dataesr/scientific-paragraphs-categorization huggingface dataset:
We then examined the broad class of cilium-related genes, bearing in mind that 2. 0% of the genes contain a U12-type intron in the human genome (748 U12 vs. 37,173 U2 genes). Since we observed 7. 6% (23 U12 genes vs. 279 U2 genes, Dataset S2) of U12 genes among the curated ciliary "Gold_Standard" genes (17), we concluded that there is an enrichment of U12 genes among them (hypergeometric test P value =1. 0e-8). By broadening this list through the compilation of several databases (1,426 genes in total, see Materials and Methods), we identified 86 U12 genes (86/1426, 6%) (Fig. 2B  and Dataset S2). Finally, among the 329 ciliopathy-related genes (18-20) (Dataset S2), 23 (~7%) are U12 genes (hypergeometric test P value = 5. 2e-8). Strikingly, nearly a third of them are associated with JBTS (ARMC9, CEP41, KATNIP, PDE6D, TCTN1, TCTN3, TMEM107, and TMEM231) (Fig.
3A  and Dataset S3). Most U12 introns (~96%) have a dPSI<10%, which suggests that fibroblasts are not the best-suited cell type to study minor spliceosome deficiency. The RNA-seq data indicate also that U12-type IR is not associated with drastic alterations of gene expression level (Dataset S3), as previously seen  (12). We further analyzed U12-type IR in a few ciliary genes: TMEM107, TMEM231, and TCTN1 that are JBTS-related genes with, respectively, high or low U12-type IR in TALS and P1 datasets; RABL2A that is a ciliary gene with a high dPSI in TALS dataset only; IFT80 that is a ciliopathy gene with a null dPSI in both datasets. Sashimi plots, RT-PCR and qRT-PCR analyses of U12type IR in these five genes showed for all of them a higher IR level in patients' cells than in controls, with a stronger effect seen in P1 compared to a TALS patient cell line (Fig.
We coinjected u4atac 5'SL MO with human U4atac carrying either the n. 16G>A, n. 51G>A, or n. 55G>A mutation. These mutations have been identified at the homozygous state in 4, 31, and 8 patients or fetuses, respectively  (9). They are associated with slightly different presentations (Dataset S4) and large differences in life expectancies: mean age at death is 10 mo for patients homozygous for n. 51G>A (three surviving patients, ≤ 2 y old), while 3/4 and 4/8 of those with n. 16G>A or n. 55G>A were still alive at the time of publication at, respectively, 6, 6, and 38, or 2. 5, 5. 5, 9, and 18 y of age. Stability of injected human U4atac snRNA was validated by Northern blot (SI Appendix, Fig. S4F ), and the abovementioned phenotypes were recorded. We observed that 16A, 51A, and 55A snRNAs had little capacity to rescue the phenotype, with a gradation between their effect, 55A U4atac coinjected embryos having a slightly milder phenotype than those coinjected with 16A and 51A U4atac (Fig.
For P5, a WGS was performed at the SeqOIA Lab (Plan France Médecine Génomique 2025, Paris, France) (see details in SI Appendix). The segregation of the variants identified in patient P5 was verified in her brother, patient P4, using Sanger sequencing as for patient P3. Bioinformatic Analyses. U12 genes were identified by running the U12db  (22)  annotation pipeline on the GRCh38 version of the human genome, with the gencode38 version of the annotations, or the GRCz11 version of the zebrafish genome. GO term analysis was performed with the TopGO (v2. 38. 1) R tool  (37) , with the default "weight01" algorithm, the Fisher-test and the org. Hs. eg. db (v3. 10. 0) R database of the genome-wide annotation for humans. Genes without any GO annotation were discarded. To constitute a list of cilium-related genes, we combined three existing databases and defined a gene as cilium-related if 1) it was part of the Gene_Ontology (GO = Cilium) of the Gold_Standard (SysCilia, a curated list of known ciliary components)  (17)  or of the Predicted candidates based on a bayesian integration in CiliaCarta  (38)  (last updated version of March, 18th 2018); 2) it was in the CilDB table v3.
