dataesr/scientific-paragraphs-categorization huggingface dataset:
As a result, each identified latent class captured individual patterns of changes of HRQoL and disease activity and the dynamics of their temporal codependencies. With GBTM, no prior defined classes are presumed, and therefore, heterogeneity in a population that is not attributed to any known factor can be uncovered. Models with increasing numbers of classes were run (from 1 up to 7) to determine the number of latent classes (class-enumeration) with SAS procedure PROC TRAJ. 28 We resorted to the Fit-Criteria Assessment Plot (FCAP) R-code to assist the process of class-enumeration. 29 FCAPs are graphical displays providing eight goodness-of-fit and model-adequacy criteria (Bayesian Information Criterion, Akaike's Information Criterion, likelihood of assignment, average posterior probability of assignment, mismatch between estimated and assigned group probabilities, SD of group membership probabilities, odds of correct classification, proportion of individuals estimated to be assigned to the smallest group).
Loss to follow-up, that is, non-random attrition occurred. To test for differential drop-out, we computed for all classes the proportion of individuals with two or more missing values in the final and immediate preceding time points. Their frequencies were then compared. Analyses were performed using SAS V. 9. 4, SPSS V. 21 and R V. 3. 2. 0. The significance level was set at 0. 05.
Sometimes, individual patients missed measurement points. At time point 0, data from 411 patients were available, after 2 years from 363 patients, after 4 years from 290 patients, after 6 years from 238 patients, and after 8 years from 158 patients. Identifying latent HRQol-disease activity trajectory groups Baseline characteristics of the overall patient population and separately for each cohort are provided in table 1. Patients included in OASIS were characterised by older age, longer symptom duration and higher proportion of (bridging) syndesmophytes in comparison to the GLAS population. Due to the inclusion criteria of GLAS, these patients were characterised by higher CRP, BASDAI and proportion prescribed TNFα-inhibitors. According to model-adequacy criteria, the five-class solution provided the best fit to the data (online supplementary figure  1  and online supplementary table  1 ).
Construction of phylogenetic trees Nucleotide sequences were aligned using the MEGA7 software (Molecular Evolutionary Genetics Analysis version 7. 0. 18 [19] ), with the ClustalW program. In order to build phylogenetic trees, the sequences of each locus obtained in this study were aligned with A. phagocytophilum sequences from cow, horse, dog, and roe deer hosts from Chastagner et al. [9]  (GenBank: KJ832158-KJ833031) (Additional file 1: Table  S1 ). Moreover, sequences of American human, dog, rodent, and tick A. phagocytophilum strains (HZ, Webster, HGE1, Dog2, JM and CRT), and a Norwegian sheep (Ovis aries) strain (Norway_variant2), were added to the alignments  [9]. Phylogenetic trees were built after concatenation of three to six loci. Concatenated sequences were imported and neighbor joining trees (NJ trees) were constructed from the alignment using BioNumerics version 7.
Ambiguities were only identified at particular polymorphic sites. In those samples with double peaks, the majority occurred at either typA or msp4 loci, and five samples had ambiguous sites at both loci (Tables  5, 6 ). We excluded all samples with sequences presenting at least one ambiguous site from subsequent analyses, to avoid incongruence between loci. Nineteen samples (four German samples from four cows, and 15 French samples from 11 cows) generated complete profiles for the six markers, without any ambiguities (Table  6 ). The sequences obtained in this study are available in the GenBank database under the accession numbers MF580591-MF580636.
Discussion Our results reveal the co-existence of two major groups of bovine A. phagocytophilum strains among all cattle samples analyzed in this study. These groups did not associate with geographical origin, as cattle from the study by Chastagner et al. [9]  originated from several French regions and clustered into either group. Moreover, these two groups remained stable over time according to MLST profiles, as identical sequences were obtained 31 months apart in the French herd. Although the bovine strains of these two groups are clearly distinct in NJ trees, the variant diversity within them remains high, as has already been described  [20]. The variability of A. phagocytophilum strains within defined sheep flocks was already mentioned  [10, [21] [22] [23]. Even so, there is no molecular typing data from any longitudinal study of A.
Acknowledgements The authors thank  Juliette Bavouzet ,  Perrine Lequitte-Charransol ,  Christelle Gandouin , and  Corinne Bouillin  for their technical support. We also thank  Rémi Nantois  and  Brigitte Macé , the French cattle owners and the family of the owner of the German cattle herd for their great cooperation and for allowing sampling of their cattle. The work of MP and CS was performed under the umbrella of the EurNegVec  COST Action   TD1301.
