dataesr/scientific-paragraphs-categorization huggingface dataset:
Conclusions We introduced FiLT3r, a time and memory efficient algorithm implemented in an opensource C++ software, which showed very good detection and quantification performances compared to state-of-the-art software. On our capture dataset, FiLT3r had a perfect recall, which was not the case of the other software. Even the reference fragment analysis method, exhibited two false negatives, as shown by further Sanger sequencing of the samples. Similarly to the other software, FiLT3r had a perfect precision. FiLT3r performances were better than that of FLT3-ITD-ext, the best software identified so far by an independent benchmark, which is alignment-based. Moreover FLT3-ITD-ext could not run on several RNA-seq dataset due to large resource requirements (both time and memory). In two cases on RNA-seq dataset, FLT3-ITD-ext reported quantification that appeared largely overestimated.
Background: Brain-derived neurotrophic factor (BDNF) plays an important role in brain development by regulating multiple pathways within the central nervous system. In the Human Biomonitoring for Europe Project (HBM4EU), this neurotrophin is being implemented as a novel effect biomarker to evaluate the potential threats of environmental chemicals on neurodevelopment. Objectives: To explore the relationships among exposure to environmental metals, BDNF biomarkers at two levels of biological complexity, and behavioral function in adolescent males. Methods: Data were gathered from 125 adolescents on: spot urine sample total concentrations of the neurotoxic metal(oid)s arsenic (As), cadmium (Cd), mercury (Hg), and lead (Pb); serum BDNF protein concentrations; and concurrent behavioral functioning according to the Child Behavior Check List (CBCL/6-18).
Covariates Data on sociodemographic characteristics and lifestyle factors were collected by administering ad hoc questionnaires to the participants and their parents/guardians. The weight, height, and body mass index (BMI) of participants were measured following standardized procedures, extensively detailed in  Castiello et al. (2020). Covariates used in the present study included data collected at the 15-to 17-year-old follow up visit on the characteristics of the adolescents: age (in months, continuous), area of residence (categorized as urban or sub-urban/rural), annual family income (<25000, 25000-35000, or >35000 €), and passive smoking (yes or no); on the characteristics of their mothers: age (in years, continuous), intelligence (verbal reasoning measured by the similarities subtest of WAIS-III at the 9-to 10-year-old follow-up), marital status (stable partner: yes or no), schooling (up to primary, secondary, or university), current employment status (employed or unemployed) and alcohol consumption (yes or no).
Funding and acknowledgements This research would not have been achieved without the selfless collaboration of the INMA-Granada adolescents and families who took part in the study. The authors also acknowledge the Human Genotyping Laboratory at the Spanish National Cancer Research Center, CeGen-PRB3, which is supported by grant no. PT17/0019, of the PE I+D+i 2013-2016, funded by the Instituto de Salud Carlos III (ISCIII) and ERDF. They thank the European Union's Horizon 2020 research and innovation program HBM4EU for financial support under Grant Agreement No. 733032. The study was also supported by the ISCIII with grant no. CP16/00085. The authors also acknowledge the funding received from the University of Granada for the open access publishing costs and the support of the Biomedical Research Networking Center-CIBER de Epidemiología y Salud Pública (CIBERESP), and the ISCIII (FIS 17/ 01526, FIS-PI16/01820 and FIS-PI16/01858).
Vicente Mustieles and Shereen Cynthia D'Cruz were under contract with the HBM4EU project. A. Rodríguez-Carrillo received a predoctoral fellowship (FPU 16/03011) from the Spanish Ministry of Education and C. Freire (grant no. MS16/ 00085) received a grant under the Miguel Servet Type I program of the ISCIII ''Fondo Europeo de Desarrollo Regional'' (ISCIII/FEDER). This article forms part of the doctoral thesis developed by Andrea Rodríguez-Carrillo in the context of the "Clinical Medicine and Public Health Program" of the University of Granada (Spain).
