bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae
Authors: Haley Bradd J , Grim Christopher J , Hasan Nur A , Choi Seon-Young , Chun Jongsik , Brettin Thomas S , Bruce David C , Challacombe Jean F , Detter J Chris , Han Cliff S , Huq Anwar , Colwell Rita R 
Published: May 2010

Abstract

Background
In recent years genome sequencing has been used to characterize new bacterial species, a method of analysis available as a result of improved methodology and reduced cost. Included in a constantly expanding list of Vibrio species are several that have been reclassified as novel members of the Vibrionaceae. The description of two putative new Vibrio species, Vibrio sp. RC341 and Vibrio sp. RC586 for which we propose the names V. metecus and V. parilis, respectively, previously characterized as non-toxigenic environmental variants of V. cholerae is presented in this study.

Results
Based on results of whole-genome average nucleotide identity (ANI), average amino acid identity (AAI), rpoB similarity, MLSA, and phylogenetic analysis, the new species are concluded to be phylogenetically closely related to V. cholerae and V. mimicus. Vibrio sp. RC341 and Vibrio sp. RC586 demonstrate features characteristic of V. cholerae and V. mimicus, respectively, on differential and selective media, but their genomes show a 12 to 15% divergence (88 to 85% ANI and 92 to 91% AAI) compared to the sequences of V. cholerae and V. mimicus genomes (ANI <95% and AAI <96% indicative of separate species). Vibrio sp. RC341 and Vibrio sp. RC586 share 2104 ORFs (59%) and 2058 ORFs (56%) with the published core genome of V. cholerae and 2956 (82%) and 3048 ORFs (84%) with V. mimicus MB-451, respectively. The novel species share 2926 ORFs with each other (81% Vibrio sp. RC341 and 81% Vibrio sp. RC586). Virulence-associated factors and genomic islands of V. cholerae and V. mimicus, including VSP-I and II, were found in these environmental Vibrio spp.

Conclusions
Results of this analysis demonstrate these two environmental vibrios, previously characterized as variant V. cholerae strains, are new species which have evolved from ancestral lineages of the V. cholerae and V. mimicus clade. The presence of conserved integration loci for genomic islands as well as evidence of horizontal gene transfer between these two new species, V. cholerae, and V. mimicus suggests genomic islands and virulence factors are transferred between these species.
Wheat beta-expansin (EXPB11) genes: Identification of the expressed gene on chromosome 3BS carrying a pollen allergen domain
Authors: Breen James , Li Dora , Dunn David S , Békés Ferenc , Kong Xiuying , Zhang Juncheng , Jia Jizeng , Wicker Thomas , Mago Rohit , Ma Wujun , Bellgard Matthew , Appels Rudi 
Published: May 2010

Abstract

Background
Expansins form a large multi-gene family found in wheat and other cereal genomes that are involved in the expansion of cell walls as a tissue grows. The expansin family can be divided up into two main groups, namely, alpha-expansin (EXPA) and beta-expansin proteins (EXPB), with the EXPB group being of particular interest as group 1-pollen allergens.

Results
In this study, three beta-expansin genes were identified and characterized from a newly sequenced region of the Triticum aestivum cv. Chinese Spring chromosome 3B physical map at the Sr2 locus (FPC contig ctg11). The analysis of a 357 kb sub-sequence of FPC contig ctg11 identified one beta-expansin genes to be TaEXPB11, originally identified as a cDNA from the wheat cv Wyuna. Through the analysis of intron sequences of the three wheat cv. Chinese Spring genes, we propose that two of these beta-expansin genes are duplications of the TaEXPB11 gene. Comparative sequence analysis with two other wheat cultivars (cv. Westonia and cv. Hope) and a Triticum aestivum var. spelta line validated the identification of the Chinese Spring variant of TaEXPB11. The expression in maternal and grain tissues was confirmed by examining EST databases and carrying out RT-PCR experiments. Detailed examination of the position of TaEXPB11 relative to the locus encoding Sr2 disease resistance ruled out the possibility of this gene directly contributing to the resistance phenotype.

