dataesr/scientific-paragraphs-categorization huggingface dataset:
Differential scanning calorimetry Differential scanning calorimetry (DSC) experiments were performed using a Micro DSC III differential scanning calorimeter (Setaram, France). The aluminum capsules containing the samples were filled with 500 µL of 0. 1% and 0. 2% (w/v) solutions of DPPC and DP-DGTS, respectively. The lipid suspensions were extruded with a thermostated extrusion kit from Avanti Polar Lipids (Alabaster, AL, USA) by passing the suspensions 11 times through 0. 1 µm pore diameter polycarbonate membranes. The two samples were heated and cooled between -4° and 55 °C, with a heating rate of 0. 5 °C/min. Only the last three of four cycles were identical and used in the data analysis, the first one being always different from the following cycles due to the annealing of the vesicles after the extrusion step.
Small angle neutron scattering (SANS) For the SANS experiments, aqueous solutions of DPPC and DGTS were prepared in pure D 2 O at 10% (w/v) and 3% (w/v), respectively, and then vortexed before transfer into 1-mm path length quartz cells (Hellma, Germany) for the data acquisition. For DPPC, this is well above the swelling limit commonly observed at 40% water for phosphatidylcholines. SANS data were collected at the D16 cold neutron diffractometer of the Institut Laue-Langevin (ILL, Grenoble, France). D16 uses a monochromator made of nine highly oriented pyrolytic graphite (HOPG) crystals whose orientation can be set to focus the beam vertically in a continuous manner from unfocussed to detector or sample focusing. For the SANS experiments, the D16 instrument was set to pinhole geometry by collimating the beam both horizontally and vertically to produce a symmetrical angular resolution and beam size in the two directions.
In detail, the nitrogen group and the lipid tails are identical and the additional methylene groups are taken from the OPLS force field which results in total charge neutrality on the betaine headgroup. All headgroup bonded parameters stem from OPLS. An initial structure of a DP-DGTS molecule was created using the geometry optimization of the Avogadro simulation package  [86]. All the simulation input files are available at https:// doi. org/ 10. 18419/ darus-2360 and corresponding molecular topologies are displayed in Additional file 7.
Computer simulations All atomistic Molecular Dynamic (MD) simulations are performed using versions 2020 and 2021 of the GROMACS simulation package  [87]. All simulations are performed with an integration time step of 1 fs in the canonical constant pressure ensemble as described above. Temperature was maintained at T = 300 K for the gel phase and T = 330 K for the fluid phase using the canonical velocity rescaling thermostat  [88]  with a characteristic time of 0. 5 ps. The time constant for the pressure coupling is set to 1 ps. Lennard-Jones interactions are truncated and shifted to zero at r c = 1. 4nm. Water molecules are kept rigid using the SETTLE algorithm  [89]. Analysis of the simulations is performed using our freely available MAICoS package (https:// www. maicos-analy sis. org/) and chemical potentials are evaluated using the multistate Bennet acceptance ratio method (MBAR)  [90]  and the toolchain of the Alchemistry project (https:// alche mistry.
While by definition µ is constant over the simu- lation volume in thermal equilibrium, its contributions µ ex and µ id are not due to the inhomogeneous water dis- tribution perpendicular and depend on the coordinate (8) � = -µµ 0 v 0 w perpendicular to the membrane surface. We thus choose to measure the chemical potential at the center of the water slab between the bilayers and fix the test particle in the plane parallel to the membrane surface using a harmonic potential acting on its center of mass. To overcome potential sampling issues due to the slow dynamics of lipids in the gel phase five independent systems are constructed as described above at n w = 30 water per lipid and then step-wise dehydrated by a 100 ns equilibration run. The five equilibrated systems at each n w are then sampled at each state for 100 ns, corresponding to 5 × 38 × 100ns = 19µs sampling time per data point shown in Fig.
After back transform, this yields NSLD profiles from which the bilayer thickness d b is evaluated. Note that the phases ν n obtained from the simulations perfectly agree with the experimental analysis. We observe a constant shift in the d curves in Additional file 5 when comparing our simulation results to the experimental data of Δd fluid =3Å for the fluid phase and Δd gel =8Å for the gel phase, which we attribute to the united-atom representation of the lipid tails and consequent underestimation of the chainchain repulsion between lipid monolayers. This explanation agrees well with the observed larger shift for the gel phase where the tails are more ordered and stretched. Consequently, simulation data for d and d b have been shifted by d in Additional file 5. Density profiles for Fig. 5  as well as for the NSLD profiles have been extracted from the simulation trajectory using our open-source analysis framework MAICoS (https:// www.
