bluuebunny/crossref_metadata_2025_split huggingface dataset:
Consolidating the State of Knowledge: A Synoptical Review of Wind Energy’s Wildlife Effects
Authors: Schuster Eva , Bulling Lea , Köppel Johann 
Published: April 2015

Abstract

Wind energy development contributes substantially to achieve climate protection goals. Unintended side effects, especially on wildlife, have long been discussed and substantial research has evolved over the last decade. At this stage, it is important to identify what we have learnt so far, as well as which predominant uncertainties and gaps remain. This review article aims to consolidate the state of knowledge, providing a qualitative analysis of the main effects of wind energy development on- and offshore, focusing on frequently studied species groups (bats, breeding and resting birds, raptors, migratory birds, marine mammals). We reviewed over 220 publications from which we identified predominant hypotheses that were summarized and displayed in tables. Journal publications, conference contributions, and further studies have been considered. We found that research focusing on offshore wind energy within the last couple of years has increased significantly as well, catching up with the vast amount of onshore studies. Some hypotheses have been verified by numerous publications and a consensus has been reached (e.g., correlation between bat activity and weather factors), while others are still being debated more (e.g., determination of migratory corridors) or remain unknown (e.g., effect on population level). Factors influencing potential effects were mainly related to species characteristics (morphology, phenology, abundance, behavior, and response to turbines) or site characteristics (landscape features, weather, and habitat quality). Consolidating the state of research provides the groundwork for the identification of mitigation measures and advanced planning approaches. However, the quantification of effects remains challenging and uncertainties will always persist.
Clinical factors associated with the survival of patients with intrahepatic cholangiocarcinoma
Authors: Ting Chun‐Fu , Huang Wen‐Hsin , Feng Chun‐Lung , Yu Cheng‐Ju , Peng Cheng‐Yuan , Su Wen‐Pang , Lai Hsueh‐Chou , Cheng Ken‐Sheng , Chuang Po‐Heng , Kao Jung‐Ta 
Published: April 2015

SummaryBackground and aimIntrahepatic cholangiocellular carcinoma (ICC) is an uncommon but lethal cancer. The aim of this study is to assess the factors affecting the survival of ICC patients and to evaluate the benefit of these factors when various therapeutic modalities are used.MethodsBetween October 2007 and June 2012, 66 ICC cases among 2255 liver cancer patients were identified by pathology and divided into two groups: Group I (surgery group; n = 17) and Group II (nonsurgery group; n = 49). Group II was further divided into Group IIa (those receiving palliative treatment; n = 19) and Group IIb (no treatment received; n = 30). Factors affecting patient survival over the study period were assessed (3‐ and 6‐month results were reported) and therapeutic benefits identified within each of the groups were evaluated.ResultsOf the 66 patients identified (male/female = 36/30), 10.6% (7/66) were in the early stages of illness. Overall, the mean patient survival duration was 3.50 ± 0.92 months (1.69–5.31 months). The mean survival duration of Group I patients was 10.50 ± 2.84 months (4.94–16.06 months). The mean survival duration of Group II patients was 3.50 ± 0.65 months (2.24–4.76 months) with Group IIa patients surviving on average 9.50 ± 3.27 months (3.10–15.90 months) and Group IIb patients surviving on average 1.50 ± 0.12 months (1.26–1.74 months). Better survival outcomes were observed in the groups receiving treatment, Group I and Group IIa, than in Group Iib, which did not receive treatment [9.50 ± 1.73 months (6.12–12.89 months) vs. 1.50 ± 0.12 months (1.26–1.74 months), p < 0.001]. Lower albumin, higher bilirubin, higher CA19‐9, advanced tumor stage, and no treatment were identified as important predictors of patient mortality at the 3‐ and 6‐month time‐points. These factors remained relevant throughout the entire study period (p = 0.002, 0.029, 0.027, 0.028, < 0.001, respectively).ConclusionThis study identified surgery as the treatment that provided the best survival prognosis for patients with ICC. Treatment involving either chemotherapy or radiotherapy could also prolong ICC patient survival. Better liver preservation, lower CA19‐9, and less aggressive tumor conditions were identified as factors which play crucial roles in enhancing patient survival.
Florbetapir positron emission tomography and cerebrospinal fluid biomarkers
Authors: Hake Ann , Trzepacz Paula T. , Wang Shufang , Yu Peng , Case Michael , Hochstetler Helen , Witte Michael M. , Degenhardt Elisabeth K. , Dean Robert A. ,   Alzheimer's Disease Neuroimaging Initiative
Published: April 2015

