dataesr/scientific-paragraphs-categorization huggingface dataset:
W I T H D R A W N a threshold calculated by the mean of negative probes plus two standard deviations. We discarded those genes below the defined threshold. Differences in sample input were corrected by selecting the optimal number and best reference candidates from the set of HK genes included in the panel. GeNorm algorithm  50  implemented in the R package CrtlGene 51 was used to test not only the most stable reference genes but also the optimal number to carry out the normalization step. We disregarded HK candidate genes with less than 50 raw counts in any of the sample comparisons.
After adjusting for sample volume, samples with an estimated bacterial load above the detection limit of 1. In the present manuscript, we found CD5L under-expressed in the granuloma compared with the healthy tissue, as well as lower CD5L plasma levels in patients requiring surgery compared to those who didn't. Consequently, CD5L was included both in the TB lesion 11-gene signature and in the 6-plasma protein TB signature described in the present manuscript. C. V is an unpaid board member of the following non-profit organizations: the FUITB foundation and the ACTMON foundation. Neither the ISCIII, the IGTP, the FUITB nor ACTMON have had any role in the conceptualization, design, data collection, analysis, decision to publish, or preparation of the manuscript.
ACKNOWLEDGEMENTS The authors would like to thank the patients who agreed to participate in the study and the staff from the  NCTLD  who helped with the SH-TBL project. The authors also thank the patients,  Arantxa Romero  and the medical staff ( Zoran Stojanovic ,  Adrián Antuori ,  Sílvia Roure ,  Antoni Noguera-Julian ,  Antoni Soriano-Arandes ,  Andrea Martín ,  Maria Espiau ,  Maria Teresa Tortola ,  Malú De Souza ,  Mª Ángeles Jiménez ,  Israel Molina ,  Xavier Casas ,  Núria López ,  Marisol Domínguez-Álvarez ,  Adrián Sánchez-Montalvá ,  Joan Pau Millet ) from the hospitals involved in STAGE-TB Project, who participated in the samples collection that was used as controls for the biomarkers assessment in plasma. We would also like to thank  Eric Garcia  for their technical support in acquiring the data.
FUNDING This work was supported by: 1) the  Plan Nacional  I + D + I co-financed by  ISCIII-Subdirección General de Evaluación and Fondo-EU de Desarrollo Regional (FEDER)  through  PI16/01511 ,  PI20/01424 ,  CP13/00174 ,  CPII18/00031  and  CB06/06/0031. 2 ) The European Union's  Horizon 2020 research and innovation program  under grant agreement No  847762. 3 ) The  Catalan Agency for Management of University and Research Grants (AGAUR)  through  2017SGR500  and  2017 FI_B_00797. 4 ) The " Spanish Society of Pneumology and Thoracic Surgery" (SEPAR)  ( 16/023 ). 5) The  Wellcome Trust , the  Medical Research Foundation  grants ( 206508/Z/17/Z  and  MRF-160-0008-ELP-KAFO-C0801 ) and the  NIHR Imperial College BRC  to M. K. 6). N. G. , registered in the EMJMD LIVE ( Erasmus+ Mundus Joint Master Degree Leading International Vaccinology Education ), co-funded by the  EACEA (Education, Audiovisual and Culture Executive Agency , award  2018-1484 ) of the European commission, receives a scholarship from the  EACEA.
surgical intervention. We provide evidence that some circulating biomarkers mirror what is happening in situ in the lung, which may help for the development of new diagnostic and prognostic tools, and treatment strategies. Moreover, this is the first study showing different pulmonary transcriptomic patterns associated with sputum culture conversion s e e m a n u s c r i p t D O I f o r d e t a i l s W I T H D R A W N status, enabling the stratification of patients at an early timepoint in the clinical management of TB disease (month 2 after starting treatment) as part of a patient cantered approach to TB treatment. s e e m a n u s c r i p t D O I f o r d e t a i l s W I T H D R A W N ONLINE METHODSEthicsThis paper is part of the SH-TBL project (ClinicalTrials. gov Identifier: NCT02715271).
