bluuebunny/crossref_metadata_2025_split huggingface dataset:
GWASinlps: non-local prior based iterative SNP selection tool for genome-wide association studies
Authors: Sanyal Nilotpal , Lo Min-Tzu , Kauppi Karolina , Djurovic Srdjan , Andreassen Ole A , Johnson Valen E , Chen Chi-Hua 
Published: June 2018

AbstractMotivationMultiple marker analysis of the genome-wide association study (GWAS) data has gained ample attention in recent years. However, because of the ultra high-dimensionality of GWAS data, such analysis is challenging. Frequently used penalized regression methods often lead to large number of false positives, whereas Bayesian methods are computationally very expensive. Motivated to ameliorate these issues simultaneously, we consider the novel approach of using non-local priors in an iterative variable selection framework.ResultsWe develop a variable selection method, named, iterative non-local prior based selection for GWAS, or GWASinlps, that combines, in an iterative variable selection framework, the computational efficiency of the screen-and-select approach based on some association learning and the parsimonious uncertainty quantification provided by the use of non-local priors. The hallmark of our method is the introduction of ‘structured screen-and-select’ strategy, that considers hierarchical screening, which is not only based on response-predictor associations, but also based on response-response associations and concatenates variable selection within that hierarchy. Extensive simulation studies with single nucleotide polymorphisms having realistic linkage disequilibrium structures demonstrate the advantages of our computationally efficient method compared to several frequentist and Bayesian variable selection methods, in terms of true positive rate, false discovery rate, mean squared error and effect size estimation error. Further, we provide empirical power analysis useful for study design. Finally, a real GWAS data application was considered with human height as phenotype.Availability and implementationAn R-package for implementing the GWASinlps method is available at https://cran.r-project.org/web/packages/GWASinlps/index.html.Supplementary informationSupplementary data are available at Bioinformatics online.
ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts
Authors: Laajala Teemu D , Murtojärvi Mika , Virkki Arho , Aittokallio Tero 
Published: June 2018

Abstract

Motivation
Prognostic models are widely used in clinical decision-making, such as risk stratification and tailoring treatment strategies, with the aim to improve patient outcomes while reducing overall healthcare costs. While prognostic models have been adopted into clinical use, benchmarking their performance has been difficult due to lack of open clinical datasets. The recent DREAM 9.5 Prostate Cancer Challenge carried out an extensive benchmarking of prognostic models for metastatic Castration-Resistant Prostate Cancer (mCRPC), based on multiple cohorts of open clinical trial data.

Results
We make available an open-source implementation of the top-performing model, ePCR, along with an extended toolbox for its further re-use and development, and demonstrate how to best apply the implemented model to real-world data cohorts of advanced prostate cancer patients.

Availability and implementation
The open-source R-package ePCR and its reference documentation are available at the Central R Archive Network (CRAN): https://CRAN.R-project.org/package=ePCR. R-vignette provides step-by-step examples for the ePCR usage.

Supplementary information
Supplementary data are available at Bioinformatics online.
Prediction of kinetics of protein folding with non-redundant contact information
Authors: Censoni Luciano , Martínez Leandro 
Published: June 2018

Abstract

Motivation
The majority of the inter-residue distances in a protein structure are correlated given a fixed topology. Here, we investigate whether we are able to predict a structure’s folding rate, which is known to depend on the complexity of its fold, while considering only a small, uncorrelated fraction of its contacts.

Results
We define an expression for the probabilistic information content associated to the relative position of a pair of amino acid residues in a protein structure. By means of fitting the protein chain to a self-avoiding random walk model, we derive a probability distribution for the distance between residues as a function of their separation along the sequence. We then show that the average information content for all residue pairs in a structure, considered as an estimate of its fold’s complexity, is well correlated to the logarithm of its folding rate. Moreover, the same information content measure may be exploited to rank contacts and identify redundancies, allowing the prediction the structure’s folding rate with similar accuracy while taking into account less than 5% of its contacts.

