bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationship between Permeability Glycoprotein (P-gp) Gene Expression and Enrofloxacin Metabolism in Nile Tilapia
Authors: Hu Kun , Cheng Gang , Zhang Haixin , Wang Huicong , Ruan Jiming , Chen Li , Fang Wenhong , Yang Xianle 
Published: June 2014

Abstract
The aim of this study was to analyze the influence of permeability glycoprotein (P-gp) gene expression on enrofloxacin (ENR) metabolism in aquatic animals. Nile Tilapia Oreochomis niloticus were fed different doses of ENR ranging from 0 to 80 mg/kg. The P-gp gene expression levels were determined by quantitative real-time PCR (qRT-PCR) at indicated time points after drug administration. Drug metabolism was determined by HPLC. The P-gp gene expression in liver and kidney was greatly enhanced 30 min after ENR administration at 40 mg/kg, peaked 3 h after drug administration, and then gradually decreased. Thirty minutes after a single oral administration of ENR (0, 20, 40, or 80 mg/kg), the P-gp gene expression increased in a dose-dependent manner. The P-gp gene expression levels in the kidney were significantly higher than those in the liver. Additionally, the metabolic rate of ENR in kidney was more rapid than that in liver. Furthermore, a close correlation was found between P-gp gene expression and ENR concentrations. These results suggest that P-gp may be involved in the ENR metabolism process in Nile Tilapia, providing a novel model for the potential utility of gene expression and drug metabolism studies in aquatic animals.
Received July 9, 2013; accepted October 17, 2013
Investigation of the Link between Broodstock Infection, Vertical Transmission, and Prevalence of Flavobacterium psychrophilum in Eggs and Progeny of Rainbow Trout and Coho Salmon
Authors: Long Amy , Call Douglas R. , Cain Kenneth D. 
Published: June 2014

Abstract
The etiological agent of bacterial coldwater disease (BCWD), Flavobacterium psychrophilum, can be transmitted both vertically and horizontally. Outbreaks of BCWD can result in significant losses in salmonid aquaculture. Reduction of outbreaks in fry may be possible through implementation of a management strategy in which progeny of heavily infected broodstock are culled from the general population. Diagnostic assays to quantify F. psychrophilum concentrations in tissue samples and confirm presence of the bacterium in ovarian fluid have been previously validated. In the current study, these assays were used to screen 60 female Rainbow Trout Oncorhynchus mykiss and 60 female Coho Salmon O. kisutch broodstock at two aquaculture facilities. Eyed eggs from 10 female broodstock (five fish from each facility) exhibiting graded levels of infection were transferred to the University of Idaho and monitored through early life stages for the presence of F. psychrophilum. Female Rainbow Trout broodstock were not positive for F. psychrophilum by enzyme-linked immunosorbent assay (ELISA) and prevalence was low in these progeny. However, ELISA optical density values for kidney correlated to F. psychrophilum prevalence in progeny (r = 0.938, P &lt; 0.05) of Coho Salmon. Nested PCR on ovarian fluid was not a reliable indicator of vertical transmission in either species as broodstock ovarian fluid results did not correlate to F. psychrophilum prevalence in eyed eggs. Further research with these assays is necessary; however, results from this study indicate that broodstock screening may be a potential tool for evaluating F. psychrophilum infection levels, which could become an important component for disease management.
Received December 19, 2012; accepted December 8, 2013
Comparative Susceptibility of Channel Catfish, Blue Catfish, and their Hybrid Cross to Experimental Challenge with Bolbophorus damnificus (Digenea: Bolbophoridae) Cercariae
Authors: Griffin Matt J. , Reichley Stephen R. , Khoo Lester H. , Ware Cynthia , Greenway Terrence E. , Mischke Charles C. , Wise David J. 
Published: June 2014

