dataesr/scientific-paragraphs-categorization huggingface dataset:
Therefore, a trend toward lower mortality and better prognosis in the treatment groups should be taken with a lot of caution. Last, our findings were obtained in a seriously ill population and may not be generalized in less severe patients and sooner after the onset of the illness. While our analysis was unpowered to demonstrate any beneficial or harmful effects of treatments on the prognosis of critically ill patients with SARS-CoV-2-related pneumonia, our findings may be useful in the conjunction of others in the perspective of individual metaanalysis to better investigate the potential interest of such drugs. Very recently, preliminary unpublished data from the RECOVERY trial (NCT 04381936) reported no significant difference in the primary endpoint of mortality (25. 7% hydroxychloroquine vs.
Acknowledgments The authors would like to thank participants of the  Fourth Annual Conference of the Japan Economy Network held at the Bank of Japan in August 2019  and the ADBI workshop on ' Green Infrastructure Development in Asia: Investment, Financing and Economic Impacts ' held in November 2019 for valuable feedback. Hugues Chenet acknowledges the support of the Chair Energy and Prosperity, under the aegis of the  Fondation du Risque. Kim Schumacher  acknowledges the support of the  ESRC  through its  IAA Innovation Fellowship scheme (Grant Nr. 1709-NPIF-348 ). The usual disclaimer applies.
Statistical Analysis Statistical analysis was performed using the SPSS Statistics 20 software. Variables were presented as mean, standard deviation, median, minimum, and maximum. The normality was tested by the Kolmogorov-Smirnov test, while the homogeneity of variance was assessed by Levene's test. The independent t-test and one-way analysis of variance were used to examine the differences in quantitative variables. The level of statistical significance was adopted at p < 0. 05.
We therefore aim to analyse the geno-phenotype profile in a well characterized pediatric ADPKD cohort. Methods: Clinical, familial, biological and imaging data were collected longitudinally in children diagnosed with ADPKD. Genotypic analysis was done using a custom Agilent SureSelect gene panel containing 136 ciliopathy-associated genes, including PKD1 and PKD2. Mutations and/or variants identified were individually evaluated for pathogenicity. Results: 58 ADPKD children from 44 families were diagnosed at a mean (AE SD) age of 4. 3 (AE5. 0) years. ADPKD diagnosis was made in 33 children (57%) because of asymptomatic screening as requested by the family; 7 (12%) due to presenting symptoms (6 due to urinary tract infection and 1 due to post-traumatic macroscopic hematuria); 9 (15. 5%) due to a coincidental finding of renal cysts on US performed for another reason and in 9 cases (15.
SAT-445 ASSESSMENT OF MICROALBUMINURIA AND ITS CLINICAL AND BIOCHEMICAL CORRELATES IN INDIVIDUALS WITH SICKLE CELL GENE The aim of this study was to determine the prevalence of MA in sickle cell disease and trait and to also determine the clinical and biochemical correlates of MA in individuals with the sickle cell gene. Methods: This cross-sectional study involved a total of 300 individuals with sickle cell disease, sickle cell trait and haemoglobin AA as controls diagnosed using haemoglobin electrophoresis. A structured pro-forma was administered and detailed physical examination performed. Data was analysed on a personal computer using Statistical Package for Social Sciences (SPSS) software version 20. 0. Normally distributed numeric variables were summarised using their mean and standard deviation (MeanAE SD).
Clinico-laboratory parameters were assessed, including presenting complaints, presence of extra-renal features, family history of ADPKD, serum chemistry and haematologic parameters. Data was analyzed using SPSS statistical software version 21. Results: A total of 94 patients fulfilled the diagnostic criteria and there was an equal sex ratio of 1:1 and mean age at diagnosis was 42. 78 (AE 14. 87) years. Age of diagnosis was slightly higher in females though this was not significant. (44. 19AE14. 54 vs. 41. 38 AE 15. 21 years). Median (range) follow up period for all patients was 16 (0. 25-196) months. Majority of the patients presented with hypertension (76; 80. 9%), loin pain was seen in 66 (70. 2%) patients and nocturia in 51(54. 3%). The commonest extra renal feature was liver cysts present in 31.