Availability and implementation
An implementation of the described model and the experimental data are available at http://github.com/luciano-censoni/sarw-lnkf.
Life After Exile: Former Catholic Émigrés and the Legacy of Flight in Marian England
Authors: Smith Frederick E 
Published: June 2018

Abstract
Over the last twenty years, a wealth of studies on early modern exile movements across Europe have emphasised the many problems experienced by émigrés, in particular when justifying their flight in the eyes of their compatriots back home. However, most of these studies see such difficulties coming to an end upon the return of émigrés to their native lands. Homecoming exiles were supposedly treated as quasi-martyrs for the faith and lauded as heroes. Taking as its case-study those English Catholic émigrés from the reigns of Henry VIII and Edward VI who returned home following Mary I’s accession, this article challenges the idea that the difficulties of dislocation ended abruptly upon repatriation. It shows that, while on the face of it they were awarded unparalleled levels of patronage for their sacrifices for the faith, being appointed to positions of power and influence within the Marian Church and state, former émigrés continued to grapple with the baggage of exile status long after they set foot on English soil. In this way, this study not only highlights the need to reconsider some recent assessments of the success of the Marian Counter-Reformation, but, more broadly, it suggests that prevailing narratives regarding the heroic homecomings of early modern exiles may be the legacy of the exiles’ own attempts to mitigate the lingering difficulties of dislocation.
Prayer and Faith: Spiritual Coping among American Indian Women Cancer Survivors
Authors: Roh Soonhee , Burnette Catherine E , Lee Yeon-Shim 
Published: June 2018

Abstract
Although cancer disparities among American Indian (AI) women are alarming, research on spiritual coping among this population is virtually nonexistent. This is particularly problematic, given the importance of medical practitioners’ discussing the topic with cancer patients, along with the centrality of spirituality to many AI patients. The purpose of this article was to explore AI women cancer survivors’ spiritual coping with their experiences. Using a community-based participatory research approach, this qualitative descriptive study included a sample of 43 AI women cancer survivors (n = 14 breast cancer, n = 14 cervical cancer, and n = 15 colon and other types of cancer). Qualitative content analysis revealed that most participants (76 percent, n = 32) cited prayer as an important part of their cancer recovery and coping strategies. Many participants expressed how prayer and spirituality connected them to family, to faith communities, and to others. In addition to prayer, over a third (36 percent, n = 15) of participants emphasized faith as a recovery and coping strategy. Results indicate that most women drew great comfort, strength, hope, and relief from their spiritual and faith traditions, indicating that religious and spiritual practices may be an important protective factor against the strain of the cancer experience.
Feeding plasticity more than metabolic rate drives the productivity of economically important filter feeders in response to elevated CO2 and reduced salinity
Authors: Rastrick Samuel P S , Collier Victoria , Graham Helen , Strohmeier Tore , Whiteley Nia M , Strand Øivind 
Published: June 2018

AbstractClimate change driven alterations in salinity and carbonate chemistry are predicted to have significant implications particularly for northern costal organisms, including the economically important filter feeders Mytilus edulis and Ciona intestinalis. However, despite a growing number of studies investigating the biological effects of multiple environmental stressors, the combined effects of elevated pCO2 and reduced salinity remain comparatively understudied. Changes in metabolic costs associated with homeostasis and feeding/digestion in response to environmental stressors may reallocate energy from growth and reproduction, affecting performance. Although these energetic trade-offs in response to changes in routine metabolic rates have been well demonstrated fewer studies have investigated how these are affected by changes in feeding plasticity. Consequently, the present study investigated the combined effects of 26 days’ exposure to elevated pCO2 (500 µatm and 1000 µatm) and reduced salinity (30, 23, and 16) on the energy available for growth and performance (Scope for Growth) in M. edulis and C. intestinalis, and the role of metabolic rate (oxygen uptake) and feeding plasticity [clearance rate (CR) and absorption efficiency] in this process. In M. edulis exposure to elevated pCO2 resulted in a 50% reduction in Scope for Growth. However, elevated pCO2 had a much greater effect on C. intestinalis, with more than a 70% reduction in Scope for Growth. In M. edulis negative responses to elevated pCO2 are also unlikely be further affected by changes in salinity between 16 and 30. Whereas, under future predicted levels of pCO2C. intestinalis showed 100% mortality at a salinity of 16, and a &gt;90% decrease in Scope for Growth with reduced biomass at a salinity of 23. Importantly, this work demonstrates energy available for production is more dependent on feeding plasticity, i.e. the ability to regulate CR and absorption efficiency, in response to multiple stressors than on more commonly studied changes in metabolic rates.
Dirac Induction for Rational Cherednik Algebras
Authors: Ciubotaru Dan , De Martino Marcelo 
Published: June 2018

