bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Divergence and Effective Size among Lane Snapper in U.S. Waters of the Western Atlantic Ocean
Authors: Gold John R. , Saillant Eric , Cummings Nancie J. , Renshaw Mark A. 
Published: December 2011

Abstract
Population structure of lane snapper Lutjanus synagris in U.S. waters in the northern Caribbean Sea was assessed using nuclear-encoded microsatellites and mitochondrial DNA (mtDNA) from samples from four localities in the U.S. Caribbean and one locality in the Florida Keys. Significant heterogeneity was detected for both allele and genotype distributions (microsatellites) and for haplotype distribution (mtDNA). Pairwise comparisons revealed that fish in the Florida Keys differed significantly from fish in the U.S. Caribbean with respect to both microsatellites and mtDNA. A parsimony network of mtDNA haplotypes was consistent with division of the five sample localities into two distinct populations. Genetic diversity at both microsatellites and mtDNA was greater among fish from the Florida Keys. The average, long-term migration rate from the U.S. Caribbean westward to the Florida Keys was approximately 1.75-fold greater than the reverse, suggesting that the elevated genetic variability among fish from the Florida Keys reflects the westward movement of alleles as a function of westward-flowing surface currents in the region. Bayesian coalescent analysis (microsatellites) indicated that each of the two populations has experienced a 10-fold decline in effective population size (Ne). Estimates of long-term effective size, generated using a coalescent, maximum-likelihood method, were 1,671.9 (Florida Keys) and 2,923.2 (U.S. Caribbean). Estimates of contemporaneous effective size, generated using a linkage-disequilibrium approach with minor alleles (those with frequencies of 0.02 or less) being excluded, were 275.6 (Florida Keys) and 668.9 (U.S. Caribbean) and differed significantly from one another. Because the samples contained mixed cohorts, the short-term estimates reflect the effective number of breeders (Nb) that produced the cohort(s) from which the samples were taken. The difference between the long-term and short-term estimates of Ne (or Nb) suggests that the declines in the effective size of both populations are relatively recent and that management concern over lane snapper in the Florida Keys is justified.
Received July 23, 2010; accepted December 14, 2010
Accurate Estimation of Salmonid Abundance in Small Streams using Nighttime Removal Electrofishing: an Evaluation using Marked Fish
Authors: Saunders W. Carl , Fausch Kurt D. , White Gary C. 
Published: December 2011

Abstract
Estimation of stream fish abundance using removal electrofishing is common and allows sampling of fish populations during a single site visit. However, recent evaluations have demonstrated that removal estimators can substantially underestimate fish abundance, raising concerns about using this method. We evaluated removal estimates of trout (family Salmonidae) abundance using night electrofishing in 200–300-m reaches of 8 Rocky Mountain streams and analyzed the data using new methods in Program MARK to account for potential sources of bias. The removal estimates were validated using populations of previously captured and marked resident fish. Overall, removal estimates were accurate estimates of the number of marked fish in study reaches (mean bias, −2.4% [&lt;1 fish/reach]), and removal and mark–recapture estimates of total fish abundance also differed by less than 1 fish/reach on average. In general, capture probabilities were high (average = 97% over three passes), and removal estimates had narrow 95% confidence intervals that included the known number of marked fish for all but 1 of 17 estimates for three trout species. Capture probability increased with fish length and was greater on the first than on subsequent electrofishing passes. Capture probability also varied among sites, but this variation was not accounted for by any measured habitat variable. Finally, fish that had been previously marked were slightly more likely to be captured during electrofishing, even though the recovery periods for most fish exceeded 24 h. Simulations confirmed our finding that accounting for the heterogeneity in capture probability owing to individual fish size reduced the bias in removal estimates. Our results demonstrate that three-pass removal electrofishing can provide accurate estimates of fish abundance when field methods are designed to maximize capture probability and when modern analytical tools are used to account for the heterogeneity in capture probability.
Received June 18, 2010; accepted January 27, 2011
Fork Length–Total Length Conversions for Haddock and Pollock
Authors: Pol Michael V. , Szymanski Mark J. , Chosid David M. , Salerno Daniel 
Published: December 2011

