bluuebunny/crossref_metadata_2025_split huggingface dataset:
Encouraging practitioners in infection prevention and control to publish: a cross-sectional survey
Authors: Melone Lynn , Price Lesley , Wilson Jennie 
Published: September 2016

Aim: The aim of this cross-sectional survey was to determine the views of infection prevention and control practitioners (IPCPs) on publishing research. Methods: A convenience sample was obtained by approaching delegates at the 2015 Infection Prevention Society conference and data were captured via a hand-held electronic device. Findings: Of the 79 respondents, most (83%) read the Journal of Infection Prevention ( JIP) and found it useful for informing their practice (72%). However, most (91%) had never published in JIP, and less than half (40%) published elsewhere. The main barrier to publication was not having work suitable for publication (38%). Support (37%), training in writing for publication (10%) and time (9%) were considered to be important facilitators in encouraging respondents to publish. Discussion: Strategies that support IPCPs in developing their writing skills may encourage more IPCPs to disseminate evidence to support best practice by publishing their work in peer-reviewed journals.
Use of an Integrated Tool for Interpretation of Blood Glucose Data Improves Correctness of Glycemic Risk Assessment in Individuals With Type 1 and Type 2 Diabetes
Authors: Parkin Christopher G. , Schwenke Stephanie , Ossege Anna Katharina , Gruchmann Torsten 
Published: September 2016

Background: Manufacturers now incorporate blood glucose (bG) value interpretation tools into their monitoring systems; however, usability of these support tools has not been well studied. We evaluated the utility and perceived benefits of support tool use by individuals with type 1 (T1D) and type 2 diabetes (T2D). Methods: This 3-arm, randomized, simulation study assessed the impact of use of bG value interpretation support tools on participants’ ability to correctly interpret bG values, using 1 of 3 tools: a new tool that uses colored scales with target range indicator (TRI), Colors and Smiley icons (already available). Participants assessed 50 bG values without use of any tool and repeated the assessment using 1 of the 3 tool configurations. Changes in percentage of correct responses when using a support tool and user perceptions were assessed. Results: Data sets from 140 participants were analyzed. Increases in correct responses were seen in all study groups but most notably in the TRI group (26%, P < .001) versus the Colors (3%, P = .018) and Smiley icons (6%, P < .001) groups. Significant improvements in confidence were seen among TRI users ( P = .023) but not among other tool users ( P > .627). Most TRI users felt confident (94%), agreed the tool will help them identify high and low values (96%) and will help them to make correct insulin dosage decisions (80%). Conclusions: Use of the TRI significantly increases users’ ability to correctly and confidently determine their glycemic risk when self-monitoring bG levels. This suggests the tool may offer clinical value to individuals with T1D and T2D.
Quantitative Improvements in Hop Test Scores After a 6-Week Neuromuscular Training Program
Authors: Meierbachtol Adam , Rohman Eric , Paur Eric , Bottoms John , Tompkins Marc 
Published: September 2016

