bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lessons From a Quality Improvement Project to Standardize the Process of Gastric Biopsy Culture for Helicobacter pylori
Authors: Bonilla Silvana , Bousvaros Athos , Cardini Jeff , Estrella-Pimentel Loida , Mitchell Paul D. , Goldshine Jana , Hirsch Rebecca , Jonas Maureen , Fox Victor 
Published: August 2021

Background:
Despite expert recommendations, clinician’s adherence to pediatric societal clinical practice guidelines is variable, particularly with respect to the use of gastric biopsy culture in the initial diagnosis of Helicobacter pylori infection. In addition, the implementation of routine use of gastric biopsy culture has been challenging with several factors affecting the rate of successful primary H pylori culture.

Methods:
We conducted a quality improvement (QI) project with the aims of increasing the rate of successful primary culture. The QI project involved educational efforts among our gastroenterologists, endoscopy suite personnel, and laboratory personnel. We compared the frequency of gastric biopsy culture sent in patients with international classification of diseases 9th revision code 041.86, and 10th revision codes B96.81 evaluated by pediatric gastroenterologists at Boston Children’s Hospital during the 9 months before the QI intervention (February 1, 2019 to October 31, 2019) and 9 months after the QI intervention (November 1 2019 to July 31 2020). We also compared the rate of culture growth in patients with positive histology (culture positivity), and antimicrobial susceptibilities before and after November 1, 2019.

Results:
We observed an increased frequency of gastric biopsy acquisition by any gastroenterologist, obtained in 39% (28 of 71) preintervention patients compared with 67% (36 of 54) intervention patients (P = 0.004). There was an increase in the percentage of culture positivity across study periods from 21% (3 of 14) preintervention to 45% (5 of 11) postintervention (P = 0.39; 95% confidence interval, 0.64-7.00).

Conclusion:
Educational initiatives and collaborative work with staff physicians, endoscopy personnel, and hospital laboratory appear to be effective tools to increase usage of gastric biopsy culture as a diagnostic tool for H pylori infection and to increase culture positivity. Improving the surveillance of local resistance rates will improve the selection of the most effective primary treatment in specific geographic areas.
Prevalence of Diaphragmatic Dysfunction in the Long-Term Acute Care Setting and Its Effects on Ventilator Weaning Outcomes
Authors: Barchuk Alex , Barchuk Sofia A. , Roebken Curtis K. , Ahn Jaeil 
Published: August 2021

Objective
To determine the prevalence of undiagnosed diaphragmatic dysfunction in a long-term acute care hospital setting in patients on prolonged mechanical ventilation and its association with weaning outcomes.

Design
This is a single-center, retrospective cohort study including 451 patients on prolonged mechanical ventilation admitted to a long-term acute care hospital facility between 2012 and 2017. Diaphragmatic dysfunction was assessed using fluoroscopy.

Results
Three hundred nineteen patients on prolonged mechanical ventilation were assessed for diaphragmatic dysfunction. Nine patients were diagnosed with diaphragmatic dysfunction before admission. Eighty (72.7%) without diaphragmatic dysfunction were successfully weaned and 30 (27.3%) failed to wean, whereas 51 participants (31.9%) with diaphragmatic dysfunction were successfully weaned and 109 (68.1%) failed to wean (P < 0.001). When analyzing days to wean, the median was 13 days for those with no diaphragmatic dysfunction, 19 days with unilateral diaphragmatic dysfunction, and 28 days with bilateral diaphragmatic dysfunction (P < 0.001). Weaning success was not statistically associated with generalized neuromuscular disorders, age, sex, body mass index, smoking history, or diabetes.

