bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Potential Impact of a Gel-Based Point-of-Sex Intervention in Reducing Gonorrhea Incidence Among Gay and Bisexual Men: A Modeling Study
Authors: Traeger Michael W. , Tidhar Tom , Holt Martin , Williams Chris , Wright Edwina J. , Stoové Mark A. , Scott Nick , Hellard Margaret E. 
Published: July 2020

Background
Increases in sexually transmitted infections among gay and bisexual men (GBM) over the past decade have coincided with declines in condom use and rapid uptake of HIV preexposure prophylaxis (PrEP). We explored the impact of an antimicrobial gel-based point-of-sex intervention (gel-PSI) with a lower efficacy for reducing gonorrhea transmission risk than condoms on population-level gonorrhea incidence among GBM in Victoria, Australia.

Methods
A deterministic compartmental model of HIV and gonorrhea transmission was used to project annual gonorrhea incidence from 2020 to 2025. Individuals were classified as HIV-negative (PrEP or non-PrEP users) or HIV-positive, and further stratified by gonorrhoea risk (high/low). All possible scenarios where between 0% and 100% of GBM using condoms transitioned to gel-PSI (considered a downgrade in protection) and 0% and 100% of GBM not using condoms transitioned to gel-PSI (considered an upgrade in protection), with gel-PSI efficacy ranging from 20% to 50%, were run.

Results
The baseline scenario of no gel-PSI uptake (status quo) projected 94,367 gonorrhea infections between 2020 and 2025, with an exponentially increasing trend in annual infections. For a gel-PSI efficacy of 30%, a net reduction in cumulative gonorrhea incidence was projected, relative to the status quo, for any ratio of proportion of condom users “downgrading” to proportion of noncondom users “upgrading” to gel-PSI use of less than 2.6. Under the supposition of equal proportions of condom users and noncondom users switching to gel-PSI, a relative reduction was projected for any gel-PSI efficacy greater than 16%.

Conclusions
Our model suggests that the introduction of a gel-PSI could have benefits for controlling gonorrhea transmission among GBM, even in scenarios where the gel-PSI is considerably less efficacious than condoms and when gel-PSI uptake leads to consequent reductions in consistent condom use.
Clinical characteristics, comorbidities and outcomes among persons with HIV hospitalized with coronavirus disease 2019 in Atlanta, Georgia
Authors: Collins Lauren F. , Moran Caitlin A. , Oliver Nora T. , Moanna Abeer , Lahiri Cecile D. , Colasanti Jonathan A. , Kelley Colleen F. , Nguyen Minh L. , Marconi Vincent C. , Armstrong Wendy S. , Ofotokun Ighovwerha , Sheth Anandi N. 
Published: July 2020

Background:
There are limited data describing the presenting characteristics and outcomes among US persons with HIV (PWH) requiring hospitalization for coronavirus disease 2019 (COVID-19).

Methods:
We performed a case series of all PWH sequentially admitted with COVID-19 from 8 March 2020 to 23 April 2020 at three hospitals in Atlanta, Georgia. Sociodemographic, clinical and HIV-associated characteristics were collected.

Results:
Of 530 confirmed COVID-19 cases hospitalized during this period, 20 occurred among PWH (3.8%). The median age was 57 (Q1–Q3, 48–62) years, 65% were men, and 85% were non-Hispanic Black. Presenting median symptom duration was 5 (Q1–Q3, 3–7) days; cough (90%), fever (65%), malaise (60%) and dyspnea (60%) were most common. On admission, 40% of patients required oxygenation support and 65% had an abnormal chest radiograph. Median length of hospitalization was 5 (Q1–Q3, 4–12) days, 30% required intensive care, 15% required intubation, and 15% died. Median CD4+ cell count prior to admission was 425 (Q1–Q3, 262–815) cells/μl and 90% of patients had HIV-1 RNA less than 200 copies/ml. Half of the patients had at least five comorbidities; hypertension (70%), dyslipidemia (60%) and diabetes (45%) were most prevalent. All three patients who died had CD4+ cell count more than 200, HIV suppression and each had a total of five comorbidities.

