bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human fetal heart specific coexpression network involves congenital heart disease/defect candidate genes
Authors: Wang Bo , You Guoling , Fu Qihua 
Published: April 2017

AbstractHeart development is a complex process requiring dynamic transcriptional regulation. Disturbance of this process will lead to severe developmental defects such as congenital heart disease/defect (CHD). CHD is a group of complex disorder with high genetic heterogeneity, common pathways associated with CHD remains largely unknown. In the manuscript, we focused on the tissue specific genes in human fetal heart samples to explore such pathways. We used the RNA microarray dataset of human fetal tissues from ENCODE project to identify genes with heart tissue specific expression. A transcriptional network was constructed for these genes based on the Pearson correlation coefficients of their expression levels. Function, selective constraints and disease associations of these genes were then examined. Our analysis identified a network consisted of 316 genes with human fetal heart specific expression. The network was highly co-regulated and showed evolutionary conserved tissue expression pattern in tetrapod. Genes in this network are enriched in CHD specific genes and disease mutations. Using the transcriptomic data, we discovered a highly concerted gene network that might reflect a common pathway associated with the etiology of CHD. Such analysis should be helpful for disease associated gene identification in clinical studies.
Anti-inflammatory, Antipyretic, and Antinociceptive Effects of a Cressa cretica Aqueous Extract
Authors: Abdallah Heba , Elshamy Abdelsamed , El Gendy Abd , Abd El-Gawad Ahmed , Omer Elsayed , De Leo Marinella , Pistelli Luisa 
Published: April 2017

Abstract
Cressa cretica is a widely grown halophytic plant traditionally used for the treatment of different ailments. Previous investigations reported its biological activity on a wide spectrum of diseases. In this study, in vivo antinociceptive, anti-inflammatory, and antipyretic activities of C. cretica aqueous extract whole plant were evaluated. In addition, the total polyphenol content, the total flavonoid content, and the chemical characterization of the extract were performed. C. cretica showed writhing inhibition in acetic acid-induced peripheral nociception of 43 and 48 % at doses of 50 and 100 mg/kg, respectively. The same doses increased latency time in a hot plate model of central analgesia by 66 and 78 % compared to the control group, respectively. The acute anti-inflammatory effect of the extract was explored in the carrageenan-induced rat hind paw test. The inhibition of paw volume was better than that of the standard drug indomethacin. C. cretica significantly decreased rectal temperature in the rats injected with Brewerʼs yeast. C. cretica aqueous extract showed both central and peripheral antinociceptive activities and was effective as an anti-inflammatory and antipyretic. Phenolic compounds, including chlorogenic acids and flavonol glycosides, were identified by HPLC-PDA-ESI-MS techniques. These findings indicate the medicinal importance of this traditionally used plant as a therapeutic remedy for different ailments.
Potential of Bryophyllum pinnatum as a Detrusor Relaxant: An in Vitro Exploratory Study
Authors: Bachmann Simon , Betschart Cornelia , Gerber Julia , Fürer Karin , Mennet Mónica , Hamburger Matthias , Potterat Olivier , von Mandach Ursula , Simões-Wüst Ana 
Published: April 2017

AbstractAn earlier prospective, randomised, placebo-controlled clinical trial had suggested that Bryophyllum pinnatum might have potential in the treatment of overactive bladder. Here we investigated the effects of B. pinnatum leaf press juice, fractions enriched in flavonoids and bufadienolides, and a flavonoid aglycon mixture and individual aglycons on detrusor contractility as a major target in overactive bladder treatment. The strength of the detrusor contractions was investigated using porcine muscle strips stimulated with KCl. B. pinnatum leaf press juice increased the contraction force of muscle strips. Treatment with the flavonoid-enriched fraction had almost no effect on contractility, while the bufadienolide-enriched fraction and flavonoid aglycons led to a concentration-dependent lowering of the contraction force. The data indicate that several components of B. pinnatum leaf press juice may contribute to the inhibitory effect on detrusor contractility, which in turn provides support to overactive bladder treatment with B. pinnatum.
« Obscur à soi-même », obscur au lecteur ?
Authors: Rey Pierre-Louis 
Published: April 2017

