dataesr/scientific-paragraphs-categorization huggingface dataset:
g. Martínez-Minaya et al. , 2018). Conversely, if no temporal variability has been detected, a possible tracked populations, so the weight of each population in the species distribution is proportional to its size  (Beal, Dias, et al. , 2021; Beal, Oppel, et al. , 2021; Carneiro et al. , 2020; Davies et al. , 2021). In our simulated datasets, the indEffectTest was able to detect the effect of ISF as intended, as the WBR value increased with increasing simulated ISF. These datasets were simulated as noncolonial but central place forager individuals (i. e. each individual had a different starting position, but all trips from one individual started in the same location). These particular settings are just an example of the conditions under which tracking data may be collected, but users can use the code provided (see Section 2) and modify it to but simulate trips with characteristics similar to their real data (duration, number of positions and step length), in order to know the ability of the function to detect ISF in a dataset of those particular characteristics.
Applied to our GLS dataset of nonbreeding distributions of Cory's, Scopoli's and Cape Verde shearwaters, the proposed method detected an effect of the ISF in the distributions of two out of the 31 colonies tested. It did not detect an effect of temporal variability for any of the colonies, and there was spatial variability in species among the 21 colonies that were representative enough to enter the analysis. For most of the sampled colonies, the WBR value was high. For the colony of Filfla (Scopoli's shearwater), where the function detected a WBR of 53. 1% (i. e. the median within-individual overlap is above the majority of between-individual overlap values) indicating an effect of ISF in the population-level space use, the correct course of action to take was to select one single trip per individual.
For the rest of the colonies, no effect of the ISF was found, and we did not take any action on them. The general lack of ISF found in our shearwater dataset agrees with published evidence suggesting a lack of individual consistency in the use of foraging areas during breeding and in several migratory and nonbreeding parameters for both Cory's and Scopoli's shearwaters  (Courbin et al. , 2018; Dias et al. , 2011; Müller et al. , 2014; Zango et al. , 2019). At a population level, there are studies reporting interannual consistency in nonbreeding distribution and migration phenology of seabirds  (Bogdanova et al. , 2014; Legrand et al. , 2016) , and our results agreed with these findings, showing that withinindividual overlaps were mainly inside the 95% CI of betweenindividual overlaps for the three species.
y)p 2 (x, y)dx dy F I G U R E 1 Example results of the individual site fidelity (ISF) function. On the top panel, a simulated dataset with high ISF, with a WBR of 95%, and on the bottom panel a simulated dataset without ISF, with a WBR of 45%. The vertical blue line represents de median within-individual overlap, while the horizontal lines represent the 95% CI of each between-individual overlap. The CI represented in orange does not contain the median within-individual overlap, while those represented in green do. High proportion of orange intervals indicates high levels of ISF.
Downloaded from https://onlinelibrary. wiley. com/doi/10. 1111/ddi. 13642 by Readcube (Labtiva Inc. ), Wiley Online Library on [21/11/2022]. See the Terms and Conditions (https://onlinelibrary. wiley. com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License generate random points within a known distribution of the species (e. g. those provided by the BirdLife database for birds, or the International Union for Conservation of Nature, IUCN, website for species with a red list assessment), thus starting the process at step II in Figure 2. Although this second procedure simplifies the process, it has the drawback that the relative abundances within different regions of the distribution will not be correctly represented, and thus, the representativeness of each subpopulation will not be accurately represented.
The inclusion value is calculated as the number of locations from the simulated species distribution (created on the previous step) included in this subsample core area. This inclusion value is estimated sequentially from n = 1 trip until n = total of trips and for a user-defined number of iterations at each step. If the subsample is correctly representing the population distribution, the inclusion value should approximate the quantile for the UD (in this case 50%). As the number of randomly selected trips increases, the inclusion value increases as well, until it stabilizes at a point (an asymptote) when adding more trips to the dataset no longer increases the inclusion value. To calculate the asymptote, a nonlinear least squares model (nls function in R) is fitted, with the formula: where a and b are given start values of 1 and 0.
for each individual. It detects instances when trips from the same individual are more similar than trips from different individuals, which causes the areas preferred by the more represented individual to be overrepresented in the distribution at a population level, and it can help designing future tracking studies to avoid this effect. The solution will largely depend on the type of data, size of the dataset, the type of analysis to develop and the aims of each particular study. In general, researchers should aim to (a) subset the data so the sampling effort is evenly distributed among all individuals, for example, sequentially removing one random track from the repeatedly sampled individuals and testing for the effect of ISF again until the effect is no longer detected or (b) apply different weights to each track, with larger weights applied to trips of underrepresented individuals.
