bluuebunny/crossref_metadata_2025_split huggingface dataset:
Social Contact Patterns and Implications for Infectious Disease Transmission: A Systematic Review and Meta-Analysis of Contact Surveys
Authors: Mousa Andria , Winskill Peter , Watson Oliver J , Ratmann Oliver , Monod Mélodie , Ajelli Marco , Diallo Aldiouma , Dodd Peter J , Grijalva Carlos G , Kiti Moses Chapa , Krishnan Anand , Kumar Rakesh , Kumar Supriya , Kwok Kin On , Lanata Claudio F , de Waroux Olivier Le Polain , Leung Kathy , Mahikul Wiriya , Melegaro Alessia , Morrow Carl D , Mossong Joël , Neal Eleanor FG , Nokes David J , Pan-ngum Wirichada , Potter Gail E , Russell Fiona M , Saha Siddhartha , Sugimoto Jonathan D , Wei Wan In , Wood Robin R , Wu Joseph T , Zhang Juanjuan , Walker Patrick GT , Whittaker Charles 
Published: June 2021

AbstractBackgroundTransmission of respiratory pathogens such as SARS-CoV-2 depends on patterns of contact and mixing across populations. Understanding this is crucial to predict pathogen spread and the effectiveness of control efforts. Most analyses of contact patterns to date have focussed on high-income settings.MethodsHere, we conduct a systematic review and individual-participant meta-analysis of surveys carried out in low- and middle-income countries and compare patterns of contact in these settings to surveys previously carried out in high-income countries. Using individual-level data from 28,503 participants and 413,069 contacts across 27 surveys we explored how contact characteristics (number, location, duration and whether physical) vary across income settings.ResultsContact rates declined with age in high- and upper-middle-income settings, but not in low-income settings, where adults aged 65+ made similar numbers of contacts as younger individuals and mixed with all age-groups. Across all settings, increasing household size was a key determinant of contact frequency and characteristics, but low-income settings were characterised by the largest, most intergenerational households. A higher proportion of contacts were made at home in low-income settings, and work/school contacts were more frequent in high-income strata. We also observed contrasting effects of gender across income-strata on the frequency, duration and type of contacts individuals made.ConclusionsThese differences in contact patterns between settings have material consequences for both spread of respiratory pathogens, as well as the effectiveness of different non-pharmaceutical interventions.FundingThis work is primarily being funded by joint Centre funding from the UK Medical Research Council and DFID (MR/R015600/1).
Inducing Body-Weight Supported Postural Perturbations during Gait and Balance Exercises to Improve Balance after Stroke – A Pilot Study
Authors: Meyer Amanda , Cutler Erica , Hellstrand Jill , Meise Emily , Rudolf Kaitlyn , Hrdlicka Henry C. , Grevelding Peter , Nankin Matthew 
Published: June 2021

ABSTRACTIntroductionImpaired balance-regulation after stroke put patients and therapists at risk for injury during rehabilitation. Body-weight-support systems (BWSSs) minimize this risk and allow patients to safely practice balance activities during therapy. Treadmill based balance perturbation systems with BWSSs are known to improve balance in patients with age or disease related impairments. However, these stationary systems are unable accommodate complex exercises requiring more freedom of movement.ObjectiveTo evaluate the impact of a new balance perturbation module, which is directly integrated to a track-mounted BWSS, has on patient balance after acute stroke.DesignUnblinded quasi-randomized controlled pilot study.SettingRehabilitation centered long-term acute care hospital.ParticipantsStroke rehabilitation inpatients with an admission Berg Balance Scale (BBS) assessment score ≥21/56.InterventionsBWSS and BWSS with perturbation (BWSS-P) training was incorporated into the participants’ regular treatment. While both groups conducted the same balance and gait activities during their treatment sessions, the BWSS-P sessions included lateral and anterior/posterior resistive or assistive balance perturbations.Main outcome measuresBBS and Activities-Specific Balance-Confidence (ABC) assessments were the main outcome measure collected. Institutional BBS data from fiscal-year 2018, prior to installation of the track mounted BWSS, was used as a historical standard-of-care (SOC) baseline.ResultsImproved post-intervention BBS and ABC assessment scores showed all participants benefited from therapy (p≤0.0438). The BBS percent-change of the BWSS-P [mean (SD) n] [66.95% (43.78%) 14] and BWSS control [53.29% (24.13%) 15] were greater than the SOC group [28.31% (17.25%) 30] (p≤0.0178), with no difference between BWSS groups (p=0.6669); ABC percent score-changes were also similar (p≥0.8036).ConclusionsBWSS groups demonstrated similar BBS and ABC score improvements, indicating balance perturbations are not detrimental to post-acute stroke rehabilitation and are safe to use. This data provides strong rationale for conducting a larger follow-up study to further assess if this new perturbation system provides additional benefit to stroke patient balance during rehabilitation.Clinical Trial RegistrationNCT04919161
A row-generation approach for simultaneous multiple needle trajectory planning in radiofrequency ablation
Authors: Kulkarni-Thaker Shefali , Aleman Dionne , Fenster Aaron 
Published: June 2021

