dataesr/scientific-paragraphs-categorization huggingface dataset:
5 (whole brain), P7 and P60 Single cell RNA Seq: Smart-seq2. Database: https:// accessed on 1 October 2022 myeloidsc. appspot. com/, In vivo P60 clusters: 0-0. 1 CPM P7 clusters: 0-0. 1 CPM threshold of >2CPM) (Did not reach cut-off Embryo cluster: 0-0. 1 CPM None Not applicable [172] Nat. Neurosci. FACS-sorted microglia from male C57BL/6 mice P90 Single cell RNA Seq: Illumina NextSeq500 In vivo No None Not applicable.
MATERIALS AND METHODS This is an international descriptive retrospective study collecting data obtained on routine clinical care visits from patients with MSP. Fifty-two centres from 24 countries participated. The inclusion criteria were (1) patients heterozygous for a pathogenic(P)/likely pathogenic (LP) variant in the VCP gene (transcript reference NM_007216. 3)  28 and (2) sufficient data available in the clinical notes to answer some of the following clinical questions: age of disease onset, genetic diagnosis, signs/symptoms at onset, clinical progression, ambulatory status and ancillary test results, if performed. Patients who harboured a variant of unknown significance (VUS) were included if disease causality was supported by in silico analysis and clinical judgement based on item (2) of the inclusion criteria and/or the pedigree indicated a dominant disease.
9 As FTD and particularly respiratory involvement speed-up disease progression, patients showing these symptoms requires a closer follow-up and improved care. Limitations of this study include its retrospective design. Data was obtained from clinical notes implying missing data, nonhomogeneous collection of data, as manifested in the variability of the number of patients in which the data was reported, and underestimation of mortality rates. Bone, cardiac and cognitive impairment might be underestimated as specific and repeated diagnostic tests were not required. In addition, the prevailing participation of neuromuscular specialist without consistently reaching out other specialists, including neurologists working primarily on dementia, and the autonomous nervous system or rheumatologists, might have led to information selection preferences.
Describing gradients requires a class of techniques that can characterize gradual changes in features. Bajada et al. (2020)  introduce the Vogt-Bailey (VB) index, which quantifies across the cortical mantle on how sharply inter-areal boundaries are defined and released open tools for VB index calculation and gradient mapping ( https:// github. com/VBIndex/ ). Arguing for potential benefits of a gradient perspective for functional cartography,  Haak and Beckmann (2020)  outline that gradient models may capture both functional heterogeneity as well as functional multiplicity across the cortical mantle, and thus complement arealization approaches that posit discrete boundaries and assume functional uniformity within regions. In  Glomb et al. (2020)  , the authors present a graph signal processing framework that, applied to EEG data, identifies harmonic basis functions to compactly describe neurophysiological brain activity.
These harmonics are or- dered by the degree of smoothness/variation along the cortex, leading to a multi-scale representation of brain connectivity. They demonstrate that the sparse harmonics representation with only a few components can track large-scale cortical activity during a face detection task. Dohmatob et al. (2021)  study the predictability of task fMRI contrast data from resting fMRI. They demonstrate that the combination of data from multiple parcellations is the best representation of local functional gradients, offering highest performance in rest-to-task mapping. Using a sparse matrix factorization algorithm trained on multiple, diverse fMRI datasets  Dadi et al. (2020)  , Dadi and colleagues identify a novel dictionary of fine-grained high-dimensional functional modes for fMRI representation.
Their study provides several recommendations to enhance reproducibility and reliability, and they demonstrate that the low-dimensional connectivity gradient approaches can outperform conventional edge-based analyses in terms of predicting phenotypic scores based on the human connectome dataset. In addition to deriving lower dimensional representations of functional or structural data, the field is increasingly exploring new formal ways to contextualize MRI-derived measures with other markers of neural architecture. Patel et al. (2020)  present a virtual histology approach, relating different MRI measures with post mortem gene expression data. They report that many MRI measures, including T1 and T2 relaxation times, T1w/T2w ratio, MWF, MTR, FA and cortical thickness reflect expression profiles of genes specific to CA1 pyramidal cells; genes enriched in processes related to dendritic arborization.
