bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultra-mini Percutaneous Hepatolithotomy in Patients With Large and Multiple Hepatolithiasis
Authors: Öztürk Ahmet , Sönmez Mehmet Giray , Bakdik Süleyman , Ecer Gökhan , Altinkaya Nurullah , Ataseven Hüseyin , Aksoy Faruk 
Published: September 2020

Background:
In this study, we applied the ultra-mini percutaneous hepatolithotomy (UM-PHL) technique on hepatolithiasis patients with multiple and large stones on which other minimally invasive methods failed, and our aim was to report its results, sharing in series for the first time.

Materials and Methods:
Preoperative and postoperative data, laboratory parameters, radiologic findings, and preoperative and postoperative details were recorded for a total of 14 patients for whom the UM-PHL technique was applied between April 2017 and December 2019. As all patients had multiple stones and extreme stone load and had bile duct surgery, they did not have a normal anatomy. All patients were radiologically confirmed to have had preprocedural magnetic retrograde cholangiopancreatography.

Results:
Operation duration of the patients was 137.6±44.9 minutes, while intraoperative blood loss was 69.2±24.9 mL, drainage catheter removal time was 2.85±0.86 days, and the hospitalization time was 4.28±2.55 days. Intraoperative balloon dilation was applied to enlarge the stricture area in 5 patients (35.7%). On the basis of the Clavien-Dindo classification, grade 2 complication was observed in 2 patients (14.2%) due to postoperative cholangitis. Patients were followed up for an average of 15 months, and nonsymptomatic radiologic stone recurrence was detected in the 12th month control of 1 patient (7.1%).

Conclusion:
The UM-PHL technique is a successful method that facilitates stone clearance by providing minimal dilatation through percutaneous intervention and by using instruments with small diameter, and it can safely be applied with its low complication level, low recurrence ratio, and short hospitalization time.
Using Digital Ethnography to Understand the Experience of Women With Pelvic Organ Prolapse
Authors: Gonzalez Gabriela , Vaculik Kristina , Khalil Carine , Zektser Yuliya , Arnold Corey , Almario Christopher V. , Spiegel Brennan M.R. , Anger Jennifer T. 
Published: September 2020

Objective
To characterize the decision-making process and illness experience of women with pelvic organ prolapse (POP) using large-scale social media analysis.

Methods
Digital ethnographic analysis of online posts identified through data mining was performed. Grounded theory methodology was applied to 200 posts via traditional hand coding. To supplement our qualitative approach, we applied a Latent Dirichlet Allocation probabilistic topic modeling process to review the entire data set of identified posts to ensure thematic saturation.

Results
There were 3451 posts by 2088 unique users from 117 websites worldwide that were identified via social media data mining. We found that the anonymity of online forums allowed for information and support exchange among women with POP. Our analysis revealed that the exchange of online information aids in the decision-making process and, in some instances, appears to be the primary source of information. There was confusion about the anatomical and surgical complexities of prolapse. Our study also identified misconceptions, perceived risk factors, prevention methods, and management recommendations that were discussed online.

Conclusions
This large-scale online community-based analysis demonstrated the utility of social media to better understand women’s experiences with POP. Thematic findings highlighted essential concerns and challenges involved in the surgical decision-making process and the understating of the anatomical complexity of sector defects, specifically to cystocele, rectocele, State specific defects.
Operationalizing Postdischarge Recovery From Laparoscopic Sacrocolpopexy for the Preoperative Consultative Visit
Authors: Heit Michael , Carpenter Janet S. , Chen Chen X. , Rand Kevin L. 
Published: September 2020

Objective
The objective was to establish a threshold for postdischarge surgical recovery from laparoscopic sacrocolpopexy for the preoperative consultative visit to answer the “what is my recovery time?” question.

