bluuebunny/crossref_metadata_2025_split huggingface dataset:
The ratio of BRAFV600E alleles can be used to assess the biological behavior of papillary thyroid carcinoma
Authors: Luo Dingcun , Ni Yeqin , Zhang Shirong , Xun Yanping , Zhao Pan , Wu Fan , Zhou Tianhan , Shi Jingjing , Lu Si , Sun Sihan , Lu Kaining 
Published: November 2020

ABSTRACTBackgroundThe BRAFV600E mutations is an important molecular event in the occurrence and development of papillary thyroid carcinoma (PTC). A qualitative detection of the BRAFV600E mutation is still insufficient to explain the biological behavior of PTC. Though quantitative detection of the BRAFV600E mutation can reflect certain characteristics of PTC, its clinical value is still controversial. We aimed to investigate the association between the ratio of BRAFV600E alleles and clinicopathological parameters in PTC patients.MethodsGenomic DNA was extracted from specimens obtained from 329 PTC patients undergoing thyroidectomy. The ratio of BRAFV600E alleles was determined by amplification refractory mutation system (ARMS) and droplet digital polymerase chain reaction (ddPCR). Inconsistent results were further verified by next-generation sequencing (NGS). The clinicopathologic features, clinical tumor stage, and tumor recurrence risk stratification of all patients were correlated with the ratio of BRAFV600E alleles.ResultsThe sensitivity of ddPCR was superior to that of ARMS and almost the same as that of NGS. In total, 275 of 329 patients had the BRAFV600E mutation as determined by ARMS, ddPCR and NGS. The ratio of BRAFV600E alleles ranged from 0.17%-48.0%, with a median ratio of 12.58%, and significantly correlated with tumor size (p<0.001), capsule or extrathyroidal invasion (p<0.001), the number or rate of lymph node metastases (p<0.001), tumor stage (p=0.006) and tumor recurrence risk (p<0.001) but not with sex, age or multifocality. The ratio of BRAFV600E alleles was much lower in PTC patients with Hashimoto’s thyroiditis than in those without (p<0.001).ConclusionsThe ratio of BRAFV600E alleles can reliably reflect the biological behavior of PTC, making it a molecular-based stratification index of recurrence risk. The quantitative detection of BRAFV600E has the potential to guide the clinical diagnosis and treatment of PTC.
A service user evaluation of eConsult use by Defence Primary Healthcare Primary Care Clinicians using a mixed-method approach
Authors: Willman Antony S 
Published: November 2020

ABSTRACTIntroductioneConsult has been recently introduced into Defence Primary Healthcare to allow patients electronic access to healthcare. Using mixed methods, this service evaluation sought the views of primary care clinicians using eConsult.MethodsA two-phase sequential exploratory mixed-method approach was used. An inductive thematic analysis of feedback from primary care clinicians in the Salisbury Plain Area identified themes around eConsult use. These were used to construct an 18-item survey instrument. This was then distributed to primary care clinicians in Defence Primary Healthcare to assess the broader applicability of the themes.ResultsFour themes were identified: the impact on accessibility, the effects on working practices, the impact on the dynamics of the consultation and the effect of training and administrative support. eConsult did not save time for clinicians but was generally more convenient for patients. eConsult was often used in conjunction with telephone and face to face follow up, forming a ‘blended consult’. Accessibility was improved, but cultural factors may affect some patients engaging.ConclusionseConsult improves accessibility and can reduce telephone and face to face consultations but does not reduce workload. It should be used alongside conventional access methods, not instead of. It is useful for straightforward clinical and administrative problems but is less useful for more complex cases unless part of a ‘blended consult’. Future use could be modified to provide greater data gathering for occupational health and chronic disease monitoring and should be monitored to ensure it is inclusive of all demographic groups.KEY MESSAGESThe increased accessibility to a clinician that eConsult offered for patients was positive.There was no workload saving for clinicians using eConsult.EConsult was often the first part of a ‘blended consult’ which subsequently involved telephone and face to face consults.While the dynamics of the consultation were changed, this was generally perceived as positive.EConsult should exist alongside current systems for accessing primary care.The efficiency of the eConsult system could be improved with better administrative support and training.
Modelling the impact of COVID-19-related control programme interruptions on progress towards the WHO 2030 target for soil-transmitted helminths
Authors: Malizia Veronica , Giardina Federica , Vegvari Carolin , Bajaj Sumali , McRae-McKee Kevin , Anderson Roy M , de Vlas Sake J , Coffeng Luc E 
Published: November 2020

