bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sample Size Estimation for On-Site Creel Surveys
Authors: McCormick Joshua L. , Meyer Kevin A. 
Published: August 2017

Abstract
Conducting sample size analysis is important to ensure that sample sizes are adequate to meet objectives for precision but not so large that valuable resources are wasted. When simple survey designs are used, sample size analysis is straightforward. However, creel surveys often follow complex designs that can make sample size estimation difficult. The objectives of this study were to provide sample size estimators for commonly used creel survey designs and investigate sample size requirements to achieve varying levels of precision. For estimates of angling effort, the average sample size among fisheries required to achieve relative 95% confidence intervals of 40% (i.e., coefficient of variation of approximately 0.2) was 16 d (range = 7–40 d). To estimate mean catch rate with the same level of precision, 43 survey days (range = 8–95 d) were required when the daily catch rate estimator was used, and 11 d (range = 3–30 d) were required when the multi-day estimator was used. Fifty-five days (range = 14–89 d) and 57 d (range = 19–140 d) were required to estimate total catch with relative 95% confidence intervals of 40% when the daily and multi-day estimators were used, respectively. Although absolute precision will vary among fisheries, our results suggest that approximately 30 d of surveying may serve as a reasonable starting point for planning creel surveys when no prior information is available on expected sample variance, as relatively large increases in sample size beyond 30 d were needed to achieve relatively small increases in precision.
Received February 14, 2017; accepted June 9, 2017 Published online August 4, 2017
Do advanced glycation end-products cause food allergy?
Authors: Smith Peter K. 
Published: August 2017

Purpose of review
The aim of this study was to appraise the evidence relating to dietary advanced glycation end-products (AGEs), their influence on innate and adaptive immune responses and their possible role in the increasing rate of food allergy that is being observed globally.

Recent findings
The western pattern of diet is high in both AGEs and their substrates and this has been increasing in the last 30 years. AGEs mimic alarmins such as S100 proteins and the high molecular group box 1 (HMBG1), binding to the Receptor for Advanced Glycation End Products (RAGE), which in turn influences innate and adaptive immune responses. AGEs can directly cause mast cell activation and degranulation. Population data from USA and Australia have correlates with the rise in food allergy and sources of AGEs in the diet and this is also reinforced by urban and regional data within countries. The function of the RAGE receptor is inter-twined with Toll-like receptor (TLR) signalling and vitamin D levels. Activation of the RAGE receptor results in loss of epithelial integrity. Animal models studies have shown that dietary compounds that reduce the formation of AGEs can protect from the development of food allergies; however, this has not been shown in humans.

Summary
Dietary sources of AGEs and their substrates are a plausible contributor to the increasing prevalence of food allergy, which requires prospective evaluation in human populations.
Examining the impact of succession management practices on organizational performance: A national study of U.S. hospitals
Authors: Groves Kevin S. 
Published: August 2017

Background:
Spearheaded by the industry's transition from volume- to value-based care, the health care reform movement has spurred both unprecedented challenges and opportunities for developing more effective and sustainable health care delivery organizations. Whereas the formidable challenges of leading hospitals and health systems have been widely discussed, including reimbursement degradation, the rapidly aging workforce, and the imminent wave of executive retirements, the opportunity to leverage succession management and talent development capabilities to overcome these challenges has been largely overlooked.

Purpose:
To address this key research and practice need, this multiphase study develops and validates an assessment of succession management practices for health care organizations.

Methodology:
Utilizing data collected from two national samples of hospital organizations, the results provide a 32-item succession management assessment comprising seven distinct sets of succession management practices.

Results:
The results indicate that succession management practices are strongly associated with multiple hospital performance metrics, including patient satisfaction and Medicare Spending per Beneficiary, leadership bench strength, and internal/external placement rate for executive level positions.