Saccharomyces cerevisiae Rotary cell culture system Modification of budding. [22]  Saccharomyces cerevisiae HARV Modification of budding and clusters formation. [23]  Aspergillus fumigatus ISS Increase in growth and virulence. [24]  ISS: International Space Station. HARV: high aspect ratio vessel. Due to its presence in space stations and its major pathogenicity in humans, we studied the effect of simulated microgravity on the physiological aspects of the Fusarium solani species complex. Indeed, it is essential to understand these effects to determine the potential risks to the health of crew members and to propose the necessary countermeasures. To our knowledge, no data are currently available for this pathogen. In a first descriptive approach, essential given the current lack of knowledge, we evaluated the physiological parameters of growth, germination, and ability to generate biofilms under RPM exposure.
Acknowledgments: We express our gratitude to  Lisiane Cunat  for her efficient technical support and the  Imaging and Cellular Biophysics Platform of the University of Lorraine  for confocal microscopy analyses. We also acknowledge the  French Space Agency (CNES) , the  French Ministry of Higher Education and Research , the  Université de Lorraine , and the  French State-Region  Project Contract (CPER) for their support. This work was presented in part at the  Congress of the French Society of Medical Mycology, Lyon, France ,  2021.
Methods: First, the most essential stakeholders in the health care sector were identified by a scoping review and grounded theory approach. Second, the effects on these stakeholders were assessed. PubMed, Web of Science, and Dimensions were searched for relevant studies. On the basis of an integrative review and grounded theory methodology, the relevant academic literature was systematized and quantitatively and qualitatively analyzed to evaluate the impact on the value creation of, and the relationships among, the stakeholders. Third, the findings were synthesized into a conceptual model of the health care sector under digital transformation. Results: A total of 2505 records were identified from the database search; of these, 140 (5. 59%) were included and analyzed. The results revealed that providers of medical treatments, patients, governing institutions, and payers are the most essential stakeholders in the health care sector.
Search Strategy Conducting the integrative review, we complied with the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) extension for Scoping Reviews statement, and the completed checklist is provided in Multimedia Appendix 1  [59]. Before the actual literature search, a pilot search was conducted to assess the feasibility of the literature search and to identify relevant keywords. This step indicated that a large number of potentially relevant articles associated digital transformation in health care with terms such as "Health Care 4. 0," "Healthcare 4. 0," and "Health 4. 0. " Furthermore, no relevant synonyms for the term "digital transformation" could be identified in Web of Science or PubMed articles. Test runs in databases showed that the identification of relevant articles would not benefit from adding specific technologies to the search terms, as these terms are predominantly accompanied by digital transformation-related and Healthcare 4.
0-related constructs. Accordingly, the search term (health* AND digital transformation) OR Health Care 4. 0 OR Healthcare 4. 0 OR Health 4. 0 was used to combine the domains of health care and digital transformation. The databases Web of Science, PubMed, and Dimensions were chosen to carry out the literature search. Web of Science and PubMed qualify as principal resources for literature searches and capture the involved disciplines  [60]. Dimensions complements these 2 databases by providing a larger data set and additional nonindexed publications  [61]. The search terms were generated in compliance with the specific syntax requirements of each of the databases (Multimedia Appendix 2). The following inclusion and exclusion criteria were based on the research questions. First, the search results must address the spectrum of digital transformation in the context of the health care sector.
Although the literature indicates that the vast majority of high-quality publications on digital transformation emerged after 2010  [62] , a pilot search revealed that only a fraction of the search results is expected to be published before 2010, allowing the inclusion of these results with reasonable effort. Two independent researchers screened and evaluated the identified records. Disagreements were discussed and resolved by consensus (Figure  1  depicts the PRISMA flow diagram  [63] ). [2, 3] , improved satisfaction of needs inside the ecosystem or satisfied at lower cost  [3, 30] , and redefinition of value proposition or relationship  [2, 3, 30]  Outcome of strategic change Other entities than stakeholders Identified stakeholders Considered entities Not English or German English or German Language The systematic database search for the integrative review process yielded 2505 records, of which 140 (5.