After several washes with PBS, secondary antibodies (1:1,000, A32731, A32728, Invitrogen) were incubated for 1. 5 h, followed by DAPI for 10 min, prior to coverslip mounting using FluorPreserveTM Reagent (EMD Millipore, 3457870). Z-stack images were taken using a Zeiss LSM880 confocal microscope, and measurement of the cilium length was performed manually on images of maximum intensity projection of z-stacks, using ImageJ software. Zebrafish Husbandry and Microinjection of Embryos. Zebrafish (Danio rerio) adults and embryos were maintained at 28. 5 °C under standard protocols  (41). The following strains were used: the mixed wild-type ABxTU, Tg(wt1b:EGFP) li1  (42) , Tg(cmlc2:GFP), and Tg(bactin:arl13bGFP)hsc5Tg  (43)  to label proximal pronephros, heart, and cilia, respectively. MO, designed to target the 5′ Stem-Loop (5'SL) (5′-GATGTTCTCAGTTAACCTTCATTGA-3′) or the Stem II (SII) (5′-AAACCACCCCCAGACAAGGAA-GGTT-3′) regions of u4atac_chr11, were provided by GeneTools, LCC and into the yolk at the one-cell stage (quantity ranging from 0.
Z-stacks were performed to acquire the whole organs and quantification of cilium number, and range of motion was done manually and blinded on images of maximum intensity projection of z-stacks, using ImageJ software. Statistics. All the data are reported as the mean of at least three independent experiments with SEM. All hypothesis tests were two-sided, and statistically significant differences (P < 0. 05) were calculated by one-way ANOVA or t tests as indicated in figure legends. When the sample size was too small or when normality was not reached (following the Shapiro-Wilk test), a nonparametric test was used. Statistical analyses were performed using GraphPad Prism software. Study Approval. Written informed consent was obtained from parents for the genetic study and for the publication of clinical information.
The study on patient' cells was approved by the French national ethical committee Comité de Protection des Personnes (number 2021-A01551-40). Animal studies (zebrafish) were conducted in accordance with the European regulations on animal use. Data, Materials, and Software Availability. Raw RNAseq data: The consent form signed by the parents of the child whose RNA was sequenced does not include agreement to dataset deposition on public databases. Therefore, as stated in the manuscript, the raw sequencing data can be obtained upon request.
ACKNOWLEDGMENTS. We thank the families for their contribution to this project. We thank the  Centre de Biotechnologie Cellulaire Biotec biobank  for biosample management ( Emilie Chopin ,  Isabelle Rouvet ), the  Plateau de Recherche Expérimentale en Criblage In vivo aquatic core facility  ( Laure Bernard ,  Robert Renard ), the  Tefor facility , and the Gendev team members for stimulating discussions. This work was supported by  CNRS ,  Inserm ,  Université de Montpellier ,  Université Paris 7  and  Université Lyon  1 through recurrent funding; the  Fondation Maladies Rares  (" Small Animal Models and Rare Diseases" program , no. 20161207 ); the  Agence Nationale de la Recherche  (no. ANR-18CE12-0007-01 ); and the  Fondation pour la recherche sur le Cerveau  « Espoir en tête » (confocal microscope).
In nuclear astrophysics, several dedicated compilations (NACRE-I and II) and theoretical reaction rate databases (REACLIB  [2] , BRUSLIB  [3] , KADONIS  [4] , NUCASTRODATA. ORG  [5] ) have been made available to meet the needs of the stellar nucleosynthesis calculations. On the other hand, the evaluated nuclear data libraries maintained by national or international coordinated efforts (ENDF, JEFF, JENDL, CENDL) are to date, incomplete as far as charged-particle-induced reactions in the resolved resonance region are concerned. For example, (α,xn) evaluated cross-section data are provided in two evaluated libraries only, JENDL-AN  [6]  which was produced in 2005, and the TENDL libraries (version 2021)  [7]. Neutron-induced reactions on light elements in the resolved resonance region are also studied because of their relevance in nuclear criticality and safety studies.
Charged-particle-induced reactions The capabilities of existing R-matrix codes to perform charged-particle R-matrix analysis has been assessed by means of an inter-comparison of the R-matrix algorithms implemented in the codes  [8]. The following R-matrix codes have been used in these exercises: AMUR  [9] , AZURE  [10] , CONRAD  [11] , EDA (LANL), FRESCO  [12] , GECCCOS (TUW), RAC (Tsinghua), SAMMY  [13]. Furthermore, the Ferdinand code was developed to ensure translatability of the corresponding Rmatrix calculations. Two additional exercises have been performed, one on minimization techniques used in the different codes and the other one on the evaluation of the 7 Be system. The former evaluation includes the two incident channels 3 He+ 4 He and p+ 6 Li and excitation energies up to 20 MeV.
