bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing inertial measurement unit locations for freezing of gait detection and patient preference
Authors: O’Day Johanna , Lee Marissa , Seagers Kirsten , Hoffman Shannon , Jih-Schiff Ava , Kidziński Łukasz , Delp Scott , Bronte-Stewart Helen 
Published: September 2021

ABSTRACTBackgroundFreezing of gait, a common symptom of Parkinson’s disease, presents as sporadic episodes in which an individual’s feet suddenly feel stuck to the ground. Inertial measurement units (IMUs) promise to enable at-home monitoring and personalization of therapy, but there is a lack of consensus on the number and location of IMUs for detecting freezing of gait. The purpose of this study was to assess IMU sets in the context of both freezing of gait detection performance and patient preference.MethodsSixteen people with Parkinson’s disease were surveyed about sensor preferences. Raw IMU data from seven people with Parkinson’s disease, wearing up to eleven sensors, were used to train convolutional neural networks to detect freezing of gait. Models trained with data from different sensor sets were assessed for technical performance; a best technical set and minimal IMU set were identified. Clinical utility was assessed by comparing model- and human-rater-determined percent time freezing and number of freezing events.ResultsThe best technical set consisted of three IMUs (lumbar and both ankles, AUROC = 0.83), all of which were rated highly wearable. The minimal IMU set consisted of a single ankle IMU (AUROC = 0.80). Correlations between these models and human raters were good to excellent for percent time freezing (ICC = 0.93, 0.89) and number of freezing events (ICC = 0.95, 0.86) for the best technical set and minimal IMU set, respectively.ConclusionsSeveral IMU sets consisting of three IMUs or fewer were highly rated for both technical performance and wearability, and more IMUs did not necessarily perform better in FOG detection. We openly share our data and software to further the development and adoption of a general, open-source model that uses raw signals and a standard sensor set for at-home monitoring of freezing of gait.
Young adults vulnerability to COVID-19 in Brazil: an overview across the country
Authors: de Souza Fernanda Sumika Hojo , Hojo-Souza Natália Satchiko , de Oliveira Daniela Carine Ramires , da Silva Cristiano Maciel , Guidoni Daniel Ludovico 
Published: September 2021

ABSTRACTBrazil is a country of continental dimensions, where many smaller countries would fit. In addition to demographic, socioeconomic, and cultural differences, hospital infrastructure and healthcare varies across all 27 federative units. Therefore, the evolution of COVID-19 pandemic did not manifest itself in a homogeneous and predictable trend across the nation. In late 2020 and early 2021, new waves of the COVID-19 outbreak have caused an unprecedented sanitary collapse in Brazil. Unlike the first COVID-19 wave, in subsequent waves, preliminary evidence has pointed to an increase in the daily reported cases among younger people being hospitalized, overloading the healthcare system. In this comprehensive retrospective study, confirmed cases of hospitalization, ICU admission, IMV requirement and in-hospital death from Brazilian COVID-19 patients throughout 2020 until the beginning of 2021 were analyzed through a spatio-temporal study for patients aged 20-59 years. All Brazilian federative units had their data disaggregated in six periods of ten epidemiological weeks each. We found that there is a wide variation in the waves dynamic due to SARS-CoV-2 infection, both in the first and in subsequent outbreaks in different federative units over the analyzed periods. As a result, atypical waves can be seen in the Brazil data as a whole. The analysis showed that Brazil is experiencing a numerical explosion of hospitalizations and deaths for patients aged 20-59 years, especially in the state of São Paulo, with a similar proportion of hospitalizations for this age group but higher proportion of deaths compared to the first wave.
Perfusate metabolomics content and tubular transporters expression during kidney graft preservation by hypothermic machine perfusion
Authors: Faucher Quentin , Alarcan Hugo , Sauvage François-Ludovic , Forestier Lionel , Miquelestorena-Standley Elodie , Nadal-Desbarats Lydie , Arnion Hélène , Venhard Jean-Christophe , Brichart Nicolas , Bruyère Franck , Marquet Pierre , Guellec Chantal Barin-Le 
Published: September 2021