Phylogeny The Microchloropsis gaditana locus Naga_100016g36 (annotated as Protein of unknown function DUF3419) was identified as putative betaine lipid synthase by homology with Nannochloropsis oceanica BTA1  [45]. The Naga_100016g36 CDS was translated and the amino acid sequence used as a query for a series of BLAST searches in all the publicly available databases. Both tBLASTn and PSI-BLAST  [91, 92]  were performed together with a human-curated process in order to obtain the widest dataset possible and the most robust one. The same was done with all the sequences used by  [45]. The final dataset contained amino acid sequences from at least 14 families of eukaryotes, bacteria, and archaea. Because in most eukaryotes the two domains of the BTA protein (the 3-amino-3-carboxypropyl-transferase and the S-adenosyl-L-methionine-dependent methyltransferase (SAM) domains) are arranged in two different configurations, two separate alignments were produced.
The amino acid sequences of the two domains were compiled in two separate fasta files and aligned using MUSCLE  [93]  then curated using BMGE (Block Mapping and Gathering with Entropy) software  [94]  to select the phylogenetic informative regions. For each alignment, the substitution model that best fits the data was selected by running the "Find Best DNA/Protein Model" utility implemented in MEGA X (Molecular Evolutionary Genetics Analyses) software  [95]. The Le-Gascuel substitution model for Maximum Likelihood (ML) phylogenetic inference method was chosen as the best fitting for both datasets  [96]. Non-uniformity of evolutionary rates among sites was modeled using a discrete Gamma distribution (+ G). For the SAM domain alignment, a certain fraction of sites were considered to be evolutionarily invariable (+ I).
For each analysis, a total of 1,600,000 generations was implemented, with successive samples separated by 100 generations after an initial "burn in" period of 25% of the number of samples. The Bayesian posterior probabilities (BPP) were estimated by two independent runs of four Metropolis Coupled chains (MCMCMC). For each dataset, the model selection was done during the analysis by estimating the posterior probabilities of the different models together with their parameters.
Availability of data and materials All data generated or analyzed during this study are included in this published article, its supplementary information files and publicly available repositories. The neutron data that support the findings of this study are available upon request at the ILL with this link https:// doi. ill. fr/ 10. 5291/ ILL-DATA. 8-02-820, https:// doi. ill. fr/ 10. 5291/ ILL-DATA. TEST-3119 and the data that support the MD simulation are publicly available at https:// doi. org/ 10. 18419/ darus-2360.
Cell Migration Assay The migration of primary mouse muscle cells was quantified using time-lapse microscopy. Myoblasts were seeded in gelatin-coated eight-well Ibidi plates and maintained in a rich medium. The next day, cells were filmed using an inverted Axio Observer Z1 microscope (Zeiss) with an LCI PlN 20×/0. 8 W DICII objective and an incubation chamber at 37 • C and 5% CO 2. Live cells were monitored every 6 min for 4 h and 30 min with brightfield and Metamorph 7. 7. 5 software. Cell velocities were calculated in µm per minute using ImageJ (National Institutes of Health) by tracking the paths of cells. At least 100 cells were tracked for each group of two independent cell cultures.
Affymetrix Microarrays Microarray analysis was performed from three independent control and mutant cell cultures. Total RNAs were obtained from cells at day 0 (corresponding to myoblasts), day 1 (corresponding to myocytes), and day 3 (corresponding to myotubes) of differentiation, using RNeasy Mini kit (Qiagen, Les Ulis, France) and DNase treatment (Qiagen, Les Ulis, France). RNA integrity was certified on a bioanalyzer (Agilent, Santa Clara, CA, USA). Hybridization to Mouse Gene 2. 0-ST arrays (Affymetrix) and scans (GCS3000 7G Expression Console software V1. 4) were performed on the Genom'ic platform (Institut Cochin, Paris, France). Probe data normalization and gene expression levels were processed using the robust multiarray average (RMA) algorithm in the expression Console (Affymetrix, Santa Clara, CA, USA).
