bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mitochondrial membrane tension governs fission
Authors: Mahecic Dora , Carlini Lina , Kleele Tatjana , Colom Adai , Goujon Antoine , Matile Stefan , Roux Aurélien , Manley Suliana 
Published: January 2018

AbstractDuring mitochondrial fission, key molecular and cellular factors assemble on the outer mitochondrial membrane, where they coordinate to generate constriction. Constriction sites can eventually divide, or reverse upon disassembly of the machinery. However, a role for membrane tension in mitochondrial fission, although speculated, has remained undefined. We captured the dynamics of constricting mitochondria in mammalian cells using live-cell structured illumination microscopy (SIM). By analyzing the diameters of tubules that emerge from mitochondria and implementing a fluorescence lifetime-based mitochondrial membrane tension sensor, we discovered that mitochondria are indeed under tension. Under perturbations that reduce mitochondrial tension, constrictions initiate at the same rate, but are less likely to divide. We propose a model based on our estimates of mitochondrial membrane tension and bending energy in living cells which accounts for the observed probability distribution for mitochondrial constrictions to divide.
Cotranslational folding of a pentarepeat β-helix protein
Authors: Notari Luigi , Martínez-Carranza Markel , Farias-Rico Jose Arcadio , Stenmark Pål , von Heijne Gunnar 
Published: January 2018

AbstractIt is becoming increasingly clear that many proteins start to fold cotranslationally, before the entire polypeptide chain has been synthesized on the ribosome. One class of proteins that a priori would seem particularly prone to cotranslational folding is repeat proteins, i.e., proteins that are built from an array of nearly identical sequence repeats. However, while the folding of repeat proteins has been studied extensively in vitro with purified proteins, only a handful of studies have addressed the issue of cotranslational folding of repeat proteins. Here, we have determined the structure and studied the cotranslational folding of a β-helix pentarepeat protein from the human pathogen Clostridium botulinum – a homolog of the Fluoroquinolone Resistance Protein MfpA – using an assay in which the SecM translational arrest peptide serves as a force sensor to detect folding events. We find that cotranslational folding of a segment corresponding to the first four of the eight β-helix coils in the protein produces enough force to release ribosome stalling, and that folding starts when this unit is ~35 residues away from the P-site, near the distal end of the ribosome exit tunnel. An additional folding transition is seen when the whole PENT moiety emerges from the exit tunnel. The early cotranslational formation of a folded unit may be important to avoid misfolding events in vivo, and may reflect the minimal size of a stable β-helix since it is structurally homologous to the smallest known β-helix protein, a four-coil protein that is stable in solution.
A role for RNA and DNA:RNA hybrids in the modulation of DNA repair by homologous recombination
Authors: D’Alessandro Giuseppina , Adamowicz Marek , Whelan Donna , Howard Sean Michael , Jones-Weinert Corey Winston , Matti Valentina , Rothenberg Eli , Cejka Petr , d’Adda di Fagagna Fabrizio 
Published: January 2018

AbstractDNA double-strand breaks (DSBs) are toxic DNA lesions which, if not properly repaired, may lead to genomic instability, cell death and senescence. Damage-induced long non-coding RNAs (dilncRNAs) are transcribed from broken DNA ends and contribute to DNA damage response (DDR) signaling. Here we show that dilncRNAs play a role in DSB repair by homologous recombination (HR) by contributing to the recruitment of the HR proteins BRCA1, BRCA2, and RAD51, without affecting DNA-end resection. In S/G2-phase cells, dilncRNAs pair to the resected DNA ends and form DNA:RNA hybrids, which are recognized by BRCA1 and promote its recruitment to DSBs. We also show that RNase H2 is in a complex with the HR proteins BRCA1, PALB2, BRCA2, and RAD51, and that it localizes to DSBs in the S/G2 cell-cycle phase. BRCA2 controls DNA:RNA hybrid levels at DSBs by mediating RNase H2 recruitment and, therefore, hybrids degradation. These results demonstrate that regulated DNA:RNA hybrid levels at DSBs contribute to HR-mediated repair.
Determining a reasonable range of relative numerical tolerance values for simulating deterministic models of biochemical reactions
Authors: Yang Ming , Yang Louis Z. 
Published: January 2018

