bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cyclo-lib: a database of computational molecular dynamics simulations of cyclodextrins
Authors: Mixcoha Edgar , Rosende Roberto , Garcia-Fandino Rebeca , Piñeiro Ángel 
Published: June 2016

Abstract
Motivation: Cyclodextrins (CDs) are amongst the most versatile/multi-functional molecules used in molecular research and chemical applications. They are natural cyclic oligosaccharides typically employed to encapsulate hydrophobic groups in their central cavity. This allows solubilizing, protecting or reducing the toxicity of a large variety of different molecules including drugs, dyes and surfactant agents. In spite of their great potential, atomic level information of these molecules, which is key for their function, is really scarce. Computational Molecular Dynamics (MD) simulations have the potential to efficiently fill this gap, providing structural-dynamic information at atomic level in time scales ranging from ps to μs.
Results: Cyclo-lib is a database with a publicly accessible web-interface containing structural and dynamic analysis obtained from computational MD simulation trajectories (250 ns long) of native and modified CDs in explicit water molecules. Cyclo-lib currently includes 70 CDs typically employed for fundamental and industrial research. Tools for comparative analysis between different CDs, as well as to restrict the analysis to specific time-segments within the trajectories are also available. Cyclo-lib provides atomic resolution information aimed to complement experimental results performed with the same molecules.
Availability and Implementation: The database is freely available under http://cyclo-lib.mduse.com/ .
Contact: Angel.Pineiro@usc.es
pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC
Authors: Jia Jianhua , Zhang Liuxia , Liu Zi , Xiao Xuan , Chou Kuo-Chen 
Published: June 2016

AbstractMotivation: Sumoylation is a post-translational modification (PTM) process, in which small ubiquitin-related modifier (SUMO) is attaching by covalent bonds to substrate protein. It is critical to many different biological processes such as replicating genome, expressing gene, localizing and stabilizing proteins; unfortunately, it is also involved with many major disorders including Alzheimer’s and Parkinson’s diseases. Therefore, for both basic research and drug development, it is important to identify the sumoylation sites in proteins.Results: To address such a problem, we developed a predictor called pSumo-CD by incorporating the sequence-coupled information into the general pseudo-amino acid composition (PseAAC) and introducing the covariance discriminant (CD) algorithm, in which a bias-adjustment term, which has the function to automatically adjust the errors caused by the bias due to the imbalance of training data, had been incorporated. Rigorous cross-validations indicated that the new predictor remarkably outperformed the existing state-of-the-art prediction method for the same purpose.Availability and implementation: For the convenience of most experimental scientists, a user-friendly web-server for pSumo-CD has been established at http://www.jci-bioinfo.cn/pSumo-CD, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.Contact: jjia@gordonlifescience.org, xxiao@gordonlifescience.org or kcchou@gordonlifescience.orgSupplementary information: Supplementary data are available at Bioinformatics online.
CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets
Authors: Dao David , Fraser Adam N. , Hung Jane , Ljosa Vebjorn , Singh Shantanu , Carpenter Anne E. 
Published: June 2016

Abstract
Summary: CellProfiler Analyst allows the exploration and visualization of image-based data, together with the classification of complex biological phenotypes, via an interactive user interface designed for biologists and data scientists. CellProfiler Analyst 2.0, completely rewritten in Python, builds on these features and adds enhanced supervised machine learning capabilities (Classifier), as well as visualization tools to overview an experiment (Plate Viewer and Image Gallery).
Availability and Implementation: CellProfiler Analyst 2.0 is free and open source, available at http://www.cellprofiler.org and from GitHub (https://github.com/CellProfiler/CellProfiler-Analyst) under the BSD license. It is available as a packaged application for Mac OS X and Microsoft Windows and can be compiled for Linux. We implemented an automatic build process that supports nightly updates and regular release cycles for the software.
Contact: anne@broadinstitute.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Dynastic Politics, International Protestantism and Royal Rebellion: Prince George of Denmark and the Glorious Revolution
Authors: Farguson Julie 
Published: June 2016

Abstract
This article reveals the importance of Prince George of Denmark to James II and William of Orange. It places George in the world of early modern European politics, when foreign policy and international relations were inextricably linked with dynastic politics, and many were concerned about the future well-being of Protestantism. The religious component is crucial as the evidence strongly suggests that George felt he belonged to a ‘Protestant International’, not defined by membership of a particular nation. By drawing attention to the polycentric nature of the Stuart court in the 1680s, the workings of dynastic politics in the international arena that involved secret political manoeuvrings in the run up to the invasion, and then detailing the way in which George behaved following William’s arrival, this article argues that Prince George played a crucial role in the Glorious Revolution. It will also demonstrate that in the 1690s George helped to consolidate and promote the new regime. During the period in question the Prince and Princess of Denmark were a political partnership, and rather than being led by others, they joined forces with William and Mary because they each had a distinct political agenda. George pursued policies he believed would benefit the Stuart–Oldenburg dynasty in England, and its related houses in Europe, and the cause of international Protestantism. A subsidiary theme of this article will be the continuing importance of ceremonies involving royalty to the political culture of urban communities in early modern England.
Organisational Responses to the Abolition of Mandatory Retirement: Case Studies of Australian University Practice
Authors: Blackham Alysia 
Published: June 2016

