dataesr/scientific-paragraphs-categorization huggingface dataset:
The ne lines represent the snow free dates for all MODIS satellite image pixels within the study area and the thick line connects the annual median values across pixels. Map data from Natural Earth (naturalearthdata. com), Landsat 5 and topographic model was downloaded from mapbox (www. mapbox. com). Note: The designations employed and the presentation of the material on this map do not imply the expression of any opinion whatsoever on the part of Research Square concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. This map has been provided by the authors. The designations employed and the presentation of the material on this map do not imply the expression of any opinion whatsoever on the part of Research Square concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries.
Acknowledgements Thanks are due to  Chris Fiedler ,  Ursula Scuderi  and  Liam Kelly  who contributed to environmental data collection, nest monitoring and banding, including geolocator deployment and retrieval. We are also grateful to  Heiko Schmaljohann  for giving speci c advice for eldwork methods and trapping, to  Michele Ottino  and staff of the  Ente di Gestione delle Aree Protette delle Alpi Cozie  for logistical support, and  Enrico Caprio  and ornitho. itfor providing the citizen science data. We further thank the  German Ornithologists' Society  for supporting this project with a research grant (designated to MM Sander) to fund the Migrate Technology Ltd. geolocators. This work is a collaboration between the  University of Turin  and the  Alfred-Wegener Institute Helmholtz Centre for Polar and Marine Biology in Potsdam , which was the hosting institute during data analysis and manuscript writing.
Data availability Geolocator data including the raw light recordings, the annotated twilight les, the location estimates with credibility intervals and the R code will be uploaded onto Movebank (www. movebank. org) upon paper acceptance. R code for Satellite data manipulation and Northern wheatear sightings can be accessed at https://github. com/slisovski/Sander_et_al_Analyses and will be uploaded to a public repository (Zotero) upon paper acceptance. Field observations including nest site occupation, clutch size, hatching and edging success as well as snow and vegetation monitoring data is available upon request.
, 2020). QTLs were identified on the genetic maps for frost tolerance, as well as bruchid and aphanomyces resistance. Bruchid beetle infestation is particularly problematic in faba bean with increasing restrictions on insecticide use. Syntenic relationships between frost tolerance QTLs in pea and faba bean were revealed. New sources of frost tolerance and bruchid resistance were identified  (Carrillo-Perdomo, Klein, et al. , 2019; Carrillo-Perdomo, Raffiot, et al. , 2019)  in a reference faba bean collection. This collection was exome sequenced, and seeds were phenotyped using X-ray 3-D tomography (to detect and quantify bruchid infestation in the bean) for further GWAS analyses. Proteomics, volatile organic compounds (VOCs), and/or RNAseq data were obtained for RIL parental lines and families in order to identify molecular pathways underlying bruchid and Aphanomyces resistance.
| BIOINFORMATICS AND DATA MANAGEMENT SUPPORT The project was supported by data management and computing services. A data repository was created specifically for the project, which made all data available to partners directly after their production and which has facilitated data integration in public and private repositories. The latest genotyping and sequencing technologies were used for producing numerous genomic resources for pea and faba bean (exome capture SNP detection and genotyping databases on large pea and faba bean panels, transcriptome unigene resources in faba bean). To assure access after project end, results will be integrated and maintained for the Pea community on the GnpIS database at URGI. Some data are already published and can be accessed through the PeaMUST-dedicated web page: https://urgi.
Study design and procedures This was a cross-sectional community-based study. The investigators were organized in three teams, each team consisting of a final-year medical student from the"Hopital de l'Amitie" in Bangui and a local village resident who had been involved in previous surveys. NS cases were identified using an active case detection approach via door-to-door visits in the first district of Landja. This district was chosen for two reasons: firstly, it was in this district that the Fracarita focal point initially suspected HN cases among children and issued the alert; secondly, for logistical reasons in particular the easy access to the zone. Of note, no data on Onchocerca volvulus endemicity were available in this area at that time. All the households were investigated and after presenting the study objectives, informed consent was obtained from the household head or his representative.
