bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geographical variations inSalmonellaincidence in Israel 1997–2006: the effect of rural residency
Authors: WEINBERGER M. , AGMON V. , YARON S. , NISSAN I. , PERETZ C. 
Published: December 2012

SUMMARYThe overall incidence and serotype distribution of non-typhoidSalmonella(NTS) may vary between different geographical localities. To investigate possible regional differences and the effect of demographic factors, we studied 15 865 episodes of laboratory-confirmed NTS infection in Israel. Using Poisson models we found significant variation in the average annual incidence rate of NTS in 15 administrative sub-districts, which was inversely associated with the percent of rural residency (incidence rate ratio 0·75, 95% confidence interval 0·65–0·86,P < 0·001). Variation was also found in the relative incidence of the most prominent serotypes (Enteritidis, Virchow, Typhimurium, Hadar, Infantis), which was affected by rural residency, the percent of non-Jewish population in the sub-district, and the percent of population aged ⩾55 years in the sub-district. Rural residency had a major effect on the epidemiology of salmonellosis in Israel. Future research is required to understand whether decreased incidence in rural areas is an under-detection bias or reflects true differences in NTS illnesses.
Factors reducing the cut-off frequency of resonant tunneling diodes
Authors: Alkeev Nikolay , Averin Stanislav , Dorofeev Aleksey , Gladysheva Nadezda 
Published: December 2012

The impedance dependence of resonant tunneling diodes (RTDs) based on the GaAs/AlAs heterosystem is investigated in the range of 0.1–40 GHz. The analysis shows that the impedance of about 90% of unbiased RTDs is well described by an equivalent circuit (EC) consisting of parallel-connected resistance and capacitance and an additional resistance connected in series with this parallel combination. When a bias voltage is applied to these RTDs, one needs a “quantum” inductance LQ to describe the impedance behavior. We find the value of LQ and calculate the delay time of electrons in the quantum well (QW) of an RTD. The impedance of the rest 10% of the RTDs is well described by an EC that takes into account the recharge of localized electron states at the heterointerfaces of the active layers. Expressions for the cut-off frequencies that take into account the delay of electrons in the QW and the localized electron states at the heterointerfaces are derived. It is shown that the delay of electrons in the QW and localized electron states at the heterointerfaces may significantly reduce the cut-off frequency of RTDs.
Estimating Spatial and Temporal Components of Variation for Fisheries Count Data Using Negative Binomial Mixed Models
Authors: Irwin Brian J. , Wagner Tyler , Bence James R. , Kepler Megan V. , Liu Weihai , Hayes Daniel B. 
Published: December 2012

AbstractPartitioning total variability into its component temporal and spatial sources is a powerful way to better understand time series and elucidate trends. The data available for such analyses of fish and other populations are usually nonnegative integer counts of the number of organisms, often dominated by many low values with few observations of relatively high abundance. These characteristics are not well approximated by the Gaussian distribution. We present a detailed description of a negative binomial mixed‐model framework that can be used to model count data and quantify temporal and spatial variability. We applied these models to data from four fishery‐independent surveys of Walleyes Sander vitreus across the Great Lakes basin. Specifically, we fitted models to gill‐net catches from Wisconsin waters of Lake Superior; Oneida Lake, New York; Saginaw Bay in Lake Huron, Michigan; and Ohio waters of Lake Erie. These long‐term monitoring surveys varied in overall sampling intensity, the total catch of Walleyes, and the proportion of zero catches. Parameter estimation included the negative binomial scaling parameter, and we quantified the random effects as the variations among gill‐net sampling sites, the variations among sampled years, and site × year interactions. This framework (i.e., the application of a mixed model appropriate for count data in a variance‐partitioning context) represents a flexible approach that has implications for monitoring programs (e.g., trend detection) and for examining the potential of individual variance components to serve as response metrics to large‐scale anthropogenic perturbations or ecological changes.
Longitudinal Length Back‐Calculations from Otoliths and Scales Differ Systematically in Haddock
Authors: Baumann Hannes , Sutherland Sandra J. , McBride Richard S. 
Published: December 2012