Multivariate data processing Mixomics package (6. 8. 2 version in RStudio software, Boston, MA, 1. 0. 44 version) was used to build first a principal component analysis based on the compilation of all data present in the study; secondly, a partial leastsquares discriminant analysis (PLS-DA) was built to depict immune signature associated with BPs treatment. PLS-DA is a multivariate supervised approach that operates by projecting the samples (X) onto a lowdimensional space of so-called latent variables that maximizes the separation between different groups of samples according to their class labels (Y = mice BPs treatments). Repeated Mfold cross-validations were used to select the optimal number of latent variables for PLS-DA models with minimal error rate.
Statistical analysis Statistical analysis was performed using GraphPad Prism version 6. 00 (GraphPad Software, San Diego, California, USA). Results were expressed as means +/-SEM. Kuskal-Wallis one-way ANOVA followed by Dunn's post hoc test for multiple comparisons were used for statistical analysis. P-values < 0. 05 were considered significant (indicated by asterisks in figures): *p < 0. 05; **p < 0. 01; ***p < 0. 001; ****p < 0. 0001.
Mesopelagic resources are central to the ecosystem but remain poorly studied mainly due to the lack of observations. This paper investigates the assemblages of micronekton organisms and their habitat in the Natural Park of the Coral Sea around New Caledonia (southwest Pacific) using data from 141 pelagic trawls. A total of 67,130 micronekton individuals (fish, crustaceans, and mollusks) were collected with 252 species identified among 152 genus and 76 families. In the analyses, we focused on 22 species; each were present in more than 33 trawls (i. e. , in more than 25% of the total number of trawls) and studied their spatial distribution and vertical dynamic behavior. Community structure was investigated through region of common profile (RCP), an innovative statistical multivariate method allowing the study of both species assemblages and environmental conditions' influence on species occurrence probability.
, 2013; Gardes et al. , 2014). Additional information on micronekton assemblages and diversity will contribute to designing the Natural Park management plan, accounting for the conservation of the food stock of all top predators. In this context, the large diversity of predators and micronekton makes the New Caledonian EEZ a good case study to understand the pelagic ecosystem functioning and to implement a management tool. The present study focuses especially on micronekton assemblage diversity, one of the most poorly understood links in pelagic ecosystems  (St. John et al. , 2016; Hidalgo and Browman, 2019). Using data from 141 mesopelagic hauls conducted in the New Caledonian EEZ in 2011-2016, we applied region of common profile (RCP) methodology to quantitatively characterize the micronektonic assemblages, to identify the environmental conditions influencing those assemblages, and to determine their spatial distribution.
The 1 doi: 10. 18142/243 sampling was conducted as much as possible to balance the day and night and the depth according to the ship's arrival time at the station and avoiding dawn and dusk when micronekton migrates. At each station one, two, or three trawl hauls were conducted within 4 h at different depths. Depth sampled was selected according to an echosounder signal targeting the layers where the acoustic signal was the strongest. Given all these limitations, the data sampling remains rather well balanced (Figure  1B  and Supplementary Table  S2 ). Acoustic data were recorded continuously during cruises using an EK60 echosounder (SIMRAD Kongsberg Maritime AS, Horten, Norway) connected to four split-beam transducers at 38, 70, 120, and 200 kHz. Micronekton organisms were sampled at each station with a mid-water trawl with a 10-mm mesh.
Environmental Variables Environmental variables were selected to explore the sampling conditions of micronekton assemblages (Table  1 ). For each haul, environmental data were extracted at the date and position of the sample. Sun inclination was calculated as a function of spatial position and date  (Michalsky, 1988; Blanc and Wald, 2012) , and hauls were categorized into "Day" and "Night" periods (negative values corresponding to Night and positive values to Day). Bathymetry data was extracted from the ZoNéCo database at a 500 m spatial resolution (ZoNéCo, 2013), 2 and the slope of the bottom was calculated as the spatial derivate of bottom depth. The depth of the 20 • C isotherm (referred as "isotherm depth" hereafter) were extracted from the Armor3D data set  (Guinehut et al. , 2012)  available at a weekly time scale.
The higher this index, the higher the diversity of one RCP. Trawl hauls were different in terms of duration (from 16 to 56 min). Moreover, the total number of sampled individuals strongly varied among trawls (from 1 to 1544). To take into account these two factors, we added into the model the total number of individuals divided by the volume filtered as a sampling factor  (Foster et al. , 2017). We used the Bayesian information criteria (BIC)  (Raftery, 1995; Hui et al. , 2015)  and our personal knowledge of the region based on acoustics data analyses  (Receveur et al. , 2019 (Receveur et al. , , 2020) )  to choose the appropriate number of RCPs.
