bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Latent Tuberculosis Infection on Neurocognitive Functioning and Inflammation in HIV-Infected and Uninfected South Indians
Authors: LaVergne Stephanie , Umlauf Anya , McCutchan Allen , Heaton Robert , Benson Constance , Kumarasamy Nagalingeswaran , Bharti Ajay R. 
Published: April 2020

Background:
HIV-associated neurocognitive disorder persists in some people living with HIV despite optimal antiretroviral therapy. Latent tuberculosis infection (LTBI) may cause systemic inflammation and immune activation that may impair brain function. We assessed cognition and biomarkers of inflammation in both HIV+ and HIV− South Indians with and without LTBI.

Methods:
Adults (≥18 years old) with and without HIV infection were screened for LTBI by interferon-gamma release assays, completed comprehensive neurocognitive assessments, and underwent measurement of serum inflammatory biomarker levels.

Results:
The participants (n = 119) were HIV+/LTBI+ (n = 15), HIV+/LTBI− (n = 50), HIV−/LTBI+ (n = 26), and HIV−/LTBI− (n = 28). HIV+ participants, regardless of LTBI status, had more impaired global deficit scores than HIV− participants (odds ratio = 3.42, P = 0.028, adjusted for sex and education differences). Neither global deficit scores nor impairment rates differed in the LTBI+ group compared with the LTBI− group (P = 0.79 and P = 0.41, respectively). The mean log10 interleukin (IL)-6 and monocyte chemoattractant protein-1 values were significantly higher and high sensitivity C-reactive protein lower in the LTBI+ group than the LTBI− group (P = 0.044, 0.023, and 0.03, respectively, adjusting for HIV status and sex).

Conclusions:
In this cross-sectional study of South Indians, HIV infection, but not LTBI, was associated with increased neurocognitive impairment. Proinflammatory biomarkers (IL-6 and monocyte chemoattractant protein-1, but not tumor necrosis factor-α) were elevated in the LTBI+ groups compared with the LTBI− groups. Biomarkers of immune activation (interferon-γ, macrophage inflammatory protein-1β, IL-2, interferon gamma inducible protein-10, RANTES, and IL-22) did not differ between these groups. Larger longitudinal studies should be conducted to confirm our findings that the effect of LTBI on systemic inflammation or neurocognitive impairment is likely small.
Compounding Benefits of Sentinel Lymph Node Biopsy for Perineal Melanoma
Authors: Patel Ronak A. , Patel Priyanka D. , Ashack Kurt , Borrelli Mimi R. , Trickey Amber , Wan Derrick C. 
Published: April 2020

Introduction
Sentinel lymph node biopsy (SLNB) in the treatment of melanoma is known to provide valuable prognostic information. However, there is no literature describing an overall or disease-specific survival (DDS) benefit of SLNB. In the perineum, melanoma is often more advanced at presentation with current treatment guidelines translated from nonanatomic specific melanoma. As a result, there is little understanding surrounding the role of SLNB in melanoma of the perineum. Our objective is to better understand the therapeutic benefits of SLNB in perineal melanoma.

Methods
The Surveillance, Epidemiology, and End Results program is a large population-based cancer registry including survival data from millions of patients in the United States. The registry was used to generate patient data for analysis from 2004 to 2016. Inclusion criteria included melanoma of the perineum; Breslow depth of 0.80 mm or greater and less than 0.80 mm with ulceration; SLNB or no intervention; clinically negative nodal disease; and available overall survival data.

Results
For 879 patients from 2004 to 2016 with perineal melanoma, significant predictors of reduced survival include older than 75 years, Clark level IV–V, Breslow depth of greater than 4.00 mm, positive ulceration status, regional and distant nodal micrometastases, and clinically positive nodes on presentation. Aggregates for overall survival (OS) and disease-specific survival (DSS) were improved with implementation of SLNB. The 5-year survival rates with SLNB versus no SLNB were 54.0% and 43.0% for OS (P = 0.001) and 57.8% and 53.1% for DSS (P = 0.044). Stratification by Breslow depth yielded significant OS and DSS advantage for greater than 1.00 to 2.00 mm (21.3% benefit, P =0.021, and 16.8% benefit, P = 0.044) and greater than 4.00 mm (30.3% benefit, P = 0.005, and 21.0% benefit, P = 0.007) Breslow depths.

