bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coronavirus 2019 and People Living With Human Immunodeficiency Virus: Outcomes for Hospitalized Patients in New York City
Authors: Sigel Keith , Swartz Talia , Golden Eddye , Paranjpe Ishan , Somani Sulaiman , Richter Felix , De Freitas Jessica K , Miotto Riccardo , Zhao Shan , Polak Paz , Mutetwa Tinaye , Factor Stephanie , Mehandru Saurabh , Mullen Michael , Cossarini Francesca , Bottinger Erwin , Fayad Zahi , Merad Miriam , Gnjatic Sacha , Aberg Judith , Charney Alexander , Nadkarni Girish , Glicksberg Benjamin S 
Published: June 2020

AbstractBackgroundThere are limited data regarding the clinical impact of coronavirus disease 2019 (COVID-19) on people living with human immunodeficiency virus (PLWH). In this study, we compared outcomes for PLWH with COVID-19 to a matched comparison group.MethodsWe identified 88 PLWH hospitalized with laboratory-confirmed COVID-19 in our hospital system in New York City between 12 March and 23 April 2020. We collected data on baseline clinical characteristics, laboratory values, HIV status, treatment, and outcomes from this group and matched comparators (1 PLWH to up to 5 patients by age, sex, race/ethnicity, and calendar week of infection). We compared clinical characteristics and outcomes (death, mechanical ventilation, hospital discharge) for these groups, as well as cumulative incidence of death by HIV status.ResultsPatients did not differ significantly by HIV status by age, sex, or race/ethnicity due to the matching algorithm. PLWH hospitalized with COVID-19 had high proportions of HIV virologic control on antiretroviral therapy. PLWH had greater proportions of smoking (P &lt; .001) and comorbid illness than uninfected comparators. There was no difference in COVID-19 severity on admission by HIV status (P = .15). Poor outcomes for hospitalized PLWH were frequent but similar to proportions in comparators; 18% required mechanical ventilation and 21% died during follow-up (compared with 23% and 20%, respectively). There was similar cumulative incidence of death over time by HIV status (P = .94).ConclusionsWe found no differences in adverse outcomes associated with HIV infection for hospitalized COVID-19 patients compared with a demographically similar patient group.
Comparing Nasopharyngeal and Midturbinate Nasal Swab Testing for the Identification of Severe Acute Respiratory Syndrome Coronavirus 2
Authors: Pinninti Swetha , Trieu Connie , Pati Sunil K , Latting Misty , Cooper Joshua , Seleme Maria C , Boppana Sushma , Arora Nitin , Britt William J , Boppana Suresh B 
Published: June 2020

Abstract
Testing of paired midturbinate (MT) nasal and nasopharyngeal (NP) swabs, collected by trained personnel from 40 patients with coronavirus disease 2019 (COVID-19), showed that more NP (76/95 [80%]) than MT swabs tested positive (61/95 [64%]) (P = .02). Among samples collected a week after study enrollment, fewer MT than NP samples were positive (45% vs 76%; P = .001).
Response to multiple rapid swallows shows impaired inhibitory pathways in distal esophageal spasm patients with and without concomitant esophagogastric junction outflow obstruction
Authors: Hernandez Patricia V , Valdovinos Luis R , Horsley-Silva Jennifer L , Valdovinos Miguel A , Crowell Michael D , Vela Marcelo F 
Published: June 2020

