bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes
Authors: Liu Yiyi , Zhao Hongyu 
Published: August 2016

Motivation: Combinatorial therapies have been under intensive research for cancer treatment. However, due to the large number of possible combinations among candidate compounds, exhaustive screening is prohibitive. Hence, it is important to develop computational tools that can predict compound combination effects, prioritize combinations and limit the search space to facilitate and accelerate the development of combinatorial therapies.Results: In this manuscript we consider the NCI-DREAM Drug Synergy Prediction Challenge dataset to identify features informative about combination effects. Through systematic exploration of differential expression profiles after single compound treatments and comparison of molecular structures of compounds, we found that synergistic levels of combinations are statistically significantly associated with compounds’ dissimilarity in structure and similarity in induced gene expression changes. These two types of features offer complementary information in predicting experimentally measured combination effects of compound pairs. Our findings offer insights on the mechanisms underlying different combination effects and may help prioritize promising combinations in the very large search space.Availability and Implementation: The R code for the analysis is available on https://github.com/YiyiLiu1/DrugCombination.Contact: hongyu.zhao@yale.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Higher classification sensitivity of short metagenomic reads with CLARK-S
Authors: Ounit Rachid , Lonardi Stefano 
Published: August 2016

Summary: The growing number of metagenomic studies in medicine and environmental sciences is creating increasing demands on the computational infrastructure designed to analyze these very large datasets. Often, the construction of ultra-fast and precise taxonomic classifiers can compromise on their sensitivity (i.e. the number of reads correctly classified). Here we introduce CLARK-S, a new software tool that can classify short reads with high precision, high sensitivity and high speed.
Availability and Implementation: CLARK-S is freely available at http://clark.cs.ucr.edu/
Contact: stelo@cs.ucr.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Chronic Headache and Backache are Long-term Sequelae of Unintentional Dural Puncture in the Obstetric Population
Authors: Ranganathan P. , Golfeiz C. , Phelps A.L. , Singh S. , Shnol H. , Paul N. , Attaallah A.F. , Vallejo M.C. 
Published: August 2016

(J Clin Anesth. 2015;27(3):201–206)
Although unintentional dural puncture (UDP) with an epidural needle and the resulting postdural puncture headache (PDPH) occur in 1% to 5% of patients who undergo neuraxial anesthesia, there are very few studies that have addressed long-term UDP and PDPH sequelae, as parturients with PDPH are not routinely followed for the development of long-term complications. The current study examined the long-term (>6 wk) effects of PDPH by interviewing parturients who had UDP (recognized or unrecognized) associated with labor epidural analgesia.
Association Between Preeclampsia and Congenital Heart Defects
Authors: Auger N. , Fraser W.D. , Healy-Profitós J. , Arbour L. 
Published: August 2016

(JAMA. 2015;314(15):1588–1598)
Congenital heart defects are the most common anomaly in infants and are a major cause of infant morbidity and mortality. The origins of congenital heart defects, therefore, need to be better studied in order to improve prevention and earlier detection. Recent studies have tried to identify biomarkers for congenital heart defects as well as preeclampsia. Biomarker findings associated with heart defects include imbalances in proangiogenic signaling proteins, such as vascular endothelial growth factor and placental growth factor, and antiangiogenic proteins, such as soluble endoglin and fms-like tyrosine kinase 1. Imbalances in these same biomarkers have been found with preeclampsia, where there is an excess of soluble endoglin and fms-like tyrosine kinase 1 relative to placental growth factor and vascular endothelial growth factor. Angiogenic mechanisms may be part of a shared pathologic pathway for preeclampsia and congenital heart defects. Studies have shown that the pathologic changes associated with preeclampsia begin early in pregnancy, around the time that fetal heart development is occurring. This current study tried to determine the relationship between preeclampsia and the prevalence of congenital heart defects in infants whose mothers had the disorder.
Guideline-based Development of Quality Indicators for Prevention and Management of Postpartum Hemorrhage
Authors: Woiski M.D. , Scheepers H.C. , Liefers J. , Lance M. , Middeldorp J.M. , Lotgering F.K. , Grol R.P. , Hermens R.P. 
Published: August 2016

