bluuebunny/crossref_metadata_2025_split huggingface dataset:
A global network of biomedical relationships derived from text
Authors: Percha Bethany , Altman Russ B 
Published: February 2018

AbstractMotivationThe biomedical community’s collective understanding of how chemicals, genes and phenotypes interact is distributed across the text of over 24 million research articles. These interactions offer insights into the mechanisms behind higher order biochemical phenomena, such as drug-drug interactions and variations in drug response across individuals. To assist their curation at scale, we must understand what relationship types are possible and map unstructured natural language descriptions onto these structured classes. We used NCBI’s PubTator annotations to identify instances of chemical, gene and disease names in Medline abstracts and applied the Stanford dependency parser to find connecting dependency paths between pairs of entities in single sentences. We combined a published ensemble biclustering algorithm (EBC) with hierarchical clustering to group the dependency paths into semantically-related categories, which we annotated with labels, or ‘themes’ (‘inhibition’ and ‘activation’, for example). We evaluated our theme assignments against six human-curated databases: DrugBank, Reactome, SIDER, the Therapeutic Target Database, OMIM and PharmGKB.ResultsClustering revealed 10 broad themes for chemical-gene relationships, 7 for chemical-disease, 10 for gene-disease and 9 for gene–gene. In most cases, enriched themes corresponded directly to known database relationships. Our final dataset, represented as a network, contained 37 491 thematically-labeled chemical-gene edges, 2 021 192 chemical-disease edges, 136 206 gene-disease edges and 41 418 gene–gene edges, each representing a single-sentence description of an interaction from somewhere in the literature.Availability and implementationThe complete network is available on Zenodo (https://zenodo.org/record/1035500). We have also provided the full set of dependency paths connecting biomedical entities in Medline abstracts, with associated sentences, for future use by the biomedical research community.Supplementary informationSupplementary data are available at Bioinformatics online.
Mitigating the adverse impact of batch effects in sample pattern detection
Authors: Fei Teng , Zhang Tengjiao , Shi Weiyang , Yu Tianwei 
Published: February 2018

Abstract

Motivation
It is well known that batch effects exist in RNA-seq data and other profiling data. Although some methods do a good job adjusting for batch effects by modifying the data matrices, it is still difficult to remove the batch effects entirely. The remaining batch effect can cause artifacts in the detection of patterns in the data.

Results
In this study, we consider the batch effect issue in the pattern detection among the samples, such as clustering, dimension reduction and construction of networks between subjects. Instead of adjusting the original data matrices, we design an adaptive method to directly adjust the dissimilarity matrix between samples. In simulation studies, the method achieved better results recovering true underlying clusters, compared to the leading batch effect adjustment method ComBat. In real data analysis, the method effectively corrected distance matrices and improved the performance of clustering algorithms.

Availability and implementation
The R package is available at: https://github.com/tengfei-emory/QuantNorm.

Supplementary information
Supplementary data are available at Bioinformatics online.
CAR T-cell therapy for glioblastoma: recent clinical advances and future challenges
Authors: Bagley Stephen J , Desai Arati S , Linette Gerald P , June Carl H , O’Rourke Donald M 
Published: February 2018

Abstract
In patients with certain hematologic malignancies, the use of autologous T cells genetically modified to express chimeric antigen receptors (CARs) has led to unprecedented clinical responses. Although progress in solid tumors has been elusive, recent clinical studies have demonstrated the feasibility and safety of CAR T-cell therapy for glioblastoma. In addition, despite formidable barriers to T-cell localization and effector function in glioblastoma, signs of efficacy have been observed in select patients. In this review, we begin with a discussion of established obstacles to systemic therapy in glioblastoma and how these may be overcome by CAR T cells. We continue with a summary of previously published CAR T-cell trials in GBM, and end by outlining the key therapeutic challenges associated with the use of CAR T cells in this disease.
The Importance of Wall Apposition in Flow Diverters
Authors: Aquarius René , de Korte Antonius , Smits Debby , Gounis Matthew , Verrijp Kiek , Driessen Léon , Leenders William , de Vries Joost 
Published: February 2018

Abstract

BACKGROUND
It is assumed that high pore densities in flow diverters (FDs) are beneficial for intracranial aneurysm (IA) healing. However, various animal studies are not conclusive on the issue, suggesting that other factors are in play. One important factor might be wall apposition.