Summary
Distal esophageal spasm (DES) is a motility disorder characterized by premature contraction of the esophageal body during single swallows. It is thought to be due to impairment of esophageal inhibitory pathways, but studies to support this are limited. The normal response to multiple rapid swallows (MRS) is deglutitive inhibition of the esophageal body during the MRS sequence. Our aim was to compare the response to MRS in DES patients and healthy control subjects. Response to MRS during HRM was evaluated in 19 DES patients (8 with and 11 without concomitant esophagogastric junction outflow obstruction [EGJOO]) and 24 asymptomatic healthy controls. Patients with prior gastroesophageal surgery, peroral endoscopic myotomy, pneumatic dilation, esophageal botulinum toxin injection within 6 months of HRM, opioid medication use, and esophageal stricture were excluded. Response to MRS was evaluated for complete versus impaired inhibition (esophageal body contractility with distal contractile integral [DCI] &gt; 100 mmHg-sec-cm during MRS), presence of post-MRS contraction augmentation (DCI post MRS greater than single swallow mean DCI), and integrated relaxation pressure (IRP). Impaired deglutitive inhibition during MRS was significantly more frequent in DES compared to controls (89% vs. 0%, P &lt; 0.001), and frequency was similar for DES with versus without concomitant EGJOO (100% vs. 82%, P = 0.48). The proportion of subjects with augmentation post MRS was similar for both groups (37% vs. 38%, P = 1.00), but mean DCI post MRS was higher in DES than controls (3360.0 vs. 1238.9, P = 0.009). IRP was lower during MRS compared to single swallows in all patients, and IRP during MRS was normal in 5 of 8 patients with DES and EGJOO. Our study suggests that impaired deglutitive inhibition during MRS is present in the majority of patients with DES regardless of whether they have concomitant EGJOO, and future studies should explore the usefulness of incorporating response to MRS in the diagnosis of DES.
Early experience with a nutrition and survivorship clinic in esophageal cancer
Authors: Murphy Conor F , Fanning Michelle , Raftery Nicola , Elliott Jessie A , Docherty Neil G , Donohoe Claire L , Ravi Narayanasamy , le Roux Carel W , Reynolds John V 
Published: June 2020

Summary
Improved cure rates in esophageal cancer care have increased focus on health-related quality of life (HRQL) in survivorship. To optimize recovery after esophagectomy, particularly nutritional well-being, a personalized multidisciplinary survivorship clinic was established at this center. Assessments at 6 and 12 months postoperatively include validated European Organization for the Research and Treatment of Cancer (EORTC) symptom and health-related quality of life (HRQL) questionnaires, functional status review, anthropometry, and biochemical screening for micronutrient deficiencies. 75 patients, at a mean age of 63 years, 84% male, 85% with adenocarcinoma, and 73% receiving multimodal therapy were included. Mean preoperative body mass index (BMI) was 27.5 (4.3) kg m −2. 6- and 12-month assessments were completed by 66 (88%) and 37 (93%) recurrence-free patients, respectively. Mean body weight loss at 6 months was 8.5 ± 6.6% and at 12 months 8.8 ± 7.3%. Of the 12-month cohort, micronutrient deficiency was present in 27 (79.4%) preoperatively and 29 (80.6%) after 1 year (P = 0.727), most commonly iron deficiency (preoperative: 16 [43.2%] and postoperative: 17 [45.9%] patients, P = 0.100). 26 (70.3%) of these patients also had clinically significant dumping syndrome persisting to 12 months after surgery. We describe a novel follow-up support structure for esophageal cancer patients in the first year of survivorship. This may serve as an exemplar model with parallel application across oncological care.
Varicella Zoster Virus in Inflammatory Bowel Disease Patients: What Every Gastroenterologist Should Know
Authors: Schreiner Philipp , Mueller Nicolas J , Fehr Jan , Maillard Michel H , Brand Stephan , Michetti Pierre , Schoepfer Alain , Restellini Sophie , Vulliemoz Marianne , Vavricka Stephan R , Juillerat Pascal , Rogler Gerhard , Biedermann Luc 
Published: June 2020

AbstractPrimary varicella zoster virus [VZV] infection results in varicella [chickenpox] and its reactivation results in herpes zoster [HZ; shingles]. Patients with inflammatory bowel disease [IBD] are susceptible to complications of primary VZV infection and have an increased risk of HZ. Concerns of VZV and HZ infection in the IBD population have been highlighted by the emergence of JAK inhibitors and their safety profile in this patient population, as with tofacitinib for the treatment of ulcerative colitis [UC]. The current pipeline of emerging therapies includes novel molecules targeting multiple pathways, including JAK/signal transducer and cytokine signalling pathways, such as JAK/STAT. Hence VZV and HZ will be increasingly relevant for gastroenterologists treating IBD patients in light of these emerging therapies. This review will focus on the epidemiology, disease course, prevention, and management of these two distinct infections in patients with IBD.
Essential information on surgical heart valve characteristics for optimal valve prosthesis selection: expert consensus document from the European Association for Cardio-Thoracic Surgery (EACTS)–The Society of Thoracic Surgeons (STS)–American Association for Thoracic Surgery (AATS) Valve Labelling Task Force
Authors: Durko Andras P , Pibarot Philippe , Atluri Pavan , Bapat Vinayak , Cameron Duke E , Casselman Filip P.A , Chen Edward P , Dahle Gry , Elefteriades John A , Lancellotti Patrizio , Prager Richard L , Rosenhek Raphael , Speir Alan , Stijnen Marco , Tasca Giordano , Yoganathan Ajit , Walther Thomas , De Paulis Ruggero ,   (Task Force Chairman); EACTS–STS–AATS Valve Labelling Task Force
Published: June 2020

