dataesr/scientific-paragraphs-categorization huggingface dataset:
This study is listed on clinicaltrials. gov (NCT 03448458). The radiotracer was labeled using a provided NETSpot kit (Advanced Accelerator Applications USA, Inc. Millburn, NJ, USA) and generator produce [ 68 Ga]Ga (Eckert & Ziegler Radio-pharma, Inc. Berlin, Germany). Safety monitoring during the drug infusion was performed, and no adverse events were recorded. Written informed consent was obtained from every study participant. This study did not interfere with standard patient evaluation or delayed therapy. Male patients with known biopsy proven mCRPC were selected under the inclusion criteria of 18 years of age or older, with skeletal, visceral and/or nodal involvement, and able to undergo [ 68 Ga]Ga-DOTATATE PET-CT. Patients were previously treated with a combination of ADT ± antiandrogen therapy or chemotherapy prior to diagnosis of mCRPC and subsequently were treated with either hormonal therapy or chemotherapy after mCRPC status (Table  1 ).
The data were gathered from a convenience sample of adult participants and therefore may not generalize to all people or communities in the United States. Additionally, behavioral intention and willingness were measured with single survey items, thereby preventing reliability estimates. Future research might explore behavioral beliefs related to mitigation behaviors as well as the mitigation behaviors directly with additional samples and using alternative instruments. Despite limitations, the results have actionable implications. Taken together, findings from this study can be used to inform communication efforts that empower people to find accurate information regarding their health decisions, including engagement in mitigation efforts during the COVID-19 pandemic. Lessons can also be applied to the development of relevant messages targeting specific beliefs and encouraging behaviors that promote public health more quickly and effectively during the next pandemic or another public health crisis.
Quality tests for loci and samples There was a substantial number of blanks (Bs) (no amplification) and unreadable genotypes (Us) (Supplementary file S1, available at https://zenodo. org/record/7234790). We thus used the same approach as the one developed by Kaboré et al. (Kaboré, MacLeod et al. , 2011). If missing data (Bs and Us) translates into poor quality of corresponding isolates (poor conservation conditions of the extract, poor PCR conditions and/or outlier individuals displaying poor match of primers with targeted flanking sequences), this should then also correlate with an increase of dropouts of one allele in heterozygous individuals (fake homozygous profiles). We thus expected a negative correlation between the number of blanks (NBs) and the number of heterozygous loci (NHz), in the same individual, and between the number of unreadable loci (NUs) and NHz.
Finding the relevant structure levels Population genetics analyses were performed on dataset previously converted into the appropriate format by Create v2. 37  (Coombs, Letcher et al. , 2008). We first tried to study the effect of cohorts. To do this, we tested subdivision between each possible cohort of the same quarter. This was done with the G-based test  (Goudet, Raymond et al. , 1996)  over all loci with 10,000 randomizations of individuals between subsample pairs. This procedure was identified as the most powerful way to combine tests over loci  (De Meeûs, Guégan et al. , 2009). This procedure could only be undertaken in Cotonou subsamples, more precisely in Agla, Ladji and Saint-Jean neighborhoods, and between cohorts 37 and 39 (see Table  1  and Supplementary File S1, available at https://zenodo.
This was tested with a two-sided Spearman rank correlation test with rcmdr. For FIS comparisons between data with or without cohorts, we used a one-sided Wilcoxon signed rank test for paired data with rcmdr, the pairing unit being the locus. To test for the effect of neighborhoods (quarters), we could only use subsamples from Benin, cohorts 37 and 39 separately, because of temporal issues or missing information. We measured the subdivision index (FST) in each cohort, and tested its significance with the G-based test in Fstat 2. 9. 4. We then averaged the FST, and FST', and combined the two p-values with MultiTest, as described above. We also used 95% confidence intervals (95%CI) obtained by 5,000 bootstraps over loci in Fstat 2. 9. 4.
We used the Cavalli-Sforza and Edward's chord distance  (Cavalli-Sforza & Edwards, 1967)  computed in FreeNA  (Chapuis & Estoup, 2007)  without null allele correction. This method is expected to provide the most accurate tree topology between Operational Taxonomic Units (UTOs) (here subsamples)  (Takezaki & Nei, 1996). Statistical scripts (simple R commands) are provided in the Material and Methods section.