In  Burt et al. (2020)  , the authors present an autocorrelation preserving null model and corresponding open access software ( https://github. com/murraylab/brainsmash ), which can help to statistically evaluate the correspondence between gradients and other aspects of brain organization while controlling for autocorrelation. Expanding even further upon the search for correspondence of different imaging features,  Haueis (2021)  advocates for the use of formal multi-scale models, which could provide a mechanistic link between microcircuit organization and macrolevel brain function.
In future work, systematic comparisons of structural and functional gradients across a wider range of species will be an important step towards the formulation of different evolutionary theory, a research goal which is likely to become increasingly feasible with growing availability of open multispecies in vivo datasets  ( Messinger et al. , 2021 ; Milham et al. , 2018 ). Similarly, studies have begun to chart gradient reconfigurations across the lifespan  ( Sydnor et al. , 2021 ) , and to assess gradient changes as a result of environmental and disease related factors  ( Valk et al. , 2021a ). These perspectives will provide important insight into the invariance, as well as malleability of cortical gradients.
Acknowledgements We would like to thank all contributors who made this Special Issue possible. We would furthermore like to express our gratitude to all reviewers who generously offered their time to provide thought-and helpful feedback to the authors and contributed to the editorial process. BCB acknowledges research support from the  National Science and Engineering Research Council of Canada  ( NSERC Discovery-1304413 ),  CIHR  ( FDN-154298 ,  PJT-174995 ),  SickKids Foundation  ( NI17-039 ),  Azrieli Center for Autism Research  ( ACAR-TACC), Brain-Canada, Helmholtz International Bigbrain Analytics and Learning Laboratory (Hiball ),  FRQ-S , the  Montreal Neurological Institute , and the Tier-2  Canada  Research Chairs program. DSM acknowledges support from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (grant agreement No.
Experimental outline Naïve Sprague-Dawley rats (n = 63) were randomly assigned into seven experimental groups receiving PFFs and AAV-vector overexpressing h-␣Syn or GFP either alone or in combination (see Fig. 1  and Table  1 ). In the combination groups, one group received both PFFs and AAV simultaneously (h-␣Syn/PFFs and GFP/PFFs) and in the other group PFFs inoculation followed the AAV injection sequentially after a four-week delay (h-␣Syn + PFFs and GFP + PFFs). All rodents were subjected to a battery of behavioral tests at four-weeks intervals (i. e. , week 4, 8, and 12 after the first injection). Twelve weeks after the first surgical session we performed electrochemical recordings for dopamine (DA) from three anaesthetized rats per group. After all data was collected, we either perfused the animals with PFA and harvested the brains for immunohistochemistry (5-7 rats per group) or we harvested the brains (three rats per group) for dissections of midbrain and striatum, and snap-froze the tissue for subsequent quantification of phosphorylated ␣Syn protein.
Drug-induced rotations Rats were injected i. p. with 2. 5 mg/kg d-amphetamine (Apotheksbolaget) and placed in automated rotameter bowels modelled after the design of Ungerstedt  [6, 46]. All full ipsilateral and contralateral rotations, with respect to the side of injection, were quantified over 90 min. The data are presented as average rotations per minute.
Stepping test Forelimb akinesia was assessed by quantifying forelimb adjusting steps as previously described  [47, 48]. In brief, rats were constrained by the experimenter so that only one forelimb was freely movable. The animal was moved sideways over 90 cm at a constant speed. The number of both backward and forward adjusting steps was counted three consecutive times for each paw. Out of the three trials, the best two trials, in terms of number of steps performed, were averaged, and adjusting steps data was presented as percentage bias.
Densitometry High resolution scans were taken with an Epson flatbed scanner at 600 DPI. The level of staining intensity was measured from 4 striatal sections (AP + 1. 6, + 0. 7, -0. 26, and -0. 6 mm) for ␣Syn211-DAB, GFP-DAB and TH-DAB and one midbrain section (AP: -5. 6 mm) for OX42-DAB, using ImageJ software (NIH, Version 1. 8. 0). Before measurement, each image was transformed into grayscale 8-bit and calibrated using a step-tablet from Epson with known OD values using the Rodbard function (https://ima gej. nih. gov/ij/docs/examples/calibration/). Correction for non-specific background was done by subtracting values obtained from the corpus callosum to the measured values. The regions of interest were outlined, and the grey-pixel intensity value average was measured. The data are expressed as optical density values of contralateral vs ipsilateral striatum or midbrain.