Acknowledgements This work is performed under the auspices of the  International Atomic Energy Agency  within the  International Nuclear Data Evaluation Network for Light Elements (INDEN -LE). The work of  I. J. Thompson  was performed under the auspices of the  U. S. Department of Energy  by  Lawrence Livermore National Laboratory  under Contract  DE-AC52-07NA27344. The work of  G. Hale  and M. Paris was supported by the  U. S. Department of Energy  through the  Los Alamos National Laboratory. Los Alamos National Laboratory  is operated by  Triad National Security, LLC , for the  National Nuclear Security Administration of U. S. Department of Energy  (Contract No. 89233218CNA000001 ). [ LA-UR-21-29650 ] This research utilized resources from the  Notre Dame Center for Research Computing  and was funded by the  National Science Foundation  through Grant No.
Despite this, the results from CLARITY showed that short-course treatment with cladribine tablets significantly reduced relapse rates, the risk of disability progression, and improved magnetic resonance imaging (MRI) outcomes. 5 In turn, CLARITY Extension provided further evidence of the sustained efficacy of cladribine tablets. 6 ubsequent analysis of CLARITY Extension has indicated the sustained benefits of cladribine tablets in terms of no evidence of disease activity (NEDA-3), and for up to 6 years from the baseline of CLARITY. 8 e CLASSIC-MS study (NCT03961204) was designed to further explore the long-term efficacy and durability of the effect of cladribine tablets beyond the two annual treatment courses in patients enrolled in the parent trials of the Phase III development program (CLARITY, CLARITY Extension, and ORACLE MS [ORAl CLadribine in Early Multiple Sclerosis]).
To be eligible for inclusion in the current analysis, patients must have received ⩾1 course of cladribine tablets or placebo during the parent studies and must have been able to provide informed consent at the time of enrollment. During the first study visit of CLASSIC-MS (hereafter referred to as "Study Visit 1"), retrospective data on Expanded Disability Status Scale (EDSS) score,  9  use of ambulatory device(s), relapses, and subsequent use of DMTs were collected along with employment status. For the purposes of analysis, "actively employed" included people who were "employed for wages," "self-employed," or considered themselves a "homemaker" at the time of Study Visit 1. The primary objective of CLASSIC-MS was to evaluate long-term mobility by determining the proportion of patients not using a wheelchair in the 3 months prior to Study Visit 1 and not bedridden at any time since LPSD, as determined by a level of functioning consistent with an EDSS score <7.
Study limitations Due to the exploratory nature of the CLASSIC-MS study, no formal sample size calculations were conducted. The study planned to enroll 788 patients, yet a final population of 662 patients was actually included. Feasibility assessments were conducted, and there were various reasons why some of the original parent study sites were not included in CLASSIC-MS, including the absence of the former/a new site investigator, a limited number/no patients at a site, and no retrospective data on file. Although it is unknown what happened to patients who did not enroll to the CLASSIC-MS study, baseline disease characteristics of patients who did enroll were considered to be generally representative of patients from the parent studies and therefore partially addresses the potential selection bias (Supplemental Table  1 ).
The population of CLASSIC-MS is also considered representative of the general MS population due to similarities with the recently reported mean age of MS diagnosis (32 years) and the higher proportion of female patients living with MS. 19  The MRI data collected during the CLASSIC-MS study were limited, and therefore, it was not possible to calculate responder rates for definitions based on imaging findings. Similarly, employment status at parent study baseline was not collected, thus limiting the interpretation of employmentrelated results. An important consideration, in terms of contextualizing the study findings, is that we do not know why more patients appeared to have disease reactivation than had another DMT (and the reason for switching), while the subsequent DMTs used by patients after the completion of the parent studies were reflective of those available in the intervening follow-up period (2010-2021).
Acknowledgements The authors thank patients and their families, investigators, co-investigators, and study teams at each of  Teva, TG Therapeutics , Excemed,  MSIF , and  NMSS. K. R. has received honoraria for lectures and steering committee meetings from  Acorda ,  Biogen ,  EMD Serono Research & Development Institute, Inc. ,  Billerica, MA, USA , an affiliate of  Merck KGaA ,  Novartis ,  Roche ,  Sanofi , and  Teva. D. S. has received consulting fees from  Acorda ,  Biogen ,  EMD Serono Research & Development Institute, Inc. ,  Billerica, MA, USA , an affiliate of  Merck KGaA , and  Teva , and speaker fees from  Acorda ,  Biogen ,  Elan ,  EMD Serono Research & Development Institute, Inc. ,  Billerica, MA, USA , an affiliate of  Merck KGaA , and  Teva. B. Y. has received honoraria for lectures and advisory boards from  Bayer ,  Biogen ,  Genpharm ,  Merck ,  Novartis , and  Sanofi , and has received research grants from  Bayer ,  Biogen ,  Merck ,  Novartis , and  Pfizer.