AbstractRadiofrequency ablation is a thermal therapy for moderately-sized cancerous tumors. A target is killed with high temperatures obtained due to the current passed through one or more electrodes (needles) inserted into it. The needles’ trajectory must be meticulously planned to prevent interference with dense organs like bone or puncturing of critical structures like veins. By approximating the thermal lesion to an ellipse, we predefine several valid needle trajectories and then solve an integer programming model to identify pairwise valid needle positions, that meet clinical criteria, using a variation of the classic set cover model. To improve the models’ tractability and scalability, we use row generation-based decomposition techniques that determines pairwise validity using two different types of cuts. Finally, we analyze target and organ-at-risk (OAR) damage using several thermal damage models. Our method is tested on 12 liver targets: three targets each with four different surgical margins. We show promising results that meet clinical guidelines while obtaining full target coverage.
Natural and cryptic peptides dominate the immunopeptidome of atypical teratoid rhabdoid tumors
Authors: Marcu Ana , Schlosser Andreas , Keupp Anne , Trautwein Nico , Johann Pascal , Wölfl Matthias , Lager Johanna , Monoranu Camelia , Walz Juliane Sarah , Henkel Lisa M. , Krauß Jürgen , Ebinger Martin , Schuhmann Martin , Thomale Ulrich , Pietsch Torsten , Klinker Erdwine , Schlegel Paul G. , Oyen Florian , Reisner Yair , Rammensee Hans-Georg , Eyrich Matthias 
Published: June 2021

AbstractAtypical teratoid/rhabdoid tumors (AT/RT) are highly aggressive CNS-tumors of infancy and early childhood. Hallmark is the surprisingly simple genome with inactivating mutations or deletions in the SMARCB1 gene as the oncogenic driver. Nevertheless, AT/RTs are infiltrated by immune cells and even clonally expanded T cells. However, it is unclear, which epitopes T-cells might recognize on AT/RT cells. Here, we report a comprehensive MS-based analysis of naturally presented HLA-class-I and class-II ligands on 23 AT/RTs. Comparative HLA ligandome analysis of the HLA-ligandome revealed 55 class-I and 139 class-II tumor-exclusive peptides. No peptide originated from the SMARCB1-region. In addition, 61 HLA-class I tumor-exclusive peptide sequences derived from non-canonically translated proteins. Combination of peptides from natural and cryptic class I and class II origin gave optimal representation of tumor cell compartments. Substantial overlap existed with the cryptic immunopeptidome of glioblastomas but no concordance was found with extracranial tumors. More than 80% of AT/RT-exclusive peptides were able to successfully prime CD8+T-cells, whereas naturally occurring memory responses in AT/RT-patients could only be detected for class-II epitopes. Interestingly, >50% of AT/RT-exclusive class-II ligands were also recognized by T-cells from glioblastoma patients but not from healthy donors. These findings highlight that AT/RTs, potentially paradigmatic for other pediatric tumors with a low mutational load, present a variety of highly immunogenic HLA-class-I and class-II peptides from canonical as well as non-canonical protein sources. Inclusion of such cryptic peptides into therapeutic vaccines would enable an optimized mapping of the tumor cell surface, thereby reducing the likelihood of immune evasion.One Sentence SummaryThe HLA-ligandome of atpyical teratoid-rhabdoid tumors contains immunogenic, tumor-exclusive peptides derived from natural and cryptic source proteins.
Decreased tissue stiffness in glioblastoma by MR Elastography is associated with increased cerebral blood flow
Authors: Svensson Siri Fløgstad , Fuster-Garcia Elies , Latysheva Anna , Fraser-Green Jorunn , Nordhøy Wibeke , Darwish Omar Isam , Hovden Ivar Thokle , Holm Sverre , Vik-Mo Einar O. , Sinkus Ralph , Emblem Kyrre Eeg 
Published: June 2021