ABSTRACTWhat values of relative numerical tolerance should be chosen in simulation of a deterministic model of a biochemical reaction is unclear, which impairs the modeling effort since the simulation outcomes of a model may depend on the relative numerical tolerance values. In an attempt to provide a guideline to selecting appropriate numerical tolerance values in simulation of in vivo biochemical reactions, reasonable numerical tolerance values were estimated based on the uncertainty principle and assumptions of related cellular parameters. The calculations indicate that relative numerical tolerance values can be reasonably set at or around 10−4 for the concentrations expressed in ng/L. This work also suggests that further reducing relative numerical values may result in erroneous simulation results.
Artefactual formation of pyruvate from in-source conversion of lactate
Authors: Trefely Sophie , Mesaros Clementina , Xu Pening , Doan Mary T. , Jiang Helen , Altinok Oya , Orynbayeva Zulfiya , Snyder Nathaniel W. 
Published: January 2018

AbstractRationaleLactate and pyruvate are high abundance products of glucose metabolism. Analysis of both molecules as part metabolomics studies in cellular metabolism and physiology have been aided by advances in liquid chromatography-mass spectrometry (LC-MS).MethodsWe used ion pairing-chromatography and negative ion mode ESI on an QExactive HF to perform stable isotope assisted metabolomics profiling of lactate and pyruvate metabolism.ResultsUsing an LC-MS method for polar metabolite analysis we discovered an artefactual formation of pyruvate from in-source fragmentation of lactate. Surprisingly, this in-source fragmentation has not been previously described, thus we report this identification to warn other investigators. This artefact was detected by baseline chromatographic resolution of lactate and pyruvate by LC with confirmation of this artefact by stable isotope labeling of lactate and pyruvate.ConclusionsThese findings have immediate implications for metabolomics studies by LC-MS and direct infusion MS, especially in negative ion mode, whereby users should resolve lactate from pyruvate or robustly quantify the potential formation of pyruvate from higher abundance lactate in their assays.
Machine-learning dissection of Human Accelerated Regions in primate neurodevelopment
Authors: Whalen Sean , Inoue Fumitaka , Ryu Hane , Fairr Tyler , Markenscoff-Papadimitriou Eirene , Keough Kathleen , Kircher Martin , Martin Beth , Alvarado Beatriz , Elor Orry , Cintron Dianne Laboy , Williams Alex , Samee Md. Abul Hassan , Thomas Sean , Krencik Robert , Ullian Erik M. , Kriegstein Arnold , Rubenstein John L. , Shendure Jay , Pollen Alex A. , Ahituv Nadav , Pollard Katherine S. 
Published: January 2018

AbstractUsing machine learning (ML), we interrogated the function of all human-chimpanzee variants in 2,645 Human Accelerated Regions (HARs), some of the fastest evolving regions of the human genome. We predicted that 43% of HARs have variants with large opposing effects on chromatin state and 14% on neurodevelopmental enhancer activity. This pattern, consistent with compensatory evolution, was confirmed using massively parallel reporter assays in human and chimpanzee neural progenitor cells. The species-specific enhancer activity of assayed HARs was accurately predicted from the presence and absence of transcription factor footprints in each species. Despite these striking cis effects, activity of a given HAR sequence was nearly identical in human and chimpanzee cells. These findings suggest that HARs did not evolve to compensate for changes in the trans environment but instead altered their ability to bind factors present in both species. Thus, ML prioritized variants with functional effects on human neurodevelopment and revealed an unexpected reason why HARs may have evolved so rapidly.
Knowledge management infrastructures and organizational intelligence in Iranian research centers
Authors: Keshavarz Hamid , Esmaili Givi Mohammad Reza , Shekari Mohammad Reza 
Published: January 2018

Purpose
The purpose of this paper is to explore the possible relationship between knowledge management infrastructures (KMI) and organizational intelligence (OI) in two country-wide research centers dependent to Ministry of Science, Research and Technology, namely, Iranian Research Institute for Information Science and Technology (IRIIST) and Institute for Humanities and Cultural Studies (IHCS).

