bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning accelerates MD-based binding pose prediction between ligands and proteins
Authors: Terayama Kei , Iwata Hiroaki , Araki Mitsugu , Okuno Yasushi , Tsuda Koji 
Published: October 2017

Abstract

Motivation
Fast and accurate prediction of protein–ligand binding structures is indispensable for structure-based drug design and accurate estimation of binding free energy of drug candidate molecules in drug discovery. Recently, accurate pose prediction methods based on short Molecular Dynamics (MD) simulations, such as MM-PBSA and MM-GBSA, among generated docking poses have been used. Since molecular structures obtained from MD simulation depend on the initial condition, taking the average over different initial conditions leads to better accuracy. Prediction accuracy of protein–ligand binding poses can be improved with multiple runs at different initial velocity.

Results
This paper shows that a machine learning method, called Best Arm Identification, can optimally control the number of MD runs for each binding pose. It allows us to identify a correct binding pose with a minimum number of total runs. Our experiment using three proteins and eight inhibitors showed that the computational cost can be reduced substantially without sacrificing accuracy. This method can be applied for controlling all kinds of molecular simulations to obtain best results under restricted computational resources.

Availability and implementation
Code and data are available on GitHub at https://github.com/tsudalab/bpbi.

Supplementary information
Supplementary data are available at Bioinformatics online.
Beyond similarity assessment: selecting the optimal model for sequence alignment via the Factorized Asymptotic Bayesian algorithm
Authors: Takeda Taikai , Hamada Michiaki 
Published: October 2017

AbstractMotivationPair Hidden Markov Models (PHMMs) are probabilistic models used for pairwise sequence alignment, a quintessential problem in bioinformatics. PHMMs include three types of hidden states: match, insertion and deletion. Most previous studies have used one or two hidden states for each PHMM state type. However, few studies have examined the number of states suitable for representing sequence data or improving alignment accuracy.ResultsWe developed a novel method to select superior models (including the number of hidden states) for PHMM. Our method selects models with the highest posterior probability using Factorized Information Criterion, which is widely utilized in model selection for probabilistic models with hidden variables. Our simulations indicated that this method has excellent model selection capabilities with slightly improved alignment accuracy. We applied our method to DNA datasets from 5 and 28 species, ultimately selecting more complex models than those used in previous studies.Availability and implementationThe software is available at https://github.com/bigsea-t/fab-phmm.Supplementary informationSupplementary data are available at Bioinformatics online.
AEGS: identifying aberrantly expressed gene sets for differential variability analysis
Authors: Guan Jinting , Chen Moliang , Ye Congting , Cai James J , Ji Guoli 
Published: October 2017

Abstract

Motivation
In gene expression studies, differential expression (DE) analysis has been widely used to identify genes with shifted expression mean between groups. Recently, differential variability (DV) analysis has been increasingly applied as analyzing changed expression variability (e.g. the changes in expression variance) between groups may reveal underlying genetic heterogeneity and undetected interactions, which has great implications in many fields of biology. An easy-to-use tool for DV analysis is needed.

Results
We develop AEGS for DV analysis, to identify aberrantly expressed gene sets in diseased cases but not in controls. AEGS can rank individual genes in an aberrantly expressed gene set by each gene’s relative contribution to the total degree of aberrant expression, prioritizing top genes. AEGS can be used for discovering gene sets with disease-specific expression variability changes.

Availability and implementation
AEGS web server is accessible at http://bmi.xmu.edu.cn:8003/AEGS, where a stand-alone AEGS application can also be downloaded.
Characterizing Cefepime Neurotoxicity: A Systematic Review
Authors: Appa Ayesha A , Jain Rupali , Rakita Robert M , Hakimian Shahin , Pottinger Paul S 
Published: October 2017

Abstract
Neurotoxicity due to cefepime has not been well characterized. We performed a systematic review of the literature and included 5 additional cases from our center. Of the 198 cases found, the mean age was 67 years and 87% of patients had renal dysfunction. The most common clinical features were diminished level of consciousness (80%), disorientation/agitation (47%), and myoclonus (40%). It is worth noting that nonconvulsive status epilepticus was relatively common with 31% of cases, whereas only 11% had convulsive seizures. Single-center estimate of incidence was 1 in 480 courses of cefepime. Cefepime neurotoxicity should be considered in older patients with renal dysfunction and new onset encephalopathy, especially if concurrent myoclonus is present. More work is needed to prospectively assess incidence and outcomes related to cefepime neurotoxicity.
The Return to Literature—Making Doctors Matter in the New Era of Medicine
Authors: Marchalik Daniel 
Published: October 2017

