and fused this engineered promoter with multiple EBEs (ProBs3 14EBE ) to either the β-glucuronidase (GUS) reporter gene or the coding sequence (cds) of the pepper gene, Bs3. TALE-induced expression of the Bs3 cds in citrus leaves resulted in no visible hypersensitive response (HR). Therefore, we utilized a different approach in which ProBs3 1EBE and ProBs3 14EBE were fused to the Xanthomonas gene, avrGf1, which encodes a bacterial effector that elicits an HR in grapefruit and sweet orange. We demonstrated, in transient assays, that activation of ProBs3 14EBE by X. citri TALEs is T3SS dependent, and that the expression of AvrGf1 triggers HR and correlates with reduced bacterial growth. We further demonstrated that all tested virulent X. citri strains from diverse geographical locations activate ProBs3 14EBE . TALEs are essential for the virulence of X. citri strains and, because the engineered promoter traps are activated by multiple TALEs, this concept has the potential to confer broad-spectrum, durable resistance to citrus canker in stably transformed plants. © 2016 BSPP AND JOHN WILEY & SONS LTD.

Pathogenic mutations of TGFBI and CHST6 genes in Chinese patients with Avellino, lattice, and macular corneal dystrophies

PubMed Central

Huo, Ya-nan; Yao, Yu-feng; Yu, Ping

2011-01-01

Objective: To investigate gene mutations associated with three different types of corneal dystrophies (CDs), and to establish a phenotype-genotype correlation. Methods: Two patients with Avellino corneal dystrophy (ACD), four patients with lattice corneal dystrophy type I (LCD I) from one family, and three patients with macular corneal dystrophy type I (MCD I) were subjected to both clinical and genetic examinations. Slit lamp examination was performed for all the subjects to assess their corneal phenotypes. Genomic DNA was extracted from peripheral blood leukocytes. The coding regions of the human transforming growth factor β-induced (TGFBI) gene and carbohydrate sulfotransferase 6 (CHST6) gene were amplified by polymerase chain reaction (PCR) and subjected to direct sequencing. DNA samples from 50 healthy volunteers were used as controls. Results: Clinical examination showed three different phenotypes of CDs. Genetic examination identified that two ACD subjects were associated with homozygous R124H mutation of TGFBI, and four LCD I subjects were all associated with R124C heterozygous mutation. One MCD I subject was associated with a novel S51X homozygous mutation in CHST6, while the other two MCD I subjects harbored a previously reported W232X homozygous mutation. Conclusions: Our study highlights the prevalence of codon 124 mutations in the TGFBI gene among the Chinese ACD and LCD I patients. Moreover, we found a novel mutation among MCD I patients. PMID:21887843

Prediction of selenoprotein T structure and its response to selenium deficiency in chicken immune organs.

PubMed

You, Lu; Liu, Ci; Yang, Zi-Jiang; Li, Ming; Li, Shu

2014-08-01

Selenoprotein T (SelT) is associated with the regulation of calcium homeostasis and neuroendocrine secretion. SelT can also change cell adhesion and is involved in redox regulation and cell fixation. However, the structure and function of chicken SelT and its response to selenium (Se) remains unclear. In the present study, 150 1-day-old chickens were randomly divided into a low Se group (L group, fed a Se-deficient diet containing 0.020 mg/kg Se) and a control group (C group, fed a diet containing sodium selenite at 0.2 mg/kg Se). The immune organs (spleen, thymus, and bursa of Fabricius) were collected at 15, 25, 35, 45, and 55 days of age. We performed a sequence analysis and predicted the structure and function of SelT. We also investigated the effects of Se deficiency on the expression of SelT, selenophosphate synthetase-1 (SPS1), and selenocysteine synthase (SecS) using RT-PCR and the oxidative stress in the chicken immune organs. The data showed that the coding sequence (CDS) and deduced amino acid sequence of SelT were highly similar to those of 17 other animals. Se deficiency induced lower (P < 0.05) levels of SelT, SPS1, and SecS, reduced the catalase (CAT) activity, and increased the levels of hydrogen peroxide (H2O2) and hydroxyl radical (-OH) in immune organs. In conclusion, the CDS and deduced amino acid sequence of chicken SelT are highly homologous to those of various mammals. The redox function and response to the Se deficiency of chicken SelT may be conserved. A Se-deficient diet led to a decrease in SelT, SecS, and SPS1 and induced oxidative stress in the chicken immune organs. To our knowledge, this is the first report of predictions of chicken SelT structure and function. The present study demonstrated the relationship between the selenoprotein synthases (SPS1, SecS) and SelT expression in the chicken immune organs and further confirmed oxidative stress caused by Se deficiency. Thus, the information presented in this study is helpful to understand chicken SelT structure and function. Meanwhile, the present research also confirmed the negative effects of Se deficiency on chicken immune organs.

First comparative characterization of three distinct ferritin subunits from a teleost: Evidence for immune-responsive mRNA expression and iron depriving activity of seahorse (Hippocampus abdominalis) ferritins.

PubMed

Oh, Minyoung; Umasuthan, Navaneethaiyer; Elvitigala, Don Anushka Sandaruwan; Wan, Qiang; Jo, Eunyoung; Ko, Jiyeon; Noh, Gyeong Eon; Shin, Sangok; Rho, Sum; Lee, Jehee

2016-02-01

Ferritins play an indispensable role in iron homeostasis through their iron-withholding function in living beings. In the current study, cDNA sequences of three distinct ferritin subunits, including a ferritin H, a ferritin M, and a ferritin L, were identified from big belly seahorse, Hippocampus abdominalis, and molecularly characterized. Complete coding sequences (CDS) of seahorse ferritin H (HaFerH), ferritin M (HaFerM), and ferritin L (HaFerL) subunits were comprised of 531, 528, and 522 base pairs (bp), respectively, which encode polypeptides of 177, 176, and 174 amino acids, respectively, with molecular masses of ∼20-21 kDa. Our in silico analyses demonstrate that these three ferritin subunits exhibit the typical characteristics of ferritin superfamily members including iron regulatory elements, domain signatures, and reactive centers. The coding sequences of HaFerH, M, and L were cloned and the corresponding proteins were overexpressed in a bacterial system. Recombinantly expressed HaFer proteins demonstrated detectable in vivo iron sequestrating (ferroxidase) activity, consistent with their putative iron binding capability. Quantification of the basal expression of these three HaFer sequences in selected tissues demonstrated a gene-specific ubiquitous spatial distribution pattern, with abundance of mRNA in HaFerM in the liver and predominant expression of HaFerH and HaFerL in blood. Interestingly, the basal expression of all three ferritin genes was found to be significantly modulated against pathogenic stress mounted by lipopolysaccharides (LPS), poly I:C, Streptococcus iniae, and Edwardsiella tarda. Collectively, our findings suggest that the three HaFer subunits may be involved in iron (II) homeostasis in big belly seahorse and that they are important in its host defense mechanisms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Study on the binding of procaine hydrochloride to DNA/DNA bases and the effect of CdS nanoparticles on the binding behavior.

PubMed

Ping, Gang; Lv, Gang; Gutmann, Sebastian; Chen, Chen; Zhang, Renyun; Wang, Xuemei

2006-01-01

The interaction between procaine hydrochloride and DNA/DNA bases in the absence and presence of cadmium sulfide (CdS) nanoparticles has been explored in this study by using differential pulse voltammetry, atomic force microscopy (AFM) and so on, which illustrates the different binding behaviors of procaine hydrochloride with different DNA bases. The results clearly indicate that the binding of purines to procaine hydrochloride is stronger than that of pyrimidines and the binding affinity is in the order of G > A > T > C. In addition, it was observed that the presence of CdS nanoparticles could remarkably enhance the probing sensitivity for the interaction between procaine hydrochloride and DNA/DNA bases. Furthermore, AFM study illustrates that procaine hydrochloride can bind to some specific sites of DNA chains, which indicates that procaine hydrochloride may interact with some special sequences of DNA.

[Cloning and sequencing of KIR2DL1 framework gene cDNA and identification of a novel allele].

PubMed

Sun, Ge; Wang, Chang; Zhen, Jianxin; Zhang, Guobin; Xu, Yunping; Deng, Zhihui

2016-10-01

To develop an assay for cDNA cloning and haplotype sequencing of KIR2DL1 framework gene and determine the genotype of an ethnic Han from southern China. Total RNA was isolated from peripheral blood sample, and complementary DNA (cDNA) transcript was synthesized by RT-PCR. The entire coding sequence of the KIR2DL1 framework gene was amplified with a pair of KIR2DL1-specific PCR primers. The PCR products with a length of approximately 1.2 kb were then subjected to cloning and haplotype sequencing. A specific target fragment of the KIR2DL1 framework gene was obtained. Following allele separation, a wild-type KIR2DL1*00302 allele and a novel variant allele, KIR2DL1*031, were identified. Sequence alignment with KIR2DL1 alleles from the IPD-KIR Database showed that the novel allele KIR2DL1*031 has differed from the closest allele KIR2DL1*00302 by a non-synonymous mutation at CDS nt 188A>G (codon 42 GAG>GGG) in exon 4, which has caused an amino acid change Glu42Gly. The sequence of the novel allele KIR2DL1*031 was submitted to GenBank under the accession number KP025960 and to the IPD-KIR Database under the submission number IWS40001982. A name KIR2DL1*031 has been officially assigned by the World Health Organization (WHO) Nomenclature Committee. An assay for cDNA cloning and haplotype sequencing of KIR2DL1 has been established, which has a broad applications in KIR studies at allelic level.

Comparative effectiveness of childhood obesity interventions in pediatric primary care: a cluster-randomized clinical trial.

PubMed

Taveras, Elsie M; Marshall, Richard; Kleinman, Ken P; Gillman, Matthew W; Hacker, Karen; Horan, Christine M; Smith, Renata L; Price, Sarah; Sharifi, Mona; Rifas-Shiman, Sheryl L; Simon, Steven R

2015-06-01

Evidence of effective treatment of childhood obesity in primary care settings is limited. To examine the extent to which computerized clinical decision support (CDS) delivered to pediatric clinicians at the point of care of obese children, with or without individualized family coaching, improved body mass index (BMI; calculated as weight in kilograms divided by height in meters squared) and quality of care. We conducted a cluster-randomized, 3-arm clinical trial. We enrolled 549 children aged 6 to 12 years with a BMI at the 95% percentile or higher from 14 primary care practices in Massachusetts from October 1, 2011, through June 30, 2012. Patients were followed up for 1 year (last follow-up, August 30, 2013). In intent-to-treat analyses, we used linear mixed-effects models to account for clustering by practice and within each person. In 5 practices randomized to CDS, pediatric clinicians received decision support on obesity management, and patients and their families received an intervention for self-guided behavior change. In 5 practices randomized to CDS + coaching, decision support was augmented by individualized family coaching. The remaining 4 practices were randomized to usual care. Smaller age-associated change in BMI and the Healthcare Effectiveness Data and Information Set (HEDIS) performance measures for obesity during the 1-year follow-up. At baseline, mean (SD) patient age and BMI were 9.8 (1.9) years and 25.8 (4.3), respectively. At 1 year, we obtained BMI from 518 children (94.4%) and HEDIS measures from 491 visits (89.4%). The 3 randomization arms had different effects on BMI over time (P = .04). Compared with the usual care arm, BMI increased less in children in the CDS arm during 1 year (-0.51 [95% CI, -0.91 to -0.11]). The CDS + coaching arm had a smaller magnitude of effect (-0.34 [95% CI, -0.75 to 0.07]). We found substantially greater achievement of childhood obesity HEDIS measures in the CDS arm (adjusted odds ratio, 2.28 [95% CI, 1.15-4.53]) and CDS + coaching arm (adjusted odds ratio, 2.60 [95% CI, 1.25-5.41]) and higher use of HEDIS codes for nutrition or physical activity counseling (CDS arm, 45%; CDS + coaching arm, 25%; P < .001 compared with usual care arm). An intervention that included computerized CDS for pediatric clinicians and support for self-guided behavior change for families resulted in improved childhood BMI. Both interventions improved the quality of care for childhood obesity. clinicaltrials.gov Identifier: NCT01537510.

Sequence Based Structural Characterization and Genetic Diversity Analysis of Full Length TLR4 CDS in Crossbred and Indigenous Cattle.

PubMed

Mishra, Chinmoy; Kumar, Subodh; Sonwane, Arvind Asaram; Yathish, H M; Chaudhary, Rajni

2017-01-02

The exploration of candidate genes for immune response in cattle may be vital for improving our understanding regarding the species specific response to pathogens. Toll-like receptor 4 (TLR4) is mostly involved in protection against the deleterious effects of Gram negative pathogens. Approximately 2.6 kb long cDNA sequence of TLR4 gene covering the entire coding region was characterized in two Indian milk cattle (Vrindavani and Tharparkar). The phylogenetic analysis confirmed that the bovine TLR4 was apparently evolved from an ancestral form that predated the appearance of vertebrates, and it is grouped with buffalo, yak, and mithun TLR4s. Sequence analysis revealed a 2526-nucleotide long open reading frame (ORF) encoding 841 amino acids, similar to other cattle breeds. The calculated molecular weight of the translated ORF was 96144 and 96040.9 Da; the isoelectric point was 6.35 and 6.42 in Vrindavani and Tharparkar cattle, respectively. The Simple Modular Architecture Research Tool (SMART) analysis identified 14 leucine rich repeats (LRR) motifs in bovine TLR4 protein. The deduced TLR4 amino acid sequence of Tharparkar had 4 different substitutions as compared to Bos taurus, Sahiwal, and Vrindavani. The signal peptide cleavage site predicted to lie between 16th and 17th amino acid of mature peptide. The transmebrane helix was identified between 635-657 amino acids in the mature peptide.

Phenotypic comparison of individuals with homozygous or heterozygous mutation of NOTCH3 in a large CADASIL family.

PubMed

Abou Al-Shaar, Hussam; Qadi, Najeeb; Al-Hamed, Mohamed H; Meyer, Brian F; Bohlega, Saeed

2016-08-15

Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a hereditary microangiopathy caused by mutations in NOTCH3, very rarely homoallelic. To describe the clinical, radiological, and neuropsychological features in an extended CADASIL family including members with either a homozygous or heterozygous NOTCH3 R1231C mutation. The pedigree included 3 generations of a family with 13 affected individuals. The patients were examined clinically and radiologically. Neuropsychological testing was performed on the proband. Sequencing of the entire coding DNA sequence (CDS) and flanking regions of NOTCH3 was undertaken using PCR amplification and direct Sanger sequencing. Homozygous C3769T mutation, predicting R1231C in exon 22 of NOTCH3 was found in 7 family members. Six other family members harbored the same in the heterozygous state. Homozygous individuals showed a slightly more severe clinical and radiological phenotype of earlier onset compared to their heterozygous counterparts. This study reports the largest number of patients with homozygous NOTCH3 mutation. The phenotype and imaging features of homozygous individuals is within the spectrum of CADASIL, although slightly at the severe end when compared to heterozygotes carrying the same mutation. Both genetic modifiers and environmental factors may play an essential role in modification and alteration of the clinical phenotype and white matter changes among CADASIL patients. Copyright © 2016 Elsevier B.V. All rights reserved.

Complete genome sequence of Yersinia ruckeri str. CSF007-82, etiologic agent of enteric redmouth disease in salmonid fish

USDA-ARS?s Scientific Manuscript database

We present the complete, closed and finished chromosomal and extra-chromosomal genome sequences of Y. ruckeri strain CSF007-82, etiologic agent of enteric red mouth disease in salmonid fish. The chromosome is 3,799,036 bp with a G+C content of 47.5% and encodes 3,530 predicted CDS, 7 ribosomal opero...

RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit.

PubMed

Garcia-Seco, Daniel; Zhang, Yang; Gutierrez-Mañero, Francisco J; Martin, Cathie; Ramos-Solano, Beatriz

2015-01-22

There is an increasing interest in berries, especially blackberries in the diet, because of recent reports of their health benefits due to their high content of flavonoids. A broad range of genomic tools are available for other Rosaceae species but these tools are still lacking in the Rubus genus, thus limiting gene discovery and the breeding of improved varieties. De novo RNA-seq of ripe blackberries grown under field conditions was performed using Illumina Hiseq 2000. Almost 9 billion nucleotide bases were sequenced in total. Following assembly, 42,062 consensus sequences were detected. For functional annotation, 33,040 (NR), 32,762 (NT), 21,932 (Swiss-Prot), 20,134 (KEGG), 13,676 (COG), 24,168 (GO) consensus sequences were annotated using different databases; in total 34,552 annotated sequences were identified. For protein prediction analysis, the number of coding DNA sequences (CDS) that mapped to the protein database was 32,540. Non redundant (NR), annotation showed that 25,418 genes (73.5%) has the highest similarity with Fragaria vesca subspecies vesca. Reanalysis was undertaken by aligning the reads with this reference genome for a deeper analysis of the transcriptome. We demonstrated that de novo assembly, using Trinity and later annotation with Blast using different databases, were complementary to alignment to the reference sequence using SOAPaligner/SOAP2. The Fragaria reference genome belongs to a species in the same family as blackberry (Rosaceae) but to a different genus. Since blackberries are tetraploids, the possibility of artefactual gene chimeras resulting from mis-assembly was tested with one of the genes sequenced by RNAseq, Chalcone Synthase (CHS). cDNAs encoding this protein were cloned and sequenced. Primers designed to the assembled sequences accurately distinguished different contigs, at least for chalcone synthase genes. We prepared and analysed transcriptome data from ripe blackberries, for which prior genomic information was limited. This new sequence information will improve the knowledge of this important and healthy fruit, providing an invaluable new tool for biological research.

Large-Scale Sequencing of Two Regions in Human Chromosome 7q22: Analysis of 650 kb of Genomic Sequence around the EPO and CUTL1 Loci Reveals 17 Genes

PubMed Central

Glöckner, Gernot; Scherer, Stephen; Schattevoy, Ruben; Boright, Andrew; Weber, Jacqueline; Tsui, Lap-Chee; Rosenthal, André

1998-01-01

We have sequenced and annotated two genomic regions located in the Giemsa negative band q22 of human chromosome 7. The first region defined by the erythropoietin (EPO) locus is 228 kb in length and contains 13 genes. Whereas 3 genes (GNB2, EPO, PCOLCE) were known previously on the mRNA level, we have been able to identify 10 novel genes using a newly developed automatic annotation tool RUMMAGE-DP, which comprises >26 different programs mainly for exon prediction, homology searches, and compositional and repeat analysis. For precise annotation we have also resequenced ESTs identified to the region and assembled them to build large cDNAs. In addition, we have investigated the differential splicing of genes. Using these tools we annotated 4 of the 10 genes as a zonadhesin, a transferrin homolog, a nucleoporin-like gene, and an actin gene. Two genes showed weak similarity to an insulin-like receptor and a neuronal protein with a leucine-rich amino-terminal domain. Four predicted genes (CDS1–CDS4) CDS that have been confirmed on the mRNA level showed no similarity to known proteins and a potential function could not be assigned. The second region in 7q22 defined by the CUTL1 (CCAAT displacement protein and its splice variant) locus is 416 kb in length and contains three known genes, including PMSL12, APS, CUTL1, and a novel gene (CDS5). The CUTL1 locus, consisting of two splice variants (CDP and CASP), occupies >300 kb. Based on the G,C profile an isochore switch can be defined between the CUTL1 gene and the APS and PMSL12 genes. [Clones 37G3, 164c7, and 235f8 are deposited in GenBank under accession no. AF053356; clone 123e15, accession no. AF024533; 186d2, accession no. AF024534; 46f6, accession no. AF006752; 50h2, accession no. AF047825; and 76h2, accession no. AF030453] PMID:9799793

Identification of unannotated exons of low abundance transcripts in Drosophila melanogaster and cloning of a new serine protease gene upregulated upon injury.

PubMed

Maia, Rafaela M; Valente, Valeria; Cunha, Marco A V; Sousa, Josane F; Araujo, Daniela D; Silva, Wilson A; Zago, Marco A; Dias-Neto, Emmanuel; Souza, Sandro J; Simpson, Andrew J G; Monesi, Nadia; Ramos, Ricardo G P; Espreafico, Enilza M; Paçó-Larson, Maria L

2007-07-24

The sequencing of the D.melanogaster genome revealed an unexpected small number of genes (~ 14,000) indicating that mechanisms acting on generation of transcript diversity must have played a major role in the evolution of complex metazoans. Among the most extensively used mechanisms that accounts for this diversity is alternative splicing. It is estimated that over 40% of Drosophila protein-coding genes contain one or more alternative exons. A recent transcription map of the Drosophila embryogenesis indicates that 30% of the transcribed regions are unannotated, and that 1/3 of this is estimated as missed or alternative exons of previously characterized protein-coding genes. Therefore, the identification of the variety of expressed transcripts depends on experimental data for its final validation and is continuously being performed using different approaches. We applied the Open Reading Frame Expressed Sequence Tags (ORESTES) methodology, which is capable of generating cDNA data from the central portion of rare transcripts, in order to investigate the presence of hitherto unnanotated regions of Drosophila transcriptome. Bioinformatic analysis of 1,303 Drosophila ORESTES clusters identified 68 sequences derived from unannotated regions in the current Drosophila genome version (4.3). Of these, a set of 38 was analysed by polyA+ northern blot hybridization, validating 17 (50%) new exons of low abundance transcripts. For one of these ESTs, we obtained the cDNA encompassing the complete coding sequence of a new serine protease, named SP212. The SP212 gene is part of a serine protease gene cluster located in the chromosome region 88A12-B1. This cluster includes the predicted genes CG9631, CG9649 and CG31326, which were previously identified as up-regulated after immune challenges in genomic-scale microarray analysis. In agreement with the proposal that this locus is co-regulated in response to microorganisms infection, we show here that SP212 is also up-regulated upon injury. Using the ORESTES methodology we identified 17 novel exons from low abundance Drosophila transcripts, and through a PCR approach the complete CDS of one of these transcripts was defined. Our results show that the computational identification and manual inspection are not sufficient to annotate a genome in the absence of experimentally derived data.

Identification of unannotated exons of low abundance transcripts in Drosophila melanogaster and cloning of a new serine protease gene upregulated upon injury

PubMed Central

Maia, Rafaela M; Valente, Valeria; Cunha, Marco AV; Sousa, Josane F; Araujo, Daniela D; Silva, Wilson A; Zago, Marco A; Dias-Neto, Emmanuel; Souza, Sandro J; Simpson, Andrew JG; Monesi, Nadia; Ramos, Ricardo GP; Espreafico, Enilza M; Paçó-Larson, Maria L

2007-01-01

Background The sequencing of the D.melanogaster genome revealed an unexpected small number of genes (~ 14,000) indicating that mechanisms acting on generation of transcript diversity must have played a major role in the evolution of complex metazoans. Among the most extensively used mechanisms that accounts for this diversity is alternative splicing. It is estimated that over 40% of Drosophila protein-coding genes contain one or more alternative exons. A recent transcription map of the Drosophila embryogenesis indicates that 30% of the transcribed regions are unannotated, and that 1/3 of this is estimated as missed or alternative exons of previously characterized protein-coding genes. Therefore, the identification of the variety of expressed transcripts depends on experimental data for its final validation and is continuously being performed using different approaches. We applied the Open Reading Frame Expressed Sequence Tags (ORESTES) methodology, which is capable of generating cDNA data from the central portion of rare transcripts, in order to investigate the presence of hitherto unnanotated regions of Drosophila transcriptome. Results Bioinformatic analysis of 1,303 Drosophila ORESTES clusters identified 68 sequences derived from unannotated regions in the current Drosophila genome version (4.3). Of these, a set of 38 was analysed by polyA+ northern blot hybridization, validating 17 (50%) new exons of low abundance transcripts. For one of these ESTs, we obtained the cDNA encompassing the complete coding sequence of a new serine protease, named SP212. The SP212 gene is part of a serine protease gene cluster located in the chromosome region 88A12-B1. This cluster includes the predicted genes CG9631, CG9649 and CG31326, which were previously identified as up-regulated after immune challenges in genomic-scale microarray analysis. In agreement with the proposal that this locus is co-regulated in response to microorganisms infection, we show here that SP212 is also up-regulated upon injury. Conclusion Using the ORESTES methodology we identified 17 novel exons from low abundance Drosophila transcripts, and through a PCR approach the complete CDS of one of these transcripts was defined. Our results show that the computational identification and manual inspection are not sufficient to annotate a genome in the absence of experimentally derived data. PMID:17650329

Chromosomal flhB1 gene of the alphaproteobacterium Azospirillum brasilense Sp245 is essential for correct assembly of both constitutive polar flagellum and inducible lateral flagella.

PubMed

Filip'echeva, Yulia; Shelud'ko, Andrei; Prilipov, Alexei; Telesheva, Elizaveta; Mokeev, Dmitry; Burov, Andrei; Petrova, Lilia; Katsy, Elena

2018-03-01

Azospirillum brasilense has the ability of swimming and swarming motility owing to the work of a constitutive polar flagellum and inducible lateral flagella, respectively. The interplay between these flagellar systems is poorly understood. One of the key elements of the flagellar export apparatus is the protein FlhB. Two predicted flhB genes are present in the genome of A. brasilense Sp245 (accession nos. HE577327-HE577333). Experimental evidence obtained here indicates that the chromosomal coding sequence (CDS) AZOBR_150177 (flhB1) of Sp245 is essential for the production of both types of flagella. In an flhB1:: Omegon-Km mutant, Sp245.1063, defects in polar and lateral flagellar assembly and motility were complemented by expressing the wild-type flhB1 gene from plasmid pRK415. It was found that Sp245.1063 lost the capacity for slight but statistically significant decrease in mean cell length in response to transfer from solid to liquid media, and vice versa; in the complemented mutant, this capacity was restored. It was also shown that after the acquisition of the pRK415-harbored downstream CDS AZOBR_150176, cells of Sp245 and Sp245.1063 ceased to elongate on solid media. These initial data suggest that the AZOBR_150176-encoded putative multisensory hybrid sensor histidine kinase-response regulator, in concert with FlhB1, plays a role in morphological response of azospirilla to changes in the hardness of a milieu.

GS6, a member of the GRAS gene family, negatively regulates grain size in rice.

PubMed

Sun, Lianjun; Li, Xiaojiao; Fu, Yongcai; Zhu, Zuofeng; Tan, Lubin; Liu, Fengxia; Sun, Xianyou; Sun, Xuewen; Sun, Chuanqing

2013-10-01

Grain size is an important yield-related trait in rice. Intensive artificial selection for grain size during domestication is evidenced by the larger grains of most of today's cultivars compared with their wild relatives. However, the molecular genetic control of rice grain size is still not well characterized. Here, we report the identification and cloning of Grain Size 6 (GS6), which plays an important role in reducing grain size in rice. A premature stop at the +348 position in the coding sequence (CDS) of GS6 increased grain width and weight significantly. Alignment of the CDS regions of GS6 in 90 rice materials revealed three GS6 alleles. Most japonica varieties (95%) harbor the Type I haplotype, and 62.9% of indica varieties harbor the Type II haplotype. Association analysis revealed that the Type I haplotype tends to increase the width and weight of grains more than either of the Type II or Type III haplotypes. Further investigation of genetic diversity and the evolutionary mechanisms of GS6 showed that the GS6 gene was strongly selected in japonica cultivars. In addition, a "ggc" repeat region identified in the region that encodes the GRAS domain of GS6 played an important historic role in the domestication of grain size in rice. Knowledge of the function of GS6 might aid efforts to elucidate the molecular mechanisms that control grain development and evolution in rice plants, and could facilitate the genetic improvement of rice yield. © 2013 Institute of Botany, Chinese Academy of Sciences.

Comparative de novo transcriptome analysis of male and female Sea buckthorn.

PubMed

Bansal, Ankush; Salaria, Mehul; Sharma, Tashil; Stobdan, Tsering; Kant, Anil

2018-02-01

Sea buckthorn is a dioecious medicinal plant found at high altitude. The plant has both male and female reproductive organs in separate individuals. In this article, whole transcriptome de novo assemblies of male and female flower bud samples were carried out using Illumina NextSeq 500 platform to determine the role of the genes involved in sex determination. Moreover, genes with differential expression in male and female transcriptomes were identified to understand the underlying sex determination mechanism. The current study showed 63,904 and 62,272 coding sequences (CDS) in female and male transcriptome data sets, respectively. 16,831 common CDS were screened out from both transcriptomes, out of which 625 were upregulated and 491 were found to be downregulated. To understand the potential regulatory roles of differentially expressed genes in metabolic networks and biosynthetic pathways: KEGG mapping, gene ontology, and co-expression network analysis were performed. Comparison with Flowering Interactive Database (FLOR-ID) resulted in eight differentially expressed genes viz. CHD3-type chromatin-remodeling factor PICKLE ( PKL ), phytochrome-associated serine/threonine-protein phosphatase ( FYPP ), protein TOPLESS ( TPL ), sensitive to freezing 6 ( SFR6 ), lysine-specific histone demethylase 1 homolog 1 ( LDL1 ), pre-mRNA-processing-splicing factor 8A ( PRP8A ), sucrose synthase 4 ( SUS4 ), ubiquitin carboxyl-terminal hydrolase 12 ( UBP12 ), known to be broadly involved in flowering, photoperiodism, embryo development, and cold response pathways. Male and female flower bud transcriptome data of Sea buckthorn may provide comprehensive information at genomic level for the identification of genetic regulation involved in sex determination.

Fever of unknown origin as initial manifestation of large vessel giant cell arteritis: diagnosis by colour-coded sonography and 18-FDG-PET.

PubMed

Czihal, M; Tatò, F; Förster, S; Rademacher, A; Schulze-Koops, H; Hoffmann, U

2010-01-01

To evaluate the clinical characteristics and imaging results (CDS, 18-FDG-PET) of patients with large vessel giant cell arteritis (LV-GCA) presenting as fever of unknown origin (FUO). From a series of 82 patients with GCA we identified 8 patients with FUO as initial disease manifestation. Clinical characteristics and results of CDS and 18-FDG-PET were analysed. Patients with FUO and those with other clinical manifestations of GCA were compared. 18-FDG-PET-scans were available for 6/8 patients, revealing enhanced tracer uptake of the thoracic aorta and the aortic branches in all patients. CDS was performed in 8/8 patients, with detection of hypoechogenic wall thickening related to LV-GCA in 7/8 patients. Subjects with FUO were significantly younger (60.9 vs. 69.3 years, p<0.01) and had a stronger humoral inflammatory response (CRP 12.6 vs. 7.1 mg/dl, p<0.01; ESR 110 vs. 71 mm/hour, p<0.01), when compared to the other GCA-patients. LV-GCA should be considered as important differential diagnosis in patients with FUO. In addition to 18-FDG-PET, which is known to be a valuable method in the diagnostic work-up of FUO, we recommend CDS of the supraaortal and femoropopliteal arteries for the initial diagnostic work-up.

High-Resolution Near-Infrared Speckle Interferometry and Radiative Transfer Modeling of the OH/IR Star OH 26.5+0.6

NASA Astrophysics Data System (ADS)

Driebe, T.; Riechers, D.; Balega, Y. Y.; Hofmann, K.-H.; Men'shchikov, A. B.; Weigelt, G.

We present near-infrared speckle interferometry of the OH/IR star OH 26.5+0.6 in the K' band obtained with the 6m telescope of the Special Astrophysical Observatory (SAO) in Oct. 2003. At a wavelength of λ = 2.13 μm the diffraction-limited resolution of 74 mas was attained. The reconstructed visibility reveals a spherically symmetric, circumstellar dust shell (CDS) surrounding the central star. In accordance with the deep silicate absorption feature in the spectral energy distribution (SED), the drop of the visibility function to a value of 0.36 at the cutoff frequency indicates a rather large optical depth of the CDS. To determine the structure and the properties of the CDS of OH 26.5+0.6, radiative transfer calculations using the code DUSTY[3] were performed to simultaneously model its visibility and the SED. Since OH 26.5+0.6 is highly variable, the observational data taken into consideration for the modeling correspond to different phases of the object's variability cycle. As in the case of another OH/IR star, OH 104.9+2.4 (see [5] and Riechers et al., this volume), we used these observational constraints at different epochs to derive several physical parameters of the central star and the CDS of OH 26.5+0.6 as a function of phase

Cloning, Phylogenetic Analysis, and Distribution of Free Fatty Acid Receptor GPR120 Expression along the Gastrointestinal Tract of Housing versus Grazing Kid Goats.

PubMed

Ran, Tao; Li, Hengzhi; Liu, Yong; Zhou, Chuanshe; Tang, Shaoxun; Han, Xuefeng; Wang, Min; He, Zhixiong; Kang, Jinghe; Yan, Qiongxian; Tan, Zhiliang; Beauchemin, Karen A

2016-03-23

G-protein-coupled receptor 120 (GPR120) is reported as a long-chain fatty acid (LCFA) receptor that elicits free fatty acid (FFA) regulation on metabolism homeostasis. The study aimed to clone the gpr120 gene of goats (g-GPR120) and subsequently investigate phylogenetic analysis and tissue distribution throughout the digestive tracts of kid goats, as well as the effect of housing versus grazing (H vs G) feeding systems on GPR120 expression. Partial coding sequence (CDS) of g-GPR120 was cloned and submitted to NCBI (accession no. KU161270 ). Phylogenetic analysis revealed that g-GPR120 shared higher homology in both mRNA and amino acid sequences for ruminants than nonruminants. Immunochemistry, real-time PCR, and Western blot analysis showed that g-GPR120 was expressed throughout the digestive tracts of goats. The expression of g-GPR120 was affected by feeding system and age, with greater expression of g-GPR120 in the G group. It was concluded that the g-GPR120-mediated LCFA chemosensing mechanism is widely present in the tongue and gastrointestinal tract of goats and that its expression can be affected by feeding system and age.

Novel Insights into the Transcriptome of Dirofilaria immitis

PubMed Central

Zhang, Zhihe; Hou, Rong; Wu, Xuhang; Yang, Deying; Zhang, Runhui; Zheng, Wanpeng; Nie, Huaming; Xie, Yue; Yan, Ning; Yang, Zhi; Wang, Chengdong; Luo, Li; Liu, Li; Gu, Xiaobin; Wang, Shuxian; Peng, Xuerong; Yang, Guangyou

2012-01-01

Background The heartworm Dirofilaria immitis is the causal agent of cardiopulmonary dirofilariosis in dogs and cats, and also infects a wide range of wild mammals as well as humans. One bottleneck for the design of fundamentally new intervention and management strategies against D. immitis may be the currently limited knowledge of fundamental molecular aspects of D. immitis. Methodology/Principal Findings A next-generation sequencing platform combining computational approaches was employed to assess a global view of the heartworm transcriptome. A total of 20,810 unigenes (mean length  = 1,270 bp) were assembled from 22.3 million clean reads. From these, 15,698 coding sequences (CDS) were inferred, and about 85% of the unigenes had orthologs/homologs in public databases. Comparative transcriptomic study uncovered 4,157 filarial-specific genes as well as 3,795 genes potentially involved in filarial-Wolbachia symbiosis. In addition, the potential intestine transcriptome of D. immitis (1,101 genes) was mined for the first time, which might help to discover ‘hidden antigens’. Conclusions/Significance This study provides novel insights into the transcriptome of D. immitis and sheds light on its molecular processes and survival mechanisms. Furthermore, it provides a platform to discover new vaccine candidates and potential targets for new drugs against dirofilariosis. PMID:22911833

Transcriptome Analysis of the Chrysanthemum Foliar Nematode, Aphelenchoides ritzemabosi (Aphelenchida: Aphelenchoididae)

PubMed Central

Li, Jun-Yi; Xie, Hui; Xu, Chun-Ling; Li, Yu

2016-01-01

The chrysanthemum foliar nematode (CFN), Aphelenchoides ritzemabosi, is a plant parasitic nematode that attacks many plants. In this study, a transcriptomes of mixed-stage population of CFN was sequenced on the Illumina HiSeq 2000 platform. 68.10 million Illumina high quality paired end reads were obtained which generated 26,817 transcripts with a mean length of 1,032 bp and an N50 of 1,672 bp, of which 16,467 transcripts were annotated against six databases. In total, 20,311 coding region sequences (CDS), 495 simple sequence repeats (SSRs) and 8,353 single-nucleotide polymorphisms (SNPs) were predicted, respectively. The CFN with the most shared sequences was B. xylophilus with 16,846 (62.82%) common transcripts and 10,543 (39.31%) CFN transcripts matched sequences of all of four plant parasitic nematodes compared. A total of 111 CFN transcripts were predicted as homologues of 7 types of carbohydrate-active enzymes (CAZymes) with plant/fungal cell wall-degrading activities, fewer transcripts were predicted as homologues of plant cell wall-degrading enzymes than fungal cell wall-degrading enzymes. The phylogenetic analysis of GH5, GH16, GH43 and GH45 proteins between CFN and other organisms showed CFN and other nematodes have a closer phylogenetic relationship. In the CFN transcriptome, sixteen types of genes orthologues with seven classes of protein families involved in the RNAi pathway in C. elegans were predicted. This research provides comprehensive gene expression information at the transcriptional level, which will facilitate the elucidation of the molecular mechanisms of CFN and the distribution of gene functions at the macro level, potentially revealing improved methods for controlling CFN. PMID:27875578

Extremely High Peak Power Pulsed RF and UWB EMR Effects on Genomic Transcription - Microarray Assessment

DTIC Science & Technology

2008-06-26

Homo sapiens decorin variant C mRNA, complete cds. 2.117 PKNOX2 HUM408A08B Human fetal brain (TFujiwara) Homo sapiens cDNA clone GEN -408A08 5’, mRNA...mRNA, complete cds. 2.117 PKNOX2 HUM408A08B Human fetal brain (TFujiwara) Homo sapiens cDNA clone GEN -408A08 5’, mRNA sequence. 2.076 SEC23B...RAS oncogene family ; RAB33B, member RAS oncogene family 205300_s_at 0.37 U1SNRNPBP U11/U12 snRNP 35K 220728_at 0.349 218689_at 0.342 FANCF Fanconi

A composite six bp in-frame deletion in the melanocortin 1 receptor (MC1R) gene is associated with the Japanese brindling coat colour in rabbits (Oryctolagus cuniculus).

PubMed

Fontanesi, Luca; Scotti, Emilio; Colombo, Michela; Beretti, Francesca; Forestier, Lionel; Dall'Olio, Stefania; Deretz, Séverine; Russo, Vincenzo; Allain, Daniel; Oulmouden, Ahmad

2010-07-01

In the domestic rabbit (Oryctolagus cuniculus), classical genetic studies have identified five alleles at the Extension locus: ED (dominant black), ES (steel, weaker version of ED), E (wild type, normal extension of black), eJ(Japanese brindling, mosaic distribution of black and yellow) and e (non-extension of black, yellow/red with white belly). Sequencing almost the complete coding sequence (CDS) of the rabbit MC1R gene, we recently identified two in-frame deletions associated with dominant black (c.280_285del6; alleles ED or ES) and recessive red (c.304_333del30; allele e) coat colours. It remained to characterize the eJallele whose phenotypic effect is similar to the Orange and Sex-linked yellow loci of cat and Syrian hamster. We sequenced the whole CDS in 25 rabbits of different coat colours including 10 Japanese and 10 Rhinelander (tricolour) rabbits and identified another 6 bp-in frame deletion flanked by a G > A transition in 5' (c.[124G>A;125_130del6]) that was present in all animals with Japanese brindling coat colour and pattern. These mutations eliminate two amino acids in the first transmembrane domain and, in addition, cause an amino acid substitution at position 44 of the wild type sequence. Genotyping 371 rabbits of 31 breeds with different coat colour this allele (eJ) was present in homozygous state in Japanese, Rhinelander and Dutch tricolour rabbits only (except one albino rabbit). Rabbits with eJ/eJ genotype were non fixed at the non-agouti mutation we previously identified in the ASIP gene. Segregation in F1 and F2 families confirmed the order of dominance already determined by classical genetic experiments with a possible dose effect evident comparing eJ/eJ and eJ/e animals. MC1R mRNA was expressed in black hair skin regions only. The c.[124A;125_130del6] allele may be responsible for a MC1R variant determining eumelanin production in the black areas. However, the mechanism determining the presence of both red and black hairs in the same animal seems more complex. Expression analyses of the c.[124A;125_130del6] allele suggest that MC1R transcription may be regulated epigenetically in rabbits with the Japanese brindling phenotype. Further studies are needed to clarify this issue.

Transcriptome analysis of pecan seeds at different developing stages and identification of key genes involved in lipid metabolism

PubMed Central

Shah, Faheem Afzal; Wang, Qiaojian; Wang, Zhaocheng; Wu, Lifang

2018-01-01

Pecan is an economically important nut crop tree due to its unique texture and flavor properties. The pecan seed is rich of unsaturated fatty acid and protein. However, little is known about the molecular mechanisms of the biosynthesis of fatty acids in the developing seeds. In this study, transcriptome sequencing of the developing seeds was performed using Illumina sequencing technology. Pecan seed embryos at different developmental stages were collected and sequenced. The transcriptomes of pecan seeds at two key developing stages (PA, the initial stage and PS, the fast oil accumulation stage) were also compared. A total of 82,155 unigenes, with an average length of 1,198 bp from seven independent libraries were generated. After functional annotations, we detected approximately 55,854 CDS, among which, 2,807 were Transcription Factor (TF) coding unigenes. Further, there were 13,325 unigenes that showed a 2-fold or greater expression difference between the two groups of libraries (two developmental stages). After transcriptome analysis, we identified abundant unigenes that could be involved in fatty acid biosynthesis, degradation and some other aspects of seed development in pecan. This study presents a comprehensive dataset of transcriptomic changes during the seed development of pecan. It provides insights in understanding the molecular mechanisms responsible for fatty acid biosynthesis in the seed development. The identification of functional genes will also be useful for the molecular breeding work of pecan. PMID:29694395

Transcriptome analysis of pecan seeds at different developing stages and identification of key genes involved in lipid metabolism.

PubMed

Xu, Zheng; Ni, Jun; Shah, Faheem Afzal; Wang, Qiaojian; Wang, Zhaocheng; Wu, Lifang; Fu, Songling

2018-01-01

Pecan is an economically important nut crop tree due to its unique texture and flavor properties. The pecan seed is rich of unsaturated fatty acid and protein. However, little is known about the molecular mechanisms of the biosynthesis of fatty acids in the developing seeds. In this study, transcriptome sequencing of the developing seeds was performed using Illumina sequencing technology. Pecan seed embryos at different developmental stages were collected and sequenced. The transcriptomes of pecan seeds at two key developing stages (PA, the initial stage and PS, the fast oil accumulation stage) were also compared. A total of 82,155 unigenes, with an average length of 1,198 bp from seven independent libraries were generated. After functional annotations, we detected approximately 55,854 CDS, among which, 2,807 were Transcription Factor (TF) coding unigenes. Further, there were 13,325 unigenes that showed a 2-fold or greater expression difference between the two groups of libraries (two developmental stages). After transcriptome analysis, we identified abundant unigenes that could be involved in fatty acid biosynthesis, degradation and some other aspects of seed development in pecan. This study presents a comprehensive dataset of transcriptomic changes during the seed development of pecan. It provides insights in understanding the molecular mechanisms responsible for fatty acid biosynthesis in the seed development. The identification of functional genes will also be useful for the molecular breeding work of pecan.

Sexual differences in the sialomes of the zebra tick, Rhipicephalus pulchellus

PubMed Central

Tan, Angelina W. L.; Francischetti, Ivo M.B.; Slovak, Mirko; Manjunatha, Kini R.; Ribeiro, José M. C.

2015-01-01

Ticks rely exclusively on vertebrate blood for their survival. During feeding ticks inject into their hosts a sophisticated salivary potion that overcomes host hemostasis and adverse inflammatory responses. These mediators may also enhance pathogen transmission. Knowledge of the tick salivary protein repertoire may lead to vaccine targets to disrupt feeding and/or parasite transmission as well as to the discovery of novel pharmacological agents. Male saliva may also assist reproduction because males use their mouthparts to lubricate and introduce their spermatophores into the females’ genital pore. The analyses of the sialomes of male and female ticks independently allow us to understand the strategy used by each gender to feed successfully.We sequenced cDNA libraries from pools of salivary glands from adult male and female R. pulchellus feeding at different time points, using the Illumina HiSeq protocol. De novo assembly of a total of 241,229,128 paired-end reads lead to extraction of 50,460 coding sequences (CDS), 11,277 of which had more than 75% coverage to known transcripts, or represented novel sequences, and were submitted to GenBank. Additionally, we generated the proteome, from the salivary gland extracts of male and female R. pulchellus, yielding a total of 454 and 2,063 proteins respectively which were identified by one or more peptides with at least 95% confidence. The data set is presented as an annotated hyperlinked Excel spreadsheet, describing 121 putative secreted protein families. Female and male specific transcripts were identified. PMID:25576852

Coal Market Module - NEMS Documentation

EIA Publications

2014-01-01

Documents the objectives and the conceptual and methodological approach used in the development of the National Energy Modeling System's (NEMS) Coal Market Module (CMM) used to develop the Annual Energy Outlook 2014 (AEO2014). This report catalogues and describes the assumptions, methodology, estimation techniques, and source code of CMM's two submodules. These are the Coal Production Submodule (CPS) and the Coal Distribution Submodule (CDS).

Delineation and analysis of chromosomal regions specifying Yersinia pestis.

PubMed

Derbise, Anne; Chenal-Francisque, Viviane; Huon, Christèle; Fayolle, Corinne; Demeure, Christian E; Chane-Woon-Ming, Béatrice; Médigue, Claudine; Hinnebusch, B Joseph; Carniel, Elisabeth

2010-09-01

Yersinia pestis, the causative agent of plague, has recently diverged from the less virulent enteropathogen Yersinia pseudotuberculosis. Its emergence has been characterized by massive genetic loss and inactivation and limited gene acquisition. The acquired genes include two plasmids, a filamentous phage, and a few chromosomal loci. The aim of this study was to characterize the chromosomal regions acquired by Y. pestis. Following in silico comparative analysis and PCR screening of 98 strains of Y. pseudotuberculosis and Y. pestis, we found that eight chromosomal loci (six regions [R1pe to R6pe] and two coding sequences [CDS1pe and CDS2pe]) specified Y. pestis. Signatures of integration by site specific or homologous recombination were identified for most of them. These acquisitions and the loss of ancestral DNA sequences were concentrated in a chromosomal region opposite to the origin of replication. The specific regions were acquired very early during Y. pestis evolution and were retained during its microevolution, suggesting that they might bring some selective advantages. Only one region (R3pe), predicted to carry a lambdoid prophage, is most likely no longer functional because of mutations. With the exception of R1pe and R2pe, which have the potential to encode a restriction/modification and a sugar transport system, respectively, no functions could be predicted for the other Y. pestis-specific loci. To determine the role of the eight chromosomal loci in the physiology and pathogenicity of the plague bacillus, each of them was individually deleted from the bacterial chromosome. None of the deletants exhibited defects during growth in vitro. Using the Xenopsylla cheopis flea model, all deletants retained the capacity to produce a stable and persistent infection and to block fleas. Similarly, none of the deletants caused any acute flea toxicity. In the mouse model of infection, all deletants were fully virulent upon subcutaneous or aerosol infections. Therefore, our results suggest that acquisition of new chromosomal materials has not been of major importance in the dramatic change of life cycle that has accompanied the emergence of Y. pestis.

Direct electrochemical stripping detection of cystic-fibrosis-related DNA linked through cadmium sulfide quantum dots

NASA Astrophysics Data System (ADS)

Marin, Sergio; Merkoçi, Arben

2009-02-01

Electrochemical detection of a cadmium sulfide quantum dots (CdS QDs)-DNA complex connected to paramagnetic microbeads (MB) was performed without the need for chemical dissolving. The method is based on dropping 20 µl of CdS QD-DNA-MB suspension on the surface of a screen-printed electrode. It is followed by magnetic collection on the surface of the working electrode and electrochemical detection using square-wave voltammetry (SWV), giving a well-shaped and sensitive analytical signal. A cystic-fibrosis-related DNA sequence was sandwiched between the two DNA probes. One DNA probe is linked via biotin-streptavidin bonding with MB and the other one via thiol groups with the CdS QD used as tags. Nonspecific signals of DNA were minimized using a blocking agent and the results obtained were successfully employed in a model DNA sensor with an interest in future applications in the clinical field. The developed nanoparticle biosensing system may offer numerous opportunities in other fields where fast, low cost and efficient detection of small volume samples is required.

Report on Disclosure Issues Related to the Use of Copy Control and Digital Rights Management Technologies. OECD Digital Economy Papers, No. 115

ERIC Educational Resources Information Center

OECD Publishing (NJ1), 2006

2006-01-01

This report analyses the disclosure issues raised by technically-imposed restrictions on the use of digital content. It focuses on the application of copy control and digital rights management technologies in three areas: copy-protected CDs; online music, and DVD regional coding. In each of these areas, the report examines the kinds of…

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.

Genome-Wide Characterization and Linkage Mapping of Simple Sequence Repeats in Mei (Prunus mume Sieb. et Zucc.)

PubMed Central

Sun, Lidan; Yang, Weiru; Zhang, Qixiang; Cheng, Tangren; Pan, Huitang; Xu, Zongda; Zhang, Jie; Chen, Chuguang

2013-01-01

Because of its popularity as an ornamental plant in East Asia, mei (Prunus mume Sieb. et Zucc.) has received increasing attention in genetic and genomic research with the recent shotgun sequencing of its genome. Here, we performed the genome-wide characterization of simple sequence repeats (SSRs) in the mei genome and detected a total of 188,149 SSRs occurring at a frequency of 794 SSR/Mb. Mononucleotide repeats were the most common type of SSR in genomic regions, followed by di- and tetranucleotide repeats. Most of the SSRs in coding sequences (CDS) were composed of tri- or hexanucleotide repeat motifs, but mononucleotide repeats were always the most common in intergenic regions. Genome-wide comparison of SSR patterns among the mei, strawberry (Fragaria vesca), and apple (Malus×domestica) genomes showed mei to have the highest density of SSRs, slightly higher than that of strawberry (608 SSR/Mb) and almost twice as high as that of apple (398 SSR/Mb). Mononucleotide repeats were the dominant SSR motifs in the three Rosaceae species. Using 144 SSR markers, we constructed a 670 cM-long linkage map of mei delimited into eight linkage groups (LGs), with an average marker distance of 5 cM. Seventy one scaffolds covering about 27.9% of the assembled mei genome were anchored to the genetic map, depending on which the macro-colinearity between the mei genome and Prunus T×E reference map was identified. The framework map of mei constructed provides a first step into subsequent high-resolution genetic mapping and marker-assisted selection for this ornamental species. PMID:23555708

Silencing the HaHR3 Gene by Transgenic Plant-mediated RNAi to Disrupt Helicoverpa armigera Development

PubMed Central

Xiong, Yehui; Zeng, Hongmei; Zhang, Yuliang; Xu, Dawei; Qiu, Dewen

2013-01-01

RNA interference (RNAi) caused by exogenous double-stranded RNA (dsRNA) has developed into a powerful technique in functional genomics, and to date it is widely used to down-regulate crucial physiology-related genes to control pest insects. A molt-regulating transcription factor gene, HaHR3, of cotton bollworm (Helicoverpa armigera) was selected as the target gene. Four different fragments covering the coding sequence (CDS) of HaHR3 were cloned into vector L4440 to express dsRNAs in Escherichia coli. The most effective silencing fragment was then cloned into a plant over-expression vector to express a hairpin RNA (hpRNA) in transgenic tobacco (Nicotiana tabacum). When H. armigera larvae were fed the E. coli or transgenic plants, the HaHR3 mRNA and protein levels dramatically decreased, resulting developmental deformity and larval lethality. The results demonstrate that both recombinant bacteria and transgenic plants could induce HaHR3 silence to disrupt H. armigera development, transgenic plant-mediated RNAi is emerging as a powerful approach for controlling insect pests. PMID:23630449

Melanin deposition ruled out as cause of color changes in the red-eared sliders (Trachemys scripta elegans).

PubMed

Cao, Dainan; Gong, Shiping; Yang, Jiangbo; Li, Weiye; Ge, Yan; Wei, Yufeng

2018-03-01

Animal coloration primarily depends on the presence of pigments and the mixing ratio of eumelanin and pheomelanin. The color of red-eared slider's carapace varies with age, from an olive green to a yellow green, and then to a yellow brown in juveniles, generally. The purpose of the present study was to investigate whether this color change is related to the difference in melanin expression. Melanin deposition levels were examined in the carapace, skin, eye and muscle of the three color-types using hematoxylin and eosin staining. Moreover, the full-length coding sequence (CDS) of red-eared slider turtle melanin biosynthesis regulatory genes TYR, TYRP1, MITF and SLC24A5 were cloned, sequenced and quantitatively analyzed. Both histological view of melanin deposition and quantitative real-time PCR test of melanin-regulated gene expressions showed that there are significant differences among different tissues of red-eared slider, but no significant difference among different color-types, indicating that melanin deposition is not associated with ontogenetic color change in the carapace of red-eared slider. This study initially explore the melanin deposition and the mRNA expression of melanin biosynthesis regulatory genes in red-eared slider, which serve as a foundation for further insight into the pigmentation patterns and the mechanism of body color change in turtles. Copyright © 2017 Elsevier Inc. All rights reserved.

Evolution of Synonymous Codon Usage in Neurospora tetrasperma and Neurospora discreta

PubMed Central

Whittle, C. A.; Sun, Y.; Johannesson, H.

2011-01-01

Neurospora comprises a primary model system for the study of fungal genetics and biology. In spite of this, little is known about genome evolution in Neurospora. For example, the evolution of synonymous codon usage is largely unknown in this genus. In the present investigation, we conducted a comprehensive analysis of synonymous codon usage and its relationship to gene expression and gene length (GL) in Neurospora tetrasperma and Neurospora discreta. For our analysis, we examined codon usage among 2,079 genes per organism and assessed gene expression using large-scale expressed sequenced tag (EST) data sets (279,323 and 453,559 ESTs for N. tetrasperma and N. discreta, respectively). Data on relative synonymous codon usage revealed 24 codons (and two putative codons) that are more frequently used in genes with high than with low expression and thus were defined as optimal codons. Although codon-usage bias was highly correlated with gene expression, it was independent of selectively neutral base composition (introns); thus demonstrating that translational selection drives synonymous codon usage in these genomes. We also report that GL (coding sequences [CDS]) was inversely associated with optimal codon usage at each gene expression level, with highly expressed short genes having the greatest frequency of optimal codons. Optimal codon frequency was moderately higher in N. tetrasperma than in N. discreta, which might be due to variation in selective pressures and/or mating systems. PMID:21402862

Working at the intersection of context, culture, and technology: Provider perspectives on antimicrobial stewardship in the emergency department using electronic health record clinical decision support.

PubMed

Chung, Phillip; Scandlyn, Jean; Dayan, Peter S; Mistry, Rakesh D

2017-11-01

Antibiotic stewardship programs (ASPs) have not been fully developed for the emergency department (ED), in part the result of the barriers characteristic of this setting. Electronic health record-based clinical decision support (EHR CDS) represents a promising strategy to implement ASPs in the ED. We aimed to determine the cultural beliefs and structural barriers and facilitators to implementation of antimicrobial stewardship in the pediatric ED using EHR CDS. Interviews and focus groups were conducted with hospital and ED leadership, attending ED physicians, nurse practitioners, physician assistants, and residents at a single health system in Colorado. We reviewed and coded the data using constant comparative analysis and framework analysis until a final set of themes emerged. Two dominant perceptions shaped providers' perspectives on ASPs in the ED and EHR CDS: (1) maintaining workflow efficiency and (2) constrained decision-making autonomy. Clinicians identified structural barriers to ASPs, such as pace of the ED, and various beliefs that shaped patterns of practice, including accommodating the prescribing decisions of other providers and managing parental expectations. Recommendations to enhance uptake focused on designing a simple yet flexible user interface, providing clinicians with performance data, and on-boarding clinicians to enhance buy-in. Developing a successful ED-based ASP using EHR CDS should attend to technologic needs, the institutional context, and the cultural beliefs of practice associated with providers' antibiotic prescribing. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Assessment of the management factors that influence the development of preventive care in the New South Wales public dental service.

PubMed

Masoe, Angela V; Blinkhorn, Anthony S; Taylor, Jane; Blinkhorn, Fiona A

2015-01-01

Oral diseases, particularly dental caries, remain one of the most common chronic health problems for adolescents, and are a major public health concern. Public dental services in New South Wales, Australia offer free clinical care and preventive advice to all adolescents under 18 years of age, particularly those from disadvantaged backgrounds. This care is provided by dental therapists and oral health therapists (therapists). It is incumbent upon clinical directors (CDs) and health service managers (HSMs) to ensure that the appropriate clinical preventive care is offered by clinicians to all their patients. The aims of this study were to 1) explore CDs' and HSMs' perceptions of the factors that could support the delivery of preventive care to adolescents, and to 2) record the strategies they have utilized to help therapists provide preventive care to adolescents. In-depth, semistructured interviews were undertaken with 19 CDs and HSMs from across NSW local health districts. A framework matrix was used to systematically code data and enable key themes to be identified for analysis. The 19 CDs and HSMs reported that fiscal accountability and meeting performance targets impacted on the levels and types of preventive care provided by therapists. Participants suggested that professional clinical structures for continuous quality improvement should be implemented and monitored, and that an adequate workforce mix and more resources for preventive dental care activities would enhance therapists' ability to provide appropriate levels of preventive care. CDs and HSMs stated that capitalizing on the strengths of visiting pediatric dental specialists and working with local health district clinical leaders would be a practical way to improve models of preventive oral health care for adolescents. The main issue raised in this study is that preventive dentistry per se lacks strong support from the central funding agency, and that increasing prevention activities is not a simple task of changing regulations or increasing professional education.

Ancient DNA sequence revealed by error-correcting codes.

PubMed

Brandão, Marcelo M; Spoladore, Larissa; Faria, Luzinete C B; Rocha, Andréa S L; Silva-Filho, Marcio C; Palazzo, Reginaldo

2015-07-10

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code.

Ancient DNA sequence revealed by error-correcting codes

PubMed Central

Brandão, Marcelo M.; Spoladore, Larissa; Faria, Luzinete C. B.; Rocha, Andréa S. L.; Silva-Filho, Marcio C.; Palazzo, Reginaldo

2015-01-01

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code. PMID:26159228

Two-terminal video coding.

PubMed

Yang, Yang; Stanković, Vladimir; Xiong, Zixiang; Zhao, Wei

2009-03-01

Following recent works on the rate region of the quadratic Gaussian two-terminal source coding problem and limit-approaching code designs, this paper examines multiterminal source coding of two correlated, i.e., stereo, video sequences to save the sum rate over independent coding of both sequences. Two multiterminal video coding schemes are proposed. In the first scheme, the left sequence of the stereo pair is coded by H.264/AVC and used at the joint decoder to facilitate Wyner-Ziv coding of the right video sequence. The first I-frame of the right sequence is successively coded by H.264/AVC Intracoding and Wyner-Ziv coding. An efficient stereo matching algorithm based on loopy belief propagation is then adopted at the decoder to produce pixel-level disparity maps between the corresponding frames of the two decoded video sequences on the fly. Based on the disparity maps, side information for both motion vectors and motion-compensated residual frames of the right sequence are generated at the decoder before Wyner-Ziv encoding. In the second scheme, source splitting is employed on top of classic and Wyner-Ziv coding for compression of both I-frames to allow flexible rate allocation between the two sequences. Experiments with both schemes on stereo video sequences using H.264/AVC, LDPC codes for Slepian-Wolf coding of the motion vectors, and scalar quantization in conjunction with LDPC codes for Wyner-Ziv coding of the residual coefficients give a slightly lower sum rate than separate H.264/AVC coding of both sequences at the same video quality.

Clinical decision support improves quality of telephone triage documentation - an analysis of triage documentation before and after computerized clinical decision support

PubMed Central

2014-01-01

Background Clinical decision support (CDS) has been shown to be effective in improving medical safety and quality but there is little information on how telephone triage benefits from CDS. The aim of our study was to compare triage documentation quality associated with the use of a clinical decision support tool, ExpertRN©. Methods We examined 50 triage documents before and after a CDS tool was used in nursing triage. To control for the effects of CDS training we had an additional control group of triage documents created by nurses who were trained in the CDS tool, but who did not use it in selected notes. The CDS intervention cohort of triage notes was compared to both the pre-CDS notes and the CDS trained (but not using CDS) cohort. Cohorts were compared using the documentation standards of the American Academy of Ambulatory Care Nursing (AAACN). We also compared triage note content (documentation of associated positive and negative features relating to the symptoms, self-care instructions, and warning signs to watch for), and documentation defects pertinent to triage safety. Results Three of five AAACN documentation standards were significantly improved with CDS. There was a mean of 36.7 symptom features documented in triage notes for the CDS group but only 10.7 symptom features in the pre-CDS cohort (p < 0.0001) and 10.2 for the cohort that was CDS-trained but not using CDS (p < 0.0001). The difference between the mean of 10.2 symptom features documented in the pre-CDS and the mean of 10.7 symptom features documented in the CDS-trained but not using was not statistically significant (p = 0.68). Conclusions CDS significantly improves triage note documentation quality. CDS-aided triage notes had significantly more information about symptoms, warning signs and self-care. The changes in triage documentation appeared to be the result of the CDS alone and not due to any CDS training that came with the CDS intervention. Although this study shows that CDS can improve documentation, further study is needed to determine if it results in improved care. PMID:24645674

Clinical decision support improves quality of telephone triage documentation--an analysis of triage documentation before and after computerized clinical decision support.