14724642, 0 , 0 Downloaded from https://onlinelibrary. wiley. com/doi/10. 1111/ddi. 13642 by Readcube (Labtiva Inc. ), Wiley Online Library on [21/11/2022]. See the Terms and Conditions (https://onlinelibrary. wiley. com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License generate random points within a known distribution of the species (e. g. those provided by the BirdLife database for birds, or the International Union for Conservation of Nature, IUCN, website for species with a red list assessment), thus starting the process at step II in Figure 2. Although this second procedure simplifies the process, it has the drawback that the relative abundances within different regions of the distribution will not be correctly represented, and thus, the representativeness of each subpopulation will not be accurately represented.
Results of the ISF test on simulated datasets Continuous predictors are mean-centred and scaled by 1 standard deviation. Effects with a p value <. 05 and/or a CI not overlapping 0 are considered significant and highlighted in bold. A parameter of the goodness of fit (adjusted R 2 ) is also shown. TA B L E 3 Within-between ratio (WBR, %) Resistance Noncolonial 0. 0 4. 8 0. 1 6. 3 0. 2 4. 3 0. 3 8. 3 0. 4 12. 2 0. 5 12. 9 0. 6 23. 4 0. 7 21. 6 0. 8 30. 7 0. 9 54. 7 1. 0 85. 8 Note: For resistances outside the allowed polygon from 0 to 1, simulating ISF from low to high (see Section 2), we calculated how many within-individual overlap values fell below, inside and above the 95% CI of the between-individual overlap, for datasets simulating both a noncolonial and a colonial species. Species Effect Estimate p Value 95% CI Cory's Intercept 41.
1 mm × 150 mm, MilliporeSigma) at 45°C. All samples were analyzed by full MS with polarity switching, and the QC sample was also analyzed by data-dependent MS/MS with separate runs for positive and negative polarities. Raw data were analyzed using Compound Discoverer 3. 1 (Thermo Fisher Scientific). Metabolites were identified either by accurate mass and retention time using an in-house database generated from pure standards or by querying the mzCloud database (https://www. mzcloud. org) with MS/MS spectral data and selecting matches with 50 or greater scores. Metabolite quantification used integrated peak areas from full MS runs. These values were corrected based on the periodic QC runs and normalized to the total signal from identified metabolites in each sample. Reporter assay for Dectin-1 activation by β-glucan.
Acknowledgments This study is supported by a  Campbell Foundation  grant to MAM; Commonwealth of Pennsylvania -COVID-19 funding to MAM;  NIH R01AA029859  to AK and MAM; a supplement to  NIH   R01 DK123733  to MAM, AL, and AK; and a supplement to  NIH   R24 AA026801  to AK. The  Wistar Proteomics and Metabolomics Shared Resource  is supported in part by  NIH Cancer Center Support  Grant  CA010815. The Thermo Fisher Scientific Q Exactive HF-X mass spectrometer was purchased with  NIH  grant  S10 OD023586. The LIINC study is supported by  NIH/National Institute of Allergy and Infectious Diseases   3R01AI141003-03S1  and  NIH/National Institute of Allergy and Infectious Diseases   R01AI158013. The  Rush University Medical Center Post-COVID-19 Clinic and Biorepository  is supported by an  Abbott Laboratories  grant to HW.
Fluorescent mAb staining Cells were stained for extracellular protein expression by incubation with fluorochrome conjugated mAbs in the dark at room temperature (RT) for 15 min. The Cells were then washed in phosphate buffered saline (PBS, ThermoFisher Scientific, Waltham, USA) supplemented with 0. 1% bovine serum albumin (BSA, Sigma-Aldrich, St Louis, USA) and centrifuged on a Beckman Coulter (Brea, USA) Allegra X-15R centrifuged for 7 min at 335 g before being fixed with 0. 5% paraformaldehyde (PFA; ProSciTech, Kirwan, Australia) in PBS and data acquired within 1 h.
