bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Dual-Platform Point-of-Care Test for Neurosyphilis Diagnosis
Authors: Gonzalez Hemil , Koralnik Igor Jerome , Huhn Gregory D. , Tantalo Lauren C. , Ritz Ethan M. , Orban Zachary , Marra Christina M. 
Published: April 2021

Background
The diagnosis of neurosyphilis relies on cerebrospinal fluid (CSF) abnormalities (pleocytosis, elevated protein) and CSF–Venereal Disease Research Laboratory (VDRL) test. In resource-limited settings, the CSF-VDRL test may not be widely available.

Methods
We optimized a commercial immunochromatographic strip test, the DPP Chembio syphilis assay, for performance with CSF and tested centrifuged CSF samples of 71 patients with syphilis (35 with neurosyphilis and 36 without neurosyphilis). A CSF dilution of 1:4 was chosen based on agreement with CSF pools with documented results from the CSF-VDRL test and fluorescent treponemal antibody absorption test on CSF. Using an electronic reader, we obtained unit values of treponemal and nontreponemal antibodies for all study samples and generated a receiver operating characteristic curve; using the Youden index, we established diagnostic cutoffs with optimal sensitivity and specificity.

Results
Diagnostic sensitivity of the nontreponemal test was 80% (95% confidence interval, 63%–92%) and specificity was 97% (95% confidence interval, 85%–100%) for neurosyphilis diagnosis using a reactive CSF-VDRL that improved after neurosyphilis therapy as a criterion standard.

Conclusions
In this small study, the DPP Chembio test showed promising results for neurosyphilis diagnosis. Further studies are needed to assess its performance in resource-limited settings.
A scoping review of chronic pain in emerging adults
Authors: Brown Donnamay , Schenk Sabrina , Genent Dunja , Zernikow Boris , Wager Julia 
Published: April 2021

Abstract
Much of the adult chronic pain literature addresses pain in typical pain cohorts of middle-aged to older individuals. To date, little research has focused on chronic pain in younger adults, who likely have a completely different pain experience. This scoping review aimed to address this gap by describing the emerging adult (18–29 years) chronic pain experience regarding prevalence, associated factors, outcomes, and pain management. Searches of primary electronic databases including PubMed, Embase, PsycINFO, and CINAHL were performed on February 26, 2020, restricting the publication date from database inception to December 31, 2019. The search strategy, conducted in English, covered search term combinations of “chronic pain” and “young adults.” A total of 6,612 records were considered—3,141 after removing duplicates. These records were screened by title and abstract; 871 through full-text screening. Of these, 78 articles covered the topic of emerging adults with chronic pain. Collectively, results indicated that between 5% and 30% of emerging adults experience chronic pain, depending on the sample and exact chronic pain definition. The most consistent associated factors were female sex, familial chronic pain, and previous experiences of chronic pain in childhood. Anxiety, depression, and sleep issues appeared associated both before and after the onset of chronic pain. Outcomes of pain included interruptions to study and work, poorer physical functioning, and pain-related interference to socializing. We observed that few pain treatments have been tested specifically in this cohort. A greater ongoing focus on chronic pain in emerging adults is required to improve long-lasting outcomes.
Microaggressions and Implicit Bias in Surgical Training: An Undocumented but Pervasive Phenomenon
Authors: Alimi Yewande , Bevilacqua Lisa A. , Snyder Rebecca A. , Walsh Danielle , Jackson Patrick G. , DeMaria Eric J. , Tuttle Janet E. , Altieri Maria S. 
Published: April 2021

Objective:
To examine the prevalence, nature, and source of microaggressions experienced by surgical residents during training.

Summary and Background Data:
The role of microaggressions in contributing to workplace culture, individual performance, and professional satisfaction has become an increasingly studied topic across various fields. Little is known about the prevalence and impact of microaggressions during surgical training.

Methods:
A 46-item survey distributed to current surgical residents in training programs across the United States via the Association of Program Directors in Surgery listserv and social media platforms between January and May 2020. Survey questions explored the frequency and extent of events of experiencing, witnessing, and responding to microaggressions in the workplace. The primary outcome was the occurrence of microaggressions experienced by surgical residents. Secondary outcomes included the nature, impact, and responses to these events.