Conclusions and Relevance
Sentinel lymph node biopsy may provide therapeutic benefits in addition to prognostic information for melanoma of the perineum through an increase in 5-year OS.
Incidence and Risk Factors for Postoperative Complications of Rectovaginal Fistula Repairs, Based on Different Surgical Routes
Authors: Chong Woojin , Liu Tracey , Bui Anthony 
Published: April 2020

Objective
To investigate incidence and risk factors for postoperative complications after rectovaginal fistula (RVF) repairs, based on different surgical routes.

Methods
This retrospective cohort study utilized CPT codes to identify RVF repairs performed during 2005 to 2017 from the American College of Surgeons National Surgical Quality Improvement Program database. Demographic/clinical characteristics were compared among different surgical routes. Logistic regression was performed to identify associations.

Results
Among 1398 RVF cases, 1391 were included for final analysis: 159 (11.4%) were performed transabdominally (group 1), 253 (18.2%) transperineally (group 2), and 979 (70.4%) transvaginally/transanally (group 3). Group 1 was older compared with groups 2 and 3 (58.72 ± 15.23 years vs 44.11 ± 13.51 years vs 46.23 ± 14.31 years, P < 0.0001). Race/ethnicity was comparable in all groups with non–Hispanic-White most common. Comparably, group 1 had higher preoperative comorbidities: hypertension requiring medication (P < 0.0001), chronic obstructive pulmonary disease (COPD) (P = 0.0347), preoperative infection (P = 0.002), functional dependence (P = 0.0001), and longer time between hospital admission to operation (P < 0.0001). Group 1 also had longer operating time (P < 0.0001); more American Society of Anesthesiologist ≥ 3 classification (P < 0.0001); and more likely inpatient status (P < 0.0001). The overall incidence of any postoperative complications was 13.2% (25.2%, group 1 vs 15.8%, group 2 vs 10.6%, group 3; P < 0.0001). The most common postoperative complications included unplanned readmission, postoperative superficial surgical site infection, and reoperation. The incidence of severe postoperative complications was 7.9% (17%, group 1 vs 7.1%, group 2 vs 6.6%, group 3, P < 0.0001): group 1 had highest rates of pulmonary embolism (P = 0.0004), deep venous thrombosis (P = 0.0453), bleeding requiring transfusion (P < 0.0001), stroke (P = 0.0207), unplanned reintubation (P = 0.0052), and death (P = 0.0004). Group 1 also had highest rates of minor postoperative complications like urinary tract infection (P = 0.0151), superficial surgical site infection (P = 0.0189), and pneumonia (P = 0.0103). In addition, group 1 had the greatest postoperative length of stay (P < 0.0001). In multivariate analysis, age (P = 0.0096), inpatient status at the time of surgery (P = 0.0004), and operating time >2 to 3 hours (P = 0.0023) were significant predictors of postoperative complications within 30 days after surgery.

Conclusions
The overall incidence of complications after RVF repairs+/−concomitant procedures was 13.2%. The overall incidence of severe complications was 7.9%. The abdominal approach had more postoperative complications but it was not an independent predictor of postoperative complications after RVF repair.
Prevalence and Treatment of Postpartum Stress Urinary Incontinence: A Systematic Review
Authors: Gonzales Alicia L. , Barnes K. Lauren , Qualls Clifford R. , Jeppson Peter C. 
Published: April 2020

Objectives
Many women present for treatment of stress urinary incontinence (SUI) after childbirth. This systematic review describes the efficacy of treatment options for SUI initiated during the 12 months after delivery.

Methods
We conducted a systematic review to identify studies comparing treatment options for SUI initiated in the 12 months after parturition. We searched MEDLINE from inception to February 2019, using Medical Subject Heading terms related to pregnancy and urinary incontinence. Preintervention and postintervention populations were compared using analysis of variance with Fisher least significant difference method used to determine efficacy between groups. Grades for Recommendation, Assessment, Development and Evaluation system was used to categorize quality of evidence as high, moderate, low, or very low.