Flow cytometry data acquisition and analysis Cells were analyzed on a four-laser LSRII flow cytometer (BD), with a minimum of 100 000 events collected. Daily QC was done using cytometer setup and tracking beads (IAW instrument operator manual) and compensation was performed with unstained cells and cells stained with a single mAb per tube conjugated to fluorochromes used in experimental sample analysis. Analysis was performed using FlowJo software (BD), with gated cell populations only included in the analysis if they contained a minimum of 20 events to minimize stochastic variation.
ACKNOWLEDGMENTS The authors thank all the healthy donors for their cooperation in providing blood samples and  Ms Michelle Bailey  and  Dr Yin Xu  for assistance with flow cytometric isolation of T cell populations. This work was funded by the following sources:  Australian Government Department of Health  and Aging; the  NHMRC  via a Program (510448) grant, a  Practitioner Fellowship  (ADK); and an  Australian Postgraduate Award  and a  UNSW Research Excellence Scholarship (LC). NS, JZ and ADK, in conjunction with  St Vincent's Hospital, Sydney, Australia , hold a patent for the  CD25 + CD134 + CD39 + assay (PCT/ AU2008/001407 ). Open access publishing facilitated by  The University of Melbourne , as part of the  Wiley -The University of Melbourne agreement via the Council of Australian University Librarians.
17, 18 e aim of the FUSION NHL 001 study was to determine the safety and tolerability of durvalumab when given in combination with lenalidomide ± rituximab, ibrutinib, or rituximab ± bendamustine in patients with lymphoma or CLL. The safety and efficacy of durvalumab were also assessed in patients receiving the recommended phase 2 dose (RP2D) of these treatment regimens as well as durvalumab monotherapy. Previously reported data showed that PD-L1 expression is associated with poor prognosis in patients with DLBCL. 19 In addition, in patients with non-small cell lung cancer or urothelial cancer receiving durvalumab monotherapy, elevated PD-L1 expression and interferon (IFN)-γ scores in baseline tumor biopsy samples were associated with higher overall reaponse rate (ORR) or improved survival.
| Statistical analysis Sample-size determination established that a maximum of 60 patients was required for the dose-finding part, and a maximum of 100 patients was required for the dose-confirmation part. Celgene, together with AstraZeneca/MedImmune, decided that the dose-expansion part was not to be opened. As a consequence, the entire study was to enroll a maximum of approximately 160 patients. All primary and secondary statistical analyses were conducted with SAS ® version 9. 1 or higher (SAS Institute, Inc. , Cary, North Carolina, USA). The safety population included all patients who received at least one dose of study drug. The efficacy population included all patients who completed at least one cycle of their assigned treatment and had baseline and at least one post-baseline tumor response assessment.
| DISCUSSION Many existing studies have reported additional benefits of the combination therapies included in the current report in patients with various hematologic malignancies. In the phase 2 PCYC-1104 study (NCT01236391),  26  111 patients with R/R MCL received ibrutinib 560 mg daily and had an ORR of 68% (n = 75), with a complete response rate of 21% and a partial response rate of 47%. With a median follow-up of 15. 3 months, median PFS was 13. 9 months and median overall survival was not reached. RESONATE was a multicenter, open-label, phase 3 study (NCT01578707) in which 391 patients with R/R CLL or SLL were randomly assigned to receive daily ibrutinib or the anti-CD20 antibody ofatumumab. In this study, the investigator-assessed ORR was significantly greater in the ibrutinib group than in the ofatumumab group (85% vs.
This was a phase 1/2, openlabel, international, multicenter study (NCT02733042) initially planned in three parts with four treatments. Phase 1 consisted of a dose-finding and a dose-confirmation part, and phase 2 was a planned dose-expansion part. Patients were assigned to one of the four treatment arms that evaluated durvalumab in combination with lenalidomide ± rituximab (Arm A), ibrutinib (Arm B), rituximab ± bendamustine (Arm C), or as monotherapy (Arm D). The entire study was anticipated to last approximately 8 years, with an anticipated study duration for any patient of up to approximately 3-8 years depending on the assigned treatment arm and patient's disease histology. The first patient visit was on May 3, 2016. On September 5, 2017, enrollment of new patients into Arm A was discontinued, based on a partial clinical hold placed by the US Food and Drug Administration resulting from risks identified in trials of pembrolizumab in combination with immunomodulatory agents in patients with multiple myeloma.
