bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross-reactive Antibody Response to mRNA SARS-CoV-2 Vaccine After Recent COVID-19-Specific Monoclonal Antibody Therapy
Authors: Schultz-Cherry Stacey , McGargill Maureen A , Thomas Paul G , Estepp Jeremie H , Gaur Aditya H , Allen E Kaitlynn , Allison Kim J , Tang Li , Webby Richard J , Cherry Sean D , Lin Chun-Yang , Fabrizio Thomas , Tuomanen Elaine I , Wolf Joshua ,   SJTRC Investigative Team, Kirkpatrick Roubidoux Ericka , Freiden Pamela , Mori Tomi , Hijano Diego R , Hakim Hana , Brice David C , Castellaw Ashley , Krammer Florian , Wittman David E , Hodges Jason , Dallas Ronald H , Cortez Valerie , Vazquez-Pagan Ana , Bajracharya Resha , Clark Brandi L , Van de Velde Lee-Ann , Awad Walid , Wilson Taylor L , Kirk Allison M , Hayden Randall T , Hoffman James , Russell-Bell Jamie , Sparks James 
Published: August 2021

Abstract

The efficacy of coronavirus disease 2019 (COVID-19) vaccines administered after COVID-19-specific monoclonal antibody is unknown, and “antibody interference” might hinder immune responses leading to vaccine failure. In an institutional review board–approved prospective study, we found that an individual who received mRNA COVID-19 vaccination &lt;40 days after COVID-19-specific monoclonal antibody therapy for symptomatic COVID-19 had similar postvaccine antibody responses to SARS-CoV-2 receptor binding domain (RBD) for 4 important SARS-CoV-2 variants (B.1, B.1.1.7, B.1.351, and P.1) as other participants who were also vaccinated following COVID-19. Vaccination against COVID-19 shortly after COVID-19-specific monoclonal antibody can boost and expand antibody protection, questioning the need to delay vaccination in this setting.

Trial registration.
The St. Jude Tracking of Viral and Host Factors Associated with COVID-19 study; NCT04362995; https://clinicaltrials.gov/ct2/show/NCT04362995.
The Timing, Duration and Conditions of UHT Metamorphism in Remnants of the Former Eastern Gondwana
Authors: Durgalakshmi   , Sajeev K , Williams Ian S , Reddy D Harinadha , Satish-Kumar M , Jöns Niels , Malaviarachchi Sanjeewa P K , Samuel Vinod O , George P M 
Published: August 2021

AbstractEarly Palaeozoic ultrahigh-temperature (UHT) metamorphism in eastern Gondwana was an event that started with Gondwana amalgamation at c. 580 Ma and lasted at least 50 Myr. Sapphirine + quartz, Mg–Al granulites preserve a record of the timing and duration of the event along the metamorphic belt. U–Th–Pb dating of zircon and monazite shows that metamorphism peaked almost simultaneously in Antarctica (554.0 ± 4.7 Ma), Sri Lanka (555.5 ± 4.6 Ma), southern India (548.1 ± 8.1 Ma) and Madagascar (550.6 ± 6.0 Ma), and ended in all locations at the same time, 530–520 Ma. Rare earth element (REE) compositions of the metamorphic zircon zones can be matched to the REE zoning in the associated garnet. Phase-diagram modelling indicates that the peak UHT P–T conditions in Antarctica, Sri Lanka, and India were very similar, 1020–1040 °C at 0.8 GPa. Peak conditions in Madagascar were at higher T and similar P: 1090 °C and 0.8 GPa. The East African Orogeny before 600 Ma preconditioned the crust of the eastern Gondwanan terranes by thickening it and harbouring heat-producing elements, heating the crust over c. 60 Myr; such that UHT conditions were reached when East and West Gondwana collided.
Reciprocal Influence of Mobility and Speech-Language: Advancing Physical Therapy and Speech Therapy Cotreatment and Collaboration for Adults With Neurological Conditions
Authors: Schwab Sarah M , Dugan Sarah , Riley Michael A 
Published: August 2021

