bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors
Authors: Megjhani Murad , Rey-Villamizar Nicolas , Merouane Amine , Lu Yanbin , Mukherjee Amit , Trett Kristen , Chong Peter , Harris Carolyn , Shain William , Roysam Badrinath 
Published: February 2015

Abstract
Motivation: The arbor morphologies of brain microglia are important indicators of cell activation. This article fills the need for accurate, robust, adaptive and scalable methods for reconstructing 3-D microglial arbors and quantitatively mapping microglia activation states over extended brain tissue regions.
Results: Thick rat brain sections (100–300 µm) were multiplex immunolabeled for IBA1 and Hoechst, and imaged by step-and-image confocal microscopy with automated 3-D image mosaicing, producing seamless images of extended brain regions (e.g. 5903 × 9874 × 229 voxels). An over-complete dictionary-based model was learned for the image-specific local structure of microglial processes. The microglial arbors were reconstructed seamlessly using an automated and scalable algorithm that exploits microglia-specific constraints. This method detected 80.1 and 92.8% more centered arbor points, and 53.5 and 55.5% fewer spurious points than existing vesselness and LoG-based methods, respectively, and the traces were 13.1 and 15.5% more accurate based on the DIADEM metric. The arbor morphologies were quantified using Scorcioni’s L-measure. Coifman’s harmonic co-clustering revealed four morphologically distinct classes that concord with known microglia activation patterns. This enabled us to map spatial distributions of microglial activation and cell abundances.
Availability and implementation: Experimental protocols, sample datasets, scalable open-source multi-threaded software implementation (C++, MATLAB) in the electronic supplement, and website (www.farsight-toolkit.org). http://www.farsight-toolkit.org/wiki/Population-scale_Three-dimensional_Reconstruction_and_Quanti-tative_Profiling_of_Microglia_Arbors
Contact: broysam@central.uh.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Oasis: online analysis of small RNA deep sequencing data
Authors: Capece Vincenzo , Garcia Vizcaino Julio C. , Vidal Ramon , Rahman Raza-Ur , Pena Centeno Tonatiuh , Shomroni Orr , Suberviola Irantzu , Fischer Andre , Bonn Stefan 
Published: February 2015

Abstract
Summary: Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. It was designed for the end user in the lab, providing an easy-to-use web frontend including video tutorials, demo data and best practice step-by-step guidelines on how to analyze sRNA-seq data. Oasis’ exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. Oasis generates downloadable interactive web reports for easy visualization, exploration and analysis of data on a local system. Finally, Oasis’ modular workflow enables for the rapid (re-) analysis of data.
Availability and implementation: Oasis is implemented in Python, R, Java, PHP, C++ and JavaScript. It is freely available at http://oasis.dzne.de.
Contact: stefan.bonn@dzne.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Influenza Circulation in United States Army Training Camps Before and During the 1918 Influenza Pandemic: Clues to Early Detection of Pandemic Viral Emergence
Authors: Chertow Daniel S. , Cai Rongman , Sun Junfeng , Grantham John , Taubenberger Jeffery K. , Morens David M. 
Published: February 2015

AbstractBackground.  Surveillance for respiratory diseases in domestic National Army and National Guard training camps began after the United States’ entry into World War I, 17 months before the “Spanish influenza” pandemic appeared.Methods.  Morbidity, mortality, and case-fatality data from 605 625 admissions and 18 258 deaths recorded for 7 diagnostic categories of respiratory diseases, including influenza and pneumonia, were examined over prepandemic and pandemic periods.Results.  High pandemic influenza mortality was primarily due to increased incidence of, but not increased severity of, secondary bacterial pneumonias.Conclusions.  Two prepandemic incidence peaks of probable influenza, in December 1917–January 1918 and in March–April 1918, differed markedly from the September–October 1918 pandemic onset peak in their clinical-epidemiologic features, and they may have been caused by seasonal or endemic viruses. Nevertheless, rising proportions of very low incidence postinfluenza bronchopneumonia (diagnosed at the time as influenza and bronchopneumonia) in early 1918 could have reflected circulation of the pandemic virus 5 months before it emerged in pandemic form. In this study, we discuss the possibility of detecting pandemic viruses before they emerge, by surveillance of special populations.
Modeling non-local thermodynamic equilibrium plasma using the Flexible Atomic Code data
Authors: Han Bo , Wang Feilu , Salzmann David , Zhao Gang 
Published: February 2015