AbstractBackgroundOn the 1st of April 2020, the World Health Organization (WHO) recommended an interruption of all neglected tropical disease control programmes, including soil-transmitted helminths (STH), in response to the COVID-19 pandemic. This paper investigates the impact of this disruption on the achieved progress towards the WHO 2030 target for STH.MethodsWe used two stochastic individual-based models to simulate the impact of missing one or more preventive chemotherapy (PC) rounds in different endemicity settings. We also investigate the extent to which the impact can be lessened by mitigation strategies, such as semi-annual or community-wide PC.ResultsBoth models show that even without a mitigation strategy, control programmes will catch up by 2030. The catch-up time is limited to a maximum of 4.5 years after the interruption. Mitigations strategies may reduce this catch-up time by up to two years and can even increase the probability of achieving the 2030 target.ConclusionsThough a PC interruption will only temporarily impact the progress towards the WHO 2030 target, programmes are encouraged to restart as soon as possible to minimise the impact on morbidity. The implementation of suitable mitigation strategies can turn the interruption into an opportunity to accelerate the progress toward reaching the target.
Hospital based contact tracing of COVID-19 patients and health care workers and risk stratification of exposed health care workers during the COVID-19 Pandemic in Eastern India
Authors: Sahoo Durgesh Prasad , Singh Arvind Kumar , Sahu Dinesh Prasad , Pradhan Somen Kumar , Patro Binod Kumar , Batmanabane Gitanjali , Mishra Baijayantimala , Behera Bijayini , Dash Ambarish , Dora G Susmita , L Anand , S M Azhar , Nair Jyolsna , Panigrahi Sasmita , R Akshaya , Sahoo Bimal Kumar , Sahoo Subhakanta , Sahoo Suchismita 
Published: November 2020

AbstractIntroductionContact tracing and subsequent quarantining of Health Care Workers (HCWs) is essential to minimize further transmission of COVID-19 infection. In this study, we have reported the yield of Contact Tracing of COVID-19 Patients and HCWs and risk stratification of exposed HCWs.MethodologyThis is a secondary analysis of routine data collected for contact tracing from 19th March to 31st August 2020 at All India Institute of Medical Sciences, Bhubaneswar, Odisha, India. HCWs exposed to COVID-19 infections were categorized as per the risk stratification guidelines and the high-risk contacts were quarantined for 14 days and tested on 7thday from last day of exposure. The low risk contacts were encouraged to closely monitor their symptoms while continuing to work.ResultsOut of 3411 HCWs exposed to COVID 19 patients (n=269) and HCWs (n=91), 890 (26.1%) were high risk contacts and 2521 (73.9%) were low risk contacts. The test positivity rate of high-risk contact was 3.82% and for low risk contact was 1.90%. Average number of high-risk contacts was significantly higher; for admitted patients (6.6) as compared to HCWs (4.0) and outpatients (0.2), p value = 0.009; for patients admitted in non-COVID areas (15.8) as compared to COVID areas (0.27), p value < 0.001; and when clustering of cases was present (14.3) as compared to isolated cases (8.2); p value < 0.001. Trend analysis (15 days block period) showed a significant decline in number of mean numbers of high-risk contacts during the study period.ConclusionContact tracing and risk stratification was effective and helped in reducing the number of HCWs going for quarantine. There was also a decline in high-risk contacts during study period suggesting role of implementation of hospital based COVID related infection control strategies. This contact tracing and risk stratification approach designed in the current study can also be implemented in other healthcare settings.
Experience from a COVID-19 screening centre of a tertiary care institution: A retrospective hospital-based study
Authors: Pradhan Somen Kumar , Sahu Dinesh Prasad , Sahoo Durgesh Prasad , Singh Arvind Kumar , Patro Binod Kumar , Mohanty Sachidananda 
Published: November 2020