Results:
A total of 1624 responses were collected, with an equal distribution by self-identified gender (female, n = 815; male, n = 809). The majority of trainees considered themselves heterosexual (n = 1490, 91.7%) and White (n = 1131, 69.6%). A majority (72.2%, n = 1173) of respondents reported experiencing microaggressions, most commonly from patients (64.1%), followed by staff (57.5%), faculty (45.3%), and co-residents (38.8%). Only a small proportion (n = 109, 7.0%) of residents reported these events to graduate medical education office/program director. Nearly one third (30.8%) of residents said they experienced retaliation due to reporting of micro-aggressions.

Conclusions:
Based on this large, national survey of general surgery and surgical subspecialty trainees, microaggressions appear to be pervasive in surgical training. Microaggressions are rarely reported to program leadership, and when reported, can result in retaliation.
Comamonas suwonensis sp. nov., isolated from stream water in the Republic of Korea
Authors: Park Kyu-Hyun , Yu Zhi , Dong Ke , Lee Sang-Seob 
Published: April 2021

A novel bacterial strain, EJ-4T, isolated from stream water collected at Seo-ho in Suwon, Republic of Korea, was characterized based on a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EJ-4T belonged to the genus

Comamonas

. The isolate is Gram-stain-negative, non-motile, aerobic, rod-shaped and forms pale yellow colonies on trypticase soy agar. The optimal growth of this strain was observed aerobically at 30 °C, pH 7 and 0.5 % NaCl. The major fatty acids were summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c; 39.7 %) and C16 : 0 (32.0 %). The G+C content of strain EJ-4T was 58.4mol %. The average nucleotide identity and digital DNA–DNA hybridization values between strain EJ-4T and Comamoas testosteroni were 91.8 and 31.2 %, respectively. The major polar lipids detected in the isolate were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant isoprenoid quinone was ubiquinone-8. Based on the results of polyphasic taxonomic analysis of strain EJ-4T, we describe a novel species of the genus

Comamonas

, for which the name Comamonas suwonensis sp. nov. has been proposed, with EJ-4T (=KCTC 82074T=JCM 34179T=KEMB 1602-279T) as the type strain.
Assessment of the COVID-19 Vaccine Program: Impact of the No Mask Mandate Executive Order in the State of Texas
Authors: Richardson Ariana , Ruffin Rachel , Iboi Enahoro A. 
Published: April 2021

AbstractOn March 10, 2021, a new executive order to lift the mask mandate and allow businesses to open at 100 percent capacity, went into effect in the U.S. state of Texas. This was due to the decrease in the daily number of COVID-19 cases and deaths as the state continues to vaccinate the population. A simple compartmental model was used to assess the implications of the executive order on the ongoing vaccination program. Our simulation shows that approximately 51% of the entire population needs to be fully vaccinated to bring the control reproduction number to a value less than one (threshold condition needed for disease elimination) as compared to the 14.32% that has been fully vaccinated as of March 31, 2021. Hence, the need for an aggressive vaccination program if the state is to open businesses to full capacity and do not require the use of a face mask by the general public.
Compliance with Covid-19 measures: evidence from New Zealand
Authors: Kaine Geoff , Greenhalgh Suzie , Wright Vic 
Published: April 2021

AbstractGovernments around the world are seeking to slow the spread of Covid-19 by implementing measures that encourage, or mandate, changes in people’s behaviour. These changes include the wearing of face masks, social distancing, and testing and self-isolating when unwell. The success of these measures depends on the commitment of individuals to change their behaviour accordingly. Understanding and predicting the motivation of individuals to change their behaviour is therefore critical in assessing the likely effectiveness of these measures in slowing the spread of the virus.In this paper we draw on a novel framework, the I3Compliance Response Framework, to understand and predict the motivation of residents in Auckland, New Zealand, to comply with measures to prevent the spread of Covid-19. The Framework is based on two concepts. The first uses the involvement construct to predict the motivation of individuals to comply. The second separates the influence of the policy measure from the influence of the policy outcome on the motivation of individuals to comply.In short, the Framework differentiates between the strength of individuals’ motivation and their beliefs about the advantages and disadvantages of policy outcomes and policy measures. We found this differentiation was useful in predicting an individual’s possible behavioural responses to a measure and discuss how it could assist government agencies to develop strategies to enhance compliance.
Cone Rescue with Laser Photobiomodulation in Murine and Human Retinal Dystrophy
Authors: Casson Robert J. , Wood John P.M. , Ao Jack , Gilhotra Jagjit S. , Durkin Shane R. , Chan WengOnn , Chidlow Glyn 
Published: April 2021