The protocol and research methodology, as well as associated documents (informed consent sheet, informed consent form) were reviewed and approved by both ethics' committees at the NCTLD (IRB00007705 NCTLD Georgia #1, IORG0006411) and the Germans Trias i Pujol University Hospital (EC: PI-16-171). For the analysis of biomarkers in plasma, we used a pre-existing collection of samples from patients with TB from the STAGE-TB cohort (ClinicalTrials. gov Identifier: NCT03691883) approved by the ethics committees of the Germans Trias i Pujol University Hospital (CEI PI-17-064).
The file format was set following GSEA instructions for RNA-Seq projects. The gene sets database was established with the [Hallmarks] option and the chip platform as "Human ENSEMBL Gene ID MSigDB. v7. 0. chip" as a reference database for GSEA analysis. A Statistical significance for every enrichment score per gene set was given by s e e m a n u s c r i p t D O I f o r d e t a i l s W I T H D R A W N the nominal p-value, considering values <0. 05 as significant. False Discovery Rate (FDR) was set at 25%, reducing the probability that a gene set with a given NES becomes a falsepositive result. The rank metric score indicates the position of the gene within the gene set after a calculated score. The Running ES is the ES in the corresponding gene set at this point in the ranked list of genes.
Simulation The spontaneous emission and amplified spontaneous emission of the QDCLC stack in the perpendicular direction is simulated by an in-house developed software written in Matlab  24. The calculation is based on spontaneous emission from isotropic electrical dipole emitters with distribution according to the intrinsic emission spectrum, and on a matrix method for transmission and reflection on homogeneous anisotropic slabs. The spectral dependent gain in the QD layer is represented by a complex imaginary part in the refractive index, which is assumed to be proportional to the intrinsic emission spectrum. The parameters for the layers are given in Table  S1  (Supplementary).
Study Design and Participants We used data from Rapport au Sexe 2021, a large, cross-sectional online survey of MSM in France conducted between 26 February and 11 April 2021. Respondents who self-identified as homosexual or bisexual or have had sex with a man in their lifetime are considered MSM. The survey was anonymous, self-administered, and voluntary. Participants were recruited through different digital media. Banners were posted directly on gay dating websites, gay geolocation dating applications, gay affinity news sites, and social media networks (Facebook). They were also posted via programmatic platforms targeting men aged 18 years old and over and on browsing pages containing keywords related to homosexuality and male dating. By clicking on these banners, people were directed to the survey site, where information about its objectives was presented as well as the conditions of participation and data confidentiality.
Statistical Analysis We performed univariate analyses to describe respondents' characteristics. Median and interquartile range (IQR) were computed for continuous variables. Categorical variables were expressed as proportions. Chi-squared tests were used to compare categorical data. To identify factors associated with intention to vaccinate against COVID-19, multinomial logistic models were used. A backward procedure was employed to select statistically significant factors in the multivariate models (entry threshold, p < 0. 20). Only factors with a p < 0. 05 were kept in the final multivariate model. Statistical analyses were performed using Stata software version 15 (StataCorp, College Station, TX, USA).
Powder samples were also observed with an optical microscope (Olympus DSX510) and image analysis were performed using Fiji Is Just Image-J software  [12]  to determine the elongation. Because of the microscope resolution, only particles with a diameter greater than around 100 μm were considered. Each particle was fitted to an ellipse with the same area as the considered particle and the elongation was calculated as: Elongation ¼ 1- minor axis length of the fitted ellipse major axis length of the f itted ellipse ð2Þ It should be noted that surface roughness does not affect the elongation value. Image analysis was carried out for around 2000 particles per sample and a cumulative frequency (in number) was recorded.
Mechanical properties Mechanical properties of agglomerates were characterized by uniaxial compression tests, through a compression between two punches in a mechanical testing machine (Instron 3400). An agglomerate was placed on the lower fixed punch and it was crushed by the upper punch at a constant speed of 0. 8 mm/min. This experiment allowed to determine the force at breakage F and to estimate the stress to failure, using the following relation  [13] : σ r ¼ 0:7F πr 2 ð3Þ Thirty agglomerates were analysed for each powder sample. A probabilistic treatment of the data was carried out based on the Weibull theory  [14] , which allowed the determination of the failure probability of the sample P f by the formula: P f ¼ 1-exp σ r σ 0 m ð4Þ where σ r is the stress to failure, m is the Weibull modulus and σ 0 is the Weibull constant.