Background: In patients who have undergone anterior cruciate ligament reconstruction (ACLR), the effect of neuromuscular re-education (NMR) programs on standard hop tests outcomes, including limb symmetry indices (LSIs), is unknown. Hypothesis: Both legs will show improvement in hop test–measured units after neuromuscular training, but the involved leg will show relatively greater improvement leading to improved limb symmetry. Patients younger than 18 years will show more improvement than patients who are older. Study Design: Retrospective cohort study. Level of Evidence: Level 3. Methods: Patients self-selected their participation in this NMR program, which was completed after traditional outpatient physical therapy. Pre– and post–hop test scores were recorded as the primary outcome measure. Results: Seventy-one patients met the inclusion criteria and completed hop testing. Overall, the involved leg showed significant improvements (pretest/posttest) for single-leg hop (138.30 cm/156.89 cm), triple crossover hop (370.05 cm/423.11 cm), and timed hop (2.21 s/1.99 s). Similarly, on the uninvolved leg, improvements were seen for the single-leg hop (159.30 cm/171.87 cm) and triple crossover hop (427.50 cm/471.27 cm). Overall mean limb symmetry improved across all 4 hop tests, but there was significant improvement only on the single-leg hop (87% pretest to 92% posttest). Patients younger than 18 years showed mean significant LSI improvement on the triple crossover hop. Conclusion: Utilizing an intensive 6-week NMR program after ACLR prior to return to sport can improve quantitative hop test measurements. Patients younger than 18 years had greater improvement than those 18 years and older. Clinical Relevance: Advanced NMR programs can be successfully utilized in the postoperative ACLR setting to improve quantitative limb symmetry.
Evaluation of the potential therapeutic benefits of macrophage reprogramming in multiple myeloma
Authors: Gutiérrez-González Alejandra , Martínez-Moreno Mónica , Samaniego Rafael , Arellano-Sánchez Noemí , Salinas-Muñoz Laura , Relloso Miguel , Valeri Antonio , Martínez-López Joaquín , Corbí Ángel L. , Hidalgo Andrés , García-Pardo Ángeles , Teixidó Joaquín , Sánchez-Mateos Paloma 
Published: September 2016

Key Points
We report strategies to reprogram macrophages as a novel approach to treat MM mouse models using pro-M1 and blocking M2 signals. MIF is upregulated in the bone marrow microenvironment of MM patients and plays an autocrine role in protumoral MØ polarization.
Protein complex detection based on partially shared multi-view clustering
Authors: Ou-Yang Le , Zhang Xiao-Fei , Dai Dao-Qing , Wu Meng-Yun , Zhu Yuan , Liu Zhiyong , Yan Hong 
Published: September 2016

Abstract
Background
Protein complexes are the key molecular entities to perform many essential biological functions. In recent years, high-throughput experimental techniques have generated a large amount of protein interaction data. As a consequence, computational analysis of such data for protein complex detection has received increased attention in the literature. However, most existing works focus on predicting protein complexes from a single type of data, either physical interaction data or co-complex interaction data. These two types of data provide compatible and complementary information, so it is necessary to integrate them to discover the underlying structures and obtain better performance in complex detection.

Results
In this study, we propose a novel multi-view clustering algorithm, called the Partially Shared Multi-View Clustering model (PSMVC), to carry out such an integrated analysis. Unlike traditional multi-view learning algorithms that focus on mining either consistent or complementary information embedded in the multi-view data, PSMVC can jointly explore the shared and specific information inherent in different views. In our experiments, we compare the complexes detected by PSMVC from single data source with those detected from multiple data sources. We observe that jointly analyzing multi-view data benefits the detection of protein complexes. Furthermore, extensive experiment results demonstrate that PSMVC performs much better than 16 state-of-the-art complex detection techniques, including ensemble clustering and data integration techniques.

Conclusions
In this work, we demonstrate that when integrating multiple data sources, using partially shared multi-view clustering model can help to identify protein complexes which are not readily identifiable by conventional single-view-based methods and other integrative analysis methods. All the results and source codes are available on https://github.com/Oyl-CityU/PSMVC.
CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data
Authors: duVerle David A. , Yotsukura Sohiya , Nomura Seitaro , Aburatani Hiroyuki , Tsuda Koji 
Published: September 2016

Abstract
Background
Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality reduction techniques, have been suggested to help infer and visualise the underlying structure of cell populations from single-cell expression levels, yet their models generally lack proper biological grounding and struggle at identifying complex differentiation paths.

Results
Here we introduce cellTree: an R/Bioconductor package that uses a novel statistical approach, based on document analysis techniques, to produce tree structures outlining the hierarchical relationship between single-cell samples, while identifying latent groups of genes that can provide biological insights.

Conclusions
With cellTree, we provide experimentalists with an easy-to-use tool, based on statistically and biologically-sound algorithms, to efficiently explore and visualise single-cell RNA data. The cellTree package is publicly available in the online Bionconductor repository at: http://bioconductor.org/packages/cellTree/.
BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori
Authors: Zhou Qiu-Zhong , Zhang Bindan , Yu Quan-You , Zhang Ze 
Published: September 2016

Abstract
Background
Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rare information about them in the only completely domesticated insect, silkworm (Bombyx mori).