Flow cytometry Flow cytometry data were acquired with a LSRFortessa flow cytometer (Becton Dickinson) and analyzed with FlowJo software (Tree Star). Dead cells were eliminated by exclusion with propidium iodide. Cells were stained intracellularly after permeabilization and fixation with True Nuclear Transcription Factor Buffer Set (BioLegend). Cells were purified with a FACSAria III (Becton Dickinson) and recovered in tubes or in 96-well quantitative PCR (qPCR) plates for gene expression analysis. antibodies All antibodies were from BD Biosciences, eBioscience, BioLegend, Cell Signaling Technology, or R&D Systems. Antibodies were biotinylated or conjugated to fluorochromes (fluorescein isothiocyanate, phycoerythrin, PECy5, PerCPCy5. 5, PECy7, allophycocyanin, Alexa Fluor 647, APCCy7, Pacific Blue, BV421, eFluor450, V500, BV605, BV655, BV700, and BV786) and were specific for the following mouse antigens: Ly76 (TER119), Gr-1 (RB6-8C5), CD3e (145-2C11), CD19 (6D5), NK1.
Bioinformatic analyses For visualization, the dimensionality of the datasets was further reduced using the "Barnes-hut" approximate version of t-SNE. This was implemented using the Rtsne function from the Rtsne R package using 800 iterations and a perplexity setting that varied from 10 to 30 depending on the size of the dataset. PhenoGraph takes as input a matrix of N single-cell measurements and partitions them into subpopulations by clustering a graph that represents their phenotypic similarity. PhenoGraph builds this graph in two steps. First, it finds the k nearest neighbors for each cell (using Euclidean distance), resulting in N sets of k-neighborhoods. Second, it operates on these sets to build a weighted graph such that the weight between nodes scales with the number of neighbors they share.
The Louvain community detection method is then used to find a partition of the graph that maximizes modularity. Given a dataset of N d-dimensional vectors, M distinct classes, and a vector providing the class labels for the first L samples, the PhenoGraph classifier assigns labels to the remaining N_L unlabeled vectors. First, a graph is constructed as described above. The classification problem then corresponds to the probability that a random walk originating at unlabeled node x will first reach a labeled node from each of the M classes. This defines an M-dimensional probability distribution for each node x that records its affinity for each class.
Introduction Rabies is a zoonotic disease still present in Europe; the red fox (Vulpesvulpes) is the virus's main reservoir and vector  [1]. Epidemiological data have confirmed the presence of rabies in wildlife since 1977 (except on the Croatian islands)  [2] ; thus, it presents a major veterinary and public health threat. Between 1977 and 2010, a total of 108,190 domestic and wild animals were sent to the National Reference Laboratory for Rabies at the Croatian Veterinary Institute for rabies testing. Of these, 16,723 (15. 5%) showed positive rabies findings (unpublished). Foxes were the most commonly tested of all animals (60. 9%). Of 65, 887 tested foxes, 23. 6% had positive rabies findings  [2]. The last human rabies case was recorded in 1964  [3, 4]. The fact that no further human rabies cases have been recorded is mainly attributed to the forceful implementation of prophylactic measures, such as quarantine, registration, and mandatory vaccination of dogs; capture and culling of stray dogs and cats; preventive vaccination of individuals in high-risk occupational groups; strict application of post-exposure prophylaxis; educational campaigns; and close cooperation between veterinary and public health institutions.
Randomly selected samples from rabies-positive animals between 2008 and 2010 have already been tested  [16]. This study reports sequencing data on 31 randomly selected positive cases from surveillance detected between 2011 and 2014. Thirty-one further positive samples were selected for phylogenetic analysis as a part of monitoring from 2011 and 2012 to differentiate animal rabies cases due to vaccine-associated infections from cases due to field strains and to assess similarities with strains in other countries. Phylogenetic analysis. For the extraction of RNA and RT-PCR, 10% (w/v) brain material suspensions were prepared using Dulbecco's Modified Eagles Medium. RNA was automatically extracted from the supernatant of centrifuged suspensions using the iPrep Pure Link Virus kit and iPrep Instrument (Invitrogen) according to the manufacturer's instructions.