Abstract
We present a new code, RCF (“Radiative–Collisional code based on FAC”), which is used to simulate steady-state plasmas under non-local thermodynamic equilibrium condition, especially photoinization-dominated plasmas. RCF takes almost all of the radiative and collisional atomic processes into a rate equation to interpret the plasmas systematically. The Flexible Atomic Code (FAC) supplies all the atomic data needed for RCF, which insures calculating completeness and consistency of atomic data. With four input parameters relating to the radiation source and target plasma, RCF calculates the population of levels and charge states, as well as potential emission spectrum. In a preliminary application, RCF successfully reproduced the results of a photoionization experiment with reliable atomic data. The effects of the most important atomic processes on the charge state distribution are also discussed.
An Evaluation of Shared Mental Models and Mutual Trust on General Medical Units: Implications for Collaboration, Teamwork, and Patient Safety
Authors: McComb Sara A. , Lemaster Matthew , Henneman Elizabeth A. , Hinchey Kevin T. 
Published: February 2015

Objectives
This study examines nurse-physician teamwork and collaboration, a critical component in the delivery of safe patient care, on general medical units. To that end, we assess shared mental models and mutual trust, 2 coordinating mechanisms that help facilitate teamwork, among nurses and physicians working on general medical units.

Methods
Data were collected from 37 nurses and 42 physicians at an urban teaching medical center in the Northeastern United States. Shared mental model questionnaire items were iteratively developed with experts' input to ensure content validity. Mutual trust items were adapted from an existing scale; items were reliable. Data were analyzed using χ2 and independent 2-tailed t tests.

Results
Physicians and nurses reported significant differences in their perceptions of the professional responsible for a variety of roles (e.g., advocating for the patient [P = 0.0007], identifying a near miss/error [P = 0.003]). Medication reconciliation is only role for which nurses perceive less responsibility than physicians perceive nurses have. Regarding mutual trust, both groups reported significantly more trust within their own professions; both groups reported similar levels of trust in physicians, with physicians reporting significantly less trust in their nursing colleagues than nurses perceive (P < 0.0001).

Conclusions
Although many efforts have been directed at improving nurse-physician collaboration, more work is needed. To that end, we propose increasing knowledge about their respective roles, providing opportunities for nurse and physician collaboration through rounding or committee work and enhancing the preparedness and professionalism of interactions.
Transparency When Things Go Wrong: Physician Attitudes About Reporting Medical Errors to Patients, Peers, and Institutions
Authors: Bell Sigall K. , White Andrew A. , Yi Jean C. , Yi-Frazier Joyce P. , Gallagher Thomas H. 
Published: February 2015

Objectives
Transparent communication after medical error includes disclosing the mistake to the patient, discussing the event with colleagues, and reporting to the institution. Little is known about whether attitudes about these transparency practices are related. Understanding these relationships could inform educational and organizational strategies to promote transparency.

Methods
We analyzed responses of 3038 US and Canadian physicians to a medical error communication survey. We used bivariate correlations, principal components analysis, and linear regression to determine whether and how physician attitudes about transparent communication with patients, peers, and the institution after error were related.

Results
Physician attitudes about disclosing errors to patients, peers, and institutions were correlated (all P's < 0.001) and represented 2 principal components analysis factors, namely, communication with patients and communication with peers/institution. Predictors of attitudes supporting transparent communication with patients and peers/institution included female sex, US (vs Canadian) doctors, academic (vs private) practice, the belief that disclosure decreased likelihood of litigation, and the belief that system changes occur after error reporting. In addition, younger physicians, surgeons, and those with previous experience disclosing a serious error were more likely to agree with disclosure to patients. In comparison, doctors who believed that disclosure would decrease patient trust were less likely to agree with error disclosure to patients. Previous disclosure education was associated with attitudes supporting greater transparency with peers/institution.