AbstractRetinitis pigmentosa (RP) encompasses a genetically diverse group of blinding inherited retinal diseases. In most subtypes the gene defect is expressed in the rod photoreceptors, yet in many affected individuals the cone photoreceptors undergo secondary degeneration, leading to loss of the remaining central vision. There is evidence that bioenergetic and oxidative stress are involved in this secondary cone loss. Photobiomodulation (PBM) uses low energy light in the far red or near-infrared spectrum to manipulate cellular activity. We have used a novel slit lamp-mounted retinal PBM laser to deliver precise energy levels to targeted retina. We showed that PBM laser attenuates oxidative and bioenergetic stress-induced photoreceptor loss in vitro and rescues cones in the rd1 murine model of RP. In a phase I trial (ACTRN12618000651280), foveal laser treatment was safe in humans with RP and temporarily recovered, on average, 5 letters of visual acuity.
Informed decision making on the uptake of evidence-based smoking cessation assistance: A needs assessment among end users and experts to inform decision aid development
Authors: Gültzow Thomas , Smit Eline Suzanne , Hudales Raesita , Dirksen Carmen D. , Hoving Ciska 
Published: April 2021

AbstractIntroductionEvidence-based cessation assistance is known to increase cessation rates. Activating personal preferences as part of the decision for smoking cessation assistance tools could further improve tools’ effectiveness. Decision aids (DAs) help individuals to choose amongst the various options by taking these preferences into account and, therefore, could have a positive effect on cessation rates. To develop attractive and effective DAs, potential end users’ needs, and experts’ viewpoints should be considered during development processes. Therefore, the aim of this study was: (1) To explore smokers’ needs and viewpoints regarding a smoking cessation assistance DA, and (2) to obtain consensus among smoking cessation counsellors and scientific experts about the content and format of such a DA.Materials and methodsData was gathered via two approaches applied across three studies: (1) 20 semi-structured interviews with potential end users, (2) two three-round Delphi studies with 61 smoking cessation counsellors and 44 scientific experts. Data from the interviews and the first round of the Delphi studies were analysed qualitatively using the Framework method, while data from the second and third round of the Delphi studies were analysed quantitatively using medians and interquartile ranges.ResultsPotential end users reported to acquire information in different ways: Via own experiences, their social environment, and the media. Important characteristics to decide between tools also varied, however effectiveness and costs were commonly reported as the most important characteristics. The experts reached consensus on 38 (smoking cessation counsellors) and 40 (scientific experts) statements regarding important cessation assistance tools’ characteristics and their viewpoints on a smoking cessation assistance DA, e.g., that a tool should be appropriate for users’ level of addiction.Discussion and conclusionSome clear trends emerged among the potential end users (especially regarding important characteristics). Experts also reached consensus among a number of statements. However, there was some variation in the needs and wishes among the (different) stakeholders. The combination of these studies highlights that a ‘one size fits all’ approach is not desirable. In the development of DAs, this heterogeneity should be taken into account, e.g., by enabling users to customize a DA based on their personal preferences while safeguarding essential elements.HighlightsPotential end users’ needs for a smoking cessation DA vary greatlyHowever, tools’ effectiveness and costs were commonly named as importantCustomizable elements within a DA could be used to deal with this heterogeneityConceptualizations (e.g., of effectiveness) may vary between stakeholdersInformation should be provided to end users in an easily understandable manner
SARS-CoV-2 UK, South African and Brazilian Variants in Karachi- Pakistan
Authors: Khan Adnan , Hanif Muhammad , Syed Sarosh , Ahmed Akhtar , Ghazali Saqib , Khanani Rafiq 
Published: April 2021