Abstract

Mobility and speech-language impairments and limitations in adults with neurological conditions manifest not in isolated anatomical components but instead in the individual-environment system and are task-dependent. Optimization of function thus requires interprofessional care to promote participation in meaningful life areas within appropriate task and environmental contexts. Cotreatment guidelines (ie, the concurrent intervention of disciplines) were established by the physical therapy, occupational therapy, and speech-language and hearing professional organizations nearly 2 decades ago to facilitate seamless interprofessional care. Despite this, cotreatment between physical therapy and speech therapy remains limited. The purpose of this Perspective article is to encourage physical therapists and speech-language pathologists to increase interprofessional collaboration through cotreatment in the management of adults with neurological conditions. Evidence from pediatrics and basic motor control literature points toward reciprocal interactions between speech-language and mobility. We provide recommendations for clinical practice with an emphasis on the gains each discipline can provide the other. This Perspective is rooted in the International Classification of Functioning, Disability and Health model and ecological theory.

Impact
The goals of speech therapy and physical therapy are complementary and mutually supportive. Enhanced cotreatment, and collaboration more generally, between physical therapists and speech-language pathologists in the management of adults with neurological conditions can augment task-relevant conditions to improve function.
It takes two to tango: Examining productive interactions in urban research collaboration
Authors: Kalliomäki Helka , Ruoppila Sampo , Airaksinen Jenni 
Published: August 2021

Abstract
The science–society relations of social sciences and humanities have been increasingly discussed under the concept of productive interactions, which refers to the mutual learning processes between researchers and stakeholders for the benefit of societal development. While most studies have analysed the societal impact from the research performers’ perspective, in this article, we examine the practitioners’ side. We contribute to the evaluation theory by offering a new perspective to examine the emergence of productive interactions. Based on an empirical analysis of collaborative practices in two Finnish urban research programmes and how the practitioners reflected on them, we argue that practitioners’ competencies are essential in leveraging societal impact. The improvement of these ‘pracademic competencies’ need to be raised as an issue in research policy and evaluation promoting responsible research and innovation.
Moving from nature to nurture: a systematic review and meta-analysis of environmental factors associated with juvenile idiopathic arthritis
Authors: Clarke Sarah L N , Mageean Katie S , Maccora Ilaria , Harrison Sean , Simonini Gabriele , Sharp Gemma C , Relton Caroline L , Ramanan Athimalaipet V 
Published: August 2021

Abstract

Objectives
JIA is the most common paediatric rheumatic disease, thought to be influenced by both genetics and the environment. Identifying environmental factors associated with disease risk will improve knowledge of disease mechanism and ultimately benefit patients. This review aimed to collate and synthesize the current evidence of environmental factors associated with JIA.

Methods
Four databases (MEDLINE, Embase, Web of Science and Cumulative Index to Nursing and Allied Health Literature) were searched from inception to January 2020. Study quality was rated using the Newcastle-Ottawa Scale. Pooled estimates for each environmental factor were generated using a random-effects, inverse-variance method, where possible. The remaining environmental factors were synthesized in narrative form.

Results
This review includes 66 environmental factors from 39 studies (11 cohort and 28 case-control studies) over 45 years. Study sample sizes ranged from 41 to 1.9 million participants. Eight environmental factors from ten studies were meta-analysed. Caesarean section delivery was associated with increased JIA risk [pooled odds ratio (OR) 1.11, 95% CI: 1.01, 1.22]. Conversely, presence (vs absence) of siblings (pooled OR 0.60, 95% CI: 0.44, 0.81) and maternal prenatal smoking (pooled OR 0.70, 95% CI: 0.58, 0.84) were associated with decreased JIA risk.

Conclusion
This review identifies several environmental factors associated with JIA and demonstrates the huge breadth of environmental research undertaken over five decades. We also highlight the challenges of combining data collected over this period due to limited between study comparability, evolution in healthcare and social practices, and changing environment, which warrant consideration when planning future studies.
Neuromodulation by means of phase-locked auditory stimulation affects key marker of excitability and connectivity during sleep
Authors: Sousouri Georgia , Krugliakova Elena , Skorucak Jelena , Leach Sven , Snipes Sophia , Ferster Maria Laura , Da Poian Giulia , Karlen Walter , Huber Reto 
Published: August 2021

