bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatiotemporal Expression of EAPP Modulates Neuronal Apoptosis and Reactive Astrogliosis After Spinal Cord Injury
Authors: Chen Minhao , Ni Yingjie , Liu Yonghua , Xia Xiaopeng , Cao Jianhua , Wang Chengniu , Mao Xingxing , Zhang Weidong , Chen Chen , Chen Xinlei , Wang Youhua 
Published: February 2015

ABSTRACTE2F‐associated phosphoprotein (EAPP) is a novel E2F binding protein that interacts with the activating members of the E2F transcription factors family and involved in various biological processes. However, the expression and function of EAPP in central nervous system (CNS) are still unknown. In this study, we performed an acute spinal cord injury (SCI) model in adult rats, we found that EAPP protein levels were significantly increased and reached a peak at day 3, and then gradually returned to normal level at day 14 after spinal cord injury and we observed that the expression of EAPP is enhanced in the gray and white matter. Spatially, increased levels of EAPP were striking in neurons and astrocytes. Moreover, colocalization of EAPP/active caspase‐3 was detected in neurons, and colocalization of EAPP/proliferating cell nuclear antigen (PCNA) was detected in astrocytes after spinal cord injury. These results indicated that EAPP might play an important role in neuronal apoptosis and reactive astrogliosis. Furthermore in vitro, EAPP depletion by siRNA inhibited astrocyte proliferation, migration and CDK4/cyclinD1 expression. Meanwhile, EAPP knockdown also reduce neuronal apoptosis and cell cycle related proteins. Which indicated that EAPP might integrate cell cycle progression and play a crucial role in cell proliferation and apoptosis. Taken together, we speculated that EAPP was involved in biochemical and physiological responses after SCI. J. Cell. Biochem. 116: 1381–1390, 2015. © 2015 Wiley Periodicals, Inc.
Databases and Web Tools for Cancer Genomics Study
Authors: Yang Yadong , Dong Xunong , Xie Bingbing , Ding Nan , Chen Juan , Li Yongjun , Zhang Qian , Qu Hongzhu , Fang Xiangdong 
Published: February 2015

Abstract
Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge. Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and user experience. The resources reviewed include data repository and analysis tools; and we hope such introduction will promote the awareness and facilitate the usage of these resources in the cancer research community.
Injury Patterns at Isle Royale National Park: An Epidemiologic Review of Injuries and Illnesses Sustained in a Remote Environment
Authors: Saxon Kathleen D. , White Jenna M.B. , Eddy Mary M. , Albertus Daniel L. , Bassin Benjamin S. 
Published: February 2015

Objective Isle Royale National Park is a remote island in northern Lake Superior that attracts 16,000 visitors annually. The epidemiology of injuries and illnesses sustained by Isle Royale׳s visitors has not been previously studied. The purpose of this study is to examine these data and evaluate them for injury patterns. Methods This is a retrospective observational study examining the epidemiology of injuries and illnesses sustained during the period from 2008 to 2012. Incident reports completed by park rangers were reviewed and the data sorted according to time of year, time of day, type of medical encounter, and whether the patient was stable, unstable, or required transport. Results Two hundred and seventy patient care reports were obtained from the National Park Service. Sixty-four percent of encounters occurred in July and August, and most patients sought care in the afternoon. Care was provided by park rangers, the majority of whom were trained to the level of emergency medical technician. Fifty-eight percent of cases were trauma related, and 20% of all cases were evacuated. Conclusions The majority of incidents were trauma related. The majority of the rangers on the island are trained to the level of emergency medical technician-B and appear to offer appropriate care to the island’s many visitors, utilizing the National Park Service treatment protocols and comprehensive medical kits. In addition, access to advanced medical care is readily available by air and water evacuation.
Injury Trends in Rock Climbers: Evaluation of a Case Series of 911 Injuries Between 2009 and 2012
Authors: Schöffl Volker , Popp Dominik , Küpper Thomas , Schöffl Isabelle 
Published: February 2015