AbstractBackgroundWe evaluated the relationship between florbetapir‐F18 positron emission tomography (FBP PET) and cerebrospinal fluid (CSF) biomarkers.MethodsAlzheimer's Disease Neuroimaging Initiative‐Grand Opportunity and Alzheimer's Disease Neuroimaging Initiative 2 (GO/2) healthy control (HC), mild cognitive impairment (MCI), and Alzheimer's disease (AD) dementia subjects with clinical measures and CSF collected ±90 days of FBP PET data were analyzed using correlation and logistic regression.ResultsIn HC and MCI subjects, FBP PET anterior and posterior cingulate and composite standard uptake value ratios correlated with CSF amyloid beta (Aβ1–42) and tau/Aβ1–42 ratios. Using logistic regression, Aβ1–42, total tau (t‐tau), phosphorylated tau181P (p‐tau), and FBP PET composite each differentiated HC versus AD. Aβ1–42 and t‐tau distinguished MCI versus AD, without additional contribution by FBP PET. Total tau and p‐tau added discriminative power to FBP PET when classifying HC versus AD.ConclusionBased on cross‐sectional diagnostic groups, both amyloid and tau measures distinguish healthy from demented subjects. Longitudinal analyses are needed.
Data-Based Decision Making in Professional Learning for School Speech-Language Pathologists
Authors: Murza Kimberly A. , Ehren Barbara J. 
Published: April 2015

Purpose
School-based speech-language pathologists (SLPs) are often asked to adopt new policies or practices at the school, district, or state level. Professional learning (PL) opportunities usually accompany these changes but are often delivered in a one-size-fits-all workshop format. The authors challenge school-based SLPs and district leadership to consider PL in a new light, guided by data-based decision making to ultimately improve student outcomes.

Method
This article discusses the research supporting the assessment and delivery of high-quality PL for school professionals, including SLPs, and a specific model for measuring change: the concerns-based adoption model (CBAM; Hall & Hord, 2015). An example of how CBAM was used to examine the adoption process with school-based SLPs in a large school district is provided.

Conclusion
Based on the review of the literature, the current approach to PL experienced by most SLPs is problematic. High-quality PL should target improvement in student outcomes and should be focused, ongoing, supported, and evaluated.
Addressing false discoveries in network inference
Authors: Petri Tobias , Altmann Stefan , Geistlinger Ludwig , Zimmer Ralf , Küffner Robert 
Published: April 2015

AbstractMotivation: Experimentally determined gene regulatory networks can be enriched by computational inference from high-throughput expression profiles. However, the prediction of regulatory interactions is severely impaired by indirect and spurious effects, particularly for eukaryotes. Recently, published methods report improved predictions by exploiting the a priori known targets of a regulator (its local topology) in addition to expression profiles.Results: We find that methods exploiting known targets show an unexpectedly high rate of false discoveries. This leads to inflated performance estimates and the prediction of an excessive number of new interactions for regulators with many known targets. These issues are hidden from common evaluation and cross-validation setups, which is due to Simpson’s paradox. We suggest a confidence score recalibration method (CoRe) that reduces the false discovery rate and enables a reliable performance estimation.Conclusions: CoRe considerably improves the results of network inference methods that exploit known targets. Predictions then display the biological process specificity of regulators more correctly and enable the inference of accurate genome-wide regulatory networks in eukaryotes. For yeast, we propose a network with more than 22 000 confident interactions. We point out that machine learning approaches outside of the area of network inference may be affected as well.Availability and implementation: Results, executable code and networks are available via our website http://www.bio.ifi.lmu.de/forschung/CoRe.Contact: robert.kueffner@helmholtz-muenchen.deSupplementary information: Supplementary data are available at Bioinformatics online.
Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from matched micro-RNA and gene expression data
Authors: Patrick Ellis , Buckley Michael , Müller Samuel , Lin David M. , Yang Jean Y. H. 
Published: April 2015

