bluuebunny/crossref_metadata_2025 huggingface dataset:
Screening of different species of Bacillus against broad spectrum antibiotics
Authors: Bajpai Vivek , Singh Sisodia Yamini , Sharma Pallavi , Jain Pankaj
Published: December 2011

Sewage is waste suspended in water that is intended to flow away from a community. Sewage effluent contains a wide range of pathogenic microorganisms which may pose health hazards to the human population when they are discharged into the environment. This study is carried out to systematically examine the pathogenic microorganisms in sewage samples isolated from the Shekhawati region of Rajasthan. For this purpose a survey was carried out at the Sewage Treatment plant of the Mody Institute of Technology & Science, Laxmangarh, Sikar. In this survey we isolated 26 bacterial strains and identified them using biochemical and molecular methods. Different biochemical tests were performed during the study and in molecular identification by DNA isolation, PCR amplification using 16s rRNA primer and partial sequencing of purified product was done. The isolates were sequenced and out of 26, 10 sequences were submitted in NCBI which designated accession numbers. Out of these 10 isolates Bacillus pumilis, Bacillus subtilis and Bacillus licheniformis were taken for further studies. The growth pattern of these isolates was observed on different pH and Temperature. There is growing awareness of the need for development of new antimicrobial agents for the treatment of human, animal and plant diseases. Keeping this fact in view, we have also examined the antibiotic susceptibility of these isolates against various antibiotics (Ampicillin, Kanamycin, Chloramphenicol etc.) by measuring zone of inhibition in Mueller Hinton agar plates by Kirby Bauer method. Results of the present studies indicates that the strains isolated from sewage water are resistant to most of the antibiotics available in market, showing the necessity of new antibiotics to be developed to check the increasing ratio of bacillus infections through contaminated water.
Constraint rescaling in refined algebraic quantisation: Momentum constraint
Authors: Louko Jorma , Martínez-Pascual Eric
Published: December 2011

We investigate refined algebraic quantisation within a family of classically equivalent constrained Hamiltonian systems that are related to each other by rescaling a momentum-type constraint. The quantum constraint is implemented by a rigging map that is motivated by group averaging but has a resolution finer than what can be peeled off from the formally divergent contributions to the averaging integral. Three cases emerge, depending on the asymptotics of the rescaling function: (i) quantisation is equivalent to that with identity scaling; (ii) quantisation fails, owing to nonexistence of self-adjoint extensions of the constraint operator; (iii) a quantisation ambiguity arises from the self-adjoint extension of the constraint operator, and the resolution of this purely quantum mechanical ambiguity determines the superselection structure of the physical Hilbert space. Prospects of generalising the analysis to systems with several constraints are discussed.
Antiferroelectric–ferroelectric phase boundary enhances polarization extension in rhombohedral Pb(Zr,Ti)O3
Authors: Ghosh Anirban , Damjanovic Dragan
Published: December 2011

The main mechanism of properties enhancement in the morphotropic phase boundary region separating tetragonal and rhombohedral phases of Pb(Zr1-xTix)O3 (PZT) is related to polarization rotation. It is shown here that in proximity of the morphotropic phase boundary separating antiferroelectric and rhombohedral phases (near x = 0.1) and at elevated temperatures the properties are dominated by polarization extension. These results may provide a guideline for developing alternative piezoelectric materials to PZT.
Locating faunal breaks in the nearshore fish assemblage of Victoria, Australia
Authors: Colton Madhavi A. , Swearer Stephen E.
Published: December 2011

Marine communities are frequently biogeographically structured, despite the potential for dispersal. Previous research on a variety of marine taxa in south-eastern Australia has suggested that a biogeographic break occurs along the coastline of Victoria. However, little of this research has focussed on nearshore ichthyofauna and the location of the break remains debated. Using fish abundance measured by two methods: underwater visual census (UVC); and baited remote underwater video (BRUV) at six locations along the open coast of Victoria, we examined (1) whether there is sufficient concordance among species to indicate the presence of a faunal break; and if present (2) where any such breaks occur. Differences in assemblage composition between locations were tested with analyses of similarity and examination of residuals from regressions of pairwise dissimilarities against coastline distance. Data collected using UVC revealed two large faunal breaks co-located with a habitat discontinuity, the convergence of two currents and a thermal gradient. Data collected by BRUV revealed only a gradation of change across the study region. Greater understanding of the biogeographic structure of these communities will facilitate more effective management, especially in light of anticipated range shifts in response to global climate change.
223 ISOLATION OF RABBIT PLURIPOTENCY GENES TO GENERATE RABBIT INDUCED PLURIPOTENT STEM CELLS
Authors: Tancos Z. , Ujhelly O. , Pirity M. K. , Dinnyes A.
Published: December 2011