Conclusions
Diaphragmatic dysfunction was found to be strongly associated with time to wean and weaning success in the long-term acute care hospital setting. Very few patients despite being on prolonged mechanical ventilation were diagnosed with diaphragmatic dysfunction before long-term acute care hospital admission. Given this information, early diagnosis of diaphragmatic dysfunction among prolonged mechanical ventilation patients in the long-term acute care hospital setting is paramount in preventing secondary complications associated with mechanical ventilation.
Five Years With Dolutegravir Plus Lamivudine as a Switch Strategy: Much More Than a Positive Finding
Authors: Ciccullo Arturo , Borghi Vanni , Giacomelli Andrea , Cossu Maria Vittoria , Sterrantino Gaetana , Latini Alessandra , Giacometti Andrea , De Vito Andrea , Gennari William , Madeddu Giordano , Capetti Amedeo , d’Ettorre Gabriella , Mussini Cristina , Rusconi Stefano , Di Giambenedetto Simona , Baldin Gianmaria 
Published: August 2021

Background:
Results from clinical trials and observational studies suggest that dolutegravir plus lamivudine could be an effective and well-tolerated option for simplification in HIV-1–positive patients. We aimed to assess long-time efficacy and safety in our multicenter cohort.

Methods:
This was a retrospective study enrolling HIV-1–infected, virologically suppressed patients switching to dolutegravir + lamivudine. We performed survival analysis to evaluate time to virological failure (VF, defined by a single HIV-RNA ≥1000 copies/mL or by 2 consecutive HIV-RNA ≥ 50 copies/mL) and treatment discontinuation (defined as the interruption of either 3TC or dolutegravir), assessing predictors via Cox regression analyses.

Results:
Seven-hundred eighty-five patients were considered for the analysis: 554 were men (70.6%), with a median age of 52 years (interquartile range 45–58 years). Estimated probabilities of maintaining virological suppression at weeks 96, 144, and 240 were 97.7% (SD ±0.6), 96.9% (SD ±0.8), and 96.4% (SD ±0.9), respectively. A non-B HIV subtype (P = 0.014) and a previous VF (P = 0.037) resulted predictors of VF. We did not observe differences in probability of VF in people living with HIV with an M184V resistance mutation (P = 0.689); however, in a deeper analysis, M184V mutation was a predictor of VF (P = 0.038) in patients with time of virological suppression <88 months. Estimated probabilities of remaining on study regimen at 96, 144, and 240 weeks were 82.9% (SD ±1.4), 79.7% (SD ±1.6) and 74.3% (SD ±2.2), respectively.

Conclusions:
Our findings show the long-term efficacy and tolerability of dolutegravir plus lamivudine in virologically suppressed patients.
Threat imminence reveals links among unfolding of anticipatory physiological response, cortical-subcortical intrinsic functional connectivity, and anxiety
Authors: Abend Rany , Ruiz Sonia G. , Bajaj Mira A. , Harrewijn Anita , Linke Julia O. , Atlas Lauren Y. , Pine Daniel S. 
Published: August 2021

AbstractExcessive expression of threat-anticipatory defensive responses is central in anxiety. Animal research indicates that anticipatory responses are dynamically organized by threat imminence and rely on conserved circuitry. Insight from translational work on threat imminence could guide mechanistic research mapping abnormal function in this circuitry to aberrant defensive responses in anxiety. Here, we initiate such research.Fifty pediatric anxiety patients and healthy-comparisons (33 females) completed a threat-anticipation task whereby cues signaled delivery of highly-painful (threat) or non-painful (safety) heat. Temporal changes in skin-conductance indexed defensive responding as function of threat imminence. Resting-state functional connectivity data were used to identify intrinsic-function correlates of anticipatory response within a specific functional network derived from translational research.Results indicate that anxiety was associated with greater increase in anticipatory response as threats became more imminent. Magnitude of increase in threat-anticipatory responses corresponded to intrinsic connectivity within a cortical-subcortical circuit; importantly, more severe anxiety was associated with greater connectivity between ventromedial prefrontal cortex and hippocampus and basolateral amygdala, a circuit implicated in animal models of anxiety. These findings link basic-translational and clinical research, highlighting aberrant intrinsic function in conserved defensive circuitry as potential pathophysiological mechanism in anxiety.
Toward Using Twitter for PrEP-Related Interventions: An Automated Natural Language Processing Pipeline for Identifying Gay or Bisexual Men in the United States
Authors: Klein Ari Z. , Meanley Steven , O’Connor Karen , Bauermeister José A. , Gonzalez-Hernandez Graciela 
Published: August 2021