Conclusions
Physician attitudes about discussing errors with patients, colleagues, and institutions are related. Several predictors of transparency affect all 3 practices and are potentially modifiable by educational and institutional strategies.
“The Jackson Table Is a Pain in the…”: A Qualitative Study of Providers’ Perception Toward a Spinal Surgery Table
Authors: Asiedu Gladys B. , Lowndes Bethany R. , Huddleston Paul M. , Hallbeck Susan 
Published: February 2015

Objective
The aim of this study was to define health care providers’ perceptions toward prone patient positioning for spine surgery using the Jackson Table, which has not been hitherto explored.

Methods
We analyzed open-ended questionnaire data and interviews conducted with the spine surgical team regarding the current process of spinal positioning/repositioning using the Jackson Table. Participants were asked to provide an open-ended explanation as to whether they think the current process of spinal positioning/repositioning is safe for the staff or patients. Follow-up qualitative interviews were conducted with 11 of the participants to gain an in-depth understanding of the challenges and safety issues related to prone patient positioning.

Results
Data analysis resulted in 6 main categories: general challenges with patient positioning, role-specific challenges, challenges with the Jackson Table and the “sandwich” mechanism, safety concerns for patients, safety concerns for the medical staff, and recommendations for best practices.

Conclusions
This study is relevant to everyday practice for spinal surgical team members and advances our understanding of how surgical teams qualitatively view the current process of patient positioning for spinal surgery. Providers recommended best practices for using the Jackson Table, which can be achieved through standardized practice for transfer of patients, educational tools, and checklists for equipment before patient transfer and positioning. This research has identified several important practice opportunities for improving provider and patient safety in spine surgery.
Site-Specific Nitrosoproteomic Identification of EndogenouslyS-Nitrosylated Proteins in Arabidopsis
Authors: Hu Jiliang , Huang Xiahe , Chen Lichao , Sun Xuwu , Lu Congming , Zhang Lixin , Wang Yingchun , Zuo Jianru 
Published: February 2015

AbstractNitric oxide (NO) regulates multiple developmental events and stress responses in plants. A major biologically active species of NO is S-nitrosoglutathione (GSNO), which is irreversibly degraded by GSNO reductase (GSNOR). The major physiological effect of NO is protein S-nitrosylation, a redox-based posttranslational modification mechanism by covalently linking an NO molecule to a cysteine thiol. However, little is known about the mechanisms of S-nitrosylation-regulated signaling, partly due to limited S-nitrosylated proteins being identified. In this study, we identified 1,195 endogenously S-nitrosylated peptides in 926 proteins from the Arabidopsis (Arabidopsis thaliana) by a site-specific nitrosoproteomic approach, which, to date, is the largest data set of S-nitrosylated proteins among all organisms. Consensus sequence analysis of these peptides identified several motifs that contain acidic, but not basic, amino acid residues flanking the S-nitrosylated cysteine residues. These S-nitrosylated proteins are involved in a wide range of biological processes and are significantly enriched in chlorophyll metabolism, photosynthesis, carbohydrate metabolism, and stress responses. Consistently, the gsnor1-3 mutant shows the decreased chlorophyll content and altered photosynthetic properties, suggesting that S-nitrosylation is an important regulatory mechanism in these processes. These results have provided valuable resources and new clues to the studies on S-nitrosylation-regulated signaling in plants.
Proposing a new approach for evaluating the situational leadership theory based on the Kano model
Authors: Salehzadeh Reza , Shahin Arash , Kazemi Ali , Shaemi Barzoki Ali 
Published: February 2015

Purpose
– The purpose of this paper is to propose a new approach for evaluating the situational leadership theory (SLT).

Design/methodology/approach
– Statistical population includes the undergraduate, postgraduate and PhD students of the University of Isfahan. For data analysis, 727 accurate completed questionnaires have been used. Initially, questions were developed for each SLT style, followed by analysis in which the type of styles were determined and classified using the Kano evaluation table.

Findings
– Based on the Kano's classifications, findings imply that, the appropriate leadership styles for undergraduate, postgraduate and PhD students are directing, coaching and supporting styles, respectively.