Conclusions
Through 3-D structural protein comparisons with Zea mays EXPB1, we proposed that variations within the coding sequence of TaEXPB11 in wheats may produce a functional change within features such as domain 1 related to possible involvement in cell wall structure and domain 2 defining the pollen allergen domain and binding to IgE protein. The variation established in this gene suggests it is a clearly identifiable member of a gene family and reflects the dynamic features of the wheat genome as it adapted to a range of different environments and uses.
Accession Numbers: ctg11 =FN564426
Survey sequences of TaEXPB11ws and TsEXPB11 are provided request.
Central obesity and atherogenic dyslipidemia in metabolic syndrome are associated with increased risk for colorectal adenoma in a Chinese population
Authors: Liu Chiu-Shong , Hsu Hua-Shui , Li Chia-Ing , Jan Chia-Ing , Li Tsai-Chung , Lin Wen-Yuan , Lin Tsann , Chen Ya-Chien , Lee Cheng-Chun , Lin Cheng-Chieh 
Published: May 2010

AbstractBackgroundMetabolic syndrome (MetS) is composed of cardiovascular risk factors including insulin resistance, obesity, dyslipidemia, and hypertension. Most of the components of MetS have been linked to the development of neoplasm. The purpose of this study was to evaluate the relationship between individual components of MetS and colorectal adenoma.MethodsThe study subjects were recruited from a pool of 4872 individuals who underwent a health check-up examination during the period January 2006 to May 2008. Each participant fulfilled a structured questionnaire. MetS was defined based on the America Heart Association and National Heart Lung Blood Institute criteria. Subjects with history of colon cancer, colon polyps, colitis, or prior colonic surgery were excluded.ResultsA total of 4122 subjects were included for final analysis (2367 men and 1755 women; mean age, 49.6 ± 11.7 years). Of them, MetS was diagnosed in 708 men (29.9%) and in 367 women (20.9%). Among the patients with MetS, 34.6% had adenoma, 31.7% had hyperplastic polyps and 23.3% were polyp-free (p < 0.0001, Chi-square test). The adjusted OR for colorectal adenoma was significantly higher in the subjects with MetS (OR, 1.31, CI: 1.09-1.57). A stronger association between MetS and colorectal adenoma was found in men (OR:1.44, CI:1.16-1.80) than in women (OR:1.04, CI:0.74-1.46). The adjusted OR for adenoma increased as the number of MetS components increased (p for trend = 0.0001 ). When the individual components of MetS were analyzed separately, only central obesity (OR:1.36, CI:1.14-1.63), low HDL cholesterol levels (OR:1.30, CI:1.10-1.54) and high triglyceride levels (OR:1.26, CI:1.04-1.53) were independently associated with colorectal adenoma.ConclusionsOf the components of MetS analyzed in this study, central obesity and dyslipidemia are independent risk factors for colorectal adenoma. With regard to the prevention of colorectal neoplasm, life-style modification such as weight reduction is worthwhile.
Can HIV incidence testing be used for evaluating HIV intervention programs? A reanalysis of the Orange Farm male circumcision trial (ANRS-1265)
Authors: Fiamma Agnès , Lissouba Pascale , Amy Oliver E , Singh Beverley , Laeyendecker Oliver , Quinn Thomas C , Taljaard Dirk , Auvert Bertran 
Published: May 2010

Abstract

Background
The objective of this study was to estimate the effect of male circumcision (MC) on HIV acquisition estimated using HIV incidence assays and to compare it to the effect measured by survival analysis.

Methods
We used samples collected during the MC randomized controlled trial (ANRS-1265) conducted in Orange Farm (South Africa) among men aged 18 to 24. Among the 2946 samples collected at the last follow-up visit, 194 HIV-positive samples were tested using two incidence assays: Calypte HIV-EIA (BED) and an avidity assay based on the BioRad HIV1/2+O EIA (AI). The results of the assays were also combined (BED-AI). The samples included the 124 participants (4.2% of total) who were HIV-positive at randomization. The protective effect was calculated as one minus the intention-to-treat incidence rate ratio in an uncorrected manner and with correction for misclassifications, with simple theoretical formulae. Theoretical calculations showed that the uncorrected intention-to-treat effect was approximately independent of the value of the incidence assay window period and was the ratio of the number tested recent seroconverters divided by the number tested HIV-negative between the randomization groups. We used cut-off values ranging from 0.325 to 2.27 for BED, 31.6 to 96 for AI and 0.325-31.6 to 1.89-96 for BED-AI. Effects were corrected for long-term specificity using a previously published formula. 95% Confidence intervals (CI) were estimated by bootstrap resampling.