Detecting emergency events on social media could facilitate disaster monitoring by categorizing and prioritizing tweets in catastrophic situations to assist emergency service operators. However, the high noise levels in tweets, combined with the limited publicly available datasets have rendered the task difficult. In this paper, we propose an enhanced multitask Transformer-based model that highlights the importance of entities, event descriptions, and hashtags in tweets. This approach includes a Transformer encoder with several layers over the sequential token representation provided by a pre-trained language model that acts as a task adapter for detecting emergency events in noisy data. We conduct an evaluation on the Text.
TREC-IS For standardized evaluations of systems, TREC-IS provided participants with training and test datasets, comprised of three components: the ontology of highlevel information types, a collection of crisis-event descriptions, and the tweets for each event to be categorized. The participant TREC-IS systems are intended to produce two outputs for crisis-related social media content: 1. Classifying tweets by information type, where each tweet should be assigned as many categories as are appropriate; 2. Ranking tweets by their criticality (priority). TREC-IS provided multiple Twitter datasets collected from a range of past wildfires, earthquakes, floods, typhoons/hurricanes, bombings, and shooting events. The information types as either top-level intent, high-level or low-level.
EXPERIMENTS & RESULTS The TREC-IS dataset has a number of emergency events covering different types: earthquakes, tropical storms (e. g. , hurricanes), mass violence (e. g. , shootings, bombings), public health emergencies (e. g. , epidemics), etc. Each incident is accompanied by a brief topic statement that contains the event title (e. g. , 2015 Paris attacks), event type (e. g. , bombing), and a narrative or description of the event. The provided dataset consisted of a total of 73,499 tweets that covered 75 topics. We did not perform any pre-processing on the data. In our internal experimental setup, we produced a data split for simulating the official TREC-IS split that contains unknown event types in the test set  7. In order to ensure this, for the training set, we selected   the event types from 0 to 64 (60,577 tweets), and from 65 to 75 (12,923 tweets), for the test set 8.
Modeling and Structure Generation The architected structures were generated using the "Engineering_Lattice" module of the CAD software "PTC Creo 7. 0" (Parametric Technology Corporation, France), based on Voronoi diagrams. The first step is to create a basic pattern cell with circular struts (Figure  1a ), which is defined by its diagonal size and the diameter of the struts. Then, the study volume (10 × 10 × 10 mm 3 ) in which it will repeat to obtain the architected structure (Figure  1b ) is defined. To facilitate the installation of the samples during the manufacturing process as well as the eventual characterization of their mechanical behavior, which will not be discussed here, two plates were added on the top and bottom faces (Figure  1c ) to facilitate the fabrication and possible mechanical testing.
Apart from the layer height, the other printing parameters were fixed and cannot be modified by the slicing software. Thus, given the precision required for the architected structures, a layer height of 25 µm was chosen. Once the layer height has been chosen, the structures were placed in the virtual bed of the slicing software, "PreForm" (Formlabs, France), which is specific to the machine and enables the orientation of the samples and to generate the necessary supports to finally prepare the G-code file for printing. When importing the files into the slicing software, we checked that the structure and its dimensions are not affected in comparison with the CAD model. After printing, each sample is immersed into a tank filled with isopropyl alcohol (IPA) and shaken several times. This post-treatment removes all the non-polymerized residues that close the internal cavities.
When importing the files into the slicing software, we checked that the structure and its dimensions are not affected in comparison with the CAD model. The G-code thus obtained is sent to the machine that will print the part that is cleaned of the printing residues with a cutter afterwards. For this process, there is no additional specific post-processing. The Lisa Pro machine (Sinterit, Poland) was used for the SLS process, which is based on the powder bed sintering technique where a laser selectively sinters powder particles of a thermoplastic polymer to build a part layer by layer. Similar to the SLA process, the machine does not allow modification of the printing parameters, which are already set by the manufacturer, except for the layer height. According to the data sheet of the equipment, this machine can print layer heights from 75 µm to 150 µm and a minimum width of 0.
