dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2014). Although in previous reports expressions of flavodoxin in Fragilariopsis cylindrus, Cylindrotheca closterium and Thlassiosiroid pseudonana appeared not to be sensitive to iron concentration  (Pankowski & McMinn, 2008; Whiteley et al. , 2017) , these species were not detected in our metabarcoding data. Therefore, we cannot rule out the possibility that at the sampling time of the diatom bloom in Lake Pavin, the community could be confronted with iron limitation. On the other hand, according to our metatranscriptomics data during the chytrid epidemic, higher proportions of iron-containing proteins were up-regulated, including cytochromes, ferredoxin and ferritin, but not flavodoxin (Table  7 ), suggesting iron was no longer limited. Further sampling and investigation of iron concentrations in Lake Pavin throughout this period should clarify the question of whether the community was confronted with iron limitation during the spring diatom bloom and whether the chytrid epidemic relieved the iron limitation.
with whole genome sequences available to date, Phaeodactylum and Thalassiosira are the most well-studied genera and with more information on annotated genes in databases. Hence, it is not surprising that the majority of diatom functions matched gene homologues in Phaeodactylum or Thalassiosira after blastx searches. Nonetheless, neither Phaeodactylum nor Thalassiosira appeared in our metabarcoding data. Since the diatom community was dominated by Au. TA B L E 4 Number of up-regulated Chytridiomycota functions during the diatom bloom and the chytrid epidemic Number of up-regulated diatom functions during the diatom bloom and the chytrid epidemic.
Conclusions We have reported results from electron cloud build-up simulations for the FCC-ee DR and positron collider ring. PyECLOUD and VSim software were used to calculate the electron build up, including the electron kinetic energies. In passing, we have also identified a few cases where two different SEY models lead to similar electron density values. The photoelectron generation rate was varied over a realistic range of values  [32]. For the damping ring (DR), our simulation results show that with small beam sizes at extraction, the kinetic energy of electrons close to the centre of the beam pipe can exceed 2. 5 keV. Regardless, in the DR, both at injection and at extraction, a peak SEY value below 2. 0 is sufficient to avoid any avalanche-like accumulation of electrons. Such SEY value is easily achieved with standard surfaces made of copper, stainless steel or NEG coating.
Background: Coffee consumption in relation to female hormone-related cancers has been investigated but metaanalyses regarding breast and ovarian cancer include studies published up to 2012 with inconsistent results for ovarian cancer. Methods: We conducted two updated meta-analyses of studies published up to June 2016 to quantify the association of coffee intake with breast and ovarian cancer risk with random effects models. We used the dataset developed by the International Agency for Research on Cancer Working Group for Monograph 116 meeting (May 2016). We additionally performed a PubMed search in June 2016. Results: Summary relative risks (RRs) (95% confidence intervals (CI)) for the study-specific highest vs. lowest coffee consumption were for breast and ovarian cancer respectively: 0.
Study selection The flow chart for the selection procedure supplementary to IARC search is shown in Supplementary Figure  1. This search identified 6,352 articles included in the PubMed database. On the basis of the titles and abstracts 6,187 were initially excluded whereas the remaining 165 were fully examined. From these, the following articles were not considered: 83 because they did not report information on the association of coffee consumption with breast and/or ovarian cancer; 1 study because it reported the association between total caffeine (not coffee) and breast cancer risk  [26] ; 3 studies considering coffee only together with tea consumption  [27] [28] [29] ; 3 studies on male breast cancer  [30] [31] [32] ; 3 studies on BRCA1 or BRCA2 mutation carriers  [33] [34] [35] ; 3 studies  [36] [37] [38]  which used the same study population as more informative studies that were included in the meta-analyses  [39] [40] [41].
Data extraction For each study, data were extracted on study design, country, duration of follow-up (for cohort studies), enrolment period, number of subjects (cases and controls/non-cases or cohort size), age of the study population, type of coffee (e. g. , total, regular/caffeinated, decaffeinated), coffee-drinking categories, estimates of RR (e. g. HR, OR etc. ) and their corresponding 95% CIs, number of cases/non-cases, or, person(time)-at-risk for each coffeedrinking category (if available), and covariates adjusted for in the analysis. We selected from each study RR estimates adjusted for the largest number of confounding factors. For case-control studies providing OR estimates separately for population and hospital controls, we considered the ORs based on population controls  [28, 66].