Description
In this study, we systematically scanned lncRNAs using the available silkworm RNA-seq data and public unigenes. Finally, we identified and collected 6281 lncRNAs in the silkworm. Besides, we also collected 1986 microRNAs (miRNAs) from previous studies. Then, we organized them into a comprehensive and web-based database, BmncRNAdb. This database offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA.

Conclusions
We have systematically identified and collected the silkworm lncRNAs and constructed a comprehensive database of the silkworm lncRNAs and miRNAs. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. The BmncRNAdb is freely available at http://gene.cqu.edu.cn/BmncRNAdb/index.php.
Robot development project with human- and eco-friendly smart materials
Authors: Itoh Yoshiaki , Yamazaki Toru , Lim Hun-ok , Takemura Kenichi 
Published: September 2016

Abstract
The social need for robotic technology is rapidly increasing to prepare for the aging society in Japan. Many political action plans concerning Japan’s robot strategy have been proposed and carried out nationwide. This project focused on the social implementation of life support robots and developing corresponding robotic technology. The project’s participants were mainly selected from four laboratories in the department of Mechanical Engineering of Kanagawa University. In addition to robotic technology, there was participation and collaboration in this project from several specialized fields of mechanical engineering, such as material properties, material development, and mechanical vibration. Developing academia–industry–government collaboration was another key project aim. Prior to this project, joint research on dynamics and design concerning mechanical vibration and noise has been undertaken since 2011 by Kanagawa University and Kanagawa Industrial Technology Center. Based on this experience in project-based research, we extended our collaborative research, and the joint research project “Robot development project with human- and eco-friendly smart materials” started in April 2012 and ended in March 2014. In this paper, we report the research activities and results for this collaboration within the regional research community. First, we introduce the project planning. We discuss the relationship between the main theme of robotic technology and the subthemes, determined by the expertise of the members. We considered the safety and reliability of robotic technology in addition to developing materials and robot mechanics. In particular, we decided to pursue participation from fields that do not always engage directly with robotic technology. Second, we outline how we determined the subthemes of the project and we examine the contribution of each subtheme to the results of the main project. Moreover, we discuss our future development work. Finally, as a first step to implementing robotic technology in the regional social system, we report a recognition survey about the practical use and materials of robots that was performed among small and medium-sized enterprises related to robotic technology in the Kanagawa area. Through the survey, we improved the development and direction of the project. Furthermore, the exhibition “Robot Innovation 2012” held in the Tokyo International Exhibition Center communicated our project results to the public.
Everolimus for the Treatment of Advanced Pancreatic Neuroendocrine Tumors: Overall Survival and Circulating Biomarkers From the Randomized, Phase III RADIANT-3 Study
Authors: Yao James C. , Pavel Marianne , Lombard-Bohas Catherine , Van Cutsem Eric , Voi Maurizio , Brandt Ulrike , He Wei , Chen David , Capdevila Jaume , de Vries Elisabeth G.E. , Tomassetti Paola , Hobday Timothy , Pommier Rodney , Öberg Kjell 
Published: September 2016