Data Analysis During the data analysis stage, grounded theory  [45]  was used to systematically structure the insights from the identified relevant literature. According to a comparison of theory-building methods  [67] , grounded theory is particularly valuable for generating new insights through the continuous interplay between analysis and data collection. It is an inductive-driven qualitative research method used for the conceptual development phase of the theory-building process  [67] , which makes it an appropriate method for this study. For the actual data analysis, the MAXQDA software (version 2020. 4. 2; VERBI GmbH), a tool for computer-assisted qualitative and mixed methods data analysis  [68] , was used. The included literature was analyzed line by line to detect statements that refer to digital transformation, health care, and value creation.
Principal Findings This study systematizes the relevant academic literature at the intersection of digital transformation and health care. The aim was to provide a conceptual model, giving a holistic view on the sector that goes beyond the technological aspects. The results were obtained from a systematic literature search. The aggregation of qualitative data was conducted using a grounded theory approach, which is an inductive and systematic data analysis methodology that yields strong descriptive and explanatory power at the intersection of theory and data  [67]. We provide an in-depth overview of the relevant literature through the lenses of value creation of, and relationships among, stakeholders. The conceptual model highlights the interdependencies of various stakeholders in the health care sector.
An imperative element is the ability to integrate new data into the organization. In a home-based recovery setting,  Dimitrov [128]  highlighted the need for an entity to distribute information across entities inside the health care systems. From a microlevel perspective, these conceptualizations implicitly highlight the need for interorganizational data exchange and the lack of respective capabilities of the current health care stakeholders to orchestrate such an exchange. Other streams of research in information systems literature consider the workforce transformation  [218]  or the transformation process of organizational change [219], both driven by technological change. Although the microlevel perspective is common for transformation process conceptualizations, it is worth considering that key elements such as the impact of technologies on the external and internal dimensions of organizations are key elements of these models as well.
Given the novelty of this study, the sufficiency of the data involved in the research process was judged by 2 measures, the data basis of other studies and "theoretical saturation"  [45]. This study included 140 literature results in the data evaluation, which is well above the number of publications included in other studies. For example, Kraus et al  [31]  evaluated the current state of research of digital transformation in health care and included 27 articles; the work of  Kutnjak et al [225] , analyzing the effect of digital transformation in health care in practice, included 7 case studies;  Hermes et al [157]  investigated the digital transformation of the health care industry based on 110 literature results;  Marques and Ferreira [180]   Looking at the theoretical saturation, the number of codes applied to text segments was >700.
Materials and Methods All patients registered in the French AA syndrome register (Freedom of Information Act-Commission nationale de l'informatique et de la liberté-99. 149, June 1999) from 1999 to 2020 were included. New French cases were added to the register once reported by physicians and/or through the members of the French National Society for Internal Medicine (Société Nationale Française de Médecine Interne-SNFMI). The study was approved by the local Ethics Committee (IRB00013412, "CHU de Clermont Ferrand IRB #1", IRB number 2022-CF020) with compliance to the French policy of individual data protection. The patients' evolution was recorded from medical records and by communication with the physicians or patients themselves via email or telephone. A total of 20 patients belonged to the 2007 case series  [3]  and their updated evolution data were collected.
We collected epidemiological, clinical, biological, radiological, histological, and evolution data. Diagnosis of associated diseases was left to the discretion of each patient's primary physician. Relapse was defined as the occurrence of new abscesses, either clinical or revealed on imaging, with or without other symptoms (such as fever or pain) and/or biological signs (increased CRP or PMN hyperleukocytosis) following a period of clinical remission. Continuous data were expressed according to statistical distribution as mean and standard deviation or median and interquartile range. The assumption of normality was assessed by the Shapiro-Wilk test. Categorical parameters were compared between groups using chi-squared or Fisher's exact tests, whereas continuous variables were compared between groups by Student's t-test or the Mann-Whitney test when the assumptions of the t-test were not met.
The homoscedasticity was analysed using the Fisher-Snedecor test. Estimates of relapse-free survival were constructed using the Kaplan-Meier method. As a patient could present several relapses, the marginal Cox proportional hazards regression model for repeated data was used to investigate associated prognostic factors in univariate and multivariable analysis, taking into account between and within patient variability. For multivariable analysis, the covariates were determined according to univariate results and to the clinical relevance with a particular attention paid on multicollinearity, (1) studying the relationships between the covariables and (2) evaluating the impact to add or delete variables on the multivariable model. IBD, relapsing polychondritis (RP), and pyoderma gangrenosum were treated independently in multivariable analyses.