Ovarian cancer Individual studies Table  1b  shows the main characteristics of the 13   All studies were included in the overall meta-analysis except for the study by Kuper et al  [84] , as the study of Kotsopoulos et al  [78]  included the same case-control dataset, but was more informative. The study by Kuper et al  [84]  was, however, included in stratified analyses by BMI. From the indicated 13 cohort and 18 case-control studies included in the overall meta-analysis 14 were conducted in North America, 13 in Europe, 3 in Asia and 1 in Australia. The RRs for ovarian cancer comparing the highest with the lowest coffee intake are shown in Figure  2. The study by Kotsopoulos et al  [78]  was included twice in the meta-analysis -one as a cohort and one as a case-control study, because it included the pooled estimates from the Nurses' Health Study and the Nurses' Health Study II (cohort studies) and the estimate of the NEEC study (a case-control study).
SupS6B ). The DNM2 protein expression was then quantified using western blot and densitometric analysis. In untreated HTZ muscles, a two-fold increase in DNM2 expression was observed compared to WT muscles while DNM2 expression was similar in WT and HTZ treated muscle (Figure  3C ). Altogether, these data demonstrated that allele-specific silencing was maintained 1 year after a single AAV1-sh9 intramuscular injection. These results also highlighted an age-related accumulation of the DNM2 protein without increase in mRNA expression in muscle of HTZ mice at 1 year of age.
Data Analysis and Statistics Graphics and statistical analyses were performed with GraphPad Prism software version 9. Values were expressed as means ± SEM. The number of samples (n), representing the number of independent biological replicates, was indicated in the figure legends. For molecular analysis the experiments were repeated at least three times per biological replicate and averaged. We used nonparametric statistical tests to analyze our data since the normality could not be assume or tested or the variance were not equal between groups. Statistical comparisons between two groups were performed using unpaired two-tailed Mann-Whitney U-test as specified. Spearman correlation analysis was used to evaluate the strength of relationship between DNM2 protein content and age. Statistical tests applied are indicated in the figure legends.
For this assay, the half of the PCR products was digested using 2U of EcoNI (New England Biolabs, France) for 2 h at 37°C. Image acquisition of PCR products after agarose gel electrophoresis was performed using a Geni2 gel imaging system (Ozyme, France) and associated-signal was quantified using ImageJ Software (NIH; http://rsbweb. nih. gov/ij). Semi-quantitative RT-PCR was also used to determine the total expression of two interferoninduced genes (Oas1 and Stat1) with appropriate number of PCR cycles selected in order to have the amplification in the exponential range (i. e. 34 cycles to amplify OasI, 36 cycles to amplify Stat1). Sequences of the primers were indicated previously. 22 Pax7, Gabarapl1, p62 Atg4, Murf1 and Atrogin 1 mRNA quantification was performed by real-time PCR using a Lightcycler 480 II (Roche, Switzerland) and 1X SYBR Green (Roche, Switzerland) reactions using 0.
1%, milk 1% overnight at 4°C. Membranes were rinsed in PBS-Tween-20 0. 1% and incubated 1h at room temperature with horseradish peroxidase-conjugated secondary antibody (anti-rabbit from Jackson ImmunoResearch, United Kingdom) in PBS-Tween-20 0. 1%. Chemiluminescence was detected using ECL detection Kit (Merck-Millipore, Germany) in a Chemidoc Imaging Systems (Biorad, France) and signal quantification was performed using ImageJ software.
Histomorphological analyses TA muscles were frozen in liquid nitrogen-cooled isopentane. Transverse sections of TA muscle (8 µm thick) were stained with hematoxylin and eosin (HE), Succinate Dehydrogenase staining (SDH) and reduced diphosphopyridine nucleotide diaphorase staining (DPNH) by standard methods. Light microscopy was performed using an Axioscope Z1 Slide scanners (Zeiss, France) at 20X magnification. Exposure settings were identical between compared samples and viewed at room temperature. Histomorphological abnormalities were manually counted on SDH staining using cell counter plugin Fiji software  48  , 8 untreated and 8 treated heterozygous Tibialis anterior sections from different animals were counted.