Objective Rock climbing is a widely performed sport. This prospective single-institution study evaluated the demographics of climbing-related injuries to improve our comprehension of current injury characteristics. Methods During a 4-year period, 836 patients with a total of 911 independent climbing injuries were prospectively evaluated using a standard questionnaire and examination protocol. Results Of all injuries, 833 were on the upper extremities, 58 on the lower. Seventeen injuries were Union International des Associations d’Alpinisme (UIAA) grade 1 injuries, 881 were grade 2, and 13 were grade 3. No higher UIAA graded injuries occurred. Overall, 380 were acute injuries (359 were seen in clinic, 21 were seen through the emergency department), and 531 were overstrain injuries (all seen in clinic). Finger injuries accounted for 52% of all injuries, the shoulder being the second most frequent location. Pulley injuries were the most frequent finger injuries. Of 20 injured young climbers under the age of 15 years, 14 had an epiphyseal fracture (all epiphyseal fractures: mean age 14 years, range 12 to 15 years). Male climbers were significantly older ( P < .05), had more climbing years ( P < .05), and were climbing at a higher climbing level ( P < .01). Older, more experienced climbers had significantly more overstrain injuries than acute injuries ( P < .05). Conclusions When comparing this study with our previous study from 1998 to 2001, there are some notable differences. Although pulley injuries are still the most common climbing injury, there are now more A4 pulley injuries than A2. Shoulder injuries are becoming more common, as are epiphyseal fractures among young climbers. It is important to understand current patterns of climbing injuries so that health providers can target interventions appropriately.
The Effect of Acetazolamide on Saccadic Latency at 3459 Meters
Authors: Faull Olivia K. , Robertson Josephine , Thomas Owen , Bradwell Arthur R. , Antoniades Chrystalina A. , Pattinson Kyle T.S. 
Published: February 2015

Objective The effect of altitude on brain function is not yet well understood, nor is the influence of height and speed of ascent. Additionally, the relationship between acute mountain sickness (AMS) symptoms and brain function at altitude is unclear. We hypothesized that a deterioration from baseline measures of brain function occurs after rapid, mechanical ascent to 3459 m and would be less pronounced in persons taking acetazolamide. Methods In this double blind, randomized, placebo-controlled study, 20 healthy volunteers (14 men, 6 women; mean age [±SD] 43 ± 16 years) were alternately allocated to acetazolamide 250 mg or to placebo, taken every 12 hours commencing 3 days before ascent. Prosaccadic and antisaccadic eye movements, heart rate, arterial saturation, and Lake Louise AMS scores were assessed at sea level and 15 to 22 hours after ascent to 3459 m. Results Arterial oxygen saturation was significantly lower in the placebo group compared to the acetazolamide group at altitude (Wilcoxon signed-rank test, median [interquartile range]: acetazolamide vs placebo: 92% [5] vs 85% [5]; P = .007), with no differences in prosaccadic latency, heart rate, or Lake Louise score. No differences in saccadic latencies from baseline to altitude were observed in the placebo group, whereas prosaccadic latencies were significantly longer at altitude with acetazolamide (altitude vs baseline: 153 ms [41] vs 176 ms [52], P = .008). Conclusions Brain function, measured by saccadic eye movements, appears to be unimpaired after rapid ascent to 3459 m. Although acetazolamide improves oxygen saturations, it may worsen prosaccades, possibly indicating adverse effects of acetazolamide on brain function at moderate altitude.
Preventing Central Line–Associated Bloodstream Infections: A Qualitative Study of Management Practices
Authors: Scheck McAlearney Ann , Hefner Jennifer L. , Robbins Julie , Harrison Michael I. , Garman Andrew 
Published: February 2015