AbstractBackgroundIschemia-related injury during the pre-implantation period impacts kidney graft outcome. Evaluating these lesions by a non-invasive approach before transplantation could help to understand the mechanisms of graft injury and identify potential biomarkers predictive of graft outcomes. This study aims to determine metabolomic content of graft perfusion fluids and its dependence on preservation time and to explore whether tubular transporters are possibly involved in the metabolomics variations observed.MethodsKidneys were stored on hypothermic perfusion machines. We evaluated the metabolomic profiles of perfusion fluids (n=35) using Liquid Chromatography coupled with tandem Mass Spectrometry and studied the transcriptional expression of tubular transporters on pre-implantation biopsies (n=26). We used univariate and multivariate analyses to assess the impact of perfusion time on these parameters and their relationship with graft outcome.ResultsSeventy-two metabolites were found in preservation fluids at the end of perfusion, of which 40% were already present in the native conservation solution. We observed an increase of 23 metabolites with longer perfusion time and a decrease for 8. The predictive model for time-dependent variation of metabolomics content showed good performance (R2= 76%, Q2= 54%, accuracy= 41%, permutations test significant). Perfusion time had no effect on the mRNA expression of transporters. We found no correlation between metabolomics and transporters expression. Neither the metabolomics profile nor the transporters expression were predictive of graft outcome.ConclusionOur results open the way for further studies, focusing on both intra- and extra-tissue metabolome, to investigate whether transporter alterations can explain the variations observed in pre-implantation period.
Metric selection and promotional language in health artificial intelligence
Authors: Graham S. Scott , Ghotra Trisha 
Published: September 2021

AbstractBackgroundRecent advances in Artificial intelligence (AI) have the potential to substantially improve healthcare across clinical areas. However, there are concerns health AI research may overstate the utility of newly developed systems and that certain metrics for measuring AI system performance may lead to an overly optimistic interpretation of research results. The current study aims to evaluate the relationship between researcher choice of AI performance metric and promotional language use in published abstracts.Methods and findingsThis cross-sectional study evaluated the relationship between promotional language and use of composite performance metrics (AUC or F1). A total of 1200 randomly sampled health AI abstracts drawn from PubMed were evaluated for metric selection and promotional language rates. Promotional language evaluation was accomplished through the development of a customized machine learning system that identifies promotional claims in abstracts describing the results of health AI system development. The language classification system was trained with an annotated dataset of 922 sentences. Collected sentences were annotated by two raters for evidence of promotional language. The annotators achieved 94.5% agreement (κ = 0.825). Several candidate models were evaluated and, the bagged classification and regression tree (CART) achieved the highest performance at Precision = 0.92 and Recall = 0.89. The final model was used to classify individual sentences in a sample of 1200 abstracts, and a quasi-Poisson framework was used to assess the relationship between metric selection and promotional language rates. The results indicate that use of AUC predicts a 12% increase (95% CI: 5-19%, p = 0.00104) in abstract promotional language rates and that use of F1 predicts a 16% increase (95% CI: 4% to 30%, p = 0. 00996).ConclusionsClinical trials evaluating spin, hype, or overstatement have found that the observed magnitude of increase is sufficient to induce misinterpretation of findings in researchers and clinicians. These results suggest that efforts to address hype in health AI need to attend to both underlying research methods and language choice.
Predictors of parents’ intention to vaccinate their children against the COVID-19 in Greece: a cross-sectional study
Authors: Galanis Petros , Vraka Irene , Siskou Olga , Konstantakopoulou Olympia , Katsiroumpa Aglaia , Moisoglou Ioannis , Kaitelidou Daphne 
Published: September 2021