Design/methodology/approach
The research is a survey in a descriptive manner. Using two validated questionnaires related to KMI and OI, the research was conducted among 175 faculty members and staffs of the two research centers. Using structural equation modeling (SEM) procedures, collected data were then analyzed by software SPSS and partial least squares.

Findings
Factor analysis showed a high factor loading related to the two main variables and all of the items indicated goodness of fit (GoF) related to the questions. The variance-mean ratio between two variables was higher than 0.5 indicating a high convergent validity. R2 for OI showed fitness of SEM. The GoF for IRIIST was 0.642 lower than IHCS with 0.645. Also, path analysis indicated a significant relationship between two variables by 95 percent degree of confidence accepting the two research hypothesis.

Originality/value
By comparison, KMI was more correlated with OI in IHCS than IRIIST. KMI in IRIIST predicted OI by 0.826 percent while in the IHCS by 0.848 percent.
Are electronic theses and dissertations (still) grey literature in the digital age? A FAIR debate
Authors: Schopfel Joachim , Rasuli Behrooz 
Published: January 2018

PurposeWhile distribution channels of theses and dissertations have changed significantly in the digital age, they are generally still considered grey literature. This paper aims to argue the applicability of the concept of grey to electronic theses and dissertations (ETDs).Design/methodology/approachThe paper is presented as a debate between two contradictory opinions on the application of the grey literature concept to ETDs.FindingsThe paper provides a definition of grey literature and then discusses its application to electronic dissertations and theses. In particular, it assesses the aspects of acquisition, quality, access and preservation. Some arguments highlight the “grey nature” of ETDs, such as the limited access via institutional and other repositories. Other arguments (e.g. the development of ETD infrastructures and the quality of ETDs) question this grey approach to ETDs. The paper concludes that “greyness” remains a challenge for ETDs, a problem waiting for solution on the way to open science through the application of the FAIR (findability, accessibility, interoperability reusability) principles.Research limitations implicationsLibrary and information science (LIS) professionals and scientists should be careful about using the concept of grey literature. The debate will help academic librarians and LIS researchers to better understand the nature of grey literature and its coverage, here in the field of ETDs.Originality/valueSome definitions from the print age may not be applicable to the digital age. The contradictory character of the debate helps clarify the similitudes and differences of grey literature and ETDs and highlights the challenge of ETDs, in particular, their accessibility and findability.
Measurement and analysis of collaboration ability
Authors: Zhao Rongying , Wei Xuqiu 
Published: January 2018

Purpose
Collaboration is an important way for scientific research. It attracts a large number of researchers, and forms a series of measurement evaluation indicators. The purpose of this study further enriches the evaluation system of collaboration and provides new indicators to measure collaboration ability at author level in order to identify the most appropriate potential partners.

Design/methodology/approach
The papers published during the period 2006-2015 and collected from Web of Science Core Collection in library and information science (LIS) are regarded as data source. And it defines and measures the collaborative rate, collaborative breadth and collaborative depth at author level.

Findings
The authors’ research shows that collaboration is an important way in the scientific research activities in LIS. Unfortunately, most author’s collaborative breadth and the collaborative depth are lower than mean. Therefore, the author’s scope and stability of collaboration is further strengthened in future. Authors can identify the most appropriate potential partners according to author’s research purpose and the region of the collaborative breadth – the collaborative depth.

Originality/value
It further enriches the evaluation system of collaboration and provides new indicators to evaluate collaboration ability at author level. Authors can identify the most appropriate potential partners according to author’s collaboration ability.
E-readiness assessment of academic libraries: a case study in Iran
Authors: Motahari-Nezhad Hossein , Shekofteh Maryam , Kazerani Maryam 
Published: January 2018

Purpose
The purpose of this study is to assess the e-readiness status of libraries in the Shahid Beheshti University of Medical Sciences in terms of four dimensions – human resources, electronical infrastructure, network services and programs and enhancers of the networked world.

Design/methodology/approach
The study population consists of 11 libraries of the Shahid Beheshti University of Medical Sciences, including the central library and 10 faculty libraries. The data collection instrument is a questionnaire prepared by the researchers that has been designed on the basis of the “e-readiness assessment of Iranian academic libraries model”. Depending on the respondents there are three parts to the questionnaire: questionnaire for managers, staff and information and communication technology (ICT) officials. Their reliability and validity have been proved.