OBJECTIVETo identify factors that may explain hospital-level differences in outcomes of programs to prevent central line–associated bloodstream infections.DESIGNExtensive qualitative case study comparing higher- and lower-performing hospitals on the basis of reduction in the rate of central line–associated bloodstream infections. In-depth interviews were transcribed verbatim and analyzed to determine whether emergent themes differentiated higher- from lower-performing hospitals.SETTINGEight US hospitals that had participated in the federally funded On the CUSP—Stop BSI initiative.PARTICIPANTSOne hundred ninety-four interviewees including administrative leaders, clinical leaders, professional staff, and frontline physicians and nurses.RESULTSA main theme that differentiated higher- from lower-performing hospitals was a distinctive framing of the goal of “getting to zero” infections. Although all sites reported this goal, at the higher-performing sites the goal was explicitly stated, widely embraced, and aggressively pursued; in contrast, at the lower-performing hospitals the goal was more of an aspiration and not embraced as part of the strategy to prevent infections. Five additional management practices were nearly exclusively present in the higher-performing hospitals: (1) top-level commitment, (2) physician-nurse alignment, (3) systematic education, (4) meaningful use of data, and (5) rewards and recognition. We present these strategies for prevention of healthcare-associated infection as a management “bundle” with corresponding suggestions for implementation.CONCLUSIONSSome of the variance associated with CLABSI prevention program outcomes may relate to specific management practices. Adding a management practice bundle may provide critical guidance to physicians, clinical managers, and hospital leaders as they work to prevent healthcare-associated infections.Infect Control Hosp Epidemiol 2015;00(0): 1–7
Asymptomatic fibrous dysplasia of the temporal bone
Authors: Kimitsuki T , Komune S 
Published: February 2015

AbstractIntroduction:Fibrous dysplasia is a bone disorder of unknown origin in which normal bone is replaced with fibrotic tissue and disorganised bone trabeculae. The temporal bone is rarely affected. Because of the slowly progressive course of the disease, many mild cases may never be recognised and are found incidentally. We present a patient with fibrous dysplasia of the right temporal bone, who had few complaints.Objective:A 62-year-old man was incidentally found to have fibrous dysplasia of the temporal bone on routine computed tomography scan.Method:One case report.Results:Computed tomography showed a thickening of the right temporal bone with a ground-glass appearance. The 62-year-old man opted for watchful waiting.Conclusion:We have presented an asymptomatic fibrous dysplasia of the temporal bone. Mild cases may never be recognised and are found incidentally because of their slow progression.
Is there a role of adjuvant treatment for salivary duct carcinoma?
Authors: Nakashima T , Yasumatsu R , Toh S , Hashimoto K , Shinoto M , Nakamura K , Komune S 
Published: February 2015

AbstractObjective:To determine the clinical effect of post-operative radiotheraphy and systemic chemotherapy for the treatment of salivary duct carcinoma.Study design:Retrospective review.Design:The medical records of 26 patients treated by surgery with or without radiotheraphy and/or systemic chemotherapy for salivary duct carcinoma were retrospectively reviewed to investigate the role of post-operative adjuvant treatment for the patients' prognosis.Results:The overall three-year and five-year survival rates were 54 and 48.1 per cent, respectively. There was no correlation with the clinical stage and the patients' prognosis. The overall three-year survival of the patients with or without post-operative radiotheraphy was 64 and 33 per cent, respectively (p = 0.29). The overall three-year survival of the patients with or without post-operative chemotherapy was 53 and 56 per cent, respectively (p = 0.78).Conclusion:Post-operative adjuvant therapy did not improve the patients' overall prognosis with salivary duct carcinoma. Developing novel treatment modalities may be necessary to improve the prognosis of this aggressive disease.
Zur Lage der Psychologie
Authors: Margraf Jürgen 
Published: February 2015