Thus, we distinguished between patients with the so-called mild depression, with an HDRS score between 8 and 15, and those with major depression, with an HDRS score ≥ 16. Finally, their inclusion in the study required that they completed a course of rTMS treatment (low frequency, with right dorsolateral prefrontal cortex stimulation) comprising five sessions per week for three weeks, along with complete data on the relevant psychometric scales. The only contraindications were those classically associated with rTMS treatment: the presence of a pacemaker, a cardiac or cerebral stimulator, or metal splinters in the head; brain injury; active comitiality; pregnancy; and intracranial hypertension. Participation in another biomedical research study was also not allowed. The clinical evaluations and corresponding data have been collected since 2007 in the patients' files.
Here we explore the latest four years (2019-2022) of using satellite data to objectively analyze tropical cyclones (TC) and issue recommendations for improved analysis. We first discuss new methods of direct retrieval from SAR and geostationary imagers. Next, we survey some of the most prominent new techniques in AI and discuss their major capabilities (especially accuracy in nonlinear TC behavior, characterization of model uncertainty and creation of synthetic satellite imagery) and limitations (especially lack of transparency and limited amount of training data). We also identify concerns with biases and unlabeled uncertainties in the Best Track records as being a first-order limitation for further progress in objective methods. The article concludes with recommendations to improve future objective methods, especially in the area of more accurate and reliable training data sets.
Introduction Objective satellite methods are essential to help forecasters characterize tropical cyclones in terms of position, intensity and structure from a steadily increasing number of satellite observations and issue reliable warnings. In the past four years, sensors with higher spatiotemporal resolution have been made more widely available. The use of AI techniques for processing TC satellite imagery has been explored and led to some operational tools. Section 2 describes major sensors and conventional methods that improve TC analyses, notably in the innercore. Section 3 specifically focuses on the development of AI methods for TC analysis and short-term forecasting, discussing their characteristics, the challenges that arise with them and the opportunities for emerging application. Section 4 highlights a drift in TC characteristics archived in the historical Best Track dataset due to evolving observing systems, which is a major concern for the development of accurate objective satellite methods.
2. Fix extraction: this type of analysis focuses on extracting fixes related to a tropical cyclone, such as its center position, maximum sustained wind (MSW), mean sea-level pressure (MSLP), radius of maximum winds (RMW), and wind radii at different speeds (34-, 50-, and 64-kt) for each quadrant. These fixes are then archived in the Best Track dataset, providing a global view of the TC at the surface level. 3. TC analyses/reanalyses with NWP/data assimilation: this type of analysis goes beyond TC-specific tasks and involves data assimilation and numerical weather prediction (NWP). Data assimilation aims to combine the latest observations with a short-range forecast to obtain the best possible estimate of the current state of the atmosphere. It provides a comprehensive, gridded description of model variables at multiple vertical levels within the TC and its large-scale environment.
, 2021). The National Environmental Satellite Data and Information Service (NESDIS) produces fix data from the 3-km SAR wind speeds that are now accessible to operational forecast centers. The fix values (MSW, RMW, R34, R50, & R64) are determined from the 95th percentile found in azimuthal/quadrant averages  (Jackson et al. , 2021, Fig. 1). These are impacting operations positively, along with SMAP/SMOS and AMSR-2, providing a good 2-D estimate of the surface winds at times and intensities  (Howell et al. , 2022)  These offer a limited but very detailed view of the TC wind field used to influence the working and final best tracks  (Knaff et al. , 2021) , and are being used for research studies(e. g. Combot et al. , 2020).
AI specific characteristics Certainly, the most active area of development in TC analysis over this last period has been the proliferation of techniques using AI to improve on existing objective methods. The highly data science-driven nature of this line of research has enabled approaches with often greater capability, but this comes from methods that may lie entirely outside the traditional skill set of forecasters and other meteorologists. Several of the most promising aspects of AI include: • The ability to resolve non-linear relationships between atmospheric variables and the TC system, • The ability to mine complex spatial and temporal structures in TC datasets, • The ability to easily combine wide varieties of data comprehensively (imagery, NWP, scalar observations, vector fields), • The ability to easily characterize model uncertainty with probabilistic output for binary yes/no predictions, and uncertainty spreads for numerical output, and • Modularity, such that one successful deep learning model can be expanded for new applications.