Findings
The libraries of Shahid Beheshti University of Medical Sciences had an average to high status in terms of “human resources” with a score of 2.32, “electronic infrastructure” with a score of 2.48, “network services and programs” with a score of 2.09 and “networked world enhancers” with a score of 2.37 out of 4. In total, these libraries had an average to high status in terms of e-readiness, with a score of 2.29.

Originality/value
The findings of this study can help the library administrators and officials of Shahid Beheshti University of Medical Sciences to plan improvements to the situation of ICT.
Improving flow in the OR
Authors: Blouin-Delisle Charles Hubert , Drolet Renee , Gagnon Serge , Turcotte Stephane , Boutet Sylvie , Coulombe Martin , Daneau Eric 
Published: January 2018

PurposeThe purpose of this paper is to increase efficiency in ORs without affecting quality of care by improving the workflow processes. Administrative processes independent of the surgical act can be challenging and may lead to clinical impacts such as increasing delays. The authors hypothesized that a Lean project could improve efficiency of surgical processes by reducing the length of stays in the recovery ward.Design/methodology/approachTwo similar Lean projects were performed in the surgery departments of two hospitals of the Centre Hospitalier Universitaire de Québec: Hôtel Dieu de Quebec (HDQ) and Hôpital de l'Enfant Jesus (HEJ). The HDQ project designed around a Define, Measure, Analyse, Improve and Control process revision and a Kaizen workshop focused on patients who were hospitalized in a specific care unit after surgery and the HEJ project targeted patients in a post-operative ambulatory context. The recovery ward output delay was measured retrospectively before and after project.FindingsFor the HDQ Lean project, wasted time in the recovery ward was reduced by 62 minutes (68 percent reduction) between the two groups. The authors also observed an increase of about 25 percent of all admissions made in the daytime after the project compared to the time period before the project. For the HEJ Lean project, time passed in the recovery ward was reduced by 6 min (29 percent reduction).Originality/valueThese projects produced an improvement in the flow of the OR without targeting clinical practices in the OR itself. They demonstrated that change in administrative processes can have a great impact on the flow of clinical pathways and highlight the need for comprehensive and precise monitoring of every step of the elective surgery patient trajectory.
Implementation of a multimodal patient safety improvement program “SafetyLEAP” in intensive care units
Authors: Backman Chantal , Hebert Paul C. , Jennings Alison , Neilipovitz David , Choudhri Omar , Iyengar Akshai , Rigal Romain , Forster Alan J. 
Published: January 2018

Purpose
Patient safety remains a top priority in healthcare. Many organizations have developed systems to monitor and prevent harm, and have invested in different approaches to quality improvement. Despite these organizational efforts to better detect adverse events, efficient resolution of safety problems remains a significant challenge. The authors developed and implemented a comprehensive multimodal patient safety improvement program called SafetyLEAP. The term “LEAP” is an acronym that highlights the three facets of the program including: a Leadership and Engagement approach; Audit and feedback; and a Planned improvement intervention. The purpose of this paper is to evaluate the implementation of the SafetyLEAP program in the intensive care units (ICUs) of three large hospitals.

Design/methodology/approach
A comparative case study approach was used to compare and contrast the adherence to each component of the SafetyLEAP program. The study was conducted using a convenience sample of three (n=3) ICUs from two provinces. Two reviewers independently evaluated major adherence metrics of the SafetyLEAP program for their completeness. Analysis was performed for each individual case, and across cases.

Findings
A total of 257 patients were included in the study. Overall, the proportion of the SafetyLEAP tasks completed was 64.47, 100, and 26.32 percent, respectively. ICU nos 1 and 2 were able to identify opportunities for improvement, follow a quality improvement process and demonstrate positive changes in patient safety. The main factors influencing adherence were the engagement of a local champion, competing priorities, and the identification of appropriate resources.

Practical implications
The SafetyLEAP program allowed for the identification of processes that could result in patient harm in the ICUs. However, the success in improving patient safety was dependent on the engagement of the care teams.