Abstract
Fork length–total length conversions for haddock Melanogrammus aeglefinus from Georges Bank and pollock Pollachius virens from the Gulf of Maine were developed by linear regression with data from fish caught during gear comparison studies. These conversions were developed to replace previous conversions that were inaccurate or insufficiently documented. Total lengths (TLs) and fork lengths (FLs) were obtained from 216 haddock ranging from 35 to 73 cm TL (median = 57 cm) and 220 pollock ranging from 43 to 107 cm TL (median = 75 cm). The conversion equation for haddock was FL = 0.95 × TL + 0.65. For pollock, it was FL = 0.94 × TL − 0.62. Reciprocal equations were also determined.
Received August 27, 2010; accepted February 17, 2011
Efficacy of a Light Attractant for Increasing Trap Net Catches of White Crappies
Authors: Binion Greg R. , Daugherty Daniel J. , Schlechte J. Warren , Ott Richard A. , Bister Timothy J. 
Published: December 2011

Abstract
We evaluated the efficacy of trap nets fitted with a battery-operated, submersible light in the net mouth in increasing the catch rates of white crappies Pomoxis annularis by comparing the catch rate and size structure of white crappies collected by these nets with those of fish collected by standard (i.e., unlighted) trap nets in six Texas reservoirs. The catch rates of standard (mean = 16.3/net-night) and lighted trap nets (12.1/net-night) did not differ significantly. We found no significant difference in the catch of stock-size white crappies (≥130 mm total length [TL]) by standard (12.7 fish/net-night) versus lighted trap nets (9.9 fish/net-night); however, significantly fewer preferred sizes (≥250 mm TL) were taken by lighted (1.9 fish/net-night) than by standard sets (2.9 fish/net-night). The length-frequency distributions of the white crappies collected by each trap net treatment were similar and did not significantly differ in four of the five lakes tested. Our results suggest that trap nets fitted with artificial lights in the net mouth do not effectively increase catch rates for white crappies and may favor the collection of smaller size-classes than standard trap nets.
Received June 24, 2010; accepted February 18, 2011
Reproducibility of Emergent Plant Mapping on Lakes
Authors: Radomski Paul , Woizeschke Kevin , Carlson Kristin , Perleberg Donna 
Published: December 2011

Abstract
Bulrushes Schoenoplectus spp. are widely distributed emergent plants that provide important fish habitat. Despite their importance, the precision of aquatic plant surveys conducted within lakes is rarely studied. Reproducibility of field-based bulrush stand coverage was assessed by using three different surveyors to conduct repeated delineations of bulrush stands in five north-central Minnesota lakes. Lakes were mapped by means of Global Positioning System delineation. The reproducibility trial of this study demonstrated that coverage mapping of bulrush stands could be completed in a timely manner and with reasonable precision. No significant differences were found among surveyor estimates of whole-lake bulrush stand coverage. The ability to detect a change in bulrush coverage over time appears to depend on the extent of mixed stands of bulrushes and perhaps on stand size. For lakes with monospecific bulrush stands, it may be reasonable to detect a whole-lake change of 10% or greater by using the techniques described here.
Received July 28, 2010; accepted December 6, 2010
Demand for Whole‐grain Bread Before and After the Release of Dietary Guidelines
Authors: Mancino Lisa , Kuchler Fred 
Published: December 2011

AbstractThe federal government has issued Dietary Guidelines for Americans seven times since 1980, but the 2005 whole‐grain recommendation was the first instance in which consumers were given a specific dietary target, that whole grains should be at least half of their grain consumption. Anecdotal evidence pointed to a unique result, an increase in demand for whole‐grain foods. Contemporaneous decreases in prices of whole‐grain foods, relative to refined‐grain foods, however, confound the evidence. We show that for whole‐grain bread, there was an increase in retail demand even after accounting for price changes. Separate models for higher‐ and lower‐income consumers show that the demand shift occurred among higher‐income consumers, but not for lower‐income consumers.
BPDA2d—a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph–mass spectrometry
Authors: Sun Youting , Zhang Jianqiu , Braga-Neto Ulisses , Dougherty Edward R. 
Published: December 2011