AbstractBackgroundParents’ intention to vaccinate their children against the COVID-19 is envisaged as critical strategy to control the pandemic.ObjectiveTo investigate the intention of parents to vaccinate their children against the COVID-19 and the factors influencing this intention.MethodsWe conducted an online cross-sectional study in Greece and we collected data during the first week of September 2021. A convenience sample was used by collecting questionnaires through social media. Our study population included adult parents with children aged 12-17 years who were eligible for a COVID-19 vaccine.ResultsStudy population included 813 parents with a mean age of 42.3 years. Among parents, 36% reported that they will vaccinate their children against the COVID-19, 33.5% denied vaccination and 30.5% were undecided. Concerns about the safety, effectiveness and side effects of COVID-19 vaccines were the most important reasons for decline of COVID-19 vaccination. Parents who took the flu vaccine in 2020 and those who had more knowledge and fewer concerns about COVID-19 vaccines had a greater probability to vaccinate their children against the COVID-19. Increased self-perceived severity of COVID-19, and increased trust in COVID-19 vaccines and the government regarding the information about the COVID-19 vaccines were associated with parents’ intention to vaccinate their children. However, increased knowledge regarding COVID-19 was associated with decreased intention of parents to vaccinate their children.ConclusionsParents’ intention to vaccinate their children against the COVID-19 was low. Our findings could contribute to the development of target strategies to implement adherence to COVID-19 vaccination campaigns.
Does Time to Theatre Affect The Ability to Achieve Fracture Reduction in Tibial Plateau Fractures?
Authors: Kitchen David S. , Richards Jack , Smitham Peter J. , Atkins Gerald J. , Solomon Lucian B. 
Published: September 2021

AimsThe primary aim of this study was to assess the effect of time to surgery on fracture reduction, assessed as residual articular step, in cases of tibial plateau fracture (TPF). The secondary aim was to assess the effect of pre-operative demographics and residual articular step on patient reported outcomes (PROMs) following TPF.MethodBetween 2006 and 2017 all surgically treated TPF patients managed by a single surgeon at our institution were prospectively consented for the study of fracture outcomes. Timing to surgical intervention, reduction of articular step, age, gender, medical background, fracture classification, mechanism of injury and PROMs (Lysholm Scores and Knee Injury and Osteoarthritis Outcome Scores (KOOS)) were recorded and analysed. Reduction of articular step, defined as <2mm, was assessed by a single blinded examiner using measurements on plain radiographs on PACS.ResultsOne hundred seventeen patients were enrolled, 52 with Schatzker II, four with Schatzker IV and 61 with Schatzker VI fractures. Patients were followed-up to a mean time of 3.9 years. The ability to achieve fracture reduction was negatively influenced by time to theatre with the odds of achieving reduction decreasing 17% each day post-injury (p = 0.002). An increased time to theatre was associated with reduced Lysholm scores at the one-year mark (p = 0.01). The ability to achieve fracture reduction did not influence PROMs within the study period.ConclusionDelay in surgical fixation negatively affects fracture reduction in TPF and may delay recovery. However, residual articular step did not influence the investigated PROMs in the cohort investigated over the mid-term (mean of 3.9 years).
Re-evaluation of ethylene role in Arabidopsis cauline leaf abscission induced by water stress and rewatering
Authors: Meir Shimon , Philosoph-Hadas Sonia , Salim Shoshana , Segev Adi , Riov Joseph 
Published: September 2021

ABSTRACTPatharkar and Walker (2016) reported that cauline leaf abscission in Arabidopsis is induced by a cycle of water stress and rewatering, which is regulated by the complex of INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), HAESA (HAE), and HAESA-LIKE2 (HSL2) kinases. However, they stated without presenting experimental results that ethylene is not involved in this process. Since this statement contradicts the well-established role of ethylene in organ abscission induced by a cycle of water stress and rewatering, our present study was aimed to re-evaluate the possible involvement of ethylene in this process. For this purpose, we examined the endogenous ethylene production during water stress and following rewatering, as well as the effects of exogenous ethylene and 1-methylcyclopropene (1-MCP), on cauline leaf abscission of Arabidopsis wild type. Additionally, we examined whether this stress induces cauline leaf abscission in ethylene-insensitive Arabidopsis mutants. The results of the present study demonstrated that ethylene production rates increased significantly in cauline leaves at 4 h after rewatering of stressed plants, and remained high for at least 24 h in plants water-stressed to 40 and 30% of system weight. Ethylene treatment applied to well-watered plants induced cauline leaf abscission, which was inhibited by 1-MCP. Cauline leaf abscission was also inhibited by 1-MCP applied during a cycle of water stress and rewatering. Finally, no abscission occurred in two ethylene-insensitive mutants,ein2-1andein2-5, following a cycle of water stress and rewatering. Taken together, these results clearly indicate that ethylene is involved in Arabidopsis cauline leaf abscission induced by water stress.One sentence summaryUnlike Patharker and Walker (2016), our results show that ethylene is involved in Arabidopsis cauline leaf abscission induced by water stress and rewatering, similar to leaf abscission in other plants.
Mapping Spatial Frequency Preferences Across Human Primary Visual Cortex
Authors: Broderick William F. , Simoncelli Eero P. , Winawer Jonathan 
Published: September 2021