AbstractIntroductionThe COVID-19 pandemic continuing to be a significant public health concern across the whole world, including India. In the absence of any specific treatment or vaccine against COVID-19., the role of efficient testing and reporting has been uncontested so far as the number of cases is rising daily. In order to strengthen the screening activities and to prevent nosocomial infection, facility-based screening centres have been designed and operated at various level of healthcare, including tertiary care institutions.MethodsThe present study has been planned with an objective to understand the patient profile and evaluate the functioning of COVID-19 screening OPD(CS-OPD) at a tertiary care hospital. In this hospital-based retrospective study, data from individuals visiting the COVID-19 screening OPD during the period from 17th March 2020 to 31st July 2020 were collected. We documented and analysed relevant demographic, epidemiological and clinical characteristics of the patients.ResultsA total of 10,735 patients visited the COVID-19 screening OPD during the defined study period out of which 3652 individuals were tested. Majority of the patients, i.e. 65.67% (7050) were male and in 15-59 years age group (84.68%). Most common symptoms among patients visiting CS-OPD was Cough (9.86%). Out of the total, 17.17% (1843) of patient reported to the CS-OPD with contact history of COVID-19 positive patient. On the other hand, 13.49% (1448) of patients were with either domestic or international travel history. The overall testing rate and positivity rate for CS-OPD during this period were found to be 34.02% and 7.94% respectively.ConclusionThe clinical, demographic and epidemiological characteristics of patients visiting CS-OPD varied across the study period depending upon the containment and testing strategy. The CS-OPD played a crucial role in preventing nosocomial infection and maintaining non-COVID care at the tertiary care hospital.
COVID-19 Medical Vulnerability Indicators: A Local Data Model for Equity in Public Health Decision-Making
Authors: Ong Paul M. , Pech Chhandara , Gutierrez Nataly Rios , Mays Vickie 
Published: November 2020

AbstractObjectiveTo develop indicators of vulnerability for coronavirus disease 2019 (covid-19) infection in Los Angeles County (LAC) by race and neighborhood characteristics.DesignDevelopment of indicators that combines pre-existing medical vulnerabilities with social and built-environment data by zip code tabulation areas (ZCTAs).SettingNeighborhoods in LAC categorized by race/ethnicity ranked into quintiles by relative vulnerability: Non-Hispanic white; Black; Latinx; Cambodians, Hmong and Laotians combined (CHL); and Other Asians.Data SourcesAskCHIS Neighborhood Edition, American Community Survey 2014-2018, and California Department of Parks and Recreation.Main Outcome Measures1) Pre-Existing Health Condition, 2) Barriers to Accessing Healthcare, 3) Built Environment Risk, and 4) CDC’s Social Vulnerability.ResultsNeighborhoods most vulnerable to COVID-19 are characterized by significant clustering of racial minorities, low income households and unmet medical needs. An overwhelming 73% of Blacks reside in the neighborhoods with the two highest quintiles of pre-existing health conditions, followed by Latinx (70%) and CHL (60%), while 60% of whites reside in low or the lowest vulnerable neighborhoods. For the Barriers to Accessing Healthcare indicator, 40% of Latinx reside in the highest vulnerability places followed by Blacks, CHL and other Asians (29%, 22%, and 16% respectively), compared with only 7% of Whites reside in such neighborhoods. The Built Environment Indicator finds CHL (63%) followed by Latinx (55%) and Blacks (53%) reside in the neighborhoods designated as high or the highest vulnerability compared to 32% of Whites residing in these neighborhoods. The Social Vulnerability Indicator finds 42% of Blacks and Latinx and 38% of CHL residing in neighborhoods of high vulnerability compared with only 8% of Whites residing these neighborhoods.ConclusionsVulnerability to covid-19 infections differs by neighborhood and racial/ethnic groups. Our vulnerability indicators when utilized in decision-making of re-openings or resource distribution such as testing, vaccine distribution, hotel rooms for quarantine and other covid-19-related resources can provide an equity driven data approach for the most vulnerable.
An evaluation of assumptions underlying respondent-driven sampling and the social contexts of sexual and gender minority youth participating in HIV clinical trials in the United States
Authors: Wirtz AL , Iyer J , Brooks D , Hailey-Fair K , Galai N , Beyrer C , Celentano D , Arrington-Sanders R. ,   PUSH Study Group
Published: November 2020