The proportional hazard hypothesis was verified using Schoenfeld's test and plotting residuals. To ensure the robustness of our results, the final model was validated by a two-step bootstrapping process. In each step, 1000 bootstrap samples with replacements were created from the training set. In the first one, using the stepwise procedure, we determined the percentage of models including each of the initial variables. In the second step, we independently estimated the marginal Cox model parameters of the final model. The bootstrap estimates of each covariate coefficient and standard errors were averaged from those replicates. Results were expressed as a hazard ratio (HR) and 95% confidence interval. Statistical analysis was performed using Stata software (version 15, StataCorp LP, College Station, TX, USA).
The primer pairs Ptat (5'-ACAAAGATGGCTWGCWATGCTTA-3 ′ , nt 5807) and Penv (5'-ATGCCAGCAATCCAATTCWTGGT-3' ′ , nt 8179) were designed by aligning several env sequences from GenBank and were used in the first round of PCR. Primer pairs A51/B31 and 567/564 were used in the second round for the amplification of the V1-V2 and V4-V5 fragments, respectively  (Germain and Valas, 2006; Mordasini et al. , 2006). For region V1-V2, PCR products were obtained from six animals (Br295 (20G-MG/10), Br329 (24H-PB/10), Br628 (43U-MA/11), Br9007, Br7003, and Br198), and for V4-V5, seven animals were used (Br295 (20G-MG/10), Br195 (21G-MG-10), Br329 (24H-PB/10), Br628 (43 U-MA/11), Br1163, Br9007, and Br7003). Additionally, the gag fragment (990 bp), containing the whole capsid (CA) and a nearly complete matrix (MA) sequence, was amplified using The partial env (V1-V2 and V4-V5) and gag amplicons were purified from agarose gels using a QIAquick Gel Extraction Kit (Qiagen, Courtaboeuf, France) and sequenced in both directions using a standard ABI BigDye terminator reaction.
Nucleotide and amino acid (aa) sequences were aligned to perform tree construction and aa analysis, respectively, using Clustal W in MEGA version X and Bioedit version 7. 2. 6  (Hall, 1999; Kumar et al. , 2018). Manual rearrangements of the alignments, including gap exclusion and length adjustment, were applied to achieve optimal results. Pairwise genetic distances were calculated using MEGA version X with Kimura 2-parameter mode  (Kimura, 1980). Phylogenetic construction was carried out using the neighbor-joining method implemented in MEGA with the Kimura 2-parameter gamma distance  (Saitou and Nei, 1987). The statistical confidence limits of the phylogram topologies were assessed with 1000 bootstrap replicates. The SRLV Brazilian sequences in this study are available under accession number in the GenBank database KF861573 (Br195 (21G-MG/Br)), KF861572 (Ovine Br198), KF861555 (Ovine Br200), and KF861574 (Br1163) for gag sequences; MZ367335 (Br9007), MZ367338 (ovine Br198), MZ367339 (Br7003), MZ367331 (Br628/43 U-MA/Br), MZ367322 (Br295/20G-MG/Br), and MZ367323 (Br329/24H-PB/Br) for V1V2 env sequences.
Statistical and network analyses Statistical analyses were carried out using R (R Development Core Team 2017). Diversity indexes, nonmetric multidimensional scaling (NMDS) ordination analyses, and correlations were conducted using the "Vegan" R package  (Oksanen et al. 2011 ). These tests were based on Bray-Curtis (BC) dissimilarities  (Bray and Curtis 1957)  between community structures in the different planktonic communities. Statistical differences between microbial communities were analyzed using a permutational multivariate ANOVA (PERMANOVA) test. A Mantel test based on the BC distance matrix and a matrix of Euclidean distances of the physicochemical parameters observed (chemical parameters and depth) was applied to test whether microbial diversity was significantly correlated to the environmental variables.