AbstractPURPOSEUnderstanding how mechanical properties relate to functional changes in glioblastomas may help explain different treatment response between patients. The aim of this study was to map differences in biomechanical and functional properties between tumor and healthy tissue, to assess any relationship between them and to study their spatial distribution.METHODSTen patients with glioblastoma and 17 healthy subjects were scanned using MR Elastography, perfusion and diffusion MRI. Stiffness and viscosity measurements G′ and G′′, cerebral blood flow (CBF), apparent diffusion coefficient (ADC) and fractional anisotropy (FA) were measured in patients’ contrast-enhancing tumor, necrosis, edema, and gray and white matter, and in gray and white matter for healthy subjects. A regression analysis was used to predict CBF as a function of ADC, FA, G′ and G′′.RESULTSMedian G′ and G′′ in contrast-enhancing tumor were 13% and 37% lower than in normal-appearing white matter (P<0.01), and 8% and 6% lower in necrosis than in contrast-enhancing tumor, respectively (P<0.05). Tumors showed both inter-patient and intra-patient heterogeneity. Measurements approached values in normal-appearing tissue when moving outward from the tumor core, but abnormal tissue properties were still present in regions of normal-appearing tissue. Using both a linear and a random-forest model, prediction of CBF was improved by adding MRE measurements to the model (P<0.01).CONCLUSIONSThe inclusion of MRE measurements in statistical models helped predict perfusion, with stiffer tissue associated with lower perfusion values.
Xpert MTB/RIF Ultra is highly sensitive for the diagnosis of tuberculosis lymphadenitis in an HIV-endemic setting
Authors: Minnies Stephanie , Reeve Byron W.P. , Rockman Loren , Nyawo Georgina , Naidoo Charissa C. , Kitchin Natasha , Rautenbach Cornelia , Wright Colleen A. , Whitelaw Andrew , Schubert Pawel , Warren Robin M. , Theron Grant 
Published: June 2021

AbstractBackgroundTuberculosis lymphadenitis (TBL) is the most common extrapulmonary TB (EPTB) manifestation. Xpert MTB/RIF Ultra (Ultra) is a World Health Organization-endorsed diagnostic test, but performance data for TBL, including on non-invasive specimens, are limited.MethodsFine needle aspiration biopsies (FNABs) from outpatients (≥18 years) with presumptive TBL (n=135) underwent: 1) routine Xpert (later Ultra once programmatically available), 2) a MGIT960 culture (if Xpert- or Ultra-negative, or rifampicin-resistant), and 3) study Ultra. Concentrated paired urine underwent Ultra. Primary analyses used a microbiological reference standard (MRS).ResultsIn a head-to-head comparison (n=92) of FNAB study Ultra and Xpert, Ultra had increased sensitivity [91% (95% confidence interval 79, 98) vs. 72% (57, 84); p=0.016] and decreased specificity [76% (61, 87) vs. 93% (82, 99); p=0.020], and detected patients not on treatment. HIV nor alternative reference standards affected sensitivity and specificity. In patients with both routine and study Ultras, the latter detected more cases [+20% (0, 42); p=0.034] and, further indicative of potential laboratory-based room-for-improvement, false-negative study Ultras had more PCR inhibition than true-positives. Study Ultra “false-positives” had less mycobacterial DNA than “true-positives” [trace-positive proportions 59% (13/22) vs. 12% (5/51); p<0.001]. Exclusion or recategorization of “traces” removed potential benefits offered over Xpert. Urine Ultra had low sensitivity [18% (7, 35)].ConclusionsUltra on FNABs is highly sensitive and detects more TBL than Xpert. Patients with FNAB Ultra-positive “trace” results, most of whom will be culture-negative, may require additional clinical investigation. Urine Ultra could reduce the number of patients needing invasive sampling.
Retention in care and viral suppression after same-day ART initiation: One-year outcomes of the SLATE I and II individually randomized clinical trials in South Africa
Authors: Maskew Mhairi , Brennan Alana T , Fox Matthew P , Vezi Lungisile , Venter Willem DF , Rosen Sydney 
Published: June 2021