ACKNOWLEDGMENTS The authors would like to thank the patients enrolled in the study as well as associated clinical trial teams. Several former and current BMS employees contributed to various aspects of this study:  Suzana Couto ,  Katie Newhall , and  Lara Stepan  contributed to the biomarker analyses;  Sabine De Bedout  had key contributions to designing, overseeing, and leading the study. The authors received editorial support in the preparation of this manuscript from  Lauren Gallagher ,  RPh, PhD , of  Peloton Advantage, LLC , an  OPEN Health company, Parsippany, NJ, USA , sponsored by  Celgene , a  Bristol Myers Squibb company, Princeton, NJ, USA. The authors, however, directed and are fully responsible for all content and editorial decisions for this manuscript.
Measure of wings Adult flies were kept in 70% ethanol for 48 h and transferred into PBS glycerol (1:1 v/v). Wings were dissected and mounted on glass slides, dorsal side up, in Hoyer's medium. Slides were scanned with a Hamamatsu Nanozoomer Digital Slide scanner, running the Nanozoomer software with a 20x objective and an 8 bit camera. Wing pictures were separately exported into TIF format using NDP. view and the 5 x lens. Measurements of wing length were performed as described in  [28].
72). Reads were then aligned against the D. melanogaster genome (dm6 genome assembly, release 6. 30) using STAR (Galaxy Version 2. 6. 0b-2). Reads were counted using FeatureCounts (Galaxy Version 1. 6. 0. 6). Differential analysis was performed using DESeq2 version 1. 32. 0. Gene ontology was analysed with DAVID (https://david. abcc. ncifcrf. gov/home. jsp). The RNA-Seq gene expression data and raw fastq files are available at the GEO repository (https://www. ncbi. nlm. nih. gov/geo/ info/seq. html) under accession number GSE181926. RT-qPCR were performed on wing imaginal disc cDNAs as described in  [28]. Expression levels were quantified with the Pfaffl method  [33]  and normalized to the geometric mean of two reference genes, GAPDH and Spt6, the expression of which did not vary in the mutants.
Study Population Normal weight and obese adolescents  (12-17 year)  were recruited to participate in this study. Adolescents enrolled in a pediatric weight management clinic in the south of France who had a body mass index (BMI) z-score > 3 (defined as severe obesity) were invited to participate. Eighteen puberty-matched normal-weight volunteers were recruited from the community to serve as controls. In order to avoid seasonal variations, all adolescents were considered for inclusion between March-April 2015 and March-April 2016. Written informed consent was obtained from all adolescents and their parents. The study was approved by Ethics Committee CPP Sud-Mediterranee III (2015-000060-34) and performed in accordance with the principles outlined in the Declaration of Helsinki. The larger VIDADO study was registered in the ClinicalTrials.
gov database (NCT02400151, last update posted 19 June 2017), and the detailed experimental design and population recruitment procedure have been previously reported  [15]. Obese adolescents were randomized by blocks of random size (2 or 4), with a 1:1 ratio into two groups (SAS software version 9. 4, SAS Institute, Cary, NC, USA). All obese participants followed a three-month weight-loss program. As this was a double-blind trial, all participants were also asked to drink a fruit juice each morning with (OS, n = 13) or without (ONS; n = 13) VD supplementation (4000 IU/day of VD 3 Uvedose ® (Crinex, Gentilly, France) 100,000 IU/2 mL)  [16, 17]. Two adolescents in the OS group left the clinic before the end of the program for personal reasons (at 3 months, OS = 11) (Figure  1 ). Throughout the clinic program, participants received both standard and personalized balanced meals prescribed by dieticians and based on a balanced distribution of macronutrients carbohydrates (55%), proteins (15%) and lipids (30% total, with less than 10% saturated fat).
The carotid IMT (mm), defined as the distance from the leading edge of the lumenintima interface to the leading edge of the media-adventitia interface of the far wall, was measured and averaged automatically by the analysis software (MyLabDesk, Esaote, Italy) according to the Mannheim consensus. Carotid artery compliance (CAC, mm 2 /mmHg) was calculated as CAC = π(Ds2-Dd2)/4PP (Ds and Dd are systolic and diastolic arterial diameters, respectively; PP is pulse pressure, measured on the left arm by an automated system (Dinamap, GE Medical Systems, Milwaukee, WI, USA)). Within-subject variation was 1. 8% for arterial diameters  [19].