Results
With the highest cut-off values, the uncorrected protective effects evaluated by BED, AI and BED-AI were 50% (95%CI: 27% to 66%), 50% (21% to 69%) and 63% (36% to 81%). The corrections for misclassifications were lower than 50% of the number of tested recent. The corrected effects were 53% (30% to 70%), 55% (25% to 77%) and 67% (38% to 86%), slightly higher than the corresponding uncorrected values. These values were consistent with the previously reported protective effect of 60% (34% to 76%) obtained with survival analysis.

Conclusions
HIV incidence assays may be employed to assess the effect of interventions using cross-sectional data.
Hematopoietic Pyk2 regulates migration of differentiated HL-60 cells
Authors: Wang Lin , Learoyd Jonathan , Duan Yingli , Leff Alan R , Zhu Xiangdong 
Published: May 2010

AbstractBackgroundPyk2 is a non-receptor cytoplasmic tyrosine kinase that belongs to the focal adhesion kinase family and has been implicated in neutrophil spreading and respiratory burst activity caused by TNF-α. However, the role of Pyk2 in neutrophil migration is incompletely defined. In this study, we tested the hypothesis that Pyk2 regulates the migration of neutrophil-like differentiated HL-60 cells subsequent to β2-integrin mediated cell adhesion.MethodsHL-60 cells were induced to differentiate into neutrophil-like cells (dHL60) by incubation in medium containing 1.25% DMSO for up to 4 days. Pyk2 expression and tyrosine phosphorylation was measured by Western blot analysis. Adhesion of dHL60 cells to plated fibrinogen was measured by residual myeloperoxidase activity. dHL60 cell migration was evaluated using a 96-well chemoTx chamber.ResultsWestern blot analysis demonstrated that hematopoietic Pyk2 was predominantly expressed after HL60 cell differentiation. Pyk2 was tyrosine phosphorylated upon adhesion of dHL60 cells to plated fibrinogen in the presence of fMLP. By contrast, tyrosine phosphorylation of Pyk2 was insignificant in dHL60 cells treated in suspension with fMLP. Antibodies against CD18 blocked both phosphorylation of Pyk2 and adhesion of dHL60 cells to fibrinogen, demonstrating that phosphorylation of Pyk2 was β2-integrin dependent. TAT-Pyk2-CT, a dominant negative fusion protein in which the TAT protein transduction domain was fused to the c-terminal Pyk2, attenuated fMLP-stimulated spreading, migration and phosphorylation of endogenous Pyk2 without blocking adhesion of dHL-60 cells to fibrinogen. Similarly, silencing of Pyk2 expression by siRNA in dHL60 cells also attenuated dHL60 cell migration caused by fMLP. Phospho-Pyk2 was evenly distributed around cell membrane circumferentially in unstimulated dHL-60 cells adherent to plated fibrinogen. In dHL60 cells treated with fMLP to cause cell spreading and polarization, Pyk2 was concentrated at the leading edge of pseudopods or at the trailing edge of uropods during migration of neutrophilic dHL-60 cells.ConclusionsWe conclude that Pyk2 is activated by β2-integrin adhesion. The activated concentration of Pyk2 and colocalization with F-actin in pseudopodia suggests that Pyk2 may regulate cell spreading and migration in dHL60 cells.
Validation of an ambulatory cough detection and counting application using voluntary cough under different conditions
Authors: Vizel Eldad , Yigla Mordechai , Goryachev Yulia , Dekel Eyal , Felis Vered , Levi Hanna , Kroin Isaac , Godfrey Simon , Gavriely Noam 
Published: May 2010

Abstract

Background
While cough is an important defence mechanism of the respiratory system, its chronic presence is bothersome and may indicate the presence of a serious disease. We hereby describe the validation process of a novel cough detection and counting technology (PulmoTrack-CC™, KarmelSonix, Haifa, Israel).