Conclusion:
The multisite series in the Southern United States provides characteristics and early outcomes of hospitalized PWH with COVID-19. Nearly all patients had controlled HIV and a high comorbidity burden. Additional study of COVID-19 among PWH is needed to determine the role of age, comorbidities and HIV control in mediating COVID-19 presentation and its sequelae.
Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation
Authors: Charre Caroline , Ginevra Christophe , Sabatier Marina , Regue Hadrien , Destras Grégory , Brun Solenne , Burfin Gwendolyne , Scholtes Caroline , Morfin Florence , Valette Martine , Lina Bruno , Bal Antonin , Josset Laurence 
Published: July 2020

AbstractSince the beginning of the COVID-19 outbreak, SARS-CoV-2 whole-genome sequencing (WGS) has been performed at unprecedented rate worldwide with the use of very diverse Next Generation Sequencing (NGS) methods. Herein, we compare the performance of four NGS-based approaches for SARS-CoV-2 WGS. Twenty four clinical respiratory samples with a large scale of Ct values (from 10.7 to 33.9) were sequenced with four methods. Three used Illumina sequencing: an in-house metagenomic NGS (mNGS) protocol and two newly commercialized kits including a hybridization capture method developed by Illumina (DNA Prep with Enrichment kit and Respiratory Virus Oligo Panel, RVOP) and an amplicon sequencing method developed by Paragon Genomics (CleanPlex SARS-CoV-2 kit). We also evaluated the widely used amplicon sequencing protocol developed by ARTIC Network and combined with Oxford Nanopore Technologies (ONT) sequencing. All four methods yielded near-complete genomes (>99%) for high viral loads samples, with mNGS and RVOP producing the most complete genomes. For mid viral loads, 2/8 and 1/8 genomes were incomplete (<99%) with mNGS and both CleanPlex and RVOP, respectively. For low viral loads (Ct ≥25), amplicon-based enrichment methods were the most sensitive techniques yielding complete genomes for 7/8 samples. All methods were highly concordant in terms of identity in complete consensus sequence. Just one mismatch in two samples was observed in CleanPlexvsthe other methods, due to the dedicated bioinformatics pipeline setting a high threshold to call SNP compared to reference sequence. Importantly, all methods correctly identified a newly observed 34-nt deletion in ORF6 but required specific bioinformatic validation for RVOP. Finally, as a major warning for targeted techniques, a default of coverage in any given region of the genome should alert to a potential rearrangement or a SNP in primer annealing or probe-hybridizing regions and would require regular updates of the technique according to SARS-CoV-2 evolution.
Physical activity, mental health and well-being of adults during early COVID-19 containment strategies: A multi-country cross-sectional analysis
Authors: Faulkner James , O’Brien Wendy J. , McGrane Bronagh , Wadsworth Daniel , Batten John , Askew Christopher D. , Badenhorst Claire , Byrd Erin , Coulter Maura , Draper Nick , Elliot Catherine , Fryer Simon , Hamlin Michael J. , Jakeman John , Mackintosh Kelly A. , McNarry Melitta A. , Mitchelmore Andrew , Murphy John , Ryan-Stewart Helen , Saynor Zoe , Schaumberg Mia , Stone Keeron , Stoner Lee , Stuart Beth , Lambrick Danielle 
Published: July 2020

ABSTRACTObjectivesTo assess how the early stages of National governments Coronavirus disease (COVID-19) containment strategies impacted upon the physical activity, mental health and well-being of adults in the UK, Ireland, New Zealand and AustraliaDesignObservational, cross-sectionalSettingOnline survey disseminated in the UK, Ireland, New Zealand and Australia within the first 2-6 weeks of government mandated COVID-19 restrictionsParticipantsAdults (n = 8,425; 44.5 ± 14.8 y), ≥ 18 y who were residing in the surveyed countriesMain outcome measuresStages of Change scale for exercise behaviour change, International Physical Activity Questionnaire (short-form), World Health Organisation-5 Well-being Index and the Depression Anxiety and Stress Scale-9ResultsParticipants who reported a negative change in exercise behaviour between pre- and during the early COVID-19 restrictions demonstrated poorer mental health and well-being compared to those who had either a positive change- or no change in their exercise behaviour (p<0.001). Whilst women reported more positive changes in exercise behaviour, young people (18-29y) reported more negative changes (both p<0.001). Individuals who engaged in more physical activity reported better mental health and well-being (p<0.001). Although there were no differences in physical activity between countries, individuals in New Zealand reported better mental health and well-being (p<0.001).ConclusionThe COVID-19 restrictions have differentially impacted upon the physical activity habits of individuals based upon their age and sex, and therefore have important implications for international policy and guideline recommendations. Public health interventions that encourage physical activity should target specific groups (e.g., men, young adults) who are most vulnerable to the negative effects of physical distancing and/or self-isolation.
Seasonality of non-SARS, non-MERS Corona viruses and the impact of meteorological factors
Authors: Anastasiou Olympia E. , Hüsing Anika , Korth Johannes , Theodoropoulos Fotis , Taube Christian , Jöckel Karl-Heinz , Stang Andreas , Dittmer Ulf 
Published: July 2020