Abstract
Comprehensive information on the characteristics of surgical heart valves (SHVs) is essential for optimal valve selection. Such information is also important in assessing SHV function after valve replacement. Despite the existing regulatory framework for SHV sizing and labelling, this information is challenging to obtain in a uniform manner for various SHVs. To ensure that clinicians are adequately informed, the European Association for Cardio-Thoracic Surgery (EACTS), The Society of Thoracic Surgeons (STS) and American Association for Thoracic Surgery (AATS) set up a Task Force comprised of cardiac surgeons, cardiologists, engineers, regulatory bodies, representatives of the International Organization for Standardization and major valve manufacturers. Previously, the EACTS–STS–AATS Valve Labelling Task Force identified the most important problems around SHV sizing and labelling. This Expert Consensus Document formulates recommendations for providing SHV physical dimensions, intended implant position and haemodynamic performance in a transparent, uniform manner. Furthermore, the Task Force advocates for the introduction and use of a standardized chart to assess the probability of prosthesis–patient mismatch and calls valve manufacturers to provide essential information required for SHV choice on standardized Valve Charts, uniformly for all SHV models.
Contexts for Couperin’s L’art de toucher le clavecin
Authors: Demeilliez Marie 
Published: June 2020

Abstract
One of the best-known texts on 18th-century French harpsichord playing, Couperin’s L’art de toucher le clavecin (1716), has long been considered a valuable source for performers of French Baroque keyboard music. This article investigates the cultural contexts that shaped its text and its aesthetic preoccupations. Various passages dealing with the human body (on seating and position, and on fingering) can be related to the rules of civility and personal control taught by 17th-century etiquette books. Other passages such as the practical exercises show resemblances with vocal pedagogy and graded exercises used in school teaching of the time. Although Couperin claimed that his was the first and only method to deal with good keyboard playing, the book is shaped by a close relationship with other musical treatises (whether for harpsichord or other instruments) published in France during the previous few decades.
‘May she who was once beautiful be transformed into a monster’: magic and witchcraft in Veneno es de amor la envidia (Madrid, 1711)
Authors: Acuña Maria Virginia 
Published: June 2020

Abstract
Through the lenses of magic, witchcraft and superstition, this article explores Veneno es de amor la envidia (Biblioteca Nacional de España, Ms. 19254), a little-known zarzuela by Sebastián Durón and Antonio de Zamora. I consider this zarzuela within its wider cultural context, looking at changing attitudes towards magic and witchcraft in early modern Spain, as well as within the context of Zamora’s literary output. I propose that Veneno es de amor la envidia was intended to attract large crowds of theatregoers fascinated with depictions of the supernatural while also helping to debunk beliefs in witchcraft through the use of humour and parody. An examination of this rather intriguing zarzuela contributes to our understanding of an often-overlooked corpus of theatrical music of the Baroque.
Genetic variance distribution of SSR markers and economically important quantitative traits in a progeny trial ofProsopis chilensis(Leguminosae): implications for the ‘Algarrobo’ management programme
Authors: Chequer Charan Daniela , Pometti Carolina , Cony Mariano , Vilardi Juan Cesar , Saidman Beatriz O , Bessega Cecilia 
Published: June 2020