Originality/value
– The approach and findings of this research contribute to the literature of SLT and the Kano model. Findings can be used as a guideline for lecturers in leading and motivating students.
How salespeople see organizational citizenship behaviors: an exploratory study using the laddering technique
Authors: Guenzi Paolo , Panzeri Federico 
Published: February 2015

Purpose
– The purpose of this paper is to more thoroughly investigate the role of organizational citizenship behaviors (OCBs) in sales force settings and the reason why salespeople should practice OCBs. In fact, in spite of the huge body of literature on OCBs and their impact on performance, some important knowledge gaps still remain to be filled. Inconsistent and unexpected findings are particularly apparent in the relatively few studies investigating OCBs in sales forces. The authors argue that some specific characteristics of the selling job and related tasks make the analysis of the practice of these behaviors in the sales context particularly interesting.

Design/methodology/approach
– The authors explore which OCBs salespeople engage in, and analyze the perceived consequences of such behaviors using means-end theory and the laddering technique. They apply means-end theory and the laddering technique to interview a sample of salespersons from three companies operating in different business-to-business settings.

Findings
– The end result of the empirical analysis is the hierarchical value map showing a set of linkages among OCBs and their perceived consequences. In the perceptions of salespeople, OCBs play a strong utilitarian role in that they facilitate personal goal attainment. In salespeople’s minds, there are no relevant trade-offs between OCBs and task-performance as long as the former can be used to improve the latter. For salespeople, the path from OCBs to performance may vary, depending on whether the performance in question is organizational, individual or customer-focused. Finally, some OCBs apparently contribute to creating customer trust in the salesperson.

Research limitations/implications
– The findings add some interesting insights to the discussion regarding some controversies in OCBs literature, especially the interplay of contextual performance and task performance.

Practical implications
– Various types of OCBs can be encouraged through different managerial interventions. As an example, altruism can be fostered by appropriate recruiting criteria (e.g. using “attitude toward teamwork” as a key personnel selection factor), and by training initiatives and leadership style. Altruism can also be stimulated by an adequately designed organizational structure (e.g. team-based) as well as by adopting appropriate integration mechanisms that facilitate interpersonal and interfunctional cooperation. Sales managers can foster some OCBs by promoting knowledge sharing and reciprocal learning among members of the sales team, and by emphasizing the positive consequences of OCBs in all communication with salespeople.

Originality/value
– Findings from this study challenge some widespread assumptions about OCBs in general. In fact, most of the literature holds that OCBs are an example of prosocial behaviors. Actually, the findings suggest that in the specific case of salespeople, OCBs are ultimately self-directed, for the most part.
Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology
Authors: Pukk Lilian , Ahmad Freed , Hasan Shihab , Kisand Veljo , Gross Riho , Vasemägi Anti 
Published: February 2015

AbstractMassively parallel sequencing a small proportion of the whole genome at high coverage enables answering a wide range of questions from molecular evolution and evolutionary biology to animal and plant breeding and forensics. In this study, we describe the development of restriction‐site associated DNA (RAD) sequencing approach for Ion Torrent PGM platform. Our protocol results in extreme genome complexity reduction using two rare‐cutting restriction enzymes and strict size selection of the library allowing sequencing of a relatively small number of genomic fragments with high sequencing depth. We applied this approach to a common freshwater fish species, the Eurasian perch (Perca fluviatilis L.), and generated over 2.2 MB of novel sequence data consisting of ~17 000 contigs, identified 1259 single nucleotide polymorphisms (SNPs). We also estimated genetic differentiation between the DNA pools from freshwater (Lake Peipus) and brackish water (the Baltic Sea) populations and identified SNPs with the strongest signal of differentiation that could be used for robust individual assignment in the future. This work represents an important step towards developing genomic resources and genetic tools for the Eurasian perch. We expect that our ddRAD sequencing protocol for semiconductor sequencing technology will be useful alternative for currently available RAD protocols.
Opioid treatment at release from jail using extended‐release naltrexone: a pilot proof‐of‐concept randomized effectiveness trial
Authors: Lee Joshua D. , McDonald Ryan , Grossman Ellie , McNeely Jennifer , Laska Eugene , Rotrosen John , Gourevitch Marc N. 
Published: February 2015