Moreover, since these observations were made from outside, we cannot distinguish the printing quality in the core of the samples where struts may not be printed or even material may be trapped. To support these hypotheses, we proposed first to make tomographic observations and then mass comparisons. To enhance the macroscopic observations, X-ray tomography observations were performed on the printed samples. The principle of this technique consists of making an X-ray beam pass through the sample at a specific position and recording the beam transmitted by a detector in the form of an image (Figure  4 ). Several 2D images are acquired at different rotation angles and the slices obtained are then used to reconstruct the three-dimensional image using dedicated algorithms  [22]. Using this technique and by post-processing the reconstructed volumes with the VGSTUDIO MAX software (Volume Graphics, Charlotte, NC, USA) from the VOLUME GRAPHICS products, one can make non-destructive analyses that give access to the various details of the internal structure: local dimensions, shape, local defects, porosities, etc.
Dimensional and Geometric Analysis The tomographic analyses also enabled measurements to be taken to evaluate the dimensional and geometrical accuracy of the printed structures. For the dimensional analysis, the volume of each reconstructed structure after the tomographic scan is compared to the CAD model, which is used as a reference, to evaluate the dimensional devi-ation of both the elements (struts, nodes and plates) and the structure. This comparison was performed using the "CloudCompare" software (Open source, France), which compares two volumes. The results obtained on three samples 05 obtained with the three processes are shown in Figure  6 , where the maximum and mean deviations are plotted. The value given on the bars corresponds to the standard deviation of the measured mean deviations for each configuration.
This confirms the previous observations and conclusions that the SLA process is the process with the best dimensional accuracy, followed by the FFF process. To complete this eccentricity indicator, measurements of the two diameters a and b were performed for each direction for the three processes using an algorithm under "Fi-Ji-ImageJ" software (Open Source, Germany). To consider only the struts and to avoid as much as possible including the measurements of the nodes contained in each slice, since the measurements were made automatically, a domain was defined in advance. This domain includes all sections with diameters between 0. 1 mm and 1 mm, representing struts with a diameter of about ±2 times the targeted diameter (0. 5 mm) and sections whose axis was not perpendicular to the projection slice.
Mass Deviations For each configuration considered in this study, the real mass of each sample was measured and then compared to its theoretical mass, calculated based on CAD model geometry. The real mass was measured after printing the samples using a digital scale with an accuracy of 1/1000 g. The theoretical mass was calculated by multiplying the volume of the CAD model by the real density of the material concerned. The latter was measured, using the printed filled structures, by the double weighing method based on Archimedes' principle. The choice to measure the real density of each material instead of considering the one given by the supplier's data sheet was made to consider the potential effect of the process on the material and/or the eventual possible deviations. The density measured for the polymerized resin used by the SLA process is 1.
The region of interest used by the optical system was 10 mm × 100 mm. DIC works on the principle of correlation whereby a series of digitally acquired images are successively taken of a deforming sample surface throughout the test. Before testing, specimen surfaces were sprayed with a fine black colored acrylic resin-based spray, creating stochastic black and white contrast patterns for the subsequent DIC procedure. Sets of digital gray scale pictures of the surface contrast were taken every second during testing, and They served as input to calculate the displacement field using ARAMIS software  [31].
Methods A systematic approach with some consideration to the "preferred reporting items for systematic reviews and metaanalyses (PRISMA) method was used. Specifically, predetermined stem keywords (and variants), and combinations thereof ("AND") were used to search databases on ISI Web of Science, Proquest, and Google Scholar. Search terms were: "cuttlefish"; "bycatch"; "conservation initiatives"; "conservation interventions"; "protection"; "sustainable"; "management"; "Sepia"; and "unaccounted fishing mortality". Papers were filtered for content beyond the main points above, and any additional specific examples were reviewed and, if relevant, included to support the identified conservation methods. Evidence was submitted from Europe, Africa, Asia, and Australia and organized into six broad categories of conservation methods (Table  1 ).