AbstractParallel macrostructure analysis of otoliths versus scales was conducted on Georges Bank Haddock Melanogrammus aeglefinus sampled in spring 2011 to test whether annuli widths of both structures yield comparable estimates of back‐calculated length at age. While generally similar in number, scale and otolith annuli were found to differ systematically in their relative widths, mainly because initial annuli are deposited closer to the origin in scales than in otoliths. Accounting for the delayed onset of scale versus otolith formation did not remove the systematic bias. To make both structures comparable, we developed an age‐independent correction approach that can adjust cumulative relative annuli widths (RAWs) of Haddock scales to otolith RAWs by the quadratic formula loge(RAWoto) = 0.7244·loge(RAWscale) + 0.0751·loge(RAWscale)2. Our study comprises a necessary step towards extracting and comparing longitudinal growth data over the entire time series of archived Haddock scales (1931–1993) and otoliths (1994–present) to improve understanding of decadal drivers of growth patterns in this fish stock. Historical longitudinal growth data for exploited stocks are currently underutilized despite their high potential value, given that such data do not confound growth and mortality the way population‐based age–length relationships do. Mixed archives consisting of multiple growth structures exist not only for Haddock but for many commercial fish species; hence, prior to mining these valuable time series of longitudinal data the comparability not only of age but also of back‐calculated growth estimates between structures needs to be ascertained.
Apparent Digestibility of 12 Protein-Origin Ingredients for Pacific White Shrimp Litopenaeus vannamei
Authors: Liu Xiang-He , Ye Ji-Dan , Kong Jiang-Hong , Wang Kun , Wang An-li 
Published: December 2012

Abstract
Using 0.5% chromic oxide as an external indicator, apparent digestibility coefficients (ADCs) were determined for 12 protein feed ingredients (fish meal [FM], blood meal [BM], meat-and-bone meal [MBM], poultry byproduct meal [PBM], shrimp head meal [SHM], squid visceral meal [SVM], soybean meal [SBM], rapeseed meal [RM], cottonseed meal [CM], peanut meal [PM], corn gluten meal [CGM], and brewer's yeast [BY]) fed to Pacific white shrimp Litopenaeus vannamei (mean initial weight ± SD = 4.45 ± 0.21 g). The shrimp were randomly allocated to thirty-nine 150-L tanks (20 shrimp/tank) and were hand-fed a reference diet or test diet (70% reference diet and 30% test feed by weight) twice daily to satiation. Feces were collected by siphoning. The observed range of ADCs of the 12 ingredients was 48.6–87.0% for dry matter, 55.7–92.3% for crude protein, 2.1–92.5% for crude lipid, 52.1–79.9% for phosphorus, and 51.1–97.2% for gross energy. Relatively high ADCs were observed for dry matter in FM (87.0%) and MBM (76.5%); for crude protein in FM (90.9%), SBM (92.3%), and PM (88.8%); for crude lipid in FM (92.5%) and SVM (88.5%); and for phosphorus (79.9, 72.7, 72.5, and 78.5%) and gross energy (97.2, 82.3, 84.0, and 84.6%) in FM, MBM, PBM, and BY. The ADCs of amino acids for the 12 ingredients were 86.7–97.4% (FM), 58.4–98.8% (BM), 46.9–99.6% (MBM), 54.8–95.4% (PBM), 79.0–100.0% (SHM), 58.3–93.0% (SVM), 60.7–99.4% (SBM), 62.6–99.6% (RM), 52.9–91.4% (CM), 60.1–99.9% (PM), 15.6–97.8% (CGM), and 30.3–98.4% (BY). Fish meal, SBM, and PM showed high average ADCs for total amino acids (&gt;90%). Crude protein ADCs corresponded with amino acid ADCs. Resultant digestibility data may provide more accurate information pertinent to formulating commercial feeds for Pacific white shrimp.
RetroSeq: transposable element discovery from next-generation sequencing data
Authors: Keane Thomas M. , Wong Kim , Adams David J. 
Published: December 2012

Abstract
Summary: A significant proportion of eukaryote genomes consist of transposable element (TE)-derived sequence. These elements are known to have the capacity to modulate gene function and genome evolution. We have developed RetroSeq for detecting non-reference TE insertions from Illumina paired-end whole-genome sequencing data. We evaluate RetroSeq on a human trio from the 1000 Genomes Project, showing that it produces highly accurate TE calls.
Availabilty: RetroSeq is open-source and available from https://github.com/tk2/RetroSeq.
Contact: tk2@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Limonomyces roseipellis Causing Pink Patch on Bermudagrass in South China
Authors: Zhang W. , Nan Z. B. , Liu G. D. 
Published: December 2012