Abstract
The digenetic trematode Bolbophorus damnificus has been implicated in significant losses in catfish aquaculture since the late 1990s. The complex life cycle sequentially involves the American white pelican Pelecanus erythrorhynchos, the marsh rams horn snail Planorbella trivolvis, and Channel Catfish Ictalurus punctatus. Research supports anecdotal reports from the industry, suggesting that the hybrid of Channel Catfish×Blue Catfish I. furcatus is less susceptible to disease agents that have been historically prohibitive to Channel Catfish production, namely the gram-negative bacteria Edwardsiella ictaluri and Flavobacterium columnare, as well as the myxozoan parasite Henneguya ictaluri. This current research compared the susceptibility of Channel Catfish, Blue Catfish, and their hybrid cross to an experimental challenge by B. damnificus. Fish were exposed to 0, 100, 200, and 400 B. damnificus cercariae per fish, and the numbers of metacercariae per fish were determined 14 d postchallenge. Metacercariae were recovered from all challenged fish. There were no significant differences among fish groups challenged with the same dose, suggesting Channel and Blue Catfish and their hybrid are comparably susceptible to B. damnificus infection. As such, it is recommended that producers raising hybrid catfish remain diligent in controlling populations of the snail intermediate host to prevent production losses attributed to B. damnificus, especially when loafing pelicans have been observed at the aquaculture operation.
Received October 22, 2013; accepted January 5, 2014
Susceptibility of Fish and Turtles to Three Ranaviruses Isolated from Different Ectothermic Vertebrate Classes
Authors: Brenes Roberto , Miller Debra L. , Waltzek Thomas. B. , Wilkes Rebecca P. , Tucker Jennifer L. , Chaney Jordan C. , Hardman Rebecca H. , Brand Mabre D. , Huether Rebecca R. , Gray Matthew J. 
Published: June 2014

Abstract
Ranaviruses have been associated with mortality of lower vertebrates around the world. Frog virus 3 (FV3)-like ranaviruses have been isolated from different ectothermic vertebrate classes; however, few studies have demonstrated whether this pathogen can be transmitted among classes. Using FV3-like ranaviruses isolated from the American bullfrog Lithobates catesbeianus, eastern box turtle Terrapene carolina carolina, and Pallid Sturgeon Scaphirhynchus albus, we tested for the occurrence of interclass transmission (i.e., infection) and host susceptibility (i.e., percent mortality) for five juvenile fish and three juvenile turtle species exposed to each of these isolates. Exposure was administered via water bath (103 PFU/mL) for 3 d and survival was monitored for 28 d. Florida softshell turtles Apalone ferox experienced no mortality, but 10% and 20% of individuals became infected by the turtle and fish isolate, respectively. Similarly, 5% of Mississippi map turtles Graptemys pseudogeographica kohni were subclinically infected with the turtle isolate at the end of the experiment. Channel Catfish Ictalurus punctatus experienced 5% mortality when exposed to the turtle isolate, while Western Mosquitofish Gambusia affinis experienced 10% mortality when exposed to the turtle and amphibian isolates and 5% mortality when exposed to the fish isolate. Our results demonstrated that interclass transmission of FV3-like ranaviruses is possible. Although substantial mortality did not occur in our experiments, the occurrence of low mortality and subclinical infections suggest that fish and aquatic turtles may function as reservoirs for FV3-like ranaviruses. Additionally, our study is the first to report transmission of FV3-like ranaviruses between fish and chelonians.
Received October 22, 2013; accepted January 8, 2014.
Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series
Authors: Nueda María José , Tarazona Sonia , Conesa Ana 
Published: June 2014

Abstract
Motivation: The widespread adoption of RNA-seq to quantitatively measure gene expression has increased the scope of sequencing experimental designs to include time-course experiments. maSigPro is an R package specifically suited for the analysis of time-course gene expression data, which was developed originally for microarrays and hence was limited in its application to count data.
Results: We have updated maSigPro to support RNA-seq time series analysis by introducing generalized linear models in the algorithm to support the modeling of count data while maintaining the traditional functionalities of the package. We show a good performance of the maSigPro-GLM method in several simulated time-course scenarios and in a real experimental dataset.
Availability and implementation: The package is freely available under the LGPL license from the Bioconductor Web site ( http://bioconductor.org ).
Contact: mj.nueda@ua.es or aconesa@cipf.es
RAREMETAL: fast and powerful meta-analysis for rare variants
Authors: Feng Shuang , Liu Dajiang , Zhan Xiaowei , Wing Mary Kate , Abecasis Gonçalo R. 
Published: June 2014