The rapid explosion of medical knowledge of the 19th and 20th centuries required a transformation in medical education, which, to that point, had been marked by low educational standards. To combat the lack of regulation, the 1910 Flexner Report recommended sweeping reforms. By 1930, students hoping to enroll in a medical school would need to complete courses in chemistry, physics, and biology, leaving little room for the liberal arts.
Medicine is once again changing. The impact of artificial intelligence is being felt across all medical fields, and the nature of physicians’ jobs in the new landscape of intelligent machines will inevitably also have to change. What will the role of new physicians be? And how should medical education be amended to meet those needs?
In 2017, the Georgetown University School of Medicine graduated the first group of students from its Literature and Medicine Track—the first U.S. medical school track dedicated to the study of literature. This Invited Commentary explores the work done in, and the scholarship resulting from, this novel educational program and suggests ways in which literature could be used to prepare future doctors for the evolving demands of the medical field.
Do Changes in Sensory Processing Precede Low Back Pain Development in Healthy Individuals?
Authors: Hwang Ching-Ting , Van Dillen Linda R. , Haroutounian Simon 
Published: October 2017

Objectives:
Low back pain (LBP) is the most commonly reported chronic pain condition. In this study, a clinically relevant, induced-LBP paradigm was used to study sensory processing as a risk factor and predictor for LBP development in healthy people. Our aim was to examine sensory processing in those who do develop LBP and those who do not develop LBP with the paradigm, and to examine the relationships between scores on psychosocial questionnaires and sensory processing measures in these healthy people.

Methods:
A total of 71 participants completed the Pain Catastrophizing Scale (PCS) and Hospital Anxiety and Depression Scale (HADS) and then took part in quantitative sensory testing. An induced-LBP paradigm, where participants stand for 2 hours and rate their low back symptoms over time, was used to classify participants as those who did develop LBP and those who did not develop LBP.

Results:
No differences in sensory processing were identified between those who did develop LBP and those who did not develop LBP (Ps>0.05). Scores for the PCS and HADS were similar between the groups (Ps>0.05). Small significant relationships between PCS scores and cold detection and cold pain thresholds were found (rs=0.23 to 0.31; Ps<0.05) and between the pressure pain thresholds at the thenar eminence and paraspinals (r=0.53; P<0.01).

Discussion:
These results provide evidence that altered sensory processing was not present in healthy people and thus is not a risk factor for development of LBP in standing.
Expanding Prenatal Care to Unauthorized Immigrant Women and the Effects on Infant Health
Authors: Swartz Jonas J. , Hainmueller Jens , Lawrence Duncan , Rodriguez Maria I. 
Published: October 2017

OBJECTIVE:
To measure the effect of access to prenatal care on unauthorized and low-income, new legal permanent resident immigrant women and their offspring.

METHODS:
We used a difference-in-differences design that leverages the staggered rollout of Emergency Medicaid Plus by county from 2008 to 2013 as a natural experiment to estimate the effect on health service utilization for women and health outcomes for their infants. Regular Medicaid pregnancies were used as an additional control in a triple difference design.

RESULTS:
Our sample included pregnancies covered by Emergency Medicaid (35,182), Emergency Medicaid Plus (12,510), and Medicaid (166,054). After expansion of access to prenatal care, there was an increase in prenatal visits (7.2 more visits, 95% CI 6.45–7.96), receipt of adequate prenatal care (28% increased rate, CI 26–31), rates of diabetes screening (61% increased rate, CI 56–66), and fetal ultrasonograms (74% increased rate, CI 72–76). Maternal access to prenatal care was also associated with an increased number of well child visits (0.24 more visits, CI 0.07–0.41), increased rates of recommended screenings and vaccines (0.04 increased probability, CI 0.002–0.074), and reduced infant mortality (−1.01/1,000, CI −1.42 to −0.60) and rates of extremely low birth weight (less than 1,000 g) (−1.33/1,000, CI −2.44 to −0.21).