Results
We double screened 4548 abstracts, identifying 98 articles for full-text review. Seven studies met the eligibility criteria and were included. Compared with a control group, the 4 interventions identified outperformed the control group (P < 0.001) using Fisher (with effect sizes noted): (1) supervised pelvic floor physical therapy (0.76), (2) electrical stimulation (0.77), (3) home physical therapy (PT) (0.44), and (4) surgery (not applicable). Based on Grades for Recommendation, Assessment, Development and Evaluation assessment, there was moderate evidence to support PT and electrical stimulation, with insufficient evidence for surgery. There were no significant differences in parity, age, or body mass index via analysis of variance. The overall strength of evidence is poor for the treatment of postpartum SUI; more data are needed to fully evaluate other treatment options.

Conclusions
All identified interventions demonstrated greater improvement for postpartum SUI over no treatment. Supervised PT ± electrostimulation was the most effective nonsurgical intervention.
#Urogyn: What’s Trending on Instagram? A Cross-sectional Observational Study
Authors: Qin Lei Alexander , El-Neemany Diana , Winkler Harvey , Shalom Dara 
Published: April 2020

Objective
The aim of the study was to identify the prevalence, authorship, and type of information pertaining to topics in urogynecology on Instagram via hashtag and content analysis.

Methods
A list of 20 hashtags consisting of common urogynecologic diagnoses, procedures, and lay terms was derived from the American Urogynecologic Society’s “Patient Fact Sheets.” The top 9 and most recent 30 posts for each hashtag were reviewed for authorship and content type. Content type was divided into the following categories: educational; tagged but unrelated posts; pertinent patient experiences; community building and outreach; advertisements; and humor. Searches were limited to English language posts.

Results
Our search yielded 561,133 posts. The 5 most popular hashtags were pelvic floor (30.6%, n = 171,855), interstitial cystitis (12.8%, n = 71,977), pelvic pain (10.0%, n = 56,505), incontinence (9.3%, n = 52,169), and prolapse (3.9%, n = 21,839). The authorship of the top 9 and most recent 30 posts (n = 537) were as follows: patients (34.6%, n = 186), allied health professionals (29.2%, n = 157), physicians (13.4%, n = 72), and other (22.7%, n = 122). Further authorship and content analysis revealed that allied health professionals authored the most informational posts (45.6%, n = 129) and patients authored the most unrelated (69.4%, n = 43), patient experience (81.7%, n = 125), community building (55.8%, n = 53), and humorous posts (38.5%, n = 10).

Conclusions
More than 500,000 posts related to urogynecology were identified on Instagram. Most posts were authored by patients and allied health professionals with a small contribution from physicians. Greater physician participation may increase the quantity of educational posts and offer a low-cost platform for networking and connecting with patients and other providers.
Financial Feasibility Analysis of a Culturally and Linguistically Competent Hispanic Kidney Transplant Program
Authors: Wang Andrew , Caicedo Juan Carlos , McNatt Gwen , Abecassis Michael , Gordon Elisa J. 
Published: April 2020

Background.
In 2006, Northwestern Medicine implemented a culturally targeted and linguistically congruent Hispanic Kidney Transplant Program (HKTP). The HKTP has been associated with a reduction in Hispanic/Latino disparities in live donor kidney transplantation. This article assessed the financial feasibility of implementing the HKTP intervention at 2 other transplant centers.

Methods.
We examined the impact of the HKTP on staffing costs compared with the total transplant center costs using data from monthly time studies conducted among transplant staff involved in the HKTP. Time studies were conducted during the HKTP preimplementation (2016) and implementation (2017) phases. Labor costs were estimated using data from the time studies and mean salaries from the Department of Labor. We retrospectively examined kidney acquisition and transplant costs at both centers in 2016 and 2017 using data from the Medicare cost reports.

Results.
During preimplementation, center A staff (n = 21) committed 764 hours ($44 607), and center B staff (n = 15) committed 800 hours ($45 193) to establish the HKTP. During implementation, center A staff (n = 19) committed 1125 hours ($55 594), and center B staff (n = 24) committed 1396 hours ($64 170), in delivering the HKTP. Overall, the total costs from the staffing time involved in the HKTP encompassed <1.0% per year (2016 and 2017) of each center’s annual total costs.