Methods
Tracheal and chest wall sounds, ambient sounds and chest motion were digitally recorded, using the PulmoTrack® hardware, from healthy volunteers coughing voluntarily while (a) laying supine, (b) sitting, (c) sitting with strong ambient noise, (d) walking, and (e) climbing stairs, a total of 25 minutes per subject. The cough monitoring algorithm was applied to the recorded data to detect and count coughs.
The detection algorithm first searches for cough 'candidates' by identifying loud sounds with a cough pattern, followed by a secondary verification process based on detection of specific characteristics of cough. The recorded data were independently and blindly evaluated by trained experts who listened to the sounds and visually reviewed them on a sonogram display.
The validation process was based on two methods: (i) Referring to an expert consensus as gold standard, and comparing each cough detected by the algorithm to the expert marking, we marked True and False, positive and negative detections.These values were used to evaluate the specificity and sensitivity of the cough monitoring system. (ii) Counting the number of coughs in longer segments (t = 60 sec, n = 300) and plotting the cough count vs. the corresponding experts' count whereby the linear regression equation, the regression coefficient (R
2) and the joint-distribution density Bland-Altman plots could be determined.

Results
Data were recorded from 12 volunteers undergoing the complete protocol. The overall Specificity for cough events was 94% and the Sensitivity was 96%, with similar values found for all conditions, except for the stair climbing stage where the Specificity was 87% with Sensitivity of 97%. The regression equation between the PulmoTrack-CC™ cough event counts and the Experts' determination was with R

2
of 0.94.

Discussion
This validation scheme provides an objective and quantitative assessment method of a cough counting algorithm in a range of realistic situations that simulate ambulatory monitoring of cough. The ability to detect voluntary coughs under acoustically challenging ambient conditions may represent a useful step towards a clinically applicable automatic cough detector.
Sonic hedgehogexpressing and responding cells generate neuronal diversity in the medial amygdala
Authors: Carney Rosalind SE , Mangin Jean-Marie , Hayes Lindsay , Mansfield Kevin , Sousa Vitor H , Fishell Gord , Machold Robert P , Ahn Sohyun , Gallo Vittorio , Corbin Joshua G 
Published: May 2010

Abstract
Background
The mammalian amygdala is composed of two primary functional subdivisions, classified according to whether the major output projection of each nucleus is excitatory or inhibitory. The posterior dorsal and ventral subdivisions of the medial amygdala, which primarily contain inhibitory output neurons, modulate specific aspects of innate socio-sexual and aggressive behaviors. However, the development of the neuronal diversity of this complex and important structure remains to be fully elucidated.

Results
Using a combination of genetic fate-mapping and loss-of-function analyses, we examined the contribution and function of Sonic hedgehog (Shh)-expressing and Shh-responsive (Nkx2-1+ and Gli1+) neurons in the medial amygdala. Specifically, we found that Shh- and Nkx2-1-lineage cells contribute differentially to the dorsal and ventral subdivisions of the postnatal medial amygdala. These Shh- and Nkx2-1-lineage neurons express overlapping and non-overlapping inhibitory neuronal markers, such as Calbindin, FoxP2, nNOS and Somatostatin, revealing diverse fate contributions in discrete medial amygdala nuclear subdivisions. Electrophysiological analysis of the Shh-derived neurons additionally reveals an important functional diversity within this lineage in the medial amygdala. Moreover, inducible Gli1
CreER(T2)
temporal fate mapping shows that early-generated progenitors that respond to Shh signaling also contribute to medial amygdala neuronal diversity. Lastly, analysis of Nkx2-1 mutant mice demonstrates a genetic requirement for Nkx2-1 in inhibitory neuronal specification in the medial amygdala distinct from the requirement for Nkx2-1 in cerebral cortical development.

Conclusions
Taken together, these data reveal a differential contribution of Shh-expressing and Shh-responding cells to medial amygdala neuronal diversity as well as the function of Nkx2-1 in the development of this important limbic system structure.
Individual fates of mesenchymal stem cells in vitro
Authors: Krinner Axel , Hoffmann Martin , Loeffler Markus , Drasdo Dirk , Galle Joerg 
Published: May 2010

Abstract

Background

In vitro cultivated stem cell populations are in general heterogeneous with respect to their expression of differentiation markers. In hematopoietic progenitor populations, this heterogeneity has been shown to regenerate within days from isolated subpopulations defined by high or low marker expression. This kind of plasticity has been suggested to be a fundamental feature of mesenchymal stem cells (MSCs) as well. Here, we study MSC plasticity on the level of individual cells applying a multi-scale computer model that is based on the concept of noise-driven stem cell differentiation.