AbstractThe propagating pattern of sleep slow waves (high-amplitude oscillations &lt; 4.5 Hz) serves as a blueprint of cortical excitability and brain connectivity. Phase-locked auditory stimulation is a promising tool for the modulation of ongoing brain activity during sleep; however, its underlying mechanisms remain unknown. Here, eighteen healthy young adults were measured with high-density electroencephalography in three experimental conditions; one with no stimulation, one with up- and one with down-phase stimulation; ten participants were included in the analysis. We show that up-phase auditory stimulation on a right prefrontal area locally enhances cortical involvement and promotes traveling by increasing the propagating distance and duration of targeted small-amplitude waves. On the contrary, down-phase stimulation proves more efficient at perturbing large-amplitude waves and interferes with ongoing traveling by disengaging cortical regions and interrupting high synchronicity in the target area as indicated by increased traveling speed. These results point out different underlying mechanisms mediating the effects of up- and down-phase stimulation and highlight the strength of traveling wave analysis as a sensitive and informative method for the study of connectivity and cortical excitability alterations.
A web-based fuzzy risk predictive-decision model of de novo stress urinary incontinence in women undergoing pelvic organ prolapse surgery
Authors: Moosavi Seyyde Yalda , Samad-Soltani Taha , Hajebrahimi Sakineh 
Published: August 2021

Abstract

Background:
Pelvic organ prolapse (POP) and stress urinary incontinence (SUI) are common conditions affecting women's health and quality of life. In 50% of cases, SUI occurs after POP surgery, which is called de novo SUI. Predicting the risk of de novo SUI is a complex multi-attribute decision-making process. The current study made available a Decision Support System in the form of a fuzzy calculator web-based application to help surgeons predict the risk of de novo SUI.

Materials and methods:
We first identified 12 risk factors and the diagnostic criteria for de novo SUI by means of a systematic review of the literature. Then based upon an expert panel, all risk factors were prioritized. A set of 232 fuzzy rules for the prediction of de novo SUI was determined. A fuzzy expert system was developed using MATLAB software and Mamdani Inference System. The risk prediction model was then evaluated using retrospective data extracted from 30 randomly selected medical records of female patients over the age of 50 without symptoms of urinary incontinence who had undergone POP surgery. Finally, the proposed results of the predictive system were compared with the results of retrospective medical record data review.

Results:
The results of this online calculator show that the accuracy of this risk prediction model, at more than 90%, compared favorably to other SUI risk prediction models.

Conclusions:
A fuzzy logic-based clinical Decision Support System in the form of an online calculator for calculating SUI prognosis after POP surgery in women can be helpful in predicting de novo SUI.
Comparison of Renal Responses Between Continuous Mycophenolate Mofetil and Conversion from Mycophenolate Mofetil to Enteric-Coated Mycophenolate Sodium in Lupus Nephritis
Authors: Liao Yu-Wan , Hung Wei-Ting , Chen Yi-Ming , Hsu Chiann-Yi , Lin Ching-Heng , Hsieh Tsu-Yi , Chen Hsin-Hua , Hsieh Chia-Wei , Lin Ching-Tsai , Lai Kuo-Lung , Tang Kuo-Tung , Tseng Chih-Wei , Chen Yi-Hsing , Huang Wen-Nan 
Published: August 2021

Background
Mycophenolate mofetil (MMF) is extensively used for induction and maintenance therapy in patients with lupus nephritis (LN). Enteric-coated mycophenolate sodium (EC-MPS) was developed to reduce the adverse gastrointestinal effects of MMF. However, the therapeutic efficacy of MMF and EC-MPS in LN remains unclear. This study aimed to examine the treatment effects of EC-MPS in LN patients with prior MMF exposure.

Methods
In this medical records review study, we included 54 LN patients, of whom 34 converted from MMF to EC-MPS at equimolar doses in 2016–2018 (nonmedical switching group) and 20 received continuous MMF treatment. Patients achieving complete remission or partial remission before the conversion were categorized as responders, whereas those who had never achieved complete remission or partial remission were categorized as nonresponders.