OBJECTIVE
To (1) determine the relationship between FD pore density and aneurysm occlusion, and (2) determine the relationship between FD wall apposition and aneurysm occlusion.

METHODS
Saccular aneurysms were microsurgically created in the aorta of 36 Wistar rats. Twelve rats received a low pore density FD (10 pores/mm2), 12 rats received a high pore density FD (23 pores/mm2), and the remaining 12 rats served as a control group. Six animals from each group were sacrificed 1 and 3 mo after surgery. We determined aneurysm occlusion, the number of struts not in contact with the aorta wall, and the average distance from malapposed struts to aorta wall through histology.

RESULTS
No significant differences were found in aneurysm occlusion between the low pore density and high pore density groups (P > .05) after 1 and 3 mo of follow-up. The average number of malapposed struts was lower for the occluded aneurysm group (4.4 ± 1.9) compared to the nonoccluded aneurysm group (7.7 ± 2.6, P < .01). The average distance between malapposed struts and parent artery wall was lower for the occluded aneurysm group (33.9 μm ± 11.5 μm) than for the nonoccluded aneurysm group (48.7 μm ± 18.8 μm, P < .05).

CONCLUSION
Wall apposition is more important than pore density for aneurysm occlusion.
Satisfaction With an Intensive Interdisciplinary Pain Treatment for Children and Adolescents
Authors: Stahlschmidt Lorin , Zernikow Boris , Wager Julia 
Published: February 2018

Objectives:
Although treatment satisfaction is recommended in the Pediatric Initiative on Methods, Measurement, and Pain Assessment in Clinical Trials (PedIMMPACT) as a core outcome measure in pediatric chronic pain clinical trials, no results regarding this outcome measure have been reported to date for intensive interdisciplinary pain treatment in children and adolescents. The aim of the present study was to close this gap and investigate the treatment satisfaction of pediatric patients with different chronic pain disorders who received intensive interdisciplinary pain treatment and who were followed up over 4 years.

Methods:
Treatment satisfaction and treatment outcome were assessed immediately after and 6, 12, and 48 months after intensive interdisciplinary pain treatment for N=104 patients (Mage=13.5; SD=2.2).

Results:
Patients and their parents were highly satisfied with the treatment and strongly agreed in their ratings. Emotional distress before treatment and younger age increased the risk of being dissatisfied. Analyses revealed that treatment satisfaction was independent of treatment outcome.

Discussion:
Taken together, the results show that treatment satisfaction is not associated with treatment outcome. A global judgment of satisfaction seems to be an independent outcome measure but may be inappropriate for measuring the multifaceted construct of satisfaction. Instead, separate satisfaction ratings in specific areas, for example, treatment methods or outcome, may be more suitable.
Maternal Mental Representations of the Child and Mobile Phone Use During Parent-Child Mealtimes
Authors: Radesky Jenny , Leung Christy , Appugliese Danielle , Miller Alison L. , Lumeng Julie C. , Rosenblum Katherine L. 
Published: February 2018

ABSTRACT

Objective:
Qualities of the parent-child relationship have not been explored as predictors of parent mobile device use during parent-child activities.

Methods:
In 195 mother-child dyads enrolled in an ongoing cohort study, maternal mental representations of their child (ability to reflect on their child's characteristics, emotional state, and their parenting role) were evaluated through the Working Model of the Child Interview (WMCI), a validated semistructured interview. WMCI scale scores were examined as predictors of active maternal mobile device use during parent-child eating encounters (videotaped home mealtimes and a structured laboratory-based protocol) in multivariate logistic regression models.