Induced pluripotent stem cells (iPSC) technology, which allows direct reprogramming of somatic cells to a pluripotent state, is a promising tool for gene-function studies disease modelling, drug screening, toxicology tests and to generate knockout animal models. The goal of the current work was to close the gap in knowledge with regard to the molecular biological background for rabbit iPS work by isolating the putative pluripotency genes from the rabbit, based on the sequences published for other species. The sequence of known pluripotency genes (Oct4, Sox2, Klf4, c-Myc, Nanog) were analysed and primers designed based on the similarity of sequences. Sequences of each individual rabbit pluripotency gene was compared to other vertebrates (e.g. human, mouse, bovine) phylogenetically. Rabbit ESCs and blastocyst stage embryos were collected from superovulated rabbits to isolate total RNA. Genes of interest were amplified using RT-PCR and electrophoretically separated for cDNA fragment isolation. Isolated and subcloned cDNA fragments were sequenced and analysed. Our results showed that after restriction digestion the size of amplified and cloned rabbit Oct4, Sox2, Klf4, c-Myc and Nanog gene fragments correspond to the expected amplicon size. Furthermore, sequence confirmation by DNA sequencing has been completed in the case of Oct4, c-Myc, Klf4 and Nanog. The homology of these genes to that of their mouse and human orthologs were as follows: Oct4: at Na level 79% homologue to mouse, 85% homologue to human, at Aa level 81% homologue to mouse, 90% homologue to human; Klf4: at Na level 98% homologue to mouse, 85% homologue to human, at Aa level 95% homologue to mouse, 84% homologue to human; c-myc: at Na level 88% homologue to mouse, 92% homologue to human, at Aa level 91% homologue to mouse and 94% homologue to human; Nanog: at Na level 71% homologue to mouse, 78% homologue to human, at Aa level 55% homologue to mouse, 66% homologue to human. In conclusion, we have revealed differences at both Na and Aa level in all four major rabbit pluripotency gene sequences in comparison to their mammalian orthologs which might partially explain difficulties in generation of rabbit iPSC capable of germline transmission. Our further goal is to apply rabbit specific pluripotency genes to reprogram somatic cells and generate iPSC more efficiently than by using mouse or human genes.
This work was supported by grants from Plurabbit, OMFB-00130/2010 ANR-NKTH; NKTH-OTKA-EU-7KP HUMAN-MB08-C-80-205; EU FP7 (AniStem, PIAP-GA-2011-286264PartnErS, PIAP-GA-2008-218205; InduStem, PIAP-GA-2008-230675; InduHeart, PEOPLE-IRG-2008-234390; InduVir, PEOPLE-IRG-2009-245808; PluriSys, HEALTH-2007-B-223485).
Developing User-Friendly Habitat Suitability Tools from Regional Stream Fish Survey Data
Authors: Zorn Troy G. , Seelbach Paul W. , Wiley Michael J.
Published: December 2011

We developed user-friendly fish habitat suitability tools (plots) for fishery managers in Michigan; these tools are based on driving habitat variables and fish population estimates for several hundred stream sites throughout the state. We generated contour plots to show patterns in fish biomass for over 60 common species (and for 120 species grouped at the family level) in relation to axes of catchment area and low-flow yield (90% exceedance flow divided by catchment area) and also in relation to axes of mean and weekly range of July temperatures. The plots showed distinct patterns in fish habitat suitability at each level of biological organization studied and were useful for quantitatively comparing river sites. We demonstrate how these plots can be used to support stream management, and we provide examples pertaining to resource assessment, trout stocking, angling regulations, chemical reclamation of marginal trout streams, indicator species, instream flow protection, and habitat restoration. These straightforward and effective tools are electronically available so that managers can easily access and incorporate them into decision protocols and presentations.