(Acta Obstet Gynecol Scand. 2015;94:1118–1127)
Postpartum hemorrhage (PPH) is a major cause of maternal mortality worldwide, and it has been reported that many mothers suffering from hemorrhage received substandard care. Two recent studies have shown that 30% to 90% of women with PPH received care that is less than optimal, while a third study has shown that hospitals with a fetal maternal specialist experienced a lower rate of PPH. Research has also shown that a lack of training and education among health care providers could play a significant role in the development of severe hemorrhage. The authors of this paper developed a series of quality indicators to evaluate whether providers are adhering to the optimal guidelines when caring for patients with PPH.
Maternal Cardiac and Obstetric Performance in Consecutive Pregnancies in Women With Heart Disease
Authors: Gelson E. , Curry R. , Gatzoulis M.A. , Swan L. , Lupton M. , Steer P.J. , Johnson M.R. 
Published: August 2016

(BJOG. 2015;122(11):1552–1559)
Pregnant women with preexisting cardiac disease often experience cardiac decompensation due to the physiological stresses of pregnancy. Some studies have suggested that these adverse effects on cardiac function might not be reversible once the pregnancy is completed. Therefore, women with cardiac disease might be expected to experience increased complications and poorer outcomes with subsequent pregnancies. This current study was undertaken to determine the effect of a second pregnancy on cardiac, obstetric, and perinatal complications in women with heart disease, compared with the first pregnancy in the same women. It secondarily estimated the effect of a second pregnancy on birth weight in women with heart disease.
Midwifery Facilitation: Exploring the Functionality of Labor Discomfort
Authors: Sanders R. 
Published: August 2016

(Birth. 2015;42(3):202–205)
Currently, only 36% of labors in the United Kingdom are performed without anesthesia. This commentary explores the increasing trend of women choosing to medicate during labor. The practice of midwifery focuses on supporting women through the birthing process. Putting the emphasis on facilitating labor—making it as easy, not as painless, as possible—could reduce the reliance on pharmacological methods of anesthesia. As the perception of how painful labor is can be altered by the woman’s labor experience, changing the language used in describing labor pain could help alter the cultural perception of it.
A Phase 1, Dose-escalation, Double-blind, Block-randomized, Controlled Trial of Safety and Efficacy of Neosaxitoxin Alone and in Combination With 0.2% Bupivacaine, With and Without Epinephrine, for Cutaneous Anesthesia
Authors: Lobo K. , Donado C. , Cornelissen L. , Kim J. , Ortiz R. , Peake R.W. , Kellogg M. , Alexander M.E. , Zurakowski D. , Kurgansky K.E. , Peyton J. , Bilge A. , Boretsky K. , McCann M.E. , Berde C.B. , Cravero J. 
Published: August 2016

(Anesthesiology. 2015;123(4):873–885)
Prolonged local anesthesia has been successfully achieved in both animals and humans using a site-1 sodium channel blocker called Neosaxitoxin (NeoSTX). The purpose of this study was to assess the safety of NeoSTX when administered through injection by itself, combined with bupivacaine, and combined with bupivacaine and epinephrine. The authors hypothesized that the drug would prove safe from a cardiovascular, neuromuscular, and respiratory standpoint. A secondary aim for this study was to evaluate the association between plasma concentrations of NeoSTX and any possible negative symptoms or bodily changes.
Second Curettage for Low-Risk Nonmetastatic Gestational Trophoblastic Neoplasia
Authors: Osborne Raymond J. , Filiaci Virginia L. , Schink Julian C. , Mannel Robert S. , Behbakht Kian , Hoffman James S. , Spirtos Nick M. , Chan John K. , Tidy John A. , Miller David S. 
Published: August 2016

OBJECTIVE:
To evaluate the efficacy and safety of second uterine curettage in lieu of chemotherapy for patients with low-risk, nonmetastatic gestational trophoblastic neoplasia (GTN) and to evaluate whether response to second curettage is independent of patient age, World Health Organization (WHO) risk score, registration human chorionic gonadotropin (hCG) level, lesion size, and depth of myometrial invasion measured on ultrasound examination.