For partial sequencing, a one-step RT-PCR was performed with 5 μl of RNA and 2 pmol of panlyssavirus primer JW12 (5'-ATGTAACACCYCTACAATG-3') and JW6DPL (5'-CAATTC GCACACATTTTGTG-3') as described  [15]  using Superscript III with Platinum Taq polymerase (Invitrogen, Carlsbad, USA). Amplified products (606 bp) were visualised using agarose gel electrophoresis and subsequently purified using Exosap (USB, Staufen, Germany). Purified PCR products were sequenced in both directions by Macrogen Inc. (Seoul, Korea). The nucleotide sequences generated in this study were subsequently submitted to GenBank and assigned the following accession numbers: KX929097-KX929159. The sequences obtained were assembled and edited using MEGA version 6  [17]. A 367 bp part (nucleotides 75-441 of the challenge virus standard reference strain; GenBank accession no.
D42112) was used for further analysis. A phylogenetic tree of classic RABV nucleoprotein sequences was constructed using the Kimura2-parameter neighbor joining method with MEGA version 6 and rooted with the RABV sequence present in the Lysvulpen vaccine. A phylogenetic tree was established among 63 Croatian RABV N sequences (2013-2014), two previously published Croatian sequences with GenBank accession numbers GU134624 and JF683628, and nine representative sequences from GenBank. Enhanced ORV monitoring. The objective of monitoring is to assess the effectiveness of the vaccination campaigns by determining the bait uptake and seroconversion rates in the target animals sampled in vaccinated areas  [9]. To obtain a sufficient number of samples, authorised hunter associations and official veterinary stations were offered a financial incentive for hunted animals in the field (through a budget provided by competent national authorities).
Bait uptake Between 2011 and 2017, 14,223 samples were tested for oxytetracycline (Table  2 ). The age determination data for 2015 and 2016 are not shown because the age was not determined from January to March 2015 and from June to December 2016. The annual number of oxytetracycline-positive foxes over the 2011-2016 period increased from 24. 86% to 84. 70% (Table  2 ); that over the 2011-2014 period ranged from 18. 87% to 86. 47% in the foxes older than 1 year and from 29% to 74. 20% in the foxes younger than 1 year (Table  2 ). The differences in the bait uptake between the adult (>1 year of age) and juvenile (<1 year of age) foxes were significant in 2011, 2012, and 2013 (p<0. 01). In 2014, the bait uptake between the adult and juvenile foxes was not significantly different (p = 0. 2026).
Hayes et al. discuss the physics and theory of DTI  [50] , while also noting that difficulty in data interpretation must be overcome. They suggest that DTI should be the procedure of choice for war/combat veterans suffering from mTBI/concussion or head trauma. Hayes et al. and Militana [51]  approach axonal injury from a 'connectivity disruption' perspective to make the mTBI/concussed brain injury more visible. The science and physics described by Hayes is based on the orientation of water molecules along normal, injured or inflamed axonal tracts. DTI could be used in separating the symptoms of PTS(D) from the overlapping symptoms of mTBI as noted above, and enhance therapy for both once the true cause of symptoms is established by serial DTI studies  [50]. Militana et al. [51]  also reported the use of fMRI (functional MRI) to measure increases in cerebrovascular activity within one (1) week after a college athletic concussion.
Acknowledgments We thank the patients and their families for participating in this study. We thank  P. Rameau  for flow cell sorting and flow cytometry analysis (PFIC,  Gustave Roussy, Villejuif, France ),  G. Meurice  for transcriptome analysis (UMS AMMICA,  INSERM US23/CNRS UMS S3665 ,  Gustave Roussy, Villejuif, France ),  Gabriel Correa  ( Instituto Lanari, University of Buenos Aires, Argentina ) for coagulation studies,  Mirta Schattner  ( IMEX-CONICET, Buenos Aires, Argentina ) for help with the flow chamber assay and  Daniela Ayala  ( UE IDIM-CONICET ) for help with Western blot experiments.
Funding This study was supported by a  French grant  from the  Ligue National Contre le Cancer  (LNCC, équipe labellisée to HR, 2013 and 2016), the  European grant ERA-NET  (to  C. Balduini , 2013), the  Argentinian grant  from the  National Agency for Scientific and Technological Research  (to PH, 2012), a grant from the  Fondation Nelia et Amadeo Barletta  (to PH, 2017) and the cooperation program between France and  Argentina, Ecos-Sud-Ministerio de Ciencia, Tecnología e Innovación Productiva (MINCyT)  (to HR and PH, 2016). DS was supported by a postdoctoral fellowship from  LNCC. The microarray was funded by the apprenticeship tax from  Gustave Roussy, Villejuif, France.
