dataesr/scientific-paragraphs-categorization huggingface dataset:
For this, we used a meta-regression approach implemented using the "rma" function in the metafor R package  (Viechtbauer, 2010) , using the Mann-Kendall test trend (S-statistics) and its respective variance as an effect size for the model  (Hamed & Rao, 1998; Pilotto et al. , 2020)  and applied it to abundances i-iii to infer their respective trend's directionality.
Biotic homogenization of recipient communities We investigated if homogenization of recipient communities occurred in conjunction with the increasing presence of Ponto-Caspian macroinvertebrates (our fourth hypothesis). For this purpose, we examined compositional similarity between communities at all sites sampled within de ned periods of four years using the Jaccard similarity index (bounded scale between 0-1) as a richness-based proxy of ß-diversity estimates using the "vegdist" function in the vegan R package  (Oksanen et al. , 2013). We split the study period (i. e. 1968-2020) into 13 four-year periods, but due to differences in the number of sampled sites between periods, the rst three  (i. e. 1968-1979)  and the year 2020 were removed to ensure comparability among communities (Table  S4 ).
In addition, we evaluated the in uence of the number of sampled sites in each period on temporal variability in the Jaccard similarity index. For this, we used Linear Mixed Models (LMMs) with the number of sampled sites as a random effect and the studied period as a xed effect using the "lmer" function of the lme4 R package  (Bates et al. , 2015). We also calculated the marginal R 2 (Rm; the variance explained by xed effects) and conditional R 2 (Rc; the variance explained by both xed and random effects) using the "r. squaredGLMM" function of the MuMIn R package  (Barton, 2020) , to infer the strength of the relationship between the number of sampled sites in each period and the Jaccard similarity index.
Discussion Overall, we identi ed 29 Ponto-Caspian macroinvertebrate species in our European dataset, which is considerably higher than the numbers reported in previous studies (Bij  de Vaate et al. , 2002; Gallardo & Aldridge, 2015). However, differences in sampling effort could have created biases and delays in detecting Ponto-Caspian macroinvertebrates at local and regional scales, particularly as the available time series began at variable times relative to actual invasion histories  (Aikio et al. , 2011; Dawson et al. , 2017). The countries represented in our data were between 1,312-4,670 km from the Ponto-Caspian region, whereas countries were not covered by our data (e. g. Italy, Belarus, Ireland). The vast majority of the Ponto-Caspian macroinvertebrates recorded were found in countries through which the Rhine-Main-Danube (RMD) Canal ows (e.
3a ;  Haubrock et al. , 2022b; Kot, 2001; Simpson et al. , 2022). Although based on correlation and not causation, the exponential growth of Ponto-Caspian macroinvertebrates in the years following the opening of the RMD Canal in 1992  (Vučković et al. , 2021)  suggests that it acted as a primary invasion corridor  (Leuven et al. , 2009). A plateau stage followed this trend later, with only a single new Ponto-Caspian macroinvertebrate species (the amphipod N. hrabei) recorded since 2012. Nevertheless, the saturation observed in recent years was based on the available data and thus may re ect the reduced number of sampled sites in the most recent years (i. e. 2015-2019). Additionally, a lag time in reporting, albeit being reduced in recent years due to increasing propagule pressure  (Gallardo & Aldridge, 2015) , could have in uenced observed trends, alongside possible differential taxonomic expertise within long term biomonitoring due to an exchange of taxonomic experts through time  (Rouget et al.
, 2016). Despite the increasing rate of invasions, some widespread alien species could show declining interregional spread rates  (Seebens et al. , 2018). Dreissena polymorpha, for example, has already been established in most countries with Ponto-Caspian species in our database (but not Austria and Belgium) and therefore has less scope to spread to new countries in Europe. Similarly, in the North American Great Lakes, Ponto-Caspian shes and invertebrates have become dominant components of food webs  (Ricciardi, 2001; Vanderploeg et al. , 2002) ; they comprise > 30% of the alien species established in the past few decades -the highest rate of introduction for this group of taxa recorded in the basin's history  (Ricciardi, 2006). This increase could be explained by colonization and propagule pressures driven by the ongoing construction of shipping canals and human modi cation of rivers, as well as deliberate introductions into human-altered waters (Bij de  Vaate et al.