Advancements The last several years has seen the publication of many AI applications for the TC center fixing (e. g. ,  Smith and Toumi 2021) , TC intensity and size estimation (e. g. ,  Wimmers et al. , 2019 -DeepMicroNet; Zhuo and Tan, 2021 -DeepTCNet; Olander et al. , 2021 -AiDT) , and TC track and intensity forecasting (e. g. ,  Su et al. , 2020; Xu et al. , 2021) , to name a few. For TC intensity though, this topic is already quite advanced and approaching the limit of precision. This is obviously due to the availability of a labeled dataset in the form of the Best Track  (Chu et al. , 2002; Landsea et al. , 2015). Recent AI model estimates of TC intensity have reached 7-10 kt RMS error, though all share the highest uncertainty in the Category 5 range of intensities. This is due to the natural imbalance of data with TC intensity, which highlights the difficulty in using AI tools to model any comparatively rare event in TC evolution.
The great challenge posed by AI in the near future is to bring the methods of the most successful models to a level of transparency that they allow the forecaster to actively engage with them. The other significant challenge is in dealing with small and unbalanced training datasets. As stated in Section 3. 2, AIbased TC intensity models show a major in estimating TC intensity in the Category 5 range because of the relatively low case number. A similar challenge is to be expected from other rare TC structures such as small but intense storms. More generally, detailed and high standard labeled datasets data are paramount for research on valuable scientific or user-oriented matters and beneficial for the quality of objective models. Some progress, however, has been made on labeled datasets and TC-centric microwave imagery and homogeneous large scale diagnostics  (Razin et al.
As one of the closest and brightest CTTSs, TW Hya has been repeatedly observed because it is a remarkable object, a cornerstone for studies of accretion, and a common target of radial velocity searches for young exoplanets. We compile and analyze 1169 high-resolution optical spectra from CFHT/ ESPaDOnS, MPG-ESO 2. 2 m/FEROS, Magellan/MIKE, La Silla 3. 6 m/HARPS, VLT/UVES, VLT/ESPRESSO, Keck/ HIRES, McDonald 2. 7 m/2coude, and CTIO 4 m/Cassegrain Echelle to conduct the largest analysis of veiling for a single star. The veiling measurements are then converted to accretion luminosity, guided by 26 flux-calibrated spectra, most obtained at low resolution. The paper is organized as follows: Section 2 describes the properties of TW Hya; Section 3 introduces the archival data and data reduction process; Section 4 describes the veiling decomposition technique and how veiling is converted into accretion rate; Section 5 describes our use of low-resolution spectra to convert veiling to accretion rate; Section 6 compares veiling measurements to emission line diagnostics of accretion; and finally Section 7 discusses the accretion variability and searches for timescales.
The individual orders were backed out from the 1D spectra and then recombined using the hrs_merge IDL routine, with final spectra that are oversampled at ∼0. 01 Å (a factor of a few smaller than the actual pixel scale for ESPaDOnS). Most MIKE spectra were obtained and published by  Dupree et al. (2012)  and  Dupree et al. (2014) , with detailed descriptions of the reductions and calibrations. Most HARPS, UVES, and FEROS spectra were automatically reduced and then downloaded from the ESO archive. 44  Of the FEROS spectra, 54 spectra were reduced and published by  Alencar & Batalha (2002)  and  Batalha et al. (2002). Most Keck/HIRES spectra were obtained from the Keck Observatory Archive, with automated reductions using the MAKEE 45  pipeline. The Keck spectra obtained on 2008 January 23 and 2008 May 23 were reduced using a custom-written code in IDL.
Balmer Continuum Spectra Accretion rates are most accurately measured from fluxcalibrated spectra that cover the Balmer jump at ∼3646 Å (see review by  Hartmann et al. 2016). Our Balmer continuum measurements of TW Hya are listed in Table  1  (see also Table  6 ). The STIS data were obtained from the archive in a fully reduced and flux-calibrated format. The X-Shooter data were reduced following procedures described in  Alcalá et al. (2014). The DBSP, LRIS, and SNIFS data were reduced with custom-build routines in IDL, following  Herczeg & Hillenbrand (2014)  and  Guo et al. (2018). The ground-based spectra have fluxes calibrated to ∼10% with a contemporaneous (within ∼1 hr) spectrum of the spectrophotometric standard LTT 3864, obtained at similar airmass.