Abstract
The abolition of the UK default retirement age (DRA) poses particular challenges for universities. However, it is still unclear how UK universities will respond to this change. To investigate these issues, this article considers theoretical perspectives regarding how organisations respond to change, with a particular focus on reflexive law. It then compares this literature with the results of comparative organisational case studies undertaken with six Australian universities in November 2013. Drawing on comparative analysis of labour laws in Australia and the UK, it considers the extent to which these responses may inform the future reactions of UK universities to the abolition of the DRA.
Creating advanced health informatics certification
Authors: Gadd Cynthia S , Williamson Jeffrey J , Steen Elaine B , Fridsma Douglas B 
Published: June 2016

Abstract
In 2005, AMIA leaders and members concluded that certification of advanced health informatics professionals would offer value to individual practitioners, organizations that hire them, and society at large. AMIA’s work to create advanced informatics certification began by leading a successful effort to create the clinical informatics subspecialty for American Board of Medical Specialties board-certified physicians. Since 2012, AMIA has been working to establish advanced health informatics certification (AHIC) for all health informatics practitioners regardless of their primary discipline. In November 2015, AMIA completed the first of 3 key tasks required to establish AHIC, with the AMIA Board of Directors’ endorsement of proposed eligibility requirements. This AMIA Board white paper describes efforts to establish AHIC, reports on the current status of AHIC components, and provides a context for the proposed AHIC eligibility requirements.
Differences in Impact of Definitional Elements on Mortality Precludes International Comparisons of Sepsis Epidemiology—A Cohort Study Illustrating the Need for Standardized Reporting*
Authors: Shankar-Hari Manu , Harrison David A. , Rowan Kathryn M. 
Published: June 2016

Objectives:
Sepsis generates significant global acute illness burden. The international variations in sepsis epidemiology (illness burden) have implications for region specific health policy. We hypothesised that there have been changes over time in the sepsis definitional elements (infection and organ dysfunction), and these may have impacted on hospital mortality.

Design:
Cohort study.

Setting:
We evaluated a high quality, nationally representative, clinical ICU database including data from 181 adult ICUs in England.

Patients:
Nine hundred sixty-seven thousand five hundred thirty-two consecutive adult ICU admissions from January 2000 to December 2012.

Interventions:
None.

Measurements and Main Results:
To address the proposed hypothesis, we evaluated a high quality, nationally representative, clinical, ICU database of 967,532 consecutive admissions to 181 adult ICUs in England, from January 2000 to December 2012, to identify sepsis cases in a robust and reproducible way. Multinomial logistic regression was used to report unadjusted trends in sepsis definitional elements and in mortality risk categories based on organ dysfunction combinations. We generated logistic regression models and assessed statistical interactions with acute hospital mortality as outcome and cohort characteristics, sepsis definitional elements, and mortality risk categories as covariates. Finally, we calculated postestimation statistics to illustrate the magnitude of clinically meaningful improvements in sepsis outcomes over the study period. Over the study period, there were 248,864 sepsis admissions (25.7%). Sepsis mortality varied by infection sources (19.1% for genitourinary to 43.0% for respiratory; p < 0.001), by number of organ dysfunctions (18.5% for 1 to 69.9% for 5; p < 0.001), and organ dysfunction combinations (18.5% for risk category 1 to 58.0% for risk category 4). The rate of improvement in adjusted hospital mortality was significant (odds ratio, 0.939 [0.934–0.945] per year; p < 0.001), but showed different secular trends in improvement between infection sources.