AbstractWe introduce the local and global indices of Dirac operators for the rational Cherednik algebra $\mathsf{H}_{t,c}(G,\mathfrak{h})$, where $G$ is a complex reflection group acting on a finite-dimensional vector space $\mathfrak{h}$. We investigate precise relations between the (local) Dirac index of a simple module in the category $\mathcal{O}$ of $\mathsf{H}_{t,c}(G,\mathfrak{h})$, the graded $G$-character of the module, the Euler–Poincaré pairing, and the composition series polynomials for standard modules. In the global theory, we introduce integral-reflection modules for $\mathsf{H}_{t,c}(G,\mathfrak{h})$ constructed from finite-dimensional $G$-modules. We define and compute the index of a Dirac operator on the integral-reflection module and show that the index is, in a sense, independent of the parameter function $c$. The study of the kernel of these global Dirac operators leads naturally to a notion of dualised generalised Dunkl–Opdam operators.
Providers’ assessment of a novel interactive health information technology in a pediatric intensive care unit
Authors: Asan Onur , Holden Richard J , Flynn Kathryn E , Murkowski Kathy , Scanlon Matthew C 
Published: June 2018

AbstractObjectiveTo explore perceptions of critical care providers about a novel collaborative inpatient health information technology (HIT) in a pediatric intensive care unit (PICU) setting.MethodsThis cross-sectional, concurrent mixed methods study was conducted in the PICU of a large midwestern children’s hospital. The technology, the Large Customizable Interactive Monitor (LCIM), is a flat panel touch screen monitor that displays validated patient information from the electronic health record. It does not require a password to login and is available in each patient’s room for viewing and interactive use by physicians, nurses, and families. Quantitative data were collected via self-administered, standardized surveys, and qualitative data via in-person, semistructured interviews between January and April 2015. Data were analyzed using descriptive statistics and inductive thematic analysis.ResultsThe qualitative analysis showed positive impacts of the LCIM on providers’ workflow, team interactions, and interactions with families. Providers reported concerns regarding perceived patient information overload and associated anxiety and burden for families. Sixty percent of providers thought that LCIM was useful for their jobs at different levels, and almost 70% of providers reported that LCIM improved information sharing and communication with families. The average overall satisfaction score was 3.4 on a 0 to 6 scale, between “a moderate amount” and “pretty much.”Discussion and ConclusionThis study provides new insight into collaborative HIT in the inpatient pediatric setting and demonstrates that using such technology has the potential to improve providers’ experiences with families and just-in-time access to EHR information in a format more easily shared with families.
Oral Contraceptive Use and Breast Cancer Risk: Retrospective and Prospective Analyses From a BRCA1 and BRCA2 Mutation Carrier Cohort Study
Authors: Schrijver Lieske H , Olsson Håkan , Phillips Kelly-Anne , Terry Mary Beth , Goldgar David E , Kast Karin , Engel Christoph , Mooij Thea M , Adlard Julian , Barrowdale Daniel , Davidson Rosemarie , Eeles Ros , Ellis Steve , Evans D Gareth , Frost Debra , Izatt Louise , Porteous Mary E , Side Lucy E , Walker Lisa , Berthet Pascaline , Bonadona Valérie , Leroux Dominique , Mouret-Fourme Emmanuelle , Venat-Bouvet Laurence , Buys Saundra S , Southey Melissa C , John Esther M , Chung Wendy K , Daly Mary B , Bane Anita , van Asperen Christi J , Gómez Garcia Encarna B , Mourits Marian J E , van Os Theo A M , Roos-Blom Marie-José , Friedlander Michael L , McLachlan Sue-Anne , Singer Christian F , Tan Yen Y , Foretova Lenka , Navratilova Marie , Gerdes Anne-Marie , Caldes Trinidad , Simard Jacques , Olah Edith , Jakubowska Anna , Arver Brita , Osorio Ana , Noguès Catherine , Andrieu Nadine , Easton Douglas F , van Leeuwen Flora E , Hopper John L , Milne Roger L , Antoniou Antonis C , Rookus Matti A ,   EMBRACE, GENEPSO, BCFR, HEBON, kConFab, and IBCCS
Published: June 2018

Abstract

Background
For BRCA1 and BRCA2 mutation carriers, the association between oral contraceptive preparation (OCP) use and breast cancer (BC) risk is still unclear.

Methods
Breast camcer risk associations were estimated from OCP data on 6030 BRCA1 and 3809 BRCA2 mutation carriers using age-dependent Cox regression, stratified by study and birth cohort. Prospective, left-truncated retrospective and full-cohort retrospective analyses were performed.