, 2021) , reducing its biotic resistance and potentially triggering an invasional meltdown  (De Rivera et al. , 2005; Gallardo & Aldridge, 2015; Hui et al. , 2016). This is particularly crucial, considering that although only 5-20% of established species develop harmful impacts  (Williamson & Gri ths, 1996) , the observed gradual increase in the number of shared species (i. e. biotic homogenization) across Europe contributes to the major concern of global change and biodiversity loss  (Iacarella et al. , 2015; Olden et al. , 2004). Based on these results, we con rmed our fourth hypothesis, however, are not able to attribute this result solely to Ponto-Caspian macroinvertebrates since other impactful alien invasive species are present in our dataset (e. g. Pacifastacus leniusculus and Corbicula uminea), while anthropogenic stressors such as climate change, pollution and habitat loss also play a substantial role in biotic homogenization  (Capinha et al.
Acknowledgements R. N. C. acknowledges funding from the  Leverhulme Trust   Early Career Fellowship  ( ECF-2021-001 ). P. H. received funding from the  EU   Horizon 2020 project eLTER PLUS  (Grant Agreement No. 871128 ). NB and MC were supported by the  Serra-Hunter programme  ( Generalitat de Catalunya ). The  FEHM (Freshwater Ecology, Hydrology and Management) research group  (to which NB and MC belong) was funded by the  "Agència de Gestió d'Ajuts Universitaris i de Recerca" (AGAUR) at the "Generalitat de Catalunya " (2017SGR1643).
Statistical Method Biological parameters were compared from baseline to D90 by using the Wilcoxon signed-rank test, with an alpha risk (two-sided) of 0. 05. Statview ® F-4. 5 software (SAS Institute Inc. , Cary, NC, USA) was used for all analyses. Paired t-test was performed using Prism 8 (GraphPad, San Diego, CA, USA). Only significant differences are indicated. The results are expressed as medians (range).
Proliferation Versus Apoptosis We measured the proliferation of T-cells by the expression of the Ki67 marker. For all the 6 patients studied, the value for the proliferation of CD4 T-cells at baseline was 2. 1% (0. 8-5. 0), which reached 7. 2% (1. 5-14. 2) on day 90 and 4. 9% on day 150 (1. 2-9. 4). For CD8 T-cells, the values were 1. 6% (0. 9-2. 7), 3. 2% (0. 5-13. 2), and 2. 6% (1. 2-9. 4) respectively (Figure  3 ). (13) (14) (15) (16) (17) (18) (19) (20) (21) (22) (23) (24) (25) (26) (27) , which gradually went down to 12. 5% (2-23) on day 90, being 25% (17-33%) on day 150. For CD8 T-cells, respective values were 14% (1-53), 20% (3-56), and 43% (21-50) (Figure  3 ). Our data clearly shows a positive outcome under RLT, suggesting the biological effect of inclusion, and worsening or returning to baseline after withdrawal.
2. 12. 1, BA. 4 and BA. 5, or the regular detection of BA. 2, in this cohort. As a proxy for immune response to SARS-CoV-2, we used antibody titers against the ancestral SARS-CoV-2 (WA1) strain spike protein measured prior to the administration of booster doses, but predominantly after primary vaccination. We interpreted the data in two ways. First, we estimated the probability of an individual having a PCR cycle threshold (Ct) value less than 30, as a proxy for infectiousness, on each day post detection using a logistic regression model. Second, we estimated the peak viral RNA concentrations, viral RNA proliferation rate, and viral RNA clearance rate across variants, immune statuses and age using a semi-mechanistic model. Our findings provide key estimates for the duration and magnitude of viral RNA shedding in the upper respiratory tract and its variation across symptom status, variants, immune states, and individuals.
Data We identified 2,875 distinct infections from 2,678 individuals in this cohort (Supplementary Figure  1 ). By the time of their final test, 2,460 (91. 9%) individuals had one detected infection, 214 (7. 99%) had two detected infections, three (0. 11%) had three detected infections, and one (0. 04%) had four detected infections. A total of 587 infections were detected within one day of a prior negative PCR test result, and thus the timing of the onset of test positivity can be assumed with reasonable accuracy. We defined these infections as the "frequent testing" group. The remaining 2,288 infections were detected two days or more from a previous negative test result or were detected with no prior negative test in the dataset. These were predominantly tests following suspected exposure, recent symptom onset, or periodic clearance for occupational health requirements, and thus we consider this latter group of detections as a reasonable proxy for infection detection in the absence of frequent testing, which is the case for most populations.