Practice Implications:
The author concludes this article with a discussion of several practical implications for health care executives and boards, including employing the succession management assessment for diagnosing development opportunities, benchmarking succession planning and talent development practices against similar hospitals or health systems, and elevating the profile of succession management as a strategic priority in today's increasingly uncertain health care landscape.
Hospital Readmission From the Perspective of Medicaid and Uninsured Patients
Authors: Misky Gregory J. , Burke Robert E. , Johnson Teresa , del Pino Jones Amira , Hanson Janice L. , Reid Mark B. 
Published: August 2017

Background:
Patients with little or no health insurance are frequently readmitted to the hospital, yet few previous studies have listened to patients' explanations of why they returned to the hospital after discharge. Enhanced understanding of patient perspectives may facilitate targeted services and improve care.

Methods:
We enrolled 18 patients with Medicaid or no insurance during a hospital readmission within 30 days in a major metropolitan area, and conducted semi-structured qualitative interviews to explore the impact of patients' experiences around readmission using a grounded theory approach.

Results:
We identified five themes contributing to readmission: (1) therapeutic misalignment; (2) accountability; (3) social fragility; (4) access failures; and (5) disease behavior. Medical conditions were complicated by social influences and insufficiently addressed by our health system. Patients understood the need to manage their own health but were unable to effectively execute care plans because of competing life demands and compromised relationships with health providers.

Conclusions:
Our study using interviews of readmitted Medicaid and uninsured patients revealed complex illnesses complicated by social instability and health system failures. Improved patient-provider trust and shared decision-making, while addressing social determinants and expanding care coordination with community partners, provide opportunity to better meet patients' needs and decrease hospital readmission in high-risk patients.
Norepinephrine Contributes to Enterocyte Damage in Septic Shock Patients: A Prospective Cohort Study
Authors: Habes Quirine L.M. , van Ede Lisa , Gerretsen Jelle , Kox Matthijs , Pickkers Peter 
Published: August 2017

ABSTRACT

Objectives:
In septic patients, both systemic inflammation and splanchnic hypoperfusion may cause enterocyte damage. Catecholamines may exert additional detrimental effects on mesenteric blood flow in these patients, and thereby contribute to this damage. Enterocyte damage itself results in impairment of gut barrier function and consequent translocation of bacteria/toxins. This may contribute to multiple organ failure and death by sustaining or amplifying the systemic inflammatory response. The aim of the study was 2-fold: to investigate which factors contribute to enterocyte damage in septic patients, and to assess whether enterocyte damage is associated with a sustained or amplified systemic inflammatory response.

Methods:
In this prospective observational cohort study in 129 patients with septic shock admitted to the ICU, we serially measured plasma levels of Intestinal Fatty Acid-Binding Protein (I-FABP, a marker for enterocyte damage) and of cytokines Tumor Necrosis Factor (TNF)-α, Interferon (IFN)-y, Interleukin (IL)-1β, IL-6, IL-8, IL-1 Receptor Antagonist (RA), and IL-10. Clinical data were collected from electronic patient files.

Results:
A total of 129 patients were included in the study. The median age of the patients was 67 years [56–74]. The median norepinephrine infusion rate was 0.2 μg/kg/min [0.1–0.5]. Overall, 28-day mortality was 31 (24%). Similar to previous work, I-FABP levels at admission were independently associated with mortality (odds ratio 3.101 [1.138–8.448]). Acute Physiology and Chronic Health Evaluation II score and an increase in norepinephrine infusion rate between days 1 and 3 were independently associated with area under curve I-FABP levels, whereas mean arterial pressure and creatinine levels were not. No correlations were found between any of the measured cytokines and plasma I-FABP levels. Furthermore, high I-FABP levels were not related with the subsequent course of cytokine levels.