AbstractCOVID-19 pandemic has been evolving in Pakistan since the UK, South African and Brazilian variants have started surfacing which are known for increase transmissibility and can also be responsible for escape from immune responses. The gold standard to detect these variants of concern is sequencing, however routine genomic surveillance in resource limited countries like Pakistan is not always readily available. With the emergence of variants of concern and a dearth of facilities for genomic scrutiny leaves policy makers and health authorities an inconsistent and twisted image to make decisions. The inadvertent detection of B.1.1.7 by target failure because of a key deletion in spike Δ69-70 in the UK by commercially available COVID-19 PCR assay helps to understand target failures as an alternative approach to detect variants. It was ascertained further that a deletion in the ORF1a gene (ORF1a Δ3675-3677) found common in B.1.1.7, B.135 and P.1 variants of concern. The Real Time Quantitative PCR (RT-qPCR) assay for detection of emergence and spread of SARS-CoV-2 variants, by these target failures is used here. The positive samples archived in respective labs were divided in two groups used in the present study. Group I constitutes 261 positive samples out of 16964 (1.53%) collected from August till September 2020. Group II include 3501 positive samples out of 46041 (7.60%) from November 2020 till January 2021. In positive samples of group I, no variant of concern was found. A staggering difference in results was noted in group II where positivity ratio increased exponentially and the variants of concern started appearing in significant numbers (53.64% overall). This is indicative that the third wave in Pakistan is due to the importation of SARS-CoV-2 variants. This calls for measures to increase surveillance by RT-qPCR which would help authorities in decision making.
End-to-End Deep Learning for Detecting Metastatic Breast Cancer in Axillary Lymph Node from Digital Pathology Images
Authors: Turki Turki , Al-Sharif Anmar , Taguchi Y-h. 
Published: April 2021

AbstractMetastatic breast cancer is one of the attributed leading causes of women deaths worldwide. Accurate diagnosis to the spread of breast cancer to axillary lymph nodes (ALNs) is done by breast pathologist, utilizing the microscope to inspect and then providing the biopsy report. Because such a diagnosis process requires special expertise, there is a need for artificial intelligence-based tools to assist breast pathologists to automatically detect breast cancer metastases. This study aims to detect breast cancer metastasized to ALN with end-to-end deep learning (DL). Also, we utilize several DL architectures, including DenseNet121, ResNet50, VGG16, Xception as well as a customized lightweight convolutional neural network. We evaluate the DL models on NVIDIA GeForce RTX 2080Ti GPU using 114 processed microscopic images pertaining to ALN metastases in breast cancer patients. Compared to all DL models employed in this study, experimental results show that DenseNet121 generates the highest performance results (64– 68%) based on AUC and accuracy.
Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus
Authors: Kasela Silva , Daniloski Zharko , Jordan Tristan X. , tenOever Benjamin R. , Sanjana Neville E. , Lappalainen Tuuli 
Published: April 2021

AbstractTo date the locus with the most robust human genetic association to COVID-19 susceptibility is 3p21.31. Here, we integrate genome-scale CRISPR loss-of-function screens and eQTLs in diverse cell types and tissues to pinpoint genes underlying COVID-19 risk. Our findings identify SLC6A20 and CXCR6 as putative causal genes that mediate COVID-19 risk and highlight the usefulness of this integrative approach to bridge the divide between correlational and causal studies of human biology.
The Importance of Automation in Genetic Diagnosis: Lessons from Analyzing an Inherited Retinal Degeneration Cohort with the Mendelian Analysis Toolkit (MATK)
Authors: Zampaglione Erin , Maher Matthew , Place Emily M. , Wagner Naomi E. , DiTroia Stephanie , Chao Katherine R. , England Eleina ,   Broad CMG, Catomeris Andrew , Nassiri Sherwin , Himes Seraphim , Pagliarulo Joey , Ferguson Charles , Galdikaité-Braziené Eglé , Cole Brian , Pierce Eric A. , Bujakowska Kinga M. 
Published: April 2021

