bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrogeographic Vicariance Determines the Genetic Structure of Northwestern Walleye Populations
Authors: Burke Lindsey A. , Jobin Richard M. , Coltman David W. 
Published: May 2012

AbstractWalleye Sander vitreus is one of the most important freshwater commercial and sport fishes in western Canada. It is an intensively managed species that is under considerable harvest pressure, yet little is known about the patterns of genetic variation and diversity of walleyes between connected water bodies and among river basins in this region. We examined the genetic variation of walleyes from 12 lakes in five different river basins of northern Alberta. Each lake contained a genetically distinct walleye subpopulation nested within a larger population of the river basin in which the lake was situated. Differentiation between subpopulations varied (FST = 0.05–0.29) and exhibited a broad‐scale isolation‐by‐distance pattern. Patterns of genetic divergence aligned closely with the current hydrogeographical landscape, as subpopulations in the same river basin were more similar than those in different river basins. The clear and distinct pattern of genetic structure is likely to have been generated and maintained by historical vicariance and natal philopatry. Because walleye populations are so clearly genetically structured by hydrogeography in western Canada, these data can be used to monitor population status, assess stocking programs, delineate management units, and enable forensic enforcement of harvest restrictions in this region.
Recruitment of Juvenile Gags in the Eastern Gulf of Mexico and Factors Contributing to Observed Spatial and Temporal Patterns of Estuarine Occupancy
Authors: Switzer Theodore S. , MacDonald Timothy C. , McMichael Robert H. , Keenan Sean F. 
Published: May 2012

AbstractWe conducted a comprehensive examination of long‐term (10+ years) fisheries‐independent data to characterize the spatial and temporal patterns of habitat selection and recruitment of juvenile gags Mycteroperca microlepis in four eastern Gulf of Mexico estuaries in Florida: Apalachicola Bay, Cedar Key, Tampa Bay, and Charlotte Harbor. Results from generalized linear modeling and habitat suitability analyses indicated that juvenile gags selected euhaline or polyhaline habitats with sloping bottoms and extensive coverage of submerged aquatic vegetation; the observed patterns were similar among estuaries. Latitudinal differences in the timing and duration of estuarine occupancy by juvenile gags were evident, with individuals appearing earlier and remaining later in more southerly estuaries. Significant interannual variability in recruitment of juvenile gags was evident within all estuaries, with high juvenile recruitment evident every 2 to 4 years. Continued efforts toward characterizing year‐class strength through the development of a regional index of juvenile gag recruitment may be useful in forecasting fisheries productivity, although such efforts would benefit greatly from an increased understanding of the relative contribution of presumed estuarine nurseries to nearshore populations.
‘Learning from research’: Therapist perspectives on the benefits and challenges of participating in a longitudinal, systematic case‐study
Authors: Grafanaki Soti 
Published: May 2012

AbstractObjectives: In psychotherapy research we have often neglected to examine the impact of research procedures on therapy process and outcome. Such information is extremely important in helping us evaluate the validity of our findings, increase relevance of research for practice, and choose appropriate methods for future projects. The aim of this paper is to share the experience of six person‐centered therapists, who participated in a longitudinal, systematic study, and present their reflections about the impact of research on therapy process, therapeutic engagement and professional development. Methods: The findings have emerged from semi‐structured interviews that took place after the first, sixth (middle) and last therapy session. In total 18 interviews were conducted. These data were part of a much larger research protocol that included a number of outcome and process measures. Results & Conclusions: The analysis of therapist narratives revealed important benefits for those participating in systematic case study research. The use of Brief Structured Recall methods and qualitative interviewing was an important factor in promoting therapist reflexivity and professional development. The importance of a strong research alliance and the active involvement of the client in the research process is discussed.
Magnetic and electric property evolution of amorphous cobalt-rich alloys driven by field annealing
Authors: Song Yujun , Li Zaidao , Sun Qiangqiang , Tang Zhaowei , Zhang Tao , Jiang Yanwei 
Published: May 2012

