bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast, accurate, and reliable molecular docking with QuickVina 2
Authors: Alhossary Amr , Handoko Stephanus Daniel , Mu Yuguang , Kwoh Chee-Keong 
Published: February 2015

AbstractMotivation: The need for efficient molecular docking tools for high-throughput screening is growing alongside the rapid growth of drug-fragment databases. AutoDock Vina (‘Vina’) is a widely used docking tool with parallelization for speed. QuickVina (‘QVina 1’) then further enhanced the speed via a heuristics, requiring high exhaustiveness. With low exhaustiveness, its accuracy was compromised. We present in this article the latest version of QuickVina (‘QVina 2’) that inherits both the speed of QVina 1 and the reliability of the original Vina.Results: We tested the efficacy of QVina 2 on the core set of PDBbind 2014. With the default exhaustiveness level of Vina (i.e. 8), a maximum of 20.49-fold and an average of 2.30-fold acceleration with a correlation coefficient of 0.967 for the first mode and 0.911 for the sum of all modes were attained over the original Vina. A tendency for higher acceleration with increased number of rotatable bonds as the design variables was observed. On the accuracy, Vina wins over QVina 2 on 30% of the data with average energy difference of only 0.58 kcal/mol. On the same dataset, GOLD produced RMSD smaller than 2 Å on 56.9% of the data while QVina 2 attained 63.1%.Availability and implementation: The C++ source code of QVina 2 is available at (www.qvina.org).Contact: aalhossary@pmail.ntu.edu.sgSupplementary information: Supplementary data are available at Bioinformatics online.
GlycanAnalysis Plug-in: a database search tool for N-glycan structures using mass spectrometry
Authors: Morimoto Kentaro , Nishikaze Takashi , Yoshizawa Akiyasu C. , Kajihara Shigeki , Aoshima Ken , Oda Yoshiya , Tanaka Koichi 
Published: February 2015

Abstract
Summary: Tandem mass spectrometry (MS/MS or MSn) is a potent technique for characterizing N-glycan structures. GlycanAnalysis searches a glycan database to support the identification of glycan structures from MS/MS spectra. It also calculates diagnostic ions of glycan structures registered in a glycan database (GlycomeDB or KEGG GLYCAN) and searches for MS/MS spectra of N-glycans that match diagnostic ions to determine the structures. This program functions as a plug-in for Mass++, a freeware mass spectrum visualization and analysis program.
Availability and implementation: The executable files of Mass++ are available for free at http://www.first-ms3d.jp/english/. The GlycanAnalysis plug-in is included in the standard package of Mass++ for Windows.
Contact: k-morimt@shimadzu.co.jp or nishikaz@shimadzu.co.jp or acyshzw@shimadzu.co.jp
Supplementary information: Supplementary material are available at Bioinformatics online.
Normalization and noise reduction for single cell RNA-seq experiments
Authors: Ding Bo , Zheng Lina , Zhu Yun , Li Nan , Jia Haiyang , Ai Rizi , Wildberg Andre , Wang Wei 
Published: February 2015

Abstract
A major roadblock towards accurate interpretation of single cell RNA-seq data is large technical noise resulted from small amount of input materials. The existing methods mainly aim to find differentially expressed genes rather than directly de-noise the single cell data. We present here a powerful but simple method to remove technical noise and explicitly compute the true gene expression levels based on spike-in ERCC molecules.
Availability and implementation: The software is implemented by R and the download version is available at http://wanglab.ucsd.edu/star/GRM.
Contact: wei-wang@ucsd.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
RepExplore: addressing technical replicate variance in proteomics and metabolomics data analysis
Authors: Glaab Enrico , Schneider Reinhard 
Published: February 2015