For example, several fishers have altered their onboard handling methods to decrease the destruction of cuttlefish eggs after hearing about this issue from the CCSP's public engagement programme and other organizations that are concerned with this issue (e. g. Devon & Severn IFCA, and SeaSearch-a community of recreational scuba divers trained to record habitat information and species records from their dives, along with environmental parameters, with data submitted to the Marine Conservation Society: www. seasearc h. org. uk). The CCSP has also brought together groups of people who have been saving, hatching, and returning cuttlefish eggs that washed up on shore. They have produced guides to aid local stakeholders in how best to hatch cuttlefish eggs with limited equipment and knowledge (e.
Discussion The main findings of our study are three-fold: (a) transcriptomic signatures of endstage DCM hearts, (b) gene expression (mRNA) changes post-LVAD use, and (c) gene regulation (miRNA) changes post-LVAD use (Figure  7 ). The majority of differentially expressed genes in this study were down-regulated, suggesting a general loss-of-function model of pathogenesis and only the most significantly enriched transcripts in our dataset were considered.
Discussion The main findings of our study are three-fold: (a) transcriptomic signatures of endstage DCM hearts, (b) gene expression (mRNA) changes post-LVAD use, and (c) gene regulation (miRNA) changes post-LVAD use (Figure  7 ). The majority of differentially expressed genes in this study were down-regulated, suggesting a general loss-of-function model of pathogenesis and only the most significantly enriched transcripts in our dataset were considered. Figure  7. Summary of the findings from this study illustrating the seminal impact of LVAD therapy on reverse remodelling in the left ventricle and right ventricle. Processes that were normalized are italicized in red, and an asterisk (*) indicates pathways where the concerned genes also had corresponding changes at the miRNA level. DCM, dilated cardiomyopathy; LVAD, left ventricular assist device.
Study Patients and Protocol The study protocol (Pro00011739) was reviewed and approved by the Health Research Ethics Board at the University of Alberta. The inclusion criteria were broad and included consecutive patients having heart transplantation at the Mazankowski Alberta Heart Institute and we were able to consent 99% of our patients. The only exclusion criterion was lack of written consent. All patients who participated in the study provided written informed consent in accordance with the Declaration of Helsinki. Clinical information for patients with DCM was collected via review of medical records from electronic databases maintained by Alberta Health Services based on the Human Explanted Heart Program (HELP) at the University of Alberta  [4, 54]. Available information on non-failing donor hearts was provided by the Human Organ Procurement and Exchange (HOPE) program in Northern Alberta.
Data Generation and Analysis Transcriptomic data, both mRNA and miRNA, were normalized and analysed using Transcriptome Analysis Console (Version 4. 0. 1) (Thermo Fisher). One-Way Between-Subject ANOVA was used to calculate p-values, and a p-value of less than 0. 05 was considered significant. Cut-off fold change (FC) for differentially expressed transcripts was set at 2 (≥2 for up regulation or ≤-2 for down-regulation). For analysis of transcript expression normalization after treatment with LVAD, only the p-value cut-off was applied in order to capture all effects of treatment on transcript expression. To identify significantly enriched functional pathways and gene ontology (GO) terms related to biological processes and molecular functions, differentially expressed genes were analysed using Enrichr (Available online: https://amp.
Statistical Analysis Parametric continuous variables were expressed as means with their respective standard deviations (SDs). Non-parametric continuous variables were expressed as medians with their respective interquartile ranges (IQRs). Categorical variables were expressed as the total number in each category and the corresponding percentage of the study group they represented. Data distribution was assessed by the Kolmogorov-Smirnov test, D'Agostino-Pearson omnibus normality test, and Shapiro-Wilk normality test. All statistical analyses were performed using SPSS Statistics version 25 (IBM, New York, NY, USA). ANOVA followed by post hoc Tukey's multiple comparison test, student's t-test, two-tailed Mann-Whitney test, and two-sided Fisher's exact test and were used for parametric continuous, non-parametric continuous, and categorical data, respectively.