AbstractIntroductionSame-day initiation (SDI) of antiretroviral therapy (ART) for HIV consistently increases ART uptake, but concerns remain about higher attrition from care after initiation. We analysed twelve-month retention in the SLATE SDI trials.MethodsSLATE I and SLATE II were individually randomized trials at public outpatient clinics in Johannesburg that enrolled patients not yet on ART and administered the SLATE I or II algorithm, which included a symptom self-report, medical history, brief physical examination, and readiness questionnaire, to assess eligibility for SDI. ART uptake and early retention have been reported. Using routine clinic records, we conducted a pooled analysis of retention in care and HIV viral suppression 14 months after study enrolment.Results and discussionWe enrolled 1,193 study participants (standard arms, n=599, 50%; intervention arms, n=594, 50%) and analysed by originally assigned groups. By 14 months after study enrolment (equivalent to 12-month retention in care), 50% of intervention arm patients and 46% of standard arm patients remained in care at the initiating site (crude risk difference 4% (95% confidence interval −1% to 10%; crude relative risk 1.10 (0.97-1.23), with similar viral suppression between arms. Observed attrition from care at site by 14 months was high in both study arms, but we found no evidence that the offer of SDI led to greater overall attrition or lower rates of viral suppression one year after starting ART and may have led to small improvements. Same-day initiation may have shifted some attrition from before to after dispensing of the first dose of medication.ConclusionsAn offer of same-day initiation of ART, following a carefully designed protocol to identify patients who are eligible and ready to start treatment, is not inherently associated with an overall increase in patient attrition from care.Trial registrationClinicaltrials.govNCT02891135, registered September 1, 2016. First participant enrolled March 6, 2017 in South Africa.Clinicaltrials.govNCT03315013, registered October 19, 2017. First participant enrolled 14 March 2018.
Evaluation of saliva molecular point of care for detection of SARS-CoV-2 in ambulatory care
Authors: LeGoff Jérôme , Kernéis Solen , Elie Caroline , Mercier Delarue Séverine , Gastli Nabil , Choupeaux Laure , Fourgeaud Jacques , Alby Marie-Laure , Quentin Pierre , Pavie Juliette , Brazille Patricia , Néré Marie Laure , Minier Marine , Gabassi Audrey , Leroy Chrystel , Parfait Béatrice , Tréluyer Jean-Marc , Delaugerre Constance 
Published: June 2021

AbstractBackgroundRapid identification of SARS-Cov-2 infected individuals is a cornerstone in strategies for the control of virus spread. The sensitivity of SARS-CoV-2 RNA detection by RT-PCR is similar in saliva and nasopharyngeal swab. Rapid molecular point-of-care tests in saliva could facilitate, broaden and speed up the diagnosis.Objectives and methodsWe conducted a prospective study in two community COVID-19 screening centers to evaluate the performances of a CE-marked RT-LAMP assay (EasyCoV™) specifically designed for the detection of SARS-CoV2 RNA from fresh saliva samples, compared to nasopharyngeal RT-PCR (reference test), to saliva RT-PCR and to nasopharyngeal antigen testing.ResultsOverall, 117 of the 1718 participants (7%) were tested positive with nasopharyngeal RT-PCR. Compared to nasopharyngeal RT-PCR, the sensitivity and specificity of the RT-LAMP assay in saliva were 34% (95%CI: 26-44) and 97% (95%CI: 96-98) respectively. The performance was similar in symptomatic and asymptomatic participants. The Ct values of nasopharyngeal RT-PCR were significantly lower in the 40 true positive subjects with saliva RT-LAMP (Ct 25.9) than in the 48 false negative subjects with saliva RT-LAMP (Ct 28.4) (p=0.028). Considering six alternate criteria for reference test, including saliva RT-PCR and nasopharyngeal antigen, the sensitivity of saliva RT-LAMP ranged between 27 and 44%.ConclusionIn the ambulatory setting, the detection of SARS-CoV-2 from crude saliva samples with the RT-LAMP assay had a lower sensitivity than nasopharyngeal RT-PCR, saliva RT-PCR and nasopharyngeal antigen testing.Registration numberNCT04578509Funding SourcesFrench Ministry of Health and the Assistance Publique-Hôpitaux de Paris Foundation.
Predicted domination of variant Delta of SARS-CoV-2 before Tokyo Olympic games, Japan
Authors: Ito Kimihito , Piantham Chayada , Nishiura Hiroshi 
Published: June 2021

AbstractUsing numbers of SARS-CoV-2 variants detected in Japan, the relative instantaneous reproduction numbers of the R.1, Alpha, and Delta variants with respect to other strains circulating in Japan were estimated at 1.245, 1.437, and 1.948, respectively. The numbers can vary within 1.190–1.319 for R.1, 1.335–1.580 for Alpha, and 1.703–2.30 for Delta depending on the assumed serial interval distributions. The frequency of the Delta is expected to take over the Alpha in Japan around July 12, 2021.
Analysis of Social Combinations of Coronavirus Vaccination: Evidence from a Conjoint Analysis
Authors: Ohmura Hanako 
Published: June 2021