AbstractIntroductionRespondent-driven sampling has been an effective sampling strategy for HIV research in many settings, but has had limited success among some youth in the United States. We evaluated a modified RDS approach for sampling Black and Latinx sexual and gender minority youth (BLSGMY) and evaluates how lived experiences and social contexts of BLSGMY youth may impact traditional RDS assumptions.MethodsRDS was implemented in three cities to engage BLSGMY in HIV prevention or care intervention trials. RDS was modified to include targeted seed recruitment from venues, internet, and health clinics, and provided options for electronic or paper coupons. Qualitative interviews were conducted among a sub-sample of RDS participants to explore their experiences with RDS. Interviews were coded using RDS assumptions as an analytic framework.ResultsBetween August 2017 and October 2019, 405 participants were enrolled, 1,670 coupons were distributed, with 133 returned, yielding a 0.079 return rate. The maximum recruitment depth was 4 waves among seeds that propagated. Self-reported median network size was 5 (IQR 2-10) and reduced to 3 (IQR 1-5) when asked how many peers were seen in the past 30 days. Qualitative interviews (n=27) revealed that small social networks, peer trust, and targeted referral of peers with certain characteristics challenged network, random recruitment, and reciprocity assumptions of RDS. HIV stigma and research hesitancy were barriers to participation and peer referral.ConclusionsSmall social networks and varying relationships with peers among BLSGMY challenge assumptions that underlie traditional RDS. Modified RDS approaches, including those that incorporate social media, may support recruitment for community-based research but may challenge assumptions of reciprocal relationships. Research hesitancy and situational barriers must be addressed in recruitment and study designs.
SARS-CoV-2 responsive T cell numbers and anti-Spike IgG levels are both associated with protection from COVID-19: A prospective cohort study in keyworkers
Authors: Wyllie David , Jones Hayley E , Mulchandani Ranya , Trickey Adam , Taylor-Phillips Sian , Brooks Tim , Charlett Andre , Ades AE ,   EDSAB-HOME investigators, Moore Philippa , Boyes John , Hormis Anil , Todd Neil , Reckless Ian , Makin Andrew , Oliver Isabel 
Published: November 2020

AbstractImmune correlates of protection from COVID-19 are incompletely understood. 2,826 keyworkers had T-SPOT®DiscoverySARS-CoV-2 tests (measuring interferon-γ secreting, SARS-CoV-2 responsive T cells, Oxford Immunotec Ltd), and anti-Spike S1 domain IgG antibody levels (EuroImmun AG) performed on recruitment into a cohort study. 285/2,826 (10.1%) of participants had positive SARS-CoV-2 RT-PCR tests, predominantly associated with symptomatic illness, during 200 days followup. T cell responses to Spike, Nucleoprotein and Matrix proteins (SNM responses) were detected in some participants at recruitment, as were anti-Spike S1 IgG antibodies; higher levels of both were associated with protection from subsequent SARS-CoV-2 test positivity. In volunteers with moderate antibody responses, who represented 39% (252/654) of those with detectable anti-Spike IgG, protection was partial, and higher with higher circulating T cell SNM responses. SARS-CoV-2 responsive T cell numbers predict protection in individuals with low anti-Spike IgG responses; serology alone underestimates the proportion of the population protected after infection.
Longitudinal testing for respiratory and gastrointestinal shedding of SARS-CoV-2 in day care centres in Hesse, Germany. Results of the SAFE KiDS Study
Authors: Hoehl Sebastian , Kreutzer Emilie , Schenk Barbara , Westhaus Sandra , Foppa Ivo , Herrmann Eva , Ettrich India , Schaible Alexander , Rudych Olga , Rabenau Holger , Berger Annemarie , Ciesek Sandra 
Published: November 2020

