bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Eight-Week Online Cognitive Training in Parkinson’s Disease: A Randomized Controlled Trial
Authors: van Balkom Tim D. , Berendse Henk W. , van der Werf Ysbrand D. , Twisk Jos W.R. , Peeters Carel F.W. , Hagen Rob H. , Berk Tanja , van den Heuvel Odile A. , Vriend Chris 
Published: March 2021

AbstractBackgroundCognitive training (CT) has been proposed as a non-pharmacological treatment option for the frequent cognitive impairments occurring in PD.ObjectiveAssess the efficacy of CT on cognitive function in PD.MethodsIn this double-blind, randomized controlled trial we enrolled 140 PD patients with significant subjective cognitive complaints. In eight weeks, participants underwent 24 sessions of computerized multi-domain CT or an active control condition for 45 minutes each (n=70 vs. n=70). The primary outcome was the accuracy on a computerized Tower of London task; secondary outcomes included effects on other neuropsychological outcomes and subjective cognitive complaints. Outcomes were assessed before and after training and at six-months follow-up, and were analyzed with multivariate mixed-model analyses.ResultsThe intention-to-treat population consisted of 136 participants. Multivariate mixed-model analyses showed no group difference on the Tower of London accuracy corrected for baseline performance: B: −0.06, 95% CI: −0.27 to 0.15, p=0.562. Participants in the CT group were on average 0.30 SD (i.e., 1.5 seconds) faster on the Tower of London, difficulty load 4 (secondary outcome): 95% CI: −0.55 to −0.06, p=0.015. CT had similar positive effects on other processing speed-related executive function tasks, although these did not reach statistical significance. At follow-up, no group differences were present.ConclusionsThe results show tentative but consistent positive effects of CT on processing speed during executive functioning. Future studies should investigate booster sessions to increase durability, optimize training duration, and study different sub-groups of PD patients along the continuum of cognitive decline towards PD dementia.
Detection and genome sequencing of SARS-CoV-2 belonging to the B.1.1.7 lineage in the Philippines
Authors: Tablizo Francis A. , Saloma Cynthia P. , Castro Marc Jerrone R. , Kim Kenneth M. , Yangzon Maria Sofia L. , Lapid Carlo M. , Maralit Benedict A. , Ayes Marc Edsel C. , Yap Jan Michael C. , Llames Jo-Hannah S. , Araiza Shiela Mae M. , Punayan Kris P. , Asin Irish Coleen A. , Tambaoan Candice Francheska B. , Chong Asia Louisa U. , Padilla Karol Sophia Agape R. , Cruz Rianna Patricia S. , Morado El King D. , Dizon Joshua Gregor A. , Cutiongco-de la Paz Eva Maria , de Guzman Alethea R. , Hao Razel Nikka M. , Zamora Arianne A. , Pacial Devon Ray , Magalang Juan Antonio R. , Alejandria Marissa , Carlos Celia , Ong-Lim Anna , Salvaña Edsel Maurice , Wong John Q. , Montoya Jaime C. , Singh-Vergeire Maria Rosario 
Published: March 2021

ABSTRACTWe report the sequencing and detection of 39 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples containing lineage-defining mutations specific to viruses belonging to the B.1.1.7 lineage (UK variant) in the Philippines.
SARS-CoV-2-specific T Cell Memory is Sustained in COVID-19 Convalescents for 8 Months with Successful Development of Stem Cell-like Memory T Cells
Authors: Jung Jae Hyung , Rha Min-Seok , Sa Moa , Choi Hee Kyoung , Jeon Ji Hoon , Seok Hyeri , Park Dae Won , Park Su-Hyung , Jeong Hye Won , Choi Won Suk , Shin Eui-Cheol 
Published: March 2021