Methods
Study participants (N = 171) with stage 2 or worse pelvic organ prolapse undergoing laparoscopic sacrocolpopexy who completed postoperative surveys at 4 time points. Postdischarge Surgical Recovery 13 (PSR13) scores were anchored to a Global Surgical Recovery (GSR) tool (if 100% recovery is back to your usual health, what percentage of recovery are you now?). Weighted mean PSR13 scores were calculated as a sum of the products variable when patients considered themselves 80 to less than 85, 85 to less than 90, 90 to less than 95, or 95 to 100 percent recovered on the GSR tool. The percentage of study participants recovered at postdischarge day 7, 14, 42, and 90 was calculated based on a comparison between the GSR scores and weighted mean PSR13 scores.

Results
A PSR13 score of 80 or greater, corresponding to 85% or greater recovery, was seen in 55.6% (42 days) and 50.9% (90 days) of study participants, respectively, establishing this numeric threshold as representing “significant” postdischarge recovery after laparoscopic sacrocolpopexy. At 14 days after discharge, only 16.4% of the study population achieved this PSR13 score.

Conclusions
Most study subjects were “significantly” recovered at 42 days after laparoscopic sacrocolpopexy using a PSR13 score of 80 or greater as a numeric threshold. There is a need to determine the population percentage of recovered study subjects at 30, 60, and beyond 90 days from laparoscopic sacrocolpopexy.
Composite Outcomes After Posterior Colporrhaphy With and Without Biologic Graft Augmentation
Authors: Winkelman William D. , Macharia Annliz , Bharadwa Sonya , Bharadwaj Maheetha , Hacker Michele R. , Rosenblatt Peter L. 
Published: September 2020

Objectives
To compare subjective and objective failure after posterior colporrhaphy with and without biologic graft augmentation.

Methods
We conducted a retrospective chart review and telephone survey of patients who underwent a posterior colporrhaphy with and without biologic graft augmentation from 2005 to 2019. Patients who underwent a sacrocolpopexy, uterosacral ligament suspensions, or anterior sacrospinous ligament fixation were excluded. We determined objective, subjective, and composite failure rates.

Results
Although 137 patients met eligibility criteria, 56 did not have valid contact information and, therefore, were excluded from the study. Of the 81 with valid contact information, 67 (83%) agreed to participate. There were 24 (36%) who had a native tissue repair and 43 (64%) who had biologic graft augmentation. Median telephone follow-up was 73 months (interquartile range [IQR], 36–117). Objective failure was similar for the biologic graft (37%) and the native tissue (42%) groups (P = 0.72). Subjective failure was twice as likely among the biologic graft group (60%) compared with the native tissue group (33%, P = 0.03). Patients with a biologic graft reported a median Pelvic Floor Distress Inventory-Short Form 20 improvement of 31 (IQR, 8–33), while those with a native tissue repair reported a median improvement of 45 (IQR, 4–46). Overall, 78% were satisfied, 85% would recommend the procedure, and 84% reported symptomatic improvement. Reoperation occurred for 15% of patients.

Conclusion(s)
Although biologic graft-augmented posterior colporrhaphy may be a safe and effective treatment option, the use of biologic grafts in the posterior compartment does not appear to confer a significant long-term benefit to traditional posterior colporrhaphy.
Self-Supervised Natural Image Reconstruction and Large-Scale Semantic Classification from Brain Activity
Authors: Gaziv Guy , Beliy Roman , Granot Niv , Hoogi Assaf , Strappini Francesca , Golan Tal , Irani Michal 
Published: September 2020

AbstractReconstructing natural images and decoding their semantic category from fMRI brain recordings is challenging. Acquiring sufficient pairs of images and their corresponding fMRI responses, which span the huge space of natural images, is prohibitive. We present a novelself-supervisedapproach that goes well beyond the scarce paired data, for achieving both: (i) state-of-the art fMRI-to-image reconstruction, and (ii) first-ever large-scale semantic classification from fMRI responses. By imposing cycle consistency between a pair of deep neural networks (from image-to-fMRI & from fMRI-to-image), we train our image reconstruction network on a large number of “unpaired” natural images (images without fMRI recordings) from many novel semantic categories. This enables to adapt our reconstruction network to a very rich semantic coverage without requiring any explicit semantic supervision. Specifically, we find that combining our self-supervised training withhigh-level perceptual losses, gives rise to new reconstruction & classification capabilities. In particular, this perceptual training enables to classify well fMRIs of never-before-seen semantic classes,without requiring any class labels during training. This gives rise to: (i) Unprecedented image-reconstruction from fMRI of never-before-seen images (evaluated by image metrics and human testing), and (ii) Large-scale semantic classification of categories that were never-before-seen during network training.Such large-scale (1000-way) semantic classification from fMRI recordings has never been demonstrated before. Finally, we provide evidence for the biological consistency of our learned model.
A neural network-based framework to understand the Type 2 Diabetes (T2D)-related alteration of the human gut microbiome
Authors: Guo Shun , Zhang Haoran , Chu Yunmeng , Jiang Qingshan , Ma Yingfei 
Published: September 2020