Specificity of primers Raw data are available online in file S1 (https://zenodo. org/record/7234790). Among the 225 investigated rodents, 183 (81%) were found qPCR-positive for T. lewisi, 16 (7%) were qPCR-negative, and 26 (12%) were not tested or provided inconclusive results (NA). Several NA individuals nevertheless provided usable microsatellite profiles. The specificity for T. lewisi of the nine microsatellite primer pairs was tested using DNA from 15 other Trypanosomatidae species: none of these was amplified by any of the nine primer pairs (data not shown).
Quality tests for loci over the entire dataset All correlation tests between number of heterozygous sites and amplification failures were highly significant: ρ=-0. 65 (p-values<0. 0001) between NBs and NHz; ρ=-0. 27 (p-values<0. 0001) between  NUs and NHz; ) between NBs and NUs. We thus pooled NBs and NUs as the number of missing genotypes (NMs) which was strongly correlated with NHz (ρ=-0. 67, p-value<0. 0001) (Figure  1 ). This means that missing data corresponded to individuals with amplification problems, such as null alleles or allelic dropouts. Because of the probable importance of clonality in T. lewisi reproduction, it was not possible to correct for these issues, and we chose to keep only isolates with complete genotypes since the absence of missing data most probably reflect no or minimal amplification failures.
Finding the relevant structure levels The correlation between GST and HS was significantly negative both considering cohorts (ρ=-0. 3571, p-value=0. 0288) and ignoring those (ρ=-0. 7381, p-value=0. 0229). There was a small and marginally not significant differentiation between cohorts 37 and 39 (FST'=0. 0347, p-value=0. 0794). Nevertheless, some evidence of a Wahlund effect was detected when cohorts were ignored: data with cohorts outputted a slightly smaller FIS=0. 015 than the data ignoring them (FIS=0. 025), but the difference was not significant (p-value=0. 1563). There was no Wahlund effect signature with the nLD/HT criterion in the dataset without cohorts (p-value=0. 6512). However, the theoretical behavior of this criterion in clonal populations has never been explored. Moreover, the p-values of LD tests when cohorts were ignored were significantly smaller than in the data with cohorts (p-value=0.
Tracking amplification problems in complete genotypes within cohorts and quarters For these analyses, both Cotonou (Benin, cohorts 37 and 39) and Niamey (Niger, cohort 12) neighborhoods were included. There was a non-significant but highly variable FIS=0. 021 in 95%CI=[-0. 134, 0. 165], (p-value=0. 5486), across loci. The standard error ratio was RS=2. 7. This may be explained by rare sexual recombination events  (De Meeûs et al. , 2006)  and/or by null alleles and/or SAD  (Séré et al. , 2014). The correlation between FIS and FST was strongly negative (ρ=-0. 8333). The absence of significant correlation between FIS and the number of missing genotypes that the initial dataset displayed  (ρ=-0. 5714, p-value=0. 9339) suggested that null alleles poorly explain the observed patterns. In order to counteract the uneasy detection and test of stuttering in clonal populations (De Meeûs & Noûs, 2022), we directly corrected loci with stuttering suspicion (i.
e. loci LEW2, LEW12, LEW32, LEW42 and LEW55) following recent recommendations  (De Meeûs et al. , 2021). As such, allele 126 and 124 of locus LEW2 were pooled. In the same manner, we pooled alleles 160 and 158 for LEW12; 261 and 263, 289 and 287 for LEW32; 314 and 312 for LEW42; as well as 343-349 and 341 for LEW55. The resulting dataset led to a clear decrease of FIS for all loci but LEW32, which displayed only a very weak decrease (Table  4 ). As a consequence, stuttering corrections were applied in all subsequent analyses. Among the 27 locus pairs for which a test was possible, there were seven locus pairs in significant LD (25. 9%), three of which remaining significant even after BY correction (11%). There was a global and significant heterozygote excess within subsamples: F IS =-0. 105 in 95%CI=[-0.
309, 0. 079] (p-value=0. 0326), with an important variation across loci, as illustrated by the jackknife over loci (SE=0. 11) being 2. 44 times the SE of FST. The fact that the correlation was negative between FIS values on the one hand, and FST or the number of missing genotypes in the initial dataset on the other hand, confirmed a minor role for null alleles. No evidence of SAD could be found. Differentiation between Niamey-Gamkalley-C12 and Cotonou-Saint-Jean-C37, the genetically two most distant subsamples, was FST=0. 4032, with two loci (LEW44 and 53) showing a FST>0. 67. Standardized subdivision reached very high values (FST'=0. 5117), with some loci displaying values above 0. 9. The general MLG diversity was quite high (Table  5 ), with much higher values in Cotonou subsamples than those obtained in Niamey.