Slides were then stained with 4',6diamidino-2-phenylindole (DAPI) for nuclei staining. The slides were mounted with Vectashield mounting medium (Vector Laboratories, United Kingdom). Fluorescent images acquisition was performed at 20X magnification on Axioscope Z1 Slide scanners (Zeiss, France) for Laminin and on a Nikon Ti2 microscope, driven by Metamorph Software (Roper), equipped with a motorized stage and a Yokogawa CSU-W1 spinning disk head coupled with a Prime 95 sCMOS camera (Photometrics) for PAX7. For quantification of fibre size, images of TA muscle sections labelled with anti-laminin antibody were used to automatically determine the Feret diameter of each fibre after manual segmentation using the Fiji software. The normal distribution of the values was plotted using Microsoft Excel software (8 heterozygous untreated, 8 heterozygous treated and 6 wild-type Tibialis anterior sections from different animals were analyzed).
Acknowledgments We thank the  Histomics Platform  from the  Brain and Spinal cord Institute (Paris, France ) for light microscopy imaging, the  MyoBank-AFM  and the  Histopathology Laboratory  from the  Institut de Myologie (Paris, France)  for providing human muscles samples, the  Penn Vector Core ,  Gene Therapy Program  ( University of Pennsylvania, Philadelphia, USA ) for providing pAAV1 plasmid (p0001). We would like to thank  Catherine Coirault  for fruitful discussions and comments. This work was supported by the  Institut National de la Santé et de la Recherche Médicale  (INSERM), INSERM transfert ( CoPoC grant ), the  Association Institut de Myologie.
Animals and Rearing Factors The individual data of 371 Charolais cull cows from 39 French commercial farms in the Auvergne-Rhône-Alpes area (the second main area of sulking cattle production in France) were used in this study. The cull cows were born between December 2003 and December 2017 and slaughtered between April 2019 and December 2020. From one face-to-face rearing survey per farm, information on the rearing management (RM) applied throughout the cull cows' life were collected using questionnaires and establishing batch management practices with each farmer  [17]. The cull cows' life was divided into 4 key periods: pre-weaning period (PWP), growth period (GP), breeding period (BP) and fattening period (FP), as described in Figure  1. In addition to the rearing surveys, the composition and the nutritional values of the different concentrates used in the different diets throughout the cull cow's life were collected from the manufacture.
Sensory Analysis In accordance with ISO 8586  [26] , 50 persons were trained (six 1-h training sessions) to evaluate 10 sensory descriptors and one hedonic descriptor (Table  2 ) using a 10-cm unstructured scale (from 0 = no perception to 10 = perception very intense) and a scale anchoring (from 0 = "I don't like at all" to 10 = "I like very much"), respectively  [24]. The sensory descriptors were evaluated by sensory survey using Tastel software ® (ABT Informatique, Rouvroy-sur-Marne, France). Flavor associated with aromas that should not normally be present in meat (e. g. , aftertaste, rancid) (0 = none to 10 = very intense).
Texture Profile Analysis After thawing (around 25 min), the LM samples were cut using a cookie cutter to obtain regular cylinders (1 cm thick × 1 cm in diameter) conserved at +4 • C until the analyses. Then, each meat cylinder underwent 2 cycles of 20% compression at 4 • C using a rheometer (Kinexus pro+, Malvern Instruments, Malvern, UK) and rSpace 1. 61 software (Kinexus, Malvern, UK). From the force-deformation curve, six parameters: springiness, hardness, cohesiveness, resilience, gumminess, and chewiness were calculated  [27, 28]. A texture profile analysis was carried out for a meat sample only when it was possible to perform the measurement on at least two meat cylinders.
Shear Force Measurement The SV samples were thawed at +4 • C (around 24 h), and for each sample, around 14 meat portions (between 0. 9 and 1. 1 cm thick × 1 cm wide) were cut in parallel to the fibers. On each raw meat portion, two shear force measurements (cut perpendicular to fibers) were carried out, using the Warner-Braztler method (Instron 5944, Elancourt, France) and Bluehill 2 software (Instron, Elancourt, France).