CONCLUSION:
Our results provide evidence of increased utilization and improved health outcomes for unauthorized immigrants and their children who are U.S. citizens after introduction of prenatal care expansion in Oregon. This study contributes to the debate around reauthorization of the Children's Health Insurance Program in 2017.
First-Trimester Serum Fatty Acid-Binding Protein 4 and Subsequent Gestational Diabetes Mellitus
Authors: Tu Wen-Jun , Guo Min , Shi Xiao-Dong , Cai Yan , Liu Qiang , Fu Chen-Wei 
Published: October 2017

OBJECTIVE:
To examine whether plasma fatty acid-binding protein 4 concentrations, measured in the first trimester, are associated with gestational diabetes mellitus (GDM).

METHODS:
This prospective, multicenter cohort study was conducted at three maternity centers in two cities (Harbin and Beijing) in China from July 2015 to June 2016. Data for fasting plasma glucose and fatty acid-binding protein 4 concentrations in the first trimester and one-step GDM screening with a 75-g oral glucose tolerance test performed between 24 and 28 weeks of gestation were collected and analyzed.

RESULTS:
Plasma from women in the first trimester was available for 1,150 women, of whom 135 (11.7%) developed GDM. The GDM distribution across the fatty acid-binding protein 4 quartiles ranged from 3.8% (first quartile) to 21.6% (fourth quartile). In multivariate models comparing the second (quartile 2), third, and fourth quartiles against the first quartile of fatty acid-binding protein 4, concentrations of fatty acid-binding protein 4 in quartile 2, quartile 3, and quartile 4 were associated with the development of GDM with respective associated adjusted odds ratios (95% CIs) of 1.76 (1.21–2.58), 2.36 (1.55–4.29), and 3.57 (1.99–6.11). A significant difference in the area under receiver operating characteristic curve between established risk factors alone and the addition of fatty acid-binding protein 4 concentrations was observed (difference 0.042 [95% CI 0.028–0.055]; P=.03).

CONCLUSIONS:
Higher fatty acid-binding protein 4 concentrations in the first trimester visit were associated with increased risk of GDM and might be useful in identifying women at risk for GDM for early prevention strategies.
A Gartner Duct Cyst Masquerading as Anterior Vaginal Prolapse
Authors: Davidson Emily R. W. , Barber Matthew D. 
Published: October 2017

BACKGROUND:
Gartner duct cysts are embryologic remnants of the mesonephric ducts that may present as a vaginal mass or cyst.

CASE:
A patient was referred for surgical management of prolapse whose bulging anterior vagina was actually a Gartner duct cyst that required excision as a result of symptoms. Preoperative magnetic resonance imaging helped confirm the diagnosis.

CONCLUSION:
A Gartner duct cyst may present as a vaginal cyst that, if large, may mimic pelvic organ prolapse. The diagnosis should be considered when a patient's individual prolapse compartments are inconsistent or when physical examination is suggestive of another process.
Neonatal Morbidity and Maternal Complication Rates in Women With a Delivery Body Mass Index of 60 or Higher
Authors: Kim Tana , Burn Sabrina C. , Bangdiwala Ananta , Pace Samantha , Rauk Phillip 
Published: October 2017

OBJECTIVE:
To investigate neonatal morbidity and maternal complication rates with delivery body mass index (BMI) 60 or greater.

METHODS:
This retrospective, multicenter cohort study included singleton pregnancies between 23 and 42 weeks of gestation from January 2005 to April 2016. Women with BMI 60 or greater were compared with a random sample of women with BMI 30–59. The primary outcome, composite neonatal morbidity, was defined as 5-minute Apgar score less than 7, hypoglycemia, respiratory distress syndrome, sepsis, hospital stay greater than 5 days, neonatal intensive care unit admission, or neonatal death. Secondary outcomes included maternal labor and delivery characteristics and complication rates. Kruskal-Wallis tests and χ2 or Fisher exact tests were used to compare BMI categories. Multivariable logistic regression was used for adjusted analysis.