Abstract
Summary: High-throughput omics datasets often contain technical replicates included to account for technical sources of noise in the measurement process. Although summarizing these replicate measurements by using robust averages may help to reduce the influence of noise on downstream data analysis, the information on the variance across the replicate measurements is lost in the averaging process and therefore typically disregarded in subsequent statistical analyses.
We introduce RepExplore, a web-service dedicated to exploit the information captured in the technical replicate variance to provide more reliable and informative differential expression and abundance statistics for omics datasets. The software builds on previously published statistical methods, which have been applied successfully to biomedical omics data but are difficult to use without prior experience in programming or scripting. RepExplore facilitates the analysis by providing a fully automated data processing and interactive ranking tables, whisker plot, heat map and principal component analysis visualizations to interpret omics data and derived statistics.
Availability and implementation: Freely available at http://www.repexplore.tk
Contact: enrico.glaab@uni.lu
Supplementary information: Supplementary data are available at Bioinformatics online.
An event-driven approach for studying gene block evolution in bacteria
Authors: Ream David C. , Bankapur Asma R. , Friedberg Iddo 
Published: February 2015

Abstract
Motivation: Gene blocks are genes co-located on the chromosome. In many cases, gene blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. The conservation is rarely absolute: gene loss, gain, duplication, block splitting and block fusion are frequently observed. An open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed. These models, however, are not generally applicable to all types of gene blocks, and consequently cannot be used to broadly compare and study gene block evolution. To address this problem, we introduce an event-based method for tracking gene block evolution in bacteria.
Results: We show here that the evolution of gene blocks in proteobacteria can be described by a small set of events. Those include the insertion of genes into, or the splitting of genes out of a gene block, gene loss, and gene duplication. We show how the event-based method of gene block evolution allows us to determine the evolutionary rateand may be used to trace the ancestral states of their formation. We conclude that the event-based method can be used to help us understand the formation of these important bacterial genomic structures.
Availability and implementation: The software is available under GPLv3 license on http://github.com/reamdc1/gene_block_evolution.git. Supplementary online material: http://iddo-friedberg.net/operon-evolution
Contact: i.friedberg@miamioh.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Combined application of biophysical habitat mapping and systematic conservation planning to assess efficiency and representativeness of the existing High Seas MPA network in the Northeast Atlantic
Authors: Evans Jon L. , Peckett Frances , Howell Kerry L. 
Published: February 2015

AbstractThe High Seas are increasingly the subject of exploitation. Although Marine Protected Areas (MPAs) are seen as a useful tool in the sustainable management of the oceans, progress in the implementation of MPA networks in areas beyond national jurisdiction has been limited. Specifically, the criteria of “representativeness” has received little consideration. This study uses the systematic conservation planning software Marxan coupled with a biologically meaningful biophysical habitat map to investigate representative MPA network scenarios and to assess the efficiency and representativeness of the existing High Seas MPA network in the Northeast Atlantic. Habitat maps were created based on the layers of water mass structure and seabed topography resulting in 30 different habitats, in six distinct regions. Conservation targets were set at 10 and 30% representation of each habitat within the final network. Two portfolios were created. The first portfolio (P1) ignored the presence of the existing MPA network within the study area allowing a non-biased selection of planning units (PUs) or sites to be chosen. The second (P2) enforced the selection of areas within the existing MPA network. Efficiency was measured as the difference in the percentage area contained within the “best scenario” MPAs from the un-bias run (P1) compared with (P2). Representativety of the existing network was assessed through the investigation of the properties of PUs included within MPAs in the “best scenario” Marxan output of P2. The results suggest that the current MPA network is neither efficient nor representative. There were clear differences in the spatial distribution of PUs selected in P1 compared with P2. The area required to be protected to achieve that the representation of 10 and 30% of each habitat was 8–10 and 1–4% higher, respectively, in P2 compared with P1. Abyssal areas in all regions are underrepresented within the current MPA network.
Sverdrup critical depth and the role of water clarity in Norwegian Coastal Water
Authors: Aksnes D. L. 
Published: February 2015