AbstractMemory T cells contribute to rapid viral clearance during re-infection, but the longevity and differentiation of SARS-CoV-2-specific memory T cells remain unclear. We conducted direct ex vivo assays to evaluate SARS-CoV-2-specific CD4+ and CD8+ T cell responses in COVID-19 convalescents up to 254 days post-symptom onset (DPSO). Here, we report that memory T cell responses were maintained during the study period. In particular, we observed sustained polyfunctionality and proliferation capacity of SARS-CoV-2-specific T cells. Among SARS-CoV-2-specific CD4+ and CD8+ T cells detected by activation-induced markers, the proportion of stem cell-like memory T (TSCM) cells increased, peaking at approximately 120 DPSO. Development of TSCM cells was confirmed by SARS-CoV-2-specific MHC-I multimer staining. Considering the self-renewal capacity and multipotency of TSCM cells, our data suggest that SARS-CoV-2-specific T cells are long-lasting after recovery from COVID-19. The current study provides insight for establishing an effective vaccination program and epidemiological measurement.
Language disorder in progressive supranuclear palsy and corticobasal syndrome: neural correlates and detection by the MLSE screening tool
Authors: Peterson Katie A. , Jones P. Simon , Patel Nikil , Tsvetanov Kamen A. , Ingram Ruth , Cappa Stefano F. , Ralph Matthew A. Lambon , Patterson Karalyn , Garrard Peter , Rowe James B. 
Published: March 2021

AbstractBackgroundProgressive supranuclear palsy (PSP) and corticobasal syndrome (CBS) affect speech and language as well as motor functions. Clinical and neuropathological data indicate a close relationship between these two disorders and the non-fluent variant of primary progressive aphasia (nfvPPA). We use the recently developed Mini Linguistic State Examination tool (MLSE) to study speech and language disorders in patients with PSP, CBS, and nfvPPA, in combination with structural magnetic resonance imaging (MRI).MethodsFifty-one patients (PSP N = 13, CBS N = 19, nfvPPA N = 19) and 30 age-matched controls completed the MLSE, the short form of the Boston Diagnostic Aphasia Examination (BDAE), and the Addenbrooke’s Cognitive Examination III. Thirty-eight patients and all controls underwent structural MRI at 3 Tesla, with T1 and T2-weighted images processed by surface-based and subcortical segmentation within FreeSurfer 6.0.0 to extract cortical thickness and subcortical volumes. Morphometric differences were compared between groups and correlated with severity of speech and language impairment.ResultsCBS and PSP patients showed impaired MLSE performance, compared to controls, with a similar language profile to nfvPPA, albeit less severe. All patient groups showed reduced cortical thickness in bilateral frontal regions and striatal volume. PSP and nfvPPA patients also showed reduced superior temporal cortical thickness, with additional thalamic and amygdalo-hippocampal volume reductions in nfvPPA. Multivariate analysis of brain-wide cortical thickness and subcortical volumes with MLSE domain scores revealed associations between performance on multiple speech and language domains with atrophy of left-lateralised fronto-temporal cortex, amygdala, hippocampus, putamen and caudate.ConclusionsThe effect of PSP and CBS on speech and language overlaps with nfvPPA. These three disorders cause a common anatomical pattern of atrophy in the left frontotemporal language network and striatum. The MLSE is a short clinical screening tool that can identify the language disorder of PSP and CBS, facilitating clinical management and patient access to future clinical trials.
Measuring the exposure of Black, Asian and other ethnic groups to Covid-infected neighbourhoods in English towns and cities
Authors: Harris Richard , Brunsdon Chris 
Published: March 2021

AbstractDrawing on the work of The Doreen Lawrence Review – a report on the disproportionate impact of Covid-19 on Black, Asian and minority ethnic communities in the UK – this paper develops an index of exposure, measuring which ethnic groups have been most exposed to Covid-19 infected residential neighbourhoods during the first and second waves of the pandemic in England. The index is based on a Bayesian Poisson model with a random intercept in the linear predictor, allowing for extra-Poisson variation at neighbourhood and town/city scales. This permits within-city differences to be decoupled from broader regional trends in the disease. The research finds that members of ethnic minority groups tend to be living in areas with higher infection rates but also that the risk of exposure is distributed unevenly across these groups. Initially, in the first wave, the disease disproportionately affected Black residents. As the pandemic has progressed, especially the Pakistani but also the Bangladeshi and Indian groups have had the highest exposure. This higher exposure of the Pakistani group is not straightforwardly a function of neighbourhood deprivation because it is present across a range of average house prices. However, we find evidence to support the view, expressed in The Doreen Lawrence Review, that it is linked to occupational and environmental exposure, particularly residential density.
Predictive Capacity of COVID-19 Test Positivity Rate
Authors: Fenga Livio , Gaspari Mauro 
Published: March 2021