The study was approved by the Ethical Committee of AOU Maggiore della Carità, Novara (Protocol 571/CE date of approval 20/05/2020). Statistical data analysis was performed by the use of SPSS Statistics Software 23. 0 (IBM SPSS Inc. , Chicago, IL, USA). Quantitative variables were described using median and interquartile range. Absolute frequencies and percentages were used for qualitative variables. ANOVA or the Mann-Whitney and chi-square test were used for continuous and categorical variables, respectively. Normal distribution of continuous variables was tested by the Kolmogorov-Smirnov test). Primary study endpoint was in-hospital mortality. Secondary study endpoints were postprocedural TIMI 3 flow and 30-day mortality. We used the propensity score technique to account for potential confounding between groups, as previously described  [33, 34].
Participant sampling The interviewed GPs were recruited from a list provided by the French national public health insurance system (CNAM). The women were recruited by snowball sampling or through their GPs (but not those interviewed for the study). Other healthcare professionals were recruited using snowball sampling. Sampling was purposive for all types of participants. Nobody refused to participate. Diversification criteria were applied in order to obtain a broad range of participants and points of view. Diversification criteria were discussed with the research team for all participants and were completed during data collection (table  1 ). Each interviewee gave her/his verbal and written informed consent prior to inclusion.
Data collection Audiotaped, semi-structured interviews were held faceto-face at the healthcare professional's office or at home. One of the midwives and one of the screening programme managers underwent a phone interview. The interview guides, developed by the investigators, were similar between the groups interviewed but each had some specificities. They explored perceptions, Open access attitudes and expectations related to breast cancer, diagnosis, prevention, screening and the DA. 6] [17] [18] [19] [20] [21]  This enabled participants to state their opinions and expectations with regard to these tools and to describe the tools' strengths and limitations. Field notes were made during and after the interviews. A woman with history of breast cancer helped to build the interview guide of women's and GPs' groups and pilot tested it.
Data analysis All interviews were transcribed verbatim and subjected to an inductive analysis based on grounded theory to analyse social interactions. 22 Next, the interview data were coded jointly by two pairs of investigators (MH+AB, A-AE+LB) and, in order to enhance intercoder reliability, individually by four other investigators (BF, EF, YR and IA). We used MAXQDA software (V. 12, VERBI Software, Consult-Sozialforschung GmbH, Berlin, Germany) for the analysis. Similarities and differences in the codes from the interviews were assessed and discussed by all the investigators until a consensus was formed. Data collection was achieved for each kind of participants after two interviews without new codes.
With DISCO, the DIachronic Spanish Sonnet COrpus, we collected 4,085 sonnets written from the fiftheenth to nineteenth centuries, including canonical and lesser-studied authors from both Spain and Latin-America, with detailed author metadata, metrics, rhyme scheme, and enjambment annotations. The dataset is available in public repositories, offered in plain text and TEI, and enriched with RDFa, a linked data format. The corpus was intended for research and teaching, as well as for non-specialist use. Some questions naturally emerge: How can we easily navigate this corpus and its rich metadata? How can we identify trends using its annotations? How can users not proficient in XML query languages and linked data benefit from such a dataset? To address these issues, we have created DISCOver, a user-friendly web interface that allows users to explore the DISCO corpus.
Introduction In this chapter, we would like to present DISCOver (https://prf1. org/discover/), an interface that provides both descriptive and analytical tools that allow users to explore the DIachronic Spanish Sonnet COrpus (DISCO). This is a dataset we started creating in 2017 that is available on GitHub 1 and Zenodo, 2 offered in plain text and XML-TEI, and enriched with RDFa, a linked data format  (Ruiz Fabo et al. , 2021). The sonnet is of prime importance in European poetry; an interface that allows users to explore a comprehensive corpus of sonnets is thus relevant for literary scholarship. One goal of this interface is to offer a set of functions that help users to explore the corpus in an intuitive way. The target users are not just literary scholars but also students and non-specialists.