AbstractBackgroundSeasonality is a characteristic of some respiratory viruses. The aim of our study was to evaluate the seasonality and the potential effects of different meteorological factors on the detection rate of the non-SARS Corona Virus detection by PCR.MethodsWe performed a retrospective analysis of 12763 respiratory tract sample results (288 positive and 12475 negative) for non-SARS, non-MERS Corona viruses (NL63, 229E, OC43, HKU1). The effect of seven single weather factors on the Corona virus detection rate was fitted in a logistic regression model with and without adjusting for other weather factors.ResultsCorona virus infections followed a seasonal pattern peaking from December to March and plunging from July to September. The seasonal effect was less pronounced in immunosuppressed patients compared to immunocompetent. Different automatic variable selection processes agreed to select the predictors temperature, relative humidity, cloud cover and precipitation as remaining predictors in the multivariable logistic regression model including all weather factors, with low ambient temperature, low relative humidity, high cloud cover and high precipitation being linked to increased Corona virus detection rates.ConclusionsCorona virus infections followed a seasonal pattern, which was more pronounced in immunocompetent patients compared to immunosuppressed. Several meteorological factors were associated with the Corona virus detection rate. However, when mutually adjusting for all weather factors, only temperature, relative humidity, precipitation and cloud cover contributed independently to predicting the Corona virus detection rate.
Observational Study of Chlorpromazine in Hospitalized Patients with Covid-19
Authors: Hoertel Nicolas , Rico Marina Sanchez , Vernet Raphaël , Jannot Anne-Sophie , Neuraz Antoine , Blanco Carlos , Lemogne Cédric , Airagnes Guillaume , Paris Nicolas , Daniel Christel , Gramfort Alexandre , Lemaitre Guillaume , Bernaux Mélodie , Bellamine Ali , Beeker Nathanaël , Limosin Frédéric 
Published: July 2020

ABSTRACTOn the grounds of its anti-inflammatory and potential antiviral effects, chlorpromazine has been suggested to be effective treatment for Covid-19. We examined the association between chlorpromazine use and respiratory failure among all hospitalized adults with Covid-19 at the 39 Greater Paris University hospitals since the beginning of the epidemic. Study baseline was defined as the date of hospital admission. The primary endpoint was a composite of intubation or death in a time-to-event analysis adjusting for numerous potential confounders. We used a multivariable Cox model with inverse probability weighting according to the propensity score. Of the 12,217 adult inpatients with a positive Covid-19 RT-PCR test included in the analyses, 57 (0.47%) received chlorpromazine. Over a mean follow-up of 20.8 days, the primary endpoint occurred in 29 patients (50.9%) exposed to chlorpromazine and 1,899 patients (15.6%) who were not. In the main analysis, there was a positive significant association between chlorpromazine use and the outcome (HR, 1.67; 95% CI, 1.09 to 2.56, p=0.019), while a Cox regression in a matched analytic sample yielded non-significant association (1.38; 95% CI, 0.91 to 2.09, p=0.123). These findings suggest that chlorpromazine is unlikely to have a clinical efficacy for Covid-19.
Canine tumor mutation rate is positively correlated with TP53 mutation across cancer types and breeds
Authors: Alsaihati Burair A. , Ho Kun-Lin , Watson Joshua , Feng Yuan , Wang Tianfang , Zhao Shaying 
Published: July 2020