Hybrid bermudagrass (Cynodon dactylon (L.) Pers. × C. transvaalensis Burtt-Davy) is widely used on golf course putting greens in southern China. In September 2011, circular pink patches ranging from 10 to 20 cm in diameter were observed on putting greens established with cv. ‘Tifgreen’ on a golf course in Haikou, Hainan Province. There were approximately 50 pink patches on a putting green. Infected leaves were covered with pink, gelatinous fungal mycelium, which resulted in the production of chlorotic lesions. Lesions expanded, became water-soaked, and leaves died basipetally. A pink fungus, characterized by the presence of clamp connections, was consistently isolated from leaves of infected plants on a potato dextrose agar amended with 0.01% gentamicin sulfate. Based on morphological characteristics, the fungus was preliminary identified as Limonomyces roseipellis Stalpers & Loerakker, the causal agent of pink patch of turfgrass (2,3). To verify the identity, the internal transcribed spacer (ITS) of rDNA was amplified and sequenced using primers ITS1 and ITS4. Comparison with sequences in the GenBank database revealed that the ITS sequence (Accession No. KC193592) showed 98% homology with the sequence of L. roseipellis (EU622846). For pathogenicity tests, inoculum was prepared by culturing the fungus on an autoclaved mixture of 100 g of rye grain and 20 ml water for 3 weeks at 25°C. Six-week-old C. dactylon plants in 10-cm pots were inoculated by placing 2 g of infested grain in the center of the turf canopy, or 2 g sterilized, uninfested grain as a control, with four replications of each treatment. After inoculation, pots were covered with translucent plastic bags and placed in a greenhouse at 24 ± 2°C with a 12-h photoperiod (1). After 3 weeks, more than 70% of leaves in the infested pots showed symptoms identical to those observed under natural conditions while control plants remained asymptomatic. The fungus was reisolated from symptomatic plants. To our knowledge, this is the first report of L. roseipellis causing pink patch on hybrid bermudagrass in China. References: (1) L. L. Burpee and L. G. Goulty. Phytopathology 74:692, 1986. (2) J. D. Kaplan and N. Jackson. Plant Dis. 67:159, 1983. (3) J. A. Stalpers and W. M. Loerakker. Can. J. Bot. 60:529, 1982.
Self‐suppression of biofilm formation in the cyanobacterium Synechococcus elongatus
Authors: Schatz Daniella , Nagar Elad , Sendersky Eleonora , Parnasa Rami , Zilberman Shaul , Carmeli Shmuel , Mastai Yitzhak , Shimoni Eyal , Klein Eugenia , Yeger Orna , Reich Ziv , Schwarz Rakefet 
Published: December 2012

SummaryBiofilms are consortia of bacteria that are held together by an extracellular matrix. Cyanobacterial biofilms, which are highly ubiquitous and inhabit diverse niches, are often associated with biological fouling and cause severe economic loss. Information on the molecular mechanisms underlying biofilm formation in cyanobacteria is scarce. We identified a mutant of the cyanobacterium Synechococcus elongatus, which unlike the wild type, developed biofilms. This biofilm‐forming phenotype is caused by inactivation of homologues of type II secretion /type IV pilus assembly systems and is associated with impairment of protein secretion. The conditioned medium from a wild‐type culture represses biofilm formation by the secretion‐mutants. This suggested that the planktonic nature of the wild‐type strain is a result of a self‐suppression mechanism, which depends on the deposition of a factor to the extracellular milieu. We also identified two genes that are essential for biofilm formation. Transcript levels of these genes are elevated in the mutant compared with the wild type, and are initially decreased in mutant cells cultured in conditioned medium of wild‐type cells. The particular niche conditions will determine whether the inhibitor will accumulate to effective levels and thus the described mechanism allows switching to a sessile mode of existence.
Dissociable brain signatures of choice conflict and immediate reward preferences in alcohol use disorders
Authors: Amlung Michael , Sweet Lawrence H. , Acker John , Brown Courtney L. , MacKillop James 
Published: December 2012