A fourth questionnaire (S4 File) was used by a Medical Doctor (SM) to obtain additional data from confirmed NS cases regarding the onset and natural history of NS, including antenatal and childhood history, psychomotor development, medical and surgical history, history of medication use, and symptoms experienced before/after the onset of nodding seizures. Persons with confirmed clinical NS agreed to undergo electroencephalogram (EEG) ("DELL de Natus Medical Incorporated, DBA Excel-Tech LDT. (XLTEK). 2568 Bristol Circle, Ontario, L6H5S1 Canada") performed by the neurologist (PM) from Bangui. Once diagnosed with NS, the patients received anti-epileptic treatment, and were invited to attend monthly or quarterly follow-up visits with a neurologist.
Finally, Appendix (D) contains mathematical results which constitute the skeleton of the work, but whose proof would be too long to integrate in the core of the paper. This work is based on Selma Souihel's PhD thesis where more extensive results can be found  [67]. In particular, there is an analysis of the conjugated effects of retinal and cortical anticipation, subject of a forthcoming paper, and briefly discussed in the conclusion. In all the following simulations, we use the CImg Library, an open-source C++ tool kit for image processing, in order to load the stimuli and reconstruct the retina activity. The source code is available on demand.
Angular anticipation We investigate in this subsection a two dimensional example of motion where angular anticipation takes place. The stimulus consists here of 72 frames, displayed at 100 Hz, of a bar moving at a constant angular speed of 4. 25 rad/ms. Fig. 16  shows the retina response to a rotating bar, with the angular orientation of activity as a function of time for the different models. We used Matlab to estimate the bar orientation from the displayed activity, fitting the set of activated points by an ellipse whose principal axis determines the response orientation. In the three cases, one can see that the response around the center of the bar is suppressed due to gain control adaptation. While the gain control activity orientation roughly follows the linear response ( Fig. 16 (B )), the ACells response shows a slight angular shift (frames : 250-300 ms) which is also visible on the response orientation time course.
Funding This work was supported by the National Research Agency (ANR), in the project "Trajectory", https://anr. fr/Project-ANR-15-CE37-0011, funding Selma Souihel's PhD, and by the interdisciplinary Institute for Modelling in Neuroscience and Cognition (NeuroMod http://univ-cotedazur. fr/en/idex/projetstructurant/neuromod ) of the Université Côte d'Azur.
Bacillus subtilis cells display limited width variability during rapid exponential growth It has long been accepted that, in contrast to E. coli, the cell diameter of B. subtilis cells remains virtually constant regardless of the growth rate  (32, 33). We wondered how variable the cell diameter could be in isogenic B. subtilis populations during fast exponential growth. We used MicrobeJ, a Fiji plugin  (44) (45) (46) , to perform cell segmentation and quantify cell diameter (see 'Material and methods', Table  S2 , Sup. Information). We first compared six independently acquired datasets of wild type B. subtilis cells grown to exponential phase in rich LB medium. We observed that the average width remained remarkably constant between experiments (variability below 2 %; Fig. 1A  and Table  S3 ).
The cell-to-cell variability and the average cell widths noticeably increased when measurements were performed on HCSm-acquired images but the relative difference of width between the two mutant strains and the wild type were perfectly conserved (Fig. 1C ). These control experiments showed that mutants affected for the control of width could be identified in our medium-throughput HCSm approach. Next, we screened the complete B. subtilis kanamycin-marked ordered deletion library (BKK)  (24) , which contains 3 983 single-gene deletion mutants (~93 % open reading frames coverage) of the parental 168 strain (GenBank Al009126) (Fig. 2 , see 'Materials and methods' for details). In order to prevent plate-to-plate fluctuations and to compare the widths of the mutants across plates, the width of each mutant was expressed relative to the average cell diameter per plate (ADP, see 'Materials and methods').
4A ). While the BKK ∆rpe showed thin and regular cell diameters with a dispersion of values similar to the control strain, widths of the backcrossed mutant displayed the largest variability of our dataset (Fig. 4A , Fig. 3B  and Table  S5 ). Furthermore, the backcrossed ∆rpe mutant formed small slow growing colonies while its BKK parent did not (Fig. S5 ). Taken together, these results suggest that the ∆rpe mutant present in our BKK collection had acquired some suppressor mutation(s), partially restoring its growth and reducing its width variability. The second strain with a variable diameter was ∆minJ (Fig. 3B  and Table  S5 ). This mutant of the "Min" system involved in division site selection, displays reduced septation, leading to long filamentous cells (Fig. 4B )  (52, 61). Although the average width of ∆minJ cells was marginally affected (-1%), the SD was unusually large, with widths ranging from 0.