Results
For BRCA1 mutation carriers, OCP use was not associated with BC risk in prospective analyses (hazard ratio [HR] = 1.08, 95% confidence interval [CI] = 0.75 to 1.56), but in the left-truncated and full-cohort retrospective analyses, risks were increased by 26% (95% CI = 6% to 51%) and 39% (95% CI = 23% to 58%), respectively. For BRCA2 mutation carriers, OCP use was associated with BC risk in prospective analyses (HR = 1.75, 95% CI = 1.03 to 2.97), but retrospective analyses were inconsistent (left-truncated: HR = 1.06, 95% CI = 0.85 to 1.33; full cohort: HR = 1.52, 95% CI = 1.28 to 1.81). There was evidence of increasing risk with duration of use, especially before the first full-term pregnancy (BRCA1: both retrospective analyses, P < .001 and P = .001, respectively; BRCA2: full retrospective analysis, P = .002).

Conclusions
Prospective analyses did not show that past use of OCP is associated with an increased BC risk for BRCA1 mutation carriers in young middle-aged women (40–50 years). For BRCA2 mutation carriers, a causal association is also not likely at those ages. Findings between retrospective and prospective analyses were inconsistent and could be due to survival bias or a true association for younger women who were underrepresented in the prospective cohort. Given the uncertain safety of long-term OCP use for BRCA1/2 mutation carriers, indications other than contraception should be avoided and nonhormonal contraceptive methods should be discussed.
Glycosuria amount in response to hyperglycaemia and risk for diabetic kidney disease and related events in Type 1 diabetic patients
Authors: Carpentier Charlyne , Dubois Séverine , Mohammedi Kamel , Belhatem Narimène , Bouhanick Béatrice , Rohmer Vincent , Briet Claire , Bumbu Anisoara , Hadjadj Samy , Roussel Ronan , Potier Louis , Velho Gilberto , Marre Michel 
Published: June 2018

AbstractBackgroundHyperglycaemia impairs tubulo-glomerular feedback. We tested whether variable tubulo-glomerular feedback during hyperglycaemia contributes to renal risk heterogeneity seen in Type 1 diabetes.MethodsDuring the period 1990–92, we studied the tubulo-glomerular feedback in Type 1 diabetic patients at high or low renal risk [21 of 54 with glomerular hyperfiltration and/or microalbuminuria against 11 of 55 with normal glomerular filtration rate (GFR) and urinary albumin despite uncontrolled diabetes]. The GFR, effective renal plasma flow, mean arterial pressure and fractional reabsorptions of glucose, osmols, sodium and lithium were measured sequentially during normo- and hyperglycaemia. All patients were followed up until 2016 for incident proteinuria, estimated GFR &lt;60 mL/min/1.73 m2, doubling of serum creatinine, end-stage renal disease or all-cause death.ResultsGlycaemia increased from 6.1 ± 1.3 to 15.1 ± 1.9 mmol/L in both high-risk and low-risk patients. Glycosuria was lower in the high- versus low-risk patients: 0.34 ± 0.25 versus 0.64 ± 0.44 mmol/min (P = 0.03). Both groups displayed similar kidney function during normoglycaemia. Hyperglycaemia increased more importantly GFR and fractional reabsorptions, and pre-glomerular vasodilatation in the high- than in the low-risk patients (all P &lt; 0.05). Over 21 years, 31.5% high- versus 12.7% low-risk patients developed endpoints (adjusted P = 0.006). In a multi-adjusted survival analysis of patients having undergone renal tests, each 0.10 mmol/min glycosuria during hyperglycaemia reduced the outcome risk by 0.72 (95% confidence interval 0.49–0.97, P = 0.03).ConclusionsReduced tubulo-glomerular feedback and glycosuria during hyperglycaemia indicate high renal risk for Type 1 diabetic patients. Inter-individual variability in tubulo-glomerular feedback activity determines renal risk in Type 1 diabetes.
Intraoperative Assessment of Cortical Perfusion After Intracranial-To-Intracranial and Extracranial-To-Intracranial Bypass for Complex Cerebral Aneurysms Using Flow 800
Authors: Rennert Robert C , Strickland Ben A , Ravina Kristine , Bakhsheshian Joshua , Fredrickson Vance , Carey Joseph , Russin Jonathan J 
Published: June 2018

Abstract

BACKGROUND
Revascularization strategies for complex cerebral aneurysms are largely based on subjective interpretation of flow demands, or indirect measures of perfusion in at-risk territories. Indocyanine Green -based flow analyses ((ICG-BFA); Flow 800, Carl Zeiss, Oberkochen, Germany) provide a real-time, semiquantitative measure of intraoperative cortical perfusion during cerebral bypass surgery for complex aneurysms.