We found that the absence of RhoA in SCs affected the hypertrophic growth of Plantaris muscle (Figure  6B ). To further analyze this alteration, we assessed the fusion capacities of SCs in mice subjected to CH by chronically injecting EdU (from the third to the eleventh day after surgery), to track EdU+ nuclei incorporated into growing myofibers. As expected based on TA muscle data shown in Figure  1C , no difference was evidenced between Ctl and Mut Plantaris muscles in Sham Operated condition. However, three weeks after overload, the percentage of EdU+ myofibers was significantly reduced in RhoA-deleted muscles compared to control muscles (Figure  6C ). This defect evidences an impaired fusion of RhoA-lacking SCs into wild-type growing myofibers. The fact that the fusion event was strongly affected by the absence of RhoA in SCs and that RhoA in myofiber is important to have correct muscle growth  [40] , suggests that RhoA is necessary in both SCs and myofibers to regulate fusion and muscle growth.
To better establish the fusion potential of RhoA-depleted SCs, we performed in vitro experiments on primary myoblasts. FACS-sorted SCs were collected from mutant or control mice and differentiated in culture for three days. SC-RhoA-deleted were unable to form proper myotubes (Figures  5D  and 6D ) and the number of myonuclei per myotubes was much lower in the RhoA-deleted cells compared to the control (Figure  6E ). Accordingly, the fusion index, which represents the proportion of nuclei within multinucleated cells (with at least 2 nuclei) among MyHC + cells normalized on the total nuclei number, was lower in RhoA-depleted myotubes compared to the control (Figure  6F ). these data showed that RhoA loss in SCs strongly affects myogenic fusion events. Moreover, the fact that both the fusion index and the number of myonuclei per myotube/myofiber are decreased suggests that both fusion SC/SC (primary fusion) and SC/growing myofiber (secondary fusion) are impaired.
05) (Table  S1 -Sheet 2; 4; 6), we noticed that at day 3 of differentiation, among the upstream regulator significantly predicted inhibited, there was Adam12, a disintegrin and metalloprotease identified as a potent stimulator of myoblast fusion  [45]. Interestingly, it was shown that Adam12 and α9β1 Integrin mediate a cell-cell interaction selectively involved in the fusion of mononucleated myoblasts to preformed myotubes  [14]. Among the target molecules associated in the dataset with the Adam12 upstream regulator, there are some extracellular matrix protein genes, such as the proteoglycan (collagen-associated) Decorin (Dnc) and Dermapontin (Dpt). To validate these data, we quantified by RT-qPCR the expression changes of some of the most relevant genes modulated in mutant differentiated myotubes used in the transcriptomic analysis.
23  The NSHD secondary modern women entered secondary school aged 11 years in 1957 and most left secondary school at the age of 15 in 1961. The 1000F secondary modern women followed just 1 year behind them. Although chronologically aligned, the two cohort studies evolved within very different institutional and scientific contexts, and they did not ask participants exactly the same questions. 24  Whilst the NSHD study contains a representative sample from across Britain, the 1000F study has an urban, regional, and working-class skew. 25  In general, the 1000F data have more missingness, is less qualitatively rich, and parental voices are more prominent than in the NSHD. 26  However, metadata on the Newcastle secondary modern schools were collected and it is supplemented in this article with school-level records from Tyne and Wear Archives and published, working-class memoirs.
Full details of the samples taken from the NSHD and 1000F cohorts are shown in Fig. 1. 31  Figure  2  provides key data on the female secondary modern sub-samples from each cohort. The longitudinal data collected on these cohorts are traditionally available in coded datasets. In both cases, I have worked instead from the original, archival questionnaires from a smaller, representative sample of each full cohort (from which the secondary modern women constitute a further sub-sample, see Fig. 1 ), reading thousands of pages of qualitative, free-text answers that were never coded or analysed using quantitative methods. 32  The main topics of these free-text answers are summarized in Fig. 3. In the case of the NSHD secondary modern women, these handwritten, free-text answers ranged from 52 to 214 words in length, describing their thoughts, feelings, and opinions on their everyday lives.
3  33 Data on the 1000F women were only available up to age 22, whereas quantitative data on the NSHD women were available across their entire lifecourse, and data up to age 43 were used for this article. 34  Lise Butler, 'The Social Scientific Turn in Modern British History', Twentieth Century British History, online publication 30 May 2022. 35   advantage of the birth cohort data. This methodology is the result of a recent, innovative collaboration between historians and a lifecourse studies researcher, offering the potential to unlock the birth cohort archives to a new generation of historians. 36.