AbstractMotivation: In practice, identifying and interpreting the functional impacts of the regulatory relationships between micro-RNA and messenger-RNA is non-trivial. The sheer scale of possible micro-RNA and messenger-RNA interactions can make the interpretation of results difficult.Results: We propose a supervised framework, pMim, built upon concepts of significance combination, for jointly ranking regulatory micro-RNA and their potential functional impacts with respect to a condition of interest. Here, pMim directly tests if a micro-RNA is differentially expressed and if its predicted targets, which lie in a common biological pathway, have changed in the opposite direction. We leverage the information within existing micro-RNA target and pathway databases to stabilize the estimation and annotation of micro-RNA regulation making our approach suitable for datasets with small sample sizes. In addition to outputting meaningful and interpretable results, we demonstrate in a variety of datasets that the micro-RNA identified by pMim, in comparison to simpler existing approaches, are also more concordant with what is described in the literature.Availability and implementation: This framework is implemented as an R function, pMim, in the package sydSeq available from http://www.ellispatrick.com/r-packages.Contact: jean.yang@sydney.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.
iFoldRNA v2: folding RNA with constraints
Authors: Krokhotin Andrey , Houlihan Kevin , Dokholyan Nikolay V. 
Published: April 2015

Abstract
Summary: A key to understanding RNA function is to uncover its complex 3D structure. Experimental methods used for determining RNA 3D structures are technologically challenging and laborious, which makes the development of computational prediction methods of substantial interest. Previously, we developed the iFoldRNA server that allows accurate prediction of short (&lt;50 nt) tertiary RNA structures starting from primary sequences. Here, we present a new version of the iFoldRNA server that permits the prediction of tertiary structure of RNAs as long as a few hundred nucleotides. This substantial increase in the server capacity is achieved by utilization of experimental information such as base-pairing and hydroxyl-radical probing. We demonstrate a significant benefit provided by integration of experimental data and computational methods.
Availability and implementation: http://ifoldrna.dokhlab.org
Contact: dokh@unc.eu
PDBest: a user–friendly platform for manipulating and enhancing protein structures
Authors: Gonçalves Wellisson R. S. , Gonçalves-Almeida Valdete M. , Arruda Aleksander L. , Meira Wagner , da Silveira Carlos H. , Pires Douglas E. V. , de Melo-Minardi Raquel C. 
Published: April 2015

Abstract
Summary: PDBest (PDB Enhanced Structures Toolkit) is a user-friendly, freely available platform for acquiring, manipulating and normalizing protein structures in a high-throughput and seamless fashion. With an intuitive graphical interface it allows users with no programming background to download and manipulate their files. The platform also exports protocols, enabling users to easily share PDB searching and filtering criteria, enhancing analysis reproducibility.
Availability and implementation: PDBest installation packages are freely available for several platforms at http://www.pdbest.dcc.ufmg.br
Contact: wellisson@dcc.ufmg.br, dpires@dcc.ufmg.br, raquelcm@dcc.ufmg.br
Supplementary information: Supplementary data are available at Bioinformatics online.
Data-dependent bucketing improves reference-free compression of sequencing reads
Authors: Patro Rob , Kingsford Carl 
Published: April 2015

Abstract
Motivation: The storage and transmission of high-throughput sequencing data consumes significant resources. As our capacity to produce such data continues to increase, this burden will only grow. One approach to reduce storage and transmission requirements is to compress this sequencing data.
Results: We present a novel technique to boost the compression of sequencing that is based on the concept of bucketing similar reads so that they appear nearby in the file. We demonstrate that, by adopting a data-dependent bucketing scheme and employing a number of encoding ideas, we can achieve substantially better compression ratios than existing de novo sequence compression tools, including other bucketing and reordering schemes. Our method, Mince, achieves up to a 45% reduction in file sizes (28% on average) compared with existing state-of-the-art de novo compression schemes.
Availability and implementation: Mince is written in C++11, is open source and has been made available under the GPLv3 license. It is available at http://www.cs.cmu.edu/∼ckingsf/software/mince.
Contact: carlk@cs.cmu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
CiVi: circular genome visualization with unique features to analyze sequence elements
Authors: Overmars Lex , van Hijum Sacha A. F. T. , Siezen Roland J. , Francke Christof 
Published: April 2015