Abstract
The critical depth concept was first recognized by Gran and Braarud (1935). During summer, in the Bay of Fundy, they observed an unexpected no bloom situation. Their interpretation was that high amounts of detritus of terrestrial origin caused too murky water and insufficient light for the tidally mixed phytoplankton. Almost 20 years later, this was elaborated by Sverdrup (1953) into a hypothesis for the initiation of the spring bloom in the North Atlantic Water (NAW) masses. Since then, variations in mixed layer depth have been a key in phytoplankton modelling. As illustrated by the study of Gran and Braarud, variation in the non-phytoplankton light attenuation coefficient is also a key to understand phytoplankton bloom conditions. Due to lack of accurate parameterizations, however, non-phytoplankton light attenuation is often assumed invariant in phytoplankton modelling. Here, I report spatial variation in a proxy for the pre-bloom light attenuation in Norwegian Coastal Water (NCW). It is shown that this variation can be partially accounted for by variations in salinity and dissolved oxygen. The light attenuation coefficient at 440 nm increased by 0.041 and 0.032 m−1 with drops in salinity and dissolved oxygen of 1PSU and 1 ml O2 l−1, respectively. Consequences for the euphotic depth, Sverdrup critical depth, and the nutricline depth are discussed. I conclude that phytoplankton modelling, particularly across coastal and oceanic waters, such as NCW and NAW, needs to account for variations in the non-phytoplankton light attenuation and that salinity might be a useful proxy for regional parameterizations.
Visualizing collaborative electronic health record usage for hospitalized patients with heart failure
Authors: Soulakis Nicholas D , Carson Matthew B , Lee Young Ji , Schneider Daniel H , Skeehan Connor T , Scholtens Denise M 
Published: February 2015

AbstractObjective To visualize and describe collaborative electronic health record (EHR) usage for hospitalized patients with heart failure.Materials and methods We identified records of patients with heart failure and all associated healthcare provider record usage through queries of the Northwestern Medicine Enterprise Data Warehouse. We constructed a network by equating access and updates of a patient’s EHR to a provider-patient interaction. We then considered shared patient record access as the basis for a second network that we termed the provider collaboration network. We calculated network statistics, the modularity of provider interactions, and provider cliques.Results We identified 548 patient records accessed by 5113 healthcare providers in 2012. The provider collaboration network had 1504 nodes and 83 998 edges. We identified 7 major provider collaboration modules. Average clique size was 87.9 providers. We used a graph database to demonstrate an ad hoc query of our provider-patient network.Discussion Our analysis suggests a large number of healthcare providers across a wide variety of professions access records of patients with heart failure during their hospital stay. This shared record access tends to take place not only in a pairwise manner but also among large groups of providers.Conclusion EHRs encode valuable interactions, implicitly or explicitly, between patients and providers. Network analysis provided strong evidence of multidisciplinary record access of patients with heart failure across teams of 100+ providers. Further investigation may lead to clearer understanding of how record access information can be used to strategically guide care coordination for patients hospitalized for heart failure.
Astrochemistry at work in the L1157-B1 shock: acetaldehyde formation
Authors: Codella C. , Fontani F. , Ceccarelli C. , Podio L. , Viti S. , Bachiller R. , Benedettini M. , Lefloch B. 
Published: February 2015

Abstract
The formation of complex organic molecules (COMs) in protostellar environments is a hotly debated topic. In particular, the relative importance of the gas phase processes as compared to a direct formation of COMs on the dust grain surfaces is so far unknown. We report here the first high-resolution images of acetaldehyde (CH3CHO) emission towards the chemically rich protostellar shock L1157-B1, obtained at 2 mm with the IRAM Plateau de Bure interferometer. Six blueshifted CH3CHO lines with Eu = 26–35 K have been detected. The acetaldehyde spatial distribution follows the young (∼ 2000 yr) outflow cavity produced by the impact of the jet with the ambient medium, indicating that this COM is closely associated with the region enriched by iced species evaporated from dust mantles and released into the gas phase. A high CH3CHO relative abundance, 2–3 × 10−8, is inferred, similarly to what found in hot corinos. Astrochemical modelling indicates that gas phase reactions can produce the observed quantity of acetaldehyde only if a large fraction of carbon, of the order of 0.1 per cent, is locked into iced hydrocarbons.
Formation of complex organic molecules in cold objects: the role of gas-phase reactions
Authors: Balucani Nadia , Ceccarelli Cecilia , Taquet Vianney 
Published: February 2015