Model Validation As described in the previous paragraph, we calculated species occurrence probability based on a set of environmental variables. To validate these predicted probabilities, we did a fourfold crossvalidation procedure  (Browne and Cudeck, 1989). The model was first fitted on a training data set (75% of randomly selected hauls) and then tested on a validation data set (the remaining 25% of hauls) four times. The area under the curve (AUC) was then calculated by species (a species was "present" with a predicted occurrence probability higher than 0. 5). AUC indicates the probability that the model predicts a presence when a presence is observed (called a true positive). It gives a measure of the model robustness to predict the presence of the considered species: the higher the AUC, the better the model prediction.
The two other hauls were conducted on unusual acoustic detections and targeted monospecific schools of a new species of the genus Polyipnus. This new species is currently under description. Three additional hauls were removed because environmental variables were not available at the sampling location. Therefore, the final data set analyzed was composed of the abundance of 22 species in 123 trawls. As described in Section "Model parameterization, " the statistical model included only one factorial parameter: the moment of the day. The sampling of the two levels of factor day/night was balanced as each level was sampled more than 50 times (65 hauls during the day and 58 at night; Supplementary Table  S2 ). The statistical model included sampling depth as a second variable inherent to haul. Sampled depth ranged between 10 and 600 m, done during both day and night even if daily hauls in the mesopelagic layer (i.
The present study participated in improving the understanding of how sensitive all micronekton species are to oceanographic variables (physical and biogeochemical), information needed to fully evaluate the impact that climate change could have on top predators' food  (Choy et al. , 2016). Eleven species (A. aculeatus, A. sladeni, C. scabra, H. globulosus, L. reinhardti, O. gracilirostris, P. sedentaria, P. semilunata, P. giardi, P. microlampas, and T. tricuspidata) have been observed in predators' stomach contents in the western and central Pacific Ocean database of the Pacific Community 3   (Sanchez et al. , 2018 ) (e. g. , Coryphaena hippurus, Kajikia audax, Katsuwonus pelamis, Lampris guttatus, Sphyraena barracuda, Thunnus albacares, Thunnus obesus, Xiphias gladius). Lanternfish species (or Myctophidae) are also a non-negligible part of predators' diets  (Brodeur et al.
It is possible that biases in the algorithm or the article selection process may have biased our results in some way. For example, certain types of misleading or inaccurate headlines may be underrepresented. Alternatively, it is possible that Facebook misled us and purposefully provided a set of articles that were artificially easy to classify (in an effort to cast their crowdsourcing efforts in a positive light). While we cannot rule out this possibility, we did replicate our results by analyzing a previously published dataset of researcher-selected headlines  (25)  and found that the crowd performed substantially better than for the articles provided by Facebook (see section S16), suggesting that the article set from Facebook was at least more difficult to classify than article sets often used in academic research.
Introduction: Data about the genotypes of circulating Mycobacterium tuberculosis isolates (MTB) in Lebanon are scarce. This study was undertaken to reveal the spoligotypes of MTB isolates recovered from patients in Lebanon. Methodology: MTB isolates from 49 patients living in Lebanon were recovered and identified. The samples were heat killed and subjected to DNA extraction. Spoligotyping was performed using microbeads from TB-SPOL Kit and the fluorescence intensity was measured using Luminex 200®. Generated patterns were assigned to families using the SITVIT2 international database of the Pasteur Institute of Guadeloupe and compared. Results: The spoligotyping of the 49 MTB isolates revealed that 31 isolates belonged to Lineage 4 (Euro-American, 63. 3%), 12 to Lineage 3 (East-African Indian, 24.
In this latter, the synthetic spacer oligonucleotide probes are immobilized on microspheres by means of covalent coupling. The detection is then achieved via fluorochromes attached to the beads and to the hybridized PCR product. The Luminex® platform provides greater robustness and reproducibility since it eliminates the membrane steps with its subjective visual data interpretation, replaced by mathematical cut-offs  [11, 12]. International databases, such as the World Spoligotyping Database, SpolDB4. 0 and SITVIT2, have revealed the clonal structure of MTB isolates in different geographical settings  [13, 14]. The SITVIT2 updated database includes classification for spoligotypes and description of the genetic families of MTB for 111,635 clinical isolates from 169 countries of patient origin (131 countries of isolation, representing 1032 cities); these isolates contain more than 7,100 patterns of spoligotyping that are grouped into 3882 SIT (Shared International Type) codes  [14].