Antibody titers were measured against the spike protein of the WA1 lineage, which correlate poorly with protection against the antigenically distinct Omicron lineages; thus, it is unclear how these data are associated specifically to Omicron-immunity, beyond representing a proxy for overall immune response. Variants and immune statuses interact, sometimes in unexpected ways, to produce viral kinetics that differ in duration and intensity. Collecting longitudinal viral load data in more diverse cohorts will help to ensure that isolation and quarantine policies are based on the best available evidence and will help to properly contextualize results from ongoing drug and vaccine trials. Similarly, our findings suggest that SARS-CoV-2 control measures may be better informed by measurements of immune status than proxies such as number or timing of receipt of vaccine doses or of infections.
Study design The data reported here represent a convenience sample including team staff, players, arena staff, vendors, and others affiliated with the NBA as described previously. (Kissler, Fauver, Mack, Olesen, et al. , 2021; Kissler, Fauver, Mack, Tai, et al. , 2021)  The retrospective study includes samples collected between 7th July 2020 and 26th January 2022 (Supplementary Figure  1 ). Clinical samples were obtained by combined swabs of the anterior nares and oropharynx, collected separately from each anatomical site, for each patient administered by a trained provider. Daily testing was required for most individuals prior to vaccination availability, with less frequent testing but close monitoring required after vaccination. Cycle threshold (Ct) values were generated using the Roche cobas target 1 assay.
Logistic regression models We used the RStan package brms to fit Bayesian logistic regression models estimating the probability of having Ct value <30 on each day post detection, stratified by detection speed. (Bürkner, n. d. )  As a baseline, we considered a model without variant-specific effects, using smoothing splines to estimate the probability of having a Ct value less than 30 on each day post detection. We then fitted additional logistic regression models, adding additional spline terms capturing the effect of vaccination status, cumulative number of previous exposures or days since previous exposure, and/or lineage with days since detection. We then ranked models based on the expected log predictive density calculated using k-folds cross-validation (25 folds) and evaluated their classification accuracy and area under the receiver operator curve.
Supported in part by  CDC  contract  200-2016-91779 ,  Emergent Ventures  at the  Mercatus Center , the  Huffman Family Donor Advised Fund , the  MorrisSinger Fund , the  National Basketball Association , and the  National Basketball Players Association. All code and data required to reproduce the analyses are available at https://github. com/gradlab/SC2-kinetics-immune-history. Supported in part by  CDC  contract  200-2016-91779 ,  Emergent Ventures  at the  Mercatus Center , the  Huffman Family Donor Advised Fund , the  MorrisSinger Fund , the  National Basketball Association , and the  National Basketball Players Association. CC-BY-NC-ND 4.
The CONFINS cohort The CONFINS cohort study (www. confins. org) was initiated on the 8 th of April 2020 to monitor French-speaking people's well-being and mental health during the Covid-19 lockdown. The cohort was onlinebased and participation was voluntary. Participants were recruited through social media posts, press releases, podcasts, TV programs and mailing were. The sole eligibility criterion was being aged 18+. For the purposes of this study only, we excluded subjects who had declared "other" for the sex variable since there were only 16 of them (0. 7 %). Wishing to attain sufficient statistical power, we also excluded those reporting missing data on at least one variable in the analyses. A sensitivity analysis tested result robustness and enhanced understanding of the relationships between outcome and exposure variables.
Data covered the period culminating on May 10 th , one day before the end of the first lockdown in France. The CONFINS questionnaire contained 77 items drawn up by several researchers through different stages of drafts and reviews. Participants completed the online survey after reading the written consent form and explicitly agreeing to participate. The cohort was approved by the French Committee for the Protection of Individuals (Comit e de Protection des Personnes -CPP, nr. 46-2020) and the French National Agency for Data Protection (Commission Nationale Informatique et Libert es -CNIL, nr. MLD/MFI/AR205600), and data were stored and analyzed according to the General Data Protection Regulation (EU GDPR). The study was conducted in accordance with the Declaration of Helsinki.