Abstract
Though Camus admires Faulkner, he differs from him in his accomplished novels, in as far as he lets no doubt emerge about his characters’ identity or the reality of events revealed in the plot. This is all the more evident because the short sentences in his novel L’Étranger contrast with the intricate and often abstruse parts of The Sound and the Fury. However, when Camus explores the most indefinable aspects of his self in the last chapter of Le Premier Homme, he regenerates his écriture in such a way that the resemblance critics had found with the American writer, in retrospect, seemed to be justified.
Assessing Reservoir Largemouth Bass Standardized Boat Electrofishing: Effect of Catchability on Density and Size Structure Indices
Authors: Tyszko Stephen M. , Hangsleben Matt A. , Zweifel Richard D. , Pritt Jeremy J. , Conroy Joseph D. 
Published: April 2017

Abstract
Understanding catchability—the fraction of a stock caught by a defined unit of effort—is crucial to using fisheries assessment data to index abundance. We conducted mark–recapture experiments to estimate catchability and evaluate standard boat electrofishing methods for assessing populations of Largemouth Bass Micropterus salmoides. We then used a resampling analysis to test for differences in bass CPUE (fish/h and fish/km) between two high-density reservoirs and one low-density reservoir and among surveys within each reservoir. We compared scenarios using surveys conducted only during (1) the standard time period (mid-April to mid-May) and (2) the entire assessment period (early April to mid-June). We considered the percentage of significant differences in CPUE between the high-density and low-density reservoirs to represent statistical power (i.e., the ability to detect a difference in CPUE when a difference actually exists) and the percentage of significant differences in CPUE between surveys in the same reservoir to represent the false-positive rate (i.e., the detection of a difference in CPUE when no difference in density exists). Catchability and CPUE were greatest and least variable during recapture events conducted during the standard period. The mean catchability of sub–stock length Largemouth Bass (150–200 mm) and memorable-length bass (≥510 mm) was significantly less than those for other length categories. Statistical power exceeded 80%, and the false-positive rate was generally less than 10% for sampling during the standard period at as few as six electrofishing sites. When including samples from outside the standard period, power was lower and the false-positive rate was as high as 60%. Power and false-positive rate were similar whether effort was measured in time or distance. Our results emphasize that standardized springtime boat electrofishing assessments validly index Largemouth Bass density and size structure.
Received October 7, 2016; accepted February 2, 2017 Published online April 24, 2017
Which factors to induce hearing loss in professional musicians? Extensive literature review and histopathology findings can answer it
Authors: Di Stadio A. 
Published: April 2017

Objective:
To evaluate the determining factors of noise-induced sensorineural hearing loss (SNHL) in professional musicians (PMs).

Methods:
An extensive review using Pubmed, Medscape and Google scholar research was performed and studies with the following keywords were selected: ‘hearing loss, tinnitus, hyperacusis, music, classical music, rock music, pop music, musicians, orchestra, music student, professional musician, non-professional musician, music exposure and temporary hearing loss’. A histopathology study from individuals who during life were musician in orchestra was described.

Results:
Eighty to ninety per cent of PMs are affected from noise-induced SNHL at 3000–8000 Hz frequencies. The range of the frequency of SNHL was correlated with the frequency of the specific frequency of the musical instrument and to the sound intensity which they were exposed. The two temporal bones studied, showed a severely loss hair cells at the basal turn of both cochleae and moderate loss of hair cells in medial and apical turn.

Conclusion:
The review and the results of the temporal bones (TBs) findings show that the intensity and frequency range are the more relevant factors causing noise-induced high frequency SNHL. The time exposed to sound, instead, can impact the low frequency range as supported by temporal bone results.
Discovery and genotyping of novel sequence insertions in many sequenced individuals
Authors: Kavak Pınar , Lin Yen-Yi , Numanagić Ibrahim , Asghari Hossein , Güngör Tunga , Alkan Can , Hach Faraz 
Published: April 2017