Conclusions.
Our findings suggest the financial feasibility of implementing the HKTP and present a potential business case for the HKTP’s implementation at other transplant centers to reduce health disparities in live donor kidney transplantation.
Immuno-informatics Characterization SARS-CoV-2 Spike Glycoprotein for Prioritization of Epitope based Multivalent Peptide Vaccine
Authors: Ismail Saba , Ahmad Sajjad , Azam Syed Sikander 
Published: April 2020

AbstractThe COVID-19 pandemic caused by SARS-CoV-2 is a public-health emergency of international concern and thus calling for the development of safe and effective therapeutics and prophylactics particularly a vaccine to protect against the infection. SARS-CoV-2 spike glycoprotein is an attractive candidate for vaccine, antibodies and inhibitor development because of many roles it plays in attachment, fusion and entry into the host cell. In this study, we characterized the SARS-CoV-2 spike glycoprotein by immune-informatics techniques to put forward potential B and T cell epitopes, followed by the use of epitopes in construction of a multi-epitope peptide vaccine construct (MEPVC). The MEPVC revealed robust host immune system simulation with high production of immunoglobulins, cytokines and interleukins. Stable conformation of the MEPVC with a representative innate immune TLR3 receptor was observed involving strong hydrophobic and hydrophilic chemical interactions, along with enhanced contribution from salt-bridges towards inter-molecular stability. Molecular dynamics simulation in solution aided further in interpreting strong affinity of the MEPVC for TLR3. This stability is the attribute of several vital residues from both TLR3 and MEPVC as shown by radial distribution function (RDF) and a novel analytical tool axial frequency distribution (AFD). Comprehensive binding free energies estimation was provided at the end that concluded major domination by electrostatic and minor from van der Waals. Summing all, the designed MEPVC has tremendous potential of providing protective immunity against COVID-19 and thus has the potential to be considered in experimental studies.
Healing Tissues From the Inside Out: Infusible Biomaterial for Targeting and Treating Inflammatory Tissues via Intravascular Administration
Authors: Spang Martin T. , Middleton Ryan , Diaz Miranda , Wang Raymond , Hunter Jervaughn , Mesfin Joshua , Lazerson Tori S. , Bhatia Saumya , Corbitt James , D’Elia Gavin , Sandoval-Gomez Gerardo , Kandell Rebecca , Kato Takayuki , Igata Sachiyo , Luo Colin , Osborn Kent G. , Cabrales Pedro , Kwon Ester , Contijoch Francisco , Reeves Ryan R. , DeMaria Anthony N. , Christman Karen L. 
Published: April 2020

AbstractBiomaterials, such as extracellular matrix (ECM) hydrogels, have been widely used in preclinical studies as injectable tissue engineering therapies; however, injectable therapies are limited as they can cause localized trauma or organ perforation. We have developed a new ECM therapy, the low molecular weight fraction derived from decellularized, digested ECM, for intravascular infusion. This new form of ECM can be infused after injury, specifically localize to injured tissues by coating the leaky microvasculature, and promote cell survival and tissue repair. In this study, we show the feasibility and targeting of intravascular ECM infusions using models of acute myocardial infarction (MI), traumatic brain injury, and pulmonary arterial hypertension. Furthermore, safety and efficacy were demonstrated in small and large animal models of acute MI following intracoronary infusion, which included using a clinically-relevant catheter in the large animal model. Functional improvements, specifically reduced left ventricular volumes and improved wall motion scores were observed after ECM infusions post-MI. Genes related to tissue repair and inflammation were differential expressed in response to ECM infusions. This study shows proof-of-concept for a new paradigm of delivering pro-healing ECM biomaterials via intravascular infusion to heal tissue from the inside out.
A platform for brain-wide functional ultrasound imaging and analysis of circuit dynamics in behaving mice
Authors: Brunner Clément , Grillet Micheline , Sans-Dublanc Arnau , Farrow Karl , Lambert Théo , Macé Emilie , Montaldo Gabriel , Urban Alan 
Published: April 2020