ABSTRACTTo identify the microbial markers from the complex human gut microbiome for delineating the disease-related microbial alteration is of great interest. Here, we develop a framework combining neural network (NN) and random forest (RF), resulting in 40 marker species and 90 marker genes identified from the metagenomic dataset D1 (185 healthy and 183 type 2 diabetes (T2D) samples), respectively. Using these markers, the NN model obtains higher accuracy in classifying the T2D-related samples than machine learning-based approaches. The NN-based regression analysis determines the fasting blood glucose (FBG) is the most significant association factor (P<<0.05) in the T2D-related alteration of the gut microbiome. Twenty-four marker species that vary little across the case and control samples and are often neglected by the statistic-based methods greatly shift in different stages of the T2D development, implying that the cumulative effect of the markers rather than individuals likely drives the alteration of the gut microbiome.
Gastrointestinal involvement attenuates COVID-19 severity and mortality
Authors: Livanos Alexandra E. , Jha Divya , Cossarini Francesca , Gonzalez-Reiche Ana S. , Tokuyama Minami , Aydillo Teresa , Parigi Tommaso L. , Ramos Irene , Dunleavy Katie , Lee Brian , Dixon Rebekah , Chen Steven T. , Martinez-Delgado Gustavo , Nagula Satish , Ko Huaibin M. , Reidy Jason , Naymagon Steven , Grinspan Ari , Ahmad Jawad , Tankelevich Michael , Gordon Ronald , Sharma Keshav , Britton Graham J. , Chen-Liaw Alice , Spindler Matthew P. , Plitt Tamar , Wang Pei , Cerutti Andrea , Faith Jeremiah J. , Colombel Jean-Frederic , Kenigsberg Ephraim , Argmann Carmen , Merad Miriam , Gnjatic Sacha , Harpaz Noam , Danese Silvio , Rahman Adeeb , Kumta Nikhil A. , Aghemo Alessio , Petralia Francesca , Bakel Harm van , Garcia-Sastre Adolfo , Mehandru Saurabh 
Published: September 2020

AbstractGiven that gastrointestinal (GI) symptoms are a prominent extrapulmonary manifestation of coronavirus disease 2019 (COVID-19), we investigated the impact of GI infection on disease pathogenesis in three large cohorts of patients in the United States and Europe. Unexpectedly, we observed that GI involvement was associated with a significant reduction in disease severity and mortality, with an accompanying reduction in key inflammatory proteins including IL-6, CXCL8, IL-17A and CCL28 in circulation. In a fourth cohort of COVID-19 patients in which GI biopsies were obtained, we identified severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) within small intestinal enterocytes for the first timein vivobut failed to obtain culturable virus. High dimensional analyses of GI tissues confirmed low levels of cellular inflammation in the GI lamina propria and an active downregulation of key inflammatory genes includingIFNG, CXCL8, CXCL2andIL1Bamong others. These data draw attention to organ-level heterogeneity in disease pathogenesis and highlight the role of the GI tract in attenuating SARS-CoV-2-associated inflammation with related mortality benefit.
Self-learning on COVID-19 among medical students and their preparedness to participate in government’s COVID-19 response in Bhutan: a cross-sectional study
Authors: Dorji Thinley , Tamang Saran Tenzin , Tilak TVSVGK 
Published: September 2020