Results:
Children were aged 5.9 years (SD: 0.7), mothers were aged 31.5 years (SD: 7.4), and 73.3% of mothers were of white non-Hispanic race/ethnicity. During the family mealtime, 47 (24.1%) mothers actively used a mobile device at least once, whereas during the structured eating protocol, 44 (22.6%) mothers used a device. Controlling for maternal race/ethnicity, education level, and child's sex, WMCI subscales were associated with device use during home mealtimes (higher Child Difficulty) and the eating protocol (higher Child Difficulty and lower Richness of Perceptions and Caregiving Sensitivity).

Conclusion:
Maternal mental representations of their child were significantly associated with using mobile devices during eating encounters. More research studies are needed to understand directionality and longer-term associations between mobile device use and parent-child relationship characteristics.
Symptoms of Depression and Anxiety as Barriers to Participation in Cardiac Rehabilitation Programs Among Arab and Jewish Patients in Israel
Authors: Vilchinsky Noa , Reges Orna , Leibowitz Morton , Khaskia Abdulrahim , Mosseri Morris , Kark Jeremy D. 
Published: February 2018

Purpose:
Despite its proven efficacy, low participation rates in cardiac prevention and rehabilitation programs (CPRPs) prevail worldwide, especially among ethnic minorities. This is strongly evident in Israel's Arab minority. Since psychological distress has been found to be associated with CPRP participation and minorities are subjected to higher levels of distress, it is plausible that distress may be an important barrier for CPRP participation among minority patients. The current prospective study assessed the contribution of depression and anxiety symptoms to participation in a CPRP after acute coronary syndrome, both in the enrollment phase and when considering adherence over time, among Jewish (majority) and Arab (minority) patients in Israel.

Methods:
Patients were interviewed during hospitalization about their emotional status and at a 6-mo follow-up concerning participation in a CPRP. Analyses were performed on 397 patients. The Brief Symptom Inventory was used. Logistic regression modeling was applied.

Results:
Symptoms of depression, but not anxiety, were frequently observed among Arab patients compared with their Jewish counterparts. In analyses adjusted for age, sex, ethnicity, and sociodemographic and clinical characteristics, having symptoms of anxiety was associated with less participation in a CPRP, evident for both Jews and Arabs; this association was less evident for symptoms of depression. Multivariable adjusted models did not show a significant association of symptoms of anxiety or depression with adherence in a CPRP. Accounting for psychological distress did not reduce the sharp difference between Jews and Arabs in CPRP participation.

Conclusion:
Symptoms of distress may serve as barriers to CPRP participation, regardless of ethnic origin.
Incorporating Longitudinal Comorbidity and Acute Physiology Data in Template Matching for Assessing Hospital Quality
Authors: Hu Wenqi , Chan Carri W. , Zubizarreta José R. , Escobar Gabriel J. 
Published: February 2018

Objective:We sought to build on the template-matching methodology by incorporating longitudinal comorbidities and acute physiology to audit hospital quality.Study Setting:Patients admitted for sepsis and pneumonia, congestive heart failure, hip fracture, and cancer between January 2010 and November 2011 at 18 Kaiser Permanente Northern California hospitals.Study Design:We generated a representative template of 250 patients in 4 diagnosis groups. We then matched between 1 and 5 patients at each hospital to this template using varying levels of patient information.Data Collection:Data were collected retrospectively from inpatient and outpatient electronic records.Principal Findings:Matching on both present-on-admission comorbidity history and physiological data significantly reduced the variation across hospitals in patient severity of illness levels compared with matching on administrative data only. After adjustment for longitudinal comorbidity and acute physiology, hospital rankings on 30-day mortality and estimates of length of stay were statistically different from rankings based on administrative data.Conclusions:Template matching–based approaches to hospital quality assessment can be enhanced using more granular electronic medical record data.
Implementation of an Oxytocin Checklist to Improve Clinical Outcomes
Authors: Sundin Courtney , Mazac Lauren , Ellis Kathleen , Garbo Candon 
Published: February 2018