Results
Baseline proteinuria was higher in the nonmedical switching group. Although elevation in proteinuria was observed after nonmedical switching, the serum creatinine concentration and estimated glomerular filtration rate both improved. Responders in the nonmedical switching group had lower proteinuria and higher complement 3 levels. In the subgroup analysis, albeit the modest increase in daily urine protein, anti–double-stranded DNA antibody levels, estimated glomerular filtration rate, and complements 3 and 4 seemed comparable after conversion.

Conclusion
Switching to EC-MPS demonstrated a similar short-term renal response to continuous MMF treatment in LN patients. Prospective randomized trials are required to verify our findings.
Lesion Normalization and Supervised Learning in Post-Traumatic Seizure Classification with Diffusion MRI
Authors: Akbar Md Navid , Ruf Sebastian , Rocca Marianna La , Garner Rachael , Barisano Giuseppe , Cua Ruskin , Vespa Paul , Erdoğmuş Deniz , Duncan Dominique 
Published: August 2021

AbstractTraumatic brain injury (TBI) is a serious condition, potentially causing seizures and other lifelong disabilities. Patients who experience at least one seizure one week after TBI (late seizure) are at high risk for lifelong complications of TBI, such as post-traumatic epilepsy (PTE). Identifying which TBI patients are at risk of developing seizures remains a challenge. Although magnetic resonance imaging (MRI) methods that probe structural and functional alterations after TBI are promising for biomarker detection, physical deformations following moderate-severe TBI present problems for standard processing of neuroimaging data, complicating the search for biomarkers. In this work, we consider a prediction task to identify which TBI patients will develop late seizures, using fractional anisotropy (FA) features from white matter tracts in diffusion-weighted MRI (dMRI). To understand how best to account for brain lesions and deformations, four preprocessing strategies are applied to dMRI, including the novel application of a lesion normalization technique to dMRI. The pipeline involving the lesion normalization technique provides the best prediction performance, with a mean accuracy of 0.819 and a mean area under the curve of 0.785. Finally, following statistical analyses of selected features, we recommend the dMRI alterations of a certain white matter tract as a potential biomarker.
Prediction of therapy outcomes of CLL using gene expression intensity, clustering, and ANN classification of single cell transcriptomes
Authors: Lyu Minjie , Jin Huan , Bellotti Anthony , Lin Xin , Cao Zhiwei , Keskin Derin B. , Brusic Vladimir 
Published: August 2021

BackgroundSingle cell transcriptomics is a new technology that enables us to measure the expression levels of genes from an individual cell. The expression information reflects the activity of that individual cell which could be used to indicate the cell types. Chronic lymphocytic leukemia (CLL) is a malignancy of B cells, one of the peripheral blood mononuclear cells subtypes. We applied five analytical tools for the study of single cell gene expression in CLL course of therapy. These tools included the analysis of gene expression distributions – median, interquartile ranges, and percentage above quality control (QC) threshold; hierarchical clustering applied to all cells within individual single cell data sets; and artificial neural network (ANN) for classification of healthy peripheral blood mononuclear cell (PBMC) subtypes. These tools were applied to the analysis of CLL data representing states before and during the therapy.ResultsWe identified patterns in gene expression that distinguished two patients that had complete remission (complete response), a patient that had a relapse, and a patient that had partial remission within three years of Ibrutinib therapy. Patients with complete remission showed a rapid decline of median gene expression counts, and the total number of gene counts below the QC threshold for healthy cells (670 counts) in 80% of more of the cells. These patients also showed the emergence of healthy-like PBMC cluster maps within 120 days of therapy and distinct changes in predicted proportions of PBMC cell types.ConclusionsThe combination of basic statistical analysis, hierarchical clustering, and supervised machine learning identified patterns from gene expression that distinguish four CLL patients treated with Ibrutinib that experienced complete remission, partial remission, or relapse. These preliminary results suggest that new bioinformatics tools for single cell transcriptomics, including ANN comparison to healthy PBMC, offer promise in prognostics of CLL.
Impacts of regional lockdown policies on COVID-19 transmission in India in 2020
Authors: Kalra Aarushi , Novosad Paul 
Published: August 2021