AbstractSpontaneous canine cancers are a valuable but relatively understudied and underutilized model in cancer research. To enhance their usage, we reanalyzed whole exome sequencing data published for 601 dogs with mammary cancer, osteosarcoma, oral melanoma, lymphoma, glioma or hemangiosarcoma from over 35 breeds, after rigorous quality control, including breed validation. Each cancer type harbors distinct molecular features, with major pathway alterations matching its human counterpart (e.g., PI3K for mammary cancer and p53 for osteosarcoma). On average, mammary cancer and glioma have lower mutation rates (median <0.5 mutation per Mb), whereas oral melanoma, osteosarcoma and hemangiosarcoma have higher mutation rates (median ≥1 mutation per Mb). Across cancer types and across breeds, the mutation rate is strongly associated withTP53mutation, but not withPIK3CAmutation. The mutation rate is also associated with a mutation signature enriched in osteosarcoma of Golden Retrievers, independent ofTP53mutation. Finally, compared to other breeds examined, DNA repair genes appear to be less conserved in Golden Retriever which is predisposed to numerous cancers.
gPortfolios: a pragmatic approach to online asynchronous assignments
Authors: Hickey Daniel , Duncan Jody , Gaylord Courtney , Hitchcock Christine , Itow Rebecca Chiyoko , Stephens Shelby Elizabeth 
Published: July 2020

Purpose
The purpose of this paper is sharing out basic guidelines and examples from an extended collaboration to move educators move online while avoiding synchronous meetings. “gPortfolios” are public (to the class) pages where students write responses to carefully constructed engagement routines. Students then discuss their work with instructors and peers in threaded comments. gPortfolios usually include engagement reflections, formative self-assessments and automated quizzes. These assessments support and document learning while avoiding instructor “burnout” from grading. gPortfolios can be implemented using Google Docs and Forms or any learning management system.

Design/methodology/approach
The authors report practical insights gained from design-based implementation research. This research explored the late Randi Engle’s principles for productive disciplinary engagement and expansive framing. Engle used current theories of learning to foster student discussions that were both authentic to the academic discipline at hand and productive for learning. This research also used new approaches to assessment to support Engle’s principles. This resulted in a comprehensive approach to online instruction and assessment that is effective and efficient for both students and teachers.

Findings
The approach “frames” (i.e. contextualizes) online engagement using each learners’ own experiences, perspectives and goals. Writing this revealed how this was different in different courses. Secondary biology students framed each assignment independently. Secondary English and history students framed assignments as elements of a personalized capstone presentation; the history students further used a self-selected “historical theme.” Graduate students framed each assignment in an educational assessment course using a real or imagined curricular aim and context.

Originality/value
Engle’s ideas have yet to be widely taken up in online education.
Seismic tuning of dispersive thin layers
Authors: Papageorgiou Giorgos , Chapman Mark 
Published: July 2020

ABSTRACTThe wedge model is commonly used to study the limits of seismic resolution where conventionally the thickness of sub‐resolution seismic layers can be determined from thin layer tuning curves. Tuning curves relate the layer temporal thickness to the wavelet frequency, but, to our knowledge, no systematic study has been done to date of the effects of velocity dispersion and attenuation on tuning. In this work, we study the tuning properties of a thin layer dispersing according to the standard linear solid model. We show that the first tuning curve is sensitive to the attenuation, relative polarity and magnitude of the two reflection coefficients at the top and base of the layer. We provide an analytic formula for the upper bound in the mismatch between the elastic and dispersive tuning curves. We conclude that highly attenuative thin layers can appear thicker or thinner than they actually are depending on polarity and relative magnitude of reflection coefficients at the layer interfaces. Our results are particularly relevant in the quantification of CO2 where knowledge of the temporal thickness of CO2 layers is reliant on their tuning curves.
Validation of the Simple Psoriatic Arthritis Screening (SiPAS) questionnaire in a Turkish psoriatic population
Authors: Kaymaz Serdar , Karasu Uğur , Kaçar Nida , Çınar Gökhan , Çobankara Veli , Alkan Hakan , Ulutaş Firdevs 
Published: July 2020