AbstractNeurons in primate visual cortex (area V1) are tuned for spatial frequency, in a manner that depends on their position in the visual field. Several studies have examined this dependency using fMRI, reporting preferred spatial frequencies (tuning curve peaks) of V1 voxels as a function of eccentricity, but their results differ by as much as two octaves, presumably due to differences in stimuli, measurements, and analysis methodology. Here, we characterize spatial frequency tuning at a millimeter resolution within human primary visual cortex, across stimulus orientation and visual field locations. We measured fMRI responses to a novel set of stimuli, constructed as sinusoidal gratings in log-polar coordinates, which include circular, radial, and spiral geometries. For each individual stimulus, the local spatial frequency varies inversely with eccentricity, and for any given location in the visual field, the full set of stimuli span a broad range of spatial frequencies and orientations. Over the measured range of eccentricities, the preferred spatial frequency is well-fit by a function that varies as the inverse of the eccentricity plus a small constant. We also find small but systematic effects of local stimulus orientation, defined in both absolute coordinates and relative to visual field location. Specifically, peak spatial frequency is higher for pinwheel than annular stimuli and for horizontal than vertical stimuli.
PhycoMine: A Microalgae Data Warehouse
Authors: Goitia Rodrigo R. D. , Riaño-Pachón Diego M. , Fassio Alexandre Victor , Winck Flavia V. 
Published: September 2021

AbstractPhycoMine is data warehouse system created to fostering the analysis of complex and integrated data from microalgae species in a single computational environment. The PhycoMine was developed on top of the InterMine software system, and it has implemented an extended database model, containing a series of tools that help the users in the analysis and mining of individual data and group data. The platform has widgets created to facilitate simultaneous data mining of different datasets. Among the widgets implemented in PhycoMine, there are options for mining chromosome distribution, gene expression variation via transcriptomics, proteomics sets, Gene Onthology enrichment, KEGG enrichment, publication enrichment, EggNOG, Transcription factors and transcriptional regulators enrichment and phenotypical data. These widgets were created to facilitate data visualization of the gene expression levels in different experimental setups, for which RNA-seq experimental data is available in data repositories. For comparative purposes, we have reanalyzed 200 RNA-seq datasets from Chlamydomonas reinhardtii, a model unicellular microalga, for optimizing the performance and accuracy of data comparisons. We have also implemented widgets for metabolic pathway analysis of selected genes and proteins and options for biological network analysis. The option for analysis of orthologue genes was also included. With this platform, the users can perform data mining for a list of genes or proteins of interest in an integrated way through accessing the data from different sources and visualizing them in graphics and by exporting the data into table formats. The PhycoMine platform is freely available and can be visited through the URL https://PhycoMine.iq.usp.br.
Long read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod
Authors: Pearman William S. , Wells Sarah J. , Dale James , Silander Olin K. , Freed Nikki E. 
Published: September 2021