Die Psychologie hat in Studium, Wissenschaft und Beruf messbare Fortschritte errungen, steht aber auch vor Herausforderungen. Trotz wachsenden gesellschaftlichen Bedarfs haben wir einen Studienplatzmangel, der auf Kosten unserer Nachbarländer geht. Gleichzeitig entstehen immer neue Studiengänge mit z. T. unklarem Gehalt außerhalb der klassischen Universitäten. Obwohl im Studium sehr gute Leistungen erbracht werden, bleiben der Bachelor-Master-Übergang und die ungenügenden Betreuungsverhältnisse kritisch. Während die Förderung der wissenschaftlichen Arbeit stabil ist, steigt die Publikationstätigkeit (überproportional bei englischsprachigen Arbeiten). Die Infrastruktur weist neben intensiver Einzelförderung auch Großforschungsprojekte und außeruniversitäre Institutionen unter psychologischer Leitung auf. Die Bedeutung der inzwischen nahezu flächendeckend aufgebauten Hochschulambulanzen als außergewöhnlicher Forschungsplattform ist noch nicht hinreichend erkannt. Obwohl die Zahl der Berufstätigen (104 000) deutlich höher ist, als bisher angenommen, ist die Erwerbssituation insgesamt sehr positiv. Die Arbeitslosigkeit ist außerordentlich gering (1,7 %) und mit 82 % arbeiten unsere Absolventen weitaus häufiger als die der Nachbardisziplinen im studierten Fach. Alle Quellen zeigen eindeutig, dass Psychologie ein fünfjähriges konsekutives Studium ist. Das deutlich größte Berufsfeld ist der klinische Bereich, gefolgt von Wirtschaft und einer breiten Palette anderer Einsatzgebiete. Eine negative Ausnahme ist die schwierige Lage der Psychologen während der Psychotherapieausbildung. Der Frauenanteil am akademischen Personal ist bei höher dotierten Stellen deutlich überproportional gestiegen. Die Entwicklung der DGPs verläuft mit steigenden Mitgliederzahlen und wachsender Professionalisierung weiter positiv. Zusätzliche Anstrengungen sind v. a. beim wissenschaftlichen Nachwuchs und Teildisziplinen mit nachlassender Mitgliedschaft erforderlich. Zu den großen Herausforderungen zählen negative Außeneinflüsse, Bedrohungen der Einheit unseres Faches und eine Fehlsteuerung durch fehlgeleiteten Wettbewerb. Analog zu Hochleistungssport oder Börse verstärken sich so auch die wissenschaftlichen Pendants zu Doping, Fouls und Bilanzbeschönigung. Auch in der Psychologie zeigt sich nun eine Steigerung der Artikel-Rückrufe um mehr als das Vierfache seit 1989. Neben fragwürdigen Forschungspraktiken ist eine unangemessene Ausrichtung am Mainstream, oft auch in Form eines falschen Fokus auf „Impact-starke” Themen, eine massive „Nebenwirkung”. Die systemischen Ursachen müssen angegangen werden, was ein Umdenken bei Teilen unserer Fachkultur und eine Besinnung auf die Stärken einer genuin psychologischen Wissenschaft erfordert. Die Zukunft der Psychologie muss kumulativ, kooperativ und brauchbar sein; Lehre, Forschung und Beruf benötigen eine starke proaktive Vertretung nach innen und nach außen. Wenn wir uns jedoch den Herausforderungen aktiv stellen, ist das Ganze nicht nur etwas anderes, sondern tatsächlich mehr als die Summe seiner Teile.
Comparison of the Toxicity of Wofasteril Peracetic Acid Formulations E400, E250, and Lspez to Daphnia magna, with Emphasis on the Effect of Hydrogen Peroxide
Authors: Liu Dibo , Straus David L , Pedersen Lars-Flemming , Meinelt Thomas 
Published: February 2015