Abstract
Microstructure changes of the cross-section of Co-rich amorphous ribbons (Co68.15Fe4.35Si12.5B15, atomic%) annealed at 450 °C for 30 min with a zero field, a 10 Oe longitudinal external magnetic field or a 10 Oe transverse external magnetic field are investigated by comparing with as-spun ribbons. The ribbons annealed without a field, and under the transverse or longitudinal field exhibit different gradient microstructures along the cross-section of the ribbons, forming gradient amorphous–nanocrystalline (AN) composites different from the as-spun amorphous species. These kinds of AN composites preserve unique magnetic properties and enhanced conductivities when compared with the as-spun ribbons, leading to excellent giant magneto-impedance (GMI) effects. In particular, the AN composites prepared from the ribbons annealed under the longitudinal field lose the dual-peak feature shown by the as-spun ribbons but a mono-GMI peak appears, preserving a maximum MI ratio as high as 520% and a low magnetic field (0–1 Oe) sensitivity of 80% Oe−1 at 15 MHz and a maximum field of 40 Oe. The distinctly graded AN composites prepared from the ribbons annealed under the transverse field still preserve the dual-peak feature as the as-spun ribbons, having a maximum MI ratio of 320% and a significantly enhanced low magnetic field (0–1 Oe) sensitivity of 200% Oe−1 at 10 MHz and a maximum field of 40 Oe.
Effect of Ti addition on the characteristics of titanium-zinc-tin-oxide thin-film transistors fabricated via a solution process
Authors: Do Jong Chil , Ahn Cheol Hyoun , Cho Hyung Koun , Lee Ho Seong 
Published: May 2012

Abstract
Thin-film transistors (TFTs) using a TiZnSnO (TZTO) channel layer were fabricated using a sol–gel process. The effect of Ti content on the device performance of the TZTO TFTs was investigated. With increasing content of Ti ions in ZTO, the off-current was significantly decreased and the threshold voltage shifted to the positive bias direction. This is the reason for the fact that the incorporation of Ti results in a reduction in the oxygen vacancy, acting as a carrier source, in the ZTO thin films. The TFT performance with 0.01M Ti exhibited a field-effect mobility (μFE) and an on/off current ratio of 0.52 cm2 V−1 s−1 and 4.1 × 105, respectively.
Studies on a non-thermal pulsed corona plasma between two parallel-plate electrodes in water
Authors: Sein M M , Bin Nasir Z , Telgheder U , Schmidt T C 
Published: May 2012

Abstract
A non-thermal plasma generated between two parallel-plate electrodes submerged in water was studied in this work. The surface of one of the stainless-steel electrodes (the cathode) was coated with a ceramic layer of Al2O3. This reactor cell was connected to a water cycle and the discharge was carried out in a closed loop and therefore an equilibrium was established during discharge. The dependence of hydrogen peroxide formation as an indicator for the generation of most important oxidative species OH radicals on the pulse repetition rate, the solution conductivity and the pH of the solution was investigated. The highest yield of H2O2 (3.5 mg L−1) was obtained at 20 pps in a NaCl solution with a conductivity of 400 µS cm−1 and pH 7 in 90 min. The maximum energy efficiency of ∼0.1 g kWh−1 H2O2 was obtained. The surface of the coated electrodes, before and after applying of electrical discharges, was analysed by scanning electron microscopy. During the discharge process, the coating was destroyed and the formation of H2O2 decreased to 10% after discharging of nearly 35 h.
Resistive switching characteristics of maghemite nanoparticle assembly on Al and Pt electrodes on a flexible substrate
Authors: Yoo Jae Woo , Hu Quanli , Baek Yoon-Jae , Choi Young Jin , Kang Chi Jung , Lee Hyun Ho , Lee Do-Joong , Kim Hyun-Mi , Kim Ki-Bum , Yoon Tae-Sik 
Published: May 2012

Abstract
Resistive switching characteristics of maghemite (γ-Fe2O3) nanoparticle assembly were investigated in structures of top-electrode (Al,Pt)/γ-Fe2O3-NPs (∼ 30 nm-thick)/bottom electrode (Al,Pt) on a flexible polyethersulfone substrate. The assembled NP layer with Al electrodes showed both unipolar and bipolar switchings with abrupt resistance change in multiple levels associated with formation and sequential rupture of conducting filaments, which is ascribed to Fe enrichment by the interfacial reaction. On the other hand, the NP layer with Pt electrodes exhibited memristive switching with hysteresis in current–voltage characteristics dependent on bias polarity, gradually changing the resistance with respect to bias conditions, and preserved resistance until a new state was developed by subsequent biasing.
A novel humidity sensor based on alumina nanowire films
Authors: Feng Zhe-sheng , Chen Xin-Jie , Chen Jin-ju , Hu Jing 
Published: May 2012