AbstractProsopis chilensis (Molina) Stuntz (Leguminosae) is a valuable native species in Argentina included in the Prosopis Management Programme. Natural provenances show important height and shape differentiation throughout their distribution in the Monte Desert. The availability of progeny trials provides an opportunity to quantify genetic differentiation among provenances and test the relative importance of demographic vs adaptive processes on morphological variation. We quantified both genetic and quantitative differentiation of neutral markers and five economically important traits, respectively, among four provenances in a provenance-progeny trial. We aimed to quantify the genetic basis of variations in height, basal diameter, tree shape, spine length and biomass. Two hypotheses were tested: (1) economically important traits have significant heritability, and (2) the phenotypic variation among provenances is the result of local adaptation to particular environmental conditions. Our results indicate that most morphological variation was found among individuals within families (~95 per cent). The h2 estimates were heterogeneous among traits and ranged from low (0 for number of stems) to moderate (0.22 and 0.28 for spine length and biomass, respectively). Variance among families (~5 per cent) was evenly distributed within and among provenances. Morphological differentiation among provenances was low, but significant, and could be attributed mainly to individuals from Villa Unión. Based on molecular markers, genetic differentiation among provenances was low and significant (FST = 0.03; P = 5 × 10−4) but was able to differentiate the groups from Villa Unión, Fiambalá and Mogna-Chilecito. Neutrality tests were conducted using the FST –QST test and DJSOST and δGREGORIUS alternative coefficients of differentiation. Neutrality tests yielded no evidence of local adaptation and were rather consistent in showing a trend toward stabilizing selection, particularly for spine length. The selection strategy for breeding programmes should depend on the trait to be improved and should consider both provenance and familiar information. Considering an intra-familiar ranking is encouraged in order to maximize the genetic gain. Additionally, in order to recover germplasm provenance diversity, based on morphological and microsatellite results, our recommendation would be to include seeds from individuals from at least the Villa Unión, Fiambalá and Mogna-Chilecito areas.
CandiMeth: Powerful yet simple visualization and quantification of DNA methylation at candidate genes
Authors: Thursby Sara-Jayne , Lobo Darin K , Pentieva Kristina , Zhang Shu-Dong , Irwin Rachelle E , Walsh Colum P 
Published: June 2020

Abstract

Background
DNA methylation microarrays are widely used in clinical epigenetics and are often processed using R packages such as ChAMP or RnBeads by trained bioinformaticians. However, looking at specific genes requires bespoke coding for which wet-lab biologists or clinicians are not trained. This leads to high demands on bioinformaticians, who may lack insight into the specific biological problem. To bridge this gap, we developed a tool for mapping and quantification of methylation differences at candidate genomic features of interest, without using coding.

Findings
We generated the workflow "CandiMeth" (Candidate Methylation) in the web-based environment Galaxy. CandiMeth takes as input any table listing differences in methylation generated by either ChAMP or RnBeads and maps these to the human genome. A simple interface then allows the user to query the data using lists of gene names. CandiMeth generates (i) tracks in the popular UCSC Genome Browser with an intuitive visual indicator of where differences in methylation occur between samples or groups of samples and (ii) tables containing quantitative data on the candidate regions, allowing interpretation of significance. In addition to genes and promoters, CandiMeth can analyse methylation differences at long and short interspersed nuclear elements. Cross-comparison to other open-resource genomic data at UCSC facilitates interpretation of the biological significance of the data and the design of wet-lab assays to further explore methylation changes and their consequences for the candidate genes.

Conclusions
CandiMeth (RRID:SCR_017974; Biotools: CandiMeth) allows rapid, quantitative analysis of methylation at user-specified features without the need for coding and is freely available at https://github.com/sjthursby/CandiMeth.
Bulk, shear and scattering attenuation beneath Hawaiian Volcanos and in the oceanic crust extending to the Aloha Cabled Observatory
Authors: Butler Rhett 
Published: June 2020

SUMMARYSeismic attenuation is measured from a swarm of 50 earthquakes in Kīlauea volcano in 2018, associated with caldera collapse. The traverse extends at nearly constant azimuth to the saddle between Mauna Loa and Mauna Kea, continuing to Maui beneath the distal flanks of three dormant volcanos. From Maui the traverse then extends seaward to the Aloha Cabled Observatory (ACO) on the seafloor north of O‘ahu. The effective attenuation is measured with respect to an ${\omega ^{ - 2}}$ earthquake source model. Frequency dependent ${Q_P}$ and ${Q_S}$ are derived. The initial path is shallow and uphill, the path to Maui propagates at mid-crustal depths, and the path to ACO extends through oceanic crust. The observations of ${Q_P} \le {Q_S}$ over each traverse are modelled as bulk attenuation ${Q_K}$. Several attenuation processes are observed, including ${Q_\mu }$, ${Q_K}$, $Q\sim f$, constant Q and scattering. The observation of bulk attenuation is ascribed to contrasting physical properties between basalt and water saturated vesicles. The ratio of Q values between shallow and mid-crustal propagation is used to derive an activation energy E* for the undetermined shear attenuation mechanism. A Debye relaxation peak is fit to the ${Q_S}( f )$ and ${Q_K}( f )$ observed for the mid-crustal pathway. A prior high-frequency attenuation study near Wake Island compares well with this Hawaiian Q data set, which in general shows lower values of Q than observed for Wake.
1603: a jagged succession*
Authors: Doran Susan 
Published: June 2020