Stereology Quantification of TH + cells in the substantia nigra pars compacta (SNpc) was performed according to the optical fractionator principle using ImageJ Software (NIH, Version 1. 8. 0)  [57]. In brief, z-stack images of every sixth series (section sampling fraction, ssf = 1/6) of the SNpc region were acquired at 20X magnification using a Leica DMi8 microscope, which yielded to 8-10 sections per animal. The average mounted section thickness (t) was 20 ± 2. 6 m and the heigh of optical dissector (h) used was 12 m (3 m guard zones). Grid area was set at 170x170 m and the counting frame size at 55x55 m. A maximal coefficient of error (CE) of 0. 11 for the intact side was accepted and animals with higher CE values were excluded from the analysis.
Statistics All data were analyzed using the statistical software GraphPad Prism (V 8. 4. 3) using an alpha of 0. 05 as threshold for determining statistical significance. For group and group by side analysis we performed analysis of variance with the factors Group and Side as dependent variables. For time-course analysis we performed repeated measures ANOVAs with the factors Week and Group. Post hoc testing used Sidak's correction were applied to avoid Type 1 errors/inflating alpha due to multiple comparison testing.
Loss of tyrosine-hydroxylase immunoreactivity and axonal pathology The decrease in TH is clearly indicative of changes affecting dopaminergic neurons and several studies have shown that ␣Syn overexpression can lead to a downregulation of TH  [27, 50, 79]. To address changes in the nigrostriatal DA system we first assessed the difference in TH immunoreactivity between the injected and the control striatum. Our data shows that h-␣Syn overexpression, as well as GFP overexpression, with or without PPFs, induced a strong reduction in striatal TH immunoreactivity. This downregulation was absent only in the PFFs group. This can be indicative of TH downregulation or actual denervation. Corresponding to the striatal densitometry, unbiased stereology of TH + cells in the SNpc demonstrated a loss of TH + neurons ipsilateral to the injection for all the groups except the PFFs only group.
ACKNOWLEDGMENTS MD would like to thank the  Royal Physiographic Society of Lund  ( Kungliga Fysiografiska  sällskapet), the  Royal Swedish Academy of Sciences  ( Kungliga Vetenskapsakademien ) and the  Per-Eric och Ulla Schybergs foundation  for financial support. FPM was supported by  NIH/NIDDK   R01DK108798. RM and AF are supported by the  EU Joint Programme on Neurodegenerative Disease Research and Agence National de la Recherche  (contracts  PROTEST-70 ,  ANR-17-JPCD-0005-01  and  Trans-PathND ,  ANR-17-JPCD-0002-02 ). This work has also received support from the  European Union 's  Horizon 2020 research and innovation programme and EFPIA Innovative Medicines Initiative  2 grant agreements No  116060  ( IMPRiND ) and No  821522  ( PD-MitoQUANT ), the  Swiss State Secretariat for Education‚ Research and Innovation (SERI) and Parkinson UK.
The cohort selected for this study has been described in previous studies where some data from this cohort database were already exploited  [12, [29] [30] [31]. Overall, the cohort included 600 participants. After exclusion of patients who met one of the listed exclusion criteria, the sample used in the current study included 321 participants. Assessments were carried out by experienced mental health professionals. First, the ED diagnosis of each participant was established/con rmed based on the clinical assessment by nutritionists, psychologists and psychiatrists. Second, patients who met the inclusion criteria were recruited and all provided their signed informed consent. Third, sociodemographic data, body weight and height were collected and three questionnaires were lled in: the Mini-international Neuropsychiatric Interview (MINI, Version 5.
0. 0), the Eating Disorder Examination Questionnaire (EDE-Q), and the Child Trauma Questionnaire (CTQ). The included sociodemographic and clinical data were: age, sex, tobacco consumption, current height, current weight, and highest and lowest weight since reaching the current weight. The MINI is a structured evaluation of psychiatric disorders according to the DSM-5. The interview is carried out by a mental health professional and is based on multiple branching owcharts that lead to a speci c diagnosis if several criteria are met. The aim of the MINI interview was to assess the presence of a current depressive episode in patients with ED. The EDE-Q is a 28-item self-report questionnaire used to evaluate ED symptoms over a 28-day period. It is scored based on a total score, and across four subscales that explore the four core clinical dimensions of ED: restraint, eating concern, body shape concern, weight concern  [33].