Conclusions:
In patients with septic shock, norepinephrine use is associated with more enterocyte damage. Although enterocyte damage is associated with increased 28-day mortality, it is not associated with a sustained or amplified systemic inflammatory response.
Intestinal and Limb Ischemic Preconditioning Provides a Combined Protective Effect in the Late Phase, But not in the Early Phase, Against Intestinal Injury Induced by Intestinal Ischemia–Reperfusion in Rats
Authors: Yang Bo , Chen Ye , Long Yan-Hong , Fan Xin , Liu Ke-Xuan , Wang Xiao-Bin , Zhou Jun 
Published: August 2017

ABSTRACTIntestinal ischemia/reperfusion (I/R) injury is associated with high morbidity and mortality. This study aimed to compare the protective efficacy of intestinal ischemic preconditioning (IIPC) and limb ischemic preconditioning (LIPC) against intestinal I/R injury and investigate their combined protective effect and the underlying mechanism. Male Sprague–Dawley rats were pretreated with IIPC, LIPC, or IIPC plus LIPC (combined), and intestinal I/R or sham operation was performed. The animals were sacrificed at 2 and 24 h after reperfusion and then blood and tissue samples were harvested for further analyses. In additional groups of animals, a 7-day survival study was conducted. The results showed that ischemic preconditioning (IPC) improved the survival rate and attenuated intestinal edema, injury, and apoptosis. IPC decreased the levels of tumor necrosis factor-α, interleukin -6, malondialdehyde and myeloperoxidase, and increased the activity of superoxide dismutase in serum and intestine after the I/R event. IPC downregulated the expression of Toll-like receptor-4 (TLR4) and nuclear factor-kappa B (NF-κB). The effect of combined pretreatment was better than that of single pretreatment in the late phase (24 h), but not in the early phase (2 h). The study demonstrated that IPC could significantly attenuate intestinal injury induced by intestinal I/R via inhibiting inflammation, oxidative stress, and apoptosis. IIPC and LIPC conferred no synergy in protecting I/R-induced intestinal injury in the early phase, but combined preconditioning had clearly stronger protection in the late phase, which was associated with the inhibition of the activated TLR4/NF-κB signaling pathway. It suggested that LIPC or combined preconditioning could potentially be applied in the clinical settings of surgical patient care.
A Model for Genome-First Care: Returning Secondary Genomic Findings to Participants and Their Healthcare Providers in a Large Research Cohort
Authors: Schwartz Marci L. B. , McCormick Cara Zayac , Lazzeri Amanda L. , Lindbuchler D’Andra M. , Hallquist Miranda L. G. , Manickam Kandamurugu , Buchanan Adam H. , Rahm Alanna Kulchak , Giovanni Monica A. , Frisbie Lauren , Flansburg Carroll N. , Davis F. Daniel , Sturm Amy C. , Nicastro Christine , Lebo Matthew S. , Mason-Suares Heather , Mahanta Lisa Marie , Carey David J. , Williams Janet L. , Williams Marc S. , Ledbetter David H. , Faucett W. Andrew , Murray Michael F. 
Published: August 2017

ABSTRACTBackgroundResearch cohorts with linked genomic data exist, or are being developed, at many research centers. Within any such “sequenced cohort” of more than 100 participants, it is likely that there are participants with previously undisclosed risk for life-threatening monogenic diseases that could be identified with targeted analysis of their existing data. Identification of such disease-associated findings are not usually primary to the enrollment research goals. At Geisinger Health System, MyCode®Community Health Initiative (MyCode) participants represent one such large sequenced cohort. Since 2013, MyCode participants in discovery research have been consented for secondary analysis of their existing research genomic sequences to allow delivery of medically actionable findings to them and their healthcare providers. This return of genomic results program was developed to manage an anticipated 3.5% of MyCode participants who will receive clinically confirmed genomic variants from an approved gene list out of more than 150,000 total participants. Risk-associated DNA sequences alone without any clinical parameter, prompt “genome-first” follow-up encounters.MethodsThis article describes our process for generating clinical grade results from research-based genomic sequencing data, delivering results to patients and their providers, facilitating targeted clinical evaluations of patients and promoting cascade testing of at-risk relatives. We also summarize our early data about the results generated during this process and our ability to contact patients and their providers to disclose the information.ResultsThis process has been used to generate 343 results on 339 patients. 93% of patients with a result have been successfully contacted about their results as evidenced by direct interaction about their result with the research team or a healthcare provider. 222 healthcare providers have been notified of a result on one or more patient through this result delivery process.ConclusionsHere we describe the existing GHS model to deliver genomic data into the electronic medical record and the clinical interactions that are prompted and supported. Elements of this genome-first care model can be applied in other healthcare settings and in national efforts, such as “All of Us”, that wish to establish programs for returning genomic results to research participants.
Kinesin-6 KIF20B is required for efficient cytokinetic furrowing and timely abscission in human cells
Authors: Janisch Kerstin M. , McNeely Katrina C. , Dardick Joseph M. , Lim Samuel H. , Dwyer Noelle D. 
Published: August 2017