Missing values We considered that some data were missing at random, i. e. MAR (Missing At Random) type (see Figure  1  below, n=688). A multiple imputation method using chained equations (MICE) was consequently performed as a sensitivity analysis concerning the entire sample. With complete data, the variables present in the final regression models and with missing data could be imputed. The validity of the imputation was checked by comparing the observed data with the missing data of the indicator variables used for imputation of missing data. In addition, Rubin's three diagnostic parameters were checked : low relative increase in variance, a fraction of missing information lower than the proportion of missing values and relative efficiency close to 100 %  [19]. In the end, missing values concerned the following variables : age, being a student, scale on knowledge and beliefs about vaccination, capacity to detect fake news scale and general health literacy scale.
General considerations Vaccine hesitancy is context-specific  [1]. Interpretation of our results should take into account the fact that the data were collected during the first nationwide lockdown (April-May 2020), at a time when vaccines were not developed. Now that Covid-19-related vaccines are have been developed and are readily available, hesitancy attitudes may have changed. The case of France is also peculiar, given its well-known vaccine hesitancy rate  [3] , and our results are to be interpreted that much more cautiously. Present-day proposal to the same population of the same questions on vaccine acceptability could provide new results to be compared with the 2020 findings, thereby observing the evolution of vaccine hesitancy concerning Covid-19 in France, now that vaccines are currently administered.
Acknowledgements We wish to thank all members of the CONFINS group including the i-Share, Kappa Sant e and Kap Code team members :  Christophe Tzourio , St ephane Sch€ uck, and  Nathalie Texier  conceived and designed the study cohort ;  Edwige Pereira ,  Garance Perret ,  Aude Pouymayou  and  Mathilde Pouriel  analyzed the data ;  Julie Arsandaux ,  Sh erazade Kinouani ,  M elissa Macalli  and  Ilaria Montagni  wrote and revised survey tools and manuscripts ;  Rapha€ el Germain  and Clothilde Pollet were in charge of the regulatory aspects ;  Vanessa Marie-Joseph ,  Adel Mebarki ,  Elena Milesi  and  Marie Mougin  were in charge of study communication and dissemination. The authors are also grateful to all the participants who volunteered to take part in the study.
Growth kinetics of the static cultures were determined using the Background Corrected Absorption (BCA) algorithm of the UniExplorer software (BioSense Solutions, version 9. 0). Growth kinetics of aerated cultures were monitored by taking samples at every hour and measuring the OD 600 values using a Gene Quant 1300 spectrophotometer (Biochrom, Berlin, Germany). Cell suspensions reaching an OD 600 > 0. 8 were diluted 1:10 or 1:20 with phosphate buffered saline (PBS, pH 7. 2), and the measured absorbance values were multiplied with the dilution factor. The generation times of S. epidermidis strains cultivated in TSB under aerobic conditions were determined as described in  [41].
The correct chromosomal insertion of the cassette into the respective mutant was demonstrated by PCR with an ermB-specific primer paired with a primer flanking the genetically manipulated site and subsequent sequencing of the resulting fragment (data not shown). For construction of the spoVG cis-complemented derivative of the 1457 ∆spoVG, the primer pair MBH603/MBH607 was used to amplify a ~3. 0 kb fragment including the yabJ-spoVG locus from genomic DNA of the strain 1457. The amplification product was digested with SacI/BglII and ligated into SacI/BglII-digested and dephosphorylated E. coli-S. epidermidis shuttle-plasmid pBASE6  [62]  to produce plasmid pBASE6_spoVG_comp. The temperature-sensitive plasmid was propagated in E. coli strain IM08B  [61]  and plasmids isolated from this E. coli strain were directly electroporated into 1457 ∆spoVG and cultured at 30 • C on TSA plates supplemented with chloramphenicol (10 µg/mL).
Fish biomass availability Fish biomass data were obtained to determine the link between the amount of main food species available and the amount of fledglings predated by Cape fur seals. The summer (October to December) hydro-acoustic survey biomass estimates of anchovy and sardine were obtained from the Department of Forestry, Fisheries and Environment. These surveys estimate the biomass of the adult fish between Hondeklip Bay on the West Coast and Port Alfred on the East Coast of South Africa  (Barange, Hampton & Roel, 1999; Coetzee et al. , 2008a). For the purpose of this study, we used the biomass for the stratum overlapping the foraging range of local Cape gannets  (Grémillet et al. , 2004). This overlap covers the area between Hondeklip Bay (290 km north of Lambert's Bay) and Cape Point (310 km south of Lambert's Bay) (Fig.