Abstract
Alumina nanowire (ANW) films were prepared by etching porous anodic aluminium oxide (AAO), and then humidity sensors with coplanar interdigitated electrodes based on ANWs were fabricated. The ANWs not only present tremendous surface area for water molecule adsorption but also provide efficient sites for attracting water molecules at low relative humidity (RH) levels. The sensors based on the particular morphology of ANWs with large open voids show high sensitivity and small hysteresis, and have fast response and recovery time to humidity. The capacitance rises slowly at a lower RH and increases rapidly after 70% RH, which is associated with the humidity mechanism of chemisorption at lower RH and physisorption at higher RH levels. The impendence analysis suggests that the ANWs are the main factor for sensing humidity, and AAO also contributes to humidity sensing. This study demonstrates that ANWs have promising applications in humidity monitoring.
Thin membranes versus bulk substrates: investigation of proximity effects in focused electron beam-induced processing
Authors: Walz M-M , Vollnhals F , Rietzler F , Schirmer M , Kunzmann A , Steinrück H-P , Marbach H 
Published: May 2012

Abstract
The resolution of focused electron beam induced processing techniques is limited by electron scattering processes. General wisdom holds that using a membrane, this can be effectively improved due to a cutoff of the electron interaction volume and thus diminished proximity effects. Recently, we demonstrated that in contrast to the expectation, proximity effects can be indeed larger on a 200 nm silicon nitride membrane than on the respective bulk substrate, due to charging-induced surface activation. Herein, we expand these investigations on proximity effects in electron beam-induced surface activation to other substrates and to electron beam-induced deposition followed by autocatalytic growth.
R/EBcoexpress: an empirical Bayesian framework for discovering differential co-expression
Authors: Dawson John A. , Ye Shuyun , Kendziorski Christina 
Published: May 2012

Abstract
Summary: R/EBcoexpress implements the approach of Dawson and Kendziorski using R, a freely available, open source statistical programming language. The approach identifies differential co-expression (DC) by examining the correlations among gene pairs using an empirical Bayesian approach, producing a false discovery rate controlled list of DC pairs. This interrogation of DC gene pairs complements but is distinct from differential expression analyses, under the general goal of understanding differential regulation across biological conditions.
Availability and implementation: R/EBcoexpress is freely available and hosted on Bioconductor; a source file and vignette may be found at http://www.bioconductor.org/packages/release/bioc/html/EBcoexpress.html
Contact: DrJADawson@hotmail.com or kendzior@wisc.edu
CodonLogo: a sequence logo-based viewer for codon patterns
Authors: Sharma Virag , Murphy David P. , Provan Gregory , Baranov Pavel V. 
Published: May 2012

Abstract
Motivation: Conserved patterns across a multiple sequence alignment can be visualized by generating sequence logos. Sequence logos show each column in the alignment as stacks of symbol(s) where the height of a stack is proportional to its informational content, whereas the height of each symbol within the stack is proportional to its frequency in the column. Sequence logos use symbols of either nucleotide or amino acid alphabets. However, certain regulatory signals in messenger RNA (mRNA) act as combinations of codons. Yet no tool is available for visualization of conserved codon patterns.
Results: We present the first application which allows visualization of conserved regions in a multiple sequence alignment in the context of codons. CodonLogo is based on WebLogo3 and uses the same heuristics but treats codons as inseparable units of a 64-letter alphabet. CodonLogo can discriminate patterns of codon conservation from patterns of nucleotide conservation that appear indistinguishable in standard sequence logos.
Availability: The CodonLogo source code and its implementation (in a local version of the Galaxy Browser) are available at http://recode.ucc.ie/CodonLogo and through the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/.
Contact: p.baranov@ucc.ie or brave.oval.pan@gmail.com
flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding
Authors: Ge Yongchao , Sealfon Stuart C. 
Published: May 2012