Received April 9, 2010; accepted November 8, 2010
Genetic Monitoring Reveals Genetic Stability within and among Threatened Chinook Salmon Populations in the Salmon River, Idaho
Authors: Van Doornik Donald M. , Waples Robin S. , Baird Melissa C. , Moran Paul , Berntson Ewann A.
Published: December 2011

Identifying and understanding temporal genetic changes within fish populations is important for the management of these populations, especially those of conservation concern. Such changes are often the result of genetic drift, which can be exacerbated when the size of a population decreases. Using molecular-genetics techniques, we monitored nine populations of Chinook salmon Oncorhynchus tshawytscha in the Salmon River, Idaho, to determine how the genetic characteristics within and among these populations have changed over time. We found no evidence of change in the level of heterozygosity or allelic richness over three to four generations in eight of the populations. This is probably due to the fact that the populations all maintained a sufficiently large effective size, even though a few of the populations did show a decline in effective size. Also, the genetic structure among the populations did not change appreciably over time. Populations that had been supplemented with hatchery-reared fish showed genetic similarity to the within-basin hatchery source population, presumably because of the extensive use of native fish for hatchery brood stocks and minimal out-of-basin stock transfers. The lack of a detectable decline in these populations’ levels of genetic diversity is encouraging, given the species’ threatened status under the U.S. Endangered Species Act.

Received September 22, 2010; accepted December 8, 2010
Predation on Juvenile Pacific Salmon Oncorhynchus spp. in Downstream Migrant Traps in Prairie Creek, California
Authors: Duffy Walter G. , Bjorkstedt Eric P. , Ellings Christopher S.
Published: December 2011

Downstream migrant traps are a widely applied fishery management tool for sampling anadromous Pacific salmon Oncorhynchus spp. and steelhead O. mykiss smolts along the West Coast of North America and elsewhere, yet predation on juvenile salmonids in traps has not been studied quantitatively. We assessed the frequency of occurrence and abundance of juvenile salmonids in the stomachs of coastal cutthroat trout O. clarkii clarkii, coho salmon O. kisutch, steelhead, and prickly sculpin Cottus asper (>70 mm fork length) captured in traps and in nearby stream habitats. All four predator species took juvenile salmonids with much greater frequency in traps than in stream habitats. Among free-swimming predators, only coastal cutthroat trout were observed with salmonid fry in their stomachs, but they took fewer salmonid prey and appeared to rely more heavily on insect prey than did coastal cutthroat trout captured in traps. Predators consumed up to 25% of the available prey over a broad range of prey abundances. Over the course of the study, predators consumed 2.5% of all salmonid fry captured in traps, but this fraction ranged from less than 1% to more than 10% in any given year. The number of prey taken in traps increased with predator length and with prey abundance in traps, and predation in traps peaked during the period of most intense downstream migration by salmon fry. In contrast, live-box design and trap location had little or no effect on the total number of prey taken by individual predators. We estimated that the predation mortality of juvenile salmon increased by 0.5–1.0% due to in-trap predation (i.e., a 9–10% relative increase over natural predation rates). We found no evidence that predators selected for prey on the basis of species. These results should motivate additional research on methods that reduce or eliminate predation in trap live-boxes and protocols for efficiently measuring predation associated with the trapping of downstream migrants.

Received May 11, 2010; accepted November 29, 2010
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

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

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% [<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

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

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

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

The 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

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

Aims

Low 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 results

We 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.

Conclusions

Hypoalbuminaemia 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.
Whole-exome sequencing of human pancreatic cancers and characterization of genomic instability caused by MLH1 haploinsufficiency and complete deficiency
Authors: Wang Linghua , Tsutsumi Shuichi , Kawaguchi Tokuichi , Nagasaki Koichi , Tatsuno Kenji , Yamamoto Shogo , Sang Fei , Sonoda Kohtaro , Sugawara Minoru , Saiura Akio , Hirono Seiko , Yamaue Hiroki , Miki Yoshio , Isomura Minoru , Totoki Yasushi , Nagae Genta , Isagawa Takayuki , Ueda Hiroki , Murayama-Hosokawa Satsuki , Shibata Tatsuhiro , Sakamoto Hiromi , Kanai Yae , Kaneda Atsushi , Noda Tetsuo , Aburatani Hiroyuki
Published: December 2011