Abstract

Motivation
Despite recent advances in algorithms design to characterize structural variation using high-throughput short read sequencing (HTS) data, characterization of novel sequence insertions longer than the average read length remains a challenging task. This is mainly due to both computational difficulties and the complexities imposed by genomic repeats in generating reliable assemblies to accurately detect both the sequence content and the exact location of such insertions. Additionally, de novo genome assembly algorithms typically require a very high depth of coverage, which may be a limiting factor for most genome studies. Therefore, characterization of novel sequence insertions is not a routine part of most sequencing projects.
There are only a handful of algorithms that are specifically developed for novel sequence insertion discovery that can bypass the need for the whole genome de novo assembly. Still, most such algorithms rely on high depth of coverage, and to our knowledge there is only one method (PopIns) that can use multi-sample data to “collectively” obtain a very high coverage dataset to accurately find insertions common in a given population.

Result
Here, we present Pamir, a new algorithm to efficiently and accurately discover and genotype novel sequence insertions using either single or multiple genome sequencing datasets. Pamir is able to detect breakpoint locations of the insertions and calculate their zygosity (i.e. heterozygous versus homozygous) by analyzing multiple sequence signatures, matching one-end-anchored sequences to small-scale de novo assemblies of unmapped reads, and conducting strand-aware local assembly. We test the efficacy of Pamir on both simulated and real data, and demonstrate its potential use in accurate and routine identification of novel sequence insertions in genome projects.

Availability and implementation
Pamir is available at https://github.com/vpc-ccg/pamir.

Supplementary information
Supplementary data are available at Bioinformatics online.
Retrograde accretion discs in high-mass Be/X-ray binaries
Authors: Christodoulou D. M. , Laycock S. G. T. , Kazanas D. 
Published: April 2017

Abstract
We have compiled a comprehensive library of all X-ray observations of Magellanic pulsars carried out by XMM–Newton, Chandra and RXTE in the period 1997–2014. In this work, we use the data from 53 high-mass Be/X-ray binaries in the Small Magellanic Cloud to demonstrate that the distribution of spin-period derivatives versus spin periods of spinning-down pulsars is not at all different from that of the accreting spinning-up pulsars. The inescapable conclusion is that the up and down samples were drawn from the same continuous parent population; therefore, Be/X-ray pulsars that are spinning down over periods spanning 18 yr are, in fact, accreting from retrograde discs. The presence of prograde and retrograde discs in roughly equal numbers supports a new evolutionary scenario for Be/X-ray pulsars in their spin period–period derivative diagram.
COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information
Authors: Zhang Chengxin , Freddolino Lydia , Zhang Yang 
Published: April 2017

Abstract
The COFACTOR web server is a unified platform for structure-based multiple-level protein function predictions. By structurally threading low-resolution structural models through the BioLiP library, the COFACTOR server infers three categories of protein functions including gene ontology, enzyme commission and ligand-binding sites from various analogous and homologous function templates. Here, we report recent improvements of the COFACTOR server in the development of new pipelines to infer functional insights from sequence profile alignments and protein–protein interaction networks. Large-scale benchmark tests show that the new hybrid COFACTOR approach significantly improves the function annotation accuracy of the former structure-based pipeline and other state-of-the-art functional annotation methods, particularly for targets that have no close homology templates. The updated COFACTOR server and the template libraries are available at http://zhanglab.ccmb.med.umich.edu/COFACTOR/.
Glomerular disease frequencies by race, sex and region: results from the International Kidney Biopsy Survey
Authors: O'Shaughnessy Michelle M , Hogan Susan L , Thompson Bawana D , Coppo Rosanna , Fogo Agnes B , Jennette J Charles 
Published: April 2017

Abstract

Background
Large-scale studies comparing glomerular disease frequencies across continents are lacking.

Methods
We surveyed 29 nephropathology laboratories in four continents using a standardized data collection form. We obtained recent consecutive kidney biopsy diagnosis frequencies at each center and summary demographics for each diagnosis. This report focuses on glomerular disease frequencies by region and race/ethnicity.