RESULTS:
The study included 338 women, with 39 in the BMI 60 or greater group. An association between obesity and neonatal morbidity was found. Increasing BMI correlated with increasing neonatal morbidity, with the highest rates among those with BMI 60 or greater (BMI 30–39 [17%], 40–49 [19%], 50–59 [22%], 60 or greater [56%]; P<.001). After adjustment for confounders, obese women with BMI less than 60 had at least a 75% reduction in odds of neonatal morbidity compared with women with BMI 60 or greater (BMI 30–39 adjusted odds ratio [OR] 0.22 [0.1–0.5], 40–49 adjusted OR 0.23 [0.1–0.6], 50–59 adjusted OR 0.25 [0.1–0.6]). Maternal complication rates including labor induction, cesarean delivery, wound complication, postpartum hemorrhage, and hospital stay greater than 5 days were also significantly increased with BMI 60 or greater.

CONCLUSION:
A BMI 60 or greater at the time of delivery is significantly associated with increased neonatal morbidity and increased maternal complication rates. In addition, neonatal morbidity and maternal complication rates with BMI 60 or greater were significantly higher when compared with women in any lesser obese BMI cohort between 30 and 59.
Maternal and Neonatal Outcomes in Indicated Preterm Births Based on the Intended Mode of Delivery
Authors: Kuper Spencer G. , Sievert Rachel A. , Steele Robin , Biggio Joseph R. , Tita Alan T. , Harper Lorie M. 
Published: October 2017

OBJECTIVE:
To compare maternal and neonatal outcomes in women who underwent induction of labor or planned cesarean delivery in indicated preterm births before 34 weeks of gestation.

METHODS:
We conducted a retrospective cohort study of all indicated singleton preterm births (23–34 weeks of gestation) in a tertiary center from 2011 to 2014. The primary maternal outcome was a composite of early postpartum hemorrhage, blood transfusion, operative complications, postpartum complications, and clinical chorioamnionitis. The primary neonatal outcome was a composite of neonatal death, cardiopulmonary resuscitation in the delivery room, grade 3 or 4 intraventricular hemorrhage, necrotizing enterocolitis, culture-proven sepsis, birth trauma, arterial cord gas pH less than 7 or base excess less than −12, and 5-minute Apgar score 3 or less. Outcomes were compared by intended mode of delivery (induction of labor compared with cesarean) and adjusted for confounders. In secondary analyses, maternal and neonatal outcomes based on the intended mode of delivery were stratified by gestational age (23–27 6/7, 28–31 6/7, and 32–33 6/7 weeks of gestation).

RESULTS:
Of 629 patients with indicated early preterm births during the study period, 331 (53%) underwent induction of labor, of whom 208 (63%) delivered vaginally. Induction of labor was not associated with an increased risk of the primary maternal (16.3% compared with 19.5%, adjusted odds ratio [OR] 0.8, 95% CI 0.5–1.3) or neonatal composite outcome (14.5% compared with 35.9%, adjusted OR 0.7, 95% CI 0.4–1.1). Analyses stratified by gestational age were consistent with the overall analysis.

CONCLUSION:
Maternal and neonatal outcomes do not differ based on the intended mode of delivery. Induction of labor should be considered when early preterm birth is indicated.
Characterizing the Functional Decline of Older Women With Incident Urinary Incontinence
Authors: Parker-Autry Candace , Houston Denise K. , Rushing Julia , Richter Holly E. , Subak Leslee , Kanaya Alka M. , Kritchevsky Stephen B. 
Published: October 2017

OBJECTIVE:
To characterize change in physical performance and differential prevalence of low skeletal muscle mass and strength (sarcopenia) and lower 25-hydroxyvitamin D concentrations among older women who developed urinary incontinence (UI) symptoms.

METHODS:
This is a secondary analysis of the Health, Aging, and Body Composition Study. Urinary incontinence symptoms were assessed using validated questions. The Short Physical Performance Battery measured physical performance. Sarcopenia, defined by low muscle mass and strength, was determined using validated cutoffs for gait speed, grip strength, and appendicular skeletal muscle mass. All parameters were evaluated at baseline and year 4. Serum 25-hydroxyvitamin D concentrations were assessed at year 2. The primary outcome was change in Short Physical Performance Battery total scores. Sarcopenia and lower serum 25-hydroxyvitamin D concentrations have been independently associated with poor physical performance and UI and were therefore included as secondary outcomes. Univariate and multivariate analyses were used to characterize the associations of change in physical performance from baseline to year 4, incidence of sarcopenia, and lower serum 25-hydroxyvitamin D on the development of UI symptoms.