AbstractSummary: RAREMETAL is a computationally efficient tool for meta-analysis of rare variants genotyped using sequencing or arrays. RAREMETAL facilitates analyses of individual studies, accommodates a variety of input file formats, handles related and unrelated individuals, executes both single variant and burden tests and performs conditional association analyses.Availability and implementation: http://genome.sph.umich.edu/wiki/RAREMETAL for executables, source code, documentation and tutorial.Contact: sfengsph@umich.edu or goncalo@umich.edu
PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data
Authors: Zhang Yanxiao , Lin Yu-Hsuan , Johnson Timothy D. , Rozek Laura S. , Sartor Maureen A. 
Published: June 2014

Abstract
Motivation: ChIP-Seq is the standard method to identify genome-wide DNA-binding sites for transcription factors (TFs) and histone modifications. There is a growing need to analyze experiments with biological replicates, especially for epigenomic experiments where variation among biological samples can be substantial. However, tools that can perform group comparisons are currently lacking.
Results: We present a peak-calling prioritization pipeline (PePr) for identifying consistent or differential binding sites in ChIP-Seq experiments with biological replicates. PePr models read counts across the genome among biological samples with a negative binomial distribution and uses a local variance estimation method, ranking consistent or differential binding sites more favorably than sites with greater variability. We compared PePr with commonly used and recently proposed approaches on eight TF datasets and show that PePr uniquely identifies consistent regions with enriched read counts, high motif occurrence rate and known characteristics of TF binding based on visual inspection. For histone modification data with broadly enriched regions, PePr identified differential regions that are consistent within groups and outperformed other methods in scaling False Discovery Rate (FDR) analysis.
Availability and implementation: http://code.google.com/p/pepr-chip-seq/ .
Contact : sartorma@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Mirsynergy: detecting synergistic miRNA regulatory modules by overlapping neighbourhood expansion
Authors: Li Yue , Liang Cheng , Wong Ka-Chun , Luo Jiawei , Zhang Zhaolei 
Published: June 2014

AbstractMotivation: Identification of microRNA regulatory modules (MiRMs) will aid deciphering aberrant transcriptional regulatory network in cancer but is computationally challenging. Existing methods are stochastic or require a fixed number of regulatory modules.Results: We propose Mirsynergy, an efficient deterministic overlapping clustering algorithm adapted from a recently developed framework. Mirsynergy operates in two stages: it first forms MiRMs based on co-occurring microRNA (miRNA) targets and then expands each MiRM by greedily including (excluding) mRNAs into (from) the MiRM to maximize the synergy score, which is a function of miRNA–mRNA and gene–gene interactions. Using expression data for ovarian, breast and thyroid cancer from The Cancer Genome Atlas, we compared Mirsynergy with internal controls and existing methods. Mirsynergy-MiRMs exhibit significantly higher functional enrichment and more coherent miRNA–mRNA expression anti-correlation. Based on Kaplan–Meier survival analysis, we proposed several prognostically promising MiRMs and envisioned their utility in cancer research.Availability and implementation: Mirsynergy is implemented/available as an R/Bioconductor package at www.cs.utoronto.ca/∼yueli/Mirsynergy.htmlContact: yueli@cs.toronto.edu ; zhaolei.zhang@utoronto.caSupplementary information: Supplementary data are available at Bioinformatics online.
Properties of age compositions and mortality estimates derived from cohort slicing of length data
Authors: Ailloud Lisa E. , Smith Matthew W. , Then Amy Y. , Omori Kristen L. , Ralph Gina M. , Hoenig John M. 
Published: June 2014