Results
Among 42 603 glomerular disease diagnoses reported (median age 47 years, 52% male, 57% white), from a total of 60 340 diagnoses, glomerular disease subtype frequencies differed considerably by continent. Diabetic glomerulosclerosis (GS; 19.1%) and focal segmental glomerulosclerosis (FSGS; 19.1%) predominated in North America; lupus nephritis (38.1%) and FSGS (15.8%) predominated in Latin America; IgA nephropathy (IgAN; 22.1%) and FSGS (14.9%) predominated in Europe; and IgAN (39.5%) and lupus nephritis (16.8%) predominated in Asia. After stratifying by race, diabetic GS (17.4% versus 4.3%, P < 0.001) and FSGS (17.3% versus 11.8%, P < 0.001) were more, and lupus nephritis less (15.8% versus 45.6%, P < 0.001), frequent among Latinos in North versus Latin America; FSGS was more (13.1% versus 7.1%, P < 0.001), and IgAN less (27.4% versus 40.5%, P < 0.001), frequent among Asians in North America versus Asia; and FSGS (18.9% versus 13.5%, P < 0.001) and diabetic GS (18.7% versus 6.5%, P < 0.001) were more, and IgAN less (14.4% versus 25.4%, P < 0.001), frequent among whites in North America versus Europe.

Conclusions
We determined that glomerular disease frequencies differed by continent, even among patients of similar race/ethnicity. Regional environmental and lifestyle factors, and local biopsy policies, might influence glomerular disease epidemiology independently of race/ethnicity.
Flow Diverters for Treatment of 160 Ophthalmic Segment Aneurysms: Evaluation of Safety and Efficacy in a Multicenter Cohort
Authors: Griessenauer Christoph J. , Piske Ronie L. , Baccin Carlos E. , Pereira Benedito J.A. , Reddy Arra S. , Thomas Ajith J. , Abud Thiago G. , Ogilvy Christopher S. 
Published: April 2017

Abstract

BACKGROUND: Treatment of ophthalmic segment aneurysms (OSA) remains challenging. Flow diverter stents (FDS) have evolved as a promising endovascular treatment option for aneurysms of the internal carotid artery and are associated with high occlusion rates and a favorable morbidity and mortality profile.

OBJECTIVE: To determine safety and efficacy of FDS for OSA in a large, multicenter cohort.

METHODS: A retrospective analysis of prospectively maintained databases of 127 consecutive patients harboring 160 OSA treated with FDS was performed. Aneurysms were classified based on location and morphology. Follow-up with digital subtraction angiography (DSA) was performed 6 to 18 months after treatment.

RESULTS: Follow-up DSA was available for 101 (63.1%) aneurysms with a mean follow-up of 18 months. Complete occlusion was observed in 90 aneurysms (89.1%), near-complete occlusion (>95%) in 3 (3%), and incomplete occlusion (<95%) in 8 aneurysms (7.9%). One aneurysm was retreated with another FDS (0.9%). No risk factors for incomplete occlusion were identified. The OA was occluded at the latest follow-up in 6 cases (7.1%). Permanent morbidity occurred in 4 patients (3.1%), and there was no mortality related to the FDS procedure.

CONCLUSION: Treatment of OSA with FDS was found to be safe and effective. The retreatment rate was extremely low and aneurysms that occluded did not reanalyze.
Risk of Venous Thromboembolism and Operative Duration in Patients Undergoing Neurosurgical Procedures
Authors: Bekelis Kimon , Labropoulos Nicos , Coy Shannon 
Published: April 2017

Abstract

BACKGROUND: The association of operative duration with the risk of venous thromboembolism (VTE) has not been quantified in neurosurgery.

OBJECTIVE: To investigate the association of surgical duration for several neurosurgical procedures and the incidence of VTE.

METHODS: We performed a retrospective cohort study involving patients who underwent neurosurgical procedures from 2005 to 2012 and were registered in the American College of Surgeons National Quality Improvement Project registry. In order to control for confounding, we used multivariable regression models, and propensity score conditioning.