Acknowledgements I would like to thank  Peter Mandler ,  Chris Jeppesen ,  Laura Fenton , and the 'Emmets' ( Lucy Delap ,  Lucy Bland ,  Deborah Thom ,  Helen McCarthy , and  Julia Laite ) for their generous feedback and insights on earlier drafts of this article. A version of this article was presented at the IHR 'Life Cycles' seminar in March 2022, and I am grateful for the feedback I received on that occasion. Thank you, in addition, to the four anonymous peer reviewers whose suggestions helped me to improve this article for TCBH. I would also like to acknowledge and thank  Andrew Wong  and  Maria Popham  at the  UCL Medical Research Council Unit for Lifelong Health and Ageing  for supporting this research, and for providing access to the NSHD, as well as the study members themselves for sharing their data.
Study population The HBV patients were recruited from Marseilles University Hospital. Healthy controls without chronic diseases or on regular medications were recruited using a snowball approach. Data on age, gender, weight, height, and dietary habits were collected. The HBV patients were con rmed to be positive for hepatitis B surface antigen for at least six months; the diagnosis was made according to European Association for the Study of the Liver (EASL) guidelines  [36]. Alcoholism and probiotics/or antibiotics intake in the previous month were exclusion criteria for both cases and controls. In addition, vegetarians and lactose lovers were excluded from our study. The other exclusion criteria for all patients were as follows: patients with viral hepatitis other than HBV, solid organ transplantation, smoking, immunosuppressive drugs treatment within six months, acute or chronic infectious diseases, other liver disease, metabolic disease, malignancy, and autoimmune diseases.
The colonies were identi ed using Matrix Assisted Laser Desorption/ Ionization Mass Spectrometry (MALDI-TOF/MS) according to the manufacturer's instructions  [39, 40]. Each obtained spectrum was matched against the spectra of Bruker's and the Laboratory of La Timone's home database (Accessed on October 2022). A score > 1. 9 allowed identi cation at the species level. In the case of unidenti ed colonies by MALDI-TOF (score < 1. 9), DNA from the unidenti ed colonies was extracted, ampli ed, puri ed and analyzed as described in  [20]. The sequences with a similarity percentage under 98. 65 or 95%  [41]  were identi ed as new species or new genera, respectively, and described according to the taxonogenomics concept  [42]. If the bacterial species identi cation was not interpretable, 16S ribosomal DNA gene sequencing was performed.
Bioinformatic analysis The raw sequencing data for all samples were deposited into the NCBI Sequence Read Archive database (Accession number: PRJEB62828). Noisy sequencing data were excluded, and chimeric sequences were identi ed and removed by Chimera Slayer. The clean data were clustered into operational taxonomic units (OTUs) at the 97% similarity threshold using UCLUST algorithm after the removal of singletons. The alpha and beta diversity were calculated using the Microbiome Analyst Platform (https://www. microbiomeanalyst. ca/; accessed on March 2023)  [44]. Shared taxa present in all groups were de ned as the core microbiota.
Highly signi cant different genera in both groups with LDA score 2. 0 and P < 0. 05 have been illustrated in Fig. 3. Interestingly, no signi cant difference was reported regarding abundance for the same frequent genera detected by culturomics as Clostridium (p = 0. 145) and Streptococcus (p = 0. 260). Enterocloster was not recognized as an abundant taxon by Linear discriminant analysis (LDA). Highly abundant OTUs assigned to the species level with LDA score 2. 0 and p < 0. 05 in both groups are shown in Fig. 3. Notably, 6 out of all seven species belonging to Enterocloster and Clostridium genera could be identi ed as multi-assigned OTUs in the dataset of 16S ribosomal RNA sequencing results (Enterocloster_aldenensis, Enterocloster_bolteae, Enterocloster_citroniae, Enterocloster_clostridioformis).
Background Nirmatrelvir/ritonavir treatment decreases the hospitalisation rate in immunocompetent patients with COVID-19, but data on efficacy in patients with haematological malignancy are scarce. Here, we describe the outcome of nirmatrelvir/ritonavir treatment in a large cohort of the latter patients. Methods This is a retrospective cohort study from the multicentre EPICOVIDEHA registry (NCT04733729) on patients with haematological malignancy, who were diagnosed with COVID-19 between January and September 2022.