Conclusions:
Within a sepsis cohort, we illustrate case-mix heterogeneity using definitional elements (infection source and organ dysfunction). In the context of improving outcomes, we illustrate differential secular trends in impact of these variables on adjusted mortality and propose this as a valid reason for international variations in sepsis epidemiology. Our article highlights the need to determine standardized reporting elements for optimal comparisons of international sepsis epidemiology.
Hospital safety climate and safety behavior: A social exchange perspective
Authors: Ancarani Alessandro , Di Mauro Carmela , Giammanco Maria D. 
Published: June 2016

Background:Safety climate is considered beneficial to the improvement of hospital safety outcomes. Nevertheless, the relations between two of its key constituents, namely those stemming from leader–subordinate relations and coworker support for safety, are still to be fully ascertained.Purpose:This article uses the theoretical lens of Social Exchange Theory to study the joint impact of leader–member exchange in the safety sphere and coworker support for safety on safety-related behavior at the hospital ward level. Social exchange constructs are further related to the existence of a shame-/blame-free environment, seen as a potential antecedent of safety behavior.Research Design:A cross-sectional study including 166 inpatients in hospital wards belonging to 10 public hospitals in Italy was undertaken to test the hypotheses developed.Methodology:Hypothesized relations have been analyzed through a fully mediated multilevel structural equation model. This methodology allows studying behavior at the individual level, while keeping into account the heterogeneity among hospital specialties.Findings:Results suggest that the linkage between leader support for safety and individual safety behavior is mediated by coworker support on safety issues and by the creation of a shame-free environment.Practical Implications:These findings call for the creation of a safety climate in which managerial efforts should be directed not only to the provision of new safety resources and the enforcement of safety rules but also to the encouragement of teamwork and freedom to report errors as ways to foster the capacity of the staff to communicate, share, and learn from each other.
MRI features of testicular spermatic granuloma
Authors: Huang Mengyue , Gao Xuemei , Cheng Jingliang , Han Jing , Liu Jingjing 
Published: June 2016

Abstract

Rationale:
A spermatic granuloma is a nonbacterial granulomatous disease that is clinically rare. To the best of our knowledge, there are no reports on the magnetic resonance imaging (MRI) features of a spermatic granuloma.

Patient concerns:
A 64-year-old man presented with a mass in the left testicular region for over 2 months, with a hard texture and without tenderness, redness, swelling, heat, or pain. The patient had no low-grade fever, lack of strength, lumbago, dysuria, or a history of trauma.

Diagnosis:
On MRI, the volume of the left testis and epididymis increased, and the lesion of the left testis showed slight hyperintensity on T1 weighted imaging and hypointensity on T2-weighted imaging (T2WI). Scattered small patchy higher signal could be observed in the lesions on T2WI, and the lesion showed hypointensity on diffusion-weighted imaging, with testicular hydrocele on both sides. After the contrast medium was injected, the lesion showed persistent enhancement, and the time signal intensity curve was of the “plateau type” on MR dynamic enhancement. The MRI diagnosis was a testicular tumor. The lesion was pathologically confirmed to be a spermatic granuloma.

Interventions:
The patient underwent left orchiectomy and epididymal resection.

Outcomes:
The testicular and epididymal lesions showed no recurrent, in 9 years follow-up time period.

Lessons:
Testicular sperm granuloma is a diffuse lesion with an increased volume in the testis and epididymis. Slight hyperintensity on T1 weighted imaging, hypointensity with spotted hyperintensity on T2WI, hypointensity on diffusion-weighted imaging, and persistent enhancement can be considered in the differential diagnosis.
Strategies for Postoperative Seroma Prevention: A Systematic Review
Authors: Janis Jeffrey E. , Khansa Lara , Khansa Ibrahim 
Published: June 2016

Background:
There is conflicting evidence on the effectiveness of the various strategies to prevent postoperative seroma. Many high-quality studies have been performed to evaluate those strategies, but the numbers of patients included in those studies have been small. The authors’ goal was to perform a systematic review of all Level I and II studies on the prevention of postoperative seroma.

Methods:
A PubMed search was performed of all Level I and II studies that evaluated strategies for the prevention of postoperative seroma. Only English-language comparative studies on humans, defining seroma as a postoperative serous fluid collection detectable on physical examination, were included. Data from all the studies were compiled, and a systematic review was performed to evaluate the effectiveness of each strategy.

Results:
Seventy-five studies comprising 7173 patients were included. Effective strategies for seroma prevention included the use of closed-suction drains; keeping the drains until their output volume was minimal; maintaining a high pressure gradient in the drains; using sharp or ultrasonic dissection rather than cautery; dissecting the abdomen in a place superficial to the Scarpa fascia; ligating blood vessels with sutures or clips; using quilting or progressive tension sutures; using fibrin, thrombin, or talc; and immobilizing the surgical site postoperatively. Surgical-site compression did not prevent seroma accumulation. The use of sclerosants at the initial operation actually increased the risk of seroma.