PubMed

North, Frederick; Richards, Debra D; Bremseth, Kimberly A; Lee, Mary R; Cox, Debra L; Varkey, Prathibha; Stroebel, Robert J

2014-03-20

Clinical decision support (CDS) has been shown to be effective in improving medical safety and quality but there is little information on how telephone triage benefits from CDS. The aim of our study was to compare triage documentation quality associated with the use of a clinical decision support tool, ExpertRN©. We examined 50 triage documents before and after a CDS tool was used in nursing triage. To control for the effects of CDS training we had an additional control group of triage documents created by nurses who were trained in the CDS tool, but who did not use it in selected notes. The CDS intervention cohort of triage notes was compared to both the pre-CDS notes and the CDS trained (but not using CDS) cohort. Cohorts were compared using the documentation standards of the American Academy of Ambulatory Care Nursing (AAACN). We also compared triage note content (documentation of associated positive and negative features relating to the symptoms, self-care instructions, and warning signs to watch for), and documentation defects pertinent to triage safety. Three of five AAACN documentation standards were significantly improved with CDS. There was a mean of 36.7 symptom features documented in triage notes for the CDS group but only 10.7 symptom features in the pre-CDS cohort (p < 0.0001) and 10.2 for the cohort that was CDS-trained but not using CDS (p < 0.0001). The difference between the mean of 10.2 symptom features documented in the pre-CDS and the mean of 10.7 symptom features documented in the CDS-trained but not using was not statistically significant (p = 0.68). CDS significantly improves triage note documentation quality. CDS-aided triage notes had significantly more information about symptoms, warning signs and self-care. The changes in triage documentation appeared to be the result of the CDS alone and not due to any CDS training that came with the CDS intervention. Although this study shows that CDS can improve documentation, further study is needed to determine if it results in improved care.

Structural, Optical, and Electrical Properties of Cobalt-Doped CdS Quantum Dots

NASA Astrophysics Data System (ADS)

Thambidurai, M.; Muthukumarasamy, N.; Velauthapillai, Dhayalan; Agilan, S.; Balasundaraprabhu, R.

2012-04-01

In the present work, a systematic study has been carried out to understand the influence of cobalt (Co) doping on various properties of CdS nanoparticles. CdS and Co-doped CdS quantum dots have been prepared at room temperature using a chemical precipitation method without using catalysts, capping agents, or surfactants. X-ray diffraction reveals that both undoped and Co-doped CdS nanoparticles exhibit hexagonal structure without any impurity phase, and the lattice constants of CdS nanoparticles are observed to decrease slightly with increasing cobalt concentration. High-resolution transmission electron microscopy (HRTEM) shows that the particle size of CdS and 5.02% Co-doped CdS nanoparticles is in the range of 2 nm to 4 nm. The Raman spectra of Co-doped CdS nanoparticles exhibit a red-shift compared with that of bulk CdS, which may be attributed to optical phonon confinement. The optical absorption spectra of Co-doped CdS nanoparticles also exhibit a red-shift with respect to that of CdS nanoparticles. The electrical conductivity of CdS and Co-doped CdS nanoparticles is found to increase with increasing temperature and cobalt concentration.

Prevalence of Creatine Deficiency Syndromes in Children With Nonsyndromic Autism.

PubMed

Schulze, Andreas; Bauman, Margaret; Tsai, Anne Chun-Hui; Reynolds, Ann; Roberts, Wendy; Anagnostou, Evdokia; Cameron, Jessie; Nozzolillo, Alixandra A; Chen, Shiyi; Kyriakopoulou, Lianna; Scherer, Stephen W; Loh, Alvin

2016-01-01

Creatine deficiency may play a role in the neurobiology of autism and may represent a treatable cause of autism. The goal of the study was to ascertain the prevalence of creatine deficiency syndromes (CDSs) in children with autism spectrum disorder (ASD). In a prospective multicenter study, 443 children were investigated after a confirmed diagnosis of ASD. Random spot urine screening for creatine metabolites (creatine, guanidinoacetate, creatinine, and arginine) with liquid chromatography-tandem mass spectrometry and second-tier testing with high-performance liquid chromatography methodology was followed by recall testing in 24-hour urines and confirmatory testing by Sanger-based DNA sequencing of GAMT, GATM, and SLC6A8 genes. Additional diagnostic tests included plasma creatine metabolites and in vivo brain proton magnetic resonance spectroscopy. The creatine metabolites in spot urine in the autism group were compared with 128 healthy controls controlled for age. In 443 subjects with ASD investigated for CDS, we had 0 events (event: 0, 95% confidence interval 0-0.0068), therefore with 95% confidence the prevalence of CDS is <7 in 1000 children with ASD. The autism and control groups did not vary in terms of creatine metabolites (P > .0125) in urine. Our study revealed a very low prevalence of CDS in children with nonsyndromic ASD and no obvious association between creatine metabolites and autism. Unlike our study population, we expect more frequent CDS among children with severe developmental delay, speech impairment, seizures, and movement disorders in addition to impairments in social communication, restricted interests, and repetitive behaviors. Copyright © 2016 by the American Academy of Pediatrics.

MERRA/AS: The MERRA Analytic Services Project Interim Report

NASA Technical Reports Server (NTRS)

Schnase, John; Duffy, Dan; Tamkin, Glenn; Nadeau, Denis; Thompson, Hoot; Grieg, Cristina; Luczak, Ed; McInerney, Mark

2013-01-01

MERRA AS is a cyberinfrastructure resource that will combine iRODS-based Climate Data Server (CDS) capabilities with Coudera MapReduce to serve MERRA analytic products, store the MERRA reanalysis data collection in an HDFS to enable parallel, high-performance, storage-side data reductions, manage storage-side driver, mapper, reducer code sets and realized objects for users, and provide a library of commonly used spatiotemporal operations that can be composed to enable higher-order analyses.

Adsorption, Aggregation, and Deposition Behaviors of Carbon Dots on Minerals.

PubMed

Liu, Xia; Li, Jiaxing; Huang, Yongshun; Wang, Xiangxue; Zhang, Xiaodong; Wang, Xiangke

2017-06-06

The increased production of carbon dots (CDs) and the release and accumulation of CDs in both surface and groundwater has resulted in the increasing interest in their research. To assess the environmental behavior of CDs, the interaction between CDs and goethite was studied under different environmental conditions. Electrokinetic characterization of CDs suggested that the ζ-potential and size distribution of CDs were affected by pH and electrolyte species, indicating that these factors influenced the stability of CDs in aqueous solutions. Traditional Derjaguin-Landau-Verwey-Overbeek theory did not fit well the aggregation process of CDs. Results of the effects of pH and ionic strength suggested that electronic attraction dominated the aggregation of CDs. Compared with other minerals, hydrogen-bonding interactions and Lewis acid-base interactions contributed to the aggregation of CDs, in addition to van der Waals and electrical double-layer forces. Adsorption isotherms and microscopic Fourier transformed infrared spectroscopy indicated that chemical bonds were formed between CDs and goethite. These findings are useful to understand the interaction of CDs with minerals, as well as the potential fate and toxicity of CDs in the natural environment, especially in soils and sediments.

Draft genome sequence of Bradyrhizobium paxllaeri LMTR 21T isolated from Lima bean (Phaseolus lunatus) in Peru.

PubMed

Ormeño-Orrillo, Ernesto; Rey, Luis; Durán, David; Canchaya, Carlos A; Rogel, Marco A; Zúñiga-Dávila, Doris; Imperial, Juan; Ruiz-Argüeso, Tomás; Martínez-Romero, Esperanza

2017-09-01

Bradyrhizobium paxllaeri is a prevalent species in root nodules of the Lima bean ( Phaseolus lunatus ) in Peru. LMTR 21 T is the type strain of the species and was isolated from a root nodule collected in an agricultural field in the Peruvian central coast. Its 8.29 Mbp genome encoded 7635 CDS, 71 tRNAs and 3 rRNAs genes. All genes required to stablish a nitrogen-fixing symbiosis with its host were present. The draft genome sequence and annotation have been deposited at GenBank under the accession number MAXB00000000.

Genomewide analysis indicates that queen larvae have lower methylation levels in the honey bee ( Apis mellifera)

NASA Astrophysics Data System (ADS)

Shi, Yuan Yuan; Yan, Wei Yu; Huang, Zachary Y.; Wang, Zi Long; Wu, Xiao Bo; Zeng, Zhi Jiang

2013-02-01

The honey bee is a social insect characterized by caste differentiation, by which a young larva can develop into either a queen or a worker. Despite possessing the same genome, queen and workers display marked differences in reproductive capacity, physiology, and behavior. Recent studies have shown that DNA methylation plays important roles in caste differentiation. To further explore the roles of DNA methylation in this process, we analyzed DNA methylome profiles of both queen larvae (QL) and worker larvae (WL) of different ages (2, 4, and 6 day old), by using methylated DNA immunoprecipitation-sequencing (meDIP-seq) technique. The global DNA methylation levels varied between the larvae of two castes. DNA methylation increased from 2-day- to 4-day-old QL and then decreased in 6-day-old larvae. In WL, methylation levels increased with age. The methylcytosines in both larvae were enriched in introns, followed by coding sequence (CDS) regions, CpG islands, 2 kbp downstream and upstream of genes, and 5' and 3' untranslated regions (UTRs). The number of differentially methylated genes (DMGs) in 2-, 4-, and 6-day-old QL and WL was 725, 3,013, and 5,049, respectively. Compared to 4- and 6-day-old WL, a large number of genes in QL were downmethylated, which were involved in many processes including development, reproduction, and metabolic regulation. In addition, some DMGs were concerned with caste differentiation.

Transcriptome Profiles of the Protoscoleces of Echinococcus granulosus Reveal that Excretory-Secretory Products Are Essential to Metabolic Adaptation

PubMed Central

Pan, Wei; Shen, Yujuan; Han, Xiuming; Wang, Ying; Liu, Hua; Jiang, Yanyan; Zhang, Yumei; Wang, Yanjuan; Xu, Yuxin; Cao, Jianping

2014-01-01

Background Cystic hydatid disease (CHD) is caused by the larval stages of the cestode and affects humans and domestic animals worldwide. Protoscoleces (PSCs) are one component of the larval stages that can interact with both definitive and intermediate hosts. Previous genomic and transcriptomic data have provided an overall snapshot of the genomics of the growth and development of this parasite. However, our understanding of how PSCs subvert the immune response of hosts and maintains metabolic adaptation remains unclear. In this study, we used Roche 454 sequencing technology and in silico secretome analysis to explore the transcriptome profiles of the PSCs from E. granulosus and elucidate the potential functions of the excretory-secretory proteins (ESPs) released by the parasite. Methodology/Principal Findings A large number of nonredundant sequences as unigenes were generated (26,514), of which 22,910 (86.4%) were mapped to the newly published E. granulosus genome and 17,705 (66.8%) were distributed within the coding sequence (CDS) regions. Of the 2,280 ESPs predicted from the transcriptome, 138 ESPs were inferred to be involved in the metabolism of carbohydrates, while 124 ESPs were inferred to be involved in the metabolism of protein. Eleven ESPs were identified as intracellular enzymes that regulate glycolysis/gluconeogenesis (GL/GN) pathways, while a further 44 antigenic proteins, 25 molecular chaperones and four proteases were highly represented. Many proteins were also found to be significantly enriched in development-related signaling pathways, such as the TGF-β receptor pathways and insulin pathways. Conclusions/Significance This study provides valuable information on the metabolic adaptation of parasites to their hosts that can be used to aid the development of novel intervention targets for hydatid treatment and control. PMID:25500817

Biodiversity of genes encoding anti-microbial traits within plant associated microbes

PubMed Central

Mousa, Walaa K.; Raizada, Manish N.

2015-01-01

The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters. PMID:25914708

Code Status Reconciliation to Improve Identification and Documentation of Code Status in Electronic Health Records.

PubMed

Jain, Viral G; Greco, Peter J; Kaelber, David C

2017-03-08

Code status (CS) of a patient (part of their end-of-life wishes) can be critical information in healthcare delivery, which can change over time, especially at transitions of care. Although electronic health record (EHR) tools exist for medication reconciliation across transitions of care, much less attention is given to CS, and standard EHR tools have not been implemented for CS reconciliation (CSR). Lack of CSR creates significant potential patient safety and quality of life issues. To study the tools, workflow, and impact of clinical decision support (CDS) for CSR. We established rules for CS implementation in our EHR. At admission, a CS is required as part of a patient's admission order set. Using standard CDS tools in our EHR, we built an interruptive alert for CSR at discharge if a patient did not have the same inpatient (current) CS at discharge as that prior to admission CS. Of 80,587 admissions over a four year period (2 years prior to and post CSR implementation), CS discordance was seen in 3.5% of encounters which had full code status prior to admission, but Do Not Resuscitate (DNR) CS at discharge. In addition, 1.4% of the encounters had a different variant of the DNR CS at discharge when compared with CS prior to admission. On pre-post CSR implementation analysis, DNR CS per 1000 admissions per month increased significantly among patients discharged and in patients being admitted (mean ± SD: 85.36 ± 13.69 to 399.85 ± 182.86, p<0.001; and 1.99 ± 1.37 vs 16.70 ± 4.51, p<0.001, respectively). EHR enabled CSR is effective and represents a significant informatics opportunity to help honor patients' end-of-life wishes. CSR represents one example of non-medication reconciliation at transitions of care that should be considered in all EHRs to improve care quality and patient safety.

CDS - Database Administrator's Guide

NASA Astrophysics Data System (ADS)

Day, J. P.

This guide aims to instruct the CDS database administrator in: o The CDS file system. o The CDS index files. o The procedure for assimilating a new CDS tape into the database. It is assumed that the administrator has read SUN/79.

Draft genome sequence of Thermoanaerobacterium sp. strain PSU-2 isolated from thermophilic hydrogen producing reactor.

PubMed

O-Thong, Sompong; Khongkliang, Peerawat; Mamimin, Chonticha; Singkhala, Apinya; Prasertsan, Poonsuk; Birkeland, Nils-Kåre

2017-06-01

Thermoanaerobacterium sp. strain PSU-2 was isolated from thermophilic hydrogen producing reactor and subjected to draft genome sequencing on 454 pyrosequencing and annotated on RAST. The draft genome sequence of strain PSU-2 contains 2,552,497 bases with an estimated G + C content of 35.2%, 2555 CDS, 8 rRNAs and 57 tRNAs. The strain had a number of genes responsible for carbohydrates metabolic, amino acids and derivatives, and protein metabolism of 17.7%, 14.39% and 9.81%, respectively. Strain PSU-2 also had gene responsible for hydrogen biosynthesis as well as the genes related to Ni-Fe hydrogenase. Comparative genomic analysis indicates strain PSU-2 shares about 94% genome sequence similarity with Thermoanaerobacterium xylanolyticum LX-11. The nucleotide sequence of this draft genome was deposited into DDBJ/ENA/GenBank under the accession MSQD00000000.

Comparison of Computer-based Clinical Decision Support Systems and Content for Diabetes Mellitus.

PubMed

Kantor, M; Wright, A; Burton, M; Fraser, G; Krall, M; Maviglia, S; Mohammed-Rajput, N; Simonaitis, L; Sonnenberg, F; Middleton, B

2011-01-01

Computer-based clinical decision support (CDS) systems have been shown to improve quality of care and workflow efficiency, and health care reform legislation relies on electronic health records and CDS systems to improve the cost and quality of health care in the United States; however, the heterogeneity of CDS content and infrastructure of CDS systems across sites is not well known. We aimed to determine the scope of CDS content in diabetes care at six sites, assess the capabilities of CDS in use at these sites, characterize the scope of CDS infrastructure at these sites, and determine how the sites use CDS beyond individual patient care in order to identify characteristics of CDS systems and content that have been successfully implemented in diabetes care. We compared CDS systems in six collaborating sites of the Clinical Decision Support Consortium. We gathered CDS content on care for patients with diabetes mellitus and surveyed institutions on characteristics of their site, the infrastructure of CDS at these sites, and the capabilities of CDS at these sites. The approach to CDS and the characteristics of CDS content varied among sites. Some commonalities included providing customizability by role or user, applying sophisticated exclusion criteria, and using CDS automatically at the time of decision-making. Many messages were actionable recommendations. Most sites had monitoring rules (e.g. assessing hemoglobin A1c), but few had rules to diagnose diabetes or suggest specific treatments. All sites had numerous prevention rules including reminders for providing eye examinations, influenza vaccines, lipid screenings, nephropathy screenings, and pneumococcal vaccines. Computer-based CDS systems vary widely across sites in content and scope, but both institution-created and purchased systems had many similar features and functionality, such as integration of alerts and reminders into the decision-making workflow of the provider and providing messages that are actionable recommendations.

Improving performance of DS-CDMA systems using chaotic complex Bernoulli spreading codes

NASA Astrophysics Data System (ADS)

Farzan Sabahi, Mohammad; Dehghanfard, Ali

2014-12-01

The most important goal of spreading spectrum communication system is to protect communication signals against interference and exploitation of information by unintended listeners. In fact, low probability of detection and low probability of intercept are two important parameters to increase the performance of the system. In Direct Sequence Code Division Multiple Access (DS-CDMA) systems, these properties are achieved by multiplying the data information in spreading sequences. Chaotic sequences, with their particular properties, have numerous applications in constructing spreading codes. Using one-dimensional Bernoulli chaotic sequence as spreading code is proposed in literature previously. The main feature of this sequence is its negative auto-correlation at lag of 1, which with proper design, leads to increase in efficiency of the communication system based on these codes. On the other hand, employing the complex chaotic sequences as spreading sequence also has been discussed in several papers. In this paper, use of two-dimensional Bernoulli chaotic sequences is proposed as spreading codes. The performance of a multi-user synchronous and asynchronous DS-CDMA system will be evaluated by applying these sequences under Additive White Gaussian Noise (AWGN) and fading channel. Simulation results indicate improvement of the performance in comparison with conventional spreading codes like Gold codes as well as similar complex chaotic spreading sequences. Similar to one-dimensional Bernoulli chaotic sequences, the proposed sequences also have negative auto-correlation. Besides, construction of complex sequences with lower average cross-correlation is possible with the proposed method.

Facile synthesis and luminescence characteristics of high-quality CdS: Eu/ZnS core/shell nanocrystals with biocompatibility.

PubMed

Zhang, Kexin; Zhang, Rui; Yu, Yaxin; Sun, Shuqing

2012-04-01

In this paper, we report a facile method to synthesize high quality CdS: Eu nanocrystals (NCs) and CdS: Eu/ZnS NCs with strong photoluminescence (PL). The influence of various experimental variables including the concentration of Eu3+ ions, the reaction time and the reaction temperature were investigated systematically. In addition, the PL properties of CdS: Eu NCs exhibited pH sensitive. Under the acid condition, pH value of the CdS: Eu NCs solution played an important role in determining PL emission intensity. However, under the alkaline condition, the obtained CdS: Eu NCs exhibited a tunable PL emission wavelength (from 490 nm to 610 nm) when pH value was adjusted from pH 7 to 10. After coating with ZnS shell, the CdS: Eu/ZnS NCs showed enhanced PL intensity compare with one of the CdS: Eu NCs. The CdS: Eu NCs and CdS: Eu/ZnS NCs were characterized by X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HRTEM). In addition, the biocompatibility of these NCs was measured by hemolytic test, which indicated that CdS: Eu/ZnS NCs were more biocompatible than CdS: Eu NCs at the same conditions. It can be expected that CdS: Eu/ZnS NCs are promising biolabeling materials.

Nitrogen and sulfur co-doped carbon dots with strong blue luminescence

NASA Astrophysics Data System (ADS)

Ding, Hui; Wei, Ji-Shi; Xiong, Huan-Ming

2014-10-01

Sulfur-doped carbon dots (S-CDs) with a quantum yield (QY) of 5.5% and nitrogen, sulfur co-doped carbon dots (N,S-CDs) with a QY of 54.4% were synthesized, respectively, via the same hydrothermal route using α-lipoic acid as the carbon source. The obtained S-CDs and N,S-CDs had similar sizes but different optical features. The QY of N,S-CDs was gradually enhanced when extending the reaction time to increase the nitrogen content. After careful characterization of these CDs, the doped nitrogen element was believed to be in the form of C&z.dbd;N and C-N bonds which enhanced the fluorescence efficiency significantly. Meanwhile, the co-doped sulfur element was found to be synergistic for nitrogen doping in N,S-CDs. The optimal N,S-CDs were successfully employed as good multicolor cell imaging probes due to their fine dispersion in water, excitation-dependent emission, excellent fluorescence stability and low toxicity. Besides, such N,S-CDs showed a wide detection range and excellent accuracy as fluorescent sensors for Fe3+ ions.Sulfur-doped carbon dots (S-CDs) with a quantum yield (QY) of 5.5% and nitrogen, sulfur co-doped carbon dots (N,S-CDs) with a QY of 54.4% were synthesized, respectively, via the same hydrothermal route using α-lipoic acid as the carbon source. The obtained S-CDs and N,S-CDs had similar sizes but different optical features. The QY of N,S-CDs was gradually enhanced when extending the reaction time to increase the nitrogen content. After careful characterization of these CDs, the doped nitrogen element was believed to be in the form of C&z.dbd;N and C-N bonds which enhanced the fluorescence efficiency significantly. Meanwhile, the co-doped sulfur element was found to be synergistic for nitrogen doping in N,S-CDs. The optimal N,S-CDs were successfully employed as good multicolor cell imaging probes due to their fine dispersion in water, excitation-dependent emission, excellent fluorescence stability and low toxicity. Besides, such N,S-CDs showed a wide detection range and excellent accuracy as fluorescent sensors for Fe3+ ions. Electronic supplementary information (ESI) available: Experimental details and comparable characterization of three kinds of CDs. See DOI: 10.1039/c4nr04267k

Controlling and fine tuning the physical properties of two identical metal coordination sites in de novo designed three stranded coiled coil peptides.

PubMed

Iranzo, Olga; Chakraborty, Saumen; Hemmingsen, Lars; Pecoraro, Vincent L

2011-01-19

Herein we report how de novo designed peptides can be used to investigate whether the position of a metal site along a linear sequence that folds into a three-stranded α-helical coiled coil defines the physical properties of Cd(II) ions in either CdS(3) or CdS(3)O (O-being an exogenous water molecule) coordination environments. Peptides are presented that bind Cd(II) into two identical coordination sites that are located at different topological positions at the interior of these constructs. The peptide GRANDL16PenL19IL23PenL26I binds two Cd(II) as trigonal planar 3-coordinate CdS(3) structures whereas GRANDL12AL16CL26AL30C sequesters two Cd(II) as pseudotetrahedral 4-coordinate CdS(3)O structures. We demonstrate how for the first peptide, having a more rigid structure, the location of the identical binding sites along the linear sequence does not affect the physical properties of the two bound Cd(II). However, the sites are not completely independent as Cd(II) bound to one of the sites ((113)Cd NMR chemical shift of 681 ppm) is perturbed by the metalation state (apo or [Cd(pep)(Hpep)(2)](+) or [Cd(pep)(3)](-)) of the second center ((113)Cd NMR chemical shift of 686 ppm). GRANDL12AL16CL26AL30C shows a completely different behavior. The physical properties of the two bound Cd(II) ions indeed depend on the position of the metal center, having pK(a2) values for the equilibrium [Cd(pep)(Hpep)(2)](+) → [Cd(pep)(3)](-) + 2H(+) (corresponding to deprotonation and coordination of cysteine thiols) that range from 9.9 to 13.9. In addition, the L26AL30C site shows dynamic behavior, which is not observed for the L12AL16C site. These results indicate that for these systems one cannot simply assign a "4-coordinate structure" and assume certain physical properties for that site since important factors such as packing of the adjacent Leu, size of the intended cavity (endo vs exo) and location of the metal site play crucial roles in determining the final properties of the bound Cd(II).

Evaluation of children with lymphatic malformations of the head and neck using the Cologne Disease Score.

PubMed

Wiegand, Susanne; Eivazi, Behfar; Zimmermann, Annette P; Sesterhenn, Andreas M; Werner, Jochen A

2009-07-01

To assess the disease-related impairments of children with lymphatic malformations of the head and neck and their changes after therapy using the Cologne Disease Score (CDS). 29 children with lymphatic malformations of the head and neck were evaluated regarding their symptoms before and after therapy using the CDS. The Wilcoxon test for dependent groups was used to compare the CDS at initial visit before treatment and last visit after treatment. The CDS of patients belonging to the moderate (initial CDS: more than eight points) and advanced disease group (initial CDS: five, six or seven points) significantly increased after therapy while the patients in the severe disease group (initial CDS: lower than four points) showed no significant improvement of CDS. Patients with stage IV and especially stage V lymphatic malformations according to de Serres showed considerably lower pre- and posttherapeutic CDS levels than those of stage I and II. The visual impairment is not mapped by the CDS, therefore item vision should be added to the CDS to make an evaluation of all lymphatic malformations of the head and neck possible. The present series could show that especially patients with a moderate or advanced disease according to the CDS may profit from therapeutic interventions.

Complete Genome Sequence of the Broad-Host-Range Vibriophage KVP40: Comparative Genomics of a T4-Related Bacteriophage

PubMed Central

Miller, Eric S.; Heidelberg, John F.; Eisen, Jonathan A.; Nelson, William C.; Durkin, A. Scott; Ciecko, Ann; Feldblyum, Tamara V.; White, Owen; Paulsen, Ian T.; Nierman, William C.; Lee, Jong; Szczypinski, Bridget; Fraser, Claire M.

2003-01-01

The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. KVP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early- or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from Vibrio spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved. PMID:12923095

[Transposition errors during learning to reproduce a sequence by the right- and the left-hand movements: simulation of positional and movement coding].

PubMed

Liakhovetskiĭ, V A; Bobrova, E V; Skopin, G N

2012-01-01

Transposition errors during the reproduction of a hand movement sequence make it possible to receive important information on the internal representation of this sequence in the motor working memory. Analysis of such errors showed that learning to reproduce sequences of the left-hand movements improves the system of positional coding (coding ofpositions), while learning of the right-hand movements improves the system of vector coding (coding of movements). Learning of the right-hand movements after the left-hand performance involved the system of positional coding "imposed" by the left hand. Learning of the left-hand movements after the right-hand performance activated the system of vector coding. Transposition errors during learning to reproduce movement sequences can be explained by neural network using either vector coding or both vector and positional coding.

Informational structure of genetic sequences and nature of gene splicing

NASA Astrophysics Data System (ADS)

Trifonov, E. N.

1991-10-01

Only about 1/20 of DNA of higher organisms codes for proteins, by means of classical triplet code. The rest of DNA sequences is largely silent, with unclear functions, if any. The triplet code is not the only code (message) carried by the sequences. There are three levels of molecular communication, where the same sequence ``talks'' to various bimolecules, while having, respectively, three different appearances: DNA, RNA and protein. Since the molecular structures and, hence, sequence specific preferences of these are substantially different, the original DNA sequence has to carry simultaneously three types of sequence patterns (codes, messages), thus, being a composite structure in which one had the same letter (nucleotide) is frequently involved in several overlapping codes of different nature. This multiplicity and overlapping of the codes is a unique feature of the Gnomic, language of genetic sequences. The coexisting codes have to be degenerate in various degrees to allow an optimal and concerted performance of all the encoded functions. There is an obvious conflict between the best possible performance of a given function and necessity to compromise the quality of a given sequence pattern in favor of other patterns. It appears that the major role of various changes in the sequences on their ``ontogenetic'' way from DNA to RNA to protein, like RNA editing and splicing, or protein post-translational modifications is to resolve such conflicts. New data are presented strongly indicating that the gene splicing is such a device to resolve the conflict between the code of DNA folding in chromatin and the triplet code for protein synthesis.

Sequencing and Comparative Genome Analysis of Two Pathogenic Streptococcus gallolyticus Subspecies: Genome Plasticity, Adaptation and Virulence

PubMed Central

Teng, Yu-Ting; Wu, Hui-Lun; Liu, Yen-Ming; Wu, Keh-Ming; Chang, Chuan-Hsiung; Hsu, Ming-Ta

2011-01-01

Streptococcus gallolyticus infections in humans are often associated with bacteremia, infective endocarditis and colon cancers. The disease manifestations are different depending on the subspecies of S. gallolyticus causing the infection. Here, we present the complete genomes of S. gallolyticus ATCC 43143 (biotype I) and S. pasteurianus ATCC 43144 (biotype II.2). The genomic differences between the two biotypes were characterized with comparative genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length and encode 2246 and 1869 CDS respectively. The organization and genomic contents of both genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92%) and 1607 (86%) of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively. There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus genus has a small core-genome (constitute around 30% of total CDS) and substantial evolutionary plasticity. We identified eight and five regions of genome plasticity in ATCC 43143 and ATCC 43144 respectively. Within these regions, several proteins were recognized to contribute to the fitness and virulence of each of the two subspecies. We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans. This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced. The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops. PMID:21633709

Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

NASA Astrophysics Data System (ADS)

Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

2018-01-01

The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

One pot synthesis of highly luminescent polyethylene glycol anchored carbon dots functionalized with a nuclear localization signal peptide for cell nucleus imaging.

PubMed

Yang, Lei; Jiang, Weihua; Qiu, Lipeng; Jiang, Xuewei; Zuo, Daiying; Wang, Dongkai; Yang, Li

2015-04-14

Strong blue fluorescent polyethylene glycol (PEG) anchored carbon nitride dots (CDs@PEG) with a high quantum yield (QY) of 75.8% have been synthesized by a one step hydrothermal treatment. CDs with a diameter of ca. 6 nm are well dispersed in water and present a graphite-like structure. Photoluminescence (PL) studies reveal that CDs display excitation-dependent behavior and are stable under various test conditions. Based on the as-prepared CDs, we designed novel cell nucleus targeting imaging carbon dots functionalized with a nuclear localization signal (NLS) peptide. The favourable biocompatibilities of CDs and NLS modified CDs (NLS-CDs) are confirmed by in vitro cytotoxicity assays. Importantly, intracellular localization experiments in MCF7 and A549 cells demonstrate that NLS-CDs could be internalized in the nucleus and show blue light, which indicates that CDs may serve as cell nucleus imaging probes.

Fabrication of CDs/CdS-TiO2 ternary nano-composites for photocatalytic degradation of benzene and toluene under visible light irradiation

NASA Astrophysics Data System (ADS)

Wang, Meng; Hua, Jianhao; Yang, Yaling

2018-06-01

An efficient cadmium sulfide quantum-dots (CdS QDs) and carbon dots (CDs) modified TiO2 photocatalyst (CdS/CDs-TiO2) was successfully fabricated. The as-prepared ternary nano-composites simultaneously improved the photo-corrosion of CdS and amplified its photocatalytic activity. The introduction of CdS QDs and CDs could enhance more absorbance of light, prevent the undesirable electron/hole recombination, and promote charge separation, which was important for the continuous formation of rad OH and rad O2- radicals. When the optimal mass ratio of CdS QDs to CDs was 3:1, above 90% degradation efficiencies were achieved for benzene within 1 h and toluene in 2 h, while that of pure TiO2 (P25), CdS QDs-TiO2, CDs-TiO2 nano-composites was around 15%. Owing to the symmetric structure and conjugation of methyl with benzene ring, the degradation of toluene was more difficult than benzene to carry on. The new fabricated nano-composites showed good prospective application of cleaning up refractory pollutants and the resource utilization.

Green preparation of carbon dots with papaya as carbon source for effective fluorescent sensing of Iron (III) and Escherichia coli.

PubMed

Wang, Ning; Wang, Yiting; Guo, Tingting; Yang, Ting; Chen, Mingli; Wang, Jianhua

2016-11-15

A simple one-step hydrothermal green approach was reported for the preparation of carbon dots (CDs) without any further decoration or modification with papaya powder as natural carbon source. In this economical and eco-friendly system, deionized water or 90% ethanol was used as solvent to produce water-soluble or ethanol-soluble CDs, respectively, termed as W-CDs and E-CDs. The quantum yield (QY) for W-CDs was 18.98%, while that for E-CDs was 18.39%. The potentials of the prepared carbon dots toward diverse applications were thoroughly investigated. W-CDs and E-CDs provide promising probes for fluorescence detection of Fe(3+), offering limits of detection of 0.48μmolL(-1) and 0.29μmolL(-1), respectively. W-CDs was further demonstrated to be a promising probe for fluorescence sensing of Escherichia coli O157: H7, along with a limit of detection of 9.5×10(4)cfumL(-1). Meanwhile, both W-CDs and E-CDs exhibit favorable biocompatibility, and demonstrated to be efficient for Hela cell imaging. Copyright © 2016 Elsevier B.V. All rights reserved.

Highly Efficient Photocatalytic Hydrogen Production of Flower-like Cadmium Sulfide Decorated by Histidine

PubMed Central

Wang, Qizhao; Lian, Juhong; Li, Jiajia; Wang, Rongfang; Huang, Haohao; Su, Bitao; Lei, Ziqiang

2015-01-01

Morphology-controlled synthesis of CdS can significantly enhance the efficiency of its photocatalytic hydrogen production. In this study, a novel three-dimensional (3D) flower-like CdS is synthesized via a facile template-free hydrothermal process using Cd(NO3)2•4H2O and thiourea as precursors and L-Histidine as a chelating agent. The morphology, crystal phase, and photoelectrochemical performance of the flower-like CdS and pure CdS nanocrystals are carefully investigated via various characterizations. Superior photocatalytic activity relative to that of pure CdS is observed on the flower-like CdS photocatalyst under visible light irradiation, which is nearly 13 times of pure CdS. On the basis of the results from SEM studies and our analysis, a growth mechanism of flower-like CdS is proposed by capturing the shape evolution. The imidazole ring of L-Histidine captures the Cd ions from the solution, and prevents the growth of the CdS nanoparticles. Furthermore, the photocatalytic contrast experiments illustrate that the as-synthesized flower-like CdS with L-Histidine is more stable than CdS without L-Histidine in the hydrogen generation. PMID:26337119

Highly Efficient Photocatalytic Hydrogen Production of Flower-like Cadmium Sulfide Decorated by Histidine

NASA Astrophysics Data System (ADS)

Wang, Qizhao; Lian, Juhong; Li, Jiajia; Wang, Rongfang; Huang, Haohao; Su, Bitao; Lei, Ziqiang

2015-09-01

Morphology-controlled synthesis of CdS can significantly enhance the efficiency of its photocatalytic hydrogen production. In this study, a novel three-dimensional (3D) flower-like CdS is synthesized via a facile template-free hydrothermal process using Cd(NO3)2•4H2O and thiourea as precursors and L-Histidine as a chelating agent. The morphology, crystal phase, and photoelectrochemical performance of the flower-like CdS and pure CdS nanocrystals are carefully investigated via various characterizations. Superior photocatalytic activity relative to that of pure CdS is observed on the flower-like CdS photocatalyst under visible light irradiation, which is nearly 13 times of pure CdS. On the basis of the results from SEM studies and our analysis, a growth mechanism of flower-like CdS is proposed by capturing the shape evolution. The imidazole ring of L-Histidine captures the Cd ions from the solution, and prevents the growth of the CdS nanoparticles. Furthermore, the photocatalytic contrast experiments illustrate that the as-synthesized flower-like CdS with L-Histidine is more stable than CdS without L-Histidine in the hydrogen generation.

Highly Efficient Photocatalytic Hydrogen Production of Flower-like Cadmium Sulfide Decorated by Histidine.

PubMed

Wang, Qizhao; Lian, Juhong; Li, Jiajia; Wang, Rongfang; Huang, Haohao; Su, Bitao; Lei, Ziqiang

2015-09-04

Morphology-controlled synthesis of CdS can significantly enhance the efficiency of its photocatalytic hydrogen production. In this study, a novel three-dimensional (3D) flower-like CdS is synthesized via a facile template-free hydrothermal process using Cd(NO3)2•4H2O and thiourea as precursors and L-Histidine as a chelating agent. The morphology, crystal phase, and photoelectrochemical performance of the flower-like CdS and pure CdS nanocrystals are carefully investigated via various characterizations. Superior photocatalytic activity relative to that of pure CdS is observed on the flower-like CdS photocatalyst under visible light irradiation, which is nearly 13 times of pure CdS. On the basis of the results from SEM studies and our analysis, a growth mechanism of flower-like CdS is proposed by capturing the shape evolution. The imidazole ring of L-Histidine captures the Cd ions from the solution, and prevents the growth of the CdS nanoparticles. Furthermore, the photocatalytic contrast experiments illustrate that the as-synthesized flower-like CdS with L-Histidine is more stable than CdS without L-Histidine in the hydrogen generation.

Correlation approach to identify coding regions in DNA sequences

NASA Technical Reports Server (NTRS)

Ossadnik, S. M.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Peng, C. K.; Simons, M.; Stanley, H. E.

1994-01-01

Recently, it was observed that noncoding regions of DNA sequences possess long-range power-law correlations, whereas coding regions typically display only short-range correlations. We develop an algorithm based on this finding that enables investigators to perform a statistical analysis on long DNA sequences to locate possible coding regions. The algorithm is particularly successful in predicting the location of lengthy coding regions. For example, for the complete genome of yeast chromosome III (315,344 nucleotides), at least 82% of the predictions correspond to putative coding regions; the algorithm correctly identified all coding regions larger than 3000 nucleotides, 92% of coding regions between 2000 and 3000 nucleotides long, and 79% of coding regions between 1000 and 2000 nucleotides. The predictive ability of this new algorithm supports the claim that there is a fundamental difference in the correlation property between coding and noncoding sequences. This algorithm, which is not species-dependent, can be implemented with other techniques for rapidly and accurately locating relatively long coding regions in genomic sequences.

Statistical properties of DNA sequences

NASA Technical Reports Server (NTRS)

Peng, C. K.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Simons, M.; Stanley, H. E.

1995-01-01

We review evidence supporting the idea that the DNA sequence in genes containing non-coding regions is correlated, and that the correlation is remarkably long range--indeed, nucleotides thousands of base pairs distant are correlated. We do not find such a long-range correlation in the coding regions of the gene. We resolve the problem of the "non-stationarity" feature of the sequence of base pairs by applying a new algorithm called detrended fluctuation analysis (DFA). We address the claim of Voss that there is no difference in the statistical properties of coding and non-coding regions of DNA by systematically applying the DFA algorithm, as well as standard FFT analysis, to every DNA sequence (33301 coding and 29453 non-coding) in the entire GenBank database. Finally, we describe briefly some recent work showing that the non-coding sequences have certain statistical features in common with natural and artificial languages. Specifically, we adapt to DNA the Zipf approach to analyzing linguistic texts. These statistical properties of non-coding sequences support the possibility that non-coding regions of DNA may carry biological information.

Cellulases and coding sequences

DOEpatents

Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

2001-02-20

The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

Cellulases and coding sequences

DOEpatents

Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

2001-01-01

The present invention provides three fungal cellulases, their coding sequences, recombinant DNA molecules comprising the cellulase coding sequences, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.

Clinical decision support for genetically guided personalized medicine: a systematic review

PubMed Central

Welch, Brandon M

2013-01-01

Objective To review the literature on clinical decision support (CDS) for genetically guided personalized medicine (GPM). Materials and Methods MEDLINE and Embase were searched from 1990 to 2011. The manuscripts included were summarized, and notable themes and trends were identified. Results Following a screening of 3416 articles, 38 primary research articles were identified. Focal areas of research included family history-driven CDS, cancer management, and pharmacogenomics. Nine randomized controlled trials of CDS interventions for GPM were identified, seven of which reported positive results. The majority of manuscripts were published on or after 2007, with increased recent focus on genotype-driven CDS and the integration of CDS within primary clinical information systems. Discussion Substantial research has been conducted to date on the use of CDS to enable GPM. In a previous analysis of CDS intervention trials, the automatic provision of CDS as a part of routine clinical workflow had been identified as being critical for CDS effectiveness. There was some indication that CDS for GPM could potentially be effective without the CDS being provided automatically, but we did not find conclusive evidence to support this hypothesis. Conclusion To maximize the clinical benefits arising from ongoing discoveries in genetics and genomics, additional research and development is recommended for identifying how best to leverage CDS to bridge the gap between the promise and realization of GPM. PMID:22922173

Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.).

PubMed

Sun, Lidan; Zhang, Qixiang; Xu, Zongda; Yang, Weiru; Guo, Yu; Lu, Jiuxing; Pan, Huitang; Cheng, Tangren; Cai, Ming

2013-10-06

Mei (Prunus mume Sieb. et Zucc.) is a famous ornamental plant and fruit crop grown in East Asian countries. Limited genetic resources, especially molecular markers, have hindered the progress of mei breeding projects. Here, we performed low-depth whole-genome sequencing of Prunus mume 'Fenban' and Prunus mume 'Kouzi Yudie' to identify high-quality polymorphic markers between the two cultivars on a large scale. A total of 1464.1 Mb and 1422.1 Mb of 'Fenban' and 'Kouzi Yudie' sequencing data were uniquely mapped to the mei reference genome with about 6-fold coverage, respectively. We detected a large number of putative polymorphic markers from the 196.9 Mb of sequencing data shared by the two cultivars, which together contained 200,627 SNPs, 4,900 InDels, and 7,063 SSRs. Among these markers, 38,773 SNPs, 174 InDels, and 418 SSRs were distributed in the 22.4 Mb CDS region, and 63.0% of these marker-containing CDS sequences were assigned to GO terms. Subsequently, 670 selected SNPs were validated using an Agilent's SureSelect solution phase hybridization assay. A subset of 599 SNPs was used to assess the genetic similarity of a panel of mei germplasm samples and a plum (P. salicina) cultivar, producing a set of informative diversity data. We also analyzed the frequency and distribution of detected InDels and SSRs in mei genome and validated their usefulness as DNA markers. These markers were successfully amplified in the cultivars and in their segregating progeny. A large set of high-quality polymorphic SNPs, InDels, and SSRs were identified in parallel between 'Fenban' and 'Kouzi Yudie' using low-depth whole-genome sequencing. The study presents extensive data on these polymorphic markers, which can be useful for constructing high-resolution genetic maps, performing genome-wide association studies, and designing genomic selection strategies in mei.

Efficient synthesis of highly fluorescent nitrogen-doped carbon dots for cell imaging using unripe fruit extract of Prunus mume

NASA Astrophysics Data System (ADS)

Atchudan, Raji; Edison, Thomas Nesakumar Jebakumar Immanuel; Sethuraman, Mathur Gopalakrishnan; Lee, Yong Rok

2016-10-01

Highly fluorescent nitrogen-doped carbon dots (N-CDs) were synthesized using the extract of unripe Prunus mume (P. mume) fruit by a simple one step hydrothermal-carbonization method. The N-CDs were synthesized at different pH ranges, 2.3, 5, 7, and 9. The pH of the P. mume extract was adjusted using an aqueous ammonia solution (25%). The optical properties of N-CDs were examined by UV-vis and fluorescence spectroscopy. The N-CDs synthesized at pH 9 emitted high fluorescence intensity compared to other obtained N-CDs. The N-CDs synthesized at pH 9 was further characterized by high resolution transmission electron microscopy (HR-TEM), X-ray diffraction (XRD), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), and Fourier transform-infra red (FT-IR) spectroscopy. HR-TEM showed that the average size of the synthesized N-CDs was approximately 9 nm and the interlayer distance was 0.21 nm, which was validated by XRD. The graphitic nature of the synthesized N-CDs were confirmed by Raman spectroscopy. XPS and FT-IR spectroscopy confirmed the doping of the nitrogen moiety over the synthesized CDs. The synthesized nitrogen doped CDs (N-CDs) were low toxicity and were used as a staining probe for fluorescence cell imaging.

Standard practices for computerized clinical decision support in community hospitals: a national survey

PubMed Central

McCormack, James L; Sittig, Dean F; Wright, Adam; McMullen, Carmit; Bates, David W

2012-01-01

Objective Computerized provider order entry (CPOE) with clinical decision support (CDS) can help hospitals improve care. Little is known about what CDS is presently in use and how it is managed, however, especially in community hospitals. This study sought to address this knowledge gap by identifying standard practices related to CDS in US community hospitals with mature CPOE systems. Materials and Methods Representatives of 34 community hospitals, each of which had over 5 years experience with CPOE, were interviewed to identify standard practices related to CDS. Data were analyzed with a mix of descriptive statistics and qualitative approaches to the identification of patterns, themes and trends. Results This broad sample of community hospitals had robust levels of CDS despite their small size and the independent nature of many of their physician staff members. The hospitals uniformly used medication alerts and order sets, had sophisticated governance procedures for CDS, and employed staff to customize CDS. Discussion The level of customization needed for most CDS before implementation was greater than expected. Customization requires skilled individuals who represent an emerging manpower need at this type of hospital. Conclusion These results bode well for robust diffusion of CDS to similar hospitals in the process of adopting CDS and suggest that national policies to promote CDS use may be successful. PMID:22707744

Use of Mobile Clinical Decision Support Software by Junior Doctors at a UK Teaching Hospital: Identification and Evaluation of Barriers to Engagement.

PubMed

Patel, Rakesh; Green, William; Shahzad, Muhammad Waseem; Larkin, Chris

2015-08-13

Clinical decision support (CDS) tools improve clinical diagnostic decision making and patient safety. The availability of CDS to health care professionals has grown in line with the increased prevalence of apps and smart mobile devices. Despite these benefits, patients may have safety concerns about the use of mobile devices around medical equipment. This research explored the engagement of junior doctors (JDs) with CDS and the perceptions of patients about their use. There were three objectives for this research: (1) to measure the actual usage of CDS tools on mobile devices (mCDS) by JDs, (2) to explore the perceptions of JDs about the drivers and barriers to using mCDS, and (3) to explore the perceptions of patients about the use of mCDS. This study used a mixed-methods approach to study the engagement of JDs with CDS accessed through mobile devices. Usage data were collected on the number of interactions by JDs with mCDS. The perceived drivers and barriers for JDs to using CDS were then explored by interviews. Finally, these findings were contrasted with the perception of patients about the use of mCDS by JDs. Nine of the 16 JDs made a total of 142 recorded interactions with the mCDS over a 4-month period. Only 27 of the 114 interactions (24%) that could be categorized as on-shift or off-shift occurred on-shift. Eight individual, institutional, and cultural barriers to engagement emerged from interviews with the user group. In contrast to reported cautions and concerns about the impact of clinicians' use of mobile phone on patient health and safety, patients had positive perceptions about the use of mCDS. Patients reported positive perceptions toward mCDS. The usage of mCDS to support clinical decision making was considered to be positive as part of everyday clinical practice. The degree of engagement was found to be limited due to a number of individual, institutional, and cultural barriers. The majority of mCDS engagement occurred outside of the workplace. Further research is required to verify these findings and assess their implications for future policy and practice.

A bifacial quantum dot-sensitized solar cell with all-cadmium sulfide photoanode

NASA Astrophysics Data System (ADS)

Ma, Chunqing; Tang, Qunwei; Liu, Danyang; Zhao, Zhiyuan; He, Benlin; Chen, Haiyan; Yu, Liangmin

2015-02-01

Pursuit of a high power conversion efficiency and reduction of electricity-generation cost has been a persistent objective for quantum dot-sensitized solar cells (QDSSCs). We present here the fabrication of a QDSSC comprising a nanoflower-structured CdS anode, a liquid electrolyte having S2-/Sn2- redox couples, and a transparent CoSe counter electrode. Nanoflower-structured CdS anodes are prepared by a successive ionic layer adsorption and reaction (SILAR) method and subsequently hydrothermal strategy free of any surfactant or template. The CdS nanoparticles synthesized by a SILAR method act as "seed crystal" for growth of CdS nanoflowers. The average electron lifetime is markedly elevated in nanoflower-structured CdS anode in comparison with CdS nanoparticle or nanoporous CdS microsphere anode. Herein, we study the effect of synthesis method on CdS morphology and solar cell's photovoltaic performance, showing a power conversion efficiency of 1.67% and 1.17% for nanoflower-structured CdS QDSSC under front and rear irradiations, respectively.

Implementation Pearls from a New Guidebook on Improving Medication Use and Outcomes with Clinical Decision Support

PubMed Central

Sirajuddin, Anwar M; Osheroff, Jerome A.; Sittig, Dean F.; Chuo, John; Velasco, Ferdinand; Collins, David A.

2012-01-01

Effective clinical decision support (CDS) is essential for addressing healthcare performance improvement imperatives, but care delivery organizations (CDO) typically struggle with CDS deployment. Ensuring safe and effective medication delivery to patients is a central focus of CDO performance improvement efforts, and this article provides an overview of best-practice strategies for applying CDS to these goals. The strategies discussed are drawn from a new guidebook, co-published and co-sponsored by more than a dozen leading organizations. Developed by scores of CDS implementers and experts, the guidebook outlines key steps and success factors for applying CDS to medication management. A central thesis is that improving outcomes with CDS interventions requires that the CDS five rights be addressed successfully. That is, the interventions must deliver the right information, to the right person, in the right format, through the right channel, at the right point in workflow. This paper provides further details about these CDS five rights, and highlights other important strategies for successful CDS programs. PMID:19894486

Closed depressions in the European loess belt - Natural or anthropogenic origin?

NASA Astrophysics Data System (ADS)

Kołodyńska-Gawrysiak, Renata; Poesen, Jean

2017-07-01

Closed depressions (CDs) are typical geomorphological features of the loess belt in Europe. CDs have been reported in several regions of the European loess belt, where they are described as hollows, mardeles, wymoki, crovuri, bludtsa and zapadiny. The natural and anthropogenic origins of CDs are debated in literature. Moreover, no comprehensive review of the geomorphic properties or the evolution of these depressions exists. Therefore this paper reviews the characteristics of CDs in the European loess belt and attempts to better understand their genesis based on detailed case studies. The main morphometric features as well as sediment deposits within CDs in several sub-regions of Europe were analysed and compared. Morphometric properties of CDs from the West European and East European loess belt were investigated through a comparison of CDs from two representative regions, i.e. East Poland and Central Belgium. In both study areas, CDs under cropland are similar. However, a comparison of morphological features of CDs under forest, revealed clear differences, suggesting a different origin of CDs from both regions. Infilled sediments in CDs show various litho-genetical features in different regions of the European loess belt. The morphometric features, ages and stratigraphy of infillings clearly indicate that both anthropogenic and natural processes have shaped these landforms within the loess belt of Europe. CDs observed in Eastern Europe may have a very different origin than those documented in Western Europe. Detailed analysis of CDs in Poland and in neighbouring regions of East Europe, suggest that CDs are natural landforms: thermokarst, deflation and dissolution of loess are reported as probable genetic processes. In contrast, several studies in Western Europe indicate a dominant anthropogenic origin (i.e. digging of calcareous loess or marls, bomb and mining craters, collapse of underground limestone quarries), although CDs formed by natural processes (i.e. piping, dissolution of limestone and salt lenses below the loess cover) are reported as well. CDs act as important archives, allowing one to reconstruct both natural and anthropogenic processes operating in the past. As CDs store most sediments eroded within their catchment they provide ideal sediment traps to assess long-term erosion rates in these environments which have hitherto been under-researched. More research is needed to unravel the genesis and evolution of these depressions to better understand the importance of the Late Glacial and Holocene stages for the morphogenesis of the loess belt in Europe.

Intraoperative Clinical Decision Support for Anesthesia: A Narrative Review of Available Systems.

PubMed

Nair, Bala G; Gabel, Eilon; Hofer, Ira; Schwid, Howard A; Cannesson, Maxime

2017-02-01

With increasing adoption of anesthesia information management systems (AIMS), there is growing interest in utilizing AIMS data for intraoperative clinical decision support (CDS). CDS for anesthesia has the potential for improving quality of care, patient safety, billing, and compliance. Intraoperative CDS can range from passive and post hoc systems to active real-time systems that can detect ongoing clinical issues and deviations from best practice care. Real-time CDS holds the most promise because real-time alerts and guidance can drive provider behavior toward evidence-based standardized care during the ongoing case. In this review, we describe the different types of intraoperative CDS systems with specific emphasis on real-time systems. The technical considerations in developing and implementing real-time CDS are systematically covered. This includes the functional modules of a CDS system, development and execution of decision rules, and modalities to alert anesthesia providers concerning clinical issues. We also describe the regulatory aspects that affect development, implementation, and use of intraoperative CDS. Methods and measures to assess the effectiveness of intraoperative CDS are discussed. Last, we outline areas of future development of intraoperative CDS, particularly the possibility of providing predictive and prescriptive decision support.

Green synthesis of multifunctional carbon dots from coriander leaves and their potential application as antioxidants, sensors and bioimaging agents.

PubMed

Sachdev, Abhay; Gopinath, P

2015-06-21

In the present study, a facile one-step hydrothermal treatment of coriander leaves for preparing carbon dots (CDs) has been reported. Optical and structural properties of the CDs have been extensively studied by UV-visible and fluorescence spectroscopic, microscopic (transmission electron microscopy, scanning electron microscopy) and X-ray diffraction techniques. Surface functionality and composition of the CDs have been illustrated by elemental analysis and Fourier transform infrared spectroscopy (FTIR). Quenching of the fluorescence of the CDs in the presence of metal ions is of prime significance, hence CDs have been used as a fluorescence probe for sensitive and selective detection of Fe(3+) ions. Eventually, biocompatibility and bioimaging aspects of CDs have been evaluated on lung normal (L-132) and cancer (A549) cell lines. Qualitative analysis of cellular uptake of CDs has been pursued through fluorescence microscopy, while quantitative analysis using a flow cytometer provided an insight into the concentration and cell-type dependent uptake of CDs. The article further investigates the antioxidant activity of CDs. Therefore, we have validated the practicality of CDs obtained from a herbal carbon source for versatile applications.

Preparation of highly luminescent and biocompatible carbon dots using a new extraction method

NASA Astrophysics Data System (ADS)

Zhang, Rui; Liu, Ying-Bo; Sun, Shu-Qing

2013-10-01

C dots (CDs) are among the most promising emerging fluorescent labels for biological imaging and sensing. A facile new synthesis method was developed using common organic solvents for fabricating CDs from candle soot. The common organic solvents were used as extractants and the obtained CDs have a narrow size distribution with average diameters of about 3.4 nm for ethylene glycol, 3.5 nm for ethanol, and 3.4 nm for n-butanol. This approach is simpler, easier, and more effective than other methods currently used for CD fabrication. The obtained CDs had a high quantum yield (38 %), tunable emission and are water-soluble. The mechanism for the luminescence of the CDs was investigated and the results indicate that the ability of the solvent to disperse the CDs plays a very important role in the photoluminescence of these CDs. The type of organic solvent and the surface groups on the CDs also influenced the optical properties of the CDs. Different emissive traps are shown to play the major role in the luminescence of the carbon materials. An in vitro hemolysis assay was performed and showed that the CDs are biocompatible.

Energy-efficient algorithm for broadcasting in ad hoc wireless sensor networks.

PubMed

Xiong, Naixue; Huang, Xingbo; Cheng, Hongju; Wan, Zheng

2013-04-12

Broadcasting is a common and basic operation used to support various network protocols in wireless networks. To achieve energy-efficient broadcasting is especially important for ad hoc wireless sensor networks because sensors are generally powered by batteries with limited lifetimes. Energy consumption for broadcast operations can be reduced by minimizing the number of relay nodes based on the observation that data transmission processes consume more energy than data reception processes in the sensor nodes, and how to improve the network lifetime is always an interesting issue in sensor network research. The minimum-energy broadcast problem is then equivalent to the problem of finding the minimum Connected Dominating Set (CDS) for a connected graph that is proved NP-complete. In this paper, we introduce an Efficient Minimum CDS algorithm (EMCDS) with help of a proposed ordered sequence list. EMCDS does not concern itself with node energy and broadcast operations might fail if relay nodes are out of energy. Next we have proposed a Minimum Energy-consumption Broadcast Scheme (MEBS) with a modified version of EMCDS, and aimed at providing an efficient scheduling scheme with maximized network lifetime. The simulation results show that the proposed EMCDS algorithm can find smaller CDS compared with related works, and the MEBS can help to increase the network lifetime by efficiently balancing energy among nodes in the networks.

SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss

PubMed Central

Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

2011-01-01

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/ PMID:22120661

SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss.

PubMed

Di Génova, Alex; Aravena, Andrés; Zapata, Luis; González, Mauricio; Maass, Alejandro; Iturra, Patricia

2011-01-01

SalmonDB is a new multiorganism database containing EST sequences from Salmo salar, Oncorhynchus mykiss and the whole genome sequence of Danio rerio, Gasterosteus aculeatus, Tetraodon nigroviridis, Oryzias latipes and Takifugu rubripes, built with core components from GMOD project, GOPArc system and the BioMart project. The information provided by this resource includes Gene Ontology terms, metabolic pathways, SNP prediction, CDS prediction, orthologs prediction, several precalculated BLAST searches and domains. It also provides a BLAST server for matching user-provided sequences to any of the databases and an advanced query tool (BioMart) that allows easy browsing of EST databases with user-defined criteria. These tools make SalmonDB database a valuable resource for researchers searching for transcripts and genomic information regarding S. salar and other salmonid species. The database is expected to grow in the near feature, particularly with the S. salar genome sequencing project. Database URL: http://genomicasalmones.dim.uchile.cl/

Preoperative planning of calcium deposit removal in calcifying tendinitis of the rotator cuff - possible contribution of computed tomography, ultrasound and conventional X-Ray.

PubMed

Izadpanah, Kaywan; Jaeger, Martin; Maier, Dirk; Südkamp, Norbert P; Ogon, Peter

2014-11-20

The purpose of the present study was to investigate the accuracy of Ultrasound (US), conventional X-Ray (CX) and Computed Tomography (CT) to estimate the total count, localization, morphology and consistency of Calcium deposits (CDs) in the rotator cuff. US, CX and CT imaging was performed pre-operatively in 151 patients who underwent arthroscopic removal of CDs in the rotator cuff. In all procedures: (1) total CD counts were determined, (2) the CDs appearance in each image modality was correlated to the intraoperative consistency and (3) CDs were localized in their relation to the acromion using US, CX and CT. Using US158 CDs, using CT 188 CDs and using CX 164 CDs were identified. Reliable localization of the CDs was possible with all used diagnostic modalities. CT revealed 49% of the CDs to be septated, out of which 85% were uni- and 15% multiseptated. CX was not suitable for prediction of CDs consistency. US reliably predicted viscous-solid CDs consistency only when presenting with full sound extinction (PPV 84.6%) . CT had high positive and negative predictive values for detection of liquid-soft (PPV 92.9%) and viscous-solid (PPV 87.8%) CDs. US and CX are sufficient for preoperative planning of CD removal with regards to localization and prediction of consistency if the deposits present with full sound extinction. This is the case in the majority of the patients. However, in patients with missing sound extinction CT can be recommended if CDs consistency of the deposits should be determined. Satellite deposits or septations are regularly present, which is of importance if complete CD removal is aspired.

Highly fluorescent Zn-doped carbon dots as Fenton reaction-based bio-sensors: an integrative experimental-theoretical consideration.

PubMed

Xu, Quan; Liu, Yao; Su, Rigu; Cai, Lulu; Li, Bofan; Zhang, Yingyuan; Zhang, Linzhou; Wang, Yajun; Wang, Yan; Li, Neng; Gong, Xiao; Gu, Zhipeng; Chen, Yusheng; Tan, Yanglan; Dong, Chenbo; Sreeprasad, Theruvakkattil Sreenivasan

2016-10-20

Heteroatom doped carbon dots (CDs), with high photoluminescence quantum yield (PLQY), are of keen interest in various applications such as chemical sensors, bio-imaging, electronics, and photovoltaics. Zinc, an important element assisting the electron-transfer process and an essential trace element for cells, is a promising metal dopant for CDs, which could potentially lead to multifunctional CDs. In this contribution, we report a single-step, high efficiency, hydrothermal method to synthesize Zn-doped carbon dots (Zn-CDs) with a superior PLQY. The PLQY and luminescence characteristic of Zn-CDs can be tuned by controlling the precursor ratio, and the surface oxidation in the CDs. Though a few studies have reported metal doped CDs with good PLQY, the as prepared Zn-Cds in the present method exhibited a PLQY up to 32.3%. To the best of our knowledge, there is no report regarding the facile preparation of single metal-doped CDs with a QY more than 30%. Another unique attribute of the Zn-CDs is the high monodispersity and the resultant highly robust excitation-independent luminescence that is stable over a broad range of pH values. Spectroscopic investigations indicated that the superior PLQY and luminescence of Zn-CDs are due to the heteroatom directed, oxidized carbon-based surface passivation. Furthermore, we developed a novel and sensitive biosensor for the detection of hydrogen peroxide and glucose leveraging the robust fluorescence properties of Zn-CDs. Under optimal conditions, Zn-CDs demonstrated high sensitivity and response to hydrogen peroxide and glucose over a wide range of concentrations, with a linear range of 10-80 μM and 5-100 μM, respectively, indicating their great potential as a fluorescent probe for chemical sensing.