AbstractBackground:Oxytocin is one of the most common drugs administered in obstetrics. Since its designation as a high-alert medication by the Institute for Safe Medication Practices in 2007, there has been much attention to oxytocin administration during labor. Oxytocin is generally safe when administered correctly, but adverse perinatal outcomes can occur during uterine tachysystole.Purpose:The purpose of this project was to evaluate and compare results of maternal and fetal outcomes of induction of labor for women at term prior to and after implementation of a newly developed oxytocin checklist.Project Design and Methods:To evaluate the practice change associated with the implementation of the new oxytocin checklist, 200 cases based on retrospective medical record reviews were compared with 200 cases after implementation.Results:Use of the checklist was associated with several significant clinical outcomes, including decreases in tachysystole, decreases in cesarean births for concern about fetal status based on electronic fetal monitoring data, decreases in length of first stage labor, and decreases in maximum dose of oxytocin.Clinical Implications:Results are similar to previous research. Early physician buy-in, clinical team education, and ongoing evaluation enhanced facilitation of the oxytocin checklist. Clinical outcomes were favorable.
Perceptions of Adult Women on Losing Their Mothers at an Early Age
Authors: Gunn Jennie , Huebner Carroll Gunn , McCoy Kristen 
Published: February 2018

Abstract

Purpose:
To explore the lived experience of women over the age of 21 who lost their mothers before the age of 18.

Methods:
Using qualitative methodology, motherless child–adult women were gathered through emails, word of mouth, and snowballing techniques. Interviews were conducted at the convenience of the women. The women coparticipated with identification of emerging themes using thematic analysis.

Results:
Eight women who lost their mothers before the age of 18 participated. Eight themes emerged: (1) Understanding: For wounded hearts only; (2) Coming apart: Finding my mother's daughter and self-worth; (3) Unconditional love: Grieving for and identifying with my champion; (4) Finding help: Filling the empty place with God; (5) Pitying the motherless child: Making it worse; (6) Filling in: Others as mother; (7) The ebb and flow: Grieving; and (8) Becoming mother: Taking on the Role.

Clinical Implications:
The nurse has the opportunity to improve care for women who lost their mothers before the age of 18 years. During pregnancy, childbirth, and childrearing, the woman may feel sad and anxious without the guidance of her mother. Special ways of caring may be instituted to provide her comfort such as allowing and encouraging her to bring a special item of her mother's to procedures and events so that she may feel connected with her, allowing someone to stand in for her mother, perhaps assisting in finding of another motherless child adult to be with her as needed, and the voicing of understanding of her loss while remaining nonjudgmental about her emotions during these times.
The Effect of Radiation on Quality of Life throughout the Breast Reconstruction Process: A Prospective, Longitudinal Pilot Study of 200 Patients with Long-Term Follow-Up
Authors: Devulapalli Chris , Bello Ricardo J. , Moin Emily , Alsobrooks James , Fallas Pablo Baltodano , Ohkuma Rika , Manahan Michele A. , Sacks Justin M. , Cooney Carisa M. , Rosson Gedge D. 
Published: February 2018

Background:
Despite well-established correlation of postmastectomy radiotherapy and surgical complications in breast reconstruction, its impact on patient reported outcomes is less clear. We sought to determine the effect of postmastectomy radiotherapy on patient reported outcomes throughout the breast reconstruction process.

Methods:
Patients undergoing prosthetic and autologous breast reconstruction from November 2010 to June 2013 were prospectively followed with BREAST-Q surveys (preoperatively, after expander placement, and 6 and 12 months after final reconstruction). Paired t test, Wilcoxon rank sum test, and multiple linear regression were used to determine the effect of radiation on patient reported outcomes.