SUMMARYImaging of large-scale circuit dynamics is crucial to gain a better understanding of brain function, but most techniques have a limited depth of field. Here we describe vfUSI, a platform for brain-wide volumetric functional ultrasound imaging of hemodynamic activity in awake head-fixed mice. We combined high-frequency 1024-channel 2D-array transducer with advanced multiplexing and high-performance computing for real-time 3D Power Doppler imaging at high spatiotemporal resolution (220×280×175-μm3voxel size, up to 6 Hz). In addition, we developed a standardized software pipeline for registration and segmentation based on the Allen Mouse Common Coordinate Framework, allowing for temporal analysis in 268 individual brain regions. We demonstrate the high sensitivity of vfUSI in multiple experimental situations where stimulus-evoked activity can be recorded using a minimal number of trials. We also mapped neural circuitsin vivoacross the whole brain during optogenetic activation of specific cell-types. Moreover, we revealed the sequential activation of sensory-motor regions during a grasping water droplet task. vfUSI will become a key neuroimaging technology because it combines ease of use, reliability, and affordability.
A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification
Authors: Srivastava Avi , Malik Laraib , Sarkar Hirak , Patro Rob 
Published: April 2020

AbstractMotivationDroplet based single cell RNA-seq (dscRNA-seq) data is being generated at an unprecedented pace, and the accurate estimation of gene level abundances for each cell is a crucial first step in most dscRNA-seq analyses. When preprocessing the raw dscRNA-seq data to generate a count matrix, care must be taken to account for the potentially large number of multi-mapping locations per read. The sparsity of dscRNA-seq data, and the strong 3’ sampling bias, makes it difficult to disambiguate cases where there is no uniquely mapping read to any of the candidate target genes.ResultsWe introduce a Bayesian framework for information sharing across cells within a sample, or across multiple modalities of data using the same sample, to improve gene quantification estimates for dscRNA-seq data. We use an anchor-based approach to connect cells with similar gene expression patterns, and learn informative, empirical priors which we provide to alevin’s gene multi-mapping resolution algorithm. This improves the quantification estimates for genes with no uniquely mapping reads (i.e. when there is no unique intra-cellular information). We show our new model improves the per cell gene level estimates and provides a principled framework for information sharing across multiple modalities. We test our method on a combination of simulated and real datasets under various setups.AvailabilityThe information sharing model is included in alevin and is implemented in C++14. It is available as open-source software, under GPL v3, athttps://github.com/COMBINE-lab/salmonas of version 1.1.0.Contactasrivastava@cs.stonybrook.edu,rob@cs.umd.edu
Rank-dependent social inheritance determines social network structure in a wild mammal population
Authors: Ilany Amiyaal , Holekamp Kay E. , Akçay Erol 
Published: April 2020

AbstractThe structure of animal social networks influences survival and reproductive success, as well as pathogen and information transmission. However, the general mechanisms determining social structure remain unclear. Using data on 73,767 social interactions among wild spotted hyenas over 27 years, we show that a process of social inheritance determines how offspring relationships are formed and maintained. The relationships of offspring with other hyenas are similar to those of their mothers over up to six years, and the degree of similarity increases with maternal social rank. The strength of mother-offspring relationship affects social inheritance and is positively correlated with offspring longevity. These results confirm the hypothesis that social inheritance of relationships can structure animal social networks and be subject to adaptive tradeoffs.
A Statistical Framework for Evolutionary Analysis of Recurrent Somatic Mutations in Cancers
Authors: Gu Xun 
Published: April 2020

AbstractCurrent cancer genomics databases have accumulated millions of somatic mutations that remain to be further explored, faciltating enormous high throuput analyses to explore the underlying mechanisms that may contribute to malignant initiation or progression. In the context of over-dominant passenger mutations (unrelated to cancers), the challenge is to identify somatic mutations that are cancer-driving. Under the notion that carcinogenesis is a form of somatic-cell evolution, we developed a two-component mixture model that enables to accomplish the following analyses. (i) We formulated a quasi-likelihood approach to test whether the two-component model is significantly better than a single-component model, which can be used for new cancer gene predicting. (ii) We implemented an empirical Bayesian method to calculate the posterior probabilities of a site to be cancer-driving for all sites of a gene, which can be used for new driving site predicting. (iii) We developed a computational procedure to calculate the somatic selection intensity at driver sites and passenger sites, respectively, as well as site-specific profiles for all sites. Using these newly-developed methods, we comprehensively analyzed 294 known cancer genes based on The Cancer Genome Atlas (TCGA) database.