Influence of wide band gap oxide substrates on the photoelectrochemical properties and structural disorder of CdS nanoparticles grown by the successive ionic layer adsorption and reaction (SILAR) method

PubMed Central

Malashchonak, Mikalai V; Korolik, Olga V; Streltsov, Еugene А; Kulak, Anatoly I

2015-01-01

Summary The photoelectrochemical properties of nanoheterostructures based on the wide band gap oxide substrates (ZnO, TiO2, In2O3) and CdS nanoparticles deposited by the successive ionic layer adsorption and reaction (SILAR) method have been studied as a function of the CdS deposition cycle number (N). The incident photon-to-current conversion efficiency (IPCE) passes through a maximum with the increase of N, which is ascribed to the competition between the increase in optical absorption and photocarrier recombination. The maximal IPCE values for the In2O3/CdS and ZnO/CdS heterostructures are attained at N ≈ 20, whereas for TiO2/CdS, the appropriate N value is an order of magnitude higher. The photocurrent and Raman spectroscopy studies of CdS nanoparticles revealed the occurrence of the quantum confinement effect, demonstrating the most rapid weakening with the increase of N in ZnO/CdS heterostructures. The structural disorder of CdS nanoparticles was characterized by the Urbach energy (E U), spectral width of the CdS longitudinal optical (LO) phonon band and the relative intensity of the surface optical (SO) phonon band in the Raman spectra. Maximal values of E U (100–120 meV) correspond to СdS nanoparticles on a In2O3 surface, correlating with the fact that the CdS LO band spectral width and intensity ratio for the CdS SO and LO bands are maximal for In2O3/CdS films. A notable variation in the degree of disorder of CdS nanoparticles is observed only in the initial stages of CdS growth (several tens of deposition cycles), indicating the preservation of the nanocrystalline state of CdS over a wide range of SILAR cycles. PMID:26734517

Influence of wide band gap oxide substrates on the photoelectrochemical properties and structural disorder of CdS nanoparticles grown by the successive ionic layer adsorption and reaction (SILAR) method.

PubMed

Malashchonak, Mikalai V; Mazanik, Alexander V; Korolik, Olga V; Streltsov, Еugene А; Kulak, Anatoly I

2015-01-01

The photoelectrochemical properties of nanoheterostructures based on the wide band gap oxide substrates (ZnO, TiO2, In2O3) and CdS nanoparticles deposited by the successive ionic layer adsorption and reaction (SILAR) method have been studied as a function of the CdS deposition cycle number (N). The incident photon-to-current conversion efficiency (IPCE) passes through a maximum with the increase of N, which is ascribed to the competition between the increase in optical absorption and photocarrier recombination. The maximal IPCE values for the In2O3/CdS and ZnO/CdS heterostructures are attained at N ≈ 20, whereas for TiO2/CdS, the appropriate N value is an order of magnitude higher. The photocurrent and Raman spectroscopy studies of CdS nanoparticles revealed the occurrence of the quantum confinement effect, demonstrating the most rapid weakening with the increase of N in ZnO/CdS heterostructures. The structural disorder of CdS nanoparticles was characterized by the Urbach energy (E U), spectral width of the CdS longitudinal optical (LO) phonon band and the relative intensity of the surface optical (SO) phonon band in the Raman spectra. Maximal values of E U (100-120 meV) correspond to СdS nanoparticles on a In2O3 surface, correlating with the fact that the CdS LO band spectral width and intensity ratio for the CdS SO and LO bands are maximal for In2O3/CdS films. A notable variation in the degree of disorder of CdS nanoparticles is observed only in the initial stages of CdS growth (several tens of deposition cycles), indicating the preservation of the nanocrystalline state of CdS over a wide range of SILAR cycles.

TiO2 activity enhancement through synergistic effect of photons localization of photonic crystals and the sensitization of CdS quantum dots

NASA Astrophysics Data System (ADS)

Li, Ping; Wang, Yuan; Wang, Ai-Jun; Chen, Sheng-Li

2017-02-01

In this work, the enhancement of TiO2 photocatalytic activity was studied through synergistic effect of the photons localization of photonic crystals and the sensitization of CdS quantum dots (CdS QDs). CdS QDs sensitized TiO2 membrane (denoted as CdS QDs/TiO2) was synthesized through doping the TiO2 membrane with CdS QDs by chemical bath deposition method (CBD). After TiO2 was sensitized with CdS QDs, the edge of light absorption of TiO2 was red-shifted to 470 nm and the light absorption in the range of 400 600 nm was higher than that of plain TiO2 membrane. Another type of composite membrane, CdS QDs/TiO2/SiO2 opal composite membrane was prepared by coupling SiO2 opal (a kind of photonic crystal) layer onto the CdS QDs/TiO2 membrane, and the photonic band gap of the SiO2 opal photonic crystal layer was deliberately planned at the electronic band gap of the CdS QDs. The photodegradation of gaseous CH3CHO (acetaldehyde) was used as probe reaction to test the photocatalytic activity of the as-prepared membranes, and the results showed that the CdS QDs sensitization can significantly improve the photocatalytic activity of TiO2 membrane under visible light irradiation, with the acetaldehyde degradation rate constant (k) on CdS QDs/TiO2 membranes being 1.59 times of that on plain TiO2 membranes. The acetaldehyde degradation rate constant on CdS QDs/TiO2/SiO2 opal composite membrane reached 4 times of that on plain TiO2 membrane. The photocatalytic activity of TiO2 membrane can be improved through synergistic effect of the photons localization of photonic crystals and the sensitization of CdS QDs.

Structural and optoelectronic studies on Ag-CdS quantum dots

NASA Astrophysics Data System (ADS)

Ibrahim Mohammed S., M.; Gubari, Ghamdan M. M.; Huse, Nanasaheb P.; Dive, Avinash S.; Sharma, Ramphal

2018-05-01

In the present study, we have successfully deposited CdS quantum dot thin films and Ag doped CdS on a glass slide by simple and economical chemical bath deposition at room temperature. The X-ray diffraction method analysis reveals that CdS thin films exhibit hexagonal structure when compared with standard JCPDS data. The estimated average crystallite size of the quantum dots and resulted in the least crystallite size of ˜9 nm. a comparison between the optical and electrical properties of the films before and after doping Ag was made through measuring and analyzing the curves for UV and I-V. From UV absorption spectra we observed that the samples exhibited a band edge near ˜400 nm with a slight deviation with the presence of excitonic peak for both CdS and Ag doped CdS. The presence of excitonic peak may be referred to the formation of quantum dots. The calculated band gap energy of thin films was found to be 3.45 eV and 3.15 eV for both CdS and Ag doped CdS thin films respectively, where the optical absorption spectra of Ag doped CdS nanoparticles also exhibit shift with respect to that of CdS quantum dots thin films. The photosensitive of CdS thin films show an increase in photocurrent when Ag doped CdS.

Hexagonal pencil-like CdS nanorods: Facile synthesis and enhanced visible light photocatalytic performance

NASA Astrophysics Data System (ADS)

An, Liang; Wang, Guanghui; Zhao, Lei; Zhou, Yong; Gao, Fang; Cheng, Yang

2015-07-01

In the present study, hexagonal pencil-like CdS nanorods have been successfully synthesized through a typical facile and economical one-step hydrothermal method without using any surfactant or template. The product was characterized by X-ray powder diffraction (XRD), field-emission scanning electron microscopy (FE-SEM) and energy dispersive analysis of X-ray (EDX). The results revealed that the prepared CdS photocatalyst consisted of a large quantity of straight and smooth solid hexagonal nanorods and a few nanoparticles. The photocatalytic activities of CdS nanorods and commercial CdS powders were investigated by the photodegradation of Orange II (OII) in aqueous solution under visible light, and the CdS nanorods presented the highest photocatalytic activity. Its photocatalytic efficiency enhancement was attributed to the improved transmission of photogenerated electron-hole pairs in the CdS nanostructures. The present findings may provide a facile approach to synthesize high efficient CdS photocatalysts.

Emergence of Atypical Mycoplasma agalactiae Strains Harboring a New Prophage and Associated with an Alpine Wild Ungulate Mortality Episode

PubMed Central

Tardy, Florence; Baranowski, Eric; Nouvel, Laurent-Xavier; Mick, Virginie; Manso-Silvàn, Lucía; Thiaucourt, François; Thébault, Patricia; Breton, Marc; Sirand-Pugnet, Pascal; Blanchard, Alain; Garnier, Alexandre; Gibert, Philippe; Game, Yvette; Poumarat, François

2012-01-01

The bacterium Mycoplasma agalactiae is responsible for contagious agalactia (CA) in small domestic ruminants, a syndrome listed by the World Organization for Animal Health and responsible for severe damage to the dairy industry. Recently, we frequently isolated this pathogen from lung lesions of ibexes during a mortality episode in the French Alps. This situation was unusual in terms of host specificity and tissue tropism, raising the question of M. agalactiae emergence in wildlife. To address this issue, the ibex isolates were characterized using a combination of approaches that included antigenic profiles, molecular typing, optical mapping, and whole-genome sequencing. Genome analyses showed the presence of a new, large prophage containing 35 coding sequences (CDS) that was detected in most but not all ibex strains and has a homolog in Mycoplasma conjunctivae, a species causing keratoconjunctivitis in wild ungulates. This and the presence in all strains of large integrated conjugative elements suggested highly dynamic genomes. Nevertheless, M. agalactiae strains circulating in the ibex population were shown to be highly related, most likely originating from a single parental clone that has also spread to another wild ungulate species of the same geographical area, the chamois. These strains clearly differ from strains described in Europe so far, including those found nearby, before CA eradication a few years ago. While M. agalactiae pathogenicity in ibexes remains unclear, our data showed the emergence of atypical strains in Alpine wild ungulates, raising the question of a role for the wild fauna as a potential reservoir of pathogenic mycoplasmas. PMID:22522685

Pool-based genome-wide association study identified novel candidate regions on BTA9 and 14 for oleic acid percentage in Japanese Black cattle.

PubMed

Kawaguchi, Fuki; Kigoshi, Hiroto; Nakajima, Ayaka; Matsumoto, Yuta; Uemoto, Yoshinobu; Fukushima, Moriyuki; Yoshida, Emi; Iwamoto, Eiji; Akiyama, Takayuki; Kohama, Namiko; Kobayashi, Eiji; Honda, Takeshi; Oyama, Kenji; Mannen, Hideyuki; Sasazaki, Shinji

2018-05-17

Fatty acid composition is an important indicator of beef quality. The objective of this study was to search the potential candidate region for fatty acid composition. We performed pool-based genome-wide association studies (GWAS) for oleic acid percentage (C18:1) in a Japanese Black cattle population from the Hyogo prefecture. GWAS analysis revealed two novel candidate regions on BTA9 and BTA14. The most significant single nucleotide polymorphisms (SNPs) in each region were genotyped in a population (n = 899) to verify their effect on C18:1. Statistical analysis revealed that both SNPs were significantly associated with C18:1 (p = .0080 and .0003), validating the quantitative trait loci (QTLs) detected in GWAS. We subsequently selected VNN1 and LYPLA1 genes as candidate genes from each region on BTA9 and BTA14, respectively. We sequenced full-length coding sequence (CDS) of these genes in eight individuals and identified a nonsynonymous SNP T66M on VNN1 gene as a putative candidate polymorphism. The polymorphism was also significantly associated with C18:1, but the p value (p = .0162) was higher than the most significant SNP on BTA9, suggesting that it would not be responsible for the QTL. Although further investigation will be needed to determine the responsible gene and polymorphism, our findings would contribute to development of selective markers for fatty acid composition in the Japanese Black cattle of Hyogo. © 2018 Japanese Society of Animal Science.

Molecular mechanisms of pathogenesis in hepatocellular carcinoma revealed by RNA‑sequencing.

PubMed

Liu, Yao; Yang, Zhe; Du, Feng; Yang, Qiao; Hou, Jie; Yan, Xiaohong; Geng, Yi; Zhao, Yaning; Wang, Hua

2017-11-01

The present study aimed to explore the underlying molecular mechanisms of hepatocellular carcinoma (HCC). RNA‑sequencing profiles GSM629264 and GSM629265, from the GSE25599 data set, were downloaded from the Gene Expression Omnibus database and processed by quality evaluation. GSM629264 and GSM629265 were from HCC and adjacent non‑cancerous tissues, respectively. TopHat software was used for alignment analysis, followed by the detection of novel splicing sites. In addition, the Cufflinks software package was used to analyze gene expressions, and the Cuffdiff program was used to screen for differently expressed genes (DEGs) and differentially expressed splicing variants. Gene ontology functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of DEGs were also performed. Transcription factors (TFs) and microRNAs (miRNAs) that regulate DEGs were identified, and a protein‑protein interaction (PPI) network was constructed. The hub node in the PPI network was obtained, and the TFs and miRNAs that regulated the hub node were further predicted. The quality of the sequencing data met the standards for analysis, and the clean reads were ~65%. Most sequencing reads mapped into coding sequence exons (CDS_exons), whereas other reads mapped into exon 3' untranslated regions (UTR_Exons), 5'UTR_Exons and Introns. Upregulated and downregulated DEGs between HCC and adjacent non‑cancerous tissues were screened. Genes of differentially expressed splicing variants were identified, including vesicle‑associated membrane protein 4, phosphatidylinositol glycan anchor biosynthesis class C, protein disulfide isomerase family A member 4 and growth arrest specific 5. Screened DEGs were enriched in the complement pathway. In the PPI network, ubiquitin C (UBC) was the hub node. UBC was predicted to be regulated by several TFs, including specificity protein 1 (SP1), FBJ murine osteosarcoma viral oncogene homolog (FOS), proto‑oncogene c‑JUN (JUN), FOS‑like antigen 2 (FOSL2) and SWI/SNF‑related, matrix‑associated, actin‑dependent regulator of chromatin, subfamily A, member 4 (SMARCA4), and several miRNAs, including miR‑30 and miR‑181. Results from the present study demonstrated that UBC, SP1, FOS, JUN, FOSL2, SMARCA4, miR‑30 and miR‑181 may participate in the development of HCC.

Evaluation of Freehand B-Mode and Power-Mode 3D Ultrasound for Visualisation and Grading of Internal Carotid Artery Stenosis.

PubMed

Pelz, Johann Otto; Weinreich, Anna; Karlas, Thomas; Saur, Dorothee

2017-01-01

Currently, colour-coded duplex sonography (2D-CDS) is clinical standard for detection and grading of internal carotid artery stenosis (ICAS). However, unlike angiographic imaging modalities, 2D-CDS assesses ICAS by its hemodynamic effects rather than luminal changes. Aim of this study was to evaluate freehand 3D ultrasound (3DUS) for direct visualisation and quantification of ICAS. Thirty-seven patients with 43 ICAS were examined with 2D-CDS as reference standard and with freehand B-mode respectively power-mode 3DUS. Stenotic value of 3D reconstructed ICAS was calculated as distal diameter respectively distal cross-sectional area (CSA) reduction percentage and compared with 2D-CDS. There was a trend but no significant difference in successful 3D reconstruction of ICAS between B-mode and power mode (examiner 1 {Ex1} 81% versus 93%, examiner 2 {Ex2} 84% versus 88%). Inter-rater agreement was best for power-mode 3DUS and assessment of stenotic value as distal CSA reduction percentage (intraclass correlation coefficient {ICC} 0.90) followed by power-mode 3DUS and distal diameter reduction percentage (ICC 0.81). Inter-rater agreement was poor for B-mode 3DUS (ICC, distal CSA reduction 0.36, distal diameter reduction 0.51). Intra-rater agreement for power-mode 3DUS was good for both measuring methods (ICC, distal CSA reduction 0.88 {Ex1} and 0.78 {Ex2}; ICC, distal diameter reduction 0.83 {Ex1} and 0.76 {Ex2}). In comparison to 2D-CDS inter-method agreement was good and clearly better for power-mode 3DUS (ICC, distal diameter reduction percentage: Ex1 0.85, Ex2 0.78; distal CSA reduction percentage: Ex1 0.63, Ex2 0.57) than for B-mode 3DUS (ICC, distal diameter reduction percentage: Ex1 0.40, Ex2 0.52; distal CSA reduction percentage: Ex1 0.15, Ex2 0.51). Non-invasive power-mode 3DUS is superior to B-mode 3DUS for imaging and quantification of ICAS. Thereby, further studies are warranted which should now compare power-mode 3DUS with the angiographic gold standard imaging modalities for quantification of ICAS, i.e. with CTA or CE-MRA.

Ultrasound-assisted microwave preparation of Ag-doped CdS nanoparticles.

PubMed

Ma, Jun; Tai, Guo'an; Guo, Wanlin

2010-03-01

Ag-doped CdS nanoparticles were synthesized by an ultrasound-assisted microwave synthesis method. The X-ray diffraction patterns reveal a structural evolution from cubic to hexagonal with increasing molar ratios of Ag(+)/Cd(2+) from 0% to 5%. It shows that the Ag-doped hexagonal CdS nanoparticles are polycrystal. The X-ray photoelectron spectroscopy of the CdS nanoparticles doping with 5% Ag(+) shows that the doped Ag in CdS is metallic. Simultaneously, the characteristic Raman peaks of the CdS nanoparticles enhance with increasing Ag(+) concentrations. The photocatalytic activity of different Ag-doped samples show a reasonable change due to different ratios of Ag which doped into CdS. Copyright 2009 Elsevier B.V. All rights reserved.

Nitrogen and sulfur co-doped carbon dots with strong blue luminescence.

PubMed

Ding, Hui; Wei, Ji-Shi; Xiong, Huan-Ming

2014-11-21

Sulfur-doped carbon dots (S-CDs) with a quantum yield (QY) of 5.5% and nitrogen, sulfur co-doped carbon dots (N,S-CDs) with a QY of 54.4% were synthesized, respectively, via the same hydrothermal route using α-lipoic acid as the carbon source. The obtained S-CDs and N,S-CDs had similar sizes but different optical features. The QY of N,S-CDs was gradually enhanced when extending the reaction time to increase the nitrogen content. After careful characterization of these CDs, the doped nitrogen element was believed to be in the form of C=N and C-N bonds which enhanced the fluorescence efficiency significantly. Meanwhile, the co-doped sulfur element was found to be synergistic for nitrogen doping in N,S-CDs. The optimal N,S-CDs were successfully employed as good multicolor cell imaging probes due to their fine dispersion in water, excitation-dependent emission, excellent fluorescence stability and low toxicity. Besides, such N,S-CDs showed a wide detection range and excellent accuracy as fluorescent sensors for Fe(3+) ions.

Chemical Synthesis and Optical Properties of CdS Poly(Lactic Acid) Nanocomposites and Their Transparent Fluorescent Films

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

Wang, Cai-Feng; Cheng, Yu-Peng; Xie, He-Yi

2011-01-01

This paper describes the chemical synthesis of cadmium sulfide (CdS) polymer nanocomposites by covalently grafting poly(lactic acid) (PLA) onto the surfaces of CdS nanocrystals (NCs). Synthesis of the nanocomposites involved two steps. Lactic acid (LA) capped CdS NCs were first prepared by reacting cadmium chloride (CdCl2) with sodium sulfide (Na2S) using LA as the organic ligand in H2O/N,N-dimethylformamide (DMF) solution. Next CdS PLA nanocomposites were formed by in situ ring-opening polymerization of lactide on the surface of modified CdS NCs. Transparent fluorescent films were then successfully prepared by blending as-prepared CdS PLA nanocomposites with high-molecular-weight PLA. The as-prepared CdS NCsmore » and their nanocomposites were studied by transmission electron microscopic imaging, thermogravimetric analyses, and spectroscopic measurements (ultraviolet-visible absorption and photoluminescence). The spectroscopic studies revealed that the CdS polymer nanocomposites exhibited good optical properties in terms of their photoluminescence and transparency.« less

Nucleotide sequence determination of guinea-pig casein B mRNA reveals homology with bovine and rat alpha s1 caseins and conservation of the non-coding regions of the mRNA.

PubMed Central

Hall, L; Laird, J E; Craig, R K

1984-01-01

Nucleotide sequence analysis of cloned guinea-pig casein B cDNA sequences has identified two casein B variants related to the bovine and rat alpha s1 caseins. Amino acid homology was largely confined to the known bovine or predicted rat phosphorylation sites and within the 'signal' precursor sequence. Comparison of the deduced nucleotide sequence of the guinea-pig and rat alpha s1 casein mRNA species showed greater sequence conservation in the non-coding than in the coding regions, suggesting a functional and possibly regulatory role for the non-coding regions of casein mRNA. The results provide insight into the evolution of the casein genes, and raise questions as to the role of conserved nucleotide sequences within the non-coding regions of mRNA species. Images Fig. 1. PMID:6548375

DNA barcode goes two-dimensions: DNA QR code web server.

PubMed

Liu, Chang; Shi, Linchun; Xu, Xiaolan; Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

2012-01-01

The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, "DNA barcode" actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications.

Lichenase and coding sequences

DOEpatents

Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong

2000-08-15

The present invention provides a fungal lichenase, i.e., an endo-1,3-1,4-.beta.-D-glucanohydrolase, its coding sequence, recombinant DNA molecules comprising the lichenase coding sequences, recombinant host cells and methods for producing same. The present lichenase is from Orpinomyces PC-2.

Utilization of Condensed Distillers Solubles as Nutrient Supplement for Production of Nisin and Lactic Acid from Whey

NASA Astrophysics Data System (ADS)

Liu, Chuanbin; Hu, Bo; Chen, Shulin; Glass, Richard W.

The major challenge associated with the rapid growth of the ethanol industry is the usage of the coproducts, i.e., condensed distillers solubles (CDS) and distillers dried grains, which are currently sold as animal feed supplements. As the growth of the livestock industries remains flat, alternative usage of these coproducts is urgently needed. CDS is obtained after the removal of ethanol by distillation from the yeast fermentation of a grain or a grain mixture by condensing the thin stillage fraction to semisolid. In this work, CDS was first characterized and yeast biomass was proven to be the major component of CDS. CDS contained 7.50% crude protein but with only 42% of that protein being water soluble. Then, CDS was applied as a nutrient supplement for simultaneous production of nisin and lactic acid by Lactococcus lactis subsp. lactis (ATCC 11454). Although CDS was able to support bacteria growth and nisin production, a strong inhibition was observed when CDS was overdosed. This may be caused by the existence of the major ethanol fermentation byproducts, especially lactate and acetate, in CDS. In the final step, the CDS based medium composition for nisin and lactic acid production was optimized using response surface methodology.

Preparation and characterization of photocatalytic carbon dots-sensitized electrospun titania nanostructured fibers

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

Li, Haopeng; Zhu, Yihua, E-mail: yhzhu@ecust.edu.cn; Cao, Huimin

2013-02-15

Graphical abstract: Display Omitted Highlights: ► The TiO{sub 2}-CDs nanostructured fibers are fabricated by using APS combining the electrospinning TiO{sub 2} nanostructured fibers and CDs. ► The CD can work as a photosensitizer in the degradation of rhodamine B under visible light irradiation. ► The TiO{sub 2}-CDs nanostructured fibers exhibit enhanced photocatalytic efficiency and can be easily handled and recycled. -- Abstract: The carbon dots (CDs) are new functional carbon-aceous materials. Compared to conventional dye molecules and semiconductor quantum dots, CDs are superior in chemical inertness and low toxicity. The TiO{sub 2}-CDs nanostructured fibers were fabricated by combining the electrospinningmore » technique and reflux method. Compared with the pure TiO{sub 2} nanostructured fibers and P25, the TiO{sub 2}-CDs nanostructured fibers exhibited enhanced photocatalytic efficiency of photodegradation of rhodamine B (RhB) under visible light irradiation. The enhanced photocatalytic activity of TiO{sub 2}-CDs nanostructured fibers could be attributed to the presence of CDs embedded in TiO{sub 2} nanostructured fibers. The CD can work as a photosensitizer in the degradation. Furthermore, the TiO{sub 2}-CDs nanostructured fibers could be easily handled and recycled due to their one-dimensional nanostructural property.« less

FRAGS: estimation of coding sequence substitution rates from fragmentary data

PubMed Central

Swart, Estienne C; Hide, Winston A; Seoighe, Cathal

2004-01-01

Background Rates of substitution in protein-coding sequences can provide important insights into evolutionary processes that are of biomedical and theoretical interest. Increased availability of coding sequence data has enabled researchers to estimate more accurately the coding sequence divergence of pairs of organisms. However the use of different data sources, alignment protocols and methods to estimate substitution rates leads to widely varying estimates of key parameters that define the coding sequence divergence of orthologous genes. Although complete genome sequence data are not available for all organisms, fragmentary sequence data can provide accurate estimates of substitution rates provided that an appropriate and consistent methodology is used and that differences in the estimates obtainable from different data sources are taken into account. Results We have developed FRAGS, an application framework that uses existing, freely available software components to construct in-frame alignments and estimate coding substitution rates from fragmentary sequence data. Coding sequence substitution estimates for human and chimpanzee sequences, generated by FRAGS, reveal that methodological differences can give rise to significantly different estimates of important substitution parameters. The estimated substitution rates were also used to infer upper-bounds on the amount of sequencing error in the datasets that we have analysed. Conclusion We have developed a system that performs robust estimation of substitution rates for orthologous sequences from a pair of organisms. Our system can be used when fragmentary genomic or transcript data is available from one of the organisms and the other is a completely sequenced genome within the Ensembl database. As well as estimating substitution statistics our system enables the user to manage and query alignment and substitution data. PMID:15005802

Green synthesis of carbon dots originated from Lycii Fructus for effective fluorescent sensing of ferric ion and multicolor cell imaging.

PubMed

Sun, Xiaohan; He, Jiang; Yang, Shenghong; Zheng, Mingda; Wang, Yingying; Ma, Shuang; Zheng, Haipeng

2017-10-01

Green, economical and effective method was developed for synthesis of fluorescent carbon dots (CDs), using one-pot hydrothermal treatment of Lycii Fructus. Optical and structural properties of the CDs have been extensively studied by UV-visible and fluorescence spectroscopic, x-ray diffraction (XRD) techniques, transmission electron microscopy (TEM) and high resolution TEM (HRTEM). Surface functionality and composition of CDs has been illustrated by Fourier transform infrared spectroscopy (FTIR), x-ray photoelectron spectroscopy (XPS) spectra and elemental analysis. The fabricated CDs possess stable fluorescent properties. The fluorescent quantum yield of the CDs can reach 17.2%. The prepared CDs emitted a broad fluorescence between 415 and 545nm and their fluorescence was tuned by changing excitation wavelength. Meanwhile, the fluorescence intensity of the CDs could be significantly quenched by Fe 3+ (turn-off). The CDs exhibit captivating sensitivity and selectivity toward Fe 3+ with a linear range from 0 to 30μM and a detection limit of 21nM. The prepared CDs were successfully applied to the determination of Fe 3+ in the urine samples, the water samples from the from the Yellow River and living HeLa (Henrietta Lacks) cells. Moreover, the low-toxicity and excellent biocompatibility of the CDs were evaluated through MTT assay on HeLa cells. The CDs were also employed as fluorescent probes for multicolor imaging of HeLa cells successfully. Copyright © 2017 Elsevier B.V. All rights reserved.

CIC-DUX4 Induces Small Round Cell Sarcomas Distinct from Ewing Sarcoma.

PubMed

Yoshimoto, Toyoki; Tanaka, Miwa; Homme, Mizuki; Yamazaki, Yukari; Takazawa, Yutaka; Antonescu, Cristina R; Nakamura, Takuro

2017-06-01

CIC-DUX4 sarcoma (CDS) or CIC-rearranged sarcoma is a subcategory of small round cell sarcoma resembling the morphological phenotypes of Ewing sarcoma (ES). However, recent clinicopathologic and molecular genetic analyses indicate that CDS is an independent disease entity from ES. Few ancillary markers have been used in the differential diagnosis of CDS, and additional CDS-specific biomarkers are needed for more definitive classification. Here, we report the generation of an ex vivo mouse model for CDS by transducing embryonic mesenchymal cells (eMC) with human CIC-DUX4 cDNA. Recipient mice transplanted with eMC-expressing CIC-DUX4 rapidly developed an aggressive, undifferentiated sarcoma composed of small round to short spindle cells. Gene-expression profiles of CDS and eMC revealed upregulation of CIC-DUX4 downstream genes such as PEA3 family genes, Ccnd2, Crh , and Zic1 IHC analyses for both mouse and human tumors showed that CCND2 and MUC5AC are reliable biomarkers to distinguish CDS from ES. Gene silencing of CIC-DUX4 as well as Ccnd2, Ret , and Bcl2 effectively inhibited CDS tumor growth in vitro The CDK4/6 inhibitor palbociclib and the soft tissue sarcoma drug trabectedin also blocked the growth of mouse CDS. In summary, our mouse model provides important biological information about CDS and provides a useful platform to explore biomarkers and therapeutic agents for CDS. Cancer Res; 77(11); 2927-37. ©2017 AACR . ©2017 American Association for Cancer Research.

Visual pattern image sequence coding

NASA Technical Reports Server (NTRS)

Silsbee, Peter; Bovik, Alan C.; Chen, Dapang

1990-01-01

The visual pattern image coding (VPIC) configurable digital image-coding process is capable of coding with visual fidelity comparable to the best available techniques, at compressions which (at 30-40:1) exceed all other technologies. These capabilities are associated with unprecedented coding efficiencies; coding and decoding operations are entirely linear with respect to image size and entail a complexity that is 1-2 orders of magnitude faster than any previous high-compression technique. The visual pattern image sequence coding to which attention is presently given exploits all the advantages of the static VPIC in the reduction of information from an additional, temporal dimension, to achieve unprecedented image sequence coding performance.

Optical Properties of CdS Nanobelts and Nanosaws Synthesized by Thermal Evaporation Method

NASA Astrophysics Data System (ADS)

Peng, Zhi-wei; Zou, Bing-suo

2012-04-01

By a simple one-step H2-assisted thermal evaporation method, high quality CdS nanostructures have been successfully fabricated on Au coated Si substrates in large scale. The as-synthesized CdS nanostructures consisted of sword-like nanobelts and toothed nanosaws with a single-crystal hexagonal wurtzite structure. The deposition temperature played an important role in determining the size and morphology of the CdS nanostructures. A combination of vapor-liquid-solid and vapor-solid growth mechanisms were proposed to interpret the formation of CdS nanostructures. Photoluminescence measurement indicated that the nanobelts and nanosaws have a prominent green emission at about 512 nm, which is the band-to-band emission of CdS. The waveguide characteristics of both types of CdS nanostructures were observed and discussed.

Outcomes of clinical decision support (CDS) and correlates of CDS use for home care patients with high medication regimen complexity: A randomized trial

PubMed Central

McDonald, Margaret V.; Feldman, Penny H.; Barrón-Vayá, Yolanda; Peng, Timothy R.; Sridharan, Sridevi; Pezzin, Liliana E.

2017-01-01

Objective To assess the outcomes of a clinical decision support (CDS) intervention designed for home care patients with high medication regimen complexity (MRC) and to examine the correlates of CDS use and its relationship to patient outcomes. Method The intervention randomized nurses upon identification of an eligible patient. The CDS consisted of a computerized algorithm that identified high MRC patients, electronic clinician alerts, and a care management module. Analyses were completed on full intention to treat and intervention group-only samples. Regression-adjusted outcomes were hospitalization, emergency department use and reduction in MRC. Data sources included health records and administrative data. Results Five hundred nurses were randomized with 7,919 of their patients. Approximately 20% of the intervention group was hospitalized versus 21% in the control group; 16.5% of the intervention group had an emergency department visit versus 16.7% in the control group; and 6% in each group dropped below the high MRC threshold. No statistically significant differences were found in the intention to treat analysis. Eighty-two percent of intervention nurses used the CDS but for only 42% of their patients. Among intervention patients, CDS use (versus non-use) was associated with reduced MRC and hospitalization. CDS use was more likely among older nurses, those with higher study-patient caseload and, marginally, among salaried nurses and those with longer tenure. Significant patient characteristics were clinical conditions, payer, episode length, care continuity and race. Conclusion CDS use was limited, thus negating the impact of the intervention overall. The findings on correlates of CDS use and the relationship between CDS use and positive outcomes suggest that CDS use and outcomes could be enhanced by avoiding very short patient lengths of stay, improving continuity of care, increasing reliance on salaried nurses and/or increasing per diem nurses’ incentives to use CDS. PMID:26009977

Structured representation for core elements of common clinical decision support interventions to facilitate knowledge sharing.

PubMed

Zhou, Li; Hongsermeier, Tonya; Boxwala, Aziz; Lewis, Janet; Kawamoto, Kensaku; Maviglia, Saverio; Gentile, Douglas; Teich, Jonathan M; Rocha, Roberto; Bell, Douglas; Middleton, Blackford

2013-01-01

At present, there are no widely accepted, standard approaches for representing computer-based clinical decision support (CDS) intervention types and their structural components. This study aimed to identify key requirements for the representation of five widely utilized CDS intervention types: alerts and reminders, order sets, infobuttons, documentation templates/forms, and relevant data presentation. An XML schema was proposed for representing these interventions and their core structural elements (e.g., general metadata, applicable clinical scenarios, CDS inputs, CDS outputs, and CDS logic) in a shareable manner. The schema was validated by building CDS artifacts for 22 different interventions, targeted toward guidelines and clinical conditions called for in the 2011 Meaningful Use criteria. Custom style sheets were developed to render the XML files in human-readable form. The CDS knowledge artifacts were shared via a public web portal. Our experience also identifies gaps in existing standards and informs future development of standards for CDS knowledge representation and sharing.

Biomolecule-assisted construction of cadmium sulfide hollow spheres with structure-dependent photocatalytic activity.

PubMed

Wei, Chengzhen; Zang, Wenzhe; Yin, Jingzhou; Lu, Qingyi; Chen, Qun; Liu, Rongmei; Gao, Feng

2013-02-25

In this study, we report the synthesis of monodispersive solid and hollow CdS spheres with structure-dependent photocatalytic abilities for dye photodegradation. The monodispersive CdS nanospheres were constructed with the assistance of the soulcarboxymthyi chitosan biopolymer under hydrothermal conditions. The solid CdS spheres were corroded by ammonia to form hollow CdS nanospheres through a dissolution-reprecipitation mechanism. Their visible-light photocatalytic activities were investigated, and the results show that both the solid and the hollow CdS spheres have visible-light photocatalytic abilities for the photodegradation of dyes. The photocatalytic properties of the CdS spheres were demonstrated to be structure dependent. Although the nanoparticles comprising the hollow spheres have larger sizes than those comprising the solid spheres, the hollow CdS spheres have better photocatalytic performances than the solid CdS spheres, which can be attributed to the special hollow structure. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Resonance Rayleigh scattering technique for simple and sensitive analysis of tannic acid with carbon dots

NASA Astrophysics Data System (ADS)

Shi, Ying; Yang, Liu; Zhu, Jinghui; Yang, Jidong; Liu, Shaopu; Qiao, Man; Duan, Ruilin; Hu, Xiaoli

2017-02-01

Carbon dots (CDs) are raising a substantial amount of attention owing to their many unique and novel physicochemical properties. Herein one-pot synthesized CDs, to the best of our knowledge, were first served as the robust nanoprobe for detection tannic acid (TA) based on resonance Rayleigh scattering technique. The as-prepared CDs can combine with TA via hydrogen bond, resulting in remarkable enhancement of scattering signal with no changes in the fluorescence of CDs. Therefore, a novel protocol for TA determination was established and this strategy allowed quantitative detection of TA in the linear range of 0.2-10.0 μmol L- 1 with an excellent detection limit of 9.0 nmol L- 1. Moreover, the CDs based nanoprobe can be applied to the determination of TA in water sample with satisfactory results. Our study can potentially influence our current views on CDs and particularly impressive and offers new insights into application of CDs beyond the traditional understanding of CDs.

Inspecting Engineering Samples

NASA Image and Video Library

2017-12-08

Goddard's Ritsko Wins 2011 SAVE Award The winner of the 2011 SAVE Award is Matthew Ritsko, a Goddard financial manager. His tool lending library would track and enable sharing of expensive space-flight tools and hardware after projects no longer need them. This set of images represents the types of tools used at NASA. To read more go to: www.nasa.gov/topics/people/features/ritsko-save.html Dr. Doug Rabin (Code 671) and PI La Vida Cooper (Code 564) inspect engineering samples of the HAS-2 imager which will be tested and readout using a custom ASIC with a 16-bit ADC (analog to digital converter) and CDS (correlated double sampling) circuit designed by the Code 564 ASIC group as a part of an FY10 IRAD. The purpose of the IRAD was to develop and high resolution digitizer for Heliophysics applications such as imaging. Future goals for the collaboration include characterization testing and eventually a sounding rocket flight of the integrated system. *ASIC= Application Specific Integrated Circuit NASA/GSFC/Chris Gunn

Development of a Tailored Intervention With Computerized Clinical Decision Support to Improve Quality of Care for Patients With Knee Osteoarthritis: Multi-Method Study.

PubMed

Van de Velde, Stijn; Kortteisto, Tiina; Spitaels, David; Jamtvedt, Gro; Roshanov, Pavel; Kunnamo, Ilkka; Aertgeerts, Bert; Vandvik, Per Olav; Flottorp, Signe

2018-06-11

Clinical practice patterns greatly diverge from evidence-based recommendations to manage knee osteoarthritis conservatively before resorting to surgery. This study aimed to tailor a guideline-based computerized decision support (CDS) intervention that facilitates the conservative management of knee osteoarthritis. Experts with backgrounds in clinical medicine, research, implementation, or health informatics suggested the most important recommendations for implementation, how to develop an implementation strategy, and how to form the CDS algorithms. In 6 focus group sessions, 8 general practitioners and 22 patients from Norway, Belgium, and Finland discussed the suggested CDS intervention and identified factors that would be most critical for the success of the intervention. The focus group moderators used the GUideline Implementation with DEcision Support checklist, which we developed to support consideration of CDS success factors. The experts prioritized 9 out of 22 recommendations for implementation. We formed the concept for 6 CDS algorithms to support implementation of these recommendations. The focus group suggested 59 unique factors that could affect the success of the presented CDS intervention. Five factors (out of the 59) were prioritized by focus group participants in every country, including the perceived potential to address the information needs of both patients and general practitioners; the credibility of CDS information; the timing of CDS for patients; and the need for personal dialogue about CDS between the general practitioner and the patient. The focus group participants supported the CDS intervention as a tool to improve the quality of care for patients with knee osteoarthritis through shared, evidence-based decision making. We aim to develop and implement the CDS based on these study results. Future research should address optimal ways to (1) provide patient-directed CDS, (2) enable more patient-specific CDS within the context of patient complexity, and (3) maintain user engagement with CDS over time. ©Stijn Van de Velde, Tiina Kortteisto, David Spitaels, Gro Jamtvedt, Pavel Roshanov, Ilkka Kunnamo, Bert Aertgeerts, Per Olav Vandvik, Signe Flottorp. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 11.06.2018.

Doxorubicin conjugated functionalizable carbon dots for nucleus targeted delivery and enhanced therapeutic efficacy

NASA Astrophysics Data System (ADS)

Yang, Lei; Wang, Zheran; Wang, Ju; Jiang, Weihua; Jiang, Xuewei; Bai, Zhaoshi; He, Yunpeng; Jiang, Jianqi; Wang, Dongkai; Yang, Li

2016-03-01

Carbon dots (CDs) have shown great potential in imaging and drug/gene delivery applications. In this work, CDs functionalized with a nuclear localization signal peptide (NLS-CDs) were employed to transport doxorubicin (DOX) into cancer cells for enhanced antitumor activity. DOX was coupled to NLS-CDs (DOX-CDs) through an acid-labile hydrazone bond, which was cleavable in the weakly acidic intracellular compartments. The cytotoxicity of DOX-CD complexes was evaluated by the MTT assay and the cellular uptake was monitored using flow cytometry and confocal laser scanning microscopy. Cell imaging confirmed that DOX-CDs were mainly located in the nucleus. Furthermore, the complexes could efficiently induce apoptosis in human lung adenocarcinoma A549 cells. The in vivo therapeutic efficacy of DOX-CDs was investigated in an A549 xenograft nude mice model and the complexes exhibited an enhanced ability to inhibit tumor growth compared with free DOX. Thus, the DOX-CD conjugates may be exploited as promising drug delivery vehicles in cancer therapy.Carbon dots (CDs) have shown great potential in imaging and drug/gene delivery applications. In this work, CDs functionalized with a nuclear localization signal peptide (NLS-CDs) were employed to transport doxorubicin (DOX) into cancer cells for enhanced antitumor activity. DOX was coupled to NLS-CDs (DOX-CDs) through an acid-labile hydrazone bond, which was cleavable in the weakly acidic intracellular compartments. The cytotoxicity of DOX-CD complexes was evaluated by the MTT assay and the cellular uptake was monitored using flow cytometry and confocal laser scanning microscopy. Cell imaging confirmed that DOX-CDs were mainly located in the nucleus. Furthermore, the complexes could efficiently induce apoptosis in human lung adenocarcinoma A549 cells. The in vivo therapeutic efficacy of DOX-CDs was investigated in an A549 xenograft nude mice model and the complexes exhibited an enhanced ability to inhibit tumor growth compared with free DOX. Thus, the DOX-CD conjugates may be exploited as promising drug delivery vehicles in cancer therapy. Electronic supplementary information (ESI) available: FT-IR and 1H NMR spectra of DOX-CD complexes. See DOI: 10.1039/c6nr00247a

Facile synthesis of silver nanoparticles/carbon dots for a charge transfer study and peroxidase-like catalytic monitoring by surface-enhanced Raman scattering

NASA Astrophysics Data System (ADS)

Zhao, Hongyue; Guo, Yue; Zhu, Shoujun; Song, Yubin; Jin, Jing; Ji, Wei; Song, Wei; Zhao, Bing; Yang, Bai; Ozaki, Yukihiro

2017-07-01

In this work, carbon dots (CDs) were combined with Ag nanoparticles (NPs) by a chemical reaction to form Ag NPs/CDs hybrid, which was then used as a novel surface-enhanced Raman scattering (SERS) substrate. During the synthetic process, carboxyl groups on the surface of Ag NPs were reacted with amino groups of CDs in an amidation reaction. The D and G bands of CDs in the Ag NPs/CDs hybrid could be easily detected by SERS. By employing p-aminothiophenol (PATP) molecules as SERS probes, the Ag NPs/CDs hybrid substrate could detect PATP in diluted solutions of concentration as low as 10-9 M. The charge transfer (CT) effect on SERS spectra with different excitation wavelengths in the prepared Ag NPs/CDs hybrid and PATP system was also investigated. It was found that addition of CDs changes the degree of CT between Ag NPs and PATP molecules. Since the prepared Ag NPs/CDs hybrid also showed a peroxidase-like activity toward the oxidation of 3,3‧,5,5‧-tetramethylbenzidine using H2O2, which can provide the sensitive detection of H2O2 by SERS technique.

Optimal nitrogen and phosphorus codoping carbon dots towards white light-emitting device

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

Zhang, Feng; Wang, Yaling; Miao, Yanqin

Through a one-step fast microwave-assisted approach, nitrogen and phosphorus co-doped carbon dots (N,P-CDs) were synthesized using ammonium citrate (AC) as a carbon source and phosphates as additive reagent. Under the condition of an optimal reaction time of 140 s, the influence of additive with different N and P content on fluorescent performance of N,P-CDs was further explored. It was concluded that high nitrogen content and moderate phosphorus content are necessary for obtaining high quantum yield (QY) N,P-CDs, among which the TAP-CDs (CDs synthesized using ammonium phosphate as additive reagent) show high quantum yield (QY) of 62% and red-green-blue (RGB) spectral compositionmore » of 51.67%. Besides, the TAP-CDs exhibit satisfying thermal stability within 180 °C. By virtue of good optical and thermal properties of TAP-CDs, a white light-emitting device (LED) was fabricated by combining ultraviolet chip with TAP-CDs as phosphor. The white LED emits bright warm-white light with the CIE chromaticity coordinate of (0.38, 0.35) and the corresponding color temperature (CCT) of 4450 K, indicating the potential of TAP-CDs phosphor in white LED.« less

Highly Efficient Carbon Dots with Reversibly Switchable Green-Red Emissions for Trichromatic White Light-Emitting Diodes.

PubMed

Yuan, Biao; Guan, Shanyue; Sun, Xingming; Li, Xiaoming; Zeng, Haibo; Xie, Zheng; Chen, Ping; Zhou, Shuyun

2018-05-09

Carbon dots (CDs) have potentials to be utilized in optoelectronic devices, bioimaging, and photocatalysis. The majority of the current CDs with high quantum yield to date were limited in the blue light emission region. Herein, on the basis of surface electron-state engineering, we report a kind of CDs with reversible switching ability between green and red photoluminescence with a quantum yield (QY) of both up to 80%. Highly efficient green and red solid-state luminescence is realized by doping CDs into a highly transparent matrix of methyltriethoxysilane and 3-triethoxysilylpropylamine to form CDs/gel glasses composites with QYs of 80 and 78%. The CDs/gel glasses show better transmittance in visible light bands and excellent thermal stability. A blue-pumped CDs/gel glasses phosphor-based trichromatic white light-emitting diode (WLED) is realized, whose color rendering index is 92.9. The WLED gets the highest luminous efficiency of 71.75 lm W -1 in CDs-based trichromatic WLEDs. This work opens a door for developing highly efficient green- and red-emissive switching CDs which were used as phosphors for WLEDs and have the tendency for applications in other fields, such as sensing, bioimaging, and photocatalysis.

[Influence of "prehistory" of sequential movements of the right and the left hand on reproduction: coding of positions, movements and sequence structure].

PubMed

Bobrova, E V; Liakhovetskiĭ, V A; Borshchevskaia, E R

2011-01-01

The dependence of errors during reproduction of a sequence of hand movements without visual feedback on the previous right- and left-hand performance ("prehistory") and on positions in space of sequence elements (random or ordered by the explicit rule) was analyzed. It was shown that the preceding information about the ordered positions of the sequence elements was used during right-hand movements, whereas left-hand movements were performed with involvement of the information about the random sequence. The data testify to a central mechanism of the analysis of spatial structure of sequence elements. This mechanism activates movement coding specific for the left hemisphere (vector coding) in case of an ordered sequence structure and positional coding specific for the right hemisphere in case of a random sequence structure.

Design and Development of a Sharable Clinical Decision Support System Based on a Semantic Web Service Framework.

PubMed

Zhang, Yi-Fan; Gou, Ling; Tian, Yu; Li, Tian-Chang; Zhang, Mao; Li, Jing-Song

2016-05-01

Clinical decision support (CDS) systems provide clinicians and other health care stakeholders with patient-specific assessments or recommendations to aid in the clinical decision-making process. Despite their demonstrated potential for improving health care quality, the widespread availability of CDS systems has been limited mainly by the difficulty and cost of sharing CDS knowledge among heterogeneous healthcare information systems. The purpose of this study was to design and develop a sharable clinical decision support (S-CDS) system that meets this challenge. The fundamental knowledge base consists of independent and reusable knowledge modules (KMs) to meet core CDS needs, wherein each KM is semantically well defined based on the standard information model, terminologies, and representation formalisms. A semantic web service framework was developed to identify, access, and leverage these KMs across diverse CDS applications and care settings. The S-CDS system has been validated in two distinct client CDS applications. Model-level evaluation results confirmed coherent knowledge representation. Application-level evaluation results reached an overall accuracy of 98.66 % and a completeness of 96.98 %. The evaluation results demonstrated the technical feasibility and application prospect of our approach. Compared with other CDS engineering efforts, our approach facilitates system development and implementation and improves system maintainability, scalability and efficiency, which contribute to the widespread adoption of effective CDS within the healthcare domain.

Discrete Cosine Transform Image Coding With Sliding Block Codes

NASA Astrophysics Data System (ADS)

Divakaran, Ajay; Pearlman, William A.

1989-11-01

A transform trellis coding scheme for images is presented. A two dimensional discrete cosine transform is applied to the image followed by a search on a trellis structured code. This code is a sliding block code that utilizes a constrained size reproduction alphabet. The image is divided into blocks by the transform coding. The non-stationarity of the image is counteracted by grouping these blocks in clusters through a clustering algorithm, and then encoding the clusters separately. Mandela ordered sequences are formed from each cluster i.e identically indexed coefficients from each block are grouped together to form one dimensional sequences. A separate search ensues on each of these Mandela ordered sequences. Padding sequences are used to improve the trellis search fidelity. The padding sequences absorb the error caused by the building up of the trellis to full size. The simulations were carried out on a 256x256 image ('LENA'). The results are comparable to any existing scheme. The visual quality of the image is enhanced considerably by the padding and clustering.

DNA Barcode Goes Two-Dimensions: DNA QR Code Web Server

PubMed Central

Li, Huan; Xing, Hang; Liang, Dong; Jiang, Kun; Pang, Xiaohui; Song, Jingyuan; Chen, Shilin

2012-01-01

The DNA barcoding technology uses a standard region of DNA sequence for species identification and discovery. At present, “DNA barcode” actually refers to DNA sequences, which are not amenable to information storage, recognition, and retrieval. Our aim is to identify the best symbology that can represent DNA barcode sequences in practical applications. A comprehensive set of sequences for five DNA barcode markers ITS2, rbcL, matK, psbA-trnH, and CO1 was used as the test data. Fifty-three different types of one-dimensional and ten two-dimensional barcode symbologies were compared based on different criteria, such as coding capacity, compression efficiency, and error detection ability. The quick response (QR) code was found to have the largest coding capacity and relatively high compression ratio. To facilitate the further usage of QR code-based DNA barcodes, a web server was developed and is accessible at http://qrfordna.dnsalias.org. The web server allows users to retrieve the QR code for a species of interests, convert a DNA sequence to and from a QR code, and perform species identification based on local and global sequence similarities. In summary, the first comprehensive evaluation of various barcode symbologies has been carried out. The QR code has been found to be the most appropriate symbology for DNA barcode sequences. A web server has also been constructed to allow biologists to utilize QR codes in practical DNA barcoding applications. PMID:22574113

SSBRP User Operations Facility (UOF) Overview and Development Strategy

NASA Technical Reports Server (NTRS)

Picinich, Lou; Stone, Thom; Sun, Charles; Windrem, May; Givens, John J. (Technical Monitor)

1995-01-01

This paper will present the Space Station Biological Research Project (SSBRP) User Operations Facility (UOF) architecture and development strategy. A major element of the UOF at NASA Ames Research Center, the Communication and Data System (CDS) will be the primary focus of the discussions. CDS operational, telescience, security, and development objectives will be discussed along with CDS implementation strategy. The implementation strategy discussions will include: Object Oriented Analysis & Design, System & Software Prototyping, and Technology Utilization. A CDS design overview that includes: CDS Context Diagram, CDS Architecture, Object Models, Use Cases, and User Interfaces will also be presented. CDS development brings together "cutting edge" technologies and techniques such as: object oriented development, network security, multimedia networking, web-based data distribution, JAVA, and graphical user interfaces. Use of these "cutting edge" technologies and techniques translates directly to lower development and operations costs.

Blocking the Formation of Zn2+/Dye Complexes in Dye-Sensitized Solar Cells by Inserting CdS Quantum Dots into Sandwich Layer

NASA Astrophysics Data System (ADS)

Sun, Yunfei; Liu, Chunling; Yang, Lili; Wei, Maobin; Lv, Shiquan; Sui, Yingrui; Cao, Jian; Chen, Gang; Yang, Jinghai

2018-06-01

ZnO NRAs are grown on ITO substrates by a simple chemical method. CdS QDs were deposited on ZnO NRAs by SILAR. N719 was synthesized by dipping method. J-V analysis indicates that by inserting a layer of CdS QDs, the conversion efficiency of DSSCs was improved obviously. The device with CdS QDs shows the higher conversion efficiency due to the three reasons: (1) CdS QDs enhanced adsorption spectra of DSSCs in the visible region; (2) CdS QDs block the formation of Zn2+/dye complex, it is beneficial for electros transport from dye to ZnO photoanode. It is the key to obtain higher conversion efficiency; (3) FRET dynamics exists by the introduction of CdS QDs.

Facile and eco-friendly synthesis of green fluorescent carbon nanodots for applications in bioimaging, patterning and staining

NASA Astrophysics Data System (ADS)

Shi, Lihong; Li, Yanyan; Li, Xiaofeng; Wen, Xiangping; Zhang, Guomei; Yang, Jun; Dong, Chuan; Shuang, Shaomin

2015-04-01

We report a facile and eco-friendly strategy for the fabrication of green fluorescent carbon nanodots (CDs), and demonstrate their applications for bio-imaging, patterning, and staining. A one-pot hydrothermal method using various plant petals yields bright green-emitting CDs, providing an easy way for the production of green fluorescent CDs without the need for a tedious synthetic methodology or the use of toxic/expensive solvents and starting materials. The as-prepared CDs show small size distribution and excellent dispersibility. Their strong green fluorescence is observed when the excitation wavelength is between 430 nm and 490 nm. Moreover, they exhibit high tolerance to various external conditions, such as pH values, external cations, and continuous excitation. Due to minimum toxicity as well as good photoluminescence properties, these CDs can be applied to in vitro and in vivo imaging, patterning, and staining. According to confocal fluorescence imaging of human uterine cervical squamous cell carcinoma cells, CDs penetrate into the cell and enter the cytoplasm and the nucleus. More strikingly, carp is directly fed with CDs for in vivo imaging and shows bright green fluorescence at an excitation wavelength of 470 nm. In addition, the obtained CDs are used as fluorescent inks for drawing luminescence patterns. Finally, we also apply the CDs as a fluorescent dye. Interestingly, the absorbent filter paper with staining emits dramatic fluorescence under 470 nm excitation.We report a facile and eco-friendly strategy for the fabrication of green fluorescent carbon nanodots (CDs), and demonstrate their applications for bio-imaging, patterning, and staining. A one-pot hydrothermal method using various plant petals yields bright green-emitting CDs, providing an easy way for the production of green fluorescent CDs without the need for a tedious synthetic methodology or the use of toxic/expensive solvents and starting materials. The as-prepared CDs show small size distribution and excellent dispersibility. Their strong green fluorescence is observed when the excitation wavelength is between 430 nm and 490 nm. Moreover, they exhibit high tolerance to various external conditions, such as pH values, external cations, and continuous excitation. Due to minimum toxicity as well as good photoluminescence properties, these CDs can be applied to in vitro and in vivo imaging, patterning, and staining. According to confocal fluorescence imaging of human uterine cervical squamous cell carcinoma cells, CDs penetrate into the cell and enter the cytoplasm and the nucleus. More strikingly, carp is directly fed with CDs for in vivo imaging and shows bright green fluorescence at an excitation wavelength of 470 nm. In addition, the obtained CDs are used as fluorescent inks for drawing luminescence patterns. Finally, we also apply the CDs as a fluorescent dye. Interestingly, the absorbent filter paper with staining emits dramatic fluorescence under 470 nm excitation. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00783f

Translation and validation of the Cardiac Depression Scale to Arabic.

PubMed

Papasavvas, T; Al-Amin, H; Ghabrash, H F; Micklewright, D

2016-08-01

The Cardiac Depression Scale (CDS) has been designed to measure depressive symptoms in patients with heart disease. There is no Arabic version of the CDS. We translated and validated the CDS in an Arabic sample of patients with heart disease. Forward and back translation of the CDS was followed by assessment of cultural relevance and content validity. The Arabic version of the CDS (A-CDS) and the Arabic version of the Hospital Anxiety and Depression Scale (A-HADS) were then administered to 260 Arab in-patients with heart disease from 18 Arabic countries. Construct validity was assessed using exploratory factor analysis with polychoric correlations. Internal consistency was assessed using ordinal reliability alpha and item-to-factor polychoric correlations. Concurrent validity was assessed using Pearson's correlation coefficient between the A-CDS and the depression subscale of the A-HADS (A-HADS-D). Cultural relevance and content validity of the A-CDS were satisfactory. Exploratory factor analysis revealed three robust factors, without cross-loadings, that formed a single dimension. Internal consistency was high (ordinal reliability alpha for the total scale and the three factors were .94, .91, .86, and .87, respectively; item-to-factor correlations ranged from .77 to .91). Concurrent validity was high (r=.72). The A-CDS demonstrated a closer to normal distribution of scores than the A-HADS-D. Sensitivity and specificity of the A-CDS were not objectively assessed. The A-CDS appears to be a valid and reliable instrument to measure depressive symptoms in a representative sample of Arab in-patients with heart disease. Copyright © 2016 Elsevier B.V. All rights reserved.

Temporal Trends in Anesthesia-related Adverse Events in Cesarean Deliveries, New York State, 2003-2012.

PubMed

Guglielminotti, Jean; Wong, Cynthia A; Landau, Ruth; Li, Guohua

2015-11-01

Cesarean delivery (CD) is associated with significantly increased risks of anesthesia-related adverse events (ARAEs) and nonanesthetic perioperative morbidity compared with vaginal delivery. Temporal trends in these adverse outcomes remain unknown despite efforts to improve maternal safety. This study examines temporal trends in ARAEs and nonanesthetic perioperative complications in CDs in New York hospitals. Data are from the State Inpatient Database for New York, 2003-2012. ARAEs, including minor and major ARAEs, and nonanesthetic perioperative complications were identified through International Classification of Diseases, Ninth Revision, Clinical Modification codes. Statistical significance in time trends was assessed using the Cochran-Armitage test and multivariable logistic regression. Of the 785,854 CDs studied, 5,715 (730 per 100,000; 95% CI, 710 to 750) had at least one ARAE and 7,040 had at least one perioperative complication (890 per 100,000; 95% CI, 870 to 920). The overall annual rate of ARAEs decreased from 890 per 100,000 in 2003 to 660 in 2012 (25% decrease; 95% CI, 16 to 34; P < 0.0001). The rate of minor ARAEs decreased 23% (95% CI, 13 to 32) and of major ARAEs decreased 43% (95% CI, 23 to 63). No decrease was observed in the rate of ARAEs for CDs performed under general anesthesia. The rate of nonanesthetic complications increased 47% (95% CI, 31 to 63; P < 0.0001). Anesthesia-related outcomes in cesarean deliveries appear to have improved significantly across hospitals in New York in the past decade. Perioperative nonanesthetic complications remain a serious healthcare issue.

CRITICA: coding region identification tool invoking comparative analysis

NASA Technical Reports Server (NTRS)

Badger, J. H.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

1999-01-01

Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

Flexible manipulation of terahertz wave reflection using polarization insensitive coding metasurfaces.

PubMed

Jiu-Sheng, Li; Ze-Jiang, Zhao; Jian-Quan, Yao

2017-11-27

In order to extend to 3-bit encoding, we propose notched-wheel structures as polarization insensitive coding metasurfaces to control terahertz wave reflection and suppress backward scattering. By using a coding sequence of "00110011…" along x-axis direction and 16 × 16 random coding sequence, we investigate the polarization insensitive properties of the coding metasurfaces. By designing the coding sequences of the basic coding elements, the terahertz wave reflection can be flexibly manipulated. Additionally, radar cross section (RCS) reduction in the backward direction is less than -10dB in a wide band. The present approach can offer application for novel terahertz manipulation devices.

Design and development of a chopping and deflecting system for the high current injector at IUAC

NASA Astrophysics Data System (ADS)

Kedia, Sanjay Kumar; Mehta, R.

2018-05-01

The Low Energy Beam Transport (LEBT) section of the High Current Injector (HCI) incorporates a Chopping cum Deflecting System (CDS). The CDS comprises of a deflecting system and a pair of slits that will remove dark current and produce time bunched beam of 60 ns at different repetition rates of 4, 2, 1, 0.5, 0.25 and 0.125 MHz. The distinguishing feature of the design is the use of a multi-plate deflecting structure with low capacitance to optimize the electric field, which in turn results in higher efficiency in terms of achievable ion current. To maximize the effective electric field and its uniformity, the gap between the deflecting plates has been varied and a semi-circular contour has been incorporated on the deflecting plates. Due to this the electric field variation is less than ±0.5% within the plate length. The length of deflecting plates was chosen to maximize the transmission efficiency. Since the velocity of the charged particles in the LEBT section is constant, therefore the separation between two successive sets of deflecting plates has been kept constant to match the ions transient time within the gap which is nearly 32 ns. A square pulse has been chosen, instead of a sinusoidal one, to increase the transmission efficiency and to decrease the tailing effect. The loaded capacitance of the structure was kept <10 pF to achieve fast rise/fall time of the applied voltage signal. A Python code has been developed to verify the various design parameters. The simulation also shows that one can get an efficient deflection of undesired particles resulting in >90% transmission efficiency with in the bunch length. Various simulation codes like Solid Works, TRACE 3D, CST MWS and homebrew Python codes were used to validate the design.

Noncoding sequence classification based on wavelet transform analysis: part I

NASA Astrophysics Data System (ADS)

Paredes, O.; Strojnik, M.; Romo-Vázquez, R.; Vélez Pérez, H.; Ranta, R.; Garcia-Torales, G.; Scholl, M. K.; Morales, J. A.

2017-09-01

DNA sequences in human genome can be divided into the coding and noncoding ones. Coding sequences are those that are read during the transcription. The identification of coding sequences has been widely reported in literature due to its much-studied periodicity. Noncoding sequences represent the majority of the human genome. They play an important role in gene regulation and differentiation among the cells. However, noncoding sequences do not exhibit periodicities that correlate to their functions. The ENCODE (Encyclopedia of DNA elements) and Epigenomic Roadmap Project projects have cataloged the human noncoding sequences into specific functions. We study characteristics of noncoding sequences with wavelet analysis of genomic signals.

Converting Panax ginseng DNA and chemical fingerprints into two-dimensional barcode.

PubMed

Cai, Yong; Li, Peng; Li, Xi-Wen; Zhao, Jing; Chen, Hai; Yang, Qing; Hu, Hao

2017-07-01

In this study, we investigated how to convert the Panax ginseng DNA sequence code and chemical fingerprints into a two-dimensional code. In order to improve the compression efficiency, GATC2Bytes and digital merger compression algorithms are proposed. HPLC chemical fingerprint data of 10 groups of P. ginseng from Northeast China and the internal transcribed spacer 2 (ITS2) sequence code as the DNA sequence code were ready for conversion. In order to convert such data into a two-dimensional code, the following six steps were performed: First, the chemical fingerprint characteristic data sets were obtained through the inflection filtering algorithm. Second, precompression processing of such data sets is undertaken. Third, precompression processing was undertaken with the P. ginseng DNA (ITS2) sequence codes. Fourth, the precompressed chemical fingerprint data and the DNA (ITS2) sequence code were combined in accordance with the set data format. Such combined data can be compressed by Zlib, an open source data compression algorithm. Finally, the compressed data generated a two-dimensional code called a quick response code (QR code). Through the abovementioned converting process, it can be found that the number of bytes needed for storing P. ginseng chemical fingerprints and its DNA (ITS2) sequence code can be greatly reduced. After GTCA2Bytes algorithm processing, the ITS2 compression rate reaches 75% and the chemical fingerprint compression rate exceeds 99.65% via filtration and digital merger compression algorithm processing. Therefore, the overall compression ratio even exceeds 99.36%. The capacity of the formed QR code is around 0.5k, which can easily and successfully be read and identified by any smartphone. P. ginseng chemical fingerprints and its DNA (ITS2) sequence code can form a QR code after data processing, and therefore the QR code can be a perfect carrier of the authenticity and quality of P. ginseng information. This study provides a theoretical basis for the development of a quality traceability system of traditional Chinese medicine based on a two-dimensional code.