Whole-exome sequencing (Exome-seq) has been successfully applied in several recent studies. We here sequenced the exomes of 15 pancreatic tumor cell lines and their matched normal samples. We captured 162,073 exons of 16,954 genes and sequenced the targeted regions to a mean coverage of 56-fold. This study identified a total of 1517 somatic mutations and validated 934 mutations by transcriptome sequencing. We detected recurrent mutations in 56 genes. Among them, 41 have not been described. The mutation rates varied widely among cell lines. The diversity of the mutation rates was significantly correlated with the distinct MLH1 copy-number status. Exome-seq revealed intensive genomic instability in a cell line with MLH1 homozygous deletion, indicated by a dramatically elevated rate of somatic substitutions, small insertions/deletions (indels), as well as indels in microsatellites. Notably, we found that MLH1 expression was decreased by nearly half in cell lines with an allelic loss of MLH1. While these cell lines were negative in conventional microsatellite instability assay, they showed a 10.5-fold increase in the rate of somatic indels, e.g., truncating indels in TP53 and TGFBR2, indicating MLH1 haploinsufficiency in the correction of DNA indel errors. We further analyzed the exomes of 15 renal cell carcinomas and confirmed MLH1 haploinsufficiency. We observed a much higher rate of indel mutations in the affected cases and identified recurrent truncating indels in several cancer genes such as VHL, PBRM1, and JARID1C. Together, our data suggest that MLH1 hemizygous deletion, through increasing the rate of indel mutations, could drive the development and progression of sporadic cancers.
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

The 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

A 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

The 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

The 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.
Negotiating hope with chronic obstructive pulmonary disease patients: a qualitative study of patients and healthcare professionals
Authors: Philip J. , Gold M. , Brand C. , Douglass J. , Miller B. , Sundararajan V.
Published: December 2011

Background:  The information needs of patients with chronic obstructive pulmonary disease (COPD) towards the end of life are poorly understood.

Aim:  This study explored the views of patients with COPD and healthcare professionals, focusing upon information needs and treatment preferences.

Method:  In‐depth, semi‐structured interviews were held with patients with COPD following admission to hospital with respiratory failure, and focus groups held with healthcare professionals from hospital and community settings.

Results:  Ten patients were interviewed, who had a median 4 previous hospital admissions, and had smoked for median 47 years. Five focus groups were held with 31 healthcare professionals (18 nurses, 7 doctors, 6 allied health). The theme underpinning all discussions was of tension between maintaining hope and negotiating the reality of the illness and its consequences. Within this theme, patients tended to be optimistic, viewed acute exacerbations as separate from their underlying chronic illness, and were keen for intensive treatments, including intubation if acutely unwell. They had little understanding of the complexities of decision‐making around treatment escalation. Both patients and health workers believed that information around end of life should be offered routinely, but delivered in a manner that recognises and maintains a form of hope.

Conclusion:  Patients and healthcare professionals believe information around illness course, future goals and treatment is important to care. An expanded view of hope may assist when providing such information, including when discussing goals of care in the setting of advanced illness.
Awareness regarding venous thromboembolism among internal medicine practitioners in Mexico: a national cross‐sectional study
Authors: Majluf‐Cruz A. , Castro Martinez G. , Herrera Cornejo M. A. , Liceaga‐Cravioto G. , Espinosa‐Larrañaga F. , Garcia‐Chavez J.
Published: December 2011

Background

Venous thromboembolism (VTE) affects millions of patients worldwide and is responsible for thousands of hospitalisations annually.

Aims

To evaluate the awareness regarding VTE among Mexican internists.

Methods

We designed a cross‐sectional survey using a questionnaire applied to Mexican internists mainly during academic meetings.

Results

We collected 1220 questionnaires. VTE was considered a potential complication for medical inpatients by 85% of the respondents, whereas 69% and 63%, respectively, considered pulmonary embolism to be a complication of deep vein thrombosis (DVT) and a cause of death. Awareness of some VTE risk factors was adequate, and 85% of those physicians surveyed routinely observed patients for these risk factors, although only 58% performed global risk stratification. Only 12% of the respondents considered length of hospital stay as a risk factor, and 58% assumed that the risk decreases after hospital discharge; 64% and 49% responded that the risk is higher, and VTE risk factors are more frequent in surgical versus medical inpatients respectively. VTE diagnosis was reported as easy or very easy for 59% of the respondents, but only 41% regarded phlebography as the gold standard for diagnosing DVT, although 85% of the respondents reported that d‐dimer + Doppler ultrasound was an alternative. Pulmonary arteriography or helical computed tomography CT scan was the gold standard for diagnosing pulmonary embolism for 60% of the physicians, but 55% responded that electrocardiogram, arterial gasometry and chest X‐ray are also useful.