AbstractObjectivesScreening of psoriatic arthritis (PsA) in patients with psoriasis (PsO) is critical for the prevention of irreversible joint erosions, deformity, and disability. The SiPAS questionnaire is a short, simple and useful tool designed to screen PsA. This study aimed to evaluate validity of the SiPAS questionnaire in Turkish patients with PsO.Materials and methodsThe Turkish translation of SiPAS was sent to us by the developer authors of the original index. Subjects were recruited from dermatology outpatient clinics. All patients' demographic parameters and SiPAS questionnaire results were recorded. After patients completed the questionnaire they were assessed by a rheumatologist according to standard protocol which included a complete history, detailed physical examination, laboratory tests and Classification for Psoriatic Arthritis (CASPAR) criteria. Receiver operating characteristics (ROC) were assessed to obtain sensitivity and specificity of the Turkish version of the SiPAS questionnaire.ResultsOne hundred and thirty subjects were recruited into the study. The mean age of subjects were 43.5 years and the 55.4% of subjects were female. Of these, after rheumatologic evaluation 42 patients were diagnosed as PsA. The area under the ROC curve was 0.994 which means as excellent predictor and optimum cut‐off threshold to discriminate patients diagnosed with PsA was 3 according to this ROC curve analysis. The overall sensitivity and specificity based on cut‐off threshold of 3, were 97.6% and 94.3%, respectively.ConclusionsThe Turkish version of the SiPAS questionnaire is a simple useful, time‐saving and valid tool for screening PsA in patients diagnosed with PsO with its high sensitivity and specificity. A SiPAS score ≥3 is an indication for referral to a rheumatologist.
Personal protective equipment and evidence‐based advice for surgical departments during COVID‐19
Authors: Tan Lorwai , Kovoor Joshua G. , Williamson Penny , Tivey David R. , Babidge Wendy J. , Collinson Trevor G. , Hewett Peter J. , Hugh Thomas J. , Padbury Robert T. A. , Langley Sally J. , Maddern Guy J. 
Published: July 2020

AbstractBackgroundInconsistencies regarding the use of appropriate personal protective equipment (PPE) have raised concerns for the safety of surgical staff during the coronavirus disease 2019 (COVID‐19) pandemic. This rapid review synthesizes the literature and includes input from clinical experts to provide evidence‐based guidance for surgical services.MethodsThe rapid review comprised of targeted searches in PubMed and grey literature. Pertinent findings were discussed by a working group of clinical experts, and consensus recommendations, consistent with Australian and New Zealand Government guidelines, were formulated.ResultsThere was a paucity of high‐quality primary studies specifically investigating appropriate surgical PPE for healthcare workers treating patients possibly infected with COVID‐19. SARS‐CoV‐2 is capable of aerosol, droplet and fomite transmission, making it essential to augment standard infection control measures with appropriate PPE, especially during surgical emergencies and aerosol‐generating procedures. All biological material should be treated a potential source of SARS‐COV‐2. Staff must have formal training in the use of PPE and should be supervised by a colleague during donning and doffing. Patients with suspected or confirmed COVID‐19 should wear a surgical mask during transfer to and from theatre. Potential solutions exist in the literature to extend the use of surgical P2/N95 respirators in situations of limited supply.ConclusionPPE is advised for all high‐risk procedures and when a patient's COVID‐19 status is unknown. Surgical departments should facilitate staggered rostering, remote meeting attendance, and self‐isolation of symptomatic staff. Vulnerable surgical staff should be identified and excluded from operations with a high risk of COVID‐19 infection.
Variation in lysine, threonine, and tryptophan availability in meat and bone meal as estimated by the slope‐ratio growth assay technique in growing rats
Authors: Sato Hiroyuki , Miura Makoto , Fujieda Takeshi , Taciak Marcin , Kikusato Motoi , Toyomizu Masaaki 
Published: July 2020

AbstractMeat and bone meal (MBM) is an important protein source used in animal feeds. However, as the composition and availability of amino acids (AAs) in MBM fluctuate markedly, it is important to verify the magnitude of these parameters in different MBMs. In this study, the AA compositions of 19 MBMs were analyzed to confirm variations in lysine (Lys), threonine (Thr), and tryptophan (Trp), then which were compared with those of soybean meal (SBM) and fish meal (FM). Instability in Lys, Thr, and Trp availabilities in six MBMs were also considered after estimation using the slope‐ratio growth assay technique in rats. Variations in AA composition were evaluated using the coefficient of variance (CV: Standard deviation/Mean). CVs for Lys, Thr, and Trp content were 9.40, 11.83, and 18.12 in MBM, 2.71, 2.48, and 3.19 in SBM, and 10.09, 10.44, and 13.47 in FM. Furthermore, means and SDs for Lys, Thr, and Trp availabilities in MBM were 53.3 ± 10.4% (CV: 19.5), 65.9 ± 17.6% (CV: 26.6), and 83.2 ± 11.2% (CV: 13.5), respectively. These results provide the first evidence that variations in MBM AA compositions were 3.5 to 5.7 times higher than those in SBM, but similar to FM, and that the large variation in availability substantially existed.