Abstract
Motivation: For flow cytometry data, there are two common approaches to the unsupervised clustering problem: one is based on the finite mixture model and the other on spatial exploration of the histograms. The former is computationally slow and has difficulty to identify clusters of irregular shapes. The latter approach cannot be applied directly to high-dimensional data as the computational time and memory become unmanageable and the estimated histogram is unreliable. An algorithm without these two problems would be very useful.
Results: In this article, we combine ideas from the finite mixture model and histogram spatial exploration. This new algorithm, which we call flowPeaks, can be applied directly to high-dimensional data and identify irregular shape clusters. The algorithm first uses K-means algorithm with a large K to partition the cell population into many small clusters. These partitioned data allow the generation of a smoothed density function using the finite mixture model. All local peaks are exhaustively searched by exploring the density function and the cells are clustered by the associated local peak. The algorithm flowPeaks is automatic, fast and reliable and robust to cluster shape and outliers. This algorithm has been applied to flow cytometry data and it has been compared with state of the art algorithms, including Misty Mountain, FLOCK, flowMeans, flowMerge and FLAME.
Availability: The R package flowPeaks is available at https://github.com/yongchao/flowPeaks.
Contact: yongchao.ge@mssm.edu
Supplementary information: Supplementary data are available at Bioinformatics online
Pancreatic Insufficiency Is Not a Prevalent Problem in Alagille Syndrome
Authors: Kamath Binita M. , Piccoli David A. , Magee John C. , Sokol Ronald J. ,   Childhood Liver Disease Research and Education Network (ChiLDREN)
Published: May 2012

ABSTRACTAlagille syndrome (ALGS) is an inherited multisystem disorder in which pancreatic insufficiency (PI) has been regarded a minor but important clinical manifestation. As part of a multicenter prospective study, 42 patients with ALGS underwent fecal elastase (FE) measurement to screen for exocrine PI. FE measurements were normal (>200 μg/g) in 40 (95%) and indeterminate (100–200 μg/g) in 2 (5%). As FE is the most reliable screen for PI, these data suggest that PI is not a prevalent problem in ALGS.
Serial Evaluation of Children With ALF With Advanced MRI, Serum Proinflammatory Cytokines, Thiamine, and Cognition Assessment
Authors: Srivastava Anshu , Yadav Santosh K. , Borkar Vibhor V. , Yadav Abhishek , Yachha Surender K. , Thomas Michael A. , Rathore Ram K.S. , Pandey Chandra M. , Gupta Rakesh K. 
Published: May 2012

ABSTRACTObjectives:This prospective, sequential study was done to understand changes in cerebral edema (CE) on magnetic resonance imaging and magnetic resonance spectroscopy, liver functions, and neurocognitive testing (NCT) in children with acute liver failure (ALF).Methods:A total of 11 ALF and 8 healthy controls were evaluated with advanced magnetic resonance (MR) imaging, blood proinflammatory cytokines (PCs), thiamine levels, liver functions, and NCT. Reevaluation was done at 43.5 ± 26.9 days (first follow‐up, n = 8) and 157.3 ± 52.3 days (second follow‐up, n = 6) after discharge.Results:At diagnosis, patients with ALF had vasogenic and cytotoxic CE, raised brain glutamine (23.2 ± 3.4 vs 15.3 ± 2.7), and serum PCs (tumor necrosis factor [TNF]‐α 40.1 ± 8.9 vs 7.2 ± 2.7 pg/mL, interleukin [IL]‐6 29.2 ± 14.4 vs 4.7 ± 1.2 pg/mL). The mammillary bodies (MBs) were smaller, and brain choline (1.9 ± 0.36 vs 2.6 ± 0.6) and blood thiamine (55.2 ± 6.7 vs 81.8 ± 10.2 nmol/L) were lower than controls. At first follow‐up, the brain glutamine and CE recovered. Brain choline and MBs volume showed improvement and thiamine levels normalized. Significant reduction in TNF‐α and IL‐6 was seen. The patients performed poorly on NCT, which normalized at second follow‐up. Liver biochemistry and thiamine levels were normal and TNF‐α and IL‐6 showed further reduction at second follow‐up.Conclusions:Patients with ALF have CE contributed by raised brain glutamine and PCs. MBs are small because of thiamine deficiency and show recovery in follow‐up. CE and brain glutamine recover earlier than normalization of NCT and liver functions. Persistence of raised cytokines up to 6 months after insult suggests possible contribution from liver regeneration.
Effect of Bowel Cleansing for Colonoscopy on Fecal Calprotectin Levels in Pediatric Patients
Authors: Kolho Kaija‐Leena , Alfthan Henrik , Hämäläinen Esa 
Published: May 2012