AbstractCOVID-19 infections can spread silently, due to the simultaneous presence of significant numbers of both critical and asymptomatic to mild cases. While for the former reliable data are available (in the form of number of hospitalization and/or beds in intensive care units), this is not the case of the latter. Hence, analytical tools designed to generate reliable forecast and future scenarios, should be implemented to help decision makers planning ahead (e.g. medical structures and equipment). Previous work of one of the authors shows that an alternative formulation of the Test Positivity Rate (TPR), i.e. the proportion of the number of persons tested positive in a given day, exhibits a strong correlation with the number of patients admitted in hospital and intensive care units. In this paper, we investigate the lagged correlation structure between the newly defined TPR and the hospitalized people time series, exploiting a rigorous statistical model, the Seasonal Auto Regressive Moving Average (SARIMA). The rigorous analytical framework chosen, i.e. the stochastic processes theory, allowed for a reliable forecasting about 12 days ahead, of those quantities. The proposed approach would also allow decision makers to forecast the number of beds in hospitals and intensive care units needed 12 days ahead. The obtained results show that a standardized TPR index is a valuable metric to monitor the growth of the COVID-19 epidemic. The index can be computed on daily basis and it is probably one of the best forecasting tools available today for predicting hospital and intensive care units overload, being an optimal compromise between simplicity of calculation and accuracy.
The Impact of the Variation of CT Scanner on the Prediction of human papillomavirus (HPV) Association of Oropharyngeal Cancer (OPC) using Radiomic models
Authors: Reiazi Reza , Arrowsmith Colin , Welch Mattea , Abbas-Aghababazadeh Farnoosh , Eeles Christopher , Tadic Tony , Hope Andrew J. , Bratman Scott V. , Haibe-Kains Benjamin 
Published: March 2021

ABSTRACTStudies have shown that radiomic features are sensitive to the variability of imaging parameters (e.g., scanner model) and one of the major challenges in these studies lies in improving the robustness of quantitative features against the variations in imaging datasets from multi-center studies. Here, we assess the impact of scanner choice on the computed tomography (CT)-derived radiomic features to predict association of oropharyngeal squamous cell carcinoma with human papillomavirus (HPV). This experiment was performed on CT image datasets acquired with two different scanner manufacturers. We demonstrate strong scanner dependency by developing a machine learning model to classify HPV status from radiological images. These experiments revealed the effect of scanner manufacturers on the robustness of the radiomic features, and the extent of this dependency is reflected on the performance of HPV prediction models. The results of this study highlight the importance of implementing an appropriate approach to reduce the impact of imaging parameters on radiomic features and consequently on the machine learning models.
Comparative analysis of policies and programs to support families and children during COVID-19
Authors: Kearon Joanne , Cachia Mark , Carsley Sarah , van den Heuvel Meta , Hopkins Jessica 
Published: March 2021

AbstractBackgroundPolicies and programs that promote positive social environments for young children and their families have the potential to improve early childhood development and long-term health. However, due to the community-wide public health measures implemented to reduce transmission of COVID-19, many families are experiencing health and socio-economic challenges and pre-existing supports and services may no longer be available. In this study, we compared the policies and programs countries have implemented to support maternal and child health during the first wave of COVID-19.MethodsWe compared the policies and programs implemented to support child health and well-being during the first wave of COVID-19 in Australia, Canada, the Netherlands, Singapore, the UK, and the USA. A grey literature review was performed to identify policies, announcements, and guidelines released from governmental and public health organizations within each country related to children, parents, families, early childhood development, adverse childhood experiences, child welfare, pre-school, or daycares. We also performed a manual search of government websites. Both provincial and federal government policies were included for Canada.ResultsThe main policies identified were focused on prenatal care, well-baby visit and immunization schedules, financial supports, domestic violence and housing, childcare supports, child protective services, and food security. All of the included countries implemented some of these policies, but there was a large variation in the number, size, and barriers to access these supports. None of the countries implemented supports in all of the potential areas identified.ConclusionPolitical legacy and previous redistributive policies might have influenced the variation in policies and programs introduced by governments. As the COVID-19 pandemic continues, further opportunity for governments to implement supportive programs and policies for children and families exists.
First dose mRNA vaccination is sufficient to reactivate immunological memory to SARS-CoV-2 in ex COVID-19 subjects
Authors: Mazzoni Alessio , Di Lauria Nicoletta , Maggi Laura , Salvati Lorenzo , Vanni Anna , Capone Manuela , Lamacchia Giulia , Mantengoli Elisabetta , Spinicci Michele , Zammarchi Lorenzo , Kiros Seble Tekle , Colao Maria Grazia , Parronchi Paola , Scaletti Cristina , Turco Lucia , Liotta Francesco , Rossolini Gian Maria , Cosmi Lorenzo , Bartoloni Alessandro , Annunziato Francesco ,   for the COVID-19 Research Group
Published: March 2021