AbstractBackgroundBhutan lacks a medical school and all their medical students are trained outside in Sri Lanka, Bangladesh and India. When the COVID-19 pandemic let to closure of medical schools in these countries, the Bhutanese medical students were repatriated in March-April 2020. Upon return, they were kept in government-sponsored facility quarantine for 21 days. This study assessed their knowledge on COVID-19 as a part of self-learning and attitude as part of preparedness towards participation in government’s health response to COVID-19.MethodThis was a cross-sectional study among medical students who had returned to the country. This survey was conducted through an online questionnaire while the students were in 21-day facility quarantine. The sample size calculated was 129 and a convenient sampling was used. Knowledge was assessed using 20 questions, each scored 1/20. Cumulative score of score of ≥80% was categorized as “good knowledge”, score of ≥60 – 79% was considered “satisfactory knowledge”, and score < 60% was considered “poor knowledge.” Correlation between knowledge score and duration of clinical clerkship was tested using Pearson’s correlation coefficient. Attitude of students towards their willingness to participate in the national COVID-19 response were tested using rating scales. Data were analysed using Stata 13.1.Results120 medical students responded to this survey (response rate = 93%). Eighty-eight (74%) had good knowledge, 28 (23%) had satisfactory knowledge and only four (3%) had poor knowledge on COVID-19. The students scored high on the symptomatology, mode of transmission, prevention and treatment options and on local epidemiology; and scored low on the forms of mechanical ventilations and on the home-management of non-critical cases. The knowledge score correlated with duration of clinical clerkship (r = 0.326, p = 0.001). The primary source of information were social media sites (102, 85%), television (94, 78%) and newspapers (76, 63%). The majority (78, 65%) were willing to participate in the government’s COVID-19 response but could not identify what roles they could play. The fear of contracting COVID-19 was reported in only in 8.7%.ConclusionsThe medical students had good knowledge on COVID-19 and were self-learned through social media, television and newspapers. The students held positive attitude towards participation in the government’s COVID-19 response.
Clinical Outcomes of Critically Ill Patients with COVID-19 by Race
Authors: Marmarchi Fahad , Liu Michael , Rangaraju Srikant , Auld Sara C. , Creel-Bulos Maria Christina , Kempton Christine L , Sharifpour Milad , Gaddh Manila , Sniecinski Roman , Maier Cheryl L. , Nahab Fadi ,   The Emory COVID-19 Quality and Clinical Research Collaborative (QCRC)
Published: September 2020

AbstractBackgroundStudies of COVID-19 have shown that African Americans have been affected by the virus at a higher rate compared to other races. This cohort study investigated comorbidities and clinical outcomes by race among COVID-19 patients admitted to the intensive care unit.MethodsThis is a case series of critically ill patients admitted with COVID-19 to a tertiary referral teaching hospital in Atlanta, Georgia. The study included all critically ill hospitalized patients between March 6, 2020 and May 5, 2020. Clinical outcomes during hospitalization included mechanical ventilation, renal replacement therapy and mortality stratified by race.ResultsOf 288 patients included (mean age, 63 ± 16 years; 45% female), 210 (73%) were African American. African Americans had significantly higher rates of comorbidities compared to other races, including hypertension (80% vs 59%, p=0.001), diabetes (49% vs 34%, p=0.026) and mean BMI (33 kg/m2 vs 28 kg/m2, p<0.001). Despite African Americans requiring continuous renal replacement therapy during hospitalization at higher rates than other races (27% vs 13%, p=0.011), rates of intubation, intensive care unit length of stay, and overall mortality (30% vs 24%, p=0.307) were similar.ConclusionThis racially diverse series of critically ill COVID-19 patients shows that despite higher rates of comorbidities at hospital admission in African Americans compared with other races, there was no significant difference in mortality.
Neonatal Presentations to the Children’s Emergency Department
Authors: Blakey Sarah , Lyttle Mark D , Magnus Dan 
Published: September 2020