Abstract
While astrochemical models are successful in reproducing many of the observed interstellar species, they have been struggling to explain the observed abundances of complex organic molecules. Current models tend to privilege grain surface over gas-phase chemistry in their formation. One key assumption of those models is that radicals trapped in the grain mantles gain mobility and react on lukewarm ( ≳ 30 K) dust grains. Thus, the recent detections of methyl formate (MF) and dimethyl ether (DME) in cold objects represent a challenge and may clarify the respective role of grain-surface and gas-phase chemistry. We propose here a new model to form DME and MF with gas-phase reactions in cold environments, where DME is the precursor of MF via an efficient reaction overlooked by previous models. Furthermore, methoxy, a precursor of DME, is also synthesized in the gas phase from methanol, which is desorbed by a non-thermal process from the ices. Our new model reproduces fairly well the observations towards L1544. It also explains, in a natural way, the observed correlation between DME and MF. We conclude that gas-phase reactions are major actors in the formation of MF, DME and methoxy in cold gas. This challenges the exclusive role of grain-surface chemistry and favours a combined grain-gas chemistry.
X-ray coherent pulsations during a sub-luminous accretion disc state of the transitional millisecond pulsar XSS J12270−4859
Authors: Papitto A. , de Martino D. , Belloni T. M. , Burgay M. , Pellizzoni A. , Possenti A. , Torres D. F. 
Published: February 2015

Abstract
We present the first detection of X-ray coherent pulsations from the transitional millisecond pulsar XSS J12270−4859, while it was in a sub-luminous accretion disc state characterized by a 0.5–10 keV luminosity of 5 × 1033 erg s−1 (assuming a distance of 1.4 kpc). Pulsations were observed by XMM–Newton at an rms amplitude of (7.7 ± 0.5) per cent with a second harmonic stronger than the fundamental frequency, and were detected when the source is neither flaring nor dipping. The most likely interpretation of this detection is that matter from the accretion disc was channelled by the neutron star magnetosphere and accreted on to its polar caps. According to standard disc accretion theory, for pulsations to be observed the mass inflow rate in the disc was likely larger than the amount of plasma actually reaching the neutron star surface; an outflow launched by the fast rotating magnetosphere then probably took place, in agreement with the observed broad-band spectral energy distribution. We also report about the non-detection of X-ray pulsations during a recent observation performed while the source behaved as a rotationally-powered radio pulsar.
Association of Pigmentary Glaucoma and Nonsenile Nuclear Cataracts
Authors: Mosaed Sameh , Haider Asghar , Kim Deborah , Zhang Zina 
Published: February 2015

Purpose:
To describe a new association between nonsenile nuclear cataracts and pigmentary glaucoma in patients with controlled intraocular pressure (IOP).

Design:
Retrospective consecutive case series of nonsenile nuclear cataracts seen in patients with pigmentary glaucoma with controlled IOP in a single glaucoma specialist practice. Eight eyes of 7 patients with pigmentary glaucoma and visually significant cataract who underwent cataract removal were reviewed.

Results:
Patients with pigmentary glaucoma developed rapidly progressing, nonsenile nuclear cataracts, with resulting myopic shifts between 4 and 13 D from baseline in <2 years. The patients had controlled IOP and there were no associations between medication use and cataract development.

Conclusions:
A new association between pigmentary glaucoma and nonsenile nuclear cataracts is described. In these patients, the IOP remains controlled and no association is seen between the cataract and medication use. The cataract is rapidly progressive and can cause a myopic shift between 4 and 13 D. Awareness of the purely nuclear cataract and its’ clinical presentation can assist the clinician when approaching the patient with pigment dispersion and decreasing vision. To the best of our knowledge, this is a new association and warrants further investigation.
Comparison of Optical Coherence Tomography Findings in Patients With Primary Open-angle Glaucoma and Parkinson Disease
Authors: Eraslan Muhsin , Balci Sevcan Y. , Cerman Eren , Temel Ahmet , Suer Devran , Elmaci Nese T. 
Published: February 2015