Abstract
Motivation: Peptide detection is a crucial step in mass spectrometry (MS) based proteomics. Most existing algorithms are based upon greedy isotope template matching and thus may be prone to error propagation and ineffective to detect overlapping peptides. In addition, existing algorithms usually work at different charge states separately, isolating useful information that can be drawn from other charge states, which may lead to poor detection of low abundance peptides.
Results: BPDA2d models spectra as a mixture of candidate peptide signals and systematically evaluates all possible combinations of possible peptide candidates to interpret the given spectra. For each candidate, BPDA2d takes into account its elution profile, charge state distribution and isotope pattern, and it combines all evidence to infer the candidate's signal and existence probability. By piecing all evidence together—especially by deriving information across charge states—low abundance peptides can be better identified and peptide detection rates can be improved. Instead of local template matching, BPDA2d performs global optimization for all candidates and systematically optimizes their signals. Since BPDA2d looks for the optimal among all possible interpretations of the given spectra, it has the capability in handling complex spectra where features overlap. BPDA2d estimates the posterior existence probability of detected peptides, which can be directly used for probability-based evaluation in subsequent processing steps. Our experiments indicate that BPDA2d outperforms state-of-the-art detection methods on both simulated data and real liquid chromatography–mass spectrometry data, according to sensitivity and detection accuracy.
Availability: The BPDA2d software package is available at http://gsp.tamu.edu/Publications/supplementary/sun11a/
Contact: Michelle.Zhang@utsa.edu; edward@ece.tamu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Albumin levels predict survival in patients with heart failure and preserved ejection fraction
Authors: Liu Ming , Chan Chin‐Pang , Yan Bryan P. , Zhang Qing , Lam Yat‐Yin , Li Rui‐Jie , Sanderson John E. , Coats Andrew J.S. , Sun Jing‐Ping , Yip Gabriel Wai‐Kwok , Yu Cheuk‐Man 
Published: December 2011

AimsLow serum albumin is common in patients with systolic heart failure and is associated with increased mortality. However, the relationship between albumin and outcome in patients with heart failure and preserved ejection fraction (HFPEF) is not known. The aim of this study was to investigate the effect of serum albumin level on survival in patients with HFPEF.Methods and resultsWe studied 576 consecutive HFPEF patients (left ventricular ejection fraction ≥50%) admitted to our hospital from 2006 to 2009. Standard demographics, transthoracic echocardiography, and routine blood testing including albumin levels were obtained shortly after admission. Outcome was assessed at 1 year after admission. Hypoalbuminaemia (≤34 g/L) was detected in 160 (28%) at admission; and all patients were then divided into hypoalbuminaemia and non‐hypoalbuminaemia groups. In the hypoalbuminaemia group, the prevalence of chronic renal failure history, serum creatinine, and urea nitrogen levels were higher when compared with those without hypoalbuminaemia (all P < 0.05). Kaplan–Meier analysis showed that patients with hypoalbuminaemia had a significantly lower survival rate (53% vs. 84%, log‐rank χ2 = 53.3, P < 0.001) and a higher rate of cardiovascular death (21.8% vs. 8.9%, log‐rank χ2 = 19.7, P < 0.001) when compared with those without hypoalbuminaemia. Cox regression further revealed that hypoalbuminaemia, a history of cerebrovascular disease, and older age were the most powerful independent predictors of all‐cause mortality in HFPEF patients at 1 year.ConclusionsHypoalbuminaemia is common in HFPEF patients and is associated with increased risk of death. Renal dysfunction may be the main pathophysiological mechanism underlying hypoalbuminaemia in HFPEF patients.
Involvement of transcription factor p53 and leptin in control of porcine ovarian granulosa cell functions
Authors: Sirotkin A. V. , Benčo A. , Tandlmajerová A. , Vašíček D. 
Published: December 2011