Abstract
Cohort slicing can be used to obtain catch-at-age data from length frequency distributions when directly measured age data are unavailable. The procedure systematically underestimates the relative abundance of the youngest age groups and overestimates abundance at older ages. Cohort-sliced catch-at-age data can be used to estimate total mortality rate (Z) using a regression estimator or the Chapman–Robson estimator for right truncated data. However, the effect of cohort slicing on accuracy and precision of resulting Z estimates remains to be determined. We used Monte Carlo simulation to estimate the per cent bias and per cent root mean square error of the unweighted regression, weighted regression, and Chapman–Robson mortality estimators applied to cohort-sliced data. Incompletely recruited age groups were truncated from the cohort-sliced catch-at-age data using previously established recommendations and a variety of plus groups was used to combine older age groups. The sensitivity of the results to a range of plausible biological combinations of Z, growth parameters, recruitment variability, and length-at-age error was tested. Our simulation shows that cohort slicing can work well in some cases and poorly in others. Overall, plus group selection was more important in high K scenarios than it was in low K scenarios. Surprisingly, defining the plus group to start at a high age worked well in some cases, although length and age are poorly correlated for old ages. No one estimator was uniformly superior; we therefore provide recommendations concerning the appropriate estimator and plus group to use, depending on the parameters characterizing the stock. We further recommend that simulations be performed to determine exactly which plus group would be most appropriate given the scenario at hand.
A Study of Viral Hepatitis E Infection in a Tertiary Care Hospital in Mysore, South India
Authors: Murthy Karkala Achutha Sudharshana , Khan Ismailkhan Mohammed , Kiran Pura Krishnamurthy , Hakeem Hisham 
Published: June 2014

Abstract
Background.  In this study, we aimed to explore the clinical and epidemiological profile of all patients with hepatitis E virus (HEV) who were admitted to a tertiary care hospital in Mysore, India and to further assess various factors that influence the prognosis of these patients.
Methods.  Two hundred ninety patients with HEV infection were included in the study and interviewed. They were subjected to clinical examination and laboratory investigations, including complete hemogram, renal, and liver function tests. Viral markers for HBV, HAV, HCV, and HEV by hepatitis B surface antigen, anti-HAV, anti-HCV, and anti-HEV antibodies, respectively, were done using the enzyme-linked immunosorbent assay method. Final outcome was recorded in the form of discharge or death.
Results.  Males had higher (82.8%) incidence of HEV infection. Yellowish discoloration of urine was the most common symptom, and icterus was the most common sign at presentation. Hepatomegaly was most common finding on abdominal examination. Mean duration of hospital stay was higher among diabetics (10 days vs 7.11 ± 3.52 days). Overall, mortality observed was 3.45%. A higher mean age (P = .000) and duration of hospital stay (P = .000) were associated with higher mortality. Mortality was significantly higher among patients with alcohol abuse (25% vs 0%) (P = .004). Higher mean prothrombin time-international normalised ratio (PT-INR) (1.6 ± 0.13 vs 1.21 ± 0.32), total bilirubin (20.3 ± 5.08 vs 11.33 ± 7.26 mg/dL), and direct bilirubin (15.05 ± 3.64 vs 6.35 ± 3.71 mg/dL) were associated with higher mortality, whereas lower mean serum albumin (2.6 ± 0.11 vs 3.41 ± 0.40 gm/dL) was associated with higher mortality. Increase in renal parameters (ie, urea [97 ± 33.48 vs 32.43 ± 18.41 mg/dL] and creatinine [2.9 ± 1.38 vs 1.12 ± 0.64 mg/dL]) and electrolyte imbalances (ie, hyperkalemia [5.95 ± 1.21 vs 4.29 ± 0.51 mmol/L] and hyponatremia [123 ± 3.56 vs 136.04 ± 2.97 mmol/L]) were associated with higher mortality. There were 20-fold increases in mean serum glutamic-oxaloacetic transaminase (SGOT) and serum glutamic-pyruvic transaminase (SGPT) values (SGPT: SGOT = 1.148) and a 1-fold increase in mean alkaline phosphatase.
Conclusions.  Higher mean age, duration of hospital stay, PT-INR, total bilirubin, direct bilirubin, blood urea, serum creatinine, potassium values, alcohol abuse, presence of ascites, and fulminant hepatitis were associated with higher mortality, whereas lower mean serum albumin and sodium values were associated with higher mortality. Diabetics had a higher mean duration of hospital stay.
How the tortoise beats the hare: Slow and steady adaptation in structured populations suggests a rugged fitness landscape in bacteria
Authors: Nahum Joshua R. , Godfrey-Smith Peter , Harding Brittany N. , Marcus Joseph H. , Carlson-Stevermer Jared , Kerr Benjamin 
Published: June 2014