Protection des Personnes Sud-Ouest et Outre-Mer 3" under reference 2010-A00282-37, MS10 and the French National Agency for Medicines and Health Product Safety under reference 2017051900102. For inclusion in the Cohort of Patients Infected by an Arbovirus (CARBO-ZikaSmell ancillary study, NCT01099852), informed consent was obtained for all patients and controls. All animal experiments were performed after approval of protocol from the Pasteur Institute Ethics Committee (dap190107) and authorized by the French Ministry of Research (APAFIS 19469), in compliance with French and European regulations.
de Protection des Personnes Sud-Ouest et Outre-Mer 3" under reference 2010-A00282-37, MS10 and the French National Agency for Medicines and Health Product Safety under reference 2017051900102. For inclusion in the Cohort of Patients Infected by an Arbovirus (CARBO-ZikaSmell ancillary study, NCT01099852), informed consent was obtained for all patients and controls. All animal experiments were performed after approval of protocol from the Pasteur Institute Ethics Committee (dap190107) and authorized by the French Ministry of Research (APAFIS 19469), in compliance with French and European regulations.
Background: Transcranial direct current stimulation (tDCS) has emerged as a promising and feasible method to improve motor performance in healthy and clinical populations. However, the potential of tDCS to enhance sport-specific motor performance in athletes remains elusive. Objective: We aimed at analyzing the acute effects of a single anodal tDCS session on sport-specific motor performance changes in athletes compared to sham. Methods: A systematic review and meta-analysis was conducted in the electronic databases PubMed, Web of Science, and SPORTDiscus. The meta-analysis was performed using an inverse variance method and a random-effects model. Additionally, two subgroup analyses were conducted (1) depending on the stimulated brain areas (primary motor cortex (M1), temporal cortex (TC), prefrontal cortex (PFC), cerebellum (CB)), and (2) studies clustered in subgroups according to different sports performance domains (endurance, strength, visuomotor skill).
Data extraction Two review authors (TM, RK) independently extracted the following data items from the included studies: 1. Methods: study design (crossover/parallel RCT). Disagreements were resolved by reaching a consensus or by involving a third person (PR). If data were not reported within a manuscript, the authors of the original papers were contacted or values were extracted using Webplot Digitizer version 4. 4 (https:// apps. automeris. io/wpd/).
Risk of bias assessment Risk of bias assessment for randomized trials was performed by two review authors (TM, RK) independently according to the criteria contained in the Cochrane guidelines  [38] : (1) random sequence generation (selection bias) (2) allocation concealment (selection bias), (3) blinding of participants and personnel (performance bias), (4) blinding of outcome assessment (detection bias),  (5)  incomplete outcome data (attrition bias), (6) selective reporting (reporting bias), and (7) "other bias. " For every included study, each of these items was classified as "low risk of bias" ("þ"), "high risk of bias" ("-"), or "unclear risk of bias" ("?"). For this purpose, the software Review Manager 5. 4. 1 (Cochrane Collaboration, Oxford, UK) was used. Any disagreements in ratings of risk of bias were handled by a conversation between the two evaluators and consultation with a third person (PR).
Quantitative analysis The meta-analysis was performed using Review Manager 5. 4. 1 (Cochrane Collaboration, Oxford, UK). The intervention effects of tDCS on sport-specific motor performance changes were calculated within each study using the standardized mean difference (SMD) of the continuous data at a 95% confidence interval (95%CI). Therefore, the mean difference and standard deviation in performance between anodal tDCS and sham were calculated in a sport-specific motor task closely related to competition in the sports discipline (e. g. , cycling e 20 min time trial on a bicycle ergometer). In the case of multiple motor tasks performed within one study, the motor task that best represents competition performance in the respective athlete population was selected (for selected sport-specific tasks, please see Table  1 ).
Results: A total of 6,922 subjects with CSF biomarkers data were included (mean (SD) age: 70. 6 (8. 5)   years, 51. 0% women). In the ADNI study population (n=497), the agreement between classification based on our algorithm and one based on amyloid/tau PET imaging was high with Cohen's kappa coefficient between 0. 87 and 0. 99. Applying the algorithm to 10 large cohorts of patients (n=6,425), the proportion of persons with AD ranged from 25. 9% to 43. 5%.