AbstractThe aim of our in vitro experiments was to examine the role of transcription factor p53 and the metabolic hormone leptin, in controlling basic functions (proliferation, apoptosis and secretory activity) of ovarian cells, as well as involvement of p53 in mediating or modulating actions of leptin, on ovarian cells. Porcine ovarian granulosa cells, transfected and non‐transfected with a gene construct encoding p53, were cultured with leptin (at concentrations of 0, 1, 10 or 100 ng/ml). Accumulation of p53 and of apoptosis‐related (bax) and proliferation‐related (PCNA, cyclin B1) substances was evaluated by SDS–PAGE‐western blotting. Secretion of progesterone (P4) was measured by RIA. Transfection with the p53 gene construct promoted accumulation of this transcription factor within cells. It also stimulated expression of bax (which can be thought of as a marker of apoptosis), and reduced accumulation of proliferation‐related substances PCNA and cyclin B1. Overexpression of p53 resulted in reduced P4 secretion. Leptin, when added alone, increased accumulation of p53, bax and PCNA, decreased accumulation of cyclin B1 and had no effect on P4 secretion. Transfection of cells with p53 gene construct reversed effects of leptin on cyclin B1 and induced stimulatory effects of leptin on P4 release, but did not modify leptin action on p53, bax and PCNA. These multiple effects of the p53 gene construct on granulosa cells, cultured with and without leptin, (i) demonstrate that leptin can be involved in control of porcine ovarian cell proliferation, apoptosis and expression of p53, but not on P4 release; and (ii) confirm involvement of p53 in promoting apoptosis and suppression of proliferation and P4 secretion in these cells. (iii) The similarity of p53 and leptin’s actions on bax and cyclin B1, and inability of p53 to further promote leptin action on this parameter suggest that p53 can be a mediator of leptin’s action on ovarian cell apoptosis. (iv) On the other hand, p53 can modulate, but probably not mediate the effects of leptin on ovarian cell proliferation and P4 release.
A modeling approach to evaluate growth and movement for recruitment success of Japanese sardine (Sardinops melanostictus) in the western Pacific
Authors: OKUNISHI TAKESHI , ITO SHIN‐ICHI , AMBE DAISUKE , TAKASUKA AKINORI , KAMEDA TAKAHIKO , TADOKORO KAZUAKI , SETOU TAKASHI , KOMATSU KOSEI , KAWABATA ATSUSHI , KUBOTA HIROSHI , ICHIKAWA TADAFUMI , SUGISAKI HIROYA , HASHIOKA TAKETO , YAMANAKA YASUHIRO , YOSHIE NAOKI , WATANABE TOMOWO 
Published: December 2011

AbstractA two‐dimensional individual‐based fish movement model coupled with fish bioenergetics was developed to simulate the observed migration and growth of Japanese sardine (Sardinops melanostictus) in the western North Pacific. In the model, derived from the observed ocean–environmental data as the driving force, fish movement was adapted as a kinesis behavior. The model successfully simulated the observed transport patterns during the egg and larval stages and the northward migrations during the juvenile stage in 2005, 2006 and 2007. The model results showed that both temperature during the larval stage in the Kuroshio Extension and the prey availability during the early juvenile stage in the Kuroshio–Oyashio transitional area are important factors for growth of Japanese sardine. In autumn, the observed juvenile sardine were mainly distributed in the subarctic water region off the Kuril Islands, which is an area (158–165°E, 43–47°N) with a high chlorophyll‐a (Chl‐a) concentration. The model reproduced the fish distribution, which has a high density in this region. The high Chl‐a concentration area in autumn may contribute to increasing the survival rate of Japanese sardine by cascading up the food chain, from the high primary production, and is an important habitat for recruitment success of Japanese sardine.
Climate‐induced year‐class fluctuations of whitemouth croaker Micropogonias furnieri (Pisces, Sciaenidae) in the Río de la Plata estuary, Argentina–Uruguay
Authors: ACHA E. M. , SIMIONATO C. G. , CAROZZA C. , MIANZAN H. 
Published: December 2011