Facile synthesis of fluorescence carbon dots from sweet potato for Fe3+ sensing and cell imaging.

PubMed

Shen, Jie; Shang, Shaoming; Chen, Xiuying; Wang, Dan; Cai, Yan

2017-07-01

In this study, a facile synthesis of fluorescence carbon dots (CDs) from sweet potato was performed through hydrothermal treatment. The obtained CDs with quantum yield of 8.64% have good dispersibility due to the soluble functional groups on their surfaces. The characterization of CDs was carried out and their possible formation mechanism was also discussed. In addition, the cytotoxicity results showed that the CDs exhibit non toxicity within 100μg/mL. At this concentration, the CDs were applied in cell imaging, indicating that they are promising fluorescent probes for biological imaging. In addition, the fluorescence of CDs was quenched by Fe 3+ with a linear concentration of 1 to 100μM, associated with the limit of detection of 0.32μM. Subsequently, the CDs were successfully applied for Fe 3+ probing in living cells. Copyright © 2017 Elsevier B.V. All rights reserved.

Red, green, and blue luminescence by carbon dots: full-color emission tuning and multicolor cellular imaging.

PubMed

Jiang, Kai; Sun, Shan; Zhang, Ling; Lu, Yue; Wu, Aiguo; Cai, Congzhong; Lin, Hengwei

2015-04-27

A facile approach for preparation of photoluminescent (PL) carbon dots (CDs) is reported. The three resulting CDs emit bright and stable red, green and blue (RGB) colors of luminescence, under a single ultraviolet-light excitation. Alterations of PL emission of these CDs are tentatively proposed to result from the difference in their particle size and nitrogen content. Interestingly, up-conversion (UC)PL of these CDs is also observed. Moreover, flexible full-color emissive PVA films can be achieved through mixing two or three CDs in the appropriate ratios. These CDs also show low cytotoxicity and excellent cellular imaging capability. The facile preparation and unique optical features make these CDs potentially useful in numerous applications such as light-emitting diodes, full-color displays, and multiplexed (UC)PL bioimaging. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photo current generation in RGO - CdS nanorod thin film device

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

Chakraborty, Koushik; Chakrabarty, Sankalpita; Ibrahim, Sk.

2016-05-23

Herein, we report the synthesis and characterization of reduced graphene oxide (RGO) - cadmium sulfide (CdS) nanocomposite materials. The reduction of GO, formation of CdS and decoration of CdS onto RGO sheets were done in a one- pot solvothermal process. We have observed that the PL intensity for CdS nanorods remarkably quenched after the attachment of RGO, which established the photo induced charge transformation from the CdS nanorod to RGO sheets through the RGO-CdS interface. The optoelectronic transport properties of our fabricated large area thin film device exhibits excellent photo induced charge generation under simulated solar light illumination. The photomore » sensitivity of the device increases linearly with the increase of illuminated light intensity. The RGO-CdS composite exhibits enhance photocatalytic dye degradation efficiency in compare to control CdS under simulated solar light illumination.« less

A Second Life for CDs

ERIC Educational Resources Information Center

Snoderly, Kathleen

2011-01-01

Cutting a few CDs apart with scissors, the author found that the process created somewhat brittle shards. As a result, she started to paint a few with acrylic, finding to her amazement that the paint gave the CDs a leathery, more manageable texture. Upon further experimentation, she found that if the CDs are painted somewhat translucently in…

77 FR 13668 - Self-Regulatory Organizations; Chicago Mercantile Exchange, Inc.; Order Approving Proposed Rule...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-07

... calculates each CDS Clearing Member's allocation to the CDS Guaranty Fund, with a new standard that CME believes better allocates tail risk. Currently CME rules provide that each CDS Clearing Member's allocation... that the allocation will be made on the basis of each CDS Clearing Member's potential residual loss...

Improved delivery through biological membranes. XXXL: Solubilization and stabilization of an estradiol chemical delivery system by modified beta-cyclodextrins.

PubMed

Brewster, M E; Estes, K S; Loftsson, T; Perchalski, R; Derendorf, H; Mullersman, G; Bodor, N

1988-11-01

A dihydropyridine in equilibrium pyridinium salt chemical delivery system (CDS) for estradiol (E2CDS) was complexed with various modified beta-cyclodextrins including hydroxyethyl-beta-cyclodextrin (HECD), hydroxypropyl-beta-cyclodextrin (HPCD), and heptakis(2,6-di-O-methyl)-beta-cyclodextrin (DMCD). Complex formation with all of these cyclodextrins resulted in dramatic increases in the water solubility of E2CDS. Studies on the complex of E2CDS and HPCD (E2CDS-CD) indicated that the encapsulated estrogen was approximately four times more stable than the unmanipulated CDS, producing an estimated half-life of degradation of 4 years compared with 1.2 years for the uncomplexed drug at room temperature. The complexation of E2CDS and HPCD also stabilized the dihydronicotinate in solutions containing potassium ferricyanide. This formulation was shown to be equivalent to E2CDS in dimethyl sulfoxide in delivering the oxidized, estradiol precursor (E2Q+) to the brain, and also produced similar biological responses; these included decreased luteinizing hormone (LH) secretion and a decrease in the rate of weight gain in castrated female rats.

High fidelity polycrystalline CdTe/CdS heterostructures via molecular dynamics

DOE PAGES

Aguirre, Rodolfo; Chavez, Jose Juan; Zhou, Xiaowang; ...

2017-06-20

Molecular dynamics simulations of polycrystalline growth of CdTe/CdS heterostructures have been performed. First, CdS was deposited on an amorphous CdS substrate, forming a polycrystalline film. Subsequently, CdTe was deposited on top of the polycrystalline CdS film. Cross-sectional images show grain formation at early stages of the CdS growth. During CdTe deposition, the CdS structure remains almost unchanged. Concurrently, CdTe grain boundary motion was detected after the first 24.4 nanoseconds of CdTe deposition. With the elapse of time, this grain boundary pins along the CdS/CdTe interface, leaving only a small region of epitaxial growth. CdTe grains are larger than CdS grainsmore » in agreement with experimental observations in the literature. Crystal phase analysis shows that zinc blende structure dominates over the wurtzite structure inside both CdS and CdTe grains. Composition analysis shows Te and S diffusion to the CdS and CdTe films, respectively. Lastly, these simulated results may stimulate new ideas for studying and improving CdTe solar cell efficiency.« less

Carbon dots decorated magnetic ZnFe2O4 nanoparticles with enhanced adsorption capacity for the removal of dye from aqueous solution

NASA Astrophysics Data System (ADS)

Shi, Weilong; Guo, Feng; Wang, Huibo; Liu, Changan; Fu, Yijun; Yuan, Songliu; Huang, Hui; Liu, Yang; Kang, Zhenhui

2018-03-01

Widely used synthetic dyes have been caused serious environmental pollution. Therefore, it is imperative to acquire highly efficient adsorbent to remove them. Here, we report the carbon dots/ZnFe2O4 (CDs/ZFO) composites were prepared through a facile hydrothermal route for absorption removal of dye from aqueous solution. The characterizations reveal the CDs were uniformly deposited on the surfaces of ZFO nanoparticles in the composite. The CDs/ZFO composites as adsorbents exhibit enhanced adsorption behavior for methyl orange (MO) in comparison of pristine ZFO, in which the 5% CDs/ZFO (with the CDs mass content of 5 wt%) shows the highest absorption activity. Experimental studies on adsorption isotherms of MO over the 5% CDs/ZFO composite indicate that experimental data were found to follow Langmuir model with a monolayer adsorption capacity of 181.2 mg g-1. The corresponding adsorption kinetics was fitted well with the pseudo-second-order kinetic model. Moreover, thermodynamics parameters including ΔG°, ΔH° and ΔS° were tested, demonstrating that the adsorption of MO over CDs/ZFO composite was spontaneous and exothermic in nature. The remarkably increased adsorption performance of CDs/ZFO composites can be attributed to abundant oxygen-containing groups on the surface of CDs.

Effects of bacteria on CdS thin films used in technological devices

NASA Astrophysics Data System (ADS)

Alpdoğan, S.; Adıgüzel, A. O.; Sahan, B.; Tunçer, M.; Metin Gubur, H.

2017-04-01

Cadmium sulfide (CdS) thin films were fabricated on glass substrates by the chemical bath deposition method at 70 {}^\\circ \\text{C} considering deposition times ranging from 2 h to 5 h. The optical band gaps of CdS thin films were found to be in the 2.42-2.37 eV range. CdS thin films had uniform spherical nano-size grains which had polycrystalline, hexagonal and cubic phases. The films had a characteristic electrical resistivity of the order of {{10}5} Ω \\text{cm} and n-type conductivity at room condition. CdS thin films were incubated in cultures of B.domonas aeruginosa and Staphylococcus aureus, which exist abundantly in the environment, and form biofilms. SEM images showed that S. aureus and K. pneumonia were detected significantly on the film surfaces with a few of P. aeruginosa and B. subtilis cells attached. CdS thin film surface exhibits relatively good resistance to the colonization of P. aeruginosa and B. subtilis. Optical results showed that the band gap of CdS thin films which interacted with the bacteria is 2.42 \\text{eV} . The crystal structure and electrical properties of CdS thin films were not affected by bacterial adhesion. The antimicrobial effect of CdS nanoparticles was different for different bacterial strains.

Controllable synthesis of green and blue fluorescent carbon nanodots for pH and Cu(2+) sensing in living cells.

PubMed

Shi, Lihong; Li, Yanyan; Li, Xiaofeng; Zhao, Bo; Wen, Xiangping; Zhang, Guomei; Dong, Chuan; Shuang, Shaomin

2016-03-15

We report a controllable strategy for fabrication of green and blue fluorescent carbon nanodots (CDs), and demonstrate their applications for pH and Cu(2+) sensing in living cells. Green and blue fluorescent CDs have been synthesized by hydrothermal method and pyrolysis of leeks, respectively, providing an easy way for the production of CDs without the request of tedious synthetic methodology or the use of toxic/expensive solvents and starting materials. Green fluorescent CDs (G-CDs) exhibit high tolerance to pH values and external cations. Blue fluorescent CDs (B-CDs) can be applied to pH and Cu(2+) sensing. The linear range of Cu(2+) detection is 0.01-10.00 μM and the detection limit is 0.05 μM. For pH detection, there is a good linearity in the pH range of 3.5-10.0. The linear and rapid response of B-CDs to Cu(2+) and pH is valuable for Cu(2+) and pH sensing in living cells. Confocal fluorescent imaging of human cervical carcinoma cells indicates that B-CDs could visualize Cu(2+) and pH fluctuations in living cells with negligible autofluorescence. Copyright © 2015 Elsevier B.V. All rights reserved.

In vivo characterization of hair and skin derived carbon quantum dots with high quantum yield as long-term bioprobes in zebrafish

PubMed Central

Zhang, Jing-Hui; Niu, Aping; Li, Jing; Fu, Jian-Wei; Xu, Qun; Pei, De-Sheng

2016-01-01

Carbon quantum dots (CDs) were widely investigated because of their tunable fluorescence properties and low toxicity. However, so far there have been no reports on in vivo functional studies of hair and skin derived CDs. Here, hair derived CDs (HCDs) and skin derived CDs (SCDs) were produced by using human hair and pig skin as precursors. The quantum yields (QYs) of HCDs and SCDs were quite high, compared to citric acid derived CDs (CCDs). HCDs and SCDs possess optimal photostability, hypotoxicity and biocompatibility in zebrafish, indicating that HCDs and SCDs possess the capacity of being used as fluorescence probes for in vivo biological imaging. The long-time observation for fluorescence alternation of CDs in zebrafish and the quenching assay of CDs by ATP, NADH and Fe3+ ions demonstrated that the decaying process of CDs in vivo might be induced by the synergistic effect of the metabolism process. All results indicated that large batches and high QYs of CDs can be acquired by employing natural and nontoxic hair and skin as precursors. To our knowledge, this is the first time to report SCDs, in vivo comparative studies of HCDs, SCDs and CCDs as bioprobes, and explore their mechanism of photostability in zebrafish. PMID:27886267

In vivo characterization of hair and skin derived carbon quantum dots with high quantum yield as long-term bioprobes in zebrafish.

PubMed

Zhang, Jing-Hui; Niu, Aping; Li, Jing; Fu, Jian-Wei; Xu, Qun; Pei, De-Sheng

2016-11-25

Carbon quantum dots (CDs) were widely investigated because of their tunable fluorescence properties and low toxicity. However, so far there have been no reports on in vivo functional studies of hair and skin derived CDs. Here, hair derived CDs (HCDs) and skin derived CDs (SCDs) were produced by using human hair and pig skin as precursors. The quantum yields (QYs) of HCDs and SCDs were quite high, compared to citric acid derived CDs (CCDs). HCDs and SCDs possess optimal photostability, hypotoxicity and biocompatibility in zebrafish, indicating that HCDs and SCDs possess the capacity of being used as fluorescence probes for in vivo biological imaging. The long-time observation for fluorescence alternation of CDs in zebrafish and the quenching assay of CDs by ATP, NADH and Fe 3+ ions demonstrated that the decaying process of CDs in vivo might be induced by the synergistic effect of the metabolism process. All results indicated that large batches and high QYs of CDs can be acquired by employing natural and nontoxic hair and skin as precursors. To our knowledge, this is the first time to report SCDs, in vivo comparative studies of HCDs, SCDs and CCDs as bioprobes, and explore their mechanism of photostability in zebrafish.

In vivo characterization of hair and skin derived carbon quantum dots with high quantum yield as long-term bioprobes in zebrafish

NASA Astrophysics Data System (ADS)

Zhang, Jing-Hui; Niu, Aping; Li, Jing; Fu, Jian-Wei; Xu, Qun; Pei, De-Sheng

2016-11-01

Carbon quantum dots (CDs) were widely investigated because of their tunable fluorescence properties and low toxicity. However, so far there have been no reports on in vivo functional studies of hair and skin derived CDs. Here, hair derived CDs (HCDs) and skin derived CDs (SCDs) were produced by using human hair and pig skin as precursors. The quantum yields (QYs) of HCDs and SCDs were quite high, compared to citric acid derived CDs (CCDs). HCDs and SCDs possess optimal photostability, hypotoxicity and biocompatibility in zebrafish, indicating that HCDs and SCDs possess the capacity of being used as fluorescence probes for in vivo biological imaging. The long-time observation for fluorescence alternation of CDs in zebrafish and the quenching assay of CDs by ATP, NADH and Fe3+ ions demonstrated that the decaying process of CDs in vivo might be induced by the synergistic effect of the metabolism process. All results indicated that large batches and high QYs of CDs can be acquired by employing natural and nontoxic hair and skin as precursors. To our knowledge, this is the first time to report SCDs, in vivo comparative studies of HCDs, SCDs and CCDs as bioprobes, and explore their mechanism of photostability in zebrafish.

A qualitative study of the activities performed by people involved in clinical decision support: recommended practices for success.

PubMed

Wright, Adam; Ash, Joan S; Erickson, Jessica L; Wasserman, Joe; Bunce, Arwen; Stanescu, Ana; St Hilaire, Daniel; Panzenhagen, Morgan; Gebhardt, Eric; McMullen, Carmit; Middleton, Blackford; Sittig, Dean F

2014-01-01

To describe the activities performed by people involved in clinical decision support (CDS) at leading sites. We conducted ethnographic observations at seven diverse sites with a history of excellence in CDS using the Rapid Assessment Process and analyzed the data using a series of card sorts, informed by Linstone's Multiple Perspectives Model. We identified 18 activities and grouped them into four areas. Area 1: Fostering relationships across the organization, with activities (a) training and support, (b) visibility/presence on the floor, (c) liaising between people, (d) administration and leadership, (e) project management, (f) cheerleading/buy-in/sponsorship, (g) preparing for CDS implementation. Area 2: Assembling the system with activities (a) providing technical support, (b) CDS content development, (c) purchasing products from vendors (d) knowledge management, (e) system integration. Area 3: Using CDS to achieve the organization's goals with activities (a) reporting, (b) requirements-gathering/specifications, (c) monitoring CDS, (d) linking CDS to goals, (e) managing data. Area 4: Participation in external policy and standards activities (this area consists of only a single activity). We also identified a set of recommendations associated with these 18 activities. All 18 activities we identified were performed at all sites, although the way they were organized into roles differed substantially. We consider these activities critical to the success of a CDS program. A series of activities are performed by sites strong in CDS, and sites adopting CDS should ensure they incorporate these activities into their efforts.

CdS-sensitized TiO2 nanocorals: hydrothermal synthesis, characterization, application.

PubMed

Mali, S S; Desai, S K; Dalavi, D S; Betty, C A; Bhosale, P N; Patil, P S

2011-10-01

Cadmium sulfide (CdS) nanoparticle-sensitized titanium oxide nanocorals (TNC) were synthesized using a two-step deposition process. The TiO(2) nanocorals were grown on the conducting glass substrates (FTO) using A hydrothermal process and CdS nanoparticles were loaded on TNC using successive ionic layer adsorption and reaction (SILAR) method. The TiO(2), CdS and TiO(2)-CdS samples were characterized by optical absorption, X-ray diffraction (XRD), FT-Raman, FT-IR, scanning electron microscopy (SEM) and contact angle. Further, their photoelectrochemical (PEC) performance was tested in NaOH, Na(2)S-NaOH-S and Na(2)S electrolytes, respectively. When CdS nanoparticles are coated on TNCs, the optical absorption is found to be enhanced and band edge is red-shifted towards visible region. The TiO(2)-CdS sample exhibits improved photoelectrochemical (PEC) performance with maximum short circuit current of (J(sc)) 1.04 mA cm(-2). After applying these TiO(2)-CdS electrodes in photovoltaic cells, the photocurrent was found to be enhanced by 2.7 and 32.5 times, as compared with those of bare CdS and TiO(2) nanocorals films electrodes respectively. Also, the power conversion efficiency of TiO(2)-CdS electrodes is 0.72%, which is enhanced by about 16 and 29 times for TiO(2), CdS samples. This journal is © The Royal Society of Chemistry and Owner Societies 2011

Label-free fluorimetric detection of CEA using carbon dots derived from tomato juice.

PubMed

Miao, Hong; Wang, Lan; Zhuo, Yan; Zhou, Zinan; Yang, Xiaoming

2016-12-15

A facile-green strategy to synthesize carbon dots (CDs) with a quantum yield (QY) of nearly 13.9% has been built up, while tomato juice served as the carbon source. Interestingly, not only the precursor of CDs and the whole synthesis procedure were environmental-friendly, but this type of CDs also exhibited multiple advantages including high fluorescent QY, excellent photostability, non-toxicity and satisfactory stability. Significantly, a label-free sensitive assay for detecting carcinoembryonic antigen (CEA) in a continuous and recyclable way has been proposed on the basis of adsorption and desorption of aptamers by the surface of CDs through a competitive mechanism. To be specific, the richness of carboxyl groups of the CDs enabled strong adsorption of ssDNA to the surface of CDs through π-π stacking interactions, resulting in the effective fluorescence quenching by forming CDs-aptamer complexes. The stronger binding affinity between CEA and CEA-aptamer than the π-π stacking interactions has been taken advantage to achieve immediate recovery of the fluorescence of CDs once CEA was introduced. Thereby, quantitative evaluation of CEA concentration in a broad range from 1ngmL(-1) to 0.5ngmL(-1) with the detection limit of 0.3ngmL(-1) was realized in this way. This strategy can be applied in a recyclable way, broadening the sensing application of CDs with biocompatibility. Besides, the CDs were used for cell imaging, potentiating them towards diverse purposes. Copyright © 2016 Elsevier B.V. All rights reserved.

Growth and characterization of CdS buffer layers by CBD and MOCVD

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

Morrone, A.A.; Huang, C.; Li, S.S.

1999-03-01

Thin film CdS has been widely used in thin-film photovoltaic devices. The most efficient Cu(In,&hthinsp;Ga)Se{sub 2} (CIGS) solar cells reported to date utilized a thin CdS buffer layer prepared by a reactive solution growth technique known as chemical bath deposition (CBD). Considerable effort has been directed to better understand the role and find a replacement for the CBD CdS process in CIGS-based solar cells. We reported a low temperature ({approximately}150&hthinsp;{degree}C) Metalorganic Chemical Vapor Deposition (MOCVD) CdS thin film buffer layer process for CIGS absorbers. Many prior studies have reported that CBD CdS contains a mixture of crystal structures. Recent investigationsmore » of CBD CdS thin films by ellipsometry suggested a multilayer structure. In this study we compare CdS thin films prepared by CBD and MOCVD and the effects of annealing. TED and XRD are used to characterize the crystal structure, the film microstructure is studied by HRTEM, and the optical properties are studied by Raman and spectrophotometry. All of these characterization techniques reveal superior crystalline film quality for CdS films grown by MOCVD compared to those grown by CBD. Dual Beam Optical Modulation (DBOM) studies showed that the MOCVD and CBD CdS buffer layer processes have nearly the same effect on CIGS absorbers when combined with a cadmium partial electrolyte aqueous dip. {copyright} {ital 1999 American Institute of Physics.}« less

Analysis of Nursing Clinical Decision Support Requests and Strategic Plan in a Large Academic Health System.

PubMed

Whalen, Kimberly; Bavuso, Karen; Bouyer-Ferullo, Sharon; Goldsmith, Denise; Fairbanks, Amanda; Gesner, Emily; Lagor, Charles; Collins, Sarah

2016-01-01

To understand requests for nursing Clinical Decision Support (CDS) interventions at a large integrated health system undergoing vendor-based EHR implementation. In addition, to establish a process to guide both short-term implementation and long-term strategic goals to meet nursing CDS needs. We conducted an environmental scan to understand current state of nursing CDS over three months. The environmental scan consisted of a literature review and an analysis of CDS requests received from across our health system. We identified existing high priority CDS and paper-based tools used in nursing practice at our health system that guide decision-making. A total of 46 nursing CDS requests were received. Fifty-six percent (n=26) were specific to a clinical specialty; 22 percent (n=10) were focused on facilitating clinical consults in the inpatient setting. "Risk Assessments/Risk Reduction/Promotion of Healthy Habits" (n=23) was the most requested High Priority Category received for nursing CDS. A continuum of types of nursing CDS needs emerged using the Data-Information-Knowledge-Wisdom Conceptual Framework: 1) facilitating data capture, 2) meeting information needs, 3) guiding knowledge-based decision making, and 4) exposing analytics for wisdom-based clinical interpretation by the nurse. Identifying and prioritizing paper-based tools that can be modified into electronic CDS is a challenge. CDS strategy is an evolving process that relies on close collaboration and engagement with clinical sites for short-term implementation and should be incorporated into a long-term strategic plan that can be optimized and achieved overtime. The Data-Information-Knowledge-Wisdom Conceptual Framework in conjunction with the High Priority Categories established may be a useful tool to guide a strategic approach for meeting short-term nursing CDS needs and aligning with the organizational strategic plan.

High Performance Photoluminescent Carbon Dots for In Vitro and In Vivo Bioimaging: Effect of Nitrogen Doping Ratios.

PubMed

Wang, Junqing; Zhang, Pengfei; Huang, Chao; Liu, Gang; Leung, Ken Cham-Fai; Wáng, Yì Xiáng J

2015-07-28

Photoluminescent carbon dots (CDs) have received ever-increasing attention in the application of optical bioimaging because of their low toxicity, tunable fluorescent properties, and ultracompact size. We report for the first time on enhanced photoluminescence (PL) performance influenced by structure effects among the various types of nitrogen doped (N-doped) PL CDs. These CDs were facilely synthesized from condensation carbonization of linear polyethylenic amine (PEA) analogues and citric acid (CA) of different ratios. Detailed structural and property studies demonstrated that either the structures or the molar ratio of PEAs altered the PL properties of the CDs. The content of conjugated π-domains with C═N in the carbon backbone was correlated with their PL Quantum Yield (QY) (up to 69%). The hybridization between the surface/molecule state and the carbon backbone synergistically affected the chemical/physical properties. Also, long-chain polyethylenic amine (PEA) molecule-doped CDs exhibit increasing photostability, but at the expense of PL efficiency, proving that the PL emission of high QY CDs arise not only from the sp(2)/sp(3) carbon core and surface passivation of CDs, but also from the molecular fluorophores integrated in the CDs. In vitro and in vivo bioimaging of these N-doped CDs showed strong photoluminescence signals. Good biocompatibility demonstrates their potential feasibility for bioimaging applications. In addition, the overall size profile of the as-prepared CDs is comparable to the average size of capillary pores in normal living tissues (∼5 nm). Our study provides valuable insights into the effects of the PEA doping ratios on photoluminescence efficiency, biocompatibility, cellular uptake, and optical bioimaging of CDs.

Chemically Deposited CdS Buffer/Kesterite Cu2ZnSnS4 Solar Cells: Relationship between CdS Thickness and Device Performance.

PubMed

Hong, Chang Woo; Shin, Seung Wook; Suryawanshi, Mahesh P; Gang, Myeng Gil; Heo, Jaeyeong; Kim, Jin Hyeok

2017-10-25

Earth-abundant, copper-zinc-tin-sulfide (CZTS), kesterite, is an attractive absorber material for thin-film solar cells (TFSCs). However, the open-circuit voltage deficit (V oc -deficit) resulting from a high recombination rate at the buffer/absorber interface is one of the major challenges that must be overcome to improve the performance of kesterite-based TFSCs. In this paper, we demonstrate the relationship between device parameters and performances for chemically deposited CdS buffer/CZTS-based heterojunction TFSCs as a function of buffer layer thickness, which could change the CdS/CZTS interface conditions such as conduction band or valence band offsets, to gain deeper insight and understanding about the V oc -deficit behavior from a high recombination rate at the CdS buffer/kesterite interface. Experimental results show that device parameters and performances are strongly dependent on the CdS buffer thickness. We postulate two meaningful consequences: (i) Device parameters were improved up to a CdS buffer thickness of 70 nm, whereas they deteriorated at a thicker CdS buffer layer. The V oc -deficit in the solar cells improved up to a CdS buffer thickness of 92 nm and then deteriorated at a thicker CdS buffer layer. (ii) The minimum values of the device parameters were obtained at 70 nm CdS thickness in the CZTS TFSCs. Finally, the highest conversion efficiency of 8.77% (V oc : 494 mV, J sc : 34.54 mA/cm 2 , and FF: 51%) is obtained by applying a 70 nm thick CdS buffer to the Cu 2 ZnSn(S,Se) 4 absorber layer.

Synthesis of CdS nanorods in soft template under gamma-irradiation.

PubMed

Zhao, Bing; Wang, Yanli; Zhang, Haijiao; Jiao, Zheng; Wang, Haobo; Ding, Guoji; Wu, Minghong

2009-02-01

CdS nano material which has a band gap of 2.42 eV at room temperature is a typical II-VII semiconductor having many commercial or potential applications, e.g., light-emitting diodes, solar cell and optoelectronic devices. In this paper, we use a new strategy to synthesize CdS nanorods. CdS nanorods were prepared in soft template under gamma-irradiation though the reaction of cadmium sulphide and thiacetamide (TAA). The formation process and characters of CdS nanorods was investigated in detail by transmission electron microscopy (TEM), electron diffraction (ED) pattern, X-ray powder diffraction (XRD), ultraviolet spectrophotometer (UV) and photoluminescence spectrophotometer (PL). In the experiment we proposed that the irradiation of gamma-ray accelerated the formation of S(2-) under acidic condition (pH = 3) and vinyl acetate (VAc) monomer formed pre-organized nano polymer tubules which were used as both templates and nanoreacters for the growth of CdS nanorods. In this process, we have obtained the CdS polycrystal nanorods with PVAc nano tubules and CdS single-crystal nanorods. The result of X-ray powder diffraction confirms that the crystal type of CdS nanorods is cubic F-43 m (216). The results from transmission electron microscopy and electron diffraction show that the concentrations of reactants and the dose rate of gamma-ray are key to produce appropriate CdS nanorods. Relatively low concentrations (Cd2+: 0.008-0.02 mol/L, Cd2+ : S(2-) = 1 : 2) of reactants and long time (1-2 d) of irradiation in low dose rate (6-14 Gy/min) are propitious to form CdS single-crystal nanorods with small diameter (less than 100 nm) and well length (2-5 microm). UV and PL characterizations show the sample have well optical properties.

Nitrogen-doped carbon dots originating from unripe peach for fluorescent bioimaging and electrocatalytic oxygen reduction reaction.

PubMed

Atchudan, Raji; Edison, Thomas Nesakumar Jebakumar Immanuel; Lee, Yong Rok

2016-11-15

This paper reports the robust hydrothermal synthesis of nitrogen doped carbon dots (N-CDs) using the unripe fruit of Prunus persica (peach) as the carbon precursor and aqueous ammonia as the nitrogen source. The optical properties of synthesized N-CDs were characterized by ultraviolet visible (UV-Vis) and fluorescence spectroscopy techniques. The synthesized N-CDs were emitted blue light when excitated with a portable UV lamp. The materials with the optical properties were characterized further by high resolution transmission electron microscope (HRTEM), X-ray diffraction (XRD), Raman, Fourier transform infrared (FT-IR) and X-ray photoelectron spectroscopy (XPS). The mean size of the N-CDs was approximately 8nm, as calculated from the HRTEM image. The d-spacing of N-CDs, calculated using Bragg law, was approximately 0.21nm, which was consistent with the interlayer distance calculated from the HRTEM image. FT-IR spectroscopy and XPS revealed the presence of the phytoconstituents functionalities of peach fruit over the N-CDs surface and a high level of nitrogen doping on carbon dots (CDs) was confirmed by XPS studies. These results suggest that the unripe fruit extract of peach is an ideal candidate for the preparation of N-CDs. The resulting N-CDs showed excellent optical properties in water. The synthesized N-CDs exhibited a high fluorescence quantum yield and low cytotoxicity, and can be used as fluorescence imaging probes. In addition, the N-CDs were catalytically activite towards the oxygen reduction reaction (ORR). The N-CDs exhibited good catalytic activity in an alkaline medium (0.1M KOH) with a remarkable ORR of approximately 0.72V vs reversible hydrogen electrode (RHE), and O2 reduction follows mainly a 2 electron pathway by being reduced to hydrogen peroxide. The 2-electron reduction pathway is used in industry for H2O2 production. Copyright © 2016 Elsevier Inc. All rights reserved.

Harmful impact on presynaptic glutamate and GABA transport by carbon dots synthesized from sulfur-containing carbohydrate precursor.

PubMed

Borisova, Tatiana; Dekaliuk, Mariia; Pozdnyakova, Natalia; Pastukhov, Artem; Dudarenko, Marina; Borysov, Arsenii; Vari, Sandor G; Demchenko, Alexander P

2017-07-01

Carbon nanoparticles that may be potent air pollutants with adverse effects on human health often contain heteroatoms including sulfur. In order to study in detail their effects on different physiological and biochemical processes, artificially produced carbon dots (CDs) with well-controlled composition that allows fluorescence detection may be of great use. Having been prepared from different types of organic precursors, CDs expose different atoms at their surface suggesting a broad variation of functional groups. Recently, we demonstrated neurotoxic properties of CDs synthesized from the amino acid β-alanine, and it is of importance to analyze whether CDs obtained from different precursors and particularly those exposing sulfur atoms induce similar neurotoxic effects. This study focused on synthesis of CDs from the sulfur-containing precursor thiourea-CDs (TU-CDs) with a size less than 10 nm, their characterization, and neuroactivity assessment. Neuroactive properties of TU-CDs were analyzed based on their effects on the key characteristics of glutamatergic and γ-aminobutyric acid (GABA) neurotransmission in isolated rat brain nerve terminals. It was observed that TU-CDs (0.5-1.0 mg/ml) attenuated the initial velocity of Na + -dependent transporter-mediated uptake and accumulation of L-[ 14 C]glutamate and [ 3 H]GABA by nerve terminals in a dose-dependent manner and increased the ambient level of the neurotransmitters. Starting from the concentration of 0.2 mg/ml, TU-CDs evoked a gradual dose-dependent depolarization of the plasma membrane of nerve terminals measured with the cationic potentiometric dye rhodamine 6G. Within the concentration range of 0.1-0.5 mg/ml, TU-CDs caused an "unphysiological" step-like increase in fluorescence intensity of the рН-sensitive fluorescent dye acridine orange accumulated by synaptic vesicles. Therefore, despite different surface properties and fluorescent features of CDs prepared from different starting materials (thiourea and β-alanine), their principal neurotoxic effects are analogous but displayed at a different level of efficiency. Sulfur-containing TU-CDs exhibit lower effects (by ~30%) on glutamate and GABA transport in the nerve terminals in comparison with sulfur-free β-alanine CDs. Our results suggest considering that an uncontrolled presence of carbon-containing particulate matter in the human environment may pose a toxicity risk for the central nervous system.

Differential expression of genes encoding anti-oxidant enzymes in Sydney rock oysters, Saccostrea glomerata (Gould) selected for disease resistance.

PubMed

Green, Timothy J; Dixon, Tom J; Devic, Emilie; Adlard, Robert D; Barnes, Andrew C

2009-05-01

Sydney rock oysters (Saccostrea glomerata) selectively bred for disease resistance (R) and wild-caught control oysters (W) were exposed to a field infection of disseminating neoplasia. Cumulative mortality of W oysters (31.7%) was significantly greater than R oysters (0.0%) over the 118 days of the experiment. In an attempt to understand the biochemical and molecular pathways involved in disease resistance, differentially expressed sequence tags (ESTs) between R and W S. glomerata hemocytes were identified using the PCR technique, suppression subtractive hybridisation (SSH). Sequencing of 300 clones from two SSH libraries revealed 183 distinct sequences of which 113 shared high similarity to sequences in the public databases. Putative function could be assigned to 64 of the sequences. Expression of nine ESTs homologous to genes previously shown to be involved in bivalve immunity was further studied using quantitative reverse-transcriptase PCR (qRT-PCR). The base-line expression of an extracellular superoxide dismutase (ecSOD) and a small heat shock protein (sHsP) were significantly increased, whilst peroxiredoxin 6 (Prx6) and interferon inhibiting cytokine factor (IK) were significantly decreased in R oysters. From these results it was hypothesised that R oysters would be able to generate the anti-parasitic compound, hydrogen peroxide (H(2)O(2)) faster and to higher concentrations during respiratory burst due to the differential expression of genes for the two anti-oxidant enzymes of ecSOD and Prx6. To investigate this hypothesis, protein extracts from hemolymph were analysed for oxidative burst enzyme activity. Analysis of the cell free hemolymph proteins separated by native-polyacrylamide gel electrophoresis (PAGE) failed to detect true superoxide dismutase (SOD) activity by assaying dismutation of superoxide anion in zymograms. However, the ecSOD enzyme appears to generate hydrogen peroxide, presumably via another process, which is yet to be elucidated. This corroborates our hypothesis, whilst phylogenetic analysis of the complete coding sequence (CDS) of the S. glomerata ecSOD gene is supportive of the atypical nature of the ecSOD enzyme. Results obtained from this work further the current understanding of the molecular mechanisms involved in resistance to disease in this economically important bivalve, and shed further light on the anomalous oxidative processes involved.

Is a Genome a Codeword of an Error-Correcting Code?

PubMed Central

Kleinschmidt, João H.; Silva-Filho, Márcio C.; Bim, Edson; Herai, Roberto H.; Yamagishi, Michel E. B.; Palazzo, Reginaldo

2012-01-01

Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction. PMID:22649495

Phase- and shape-controlled hydrothermal synthesis of CdS nanoparticles, and oriented attachment growth of its hierarchical architectures

NASA Astrophysics Data System (ADS)

Cao, Yali; Hu, Pengfei; Jia, Dianzeng

2013-01-01

Hydrothermal strategies were successfully used to control the phases and morphologies of CdS nanocrystals. In the absence of an external direction-controlling process, the hexagonal and cubic phase well-defined leaf- and flower-like CdS nanocrystals were controlled obtained via adjusting the reaction duration or the concentration of surfactant. Oriented attachment growth modes were suggested for the formation of CdS superstructures, which was clarified through the tracing of temporal evolution of CdS nanoparticles. The CdS superstructures were structured by primary building nanoparticles, and held excellent visible emission with a peak in the green regions. This strategy is very helpful for studying the phase and morphology controlled fabrication of sulfides nanocrystals.

Biomimetic synthesis of needle-like fluorescent calcium phosphate/carbon dot hybrid composites for cell labeling and copper ion detection.

PubMed

Guo, Shanshan; Lu, Shousi; Xu, Pingxiang; Ma, Yi; Zhao, Liang; Zhao, Yuming; Gu, Wei; Xue, Ming

2016-05-04

Herein, we report a biomimetic method to synthesize needle-like calcium phosphate (CaP) with dimensions of ∼130 nm length and ∼30 nm width using carbon dots (CDs) and sodium carboxymethylcellulose as dual templates. In addition to acting as the template, the CDs enable the CaP/CDs hybrid composites to emit blue fluorescence under UV excitation. Moreover, the prepared CaP/CDs exhibited a negligible cytotoxicity towards HeLa cells. The potential of these CaP/CDs as a fluorescent probe for cell labeling was tested. In addition, it was demonstrated that the CaP/CDs were capable of selective detection of copper ions in drinking water.

Biosynthesis of CdS nanoparticles in banana peel extract.

PubMed

Zhou, Guang Ju; Li, Shuo Hao; Zhang, Yu Cang; Fu, Yun Zhi

2014-06-01

Cadmium sulfide (CdS) nanoparticles (NPs) were synthesized by using banana peel extract as a convenient, non-toxic, eco-friendly 'green' capping agent. Cadmium nitrate and sodium sulfide are main reagents. A variety of CdS NPs are prepared through changing reaction conditions (banana extracts, the amount of banana peel extract, solution pH, concentration and reactive temperature). The prepared CdS colloid displays strong fluorescence spectrum. X-ray diffraction analysis demonstrates the successful formation of CdS NPs. Fourier transform infra-red (FTIR) spectrogram indicates the involvement of carboxyl, amine and hydroxyl groups in the formation of CdS NPs. Transmission electron microscope (TEM) result reveals that the average size of the NPs is around 1.48 nm.

Unique organogel formation with macroporous materials constructed by the freeze-drying of aqueous cyclodextrin solutions.

PubMed

Marui, Yasuhiro; Kikuzawa, Akira; Kida, Toshiyuki; Akashi, Mitsuru

2010-07-06

Macroporous cyclodextrin materials (MP-alpha-, beta-, and gamma-CDs) were easily fabricated by the freeze-drying of aqueous solutions of alpha-, beta-, and gamma-CDs. These MP-CDs showed the absorption ability toward various organic solvents and oils to give organogels at ambient temperature. The morphological changes of the MP-CD microstructures were observed through the absorption of organic solvents. In particular, the absorption of polar organic solvents with hydrogen-bond forming ability, including 1,4-dioxane and ethanol, by the MP-CDs caused remarkable morphological changes in the microstructures. The absorption of these polar solvents by MP-alpha- and gamma-CDs resulted in the formation of channel-type assemblies of alpha- and gamma-CDs, respectively.

Mn(II)-coordinated Fluorescent Carbon Dots: Preparation and Discrimination of Organic Solvents

NASA Astrophysics Data System (ADS)

Wang, Yuru; Wang, Tianren; Chen, Xi; Xu, Yang; Li, Huanrong

2018-04-01

Herein, we prepared a Mn(II)-coordinated carbon dots (CDs) with fluorescence and MRI (magnetic resonance imaging) bimodal properties by a one-pot solvothermal method and separated via silica column chromatography. The quantum yield of the CDs increased greatly from 2.27% to 6.75% with increase of Mn(II) doping, meanwhile the CDs exhibited a higher MR activity (7.28 mM-1s-1) than that of commercial Gd-DTPA (4.63 mM-1s-1). In addition, white light emitting CDs were obtained by mixing the different types of CDs. Notably, these CDs exhibited different fluorescence emissions in different organic solvents and could be used to discriminate organic solvents based on the polarity and protonation of the solvents.

Investigation of the Activity of the Microorganisms in a Reblochon-Style Cheese by Metatranscriptomic Analysis

PubMed Central

Monnet, Christophe; Dugat-Bony, Eric; Swennen, Dominique; Beckerich, Jean-Marie; Irlinger, Françoise; Fraud, Sébastien; Bonnarme, Pascal

2016-01-01

The microbial communities in cheeses are composed of varying bacteria, yeasts, and molds, which contribute to the development of their typical sensory properties. In situ studies are needed to better understand their growth and activity during cheese ripening. Our objective was to investigate the activity of the microorganisms used for manufacturing a surface-ripened cheese by means of metatranscriptomic analysis. The cheeses were produced using two lactic acid bacteria (Streptococcus thermophilus and Lactobacillus delbrueckii ssp. bulgaricus), one ripening bacterium (Brevibacterium aurantiacum), and two yeasts (Debaryomyces hansenii and Geotrichum candidum). RNA was extracted from the cheese rinds and, after depletion of most ribosomal RNA, sequencing was performed using a short-read sequencing technology that generated ~75 million reads per sample. Except for B. aurantiacum, which failed to grow in the cheeses, a large number of CDS reads were generated for the inoculated species, making it possible to investigate their individual transcriptome over time. From day 5 to 35, G. candidum accounted for the largest proportion of CDS reads, suggesting that this species was the most active. Only minor changes occurred in the transcriptomes of the lactic acid bacteria. For the two yeasts, we compared the expression of genes involved in the catabolism of lactose, galactose, lactate, amino acids, and free fatty acids. During ripening, genes involved in ammonia assimilation and galactose catabolism were down-regulated in the two species. Genes involved in amino acid catabolism were up-regulated in G. candidum from day 14 to day 35, whereas in D. hansenii, they were up-regulated mainly at day 35, suggesting that this species catabolized the cheese amino acids later. In addition, after 35 days of ripening, there was a down-regulation of genes involved in the electron transport chain, suggesting a lower cellular activity. The present study has exemplified how metatranscriptomic analyses provide insight into the activity of cheese microbial communities for which reference genome sequences are available. In the future, such studies will be facilitated by the progress in DNA sequencing technologies and by the greater availability of the genome sequences of cheese microorganisms. PMID:27148224

Impact of the Cornea Donor Study (CDS) on Acceptance of Corneas from Older Donors

PubMed Central

Sugar, Alan; Montoya, Monty M.; Beck, Roy; Cowden, John W.; Dontchev, Mariya; Gal, Robin L.; Kollman, Craig; Malling, Jackie; Mannis, Mark J.; Tennant, Bradley

2014-01-01

Purpose Evaluate retrospectively whether findings from the Cornea Donor Study (CDS) led to changes in the transplantation of corneas from older donors. Methods United States eye banks provided complete data on donor age and placement (domestic or international) for 86,273 corneas from 1998 to 2009. The data were analyzed by 3 time periods: preceding CDS (1998–1999), during CDS (2000–2007) and after publication of CDS 5 year results (2008–2009), and separately for corneas placed within vs. outside the United States. Results For corneal tissues transplanted in the United States, the percentage of donors ≥66 years old increased from 19% before CDS to 21% during CDS and 25% after CDS (p<0.001). Corresponding median (25th-75th percentile) donor ages were 53 (39–63), 54 (41–64) and 57 (46–66), respectively (p<0.001). The opposite trend was observed for corneas distributed outside the United States with the percentage of donors ≥66 years old decreasing from 56% to 42% to 34%, respectively. Donor age trends over time varied by eye bank. Conclusions There was a modest overall increase in the donor age of corneas transplanted in the United States from 1998 to 2009, but the retrospective nature of the study limits our ability to attribute this change to the CDS. The modest increases in the donor age of corneas transplanted is a positive finding, but wider acceptance of older corneal donor tissue should be encouraged based on the five-year evidence generated by the CDS. PMID:22262218

Biological and catalytic applications of green synthesized fluorescent N-doped carbon dots using Hylocereus undatus.

PubMed

Arul, Velusamy; Edison, Thomas Nesakumar Jebakumar Immanuel; Lee, Yong Rok; Sethuraman, Mathur Gopalakrishnan

2017-03-01

In this work, a simple hydrothermal route for the synthesis of fluorescent nitrogen doped carbon dots (N-CDs) is reported. The Hylocereus undatus (H. undatus) extract and aqueous ammonia are used as carbon and nitrogen source, respectively. The optical properties of synthesized N-CDs are analyzed using UV-Visible (UV-Vis) and fluorescence spectroscopy. The surface morphology, elemental composition, crystallinity and functional groups present in the N-CDs are examined using high resolution transmission electron microscopy (HR-TEM) with energy dispersive spectroscopy (EDS), selected area electron diffraction (SAED), X-ray diffraction (XRD) and Fourier transform infrared (FT-IR) spectroscopy, respectively. The synthesized N-CDs emit strong blue fluorescence at 400nm under the excitation of 320nm. Further, the excitation dependent emission properties are also observed from the fluorescence of synthesized N-CDs. The HR-TEM results reveal that synthesized N-CDs are in spherical shape with average diameter of 2.5nm. The XRD pattern exhibits, the graphitic nature of synthesized N-CDs. The doping of nitrogen is confirmed from the EDS and FT-IR studies. The cytotoxicity and biocompatibility of N-CDs are evaluated through MTT assay on L-929 (Lymphoblastoid-929) and MCF-7 (Michigan Cancer Foundation-7) cells. The results indicate that the fluorescent N-CDs show less cytotoxicity and good biocompatibility on both L-929 and MCF-7 cells. Moreover, the N-CDs show excellent catalytic activity towards the reduction of methylene blue by sodium borohydride. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural Dynamics of Carbon Dots in Water and N, N-Dimethylformamide Probed by All-Atom Molecular Dynamics Simulations.

PubMed

Paloncýová, Markéta; Langer, Michal; Otyepka, Michal

2018-04-10

Carbon dots (CDs), one of the youngest members of the carbon nanostructure family, are now widely experimentally studied for their tunable fluorescence properties, bleaching resistance, and biocompatibility. Their interaction with biomolecular systems has also been explored experimentally. However, many atomistic details still remain unresolved. Molecular dynamics (MD) simulations enabling atomistic and femtosecond resolutions simultaneously are a well-established tool of computational chemistry which can provide useful insights into investigated systems. Here we present a full procedure for performing MD simulations of CDs. We developed a builder for generating CDs of a desired size and with various oxygen-containing surface functional groups. Further, we analyzed the behavior of various CDs differing in size, surface functional groups, and degrees of functionalization by MD simulations. These simulations showed that surface functionalized CDs are stable in a water environment through the formation of an extensive hydrogen bonding network. We also analyzed the internal dynamics of individual layers of CDs and evaluated the role of surface functional groups on CD stability. We observed that carboxyl groups interconnected the neighboring layers and decreased the rate of internal rotations. Further, we monitored changes in the CD shape caused by an excess of charged carboxyl groups or carbonyl groups. In addition to simulations in water, we analyzed the behavior of CDs in the organic solvent DMF, which decreased the stability of pure CDs but increased the level of interlayer hydrogen bonding. We believe that the developed protocol, builder, and parameters will facilitate future studies addressing various aspects of structural features of CDs and nanocomposites containing CDs.

Simple and green synthesis of protein-conjugated CdS nanoparticles and spectroscopic study on the interaction between CdS and zein

NASA Astrophysics Data System (ADS)

Qin, Dezhi; Zhang, Li; Du, Xian; Wang, Yabo; Zhang, Qiuxia

2016-09-01

The present study demonstrates the role of zein molecules in synthesizing CdS nanoassemblies through protein-directed, green synthetic approach. Zein molecules can as capping ligand and stabilizing agent to regulate the nucleation and growth of CdS nanocrystals, and the obtained products are organic-inorganic nanocomposites. The analysis of surface charge and conductivity indicates that strong electrostatic force restricts mobility of ions, which creates a local supersaturation surrounding the binding sites of zein and reduces the activated energy of nucleation. The interaction between Cd2+/CdS and zein molecules was systematically investigated through spectroscopy techniques. Fourier transform infrared (FT-IR) spectra were used to envisage the binding of the functional groups of zein with the surface of CdS nanoparticles. Ultraviolet visible (UV-Vis) and photoluminescence (PL) spectra results show that Cd2+/CdS might interact with the aromatic amino acids of protein molecules and change its chemical microenvironment. The quantum-confined effect of nanocrystals is confirmed by optical absorption spectrum due to the small size (3-5 nm) of CdS particles. The data of circular dichroism (CD) spectra indicate that the formation of CdS nanocrystals could lead to the conformational change of zein molecules. Moreover, the possible mechanism of CdS nanocrystals growth in zein solution was also discussed. The weak interactions such as Van der Waals, hydrophobic forces and hydrogen bonds in zein molecules should play a crucial factor in the self-assembly of small nanoparticles.

A qualitative study of the activities performed by people involved in clinical decision support: recommended practices for success

PubMed Central

Wright, Adam; Ash, Joan S; Erickson, Jessica L; Wasserman, Joe; Bunce, Arwen; Stanescu, Ana; St Hilaire, Daniel; Panzenhagen, Morgan; Gebhardt, Eric; McMullen, Carmit; Middleton, Blackford; Sittig, Dean F

2014-01-01

Objective To describe the activities performed by people involved in clinical decision support (CDS) at leading sites. Materials and methods We conducted ethnographic observations at seven diverse sites with a history of excellence in CDS using the Rapid Assessment Process and analyzed the data using a series of card sorts, informed by Linstone's Multiple Perspectives Model. Results We identified 18 activities and grouped them into four areas. Area 1: Fostering relationships across the organization, with activities (a) training and support, (b) visibility/presence on the floor, (c) liaising between people, (d) administration and leadership, (e) project management, (f) cheerleading/buy-in/sponsorship, (g) preparing for CDS implementation. Area 2: Assembling the system with activities (a) providing technical support, (b) CDS content development, (c) purchasing products from vendors (d) knowledge management, (e) system integration. Area 3: Using CDS to achieve the organization's goals with activities (a) reporting, (b) requirements-gathering/specifications, (c) monitoring CDS, (d) linking CDS to goals, (e) managing data. Area 4: Participation in external policy and standards activities (this area consists of only a single activity). We also identified a set of recommendations associated with these 18 activities. Discussion All 18 activities we identified were performed at all sites, although the way they were organized into roles differed substantially. We consider these activities critical to the success of a CDS program. Conclusions A series of activities are performed by sites strong in CDS, and sites adopting CDS should ensure they incorporate these activities into their efforts. PMID:23999670

The GUIDES checklist: development of a tool to improve the successful use of guideline-based computerised clinical decision support.

PubMed

Van de Velde, Stijn; Kunnamo, Ilkka; Roshanov, Pavel; Kortteisto, Tiina; Aertgeerts, Bert; Vandvik, Per Olav; Flottorp, Signe

2018-06-25

Computerised decision support (CDS) based on trustworthy clinical guidelines is a key component of a learning healthcare system. Research shows that the effectiveness of CDS is mixed. Multifaceted context, system, recommendation and implementation factors may potentially affect the success of CDS interventions. This paper describes the development of a checklist that is intended to support professionals to implement CDS successfully. We developed the checklist through an iterative process that involved a systematic review of evidence and frameworks, a synthesis of the success factors identified in the review, feedback from an international expert panel that evaluated the checklist in relation to a list of desirable framework attributes, consultations with patients and healthcare consumers and pilot testing of the checklist. We screened 5347 papers and selected 71 papers with relevant information on success factors for guideline-based CDS. From the selected papers, we developed a 16-factor checklist that is divided in four domains, i.e. the CDS context, content, system and implementation domains. The panel of experts evaluated the checklist positively as an instrument that could support people implementing guideline-based CDS across a wide range of settings globally. Patients and healthcare consumers identified guideline-based CDS as an important quality improvement intervention and perceived the GUIDES checklist as a suitable and useful strategy. The GUIDES checklist can support professionals in considering the factors that affect the success of CDS interventions. It may facilitate a deeper and more accurate understanding of the factors shaping CDS effectiveness. Relying on a structured approach may prevent that important factors are missed.

Pattern recognition of electronic bit-sequences using a semiconductor mode-locked laser and spatial light modulators

NASA Astrophysics Data System (ADS)

Bhooplapur, Sharad; Akbulut, Mehmetkan; Quinlan, Franklyn; Delfyett, Peter J.

2010-04-01

A novel scheme for recognition of electronic bit-sequences is demonstrated. Two electronic bit-sequences that are to be compared are each mapped to a unique code from a set of Walsh-Hadamard codes. The codes are then encoded in parallel on the spectral phase of the frequency comb lines from a frequency-stabilized mode-locked semiconductor laser. Phase encoding is achieved by using two independent spatial light modulators based on liquid crystal arrays. Encoded pulses are compared using interferometric pulse detection and differential balanced photodetection. Orthogonal codes eight bits long are compared, and matched codes are successfully distinguished from mismatched codes with very low error rates, of around 10-18. This technique has potential for high-speed, high accuracy recognition of bit-sequences, with applications in keyword searches and internet protocol packet routing.

Facile and eco-friendly synthesis of green fluorescent carbon nanodots for applications in bioimaging, patterning and staining.

PubMed

Shi, Lihong; Li, Yanyan; Li, Xiaofeng; Wen, Xiangping; Zhang, Guomei; Yang, Jun; Dong, Chuan; Shuang, Shaomin

2015-04-28

We report a facile and eco-friendly strategy for the fabrication of green fluorescent carbon nanodots (CDs), and demonstrate their applications for bio-imaging, patterning, and staining. A one-pot hydrothermal method using various plant petals yields bright green-emitting CDs, providing an easy way for the production of green fluorescent CDs without the need for a tedious synthetic methodology or the use of toxic/expensive solvents and starting materials. The as-prepared CDs show small size distribution and excellent dispersibility. Their strong green fluorescence is observed when the excitation wavelength is between 430 nm and 490 nm. Moreover, they exhibit high tolerance to various external conditions, such as pH values, external cations, and continuous excitation. Due to minimum toxicity as well as good photoluminescence properties, these CDs can be applied to in vitro and in vivo imaging, patterning, and staining. According to confocal fluorescence imaging of human uterine cervical squamous cell carcinoma cells, CDs penetrate into the cell and enter the cytoplasm and the nucleus. More strikingly, carp is directly fed with CDs for in vivo imaging and shows bright green fluorescence at an excitation wavelength of 470 nm. In addition, the obtained CDs are used as fluorescent inks for drawing luminescence patterns. Finally, we also apply the CDs as a fluorescent dye. Interestingly, the absorbent filter paper with staining emits dramatic fluorescence under 470 nm excitation.

Rapid solid-phase microwave synthesis of highly photoluminescent nitrogen-doped carbon dots for Fe3+ detection and cellular bioimaging

NASA Astrophysics Data System (ADS)

He, Guili; Xu, Minghan; Shu, Mengjun; Li, Xiaolin; Yang, Zhi; Zhang, Liling; Su, Yanjie; Hu, Nantao; Zhang, Yafei

2016-09-01

Recently, carbon dots (CDs) have been playing an increasingly important role in industrial production and biomedical field because of their excellent properties. As such, finding an efficient method to quickly synthesize a large scale of relatively high purity CDs is of great interest. Herein, a facile and novel microwave method has been applied to prepare nitrogen doped CDs (N-doped CDs) within 8 min using L-glutamic acid as the sole reaction precursor in the solid phase condition. The as-prepared N-doped CDs with an average size of 1.64 nm are well dispersed in aqueous solution. The photoluminescence of N-doped CDs is pH-sensitive and excitation-dependent. The N-doped CDs show a strong blue fluorescence with relatively high fluorescent quantum yield of 41.2%, which remains stable even under high ionic strength. Since the surface is rich in oxygen-containing functional groups, N-doped CDs can be applied to selectively detect Fe3+ with the limit of detection of 10-5 M. In addition, they are also used for cellular bioimaging because of their high fluorescent intensity and nearly zero cytotoxicity. The solid-phase microwave method seems to be an effective strategy to rapidly obtain high quality N-doped CDs and expands their applications in ion detection and cellular bioimaging.

Facile green synthesis of fluorescent N-doped carbon dots from Actinidia deliciosa and their catalytic activity and cytotoxicity applications

NASA Astrophysics Data System (ADS)

Arul, Velusamy; Sethuraman, Mathur Gopalakrishnan

2018-04-01

Green synthesis of fluorescent nitrogen doped carbon dots (N-CDs) using Actinidia deliciosa (A. deliciosa) fruit extract as a carbon precursor and aqueous ammonia as a nitrogen dopant is reported here. The synthesized N-CDs were characterized by high resolution transmission electron microscopy (HR-TEM), energy dispersive spectroscopy (EDS), selected area electron diffraction (SAED), UV-Visible spectroscopy (UV-Vis), fluorescence spectroscopy, Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). The average size of the N-CDs was approximately 3.59 nm and the calculated inter layer distance was found to be 0.21 nm. Raman spectroscopy and SAED pattern revealed the graphitic nature of the synthesized N-CDs. The N-CDs were found to emit intense blue color at 405 nm under the excitation of 315 nm. The doping of nitrogen over the surface of the N-CDs was confirmed by EDS, FT-IR and XPS studies. The synthesized N-CDs were found to exhibit excellent catalytic activity in the reduction of Rhodamine-B using sodium borohydrate. The MTT assay was used to evaluate the cytotoxicity and biocompatibility of N-CDs towards L-929 and MCF-7 cells. From the results obtained, it was found that the N-CDs exhibit low cytotoxicity and superior biocompatibility on both L-929 and MCF-7 cells.

Development of CdS Nanostructures by Thermal Decomposition of Aminocaproic Acid-Mixed Cd-Thiourea Complex Precursor: Structural, Optical and Photocatalytic Characterization.

PubMed

Patel, Jayesh D; Mighri, Frej; Ajji, Abdellah; Chaudhuri, Tapas K

2015-04-01

The present work deals with two different CdS nanostructures produced via hydrothermal and solvothermal decompositions of aminocaproic acid (ACA)-mixed Cd-thiourea complex precursor at 175 °C. Both nanostructures were extensively characterized for their structural, morphological and optical properties. The powder X-ray diffraction characterization showed that the two CdS nanostructures present a wurtzite morphology. Scanning electron microscopy and energy-dispersive X-ray characterizations revealed that the hydrothermal decomposition produced well-shaped CdS flowers composed of six dendritic petals, and the solvothermal decomposition produced CdS microspheres with close stoichiometric chemical composition. The UV-vis absorption and photoluminescence spectra of CdS dendritic flowers and microsphere nanostructures showed that both nanostructures present a broad absorption between 200 and 700 nm and exhibit strong green emissions at 576 and 520 nm upon excitations at 290 nm and 260 nm, respectively. The transmission electron microscopy (TEM) and Brunauer-Emmett-Teller (BET) characterizations confirmed that CdS microspheres were mesoporous and were composed of small nanocrystals. A possible growth mechanism in the formation of the CdS nanostructures was proposed based on morphology evolution as a function of the reaction time. Furthermore, the as-synthesized CdS nanostructures were found to exhibit highly efficient photocatalytic activities for the degradation of methyl orange (MeO) and rhodamine B (RhB) dyes.

The excitonic photoluminescence mechanism and lasing action in band-gap-tunable CdS(1-x)Se(x) nanostructures.

PubMed

Dai, Jun; Zhou, Pengxia; Lu, Junfeng; Zheng, Hongge; Guo, Jiyuan; Wang, Fang; Gu, Ning; Xu, Chunxiang

2016-01-14

Bandgap tunable semiconductor materials have wide application in integrated-optoelectronic and communication devices. The CdS1-xSex ternary semiconductor materials covering green-red bands have been reported previously, but their basic band-gap and optical properties crucial to the performance of the CdS1-xSex-based optoelectronic devices have not been deeply understood. In this paper, we theoretically simulated and discussed the feasibility of bandgap-tunable CdS1-xSex nanomaterials for designing wavelength tunable microlasers. Then we fabricated the CdS1-xSex nanobelts with their band gap ranging from 2.4 to 1.74 eV by adjusting the composition ratio x in the vapor-phase-transport growth process. The temperature-dependent photoluminescence and exciton-related optical constants of the CdS1-xSex nanobelts were carefully demonstrated. Finally, the wavelength-tunable Fabry-Perot lasing in CdS1-xSex nanobelts was obtained, and the Fabry-Perot lasing mechanism was numerically simulated by the FDTD method. The systematic results on the mechanism of the tunable band gap, exciton properties and lasing of the CdS1-xSex nanostructure help us deeply understand the intrinsic optical properties of this material, and will build a strong foundation for future application of green-red wavelength-tunable CdS1-xSex microlasers.

Carbon dots as fluorescent probes for "off-on" detection of Cu2+ and L-cysteine in aqueous solution.