Assessment of CSF biomarkers CSF concentrations of Aβ42, Aβ40, total Tau, and p-Tau 181 were measured with commercially available immunoassays, using the manufacturer's procedures. Four different methods were used: 1. The Elecsys immunoassays using the cobas e601 analyzer (Roche Diagnostics GmbH). 2. The INNOTEST immunoassays (Fujirebio Europe, Gent, Belgium). 3. The Lumipulse G 1200 (Fujirebio Europe, Gent, Belgium). 4. The Euroimmun analyzer I-2P (Euroimmun AG, Luebeck, Germany). Some centers (Paris, Montpellier, Lille) contributed 2 patient-cohorts as they used 2 different methods over time for the dosage of biomarkers. CSF samples in the ADNI study were analyzed using Elecsys immunoassays. We decided not to include older CSF ADNI data from the Luminex platform due to the long delay, approximately 5 years, between the CSF and tau PET measures.
Amyloid and tau PET imaging (ADNI) We used data from the ADNI study on participants with data on CSF biomarkers and at least one PET imaging of beta-amyloid or tau radiotracer; further information on acquisition of PET data in ADNI is provided on the ADNI website. 29 Amyloid PET imaging was performed using florbetapir (AV-45) radioligand,  30  we used the following data: UCBERKELEYAV45_05_12_20-2. csv. Positivity for florbetapir PET imaging was defined by a global standard uptake value ratio (SUVR) higher than 1. 11 using the whole cerebellum as reference region, this cut-off was defined as the upper 95% confidence interval above the mean in a group of young, cognitively-normal controls in cross-sectional analyses. 31 sitivity for tau PET was determined using flortaucipir (AV-1451) imaging,  32  and we used the following data: UCBERKELEYAV1451_05_12_20.
Statistical analysis The characteristics of participants were examined in each cohort; proportions were calculated for categorical variables, and mean and standard deviation for continuous variables. Figure  1  illustrates the overall design of the study. The first step consisted of validation of the proposed algorithm using data from the ADNI study by comparing CSF biomarker positivity determined using our proposed algorithm with that based on tau and amyloid PET imaging. Amyloid positivity in ADNI was defined using florbetapir amyloid PET imaging (cut-off for SUVR=1. 11), and then AUC for CSF Aβ42/40 ratio and CSF Aβ42 was used to discriminate between positive and negative cases. The optimal cut-offs for CSF Aβ42/40 and CSF Aβ42 were established as the lowest distance to the top left corner in the ROC curve.
Characteristics of the participants A total of 6,922 subjects from 11 cohorts with data on CSF biomarkers were included in this study; their characteristics are shown in the eTable 1 in the Supplement. The mean (SD) age of patients ranged from 62. 8 (7. 1) to 72. 7 (8. 0) years, the mean (SD) MMSE score was between 20. 0 (5. 7) and 27. 2 (2. 0) and the proportion of women was from 43. 3% to 56. 2%. The percentage of patients with dementia in the various cohorts ranged from 13. 3% to 54. 6%. Fujirebio Lumipulse was used in 4 cohorts, Fujirebio INNOTEST and Roche Elecsys in 3 cohorts, and Euroimmun in 1 cohort. The distribution of CSF biomarkers in all cohort is shown in eFigure 1.
The main strength of this study is elaboration of a pragmatic method to determine cutoffs for CSF biomarkers for AD so that it can be readily replicated in other centers. The validity of the algorithm was established by comparing findings with amyloid and tau PET imaging. There are also a number of limitations. One, by design the CSF biomarker assessment and PET imaging was not undertaken at the same time in ADNI and whether this affects determination of cut-offs is unclear. It is worth noting that few studies have longitudinal data and they show slow change in CSF AD biomarkers. 50 Two, we used PET biomarkers to validate the algorithm but tau and amyloid imaging positivity remains Copyright © 2022 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.
Introduction The positive correlation in performance across cognitive tests can be reduced to a single dimension: the general intelligence factor (g-factor), which reflects a person's general cognitive performance. Although several studies examined the genetic and neurological basis of intelligence separately, there are relatively few studies investigating how genetic, environmental, and neurological factors simultaneously influence intelligence due to the lack of sufficiently rich and large datasets (for review  Deary et al. , 2021). Thus, this paper aims to capitalize on the richness of the UK Biobank -a large-scale prospective study with neural, genetic, environmental, and behavioral data -and identify the neuroanatomical measures (e. g. , brain volumes) mediating the effect of genetic and environmental factors on intelligence.