ABSTRACTPurposeIn Mendelian disease diagnosis, variant analysis is a repetitive, error-prone, and time-consuming process. To address this, we have developed the Mendelian Analysis Toolkit (MATK), a configurable automated variant ranking program.MethodsMATK aggregates variant information from multiple annotation sources and uses expert-designed rules with parameterized weights to produce a ranked list of potentially causal solutions. MATK performance was measured by a comparison of MATK-aided versus human domain-expert analyses of 1060 inherited retinal degeneration (IRD) families investigated with an IRD-specific gene panel (589 individuals) and exome sequencing (471 families).ResultsWhen comparing MATK-assisted analysis to expert curation in both IRD-specific and exome sequencing (1060 subjects), 97.3% of potential solutions found by experts were also identified by the MATK-assisted analysis (541 solutions identified with MATK of 556 solutions found by conventional analysis). Furthermore, MATK-assisted analysis identified 114 additional potential solutions from the 504 cases unsolved by the conventional analysis.ConclusionMATK expedites the process of identifying likely solving variants in Mendelian traits and reduces variability coming from human error and researcher bias. MATK facilitates data re-analysis to keep up with the constantly improving annotation sources and NGS processing pipelines. The software is open source, available at https://gitlab.com/matthew_maher/mendelanalysis
Antibody and T cell responses to a single dose of the AZD1222/Covishield vaccine in previously SARS-CoV-2 infected and naïve health care workers in Sri Lanka
Authors: Jeewandara Chandima , Kamaladasa Achala , Pushpakumara Pradeep Darshana , Jayathilaka Deshni , Abayrathna Inoka Sepali , Danasekara Saubhagya , Guruge Dinuka , Ranasinghe Thushali , Dayarathne Shashika , Pathmanathan Thilagaraj , Somathilaka Gayasha , Madhusanka Deshan , Tanussiya Shyrar , TPJ Tibutius , Kuruppu Heshan , Wijesinghe Ayesha , Thashmi Nimasha , Milroy Dushantha , Nandasena Achini , Sanjeewani Nilanka , Wijayamuni Ruwan , Samaraweera Sudath , Schimanski Lisa , Tan T.K. , Dong Tao , Ogg Graham S. , Townsend Alain , Malavige Gathsaurie Neelika 
Published: April 2021

AbstractBackgroundIn order to determine the immunogenicity of a single dose of the AZD1222/Covishield vaccine in a real-world situation, we assessed the immunogenicity, in a large cohort of health care workers in Sri Lanka.MethodsSARS-CoV-2 antibodies was carried out in 607 naïve and 26 previously infected health care workers (HCWs) 28 to 32 days following a single dose of the vaccine. Haemagglutination test (HAT) for antibodies to the receptor binding domain (RBD) of the wild type virus, B.1.1.7, B.1.351 and the surrogate neutralization assay (sVNT) was carried out in 69 naïve and 26 previously infected individuals. Spike protein (pools S1 and S2) specific T cell responses were measured by ex vivo ELISpot IFNγ assays in 76 individuals.Results92.9% of previously naive HCWs seroconverted to a single dose of the vaccine, irrespective of age and gender; and ACE2 blocking antibodies were detected in 67/69 (97.1%) previously naïve vaccine recipients. Although high levels of antibodies were found to the RBD of the wild type virus, the titres for B.1.1.7 and B.1.351 were lower in previously naïve HCWs. Ex vivo T cell responses were observed to S1 in 63.9% HCWs and S2 in 31.9%. The ACE2 blocking titres measured by the sVNT significantly increased (p<0.0001) from a median of 54.1 to 97.9 % of inhibition, in previously infected HCWs and antibodies to the RBD for the variants B.1.1.7 and B.1.351 also significantly increased.Discussiona single dose of the AZD1222/Covishield vaccine was shown to be highly immunogenic in previously naïve individuals inducing antibody levels greater than following natural infection. In infected individuals, a single dose induced very high levels of ACE2 blocking antibodies and antibodies to RBDs of SARS-CoV-2 variants of concern.FundingWe are grateful to the World Health Organization, UK Medical Research Council and the Foreign and Commonwealth Office.