PubMed

Zong, Jie; Yang, Xiaoling; Trinchi, Adrian; Hardin, Simon; Cole, Ivan; Zhu, Yihua; Li, Chunzhong; Muster, Tim; Wei, Gang

2014-01-15

Copper ion (Cu(2+)) and L-cysteine (L-Cys) detection is critically important since an abnormal level of Cu(2+) or L-Cys is an indicator for many diseases. In this paper, we demonstrate an "off-on" approach for highly sensitive and selective detection of Cu(2+) and L-Cys using carbon dots (CDs) as fluorescent probes. CDs were prepared by using mesoporous silica (MS) spheres as nanoreactors. The binding ability of CDs towards metal ions was examined by comparing the fluorescence intensities of CDs before and after the addition of the metal ions. The addition of Cu(2+) cations leads to their absorption on the surface of CDs and the significant fluorescence quench of CDs (turn-off). The resulting in CDs-Cu(2+) system was found to be sensitive to L-Cys. The addition of L-Cys not only serves to shelter the CDs effectively from being quenched, but also to reverse the quenching and restore the fluorescence (turn-on) due to its ability to remove Cu(2+) from the surface of CDs. This method is facile, rapid, low cost, and environment-friendly. A detection limit as low as 2.3×10(-8) M for Cu(2+) and 3.4×10(-10) M for L-Cys is obtained, which is promising for biological applications. © 2013 Elsevier B.V. All rights reserved.

Two Perspectives on the Origin of the Standard Genetic Code

NASA Astrophysics Data System (ADS)

Sengupta, Supratim; Aggarwal, Neha; Bandhu, Ashutosh Vishwa

2014-12-01

The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids. We determine the efficacy of the physico-chemical hypothesis of code origin in the absence and presence of horizontal gene transfer (HGT) by allowing a diverse collection of code-sequence sets to compete with each other. We find that in the absence of horizontal gene transfer, natural selection between competing codes distinguished by differences in the degree of physico-chemical optimization is unable to explain the structure of the standard genetic code. However, for certain probabilities of the horizontal transfer events, a universal code emerges having a structure that is consistent with the standard genetic code.

An algebraic hypothesis about the primeval genetic code architecture.

PubMed

Sánchez, Robersy; Grau, Ricardo

2009-09-01

A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D,A,C,G,U}, where symbol D represents one or more hypothetical bases with unspecific pairings. We hypothesized that the high degeneration of a primeval genetic code with five bases and the gradual origin and improvement of a primeval DNA repair system could make possible the transition from ancient to modern genetic codes. Our results suggest that the Watson-Crick base pairing G identical with C and A=U and the non-specific base pairing of the hypothetical ancestral base D used to define the sum and product operations are enough features to determine the coding constraints of the primeval and the modern genetic code, as well as, the transition from the former to the latter. Geometrical and algebraic properties of this vector space reveal that the present codon assignment of the standard genetic code could be induced from a primeval codon assignment. Besides, the Fourier spectrum of the extended DNA genome sequences derived from the multiple sequence alignment suggests that the called period-3 property of the present coding DNA sequences could also exist in the ancient coding DNA sequences. The phylogenetic analyses achieved with metrics defined in the N-dimensional vector space (B(3))(N) of DNA sequences and with the new evolutionary model presented here also suggest that an ancient DNA coding sequence with five or more bases does not contradict the expected evolutionary history.

75 FR 11589 - Order Extending Temporary Exemptions Under the Securities Exchange Act of 1934 in Connection with...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-11

... make payments under a CDS contract is triggered by a default or other credit event as to such entity or... CDS clearing by ICE Trust. We recognize, however, that there could be legal uncertainty in the event..., and the access to clearing services by independent CDS exchanges or CDS trading platforms.\\15\\ \\15...

Facile synthesis of S, N co-doped carbon dots and investigation of their photoluminescence properties.

PubMed

Zhang, Yue; He, Junhui

2015-08-21

A facile one-pot approach to prepare photoluminescent carbon dots (CDs) was developed through hydrothermal treatment of cysteine and citric acid. The obtained CDs show stable and bright blue emission with a quantum yield of 54% and an average lifetime of 11.61 ns. Moreover, the two-photon induced upconversion fluorescence of the CDs was observed and demonstrated. Interestingly, both down and up conversion fluorescence of the CDs show excitation-independent emission, which is quite different from most of the previously reported CDs. Ultrafast spectroscopy was also employed here to study the photoluminescence (PL) properties of the CDs. After characterization using various spectroscopic techniques, a unique PL mechanism for the as-prepared CDs' fluorescence was proposed accordingly. In addition, the influence of various metal ions on the CD fluorescence was examined and no quenching phenomena were observed. Meanwhile, gold nanoparticles (Au NPs) were found to be good quenchers of CD fluorescence and their quenching behavior was fitted to the Stern-Volmer equation. This provides new opportunities for fluorescence sensor designs and light energy conversion applications. Finally, the as-prepared CDs were inkjet-printed to form a desirable pattern, which is useful for fluorescent patterns, and anti-counterfeiting labeling.

Fabrication of luminescent CdS nanoparticles on short-peptide-based hydrogel nanofibers: tuning of optoelectronic properties.

PubMed

Palui, Goutam; Nanda, Jayanta; Ray, Sudipta; Banerjee, Arindam

2009-07-13

The pH-induced self-assembly of three synthetic tripeptides in water medium is used to immobilize luminescent CdS nanoparticles. These peptides form a nanofibrillar network structure upon gelation in aqueous medium at basic pH values (pH 11.0-13.0), and the fabrication of CdS nanoparticles on the gel nanofiber confers the luminescent property to these gels. Atomic force microscopy, field-emission scanning electron microscopy, and high-resolution transmission electron microscopy clearly reveal the presence of CdS nanoparticles in a well-defined array on the gel nanofibers. This is a convenient way to make organic nanofiber-inorganic nanoparticle hybrid nanocomposite systems. The size of the CdS nanoparticles remains almost same before and after deposition on the gel nanofiber. Photoluminescence (PL) measurement of the CdS nanoparticles upon deposition on the gel nanofibers shows a significant blue shift in the emission spectrum of the nanoparticles, and there is a considerable change in the PL gap energy of the CdS nanoparticles after immobilization on different gel nanofibrils. This finding suggests that the optoelectronic properties of CdS nanoparticles can be tuned upon deposition on gel nanofibers without changing the size of the nanoparticles.

Application of Quaternion in improving the quality of global sequence alignment scores for an ambiguous sequence target in Streptococcus pneumoniae DNA

NASA Astrophysics Data System (ADS)

Lestari, D.; Bustamam, A.; Novianti, T.; Ardaneswari, G.

2017-07-01

DNA sequence can be defined as a succession of letters, representing the order of nucleotides within DNA, using a permutation of four DNA base codes including adenine (A), guanine (G), cytosine (C), and thymine (T). The precise code of the sequences is determined using DNA sequencing methods and technologies, which have been developed since the 1970s and currently become highly developed, advanced and highly throughput sequencing technologies. So far, DNA sequencing has greatly accelerated biological and medical research and discovery. However, in some cases DNA sequencing could produce any ambiguous and not clear enough sequencing results that make them quite difficult to be determined whether these codes are A, T, G, or C. To solve these problems, in this study we can introduce other representation of DNA codes namely Quaternion Q = (PA, PT, PG, PC), where PA, PT, PG, PC are the probability of A, T, G, C bases that could appear in Q and PA + PT + PG + PC = 1. Furthermore, using Quaternion representations we are able to construct the improved scoring matrix for global sequence alignment processes, by applying a dot product method. Moreover, this scoring matrix produces better and higher quality of the match and mismatch score between two DNA base codes. In implementation, we applied the Needleman-Wunsch global sequence alignment algorithm using Octave, to analyze our target sequence which contains some ambiguous sequence data. The subject sequences are the DNA sequences of Streptococcus pneumoniae families obtained from the Genebank, meanwhile the target DNA sequence are received from our collaborator database. As the results we found the Quaternion representations improve the quality of the sequence alignment score and we can conclude that DNA sequence target has maximum similarity with Streptococcus pneumoniae.

The Influence of Child-Directed Speech on Word Learning and Comprehension.

PubMed

Foursha-Stevenson, Cassandra; Schembri, Taylor; Nicoladis, Elena; Eriksen, Cody

2017-04-01

This paper describes an investigation into the function of child-directed speech (CDS) across development. In the first experiment, 10-21-month-olds were presented with familiar words in CDS and trained on novel words in CDS or adult-directed speech (ADS). All children preferred the matching display for familiar words. However, only older toddlers in the CDS condition preferred the matching display for novel words. In Experiment 2, children 3-6 years of age were presented with a sentence comprehension task in CDS or ADS. Older children performed better overall than younger children with 5- and 6-year-olds performing above chance regardless of speech condition, while 3- and 4-year-olds only performed above chance when the sentences were presented in CDS. These findings provide support for the theory that CDS is most effective at the beginning of acquisition for particular constructions (e.g. vocabulary acquisition, syntactic comprehension) rather than at a particular age or for a particular task.

Fluorescent chemosensor for pyridine based on N-doped carbon dots.

PubMed

Campos, B B; Abellán, C; Zougagh, M; Jimenez-Jimenez, J; Rodríguez-Castellón, E; Esteves da Silva, J C G; Ríos, A; Algarra, M

2015-11-15

Fluorescent carbon dots (CDs) and its nitrogen doped (N-CDs) nanoparticles have been synthesized from lactose as precursor using a bottom-up hydrothermal methodology. The synthesized nanoparticles have been characterized by elemental analysis, FTIR, Raman, TEM, DLS, XPS, and steady-state and life-time fluorescence. The synthesized carbon nanoparticles, CDs and N-CDs, have a size at about 7.7±2.4 and 50±15nm, respectively, and quantum yields of 8% (CDs) and 11% (N-CDs). These techniques demonstrated the effectiveness of the synthesis procedure and the functionalization of the CDs surface with amine and amide groups in the presence of NH3 in aqueous media. The effect of excitation wavelength and pH on the luminescent properties was studied. Under the optimal conditions, the nitrogen doped nanoparticles can be used as pyridine sensor in aqueous media because they show an enhancement of its fluorescence with a good linear relationship. The analytical method is simple, reproducible and very sensitive for pyridine determination. Copyright © 2015 Elsevier Inc. All rights reserved.

Distribution of different surface modified carbon dots in pumpkin seedlings.

PubMed

Qian, Kun; Guo, Huiyuan; Chen, Guangcai; Ma, Chuanxin; Xing, Baoshan

2018-05-22

The distribution of surface modified carbon dots (CDs) in the pumpkin seedlings was studied by visualization techniques and their potential phytotoxicity was investigated at both the physiological and biochemical levels. The average size of carbon dots was approximately 4 nm. The fluorescent peaks of bared CDs, CD-PEI and CD-PAA were between 420 nm and 500 nm, indicating CDs could emit blue and green fluorescence. Fluorescent images showed that all three types of CDs could accumulate in the pumpkin roots and translocate to the shoots, although the distribution pattern of each CDs was obviously different. At the biochemical level, the elevated antioxidant enzymes in pumpkin roots suggest that all the CDs could potentially trigger the antioxidant defense systems in pumpkin seedlings. Additionally, such alteration was greater in the roots than in the shoots. Our study represents a new perspective on CD visualization in plant tissues and provide useful information for the potential toxicity of different types of CDs to terrestrial plants, which is of importance to agricultural application.

Design Recommendations for Pharmacogenomics Clinical Decision Support Systems

PubMed Central

Khelifi, Maher; Tarczy-Hornoch, Peter; Devine, Emily B.; Pratt, Wanda

2017-01-01

The use of pharmacogenomics (PGx) in clinical practice still faces challenges to fully adopt genetic information in targeting drug therapy. To incorporate genetics into clinical practice, many support the use of Pharmacogenomics Clinical Decision Support Systems (PGx-CDS) for medication prescriptions. This support was fueled by new guidelines to incorporate genetics for optimizing drug dosage and reducing adverse events. In addition, the complexity of PGx led to exploring CDS outside the paradigm of the basic CDS tools embedded in commercial electronic health records. Therefore, designing the right CDS is key to unleashing the full potential of pharmacogenomics and making it a part of clinicians’ daily workflow. In this work, we 1) identify challenges and barriers of the implementation of PGx-CDS in clinical settings, 2) develop a new design approach to CDS with functional characteristics that can improve the adoption of pharmacogenomics guidelines and thus patient safety, and 3) create design guidelines and recommendations for such PGx-CDS tools. PMID:28815136

Enhanced photo response of mesoporous nanostructured CdS thin film via electrospray aerosol deposition technique

NASA Astrophysics Data System (ADS)

Logu, T.; Soundarrajan, P.; Sankarasubramanian, K.; Sethuraman, K.

2018-04-01

In this work, a high crystalline and mesoporous nanostructured cadmium sulfide (CdS) thin film was successfully grown on the FTO substrates using facile Electrospray Aerosol Deposition (ESAD) technique. The structural, optical, morphological and electrical properties of CdS thin film have been systematically examined. CdS thin film exhibits the hexagonal wurtzite crystal structure with polycrystalline nature. The optical band gap energy of the prepared film was estimated from the Tauc plot and is 2.43 eV. The SEM and AFM images show that the well-interconnected CdS nanoparticles gives mesoporous like morphology. The fine aerosol generated from the ESAD process induces the alteration in the surface morphological structure of deposited CdS film that consequences in enhanced electrical and photo-physical properties. The photoconductivity of the sample has been studied which demonstrates significant photo current. The present study predicts that mesoporous nanostructured CdS thin film would be given a special interest for optoelectronic applications.

Arrays of Ultrathin CdS Nanoflakes with High-Energy Surface for Efficient Gas Detection.

PubMed

Liu, Xiao-Hua; Yin, Peng-Fei; Kulinich, Sergei A; Zhou, Yu-Zhu; Mao, Jing; Ling, Tao; Du, Xi-Wen

2017-01-11

It is fascinating and challenging to endow conventional materials with unprecedented properties. For instance, cadmium sulfide (CdS) is an important semiconductor with excellent light response; however, its potential in gas-sensing was underestimated owing to relatively low chemical activity and poor electrical conductivity. Herein, we demonstrate that an ideal architecture, ultrathin nanoflake arrays (NFAs), can improve significantly gas-sensing properties of CdS material. The CdS NFAs are grown directly on the interdigitated electrode to expose large surface area. Their thickness is reduced below the double Debye length of CdS, permitting to achieve a full depletion of carriers. Particularly, the prepared CdS nanoflakes are enclosed with high-energy {0001} facets exposed, which provides more active sites for gas adsorption. Moreover, the NFAs exhibit the light-trapping effect, which further enhances their gas sensitivity. As a result, the as-prepared CdS NFAs demonstrate excellent gas-sensing and light-response properties, thus being capable of dual gas and light detection.

Two Closely Related Genes of Arabidopsis Encode Plastidial Cytidinediphosphate Diacylglycerol Synthases Essential for Photoautotrophic Growth1[C

PubMed Central

Haselier, André; Akbari, Hana; Weth, Agnes; Baumgartner, Werner; Frentzen, Margrit

2010-01-01

Cytidinediphosphate diacylglycerol synthase (CDS) catalyzes the formation of cytidinediphosphate diacylglycerol, an essential precursor of anionic phosphoglycerolipids like phosphatidylglycerol or -inositol. In plant cells, CDS isozymes are located in plastids, mitochondria, and microsomes. Here, we show that these isozymes are encoded by five genes in Arabidopsis (Arabidopsis thaliana). Alternative translation initiation or alternative splicing of CDS2 and CDS4 transcripts can result in up to 10 isoforms. Most of the cDNAs encoding the various plant isoforms were functionally expressed in yeast and rescued the nonviable phenotype of the mutant strain lacking CDS activity. The closely related genes CDS4 and CDS5 were found to encode plastidial isozymes with similar catalytic properties. Inactivation of both genes was required to obtain Arabidopsis mutant lines with a visible phenotype, suggesting that the genes have redundant functions. Analysis of these Arabidopsis mutants provided further independent evidence for the importance of plastidial phosphatidylglycerol for structure and function of thylakoid membranes and, hence, for photoautotrophic growth. PMID:20442275

CeO₂ Enhanced Ethanol Sensing Performance in a CdS Gas Sensor.

PubMed

Li, Meishan; Ren, Wei; Wu, Rong; Zhang, Min

2017-07-05

CdS nanowires (NWs) were fabricated through a facile low-temperature solvothermal method, following which CeO₂ nanoparticles were modified on the NWs. The ethanol sensing characteristics of pure CdS and decorated ones with different CeO₂ content were studied. It was found that the sensing performance of CdS was significantly improved after CeO₂ decoration. In particular, the 5 at% CeO₂/CdS composite exhibited a much higher response to 100 ppm ethanol (about 52), which was 2.6 times larger than that of pure CdS. A fast response and recovery time (less than 12 s and 3 s, respectively) were obtained as well as an excellent selectivity. These results make the CeO₂-decorated CdS NWs good candidates for ethanol sensing applications.

Quick synthesis of 2-propanol derived fluorescent carbon dots for bioimaging applications

NASA Astrophysics Data System (ADS)

Angamuthu, Raja; Palanisamy, Priya; Vasudevan, Vasanthakumar; Nagarajan, Sedhu; Rajendran, Ramesh; Vairamuthu, Raj

2018-04-01

Herein, for the first time, we present a one-pot ingenious preparative method for fluorescent carbon dots from 2-propanol (2P-CDs) without external treatments. Structure, morphology, chemical composition and fluorescence properties of the 2P-CDs were examined. These results confirm that the as-synthesized 2P-CDs are amorphous, monodispersed, spherical and the average particle size is 2.5 ± 0.7 nm. Most importantly, excitation-dependent emission properties were observed, which suggest that these 2P-CDs may be used in multicolor bioimaging applications. When incubated with HeLa cells, the 2P-CDs exhibit low cytotoxicity, and positive biocompatibility. Confocal microscopy image shows the uptake of 2P-CDs by HeLa cells and the application of probable biomarker is demonstrated.

Optical characterization of CdS nanorods capped with starch

NASA Astrophysics Data System (ADS)

Roy, J. S.; Pal Majumder, T.; Schick, C.

2015-05-01

Well crystalline uniform CdS nanorods were grown by changing the concentration of maize starch. The highly polymeric (branched) structure of starch enhances the growth of CdS nanorods. The average diameter of the nanorods is 20-25 nm while length is of 500-600 nm as verified from SEM and XRD observations. The optical band gaps of the CdS nanorods are varying from 2.66 eV to 2.52 eV depending on concentration of maize starch. The photoluminescence (PL) emission bands are shifted from 526 nm to 529 nm with concentration of maize starch. We have also observed the enhanced PL intensity in CdS nanorods capped with starch. The Fourier transform infrared (FTIR) spectroscopy shows the significant effect of starch on CdS nanorods.

Functional analysis of the Brassica napus L. phytoene synthase (PSY) gene family.

PubMed

López-Emparán, Ada; Quezada-Martinez, Daniela; Zúñiga-Bustos, Matías; Cifuentes, Víctor; Iñiguez-Luy, Federico; Federico, María Laura

2014-01-01

Phytoene synthase (PSY) has been shown to catalyze the first committed and rate-limiting step of carotenogenesis in several crop species, including Brassica napus L. Due to its pivotal role, PSY has been a prime target for breeding and metabolic engineering the carotenoid content of seeds, tubers, fruits and flowers. In Arabidopsis thaliana, PSY is encoded by a single copy gene but small PSY gene families have been described in monocot and dicotyledonous species. We have recently shown that PSY genes have been retained in a triplicated state in the A- and C-Brassica genomes, with each paralogue mapping to syntenic locations in each of the three "Arabidopsis-like" subgenomes. Most importantly, we have shown that in B. napus all six members are expressed, exhibiting overlapping redundancy and signs of subfunctionalization among photosynthetic and non photosynthetic tissues. The question of whether this large PSY family actually encodes six functional enzymes remained to be answered. Therefore, the objectives of this study were to: (i) isolate, characterize and compare the complete protein coding sequences (CDS) of the six B. napus PSY genes; (ii) model their predicted tridimensional enzyme structures; (iii) test their phytoene synthase activity in a heterologous complementation system and (iv) evaluate their individual expression patterns during seed development. This study further confirmed that the six B. napus PSY genes encode proteins with high sequence identity, which have evolved under functional constraint. Structural modeling demonstrated that they share similar tridimensional protein structures with a putative PSY active site. Significantly, all six B. napus PSY enzymes were found to be functional. Taking into account the specific patterns of expression exhibited by these PSY genes during seed development and recent knowledge of PSY suborganellar localization, the selection of transgene candidates for metabolic engineering the carotenoid content of oilseeds is discussed.

Molecular cloning and evolutionary analysis of captive forest musk deer bitter taste receptor gene T2R16.

PubMed

Zhao, G J; Wu, N; Li, D Y; Zeng, D J; Chen, Q; Lu, L; Feng, X L; Zhang, C L; Zheng, C L; Jie, H

2015-12-08

Sensing bitter tastes is crucial for most animals because it can prevent them from ingesting harmful food. This process is mainly mediated by the bitter taste receptors (T2R) that are largely expressed in the taste buds. Previous studies have identified some T2R gene repertoires. Marked variation in repertoire size has been noted among species. However, research on T2Rs is still limited and the mechanisms underlying the evolution of vertebrate T2Rs remain poorly understood. In the present study, we analyzed the structure and features of the protein encoded by the forest musk deer (Moschus berezovskii) T2R16 and submitted the gene sequence to NCBI GenBank. The results showed that the full coding DNA sequence (CDS) of musk deer T2R16 (GenBank accession No. KP677279) was 906 bp, encoding 301 amino acids, which contained ATG start codon and TGA stop codon, with a calculated molecular weight of 35.03 kDa and an isoelectric point of 9.56. The T2R16 protein receptor had seven conserved transmembrane regions. Hydrophobicity analysis showed that most amino acid residues in T2R16 protein were hydrophobic, and the grand average of hydrophobicity (GRAVY) was 0.657. Phylogenetic analysis based on this gene revealed that forest musk deer had the closest association with sheep (Ovis aries), as compared to cow (Bos taurus), Tursiops truncatus, and other species, whereas it was genetically farthest from humans (Homo sapiens). We hope these results would complement the existing data on T2R16 and encourage further research in this respect.

Molecular cloning, expression and single nucleotide polymorphisms of protein phosphatase 1 (PP1) in mandarin fish (Siniperca chuatsi).

PubMed

Cheng, Xiao-Yan; He, Shan; Liang, Xu-Fang; Song, Yi; Yuan, Xiao-Chen; Li, Ling; Wen, Zheng-Yong; Cai, Wen-Jing; Tao, Ya-Xiong

2015-11-01

In the wild, mandarin fish (Siniperca chuatsi) only feed on live prey fish, refusing dead prey. When reared in ponds, training will result in some mandarin fish accepting artificial diets. However, little is currently known about the molecular mechanism of the individual difference. Serine/threonine protein phosphatase 1 (PP1) is a suppressor of learning and long-term memory (LTM) in mammals. In the present study, the relationship between PP1 and the individual difference in acceptance of artificial diets in mandarin fish was investigated. The complete CDS (coding sequence) of four PP1 isoforms (PP1caa, PP1cab, PP1cb and PP1cc) were cloned in mandarin fish. The amino acid sequences of these PP1 isoforms are highly conserved in different species. The mRNA expressions of PP1caa and PP1cb in brain of artificial diet feeders were significantly higher than those in nonfeeders, suggesting the deficiency in the maintenance of long-term memory of its natural food habit (live prey fish). The SNP loci in PP1caa and PP1cb were also found to be associated with the individual difference in acceptance of artificial diets in mandarin fish. These SNPs of PP1caa and PP1cb genes could be useful markers for gene-associated breeding of mandarin fish, which could accept artificial diets. In conclusion, different mRNA expression and SNPs of PP1caa and PP1cb genes in feeders and nonfeeders of artificial diets might contribute to understanding the molecular mechanism of individual difference in acceptance of artificial diets in mandarin fish. Copyright © 2015 Elsevier Inc. All rights reserved.

Enhanced Salt Tolerance Conferred by the Complete 2.3 kb cDNA of the Rice Vacuolar Na+/H+ Antiporter Gene Compared to 1.9 kb Coding Region with 5′ UTR in Transgenic Lines of Rice

PubMed Central

Amin, U. S. M.; Biswas, Sudip; Elias, Sabrina M.; Razzaque, Samsad; Haque, Taslima; Malo, Richard; Seraj, Zeba I.

2016-01-01

Soil salinity is one of the most challenging problems that restricts the normal growth and production of rice worldwide. It has therefore become very important to produce more saline tolerant rice varieties. This study shows constitutive over-expression of the vacuolar Na+/H+ antiporter gene (OsNHX1) from the rice landrace (Pokkali) and attainment of enhanced level of salinity tolerance in transgenic rice plants. It also shows that inclusion of the complete un-translated regions (UTRs) of the alternatively spliced OsNHX1 gene provides a higher level of tolerance to the transgenic rice. Two separate transformation events of the OsNHX1 gene, one with 1.9 kb region containing the 5′ UTR with CDS and the other of 2.3 kb, including 5′ UTR, CDS, and the 3′ UTR regions were performed. The transgenic plants with these two different constructs were advanced to the T3 generation and physiological and molecular screening of homozygous plants was conducted at seedling and reproductive stages under salinity (NaCl) stress. Both transgenic lines were observed to be tolerant compared to WT plants at both physiological stages. However, the transgenic lines containing the CDS with both the 5′ and 3′ UTR were significantly more tolerant compared to the transgenic lines containing OsNHX1 gene without the 3′ UTR. At the seedling stage at 12 dS/m stress, the chlorophyll content was significantly higher (P < 0.05) and the electrolyte leakage significantly lower (P < 0.05) in the order 2.3 kb > 1.9 kb > and WT lines. Yield in g/plant in the best line from the 2.3 kb plants was significantly more (P < 0.01) compared, respectively, to the best 1.9 kb line and WT plants at stress of 6 dS/m. Transformation with the complete transcripts rather than the CDS may therefore provide more durable level of tolerance. PMID:26834778

Green Synthesis of Bifunctional Fluorescent Carbon Dots from Garlic for Cellular Imaging and Free Radical Scavenging.

PubMed

Zhao, Shaojing; Lan, Minhuan; Zhu, Xiaoyue; Xue, Hongtao; Ng, Tsz-Wai; Meng, Xiangmin; Lee, Chun-Sing; Wang, Pengfei; Zhang, Wenjun

2015-08-12

Nitrogen and sulfur codoped carbon dots (CDs) were prepared from garlic by a hydrothermal method. The as-prepared CDs possess good water dispersibility, strong blue fluorescence emission with a fluorescent quantum yield of 17.5%, and excellent photo and pH stabilities. It is also demonstrated that the fluorescence of CDs are resistant to the interference of metal ions, biomolecules, and high ionic strength environments. Combining with low cytotoxicity properties, CDs could be used as an excellent fluorescent probe for cellular multicolor imaging. Moreover, the CDs were also demonstrated to exhibit favorable radical scavenging activity.

Circular codes revisited: a statistical approach.

PubMed

Gonzalez, D L; Giannerini, S; Rosa, R

2011-04-21

In 1996 Arquès and Michel [1996. A complementary circular code in the protein coding genes. J. Theor. Biol. 182, 45-58] discovered the existence of a common circular code in eukaryote and prokaryote genomes. Since then, circular code theory has provoked great interest and underwent a rapid development. In this paper we discuss some theoretical issues related to the synchronization properties of coding sequences and circular codes with particular emphasis on the problem of retrieval and maintenance of the reading frame. Motivated by the theoretical discussion, we adopt a rigorous statistical approach in order to try to answer different questions. First, we investigate the covering capability of the whole class of 216 self-complementary, C(3) maximal codes with respect to a large set of coding sequences. The results indicate that, on average, the code proposed by Arquès and Michel has the best covering capability but, still, there exists a great variability among sequences. Second, we focus on such code and explore the role played by the proportion of the bases by means of a hierarchy of permutation tests. The results show the existence of a sort of optimization mechanism such that coding sequences are tailored as to maximize or minimize the coverage of circular codes on specific reading frames. Such optimization clearly relates the function of circular codes with reading frame synchronization. Copyright © 2011 Elsevier Ltd. All rights reserved.

Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses

PubMed Central

Turco, Gina; Schnable, James C.; Pedersen, Brent; Freeling, Michael

2013-01-01

Conserved non-coding sequences (CNS) are islands of non-coding sequence that, like protein coding exons, show less divergence in sequence between related species than functionless DNA. Several CNSs have been demonstrated experimentally to function as cis-regulatory regions. However, the specific functions of most CNSs remain unknown. Previous searches for CNS in plants have either anchored on exons and only identified nearby sequences or required years of painstaking manual annotation. Here we present an open source tool that can accurately identify CNSs between any two related species with sequenced genomes, including both those immediately adjacent to exons and distal sequences separated by >12 kb of non-coding sequence. We have used this tool to characterize new motifs, associate CNSs with additional functions, and identify previously undetected genes encoding RNA and protein in the genomes of five grass species. We provide a list of 15,363 orthologous CNSs conserved across all grasses tested. We were also able to identify regulatory sequences present in the common ancestor of grasses that have been lost in one or more extant grass lineages. Lists of orthologous gene pairs and associated CNSs are provided for reference inbred lines of arabidopsis, Japonica rice, foxtail millet, sorghum, brachypodium, and maize. PMID:23874343

Synthesis and formation mechanistic investigation of nitrogen-doped carbon dots with high quantum yields and yellowish-green fluorescence

NASA Astrophysics Data System (ADS)

Hou, Juan; Wang, Wei; Zhou, Tianyu; Wang, Bo; Li, Huiyu; Ding, Lan

2016-05-01

Heteroatom doped carbon dots (CDs) have received increasing attention due to their unique properties and related applications. However, previously reported CDs generally show strong emission only in the blue-light region, thus restricting their further applications. And the fundamental investigation on the preparation process is always neglected. Herein, we have developed a simple and solvent-free synthetic strategy to fabricate nitrogen-doped CDs (N-CDs) from citric acid and dicyandiamide. The as-prepared N-CDs exhibited a uniform size distribution, strong yellowish-green fluorescence emission and a high quantum yield of 73.2%. The products obtained at different formation stages were detailedly characterized by transmission electron microscopy, X-ray diffraction spectrometer, X-ray photoelectron spectroscopy and UV absorbance spectroscopy. A possible formation mechanism has thus been proposed including dehydration, polymerization and carbonization. Furthermore, the N-CDs could serve as a facile and label-free probe for the detection of iron and fluorine ions with detection limits of 50 nmol L-1 and 75 nmol L-1, respectively.Heteroatom doped carbon dots (CDs) have received increasing attention due to their unique properties and related applications. However, previously reported CDs generally show strong emission only in the blue-light region, thus restricting their further applications. And the fundamental investigation on the preparation process is always neglected. Herein, we have developed a simple and solvent-free synthetic strategy to fabricate nitrogen-doped CDs (N-CDs) from citric acid and dicyandiamide. The as-prepared N-CDs exhibited a uniform size distribution, strong yellowish-green fluorescence emission and a high quantum yield of 73.2%. The products obtained at different formation stages were detailedly characterized by transmission electron microscopy, X-ray diffraction spectrometer, X-ray photoelectron spectroscopy and UV absorbance spectroscopy. A possible formation mechanism has thus been proposed including dehydration, polymerization and carbonization. Furthermore, the N-CDs could serve as a facile and label-free probe for the detection of iron and fluorine ions with detection limits of 50 nmol L-1 and 75 nmol L-1, respectively. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr02701f

Analysis of Nursing Clinical Decision Support Requests and Strategic Plan in a Large Academic Health System

PubMed Central

Bavuso, Karen; Bouyer-Ferullo, Sharon; Goldsmith, Denise; Fairbanks, Amanda; Gesner, Emily; Lagor, Charles; Collins, Sarah

2016-01-01

Summary Objectives To understand requests for nursing Clinical Decision Support (CDS) interventions at a large integrated health system undergoing vendor-based EHR implementation. In addition, to establish a process to guide both short-term implementation and long-term strategic goals to meet nursing CDS needs. Materials and Methods We conducted an environmental scan to understand current state of nursing CDS over three months. The environmental scan consisted of a literature review and an analysis of CDS requests received from across our health system. We identified existing high priority CDS and paper-based tools used in nursing practice at our health system that guide decision-making. Results A total of 46 nursing CDS requests were received. Fifty-six percent (n=26) were specific to a clinical specialty; 22 percent (n=10) were focused on facilitating clinical consults in the inpatient setting. “Risk Assessments/Risk Reduction/Promotion of Healthy Habits” (n=23) was the most requested High Priority Category received for nursing CDS. A continuum of types of nursing CDS needs emerged using the Data-Information-Knowledge-Wisdom Conceptual Framework: 1) facilitating data capture, 2) meeting information needs, 3) guiding knowledge-based decision making, and 4) exposing analytics for wisdom-based clinical interpretation by the nurse. Conclusion Identifying and prioritizing paper-based tools that can be modified into electronic CDS is a challenge. CDS strategy is an evolving process that relies on close collaboration and engagement with clinical sites for short-term implementation and should be incorporated into a long-term strategic plan that can be optimized and achieved overtime. The Data-Information-Knowledge-Wisdom Conceptual Framework in conjunction with the High Priority Categories established may be a useful tool to guide a strategic approach for meeting short-term nursing CDS needs and aligning with the organizational strategic plan. PMID:27437036

A novel fluorescent retrograde neural tracer: cholera toxin B conjugated carbon dots

NASA Astrophysics Data System (ADS)

Zhou, Nan; Hao, Zeyu; Zhao, Xiaohuan; Maharjan, Suraj; Zhu, Shoujun; Song, Yubin; Yang, Bai; Lu, Laijin

2015-09-01

The retrograde neuroanatomical tracing method is a key technique to study the complex interconnections of the nervous system. Traditional tracers have several drawbacks, including time-consuming immunohistochemical or immunofluorescent staining procedures, rapid fluorescence quenching and low fluorescence intensity. Carbon dots (CDs) have been widely used as a fluorescent bio-probe due to their ultrasmall size, excellent optical properties, chemical stability, biocompatibility and low toxicity. Herein, we develop a novel fluorescent neural tracer: cholera toxin B-carbon dot conjugates (CTB-CDs). It can be taken up and retrogradely transported by neurons in the peripheral nervous system of rats. Our results show that CTB-CDs possess high photoluminescence intensity, good optical stability, a long shelf-life and non-toxicity. Tracing with CTB-CDs is a direct and more economical way of performing retrograde labelling experiments. Therefore, CTB-CDs are reliable fluorescent retrograde tracers.The retrograde neuroanatomical tracing method is a key technique to study the complex interconnections of the nervous system. Traditional tracers have several drawbacks, including time-consuming immunohistochemical or immunofluorescent staining procedures, rapid fluorescence quenching and low fluorescence intensity. Carbon dots (CDs) have been widely used as a fluorescent bio-probe due to their ultrasmall size, excellent optical properties, chemical stability, biocompatibility and low toxicity. Herein, we develop a novel fluorescent neural tracer: cholera toxin B-carbon dot conjugates (CTB-CDs). It can be taken up and retrogradely transported by neurons in the peripheral nervous system of rats. Our results show that CTB-CDs possess high photoluminescence intensity, good optical stability, a long shelf-life and non-toxicity. Tracing with CTB-CDs is a direct and more economical way of performing retrograde labelling experiments. Therefore, CTB-CDs are reliable fluorescent retrograde tracers. Electronic supplementary information (ESI) available: PL spectra of CTB; absorption spectra of dialysate; fluorescence signal and immunohistochemical staining of CTB-CDs in L4 DRG. See DOI: 10.1039/c5nr04361a

Annealing effects on the chemical deposited CdS films and the electrical properties of CdS/CdTe solar cells

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

Han, Junfeng; Institute of Materials Science, Darmstadt University of Technology, Petersenstr. 23, 64287 Darmstadt; Liao, Cheng, E-mail: Cliao@pku.edu.cn

2011-02-15

Graphical abstract: From XPS core level spectras, compared with as-depositing CdS (sample A), the Fermi level is shifting closer to the conduction band after annealing treatment in the oxygen (sample B) while it is shifting closer to the valence band after annealing treatment in the argon-hydrogen (sample C). That might be the main reason of the different performance of the final devices. The open circuit voltage of the CdS/CdTe solar cell increases when the CBD CdS is annealed with oxygen, while the performance of the solar cell decreases when the CBD CdS is annealed with argon-hydrogen. Research highlights: {yields} Twomore » different methods (oxidation and reduction) were used to anneal CdS films for CdTe solar cells. {yields} Electrical properties were analyzed by XPS (Fermi levels of CdS films). {yields} Annealing treatment in oxidation atmosphere could shift Fermi level of CdS film to higher position and consequently improve the CdS/CdTe junction and performance of solar cells. -- Abstract: CdS layers grown by chemical bath deposition (CBD) are annealed in the oxygen and argon-hydrogen atmosphere respectively. It has been found that the open circuit voltage of the CdS/CdTe solar cell increases when the CBD CdS is annealed with oxygen before the deposition of CdTe by close spaced sublimation (CSS), while the performance of the solar cell decreases when the CBD CdS is annealed with argon-hydrogen. Electronic properties of the CdS films are investigated using X-ray photo-electron spectroscopy (XPS), which indicates that the Fermi level is shifting closer to the conduction band after annealing in the oxygen and consequently a higher open circuit voltage of the solar cell can be obtained.« less

Second-generation sequencing of entire mitochondrial coding-regions (∼15.4 kb) holds promise for study of the phylogeny and taxonomy of human body lice and head lice.

PubMed

Xiong, H; Campelo, D; Pollack, R J; Raoult, D; Shao, R; Alem, M; Ali, J; Bilcha, K; Barker, S C

2014-08-01

The Illumina Hiseq platform was used to sequence the entire mitochondrial coding-regions of 20 body lice, Pediculus humanus Linnaeus, and head lice, P. capitis De Geer (Phthiraptera: Pediculidae), from eight towns and cities in five countries: Ethiopia, France, China, Australia and the U.S.A. These data (∼310 kb) were used to see how much more informative entire mitochondrial coding-region sequences were than partial mitochondrial coding-region sequences, and thus to guide the design of future studies of the phylogeny, origin, evolution and taxonomy of body lice and head lice. Phylogenies were compared from entire coding-region sequences (∼15.4 kb), entire cox1 (∼1.5 kb), partial cox1 (∼700 bp) and partial cytb (∼600 bp) sequences. On the one hand, phylogenies from entire mitochondrial coding-region sequences (∼15.4 kb) were much more informative than phylogenies from entire cox1 sequences (∼1.5 kb) and partial gene sequences (∼600 to ∼700 bp). For example, 19 branches had > 95% bootstrap support in our maximum likelihood tree from the entire mitochondrial coding-regions (∼15.4 kb) whereas the tree from 700 bp cox1 had only two branches with bootstrap support > 95%. Yet, by contrast, partial cytb (∼600 bp) and partial cox1 (∼486 bp) sequences were sufficient to genotype lice to Clade A, B or C. The sequences of the mitochondrial genomes of the P. humanus, P. capitis and P. schaeffi Fahrenholz studied are in NCBI GenBank under the accession numbers KC660761-800, KC685631-6330, KC241882-97, EU219988-95, HM241895-8 and JX080388-407. © 2014 The Royal Entomological Society.

Effective Identification of Similar Patients Through Sequential Matching over ICD Code Embedding.

PubMed

Nguyen, Dang; Luo, Wei; Venkatesh, Svetha; Phung, Dinh

2018-04-11

Evidence-based medicine often involves the identification of patients with similar conditions, which are often captured in ICD (International Classification of Diseases (World Health Organization 2013)) code sequences. With no satisfying prior solutions for matching ICD-10 code sequences, this paper presents a method which effectively captures the clinical similarity among routine patients who have multiple comorbidities and complex care needs. Our method leverages the recent progress in representation learning of individual ICD-10 codes, and it explicitly uses the sequential order of codes for matching. Empirical evaluation on a state-wide cancer data collection shows that our proposed method achieves significantly higher matching performance compared with state-of-the-art methods ignoring the sequential order. Our method better identifies similar patients in a number of clinical outcomes including readmission and mortality outlook. Although this paper focuses on ICD-10 diagnosis code sequences, our method can be adapted to work with other codified sequence data.

Automation bias in electronic prescribing.

PubMed

Lyell, David; Magrabi, Farah; Raban, Magdalena Z; Pont, L G; Baysari, Melissa T; Day, Richard O; Coiera, Enrico

2017-03-16

Clinical decision support (CDS) in e-prescribing can improve safety by alerting potential errors, but introduces new sources of risk. Automation bias (AB) occurs when users over-rely on CDS, reducing vigilance in information seeking and processing. Evidence of AB has been found in other clinical tasks, but has not yet been tested with e-prescribing. This study tests for the presence of AB in e-prescribing and the impact of task complexity and interruptions on AB. One hundred and twenty students in the final two years of a medical degree prescribed medicines for nine clinical scenarios using a simulated e-prescribing system. Quality of CDS (correct, incorrect and no CDS) and task complexity (low, low + interruption and high) were varied between conditions. Omission errors (failure to detect prescribing errors) and commission errors (acceptance of false positive alerts) were measured. Compared to scenarios with no CDS, correct CDS reduced omission errors by 38.3% (p < .0001, n = 120), 46.6% (p < .0001, n = 70), and 39.2% (p < .0001, n = 120) for low, low + interrupt and high complexity scenarios respectively. Incorrect CDS increased omission errors by 33.3% (p < .0001, n = 120), 24.5% (p < .009, n = 82), and 26.7% (p < .0001, n = 120). Participants made commission errors, 65.8% (p < .0001, n = 120), 53.5% (p < .0001, n = 82), and 51.7% (p < .0001, n = 120). Task complexity and interruptions had no impact on AB. This study found evidence of AB omission and commission errors in e-prescribing. Verification of CDS alerts is key to avoiding AB errors. However, interventions focused on this have had limited success to date. Clinicians should remain vigilant to the risks of CDS failures and verify CDS.

Nanoniobia modification of CdS photoanode for an efficient and stable photoelectrochemical cell.

PubMed

Pareek, Alka; Paik, Pradip; Borse, Pramod H

2014-12-30

Herein we report the surface modification of a CdS film by niobia nanoparticles via thioglycerol as an organic linker and thus fabricate an efficient and a stable photoanode for a photoelectrochemical (PEC) cell. We have synthesized three differenly sized (∼3, ∼6 ,and ∼9 nm) niobia nanoparticles by a hydrothermal synthesis approach and have further investigated the particle-size-dependent PEC performance of the nanoparticle-modified CdS photoanode. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) confirm the formation of Nb2O5 nanoparticles that are prepared via decomposition of the niobium peroxo complex during the hydrothermal reaction and reveal the presence of surface OH(-) groups over niobia nanoparticles that impart a high catalytic property to a material. The nano-Nb2O5-modified photoanode displayed a 23-fold higher power conversion efficiency compared to that of CdS. This modified structure increases the open circuit voltage (OCV) from 0.65 to 0.77 V, which is attributed to the nano-Nb2O5-induced surface passivation effect over bare CdS. Linking of nanoparticles on the CdS surface improves the photocorrosion stability of the CdS photoanode for even longer than 4 h in contrast to the tens of minutes for the base CdS surface. The uniform coverage of the CdS photoanode surface by niobia nanoparticles is thus found to be the controlling parameter for achieving a higher PEC performance and stability of the photoanode. This finding directed us to design an improved CdS photoanode for efficient and prolonged PEC hydrogen generation from a PEC cell.

Antimanic-like activity of candesartan in mice: Possible involvement of antioxidant, anti-inflammatory and neurotrophic mechanisms.

PubMed

de Souza Gomes, Júlia Ariana; de Souza, Greicy Coelho; Berk, Michael; Cavalcante, Lígia Menezes; de Sousa, Francisca Cléa F; Budni, Josiane; de Lucena, David Freitas; Quevedo, João; Carvalho, André F; Macêdo, Danielle

2015-11-01

Activation of the brain angiotensin II type 1 receptor (AT1R) triggers pro-oxidant and pro-inflammatory mechanisms which are involved in the neurobiology of bipolar disorder (BD). Candesartan (CDS) is an AT1 receptor antagonist with potential neuroprotective properties. Herein we investigated CDS effects against oxidative, neurotrophic inflammatory and cognitive effects of amphetamine (AMPH)-induced mania. In the reversal protocol adult mice were given AMPH 2 mg/kg i.p. or saline and between days 8 and 14 received CDS 0.1, 0.3 or 1 mg/kg orally, lithium (Li) 47.5 mg/kg i.p., or saline. In the prevention treatment, mice were pretreated with CDS, Li or saline prior to AMPH. Locomotor activity and working memory performance were assessed. Glutathione (GSH), thiobarbituric acid-reactive substance (TBARS) and TNF-α levels were evaluated in the hippocampus (HC) and cerebellar vermis (CV). Brain-derived neurotrophic factor (BDNF) and glycogen synthase kinase 3-beta (GSK-3beta) levels were measured in the HC. CDS and Li prevented and reversed the AMPH-induced increases in locomotor activity. Only CDS prevented and reversed AMPH-induced working memory deficits. CDS prevented AMPH-induced alterations in GSH (HC and CV), TBARS (HC and CV), TNF-α (HC and CV) and BDNF (HC) levels. Li prevented alterations in BDNF and phospho-Ser9-GSK3beta. CDS reversed AMPH-induced alterations in GSH (HC and CV), TBARS (HC), TNF-α (CV) and BDNF levels. Li reversed AMPH-induced alterations in TNF-α (HC and CV) and BDNF (HC) levels. CDS is effective in reversing and preventing AMPH-induced behavioral and biochemical alterations, providing a rationale for the design of clinical trials investigating CDS׳s possible therapeutic effects. Copyright © 2015 Elsevier B.V. and ECNP. All rights reserved.

Structural and Optical Properties of Core-Shell TiO2/CdS Prepared by Chemical Bath Deposition

NASA Astrophysics Data System (ADS)

Al-Jawad, Selma M. H.

2017-10-01

Titanium dioxide (TiO2) nanorod arrays (NRAs) sensitized with cadmium sulfide (CdS) nanoparticles (NPs) were deposited by chemical bath deposition (CBD). TiO2 NRAs were also obtained by using the same method on glass substrates coated with fluorine-doped tin oxide (FTO). The structure of the FTO/TiO2/CdS core-shell was characterized by x-ray diffraction (XRD), atomic force microscopy, scanning electron microscopy, ultraviolet-visible (UV-Vis) absorption spectroscopy, photoluminescence, and photoelectrocatalysis of FTO/TiO2 and FTO/TiO2/CdS. The FTO/TiO2 conformed to anatase and rutile phase structures for different pH values and also with annealing. XRD patterns of the FTO/TiO2/CdS sample exhibited two peaks corresponding to hexagonal (100) and (101) for CdS. Scanning electron micrographs showed nanorod structures for the TiO2 thin films deposited at a pH value equal 0.7. Optical results showed the CdS deposited on nanorod TiO2 exhibited increased absorption ability in the visible light, indicating an increased photocatalytic activity for TiO2/CdS core-shell nanorods in the visible light. When illuminated with a UV-Vis light source, the TiO2/CdS core-shell films displayed high responses. A composite exists between the TiO2 nanostructure and CdS NPs because the film absorbs the incident light located in both the visible and UV-Vis regions. A higher response to UV-Vis light was attained with the use of TiO2 NRAs/CdS NPs films prepared by CBD. This approach offers a technique for fabricating photoelectrodes.

Representation of DNA sequences with virtual potentials and their processing by (SEQREP) Kohonen self-organizing maps.

PubMed

Aires-de-Sousa, João; Aires-de-Sousa, Luisa

2003-01-01

We propose representing individual positions in DNA sequences by virtual potentials generated by other bases of the same sequence. This is a compact representation of the neighbourhood of a base. The distribution of the virtual potentials over the whole sequence can be used as a representation of the entire sequence (SEQREP code). It is a flexible code, with a length independent of the sequence size, does not require previous alignment, and is convenient for processing by neural networks or statistical techniques. To evaluate its biological significance, the SEQREP code was used for training Kohonen self-organizing maps (SOMs) in two applications: (a) detection of Alu sequences, and (b) classification of sequences encoding for HIV-1 envelope glycoprotein (env) into subtypes A-G. It was demonstrated that SOMs clustered sequences belonging to different classes into distinct regions. For independent test sets, very high rates of correct predictions were obtained (97% in the first application, 91% in the second). Possible areas of application of SEQREP codes include functional genomics, phylogenetic analysis, detection of repetitions, database retrieval, and automatic alignment. Software for representing sequences by SEQREP code, and for training Kohonen SOMs is made freely available from http://www.dq.fct.unl.pt/qoa/jas/seqrep. Supplementary material is available at http://www.dq.fct.unl.pt/qoa/jas/seqrep/bioinf2002

CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments.

PubMed

Zhou, Carol L Ecale

2015-01-01

In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many multiple sequence alignment derived from a set of structure or sequence alignments, and a need was evident for creating such a tool for combining pairwise structure alignments that would allow for insertion of gaps in the reference structure. This report describes a new Python code, CombAlign, which takes as input a set of pairwise sequence alignments (which may be structure based) and generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA). The use and utility of CombAlign was demonstrated by generating gapped MSSAs using sets of pairwise structure-based sequence alignments between structure models of the matrix protein (VP40) and pre-small/secreted glycoprotein (sGP) of Reston Ebolavirus and the corresponding proteins of several other filoviruses. The gapped MSSAs revealed structure-based residue-residue correspondences, which enabled identification of structurally similar versus differing regions in the Reston proteins compared to each of the other corresponding proteins. CombAlign is a new Python code that generates a one-to-many, gapped, multiple structure- or sequence-based sequence alignment (MSSA) given a set of pairwise sequence alignments (which may be structure based). CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related proteins. CombAlign was developed in Python 2.6, and the source code is available for download from the GitHub code repository.

Complete Coding Genome Sequence for Mogiana Tick Virus, a Jingmenvirus Isolated from Ticks in Brazil

DTIC Science & Technology

2017-05-04

and capable of infecting a wide range of animal hosts (1–5). Here, we report the complete coding genome sequence (i.e., only missing portions of...segmented nature of the genome was not under- stood. Therefore, only the two genome segments with detectable sequence homolo- gies to flaviviruses were...originally reported (2). We revisited the data set of Maruyama et al. (2) and assembled the complete coding sequences for all four genome segments. We

Clinical Decision Support: a 25 Year Retrospective and a 25 Year Vision.

PubMed

Middleton, B; Sittig, D F; Wright, A

2016-08-02

The objective of this review is to summarize the state of the art of clinical decision support (CDS) circa 1990, review progress in the 25 year interval from that time, and provide a vision of what CDS might look like 25 years hence, or circa 2040. Informal review of the medical literature with iterative review and discussion among the authors to arrive at six axes (data, knowledge, inference, architecture and technology, implementation and integration, and users) to frame the review and discussion of selected barriers and facilitators to the effective use of CDS. In each of the six axes, significant progress has been made. Key advances in structuring and encoding standardized data with an increased availability of data, development of knowledge bases for CDS, and improvement of capabilities to share knowledge artifacts, explosion of methods analyzing and inferring from clinical data, evolution of information technologies and architectures to facilitate the broad application of CDS, improvement of methods to implement CDS and integrate CDS into the clinical workflow, and increasing sophistication of the end-user, all have played a role in improving the effective use of CDS in healthcare delivery. CDS has evolved dramatically over the past 25 years and will likely evolve just as dramatically or more so over the next 25 years. Increasingly, the clinical encounter between a clinician and a patient will be supported by a wide variety of cognitive aides to support diagnosis, treatment, care-coordination, surveillance and prevention, and health maintenance or wellness.

Antimicrobial activity, cytotoxicity and DNA binding studies of carbon dots

NASA Astrophysics Data System (ADS)

Jhonsi, Mariadoss Asha; Ananth, Devanesan Arul; Nambirajan, Gayathri; Sivasudha, Thilagar; Yamini, Rekha; Bera, Soumen; Kathiravan, Arunkumar

2018-05-01

In recent years, quantum dots (QDs) are one of the most promising nanomaterials in life sciences community due to their unexploited potential in biomedical applications; particularly in bio-labeling and sensing. In the advanced nanomaterials, carbon dots (CDs) have shown promise in next generation bioimaging and drug delivery studies. Therefore the knowledge of the exact nature of interaction with biomolecules is of great interest to designing better biosensors. In this study, the interaction between CDs derived from tamarind and calf thymus DNA (ct-DNA) has been studied by vital spectroscopic techniques, which revealed that the CDs could interact with DNA via intercalation. The apparent association constant has been deduced from the absorption spectral changes of ct-DNA-CDs using the Benesi-Hildebrand equation. From the DNA induced emission quenching experiments the apparent DNA binding constant of the CDs (Kapp) have also been evaluated. Furthermore, we have analyzed the antibacterial and antifungal activity of CDs using disc diffusion assay method which exhibited excellent activity against E. coli and C. albicans with inhibition zone in the range of 7-12 mm. The biocompatible nature of CDs was confirmed by an in vitro cytotoxicity test on L6 normal rat myoblast cells by using MTT assay. The cell viability is not affected till the high dosage of CDs (200 μg/mL) for >48 h. As a consequence of the work, future development of CDs for microbial control and DNA sensing among the various biomolecules is possible in view of emerging biofields.

Effect of silver doping on the elastic properties of CdS nanoparticles

NASA Astrophysics Data System (ADS)

Dey, P. C.; Das, R.

2018-05-01

CdS and Ag doped CdS (CdS/Ag) nanoparticles have been prepared via chemical method from a Cadmium acetate precursor and Thiourea. The synthesized CdS and CdS/Ag nanoparticles have been characterized by the X-ray Diffraction and High Resolution Transmission Electron Microscope. Here, these nanoparticles have been synthesized at room temperature and all the characterization have also been done at room temperature only. The XRD results reveal that the products are crystalline with cubic zinc blende structure. HRTEM images show that the prepared nanoparticles are nearly spherical in shape. Williamson-Hall method and Size-Strain Plot (SSP) have been used to study the individual contribution of crystalline sizes and lattice strain on the peak broadening of the CdS and CdS/Ag nanoparticles. The different modified model of Williamson-Hall method such as, uniform deformation model, uniform stress deformation model and uniform energy density deformation model and SSP method have been used to calculate the different physical parameter such as lattice strain, stress and energy density for all diffraction peaks of the XRD, corresponding to the CdS and silver doped CdS (CdS/Ag). The obtained results reveal that the average particle size of the prepared CdS and CdS/Ag nanoparticles estimated from the HRTEM images, Williamson-Hall analysis and SSP method are highly correlated with each other. Further, all these result confirms that doping of Ag significantly affects the elastic properties of CdS.

Tricolor White-Light-Emitting Carbon Dots with Multiple-Cores@Shell Structure for WLED Application.

PubMed

Zhang, Tianyi; Zhao, Feifei; Li, Li; Qi, Bin; Zhu, Dongxia; Lü, Jianhua; Lü, Changli

2018-06-13

The past few years have witnessed the rapid development of carbon dots (CDs) due to their outstanding optical properties and a wide range of applications. However, the design and control of CDs with long-wavelength multicolor emission are still huge challenges to be addressed for their practical use in different fields. Here, novel nitrogen-doped multiple-core@shell-structured AC-CDs with tricolor emissions of red, green, and blue were constructed via one-pot hydrothermal method from 5-amino-1,10-phenanthroline and citric acid as reactants and the growth process of AC-CDs was monitored with the reaction time in the synthetic system. The origin of different fluorescence emissions was explored using the unique coordination ability of the surface groups of AC-CDs. An obvious concentration dependence of fluorescent properties was observed for the as-prepared AC-CDs, and a highly fluorescent quantum yield (QY) of 67% for red emission at 630 nm can be obtained by adjusting concentration of AC-CDs. The pure white-light emission (0.33, 0.33; Commission Internationale de l'Elcairage coordinate) was carried out from single carbon dot with QY of 29% through regulation of the excitation and concentration of multiple-core@shell-structured AC-CDs. In addition, because of their excellent photoluminescent properties, the white-emitting AC-CDs as emitting phosphor can be easily used in the fabrication of white-light-emitting diode with good anti-photobleaching and temperature stability.

Turn-off fluorescence sensor for the detection of ferric ion in water using green synthesized N-doped carbon dots and its bio-imaging.

PubMed

Edison, Thomas Nesakumar Jebakumar Immanuel; Atchudan, Raji; Shim, Jae-Jin; Kalimuthu, Senthilkumar; Ahn, Byeong-Cheol; Lee, Yong Rok

2016-05-01

This paper reports turn-off fluorescence sensor for Fe(3+) ion in water using fluorescent N-doped carbon dots as a probe. A simple and efficient hydrothermal carbonization of Prunus avium fruit extract for the synthesis of fluorescent nitrogen-doped carbon dots (N-CDs) is described. This green approach proceeds quickly and provides good quality N-CDs. The mean size of synthesized N-CDs was approximately 7nm calculated from the high-resolution transmission electron microscopic images. X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy revealed the presence of -OH, -NH2, -COOH, and -CO functional groups over the surface of CDs. The N-CDs showed excellent fluorescent properties, and emitted blue fluorescence at 411nm upon excitation at 310nm. The calculated quantum yield of the synthesized N-CDs is 13% against quinine sulfate as a reference fluorophore. The synthesized N-CDs were used as a fluorescent probe towards the selective and sensitive detection of biologically important Fe(3+) ions in water by fluorescence spectroscopy and for bio-imaging of MDA-MB-231 cells. The limit of detection (LOD) and the Stern-Volmer quenching constant for the synthesized N-CDs were 0.96μM and 2.0958×10(3)M of Fe(3+) ions. The green synthesized N-CDs are efficiently used as a promising candidate for the detection of Fe(3+) ions and bio-imaging. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantized phase coding and connected region labeling for absolute phase retrieval.

PubMed

Chen, Xiangcheng; Wang, Yuwei; Wang, Yajun; Ma, Mengchao; Zeng, Chunnian

2016-12-12

This paper proposes an absolute phase retrieval method for complex object measurement based on quantized phase-coding and connected region labeling. A specific code sequence is embedded into quantized phase of three coded fringes. Connected regions of different codes are labeled and assigned with 3-digit-codes combining the current period and its neighbors. Wrapped phase, more than 36 periods, can be restored with reference to the code sequence. Experimental results verify the capability of the proposed method to measure multiple isolated objects.

Functional interrogation of non-coding DNA through CRISPR genome editing

PubMed Central

Canver, Matthew C.; Bauer, Daniel E.; Orkin, Stuart H.

2017-01-01

Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA. PMID:28288828

Violations of exhibiting and FDA rules at an American Psychiatric Association annual meeting.

PubMed

Lurie, Peter; Tran, Tung; Wolfe, Sidney Manuel; Goodman, Robert

2005-12-01

We conducted a cross-sectional study of all exhibit booths for the 24 pharmaceutical companies at the 2002 American Psychiatric Association (APA) convention. We collected and categorized one of each item distributed by the companies at each booth. A total of 268 items were collected from 24 companies (median=8). The most common categories of items were "reprints or pamphlets" (37%) and "noneducational gifts" (27%), including music CDs and invitations to dinners and museums. There were a total of 16 violations of the APA's own exhibit rules: eight companies had one violation and two companies had four violations. Four companies engaged in FDA-prohibited off-label promotion; one also violated the APA code. Over half of all companies (54%) were in violation of either APA rules or FDA regulations. The APA's voluntary code has failed to adequately reduce inappropriate promotional activity at the annual APA meeting.

Memorization of Sequences of Movements of the Right or the Left Hand by Right- and Left-Handers: Vector Coding.

PubMed

Bobrova, E V; Bogacheva, I N; Lyakhovetskii, V A; Fabinskaja, A A; Fomina, E V

2017-01-01

In order to test the hypothesis of hemisphere specialization for different types of information coding (the right hemisphere, for positional coding; the left one, for vector coding), we analyzed the errors of right and left-handers during a task involving the memorization of sequences of movements by the left or the right hand, which activates vector coding by changing the order of movements in memorized sequences. The task was first performed by the right or the left hand, then by the opposite hand. It was found that both'right- and left-handers use the information about the previous movements of the dominant hand, but not of the non-dom" inant one. After changing the hand, right-handers use the information about previous movements of the second hand, while left-handers do not. We compared our results with the data of previous experiments, in which positional coding was activated, and concluded that both right- and left-handers use vector coding for memorizing the sequences of their dominant hands and positional coding for memorizing the sequences of non-dominant hand. No similar patterns of errors were found between right- and left-handers after changing the hand, which suggests that in right- and left-handersthe skills are transferred in different ways depending on the type of coding.

Rapid Synthesis of Carbon Dots by Hydrothermal Treatment of Lignin

PubMed Central

Chen, Wenxin; Hu, Chaofan; Yang, Yunhua; Cui, Jianghu; Liu, Yingliang

2016-01-01

A rapid approach has been developed for the fluorescent carbon dots (CDs) by the hydrothermal treatment of lignin in the presence of H2O2. The as-synthesized CDs were found to emit blue photoluminescence with excellent photostability. Moreover, the CDs displayed biocompatibility, low cytotoxicity, and high water solubility properties. Finally, the as-resulted CDs were demonstrated to be excellent probes for bioimaging and biosensing applications. PMID:28773309

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

Li, Bo; Zhang, Xiaosong, E-mail: zhangxiaosong@tjut.edu.cn; Li, Lan

Trap-rich CdS nanocrystals were synthesized by employing CdSt{sub 2} and sulfur as precursors via thermal decomposition. Furthermore, X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), absorption and photoluminescence (PL) spectra were used to characterize structure, morphology and luminescence properties of CdS nanocrystals (NCs). CdS NCs have a broad emission across 500–700 nm under the excitation of blue light with 460 nm, consequently, white light can be produced by mixing broad emission from CdS NCs excited by blue light, with the remaining blue light. In addition, the broad emission generation is closely and inseparably related to surface defects. Moreover, LaMer modelmore » was used to explain the phenomenon that the intensity of the trap emission gradually decreases as the reaction time increases in contrast with that of the band-edge emission. - Graphical abstract: Trap-rich CdS nanocrystals were synthesized. Furthermore, white light is produced by mixing broad emission across 500–700 nm from CdS NCs excited by blue light, in combination with the remaining blue light. - Highlights: • Trap-rich CdS nanocrystals were synthesized. • CdS NCs have a broad emission across 500–700 nm under the excitation of blue light. • White light can be produced by mixing broad emission with the remaining blue light.« less

One-step hydrothermal synthesis of chiral carbon dots and their effects on mung bean plant growth.