Results:
Two hundred patients were included in the study, of which 51 (25.5 percent) received postmastectomy radiotherapy. Prosthetic reconstruction was performed in 75 patients (37.5 percent), autologous reconstruction was performed in 118 (59 percent), and pure fat grafting was performed in seven (3.5 percent). At one-year follow-up, the nonirradiated group reported higher BREAST-Q scores when compared with the irradiated group, in Satisfaction with Breasts (p = 0.003), Psychosocial Well-being (p = 0.003), Sexual Well-being (p < 0.001), Physical Well-being of Chest (p = 0.024), and Satisfaction with Outcome (p = 0.03). When accounting for baseline values, Satisfaction with Breasts and Physical Well-being of Chest significantly worsened in irradiated patients undergoing prosthetic reconstruction, an effect not seen with autologous reconstructions. All irradiated patients significantly worsened in Psychosocial Well-being and Sexual Well-being scores.

Conclusions:
Postmastectomy radiotherapy is associated with worse patient reported outcomes following breast reconstruction. Autologous reconstruction can mitigate patient dissatisfaction in some domains.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, II.
Sifting through the Evidence: A Comprehensive Review and Analysis of Neurotization in Breast Reconstruction
Authors: Weissler Jason M. , Koltz Peter F. , Carney Martin J. , Serletti Joseph M. , Wu Liza C. 
Published: February 2018

Background:
An untoward outcome following breast reconstruction is diminished or complete loss of sensation. As the reconstructive paradigm continues to evolve, sensory restoration following reconstruction remains a research focus. Despite the multitude of published outcomes, there is marked heterogeneity across studies, thus confounding published outcomes. This study critically appraises the literature to summarize outcomes and establish a framework to guide clinical practice and future research.

Methods:
A literature review was conducted according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines in an effort to perform a meta-analysis. The Ovid MEDLINE, PubMed, Embase, Scopus, Cochrane, and ClinicalTrials.gov online databases were queried to capture all publications between 1990 and 2017 that investigated postreconstruction breast sensation. The primary outcome of interest was breast sensation following both implant-based and autologous reconstruction with or without neurotization. Secondary outcomes of interest included time to sensory testing and patient-reported outcomes.

Results:
Overall, 503 titles were screened, from which 37 articles were ultimately included for analysis, accounting for 1299 patients. There was major methodologic variability and inconsistent measurable outcomes across studies. It can be deduced that postoperative sensation returns spontaneously and unpredictably, neurotization enhances the magnitude and rapidity of sensory restoration when compared to nonneurotized reconstruction, and a sensate reconstruction improves patient-reported outcomes.

Conclusions:
Significant study design discrepancies exist, making it difficult to combine data and assess results. To effectively study breast sensation and the impact of neurotization, future investigation will depend on standardizing the way in which breast sensation is measured.
Effects of Botulinum Toxin on Improving Facial Surgical Scars: A Prospective, Split-Scar, Double-Blind, Randomized Controlled Trial
Authors: Hu Li , Zou Yun , Chang Shih-Jen , Qiu Yajing , Chen Hui , Gang Ma , Jin Yunbo , Lin Xiaoxi 
Published: February 2018

Background:
Early intervention might improve the quality of surgical scars. Botulinum toxin type A has been shown to improve surgical scars in the past decade. The purpose of this study was to evaluate the effect of botulinum toxin type A on surgical facial scars.

Methods:
In this prospective, split-scar, double-blind, randomized controlled trial, 16 consecutive patients who underwent facial surgery between June and October of 2015 were enrolled. Botulinum toxin type A was injected randomly into half of each surgical wound closure immediately after surgery. The scars were assessed independently by two plastic surgeons at a 6-month follow-up visit using the Vancouver Scar Scale and the visual analogue scale. The scar width was also measured.

Results:
Fourteen patients completed the study. The visual analogue scale score and scar width measurements revealed a significant improvement in appearance and narrower scars for the botulinum toxin type A–treated halves of the scars (p = 0.046 and p = 0.001, respectively). The mean Vancouver Scar Scale score was 4.68 for the botulinum toxin type A–injected group and 5.24 for the control group (p = 0.15). In addition, the Vancouver Scar Scale height score was significantly different between the two groups (p = 0.008).

Conclusion:
This study demonstrates that early postsurgical botulinum toxin injections can produce better, narrower, and flatter facial surgical scars.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, II.