OBJECTIVE
To determine the utility of intraoperative ICG-BFA for assessing cortical perfusion in at-risk territories during cerebral bypass for complex aneurysms requiring vessel sacrifice.

METHODS
Retrospective analysis of consecutive patients from a prospective, single-institution open cerebrovascular database.

RESULTS
Intraoperative ICG-BFA confirmed adequate cortical perfusion in 2 patients with fusiform posterior circulation aneurysms, treated with a posterior inferior cerebellar artery (PICA)-PICA and occipital artery (OA)-to-third segment of the posterior cerebral artery (P3) bypass with proximal vessel sacrifice, respectively. ICG-BFA was used in a third patient that underwent clip reconstruction/ intracranial-to-intracranial bypass for a large middle cerebral artery (MCA) bifurcation aneurysm requiring sacrifice of the temporal M2 branch. In this case, a frontal M3 to temporal M3 side-to-side anastomosis was created to arborize the MCA tree and allow filling of both M2 territories through a single M2 branch. After aneurysm reconstruction, ICG-BFA identified an inadvertent occlusion of the frontal M2 that left the entire MCA distribution reliant on collateral flow but did not cause a neuromonitoring change. Repeat ICG-BFA after clip re-arrangement demonstrated aneurysm occlusion and equal flow in both frontal and temporal MCA cortical distributions from the arborization.

CONCLUSION
ICG-BFA is a useful adjunct for intraoperative cortical flow assessment during cerebral revascularization for complex aneurysms requiring vessel sacrifice.
Nanostructure of DNA repair foci revealed by superresolution microscopy
Authors: Sisario Dmitri , Memmel Simon , Doose Sören , Neubauer Julia , Zimmermann Heiko , Flentje Michael , Djuzenova Cholpon S. , Sauer Markus , Sukhorukov Vladimir L. 
Published: June 2018

ABSTRACTInduction of DNA double‐strand breaks (DSBs) by ionizing radiation leads to formation of micrometersized DNA‐repair foci, whose organization on the nanometer‐scale remains unknown because of the diffraction limit (~200 nm) of conventional microscopy. Here, we applied diffraction‐unlimited, direct stochastic optical‐reconstruction microscopy (dSTORM) with a lateral resolution of ~20 nm to analyze the focal nanostructure of the DSB marker histone γH2AX and the DNA‐repair protein kinase (DNA‐PK) in irradiated glioblastoma multiforme cells. Although standard confocal microscopy revealed substantial colocalization of immunostained γH2AX and DNA‐PK, in our dSTORM images, the 2 proteins showed very little (if any) colocalization despite their close spatial proximity. We also found that γH2AX foci consisted of distinct circular subunits (“nanofoci”) with a diameter of ~45 nm, whereas DNA‐PK displayed a diffuse, intrafocal distribution. We conclude that γH2AX nanofoci represent the elementary, structural units of DSB repair foci, that is, individual γH2AX‐containing nucleosomes. dSTORM‐based γH2AX nanofoci counting and distance measurements between nanofoci provided quantitative information on the total amount of chromatin involved in DSB repair as well as on the number and longitudinal distribution of γH2AX‐containing nucleosomes in a chromatin fiber. We thus estimate that a single focus involves between ~0.6 and ~1.1Mbp of chromatin, depending on radiation treatment. Because of their ability to unravel the nanostructure of DSB‐repair foci, dSTORM and related single‐molecule localization nanoscopy methods will likely emerge as powerful tools in biology and medicine to elucidate the effects of DNA damaging agents in cells.—Sisario, D., Memmel, S., Doose, S., Neubauer, J., Zimmermann, H., Flentje, M., Djuzenova, C. S., Sauer, M., Sukhorukov, V. L. Nanostructure of DNA repair foci revealed by superresolution microscopy. FASEB J. 32, 6469–6477 (2018). www.fasebj.org
Identifying and treating traumatic hand and wrist injuries
Authors: Kavin Michelle , Liss Frederic E. 
Published: June 2018

ABSTRACTProper identification and management of traumatic hand and wrist injuries is critical to preventing loss of function, nerve damage, joint instability, persistent pain, and delay in indicated surgery. This article uses case studies to help clinicians make accurate diagnoses and treatment plans. Physical examination findings, radiograph results, and treatment plans are reviewed for four traumatic hand and wrist fractures or dislocations.