ABSTRACTCytokinesis requires the cooperation of many cytoskeletal and membrane regulators. Most of the major players required for cytokinesis are known, but the temporal regulation and adaptations for different cell types are less understood. KIF20B (previously called MPHOSPH1 or MPP1) is a member of the Kinesin-6 family, which also includes the better-known members KIF23/MKLP1 and KIF20A/MKLP2. Previously, we showed that mouse Kif20b is involved in cerebral cortex growth and midbody organization of neural stem cells. Here we show that KIF20B has a cell-autonomous role in cytokinesis in isolated human cells. It localizes to microtubules of the central spindle and midbody throughout cytokinesis, at sites distinct from the other Kinesin-6 family members. KIF20B is not required for central spindle or midbody assembly, but affects midbody shape and late maturation steps. KIF20B appears to temporally regulate both furrow ingression and abscission.
A quantitative chemotherapy genetic interaction map reveals new factors associated with PARP inhibitor resistance
Authors: Hu Hsien-Ming , Zhao Xin , Kaushik Swati , Robillard Lilliane , Barthelet Antoine , Lin Kevin K. , Simmons Andy D. , Raponi Mitch , Harding Thomas C. , Bandyopadhyay Sourav 
Published: August 2017

SUMMARYNearly every cancer patient is treated with chemotherapy yet our understanding of factors that dictate response and resistance to such agents remains limited. We report the generation of a quantitative chemical-genetic interaction map in human mammary epithelial cells that charts the impact of knockdown of 625 cancer and DNA repair related genes on sensitivity to 29 drugs, covering all classes of cancer chemotherapeutics. This quantitative map is predictive of interactions maintained in cancer cell lines and can be used to identify new cancer-associated DNA repair factors, predict cancer cell line responses to therapy and prioritize drug combinations. We identify thatGPBP1loss in breast and ovarian cancer confers resistance to cisplatin and PARP inhibitors through the regulation of genes involved in homologous recombination. This map may help navigate patient genomic data and optimize chemotherapeutic regimens by delineating factors involved in the response to specific types of DNA damage.
First Draft Genome Sequence of the Pathogenic FungusLomentospora prolificans(formerlyScedosporium prolificans)
Authors: Luo Ruibang , Zimin Aleksey , Workman Rachael , Fan Yunfan , Pertea Geo , Grossman Nina , Wear Maggie P. , Jia Bei , Miller Heather , Casadevall Arturo , Timp Winston , Zhang Sean X. , Salzberg Steven L. 
Published: August 2017

AbstractHere we describe the sequencing and assembly of the pathogenic fungusLomentospora prolificansusing a combination of short, highly accurate Illumina reads and additional coverage in very long Oxford Nanopore reads. The resulting assembly is highly contiguous, containing a total of 37,630,066 bp with over 98% of the sequence in just 26 scaffolds. Annotation identified 8,656 protein-coding genes. Pulsed-field gel analysis suggests that this organism contains at least 7 and possibly 11 chromosomes, the two longest of which have sizes corresponding closely to the sizes of the longest scaffolds, at 6.6 and 5.7 Mb.
Applying expression profile similarity for discovery of patient-specific functional mutations
Authors: Meng Guofeng 
Published: August 2017