Abstract
This article contests the received wisdom that James I’s accession was smooth and untroubled by revealing the less smooth side – the jagged edge as it were - to both the moment of James I’s succession and the early months of his reign. It examines the uncertainty about the new king’s title; the short hiatus in effective government; unease about some of James’s actions; anxieties raised by the Bye and Main plots; grass-roots political agitation; and immediate concerns about the future direction of policy. Examining them together offers a new perspective on James I’s early reign.
Cardiac Microlesions Form During Severe BacteremicEnterococcus faecalisInfection
Authors: Brown Armand O , Singh Kavindra V , Cruz Melissa R , Kaval Karan Gautam , Francisco Liezl E , Murray Barbara E , Garsin Danielle A 
Published: June 2020

AbstractEnterococcus faecalis is a significant cause of hospital-acquired bacteremia. Herein, the discovery is reported that cardiac microlesions form during severe bacteremic E. faecalis infection in mice. The cardiac microlesions were identical in appearance to those formed by Streptococcus pneumoniae during invasive pneumococcal disease. However, E. faecalis does not encode the virulence determinants implicated in pneumococcal microlesion formation. Rather, disulfide bond forming protein A (DsbA) was found to be required for E. faecalis virulence in a Caenorhabditis elegans model and was necessary for efficient cardiac microlesion formation. Furthermore, E. faecalis promoted cardiomyocyte apoptotic and necroptotic cell death at sites of microlesion formation. Additionally, loss of DsbA caused an increase in proinflammatory cytokines, unlike the wild-type strain, which suppressed the immune response. In conclusion, we establish that E. faecalis is capable of forming cardiac microlesions and identify features of both the bacterium and the host response that are mechanistically involved.
Association of Male Sex and Obesity With Residual Plasma Human Immunodeficiency Virus 1 Viremia in Persons on Long-Term Antiretroviral Therapy
Authors: Cyktor Joshua C , Bosch Ronald J , Mar Hanna , Macatangay Bernard J , Collier Ann C , Hogg Evelyn , Godfrey Catherine , Eron Joseph J , McMahon Deborah K , Mellors John W , Gandhi Rajesh T ,   ACTG A5321 Team
Published: June 2020

Abstract

Background
Although adipose tissue has been proposed to harbor part of the human immunodeficiency virus 1 (HIV-1) reservoir, the influence of host characteristics, including sex and body mass index (BMI), on measures of HIV-1 persistence during antiretroviral therapy (ART) are incompletely understood.

Methods
We evaluated age, sex, BMI, waist circumference, years on ART, pre-ART HIV-1 RNA, pre-ART CD4+ T-cell count, and initial ART regimen with measures of HIV-1 persistence in blood (residual viremia, cellular HIV-1 DNA and RNA) in a cohort of 295 individuals with well-documented long-term virologic suppression (HIV-1 RNA &lt;50 copies/mL) on ART (AIDS Clinical Trials Group study A5321).

Results
Men were more likely than women to have detectable plasma HIV-1 RNA by single-copy assay (52% vs 29%; P = .003), and the proportion of participants with detectable residual viremia increased in a stepwise fashion by BMI category (normal weight or underweight, 38%; overweight, 50%; and obese, 55%). ART regimen type was not associated with measures of HIV-1 persistence after controlling for ART duration.

Conclusions
Sex and obesity are independently associated with residual viremia in people on long-term ART. Additional studies to confirm these relationships and to define the mechanisms by which sex and obesity affect HIV-1 persistence are needed to inform HIV-1 cure strategies.