AbstractUsing a conjoint analysis based on cases in Japan, this study attempts to identify a preferable social strategic combination of “Who is vaccinated, who is not, who waits.” The analysis shows that the most desirable choice is a “wait-and-see” strategy, allowing for a risk assessment of side effects. We also find that subjects who recalled blood relatives as their familiar entities tend to prefer a “wait-and-see” strategy for themselves and their blood relatives.
Burden of Depressive and Anxiety Disorders in Nepal, 1990-2017: An Analysis of Global Burden of Disease Data
Authors: Bhatta Deepa Kumari , Budhathoki Kreeti , Paudel Kiran , Paudel Shishir , Marhatta Sujan Babu , Banskota Avinaya , Joshi Yadav Prasad 
Published: June 2021

ABSTRACTObjectivesThis study aims to describe the burden of depressive and anxiety disorders in Nepal in terms of incidence, prevalence, YLDs, and DALYs by age and sex.DesignAn ecological study on disease burden.MethodsWe used the publicly available Global Burden of Disease (GBD) data from 1990 to 2017. The age and sex-specific incidence, prevalence rate, Years Lived with Disability (YLDs), and Disability Adjusted Life Years (DALYs) were examined among per 100,000 populations.ResultsFemales had a higher prevalence of depressive 4094.4 (95% uncertainty interval [UI]: 3761.9-4470.3 per 100,000) and anxiety 4496.8 (95% UI: 4171.9-4837.9 per 100,000) disorders. The prevalence of major depressive disorders was comparatively higher in females (2766.7) than males (1822.9). Females also had higher YLDs for both depressive and anxiety disorders. In 2017, higher DALYs of anxiety disorder were found in the females of 45-49 years (630.1). Childhood sexual abuse was found to be the main risk factor for depressive disorder, contributing to 32.5 DALYs in both sexes. Bullying, victimization had contributed to 26.7 DALYs of anxiety.ConclusionsThe high burden of disorders in females would support in identifying major mental health challenges in Nepal and develop plans and various preventive, curative, and rehabilitative strategies.Strength and limitations of this studyThis is one of the few studies that have provided the burden of depressive and anxiety disorders in developing nations such as Nepal.The data used in this study were based on the GBD studies which utilize exhaustive information sources and comprehensive investigations.Estimation of the burden of diseases was restricted to standard epidemiological measures and other financial and social burdens were not considered.Due to use of secondary data and information which were only available publicly this may not representative of the whole nation.
Designing and implementing state-level fertility preservation health insurance benefit mandates
Authors: Flores Ricardo E. , Yoeun Sara W. , Mesina Omar , Kaiser Bonnie N. , McMenamin Sara B. , Su H. Irene 
Published: June 2021

AbstractObjectiveTo describe the design and implementation of state-level fertility preservation (FP) health insurance benefit mandates and regulation and to provide stakeholders with guidance on best practices, gaps, and implementation needs.DesignLegal mapping and implementation framework-guided analysisSettingU.S. states with state-level fertility preservation health insurance benefit mandatesPatient(s)Individuals at risk of iatrogenic infertilityIntervention(s)State laws mandating health insurance benefit coverage for fertility preservation services.Main Outcome Measure(s)Design features of FP mandated benefit legislation; implementation processResult(s)Between June, 2017 and March, 2021, 11 states passed FP benefit mandate laws. On average, states took 223 days to implement their mandates from the start of the laws’ enactment dates to their corresponding effective dates, and a majority issued regulatory guidance after the law was in effect. Significant variation was observed in which FP services were specified for inclusion or exclusion in the laws and/or regulator guidance. Federal policies impacted state level implementation, with the ACA and HIPAA guiding design of fertility preservation benefits. In addition, a majority of states referenced medical society clinical practice guidelines in the design of FP mandated benefits.ConclusionsOur policy scan documented significant variation in the design and implementation of health insurance benefit mandates for FP services. Future considerations for policy development include specificity and flexibility of benefit design, reference to external clinical practice guidelines to drive benefit coverage, inclusion of Medicaid populations in required coverage, and consideration of interaction with relevant state and federal policies. In addition, key considerations for implementation include the sufficient length of time for the implementation period, regulator guidance issued prior to the law going into effect, and explicit allocation of resources for the implementation process.