Results
By simulation studies, we provide detailed insight into the kinetics of MSC organisation. Monitoring the fates of individual cells in high and low oxygen culture, we calculated the average transition times of individual cells into stem cell and differentiated states. We predict that at low oxygen the heterogeneity of a MSC population with respect to differentiation regenerates from any selected subpopulation in about two days. At high oxygen, regeneration becomes substantially slowed down. Simulation results on the composition of the functional stem cell pool of MSC populations suggest that most of the cells that constitute this pool originate from more differentiated cells.

Conclusions
Individual cell-based models are well-suited to provide quantitative predictions on essential features of the spatio-temporal organisation of MSC in vitro. Our predictions on MSC plasticity and its dependence on the environment motivate a number of in vitro experiments for validation. They may contribute to a better understanding of MSC organisation in vitro, including features of clonal expansion, environmental adaptation and stem cell ageing.
Co-expression module analysis reveals biological processes, genomic gain, and regulatory mechanisms associated with breast cancer progression
Authors: Shi Zhiao , Derow Catherine K , Zhang Bing 
Published: May 2010

AbstractBackgroundGene expression signatures are typically identified by correlating gene expression patterns to a disease phenotype of interest. However, individual gene-based signatures usually suffer from low reproducibility and interpretability.ResultsWe have developed a novel algorithm Iterative Clique Enumeration (ICE) for identifying relatively independent maximal cliques as co-expression modules and a module-based approach to the analysis of gene expression data. Applying this approach on a public breast cancer dataset identified 19 modules whose expression levels were significantly correlated with tumor grade. The correlations were reproducible for 17 modules in an independent breast cancer dataset, and the reproducibility was considerably higher than that based on individual genes or modules identified by other algorithms. Sixteen out of the 17 modules showed significant enrichment in certain Gene Ontology (GO) categories. Specifically, modules related to cell proliferation and immune response were up-regulated in high-grade tumors while those related to cell adhesion was down-regulated. Further analyses showed that transcription factors NYFB, E2F1/E2F3, NRF1, and ELK1 were responsible for the up-regulation of the cell proliferation modules. IRF family and ETS family proteins were responsible for the up-regulation of the immune response modules. Moreover, inhibition of the PPARA signaling pathway may also play an important role in tumor progression. The module without GO enrichment was found to be associated with a potential genomic gain in 8q21-23 in high-grade tumors. The 17-module signature of breast tumor progression clustered patients into subgroups with significantly different relapse-free survival times. Namely, patients with lower cell proliferation and higher cell adhesion levels had significantly lower risk of recurrence, both for all patients (p= 0.004) and for those with grade 2 tumors (p= 0.017).ConclusionsThe ICE algorithm is effective in identifying relatively independent co-expression modules from gene co-expression networks and the module-based approach illustrated in this study provides a robust, interpretable, and mechanistic characterization of transcriptional changes.
Mapping mental health finances in Ghana, Uganda, Sri Lanka, India and Lao PDR
Authors: Raja Shoba , Wood Sarah K , de Menil Victoria , Mannarath Saju C 
Published: May 2010

Abstract

Background
Limited evidence about mental health finances in low and middle-income countries is a key challenge to mental health care policy initiatives. This study aimed to map mental health finances in Ghana, Uganda, India (Kerala state), Sri Lanka and Lao PDR focusing on how much money is available for mental health, how it is spent, and how this impacts mental health services.

Methods
A researcher in each region reviewed public mental health-related budgets and interviewed key informants on government mental health financing. A total of 43 key informant interviews were conducted. Quantitative data was analyzed in an excel matrix using descriptive statistics. Key informant interviews were coded a priori against research questions.

Results
National ring-fenced budgets for mental health as a percentage of national health spending for 2007-08 is 1.7% in Sri Lanka, 3.7% in Ghana, 2.0% in Kerala (India) and 6.6% in Uganda. Budgets were not available in Lao PDR. The majority of ring-fenced budgets (76% to 100%) is spent on psychiatric hospitals. Mental health spending could not be tracked beyond the psychiatric hospital level due to limited information at the health centre and community levels.

Conclusions
Mental health budget information should be tracked and made publically accessible. Governments can adapt WHO AIMS indicators for reviewing national mental health finances. Funding allocations work more effectively through decentralization. Mental health financing should reflect new ideas emerging from community based practice in LMICs.