Transformants were selected on LB agar plates supplemented with MgSO 4 and neomycin. For the determination of generation time (GT), cells from overnight cultures were diluted to a fixed starting OD 600nm of 0. 01 in fresh LB medium supplemented with MgSO 4 in 96-well cell culture plates (CellStar) and grown in a microplate reader Synergy2 (BioTek Instruments, Vt, USA) at maximum rpm at 37°C. GT was calculated using a Matlab script available at the following link: https://github. com/CyrilleBillaudeau/GenerationTime_ofBacteria_withOD. General screening procedure. Our screening was performed on the BKK library (24) using HCSm setups (see 'High content screening microscopy'), leading to the selection of 3 974 out of the 3 983 mutants from this collection (9 clones were absent from the published library or failed to re-grow).
Epifluorescence images of the membrane-stained cells were acquired on a previously described setup equipped with a 100 × objective  (36). Image processing and cell size quantification. The post-acquisition treatment of the images was done with the Fiji software and the measures (mean cell diameter and length) with the MicrobeJ plugin  (44) (45) (46). In MicrobeJ, the cell width was calculated as the mean value along the medial axis of the cell. The parameters used for the MicrobeJ module are listed in Table  S2. Cells aggregates were excluded and segmentation was manually corrected when necessary. During high-throughput screening, the cell width of each strain was calculated as the mean of 225 cells (in average). When the four-image set contained less than 30 measurable cells, a new acquisition was performed.
2015). The obtained spectra were imported and analysed using Biotyper 3. 0 software. They were then incremented in our local mass spectrometry database (https://www. mediterranee-infection. com/urms-data-base). No identi cation was successful using MALDI-TOF MS. Therefore, sequencing of the 16S rRNA gene was performed for each of the studied strains using the primer pair fD1 and rP2  (Weisburg et al. 1991). They were sequenced using the Big Dye® Terminator v1. 1 Cycle Sequencing Kit and 3500xL Genetic Analyzer capillary3500xL sequencer (Thermo Fisher, Saint-Aubin, France), as previously described  (Lo et al. 2016 ). The 16S rRNA nucleotide sequences were assembled and corrected using CodonCode Aligner software (http://www. codoncode. com).
Genomes sequencing and analysis The total DNA of the genomes was recovered using the EZ1 biorobot (Qiagen, Courtaboeuf, France) and the EZ1 DNA tissue kit. Sequencing was performed using MiSeq technology (Illumina, San Diego, CA, USA) with the Nextera Mate Pair sample prep kit and Nextera XT paired end (Illumina), as previously described  (Morel et al. 2015). Several bioinformatics, including Velvet (Zerbino and Birney 2008), Spades  (Bankevich et al. 2012 ), and SOAPdenovo  (Luo et al. 2012 ) were used to assemble the genomes. GapCloser software  (Xu et al. 2019 ) was used to reduce assembly gaps. Scaffolds which had fewer than 800 base pairs (bp) or had a depth value lower than 25% of the mean depth were removed. The best assembly was selected using different criteria (number of scaffolds, N50, number of N).
The degree of genomic similarity of each strain was evaluated by processing sequences using the Orthologous ANI Tool (OAT) software  (Lee et al. 2016). Furthermore, the Genome-to-Genome Distance Calculator (GGDC) web server, which is available online (http://ggdc. dsmz. de), was used to calculate DNA-DNA hybridisation  (DDH)  values between the genomes of closest species, as previously described (Meier-Kolthoff et al. 2013).
The genome and 16S rRNA sequence were deposited in GenBank under accession numbers OPYI00000000 and LT972121, respectively. Description of Peptoniphilus urinimassiliensis sp. nov. Peptoniphilus urinimassiliensis (u. ri. ni. mas. si. li. en'sis composed of u. ri. ni L. masc. adj. for urine, from which strain Marseille-P3195 was isolated and mas. si. li. en'sis, L. masc. adj. massiliensis from Massilia, the Latin name for Marseille, France, where the type strain was rst isolated). Colonies are grey and circular. Bacterial cells are Gram-positive sphere-shaped, non-spore forming. Catalase or oxidase activities are not detected. growth is at 37°C in anaerobic atmosphere on sheep blood-enriched Columbia agar. Strain Marseille-P3195 exhibits positive reactions for glycerol, fucose, ra nose, maltose, lactose, melibiose, D-trehalose, esculin ferric citrate, N-acetyl-glucosamine, sorbitol, dulcitol, galactose, glucose, fructose, arabinose, ribose, xylose, esterase lipase (C8), acid phosphatase, and naphthol-AS-BI-phosphohydrolase.