Discussion Isolates from South-East Asia suffered from many amplification problems, probably due to primer mismatches and/or degradation of DNA samples, thus precluding any conclusions about this particular subdataset. Consequently, future studies of T. lewisi from that part of the world will most probably require the de novo design of dedicated loci and primers. In African isolates, though in a lesser extent, many loci obviously suffered from some amplification failures. This means that future studies would probably benefit from a refinement of the primers described here, and/or from an adaption of PCR conditions in order to improve amplification success. Isolates with a qPCR cycle threshold Ct<30 (see Appendix) provided amplification success at all 9 loci for the present data set as a probable result of a higher concentration of trypanosomes' DNA.
For future studies, we will thus recommend to select extracts with a Ct<30. Alternatively, other techniques such as those relying on highthroughput sequencing-based production of microsatellite markers  (Lepais, Chancerel et al. , 2020 ) could be of great interest for further fine-scale investigation of population genetics in T. lewisi. On the other hand, once isolates with missing data were excluded from the dataset, some characteristics of rodent-borne T. lewisi population structure could be described for the first time using the present panel of newly developed microsatellite loci. First, the most coherent genetically-defined units retrieved here clearly corresponded to West African urban neighborhoods within a two months window. It is even plausible that they could correspond to smaller areas, such as households and/or rodent demes.
If all the isolates from the entire initial dataset are taken into account, it results, on average, in K'=14 possible alleles, which gives H S '=0. 46. This value is surprisingly close to the value that we computed for the uncured dataset in West African isolates (Hs=0. 457). The fact that the superimposition criterion from Séré et al. (Séré et al. , 2014)  was not applicable, may originate from a combination of amplification problems, Wahlund effects and small subsample sizes. Another expectation in pure clones is that the probability to find two identical alleles within individuals, QI=1/K=0. 342. This value is much smaller than what was found in our African dataset before stuttering cure with QI_obs=0. 554, and does not support a total absence of sexual segregation. The absence of null allele or SAD signatures, the relatively low proportion of locus pairs in significant LD as well as of repeated MLGs in most datasets, the strong subdivision measures (with FST>0.
Acknowledgements The authors would like to thank  Marc Desquesnes CIRAD INTERTRYP Toulouse France  (secretary, with  Philippe Truc  of the  NAHIAT: Network on Atypical Human Infections by Animal Trypanosomes ) for useful discussions on T. lewisi life cycle. Sathaporn Jittapalapong  and  Anamika Karnchanabanthoeng Kritiyakan ,  Faculty of Veterinary Technology, Kasetsart University (Bangkok, Thailand ), and  Bernard Carcy provided DNAs from Thailand with the support of French ANR funded projects CERoPath  ( ANR 07 BDIV 012 ) and  FutureHealthSEA  ( ANR-17-CE35-0003 ). We thank  Anne-Laure Bañuls  for providing DNAs and samples from Senegal. Authors would also want to thank  Gabriele Schönian  and one anonymous referee for their comments and suggestions that helped improving this manuscript.
An EOL-JXA-8200 Superprobe electron microprobe was used to collect electron backscatter images and EDS spectra of the thin electrode surfaces. The electron beam current was 2. 5nA, and the hematite samples were sufficiently conductive that no other treatment (i. e. carbon coating) was needed for analysis with the electron microprobe. The composition of the surface was also characterized using a PHI VersaProbe II X-ray photoelectron spectrometer with a scanning monochromated Al source (1486. 6 eV; 50 W). The takeoff angle between the sample surface and analyzer was 45°. All data were background subtracted, smoothed using a five-point quadratic Savitzky-Golay algorithm. The binding energy scale was calibrated with respect to the C1s (set to 285 eV). Curve fitting of the Cr 2p 3/2 peak was performed using Gaussian line shaped on a Shirley-type background.
