bluuebunny/crossref_metadata_2025_split huggingface dataset:
PINA 3.0: mining cancer interactome
Authors: Du Yang , Cai Meng , Xing Xiaofang , Ji Jiafu , Yang Ence , Wu Jianmin 
Published: October 2020

AbstractProtein–protein interactions (PPIs) are crucial to mediate biological functions, and understanding PPIs in cancer type-specific context could help decipher the underlying molecular mechanisms of tumorigenesis and identify potential therapeutic options. Therefore, we update the Protein Interaction Network Analysis (PINA) platform to version 3.0, to integrate the unified human interactome with RNA-seq transcriptomes and mass spectrometry-based proteomes across tens of cancer types. A number of new analytical utilities were developed to help characterize the cancer context for a PPI network, which includes inferring proteins with expression specificity and identifying candidate prognosis biomarkers, putative cancer drivers, and therapeutic targets for a specific cancer type; as well as identifying pairs of co-expressing interacting proteins across cancer types. Furthermore, a brand-new web interface has been designed to integrate these new utilities within an interactive network visualization environment, which allows users to quickly and comprehensively investigate the roles of human interacting proteins in a cancer type-specific context. PINA is freely available at https://omics.bjcancer.org/pina/.
Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts
Authors: Freshour Sharon L , Kiwala Susanna , Cotto Kelsy C , Coffman Adam C , McMichael Joshua F , Song Jonathan J , Griffith Malachi , Griffith Obi L , Wagner Alex H 
Published: October 2020

Abstract
The Drug-Gene Interaction Database (DGIdb, www.dgidb.org) is a web resource that provides information on drug-gene interactions and druggable genes from publications, databases, and other web-based sources. Drug, gene, and interaction data are normalized and merged into conceptual groups. The information contained in this resource is available to users through a straightforward search interface, an application programming interface (API), and TSV data downloads. DGIdb 4.0 is the latest major version release of this database. A primary focus of this update was integration with crowdsourced efforts, leveraging the Drug Target Commons for community-contributed interaction data, Wikidata to facilitate term normalization, and export to NDEx for drug-gene interaction network representations. Seven new sources have been added since the last major version release, bringing the total number of sources included to 41. Of the previously aggregated sources, 15 have been updated. DGIdb 4.0 also includes improvements to the process of drug normalization and grouping of imported sources. Other notable updates include the introduction of a more sophisticated Query Score for interaction search results, an updated Interaction Score, the inclusion of interaction directionality, and several additional improvements to search features, data releases, licensing documentation and the application framework.
Prevalence of phase variable epigenetic invertons among host-associated bacteria
Authors: Huang Xueting , Wang Juanjuan , Li Jing , Liu Yanni , Liu Xue , Li Zeyao , Kurniyati Kurni , Deng Yijie , Wang Guilin , Ralph Joseph D , De Ste Croix Megan , Escobar-Gonzalez Sara , Roberts Richard J , Veening Jan-Willem , Lan Xun , Oggioni Marco R , Li Chunhao , Zhang Jing-Ren 
Published: October 2020