The major fatty acids are C 16:0 (31%), C 18:1n9 (25%), and C 18:2n6 (24. 2%). The genome size and G + C content of strain Marseille-P3195 are 1,822,830 bp and 49. 7 mol%, respectively. The type strain Marseille-P3195 T (= CSUR P3195 = DSM 103468) was isolated in a urine sample from a young man who had just received a kidney transplant for genetic focal segmental glomerulosclerosis. The genome and 16S rRNA sequence were deposited in GenBank under accession numbers FTPC00000000 and LT598577, respectively.
In the SENTINA and the ACOSOG Z1071 trials, FNRs were 12% and 14% respectively, and thus higher than the arbitrarily chosen but widely accepted cut-off value of 10% (Table  3 ). So far, however, only limited data regarding the oncologic outcome following SLNB alone are available in this setting  [3]. Marking positive lymph nodes at the time of diagnosis and prior to neoadjuvant chemotherapy with clips, coils, radioactive seeds, or other markers may improve the FNR of de-escalated surgical staging procedures  [7, 8]. The best marking technique, however, has not been unanimously identified yet. Importantly, data comparing recurrence rates and surgical morbidity among SLNB, ALND, and TAD are so far not available. As a result, the German S3 guidelines updated in 2020 recommend ALND after NACT in cN+ patients, as do Austrian and Scandinavian guidelines.
Not provided India  [17]  No specific recommendation for cN+ ycN0 patients Not provided Poland  [18]  SLNB can be an option with some limitations:   1 Sentinel nodes with isolated tumor cells [ypN0(i+)] defined as positive. 2 Only in patients with at least 2 sentinel nodes removed (pre-defined study criterion); in case of only one sentinel node removed, the false negative rate was 29. 3%  [7]. In order to shed light on this much debated topic, the European Breast Cancer Research Association of Surgical Trialists (EUBREAST) has initiated AXSANA (AXillary Surgery After NeoAdjuvant Treatment), a multinational prospective cohort study (NCT04373655) which enrolls cN+ patients undergoing NACT who convert to ycN0. The aim of AXSANA is to assess the impact of different surgical staging procedures in the axilla on the oncologic outcome and on health-related quality of life.
Still, the success of target lymph node (TLN) removal depends on the ultrasound visibility of the clip inserted before NACT. The study that brought international attention to the technique was a retrospective analysis of a prospective database at the M. D. Anderson Cancer Center (Table  5 )  [8]. Nearly all patients in this study underwent ultrasound-guided placement of a radioactive iodine-125 seed into the previously clipped node prior to surgery. This strategy offers more flexibility than wire localization, which was used in two patients only, because the seed can be inserted several days before surgery, whereas the wire placement is usually scheduled for the morning before the operation or (rarely) the day before. The study by  Caudle et al. showed that the FNR of TAD can be as low as 2.
Secondly, both the localization of iodine-125 and technetium-99 used for SLN mapping require a gamma probe so interference might potentially occur in case of down-scatter of technetium-99m into the energy spectrum of iodine-125. The first results of the RISAS trial (NCT02800317), presented by Simons et al. at the San Antonio Breast Cancer Symposium in 2020  [53] , could, however, show that the combination of the MARI technique and SLNB is feasible: TAD was successfully performed in 223 out of 227 (98%) patients. The trial was designed to test the non-inferiority of TAD over ALND, with FNR as the main endpoint. Non-inferiority was assumed if the upper bound of a 95% confidence interval around the FNR was lower than 6. 25%. Although the FNR was low (3. 5%), the prespecified primary endpoint was not met (95% confidence interval 1.