Abstract
Summary: We have developed CiVi, a user-friendly web-based tool to create custom circular maps to aid the analysis of microbial genomes and sequence elements. Sequence related data such as gene-name, COG class, PFAM domain, GC%, and subcellular location can be comprehensively viewed. Quantitative gene-related data (e.g. expression ratios or read counts) as well as predicted sequence elements (e.g. regulatory sequences) can be uploaded and visualized. CiVi accommodates the analysis of genomic elements by allowing a visual interpretation in the context of: (i) their genome-wide distribution, (ii) provided experimental data and (iii) the local orientation and location with respect to neighboring genes. CiVi thus enables both experts and non-experts to conveniently integrate public genome data with the results of genome analyses in circular genome maps suitable for publication.
Contact: L.Overmars@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Availability and implementation: CiVi is freely available at http://civi.cmbi.ru.nl
Tailoring of alerts substantially reduces the alert burden in computerized clinical decision support for drugs that should be avoided in patients with renal disease
Authors: Czock David , Konias Michael , Seidling Hanna M , Kaltschmidt Jens , Schwenger Vedat , Zeier Martin , Haefeli Walter E 
Published: April 2015

Abstract
Objective Electronic alerts are often ignored by physicians, which is partly due to the large number of unspecific alerts generated by decision support systems. The aim of the present study was to analyze critical drug prescriptions in a university-based nephrology clinic and to evaluate the effect of different alerting strategies on the alert burden.
Methods In a prospective observational study, two advanced strategies to automatically generate alerts were applied when medication regimens were entered for discharge letters, outpatient clinic letters, and written prescriptions and compared to two basic reference strategies. Strategy A generated alerts whenever drug-specific information was available, whereas strategy B generated alerts only when the estimated glomerular filtration rate of a patient was below a drug-specific value. Strategies C and D included further patient characteristics and drug-specific information to generate even more specific alerts.
Results Overall, 1012 medication regimens were entered during the observation period. The average number of alerts per drug preparation in medication regimens entered for letters was 0.28, 0.080, 0.019, and 0.011, when using strategy A, B, C, or D (P&lt;0.001, for comparison between the strategies), leading to at least one alert in 87.5%, 39.3%, 13.5%, or 7.81 % of the regimens. Similar average numbers of alerts were observed for medication regimens entered for written prescriptions.
Conclusions The prescription of potentially hazardous drugs is common in patients with renal impairment. Alerting strategies including patient and drug-specific information to generate more specific alerts have the potential to reduce the alert burden by more than 90 %.
Peanuts, brezels and bananas: food for thought on the orbital structure of the Galactic bulge
Authors: Portail Matthieu , Wegg Christopher , Gerhard Ortwin 
Published: April 2015

Abstract
Recent observations have discovered the presence of a box/peanut or X-shape structure in the Galactic bulge. Such box/peanut structures are common in external disc galaxies, and are well known in N-body simulations where they form following the buckling instability of a bar. From studies of analytical potentials and N-body models, it has been claimed in the past that box/peanut bulges are supported by ‘bananas’, or x1v1 orbits. We present here a set of N-body models where instead the peanut bulge is mainly supported by brezel-like orbits, allowing strong peanuts to form with short extent relative to the bar length. This shows that stars in the X-shape do not necessarily stream along banana orbits which follow the arms of the X-shape. The brezel orbits are also found to be the main orbital component supporting the peanut shape in our recent made-to-measure dynamical models of the Galactic bulge. We also show that in these models the fraction of stellar orbits that contribute to the X-structure account for 40–45 per cent of the stellar mass.
Dark matter-induced collapse of neutron stars: a possible link between fast radio bursts and the missing pulsar problem
Authors: Fuller Jim , Ott Christian D. 
Published: April 2015