The effect of the RM on the carcass and meat traits was evaluated by ANOVA. For the carcass traits, the slaughterhouse and operator effects were tested in the ANOVA. If these effects were significant, a new ANOVA (mixed model) was performed, considering these effects as random effects. If these effects were not significant, they were removed, and a new ANOVA was carried out. For the sensory descriptors, mixed models considering the panelist effect as a random effect were performed. A post-analysis was realized when the effect of the RM effect was significant, using the Tukey's test. The "FactoMineR" package was used to realize the FAMD and the HCPC  [30]. The ANOVAs were performed using the "agricolae" package  [31]  and the mixed models followed by Tukey's tests using the "emmeans", "multcompView", and "multcomp" packages  [32] [33] [34] [35].
Acknowledgments: The authors would first like to thank the farmers who accepted to participate in this study. The authors would also like the staff of the four breeding cooperatives (FEDER, SICABA, SICAGIEB and SICAREV) for helping us to select the surveyed farms, and the staff of the four slaughterhouses (SICABA, SICAREV, SOCOPA, and  Viandes de Bresse)  for the achievement of measuring the carcasses and the meat sampling. The authors would also like to thank the  INRAE  staff for the meat samples collection and transport, and for the meat sample preparation and rheological analyses (shear force), and the  VetAgro Sup  staff for color, sensorial and rheological (texture) analyses. Finally, the authors thank the other partners implicated in the development of the ProBA (produce suckler cattle delivering the goods of the slaughterers in the region  Auvergne-Rhône-Alpes ) project:  ARIA Auvergne-Rhône-Alpes , la  Chambre Régionale d'Agriculture Auvergne-Rhône-Alpes , and  La Cooperation Agricole Auvergne-Rhône-Alpes.
NET21 questionnaires). The expected benefit will be an increase in the efficacy of retreatment after two additional cycles of Lutathera ® compared to active surveillance in patients with an intestinal NET in relapse. The risk-benefit balance of the study will be continuously evaluated by the ICM Clinical Research Pharmacovigilance Unit and discussed in the periodic safety reports. The study was approved by a national Ethics Committee and will be performed according to Good Clinical Practice and the Declaration of Helsinki. The trial was prospectively registered on ClinicalTrials. gov: NCT04954820. The study protocol adheres to SPIRIT guidelines.
Objective: To determine the effects of behavioural interventions in people with oropharyngeal dysphagia. Methods: Systematic literature searches were conducted to retrieve randomized controlled trials in four different databases (CINAHL, Embase, PsycINFO, and PubMed). The methodological quality of eligible articles was assessed using the Revised Cochrane risk-of-bias tool for randomised trials (RoB 2), after which meta-analyses were performed using a random-effects model. Results: A total of 37 studies were included. Overall, a significant, large pre-post interventions effect size was found. To compare different types of interventions, all behavioural interventions and conventional dysphagia treatment comparison groups were categorised into compensatory, rehabilitative, and combined compensatory and rehabilitative interventions.
Systematic Review Methodological Quality and Risk of Bias. The Revised Cochrane risk-of-bias tool for randomised trials (RoB 2)  [13]  was used to assess the methodological quality of the included studies. The RoB 2 tool provides a framework for evaluating the risk of bias in the findings of any type of randomised trial. The tool is structured along five domains through which bias might be introduced into the study results: (1) the randomisation process; (2) deviations from intended interventions; (3) missing outcome data; (4) measurement of the outcome; (5) selection of the reported result. Data Collection Process. A data extraction form was created to extract data from the included studies under the following categories: methodological quality, participant diagnosis, inclusion criteria, sample size, age, gender, intervention goal, intervention agent/delivery/dosage, intervention condition, outcome measures and treatment outcome.
Meta-Analysis Data was extracted from relevant studies to compare the effect sizes for the following: (1) pre-post outcome measures of OD and (2) mean difference in outcome measures from pre to post between different types of behavioural interventions. All interventions were categorised into compensatory (e. g. , body and postural adjustments, or bolus modification), rehabilitative (e. g. , oromotor exercises or Shaker exercise), combined compensatory and rehabilitative interventions, and no dysphagia intervention. Only studies using instrumental assessment (videofluoroscopic swallow study  [VFSS]  or fiberoptic endoscopic evaluation of swallowing  [FEES] ) to confirm OD were included. Outcome measures based on visuoperceptual evaluation of instrumental assessment and clinical non-instrumental assessments, were eligible for inclusion in meta-analyses.