AbstractType I restriction-modification (R-M) systems consist of a DNA endonuclease (HsdR, HsdM and HsdS subunits) and methyltransferase (HsdM and HsdS subunits). The hsdS sequences flanked by inverted repeats (referred to as epigenetic invertons) in certain Type I R-M systems undergo invertase-catalyzed inversions. Previous studies in Streptococcus pneumoniae have shown that hsdS inversions within clonal populations produce subpopulations with profound differences in the methylome, cellular physiology and virulence. In this study, we bioinformatically identified six major clades of the tyrosine and serine family invertases homologs from 16 bacterial phyla, which potentially catalyze hsdS inversions in the epigenetic invertons. In particular, the epigenetic invertons are highly enriched in host-associated bacteria. We further verified hsdS inversions in the Type I R-M systems of four representative host-associated bacteria and found that each of the resultant hsdS allelic variants specifies methylation of a unique DNA sequence. In addition, transcriptome analysis revealed that hsdS allelic variations in Enterococcus faecalis exert significant impact on gene expression. These findings indicate that epigenetic switches driven by invertases in the epigenetic invertons broadly operate in the host-associated bacteria, which may broadly contribute to bacterial host adaptation and virulence beyond the role of the Type I R-M systems against phage infection.
The InterPro protein families and domains database: 20 years on
Authors: Blum Matthias , Chang Hsin-Yu , Chuguransky Sara , Grego Tiago , Kandasaamy Swaathi , Mitchell Alex , Nuka Gift , Paysan-Lafosse Typhaine , Qureshi Matloob , Raj Shriya , Richardson Lorna , Salazar Gustavo A , Williams Lowri , Bork Peer , Bridge Alan , Gough Julian , Haft Daniel H , Letunic Ivica , Marchler-Bauer Aron , Mi Huaiyu , Natale Darren A , Necci Marco , Orengo Christine A , Pandurangan Arun P , Rivoire Catherine , Sigrist Christian J A , Sillitoe Ian , Thanki Narmada , Thomas Paul D , Tosatto Silvio C E , Wu Cathy H , Bateman Alex , Finn Robert D 
Published: October 2020

AbstractThe InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing equivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification. Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation. Here, we report the status of InterPro (version 81.0) in its 20th year of operation, and its associated software, including updates to database content, the release of a new website and REST API, and performance improvements in InterProScan.
Determinants of Physical Activity Engagement in Patients With Nonalcoholic Fatty Liver Disease: The Need for an Individualized Approach to Lifestyle Interventions
Authors: O’Gorman Philip , Monaghan Ann , McGrath Marie , Naimimohasses Sara , Gormley John , Norris Suzanne 
Published: October 2020

Abstract

Objectives
Physical activity (PA) is an important non-pharmacological treatment for non-alcoholic fatty liver disease (NAFLD). This study investigated the determinants of PA engagement and awareness of the World Health Organization (WHO) PA guidelines in patients with NAFLD.

Methods
Study participants were 101 patients with NAFLD (median age: 54 [IQR = 15] y; 53 men and 48 women) who completed 4 questionnaires: (1) a PA guideline awareness questionnaire; (2) a PA questionnaire assessing PA levels; and (3) 2 questionnaires assessing perceived barriers and motivators for engaging in PA. Binary logistic regression was performed to assess predictors of PA levels.

Results
Twenty-four percent of participants correctly identified the recommended WHO weekly PA guidelines, and 39% adhered to the guidelines. Lack of willpower, time, and energy were the most frequently cited barrier domains. Scores for lack of willpower (odds ratio [OR] = 1.445, 95% CI = 1.088–1.919) and lack of resources (OR = 1.378, 95% CI = 1.003–1.893), and reporting 3 or more “significant” barrier domains (OR = 5.348, 95% CI = 1.792–15.873) were significant predictors of PA levels. Maintaining health and fitness was the most cited motivator domain and was a significant predictor (OR = 2.551, 95% CI = 1.253–5.208) of PA levels.

Conclusions
This study highlights the lack of awareness of the WHO PA guidelines and the key determinants of PA participation in patients with NAFLD. Determinants of PA should be identified at the individual level to create a personalized approach for PA maintenance for people with NAFLD to promote lifelong participation in PA.

Impact
This study closes a gap in the published data on the determinants of PA engagement in patients with NAFLD.

Lay Summary
Physical inactivity is the fourth leading cause of global mortality and contributes to many chronic inflammatory diseases, including obesity, type 2 diabetes, cardiovascular disease, and nonalcoholic fatty liver disease (NAFLD). People with NAFLD engage in less physical activity compared with people who are healthy, and this study provides new information that clinicians can use to help these patients increase their physical activity participation.
AIRBORNE RADIOMETRIC MAPPING FOR NATURAL RADIATION ASSESSMENT OVER OKITIPUPA SOUTHEAST BELT OF THE BITUMINOUS SAND FIELD OF NIGERIA
Authors: Faruwa Ajibola Richard , Qian Wei , Agbele Alaba Tolulope , Babinisi Ayodeji Bodunde , Yekeen Bolaji Ahmed 
Published: October 2020