AbstractBackgroundWith the pandemic of SARS-CoV-2 ongoing in Europe in July of 2020, day care centres were reopened in the state of Hesse, Germany, after the lockdown. The role young children play in the dynamics of the transmission was unknown.MethodsWe conducted a longitudinal study over a period of 12 weeks (18th of June 2020 to 10th of September, 2020) to screen attendees and staff from day care centres in the state of Hesse, Germany, for both respiratory and gastrointestinal shedding of SARS-CoV-2. 825 children (age range 3 months to 8 years) and 372 staff members from 50 day care centres, which were chosen representatively from throughout the state, participated in the study. Parents were asked to perform both a buccal mucosa and an anal swab on their children once a week. Staff were asked to self-administer the swabs. RT-PCRs for SARS-CoV-2 were performed in a multiple-swab pooling protocol.Findings7,366 buccal mucosa swabs and 5,907 anal swabs were analysed. No respiratory or gastrointestinal shedding of SARS-CoV-2 was detected in any of the children. Shedding of SARS-CoV-2 could be detected in two staff members from distinct day care centres. One was asymptomatic at the time of testing, and one was symptomatic.InterpretationRespiratory or gastrointestinal shedding of SARS-CoV-2 in children or staff members in day care centres was very rare in the context of low community activity. The data indicate day care centres do not pose a reservoir for SARS-CoV-2 in a low prevalence setting, no inapparent transmissions were observed.FundingThe study was commissioned by the Hessian Ministry of Social Affairs and Integration and was supported by Roche Diagnostics, Basel, Switzerland.
Predicting the Clinical Management of Skin Lesions using Deep Learning
Authors: Abhishek Kumar , Kawahara Jeremy , Hamarneh Ghassan 
Published: November 2020

ABSTRACTAutomated machine learning approaches to skin lesion diagnosis from images are approaching dermatologist-level performance. However, current machine learning approaches that suggest management decisions rely on predicting the underlying skin condition to infer a management decision without considering the variability of management decisions that may exist within a single condition. We present the first work to explore image-based prediction of clinical management decisions directly without explicitly predicting the diagnosis. In particular, we use clinical and dermoscopic images of skin lesions along with patient metadata from the Interactive Atlas of Dermoscopy dataset (1,011 cases; 20 disease labels; 3 management decisions) and demonstrate that predicting management labels directly is more accurate than predicting the diagnosis and then inferring the management decision (13.73 ± 3.93% and 6.59 ± 2.86% improvement in overall accuracy and AUROC respectively), statistically significant at p < 0.001. Directly predicting management decisions also considerably reduces the over-excision rate as compared to management decisions inferred from diagnosis predictions (24.56% fewer cases wrongly predicted to be excised). Furthermore, we show that training a model to also simultaneously predict the seven-point criteria and the diagnosis of skin lesions yields an even higher accuracy (improvements of 4.68 ± 1.89% and 2.24 ± 2.04% in overall accuracy and AUROC respectively) of management predictions. Finally, we demonstrate our model’s generalizability by evaluating on the publicly available MClass-D dataset and show that our model agrees with the clinical management recommendations of 157 dermatologists as much as they agree amongst each other.