AbstractThe whitemouth croaker, Micropogonias furnieri, is exploited by coastal fisheries in the Plata estuary. Its age structure shows the predominance of certain year classes, which are indicative of recruitment variability. The estuary is affected by river discharge variations associated with climatic signals (El Niño Southern Oscillation and others). We hypothesize that recruitment may correlate: (i) negatively with runoff (low runoff would promote the stronger retention of ichthyoplankton); (ii) positively with temperature (higher temperatures should enhance larvae survivorship and/or expand the spawning season); and (iii) positively with the wind zonal component (stronger onshore winds should facilitate the retention of ichthyoplankton). A time series of the relative cohort strengths was constructed for the 1938–2000 period from the age frequencies based on otolith readings. We performed a spectral analysis of the biological and physical series, and we searched for co‐movements between them, which suggested the presence of mechanistic links. The results showed co‐movements for recruitment, runoff and air temperature series at approximately 6.5, 3.4 and 2.4 yr; the temperature reinforced the runoff effects on recruitment at the 6.5‐yr peak, and it weakened them at the 3.4‐ and 2.4‐yr peaks. Wind variability was not relevant for the time scales studied. To explore the mechanisms of retention, we modeled the effects of the runoff fluctuations on the dispersal of the eggs. Both the statistical and modeling results supported the hypothesis that the effects of extreme river discharges on retention may regulate croaker recruitment by promoting high (low) recruitment during low (high) discharge periods.
Pediatric liver–kidney transplantation for hepatorenal fibrocystic disease from a living donor
Authors: Sakamoto Seisuke , Kasahara Mureo , Fukuda Akinari , Tanaka Hideaki , Kakiuchi Toshihiko , Karaki Chiaki , Kanazawa Hiroyuki , Kamei Koichi , Ito Shyuichi , Nakazawa Atsuko 
Published: December 2011

Sakamoto S, Kasahara M, Fukuda A, Tanaka H, Kakiuchi T, Karaki C, Kanazawa H, Kamei K, Ito S, Nakazawa A. Pediatric liver–kidney transplantation for hepatorenal fibrocystic disease from a living donor.  Pediatr Transplantation 2012: 16: 99–102. © 2011 John Wiley & Sons A/S.Abstract: The indications for and the timing of LT and/or KT for the patients with HRFCD are based on the severity of liver and kidney involvement. Most organs come from living donors, because the number of deceased donors is extremely low in Japan. Therefore, patients with HRFCD may need two organs from living donors. Four patients with HRFCD underwent living donor LT and KT from a single donor. The type of transplantation included combined LKT in one case, sequential LKT in two cases, and sequential KLT in one case. Although the case of combined LKT died because of sepsis, the other cases were doing well. Sequential LKT was successfully performed at the proper timing for each transplant; however, both of the donors suffered from a gastroduodenal ulcer after liver donation because of the psychological burden related to the relatively short period between two donations. In conclusion, living donation for LKT with cautious surgical procedures is not harmful for donors and recipients. However, changes in the allocation system established for deceased donors for HRFCD should be considered to avoid the need for two organ donations from the same living donor.
The Relationship Between Foraging, Learning Abilities and Neophobia in Two Species of Darwin’s Finches
Authors: Tebbich Sabine , Stankewitz Sophia , Teschke Irmgard 
Published: December 2011

AbstractThe ability to unlearn a previously established association is an important component of behavioural flexibility and may vary according to species ecology. Previously, two closely related sympatric Darwin’s finches were found to differ in their learning abilities. Small tree finches (Camarhynchus parvulus) outperformed woodpecker finches (Cactospiza pallida) in reversal learning but performed worse in an operant task. We attributed this difference to the habit of woodpecker finches to engage in long bouts of energetic pecking during extractive foraging. Persistently repeating one action without reward could favour performance in operant tasks but also limit behavioural flexibility. Here, we tested whether perseverance is the reason for woodpecker finches’ depressed reversal learning performance. Two new reversal conditions allowed the disentanglement of two sources of error in reversal learning: perseverant choice of the previously rewarded stimulus and failure to respond to the previously non‐rewarded stimulus. For the within‐species comparison, we predicted that woodpecker finches should find it more difficult to learn to avoid the previously rewarded stimulus than learning to choose the previously non‐rewarded stimulus. For the species comparison, we predicted the woodpecker finches should make more errors of perseverance than small tree finches. As performance could also be influenced by reaction to novelty, we compared neophobic responses between species and related them to reversal learning proficiency. We found no significant difference in reversal learning in the predicted direction, but found a negative correlation between neophobia and reversal learning at the inter‐ and the intraspecific level, which points towards a general relationship between reaction to novelty and flexibility.