AbstractImpulsive delayed reward discounting (DRD) is an important behavioral process in alcohol use disorders (AUDs), reflecting incapacity to delay gratification. Recent work in neuroeconomics has begun to unravel the neural mechanisms supporting DRD, but applications of neuroeconomics in relation to AUDs have been limited. This study examined the neural mechanisms of DRD preferences in AUDs, with emphasis on dissociating activation patterns based on DRD choice type and level of cognitive conflict. Heavy drinking adult men with (n = 13) and without (n = 12) a diagnosis of an AUD completed a monetary DRD task during a functional magnetic resonance imaging scan. Participant responses were coded based on choice type (impulsive versus restrained) and level of cognitive conflict (easy versus hard). AUD+ participants exhibited significantly more impulsive DRD decision‐making. Significant activation during DRD was found in several decision‐making regions, including dorsolateral prefrontal cortex (DLPFC), insula, posterior parietal cortex (PPC), and posterior cingulate. An axis of cognitive conflict was also observed, with hard choices associated with anterior cingulate cortex and easy choices associated with activation in supplementary motor area. AUD+ individuals exhibited significant hyperactivity in regions associated with cognitive control (DLPFC) and prospective thought (PPC) and exhibited less task‐related deactivation of areas associated with the brain's default network during DRD decisions. This study provides further clarification of the brain systems supporting DRD in general and in relation to AUDs.
Comparison of ProTaper and Mtwo retreatment systems in the removal of resin‐based root canal obturation materials during retreatment
Authors: İriboz Emre , Sazak Öveçoğlu Hesna 
Published: December 2012

AbstractTo evaluate the effectiveness of the ProTaper and Mtwo retreatment systems for removal of resin‐based obturation techniques during retreatment. A total of 160 maxillary anterior teeth were enlarged to size 30 using ProTaper and Mtwo rotary instruments. Teeth were randomly divided into eight groups. Resilon + Epiphany, gutta‐percha + Epiphany, gutta‐percha + AH Plus and gutta‐percha + Kerr Pulp Canal Sealer (PCS) combinations were used for obturation. ProTaper and Mtwo retreatment files were used for removal of root canal treatments. After clearing the roots, the teeth were split vertically into halves, and the cleanliness of the canal walls was determined by scanning electron microscopy. Specimens obturated with gutta‐percha and Kerr PCS displayed significantly more remnant obturation material than did specimens filled with resin‐based obturation materials. Teeth prepared with Mtwo instruments contained significantly more remnant filling material than did teeth prepared with ProTaper. ProTaper files were significantly faster than Mtwo instruments in terms of the mean time of retreatment and time required to reach working length. The Resilon + Epiphany and AH Plus + gutta‐percha obturation materials were removed more easily than were the Epiphany + gutta‐percha and Kerr PCS + gutta‐percha obturation materials. Although ProTaper retreatment files worked faster than did Mtwo retreatment files in terms of removing root canal obturation materials, both retreatment systems are effective, reliable and fast.
Effect of myopia on ganglion cell complex and peripapillary retinal nerve fibre layer measurements: a Fourier‐domain optical coherence tomography study of young Chinese persons
Authors: Zhao Zhennan , Jiang Chunhui 
Published: December 2012

AbstractBackgroundTo investigate the change of the ganglion cell complex and peripapillary retinal nerve fibre layer under different refractive conditions, as measured by optical coherence tomography.DesignCross‐sectional observational study.ParticipantsA total of 107 eyes from 107 subjects were studied.MethodsGanglion cell complex and retinal nerve fibre layer were studied by a spectral‐domain system. Their relationship against spherical equivalents and axial length was studied.Main Outcome MeasuresThe thickness of ganglion cell complex and retinal nerve fibre layer at different area and under different refractive conditions as measurements by optical coherence tomography.ResultsThe average, superior and inferior macular ganglion cell complex thickness was significantly associated with both spherical equivalents (all P < 0.05) and axial length (all P < 0.05). Peripapillary retinal nerve fibre layer thicknesses from the superior, inferior and temporal quadrants were associated with both spherical equivalents (all P < 0.01), axial length (all P < 0.05) and ganglion cell complex thickness (all P < 0.001), except for the nasal part. However, if the retinal nerve fibre layer thickness was studied in sections, then some parts of the upper and lower temporal part showed no correlation with either spherical equivalents or axial length (all P < 0.05).ConclusionsThe thicknesses of the ganglion cell complex and most of the peripapillary retinal nerve fibre layer were correlated with refraction and axial length. Therefore, when using these for clinical purposes, attention must be paid to the refractive state of the patient.
How is digit identity determined during limb development?
Authors: Suzuki Takayuki 
Published: December 2012

