bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation
Authors: Shrestha Utsab R. , Juneja Puneet , Zhang Qiu , Gurumoorthy Viswanathan , Borreguero Jose M. , Urban Volker , Cheng Xiaolin , Pingali Sai Venkatesh , Smith Jeremy C. , O’Neill Hugh M. , Petridis Loukas 
Published: September 2019

Significance
A major challenge in biology is characterizing the structural flexibility of intrinsically disordered proteins (IDPs). Ensemble-averaged experimental data do not provide the underlying protein structures. Here, we performed independently small-angle neutron and X-ray scattering experiments and unbiased molecular dynamics simulations to probe the solution structure of an IDP. We report that enhancing the sampling of the simulations can generate an ensemble of IDP structures in quantitative agreement with scattering and NMR, without the need for biasing the simulation or reweighting the results. The demonstration of established simulation technology that produces accurate physical models of flexible biosystems may pave the way to relating conformational flexibility to biological function.
Early detection and monitoring of cerebral ischemia using calcium-responsive MRI probes
Authors: Savić Tanja , Gambino Giuseppe , Bokharaie Vahid S. , Noori Hamid R. , Logothetis Nikos K. , Angelovski Goran 
Published: September 2019

Significance
The duration of cerebral ischemia is a key factor in determining the severity of brain damage and the course of action. Thus, an accurate and timely observation of the ischemic process is highly critical. Here we present a molecular neuroimaging approach that enables direct detection and real-time visualization of transient cerebral ischemia. The method relies on high-resolution observation of extracellular calcium alterations associated with the spatiotemporal dynamics of cerebral ischemia, using a selective molecular MRI probe. The rapid detection of calcium fluctuations in healthy and disease states will not only lead to essential insights for successful treatment and recovery of ischemic brain tissue but will also improve our understanding of the underlying neurobiology of neurological and psychiatric disorders.
Future epidemiological and economic impacts of universal influenza vaccines
Authors: Sah Pratha , Alfaro-Murillo Jorge A. , Fitzpatrick Meagan C. , Neuzil Kathleen M. , Meyers Lauren A. , Singer Burton H. , Galvani Alison P. 
Published: September 2019

Significance
Diminished efficacy of influenza vaccines has fueled research and funding for a broadly protective vaccine. NIAID recently proposed at least 75% efficacy against symptomatic influenza as a key criterion for a universal vaccine. Our analyses demonstrate that universal vaccines with 75% efficacy would be highly impactful in reducing the epidemiological impacts of seasonal influenza at both the national and state levels. Reduced incidence and hospitalizations due to universal vaccine distribution would save $3.5 billion influenza-related direct medical costs per year. This economic benefit surpasses the current and proposed funding of $330 million combined toward the development of a universal influenza vaccine. Our results highlight that benefits of universal vaccine rollout justify the significant investment required for development.
NanoSIMS imaging reveals metabolic stratification within current-producing biofilms
Authors: Chadwick Grayson L. , Jiménez Otero Fernanda , Gralnick Jeffrey A. , Bond Daniel R. , Orphan Victoria J. 
Published: September 2019

Significance
Electricity-producing bacteria are potential power sources, fermentation platforms, and desalination systems, if current densities could be increased. These organisms form conductive biofilms on electrodes, allowing new cell layers to contribute to current production until a limit is reached, but the biological underpinning of this limit is not well-understood. We investigated the limitation behind this phenomenon using stable isotope probing and nanoscale secondary ion mass spectrometry, showing active cells are restricted to layers closest to the electrode. This metabolic observation fundamentally changes our understanding of electron flow and cell growth within current-producing biofilms and provides constraints on the physical structure of natural communities reliant on this process for growth. We predict improvements in biofilm conductivity will yield higher current-producing systems.
Hepatitis C Virus RNA Is Commonly Detectable in Rectal and Nasal Fluids of Patients With High Viremia
Authors: Chromy David , Schmidt Ralf , Mandorfer Mattias , Lang Gerold Felician , Bauer David , Schwabl Philipp , Popow-Kraupp Theresia , Reiberger Thomas , Mayer Florian 
Published: September 2019