AbstractBackgroundPre-exposure prophylaxis (PrEP) is highly effective at preventing the acquisition of Human Immunodeficiency Virus (HIV). There is a substantial gap, however, between the number of people in the United States who have indications for PrEP and the number of them who are prescribed PrEP. While Twitter content has been analyzed as a source of PrEP-related data (e.g., barriers), methods have not been developed to enable the use of Twitter as a platform for implementing PrEP-related interventions.ObjectiveMen who have sex with men (MSM) are the population most affected by HIV in the United States. Therefore, the objective of this study was to develop and assess an automated natural language processing (NLP) pipeline for identifying men in the United States who have reported on Twitter that they are gay, bisexual, or MSM.MethodsBetween September 2020 and January 2021, we used the Twitter Streaming Application Programming Interface (API) to collect more than 3 million tweets containing keywords that men may include in posts reporting that they are gay, bisexual, or MSM. We deployed handwritten, high-precision regular expressions on the tweets and their user profile metadata designed to filter out noise and identify actual self-reports. We identified 10,043 unique users geolocated in the United States, and drew upon a validated NLP tool to automatically identify their ages.ResultsBased on manually distinguishing true and false positive self-reports in the tweets or profiles of 1000 of the 10,043 users identified by our automated pipeline, our pipeline has a precision of 0.85. Among the 8756 users for which a United States state-level geolocation was detected, 5096 (58.2%) of them are in the 10 states with the highest numbers of new HIV diagnoses. Among the 6240 users for which a county-level geolocation was detected, 4252 (68.1%) of them are in counties or states considered priority jurisdictions by the Ending the HIV Epidemic (EHE) initiative. Furthermore, the majority of the users are in the same two age groups as the majority of MSM in the United States with new HIV diagnoses.ConclusionsOur automated NLP pipeline can be used to identify MSM in the United States who may be at risk for acquiring HIV, laying the groundwork for using Twitter on a large scale to target PrEP-related interventions directly at this population.
COMORBIDITY ANALYSIS: OVERLAPPING SEMICIRCLES WITH WIGNER LAW AND RANDOM MATRIX THEORY
Authors: Nolasco-Jáuregui O. , Quezada-Téllez L. A. , Salazar-Flores Y. , Díaz-Hernández Adán 
Published: August 2021

AbstractIn December 2019 COVID-19 appeared as a new pandemic that has claimed the lives of millions of people around the world. This article presents a regional analysis of COVID-19 in Mexico. Due to the comorbidities of Mexican society, the new pandemic implies a higher risk for the population. The study period runs from April 12 to October 5, 2020 (761 665 Patients). In this proposal we apply a unique methodology of random matrix theory in the moments of a probability measure that appears as the limit of the empirical spectral distribution by the Wigner semicircle law. The graphical presentation of the results is done with Machine Learning methods in the SuperHeat maps. With this is possible to analyze the behavior of patients who tested positive for COVID-19 and their comorbidities. We conclude that the most sensitive comorbidities in hospitalized patients are the following three: COPD, Other Diseases and Renal Diseases.
Evaluation of GENECUBE® HQ SARS-CoV-2 for anterior nasal samples and saliva samples with a new rapid examination protocol
Authors: Naito Asami , Kiyasu Yoshihiko , Akashi Yusaku , Sugiyama Akio , Michibuchi Masashi , Takeuchi Yuto , Notake Shigeyuki , Nakamura Koji , Ishikawa Hiroichi , Suzuki Hiromichi 
Published: August 2021