AbstractMost animal mitochondrial genomes are small, circular, and structurally conserved. However, recent work indicates that diverse taxa possess unusual mitochondrial genomes. In Isopoda, species in multiple lineages have atypical and rearranged mitochondrial genomes. However, more species of this speciose taxon need to be evaluated to understand the evolutionary origins of atypical mitochondrial genomes in this group. In this study, we report the presence of an atypical mitochondrial structure in the New Zealand endemic marine isopod,Isocladus armatus. Data from long and short read DNA sequencing, suggests thatI. armatushas two mitochondrial chromosomes. The first chromosome consists of two mitochondrial genomes that have been inverted and fused together in a circular form, and the second chromosome consists of a single mitochondrial genome in a linearized form. This atypical mitochondrial structure has been detected in other isopod lineages, and our data from an additional divergent isopod lineage (Sphaeromatidae) lends support to the hypothesis that atypical structure evolved early in the evolution of Isopoda. Additionally, we find that a heteroplasmic site previously observed across many species within Isopoda is absent inI. armatus,but confirm the presence of two heteroplasmic sites recently reported in two other isopod species.
A combination of two human neutralizing antibodies prevents SARS-CoV-2 infection in rhesus macaques
Authors: Cobb Ronald R. , Nkolola Joseph , Gilchuk Pavlo , Chandrashekar Abishek , House Robert V. , Earnhart Christopher G. , Dorsey Nicole M. , Hopkins Svetlana A. , Snow Doris M. , Chen Rita E. , VanBlargan Laura A. , Hechenblaikner Manuel , Hoppe Brian , Collins Laura , Tomic Milan T. , Nonet Genevieve H. , Hackett Kyal , Slaughter James C. , Diamond Michael S. , Carnahan Robert H. , Barouch Dan H. , Crowe James E. 
Published: September 2021

ABSTRACTHuman monoclonal antibody (mAb) treatments are promising for COVID-19 prevention, post-exposure prophylaxis, or therapy. However, the titer of neutralizing antibodies required for protection against SARS-CoV-2 infection remains poorly characterized. We previously described two potently neutralizing mAbs COV2-2130 and COV2-2381 targeting non-overlapping epitopes on the receptor-binding domain of SARS-CoV-2 spike protein. Here, we engineered the Fc-region of these mAbs with mutations to extend their persistence in humans and reduce interactions with Fc gamma receptors. Passive transfer of individual or combinations of the two antibodies (designated ADM03820) given prophylactically by intravenous or intramuscular route conferred virological protection in a non-human primate (NHP) model of SARS-CoV-2 infection, and ADM03820 potently neutralized SARS-CoV-2 variants of concernin vitro. We defined 6,000 as a protective serum neutralizing antibody titer in NHPs against infection for passively transferred human mAbs that acted by direct viral neutralization, which corresponded to a concentration of 20 μg/mL of circulating mAb.
PD-1 checkpoint blockade activates germinal center follicular T cell programs that disrupt type 2 isotype-specific antibody homeostasis
Authors: Shuparski Andrew G. , Higgins Brett W. , Miller Karen B. , McHeyzer-Williams Louise J. , McHeyzer-Williams Michael G. 
Published: September 2021

ABSTRACTMultiple CD4 T cell dependent tolerance mechanisms control adaptive B cell immunity to environmental antigens. We recently demonstrated a PD-1 checkpoint within steady-state splenic germinal centers (GC) that constrains the maturation of type 2 IgG1 isotype-specific antibody homeostasis. Here, we utilized single cell-indexed custom RNA-sequencing to probe the follicular T cell mechanisms directly targeted by acute PD-1 blockade. We find a pre-existing subset of follicular helper T (TFH) cells that express type 2 immune response properties (TFH2) with exaggerated pathways of TCR activation, cytokine signaling, and enhanced cell-cell contact upon acute PD-1 blockade. This selective amplification of the TFH2 program significantly increases predicted molecular connections to type 2 IgG1 GC B cells that dominate limited changes in GC localized follicular regulatory T (GC TFR) cell programs. These studies demonstrate how type 2 isotype-specific adaptive B cell tolerance is selectively disrupted by acute PD-1 blockade to reveal the modular regulatory mechanisms that control splenic GC dynamics at homeostasis.One Sentence SummaryAcute PD-1 blockade alters the regulatory dynamic of the steady state germinal center to drive the maturation of IgG1 GC B cells towards PC differentiation in a process mediated by type 2 like TFH effector molecules.HIGHLIGHTS-Acute PD-1 blockade enhances the steady state splenic TFH program-PD-1 blockade selectively exaggerates a Type 2 like TFH module-GC TFR cells are minimally impacted by blockade-PD-1 restrains predicted TFH2 functional contacts with IgG1 GC B Cells