Abstract
Airborne radiometric data were used for natural radiation assessment with the view to assess its likely environmental and health impact, which is one of the major factors that may pose some dangers to both physical and biological components especially during the exploitation of bitumen and also use the assessment as a baseline study that could be useful in planning appropriate environmental management programs that will reduce the potential negative effect of exploiting the resources on the environment. To determine the radiation source effects of humans, exposure rate, absorbed dose rate and annual effective dose rate were computed. The results obtained over Okitipupa southeast belt bituminous sand field indicate that the average levels of natural background radiations are generally not considered harmful. The natural activity levels were not above average and the does appear to be well within recommended limits and norms for naturally occurring activity.
Paediatric COVID-19: Milder Presentation—A Silver Lining in Dark Cloud
Authors: Ramteke Sharmila , Tikkas Rajesh , Goel Manjusha , Mandraha Shipra , Shrivastava Jyotsna 
Published: October 2020

Abstract

Objective
To assess the clinico-epidemiological profile of paediatric patients with Corona virus disease 2019 (COVID-19) infection during the pandemic.

Methods
Clinico-epidemiological and laboratory profile of children between 1 month and 14 years were studied between 15 May and 31 July 2020, who had positive nasopharyngeal and oropharyngeal swab for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) by reverse transcriptase–polymerase chain reaction (RT-PCR).

Results
A total of 30 children with median age of 10.5 years (8 months to 14 years) were included in the present study. Sixty percent were boys. Twenty-seven (90%) belonged to an urban area and all 30 children were from a containment area. All were belonging to Kuppuswamy upper lower and lower socioeconomic class. Twenty-one (70%) were asymptomatic. All children had a positive household contact. Symptomatic children had only mild symptoms of fever, dry cough and rhinitis. All were fully vaccinated as per age. Nine (30%) had anaemia. The mean leucocyte count was 7470 ± 2427 (4300–14 100). Leucocytosis was seen in 3 (9%) children. C-reactive protein was found to be raised in only 4 (13%) children. We did not find alteration in sense of smell and taste. No mortality was reported.

Conclusion
COVID-19 in paediatric patients is usually mild. Severe acute respiratory infection is not a major manifestation of COVID 19 infection in children. All children infected by the novel Corona virus-2 in this study, have a documented household contact.
Outcomes From Re-Treatment and Cerebrospinal Fluid Analyses in Patients With Syphilis Who Had Serological Nonresponse or Lack of Seroreversion After Initial Therapy
Authors: Zhang Xiaohui , Shahum Andrea , Yang Li-Gang , Xue Yaohua , Wang Liuyuan , Yang Bin , Zheng Heping , Chen Jane S. , Radolf Justin D. , Seña Arlene C. 
Published: October 2020

Background
We conducted an observational study to determine whether patients with syphilis who do not demonstrate serological cure or lack of seroreversion in nontreponemal (NT) antibody titers after initial therapy benefit from re-treatment and cerebrospinal fluid (CSF) analysis.

Methods
We enrolled patients with syphilis from sexually transmitted disease clinics in Guangzhou, China, who had persistent NT titers after therapy. Serological nonresponse was defined as a <4-fold decline in baseline NT titers after therapy. Lack of seroreversion was defined as demonstrating a ≥4-fold NT titer decline but without seroreversion to negative, or having persistent low-level titers (i.e., 1:1–1:2) after therapy. After consent, we abstracted medical record data regarding syphilis diagnoses, initial and re-treatment regimens, and serological outcomes. Nontreponemal titers were obtained from participants at enrollment and follow-up. We evaluated CSF findings among a subgroup of participants relative to re-treatment.

Results
From March 2012 to February 2016, we enrolled 135 HIV-negative patients with syphilis with persistent NT titers after initial therapy. Among 116 participants with ≥12 months of follow-up, 60 (52%) received re-treatment of syphilis. Overall, there were no significant differences in serological response between those who were re-treated and those who were not among serological nonresponders (29% vs. 27%; P = 1.0) or among participants without seroconversion (41% vs. 37%; P = 0.8). Of 60 participants who underwent CSF analyses, 8 (13%) had CSF abnormalities, but only 2 (3%) met the neurosyphilis criteria after re-treatment.