Data Collection Participants were invited to answer a detailed questionnaire adapted to the type of graft and designed to collect the following information: Toxoplasma seroprevalence in the country (documented by articles or recent surveys); implementation of a case reporting system for toxoplasmosis in transplant recipients; annual number of transplant procedures for each organ type in the participating center and in the whole country; pretransplant serologic screening policy for recipients and donors; implementation of recipient monitoring after transplantation and methods used (PCR, serology); and chemoprophylaxis regimen and duration according to organ type (if cotrimoxazole was given primarily for preventing Pneumocystis pneumonia, this use was recorded) and according to the recipient serologic results (primary or secondary prophylaxis, whether chemoprophylaxis was given to seronegative recipients, seropositive recipients, or both).
From each center and for each organ type, we also collected the mean patient age and the mean percentage of the whole transplant patient population surviving at 2 months and at 6 months. The number of cases and clinical data were retrieved from hospital medical or laboratory databases or from local or national databases, if existing. Participants were invited to send only aggregated data generated automatically by the database. The study was approved by the Ethics Committee of the University Hospital of Rennes, France (approval no. 15. 12).
Statistical Analyses Descriptive statistics are expressed as frequency (percentage) or mean ± SE. Comparison of qualitative data between groups was based on exact χ 2 tests for equal proportions or Fisher exact tests if single table values were <5; quantitative data were compared by using analysis of variance or t-test (nonparametric test). We computed data by using SAS software version 9. 4 (SAS Institute, Cary, NC, USA).
Participating Centers, Transplantation Activity, and Case Notification Overall, 46 centers from 11 countries (1-10 centers/country) participated in the survey; countries represented were France, Germany, Greece, Italy, Romania, Serbia, Slovakia, Spain, Switzerland, Turkey, and the United Kingdom (online Technical Appendix, https://wwwnc. cdc. gov/EID/ article/24/8/18-0045-Techapp1. pdf). Responses indicated that 5 countries (Switzerland, Slovakia, Turkey, Greece and the United Kingdom) report toxoplasmosis cases in a national database. During 2010-2014, the mean annual number (range) of allo-HSCT procedures reported per country was 1,016 (13-1,900) and of auto-HSCT was 1,524 (14-3,078) (online Technical Appendix). Regarding SOT recipients, the mean annual number (range) of transplantations was 155 (10-420) for heart, 1,286 (55-3,074) for kidney, and 622 (35-1,241) for liver.
Indeed, overall survival rates were better among patients who received cotrimoxazole than among those who received no treatment; but when considering HSCT and SOT patients separately, survival rates remained significantly better for SOT patients only. This finding raises the question of the effectiveness of prophylaxis, in terms of regimen and duration. This study has several limitations. First, we used aggregated data, so individual analyses or modifications of the analysis plan were not possible after data collection. Therefore, individual data such as immunosuppressive regimen, graft versus host disease, or simultaneous infections were not recorded, and multivariate analyses to further explore mortality rates were not possible. The number of participating centers per country varied, and for some countries (particularly Germany and Turkey), these centers accounted for a small proportion of the transplantation activity in the whole country (online Technical Appendix); thus, we cannot be sure that the data collected were representative for the whole country.
Mycobacteria cultures and cell infection Methods used to generate the PGL-expressing rBCGs used in this study and experimental validation that they grow comparably and express equivalent amounts of heterologous PGLs were reported previously  (2, 8). Bacteria were grown at 37°C in suspension in Middlebrook 7H9 broth (#M0178) supplemented with ADC (#M0553) and 40 µg/ml kanamycin (#K0254), all from Sigma. Mycobacterial suspensions destined to infect BMDMs were pelleted at (3,200 × g) for 7 min, washed twice with phosphatebuffered saline (PBS), suspended in 5 ml of PBS before dissociation in M-tubes using the gentleMACS Dissociator (Miltenyi Biotec), then diluted in RPMI to the appropriate concentration. Before infection, BMDMs were washed twice with warm RPMI, followed by a 2 h infection in RPMI.