PubMed

Zhang, Mengling; Hu, Lulu; Wang, Huibo; Song, Yuxiang; Liu, Yang; Li, Hao; Shao, Mingwang; Huang, Hui; Kang, Zhenhui

2018-06-27

Chiral compounds/materials have important effects on the growth of plants. Chiral carbon dots (CDs), as an emerging chiral carbon nanomaterial, have great potential in bio-application and bio-nanotechnology. Herein, we report a hydrothermal method to synthesize chiral CDs from cysteine (cys) and citric acid. These chiral CDs were further demonstrated to have systemic effects on the growth of mung bean plants, in which case both l- and d-CDs can promote the growth of the root in mung bean plants, stem length of mung bean sprouts and water absorption of bean seeds. The elongation of mung bean sprouts presented an increasing trend with the treatment of chiral CDs of increasing concentration (below 500 μg mL-1). Furthermore, in the optimal concentration (100 μg mL-1), the l-CDs can improve root vigor and the activity of the Rubisco enzyme of bean sprouts by 8.4% and 20.5%, while the d-CDs increased by 28.9% and 67.5%. Due to more superior properties in improving root vigor and the activity of the Rubisco enzyme of mung bean sprouts, d-CDs are able to enhance photosynthesis better and accumulate more carbohydrate in mung bean plants.

Ultrasensitive detection of amifostine and alkaline phosphatase based on the growth of CdS quantum dots.

PubMed

Na, Weidan; Liu, Siyu; Liu, Xiaotong; Su, Xingguang

2015-11-01

In this study, we reported a simple and sensitive fluorescence nanosensor for rapid detection of amifostine and alkaline phosphatase (ALP). The novel nanosensor was based on the fluorescence "turn on-off" of CdS quantum dots (QDs). Firstly, Cd(2+) cation could react with S(2-) anion to generate fluorescent CdS QDs in the presence of amifostine. The fluorescence (FL) intensity of amifostine-capped CdS QDs (Amifostine-CdS QDs) was increased with the increasing amounts of amifostine, and could be used for amifostine detection. However, amifostine could be converted to 2-(3-aminopropylamino) ethanethiol (WR1065) in the presence of ALP based on the dephosphorylation of ALP. Under the optimum conditions, the affinity of WR1065 to CdS QDs was weaker than that of amifostine. Therefore the new generation of WR1065-CdS QDs would reduce the FL intensity with the increase of ALP concentration, and the fluorescence of CdS QDs was turn off. The metabolic process of amifostine in the presence of alkaline phosphatase could be also studied via the change of FL intensity of CdS QDs. The present method was cost-effective, convenient, and does not require any complicated synthetic procedures. Copyright © 2015 Elsevier B.V. All rights reserved.

One-pot synthesis of CdS nanocrystals hybridized with single-layer transition-metal dichalcogenide nanosheets for efficient photocatalytic hydrogen evolution.

PubMed

Chen, Junze; Wu, Xue-Jun; Yin, Lisha; Li, Bing; Hong, Xun; Fan, Zhanxi; Chen, Bo; Xue, Can; Zhang, Hua

2015-01-19

Exploration of low-cost and earth-abundant photocatalysts for highly efficient solar photocatalytic water splitting is of great importance. Although transition-metal dichalcogenides (TMDs) showed outstanding performance as co-catalysts for the hydrogen evolution reaction (HER), designing TMD-hybridized photocatalysts with abundant active sites for the HER still remains challenge. Here, a facile one-pot wet-chemical method is developed to prepare MS2-CdS (M=W or Mo) nanohybrids. Surprisedly, in the obtained nanohybrids, single-layer MS2 nanosheets with lateral size of 4-10 nm selectively grow on the Cd-rich (0001) surface of wurtzite CdS nanocrystals. These MS2-CdS nanohybrids possess a large number of edge sites in the MS2 layers, which are active sites for the HER. The photocatalytic performances of WS2-CdS and MoS2-CdS nanohybrids towards the HER under visible light irradiation (>420 nm) are about 16 and 12 times that of pure CdS, respectively. Importantly, the MS2-CdS nanohybrids showed enhanced stability after a long-time test (16 h), and 70% of catalytic activity still remained. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

MWCNT/CdS hybrid nanocomposite for enhanced photocatalytic activity

NASA Astrophysics Data System (ADS)

Chaudhary, Deepti; Khare, Neeraj; Vankar, V. D.

2016-05-01

Multi-walled carbon nanotubes (MWCNT)/CdS hybrid nanocomposite were synthesized by one step hydrothermal method. MWCNTs were used as a substrate for the growth of CdS nanoparticles. MWCNT/CdS nanocomposite and pure CdS were characterized by XRD, TEM, UV-vis and photoluminescence spectroscopy. HRTEM study confirms the intimate contact of CdS with MWCNT. The photocatalytic activity of nanocomposite was studied for the degradation of methylene blue dye under UV irradiation. The enhanced photocatalytic activity of MWCNT/CdS nanocomposite as compared to pure CdS has been attributed to reduced recombination of photogenerated charge carriers due to interfacial electron transfer from CdS to MWCNT.

CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison

PubMed Central

Castrignanò, Tiziana; Canali, Alessandro; Grillo, Giorgio; Liuni, Sabino; Mignone, Flavio; Pesole, Graziano

2004-01-01

The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences. Indeed, such sequences are likely to correspond to known or unknown coding exons or regulatory motifs. Here, we present a web server implementing a previously developed algorithm that, by comparing user-submitted genome sequences, is able to identify statistically significant conserved blocks and assess their coding or noncoding nature through the measure of a coding potential score. The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected conserved sequences and annotated gene features. PMID:15215464

CdS nanoparticles immobilized on porous carbon polyhedrons derived from a metal-organic framework with enhanced visible light photocatalytic activity for antibiotic degradation

NASA Astrophysics Data System (ADS)

Yang, Cao; Cheng, Jianhua; Chen, Yuancai; Hu, Yongyou

2017-10-01

The CdS/MOF-derived porous carbon (MPC) composite as an efficient visible-light-driven photocatalyst was prepared through the pyrolysis of ZIF-8 and subsequent growth of CdS. The porous and functionalized MPC enables intimate and discrete growth of CdS nanoparticles. This unique structure not only reduces the bulk recombination owing to nano-size effect of CdS, but also suppresses the surface recombination due to the discrete growth of CdS nanoparticles on MPC polyhedrons, which facilitates electron transfer and charge separation. Moreover, such a composite material possessed good adsorption ability toward the antibiotic pollutants because of the amino-functionalized surface. As a result, the as-prepared CdS/MPC composites showed excellent photocatalytic performance for the antibiotic degradation, significantly improving the photoactivity of CdS. Importantly, the CdS/MPC composite with the CdS loading of 20 wt% exhibited the highest photocatalytic efficiency of approximately 91% and apparent rate constant of 0.024 min-1.

Synthesis of pore-variable mesoporous CdS and evaluation of its photocatalytic activity in degrading methylene blue

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

Zhang, Wei-Min, E-mail: chm_zhangwm@ujn.edu.cn; Jiang, Yao-Quan; Cao, Xiao-Yan

2013-10-15

Graphical abstract: - Highlights: • Self-templated synthesis of tubular CdS. • Cadmium complexes of aliphatic acids sustain the network of mesoporous structures. • Aliphatic acids affect the phase composition and particle size. • Pore size and volume vary with aliphatic acids having different hydrocarbonyl. - Abstract: In this study, mesoporous CdS polycrystallites have been synthesized using aliphatic acids of hexanoic acid, octanoic acid, and oleic acid as coordinating and capping agents, respectively. The fibrous Cd–fatty acid salts act as a template to form the tubular CdS. The organic species are found to be necessary for maintaining the network of mesoporousmore » CdS. The characterization results indicate that the shorter carbon chain length in aliphatic acids favors the wurtzite phase and particle size growth the specific surface area, pore diameter and pore volume show a monotonic raise with increasing carbon chain. The photocatalytic activities of mesoporous CdS tubes exhibit much higher efficiency than those of nanosized CdS powders in decolorizing methylene blue under simulated visible light.« less

Structural and Spectroscopic Studies of Sm3+/CdS Nanocrystallites in Sol-Gel TiO2-ZrO2 Matrix

NASA Astrophysics Data System (ADS)

Karthika, S.; Prathibha, Vasudevan; Ann, Mary K. A.; Viji, Vidyadharan; Biju, P. R.; Unnikrishnan, N. V.

2014-02-01

A sol-gel method was used to prepare titania-zirconia matrices doped with Sm3+/CdS nanocrystallites. The structural properties of the matrices were characterized using transmission electron microscopy (TEM), thermogravimetric analysis (TGA), differential thermal analysis (DTA), and Fourier-transform infrared spectroscopy studies. The thermal stability of the material was determined by TGA/DTA analysis. The absorption spectrum shows the characteristic peaks of the Sm3+ ions and the absorption peak corresponding to the CdS nanocrystallites. The optical bandgap and size of the CdS nanoparticles were calculated from the absorption spectrum. From TEM, the interplanar distance ( d) was estimated to be 3.533 Å, which matches with the (1 0 0) plane of bulk CdS. The measurements yield a nanocrystallite size of around 7.8 nm. The optical absorption and emission spectra confirmed the formation of CdS nanoparticles along with samarium ions in the titania-zirconia matrices. The fluorescence intensity of the samarium ions was found to be greatly enhanced by codoping with CdS nanocrystallites.

Effects of air annealing on CdS quantum dots thin film grown at room temperature by CBD technique intended for photosensor applications

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

Shaikh, Shaheed U.; Desale, Dipalee J.; Siddiqui, Farha Y.

2012-11-15

Graphical abstract: The effect of different intensities (40, 60 100 and 200 W) of light on CdS quantum dots thin film annealed at 350 °C indicating enhancement in (a) photo-current and (b) photosensitivity. Highlights: ► The preparation of CdS nanodot thin film at room temperature by M-CBD technique. ► Study of air annealing on prepared CdS nanodots thin film. ► The optimized annealing temperature for CdS nanodot thin film is 350 °C. ► Modified CdS thin films can be used in photosensor application. -- Abstract: CdS quantum dots thin-films have been deposited onto the glass substrate at room temperature usingmore » modified chemical bath deposition technique. The prepared thin films were further annealed in air atmosphere at 150, 250 and 350 °C for 1 h and subsequently characterized by scanning electron microscopy, ultraviolet–visible spectroscopy, electrical resistivity and I–V system. The modifications observed in morphology and opto-electrical properties of the thin films are presented.« less

Additive interaction of carbon dots extracted from soluble coffee and biogenic silver nanoparticles against bacteria

NASA Astrophysics Data System (ADS)

Andrade, Patricia F.; Nakazato, Gerson; Durán, Nelson

2017-06-01

It is known the presence of carbon dots (CDs) in carbohydrate based foods. CDs extracted from coffee grounds and instant coffee was also published. CDs from soluble coffee revealed an average size of 4.4 nm. CDs were well-dispersed in water, fluorescent and we have characterized by XPS, XRD analysis, fluorescence and by FTIR spectra. The MIC value by serial micro-dilution assays for CDs on S. aureus ATCC 25923 was 250 μg/mL and E. coli ATCC 25922 >1000 ug/mL. For silver nanoparticles biogenically synthesized was 6.7 μg/mL. Following the checkerboard assay with combining ½ MIC values of the MICs of 125 μg/mL of carbon dots and 3.4 μg/mL of silver nanoparticles, following the fractionated inhibitory concentration (FIC) index methodology, on S. aureus gave a fractionated inhibitory concentration (FIC) value of 1.0, meaning additive interaction. In general, the unfunctionalized CDs showed to be inefficient as antibacterial compounds, however the CDs extracted from Coffee powder and together silver nanoparticles appeared interesting as antibacterial association.

Damage tolerance protein Mus81 associates with the FHA1 domain of checkpoint kinase Cds1.

PubMed

Boddy, M N; Lopez-Girona, A; Shanahan, P; Interthal, H; Heyer, W D; Russell, P

2000-12-01

Cds1, a serine/threonine kinase, enforces the S-M checkpoint in the fission yeast Schizosaccharomyces pombe. Cds1 is required for survival of replicational stress caused by agents that stall replication forks, but how Cds1 performs these functions is largely unknown. Here we report that the forkhead-associated-1 (FHA1) protein-docking domain of Cds1 interacts with Mus81, an evolutionarily conserved damage tolerance protein. Mus81 has an endonuclease homology domain found in the XPF nucleotide excision repair protein. Inactivation of mus81 reveals a unique spectrum of phenotypes. Mus81 enables survival of deoxynucleotide triphosphate starvation, UV radiation, and DNA polymerase impairment. Mus81 is essential in the absence of Bloom's syndrome Rqh1 helicase and is required for productive meiosis. Genetic epistasis studies suggest that Mus81 works with recombination enzymes to properly replicate damaged DNA. Inactivation of Mus81 triggers a checkpoint-dependent delay of mitosis. We propose that Mus81 is involved in the recruitment of Cds1 to aberrant DNA structures where Cds1 modulates the activity of damage tolerance enzymes.

Primer development to obtain complete coding sequence of HA and NA genes of influenza A/H3N2 virus.

PubMed

Agustiningsih, Agustiningsih; Trimarsanto, Hidayat; Setiawaty, Vivi; Artika, I Made; Muljono, David Handojo

2016-08-30

Influenza is an acute respiratory illness and has become a serious public health problem worldwide. The need to study the HA and NA genes in influenza A virus is essential since these genes frequently undergo mutations. This study describes the development of primer sets for RT-PCR to obtain complete coding sequence of Hemagglutinin (HA) and Neuraminidase (NA) genes of influenza A/H3N2 virus from Indonesia. The primers were developed based on influenza A/H3N2 sequence worldwide from Global Initiative on Sharing All Influenza Data (GISAID) and further tested using Indonesian influenza A/H3N2 archived samples of influenza-like illness (ILI) surveillance from 2008 to 2009. An optimum RT-PCR condition was acquired for all HA and NA fragments designed to cover complete coding sequence of HA and NA genes. A total of 71 samples were successfully sequenced for complete coding sequence both of HA and NA genes out of 145 samples of influenza A/H3N2 tested. The developed primer sets were suitable for obtaining complete coding sequences of HA and NA genes of Indonesian samples from 2008 to 2009.

GATA: A graphic alignment tool for comparative sequenceanalysis

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

Nix, David A.; Eisen, Michael B.

2005-01-01

Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dotplot analysis is often used to estimate non-coding sequence relatedness. Yet dotmore » plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments.« less

Phylogenetic Network for European mtDNA

PubMed Central

Finnilä, Saara; Lehtonen, Mervi S.; Majamaa, Kari

2001-01-01

The sequence in the first hypervariable segment (HVS-I) of the control region has been used as a source of evolutionary information in most phylogenetic analyses of mtDNA. Population genetic inference would benefit from a better understanding of the variation in the mtDNA coding region, but, thus far, complete mtDNA sequences have been rare. We determined the nucleotide sequence in the coding region of mtDNA from 121 Finns, by conformation-sensitive gel electrophoresis and subsequent sequencing and by direct sequencing of the D loop. Furthermore, 71 sequences from our previous reports were included, so that the samples represented all the mtDNA haplogroups present in the Finnish population. We found a total of 297 variable sites in the coding region, which allowed the compilation of unambiguous phylogenetic networks. The D loop harbored 104 variable sites, and, in most cases, these could be localized within the coding-region networks, without discrepancies. Interestingly, many homoplasies were detected in the coding region. Nucleotide variation in the rRNA and tRNA genes was 6%, and that in the third nucleotide positions of structural genes amounted to 22% of that in the HVS-I. The complete networks enabled the relationships between the mtDNA haplogroups to be analyzed. Phylogenetic networks based on the entire coding-region sequence in mtDNA provide a rich source for further population genetic studies, and complete sequences make it easier to differentiate between disease-causing mutations and rare polymorphisms. PMID:11349229

Effects of experimental conditions on the morphologies, structures and growth modes of pulsed laser-deposited CdS nanoneedles

PubMed Central

2014-01-01

CdS nanoneedles with different morphologies, structures, and growth modes have been grown on Ni-coated Si(100) surface under different experimental conditions by pulsed laser deposition method. The effects of catalyst layer, substrate temperature, and laser pulse energy on the growth of the CdS nanoneedles were studied in detail. It was confirmed that the formation of the molten catalyst spheres is the key to the nucleation of the CdS nanoneedles by observing the morphologies of the Ni catalyst thin films annealed at different substrate temperatures. Both the substrate temperature and laser pulse energy strongly affected the growth modes of the CdS nanoneedles. The secondary growth of the smaller nanoneedles on the top of the main nanoneedles was found at appropriate conditions. A group of more completed pictures of the growth modes of the CdS nanoneedles were presented. PMID:24559455

Recommendations for Clinical Decision Support Deployment: Synthesis of a Roundtable of Medical Directors of Information Systems

PubMed Central

Jenders, Robert A.; Osheroff, Jerome A.; Sittig, Dean F.; Pifer, Eric A.; Teich, Jonathan M

2007-01-01

Background: Ample evidence exists that clinical decision support (CDS) can improve clinician performance. Nevertheless, additional evidence demonstrates that clinicians still do not perform adequately in many instances. This suggests an ongoing need for implementation of CDS, in turn prompting development of a roadmap for national action regarding CDS. Objective: Develop practical advice to aid CDS implementation in order to improve clinician performance. Method: Structured group interview during a roundtable discussion by medical directors of information systems (N = 30), with subsequent review by participants and synthesis. Results: Participant consensus was that CDS should be comprehensive and should involve techniques such as order sets and facilitated documentation as well as alerts; should be subject to ongoing feedback; and should flow from and be governed by an organization’s clinical goals. Conclusion: A structured roundtable discussion of clinicians experienced in health information technology can yield practical, consensus advice for implementation of CDS. PMID:18693858

Hydrothermal synthesis of nitrogen-doped carbon dots with real-time live-cell imaging and blood-brain barrier penetration capabilities.

PubMed

Lu, Shousi; Guo, Shanshan; Xu, Pingxiang; Li, Xiaorong; Zhao, Yuming; Gu, Wei; Xue, Ming

Nitrogen-doped carbon dots (N-CDs) were synthesized using a one-pot hydrothermal treatment with citric acid in the presence of polyethylenimine. Transmission electron microscopy analysis revealed that the N-CDs were monodispersed and quasi-spherical with an average size of ~2.6 nm. Under ultraviolet irradiation the N-CDs emitted a strong blue luminescence with a quantum yield as high as 51%. Moreover, the N-CDs exhibited a negligible cytotoxicity and could be applied as efficient nanoprobes for real-time imaging of live cells. In addition, the ability of the N-CDs to cross the blood-brain barrier (BBB) in a concentration-dependent manner was demonstrated using an in vitro BBB model. Therefore, these PEI-passivated N-CDs with real-time live-cell imaging and BBB-penetration capabilities hold promise for traceable drug delivery to the brain.

Highly fluorescent carbon dots for visible sensing of doxorubicin release based on efficient nanosurface energy transfer.

PubMed

Wang, Beibei; Wang, Shujun; Wang, Yanfang; Lv, Yan; Wu, Hao; Ma, Xiaojun; Tan, Mingqian

2016-01-01

To prepare fluorescent carbon dots for loading cationic anticancer drug through donor-quenched nanosurface energy transfer in visible sensing of drug release. Highly fluorescent carbon dots (CDs) were prepared by a facile hydrothermal approach from citric acid and o-phenylenediamine. The obtained CDs showed a high quantum yield of 46 % and exhibited good cytocompatibility even at 1 mg/ml. The cationic anticancer drug doxorubicin (DOX) can be loaded onto the negatively charged CDs through electrostatic interactions. Additionally, the fluorescent CDs feature reversible donor-quenched mode nanosurface energy transfer. When loading the energy receptor DOX, the donor CDs' fluorescence was switched "off", while it turned "on" again after DOX release from the surface through endocytic uptake. Most DOX molecules were released from the CDs after 6 h incubation and entered cell nuclear region after 8 h, suggesting the drug delivery system may have potential for visible sensing in drug release.

One-pot synthesis of fluorescent nitrogen-doped carbon dots with good biocompatibility for cell labeling.

PubMed

Zhang, Zhengwei; Yan, Kun; Yang, Qiulian; Liu, Yanhua; Yan, Zhengyu; Chen, Jianqiu

2017-12-01

Here we report an easy and economical hydrothermal carbonization approach to synthesize the fluorescent nitrogen-doped carbon dots (N-CDs) that was developed using citric acid and triethanolamine as the precursors. The synthesis conditions were optimized to obtain the N-CDs with superior fluorescence performances. The as-prepared N-CDs are monodispersed sphere nanoparticles with good water solubility, and exhibited strong fluorescence, favourable photostability and excitation wavelength-dependent behavior. Furthermore, the in vitro cytotoxicity and cellular labeling of N-CDs were investigated using the rat glomerular mesangial cells. The results showed the N-CDs have more inconspicuous cytotoxicity and better biosafety in comparison with ZnSe quantum dots, although both targeted the cells successfully. Considering their admirable photostability, low toxicity and good compatibility, the as-obtained N-CDs could have potential applications in biosensors, cellular imaging, and other fields. Copyright © 2017 John Wiley & Sons, Ltd.

Hydrothermal synthesis of nitrogen-doped carbon dots with real-time live-cell imaging and blood–brain barrier penetration capabilities

PubMed Central

Lu, Shousi; Guo, Shanshan; Xu, Pingxiang; Li, Xiaorong; Zhao, Yuming; Gu, Wei; Xue, Ming

2016-01-01

Nitrogen-doped carbon dots (N-CDs) were synthesized using a one-pot hydrothermal treatment with citric acid in the presence of polyethylenimine. Transmission electron microscopy analysis revealed that the N-CDs were monodispersed and quasi-spherical with an average size of ~2.6 nm. Under ultraviolet irradiation the N-CDs emitted a strong blue luminescence with a quantum yield as high as 51%. Moreover, the N-CDs exhibited a negligible cytotoxicity and could be applied as efficient nanoprobes for real-time imaging of live cells. In addition, the ability of the N-CDs to cross the blood–brain barrier (BBB) in a concentration-dependent manner was demonstrated using an in vitro BBB model. Therefore, these PEI-passivated N-CDs with real-time live-cell imaging and BBB-penetration capabilities hold promise for traceable drug delivery to the brain. PMID:27932880

[Screening for depersonalization-derealization with two items of the cambridge depersonalization scale].

PubMed

Michal, Matthias; Zwerenz, Rüdiger; Tschan, Regine; Edinger, Jens; Lichy, Marcel; Knebel, A; Tuin, Inka; Beutel, Manfred

2010-05-01

Depersonalization (DP) and derealization (DR) are considered to be highly underdiagnosed. Therefore the development of screening instruments is important. From the Cambridge Depersonalization Scale (CDS) two items were extracted discriminating best patients with clinical significant DP from patients without DP. These two Items were assembled to a short version of the CDS. This short version (CDS-2) was tested in a sample of 38 patients with clinical significant DP-DR and 49 patients without or only mild DP-DR. Scores were compared against clinical diagnoses based on a structured interview (gold standard). The CDS-2 was able to differentiate patients with clinical significant DP well from other groups (cut-off of CDS-2>or=3, sensitivity=78.9%, specifity=85.7%) and also showed high reliability (Cronbachs alpha=0.92). Therefore the CDS-2 can be considered as a useful tool for screening and identification of DP-DR.

Resources and rewards for clerkship directors: how surgery compares.

PubMed

Ephgrave, Kimberly; Ferguson, Kristi; Shaaban, Aimen; Hoshi, Hisakazu

2010-01-01

Clerkship directors (CDs) are key educators and active clinicians. In 2003, the Alliance for Clinical Education published standards for CD resources and responsibilities, but how reality compares is unknown. Representatives from each core clinical disciplines' CD organizations created an electronic survey that CDs received in 2006-2007. More than 500 CDs responded, including 71 surgeons. Surgeons reported spending approximately 27% of professional time on education. Most have codirectors, so total CD effort approximates the greater than 50% Alliance for Clinical Education guidelines. No disciplines' CDs have more than one support staff as recommended. Surgeons have the least clinic time, but the most inpatient weeks and many publications. Surgery CD concerns are curricula and simulation; few believe being a CD impairs academic advancement and more than 95% believe it enhances work satisfaction. Surgery CDs are clinically active and academically productive. Although few surgery CDs have the recommended support staff, more than 95% report being a CD enhances work satisfaction.

Cultivating Fluorescent Flowers with Highly Luminescent Carbon Dots Fabricated by a Double Passivation Method.

PubMed

Han, Shuai; Chang, Tao; Zhao, Haiping; Du, Huanhuan; Liu, Shan; Wu, Baoshuang; Qin, Shenjun

2017-07-07

In this work, we present the fabrication of highly luminescent carbon dots (CDs) by a double passivation method with the assistance of Ca(OH)₂. In the reaction process, Ca 2+ protects the active functional groups from overconsumption during dehydration and carbonization, and the electron-withdrawing groups on the CD surface are converted to electron-donating groups by the hydroxyl ions. As a result, the fluorescence quantum yield of the CDs was found to increase with increasing Ca(OH)₂ content in the reaction process. A blue-shift optical spectrum of the CDs was also found with increasing Ca(OH)₂ content, which could be attributed to the increasing of the energy gaps for the CDs. The highly photoluminescent CDs obtained (quantum yield: 86%) were used to cultivate fluorescent carnations by a water culture method, while the results of fluorescence microscopy analysis indicated that the CDs had entered the plant tissue structure.

RY-Coding and Non-Homogeneous Models Can Ameliorate the Maximum-Likelihood Inferences From Nucleotide Sequence Data with Parallel Compositional Heterogeneity.

PubMed

Ishikawa, Sohta A; Inagaki, Yuji; Hashimoto, Tetsuo

2012-01-01

In phylogenetic analyses of nucleotide sequences, 'homogeneous' substitution models, which assume the stationarity of base composition across a tree, are widely used, albeit individual sequences may bear distinctive base frequencies. In the worst-case scenario, a homogeneous model-based analysis can yield an artifactual union of two distantly related sequences that achieved similar base frequencies in parallel. Such potential difficulty can be countered by two approaches, 'RY-coding' and 'non-homogeneous' models. The former approach converts four bases into purine and pyrimidine to normalize base frequencies across a tree, while the heterogeneity in base frequency is explicitly incorporated in the latter approach. The two approaches have been applied to real-world sequence data; however, their basic properties have not been fully examined by pioneering simulation studies. Here, we assessed the performances of the maximum-likelihood analyses incorporating RY-coding and a non-homogeneous model (RY-coding and non-homogeneous analyses) on simulated data with parallel convergence to similar base composition. Both RY-coding and non-homogeneous analyses showed superior performances compared with homogeneous model-based analyses. Curiously, the performance of RY-coding analysis appeared to be significantly affected by a setting of the substitution process for sequence simulation relative to that of non-homogeneous analysis. The performance of a non-homogeneous analysis was also validated by analyzing a real-world sequence data set with significant base heterogeneity.

Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii.

PubMed

Suyama, Mikita; Lathe, Warren C; Bork, Peer

2005-10-10

We have identified 141 novel palindromic repetitive elements in the genome of euryarchaeon Methanocaldococcus jannaschii. The total length of these elements is 14.3kb, which corresponds to 0.9% of the total genomic sequence and 6.3% of all extragenic regions. The elements can be divided into three groups (MJRE1-3) based on the sequence similarity. The low sequence identity within each of the groups suggests rather old origin of these elements in M. jannaschii. Three MJRE2 elements were located within the protein coding regions without disrupting the coding potential of the host genes, indicating that insertion of repeats might be a widespread mechanism to enhance sequence diversity in coding regions.

Reliability and validity of a Japanese version of the Cambridge depersonalization scale as a screening instrument for depersonalization disorder.

PubMed

Sugiura, Miyuki; Hirosawa, Masataka; Tanaka, Sumio; Nishi, Yasunobu; Yamada, Yasuyuki; Mizuno, Motoki

2009-06-01

The Cambridge Depersonalization Scale (CDS) is an instrument that has obtained reliability and validity in some countries for use in detecting depersonalization disorder under clinical conditions, but not yet in Japan under non-psychiatric conditions. The purposes of this study were to develop a Japanese version of the CDS (J-CDS) and to examine its reliability and validity as an instrument for screening depersonalization disorder under non-clinical conditions. The CDS was translated from English into Japanese and then back-translated into English by a native English-speaking American. After making the J-CDS, we examined its reliability and validity. Questionnaires that were composed of J-CDS, the Dissociative Experience Scale (DES), the Zung self-rating scale and the Maudsley Obsessional-Compulsive Inventory were administrated to 59 participants (12 patients with depersonalization disorder, 11 individuals who had recovered from depersonalization and 36 healthy controls). Cronbach's alpha and split-half reliability were 0.94 and 0.93, respectively. The J-CDS score in the depersonalization group was significantly higher than in the healthy control group. The J-CDS score was significantly correlated with scores of total DES, and DES-depersonalization. The best compromise between the true positive and false negative rate was at a cut-off point of 60, yielding a sensitivity of 1.00 and a specificity of 0.96. In this study, J-CDS showed good reliability and validity. The best cut-off point, when we use this for distinguishing individuals with depersonalization disorder from individuals without psychiatric disorders, is 60 points.

Evaluation of the Effect of Decision Support on the Efficiency of Primary Care Providers in the Outpatient Practice

PubMed Central

Hankey, Ronald A.; Decker, Lindsay K.; Cha, Stephen S.; Greenes, Robert A.; Liu, Hongfang; Chaudhry, Rajeev

2015-01-01

Background: Clinical decision support (CDS) for primary care has been shown to improve delivery of preventive services. However, there is little evidence for efficiency of physicians due to CDS assistance. In this article, we report a pilot study for measuring the impact of CDS on the time spent by physicians for deciding on preventive services and chronic disease management. Methods: We randomly selected 30 patients from a primary care practice, and assigned them to 10 physicians. The physicians were requested to perform chart review to decide on preventive services and chronic disease management for the assigned patients. The patients assignment was done in a randomized crossover design, such that each patient received 2 sets of recommendations—one from a physician with CDS assistance and the other from a different physician without CDS assistance. We compared the physician recommendations made using CDS assistance, with the recommendations made without CDS assistance. Results: The physicians required an average of 1 minute 44 seconds, when they were they had access to the decision support system and 5 minutes when they were unassisted. Hence the CDS assistance resulted in an estimated saving of 3 minutes 16 seconds (65%) of the physicians’ time, which was statistically significant (P < .0001). There was no statistically significant difference in the number of recommendations. Conclusion: Our findings suggest that CDS assistance significantly reduced the time spent by physicians for deciding on preventive services and chronic disease management. The result needs to be confirmed by performing similar studies at other institutions. PMID:25155103

Easy Preparation and Photoelectrochemical Properties of CdS Nanoparticle/Graphene Nanosheet Nanocomposites Using Supercritical Carbon Dioxide.

PubMed

Yan, Shancheng; Xu, Xin; Jiang, Chao; Pan, Lijia; Shi, Yi; Hu, Dong; Cao, Zhenglin

2016-03-01

Graphene nanosheets (GNSs) were modified with CdS nanoparticles (NPs) using supercritical CO2 (SC CO2), which has gas-like diffusivity, low viscosity, and near-zero surface tension. The resulting CdS NP/GNS nanocomposites were characterized by field-emission scanning electron microscopy, transmission electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, Raman spectroscopy, and photoluminescence spectroscopy. Distinct morphologies of CdS NP/GNS nanocomposites decorated on the GNS surface were obtained at different SC CO2 pressures, temperatures, and durations and in different sources. Results showed that the sources and SC CO2 significantly influenced the aggregation or assembly behavior of the CdS NP/GNS nanocomposites on the GNSs. The formation mechanism of the distinct nanohybrid structures was studied by Raman mapping. A difference was noted between the Raman spectra of pristine graphene nanosheets and CdS NP/GNS nanocomposites. This result can be ascribed to the CdS NPs anchored onto the GNS defects and to the improved quality of the GNSs under SC CO2. The photo-current densities of CdS NP/GNS nanocomposites were at least three times higher than that of the pristine CdS NPs at the same applied voltage for photoelectrochemical water splitting. The findings suggested that highly efficient graphene-supported NP photoelectrocatalysts can be fabricated by the supercritical fluid method and that graphene can serve as a favorable photoelectrocatalytic carrier, with promising potential applications in environmental and energy fields. Keywords: Graphene Nanosheets, Cadmium Sulfide, Raman Spectroscopy, Photoelectrochemical.

Clinical Decision Support: a 25 Year Retrospective and a 25 Year Vision

PubMed Central

Sittig, D. F.; Wright, A.

2016-01-01

Summary Objective The objective of this review is to summarize the state of the art of clinical decision support (CDS) circa 1990, review progress in the 25 year interval from that time, and provide a vision of what CDS might look like 25 years hence, or circa 2040. Method Informal review of the medical literature with iterative review and discussion among the authors to arrive at six axes (data, knowledge, inference, architecture and technology, implementation and integration, and users) to frame the review and discussion of selected barriers and facilitators to the effective use of CDS. Result In each of the six axes, significant progress has been made. Key advances in structuring and encoding standardized data with an increased availability of data, development of knowledge bases for CDS, and improvement of capabilities to share knowledge artifacts, explosion of methods analyzing and inferring from clinical data, evolution of information technologies and architectures to facilitate the broad application of CDS, improvement of methods to implement CDS and integrate CDS into the clinical workflow, and increasing sophistication of the end-user, all have played a role in improving the effective use of CDS in healthcare delivery. Conclusion CDS has evolved dramatically over the past 25 years and will likely evolve just as dramatically or more so over the next 25 years. Increasingly, the clinical encounter between a clinician and a patient will be supported by a wide variety of cognitive aides to support diagnosis, treatment, care-coordination, surveillance and prevention, and health maintenance or wellness. PMID:27488402

Brain cDNA clone for human cholinesterase

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

McTiernan, C.; Adkins, S.; Chatonnet, A.

1987-10-01

A cDNA library from human basal ganglia was screened with oligonucleotide probes corresponding to portions of the amino acid sequence of human serum cholinesterase. Five overlapping clones, representing 2.4 kilobases, were isolated. The sequenced cDNA contained 207 base pairs of coding sequence 5' to the amino terminus of the mature protein in which there were four ATG translation start sites in the same reading frame as the protein. Only the ATG coding for Met-(-28) lay within a favorable consensus sequence for functional initiators. There were 1722 base pairs of coding sequence corresponding to the protein found circulating in human serum.more » The amino acid sequence deduced from the cDNA exactly matched the 574 amino acid sequence of human serum cholinesterase, as previously determined by Edman degradation. Therefore, our clones represented cholinesterase rather than acetylcholinesterase. It was concluded that the amino acid sequences of cholinesterase from two different tissues, human brain and human serum, were identical. Hybridization of genomic DNA blots suggested that a single gene, or very few genes coded for cholinesterase.« less

Functional interrogation of non-coding DNA through CRISPR genome editing.

PubMed

Canver, Matthew C; Bauer, Daniel E; Orkin, Stuart H

2017-05-15

Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA. Copyright © 2017 Elsevier Inc. All rights reserved.

piggyBac transposons expressing full-length human dystrophin enable genetic correction of dystrophic mesoangioblasts

PubMed Central

Loperfido, Mariana; Jarmin, Susan; Dastidar, Sumitava; Di Matteo, Mario; Perini, Ilaria; Moore, Marc; Nair, Nisha; Samara-Kuko, Ermira; Athanasopoulos, Takis; Tedesco, Francesco Saverio; Dickson, George; Sampaolesi, Maurilio; VandenDriessche, Thierry; Chuah, Marinee K.

2016-01-01

Duchenne muscular dystrophy (DMD) is a genetic neuromuscular disorder caused by the absence of dystrophin. We developed a novel gene therapy approach based on the use of the piggyBac (PB) transposon system to deliver the coding DNA sequence (CDS) of either full-length human dystrophin (DYS: 11.1 kb) or truncated microdystrophins (MD1: 3.6 kb; MD2: 4 kb). PB transposons encoding microdystrophins were transfected in C2C12 myoblasts, yielding 65±2% MD1 and 66±2% MD2 expression in differentiated multinucleated myotubes. A hyperactive PB (hyPB) transposase was then deployed to enable transposition of the large-size PB transposon (17 kb) encoding the full-length DYS and green fluorescence protein (GFP). Stable GFP expression attaining 78±3% could be achieved in the C2C12 myoblasts that had undergone transposition. Western blot analysis demonstrated expression of the full-length human DYS protein in myotubes. Subsequently, dystrophic mesoangioblasts from a Golden Retriever muscular dystrophy dog were transfected with the large-size PB transposon resulting in 50±5% GFP-expressing cells after stable transposition. This was consistent with correction of the differentiated dystrophic mesoangioblasts following expression of full-length human DYS. These results pave the way toward a novel non-viral gene therapy approach for DMD using PB transposons underscoring their potential to deliver large therapeutic genes. PMID:26682797

Cloning and characterization of the canine receptor for advanced glycation end products.

PubMed

Murua Escobar, Hugo; Soller, Jan T; Sterenczak, Katharina A; Sperveslage, Jan D; Schlueter, Claudia; Burchardt, Birgit; Eberle, Nina; Fork, Melanie; Nimzyk, Rolf; Winkler, Susanne; Nolte, Ingo; Bullerdiek, Jörn

2006-03-15

Metastasis is one of the major problems when dealing with malignant neoplasias. Accordingly, the finding of molecular targets, which can be addressed to reduce tumour metastasising, will have significant impact on the development of new therapeutic approaches. Recently, the receptor for advanced glycation end products (RAGE)-high mobility group B1 (HMGB1) protein complex has been shown to have significant influence on invasiveness, growth and motility of tumour cells, which are essential characteristics required for metastatic behaviour. A set of in vitro and in vivo approaches showed that blocking of this complex resulted in drastic suppression of tumour cell growth. Due to the similarities of human and canine cancer the dog has joined the common rodent animal model for therapeutic and preclinical studies. However, complete characterisation of the protein complex is a precondition to a therapeutic approach based on the blocking of the RAGE-HMGB1 complex to spontaneously occurring tumours in dogs. We recently characterised the canine HMGB1 gene and protein completely. Here we present the complete characterisation of the canine RAGE gene including its 1384 bp mRNA, the 1215 bp protein coding sequence, the 2835 bp genomic structure, chromosomal localisation, gene expression pattern, and its 404 amino acid protein. Furthermore we compared the CDS of six different canine breeds and screened them for single nucleotide polymorphisms.

Single-Source Molecular Precursor for Synthesis of CdS Nanoparticles and Nanoflowers

NASA Astrophysics Data System (ADS)

Salavati-Niasari, Masoud; Sobhani, Azam

2012-04-01

CdS Semiconductor nanostructures were synthesized by using two different methods. Using triphenylphosphine (C18H15P) and oleylamine (C18H37N) as surfactant, CdS semiconductor nanocrystals with a size ranging from 30 to 90 nm can be synthesized by thermal decomposition of precursor [bis(thiosemicarbazide)cadmium(II)]. CdS nanoflowers were synthesized via hydrothermal decomposition of [bis(thiosemicarbazide) cadmium(II)] without any surfactant. X-ray diffraction (XRD) patterns confirm that the resulting samples were a pure hexagonal phase of CdS. The optical property test indicates that the absorption peak of the samples shifts towards short wavelength, and the blue shift phenomenon might be ascribed to the quantum effect.

Growth and characterization of EDTA assisted CBD-CdS

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

Kumarage, W. G. C.; Wijesundera, R. P.; Seneviratne, V. A.

2017-10-01

Chemical bath deposition of CdS (CBD-CdS) thin films with the assistance of a cationic surfactant, ethylenediamine tetraacetic acid (EDTA), is reported in this work. Also the EDTA treated CdS thin films are compared with that of conventional CBD-CdS. Fabricated thin, compact, uniform and adherent EDTA treated CdS films show enhanced effective surface area and roughness compared to conventional CBD-CdS. The grazing incidence x-ray diffraction analysis shows all the fabricated CdS films are hexagonally crystallized. EDTA-treated CdS films show excellent photo activity compared to conventional CBDCdS. The flat band potential (Vfb) value was found to be tunable with EDTA concentration.

Facile synthesis of carbon dots with superior sensing ability

NASA Astrophysics Data System (ADS)

Jin, Lin; Li, Jingguo; Liu, Liyun; Wang, Zhenling; Zhang, Xingcai

2018-04-01

Carbon dots (CDs) have various applications in biomedical and environmental field, such as bio-imaging, bio-sensing and heavy metal detection. In this study, a novel class of CDs were synthesized using a one-step hydrothermal method. The fabricated CDs displayed stable photoluminescence, good water solubility, and photo stability. Moreover, the functional groups (carboxylic acid moieties and hydroxyls) on the surface of the obtained CDs enable it with superior sensing ability (e.g., very low detectable concentration for Pb2+: 5 nmol/L). With superior detection sensitivity, excellent fluorescent properties and facile fabrication method, the as-obtained CDs can find practical applications as cost-effective and sensitive chemo-sensors in water and food safety field.

CDS Re Mix

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

None

CDS (Change Detection Systems) is a mechanism for rapid visual analysis using complex image alignment algorithms. CDS is controlled with a simple interface that has been designed for use for anyone that can operate a digital camera. A challenge of complex industrial systems like nuclear power plants is to accurately identify changes in systems, structures and components that may critically impact the operation of the facility. CDS can provide a means of early intervention before the issues evolve into safety and production challenges.

Improved Dynamic Modeling of the Cascade Distillation Subsystem and Analysis of Factors Affecting Its Performance

NASA Technical Reports Server (NTRS)

Perry, Bruce A.; Anderson, Molly S.

2015-01-01

The Cascade Distillation Subsystem (CDS) is a rotary multistage distiller being developed to serve as the primary processor for wastewater recovery during long-duration space missions. The CDS could be integrated with a system similar to the International Space Station Water Processor Assembly to form a complete water recovery system for future missions. A preliminary chemical process simulation was previously developed using Aspen Custom Modeler® (ACM), but it could not simulate thermal startup and lacked detailed analysis of several key internal processes, including heat transfer between stages. This paper describes modifications to the ACM simulation of the CDS that improve its capabilities and the accuracy of its predictions. Notably, the modified version can be used to model thermal startup and predicts the total energy consumption of the CDS. The simulation has been validated for both NaC1 solution and pretreated urine feeds and no longer requires retuning when operating parameters change. The simulation was also used to predict how internal processes and operating conditions of the CDS affect its performance. In particular, it is shown that the coefficient of performance of the thermoelectric heat pump used to provide heating and cooling for the CDS is the largest factor in determining CDS efficiency. Intrastage heat transfer affects CDS performance indirectly through effects on the coefficient of performance.

Carbon dots-decorated multiwalled carbon nanotubes nanocomposites as a high-performance electrochemical sensor for detection of H2O2 in living cells.

PubMed

Bai, Jing; Sun, Chunhe; Jiang, Xiue

2016-07-01

A novel enzyme-free hydrogen peroxide sensor composed of carbon dots (CDs) and multi-walled carbon nanotubes (MWCNTs) was prepared. It was found that the carbon dots-decorated multi-walled carbon nanotubes nanocomposites (CDs/MWCNTs) modified glassy carbon (GC) electrode (CDs/MWCNTs/GCE) exhibited a significant synergistic electrocatalytic activity towards hydrogen peroxide reduction as compared to carbon dots or multi-walled carbon nanotubes alone, and the CDs/MWCNTs/GCE has shown a low detection limit as well as excellent stability, selectivity, and reproducibility. These remarkable analytical advantages enable the practical application of CDs/MWCNTs/GCE for the real-time tracking of hydrogen peroxide (H2O2) released from human cervical cancer cells with satisfactory results. The enhanced electrochemical activity can be assigned to the edge plane-like defective sites and lattice oxygen in the CDs/MWCNTs nanocomposites due to the small amount of decoration of carbon dots on the multi-walled carbon nanotubes. Based on a facile preparation method and with good electrochemical properties, the CDs/MWCNTs nanocomposites represent a new class of carbon electrode for electrochemical sensor applications. Graphical Abstract CDs/MWCNTs exhibited good electrocatalytic activity and stability to H2O2 reduction and can be used for real-time detection of H2O2 released from living cells.

One-pot synthesis and lubricity of fluorescent carbon dots applied on PCL-PEG-PCL hydrogel.

PubMed

Guo, Junde; Mei, Tangjie; Li, Yue; Hafezi, Mahshid; Lu, Hailin; Li, Jianhui; Dong, Guangneng

2018-06-12

This work presents a method for one-pot synthesis of N-doped nanometer-size carbon dots, which can be assembled with thermosensitive poly(ε-caprolactone)-poly(ethylene glycol)-poly(ε-caprolactone) (PCL-PEG-PCL, PCEC) hydrogel to achieve slow-release lubricity. The typical property of this green production was studied by fourier transform infrared (FT-IR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and transmission electron microscope (TEM). The photoluminescence of composite PCEC/CDs hydrogel and its released solutions were characterized by ultraviolet spectrum, and the rheological properties were tested by rotary rheometer. Tribological performance of the released solution from composite PCEC/CDs hydrogel was obtained to compare with PBS and pure CDs solution. The experimental results reveal that the CDs contain the chemical groups of N-H, C-OH/C-O-C and -COOH, etc. In addition, the diameter of the CDs is in the range of 6~8 nm. The phase transition behavior of PCEC/CDs hydrogel can be still kept and its viscoelasticity hydrogel is improved by approximatively 7%. Furthermore, friction coefficient of the released solution from composite PCEC/CDs hydrogel decreases by about 70% than that of PBS. Besides, the wear condition can be improved by a lubricating transfer film formed by released CDs. This novel strategy for slow-release application is valuable for drug delivery and bio-tribology.

Effect of preparation methods and doping on the structural and tunable emissions of CdS

NASA Astrophysics Data System (ADS)

Mohamed, Mohamed Bakr; Abdel-Kader, M. H.; Alhazime, Ali A.; Almarashi, Jamal Q. M.

2018-03-01

Fe, Mn and Mg doped CdS samples were prepared by thermolysis method in air and under flow of nitrogen. Structural, compositional and optical properties of the prepared samples were investigated using x-ray powder diffraction (XRD), scanning electron microscope (SEM/EDS mapping), Fourier transform infrared red (FTIR), UV-vis absorption and photoluminescence (PL) spectroscopes. Rietveld refinement of x-ray data showed that all the undoped and doped CdS samples prepared in air and under flow of nitrogen have both cubic and hexagonal structures. The percentages of hexagonal and cubic phases for all prepared samples were determined. The crystallite size increased for CdS prepared under flow of N2 compared with the sample prepared in air. The energy gap of all the samples was calculated using UV data. The intensity of PL emission changed according to the method of preparation and the kind of doping elements. PL emission revealed a blue shift for CdS prepared in air compared with CdS prepared under flow of nitrogen; also all doped samples showed a red shift of PL spectra compared with undoped samples. Undoped and doped CdS with Fe and Mg samples emitted violet and blue sub-spectra. Mn doped CdS prepared in air revealed violet, blue and yellow sub-spectra, while the sample prepared under flow of N2 emitted violet, blue and green sub-spectra.

Publication, discovery and interoperability of Clinical Decision Support Systems: A Linked Data approach.

PubMed

Marco-Ruiz, Luis; Pedrinaci, Carlos; Maldonado, J A; Panziera, Luca; Chen, Rong; Bellika, J Gustav

2016-08-01

The high costs involved in the development of Clinical Decision Support Systems (CDSS) make it necessary to share their functionality across different systems and organizations. Service Oriented Architectures (SOA) have been proposed to allow reusing CDSS by encapsulating them in a Web service. However, strong barriers in sharing CDS functionality are still present as a consequence of lack of expressiveness of services' interfaces. Linked Services are the evolution of the Semantic Web Services paradigm to process Linked Data. They aim to provide semantic descriptions over SOA implementations to overcome the limitations derived from the syntactic nature of Web services technologies. To facilitate the publication, discovery and interoperability of CDS services by evolving them into Linked Services that expose their interfaces as Linked Data. We developed methods and models to enhance CDS SOA as Linked Services that define a rich semantic layer based on machine interpretable ontologies that powers their interoperability and reuse. These ontologies provided unambiguous descriptions of CDS services properties to expose them to the Web of Data. We developed models compliant with Linked Data principles to create a semantic representation of the components that compose CDS services. To evaluate our approach we implemented a set of CDS Linked Services using a Web service definition ontology. The definitions of Web services were linked to the models developed in order to attach unambiguous semantics to the service components. All models were bound to SNOMED-CT and public ontologies (e.g. Dublin Core) in order to count on a lingua franca to explore them. Discovery and analysis of CDS services based on machine interpretable models was performed reasoning over the ontologies built. Linked Services can be used effectively to expose CDS services to the Web of Data by building on current CDS standards. This allows building shared Linked Knowledge Bases to provide machine interpretable semantics to the CDS service description alleviating the challenges on interoperability and reuse. Linked Services allow for building 'digital libraries' of distributed CDS services that can be hosted and maintained in different organizations. Copyright © 2016 Elsevier Inc. All rights reserved.

A Code Division Multiple Access Communication System for the Low Frequency Band.

DTIC Science & Technology

1983-04-01

frequency channels spread-spectrum communication / complex sequences, orthogonal codes impulsive noise 20. ABSTRACT (Continue an reverse side It...their transmissions with signature sequences. Our LF/CDMA scheme is different in that each user’s signature sequence set consists of M orthogonal ...signature sequences. Our LF/CDMA scheme is different in that each user’s signature sequence set consists of M orthogonal sequences and thus log 2 M

A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region.

PubMed

Kress, W John; Erickson, David L

2007-06-06

A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.

Combination of counterpropagation artificial neural networks and antioxidant activities for comprehensive evaluation of associated-extraction efficiency of various cyclodextrins in the traditional Chinese formula Xue-Zhi-Ning.

PubMed

Sun, Lili; Yang, Jianwen; Wang, Meng; Zhang, Huijie; Liu, Yanan; Ren, Xiaoliang; Qi, Aidi

2015-11-10

Xue-Zhi-Ning (XZN) is a widely used traditional Chinese medicine formula to treat hyperlipidemia. Recently, cyclodextrins (CDs) have been extensively used to minimize problems relative to medicine bioavailability, such as low solubility and poor stability. The objective of this study was to determine the associated-extraction efficiency of various CDs in XZN. Three various type CDs were evaluated, including native CDs (α-CD, β-CD), hydrophilic CD derivatives (HP-β-CD and Me-β-CD), and ionic CD derivatives (SBE-β-CD and CM-β-CD). An ultra high-performance liquid chromatography (UHPLC) fingerprint was applied to determine the components in CD extracts and original aqueous extract (OAE). A counterpropagation artificial neural network (CP-ANN) was used to analyze the components in different extracts and compare the selective extraction of various CDs. Extraction efficiencies of the various CDs in terms of extracted components follow the ranking, ionic CD derivatives>hydrophilic CD derivatives>native CDs>OAE. Besides, different types of CDs have their own selective extraction and ionic CD derivatives present the strongest associated-extraction efficiency. Antioxidant potentials of various extracts were evaluated by determining the inhibition of spontaneous, H2O2-induced, CCl4-induced and Fe(2+)/ascorbic acid-induced lipid peroxidation (LPO) and analyzing the scavenging capacity for DPPH and hydroxyl radicals. The order of extraction efficiencies of the various CDs relative to antioxidant activities is as follows: SBE-β-CD>CM-β-CD>HP-β-CD>Me-β-CD>β-CD>α-CD. It can be demonstrated that all of the CDs studied increase the extraction efficiency and that ionic CD derivatives (SBE-β-CD and CM-β-CD) present the highest extraction capability in terms of amount extracted and antioxidant activities of extracts. Copyright © 2015 Elsevier B.V. All rights reserved.

Boosting Quality Registries with Clinical Decision Support Functionality*. User Acceptance of a Prototype Applied to HIV/TB Drug Therapy.

PubMed

Wannheden, Carolina; Hvitfeldt-Forsberg, Helena; Eftimovska, Elena; Westling, Katarina; Ellenius, Johan

2017-08-11

The care of HIV-related tuberculosis (HIV/TB) is complex and challenging. Clinical decision support (CDS) systems can contribute to improve quality of care, but more knowledge is needed on factors determining user acceptance of CDS. To analyze physicians' and nurses' acceptance of a CDS prototype for evidence-based drug therapy recommendations for HIV/TB treatment. Physicians and nurses were involved in designing a CDS prototype intended for future integration with the Swedish national HIV quality registry. Focus group evaluation was performed with ten nurses and four physicians, respectively. The Unified Theory of Acceptance and Use of Technology (UTAUT) was used to analyze acceptance. We identified several potential benefits with the CDS prototype as well as some concerns that could be addressed by redesign. There was also concern about dependence on physician attitudes, as well as technical, organizational, and legal issues. Acceptance evaluation at a prototype stage provided rich data to improve the future design of a CDS prototype. Apart from design and development efforts, substantial organizational efforts are needed to enable the implementation and maintenance of a future CDS system.

Nitrogen and Phosphorus Co-Doped Carbon Nanodots as a Novel Fluorescent Probe for Highly Sensitive Detection of Fe(3+) in Human Serum and Living Cells.

PubMed

Shi, Bingfang; Su, Yubin; Zhang, Liangliang; Huang, Mengjiao; Liu, Rongjun; Zhao, Shulin

2016-05-04

Chemical doping with heteroatoms can effectively modulate physicochemical and photochemical properties of carbon dots (CDs). However, the development of multi heteroatoms codoped carbon nanodots is still in its early stage. In this work, a facile hydrothermal synthesis strategy was applied to synthesize multi heteroatoms (nitrogen and phosphorus) codoped carbon nanodots (N,P-CDs) using glucose as carbon source, and ammonia, phosphoric acid as dopant, respectively. Compared with CDs, the multi heteroatoms doped CDs resulted in dramatic improvement in the electronic characteristics and surface chemical activities. Therefore, the N,P-CDs prepared as described above exhibited a strong blue emission and a sensitive response to Fe(3+). The N,P-CDs based fluorescent sensor was then applied to sensitively determine Fe(3+) with a detection limit of 1.8 nM. Notably, the prepared N,P-CDs possessed negligible cytotoxicity, excellent biocompatibility, and high photostability. It was also applied for label-free detection of Fe(3+) in complex biological samples and the fluorescence imaging of intracellular Fe(3+), which indicated its potential applications in clinical diagnosis and other biologically related study.

Morphology, structure and optical properties of hydrothermally synthesized CeO2/CdS nanocomposites

NASA Astrophysics Data System (ADS)

Mohanty, Biswajyoti; Nayak, J.

2018-04-01

CeO2/CdS nanocomposites were synthesized using a two-step hydrothermal technique. The effects of precursor concentration on the optical and structural properties of the CeO2/CdS nanoparticles were systematically studied. The morphology, composition and the structure of the CeO2/CdS nanocomposite powder were studied by scanning electron microscopy (SEM), energy dispersive X-ray spectrum analysis (EDXA) and X-ray diffraction (XRD), respectively. The optical properties of CeO2/CdS nanocomposites were studied by UV-vis absorption and photoluminescence (PL) spectroscopy. The optical band gaps of the CeO2/CdS nanopowders ranged from 2.34 eV to 2.39 eV as estimated from the UV-vis absorption. In the room temperature photoluminescence spectrum of CeO2/CdS nanopowder, a strong blue emission band was observed at 400 nm. Since the powder shows strong visible luminescence, it may be used as a blue phosphor in future. The original article published with this DOI was submitted in error. The correct article was inadvertently left out of the original submission. This has been rectified and the correct article was published online on 16 April 2018.

Ratiometric, visual, dual-signal fluorescent sensing and imaging of pH/copper ions in real samples based on carbon dots-fluorescein isothiocyanate composites.

PubMed

Zhu, Xinxin; Jin, Hui; Gao, Cuili; Gui, Rijun; Wang, Zonghua

2017-01-01

In this article, a facile aqueous synthesis of carbon dots (CDs) was developed by using natural kelp as a new carbon source. Through hydrothermal carbonization of kelp juice, fluorescent CDs were prepared and the CDs' surface was modified with polyethylenimine (PEI). The PEI-modified CDs were conjugated with fluorescein isothiocyanate (FITC) to fabricate CDs-FITC composites. To exploit broad applications, the CDs-FITC composites were developed as fluorescent sensing or imaging platforms of pH and Cu 2+ . Analytical performances of the composites-based fluorescence (FL) sensors were evaluated, including visual FL imaging of pH in glass bottle, ratiometric FL sensing of pH in yogurt samples, visual FL latent fingerprint and leaf imaging detection of [Cu 2+ ], dual-signal FL sensing of [Cu 2+ ] in yogurt and human serum samples. Experimental results from ratiometric, visual, dual-signal FL sensing and imaging applications confirmed the high feasibility, accuracy, stabilization and simplicity of CDs-FITC composites-based FL sensors for the detection of pH and Cu 2+ ions in real samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantum dots coupled ZnO nanowire-array panels and their photocatalytic activities.

PubMed

Liao, Yulong; Que, Wenxiu; Zhang, Jin; Zhong, Peng; Yuan, Yuan; Qiu, Xinku; Shen, Fengyu

2013-02-01

Fabrication and characterization of a heterojunction structured by CdS quantum dots@ZnO nanowire-array panels were presented. Firstly, ZnO nanowire-array panels were prepared by using a chemical bath deposition approach where wurtzite ZnO nanowires with a diameter of about 100 nm and 3 microm in length grew perpendicularly to glass substrate. Secondly, CdS quantum dots were deposited onto the surface of the ZnO nanowire-arrays by using successive ion layer absorption and reaction method, and the CdS shell/ZnO core heterojunction were thus obtained. Field emission scanning electron microscopy and transmission electron microscope were employed to characterize the morphological properties of the as-obtained CdS quantum dots@ZnO nanowire-array panels. X-ray diffraction was adopted to characterize the crystalline properties of the as-obtained CdS quantum dots@ZnO nanowire-array panels. Methyl orange was taken as a model compound to confirm the photocatalytic activities of the CdS shell/ZnO core heterojunction. Results indicate that CdS with narrow band gap not only acts as a visible-light sensitizer but also is responsible for an effective charge separation.

Enhanced photocatalytic activity of graphitic carbon nitride/cadmium sulfide heterojunctions by protonating treatment

NASA Astrophysics Data System (ADS)

Yan, Mengdie; Ma, Yushuang; Zhang, Huanhuan; Ye, Boyong; Dong, Xiaoping

2018-05-01

Highly efficient visible-light-driven protonated g-C3N4 (pg-C3N4)/CdS heterojunctions with different weight ratios of CdS were prepared by treating g-C3N4 with hydrochloric acid and using an in-situ precipitation method. The structure and morphology of heterojunctions were investigated by X-ray powder diffraction (XRD), transmission electron microscopy (TEM), UV-vis diffuse reflectance spectroscopy (DRS), Fourier transform infrared spectroscopy (FTIR) and nitrogen adsorption technology. The as-prepared pg-C3N4/CdS heterojunction with 50 wt% of g-C3N4 exhibited much higher photocatalytic activity for photodegradation of methyl orange (MO) than pg-C3N4, CdS and g-C3N4/CdS without protonation as well, which could be contributed to the activation of hydrochloric acid treatment and the improved electron-hole separation due to their overlapping band structure of CdS and pg-C3N4. A possible photocatalytic mechanism of the pg-C3N4/CdS heterojunctions with superoxide radical species as the main active species in photocatalysis was proposed on the basis of experimental results.

Streamlined Genome Sequence Compression using Distributed Source Coding

PubMed Central

Wang, Shuang; Jiang, Xiaoqian; Chen, Feng; Cui, Lijuan; Cheng, Samuel

2014-01-01

We aim at developing a streamlined genome sequence compression algorithm to support alternative miniaturized sequencing devices, which have limited communication, storage, and computation power. Existing techniques that require heavy client (encoder side) cannot be applied. To tackle this challenge, we carefully examined distributed source coding theory and developed a customized reference-based genome compression protocol to meet the low-complexity need at the client side. Based on the variation between source and reference, our protocol will pick adaptively either syndrome coding or hash coding to compress subsequences of changing code length. Our experimental results showed promising performance of the proposed method when compared with the state-of-the-art algorithm (GRS). PMID:25520552

PVP capped CdS nanoparticles for UV-LED applications

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

Sivaram, H.; Selvakumar, D.; Jayavel, R., E-mail: rjvel@annauniv.edu

Polyvinlypyrrolidone (PVP) capped cadmium sulphide (CdS) nanoparticles are synthesized by wet chemical method. The powder X-ray diffraction (XRD) result indicates that the nanoparticles are crystallized in cubic phase. The optical properties are characterized by UV-Vis absorption. The morphology of CdS nanoparticles are studied using Scanning electron microscope (SEM). The thermal behavior of the as prepared nanoparticles has been examined by Thermo gravimetric analysis (TGA). The optical absorption study of pvp capped CdS reveal a red shift confirms the UV-LED applications.

Health Care Expenditures and Utilization for Children With Noncomplex Chronic Disease.