AbstractCharacterizing the adaptive immune response to COVID-19 vaccination in individuals who recovered from SARS-CoV-2 infection may define current and future clinical practice. To determine the effect of two doses BNT162b2 mRNA COVID-19 vaccination schedule in individuals who recovered from COVID-19 (ex COVID-19) compared to naïve subjects we evaluated SARS-CoV-2 spike-specific T and B cell responses, as well as specific IgG, IgM and neutralizing antibodies titres in 22 individuals who received BNT162b2 mRNA COVID-19 vaccine, 11 of which had a previous history of SARS-CoV-2 infection. Evaluations were performed before vaccination and then weekly until 7 days post second injection. Data obtained clearly showed that one vaccine dose is sufficient to increase both cellular and humoral immune response in ex COVID-19 subjects without any additional improvement after the second dose. On the contrary, the second dose is mandatory in naïve ones to further enhance the response. These results question whether a second vaccine jab in ex COVID-19 subjects is required and indicate that millions of vaccine doses may be redirected to naïve individuals, thus shortening the time to reach herd immunity.
Anti-Spike protein assays to determine post-vaccination antibody levels: a head-to-head comparison of five quantitative assays
Authors: Perkmann Thomas , Perkmann-Nagele Nicole , Koller Thomas , Mucher Patrick , Radakovics Astrid , Marculescu Rodrig , Wolzt Michael , Wagner Oswald F. , Binder Christoph J. , Haslacher Helmuth 
Published: March 2021

AbstractBackgroundReliable quantification of the antibody response to SARS-CoV-2 vaccination is highly relevant for identifying possible vaccine failure and estimating the time of protection. Therefore, we aimed to evaluate the performance of five different Anti-SARS-CoV-2 antibody assays regarding the quantification of anti-spike (S) antibodies induced after a single dose of BNT162b2.MethodsSera of n=69 SARS-CoV-2 naïve individuals 21±1 days after vaccination with BNT162b2 (Pfizer/BioNTech) were tested using the following quantitative SARS-CoV-2 antibody assays: Roche S total antibody, DiaSorin trimeric spike IgG, DiaSorin S1/S2 IgG, Abbott II IgG, and Serion/Virion IgG. Test agreement was assessed by Passing-Bablok regression. Results were further compared to the percent inhibition calculated from a surrogate virus neutralization test (sVNT) by correlation and ROC (receiver-operating-characteristics) analysis.ResultsIndividual values were distributed over several orders of magnitude for all assays evaluated. Although the assays were in good overall agreement (ρ=0.80-0.94), Passing-Bablok regression revealed systematic and proportional differences, which could not be eliminated by converting the results to BAU/mL as suggested by the manufacturers. 7 (10%) individuals had a negative sVNT results (i.e. <30% inhibition). These samples were reliably identified by most assays and yielded low binding antibody levels (ROC-AUCs 0.84-0.93).ConclusionsAlthough all assays evaluated showed good correlation, readings from different assays were not interchangeable, even when converted to BAU/mL using the WHO international standard for SARS-CoV-2 immunoglobulin. This highlights the need for further standardization of SARS-CoV-2 serology.
Gait-phase modulates alpha and beta oscillations in the pedunculopontine nucleus
Authors: He Shenghong , Deli Alceste , Fischer Petra , Wiest Christoph , Huang Yongzhi , Martin Sean , Khawaldeh Saed , Aziz Tipu Z. , Green Alexander L , Brown Peter , Tan Huiling 
Published: March 2021