Detection of pSrc (MW 60 kDa), MyD88 (MW 33 kDa), TRIF (MW 98 kDa), and GAPDH (MW 37 kDa) was performed in a single Western blot assay using multiple antibodies. Before using this technique, we verified that our antibodies were specific (data not shown). When only TRIF and GAPDH were analyzed, blots were sliced horizontally after transfer, then stained separately in order to capture images at optimal exposure times. Protein complexes were revealed with the ECL Prime detection reagent (GE Healthcare) and chemiluminescence reading on a Fuji LAS-4000 Luminescent Image Analyzer. IFN-β and TNF-α concentrations in BMDM culture supernatants were measured by ELISA (Biolegend, #439407 and #430901), following the manufacturer's protocol.
rna extraction and real-time Quantitative rT-Pcr Qiagen RNeasy Mini Kit (#74104) was used to extract total RNA from BMDMs. cDNA was amplified from 1 µg of total RNA using the high-capacity cDNA reverse transcription kit with added RNAse inhibitor (#4374966, Applied Biosystems). Relative mRNA levels were quantified by qRT-PCR using power SYBR green and with gene-specific primers (Table  1 ). Amplification conditions and dissociation step were as follows: 50°C for 2 min, 95°C for 10 min followed by 40 cycles (95°C for 15 s and 60°C for 1 min). ABI 7300 Sequence Detection System (Applied Biosystems) was used for data acquisition. Fold increase values were calculated for each gene transcript using the 2 -ΔΔCt method, using RPL19 as a house-keeping gene.
FUnDing This study was supported by the " Marie Skłodowska-Curie Actions " of the European Union's  Seventh Framework Programme   FP7/2007-2013 ,  REA  grant agreement no. 317057 ; the  French National Research Agency  ( ANR-11-BSV3-001 );  Institut Pasteur  and  Institut National de la Santé et de la Recherche Médicale (INSERM).
Study Population and Data Collection We performed a multicenter retrospective study in 7 patients with proven cblC deficiency and available kidney biopsy. The cases were selected in 6 different centers in France and Belgium. The diagnosis of cblC deficiency was made by complementation studies or genetic testing. The data collected included clinical (age, hypertension, edema, PAH, neurologic symptoms, and thromboembolic events), biological (hemoglobin, platelets, schizocytes, lactate dehydrogenase [LDH], haptoglobin, plasma creatinine, estimated glomerular filtration rate (eGFR), proteinuria, and complement system), and biochemical (vitamin B 12 , total homocysteinemia, MMA, and methioninemia) characteristics at initial presentation. The management and the outcome of each patient were also recorded.
The cblC cases were compared with controls with TMA of cblC-independent origin. The controls were selected in 2 different centers (Rouen University Hospital, France, and Necker Hospital, Paris, France). We included all of the patients aged 4 to 28 years who presented between 1999 and 2015 with available kidney biopsy findings revealing renal TMA. Patients with TMA lesions associated with IgA nephropathy or lupus nephritis were excluded. Data on age, proteinuria, eGFR, and cause of TMA were collected for each control. The eGFR was calculated based on the Modification of Diet in Renal Disease (MDRD) formula for adults and the Schwartz formula for children and adolescents. All of the research procedures were approved by the local ethics committee of Rouen, France (E2015-36).
ACKNOWLEDGMENTS The authors thank the clinicians ( Elisabeth Cassuto ,  Yannick Le Meur ,  Laetitia Albano ,  Hélène Leray Moragues ,  Vincent Pernin ,  Françoise Broux ,  Férielle Louillet ) and pathologists ( Isabelle Brochériou ,  Hélène Perrochia ,  Laurent Doucet ,  François Comoz ,  Céline Le Naoures-Mear ), who provided access to patients' data and kidney biopsies Q10. We thank  Soumeya Bekri ,  Metabolic Biochemistry Department, Rouen University Hospital , for her expertise in the biochemical characterization of patient 1. We express our gratitude to  Damien Genty  for his technical assistance in performing microphotography.
Patients and samples Patients were recruited in the context of the IFM/DFCI 2009 trial (#NCT01191060) and followed in the Hospital Lyon Sud. Patients under 65 years old with newly diagnosed symptomatic MM were randomized to receive, after frontline induction regimen with three cycles of bortezomib-lenalidomide-dexamethasone (VRD for Velcade/Revlimid/Dexamethasone), either SCT conditioned with high dose of Melphalan, followed by a two-cycle VRD consolidation, or five additional VRD cycles without high dose therapy. The two arms then received 1 year maintenance with single agent LEN. Patients' characteristics are summarized in Table  1  and results of the clinical trial were recently published  (19). The clinical trial protocol was initially approved by the institutional ethics committee at the coordinating center (Purpan Hospital, Toulouse, France).