Purpose Everolimus improved median progression-free survival by 6.4 months in patients with advanced pancreatic neuroendocrine tumors (NET) compared with placebo in the RADIANT-3 study. Here, we present the final overall survival (OS) data and data on the impact of biomarkers on OS from the RADIANT-3 study. Methods Patients with advanced, progressive, low- or intermediate-grade pancreatic NET were randomly assigned to everolimus 10 mg/day (n = 207) or placebo (n = 203). Crossover from placebo to open-label everolimus was allowed on disease progression. Ongoing patients were unblinded after final progression-free survival analysis and could transition to open-label everolimus at the investigator’s discretion (extension phase). OS analysis was performed using a stratified log-rank test in the intent-to-treat population. The baseline levels of chromogranin A, neuron-specific enolase, and multiple soluble angiogenic biomarkers were determined and their impact on OS was explored. Results Of 410 patients who were enrolled between July 2007 and March 2014, 225 received open-label everolimus, including 172 patients (85%) randomly assigned initially to the placebo arm. Median OS was 44.0 months (95% CI, 35.6 to 51.8 months) for those randomly assigned to everolimus and 37.7 months (95% CI, 29.1 to 45.8 months) for those randomly assigned to placebo (hazard ratio, 0.94; 95% CI, 0.73 to 1.20; P = .30). Elevated baseline chromogranin A, neuron-specific enolase, placental growth factor, and soluble vascular endothelial growth factor receptor 1 levels were poor prognostic factors for OS. The most common adverse events included stomatitis, rash, and diarrhea. Conclusion Everolimus was associated with a median OS of 44 months in patients with advanced, progressive pancreatic NET, the longest OS reported in a phase III study for this population. Everolimus was associated with a survival benefit of 6.3 months, although this finding was not statistically significant. Crossover of patients likely confounded the OS results.
Conflicting Interpretation of Genetic Variants and Cancer Risk by Commercial Laboratories as Assessed by the Prospective Registry of Multiplex Testing
Authors: Balmaña Judith , Digiovanni Laura , Gaddam Pragna , Walsh Michael F. , Joseph Vijai , Stadler Zsofia K. , Nathanson Katherine L. , Garber Judy E. , Couch Fergus J. , Offit Kenneth , Robson Mark E. , Domchek Susan M. 
Published: September 2016

Purpose Massively parallel sequencing allows simultaneous testing of multiple genes associated with cancer susceptibility. Guidelines are available for variant classification; however, interpretation of these guidelines by laboratories and providers may differ and lead to conflicting reporting and, potentially, to inappropriate medical management. We describe conflicting variant interpretations between Clinical Laboratory Improvement Amendments–approved commercial clinical laboratories, as reported to the Prospective Registry of Multiplex Testing (PROMPT), an online genetic registry. Methods Clinical data and genetic testing results were gathered from 1,191 individuals tested for inherited cancer susceptibility and self-enrolled in PROMPT between September 2014 and October 2015. Overall, 518 participants (603 genetic variants) had a result interpreted by more than one laboratory, including at least one submitted to ClinVar, and these were used as the final cohort for the current analysis. Results Of the 603 variants, 221 (37%) were classified as a variant of uncertain significance (VUS), 191 (32%) as pathogenic, and 34 (6%) as benign. The interpretation differed among reporting laboratories for 155 (26%). Conflicting interpretations were most frequently reported for CHEK2 and ATM, followed by RAD51C, PALB2, BARD1, NBN, and BRIP1. Among all participants, 56 of 518 (11%) had a variant with conflicting interpretations ranging from pathogenic/likely pathogenic to VUS, a discrepancy that may alter medical management. Conclusions Conflicting interpretation of genetic findings from multiplex panel testing used in clinical practice is frequent and may have implications for medical management decisions.
PANCREOX: A Randomized Phase III Study of Fluorouracil/Leucovorin With or Without Oxaliplatin for Second-Line Advanced Pancreatic Cancer in Patients Who Have Received Gemcitabine-Based Chemotherapy
Authors: Gill Sharlene , Ko Yoo-Joung , Cripps Christine , Beaudoin Annie , Dhesy-Thind Sukhbinder , Zulfiqar Muhammad , Zalewski Pawel , Do Thuan , Cano Pablo , Lam Wendy Yin Han , Dowden Scot , Grassin Helene , Stewart John , Moore Malcolm 
Published: September 2016