AbstractThe progress of cancer genome sequencing projects yields unprecedented information of mutations for numerous patients. However, the complexity of mutation profiles of patients hinders the further understanding of mechanisms of oncogenesis. One basic question is how to uncover mutations with functional impacts. In this work, we introduce a computational method to predict functional somatic mutations for each of patient by integrating mutation recurrence with similarity of expression profiles of patients. With this method, the functional mutations are determined by checking the mutation enrichment among a group of patients with similar expression profiles. We applied this method to three cancer types and identified the functional mutations. Comparison of the predictions for three cancer types suggested that most of the functional mutations were cancer-type-specific with one exception to p53. By checking prediction results, we found that our method effectively filtered non-functional mutations resulting from large protein sizes. In addition, this methods can also perform functional annotation to each patient to describe their association with signalling pathways or biological processes. In breast cancer, we predicted “cell adhesion” and other mutated gene associated terms to be significantly enriched among patients.
Heritable cognitive and psychopathology factors in youth are predicted by brain fronto-temporal white matter pathway
Authors: Alnæs Dag , Kaufmann Tobias , Doan Nhat Trung , Córdova-Palomera Aldo , Wang Yunpeng , Bettella Francesco , Moberget Torgeir , Andreassen Ole A. , Westlye Lars T. 
Published: August 2017

AbstractA healthy transition from adolescence to adulthood relies on a continuous individual adaptation to a dynamic environment. Here, we employed data driven multivariate approaches to derive both general cognitive and psychopathology factors as well as brain phenotypes in children and adolescents in the publicly available PNC sample. We identified a distinct brain white matter pattern which proved central for prediction of heritable cognition and psychopathology scores, highlighting the importance of fronto-temporal connections for intellectual and mental development.
An improved method for the expression screening of membrane protein-GFP fusions in yeast
Authors: Baldock Darren , Sheldon Judith , Tailor Ravi , Green Katherine , Ray John , Singh Shradha , Brocklehurst Kathryn 
Published: August 2017

AbstractThe expression and purification of membrane proteins is an extremely challenging area of work within Protein Science. Membrane proteins are required for compound screening and structure determination in industry. Here we describe some new and innovative methodology in developing the membrane protein GFP fusion primary expression screening in yeast. This methodology enables the expression of membrane proteins fused to GFP in bothSaccharomyces cerevisiaeandPichia pastorissystems. This capability helps facilitate screening of constructs to establish which are suitable for membrane protein production for compound screening and structure determinationIn terms of the primary screening work, we have developed both agar plate and liquid plate expression methodology in yeast. The two approaches correspond well, but the agar plate method is more rapid and we have shown it to have the advantage of allowing cells to be taken directly into confocal microscopy for immediate cell localisation data. Innovative work to extend the methanol induction time in thePichiaagar plate method established good differentiation from the background. A novel agar plate method was also developed forS.cerevisiaewhich is also presented. These screening methods allow triaging of constructs for either membrane protein preps for biochemical assays or progression to fluorescence size exclusion chromatography; where various detergents can be screened to determine the most appropriate for membrane protein solubilisation, the starting point for purification, crystallisation and structure determination.Membrane targets depicted to demonstrate the improved primary screening methodology are a copper transporter Ctr1p fromS.cerevisiaeand a water transporter Aqp4 from human origin.HighlightsAn improved method for the production of recombinant MP-GFP fusions in yeast is presented using agar plates.An agar plate method for MP-GFP expression screening is described forPichia pastoris, with improved induction methodology by the simple addition of methanol, allowing longer induction times for expression clarity.A new simple rapid agar plate method for MP-GFP expression screening is described forSaccharomyces cerevisiae.Cells can be taken directly from agar plates into confocal microscopy studies for immediate cell localisation data and triaging.Liquid plate based screening methods are also described for both yeasts in comparison, to show there is corresponding data, helping validate the new agar plate methods.