AbstractBackground and AimsRelapse to addiction following incarceration is common. We estimated the feasibility and effectiveness of extended‐release naltrexone (XR‐NTX) as relapse prevention among opioid‐dependent male adults leaving a large urban jail.DesignEight‐week, proof‐of‐concept, open‐label, non‐blinded randomized effectiveness trial.SettingNew York City jails and Bellevue Hospital Center Adult Primary Care clinics, USA.ParticipantsFrom January 2010 to July 2013, 34 opioid‐dependent adult males with no stated interest in agonist treatments (methadone, buprenorphine) received a counseling and referral intervention and were randomized to XR‐NTX (n = 17) versus no medication (n = 17) within one week prior to jail release.InterventionXR‐NTX (Vivitrol®; Alkermes Inc.), a long‐acting injectable mu opioid receptor antagonist.MeasuresThe primary intent‐to‐treat outcome was post‐release opioid relapse at week 4, defined as ≥10 days of opioid misuse by self‐report and urine toxicologies. Secondary outcomes were proportion of urine samples negative for opioids and rates of opioid abstinence, intravenous drug use (IVDU), cocaine use, community treatment participation, re‐incarceration and overdose.FindingsAcceptance of XR‐NTX was high; 15 of 17 initiated treatment. Rates of the primary outcome of week 4 opioid relapse were lower among XR‐NTX participants: 38 versus 88% [P<0.004; odds ratio (OR) = 0.08, 95% confidence interval (CI) = 0.01–0.48]; more XR‐NTX urine samples were negative for opioids, 59 versus 29% (P<0.009; OR = 3.5, 95% CI = 1.4–8.5). There were no significant differences in the remaining secondary outcomes, including rates of IVDU, cocaine use, re‐incarceration and overdose.ConclusionExtended‐release naltrexone is associated with significantly lower rates of opioid relapse among men in the United States following release from jail when compared with a no medication treatment‐as‐usual condition.
The Effect of Simvastatin on Infection‐Induced Inflammatory Response of Human Fetal Membranes
Authors: Basraon Sanmaan K. , Costantine Maged M. , Saade George , Menon Ramkumar 
Published: February 2015

ProblemInflammatory cytokines and matrix metalloproteinases (MMPs) contribute to preterm labor pathophysiology. The objective of this study was to test anti‐inflammatory properties of simvastatin in human fetal membranes exposed to lipopolysaccharide (LPS).Method of studyNormal term human fetal membrane explants (n = 11) were allocated to one of the six study groups: control, LPS only (100 ng/mL), simvastatin only (125 ng/mL), simvastatin given 6 hrs prior to LPS (S‐L), simvastatin given 6 hrs post‐LPS (L‐S), and simvastatin and LPS given simultaneously (L+S). Explants were incubated for 24 hrs. Multiplex ELISA for cytokines: IL‐1β, IL‐6, IL‐10, and TNF‐α; soluble cytokine receptors: sIL‐1R2, sIL‐6R, sTNFR1, and R2; MMPs (1, 2, 7, 9, and 10); and tissue inhibitor of metalloproteinase‐2 (TIMP‐2) was performed on tissue culture supernatants. Pairwise comparison between different groups was conducted by least square mean estimates.ResultsCompared with controls, LPS stimulation increased cytokine production and their tissue bioavailability (measured as the molar ratio of cytokine to its soluble receptor), thus confirming membrane immune reactivity (P < 0.01). Pre‐treatment with simvastatin (S‐L) reduced IL‐6 (P = 0.02), TNF‐α (P = 0.02), and MMP‐9 (P = 0.01); post‐treatment (L‐S) reduced IL‐1β (P = 0.02) and TNF‐α (P = 0.04), while simultaneous treatment (L+S) did not reduce any of the cytokines tested. Simvastatin reduced the molar ratio of TNF‐α/sTNFR1 or R2 and IL‐1β/sIL‐1R2 (P = 0.01 and 0.04 in S‐L group; P = 0.01 and 0.004 in L‐S group, respectively). S‐L additionally reduced MMP‐9/TIMP‐2 molar ratio (P = 0.0007).ConclusionsSimvastatin downregulates LPS‐induced inflammatory response and restores homeostasis between pro‐ and anti‐inflammatory processes. Simvastatin may reduce fetal inflammatory response associated with infection‐induced preterm birth.