RESULTS: During the study period, there were 94 747 patients, who underwent neurosurgical procedures, and met the inclusion criteria. Of these, 1358 (1.0%) developed VTE within 30 days postoperatively. Multivariable logistic regression demonstrated an association of longer operative duration with higher 30-day incidence of VTE (odds ratio [OR], 1.22; 95% confidence interval [CI], 1.19-1.25). Compared with procedures of moderate duration (third quintile, 40-60th percentile), patients undergoing the longest procedures (>80th percentile) had higher odds (OR, 3.15; 95% CI, 2.49-3.99) of developing VTE. The shortest procedures (<20th percentile) were associated with a decreased incidence of VTE (OR, 0.51; 95% CI, 0.27-0.76) in comparison to those of moderate duration. The same associations were present in propensity score-adjusted models, and models stratified by subgroups of cranial, spinal, peripheral nerve, and carotid procedures.

CONCLUSIONS: In a cohort of patients from a national prospective surgical registry, increased operative duration was associated with increased incidence of VTE for neurosurgical procedures. These results can be used by neurosurgeons to inform operative management, and to stratify patients with regard to VTE risk.
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in the surface ocean
Authors: Delmont Tom O. , Quince Christopher , Shaiber Alon , Esen Özcan C. , Lee Sonny TM , Lücker Sebastian , Murat Eren A. 
Published: April 2017

AbstractNitrogen fixation in the surface ocean impacts the global climate by regulating the microbial primary productivity and the sequestration of carbon through the biological pump. Cyanobacterial populations have long been thought to represent the main suppliers of the bio-available nitrogen in this habitat. However, recent molecular surveys of nitrogenase reductase gene revealed the existence of rare non-cyanobacterial populations that can also fix nitrogen. Here, we characterize for the first time the genomic content of some of these heterotrophic bacterial diazotrophs (HBDs) inhabiting the open surface ocean waters. They represent new lineages within Planctomycetes and Proteobacteria, a phylum never linked to nitrogen fixation prior to this study. HBDs were surprisingly abundant in the Pacific Ocean and the Atlantic Ocean northwest, conflicting with decades of PCR surveys. The abundance and widespread occurrence of non-cyanobacterial diazotrophs in the surface ocean emphasizes the need to re-evaluate their role in the nitrogen cycle and primary productivity.
The relationship of survivorship and body mass modeled by metabolic and vitality theories
Authors: Anderson James J. 
Published: April 2017

AbstractThe relationship between body mass and survivorship is explained by a model that merges metabolic theory relating metabolism to body mass, and vitality theory relating survival to vitality loss and extrinsic mortality. The resulting metabolic-vitality framework hypothesizes mortality results from replicative senescence of the hematopoietic system and predator-prey interactions. Fitting the metabolic-vitality model to body mass and maximum lifespan data of 494 nonvolant mammals yields allometric relationships of body mass to the vitality parameters, from which full survivorship profiles can be predicted from body mass. Comparisons of the mass-derived vitality parameters to those estimated directly from survival data identifies how intrinsic and extrinsic mortality processes of specific populations deviate from the aggregate. Highlighted findings include a mathematical explanation for the shift from Type I to Type II survivorship curves with decreasing body mass, a quantification of the impact of hunting on wild populations and a quantification of the reduce rate of primate aging relative to the aggregate of mammal populations. Finally, the framework allows explorations of the combined effects of animal aging and predation on survival patterns.
Stationary Analysis the Alternative Splicing Profile Reveals the Splicing Code
Authors: Li Meng 
Published: April 2017

AbstractRecent works indicated that the regulatory function of RBPs showed context dependent manners, but the details of the regulatory function of most RBPs and importance are unknown. Here we integrated hundreds of eCLIP-seq and RNA-seq from ENCODE project and used RBP-position combinations on events to predict if the events are spliced out or not and the results showed that only a small of them can regulate the alternative splicing process in a degree. We observedSRSF1, LIN28B, FMR1, SRSF7, RBM22, PRPF8, SF3B4, TIA1andhnRNP Mare important features by binding the exon or intron region respectively.SF3B4andRBM22show opposite regulatory function when binding exons downstream and upstream intron. This supports the asymmetric exon decision model that state the exon exclusion pathway compete with the exon inclusion pathway to regulate splicing. We also observed that some peaks locate in exon-exon junction regions and indicate some splicing related RBPs also bind on mRNAs.