Conclusions
Most HIV-negative patients with syphilis who have serological nonresponse or lack of seroreversion after therapy do not benefit from re-treatment in the short term, and neurosyphilis is uncommon.
Implementation of a Ponseti Clubfoot Program Decreases Major Surgery: A Quality Improvement Initiative
Authors: Carry Patrick M. , Graham Susan , Whalen Karen , Burke Deborah , Baschal Robin , Holmes Kaley S. , Kohuth Brian , Georgopoulos Gaia , Miller Nancy Hadley 
Published: October 2020

Introduction:
Clubfoot describes a congenital condition. If untreated, clubfoot can cause long-term functional issues. The Ponseti method is the gold-standard treatment; it emphasizes casting over surgery. We identified a high rate of major recurrence in patients with isolated clubfoot at our institution. We implemented a quality improvement intervention to address the recurrences.

Methods:
We established a clubfoot program that aimed to (1) develop a standardized treatment pathway; (2) improve care team education; (3) improve coordination of care with families; and (4) improve documentation. The purpose of this study was to outline our quality improvement intervention and evaluate its success. Data were retrospectively collected from isolated clubfeet before (2003–2007, phase I) and after (2012–2014, phase II) implementation of the clubfoot program. We compared the differences in treatment and major recurrence between the 2 phases using generalized logistic or linear mixed models. Modified Poisson regression models were used to evaluate the association between provider nonadherence and recurrence.

Results:
The pre- (phase I) and post- (phase II) implementation groups included 91 patients (131 feet) and 68 patients (101 feet), respectively. The incidence of major recurrence (odds ratio: 59.5, 95% confidence interval: 7.8–454.4, P < 0.0001) was lower during phase II compared to phase I. Nonadherence with the care pathway was associated with an increased risk of recurrence (risk ratio: 4.1, 95% confidence interval: 1.2–14.3, P = 0.0274).

Conclusions:
The implementation of a clubfoot program was associated with a decrease in major clubfoot surgery and improved adherence to established guidelines for clubfoot management.
Collagenase Treatment of Dupuytren’s Disease with Minimum 5-Year Follow-Up: Recurrence, Reintervention, and Satisfaction
Authors: Zhang Dafang , Earp Brandon E. , Benavent Kyra A. , Blazar Philip 
Published: October 2020

Background:
The objective of this study was to determine the rates of patient satisfaction, perceived recurrence of flexion deformity, and additional treatment after collagenase clostridium histolyticum treatment for Dupuytren’s contracture at a minimum of 5-year follow-up.

Methods:
A retrospective study was performed of 199 digits in 142 patients who underwent collagenase clostridium histolyticum treatments from April of 2010 to December of 2013 with a minimum of 5-year follow-up. Patients were contacted by telephone regarding perceived recurrence, additional treatment, satisfaction, and willingness to undergo this treatment again.

Results:
At an average 7.2-year follow-up, 160 of 199 digits (80 percent) had perceived recurrence, and 105 of 199 digits (53 percent) underwent additional treatment. Average satisfaction was 6.5 on a Likert scale ranging from 1 to 10, and 67 percent would undergo collagenase clostridium histolyticum treatment again. Multivariable logistic regression analysis showed that higher Charlson Comorbidity Index (OR, 0.77; 95 percent CI, 0.63 to 0.93) and isolated metacarpophalangeal joint involvement (OR, 0.53; 95 percent CI, 0.29 to 0.97) were associated with decreased odds of additional treatment, and higher American Society of Anesthesiologists physical status classification (OR, 2.49; 95 percent CI, 1.35 to 4.48) and nonsmoker status (OR, 0.23; 95 percent CI, 0.09 to 0.59) were associated with willingness to undergo the treatment again.