When Should Lymph Nodes Be Marked? To date, there is no consensus on the optimal timepoint of marker placement. In most studies, lymph node metastases were confirmed by fine needle aspiration or core biopsy. Such procedures, however, are not standard in some countries, and not all guidelines recommend routine minimally invasive biopsy in case of suspicious findings. Especially in case of large tumors and multiple highly suspicious nodes, clinicians may find it sufficient to perform biopsy of the breast tumor only. If a minimally invasive biopsy is performed, the marker may be inserted into the same lymph node(s) at the same session or at a second session upon confirmation of metastasis by pathology/cytology. Data on this aspect lack detail in available studies but most authors report the placement of the marker into the "previously proven" node  [44, 48].
For patients with ≥4 positive nodes before NACT, axillary radiotherapy is always indicated but patients with non-pCR are also recommended an ALND. In a cohort of 100 patients treated by TLNB (MARI) and ALND, the proposed algorithm would have led to omission of ALND in 74%, and some patients potentially risk under-(3%) or over-treatment (17%)  [65]. Whether such tailored strategies might be an acceptable compromise between high oncological safety on one side and lower arm morbidity on the other remains to be clarified in future trials. In this context, the results of the NSABP-B51 trial (NCT01872975) are expected to be published in 2023. This phase III clinical trial is designed to test whether regional nodal irradiation (RNI) improves the recurrence-free interval rate in women with cN1 breast cancer before NACT who become pathologically node-negative at the time of surgery.
Patients who undergo mastectomy are randomly assigned to observation or radiotherapy to the chest wall and undissected axilla, internal mammary nodes, and ipsilateral supraclavicular fossa, whereas women who undergo breast-conserving surgery are randomized to adjuvant whole breast irradiation vs. whole breast and regional nodal irradiation. In the ALLIANCE A011202 (NCT01901094) trial, women with node-positive status before NACT receive SLNB at the time of surgery. Patients with axillary residual disease are randomized to completion ALND and RNI vs. RNI alone.
Arm morbidity and quality of life are evaluated at baseline and after 1, 3, and 5 years, using four val-idated questionnaires (EORTC QLQ-C 30, EORTC QLQ BR 23, Lymph-ICF, and Sense of Coherence). Financial support has been provided by the AGO-B study group, the AWOgyn (German Working Group for Reconstructive Surgery in Oncology-Gynecology), Claudia von Schilling Foundation for Breast Cancer Research, EndoMag, Mammotome, and MeritMedical. AXSANA is further supported by the North-Eastern German Society of Gynecological Oncology (NOGGO) and the German Breast Group (GBG). The first AXSANA study site was opened in Germany in June 2020, and recruitment began the same month. Currently, there are 328 patients enrolled. Twenty countries are participating in the study, most of which are in the process of applying for ethical approval.
• Which staging technique should be recommended to cN+ patients converting to ycN0? • Is imaging helpful in identifying patients most likely to achieve pCR in the axilla? If yes, which method should be recommended? • Should cN1 and cN2/3 patients be offered different surgical strategies for axillary staging? • Which lymph node marking technique offers highest rates of successful TAD/TLNB? Due to high complexity and discordant recommendations, a randomized trial comparing different techniques seems hardly feasible and therefore would not clarify currently open issues within a reasonable timeframe. In the AXSANA study, patients are treated at physicians' discretion. To allow comparisons between different cohorts (SLNB, TLNB, TAD, ALND), detailed data regarding clinical and pathological parameters are obtained.
Among these 29 secreted proteins, 11 were down-regulated while 18 proteins were up-regulated. The heat map of deregulated secreted proteins (Figure  1B ) confirmed the coherence of the iTRAQ ratio (Mecp2 KO vs WT) obtained from the two independent replicates with the highest fold change for Lcn2 (iTRAQ ratio KO/WT 0. 31), Lgals1 (iTRAQ ratio KO/WT FG 0. 35), Mfap4 (iTRAQ ratio KO/WT FG 2. 83), and Enpp5 (iTRAQ ratio KO/WT FG 2. 54) (Table  1 ). Although our analysis highlighted a small number of proteins for global profiling (29 deregulated secreted proteins), this study provides the first proteomic insight into astroglial-secreted factors in RTT. The secretomic data were deposited to the Pro-teomeXchange Consortium via the MassIVE Dataset Submission  [24]  under the MassIVE MSV000085665 identifier (http://massive.