Originality/value
The authors developed an evidence-based approach to systematically and prospectively detect, improve, and evaluate actions related to patient safety.
An interdisciplinary approach to improve surgical antimicrobial prophylaxis
Authors: Conaty Oisín , Gaughan Leah , Downey Colum , Carolan Noreen , Brophy Megan Joanne , Kavanagh Ruth , McNamara Deborah A.A. , Smyth Edmond , Burns Karen , Fitzpatrick Fidelma 
Published: January 2018

Purpose
The purpose of this paper is to improve surgical antimicrobial prophylaxis (SAP) prescribing in orthopaedic surgery using the model for improvement framework.

Design/methodology/approach
Orthopaedic patients receiving joint replacements, hip fracture repairs or open-reduction internal-fixation procedures were included. Antimicrobial(s); dose, time of administration and duration of SAP were evaluated for appropriateness based on the local SAP guidelines. After baseline data collection, a driver diagram was constructed with interventions devised for plan-do-study-act cycles. Data were fed back weekly using a point prevalence design (PPD). Interventions included SAP guideline changes, reminders and tools to support key messages.

Findings
SAP in 168 orthopaedic surgeries from 15 June 2016 to 31 January 2017 was studied. Prescribing appropriateness improved from 20 to 78 per cent. Junior doctor changeover necessitated additional education and reminders.

Practical implications
Due to constant staff changeover; continuous data collection, communication, education and reminders are essential to ensure continuous compliance with clinical guidance. Patients with hip fractures are difficult to weigh, requiring weight estimation for weight-based antimicrobial dosing. Unintended consequences of interventions included the necessity to change pre-operative workflow to accommodate reconstitution time of additional antimicrobials and inadvertent continuation of new antimicrobials post-operatively.

Originality/value
Rather than perform the traditional retrospective focused audit, we established a prospective, continuous, interventional quality improvement (QI) project focusing on internal processes within the control of the project team with rapid cyclical changes and interventions. The weekly PPD was pragmatic and enabled the QI project to be sustained with no additional resources.
The NHS Bowel cancer screening programme achieves the anticipated survival improvement, but participation must be improved
Authors: Borowski David W. , Cawkwell Sarah , Zaidi Syed M. Amir , Toward Matthew , Maguire Nicola , Garg Dharmendra K. , Gill Talvinder S. 
Published: January 2018

PurposeThe NHS Bowel cancer screening programme (NHSBCSP) aims to reduce colorectal cancer (CRC) cumulative mortality by up to 23 per cent; long-term outcomes at national level are not yet known. The purpose of this paper is to examine a local population of CRC patients of screening age for their characteristics and long-term survival in relation to their presentation, including through the NHSBCSP.Design/methodology/approachRetrospective analysis of a prospectively maintained CRC database for the years 2009-2014 in a single district hospital providing bowel cancer screening and tertiary rectal cancer services.FindingsOf 528 CRC patients diagnosed in the screening age range, 144(27.3 per cent) presented through NHSBCSP, 308(58.3 per cent) electively with symptoms and 76(14.4 per cent) as emergency. NHSBCSP-diagnosed patients were younger (median 66 vs 68 and 69 years, respectively,p=0.001), had more often left-sided cancers (59(41.0 per cent) vs 82(26.6 per cent) and 24(31.6 per cent), respectively,p=0.001), more UICC-stage I (42(29.2 per cent) vs 49(15.9 per cent) and 2(2.6 per cent)), stage III (59(41.0 per cent) vs 106(34.4 per cent) and 20(26.3 per cent)) and less stage IV disease (8(5.6 per cent) vs 61(19.8 per cent) and 34 (44.7 per cent), respectively,p<0.001). Three-year overall survival was best for NHSBCSP and worst for emergency patients (87.5 per cent vs 69.0 per cent and 35.3 per cent, respectively, LogRankp<0.001).Originality/valuePatients diagnosed within the NHSBCSP have improved outcome compared to both symptomatic elective and emergency presentations. A reduction in overall cumulative mortality in order of 25 per cent may well be achieved, but continuing high levels of emergency presentations and undetected right-sided disease emphasise need for further improvement in public participation in the NHSBCSP and research into more sensitive and acceptable alternative screening methods.