Mantel tests and canonical correspondence analyses (CCA) were calculated with the "Ade4" package  (Dray and Dufour 2007). Prior to CCA analysis, we performed a forward selection of parameters with the function ordiR2step from the "Vegan" R package in order to avoid the effect produced by the occurrence of variables with strong correlation. Only significant factors (p-value from ANOVA < 0. 05) were subsequently used for CCA (see Supplementary Table  S5  for ANOVA analysis and variable selection performed for each CCA). To eliminate potential biases due to the nature of our data, NMDS and CCA analyses were performed using three different approaches: (1) rarefaction in order to obtain a data matrix with an equal number of sequences per sample; (2) Wisconsin standardization; and (3) frequency-based standardization.
Networks of dominant OTUs in Alchichica were constructed using the package SpiecEasi for R  (Kurtz et al. 2015)  with data from winter (2012) and late-spring (2014) using two approaches. First, we analyzed sparse correlations based on the model SparCC  (Friedman and Alm 2012). Second, we studied modularity and degree of connectivity using the actual SPIEC-EASI (for Sparse and Compositionally Robust Inference of Microbial Ecological Networks) model, which estimates the inverse covariance matrix, creating less indirect edges.
2021b). Although planktonic communities were significantly different from those of microbialite-associated microbial communities in NMDS analyses along axis 1 (Supplementary Fig. S8 ), we hypothesized that the salinity-alkalinity gradient was also a major driver of planktonic communities. In order to compare prokaryotic and microbial eukaryotic community structure between plankton of different TMVB lakes, we used two different ordination analyses based on Bray-Curtis distances between samples: non-metric multidimensional scaling (NMDS) and hierarchical clustering analysis (HCA). The NMDS based on a matrix using a Wisconsin double standardization, which tends to enhance patterns among datasets, clearly separated the planktonic communities of both cell size fractions (0. 2-5 μm and 5-30 μm) in lakes Alchichica and Atexcac from those of the rest of the lakes along the first axis (Fig.
Acknowledgments The authors would like to thank  A. Lopez-Archilla ,  A. Saghaï ,  N. Zeyen , and  E. Cortés  for help and discussions during the 2014 field trip, and  P. Deschamps  for bioinformatic advice. This research was funded by the  European Research Council  Grants ProtistWorld (322669, Purificaci on L opez-García) and PlastEvol (787904,  David Moreira ), and the  French ANR  project  Microbialites  ( ANR-18-CE02-0013-01 ; Purificaci on L opez-García/Karim Benzerara).
Gas exchanges, heart rate, SpO 2 and perceptual variables Breath-by-breath pulmonary gas exchange (oxygen uptake, VO 2 ; carbon dioxide production and end-tidal carbon dioxide partial pressure, P ET CO 2 ), minute ventilation ( _ V E) and respiratory frequency (Rf) were measured at rest and throughout time-trial using a portable gas analyzer (MetaMax 3B, Cortex, Leipzig, Germany) with an oronasal mask (Vmask ™ , 7,500 series; Hans Rudolph Inc. , Shawnee, United States). Heart rate (HR) and peripheral oxygen saturation (SpO 2 ) were continuously recorded (Radical-7 ® , Masimo Corporation, Irvin, United States) and stored for offline analyzes with commercially available software (Labchart software, AD Instrument, Colorado Springs, United States). The VO 2max was not measured in hypoxic conditions but estimated by decrementing the NN VO 2max (i.
Electromyographic recordings Quadriceps electromyography (EMG) was continuously recorded from the right vastus lateralis (VL) using bipolar silver chloride surface electrodes of 10-mm diameter (Kendall Meditrace 100). Electrodes were taped lengthwise on the skin over the muscle belly following SENIAM recommendations, with an interelectrode distance of 20 mm. Positions of the electrodes were marked on the skin to ensure precise replacement in other sessions. Reference electrode was attached on the patella. Low impedance (<10 kΩ) at the skin-electrode was obtained by shaving and abrading the skin with an abrasive sponge and cleaning with alcohol. EMG data were recorded at 2 kHz with Biopac system (MP150, Biopac System, Goleta, United States) and amplified with a bandwidth frequency ranging from 10 to 500 Hz.