AbstractIntroductionGENECUBE® is a rapid molecular identification system, and previous studies demonstrated that GENECUBE® HQ SARS-CoV-2 showed excellent analytical performance for the detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) with nasopharyngeal samples. However, other respiratory samples have not been evaluated.MethodsThis prospective comparison between GENECUBE® HQ SARS-CoV-2 and reference real-time reverse transcriptase polymerase chain reaction (RT-PCR) was performed for the detection of SARS-CoV-2 using anterior nasal samples and saliva samples. Additionally, we evaluated a new rapid examination protocol using GENECUBE® HQ SARS-CoV-2 for the detection of SARS-CoV-2 with saliva samples. For the rapid protocol, in the preparation of saliva samples, purification and extraction processes were adjusted, and the total process time was shortened to approximately 35 minutes.ResultsFor 359 anterior nasal samples, the total-, positive-, and negative concordance of the two assays was 99.7% (358/359), 98.1% (51/52), and 100% (307/307), respectively. For saliva samples, the total-, positive-, and negative concordance of the two assays was 99.6% (239/240), 100% (56/56), and 99.5% (183/184), respectively. With the new protocol, total-, positive-, and negative concordance of the two assays was 98.8% (237/240), 100% (56/56), and 98.4% (181/184), respectively. In all discordance cases, SARS-CoV-2 was detected by additional molecular examinations.ConclusionGENECUBE® HQ SARS-CoV-2 provided high analytical performance for the detection of SARS-CoV-2 in anterior nasal samples and saliva samples.
Use of HIV Recency Assays for HIV Incidence Estimation and Non-Incidence Surveillance Use Cases: A systematic review
Authors: Facente Shelley N. , Agyei Lillian , Maher Andrew D. , Mahy Mary , Dalal Shona , Lowrance David , Grebe Eduard , Marsh Kimberly 
Published: August 2021

ABSTRACTIntroductionHIV assays designed to detect recent infection, also known as “recency assays,” are often used to estimate HIV incidence in a specific country, region, or subpopulation, alone or as part of recent infection testing algorithms (RITAs). Recently, many countries and organizations have become interested in using recency assays within case surveillance systems and routine HIV testing services, and in measuring other indicators beyond incidence, generally referred to as “non-incidence surveillance use cases.”MethodsTo identify best methodological and field implementation practices for the use of recency assays to estimate HIV incidence and trends in recent infections for key populations or specific geographic areas, we undertook: 1) a global Call for Information released from WHO/UNAIDS; and 2) a systematic review of the literature to: (a) assess the field performance characteristics of commercially available recency assays, (b) understand the use of recency testing for surveillance in programmatic and laboratory settings, and (c) review methodologies for implementing recency testing for both incidence estimation and non-incidence use cases.Results and discussionAmong the 90 documents ultimately reviewed, 65 (88%) focused on assay/algorithm performance or methodological descriptions, with high-quality evidence of accurate age- and sex- disaggregated HIV incidence estimation at national or regional levels in general population settings, but not at finer geographic levels for prevention prioritization. The remaining 25 documents described field-derived incidence (n=14) and non-incidence (n=11) use cases, including integrating RITAs into routine surveillance and assisting with molecular genetic analyses, but evidence was generally weaker or only reported on what was done, without validation data or findings related to effectiveness of recency assays when used for these purposes.ConclusionsHIV recency assays have been widely validated for estimating HIV incidence in age- and sex-specific populations at national and sub-national regional levels; however, there was a lack of evidence validating the accuracy and effectiveness of using recency assays for non-incidence surveillance use cases. The evidence identified through this review will be used in forthcoming technical guidance on the use of HIV recency assays for surveillance use cases by WHO and UNAIDS; further evidence on methodologies and effectiveness of non-incidence use cases is needed.
Intestinal function and transit associate with gut microbiota dysbiosis in cystic fibrosis
Authors: Marsh Ryan , Gavillet Helen , Hanson Liam , Ng Christabella , Mitchell-Whyte Mandisa , Major Giles , Smyth Alan R , Rivett Damian , van der Gast Christopher 
Published: August 2021