AbstractObjectiveTo assess the impact of non-pharmaceutical interventions (NPIs) on the first wave of COVID transmission and fatalities in India.MethodsWe collected data on NPIs, using government notifications and news reports, in six major Indian states from March to August 2020, and we matched these with district-level data on COVID related deaths and Google Mobility reports. We used a district fixed effect regression approach to measure the extent to which district-level lockdowns and mobility restrictions helped reduce deaths in 2020.ResultsIn most states, COVID deaths grew most rapidly only after the initial lockdown was lifted. District-level NPIs were associated with a statistically significantly lower COVID death count in three out of five sample states (district analysis was not possible in Delhi) and in the aggregate. Interventions that were most associated with slowing fatalities were temple closures, retail closures, and curfews.DiscussionOutside of Maharashtra (the first state struck) the first fatality wave appears to have been delayed by the national lockdown. India’s NPIs, however incomplete, were successful in delaying or limiting COVID-19 deaths. Even with incomplete compliance, limiting mass gatherings in face of incipient viral waves may save lives.
Progress of the Delta variant and erosion of vaccine effectiveness, a warning from Utah
Authors: Keegan Lindsay T. , Truelove Shaun , Lessler Justin 
Published: August 2021

AbstractSince the emergence of SARS-CoV-2, vaccines have been heralded as the best way to curtail the pandemic. Clinical trials have shown SARS-CoV-2 vaccines to be highly efficacious against both disease and infection. However, those currently in use were primarily tested against early lineages. Data on vaccine effectiveness (VE) against variants of concern (VOC), including the Delta variant (B.1.617.2), remain limited. To examine the effectiveness of vaccination in Utah we compared the proportion of cases reporting vaccination to that expected at different VEs, then estimated the combined daily vaccine effectiveness using a field evaluation approach. Delta has rapidly outcompeted all other variants and, as of June 20th, represents 70% of all SARS-CoV-2 viruses sequenced in Utah. If we attribute the entire change in VE to the Delta variant, the estimated vaccine effectiveness against Delta would be 82% (95% CI: 78%, 85%). We show a modest reduction in vaccine effectiveness against COVID-19 in Utah corresponding to the expansion of the Delta lineage in the state. This reduction in the effectiveness of available vaccines correlated with the arrival of novel VOCs, rather than waning immunity, is highly concerning.
Mixed invasive molds among COVID-19 patients
Authors: Singh Vanya , Prasad Amber , Panda Prasan Kumar , Totaganti Manjunath , Tyagi Amit , Thaduri Abhinav , Rao Shalinee , Bairwa Mukesh , Singh Ashok Kumar 
Published: August 2021

AbstractPurposeDue to surge in COVID cases during the second wave of the COVID pandemic, the healthcare system collapsed in India with shortage of hospital beds, injudicious use of steroids and other immunomodulators, and poor glycaemic monitoring among a population with pre-existing risk of diabetes. Fungal epidemic was announced amid COVID pandemic with several cases of COVID-associated mucormycosis and aspergillosis being reported. But, there is no data regarding mixed fungal infections in COVID patients.Materials and MethodsThe study presented a series of ten consecutive cases with dual invasive molds in patients infected with SARS-CoV-2. Among patients hospitalized with the diagnosis of COVID in May 2021 at a tertiary care center in North India, ten microbiologically confirmed dual/mixed COVID-associated mucor-aspergillosis (CAMA) were evaluated.ResultsAll patients were diabetics with the majority having severe COVID pneumonia (6/10, 60%) either on admission or in the past one month, whilst two were each of moderate (20%) and mild (20%) categories of COVID. The patients were managed with amphotericin-B along with surgical intervention. In this case series, 70% of all CAMA (Rhizopus arrhizuswithAspergillus flavusin seven andAspergillus fumigatusin three patients) patients survived, connoting the critical importance of a high index of clinical suspicion and accurate microbiological diagnosis for managing invasive molds.ConclusionsMixed fungal infections i.e. CAMA during COVID and post-COVID periods may be an emerging disease. This outbreak is seen particularly in such patients with uncontrolled diabetes, on steroids, or cocktail therapy, or living in unhygienic environments.We believe that our findings would help gain a better insight into the risk and progression of invasive fungal mixed infections among COVID patients and thus play a pivotal role in diagnosing, classifying, and implementing an effective management strategy for treating similar cases in the future.