Conclusions:
Patients may be counseled that the long-term perceived recurrence rate of Dupuytren’s contractures after collagenase clostridium histolyticum treatment is high, and more than half of patients seek additional treatment. Satisfaction and willingness to undergo collagenase clostridium histolyticum treatment decrease with perceived recurrence.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
Videoscope-Assisted Cleft Palate Surgery: Rationale, Experience, and Technical Implementation
Authors: Levites Heather A. , Sergesketter Amanda R. , Sharif-Askary Banafesh , Hollenbeck Scott T. , Allori Alexander C. , Marcus Jeffrey R. 
Published: October 2020

Summary:
Limited visibility characteristic of cleft palate repair presents both ergonomic and educational challenges to cleft surgeons. Despite widespread recognition and reporting, posture-related spine disorders continue to represent a significant and potentially career-limiting problem for cleft/craniofacial surgeons. In addition, education and participation during palate repairs is difficult because of visual field constraints. At the authors’ institution, a novel videoscope system was designed and implemented to (1) provide visualization for all surgical team members during palate operations, (2) facilitate active resident education, and (3) improve surgeon ergonomics. The authors’ prior report demonstrated proof of concept for this method, which is now used in all cleft palate operations at their center. The purpose of this report is to share the detailed methodology to facilitate implementation by others and a retrospective review of the authors’ experience before and after implementation. Video demonstration of the videoscope setup and a representative, recorded case are provided. The use of the videoscope was feasible in palatoplasties regardless of palatal phenotype and repair technique and did not have an effect on operative time. Subjectively, the authors report reduced procedure time in cervical flexion and subjectively improved musculoskeletal strain associated with videoscope use. Importantly, use of this system also provided complete visualization for all operating room team members and enabled enhanced resident autonomy during palate operations. Finally, it has facilitated the creation and archive of high-definition educational videos with unparalleled perspective. The equipment required to implement the system is likely already available in many medical centers. Adoption of this system may provide an opportunity to improve posture and teaching capabilities for cleft surgeons.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
Identifying barriers and facilitators to physical activity for people with scleroderma: A nominal group technique study
Authors: Harb Sami , Cumin Julie , Rice Danielle B. , Peláez Sandra , Hudson Marie , Bartlett Susan J. , Roren Alexandra , Furst Daniel E. , Frech Tracy M. , Nguyen Christelle , Nielson Warren R. , Thombs Brett D. , Shrier Ian ,   SPIN-PACE Patient Advisory Team
Published: October 2020

AbstractPurposeTo identify physical activity barriers and facilitators experienced by people with systemic sclerosis (SSc; scleroderma).Materials and MethodsWe conducted nominal group technique sessions with SSc patients who shared barriers to physical activities, barrier-specific facilitators, and general facilitators. Participants rated importance of barriers and likelihood of using facilitators from 0-10, and indicated whether they had tried facilitators. Barriers and facilitators across sessions were subsequently merged to eliminate overlap; edited based on feedback from investigators, patient advisors, and clinicians; and categorized.ResultsWe conducted nine sessions (n=41 total participants) and initially generated 181 barriers, 457 barrier-specific facilitators, and 20 general facilitators. The number of consolidated barriers (barrier-specific facilitators in parentheses) for each category were: 14 (61) for health and medical; 4 (23) for social and personal; 1 (3) for time, work, and lifestyle; and 1 (4) for environmental. There were 12 consolidated general facilitators. The consolidated items with ≥ 1/3 of participants’ ratings ≥ 8 were: 15 barriers, 69 barrier-specific facilitators, and 9 general facilitators.ConclusionsPeople with SSc reported many barriers related to health and medical aspects of SSc and several barriers in other categories. They reported facilitators to remain physically active despite the barriers.Implications for RehabilitationPeople with scleroderma experience difficulty being physically active due to the diverse and often severe manifestations of the disease, including involvement of the skin, musculoskeletal system, and internal organs.In addition to regular care of scleroderma-related symptoms, patients overcome many exercise challenges by selecting physical activities that are comfortable for them, adjusting the intensity and duration of activities, adapting activities, and using adapted equipment or other materials to reduce discomfort.Rehabilitation professionals should help people with scleroderma to tailor activity options to their capacity and needs when providing care and advice to promote physical activity.