ABSTRACTThe recent development of easily applicable fecal surrogate markers of intestinal inflammation, such as fecal calprotectin (FC), has provided a new means for objectively assessing disease activity in patients with chronic inflammatory bowel disease. Because the use of these markers is about to emerge, it is important to be aware of the possible limitations of measurements. We assessed levels of FC during bowel cleansing. In patients with high FC levels at baseline, the values measured during bowel cleansing varied considerably, remaining high or even returning to normal. Thus, stool sampling for FC assessment is not recommended during bowel preparation for colonoscopy.
Endoscopic Surveillance and Primary Prophylaxis Sclerotherapy of Esophageal Varices in Biliary Atresia
Authors: Lampela Hanna , Kosola Silja , Koivusalo Antti , Lauronen Jouni , Jalanko Hannu , Rintala Risto , Pakarinen Mikko P. 
Published: May 2012

ABSTRACTObjectives:Evidence‐based recommendations on endoscopic screening and prophylactic treatment of esophageal varices in patients with biliary atresia (BA) are scarce. We assessed the efficiency of endoscopic surveillance and risk factors of esophageal varices and associated upper gastrointestinal bleeding.Methods:A total of 47 consecutive children with BA and portoenterostomy underwent yearly endoscopies and prophylactic injection sclerotherapy of esophageal varices between 1987 and 2009. The median follow‐up was 1.7 years (range 0.5–18.9) and overall 2‐year survival 71%. Disease characteristics, clearance of jaundice, laboratory tests reflecting liver function and hypersplenism, as well as sonographic signs of portal hypertension were related to endoscopic findings and bleeding episodes.Results:Grade 2 to 3 varices developed with similar frequency after failed (18/28, 64%) and successful portoenterostomy (10/19, 53%) in 28 patients. Following failed portoenterostomy, esophageal varices were encountered significantly earlier (8 [4–23] vs 19 [4–165] months, P = 0.004), and they reappeared after eradication more often (16/16 vs 4/10, P = 0.001). Varices bled only after failed portoenterostomy (13/28 vs 0/19, P < 0.001). Increased serum bilirubin concentration >40 μmol/L at 3 months after portoenterostomy was a risk factor of upper gastrointestinal bleeding (odds ratio [OR] 17, 95% confidence interval [CI] 1.7–175, P = 0.017).Conclusions:In future studies as well as clinical surveillance of BA patients' varices, successful and failed portoenterostomy patients should be approached as separate groups with divergent prognoses. After failed portoenterostomy, surveillance should start early, for example, at 6 months.
The prognostic impact of clinical and molecular features in hairy cell leukaemia variant and splenic marginal zone lymphoma
Authors: Hockley Sarah L. , Else Monica , Morilla Alison , Wotherspoon Andrew , Dearden Claire , Catovsky Daniel , Gonzalez David , Matutes Estella 
Published: May 2012

SummaryHairy cell leukaemia variant (HCL‐variant) and splenic marginal zone lymphoma (SMZL) are disorders with overlapping features. We investigated the prognostic impact in these disorders of clinical and molecular features including
IGH
VDJ
rearrangements,
IGHV
gene usage and
TP

53 mutations. Clinical and laboratory data were collected before therapy from 35 HCL‐variant and 68 SMZL cases. End‐points were the need for treatment and overall survival. 97% of HCL‐variant and 77% of SMZL cases required treatment (P = 0·009). Survival at 5 years was significantly worse in HCL‐variant [57% (95% confidence interval 38–73%)] compared with SMZL [84% (71–91%); Hazard Ratio 2·25 (1·20–4·25), P = 0·01]. In HCL‐variant, adverse prognostic factors for survival were older age (P = 0·04), anaemia (P = 0·01) and
TP

53 mutations (P = 0·02). In SMZL, splenomegaly, anaemia and
IGHV
genes with >98% homology to the germline predicted the need for treatment; older age, anaemia and
IGHV
unmutated genes (100% homology) predicted shorter survival.
IGHV
gene usage had no impact on clinical outcome in either disease. The combination of unfavourable factors allowed patients to be stratified into risk groups with significant differences in survival. Although HCL‐variant and SMZL share some features, they have different outcomes, influenced by clinical and biological factors.