Acknowledgements The authors would like to thank  Dr. Nilanjan Chatterjee  ( MIT ) for his assistance in operating the electron microprobe,  Libby Shaw  ( MIT ) for her assistance in collecting the XPS spectra for the samples,  Allison Coe  ( MIT ) for her assistance in quantifying S. putrefaciens concentrations, and  Professors Charles Harvey  (MIT) and  Harold Hemond (MIT)  for their advice on the characterization of the hematite and general feedback on this work.
Measurement of Climatic Factors: Temperature, rainfall, and relative air humidity are the three climatic factors considered in this study. Indeed, in the tropics, the abundance of Bostrichids varies according to the seasons with more or less the influence of temperature and relative air humidity  (Hodges et al. , 2003). In each department, two memory thermo-hygrometers (Data Logger EL-USB-2) were used to simultaneously record temperature and humidity during the study; and two direct-reading rain gauges were used to measure rainfall. All these measuring instruments were installed within a 5 km radius of the study sites.
ACKNOWLEDGEMENTS: The authors are grateful to the  African Centre of Excellence on Climate Change, Biodiversity and Sustainable Agriculture , the  University Agency of the Francophony (AUF) , the  Research Institut for Development (IRD) , the  International Foundation for Science (IFS)  and the  Scientific and Technological Cooperation Committee (COMSTECH) of the Organization of Islamic Cooperation (OIC)  for their financial support. They are also grateful to the technician supervising the fieldwork,  Mr. DUA Fofié Daniel , as well as to the various farmers who agreed to make their plots available.
Echocardiography Transthoracic echocardiography was performed using the Vevo 2100™ High-Resolution Imaging System (Visual Sonics, Toronto, Canada). Data were collected at baseline, the day before surgery, as well as days 1 and 7 after surgery. For image acquisition, mice were anesthetized with 2% iso urane in an oxygen mix chamber and placed on an electrical heated platform. B-mode images of the left ventricle were acquired from the parasternal long axis view in supine position. LV end diastolic (LVEDV) and systolic volumes (LVESV) were provided by the machine using the LV wall tracing tool. LV ejection fraction (EF %) was calculated from B-mode image as previously described  [26]. Additionally, images of base, midsection, and apex were acquired from short axes view. The images of the base acquired at day 1 post MI was used for calculation of fractional area change.
Blood Pressure Measurements Blood pressure (BP) was measured non-invasively using tail cuff, volume pressure recording sensor technology and CODA high-throughput monitor, (Kent Scienti c, Torrington, CT, USA). Measurements were performed at baseline and after two weeks of CS exposure to assess the impact of CS on BP in both CS exposed groups. Real-time measurements of systolic, diastolic, and mean arterial blood pressure were recorded. Each session consisted of 5 acclimatization cycles followed by 15 BP measurement cycles. On the data collection day, 2 sessions of 15 BP measurements were obtained; any irregular recordings noted as false recordings by the system were excluded. Brie y, mice were trained for 7 days by measuring BP daily, after which BP recordings were made and a set was accepted if the computer identi ed 50% successful readings.
RV and LV slices were incubated in 1% TTC for 15 min at 37 °C. The infarcted region was de ned as the unstained section following incubation with TTC. ImageJ software (National Institutes of Health, Bethesda, MD, USA) was used for infarct size measurement. The whole LV area along with the unstained region was traced and the measurement was done automatically by the program in pixels. The infarct area was expressed as a percentage of the left ventricle. As for RV area, the borders of the RV were traced, and measurement was done automatically. No infarcted area was detected on the RV tissue.
Masson's Trichrome Staining For myocardial brosis and collagen deposition, the slides of the left ventricle's mid-section were stained with Masson's trichrome. Collagen volume fractions (CVFs) and brosis were measured using ImageJ software (https://imagej. nih. gov/ij/). Brie y, after dewaxing and hydration steps, and according to manufacturer's protocol (Abcam, Connective Tissue Stain, #ab150686) tissue slides were soaked in Bouin solution for 1 h at 56 C, washed in running tap water, and rinsed in distilled water. A second washing step was done after 10 min of incubation in hematoxylin. Slides were stained in biebrich scarlet acid fuchsin for 10 min. After washing, sections were differentiated in phosphomolybdicphosphotungstic acid solution for 10 min, transferred to aniline blue solution, stained for 5 min and mounted and observed using light microscopy at 400x magni cation.