PubMed

Hoefgen, Erik R; Andrews, Annie L; Richardson, Troy; Hall, Matthew; Neff, John M; Macy, Michelle L; Bettenhausen, Jessica L; Shah, Samir S; Auger, Katherine A

2017-09-01

Pediatric health care expenditures and use vary by level of complexity and chronic illness. We sought to determine expenditures and use for children with noncomplex chronic diseases (NC-CDs). We performed a retrospective, cross-sectional analysis of Medicaid enrollees (ages 0-18 years) from January 1, 2012, through December 31, 2013, using administrative claims (the Truven MarketScan Medicaid Database). Patients were categorized by chronicity of illness by using 3M Health Information System's Clinical Risk Groups (CRGs) as follows: without chronic diseases (WO-CDs) (CRG 1-2), NC-CDs (CRG 3-5), and complex chronic diseases (C-CDs) (CRG 6-9). Primary outcomes were medical expenditures, including total annualized population expenditure and per-member per-year expenditure (PMPY). Secondary outcomes included the number of health care encounters over the 2-year period. There were 2 424 946 children who met inclusion criteria, 53% were WO-CD; 36% had an NC-CD; and 11% had a C-CD. Children with NC-CDs accounted for 33% ($2801 PMPY) of the annual spending compared with 20% ($1151 PMPY) accounted for by children WO-CDs and 47% ($12 569 PMPY) by children with C-CDs. The median outpatient visit count by group over the 2-year period was 15 (interquartile range [IQR] 10-25) for NC-CD, 8 (IQR 5-13) WO-CD, and 34 (IQR 19-72) for C-CD. Children with NC-CDs accounted for 33% of pediatric Medicaid expenditures and have significantly higher PMPY and aggregate annual expenditures than children WO-CDs. The annual aggregate expenditures of the NC-CD group represent a significant societal cost because of the high volume of children, extrapolated to ∼$34.9 billion annually in national Medicaid expenditures. Copyright © 2017 by the American Academy of Pediatrics.

Expressing clinical data sets with openEHR archetypes: a solid basis for ubiquitous computing.

PubMed

Garde, Sebastian; Hovenga, Evelyn; Buck, Jasmin; Knaup, Petra

2007-12-01

The purpose of this paper is to analyse the feasibility and usefulness of expressing clinical data sets (CDSs) as openEHR archetypes. For this, we present an approach to transform CDS into archetypes, and outline typical problems with CDS and analyse whether some of these problems can be overcome by the use of archetypes. Literature review and analysis of a selection of existing Australian, German, other European and international CDSs; transfer of a CDS for Paediatric Oncology into openEHR archetypes; implementation of CDSs in application systems. To explore the feasibility of expressing CDS as archetypes an approach to transform existing CDSs into archetypes is presented in this paper. In case of the Paediatric Oncology CDS (which consists of 260 data items) this lead to the definition of 48 openEHR archetypes. To analyse the usefulness of expressing CDS as archetypes, we identified nine problems with CDS that currently remain unsolved without a common model underpinning the CDS. Typical problems include incompatible basic data types and overlapping and incompatible definitions of clinical content. A solution to most of these problems based on openEHR archetypes is motivated. With regard to integrity constraints, further research is required. While openEHR cannot overcome all barriers to Ubiquitous Computing, it can provide the common basis for ubiquitous presence of meaningful and computer-processable knowledge and information, which we believe is a basic requirement for Ubiquitous Computing. Expressing CDSs as openEHR archetypes is feasible and advantageous as it fosters semantic interoperability, supports ubiquitous computing, and helps to develop archetypes that are arguably of better quality than the original CDS.

Exciton-Plasmon Interaction between AuNPs/Graphene Nanohybrids and CdS Quantum Dots/TiO2 for Photoelectrochemical Aptasensing of Prostate-Specific Antigen.

PubMed

Cai, Guoneng; Yu, Zhengzhong; Ren, Rongrong; Tang, Dianping

2018-03-23

A competitive-displacement reaction strategy based on target-induced dissociation of gold nanoparticle coated graphene nanosheet (AuNPs/GN) from CdS quantum dot functionalized mesoporous titanium dioxide (CdS QDs/TiO 2 ) was designed for the sensitive photoelectrochemical (PEC) aptasensing of prostate-specific antigen (PSA) through the exciton-plasmon interaction (EPI) between CdS QDs and AuNPs. To construct such an aptasensing system, capture DNA was initially conjugated covalently onto CdS QDs/TiO 2 -modified electrode, and then AuNPs/GN-labeled PSA aptamer was bound onto biofunctionalized CdS QDs/TiO 2 via hybridization chain reaction of partial bases with capture DNA. Introduction of AuNPs/GN efficiently quenched the photocurrent of CdS QDs/TiO 2 thanks to energy transfer. Upon addition of target PSA, the sandwiched aptamer between CdS QDs/TiO 2 and AuNPs/GN reacted with the analyte analyte, thus resulting in the dissociation of AuNPs/GN from the CdS QDs/TiO 2 to increase the photocurrent. Under optimum conditions, the aptasensing platform exhibited a high sensitivity for PSA detection within a dynamic linear range of 1.0 pg/mL to 8.0 ng/mL at a low limitat of detection of 0.52 pg/mL. The interparticle distance of exciton-plasmon interaction and contents of AuNPs corresponding to EPI effect in this system were also studied. Good selectivity and high reproducibility were obtained for the analysis of target PSA. Importantly, the accuracy and matrix effect of PEC aptasensor was evaluated for the determination of human serum specimens and newborn calf serum-diluted PSA standards, giving a well-matched result with the referenced PSA ELISA kit.

Amorphous MoS{sub x} on CdS nanorods for highly efficient photocatalytic hydrogen evolution

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

Li, Xiaofang; Tang, Chaowan; Zheng, Qun

Loading cocatalyst on semiconductors was crucially necessary for improving the photocatalytic hydrogen evolution. Amorphous MoS{sub x} as a novel and noble metal-free cocatalyst was loaded on CdS nanorods by a simple photodeposition method. Efficient hydrogen evolution with amount of 15 mmol h{sup −1} g{sup −1} was observed over the MoS{sub x} modified CdS nanorods, which was about 6 times higher than that by using Pt as cocatalyst. Meanwhile, with MoS{sub x} cocatalyst, the efficiency of CdS nanorods was superior to that of CdS nanoparticles and bulk CdS. No deactivation could be observed in the efficiency of MoS{sub x} modified CdSmore » nanorods under irradiation for successive 10 h. Further experimental results indicated that the efficient electrons transfer, low overpotential of hydrogen evolution and active S atoms over the MoS{sub x} modified CdS nanorods were responsible for the higher efficiency. Our results provided guidance for synthesizing noble metal-free materials as cocatalyst for photocatalytic hydrogen evolution. - Graphical abstract: Photodeposition of amorphous MoS{sub x} on CdS nanorods for highly efficient photocatalytic hydrogen evolution. - Highlights: • Amorphous MoSx cocatalyst was loaded on CdS NRs by a simple photodeposition. • MoS{sub x}/CdS NRs exhibited 6 times higher hydrogen evolution efficiency than Pt/CdS NRs. • The hydrogen evolution of MoS{sub x}/CdS NRs linearly increased with prolonging time. • Lower overpotential and efficient electron transfer were observed over MoS{sub x}/CdS NRs.« less

Development and evaluation of a comprehensive clinical decision support taxonomy: comparison of front-end tools in commercial and internally developed electronic health record systems

PubMed Central

Sittig, Dean F; Ash, Joan S; Feblowitz, Joshua; Meltzer, Seth; McMullen, Carmit; Guappone, Ken; Carpenter, Jim; Richardson, Joshua; Simonaitis, Linas; Evans, R Scott; Nichol, W Paul; Middleton, Blackford

2011-01-01

Background Clinical decision support (CDS) is a valuable tool for improving healthcare quality and lowering costs. However, there is no comprehensive taxonomy of types of CDS and there has been limited research on the availability of various CDS tools across current electronic health record (EHR) systems. Objective To develop and validate a taxonomy of front-end CDS tools and to assess support for these tools in major commercial and internally developed EHRs. Study design and methods We used a modified Delphi approach with a panel of 11 decision support experts to develop a taxonomy of 53 front-end CDS tools. Based on this taxonomy, a survey on CDS tools was sent to a purposive sample of commercial EHR vendors (n=9) and leading healthcare institutions with internally developed state-of-the-art EHRs (n=4). Results Responses were received from all healthcare institutions and 7 of 9 EHR vendors (response rate: 85%). All 53 types of CDS tools identified in the taxonomy were found in at least one surveyed EHR system, but only 8 functions were present in all EHRs. Medication dosing support and order facilitators were the most commonly available classes of decision support, while expert systems (eg, diagnostic decision support, ventilator management suggestions) were the least common. Conclusion We developed and validated a comprehensive taxonomy of front-end CDS tools. A subsequent survey of commercial EHR vendors and leading healthcare institutions revealed a small core set of common CDS tools, but identified significant variability in the remainder of clinical decision support content. PMID:21415065

Photocatalyst based on TiO2 nanotube arrays co-decorated with CdS quantum dots and reduced graphene oxide irradiated by γ rays for effective degradation of ethylene

NASA Astrophysics Data System (ADS)

Zhang, Quan; Ye, Shengying; Song, Xianliang; Luo, Shucan

2018-06-01

We report herein a means of transforming TiO2 nanotube arrays (TNAs) from an amorphous state to an anatase crystal state (denoted as ∗TNAs), and present a single-step synthetic route for preparing CdS quantum dots (CdS QDs) as well as reduced graphene oxide (rGO) through gamma-ray irradiation. The as-prepared ∗TNAs, CdS QDs, and rGO, which had all been subjected to gamma-ray irradiation, were then assembled together to produce the desired heterojunction (denoted as CdS QDs/rGO-∗TNAs). X-ray diffraction (XRD), field-emission scanning electron microscopy (FESEM), ultraviolet/visible diffuse-reflectance spectroscopy (UV/Vis DRS), Fourier-transform infrared spectroscopy (FTIR), micro-Raman spectrometry (RS), atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS) have been applied to characterize the appearance and performance of this photocatalyst. The photocatalytic activity of CdS QDs/rGO-∗TNAs towards ethylene degradation has been measured by placing it in a simulated cold-storage environment, the temperature and humidity of which were set at about 3 ± 1 °C and 75-90%, respectively. The results showed that the rate constant (K) of ethylene degradation could reach up to 1.07 × 10-3 min-1 with CdS QDs/rGO-∗TNAs, as compared to 2.30 × 10-4 min-1 with ∗TNAs and 6.25 × 10-4 min-1 with CdS QDs-∗TNAs, indicating that the constructed CdS QDs/rGO-∗TNAs constitutes a promising photocatalyst for ethylene removal in a cold storage environment.

Scalable alignment of CdS nanowires based on efficient roll-on transfer technique.

PubMed

Yan, Shancheng; Shi, Yi; Xiao, Zhongdang; Wang, Junzhuan; Hu, Dong; Xul, Xin; Lu, Tao; Liu, Aili; Gao, Fan

2013-06-01

A roll-on transfer strategy is developed to enable large-scale and uniform assembly of CdS nanowires on various rigid and flexible substrate materials. In this method, the CdS nanowires were synthesized by the hydrothermal method. The dispersed CdS NWs could be firstly aligned and selectively deposited at the micro/nanochannels between aligned nanofibers on the surface of the donor roller as a result of evaporation-induced flow and capillary action, and then the directional and aligned transfer of the CdS NWs from the donor roller to a receiver substrate via roll-on transfer technique. Finally, a device structures consisting of the nanowire channel and two metal electrodes was fabricated. The electrical property of this device was observed.

One-step, low-temperature fabrication of CdS quantum dots by watermelon rind: a green approach

PubMed Central

Lakshmipathy, Rajasekhar; Sarada, Nallani Chakravarthula; Chidambaram, K; Pasha, Sk Khadeer

2015-01-01

We investigated the one-step synthesis of CdS nanoparticles via green synthesis that used aqueous extract of watermelon rind as a capping and stabilizing agent. Preliminary phytochemical analysis depicted the presence of carbohydrates which can act as capping and stabilizing agents. Synthesized CdS nanoparticles were characterized using UV-visible, Fourier transform infrared spectroscopy, X-ray diffraction, EDX, dynamic light scattering, transmission electron microscopy, and atomic force microscopy techniques. The CdS nanoparticles were found to be size- and shape-controlled and were stable even after 3 months of synthesis. The results suggest that watermelon rind, an agro-waste, can be used for synthesis of CdS nanoparticles without any addition of stabilizing and capping agents. PMID:26491319

Enhanced photoelectrochemical properties of TiO2 nanorod arrays decorated with CdS nanoparticles

PubMed Central

Xie, Zheng; Liu, Xiangxuan; Wang, Weipeng; Liu, Can; Li, Zhengcao; Zhang, Zhengjun

2014-01-01

TiO2 nanorod arrays (TiO2 NRAs) sensitized with CdS nanoparticles were fabricated via successive ion layer adsorption and reaction (SILAR), and TiO2 NRAs were obtained by oxidizing Ti NRAs obtained through oblique angle deposition. The TiO2 NRAs decorated with CdS nanoparticles exhibited excellent photoelectrochemical and photocatalytic properties under visible light, and the one decorated with 20 SILAR cycles CdS nanoparticles shows the best performance. This can be attributed to the enhanced separation of electrons and holes by forming heterojunctions of CdS nanoparticles and TiO2 NRAs. This provides a promising way to fabricate the material for solar energy conversion and wastewater degradation. PMID:27877718

Development of a Higher Fidelity Model for the Cascade Distillation Subsystem (CDS)

NASA Technical Reports Server (NTRS)

Perry, Bruce; Anderson, Molly

2014-01-01

Significant improvements have been made to the ACM model of the CDS, enabling accurate predictions of dynamic operations with fewer assumptions. The model has been utilized to predict how CDS performance would be impacted by changing operating parameters, revealing performance trade-offs and possibilities for improvement. CDS efficiency is driven by the THP coefficient of performance, which in turn is dependent on heat transfer within the system. Based on the remaining limitations of the simulation, priorities for further model development include: center dot Relaxing the assumption of total condensation center dot Incorporating dynamic simulation capability for the buildup of dissolved inert gasses in condensers center dot Examining CDS operation with more complex feeds center dot Extending heat transfer analysis to all surfaces

Structural and photoluminescence properties of Ni doped CdS nanoparticles synthesis by sol gel method

NASA Astrophysics Data System (ADS)

Mahdi, Hadeel Salih; Parveen, Azra; Azam, Ameer

2018-05-01

Ni doped CdS nanoparticles have been successfully synthesized by sol-gel method. Nickel nitrate, cadmium nitrate, sodium sulfide has been used as precursors for the preparation of these Ni-doped CdS nanoparticles. The structural properties were studied by X-ray diffraction analysis. Surface morphology and the composition of the samples were studied by scanning electron microscope (SEM). The X-ray diffraction results revealed that the Ni-doped CdS nanoparticles were in hexagonal structure. The crystallite size was determined from Debye-Scherer equation and showed that the particle size increases with the doping of Ni. Optical absorption spectra of Ni doped CdS also was studied by Photoluminescence spectroscopy in the range of 200-600 nm.

Synthesis of Nitrogen and Sulfur Co-doped Carbon Dots from Garlic for Selective Detection of Fe3+

NASA Astrophysics Data System (ADS)

Sun, Chun; Zhang, Yu; Wang, Peng; Yang, Yue; Wang, Yu; Xu, Jian; Wang, Yiding; Yu, William W.

2016-02-01

Garlic was used as a green source to synthesize carbon dots (CDs) with a systematic study of the optical and structure properties. Ethylenediamine was added into the synthesis to improve the photoluminescence quantum yield (PL QY) of the CDs. Detailed structural and composition studies demonstrated that the content of N and the formation of C-N and C=N were critical to improve the PL QY. The as-synthesized CDs exhibited excellent stability in a wide pH range and high NaCl concentrations, rendering them applicable in complicated and harsh conditions. Quenching the fluorescence of the CDs in the presence of Fe3+ ion made these CDs a luminescent probe for selective detection of Fe3+ ion.

Synthesis of Nitrogen and Sulfur Co-doped Carbon Dots from Garlic for Selective Detection of Fe(3.).

PubMed

Sun, Chun; Zhang, Yu; Wang, Peng; Yang, Yue; Wang, Yu; Xu, Jian; Wang, Yiding; Yu, William W

2016-12-01

Garlic was used as a green source to synthesize carbon dots (CDs) with a systematic study of the optical and structure properties. Ethylenediamine was added into the synthesis to improve the photoluminescence quantum yield (PL QY) of the CDs. Detailed structural and composition studies demonstrated that the content of N and the formation of C-N and C=N were critical to improve the PL QY. The as-synthesized CDs exhibited excellent stability in a wide pH range and high NaCl concentrations, rendering them applicable in complicated and harsh conditions. Quenching the fluorescence of the CDs in the presence of Fe(3+) ion made these CDs a luminescent probe for selective detection of Fe(3+) ion.

Nanobiotechnology of Carbon Dots: A Review.

PubMed

Durán, Nelson; Simões, Mateus B; de Moraes, Ana C M; Fávaro, Wagner J; Seabra, Amedea B

2016-07-01

In recent years, carbon dots (CDs) have gained increasing attention owing to their unique properties and enormous potential for several biomedical and technological applications. CDs are biocompatible, have a small size with a relatively large surface area, are photostable, and have customizable photoluminescence properties. This review is divided into the following discussions of CDs: general definitions; an overview of recent reviews; methods of green and classical synthesis; applications in bioimaging, involving supercapacitors, nanocarriers and nanomedicine; toxicological evaluations (including cytotoxic, genotoxic and anti-cancer properties of CDs); their conjugation with enzymes, biosensors, and cell labeling. Finally the remaining drawbacks and challenges of CD applications are highlighted. In this context, this article aims to provide critical insight and inspire further developments in the synthesis and application of CDs.

Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing.

PubMed

Kanda, Kojun; Pflug, James M; Sproul, John S; Dasenko, Mark A; Maddison, David R

2015-01-01

In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced.

Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing

PubMed Central

Dasenko, Mark A.

2015-01-01

In this paper we explore high-throughput Illumina sequencing of nuclear protein-coding, ribosomal, and mitochondrial genes in small, dried insects stored in natural history collections. We sequenced one tenebrionid beetle and 12 carabid beetles ranging in size from 3.7 to 9.7 mm in length that have been stored in various museums for 4 to 84 years. Although we chose a number of old, small specimens for which we expected low sequence recovery, we successfully recovered at least some low-copy nuclear protein-coding genes from all specimens. For example, in one 56-year-old beetle, 4.4 mm in length, our de novo assembly recovered about 63% of approximately 41,900 nucleotides in a target suite of 67 nuclear protein-coding gene fragments, and 70% using a reference-based assembly. Even in the least successfully sequenced carabid specimen, reference-based assembly yielded fragments that were at least 50% of the target length for 34 of 67 nuclear protein-coding gene fragments. Exploration of alternative references for reference-based assembly revealed few signs of bias created by the reference. For all specimens we recovered almost complete copies of ribosomal and mitochondrial genes. We verified the general accuracy of the sequences through comparisons with sequences obtained from PCR and Sanger sequencing, including of conspecific, fresh specimens, and through phylogenetic analysis that tested the placement of sequences in predicted regions. A few possible inaccuracies in the sequences were detected, but these rarely affected the phylogenetic placement of the samples. Although our sample sizes are low, an exploratory regression study suggests that the dominant factor in predicting success at recovering nuclear protein-coding genes is a high number of Illumina reads, with success at PCR of COI and killing by immersion in ethanol being secondary factors; in analyses of only high-read samples, the primary significant explanatory variable was body length, with small beetles being more successfully sequenced. PMID:26716693

The Mitochondrial Cytochrome Oxidase Subunit I Gene Occurs on a Minichromosome with Extensive Heteroplasmy in Two Species of Chewing Lice, Geomydoecus aurei and Thomomydoecus minor

PubMed Central

Pietan, Lucas L.; Spradling, Theresa A.

2016-01-01

In animals, mitochondrial DNA (mtDNA) typically occurs as a single circular chromosome with 13 protein-coding genes and 22 tRNA genes. The various species of lice examined previously, however, have shown mitochondrial genome rearrangements with a range of chromosome sizes and numbers. Our research demonstrates that the mitochondrial genomes of two species of chewing lice found on pocket gophers, Geomydoecus aurei and Thomomydoecus minor, are fragmented with the 1,536 base-pair (bp) cytochrome-oxidase subunit I (cox1) gene occurring as the only protein-coding gene on a 1,916–1,964 bp minicircular chromosome in the two species, respectively. The cox1 gene of T. minor begins with an atypical start codon, while that of G. aurei does not. Components of the non-protein coding sequence of G. aurei and T. minor include a tRNA (isoleucine) gene, inverted repeat sequences consistent with origins of replication, and an additional non-coding region that is smaller than the non-coding sequence of other lice with such fragmented mitochondrial genomes. Sequences of cox1 minichromosome clones for each species reveal extensive length and sequence heteroplasmy in both coding and noncoding regions. The highly variable non-gene regions of G. aurei and T. minor have little sequence similarity with one another except for a 19-bp region of phylogenetically conserved sequence with unknown function. PMID:27589589

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

PubMed

2004-12-09

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.

Tuning band alignment by CdS layers using a SILAR method to enhance TiO2/CdS/CdSe quantum-dot solar-cell performance.

PubMed

Zhang, Bingkai; Zheng, Jiaxin; Li, Xiaoning; Fang, Yanyan; Wang, Lin-Wang; Lin, Yuan; Pan, Feng

2016-04-28

We report tuning band alignment by optimized CdS layers using a SILAR method to achieve the recorded best performance with about 6% PCE in TiO2/CdS/CdSe QDSSCs. Combining experimental and theoretical studies, we find that a better lattices match between CdS and TiO2 assists the growth of CdSe, and the combined effect of charge transfer and surface dipole moment at the TiO2/CdS/CdSe interface shifts the energy levels of TiO2 upward and increases Voc of the solar cells. More importantly, the band gap of CdS buffer layers is sensitive to the distortion induced by lattice mismatch and numbers of CdS layers. For example, the barrier for charge transfer disappears when there are more than 4 layers of CdS, facilitating the charge injection from CdSe to TiO2.

Psychometric Properties of the Persian Version of Care Dependency Scale in Nursing Homes.

PubMed

Rajabi, Gholamreza; Namadmalan, Masoume; Dijkstra, Ate; Ghasemzade, Roya; Foroughan, Mahshid; Zahednejad, Shahla

The purpose of the study was to examine the psychometric properties of the Persian version of the Care Dependency Scale (CDS) in nursing homes. Instrument development. The English version of the CDS was translated into Persian. A convenience sample of 140 (100 older people without dementia and 40 patients with dementia) Persian-speaking people were selected from the nursing homes in Ahvaz, Iran. Cronbach's alpha, discriminant validity, and construct validity (exploratory factor analysis) were examined. Exploratory factor analysis indicated that the CDS has two factors, including psychosocial and somatic factors. Discriminant validity showed that the CDS can differentiate patients with dementia from the older adults without dementia. The results of the study showed that the Persian CDS is a reliable and valid scale when used in nursing homes. The Persian version of the CDS can help clinicians and nurses to assess patients' need and the degree of care dependency among older adults in Persian-speaking areas.

Proposal for fulfilling strategic objectives of the U.S. Roadmap for national action on clinical decision support through a service-oriented architecture leveraging HL7 services.

PubMed

Kawamoto, Kensaku; Lobach, David F

2007-01-01

Despite their demonstrated effectiveness, clinical decision support (CDS) systems are not widely used within the U.S. The Roadmap for National Action on Clinical Decision Support, published in June 2006 by the American Medical Informatics Association, identifies six strategic objectives for achieving widespread adoption of effective CDS capabilities. In this manuscript, we propose a Service-Oriented Architecture (SOA) for CDS that facilitates achievement of these six objectives. Within the proposed framework, CDS capabilities are implemented through the orchestration of independent software services whose interfaces are being standardized by Health Level 7 and the Object Management Group through their joint Healthcare Services Specification Project (HSSP). Core services within this framework include the HSSP Decision Support Service, the HSSP Common Terminology Service, and the HSSP Retrieve, Locate, and Update Service. Our experiences, and those of others, indicate that the proposed SOA approach to CDS could enable the widespread adoption of effective CDS within the U.S. health care system.

Engineering iodine-doped carbon dots as dual-modal probes for fluorescence and X-ray CT imaging.

PubMed

Zhang, Miaomiao; Ju, Huixiang; Zhang, Li; Sun, Mingzhong; Zhou, Zhongwei; Dai, Zhenyu; Zhang, Lirong; Gong, Aihua; Wu, Chaoyao; Du, Fengyi

2015-01-01

X-ray computed tomography (CT) is the most commonly used imaging technique for noninvasive diagnosis of disease. In order to improve tissue specificity and prevent adverse effects, we report the design and synthesis of iodine-doped carbon dots (I-doped CDs) as efficient CT contrast agents and fluorescence probe by a facile bottom-up hydrothermal carbonization process. The as-prepared I-doped CDs are monodispersed spherical nanoparticles (a diameter of ~2.7 nm) with favorable dispersibility and colloidal stability in water. The aqueous solution of I-doped CDs showed wavelength-dependent excitation and stable photoluminescence similar to traditional carbon quantum dots. Importantly, I-doped CDs displayed superior X-ray attenuation properties in vitro and excellent biocompatibility. After intravenous injection, I-doped CDs were distributed throughout the body and excreted by renal clearance. These findings validated that I-doped CDs with high X-ray attenuation potency and favorable photoluminescence show great promise for biomedical research and disease diagnosis.

Engineering iodine-doped carbon dots as dual-modal probes for fluorescence and X-ray CT imaging

PubMed Central

Zhang, Miaomiao; Ju, Huixiang; Zhang, Li; Sun, Mingzhong; Zhou, Zhongwei; Dai, Zhenyu; Zhang, Lirong; Gong, Aihua; Wu, Chaoyao; Du, Fengyi

2015-01-01

X-ray computed tomography (CT) is the most commonly used imaging technique for noninvasive diagnosis of disease. In order to improve tissue specificity and prevent adverse effects, we report the design and synthesis of iodine-doped carbon dots (I-doped CDs) as efficient CT contrast agents and fluorescence probe by a facile bottom-up hydrothermal carbonization process. The as-prepared I-doped CDs are monodispersed spherical nanoparticles (a diameter of ~2.7 nm) with favorable dispersibility and colloidal stability in water. The aqueous solution of I-doped CDs showed wavelength-dependent excitation and stable photoluminescence similar to traditional carbon quantum dots. Importantly, I-doped CDs displayed superior X-ray attenuation properties in vitro and excellent biocompatibility. After intravenous injection, I-doped CDs were distributed throughout the body and excreted by renal clearance. These findings validated that I-doped CDs with high X-ray attenuation potency and favorable photoluminescence show great promise for biomedical research and disease diagnosis. PMID:26609232

Template-free solution approach to synthesize CdS dendrites with SCN based ionic liquid

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

Li, Kangfeng; Li, Jiajia; Cheng, Xianyi

2011-07-15

Highlights: {yields} Template-free solution approach to synthesize CdS hierarchical dendrites. {yields} The 1-butyl-3-methlyimidazole thiocyanate ([BMIM][SCN]) plays doubly functional roles in the progress. {yields} The CdS hierarchical dendrites exhibit a more intense emission at 710 nm belongs to infrared band. -- Abstract: Cadmium sulfide dendrites were synthesized by a facile hydrothermal treatment from CdCl{sub 2} and ionic liquid 1-butyl-3-methlyimidazole thiocyanate acted both as sulfur source and surfactant. The product was characterized by means of X-ray powder diffraction and scanning electron microscopy. X-ray powder diffraction studies indicated that the product was well-crystallized hexagonal phase of CdS, and the scanning electron microscopy imagesmore » showed that the obtained powders consisted of a wealth of well-defined CdS dendritic microstructures with a pronounced trunk and highly ordered branches. The UV-Vis and photoluminescence spectroscopy measurements were taken as well. The possible formation mechanism of CdS dendrites was simply proposed in the end.« less

Prominence of fusion temperature and engineering heteroatoms on multifarious emissive shifts in carbon dots.

PubMed

Velusamy, Jayaramakrishnan; Ramos-Ortiz, Gabriel; Rodríguez, Mario; Hernández-Cruz, Olivia; Ponce, Arturo

2018-05-16

We present a simple but robust strategy to engineering heteroatoms (N, S) on carbon dots (CDs) surface that results in a collection of enhanced photoluminescence (PL) emissions. The use of citric acid (CA) and 2-Imidazolidinethione (2-IZT) as precursors was envisioned to study the impact of thermolysis process on the PL properties. The proposed strategy, implemented at two different temperatures (180 °C and 200 °C), is suitable to produce CDs with tunable PL and quantum yield (QY) up to ∼32%. Similar to earlier reports of CA-based CDs, the self-assembling of fluorophores integrated into the CDs edge is hypothesized, however, in our CDs a double intriguing effect of blue- and red-shifting can be observed for PL as the wavelength of excitation is increased in the range 280-480 nm. Through a comprehensive characterization and evaluation of these CDs in water suspensions, the mechanisms that lead to PL multifarious emissions are proposed. Copyright © 2018 Elsevier Inc. All rights reserved.

Enhancements in healthcare information technology systems: customizing vendor-supplied clinical decision support for a high-risk patient population.

PubMed

Tiwari, Ruchi; Tsapepas, Demetra S; Powell, Jaclyn T; Martin, Spencer T

2013-01-01

Healthcare organizations continue to adopt information technologies with clinical decision support (CDS) to prevent potential medication-related adverse drug events. End-users who are unfamiliar with certain high-risk patient populations are at an increased risk of unknowingly causing medication errors. The following case describes a heart transplant recipient exposed to supra-therapeutic concentrations of tacrolimus during co-administration of ritonavir as a result of vendor supplied CDS tools that omitted an interaction alert. After review of 4692 potential tacrolimus-based DDIs between 329 different drug pairs supplied by vendor CDS, the severity of 20 DDIs were downgraded and the severity of 62 were upgraded. The need for institution-specific customization of vendor-provided CDS is paramount to ensure avoidance of medication errors. Individualized care will become more important as patient populations and institutions become more specialized. In the future, vendors providing integrated CDS tools must be proactive in developing institution-specific and easily customizable CDS tools.

Enhancements in healthcare information technology systems: customizing vendor-supplied clinical decision support for a high-risk patient population

PubMed Central

Tiwari, Ruchi; Tsapepas, Demetra S; Powell, Jaclyn T

2013-01-01

Healthcare organizations continue to adopt information technologies with clinical decision support (CDS) to prevent potential medication-related adverse drug events. End-users who are unfamiliar with certain high-risk patient populations are at an increased risk of unknowingly causing medication errors. The following case describes a heart transplant recipient exposed to supra-therapeutic concentrations of tacrolimus during co-administration of ritonavir as a result of vendor supplied CDS tools that omitted an interaction alert. After review of 4692 potential tacrolimus-based DDIs between 329 different drug pairs supplied by vendor CDS, the severity of 20 DDIs were downgraded and the severity of 62 were upgraded. The need for institution-specific customization of vendor-provided CDS is paramount to ensure avoidance of medication errors. Individualized care will become more important as patient populations and institutions become more specialized. In the future, vendors providing integrated CDS tools must be proactive in developing institution-specific and easily customizable CDS tools. PMID:22813760

Photochemical Fabrication of Transition Metal Nanoparticles Using CdS Template and Their Co-Catalysis Effects for TiO2 Photocatalysis

NASA Astrophysics Data System (ADS)

Badhwar, Nidhi; Gupta, Nidhi; Pal, Bonamali

2013-09-01

Transition metal nanoparticles were prepared by chemical dissolution of CdS template from metal photodeposited CdS nanorod (length = 70-85 nm and width = 5-6 nm) heterocomposites. Size (9-10 nm) of metal nanoparticles obtained after CdS removal was larger than the size (4-6 nm) of metal nanodeposits over CdS template. The obtained Au nanoparticles displayed a broad red shifted absorption band at 660 nm, whereas Pt, Pd and Rh nanoparticles exhibit featureless absorption spectra. Elemental analysis confirms the complete removal of CdS template from Au-CdS (Au — 2.65 at.%) and Ag-CdS (Ag — 2.06 at.%) composites showing no Cd peak. These metal nanoparticles imparted dissimilar co-catalytic activity of TiO2 for photocatalytic degradation of salicylic acid in the order Au > Pt > Pd > Ag > Rh as a function of their nature, electronegativity, redox potential and work function.

Highly Efficient Red-Emitting Carbon Dots with Gram-Scale Yield for Bioimaging.

PubMed

Ding, Hui; Wei, Ji-Shi; Zhong, Ning; Gao, Qing-Yu; Xiong, Huan-Ming

2017-11-07

Carbon dots (CDs) are a new class of photoluminescent (PL), biocompatible, environment-friendly, and low-cost carbon nanomaterials. Synthesis of highly efficient red-emitting carbon dots (R-CDs) on a gram scale is a great challenge at present, which heavily restricts the wide applications of CDs in the bioimaging field. Herein, R-CDs with a high quantum yield (QY) of 53% are produced on a gram scale by heating a formamide solution of citric acid and ethylenediamine. The as-prepared R-CDs have an average size of 4.1 nm and a nitrogen content of about 30%, with an excitation-independent emission at 627 nm. After detailed characterizations, such strong red fluorescence is ascribed to the contribution from the nitrogen- and oxygen-related surface states and the nitrogen-derived structures in the R-CD cores. Our R-CDs show good photostability and low cytotoxicity, and thus they are excellent red fluorescence probes for bioimaging both in vitro and in vivo.

Carbon dot/polyvinylpyrrolidone hybrid nanofibers with efficient solid-state photoluminescence constructed using an electrospinning technique

NASA Astrophysics Data System (ADS)

Zhai, Yue; Bai, Xue; Cui, Haining; Zhu, Jinyang; Liu, Wei; Zhang, Tianxiang; Dong, Biao; Pan, Gencai; Xu, Lin; Zhang, Shuang; Song, Hongwei

2018-01-01

Carbon dots (CDs) are the promising candidates for application in optoelectronic and biological areas due to their excellent photostability, unique photoluminescence, good biocompatibility, low toxicity and chemical inertness. However, the self-quenching of photoluminescence as they are dried into the solid state dramatically limits their further application. Therefore, realizing efficient photoluminescence and large-scale production of CDs in the solid state is an urgent challenge. Herein, solid-state hybrid nanofibers based on CDs and polyvinylpyrrolidone (PVP) are constructed through an electrospinning process. The resulting solid-state hybrid PVP/CD nanofibers present much enhanced photoluminescence performance compared to the corresponding pristine colloidal CDs due to the decrease in non-radiative recombination of electron-holes. Owing to the suppressed self-quenching of CDs, the photoluminescence quantum yield is considerably improved from 42.9% of pristine CDs to 83.5% of nanofibers under the excitation wavelength of 360 nm. This has great application potential in optical or optoelectronic devices.

Cultivating Fluorescent Flowers with Highly Luminescent Carbon Dots Fabricated by a Double Passivation Method

PubMed Central

Chang, Tao; Zhao, Haiping; Du, Huanhuan; Liu, Shan; Wu, Baoshuang; Qin, Shenjun

2017-01-01

In this work, we present the fabrication of highly luminescent carbon dots (CDs) by a double passivation method with the assistance of Ca(OH)2. In the reaction process, Ca2+ protects the active functional groups from overconsumption during dehydration and carbonization, and the electron-withdrawing groups on the CD surface are converted to electron-donating groups by the hydroxyl ions. As a result, the fluorescence quantum yield of the CDs was found to increase with increasing Ca(OH)2 content in the reaction process. A blue-shift optical spectrum of the CDs was also found with increasing Ca(OH)2 content, which could be attributed to the increasing of the energy gaps for the CDs. The highly photoluminescent CDs obtained (quantum yield: 86%) were used to cultivate fluorescent carnations by a water culture method, while the results of fluorescence microscopy analysis indicated that the CDs had entered the plant tissue structure. PMID:28686178

Mesoporous structured MIPs@CDs fluorescence sensor for highly sensitive detection of TNT.

PubMed

Xu, Shoufang; Lu, Hongzhi

2016-11-15

A facile strategy was developed to prepare mesoporous structured molecularly imprinted polymers capped carbon dots (M-MIPs@CDs) fluorescence sensor for highly sensitive and selective determination of TNT. The strategy using amino-CDs directly as "functional monomer" for imprinting simplify the imprinting process and provide well recognition sites accessibility. The as-prepared M-MIPs@CDs sensor, using periodic mesoporous silica as imprinting matrix, and amino-CDs directly as "functional monomer", exhibited excellent selectivity and sensitivity toward TNT with detection limit of 17nM. The recycling process was sustainable for 10 times without obvious efficiency decrease. The feasibility of the developed method in real samples was successfully evaluated through the analysis of TNT in soil and water samples with satisfactory recoveries of 88.6-95.7%. The method proposed in this work was proved to be a convenient and practical way to prepare high sensitive and selective fluorescence MIPs@CDs sensors. Copyright © 2016 Elsevier B.V. All rights reserved.

Synthesis and spectral studies on Cd(II) dithiocarbamate complexes and their use as precursors for CdS nanoparticles

NASA Astrophysics Data System (ADS)

Sathiyaraj, Ethiraj; Padmavathy, Krishnaraj; Kumar, Chandran Udhaya; Krishnan, Kannan Gokula; Ramalingan, Chennan

2017-11-01

Bis(N-cyclopropyl-N-4-chlorobenzyldithiocarbamato-S,S‧)cadmium(II) (1) and (2,2‧-bipyridine) bis(N-cyclopropyl-N-4-chlorobenzyldithiocarbamato-S,S‧)cadmium(II) (2) have been synthesized and characterized by FT-IR, 1HNMR and 13C NMR analyses. For the complex 2, single crystal X-ray diffraction analysis and computational studies (optimized geometry, HOMO-LUMO and MEP) have been executed employing DFT/B3LYP method with LANL 2DZ basic set. The optimized bond lengths and bond angles agree well with the experimental results. The complexes 1 and 2 have been used as single source precursors for the synthesis of ethyleneglycol capped CdS1 and CdS2 nanoparticles, respectively. CdS1 and CdS2 nanoparticles have been synthesized by solvothermal method. PXRD, SEM, Elemental colour mapping, EDAX, TEM and UV-Vis spectroscopy have been used to characterize the as-prepared CdS nanoparticles. The X-ray diffraction pattern confirms both their hexagonal structures.

A Partial Least Squares Based Procedure for Upstream Sequence Classification in Prokaryotes.

PubMed

Mehmood, Tahir; Bohlin, Jon; Snipen, Lars

2015-01-01

The upstream region of coding genes is important for several reasons, for instance locating transcription factor, binding sites, and start site initiation in genomic DNA. Motivated by a recently conducted study, where multivariate approach was successfully applied to coding sequence modeling, we have introduced a partial least squares (PLS) based procedure for the classification of true upstream prokaryotic sequence from background upstream sequence. The upstream sequences of conserved coding genes over genomes were considered in analysis, where conserved coding genes were found by using pan-genomics concept for each considered prokaryotic species. PLS uses position specific scoring matrix (PSSM) to study the characteristics of upstream region. Results obtained by PLS based method were compared with Gini importance of random forest (RF) and support vector machine (SVM), which is much used method for sequence classification. The upstream sequence classification performance was evaluated by using cross validation, and suggested approach identifies prokaryotic upstream region significantly better to RF (p-value < 0.01) and SVM (p-value < 0.01). Further, the proposed method also produced results that concurred with known biological characteristics of the upstream region.

Golay sequences coded coherent optical OFDM for long-haul transmission

NASA Astrophysics Data System (ADS)

Qin, Cui; Ma, Xiangrong; Hua, Tao; Zhao, Jing; Yu, Huilong; Zhang, Jian

2017-09-01

We propose to use binary Golay sequences in coherent optical orthogonal frequency division multiplexing (CO-OFDM) to improve the long-haul transmission performance. The Golay sequences are generated by binary Reed-Muller codes, which have low peak-to-average power ratio and certain error correction capability. A low-complexity decoding algorithm for the Golay sequences is then proposed to recover the signal. Under same spectral efficiency, the QPSK modulated OFDM with binary Golay sequences coding with and without discrete Fourier transform (DFT) spreading (DFTS-QPSK-GOFDM and QPSK-GOFDM) are compared with the normal BPSK modulated OFDM with and without DFT spreading (DFTS-BPSK-OFDM and BPSK-OFDM) after long-haul transmission. At a 7% forward error correction code threshold (Q2 factor of 8.5 dB), it is shown that DFTS-QPSK-GOFDM outperforms DFTS-BPSK-OFDM by extending the transmission distance by 29% and 18%, in non-dispersion managed and dispersion managed links, respectively.

Designing Real-time Decision Support for Trauma Resuscitations

PubMed Central

Yadav, Kabir; Chamberlain, James M.; Lewis, Vicki R.; Abts, Natalie; Chawla, Shawn; Hernandez, Angie; Johnson, Justin; Tuveson, Genevieve; Burd, Randall S.

2016-01-01

Background Use of electronic clinical decision support (eCDS) has been recommended to improve implementation of clinical decision rules. Many eCDS tools, however, are designed and implemented without taking into account the context in which clinical work is performed. Implementation of the pediatric traumatic brain injury (TBI) clinical decision rule at one Level I pediatric emergency department includes an electronic questionnaire triggered when ordering a head computed tomography using computerized physician order entry (CPOE). Providers use this CPOE tool in less than 20% of trauma resuscitation cases. A human factors engineering approach could identify the implementation barriers that are limiting the use of this tool. Objectives The objective was to design a pediatric TBI eCDS tool for trauma resuscitation using a human factors approach. The hypothesis was that clinical experts will rate a usability-enhanced eCDS tool better than the existing CPOE tool for user interface design and suitability for clinical use. Methods This mixed-methods study followed usability evaluation principles. Pediatric emergency physicians were surveyed to identify barriers to using the existing eCDS tool. Using standard trauma resuscitation protocols, a hierarchical task analysis of pediatric TBI evaluation was developed. Five clinical experts, all board-certified pediatric emergency medicine faculty members, then iteratively modified the hierarchical task analysis until reaching consensus. The software team developed a prototype eCDS display using the hierarchical task analysis. Three human factors engineers provided feedback on the prototype through a heuristic evaluation, and the software team refined the eCDS tool using a rapid prototyping process. The eCDS tool then underwent iterative usability evaluations by the five clinical experts using video review of 50 trauma resuscitation cases. A final eCDS tool was created based on their feedback, with content analysis of the evaluations performed to ensure all concerns were identified and addressed. Results Among 26 EPs (76% response rate), the main barriers to using the existing tool were that the information displayed is redundant and does not fit clinical workflow. After the prototype eCDS tool was developed based on the trauma resuscitation hierarchical task analysis, the human factors engineers rated it to be better than the CPOE tool for nine of 10 standard user interface design heuristics on a three-point scale. The eCDS tool was also rated better for clinical use on the same scale, in 84% of 50 expert–video pairs, and was rated equivalent in the remainder. Clinical experts also rated barriers to use of the eCDS tool as being low. Conclusions An eCDS tool for diagnostic imaging designed using human factors engineering methods has improved perceived usability among pediatric emergency physicians. PMID:26300010

Equilibrium chemistry down to 100 K. Impact of silicates and phyllosilicates on the carbon to oxygen ratio

NASA Astrophysics Data System (ADS)

Woitke, P.; Helling, Ch.; Hunter, G. H.; Millard, J. D.; Turner, G. E.; Worters, M.; Blecic, J.; Stock, J. W.

2018-06-01

We have introduced a fast and versatile computer code, GGCHEM, to determine the chemical composition of gases in thermo-chemical equilibrium down to 100 K, with or without equilibrium condensation. We have reviewed the data for molecular equilibrium constants, kp(T), from several sources and discussed which functional fits are most suitable for low temperatures. We benchmarked our results against another chemical equilibrium code. We collected Gibbs free energies, ΔGf⊖, for about 200 solid and liquid species from the NIST-JANAF database and the geophysical database SUPCRTBL. We discussed the condensation sequence of the elements with solar abundances in phase equilibrium down to 100 K. Once the major magnesium silicates Mg2SiO4[s] and MgSiO3[s] have formed, the dust to gas mass ratio jumps to a value of about 0.0045 which is significantly lower than the often assumed value of 0.01. Silicate condensation is found to increase the carbon to oxygen ratio (C/O) in the gas from its solar value of 0.55 up to 0.71, and, by the additional intake of water and hydroxyl into the solid matrix, the formation of phyllosilicates at temperatures below 400 K increases the gaseous C/O further to about 0.83. Metallic tungsten (W) is the first condensate found to become thermodynamically stable around 1600-2200 K (depending on pressure), several hundreds of Kelvin before subsequent materials such as zirconium dioxide (ZrO2) or corundum (Al2O3) can condense. We briefly discuss whether tungsten, despite its low abundance of 2 × 10-7 times the silicon abundance, could provide the first seed particles for astrophysical dust formation. GGCHEM code is publicly available at http://https://github.com/pw31/GGchemTable D.1 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/614/A1

Advising Medical Students for the Match: A National Survey of Pediatrics Clerkship Directors.

PubMed

Ryan, Michael S; Levine, Leonard J; Colbert-Getz, Jorie M; Spector, Nancy D; Fromme, H Barrett

2015-01-01

To describe the role and perspectives of pediatrics clerkship directors (CDs) who provide advice to students who apply to Pediatrics residency training programs. We developed a survey based on previous studies and data from the 2012 National Residency Matching Program- Program Director (NRMP-PD) survey. Topics included CDs roles and confidence in advising, perspectives on applicants' competitiveness, and resources used to inform advising practice. This survey was disseminated as part of the 2013 Council on Medical Student Education in Pediatrics annual survey. CDs from 63 (45%) Liaison Committee for Medical Education-accredited medical schools in the United States responded. All CDs had some advising role, and most (68%) served in a formal advising capacity. Most (58%) also participated in the intern selection process at their institution. Those with formal advising roles were not significantly more confident in their advising than those without formal roles. CDs relied heavily on subjective resources and most did not use the NRMP-PD survey data. Despite this, the perspectives of CDs were similar to those of program directors based on the most recent NRMP-PD survey. Pediatrics CDs uniformly serve in advising capacities and have perspectives that compare favorably with those of program directors. Despite this concordance, the high reliance on subjective resources and the frequency in which CDs participate in intern selection raises concern. The results of this study have several implications for key stakeholders in the residency selection process. Copyright © 2015 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

Key principles for a national clinical decision support knowledge sharing framework: synthesis of insights from leading subject matter experts.

PubMed

Kawamoto, Kensaku; Hongsermeier, Tonya; Wright, Adam; Lewis, Janet; Bell, Douglas S; Middleton, Blackford

2013-01-01

To identify key principles for establishing a national clinical decision support (CDS) knowledge sharing framework. As part of an initiative by the US Office of the National Coordinator for Health IT (ONC) to establish a framework for national CDS knowledge sharing, key stakeholders were identified. Stakeholders' viewpoints were obtained through surveys and in-depth interviews, and findings and relevant insights were summarized. Based on these insights, key principles were formulated for establishing a national CDS knowledge sharing framework. Nineteen key stakeholders were recruited, including six executives from electronic health record system vendors, seven executives from knowledge content producers, three executives from healthcare provider organizations, and three additional experts in clinical informatics. Based on these stakeholders' insights, five key principles were identified for effectively sharing CDS knowledge nationally. These principles are (1) prioritize and support the creation and maintenance of a national CDS knowledge sharing framework; (2) facilitate the development of high-value content and tooling, preferably in an open-source manner; (3) accelerate the development or licensing of required, pragmatic standards; (4) acknowledge and address medicolegal liability concerns; and (5) establish a self-sustaining business model. Based on the principles identified, a roadmap for national CDS knowledge sharing was developed through the ONC's Advancing CDS initiative. The study findings may serve as a useful guide for ongoing activities by the ONC and others to establish a national framework for sharing CDS knowledge and improving clinical care.

Reducing risk with clinical decision support: a study of closed malpractice claims.

PubMed

Zuccotti, G; Maloney, F L; Feblowitz, J; Samal, L; Sato, L; Wright, A

2014-01-01

Identify clinical opportunities to intervene to prevent a malpractice event and determine the proportion of malpractice claims potentially preventable by clinical decision support (CDS). Cross-sectional review of closed malpractice claims over seven years from one malpractice insurance company and seven hospitals in the Boston area. For each event, clinical opportunities to intervene to avert the malpractice event and the presence or absence of CDS that might have a role in preventing the event, were assigned by a panel of expert raters. Compensation paid out to resolve a claim (indemnity), was associated with each CDS type. Of the 477 closed malpractice cases, 359 (75.3%) were categorized as substantiated and 195 (54%) had at least one opportunity to intervene. Common opportunities to intervene related to performance of procedure, diagnosis, and fall prevention. We identified at least one CDS type for 63% of substantiated claims. The 41 CDS types identified included clinically significant test result alerting, diagnostic decision support and electronic tracking of instruments. Cases with at least one associated intervention accounted for $40.3 million (58.9%) of indemnity. CDS systems and other forms of health information technology (HIT) are expected to improve quality of care, but their potential to mitigate risk had not previously been quantified. Our results suggest that, in addition to their known benefits for quality and safety, CDS systems within HIT have a potential role in decreasing malpractice payments. More than half of malpractice events and over $40 million of indemnity were potentially preventable with CDS.

Cadmium sulfide quantum dots induce oxidative stress and behavioral impairments in the marine clam Scrobicularia plana.

PubMed

Buffet, Pierre-Emmanuel; Zalouk-Vergnoux, Aurore; Poirier, Laurence; Lopes, Christelle; Risso-de-Faverney, Christine; Guibbolini, Marielle; Gilliland, Douglas; Perrein-Ettajani, Hanane; Valsami-Jones, Eugenia; Mouneyrac, Catherine

2015-07-01

Cadmium sulfide (CdS) quantum dots have a number of current applications in electronics and solar cells and significant future potential in medicine. The aim of the present study was to examine the toxic effects of CdS quantum dots on the marine clam Scrobicularia plana exposed for 14 d to these nanomaterials (10 µg Cd L(-1) ) in natural seawater and to compare them with soluble Cd. Measurement of labile Cd released from CdS quantum dots showed that 52% of CdS quantum dots remained in the nanoparticulate form. Clams accumulated the same levels of Cd regardless of the form in which it was delivered (soluble Cd vs CdS quantum dots). However, significant changes in biochemical responses were observed in clams exposed to CdS quantum dots compared with soluble Cd. Increased activities of catalase and glutathione-S-transferase were significantly higher in clams exposed in seawater to Cd as the nanoparticulate versus the soluble form, suggesting a specific nano effect. The behavior of S. plana in sediment showed impairments of foot movements only in the case of exposure to CdS quantum dots. The results show that oxidative stress and behavior biomarkers are sensitive predictors of CdS quantum dots toxicity in S. plana. Such responses, appearing well before changes might occur at the population level, demonstrate the usefulness of this model species and type of biomarker in the assessment of nanoparticle contamination in estuarine ecosystems. © 2015 SETAC.

Surface and interface of epitaxial CdTe film on CdS buffered van der Waals mica substrate

NASA Astrophysics Data System (ADS)

Yang, Y.-B.; Seewald, L.; Mohanty, Dibyajyoti; Wang, Y.; Zhang, L. H.; Kisslinger, K.; Xie, Weiyu; Shi, J.; Bhat, I.; Zhang, Shengbai; Lu, T.-M.; Wang, G.-C.

2017-08-01

Single crystal CdTe films are desirable for optoelectronic device applications. An important strategy of creating films with high crystallinity is through epitaxial growth on a proper single crystal substrate. We report the metalorganic chemical vapor deposition of epitaxial CdTe films on the CdS/mica substrate. The epitaxial CdS film was grown on a mica surface by thermal evaporation. Due to the weak van der Waals forces, epitaxy is achieved despite the very large interface lattice mismatch between CdS and mica (∼21-55%). The surface morphology of mica, CdS and CdTe were quantified by atomic force microscopy. The near surface structures, orientations and texture of CdTe and CdS films were characterized by the unique reflection high-energy electron diffraction surface pole figure technique. The interfaces of CdTe and CdS films and mica were characterized by X-ray pole figure technique and transmission electron microscopy. The out-of-plane and in-plane epitaxy of the heteroepitaxial films stack are determined to be CdTe(111)//CdS(0001)//mica(001) and [1 bar2 1 bar]CdTe//[ 1 bar100]CdS//[010]mica, respectively. The measured photoluminescence (PL), time resolved PL, photoresponse, and Hall mobility of the CdTe/CdS/mica indicate quality films. The use of van der Waals surface to grow epitaxial CdTe/CdS films offers an alternative strategy towards infrared imaging and solar cell applications.

A carbon dot-based "off-on" fluorescent probe for highly selective and sensitive detection of phytic acid.

PubMed

Gao, Zhao; Wang, Libing; Su, Rongxin; Huang, Renliang; Qi, Wei; He, Zhimin

2015-08-15

We herein report a facile, one-step pyrolysis synthesis of photoluminescent carbon dots (CDs) using citric acid as the carbon source and lysine as the surface passivation reagent. The as-prepared CDs show narrow size distribution, excellent blue fluorescence and good photo-stability and water dispersivity. The fluorescence of the CDs was found to be effectively quenched by ferric (Fe(III)) ions with high selectivity via a photo-induced electron transfer (PET) process. Upon addition of phytic acid (PA) to the CDs/Fe(III) complex dispersion, the fluorescence of the CDs was significantly recovered, arising from the release of Fe(III) ions from the CDs/Fe(III) complex because PA has a higher affinity for Fe(III) ions compared to CDs. Furthermore, we developed an "off-on" fluorescence assay method for the detection of phytic acid using CDs/Fe(III) as a fluorescent probe. This probe enables the selective detection of PA with a linear range of 0.68-18.69 μM and a limit of detection (signal-to-noise ratio is 3) of 0.36 μM. The assay method demonstrates high selectivity, repeatability, stability and recovery ratio in the detection of the standard and real PA samples. We believe that the facile operation, low-cost, high sensitivity and selectivity render this CD-based "off-on" fluorescent probe an ideal sensing platform for the detection of PA. Copyright © 2015 Elsevier B.V. All rights reserved.

BASiNET-BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification.

PubMed

Ito, Eric Augusto; Katahira, Isaque; Vicente, Fábio Fernandes da Rocha; Pereira, Luiz Filipe Protasio; Lopes, Fabrício Martins

2018-06-05

With the emergence of Next Generation Sequencing (NGS) technologies, a large volume of sequence data in particular de novo sequencing was rapidly produced at relatively low costs. In this context, computational tools are increasingly important to assist in the identification of relevant information to understand the functioning of organisms. This work introduces BASiNET, an alignment-free tool for classifying biological sequences based on the feature extraction from complex network measurements. The method initially transform the sequences and represents them as complex networks. Then it extracts topological measures and constructs a feature vector that is used to classify the sequences. The method was evaluated in the classification of coding and non-coding RNAs of 13 species and compared to the CNCI, PLEK and CPC2 methods. BASiNET outperformed all compared methods in all adopted organisms and datasets. BASiNET have classified sequences in all organisms with high accuracy and low standard deviation, showing that the method is robust and non-biased by the organism. The proposed methodology is implemented in open source in R language and freely available for download at https://cran.r-project.org/package=BASiNET.

The Number, Organization, and Size of Polymorphic Membrane Protein Coding Sequences as well as the Most Conserved Pmp Protein Differ within and across Chlamydia Species.

PubMed

Van Lent, Sarah; Creasy, Heather Huot; Myers, Garry S A; Vanrompay, Daisy

2016-01-01

Variation is a central trait of the polymorphic membrane protein (Pmp) family. The number of pmp coding sequences differs between Chlamydia species, but it is unknown whether the number of pmp coding sequences is constant within a Chlamydia species. The level of conservation of the Pmp proteins has previously only been determined for Chlamydia trachomatis. As different Pmp proteins might be indispensible for the pathogenesis of different Chlamydia species, this study investigated the conservation of Pmp proteins both within and across C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci. The pmp coding sequences were annotated in 16 C. trachomatis, 6 C. pneumoniae, 2 C. abortus, and 16 C. psittaci genomes. The number and organization of polymorphic membrane coding sequences differed within and across the analyzed Chlamydia species. The length of coding sequences of pmpA,pmpB, and pmpH was conserved among all analyzed genomes, while the length of pmpE/F and pmpG, and remarkably also of the subtype pmpD, differed among the analyzed genomes. PmpD, PmpA, PmpH, and PmpA were the most conserved Pmp in C. trachomatis,C. pneumoniae,C. abortus, and C. psittaci, respectively. PmpB was the most conserved Pmp across the 4 analyzed Chlamydia species. © 2016 S. Karger AG, Basel.

A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

PubMed Central

Kress, W. John; Erickson, David L.

2007-01-01

Background A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Methodology/Principal Findings Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. Conclusions/Significance A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination. PMID:17551588

A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification.

PubMed

Cenik, Can; Chua, Hon Nian; Singh, Guramrit; Akef, Abdalla; Snyder, Michael P; Palazzo, Alexander F; Moore, Melissa J; Roth, Frederick P

2017-03-01

Introns are found in 5' untranslated regions (5'UTRs) for 35% of all human transcripts. These 5'UTR introns are not randomly distributed: Genes that encode secreted, membrane-bound and mitochondrial proteins are less likely to have them. Curiously, transcripts lacking 5'UTR introns tend to harbor specific RNA sequence elements in their early coding regions. To model and understand the connection between coding-region sequence and 5'UTR intron status, we developed a classifier that can predict 5'UTR intron status with >80% accuracy using only sequence features in the early coding region. Thus, the classifier identifies transcripts with 5 ' proximal- i ntron- m inus-like-coding regions ("5IM" transcripts). Unexpectedly, we found that the early coding sequence features defining 5IM transcripts are widespread, appearing in 21% of all human RefSeq transcripts. The 5IM class of transcripts is enriched for non-AUG start codons, more extensive secondary structure both preceding the start codon and near the 5' cap, greater dependence on eIF4E for translation, and association with ER-proximal ribosomes. 5IM transcripts are bound by the exon junction complex (EJC) at noncanonical 5' proximal positions. Finally, N 1 -methyladenosines are specifically enriched in the early coding regions of 5IM transcripts. Taken together, our analyses point to the existence of a distinct 5IM class comprising ∼20% of human transcripts. This class is defined by depletion of 5' proximal introns, presence of specific RNA sequence features associated with low translation efficiency, N 1 -methyladenosines in the early coding region, and enrichment for noncanonical binding by the EJC. © 2017 Cenik et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

A DS-UWB Cognitive Radio System Based on Bridge Function Smart Codes

NASA Astrophysics Data System (ADS)

Xu, Yafei; Hong, Sheng; Zhao, Guodong; Zhang, Fengyuan; di, Jinshan; Zhang, Qishan

This paper proposes a direct-sequence UWB Gaussian pulse of cognitive radio systems based on bridge function smart sequence matrix and the Gaussian pulse. As the system uses the spreading sequence code, that is the bridge function smart code sequence, the zero correlation zones (ZCZs) which the bridge function sequences' auto-correlation functions had, could reduce multipath fading of the pulse interference. The Modulated channel signal was sent into the IEEE 802.15.3a UWB channel. We analysis the ZCZs's inhibition to the interference multipath interference (MPI), as one of the main system sources interferences. The simulation in SIMULINK/MATLAB is described in detail. The result shows the system has better performance by comparison with that employing Walsh sequence square matrix, and it was verified by the formula in principle.

Reducing Diagnostic Error with Computer-Based Clinical Decision Support

ERIC Educational Resources Information Center

Greenes, Robert A.

2009-01-01

Information technology approaches to delivering diagnostic clinical decision support (CDS) are the subject of the papers to follow in the proceedings. These will address the history of CDS and present day approaches (Miller), evaluation of diagnostic CDS methods (Friedman), and the role of clinical documentation in supporting diagnostic decision…

Unesco Integrated Documentation Network; Computerized Documentation System (CDS).

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Paris (France). Dept. of Documentation, Libraries, and Archives.

Intended for use by the Computerized Documentation System (CDS), the Unesco version of ISIS (Integrated Set of Information Systems)--originally developed by the International Labour Organization--was developed in 1975 and named CDS/ISIS. This system has a comprehensive collection of programs for input, management, and output, running in batch or…

Preparation of CdS Nanoparticles by First-Year Undergraduates

ERIC Educational Resources Information Center

Winkelmann, Kurt; Noviello, Thomas; Brooks, Stephen

2007-01-01

The first year undergraduates use a simple method to synthesize 5-nm CdS nanoparticles in a water-in-oil microemulsion. The quantum size effect, the relationship between colors, optical absorbance, band-gap energy and the CdS particles affected by the formation of micelles are observed.

The Ever-Present Demand for Public Computing Resources. CDS Spotlight

ERIC Educational Resources Information Center

Pirani, Judith A.

2014-01-01

This Core Data Service (CDS) Spotlight focuses on public computing resources, including lab/cluster workstations in buildings, virtual lab/cluster workstations, kiosks, laptop and tablet checkout programs, and workstation access in unscheduled classrooms. The findings are derived from 758 CDS 2012 participating institutions. A dataset of 529…

Effects of coordination agents on the morphology of CdS nanocrystallites synthesized by the hydrothermal method

NASA Astrophysics Data System (ADS)

Nie, Qiulin; Yuan, Qiuli; Chen, Weixiang; Xu, Zhude

2004-05-01

CdS nanocrystallites were synthesized by the hydrothermal method and characterized by XRD, TEM, and XPS, respectively. Different coordination agents were chosen as the template to investigate their effects on the product morphology. It was found that the CdS nanocrystallites displayed a rod-like shape when ethylenediamine or methylamine were employed as the template. In contrast, only nanoparticles of CdS were observed when ammonia or pyridine were used. Based on our experimental results, a complex structure-controlling mechanism is proposed.