AbstractIn the context of Wright’s adaptive landscape, genetic epistasis can yield a multipeaked or “rugged” topography. In an unstructured population, a lineage with selective access to multiple peaks is expected to rapidly fix on one, which may not be the highest peak. Contrarily, beneficial mutations in a population with spatially restricted migration take longer to fix, allowing distant parts of the population to explore the landscape semi-independently. Such a population can simultaneous discover multiple peaks and the genotype at the highest discovered peak is expected to fix eventually. Thus, structured populations sacrifice initial speed of adaptation for breadth of search. As in the Tortoise-Hare fable, the structured population (Tortoise) starts relatively slow, but eventually surpasses the unstructured population (Hare) in average fitness. In contrast, on single-peak landscapes (e.g., systems lacking epistasis), all uphill paths converge. Given such “smooth” topography, breadth of search is devalued, and a structured population only lags behind an unstructured population in average fitness (ultimately converging). Thus, the Tortoise-Hare pattern is an indicator of ruggedness. After verifying these predictions in simulated populations where ruggedness is manipulable, we then explore average fitness in metapopulations ofEscherichia coli. Consistent with a rugged landscape topography, we find a Tortoise-Hare pattern. Further, we find that structured populations accumulate more mutations, suggesting that distant peaks are higher. This approach can be used to unveil landscape topography in other systems, and we discuss its application for antibiotic resistance, engineering problems, and elements of Wright’s Shifting Balance Process.Significance Statement:Adaptive landscapes are a way of describing how mutations interact with each other to produce fitness. If an adaptive landscape is rugged, organisms achieve higher fitness with more difficulty because the mutations to reach high fitness genotypes may not be always beneficial. By evolving populations ofEscherichia coliwith different degrees of spatial structure, we identified a Tortoise-Hare pattern, where structured populations were initially slower, but overtook less structured populations in mean fitness. These results, combined with genetic sequencing and computational simulation, indicate this bacterial adaptive landscape is rugged. Our findings address one of the most enduring questions in evolutionary biology, in addition to, providing insight into how evolution may influence medicine and engineering.
Natural variation in teosinte at the domestication locusteosinte branched1(tb1)
Authors: Vann Laura , Kono Thomas , Pyhäjärvi Tanja , Hufford Matthew B. , Ross-Ibarra Jeffrey 
Published: June 2014

AbstractPremise of the studyTheteosinte branched1(tb1)gene is a major QTL controlling branching differences between maize and its wild progenitor, teosinte. The insertion of a transposable element (Hopscotch) upstream oftb1is known to enhance the gene’s expression, causing reduced tillering in maize. Observations of the maizetb1allele in teosinte and estimates of an insertion age of theHopscotchthat predates domestication led us to investigate its prevalence and potential role in teosinte.MethodsPrevalence of theHopscotchelement was assessed across an Americas-wide sample of 837 maize and teosinte individuals using a co-dominant PCR assay. Population genetic summaries were calculated for a subset of individuals from four teosinte populations in central Mexico. Phenotypic data were also collected using seed from a single teosinte population whereHopscotchwas found segregating at high frequency.Key resultsGenotyping results indicate theHopscotchelement is found in a number of teosinte populations and linkage disequilibrium neartb1does not support recent introgression from maize. Population genetic signatures are consistent with selection on this locus revealing a potential ecological role forHopscotchin teosinte, but a greenhouse experiment does not detect a strong association betweentb1and tillering in teosinte.ConclusionsOur findings suggest the role ofHopscotchdiffers between maize and teosinte. Future work should assesstb1expression levels in teosinte with and without theHopscotchand more comprehensively phenotype teosinte to assess the ecological significance of theHopscotchinsertion and, more broadly, thetb1locus in teosinte.