Negative control contained no DNA, and positive control contained either M. bovis DNA or MTB strain H37Rv DNA provided within the kit. Only 5 µL of each biotinylated PCR-amplified DNA were applied to freshly prepared microbeads working mix in 96-well flat-bottom plate (Corning Incorporated, NY, USA) according to the multiplexed direct hybridization protocol provided in the supplier work guide (Beamedex®, Orsay, France). Fluorescence produced from Streptavidin-Phycoerythrin binding in samples and control wells is then measured, according to the presence or absence of each of the 43 groups of beads on the flow cytometry-based Luminex 200® system (Bio-Plex, Bio-Rad, Hercules, USA). Median Fluorescence Intensity (MFI) values were obtained via Bio-Plex Manager Software 6. 1 version. Raw csv files were converted with Excel spreadsheet files into.
Definition of lineage and strains genotyping For identification of genetic families and lineages, the 43-digit binary spoligotyping codes (n/o) were individually entered into the SITVIT2 database of Pasteur Institute of Guadeloupe, and compared with existing spoligotyping-based taxonomical standards  [14]. Codes that do not provide lineage information are referred to as 'orphan' when unique and 'new' whereas codes in cluster were referred as 'NEW'. Based on the regions of difference (RD) and WGS classification systems using SNPs and large sequence polymorphisms (LSP) and correlation to spoligotyping signatures, the seven major global MTB complex lineages are defined; L1 is Indo-Oceanic/named East-african Indian or EAI in spoligotyping-based nomenclature), L2 is East-Asian (and includes Beijing sublineages), L3 is East-African-Indian/also named CAS or Central Asian in spoligotyping-based nomenclature, L4 is the Euro-American, historically designated as "T" with at least 10 sublineages, L5 is M.
different national origins in SITVIT2 database (Afghanistan n = 8, China n = 10, UK n = 1, India n = 6, Iran n = 42, Iraq n = 12, Italy n = 1, Kirghizstan n = 4, Lebanon n = 1, Oman n = 1, Pakistan n = 4, Romania n = 1, and Saudi Arabia n = 7) (http://www. pasteurguadeloupe. fr:8081/SITVIT2/index. jsp).
Acknowledgements This study was made possible through the  CNRS grant  from the  Lebanese National Council for scientific Research (CNRS  grant  award N° 102913 ) to  Pr G. F. Araj  and  Pr. G. M. Matar. Dr. C. Sola  is grateful to  Luminex Corp® ,  USA  for technical support. All authors declare no conflict of interest except for  C. Sola  and  G. Refrégier  that were founders of the Beamedex® company and shareholders at the time of the study.
Study population and historical controls MSA patients from Campus Neurológico Sénior were identified from a movement disorders imaging database and selected if a 3 T MRI with a devoted movement disorders predefined protocol  [6, 7]  was performed. Clinical characteristics were assessed by two movement disorders specialists (RMS, ACC): disease duration since onset of first symptom and since diagnosis, presenting symptom, presence of cerebellar signs, Hoehn and Yahr stage [HY], levodopa equivalent daily dose  [LEDD]. Only patients with parkinsonism and fulfilling second consensus criteria for possible or probable MSA  [1]  were included. PD patients with 2 to 5 years of disease duration (PD2_5y), and healthy controls (HC), who were included in previous studies, were selected to match disease duration in our study population  [7, 11, 21, 22].
difficile genomes (14 ribotypes). RT-specific genetic polymorphisms were annotated and validated for their specificity and sensitivity against a larger dataset of 2425 C. difficile genomes covering 132 different RTs. In silico PCR ribotyping was unsuccessful due to non-specific or missing theoretical RT PCR fragments. More successfully, DBGWAS discovered a total of 47 new markers (13 in RT017, 12 in RT078, 9 in RT106, 7 in RT027, and 6 in RT001) with minimum q-values of 0 to 7. 40 × 10 -5 , indicating excellent marker selectivity. The specificity and sensitivity of individual markers ranged between 0. 92 and 1. 0 but increased to 1 by combining two markers, hence providing undisputed RT identification based on a single genome sequence. Markers were scattered throughout the C. difficile genome in intra-and intergenic regions.
In Silico PCR-Based Ribotyping We performed in silico PCR using canonical ribotyping PCR primers. Based on the reference sequences 16S-USA and 23S-USA (Table  1 ), in silico PCR was performed using the subsequence search tool in BioNumerics v7. 6 software (Applied Maths NV, Sint Martens-Latem, Belgium). Besides 7 genomes obtained from Creighton University, 23 C. difficile genomes of five selected RTs were downloaded from NCBI to verify in silico amplification of the ISR region (Supplementary Table  S1 ).