Chemical synthesis of CdS onto TiO2 nanorods for quantum dot sensitized solar cells

NASA Astrophysics Data System (ADS)

Pawar, Sachin A.; Patil, Dipali S.; Lokhande, Abhishek C.; Gang, Myeng Gil; Shin, Jae Cheol; Patil, Pramod S.; Kim, Jin Hyeok

2016-08-01

A quantum dot sensitized solar cell (QDSSC) is fabricated using hydrothermally grown TiO2 nanorods and successive ionic layer adsorption and reaction (SILAR) deposited CdS. Surface morphology of the TiO2 films coated with different SILAR cycles of CdS is examined by Scanning Electron Microscopy which revealed aggregated CdS QDs coverage grow on increasing onto the TiO2 nanorods with respect to cycle number. Under AM 1.5G illumination, we found the TiO2/CdS QDSSC photoelectrode shows a power conversion efficiency of 1.75%, in an aqueous polysulfide electrolyte with short-circuit photocurrent density of 4.04 mA/cm2 which is higher than that of a bare TiO2 nanorods array.

Bacteria-Derived Carbon Dots Inhibit Biofilm Formation of Escherichia coli without Affecting Cell Growth

PubMed Central

Lin, Fengming; Li, Chengcheng; Chen, Zhan

2018-01-01

Biofilms are deleterious in many biomedical and industrial applications and prevention of their formation has been a pressing challenge. Here, carbon dots, CDs-LP that were easily synthesized from the biomass of Lactobacillus plantarum by one-step hydrothermal carbonization, were demonstrated to prevent biofilm formation of E. coli. CDs-LP did not thwart the growth of E. coli, indicating the anti-biofilm effect was not due to the bactericidal effect. Moreover, CDs-LP did not affect the growth of the animal cell AT II, showing low cytotoxicity, good safety and excellent biocompatibility. Therefore, CDs-LP could overcome the cytotoxicity issue found in many current antibiofilm agents. CDs-LP represent a new type of anti-biofilm materials, opening up a novel avenue to the development of biofilm treatment. PMID:29503644

The preparation of ethylenediamine-modified fluorescent carbon dots and their use in imaging of cells.

PubMed

Dong, Wei; Zhou, Siqi; Dong, Yan; Wang, Jingwen; Ge, Xin; Sui, Lili

2015-09-01

In this work, fluorescent carbon dots (CDs) were synthesized using a hydrothermal method with glucose as the carbon source and were surface-modified with ethylenediamine. The properties of as-prepared CDs were analyzed by transmission electron microscopy (TEM), Fourier transform infrared (FTIR), ultraviolet-visible light (UV/vis) absorption and fluorescent spectra. Furthermore, CDs conjugated with mouse anti-(human carcinoembryonic antigen) (CEA) monoclonal antibody were successful employed in the biolabeling and fluorescent imaging of human gastric carcinoma cells. In addition, the cytotoxicity of CDs was also tested using human gastric carcinoma cells. There was no apparent cytotoxicity on human gastric carcinoma cells. These results suggest the potential application of the as-prepared CDs in bioimaging and related fields. Copyright © 2015 John Wiley & Sons, Ltd.

Photoluminescence and structural characteristics of CdS nanoclusters synthesized by hydrothermal microemulsion

NASA Astrophysics Data System (ADS)

Liu, Bing; Xu, G. Q.; Gan, L. M.; Chew, C. H.; Li, W. S.; Shen, Z. X.

2001-01-01

Spherical and uniform CdS nanoclusters were synthesized by hydrothermal microemulsion. The reaction of Cd2+ ions with S2- ions generated from the decomposition of thioacetamide proceeded in water microdroplets. The mean diameter of the CdS nanoclusters can be varied from 20 to 80 nm by increasing the reaction temperature from 30 to 120 °C. XRD results indicate that the resulting CdS nanoclusters have a reduced and distorted hexagonal lattice compared to bulk materials. Two intense luminescence bands, i.e., green and red, were observed to coexist in the CdS nanoclusters. Their peak positions and relative intensities were found to be sensitive to the size and structure of nanoclusters. These emissions are attributed to surface defects (green emission) and the Cd-Cl composite vacancies (red emission).

Enhanced photocatalytic hydrogen evolution from in situ formation of few-layered MoS2/CdS nanosheet-based van der Waals heterostructures.

PubMed

Iqbal, Shahid; Pan, Ziwei; Zhou, Kebin

2017-05-25

Here we report for the first time that the H 2 bubbles generated by photocatalytic water splitting are effective in the layer-by-layer exfoliation of MoS 2 nanocrystals (NCs) into few layers. The as-obtained few layers can be in situ assembled with CdS nanosheets (NSs) into van der Waals heterostructures (vdWHs) of few-layered MoS 2 /CdS NSs which, in turn, are effective in charge separation and transfer, leading to enhanced photocatalytic H 2 production activity. The few-layered MoS 2 /CdS vdWHs exhibited a H 2 evolution rate of 140 mmol g (CdS) -1 h -1 and achieved an apparent quantum yield of 66% at 420 nm.

A study on the enhancement of opto-electronic properties of CdS thin films: seed-assisted fabrication

NASA Astrophysics Data System (ADS)

Kumarage, W. G. C.; Wijesundera, R. P.; Seneviratne, V. A.; Jayalath, C. P.; Dassanayake, B. S.

2017-04-01

A novel method of fabricating chemical bath deposited CdS thin films (CBD-CdS) by using electrodeposited CdS (ED-CdS) as a seed layer is reported. The resulting thin, compact, uniform and adherent seed-assisted CdS films (ED/CBD-CdS) show enhanced effective surface area compared to both ED-CdS and CBD-CdS. The phase of these CdS films was determined to be hexagonal. The fabricated ED/CBD-CdS films show higher photoelectrochemical (PEC) cell efficiency than either ED-CdS and CBD-CdS thin films. Carrier concentration and flat band potential values for ED/CBD-CdS systems are also found to be superior compared to both ED-CdS and CBD-CdS systems.

Structural and optical properties of Ni-doped CdS thin films prepared by chemical bath deposition method

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

Premarani, R.; Saravanakumar, S., E-mail: sarophy84@gmail.com; Chandramohan, R.

2015-06-24

The structural and optical behavior of undoped Cadmiun Sulphide (CdS) and Ni-doped CdS thinfilms prepared by Chemical Bath Deposition (CBD) technique is reported. The crystallite sizes of the thinfilms have been characterized by X-ray diffraction pattern (XRD). The particle sizes increase with the increase of Ni content in the CdS thinfilms. Scanning Electron Microscope (SEM) results indicated that CdS thinfilms is made up of aggregate of spherical-like particles. The composition was estimated by Energy Dispersive Analysis of X-ray (EDX) and reported. Spectroscopic studies revealed considerable improvement in transmission and the band gap of the films changes with addition of Nimore » dopant that is associated with variation in crystallite sizes in the nano regime.« less

Structural, optical and photoelectric properties of sprayed CdS thin films

NASA Astrophysics Data System (ADS)

Chandel, Tarun; Dwivedi, Shailendra Kumar; Zaman, M. Burhanuz; Rajaram, P.

2018-05-01

In this study, CdS thin films were grown via a facile spray pyrolysis technique. The crystalline phase, morphological, compositional and optical properties of the CdS thin films have been studied using X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and UV-vis absorption spectroscopy, respectively. XRD patterns show that the grown CdS films crystallized in the hexagonal structure. Scanning electron microscopy (SEM) study shows that the surfaces of the films are smooth and are uniformly covered with nanoparticles. EDAX results reveal that the grown films have good stochiometry. UV-vis spectroscopy shows that the grown films have transparency above 80% over the entire visible region. The photo-electric response of the CdS films grown on glass substrates has been observed.

Construction of an all-solid-state artificial Z-scheme system consisting of Bi2WO6/Au/CdS nanostructure for photocatalytic CO2 reduction into renewable hydrocarbon fuel.

PubMed

Wang, Meng; Han, Qiutong; Li, Liang; Tang, Lanqin; Li, Haijin; Zhou, Yong; Zou, Zhigang

2017-07-07

An all-solid-state Bi 2 WO 6 /Au/CdS Z-scheme system was constructed for the photocatalytic reduction of CO 2 into methane in the presence of water vapor. This Z-scheme consists of ultrathin Bi 2 WO 6 nanoplates and CdS nanoparticles as photocatalysts, and a Au nanoparticle as a solid electron mediator offering a high speed charge transfer channel and leading to more efficient spatial separation of electron-hole pairs. The photo-generated electrons from the conduction band (CB) of Bi 2 WO 6 transfer to the Au, and then release to the valence band (VB) of CdS to recombine with the holes of CdS. It allows the electrons remaining in the CB of CdS and holes in the VB of Bi 2 WO 6 to possess strong reduction and oxidation powers, respectively, leading the Bi 2 WO 6 /Au/CdS to exhibit high photocatalytic reduction of CO 2 , relative to bare Bi 2 WO 6 , Bi 2 WO 6 /Au, and Bi 2 WO 6 /CdS. The depressed hole density on CdS also enhances the stability of the CdS against photocorrosion.

Optical and structural properties of sputtered CdS films for thin film solar cell applications

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

Kim, Donguk; Park, Young; Kim, Minha

2015-09-15

Graphical abstract: Photo current–voltage curves (a) and the quantum efficiency (QE) (b) for the solar cell with CdS film grown at 300 °C. - Highlights: • CdS thin films were grown by a RF magnetron sputtering method. • Influence of growth temperature on the properties of CdS films was investigated. • At higher T{sub g}, the crystallinity of the films improved and the grains enlarged. • CdS/CdTe solar cells with efficiencies of 9.41% were prepared at 300 °C. - Abstract: CdS thin films were prepared by radio frequency magnetron sputtering at various temperatures. The effects of growth temperature on crystallinity,more » surface morphology and optical properties of the films were characterized with X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), Raman spectra, UV–visible spectrophotometry, and photoluminescence (PL) spectra. As the growth temperature was increased, the crystallinity of the sputtered CdS films was improved and the grains were enlarged. The characteristics of CdS/CdTe thin film solar cell appeared to be significantly influenced by the growth temperature of the CdS films. Thin film CdS/CdTe solar cells with efficiencies of 9.41% were prepared at a growth temperature of 300 °C.« less

Co-sensitization of ZnO by CdS quantum dots in natural dye-sensitized solar cells with polymeric electrolytes to improve the cell stability

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

Junhom, W.; Magaraphan, R.

2015-05-22

The CdS quantum dots (QDs) were deposited on ZnO layer by chemical bath deposition method to absorb light in the shorter wavelength region and used as photoanode in the dye sensitized solar cell (DSSCs) with natural dye extracted from Noni leaves. Microstructures of CdS-ZnO from various dipping time were characterized by XRD, FE-SEM and EDX. The results showed that the CdS is hexagonal structure and the amount of CdS increases when the dipping time increases. The maximal conversion efficiency of 0.292% was achieved by the DSSCs based on CdS QDs-sensitized ZnO film obtained from 9 min-dipping time. Furthermore, the stability ofmore » DSSCs was improved by using polymeric electrolyte. Poly (acrylic acid) (PAA) and Polyacrylamide (PAM) were introduced to CdS QDs-sensitized ZnO film from 9 min-dipping time. Each polymeric electrolyte was prepared by swelling from 0.1-2.0 %w in H2O. The maximal conversion efficiency of 0.207% was achieved for DSSCs based on CdS QDs-sensitized ZnO film with PAM 1.0% and the conversion efficiency was decreased 25% when it was left for1 hr.« less

Co-sensitization of ZnO by CdS quantum dots in natural dye-sensitized solar cells with polymeric electrolytes to improve the cell stability

NASA Astrophysics Data System (ADS)

Junhom, W.; Magaraphan, R.

2015-05-01

The CdS quantum dots (QDs) were deposited on ZnO layer by chemical bath deposition method to absorb light in the shorter wavelength region and used as photoanode in the dye sensitized solar cell (DSSCs) with natural dye extracted from Noni leaves. Microstructures of CdS-ZnO from various dipping time were characterized by XRD, FE-SEM and EDX. The results showed that the CdS is hexagonal structure and the amount of CdS increases when the dipping time increases. The maximal conversion efficiency of 0.292% was achieved by the DSSCs based on CdS QDs-sensitized ZnO film obtained from 9 min-dipping time. Furthermore, the stability of DSSCs was improved by using polymeric electrolyte. Poly (acrylic acid) (PAA) and Polyacrylamide (PAM) were introduced to CdS QDs-sensitized ZnO film from 9 min-dipping time. Each polymeric electrolyte was prepared by swelling from 0.1-2.0 %w in H2O. The maximal conversion efficiency of 0.207% was achieved for DSSCs based on CdS QDs-sensitized ZnO film with PAM 1.0% and the conversion efficiency was decreased 25% when it was left for1 hr.

Cu doping concentration effect on the physical properties of CdS thin films obtained by the CBD technique

NASA Astrophysics Data System (ADS)

Albor Aguilera, M. L.; Flores Márquez, J. M.; Remolina Millan, A.; Matsumoto Kuwabara, Y.; González Trujillo, M. A.; Hernández Vásquez, C.; Aguilar Hernandez, J. R.; Hernández Pérez, M. A.; Courel-Piedrahita, M.; Madeira, H. T. Yee

2017-08-01

Cu(In, Ga)Se2 (CIGS) and Cu2ZnSnS4 (CZTS) semiconductors are direct band gap materials; when these types of material are used in solar cells, they provide efficiencies of 22.1% and 12.6%, respectively. Most traditional fabrication methods involve expensive vacuum processes including co-evaporation and sputtering techniques, where films and doping are conducted separately. On the other hand, the chemical bath deposition (CBD) technique allows an in situ process. Cu-doped CdS thin films working as a buffer layer on solar cells provide good performing devices and they may be deposited by low cost techniques such as chemical methods. In this work, Cu-doped CdS thin films were deposited using the CBD technique on SnO2:F (FTO) substrates. The elemental analysis and mapping reconstruction were conducted by EDXS. Morphological, optical and electrical properties were studied, and they revealed that Cu doping modified the CdS structure, band-gap value and the electrical properties. Cu-doped CdS films show high resistivity compared to the non-doped CdS. The appropriate parameters of Cu-doped CdS films were determined to obtain an adequate window or buffer layer on CIGS and CZTS photovoltaic solar cells.

Investigations on structural, vibrational, morphological and optical properties of CdS and CdS/Co films by ultrasonic spray pyrolysis

NASA Astrophysics Data System (ADS)

Aksay, S.; Polat, M.; Özer, T.; Köse, S.; Gürbüz, G.

2011-09-01

CdS and CdS/Co films have been deposited on glass substrates by an ultrasonic spray pyrolysis method. The effects of Co incorporation on the structural, optical, morphological, elemental and vibrational properties of these films were investigated. XRD analysis confirmed the hexagonal wurtzite structure of all films and had no impurity phase. While CdS film has (0 0 2) as the preferred orientation, CdS/Co films have (1 1 0) as the preferred orientation. The direct optical band gap was found to decrease from 2.42 to 2.39 eV by Co incorporation. The decrease of the direct energy gaps by increasing Co contents is mainly due to the sp-d exchange interaction between the localized d-electrons of Co2+ ions and band electrons of CdS. After the optical investigations, it was seen that the transmittance of CdS films decreased by Co content. The Raman measurements revealed two peaks corresponding to the 1LO and 2LO modes of hexagonal CdS. The vibrational modes of Cd-S were obtained in the wavenumber range (590-715 cm-1) using Fourier transform infrared spectroscopy (FTIR). The elemental analysis of the film was done by energy dispersive X-ray spectrometry.

Efficient color-tunable multiexcitonic dual wavelength emission from Type II semiconductor tetrapods.

PubMed

Wu, Wen-Ya; Li, Mingjie; Lian, Jie; Wu, Xiangyang; Yeow, Edwin K L; Jhon, Mark H; Chan, Yinthai

2014-09-23

We synthesized colloidal InP/ZnS seeded CdS tetrapods by harnessing the structural stability of the InP/ZnS seed nanocrystals at the high reaction temperatures needed to grow the CdS arms. Because of an unexpected Type II band alignment at the interface of the InP/ZnS core and CdS arms that enhanced the occurrence of radiative excitonic recombination in CdS, these tetrapods were found to be capable of exhibiting highly efficient multiexcitonic dual wavelength emission of equal intensity at spectrally distinct wavelengths of ∼485 and ∼675 nm. Additionally, the Type II InP/ZnS seeded CdS tetrapods displayed a wider range of pump-dependent emission color-tunability (from red to white to blue) within the context of a CIE 1931 chromaticity diagram and possessed higher photostability due to suppressed multiexcitonic Auger recombination when compared to conventional Type I CdSe seeded CdS tetrapods. By employing time-resolved spectroscopy measurements, we were able to attribute the wide emission color-tunability to the large valence band offset between InP and CdS. This work highlights the importance of band alignment in the synthetic design of semiconductor nanoheterostructures, which can exhibit color-tunable multiwavelength emission with high efficiency and photostability.

The influence of viral coding sequences on pestivirus IRES activity reveals further parallels with translation initiation in prokaryotes.

PubMed Central

Fletcher, Simon P; Ali, Iraj K; Kaminski, Ann; Digard, Paul; Jackson, Richard J

2002-01-01

Classical swine fever virus (CSFV) is a member of the pestivirus family, which shares many features in common with hepatitis C virus (HCV). It is shown here that CSFV has an exceptionally efficient cis-acting internal ribosome entry segment (IRES), which, like that of HCV, is strongly influenced by the sequences immediately downstream of the initiation codon, and is optimal with viral coding sequences in this position. Constructs that retained 17 or more codons of viral coding sequence exhibited full IRES activity, but with only 12 codons, activity was approximately 66% of maximum in vitro (though close to maximum in transfected BHK cells), whereas with just 3 codons or fewer, the activity was only approximately 15% of maximum. The minimal coding region elements required for high activity were exchanged between HCV and CSFV. Although maximum activity was observed in each case with the homologous combination of coding region and 5' UTR, the heterologous combinations were sufficiently active to rule out a highly specific functional interplay between the 5' UTR and coding sequences. On the other hand, inversion of the coding sequences resulted in low IRES activity, particularly with the HCV coding sequences. RNA structure probing showed that the efficiency of internal initiation of these chimeric constructs correlated most closely with the degree of single-strandedness of the region around and immediately downstream of the initiation codon. The low activity IRESs could not be rescued by addition of supplementary eIF4A (the initiation factor with ATP-dependent RNA helicase activity). The extreme sensitivity to secondary structure around the initiation codon is likely to be due to the fact that the eIF4F complex (which has eIF4A as one of its subunits) is not required for and does not participate in initiation on these IRESs. PMID:12515388

Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics

PubMed Central

2012-01-01

Background Detecting the borders between coding and non-coding regions is an essential step in the genome annotation. And information entropy measures are useful for describing the signals in genome sequence. However, the accuracies of previous methods of finding borders based on entropy segmentation method still need to be improved. Methods In this study, we first applied a new recursive entropic segmentation method on DNA sequences to get preliminary significant cuts. A 22-symbol alphabet is used to capture the differential composition of nucleotide doublets and stop codon patterns along three phases in both DNA strands. This process requires no prior training datasets. Results Comparing with the previous segmentation methods, the experimental results on three bacteria genomes, Rickettsia prowazekii, Borrelia burgdorferi and E.coli, show that our approach improves the accuracy for finding the borders between coding and non-coding regions in DNA sequences. Conclusions This paper presents a new segmentation method in prokaryotes based on Jensen-Rényi divergence with a 22-symbol alphabet. For three bacteria genomes, comparing to A12_JR method, our method raised the accuracy of finding the borders between protein coding and non-coding regions in DNA sequences. PMID:23282225

Nonspatial Sequence Coding in CA1 Neurons

PubMed Central

Allen, Timothy A.; Salz, Daniel M.; McKenzie, Sam

2016-01-01

The hippocampus is critical to the memory for sequences of events, a defining feature of episodic memory. However, the fundamental neuronal mechanisms underlying this capacity remain elusive. While considerable research indicates hippocampal neurons can represent sequences of locations, direct evidence of coding for the memory of sequential relationships among nonspatial events remains lacking. To address this important issue, we recorded neural activity in CA1 as rats performed a hippocampus-dependent sequence-memory task. Briefly, the task involves the presentation of repeated sequences of odors at a single port and requires rats to identify each item as “in sequence” or “out of sequence”. We report that, while the animals' location and behavior remained constant, hippocampal activity differed depending on the temporal context of items—in this case, whether they were presented in or out of sequence. Some neurons showed this effect across items or sequence positions (general sequence cells), while others exhibited selectivity for specific conjunctions of item and sequence position information (conjunctive sequence cells) or for specific probe types (probe-specific sequence cells). We also found that the temporal context of individual trials could be accurately decoded from the activity of neuronal ensembles, that sequence coding at the single-cell and ensemble level was linked to sequence memory performance, and that slow-gamma oscillations (20–40 Hz) were more strongly modulated by temporal context and performance than theta oscillations (4–12 Hz). These findings provide compelling evidence that sequence coding extends beyond the domain of spatial trajectories and is thus a fundamental function of the hippocampus. SIGNIFICANCE STATEMENT The ability to remember the order of life events depends on the hippocampus, but the underlying neural mechanisms remain poorly understood. Here we addressed this issue by recording neural activity in hippocampal region CA1 while rats performed a nonspatial sequence memory task. We found that hippocampal neurons code for the temporal context of items (whether odors were presented in the correct or incorrect sequential position) and that this activity is linked with memory performance. The discovery of this novel form of temporal coding in hippocampal neurons advances our fundamental understanding of the neurobiology of episodic memory and will serve as a foundation for our cross-species, multitechnique approach aimed at elucidating the neural mechanisms underlying memory impairments in aging and dementia. PMID:26843637

High resolution spectroscopy over 8500-8750 Å for GAIA <= 50 000 K. III. A library of synthetic spectra for 7750 <= Teff

NASA Astrophysics Data System (ADS)

Castelli, F.; Munari, U.

2001-02-01

In this paper we complete the library of synthetic spectra for the range 7650-8750 Å, which includes the 8500-8750 Å interval currently base-lined for the spectroscopic observations by GAIA, candidate ESA Cornerstone 5 mission. As for Paper II, the spectra are based on Kurucz's codes and line data. The explored metallicity, gravity and temperature ranges are -2.5<= [Z/Zsun]<= +0.5, 4.5<=log g<= 2.0 and 7750<=Teff <=50 000 K, respectively. The 698 new spectra are computed at the same lambda / bigtriangleup lambda =20 000 resolving power of the observed spectra given in Paper I (131 standard stars mapping the MKK spectral classification system) and the 254 synthetic spectra of Paper II (characterized by Teff <= 7 500 K). Tables 2-4 are only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/366/1003 or via the personal HomePage http://ulisse.pd.astro.it/Astro/Atlases/ The spectra are available in electronic form at the CDS. Figures 5-224 are only available in electronic form at http://www.edpsciences.org

Repeats of base oligomers as the primordial coding sequences of the primeval earth and their vestiges in modern genes.

PubMed

Ohno, S

1984-01-01

Three outstanding properties uniquely qualify repeats of base oligomers as the primordial coding sequences of all polypeptide chains. First, when compared with randomly generated base sequences in general, they are more likely to have long open reading frames. Second, periodical polypeptide chains specified by such repeats are more likely to assume either alpha-helical or beta-sheet secondary structures than are polypeptide chains of random sequence. Third, provided that the number of bases in the oligomeric unit is not a multiple of 3, these internally repetitious coding sequences are impervious to randomly sustained base substitutions, deletions, and insertions. This is because the recurring periodicity of their polypeptide chains is given by three consecutive copies of the oligomeric unit translated in three different reading frames. Accordingly, when one reading frame is open, the other two are automatically open as well, all three being capable of coding for polypeptide chains of identical periodicity. Under this circumstance, a frame shift due to the deletion or insertion of a number of bases that is not a multiple of 3 fails to alter the down-stream amino acid sequence, and even a base change causing premature chain-termination can silence only one of the three potential coding units. Newly arisen coding sequences in modern organisms are oligomeric repeats, and most of the older genes retain various vestiges of their original internal repetitions. Some of the genes (e.g., oncogenes) have even inherited the property of being impervious to randomly sustained base changes.

Effect of CdS Growth Time on the Optical Properties of One-Pot Preparation of CdS-Ag2S Binary Compounds

NASA Astrophysics Data System (ADS)

Karimipour, M.; Izadian, L.; Molaei, M.

2018-02-01

CdS-Ag2S binary nanoparticles were synthesized using a facile one-pot microwave irradiation method. The effect of initial nucleation of CdS quantum dots (QDs) using 3 min, 5 min, and 7 min of microwave irradiation on the optical properties of the final compound was studied. The composition and crystal structure of the compounds were verified using energy dispersive x-ray spectroscopy and x-ray diffraction. They revealed that existence of Ag and Cd elements with an atomic ratio of 0.19 crystalizes in the form of monoclinic Ag2S and hexagonal CdS. Scanning electron microscope images showed a spherical morphology of the resultant compound, and transmission electron microscope images showed the formation of fine particles of CdS-Ag2S composites with an average size of 5-7 nm and 10-14 nm for CdS and Ag2S, respectively. Photoluminescence spectroscopy revealed that the initial growth time of CdS has a crucial effect on the emission of binary compounds such that for 3 min and 5 min of irradiation of CdS solution, the binary compound obtains strong red and considerable near-IR emission (850 nm), but for longer time, it rapidly quenches. The results indicate that the strong red emission can be tuned from 600 nm up to 700 nm with prolonging nucleation time of CdS. This study also emphasized that the origin of red emission strongly depends on the size and defects created in the CdS QDs.

Reducing Risk with Clinical Decision Support

PubMed Central

Maloney, F.L.; Feblowitz, J.; Samal, L.; Sato, L.; Wright, A.

2014-01-01

Summary Objective Identify clinical opportunities to intervene to prevent a malpractice event and determine the proportion of malpractice claims potentially preventable by clinical decision support (CDS). Materials and Methods Cross-sectional review of closed malpractice claims over seven years from one malpractice insurance company and seven hospitals in the Boston area. For each event, clinical opportunities to intervene to avert the malpractice event and the presence or absence of CDS that might have a role in preventing the event, were assigned by a panel of expert raters. Compensation paid out to resolve a claim (indemnity), was associated with each CDS type. Results Of the 477 closed malpractice cases, 359 (75.3%) were categorized as substantiated and 195 (54%) had at least one opportunity to intervene. Common opportunities to intervene related to performance of procedure, diagnosis, and fall prevention. We identified at least one CDS type for 63% of substantiated claims. The 41 CDS types identified included clinically significant test result alerting, diagnostic decision support and electronic tracking of instruments. Cases with at least one associated intervention accounted for $40.3 million (58.9%) of indemnity. Discussion CDS systems and other forms of health information technology (HIT) are expected to improve quality of care, but their potential to mitigate risk had not previously been quantified. Our results suggest that, in addition to their known benefits for quality and safety, CDS systems within HIT have a potential role in decreasing malpractice payments. Conclusion More than half of malpractice events and over $40 million of indemnity were potentially preventable with CDS. PMID:25298814

Key principles for a national clinical decision support knowledge sharing framework: synthesis of insights from leading subject matter experts

PubMed Central

Hongsermeier, Tonya; Wright, Adam; Lewis, Janet; Bell, Douglas S; Middleton, Blackford

2013-01-01

Objective To identify key principles for establishing a national clinical decision support (CDS) knowledge sharing framework. Materials and methods As part of an initiative by the US Office of the National Coordinator for Health IT (ONC) to establish a framework for national CDS knowledge sharing, key stakeholders were identified. Stakeholders' viewpoints were obtained through surveys and in-depth interviews, and findings and relevant insights were summarized. Based on these insights, key principles were formulated for establishing a national CDS knowledge sharing framework. Results Nineteen key stakeholders were recruited, including six executives from electronic health record system vendors, seven executives from knowledge content producers, three executives from healthcare provider organizations, and three additional experts in clinical informatics. Based on these stakeholders' insights, five key principles were identified for effectively sharing CDS knowledge nationally. These principles are (1) prioritize and support the creation and maintenance of a national CDS knowledge sharing framework; (2) facilitate the development of high-value content and tooling, preferably in an open-source manner; (3) accelerate the development or licensing of required, pragmatic standards; (4) acknowledge and address medicolegal liability concerns; and (5) establish a self-sustaining business model. Discussion Based on the principles identified, a roadmap for national CDS knowledge sharing was developed through the ONC's Advancing CDS initiative. Conclusion The study findings may serve as a useful guide for ongoing activities by the ONC and others to establish a national framework for sharing CDS knowledge and improving clinical care. PMID:22865671

Studies on growth mechanism and physical properties of hydrothermally synthesized CdS with novel hierarchical superstructures and their photocatalytic activity

NASA Astrophysics Data System (ADS)

Jamble, Shweta N.; Ghoderao, Karuna P.; Kale, Rohidas B.

2018-03-01

A simple, facile and organic-free hydrothermal method was utilized to synthesize cadmium sulfide (CdS) superstructures. The cadmium chloride and thiourea used as a Cd2+ and S2- ion sources for the growth of CdS superstructures. The reaction was carried out at different time and temperatures. The X-ray diffraction studies confirmed that the obtained products were highly crystalline with hexagonal phase. Scanning and transmission electron microscopy images reveal a monodisperse dendrite-like CdS superstructure. It consisted of a central long trunk with secondary branches, lying parallel to each other and making a certain angle with the central trunk, and small ternary branches grew out of the secondary branches. The selected area electron diffraction altogether with high-resolution electron microscopy patterns depicted that the leaves of dendrite were single crystalline in nature and preferentially grown along (111) direction. The UV-vis absorbance and photoluminescence study illustrated that the hierarchically grown CdS superstructures revealed the good quality of optical properties. A probable growth mechanism for the formation of CdS dendritic superstructures was also discussed and demonstrated by experimental results. The photocatalytic activity of CdS superstructures was studied with the photodegradation of methylene blue (MB) in an aqueous solution, under the visible light irradiation. The results showed that the degradation ratio of MB could reach 94.93% in 220 min. Based on the results, the possible mechanism of the photocatalytic reaction of MB with CdS dendrites is useful for visible light photocatalytic applications.

Surface and interface of epitaxial CdTe film on CdS buffered van der Waals mica substrate

DOE PAGES

Yang, Y. -B.; Seewald, L.; Mohanty, Dibyajyoti; ...

2017-03-31

We report single crystal CdTe films are desirable for optoelectronic device applications. An important strategy of creating films with high crystallinity is through epitaxial growth on a proper single crystal substrate. We report the metalorganic chemical vapor deposition of epitaxial CdTe films on the CdS/mica substrate. The epitaxial CdS film was grown on a mica surface by thermal evaporation. Due to the weak van der Waals forces, epitaxy is achieved despite the very large interface lattice mismatch between CdS and mica (~21–55%). The surface morphology of mica, CdS and CdTe were quantified by atomic force microscopy. The near surface structures, orientations and texture of CdTe and CdS films were characterized by the unique reflection high-energy electron diffraction surface pole figure technique. The interfaces of CdTe and CdS films and mica were characterized by X-ray pole figure technique and transmission electron microscopy. The out-of-plane and in-plane epitaxy of the heteroepitaxial films stack are determined to be CdTe(111)//CdS(0001)//mica(001) and [more » $$\\overline{1}2\\overline{1}$$] CdTe//[$$\\overline{1}100$$] CdS//[010] mica, respectively. The measured photoluminescence (PL), time resolved PL, photoresponse, and Hall mobility of the CdTe/CdS/mica indicate quality films. Finally, the use of van der Waals surface to grow epitaxial CdTe/CdS films offers an alternative strategy towards infrared imaging and solar cell applications.« less

Surface and interface of epitaxial CdTe film on CdS buffered van der Waals mica substrate

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

Yang, Y. -B.; Seewald, L.; Mohanty, Dibyajyoti

We report single crystal CdTe films are desirable for optoelectronic device applications. An important strategy of creating films with high crystallinity is through epitaxial growth on a proper single crystal substrate. We report the metalorganic chemical vapor deposition of epitaxial CdTe films on the CdS/mica substrate. The epitaxial CdS film was grown on a mica surface by thermal evaporation. Due to the weak van der Waals forces, epitaxy is achieved despite the very large interface lattice mismatch between CdS and mica (~21–55%). The surface morphology of mica, CdS and CdTe were quantified by atomic force microscopy. The near surface structures, orientations and texture of CdTe and CdS films were characterized by the unique reflection high-energy electron diffraction surface pole figure technique. The interfaces of CdTe and CdS films and mica were characterized by X-ray pole figure technique and transmission electron microscopy. The out-of-plane and in-plane epitaxy of the heteroepitaxial films stack are determined to be CdTe(111)//CdS(0001)//mica(001) and [more » $$\\overline{1}2\\overline{1}$$] CdTe//[$$\\overline{1}100$$] CdS//[010] mica, respectively. The measured photoluminescence (PL), time resolved PL, photoresponse, and Hall mobility of the CdTe/CdS/mica indicate quality films. Finally, the use of van der Waals surface to grow epitaxial CdTe/CdS films offers an alternative strategy towards infrared imaging and solar cell applications.« less

Super-resolution depth information from a short-wave infrared laser gated-viewing system by using correlated double sampling

NASA Astrophysics Data System (ADS)

Göhler, Benjamin; Lutzmann, Peter

2017-10-01

Primarily, a laser gated-viewing (GV) system provides range-gated 2D images without any range resolution within the range gate. By combining two GV images with slightly different gate positions, 3D information within a part of the range gate can be obtained. The depth resolution is higher (super-resolution) than the minimal gate shift step size in a tomographic sequence of the scene. For a state-of-the-art system with a typical frame rate of 20 Hz, the time difference between the two required GV images is 50 ms which may be too long in a dynamic scenario with moving objects. Therefore, we have applied this approach to the reset and signal level images of a new short-wave infrared (SWIR) GV camera whose read-out integrated circuit supports correlated double sampling (CDS) actually intended for the reduction of kTC noise (reset noise). These images are extracted from only one single laser pulse with a marginal time difference in between. The SWIR GV camera consists of 640 x 512 avalanche photodiodes based on mercury cadmium telluride with a pixel pitch of 15 μm. A Q-switched, flash lamp pumped solid-state laser with 1.57 μm wavelength (OPO), 52 mJ pulse energy after beam shaping, 7 ns pulse length and 20 Hz pulse repetition frequency is used for flash illumination. In this paper, the experimental set-up is described and the operating principle of CDS is explained. The method of deriving super-resolution depth information from a GV system by using CDS is introduced and optimized. Further, the range accuracy is estimated from measured image data.

Coexpression Analysis Identifies Two Oxidoreductases Involved in the Biosynthesis of the Monoterpene Acid Moiety of Natural Pyrethrin Insecticides in Tanacetum cinerariifolium1[OPEN

PubMed Central

Moghe, Gaurav D.

2018-01-01

Flowers of Tanacetum cinerariifolium produce a set of compounds known collectively as pyrethrins, which are commercially important pesticides that are strongly toxic to flying insects but not to most vertebrates. A pyrethrin molecule is an ester consisting of either trans-chrysanthemic acid or its modified form, pyrethric acid, and one of three alcohols, jasmolone, pyrethrolone, and cinerolone, that appear to be derived from jasmonic acid. Chrysanthemyl diphosphate synthase (CDS), the first enzyme involved in the synthesis of trans-chrysanthemic acid, was characterized previously and its gene isolated. TcCDS produces free trans-chrysanthemol in addition to trans-chrysanthemyl diphosphate, but the enzymes responsible for the conversion of trans-chrysanthemol to the corresponding aldehyde and then to the acid have not been reported. We used an RNA sequencing-based approach and coexpression correlation analysis to identify several candidate genes encoding putative trans-chrysanthemol and trans-chrysanthemal dehydrogenases. We functionally characterized the proteins encoded by these genes using a combination of in vitro biochemical assays and heterologous expression in planta to demonstrate that TcADH2 encodes an enzyme that oxidizes trans-chrysanthemol to trans-chrysanthemal, while TcALDH1 encodes an enzyme that oxidizes trans-chrysanthemal into trans-chrysanthemic acid. Transient coexpression of TcADH2 and TcALDH1 together with TcCDS in Nicotiana benthamiana leaves results in the production of trans-chrysanthemic acid as well as several other side products. The majority (58%) of trans-chrysanthemic acid was glycosylated or otherwise modified. Overall, these data identify key steps in the biosynthesis of pyrethrins and demonstrate the feasibility of metabolic engineering to produce components of these defense compounds in a heterologous host. PMID:29122986

76 FR 70206 - Self-Regulatory Organizations; ICE Clear Credit LLC; Notice of Filing of Proposed Rule Change to...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-10

... highly correlated relationship between long-short positions in CDS Indices and the underlying CDS Single... currently clear CDS Single Names for customer-related transactions. Accordingly, currently, there are no customer-related positions that would qualify for portfolio margining treatment. ICC does not believe that...

78 FR 13130 - Self-Regulatory Organizations; ICE Clear Europe Limited; Order Approving Proposed Rule Change, as...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-26

... already the case for single-name CDS). Recognizing the highly correlated relationship between long-short...' proprietary positions. ICE Clear Europe does not currently clear CDS positions of customers of its Clearing Members, but it plans to introduce customer clearing for CDS upon receipt of applicable regulatory...

78 FR 9088 - Self-Regulatory Organizations; ICE Clear Europe Limited; Order Approving Proposed Rule Change To...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-07

... Customer Clearing Model for CDS Products and To Amend, Clarify, and Consolidate Certain Rules and... the proposed rule change is to provide for a Customer CDS Clearing Model whereby customers of ICE... changes that are unrelated to Customer CDS Clearing Model. Currently, ICE Clear Europe Clearing Members...

The Financial Management System: A Pivotal Tool for Fiscal Viability. CDS Spotlight. ECAR Research Bulletin

ERIC Educational Resources Information Center

Lang, Leah; Pirani, Judith A.

2014-01-01

This spotlight focuses on data from the 2013 CDS to better understand how higher education institutions approach financial management systems. Information provided for this spotlight was derived from Module 8 of Core Data Service (CDS), which asked several questions regarding information systems and applications. Responses from 525 institutions…

BI Reporting, Data Warehouse Systems, and Beyond. CDS Spotlight Report. Research Bulletin

ERIC Educational Resources Information Center

Lang, Leah; Pirani, Judith A.

2014-01-01

This Spotlight focuses on data from the 2013 Core Data Service [CDS] to better understand how higher education institutions approach business intelligence (BI) reporting and data warehouse systems (see the Sidebar for definitions). Information provided for this Spotlight was derived from Module 8 of CDS, which contains several questions regarding…

The diagnostic accuracy of Clinical Dehydration Scale in identifying dehydration in children with acute gastroenteritis: a systematic review.

PubMed

Falszewska, Anna; Dziechciarz, Piotr; Szajewska, Hania

2014-10-01

To systematically update diagnostic accuracy of the Clinical Dehydration Scale (CDS) in clinical recognition of dehydration in children with acute gastroenteritis. Six databases were searched for diagnostic accuracy studies in which population were children aged 1 to 36 months with acute gastroenteritis; index test was the CDS; and reference test was post-illness weight gain. Three studies involving 360 children were included. Limited evidence showed that in high-income countries the CDS provides strong diagnostic accuracy for ruling in moderate and severe (>6%) dehydration (positive likelihood ratio 5.2-6.6), but has limited value for ruling it out (negative likelihood ratio 0.4-0.55). In low-income countries, the CDS has limited value either for ruling moderate or severe dehydration in or out. In both settings, the CDS had limited value for ruling in or out dehydration <3% or dehydration 3% to 6%. The CDS can help assess moderate to severe dehydration in high-income settings. Given the limited data, the evidence should be viewed with caution. © The Author(s) 2014.

Emitting color tunable carbon dots by adjusting solvent towards light-emitting devices

NASA Astrophysics Data System (ADS)

Zhu, Jinyang; Bai, Xue; Bai, Jialin; Pan, Gencai; Zhu, Yongsheng; Zhai, Yue; Shao, He; Chen, Xu; Dong, Biao; Zhang, Hanzhuang; Song, Hongwei

2018-02-01

Carbon dots (CDs), one of the most significant classes of carbon-based nanophosphors, have attracted extensive attention in recent years. However, few attempts have been reported for realizing CDs with tunable emissions, especially for obtaining the red-light emissions with high photoluminescence quantum yields. Herein, we synthesized CDs with different chromatic blue, green and red emissions by facilely changing the reaction solvent during hydrothermal conditions. The photoluminescence quantum yields of 34%, 19% and 47% for the blue, green and red emissions, respectively, were achieved. Furthermore, the solid-state CD/PVA composite films were constructed through mixing the CDs with PVA polymer, in which the self-quenching of photoluminescence of CDs had been successfully avoided benefiting from the formation of hydrogen bonds between the CDs and PVA molecules. Finally, the warm white light emitting diode (WLED) was fabricated by integrating CD/PVA film on a UV-LED chip. The WLED exhibited the Commission International de l’Eclairage coordinates (CIE) of (0.38, 0.34), correlated color temperature of 3913 K and color rendering index of 91, respectively, which were comparable with the commercial WLEDs.

Microstructural and optical properties of CdS nanoparticles synthesized by sol gel method

NASA Astrophysics Data System (ADS)

Mahdi, Hadeel Salih; Parveen, Azra; Agrawal, Shraddha; Azam, Ameer

2018-05-01

Semiconductor nanoparticles of CdS are of great interest for both fundamental research and industrial development due to their unique size-dependent optical and electronic properties and their exciting utilization in the fields of light-emitting diode, electro-chemical cells, laser, hydrogen producing catalyst, biological label. We present a scheme to measure the optical properties of CdS nanoparticles The peaks were indexed by powder-x software. The XRD pattern analysis showed that CdS composition was found to have hexagonal structure with well crystalline nature. the surface morphology and the composition of the samples were investigated by SEM (JEOL, japan). The image shows the presence of large spherical aggregates of smaller individual nanoparticles of various sizes for pure cds. to check the chemical composition of the material, energy dispersive X-ray (EDX) spectroscopic analysis was also performed which further confirmed the presence of cd and s ions in the matrix. The optical absorption spectra of CdS sample was recorded by uv-vis spectrophotometer in the range of 200 to 800 nm.

Rapid microwave-assisted synthesis of highly luminescent nitrogen-doped carbon dots for white light-emitting diodes

NASA Astrophysics Data System (ADS)

Wang, Yaling; Zheng, Jingxia; Wang, Junli; Yang, Yongzhen; Liu, Xuguang

2017-11-01

Highly luminescent nitrogen-doped carbon dots (N-CDs) were synthesized rapidly by one-step microwave-assisted hydrothermal method using citric acid as carbon source and ethylenediamine as dopant. The influences of reaction temperature, reaction time and raw material ratio on the fluorescence performance of N-CDs were investigated. Then N-CDs with the highest quantum yield were selected as fluorescent materials for fabricating white light-emitting diodes (LEDs). Highly luminescent N-CDs with the quantum yield of 75.96% and blue-to-red spectral composition of 51.48% were obtained at the conditions of 180 °C, 8 min and the molar ratio of citric acid to ethylenediamine 2:1. As-prepared highly luminescent N-CDs have an average size of 6.06 nm, possess extensive oxygen- and nitrogen-containing functional groups on their surface, and exhibit strong absorption in ultraviolet region. White LEDs based on the highly luminescent N-CDs emit warm white light with color coordinates of (0.42, 0.40) and correlated color temperature of 3416 K.

Harmane and harmalan are bioactive components of classical clonidine-displacing substance.

PubMed

Parker, Christine A; Anderson, Neil J; Robinson, Emma S J; Price, Rhiannon; Tyacke, Robin J; Husbands, Stephen M; Dillon, Michael P; Eglen, Richard M; Hudson, Alan L; Nutt, David J; Crump, Matthew P; Crosby, John

2004-12-28

Elucidation of the structure of the endogenous ligand(s) for imidazoline binding sites, clonidine-displacing substance (CDS), has been a major goal for many years. Crude CDS from bovine lung was purified by reverse-phase high-pressure liquid chromatography. Electrospray mass spectrometry (ESMS) and nuclear magnetic resonance ((1)H NMR) analysis revealed the presence of L-tryptophan and 1-carboxy-1-methyltetrahydro-beta-carboline in the active CDS extract. Competition radioligand binding studies, however, failed to show displacement of specific [(3)H]clonidine binding to rat brain membranes for either compound. Further purification of the bovine lung extract allowed the isolation of the beta-carbolines harmane and harmalan as confirmed by ESMS, (1)H NMR, and comparison with synthetic standards. Both compounds exhibited a high (nanomolar) affinity for both type 1 and type 2 imidazoline binding sites, and the synthetic standards were shown to coelute with the active classical CDS extracts. We therefore propose that the beta-carbolines harmane and harmalan represent active components of classical CDS. The identification of these compounds will allow us to establish clear physiological roles for CDS.

Ultrasonic chemical synthesis of CdS-reduced graphene oxide nanocomposites with an enhanced visible light photoactivity

NASA Astrophysics Data System (ADS)

Lin, Yi-Chen; Tsai, Du-Cheng; Chang, Zue-Chin; Shieu, Fuh-Sheng

2018-05-01

In this study, we report a facile ultrasonic method to prepare a series of CdS and reduced graphene oxide (CdS/rGO) composites with different weight ratios of graphene at temperature as low as 70 °C for 20 min by employing ammonia as a complexing agent of Cd2+ ions and reducing agent of graphene oxide (GO). Pure CdS particles had a poor crystallinity and aggregated to large particles size. As GO was incorporated into CdS, a uniform dispersion of CdS particles with high crystallinity on rGO sheets was clearly observed. The as-prepared CdS/rGO composites have a wide and strong photo absorption in the visible region and display a substantially improved photocatalytic activity for the degradation of methylene blue under visible light irradiation by forming a heterojunction of rGO and CdS. However, too much rGO will shield the light of the active sites for the CdS nanoparticle surface and thus limit further improvement in the photocatalytic efficiency.

Synthesis of Novel Sea-Urchin-Like CdS and Their Optical Properties.

PubMed

Kamran, Muhammad Arshad; Liu, Ruibin; Shi, Li-Jie; Bukhtiar, Arfan; Li, Jing; Zou, Bingsuo

2015-06-01

A novel morphology of CdS sea-urchin-like microstructures is synthesized by simple thermal evaporation process. Microstructures with average size of 20-50 μm are composed of single crystalline CdS nanobelts. The structural, compositional, morphological characterization of the product were examined by X-ray diffraction, energy dispersive X-ray spectroscopy, Raman spectroscopy, scanning electron microscope, transmission electron microscopy and selected area electron diffraction while optical properties are investigated by Photoluminescence spectroscopy and time-resolved Photoluminescence measurements. The tentative growth mechanism for the growth of sea-urchin-like CdS is proposed and described briefly. A strong green emission with a maximum around 517 nm was observed from the individual CdS microstructure at room temperature, which was attributed to band-edge emission of CdS. These Novel structures exhibit excellent lasing (stimulated emission) with low threshold (9.07 μJ cm(-2)) at room temperature. We analyze the physical mechanism of stimulated emission. These results are important in the design of green luminescence, low-threshold laser and display devices in the future.

ORAC-fluorescein assay to determine the oxygen radical absorbance capacity of resveratrol complexed in cyclodextrins.

PubMed

Lucas-Abellán, C; Mercader-Ros, M T; Zafrilla, M P; Fortea, M I; Gabaldón, J A; Núñez-Delicado, E

2008-03-26

The effect of the complexation of resveratrol with hydroxypropyl-beta-cyclodextrins (HP-beta-CDs) on the antioxidant capacity of the polyphenol is studied for the first time by means of the oxygen radical absorbance capacity (ORAC) method, using fluorescein (FL) as the fluorescent probe. The method is validated through its linearity, precision, and accuracy for measuring the ORAC of resveratrol in the absence or presence of cyclodextrins (CDs). The complexation of resveratrol in CDs increased the net area under the FL decay curve (net AUC) of resveratrol up to its saturation level, at which the polyphenol showed almost double the antioxidant activity it shows in the absence of CDs. The complexation constant ( K c) between resveratrol and HP-beta-CDs was calculated by linear regression of the phase solubility diagram ( K c = 18048 M (-1)). The antioxidant activity of resveratrol was dependent on the complexed resveratrol because CDs acts as a controlled dosage reservoir that protects resveratrol against rapid oxidation by free radicals. In this way, its antioxidant activity is prolonged and only reaches its maximum when all the resveratrol is complexed.

In Situ Localized Surface Plasmon Resonance (LSPR) Spectroscopy to Investigate Kinetics of Chemical Bath Deposition of CdS Thin Films

DOE PAGES

Kalyanaraman, Ramki; Taz, Humaira; Ruther, Rose E.; ...

2015-02-11

Techniques that can characterize the early stages of thin film deposition from liquid phase processes can aid greatly in our understanding of mechanistic aspects of chemical bath deposition (CBD). Here we have used localized surface plasmon resonance (LSPR) spectroscopy to monitor in-situ the kinetics of early-stage growth of cadmium sulfide (CdS) thin films on Ag nanoparticle on quartz substrates. Real-time shift during CdS deposition showed that the LSPR wavelength red shifted rapidly due to random deposition of CdS on the substrate, but saturated at longer times. LSPR modeling showed that these features could be interpreted as an initial deposition ofmore » CdS islands followed by preferential deposition onto itself. The CdS also showed significantly enhanced Raman signals up to 170 times due to surface enhanced raman scattering (SERS) from the CdS/Ag NP regions. The ex-situ SERS effect supported the LSPR shift suggesting that these techniques could be used to understand nucleation and growth phenomena from the liquid phase.« less

Preparation of highly luminescent and color tunable carbon nanodots under visible light excitation for in vitro and in vivo bio-imaging

DOE PAGES

Zheng, Min; Li, Jing; Xie, Zhigang; ...

2015-11-10

Carbon nanodots (CDs) have generated enormous excitement because of their superiority in water solubility, chemical inertness, low toxicity, ease of functionalization and resistance to photobleaching. Here we report a facile thermal pyrolysis route to prepare CDs with high quantum yield (QY) using citric acid as the carbon source and ethylene diamine derivatives (EDAs) including triethylenetetramine (TETA), tetraethylenepentamine (TEPA) and polyene polyamine (PEPA) as the passivation agents. We find that the CDs prepared from EDAs, such as TETA, TEPA and PEPA, show relatively high photoluminescence (PL) QY (11.4, 10.6, and 9.8%, respectively) at 1 ex of 465 nm. The cytotoxicity ofmore » the CDs has been investigated through in vitro and in vivo bio-imaging studies. The results indicate that these CDs possess low toxicity and good biocompatibility. As a result, the unique properties such as the high PL QY at large excitation wave length and the low toxicity of the resulting CDs make them promising fluorescent nanoprobes for applications in optical bio-imaging and biosensing.« less

Clinical guideline representation in a CDS: a human information processing method.

PubMed

Kilsdonk, Ellen; Riezebos, Rinke; Kremer, Leontien; Peute, Linda; Jaspers, Monique

2012-01-01

The Dutch Childhood Oncology Group (DCOG) has developed evidence-based guidelines for screening childhood cancer survivors for possible late complications of treatment. These paper-based guidelines appeared to not suit clinicians' information retrieval strategies; it was thus decided to communicate the guidelines through a Computerized Decision Support (CDS) tool. To ensure high usability of this tool, an analysis of clinicians' cognitive strategies in retrieving information from the paper-based guidelines was used as requirements elicitation method. An information processing model was developed through an analysis of think aloud protocols and used as input for the design of the CDS user interface. Usability analysis of the user interface showed that the navigational structure of the CDS tool fitted well with the clinicians' mental strategies employed in deciding on survivors screening protocols. Clinicians were more efficient and more complete in deciding on patient-tailored screening procedures when supported by the CDS tool than by the paper-based guideline booklet. The think-aloud method provided detailed insight into users' clinical work patterns that supported the design of a highly usable CDS system.

Synthesis and characterization of cadmium sulphide thin films prepared by spin coating

NASA Astrophysics Data System (ADS)

Chodavadiya, Nisarg; Chapanari, Amisha; Zinzala, Jignesh; Ray, Jaymin; Pandya, Samir

2018-05-01

An II-VI group semiconductor is Wide band gap materials and has been widely studied due to their fundamental optical, structural, and electrical properties. Cadmium sulphide (CdS) is one of the most emerged materials in II-VI group. It has many applications such as buffer later in photovoltaic cell, multilayer light emitting diodes, optical filters, thin film field effect transistors, gas sensors, light detectors etc. It is fundamentally an n-type material with an optical band gap of 2.4 eV. Owing to these properties we had studied CdS thin films synthesis and characterized by Raman, Ultraviolet - Visible spectroscopy (UV-VIS) and Hot probe method. CdS thin films were prepared by spin coating of the Cadmium-thiourea precursor solution. Visual inspection after 20 minute thermolysis time the films were looks uniform and shiny pale yellow in color. Raman confirms the A1 vibration of pure CdS. UV-VIS gives the band gap about 2.52 eV, which confirms the formation of nanocrystalline form of CdS. Finally, hot probe signifies the n-type conductivity of the CdS film.

The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite.

PubMed

Tschoeke, Diogo A; Nunes, Gisele L; Jardim, Rodrigo; Lima, Joana; Dumaresq, Aline Sr; Gomes, Monete R; de Mattos Pereira, Leandro; Loureiro, Daniel R; Stoco, Patricia H; de Matos Guedes, Herbert Leonel; de Miranda, Antonio Basilio; Ruiz, Jeronimo; Pitaluga, André; Silva, Floriano P; Probst, Christian M; Dickens, Nicholas J; Mottram, Jeremy C; Grisard, Edmundo C; Dávila, Alberto Mr

2014-01-01

Leishmaniasis is an infectious disease caused by Leishmania species. Leishmania amazonensis is a New World Leishmania species belonging to the Mexicana complex, which is able to cause all types of leishmaniasis infections. The L. amazonensis reference strain MHOM/BR/1973/M2269 was sequenced identifying 8,802 codifying sequences (CDS), most of them of hypothetical function. Comparative analysis using six Leishmania species showed a core set of 7,016 orthologs. L. amazonensis and Leishmania mexicana share the largest number of distinct orthologs, while Leishmania braziliensis presented the largest number of inparalogs. Additionally, phylogenomic analysis confirmed the taxonomic position for L. amazonensis within the "Mexicana complex", reinforcing understanding of the split of New and Old World Leishmania. Potential non-homologous isofunctional enzymes (NISE) were identified between L. amazonensis and Homo sapiens that could provide new drug targets for development.

The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite

PubMed Central

Tschoeke, Diogo A; Nunes, Gisele L; Jardim, Rodrigo; Lima, Joana; Dumaresq, Aline SR; Gomes, Monete R; de Mattos Pereira, Leandro; Loureiro, Daniel R; Stoco, Patricia H; de Matos Guedes, Herbert Leonel; de Miranda, Antonio Basilio; Ruiz, Jeronimo; Pitaluga, André; Silva, Floriano P; Probst, Christian M; Dickens, Nicholas J; Mottram, Jeremy C; Grisard, Edmundo C; Dávila, Alberto MR

2014-01-01

Leishmaniasis is an infectious disease caused by Leishmania species. Leishmania amazonensis is a New World Leishmania species belonging to the Mexicana complex, which is able to cause all types of leishmaniasis infections. The L. amazonensis reference strain MHOM/BR/1973/M2269 was sequenced identifying 8,802 codifying sequences (CDS), most of them of hypothetical function. Comparative analysis using six Leishmania species showed a core set of 7,016 orthologs. L. amazonensis and Leishmania mexicana share the largest number of distinct orthologs, while Leishmania braziliensis presented the largest number of inparalogs. Additionally, phylogenomic analysis confirmed the taxonomic position for L. amazonensis within the “Mexicana complex”, reinforcing understanding of the split of New and Old World Leishmania. Potential non-homologous isofunctional enzymes (NISE) were identified between L. amazonensis and Homo sapiens that could provide new drug targets for development. PMID:25336895

Hot electron induced NIR detection in CdS films.

PubMed

Sharma, Alka; Kumar, Rahul; Bhattacharyya, Biplab; Husale, Sudhir

2016-03-11

We report the use of random Au nanoislands to enhance the absorption of CdS photodetectors at wavelengths beyond its intrinsic absorption properties from visible to NIR spectrum enabling a high performance visible-NIR photodetector. The temperature dependent annealing method was employed to form random sized Au nanoparticles on CdS films. The hot electron induced NIR photo-detection shows high responsivity of ~780 mA/W for an area of ~57 μm(2). The simulated optical response (absorption and responsivity) of Au nanoislands integrated in CdS films confirms the strong dependence of NIR sensitivity on the size and shape of Au nanoislands. The demonstration of plasmon enhanced IR sensitivity along with the cost-effective device fabrication method using CdS film enables the possibility of economical light harvesting applications which can be implemented in future technological applications.

Algae mediated synthesis of cadmium sulphide nanoparticles and their application in bioremediation

NASA Astrophysics Data System (ADS)

Prasad Mandal, Ranju; Sekh, Sanoyaz; Sarkar, Neera Sen; Chattopadhyay, Dipankar; De, Swati

2016-05-01

The present work is a study on the biological synthesis of cadmium sulphide (CdS) nanoparticles using blue-green algae that is popularly used as a food supplement. This synthesis is unique in the sense that no external sulphur precursor is required, the CdS nanoparticles are synthesized in situ in the algal medium. The CdS nanoparticles thus synthesized are photoluminescent and can act as highly efficient photocatalysts for degradation of the dye pollutant malachite green. Thus the CdS nanoparticles synthesized in situ in the algae conform to the desired criteria of waste water treatment i.e. biosorption of the pollutant and its subsequent degradation. The novelty of this work also lies in its potential for use in bioremediation by conversion of the toxic Cd(II) ion to less toxic CdS nanoparticles within the algal framework.

The Potential Application of Raw Cadmium Sulfide Nanoparticles as CT Photographic Developer

NASA Astrophysics Data System (ADS)

Wu, Qiang; Huang, Lingxin; Li, Zhan; An, Wenzhen; Liu, Dan; Lin, Jin; Tian, Longlong; Wang, Xinling; Liu, Bo; Qi, Wei; Wu, Wangsuo

2016-04-01

With the development of science and technology, new applications about nanoparticles should be explored to achieve full-scale knowledge. Therefore, in this work, the toxicity and potential application of raw cadmium sulfide nanoparticles (CdS) in vivo were further studied through ICP-OES and CTs. Surprisingly, CdS exhibited an excellent photographic property, except for finding the accumulation of CdS in the lungs, liver, spleen, and kidney with a strong dependence on time; it is also found that there were a significant uptake in the pancreas for an obvious CT imaging. And the following investigations showed that the raw CdS could damage the tissues accumulating nanoparticles. Through this work, it can be seen that the raw CdS being modified might be an excellent photographic developer for detecting cancers or other diseases.

Transparent sunlight conversion film based on carboxymethyl cellulose and carbon dots.

PubMed

You, Yaqin; Zhang, Haoran; Liu, Yingliang; Lei, Bingfu

2016-10-20

Transparent sunlight conversion film based on carboxymethyl cellulose (CMC) and carbon dots (CDs) has been developed for the first time through dispersion of CDs in CMC aqueous solution. Due to the hydrogen bonds interaction, CMC can effectively absorb the CDs, whose surfaces are functionalized by lots of polar groups. The results from atomic force microscopy (AFM), scanning electron microscopy (SEM) confirm that the composite film possesses a homogeneous and compact structure. Besides, the CMC matrix neither competes for absorbing excitation light nor absorbs the emissions of CDs, which reserves the inherent optical properties of the individual CDs. The composite films can efficiently convert ultraviolet light to blue light. What's more, the film is transparent and possesses excellent mechanical properties, expected to apply in the field of agricultural planting for sunlight conversion. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ferromagnetism in sphalerite and wurtzite CdS nanostructures

PubMed Central

2013-01-01

Room-temperature ferromagnetism is observed in undoped sphalerite and wurtzite CdS nanostructures which are synthesized by hydrothermal methods. Scanning electron microscopy and transmission electron microscopy results indicate that the sphalerite CdS samples show a spherical-like shape and the wurtzite CdS ones show a flower-like shape, both of which are aggregated by lots of smaller particles. The impurity of the samples has been ruled out by the results of X-ray diffraction, selected-area electron diffraction, and X-ray photoelectron spectroscopy. Magnetization measurements indicate that all the samples exhibit room-temperature ferromagnetism and the saturation magnetization decreases with the increased crystal sizes, revealing that the observed ferromagnetism is defect-related, which is also confirmed by the post-annealing processes. This finding in CdS should be the focus of future electronic and spintronic devices. PMID:23294671

Structural and optical properties of nano-structured CdS thin films prepared by chemical bath deposition

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

Bai, Rekha, E-mail: rekha.mittal07@gmail.com; Kumar, Dinesh; Chaudhary, Sujeet

2016-05-06

Cadmium sulfide (CdS) thin films have been deposited on conducting glass substrates by chemical bath deposition (CBD) technique. The effect of precursor concentration on the structural, morphological, compositional, and optical properties of the CdS films has been studied. Crystal structure of these CdS films is characterized by X-ray diffraction (XRD) and it reveals polycrystalline structure with mixture of cubic and wurtzite phases with grain size decreasing as precursor concentration is increased. Optical studies reveal that the CdS thin films have high transmittance in visible spectral region reaching 90% and the films possess direct optical band gap that decreases from 2.46more » to 2.39 eV with decreasing bath concentration. Our study suggests that growth is nucleation controlled.« less