Conclusions:
Seroma is a common and frustrating complication in plastic surgery. This study demonstrates that simple strategies can be used to lower the risk of seroma.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, II.
Prospective and Bidirectional Cross-Sectional Associations between Body Mass Index and Physical Activity following Liposuction: A Cohort Study
Authors: Valente Denis Souto , Padoin Alexandre Vontobel , Carvalho Lauro Aita , Pereira Filho Gustavo de Azambuja , Ribeiro Vinicius Weissheimer , Zanella Rafaela Koehler 
Published: June 2016

Background:
It has been speculated that the immediate decrease in body fat following liposuction may affect body composition by feedback mechanisms of body fat regain. Physical activity has both short- and long-term impacts on health. Although the lay public often associates higher levels of physical activity with body fat distribution changes, studies on the association between physical activity and body fat distribution present inconsistent results. The aim of this study was to investigate the cross-sectional and prospective associations between physical activity and body mass index following liposuction.

Methods:
This is a prospective, bidirectional, cross-sectional study, including 526 liposuction patients, who were followed up at a mean of 11.7 and 24.3 months after surgery.

Results:
The sum of skinfolds at 11.7 months was highly correlated with skinfolds at 24.3 months (rho = 0.74, p < 0.001). More than 85 percent of participants remained in the same quintile or changed by not more than one quintile during the 13.6-month period. Tracking of physical activity was considerably lower but still significant; the correlation was 0.24 (p < 0.001), and 61.4 percent of the patients moved one or less quintiles. In fully adjusted models, no significant cross-sectional or longitudinal associations were found between physical activity and body mass index.

Conclusions:
The authors provide evidence of tracking of physical activity and particularly body mass index following liposuction. The authors’ results do not support the hypothesis that physical activity and fatness are strongly related following liposuction.
The American Association of Plastic Surgeons Recent History, with a Review of the Past
Authors: Lawrence W. Thomas 
Published: June 2016

Summary:
The American Association of Plastic Surgeons was founded in 1921 and is the oldest of the plastic surgery societies. It was born out of the enthusiasm of reconstructive surgeons who had recently increased in numbers and expanded the scope of their activities as a result of the challenges posed by battle-injured soldiers during World War I. Early meetings were small, focused exclusively on the head and neck, and often included live surgical demonstrations. The Association has grown in size and scope with time, but it has maintained its academic focus. This article focuses on the most recent 15 years of the Association’s history, as prior publications have chronicled the history of the organization up to 2000. The organization has remained robust in the new millennium, with the national meetings being its most prominent activity. The format of the meetings has continually been improved to remain relevant and of interest to the membership and other attendees. The organization continues to support the development of young academic plastic surgeons through the Academic Scholars Program. It has established new programs such as the Constable Fellowship to support international exchange and has also sponsored two consensus conferences to help define standards of care in plastic surgery–related issues. The Association annually recognizes significant contributors to the field through the variety of awards that it bestows as well. The mission of the American Association of Plastic Surgeons is to provide scholarly leadership in plastic surgery, and the organization continues to successfully accomplish this mission.
An Analysis of the Decisions Made for Contralateral Prophylactic Mastectomy and Breast Reconstruction
Authors: Buchanan Patrick J. , Abdulghani Mariam , Waljee Jennifer F. , Kozlow Jeffrey H. , Sabel Michael S. , Newman Lisa A. , Chung Kevin C. , Momoh Adeyiza O. 
Published: June 2016

Background:
Little is known about the role breast reconstruction plays in decisions made for contralateral prophylactic mastectomy. This study explores factors critical to patient medical decision-making for contralateral prophylactic mastectomy and reconstruction among women with early stage, unilateral breast cancer.

Methods:
A mixed methods approach was used to gain an understanding of patients’ choices and experiences. Patients with stage 0 to III unilateral breast cancer who underwent reconstruction were recruited, and semistructured interviews were conducted. Patient-reported outcomes were evaluated using the Concerns About Recurrence Scale and the BREAST-Q.

Results:
Thirty patients were enrolled; 13 (43 percent) underwent unilateral mastectomy and 17 (57 percent) underwent contralateral prophylactic mastectomy. Three broad categories emerged from patient interviews: medical decision-making, quality of life after mastectomy, and breast reconstruction expectations. Patients who chose contralateral prophylactic mastectomy made the decision for mastectomy based primarily on worry about recurrence. Quality of life after mastectomy was characterized by relief of worry, especially in patients who chose contralateral prophylactic mastectomy [n = 14 (82.4 percent)]. Patients’ desires for symmetry, although not the primary reason for contralateral prophylactic mastectomy, played a role in supporting decisions made. Levels of worry after treatment were similar in both groups (72.7 percent). Patients with contralateral prophylactic mastectomy had higher mean scores for satisfaction with breast (82.4 versus 70.6) and satisfaction with outcome (89.9 versus 75.2).

Conclusions:
The choice for contralateral prophylactic mastectomy is greatly influenced by fear of recurrence, with desires for symmetry playing a secondary role in decisions made.