AbstractBackgroudThe pedunculopontine nucleus (PPN) is a reticular collection of neurons at the junction of the midbrain and pons, playing an important role in modulating posture and locomotion. Deep brain stimulation of the PPN has been proposed as an emerging treatment for patients with Parkinson’s disease (PD) or multiple system atrophy (MSA) suffering gait-related atypical parkinsonian syndromes.ObjectiveIn this study, we investigated PPN activities during gait to better understand its functional role in locomotion. Specifically, we investigated whether PPN activity is rhythmically modulated during locomotion.MethodsPPN local field potential (LFP) activities were recorded from PD or MSA patients suffering from gait difficulties during stepping in place or free walking. Simultaneous measurements from force plates or accelerometers were used to determine the phase within each gait cycle at each time point.ResultsOur results showed that activities in the alpha and beta frequency bands in the PPN LFPs were rhythmically modulated by the gait phase within gait cycles, with a higher modulation index when the stepping rhythm was more regular. Meanwhile, the PPN-cortical coherence was most prominent in the alpha band. Both gait-phase related modulation in the alpha/beta power and the PPN-cortical coherence in the alpha frequency band were spatially specific to the PPN and did not extend to surrounding regions.ConclusionsThese results raise the possibility that alternating PPN stimulation in tandem with the gait rhythm may be more beneficial for gait control than continuous stimulation, although this remains to be established in future studies.
cinaR: A comprehensive R package for the differential analyses and functional interpretation of ATAC-seq data
Authors: Karakaslar E Onur , Ucar Duygu 
Published: March 2021

AbstractSummaryATAC-seq is a frequently used assay to study chromatin accessibility levels. Differential chromatin accessibility analyses between biological groups and functional interpretation of these differential regions are essential in ATAC-seq data analyses. Although distinct methods and analyses pipelines are developed for this purpose, a stand-alone R package that combines state-of-the art differential and functional enrichment analyses pipelines is missing. To fill this gap, we developedcinaR (Chromatin Analyses inR), which is a single wrapper function and provides users with various data analyses and visualization options, including functional enrichment analyses with gene sets curated from multiple sources.Availability and implementationcinaRis an R/CRAN package which is under GPL-3 License and its source code is freely accessible athttps://CRAN.R-project.org/package=cinaR.Gene sets are available athttps://CRAN.R-project.org/package=cinaRgenesets.Bone marrow ATAC-seq data is available athttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE165120
Novel regulators of growth identified in the evolution of fin proportion in flying fish
Authors: Daane Jacob M. , Blum Nicola , Lanni Jennifer , Boldt Helena , Iovine M. Kathryn , Higdon Charles W. , Johnson Stephen L. , Lovejoy Nathan R. , Harris Matthew P. 
Published: March 2021

AbstractIdentifying the genetic foundations of trait variation and evolution is challenging as it is often difficult to parse meaningful signals from confounding signatures such as drift and epistasis. However, identification of the genetic loci underlying morphological and physiological traits can be honed through the use of comparative and complementary genetic approaches, whereby shared sets of genes that are repeatedly implicated across large evolutionary time periods as under selection can illuminate important pathways and epistatic relationships that function as novel regulators of trait development. Here we intersect comparative genomic analyses with unbiased mutagenesis screens in distantly related species to define the control of proportional growth, as changes in the size and relative proportions of tissues underlie a large degree of the variant forms seen in nature. Through a phylogenomic analysis of genome-wide variation in 35 species of flying fishes and relatives, we identify genetic signatures in both coding and regulatory regions underlying the convergent evolution of increased paired fin size and aerial gliding behaviors, key innovations for flying fishes and flying halfbeaks. To refine our analysis, we intersected convergent phylogenomic signatures with mutants identified in distantly related zebrafish with altered fin size. Through these paired approaches, we identify a surprising role for an L-type amino acid transporter,lat4a, and the potassium channel,kcnh2a, in the regulation of fin proportion. We show that specific epistatic interaction between these genetic loci in zebrafish closely phenocopies the observed fin proportions of flying fishes. The congruence of experimental and phylogenomic findings point to a conserved, non-canonical signaling interaction that integrates bioelectric cues and amino acid transport in the establishment of relative size in development and evolution.