Abstract
Commercial peracetic acid (PAA) formulations are acidic mixtures of PAA, hydrogen peroxide (H2O2), acetic acid, H2O, and stabilizers to maintain the equilibrium of the concentrations. Different PAA formulations show diverse PAA : H2O2 ratios, potentially leading to different toxicities at the same PAA concentration due to the different concentrations of H2O2 and stabilizers used. To confirm any potential differences in toxicity, we performed 24-h toxicity tests using Daphnia magna with three commercial PAA formulations (Wofasteril): E400, E250, and Lspez. The experiments were carried out in standard dilution water and with increased water hardness, salinity, or dissolved organic carbon to reflect various natural conditions. Results showed that the toxicity to Daphnia was greatest for Lspez, intermediate for E250, and lowest for E400. An E400 + H2O2 mixture, which possessed a composition theoretically identical to the E250 formulation, had toxic effects and 24-h LC50 values similar to those of E250. This indicates an additive effect of H2O2 on the toxicity of PAA formulations. Moreover, a significant positive correlation was found between Daphnia mortality and the 3-h concentration of total peroxide (PAA and H2O2), with an r-value higher than that of PAA alone. A significant negative correlation between the total peroxide : PAA molar ratio and the 24-h LC50 value was observed, indicating that the toxicity of PAA formulations to Daphnia is due to the combined effect of both PAA and H2O2.
AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction
Authors: Xu Dong , Jaroszewski Lukasz , Li Zhanwen , Godzik Adam 
Published: February 2015

Abstract
Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available.
Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets.
Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/.
Contact: adam@sanfordburnham.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum
Authors: Isakov Ofer , Bordería Antonio V. , Golan David , Hamenahem Amir , Celniker Gershon , Yoffe Liron , Blanc Hervé , Vignuzzi Marco , Shomron Noam 
Published: February 2015

Abstract
Motivation: The study of RNA virus populations is a challenging task. Each population of RNA virus is composed of a collection of different, yet related genomes often referred to as mutant spectra or quasispecies. Virologists using deep sequencing technologies face major obstacles when studying virus population dynamics, both experimentally and in natural settings due to the relatively high error rates of these technologies and the lack of high performance pipelines. In order to overcome these hurdles we developed a computational pipeline, termed ViVan (Viral Variance Analysis). ViVan is a complete pipeline facilitating the identification, characterization and comparison of sequence variance in deep sequenced virus populations.
Results: Applying ViVan on deep sequenced data obtained from samples that were previously characterized by more classical approaches, we uncovered novel and potentially crucial aspects of virus populations. With our experimental work, we illustrate how ViVan can be used for studies ranging from the more practical, detection of resistant mutations and effects of antiviral treatments, to the more theoretical temporal characterization of the population in evolutionary studies.
Availability and implementation: Freely available on the web at http://www.vivanbioinfo.org
Contact: nshomron@post.tau.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
Pattern recognition methods to relate time profiles of gene expression with phenotypic data: a comparative study
Authors: Hendrickx Diana M. , Jennen Danyel G. J. , Briedé Jacob J. , Cavill Rachel , de Kok Theo M. , Kleinjans Jos C. S. 
Published: February 2015

Abstract
Motivation: Comparing time courses of gene expression with time courses of phenotypic data may provide new insights in cellular mechanisms. In this study, we compared the performance of five pattern recognition methods with respect to their ability to relate genes and phenotypic data: one classical method (k-means) and four methods especially developed for time series [Short Time-series Expression Miner (STEM), Linear Mixed Model mixtures, Dynamic Time Warping for -Omics and linear modeling with R/Bioconductor limma package]. The methods were evaluated using data available from toxicological studies that had the aim to relate gene expression with phenotypic endpoints (i.e. to develop biomarkers for adverse outcomes). Additionally, technical aspects (influence of noise, number of time points and number of replicates) were evaluated on simulated data.
Results: None of the methods outperforms the others in terms of biology. Linear modeling with limma is mostly influenced by noise. STEM is mostly influenced by the number of biological replicates in the dataset, whereas k-means and linear modeling with limma are mostly influenced by the number of time points. In most cases, the results of the methods complement each other. We therefore provide recommendations to integrate the five methods.
Availability: The Matlab code for the simulations performed in this research is available in the Supplementary Data (Word file). The microarray data analysed in this paper are available at ArrayExpress (E-TOXM-22 and E-TOXM-23) and Gene Expression Omnibus (GSE39291). The phenotypic data are available in the Supplementary Data (Excel file). Links to the pattern recognition tools compared in this paper are provided in the main text.
Contact: d.hendrickx@maastrichtuniversity.nl
Supplementary information: Supplementary data are available at Bioinformatics online.