RESULTS:
Of the 1,583 women enrolled, 910 were excluded (730 had baseline UI; 180 with missing data). Six hundred seventy-three women were continent at baseline; 223 (33%) developed UI symptoms at year 4. SPPB total scores significantly declined in women with UI versus continent women (mean difference continent−incident UI 0.32, 95% CI 0.04–0.60, P=.02). Of subscale measures, standing balance showed the greatest decline at 0.20 (0.05–0.36; continent−incident UI, respectively; P=.009). Sarcopenia developed at a higher rate with incident UI (adjusted odds ratio [OR] 1.7, 95% CI 1.0–2.9). Low 25-hydroxyvitamin D was not associated with incident UI (adjusted OR 1.1, 95% CI 0.7–1.6 and 1.1, 95% CI 0.7–1.6 for deficient or insufficient versus sufficient status, respectively).

CONCLUSION:
We observed a significant decline in standing balance among older women who developed UI symptoms. This decline may be associated with coinciding development of sarcopenia.
Contraception and Conception After Bariatric Surgery
Authors: Menke Marie N. , King Wendy C. , White Gretchen E. , Gosman Gabriella G. , Courcoulas Anita P. , Dakin Gregory F. , Flum David R. , Orcutt Molly J. , Pomp Alfons , Pories Walter J. , Purnell Jonathan Q. , Steffen Kristine J. , Wolfe Bruce M. , Yanovski Susan Z. 
Published: October 2017

OBJECTIVE:
To examine contraceptive practices and conception rates after bariatric surgery.

METHODS:
The Longitudinal Assessment of Bariatric Surgery-2 is a multicenter, prospective cohort study of adults undergoing first-time bariatric surgery as part of routine clinical care at 10 U.S. hospitals. Recruitment occurred between 2005 and 2009. Participants completed preoperative and annual postsurgical assessments for up to 7 years until January 2015. This report was restricted to women 18–44 years old with no history of menopause, hysterectomy, or estrogen and progesterone therapy. Primary outcomes were self-reported contraceptive practices, overall conception rate, and early (less than 18 months) postsurgical conception. Contraceptive practice (no intercourse, protected intercourse, unprotected intercourse, or tried to conceive) was classified based on the preceding year. Conception rates were determined from self-reported pregnancies.

RESULTS:
Of 740 eligible women, 710 (95.9%) completed follow-up assessment(s). Median (interquartile range) preoperative age was 34 (30–39) years. In the first postsurgical year, 12.7% (95% CI 9.4–16.0) of women had no intercourse, 40.5% (95% CI 35.6–45.4) had protected intercourse only, 41.5% (95% CI 36.4–46.6) had unprotected intercourse while not trying to conceive, and 4.3% (95% CI 2.4–6.3) tried to conceive. The prevalence of the first three groups did not significantly differ across the 7 years of follow-up (P for all >.05); however, more women tried to conceive in the second year (13.1%, 95% CI 9.3–17.0; P<.001). The conception rate was 53.8 (95% CI 40.0–71.1) per 1,000 woman-years across follow-up (median [interquartile range] 6.5 [5.9–7.0] years); 42.3 (95% CI 30.2–57.6) per 1,000 woman-years in the 18 months after surgery. Age (adjusted relative risk 0.41 [95% CI 0.19–0.89] per 10 years, P=.03), being married or living as married (adjusted relative risk 4.76 [95% CI 2.02–11.21], P<.001), and rating future pregnancy as important preoperatively (adjusted relative risk 8.50 [95% CI 2.92–24.75], P<.001) were associated with early conception.

CONCLUSIONS:
Postsurgical contraceptive use and conception rates do not reflect recommendations for an 18-month delay in conception after bariatric surgery.

CLINICAL TRIAL REGISTRATION:
ClinicalTrials.gov, NCT00465829.