Digit identity has been studied using the chick embryo as a model system for more than 40 years. Using this model system, several milestone findings have been reported, such as the apical ectodermal ridge (AER), the zone of polarizing activity (ZPA), the Shh gene, and the theory of morphogen and positional information. These experimental results and models provided context for understanding pattern formation in developmental biology. The focus of this review is on the determination of digit identity during limb development. First, the history of studies on digit identity determination is described, followed by descriptions of the molecular mechanisms and current models for determination of digit identity. Finally, future questions and remarkable points will be discussed.
The Diagnostic Accuracy of Doppler Echocardiography in Assessment of Pulmonary Artery Systolic Pressure: A Meta‐Analysis
Authors: Taleb Mohammed , Khuder Sadik , Tinkel Jodi , Khouri Samer J. 
Published: December 2012

Background: Transthoracic echocardiography is commonly used to estimate pulmonary arterial systolic pressure (PASP) and to diagnose pulmonary hypertension (PH). However, some recent studies have questioned the accuracy of Doppler echocardiography (DE) in the assessment of PASP. The present meta‐analysis was performed to estimate the accuracy, sensitivity, and specificity of DE in the assessment of PASP. Methods: A literature search and data extraction of English and non‐English articles reported from May 1984 to January 2009 was performed independently by 2 investigators using MEDLINE and EMBASE databases. Articles were included if they compared DE with right heart catheterization (RHC) in the assessment of PASP. Nine articles met our criteria and were included in our meta‐analysis. We conducted a meta‐analysis of the results of these articles using fixed‐ and random‐effect models to estimate the accuracy, sensitivity, and specificity of DE in the assessment of PASP. Results: The correlation between PASP estimated by DE and RHC ranged from (r = 0.65, P < 0.001) to (r = 0.97, P < 0.001). The pooled sensitivity, specificity, and accuracy of DE for the diagnosis of PH were 88% (95% confidence interval [CI], 84–92%), 56% (95% CI, 46–66%), and 63% (95% CI, 53–73%), respectively. Conclusion: DE is a useful noninvasive modality to screen for PH and can reliably determine whether PASP is normal, mildly elevated, or markedly elevated. However, abnormal results from DE need to be confirmed by RHC.
Prognostic Stratification by Conventional Echocardiography of Patients with Aortic Stenosis: The “CAIMAN‐ECHO Score”
Authors: Cioffi Giovanni , Mazzone Carmine , Faggiano Pompilio , Tarantini Luigi , Di Lenarda Andrea , Russo Tiziano Edoardo , Selmi Alessandro , Stefenelli Carlo , Furlanello Francesco 
Published: December 2012

Background and Aim: Surgery is not recommended in asymptomatic patients with aortic stenosis (AS). However, prognosis of these patients is worse than retained. We built a simple score (named by the acronym “CAIMAN”) for stratifying asymptomatic patients with AS according to the different risk for cardiovascular events. Material and Methods: Data from 141 patients with moderate‐to‐severe AS followed up for 36 months were analyzed. The end point “outcome” was defined as death of all causes or aortic valve replacement imposed by symptoms or hospital admission for myocardial infarction and/or heart failure. The score was validated in 143 patients prospectively recruited in 2 different centers. Results: The 40 events occurred in the original cohort were associated with higher aortic transvalvular peak jet velocity, calcium score, and observed/predicted left ventricular (LV) mass ratio. Based on the hazard ratios of Cox analysis, the score was calculated as follows: calcium score 1–3 = 1 point, 4 = 6 points; transvalvular peak jet velocity ≤3.6 m/sec = 1 point, 3.6 m/sec = 3 points, observed/predicted LV mass ratio ≤110% = 1 point, >110% = 3 points. After a mean period of 28 ± 18 months, event‐free survival was 18%, 42%, 91%, and 96% in the 4 quartiles of echo score. The accuracy of the score in predicting events was 84% and 77% (P = 0.09) in the original and validation cohort, respectively. Conclusions: The CAIMAN‐ECHO score is a simple and feasible tool useful for an accurate prognostic stratification of patients with asymptomatic moderate‐to‐severe AS.