DBGWAS-Mediated Discovery New RT-Specific Markers A total number of 160 C. difficile genome assemblies (training set) of 14 different RTs including hyper-virulent RT001, RT017, RT027, RT078, and RT106 were used for the discovery of unique RT genomic markers (Table  2 ). This small training set allowed for the development of discriminatory markers to characterize the five major RTs among the 14 different RTs. Genomes were collected from the National Center for Biotechnology and Information (NCBI; www. ncbi. nlm. nih. gov), Creighton University, and the Enterobase databases (https://enterobase. warwick. ac. uk). Metadata of these genomes are summarized in Supplementary Table  S2. To identify associations between variant genetic loci and PCR RT, a hypothesis-free DBGWAS method was used. DBGWAS defines genetic variants linked to phenotypic traits via single nucleotide polymorphism (SNP), insertions, deletions, and consequences of recombination  [41, 42].
We used an open source tool (https://gitlab. com/leoisl/dbgwas) [40]. The tool is able to cover variants in coding as well as non-coding regions of bacterial genomes. DBGWAS was performed keeping the tool parameters in the default setting for different C. difficile ribotypes (RT001, RT017, RT027, RT078, and RT106) and their RT-specific genetic variants observed in the training set. Each C. difficile RT was considered independently in this study. DBGWAS identified short signature sequences called (overlapping) k-mers, yielding a compact summary of all variations across a set of genomes  [40]. Overlapping k-mers are called unitigs and were selected on the basis of their specific and unique presence in a particular RT. Q-values define test sensitivity and specificity and are Benjamini-Hochberg-transformed p-values for controlling the false-positive results in case of multiple testing  [40, 43].
Validation of Markers Validation of novel unitig markers was performed by means of BLAST searches against the test set of genomes (Table  3 ). A wide range of 2425 genomes covering 132 different C. difficile RTs was downloaded  [44]  and processed using a Linux shell script. These sequences represented PCR ribotyped strains from different countries and clinical and environmental specimens for which phylogenetic analyses were already performed by Frentrup et al. [44]  (Supplementary Table  S3 ). A database of this test set was created to perform local command line BLAST searches against the set of significant unitigs identified above. The specificity of all the unitigs was tested using strict parametric filters of 100% coverage and identity. RT001 206 RT046 3 RT127 1 RT375 1 RT002 53 RT049 9 RT129 1 RT404 15 RT003 11 RT050 4 RT137 1 RT413 13 RT005 14 RT051 1 RT138 1 RT446 2 RT006 1 RT053 5 RT149 1 RT449 2 RT009 2 RT054 2 RT150 1 RT451 1 RT010 7 RT056 5 RT153 1 RT453 1 RT011 3 RT058 1 RT156 1 RT454 1 RT012 45 RT060 1 RT157 1 RT456 1 RT013 1 RT062 2 RT158 1 RT470 1 RT014 113 RT063 1 RT176 13 RT500 21 RT015 36 RT066 3 RT193 1 RT534 1 RT017 272 RT067 1 RT194 1 RT547 1 RT018 55 RT069 1 RT212 1 RT559 1 RT019 1 RT070 4 RT220 4 RT563 1 RT020 44 RT072 1 RT225 1 RT569 1 RT022 1 RT073 2 RT226 1 RT581 1 RT023 16 RT075 1 RT236 3 RT585 1 RT024 1 RT076 2 RT238 1 RT586 1 RT026 6 RT077 1 RT239 2 RT591 1 RT027 652 RT078 492 RT241 5 RT598 8 RT029 3 RT081 2 RT244 9 RT614 1 RT031 2 RT083 1 RT251 1 RT620 2 RT032 1 RT084 2 RT262 1 RT629 1 RT033 5 RT087 8 RT284 1 RT651 1 RT035 2 RT090 1 RT289 1 RT666 1 RT036 1 RT094 1 RT290 1 RT668 1 RT037 1 RT102 1 RT305 1 RT678 1 RT039 5 RT103 2 RT316 1 RT708 1 RT042 2 RT106 55 RT321 1 RT719 1 RT043 2 RT117 2 RT328 2 RT720 1 RT044 2 RT125 1 RT336 1 RT721 1 RT045 2 RT126 79 RT356 8 RT722 1.