Purpose The standard of care for second-line therapy in patients with advanced pancreatic cancer after gemcitabine-based therapy is not clearly defined. The CONKO-003 phase III study reported a survival benefit with second-line fluorouracil (FU) and oxaliplatin using the oxaliplatin, folinic acid, and FU (OFF) regimen. 1 PANCREOX was a phase III multicenter trial to evaluate the benefit of FU and oxaliplatin administered as modified FOLFOX6 (mFOLFOX6; infusional fluorouracil, leucovorin, and oxaliplatin) versus infusional FU/leucovorin (LV) in this setting. Patients and Methods Patients with confirmed advanced pancreatic cancer who were previously treated with gemcitabine therapy and with an Eastern Cooperative Oncology Group performance status of 0-2 were eligible. A total of 108 patients were randomly assigned to receive biweekly mFOLFOX6 or infusional FU/LV until progression. Progression-free survival (PFS) was the primary end point. Results Baseline patient characteristics were similar in both arms. No difference was observed in PFS (median, 3.1 months v 2.9 months; P = .99). Overall survival (OS) was inferior in patients assigned to mFOLFOX6 (median, 6.1 months v 9.9 months; P = .02). Increased toxicity was observed with the addition of oxaliplatin, with grade 3/4 adverse events occurring in 63% of patients who received mFOLFOX6 and 11% of those who received FU/LV. More patients in the mFOLFOX6 arm withdrew from study due to adverse events than in the FU/LV arm (20% v 2%), whereas the use of postprogression therapy was significantly higher in the FU/LV arm (25% v 7%; P = .015). No significant differences were observed in time to deterioration on the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core 30 global health scale. Conclusion No benefit was observed with the addition of oxaliplatin, administered as mFOLFOX6, versus infusional FU/LV in patients with advanced pancreatic cancer previously treated with first-line gemcitabine.
Age-dependent Increases in Adrenal Cytochrome b5 and Serum 5-Androstenediol-3-sulfate
Authors: Rege Juilee , Karashima Shigehiro , Lerario Antonio M. , Smith Joshua M. , Auchus Richard J. , Kasa-Vubu Josephine Z. , Sasano Hironobu , Nakamura Yasuhiro , White Perrin C. , Rainey William E. 
Published: September 2016

Context:Adrenal production of dehydroepiandrosterone sulfate (DHEA-S) increases throughout childhood owing to expansion of the zona reticularis (ZR). ZR features cells with a steroidogenic phenotype distinct from that of the adjacent zona fasciculata, with higher expression of cytochrome b5 type A (CYB5A) and steroid sulfotransferase type 2A1 but decreased 3β-hydroxysteroid dehydrogenase type 2 (HSD3B2). In addition to DHEA-S, three adrenal Δ5-steroid sulfates could provide additional tools to define adrenal maturation.Objective:This study sought to simultaneously measure serum levels of four adrenal Δ5-steroid sulfates, pregnenolone sulfate (Preg-S), 17α-hydroxypregnenolone sulfate (17OHPreg-S), DHEA-S, and 5-androstenediol-3-sulfate (Adiol-S) as a function of age and relate their production to the age-dependent adrenal localization of CYB5A.Participants and Methods:Δ5-steroid sulfates were quantified by liquid chromatography–tandem mass spectrometry in sera from 247 normal children (129 males,118 females) age 1.5–18 y and 42 adults (20 males, 22 females). Immunofluorescence localized HSD3B2 and CYB5A in normal adrenal glands from subjects age 2–35 y. Finally, HAC15 adrenocortical cells were transduced with lentiviral short hairpin RNA to suppress CYB5A expression.Results:Of the Δ5-steroid sulfates quantified, DHEA-S was most abundant. Adiol-S increased in parallel with DHEA-S. Steroid ratios (17OHPreg-S/DHEA-S) suggested increases in 17,20-lyase activity during childhood. Immunofluorescence analysis showed age-related increases in ZR CYB5A immunoreactivity. Furthermore, silencing CYB5A in HAC15 adrenocortical cells significantly reduced DHEA-S and Adiol-S production.Conclusion:Adiol-S shows a similar age-related increase to that of DHEA-S. This likely results from the childhood expansion of CYB5A-expressing ZR, which enhances 17,20-lyase activity and the production of DHEA-S and Adiol-S.