Statistical analysis Our data were analysed to determine the influences (if any) of culling and fish biomass on Cape gannet fledgling predation probability (the response variable). In our generalised linear model (GLM), the presence/absence of culling, annual total fish biomass, and the annual total number of fledglings were set as the explanatory variables. To standardize the variables, we used the beta(model) function in the Reghelper package  (Hughes, Beiner & Team, 2017)  in R version 3. 5. 3 (R Core Team, 2017). The total fish biomass was the sum of the sardine and anchovy biomass between Hondeklip Bay and Cape Point. The annual total number of fledglings was determined by the sum of the daily successful fledglings counted within a year (this excludes the number of predations). Culling years were compared to years in which culling was not implemented.
Since the results of only three culling years are inconclusive, we have forecasted the gannet population with and without culling for twenty years using variations within our own original dataset. The sole objective of the population forecast is to compare the population size during years in which no culling was implemented (Table  S3 ), compared to the consistent implementation thereof (Table  S4 ). Our equation included annual gannet population numbers (from 15,000 individuals in year 1) summed with annual fledgling numbers, minus annual mortality of 70 and 8% for fledglings and adults respectively  (Wanless et al. , 2006). Our forecast assumes that all fledglings recruit at their natal colony. The mean gannet population between 2006 and 2018 (as estimated by CapeNature) was 15,000 individuals hence we used it as our first gannet population value to base the equations on.
Statistical analysis All the data were entered into a database and further analyzed using the statistical package for social sciences (SPSS Inc. version 24. 0). Data are presented as mean ± SD or proportions. Parametric variables with normal distribution were compared using one-way analysis of variance (ANOVA) with Tukey, as the post hoc test. The non-parametric variables were compared using Kruskal-Wallis test. The groups were compared with t test (for continued variables) and chi-square for the categoric variables. A two-sided P-value of less than 0. 05 was considered to be statistically significant.
Discussion Given the fact that the proper surgical treatment for rectal lesions still remains controversial in different patients, having a large database with a large sample size will undoubtedly help surgeons to make a better decision about each patient individually  (19) (20) (21) (22) (23) (24). In this study with a large sample size, we examined all the short-and long-term outcomes as well as fertility results and draw comparisons between the two radical and conservative surgical methods. We showed that by choosing the right patient for each technique, all these methods are feasible and could be accompanied by excellent and acceptable outcomes. Regarding the weakness of our study, we could mention the lack of comparison of hormone therapy after the surgery in the three groups and its effect on disease recurrence in addition to the lack of comparison of the lifestyle and behavior of the patients in the management of complications after the surgery.
The 3D printer communicates with the computer via an ethernet cable using the Telnet protocol. The machine is controlled by the MATLAB script developed to convert the geometry to be printed into the G-code programming language used by the 3D printer. Then, the initial design of the structure can be modified by printing new geometries over the structure. This requires just a calibration step of the initial position of the extruder in a point of reference of the structure. In this demonstration case, the reference point used to calibrate the position of the extruder is the vertex at tip of the beam. The MATLAB script described in this section to manage the experimental setup is available into the github repository https:// github. com/ jesse paixao/ EASER.
Sequence alignment and antimicrobial prediction The amino acid sequence alignment between HSV-1 gB and Aβ42 was performed using the PyMol software after having depicted the 3D structure of HSV-1-gB and Aβ42 peptide (The PyMOL Molecular Graphics System, Version 2. 0 Schrödinger, LLC  [27] ). AntiBP2 software was used, with neural networks and support vector machines (SVM) to predict the amino-acid sub-sequence for a peptide with antibacterial activity. AntiBP2 utilizes four datasets to train their models: N-terminus based, C-terminus based, N+C terminus based and amino acid composition methods. These 4 methods are SVM trained on 4 different datasets, compiled using N, C, NC and full composition peptides respectively. For antiviral activity predictions, we employed the AVPpred software, which computes various features (i.