Statistical Analysis Results were expressed as mean ± the standard error of the mean (SEM). Statistical comparisons were performed using an unpaired t-test or for multiple comparison, ANOVA followed by Tukey post hoc test was performed. P≤0. 05, P≤0. 01, and P≤0. 001 (*, **, *** respectively) were considered signi cant. GraphPad Prism software was used to perform statistical analysis.
In addition, we did not observe any gross indications that CS exposure induced stress. Fifth, it is possible that the CS protocol induces stress in mice and consequently has an impact on cardiovascular physiology; however, both sexes were subjected to the same CS protocol. Sixth, ischemia-reperfusion was not performed in our study, but will be done in future experiments; however, a signi cant percentage of MI patients are not reperfused and suffer from permanent occlusion MIs  [86, 87]. Finally, CS exposure was performed for 2 weeks before MI and it would be informative to assess longer exposure times. The key goal, however, was to eliminate the risk of CS-induced cardiomyopathy that normally occur with long-term CS exposure and focus solely on acute events. Nonetheless, our study provides novel data on sex-differences in the response of the infarcted heart to CS.
, 2007;  or spaces based on communitywide indices, e. g. ,  Rigolet et al. , 2015). The analysis and representation of stable isotope trajectories or contrasted patterns requires the use of quantitative geometric properties in 2D δ spaces often complemented by vectors in stable isotope scatter plots and/or circular representation  (Agostinho et al. , 2021; Black & Armbruster, 2021; Cucherousset et al. , 2013; Schmidt et al. , 2007). However, scientists are increasingly faced with multivariate datasets (i. e. , >2 dimensions) in stable isotope ecology in response to the potential use of (1) other isotopes to complement δ 13 C and δ 15 N (e. g. , 34 S (  [Connolly et al. , 2004] , δD  [Doucett et al. , 2007] ) and  (2)  numerous structural and functional community-wide metrics or indices  (Cucherousset & Villéger, 2015; Layman et al.
, 2007). While the availability of long-term, large-scale, and highresolution data is one of the most limiting factors to study temporal patterns in stable isotope ecology, the development of methods to analyze, synthesize, and ultimately represent the dynamics of ecological systems still remains an essential issue to complete current approaches by more quantitative and formal explicit frameworks. Building on CTA, we aim to provide a framework for the temporal analysis of stable isotope data at different levels of biological organization, from individuals to ecosystems to derive structural and functional trajectories in a new approach referred to as Stable Isotope Trajectory Analysis (SITA). We (1) provide a general definition of the trajectory concept applied in stable isotope ecology, adapted from CTA framework to stable isotope analysis,  (2)  present the package ecotraj designed for ecological trajectory analyses and here used specifically for SITA, and (3) illustrate potential applications of SITA using field, experimental or modeled data that include four main topics in stable isotope ecology: (i) individual and (ii) population levels, (iii) structural and functional trajectories of entire food webs, and (iv) modeling of stable isotope dynamics at high spatio-temporal resolutions.
Trajectory heat map Stable isotope datasets with high temporal resolutions may require special representations as they can potentially saturate TD or TR diagrams. Here, we propose the concept of a trajectory heat map (TH) to represent long-term SI dynamics. The heat map is a two-dimensional representation of data in which the changes in the distribution of a chosen trajectory metric over time are represented using cell colors (see Section Spatio-temporal variability of δ 13 C and δ 15 N modeled isoscapes in the northeast Pacific). TH allows the representation of the distribution of distance-and direction-based trajectory metrics. If users aim to favor the representation of directions in TH, angles Ɵ, ω or α can be represented in a matrix of fixed cell size whose colors vary depending of the number of a given direction range occurring in a given period.
Isoscape trajectory map The spatial distribution of SI in environmental materials can be predicted, using models of isotope-fractionating processes and data describing environmental conditions, and represented through isotopic landscape, called isoscapes  (Bowen, 2010; West et al. , 2008). We adapted the TM concept for isoscape datasets characterized by high spatial resolutions and a minimum of two temporal surveys or modeling. This particular concept of TM is inspired by wind/current map where the magnitude and the direction of wind/current are represented through multiple vector covering large areas. In the isoscape TM (ITM), the direction of arrows represents angle α in a 2D Ω δ space (e. g. , δ 13 C/δ 15 N), and size illustrates trajectory length (see Section Spatiotemporal variability of δ 13 C and δ 15 N modeled isoscapes in the northeast Pacific).