Methods All data included in this analysis were exported from the EPICOVIDEHA registry. EPICOVIDEHA (NCT04733729) is an online registry open for patients with haematologic malignancy and SARS-CoV-2 infection. Cases from various regions of the world are documented in an electronic case report form (eCRF) accessible via www. clinicalsurveys. net (EFS Summer 2021, TIVIAN, Cologne, Germany). The eCRF comprises epidemiological data, such as baseline pre-COVID-19 conditions, previous clinical management of the haematologic malignancy, anti-SARS-CoV-2 vaccination history, COVID-19 diagnosis and management, and outcome. All patients are included in a validation process for data coherence and completeness performed by experts in haematologic malignancy and infectious diseases. 19 In this validation process, data missing completely at random were reduced as possible, contacting contributors were to solve pending queries.
Exclusions from the database only happened if a patient was not fulfilling all the inclusion criteria (no haematological malignancy, not active within the last 5 years prior to COVID-19, no adult, no laboratory-based COVID-19 diagnosis). For the present analysis, patients needed to fulfil all inclusion criteria to be eligible: active haematologic malignancy within the last five years prior to COVID-19, including patients at onset or watch and wait; age ≥18 years; SARS-CoV-2 infection confirmed by either polymerase chain reaction (PCR) or antigen test; and SARS-CoV-2 diagnosis between January 1st and September 30th, 2022. Selected patients were grouped according to treatment specifically received for COVID-19. Thus, we formed the following categories: patients treated with nirmatrelvir/ritonavir ± other directed or non-directed treatments, patients receiving other SARS-CoV-2 directed antivirals or monoclonal antibodies ± other non-directed treatments, and finally patients receiving neither directed antivirals or monoclonal antibodies, nor corticosteroids or convalescent plasma.
Acknowledgments The authors thank all participating institutions for their utmost contributions and support to the project during a pandemic situation. In addition, we would like to express our gratitude to  Professor Francisco Javier Martín-Vallejo  ( Department of Statistics, Faculty of Medicine, University of Salamanca, Salamanca, Spain ) for his guidance in performing the statistical analyses of this manuscript. EPICOVIDEHA has received funds from  Optics COMMIT (COVID-19 Unmet Medical Needs and Associated Research Extension) COVID-19 RFP program  by  GILEAD Science, United States  (Project  2020-8223 ).
Background Malaria infections during pregnancy can cause adverse birth outcomes, yet many infections are undetected by microscopy. We aimed to describe the epidemiology of submicroscopic malaria infections in pregnant women in Asia, the Americas, and Africa using aggregated and individual participant data (IPD). Methods For this systematic review and meta-analysis, studies (published Jan 1, 1997 to Nov 10, 2021) with information on both microscopic and submicroscopic infections during pregnancy from Asia, the Americas, or Africa, identified in the Malaria-in-Pregnancy Library, were eligible. Studies (or subgroups or study groups) that selected participants on the basis of the presence of fever or a positive blood smear were excluded to avoid selection bias. We obtained IPD (when available) and aggregated data.
Research in context Evidence before this study We conducted a literature search for studies reviewing submicroscopic malaria infection among pregnant women in malarious areas with no language restriction using the search terms ("Polymerase chain reaction" OR "PCR" OR "submicroscopic" OR "sub-microscopic" OR "sub-patent" OR "sub-microscopic" OR "Lamp" OR "loop-mediated isothermal amplification") AND "malaria" AND "Review" AND "pregnan*". The following databases were searched: PubMed and the Malaria in Pregnancy Library, which consists of references from Web of Knowledge, Scopus, Cumulative Index to Nursing and Allied Health Literature, Bioline, the Cochrane Library databases, the WHO Global Health Library, grey literature (ie reports, unpublished studies, and theses) and conference abstracts.
Added value of this study This pooled analysis of 45 individual participant and 23 aggregated datasets provides further detailed information on the epidemiology of submicroscopic malaria in pregnancy. Submicroscopic malaria in pregnancy occurred in all malarious regions (ie, Asia, the Americas, and Africa) and was more common than microscopic malaria in most settings. Similar to reports among populations who were not pregnant, the proportion of submicroscopic malaria was higher in Asia and the Americas than in Africa, where it was more common among malaria species other than Plasmodium falciparum. This study was also able to explore the relationship between malaria infections with fever and found that submicroscopic malaria was associated with fever in Africa, but not in Asia and the Americas.