METHODS:
This was a cooperative group multicenter prospective phase II study. Prestudy testing included quantitative hCG level, pelvic ultrasonography, and chest radiography. Patients were categorized according to WHO risk scoring criteria (low risk with a score of 0–6).

RESULTS:
Sixty-four women with newly diagnosed low-risk, nonmetastatic GTN were enrolled. Four patients were excluded. Twenty-four patients (40%) (lower 95% confidence limit 27.6%) were cured after second curettage. An additional two patients (3%) achieved a complete response but did not complete follow-up. Overall, 26 of 60 patients were able to avoid chemotherapy. Surgical failure was observed in 34 women (59%) and was more common in women 19 years old or younger or 40 years old or older. One case of grade 1 uterine perforation was successfully managed by observation. Four grade 1 and one grade 3 uterine hemorrhages were reported. New metastatic disease (lung) was identified in one of these women after second curettage. In three patients (surgical failures), the second curettage pathology was placental site trophoblastic tumor, and it was placental nodule in one additional patient.

CONCLUSION:
Second uterine curettage as initial treatment for low-risk, nonmetastatic GTN cures 40% of patients without significant morbidity.

CLINICAL TRIAL REGISTRATION:

ClinicalTrials.gov, https://clinicaltrials.gov/, NCT00521118.
Accuracy of Home-Based Ultrasonographic Diagnosis of Obstetric Risk Factors by Primary-Level Health Care Workers in Rural Nepal
Authors: Kozuki Naoko , Mullany Luke C. , Khatry Subarna K. , Ghimire Ram K. , Paudel Sharma , Blakemore Karin , Bird Christine , Tielsch James M. , LeClerq Steven C. , Katz Joanne 
Published: August 2016

OBJECTIVE:
To assess the feasibility of ultrasonographic task shifting by estimating the accuracy at which primary-level health care workers can perform community-based third-trimester ultrasound diagnosis for selected obstetric risk factors in rural Nepal.

METHODS:
Three auxiliary nurse–midwives received two 1-week ultrasound trainings at Tribhuvan University Teaching Hospital in Kathmandu. At a study site in rural Nepal, pregnant women who were 32 weeks of gestation or greater were enrolled and received ultrasound examinations from the auxiliary nurse–midwives during home visits. Each auxiliary nurse–midwife screened for noncephalic presentation, multiple gestation, and placenta previa. Deidentified digital ultrasonograms were stored and uploaded onto an online server, where certified sonologists and ultrasonographers reviewed the images and made their own diagnoses for the three conditions. Accuracy of auxiliary nurse–midwife diagnoses was then calculated.

RESULTS:
A total of 804 women contributed to the analysis. Each auxiliary nurse–midwife's κ statistic for diagnosis of noncephalic presentation was above 0.90 compared with the ultrasonogram reviewers. Sensitivity, specificity, and positive and negative predictive values were between 90% and 100% for all auxiliary nurse–midwives. For multiple gestation, the auxiliary nurse–midwives were in perfect agreement with both the ultrasonogram reviewers and maternal postpartum self-report. Two placenta previa cases were detected, and the ultrasonogram reviewers agreed with both.

CONCLUSION:
With limited training, primary-level health care workers in rural Nepal can accurately diagnose selected third-trimester obstetric risk factors using ultrasonography.
Association Between Western and Mediterranean Dietary Patterns and Mammographic Density
Authors: Castelló Adela , Ascunce Nieves , Salas-Trejo Dolores , Vidal Carmen , Sanchez-Contador Carmen , Santamariña Carmen , Pedraz-Pingarrón Carmen , Moreno Maria Pilar , Pérez-Gómez Beatriz , Lope Virginia , Aragonés Nuria , Vioque Jesús , Pollán Marina ,   on behalf of the DDM-Spain Research Group
Published: August 2016

OBJECTIVE:
To examine the association between two dietary patterns (Western and Mediterranean), previously linked to breast cancer risk, and mammographic density.