AbstractBackgroundIncreasing numbers of hepatitis C virus (HCV) infections among men who have sex with men (MSM) are being observed in the Western world. The actual routes of HCV transmission during high-risk sex practices and associated drug use remain poorly understood.MethodsForty-seven patients with HCV were prospectively enrolled. Rectal and nasal swabs were collected to quantify HCV-RNA levels within rectal and nasal fluids. Contamination by occult rectal bleeding was excluded by guaiac paper test. Risk behavior was assessed by standardized questionnaires.ResultsMedian age was 41.9 years, 89% were HIV positive (+) (42/47) and 85% (40/47) were male, 58% (23/40) of whom were MSM. Acute HCV infection was diagnosed in 32% (15/47) ,with all patients being HIV+MSM and 93% (14/15) having a documented history of sexually transmitted disease. Thirty-three (70%) patients had ≥1 HCV+ swab sample (HCV+SS; 48%, 22/46 rectal; 62%, 29/47 nasal), and contamination with blood was excluded in all patients. Individuals with HCV+SS had significantly higher serum HCV-RNA levels than patients with HCV-negative SS (6.28 [IQR, 0.85] log IU/mL vs 4.08 [2.45] log IU/mL; P &lt; .001). Using ROC-curve analysis, serum HCV-RNA cutoffs for ruling in/out any HCV+SS were established at 6.02 log IU/mL and 4.02 log IU/mL, respectively.ConclusionsHCV-RNA is commonly detectable in rectal and nasal fluids of both HIV+ and HIV-negative HCV patients with high serum HCV-RNA, independently of the suspected route of HCV transmission. Accordingly, high-risk sex practices and sharing of nasal drug-sniffing “tools” might be important HCV transmission routes, especially in patients with high serum HCV-RNA.
A concise python implementation of the lattice Boltzmann method on HPC for geo-fluid flow
Authors: Mora Peter , Morra Gabriele , Yuen David A 
Published: September 2019

SUMMARY
The lattice Boltzmann method (LBM) is a method to simulate fluid dynamics based on modelling distributions of particles moving and colliding on a lattice. The Python scripting language provides a clean programming paradigm to develop codes based on the LBM, however in order to reach performance comparable to compiled languages, it needs to be carefully implemented, maximizing its vectorized tools, mostly integrated in the NumPy module. We present here the details of a Python implementation of a concise LBM code, with the purpose of offering a pedagogical tool for students and professionals in the geosciences who are approaching this technique for the first time. The first half of the paper focuses on how to vectorize a 2-D LBM code and show how if carefully done, this allows performance close to a compiled code. In the second part of the paper, we use the vectorization described earlier to naturally write a parallel implementation using MPI and test both weak and hard scaling up to 1280 cores. One benchmark, Poiseuille flow and two applications, one on sound wave propagation and another on fluid-flow through a simplified model of a rock matrix are finally shown.
Minnowbrook at 50: A Prelude
Authors: Carboni Julia L , Nabatchi Tina 
Published: September 2019

Abstract
This essay introduces the special issue on Minnowbrook at 50, a conference hosted in August 2018 by the Syracuse University Maxwell School of Citizenship and Public Affairs to celebrate the 50th anniversary of Minnowbrook I and honor the legacy of all the Minnowbrook conferences. After a brief discussion about the Minnowbrook conferences and the set-up of Minnowbrook 50, the essay offers short synopses of the seven articles included in this issue.
Margin Trading and Comovement During Crises*
Authors: Kahraman Bige , Tookes Heather 
Published: September 2019

Abstract
We exploit threshold rules governing margin trading eligibility in India to identify a causal link between margin trading and increased comovement during crises. Margin trading explains more than one-quarter of the increase return comovement that we observe during crises. To understand the mechanisms driving this result, we evaluate the relative importance of stock connections through common brokers (who provide margin financing) versus common margin traders. We find that common brokers are most important. Margin-eligible stocks that are more connected through common brokers experience larger crisis-period increases in pairwise return comovement, especially when those brokers’ clients have experienced recent portfolio losses, when their clients have outstanding margin loans in more volatile stocks, and when the brokers are large. These findings are consistent with Brunnermeier and Pedersen (2009), in which initial shocks propagate due to the tightening of margin constraints imposed by financial intermediaries.
Validation of Early Warning Scores at Two Long-Term Acute Care Hospitals
Authors: Churpek Matthew M. , Carey Kyle A. , Dela Merced Nino , Prister James , Brofman John , Edelson Dana P. 
Published: September 2019

Objectives:
Early warning scores were developed to identify high-risk patients on the hospital wards. Research on early warning scores has focused on patients in short-term acute care hospitals, but there are other settings, such as long-term acute care hospitals, where these tools could be useful. However, the accuracy of early warning scores in long-term acute care hospitals is unknown.

Design:
Observational cohort study.

Setting:
Two long-term acute care hospitals in Illinois from January 2002 to September 2017.

Patients:
Admitted adult long-term acute care hospital patients.

Interventions:
None.