Abstract
Fast radio bursts (FRBs) are an emerging class of short and bright radio transients whose sources remain enigmatic. Within the Galactic Centre, the non-detection of pulsars within the inner ∼10 pc has created a missing pulsar problem that has intensified with time. With all reserve, we advance the notion that the two problems could be linked by a common solution: the collapse of neutron stars (NS) due to capture and sedimentation of dark matter (DM) within their cores. Bramante & Linden showed that certain DM properties allow for rapid NS collapse within the high DM density environments near galactic centres while permitting NS survival elsewhere. Each DM-induced collapse could generate an FRB as the NS magnetosphere is suddenly expelled. This scenario could explain several features of FRBs: their short time scales, large energies, locally produced scattering tails, and high event rates. We predict that FRBs are localized to galactic centres, and that our own galactic centre harbours a large population of NS-mass (M ∼ 1.4 M⊙) black holes. The DM-induced collapse scenario is intrinsically unlikely because it can only occur in a small region of allowable DM parameter space. However, if observed to occur, it would place tight constraints on DM properties.
Applied catalysis for sustainable development of chemical industry in China
Authors: Xie Zaiku , Liu Zhicheng , Wang Yangdong , Jin Zhonghao 
Published: April 2015

Abstract
Progressing green chemical technologies is significant to the sustainable development of chemical industry in China, as the energy and environment problems increasingly became great challenges to the whole society. The scientific connotation of sustainable energy chemical engineering can be generalized as green carbon/hydrogen science which means optimization of carbon/hydrogen atom economics based on high efficient catalysis and low-carbon emission. This review illustrated recent advances in developing sustainable technologies for applied catalysis in chemical industry of China, including the fields of high efficient conversion of heavy oil, green petrochemical catalytic technologies, clean utilization of coal and natural gas, promoting sustainable resources and clean energy, etc. Moreover, from the view of industrial point, some important common scientific problems were discussed and summarized, such as the relation between molecular diffusion and catalyzing efficiency, homogeneous catalysis in heterogeneous catalysts, in situ or operando characterization of industrial catalysis, etc., aiming to supplying a forward roadmap to academia and/or industry.
Effects of an Innovative Psychotherapy Program for Surgical Patients
Authors: Kerper Léonie F. , Spies Claudia D. , Salz Anna-Lena , Weiß-Gerlach Edith , Balzer Felix , Neumann Tim , Tafelski Sascha , Lau Alexandra , Neuner Bruno , Romanczuk-Seiferth Nina , Glaesmer Heide , Wernecke Klaus-Dieter , Brähler Elmar , Krampe Henning 
Published: April 2015

AbstractAbstract
In 220 surgical patients with comorbid mental disorders (primarily mood, anxiety and adjustment disorders, or alcohol or tobacco abuse), those randomized to psychotherapy sessions perioperatively and up to 3 months postoperatively were more likely to participate in psychosocial mental health care 6 months after surgery than those randomized to brief written advice only.

Background:
The stepped care program Bridging Intervention in Anesthesiology (BRIA) aims at motivating and supporting surgical patients with comorbid mental disorders to engage in psychosocial mental healthcare options. This study examined the efficacy of BRIA.

Methods:
This randomized, parallel-group, open-label, controlled trial was conducted in the preoperative anesthesiological assessment clinics and surgical wards of a large university hospital in Germany. A total of 220 surgical patients with comorbid mental disorders were randomized by using the computer-generated lists to one of two intervention groups: BRIA psychotherapy sessions up to 3 months postoperatively (BRIA) versus no psychotherapy/computerized brief written advice (BWA) only. Primary outcome was participation in psychosocial mental healthcare options at month 6. Secondary outcome was change of self-reported general psychological distress (Global Severity Index of the Brief Symptom Inventory) between baseline and month 6.

Results:
At 6-month follow-up, the rate of patients who engaged in psychosocial mental healthcare options was 30% (33 of 110) in BRIA compared with 11.8% (13 of 110) in BWA (P = 0.001). Number needed to treat and relative risk reduction were 6 (95% CI, 4 to 13) and 0.21 (0.09 to 0.31), respectively. In BRIA, Global Severity Index decreased between baseline and month 6 (P < 0.001), whereas it did not change significantly in BWA (P = 0.197).

Conclusions:
Among surgical patients with comorbid mental disorders, BRIA results in an increased engagement in subsequent therapy options and a decrease of general psychological distress. These data suggest that it is reasonable to integrate innovative psychotherapy programs into the context of interdisciplinary surgical care.