METHODS:
This cross-sectional study included 3,584 women attending population-based breast cancer screening programs and recruited between October 7, 2007, and July 14, 2008 (participation rate 74.5%). Collected data included anthropometric measurements; demographic, obstetric, and gynecologic characteristics; family and personal health history; and diet in the preceding year. Mammographic density was blindly assessed by a single radiologist and classified into four categories: less than 10%, 10–25%, 25–50%, and greater than 50%. The association between adherence to either a Western or a Mediterranean dietary pattern and mammographic density was explored using multivariable ordinal logistic regression models with random center-specific intercepts. Models were adjusted for age, body mass index, parity, menopause, smoking, family history, hormonal treatment, and calorie and alcohol intake. Differences according to women's characteristics were tested including interaction terms.

RESULTS:
Women with a higher adherence to the Western dietary pattern were more likely to have high mammographic density (n=242 [27%]) than women with low adherence (n=169 [19%]) with a fully adjusted odds ratio (ORQ4vsQ1) of 1.25 (95% confidence interval [CI] 1.03–1.52). This association was confined to overweight–obese women (adjusted ORQ4vsQ1 [95% CI] 1.41 [1.13–1.76]). No association between Mediterranean dietary pattern and mammographic density was observed.

CONCLUSION:
The Western dietary pattern was associated with increased mammographic density among overweight–obese women. Our results might inform specific dietary recommendations for women with high mammographic density.
Risk Factors for Dyspareunia After First Childbirth
Authors: Alligood-Percoco Natasha R. , Kjerulff Kristen H. , Repke John T. 
Published: August 2016

OBJECTIVE:
To investigate risk factors for dyspareunia among primiparous women.

METHODS:
This was a planned secondary analysis using data from the 1- and 6-month postpartum interviews of a prospective study of women who delivered their first neonate in Pennsylvania, 2009–2011. Participants who had resumed sexual intercourse by the 6-month interview (N=2,748) constituted the analytic sample. Women reporting a big or medium problem with painful intercourse at 6 months were categorized as having dyspareunia. Multivariable logistic regression was used to evaluate the effect of patient characteristics, obstetric and psychosocial factors, and breastfeeding on dyspareunia.

RESULTS:
There were 583 women (21.2%) who reported dyspareunia at 6 months postpartum. Nearly one third of those breastfeeding at 6 months reported dyspareunia (31.5%) compared with 12.7% of those not breastfeeding (adjusted odds ratio [OR] 2.89, 95% confidence interval [CI] 2.33–3.59, P<.001); 32.5% of those reporting a big or medium problem with perineal pain at 1 month reported dyspareunia at 6 months compared with 15.9% of those who did not (adjusted OR 2.45, 95% CI 1.93–3.10, P<.001); 28.3% of women who reported fatigue all or most of the time at 1 month reported dyspareunia at 6 months compared with 18.0% of those who reported fatigue less often (adjusted OR 1.60, 95% CI 1.30–1.98, P<.001); and 24.1% of those who scored in the upper third on the stress scale at 1 month reported dyspareunia at 6 months postpartum compared with 15.6% of those who scored in the lowest third (adjusted OR 1.55, 95% CI 1.18–2.02, P=.001).

CONCLUSION:
In this prospective cohort study, we identified specific risk factors for dyspareunia in primiparous women that can be discussed at the first postpartum visit, including breastfeeding, perineal pain, fatigue, and stress.
Reverse Vesicouterine Fold Dissection for Laparoscopic Hysterectomy After Prior Cesarean Deliveries
Authors: Nezhat Camran , Grace Lindsey A. , Razavi Gity M. , Mihailide Catalina , Bamford Holden 
Published: August 2016

BACKGROUND:
Cesarean delivery adhesions, during laparoscopic hysterectomy, can present surgical challenges, including distortion of anatomy, prolonged operating time, and inadvertent injury to nearby structures.

TECHNIQUE:
At the time of laparoscopic hysterectomy, in patients with significant adhesions from prior cesarean deliveries, we use a reverse inferior to superior vesicouterine fold dissection to mobilize the scarred bladder. We use this as an alternative to the commonly practiced technique of mobilizing the bladder in a superior to inferior fashion at the time of laparoscopic hysterectomy.

EXPERIENCE:
Fifty-two patients with a median age of 42.5 years are presented. Forty-eight patients were discharged within 3–6 hours postoperatively. Sixteen patients were discharged with Foley catheters, because they were unable to void within the protocol for a fast-track discharge. The catheters were removed between postoperative days 1 and 5. There were no gastrointestinal or genitourinary complications. One patient experienced a delayed vaginal cuff abscess and bleeding, which were managed conservatively.