Conclusions

Awareness regarding VTE risk factors and the degree of diagnostic skills among Mexican internal medicine specialists are low.
Natural history of severe eosinophilia with uncertain aetiology and proposals on a practical approach to its management
Authors: Ang A. L. , Wong R. X. , Zhuang Q. Y. , Linn Y. C.
Published: December 2011

Background:  Eosinophilia is commonly encountered during clinical practice. Some can be attributed to well‐defined causes while others cannot. Optimal management of hypereosinophilia with unknown aetiology is uncertain as the natural history is not well described.

Methods:  We retrospectively studied patients with hypereosinophilia (>5 × 109/L) and described the characteristics, natural history and treatment of those with eosinophilia of uncertain aetiology.

Results:  There were 141 patients with hypereosinophilia: 87 with well‐defined causes, 54 with uncertain aetiology. The latter was managed as hypereosinophilic syndrome (HES) (n= 5), idiopathic hypereosinophilia (IH) (n= 11), presumptive helminthic infection (n= 11) and reactive eosinophilia (n= 5), while 22 were insufficiently investigated and did not have definite working diagnoses. Their median age and peak eosinophil count were 64 (22 to 94) years and 10.0 (5.2–33.9) × 109/L respectively. Forty‐six per cent had symptoms attributable to eosinophilia, with the HES and insufficiently investigated groups having the highest (100%) and lowest (27%) percentages respectively. HES and IH patients were most extensively investigated. All 14 HES or IH patients who received steroids responded. All presumptive helminthic infection patients received mebendazole: nine responded, and two had unassessable responses. For the remaining patients, seven received steroids and all responded; one received mebendazole but defaulted; 19 were not treated:11 resolved spontaneously. No non‐HES patients developed eosinophilia‐related organ dysfunction. No mortality was caused by hypereosinophilia.

Conclusions:  Patients with hypereosinophilia of uncertain aetiology can be empirically managed according to working diagnoses derived from history taking, examination and selective investigations. Most patients have benign short‐term outcomes, but longer monitoring is required to assess long‐term outcomes from untreated hypereosinophilia.
Protective effects of the dipeptidyl peptidase IV inhibitor sitagliptin in the blood–retinal barrier in a type 2 diabetes animal model
Authors: Gonçalves A. , Leal E. , Paiva A. , Teixeira Lemos E. , Teixeira F. , Ribeiro C. F. , Reis F. , Ambrósio A. F. , Fernandes R.
Published: December 2011

Aim: The aim of this study was to evaluate the efficacy of sitagliptin, a dipeptidyl peptidase IV inhibitor (DPP‐IV), in preventing the deleterious effects of diabetes on the blood–retinal barrier in male Zucker Diabetic Fatty (ZDF) rats.

Methods: ZDF rats at 20 weeks of age were treated with sitagliptin (10 mg/kg/day) during 6 weeks. The effect of the drug on glycaemia was assessed by evaluating glycated haemoglobin (HbA1c). The content and/or distribution of tight junction (TJ) proteins occludin and claudin‐5, as well as nitrotyrosine residues, interleukin (IL)‐1β, BAX and Bcl‐2 was evaluated in the retinas by western blotting and/or immunohistochemistry. Retinal cell apoptosis was assessed by the terminal deoxynucleotidyl transferase‐mediated dUTP nick‐end labelling (TUNEL) assay. The number of CD34+ cells present in peripheral circulation was assessed by flow cytometry, and endothelial progenitor cells (EPC) adhesion ability to the retinal vessels was evaluated by immunohistochemistry.

Results: Sitagliptin improved glycaemic control as reflected by a significant decrease in HbA1c levels by about 1.2%. Treatment with sitagliptin prevented the changes in the endothelial subcellular distribution of the TJ proteins induced by diabetes. Sitagliptin also decreased the nitrosative stress, the inflammatory state and cell death by apoptosis in diabetic retinas. Diabetic animals presented decreased levels of CD34+ cells in the peripheral circulation and decreased adhesion ability of EPC to the retinal vessels. Sitagliptin allowed a recovery of the number of CD34+ cells present in the bloodstream to levels similar to their number in controls and increased the adhesion ability of EPC to the retinal vessels.

Conclusions: Sitagliptin prevented nitrosative stress, inflammation and apoptosis in retinal cells and exerted beneficial effects on the blood–retinal barrier integrity in ZDF rat retinas.