ABSTRACTBackgroundPaediatric attendances to Emergency Departments (EDs) in the UK are increasing, particularly for younger children. Neonates present a challenge due to their non-specific presentations. Community services are under increasing pressure and parents may preferentially bring their children to the ED, even for non-urgent problems. Neonatal attendances have not been extensively studied, but previous reviews have shown many are well, often not requiring specific medical intervention. This study aimed to characterise the presenting features, management and disposition of neonatal attendances to a tertiary Children’s ED (CED).MethodsRetrospective observational review of medical records identified via the ED Electronic database of neonatal attendances (≤28 days) to Bristol Royal Hospital for Children (BRHC) over 12 months (01/01/2016-31/12/2016). Further information was obtained from investigation results, discharge summaries and historical admissions data.ResultsNeonatal attendances increased from 655 to 1205 from 2008-2016. The most common presenting complaints were breathing difficulty (18.1%), vomiting (8.3%) and poor feeding (8.2%). The most common diagnoses were ‘no significant medical problem’ (41.9%), bronchiolitis (10.5%) and suspected sepsis (10.0%). Just over 1/3 were admitted (23% inpatient, 12% Short Stay Unit). Median length of stay for inpatients was 2 days. Half of neonatal attendances to the ED had no investigations performed and most (77.7%) needed advice or observation only.ConclusionMany neonates presenting to the CED were well and discharged with observation only. This suggests not only that there is potential for improved community management but that increased support for community colleagues and new parents is needed. There are also implications for reviewing training in emergency medicine, especially the ability to assess ‘well’ infants and to manage common neonatal problems. Drivers of health policy should consider developing enhanced models of out of hospital care which are acceptable to clinicians and families
Efficacy and safety ofBoswelliacontaining formulations for the treatment of osteoarthritis: protocol for a systematic review and meta-analysis of randomised controlled trials
Authors: Wang Zhiqiang , Singh Ambrish , Hussain Salman , Molina García Pablo , Antony Benny 
Published: September 2020

AbstractOsteoarthritis (OA) is a common chronic joint disease with limited pharmacological management options.Boswelliaextracts (BE) or formulations containing BE are generally considered as safe and offers a modest efficacy for the treatment of OA. Although previous systematic reviews have assessed the efficacy of BE in OA, these reviews had excluded trials assessing various formulations containing BE and excluded various combinations of BE. Hence, this study aims to systematically review the evidence from RCTs assessing the efficacy and safety of both BE and formulations containing BE for the treatment of OA. Biomedical databases such as PubMed, Embase, and Google Scholar will be searched to identify the RCTs of BE or formulations containing BE in patients with OA (hand, knee, hip, or any other OA). Cochrane risk of bias tool will be used to assess the quality of included studies. Review Manager 5 (Rev Man) and STATA Version 16 will be used to conduct the statistical analysis.
Geometricus Represents Protein Structures as Shape-mers Derived from Moment Invariants
Authors: Durairaj Janani , Akdel Mehmet , de Ridder Dick , van Dijk Aalt DJ 
Published: September 2020

AbstractMotivationAs the number of experimentally solved protein structures rises, it becomes increasingly appealing to use structural information for predictive tasks involving proteins. Due to the large variation in protein sizes, folds, and topologies, an attractive approach is to embed protein structures into fixed-length vectors, which can be used in machine learning algorithms aimed at predicting and understanding functional and physical properties. Many existing embedding approaches are alignment-based, which is both time-consuming and ineffective for distantly related proteins. On the other hand, library- or model-based approaches depend on a small library of fragments or require the use of a trained model, both of which may not generalize well.ResultsWe present Geometricus, a novel and universally applicable approach to embedding proteins in a fixed-dimensional space. The approach is fast, accurate, and interpretable. Geometricus uses a set of 3D moment invariants to discretize fragments of protein structures into shape-mers, which are then counted to describe the full structure as a vector of counts. We demonstrate the applicability of this approach in various tasks, ranging from fast structure similarity search, unsupervised clustering, and structure classification across proteins from different superfamilies as well as within the same family.AvailabilityPython code available athttps://git.wur.nl/durai001/geometricusContactaaltjan.vandijk@wur.nl,janani.durairaj@wur.nl