However, if both types of data were available, instrumental assessment was preferred over non-instrumental assessment outcome data. Oral intake measures, screening tools and patient self-report measures were excluded from meta-analyses. Measures other than the authors' primary outcomes may have been selected if these measures helped to reduce heterogeneity between studies. To compare effect sizes, group means, standard deviations, and sample sizes for pre-and post-measurements were entered into Comprehensive Meta-Analysis Version 3. 3. 070 [14]. If only non-parametric data were available (i. e. , medians, interquartile ranges), then data were converted into parametric data for meta-analyses. Participants in studies of multiple intervention groups were analysed separately. Where studies used the same participants, only one study was included in the meta-analysis.
Other subgroup analyses were conducted to compare effect sizes between selected interventions (i. e. , Shaker exercise, Chin Tuck Against Resistance exercise [CTAR], and Expiratory Muscle Strength Training [EMST]), medical diagnoses, and outcome measures. Only between-subgroup meta-analyses were conducted using post-intervention data, to account for possible spontaneous recovery during the period of intervention. Using Comprehensive Data Analysis software, publication bias was assessed following the Begg and Muzumdar's rank correlation test and the fail-safe N test. The Begg and Muzumdar's rank correlation test reports the rank correlation between the standardised effect size and the variances of these effects  [17]. This statistical procedure produces tau as well as a two tailed p value; values of zero indicate no relationship, whereas deviations away from zero indicate a relationship.
Study Selection A total of 8059 studies were retrieved across four databases: CINAHL (n = 239), Embase (n = 4550), PsycINFO (n = 231), and PubMed (n = 3039). After removal of duplicate titles and abstracts (n = 1113), a total of 6946 records remained. After assessing titles and abstracts, 261 original articles were identified. Full-text records were accessed to verify all inclusion criteria. During full-text assessment, articles were divided into different types of interventions, as this systematic review reports on behavioural interventions only. Based on the inclusion criteria, 36 articles were included, after which one study was identified through reference checking of the included articles. Figure  1  presents the flow diagram of the article selection process according to PRISMA.
#25300062, Grand Island, NY, USA) and subcultured at 1. 8 × 10 5 cells/mL in 25 cm 2 or 75 cm 2 cell culture flasks with TMCM. At each passage (P), a part of the pHTMC was seeded in 48-well plates for immunofluorescence analysis. Before use in experiments, all pHTMC strains were characterized by immunohistochemistry. All studies were conducted using cells before the 7th passage, and at least three different donors' human primary cell cultures were used for each experiment. Information about pHTMC lines are available in supplementary data (Table  S1 ).
The nuclei were stained with DAPI (1/1000 dilution). Western immunoblot analysis of the myocilin induction in response to DXM was also used to characterize the pHTMC in accordance with the consensus recommendations  [28]. The analysis of myocilin induction by DXM compared two conditions: 1/TMCM + 2. 10 -3 % ethanol (control) for 6 days, and 2/TMCM + 100 nM DXM (Sigma D8893, stock solution 20 µg/mL) dissolved in ethanol for 6 days. Mouse anti-myocilin (Santa Cruz sc-137233, dilution 1/100), anti-β-actin (Cell signaling 3700, 1/5000) primary antibodies, and HRPlinked anti-mouse secondary antibody (Invitrogen) were used. Protein expression was analyzed using Quantity One software and normalized with β-actin protein.
The immunofluorescence images were taken using a Nikon ECLIPSE Ti fluorescence inverted microscope; the images were acquired with 100× and 200× magnifications and then processed using ImageJ software (NIH, Bethesda, MD, USA). The quantification was carried out using the Cellomics ArrayScanVTI (Thermo Fisher Scientific, MA, USA), an imaging system that detects, analyzes, and quantifies immunofluorescence staining on adherent cells. In each well, a central zone of 16 mm 2 was analyzed. Using the HCS Studio Cellomics Scan software (Thermo Scientific, version 6. 6. 0), we measured the total area of positive labeling, which we related to the number of nuclei. An annular analysis pattern around each nucleus was drawn. The positive labeling area was measured in each of these rings. This area was then related to the number of nuclei.