Measurements and Main Results:
Demographic characteristics, vital signs, laboratory values, nursing flowsheet data, and outcomes data were collected from the electronic health record. The accuracy of individual variables, the Modified Early Warning Score, the National Early Warning Score version 2, and our previously developed electronic Cardiac Arrest Risk Triage score were compared for predicting the need for acute hospital transfer or death using the area under the receiver operating characteristic curve. A total of 12,497 patient admissions were included, with 3,550 experiencing the composite outcome. The median age was 65 (interquartile range, 54–74), 46% were female, and the median length of stay in the long-term acute care hospital was 27 days (interquartile range, 17–40 d), with an 8% in-hospital mortality. Laboratory values were the best predictors, with blood urea nitrogen being the most accurate (area under the receiver operating characteristic curve, 0.63) followed by albumin, bilirubin, and WBC count (area under the receiver operating characteristic curve, 0.61). Systolic blood pressure was the most accurate vital sign (area under the receiver operating characteristic curve, 0.60). Electronic Cardiac Arrest Risk Triage (area under the receiver operating characteristic curve, 0.72) was significantly more accurate than National Early Warning Score version 2 (area under the receiver operating characteristic curve, 0.66) and Modified Early Warning Score (area under the receiver operating characteristic curve, 0.65; p < 0.01 for all pairwise comparisons).

Conclusions:
In this retrospective cohort study, we found that the electronic Cardiac Arrest Risk Triage score was significantly more accurate than Modified Early Warning Score and National Early Warning Score version 2 for predicting acute hospital transfer and mortality. Because laboratory values were more predictive than vital signs and the average length of stay in an long-term acute care hospital is much longer than short-term acute hospitals, developing a score specific to the long-term acute care hospital population would likely further improve accuracy, thus allowing earlier identification of high-risk patients for potentially life-saving interventions.
CASE REPORT OF THE ROLE OF OPTICAL COHERENCE TOMOGRAPHY IN RECOMBINANT GROWTH HORMONE THERAPY
Authors: Kohen Maryo C. , Orge Faruk H. 
Published: September 2019

Purpose:
To report the correlation between recombinant growth hormone (rhGH) dosage and retinal nerve fiber layer (RNFL) thickness values measured by optical coherence tomography in a case of pseudotumor cerebri syndrome (PTCS) after rhGH.

Methods:
An 11-year-old girl was receiving rhGH for panhypopituitarism. The patient developed PTCS, and her rhGH dose was adjusted using optical coherence tomography RNFL thickness measurements. The linear correlation coefficient (r) and coefficient of determination (r2) were calculated to assess the relationship between RNFL thickness and rhGH dose.

Results:
As the rhGH dosage was increased, the RNFL thickness values also increased, especially when acetazolamide was excluded because of its confounding effect. (r = 0.64) In separate subgroup analysis, a higher acetazolamide dosage strongly correlated with reduced RNFL thickness (r = 0.77).

Conclusion:
Although PTCS is a rare complication after rhGH therapy, its detrimental effects cannot be ignored. In our case report, we used optical coherence tomography RNFL values in addition to clinical findings to carefully titrate the rhGH dosage to prevent a flare-up of PTCS. Despite the obvious need for larger studies, our case report shows the value of RNFL thickness measured by optical coherence tomography and the valuable additional data it provides to refine rhGH therapy as an adjunct noninvasive method in PTCS.
The association of early life stressors with pain sensitivity and pain experience at 22 years
Authors: Waller Robert , Smith Anne J. , O'Sullivan Peter B. , Slater Helen , Sterling Michele , Straker Leon M. 
Published: September 2019

Abstract
Early life stress (ELS) can significantly influence biological pathways associated with nociception, increasing vulnerability to future heightened pain sensitivity and subsequent risk of pain events. However, very little human research has investigated the association of ELS, measured across multiple domains, with future pain sensitivity. Data from Gen1 and Gen2 of the Raine Study were used to assess the association between a wide range of early life stressors, including antenatally, and pressure and cold pain sensitivity at young adulthood. Participants were classified into 2 groups according to their cold pain sensitivity. In addition, the interaction between ELS, pain sensitivity, and pain experience (based on Örebro Musculoskeletal Pain Questionnaire) at age 22 years was examined. Analysis was performed using both a complete case and multiple imputation approach, adjusting for contemporaneous 22-year correlates, with comparable results in each model. More problematic behaviour at age 2 years was associated with less pressure pain sensitivity at 22 years (13.7 kPa, 95% CI: 1.0-27.0, P = 0.037), with no interaction between problematic behaviour and pain experience at 22 years. For those reporting a moderate/high pain experience at 22 years, poor family functioning increased the odds ratio for high cold pain sensitivity (3.0, 95% CI: 1.6-5.6), but for those reporting no/low pain experience, it did not (OR:1.2, 95% CI: 0.8-1.8). This study provides the most comprehensive investigation of the relationship between ELS and pressure and cold pain sensitivity in young adults supporting early life as a critical period of development influencing future nociceptive processing.
Using a Second Stakeholder-Driven Variance Reporting System Improves Pediatric Perioperative Safety
Authors: Kawaguchi Akemi L. , Jain Ranu , Hebballi Nutan B. , Pham Dean H. , Putnam Luke R. , Kao Lillian S. , Lally Kevin P. , Tsao Kuojen 
Published: September 2019

Introduction:
Despite recognizing the occurrence of variances, we noted a low rate of reporting with the established computer variance program. Therefore, we developed and introduced a simple, handwritten variance reporting system. The goal of this study was to compare our pediatric perioperative handwritten variance cards to our established computerized variance reporting system.