CONCLUSION:
Reverse vesicouterine fold dissection is a useful alternative technique for laparoscopic hysterectomy in women with a history of prior cesarean deliveries.
Static Compression Induces ECM Remodeling and Integrin α2β1 Expression and Signaling in a Rat Tail Caudal Intervertebral Disc Degeneration Model
Authors: Yan ZhanJun , Pan YouDong , Wang ShiHui , Cheng MaoHua , Kong HongMei , Sun ChunGuang , Hu Kai , Chen TongLei , Dong QiRong , Chen JianFeng 
Published: August 2016

Study Design.
A three-level rat tail caudal intervertebral disc (IVD) degeneration (IVDD) model was established to study effects of static compression on extracellular matrix (ECM) remodeling and integrin signaling in IVDs during IVDD.

Objective.
The aim of this study was to investigate the effect of compression force on ECM remodeling and integrin signaling in IVDs during IVDD.

Summary of Background Data.
Integrins sense mechanical environment alteration via binding to ECM ligands and trigger intracellular signaling for pathological ECM remodeling during IVDD. However, the role of compression force in ECM remodeling and integrin signaling during IVDD remains elusive.

Methods.
Compared with the classical one-level rat tail IVDD model that exerts axial stress on the 8th to 9th caudal vertebral bodies, a three-level model was established by using an Ilizarov-type apparatus to exert stress on the 7th to 10th caudal vertebral bodies in rat tails for four weeks. To exclude side effects from surgical stab injury on manipulated discs, intact coccygeal (Co) disc Co8–9 was analyzed.

Results.
In three-level IVDD model, significant degeneration of the Co8–9 disc was observed. Quantitative real-time polymerase chain reaction (qRT-PCR) showed elevated mRNA expression of collagen types I, III, and V; matrix metalloproteinases (MMPs) 2, 3, 9, 13, 14; and decreased mRNA expression of collagen type II in Co8–9 disc. Compression loading altered the expression of integrin α2β1 (upregulated) and α10β1 (downregulated) in NP cells, and activated integrin downstream signaling. By contrast, one-level model showed more severe disc degeneration and ECM remodeling. Integrin α1, α2, α11, and β1 were upregulated, whereas α10 was downregulated. Similar activation of integrin signaling was observed.

Conclusion.
Static compression altered collagen and MMP expression, and promoted β1 integrin expression and signaling in IVD. Compared with one-level rat tail IVDD model, three-level model showed milder effects on disc degeneration, ECM remodeling, and integrin expression, suggesting one-level model might involve other causes that induce IVDD via mechanisms independent of compression force.

Level of Evidence: N/A
Tablet-Based eBooks for Young Children: What Does the Research Say?
Authors: Reich Stephanie M. , Yau Joanna C. , Warschauer Mark 
Published: August 2016

ABSTRACT:

Objective:
Young children's use of electronic books (eBooks) is increasing as handheld touch screen devices, such as tablets, become increasingly available. Although older children's reading on tablets has been more broadly investigated, less is known about the impacts of digital reading for infant, toddlers, and preschoolers. This review compares the educational affordances of reading on tablets versus print books for young children's learning.

Method:
A qualitative synthesis of research on tablet-based eReading and young children's learning from screens was conducted.

Results:
When eBooks are designed well, preschool-aged children learn equally well and sometimes more than from print books. However, enhanced eBooks with sounds, animations, and games can distract children and reduce learning. When book-sharing with an adult, conversations during eBook reading are often about the platform while print book conversations are more often about the book content. For young children (0–2 yr), there is a paucity of research, but broader studies on learning from screens suggest limited educational benefits of tablet use for this age group.

Discussion:
The authors recommend that (1) the selection of eBooks (especially enhanced eBooks) be thoughtful as games or animations that are not related to the story content can be distracting for young children, (2) adults share in the reading experience as discussions of the story, text, and characters have been found to enhance comprehension, language development, and print awareness, and (3) tablet eBook use be restricted for infants and toddlers, as they benefit more from face-to-face interaction with caregivers than from interactive screens alone.