AbstractBackgroundMost people with cystic fibrosis (pwCF) suffer from gastrointestinal symptoms and are at risk of gut complications. Gut microbiota dysbiosis is apparent within the CF population across all age groups, with evidence linking dysbiosis to intestinal inflammation and other markers of health. This pilot study aimed to investigate the potential relationships between the gut microbiota and gastrointestinal physiology, transit, and health.Study DesignFaecal samples from 10 pwCF and matched controls were subject to 16S rRNA sequencing. Results were combined with clinical metadata and MRI metrics of gut function to investigate relationships.ResultspwCF had significantly reduced microbiota diversity compared to controls. Microbiota compositions were significantly different, suggesting remodelling of core and rarer satellite taxa in CF. Dissimilarity between groups was driven by a variety of taxa, including Escherichia coli, Bacteroides spp., Clostridium spp., and Faecalibacterium prausnitzii. The core taxa were explained primarily by CF disease, whilst the satellite taxa were associated with pulmonary antibiotic usage, CF disease, and gut function metrics. Species-specific ordination biplots revealed relationships between taxa and the clinical or MRI-based variables observed.ConclusionsAlterations in gut function and transit resultant of CF disease are associated with the gut microbiota composition, notably the satellite taxa. Delayed transit in the small intestine might allow for the expansion of satellite taxa resulting in potential downstream consequences for core community function in the colon.HighlightsFaecal microbiota significantly differs between pwCF and healthy controlsKey SCFA producers contributed to microbiota dissimilarity between groupsPulmonary antibiotic treatment heavily impacted gut microbiotaIntestinal physiology and transit impacted satellite microbiota composition
Enhanced neutrophil extracellular trap formation in COVID-19 is inhibited by the PKC inhibitor ruboxistaurin
Authors: Dowey Rebecca , Cole Joby , Thompson A A Roger , Huang Chenghao , Whatmore Jacob , Iqbal Ahmed , Bradley Kirsty L , McKenzie Joanne , Hull Rebecca C , Lawrie Allan , Condliffe Alison M , Kiss-Toth Endre , Sabroe Ian , Prince Lynne R 
Published: August 2021

AbstractNeutrophil extracellular traps (NETs) are web-like DNA and protein lattices which are expelled by neutrophils to trap and kill pathogens, but which cause significant damage to the host tissue. NETs have emerged as critical mediators of lung damage, inflammation and thrombosis in COVID-19 and other diseases, but there are no therapeutics to prevent or reduce NETs that are available to patients. Here, we show that neutrophils isolated from hospitalised patients with COVID-19 produce significantly more NETs in response to LPS compared to cells from healthy control subjects. A subset of patients were captured at follow-up clinics (3-4 month post-infection) and while LPS-induced NET formation is significantly lower at this time point, it remains elevated compared to healthy controls. LPS- and PMA-induced NETs were significantly inhibited by the protein kinase C (PKC) inhibitor ruboxistaurin. Ruboxistaurin-mediated inhibition of NETs in healthy neutrophils reduces NET-induced epithelial cell death. Our findings suggest ruboxistaurin could reduce proinflammatory and tissue-damaging consequences of neutrophils during disease, and since it has completed phase III trials for other indications without safety concerns, it is a promising and novel therapeutic strategy for COVID-19.
Monitoring socioeconomic inequalities across HIV knowledge, attitudes, behaviours and prevention in 18 sub-Saharan African countries
Authors: Hamidouche Mohamed , Ante-Testard Pearl Anne , Baggaley Rachel , Temime Laura , Jean Kévin 
Published: August 2021

ObjectivesSocioeconomic inequalities in HIV prevention services coverage constitute important barriers to global prevention targets, especially in sub-Saharan Africa (SSA). We aimed at monitoring these inequalities from population-based survey data in 18 SSA countries between 2010 and 2018.MethodsWe defined eight HIV indicators aimed at capturing uptake of HIV prevention services among adult participants. Country-specific wealth-related inequalities were measured using the Relative and Slope Index of Inequalities (RII and SII, respectively) and then pooled using random-effects meta-analyses. We compared inequalities between African regions using the Wilcoxon rank-sum test.ResultsThe sample consisted of 358,591 participants (66% women). Despite variability between countries and indicators, the meta-analysis revealed significant levels of relative and absolute inequalities in 6 out of 8 indicators: HIV-related knowledge, positive attitudes toward people living with HIV (PLHIV), condom use at last sexual intercourse, participation to prevention of mother-to-child transmission programs, medical male circumcision and recent HIV testing. The largest inequalities were reported in condom use, with condom use reported 5 times more among the richest versus the poorest (RII=5.02, 95% Confidence interval, CI: 2.79-9.05) and in positive attitudes toward PLHIV, with a 32-percentage point difference between the richest and poorest (SII=0.32, 95% CI: 0.26-0.39). Conversely, no significant inequalities were observed in multi-partnership and HIV seropositivity among youth. Overall, inequalities tended to be larger in West and Central vs. East and Southern African countries.ConclusionsDespite efforts to scale-up HIV-prevention programs, socioeconomic inequalities remain substantial over the continuum of HIV primary and secondary prevention in several SSA countries.