Methods:
We developed a handwritten variance card program through a stakeholder-driven quality-improvement initiative. We collected variances from handwritten cards in 4 perioperative locations and also from the established computerized variance system. We analyzed the variances and categorized them into 6 safety domains and 5 variance categories.

Results:
Over 6 consecutive years, 3,434 variances were reported (687 computerized and 2,747 handwritten). For safety domains, the computerized system was more likely to capture adverse events and near-misses (8.7% vs. 1.1%, P < 0.001; 23.5% vs. 8.6%, P < 0.001, respectively) while the handwritten system was more likely to identify the safety process and other non-safety issues (20.1% vs. 38.3%, P < 0.001). Both systems addressed policy/process issues most often, with 37.9% of the handwritten cards and 66.6% of the computerized variance reports. Of the handwritten cards with a patient identifier (n = 1,407), only 5.1% (n = 72) also had a computerized variance filed about the same event. Thus, staff reported >1,300 additional variances that were not identified with the computerized variance system alone.

Conclusion:
The handwritten, stakeholder-driven variance reporting system was essential to identify local and system issues that would not have been identified by the computerized variance reporting system alone.
High-profile sexual misconduct media triggers sex harassment recall and reinterpretation
Authors: Amber Brittney , Dinh Tuyen K. , Lewis Arielle N. , Trujillo Leidy D. , Stockdale Margaret S. 
Published: September 2019

Purpose
The purpose of this paper is to explore a possible effect of #MeToo media on individuals’ personal recall and reinterpretation of sex harassment (SH) experiences. The authors experimentally examine how exposure to high-profile stories of sexual misconduct triggers memories and reinterpretation of one’s own past SH experiences.

Design/methodology/approach
Using a sample of 393 US adults, participants were randomly assigned to read one of four media passages, two of which were news stories or transcripts of high-profile cases of sexual harassment or misconduct (e.g., the Trump Access Hollywood transcript), then completed the Sexual Experiences Questionnaire (SEQ) and follow-up questions about how the media impacted their memory of their prior SH experiences.

Findings
Sexual misconduct media stories, compared to control conditions, indirectly predicted self-report of past SH (SEQ) through both remembering and reinterpreting one’s past experiences. Gender and political ideology moderated the indirect effects such that the effects of the media stories were stronger for women and for those higher on progressive political ideology.

Practical implications
This study experimentally demonstrated what has publicly been assumed to be a driving force behind the upswing of SH reports and the seriousness by which they have been regarded during the #MeToo era: publicized stories of high-profile sexual misconduct triggers personal recall of having been sexually harassed in the past and reinterpretation of SH experiences. The #MeToo movement may be acting as a driver of social change, facilitating changes in social norms. As these social norms change, organizations should be prepared to effectively respond to a possible increase in reporting SH experiences due changes in norms around reporting SH.

Originality/value
This study uses an experimental design to investigate the role of high-profile media stories about SH as a driving force behind the #MeToo movement.
Thematic mapping of cloud computing based on a systematic review: a tertiary study
Authors: Delavari Vahid , Shaban Elahi , Janssen Marijn , Hassanzadeh Alireza 
Published: September 2019

Purpose
A large number of systematic reviews (SRs) studies have been performed in the cloud computing field, demonstrating miscellaneous outcomes and utilizing different approaches. Accordingly, a meta-review of cloud SRs is needed to appraise the results of such studies and create an integrated understanding. The paper aims to discuss these issues.

Design/methodology/approach
A tertiary study was conducted using a systematic method to analyze SRs including two stages: searching and screening the SRs and thematic synthesis of results. As a qualitative data management tool, Nvivo software was used to support the research process, for data coding and synthesis.

Findings
First, by searching electronic sources between the year of 2011–2016, out of a total of 142 identified articles, 94 articles were included according to pre-determined criteria, of which 76 articles were approved after qualitative evaluation. In the second stage, identifying the research themes, a map of the concepts and issues related to each theme was drawn up. The analysis shows that the quality of articles has improved but can be further enhanced using methodological guidelines as well as supporting tools. The research has focused more on the technical aspect, although there is an equal demand for synthesizing of cloud governance concepts.

Originality/value
This is the first tertiary study which presents the main research themes and concepts of cloud SRs in form of thematic maps by using the thematic synthesis and SR methods. This paper also provides some recommendations to improve reviews after evaluating the quality of papers. This study can support reviewers for future SRs in the field and also helps practitioners and managers to have a better understanding of different aspects of cloud computing.