Purpose:To evaluate the peripapillary retinal nerve fiber layer (RNFL), ganglion cell complex, and macular thickness as well as their correlation with the severity of diseases.Materials and Methods:This is a cross-sectional study and comparing both eyes of 26 patients with primary open-angle glaucoma, 25 patients with Parkinson disease (PD), and 23 healthy subjects. RNFL, ganglion cell complex, and macular thickness were measured and analyzed with optical coherence tomography (OCT) in all cases and correlation with severity of the disease was assessed in PD group.Results:The mean RNFL of PD was significantly thinner compared with controls (P=0.002). In glaucoma group, the mean RNFL was significantly thinner (96.28±12.49 μm) than PD (105.43±13.45 μm) and the controls (113.75±8.53 μm) (P<0.001;P<0.001, respectively). The global loss volume (GLV) rates in the glaucoma and PD group were significantly higher than controls, respectively (P=0.006;P<0.001/P=0.002,P=0.013). However, the GLV rate was significantly lower in PD group compared with glaucoma group (P=0.001). There was no significant correlation between OCT measurements and disease duration or severity in the PD patients.Conclusions:Although RNFL thickness and GLV changes may show the ganglion cell loss in both disease but none of the OCT parameters are correlated with the severity of PD. OCT may help to reveal the ganglion cell damage but may not help in determination of severity during the clinical follow-up of PD patients.
Vascular Endothelial Growth Factor is Increased in Aqueous Humor of Acute Primary Angle-Closure Eyes
Authors: Huang Wenbin , Gao Xinbo , Chen Shida , Li Xingyi , Zhang Xinyu , Zhang Xiulan 
Published: February 2015

Purpose:
To measure and compare the levels of vascular endothelial growth factor (VEGF) in the aqueous humor of patients with acute primary angle closure (APAC), primary angle-closure glaucoma (PACG), and normal cataract (controls).

Methods:
Aqueous humor samples were prospectively collected from 38 APAC eyes, 36 PACG eyes, and 25 nonglaucomatous cataract control eyes. The levels of aqueous humor VEGF were measured using enzyme-linked immunoassays. The clinical characteristics of participants were also collected for correlation analysis.

Results:
VEGF was detected in aqueous humor samples of 35 of 38 APAC patients (mean±SE of the mean, 935±258 pg/mL), 30 of 36 PACG patients (165±37.5 pg/mL), and 16 of 25 cataract controls (69.5±13.5 pg/mL). The mean concentration of VEGF in APAC eyes was 13.5 and 5.7 times higher than that in controls and PACG eyes, respectively, and these differences were statistically significant (both P<0.0167). In the correlation analysis that included all participants, the aqueous humor VEGF level was found to correlate negatively with axial length (ρ=−0.342, P=0.001), and positively with intraocular pressure (ρ=0.434, P<0.001).

Conclusions:
VEGF was significantly increased in aqueous humor of APAC eyes. An increase in aqueous humor VEGF may be the result of the characteristic ocular ischemia and hypoxia observed in APAC eyes as a consequence of sudden excessive increases in intraocular pressure during the acute episode.
Prescriptions for Bedtime Sedatives After the Introduction of a General Admission Order Set at an Academic Health Center: The Potential and Pitfalls of Order Sets
Authors: Kara Areeba , Isaacs Alex N. , Nisly Sarah A. 
Published: February 2015

Objective
This study describes the impact of modifications to a general admission order set on physician prescribing of 2 as-needed or pro re nata (PRN) bedtime sedatives.

Methods
The hospitalists at our institution have used a general medical admission order set since 2005. Zolpidem was the only as-needed (PRN) bedtime sedative option on the order set until trazodone was added in December 2008. Trazodone is preferred over zolpidem in the geriatric population. We identified patients admitted by the hospitalists between January 2007 and August 2013 who were prescribed with either zolpidem or trazodone as a PRN sedative. Patient demographics, date and time of the order, and number of sedative doses administered during the hospitalization were recorded. Orders placed within 12 hours of admission were attributed to admission orders.

Results
Between 2007 and 2013, the number of patients admitted by the hospitalists with an order for PRN trazodone on admission increased by 18-fold. During the same period, the number of admissions by the hospitalists increased by 2.3 times. Zolpidem orders exceeded those for trazodone in all age groups until 2008. After the addition of trazodone, its use exceeded that of zolpidem. Almost half (48%) of all patients did not have a dose of the PRN trazodone administered.

Conclusions
Although order sets can be leveraged to align practitioners with established guidelines, the expediency of using medications on an order set may overcome physicians' clinical judgment. The content of an order set therefore deserves careful scrutiny before implementation.