dataesr/scientific-paragraphs-categorization huggingface dataset:
General Experimental Procedure The 1D ( 1 H, 13 C, APT and DEPT 135) and 2D (HMBC, COSY and HSQC) NMR spectra were acquired using standard pulse sequences on a Bruker model AMX 400 NMR spectrometer operating at 400 MHz and 100 MHz in 1 H NMR and 13 C NMR, respectively. Results for the chemical shift (δ) were provided in parts per million units (ppm). J values for coupling constants were provided in Hertz (Hz). The HSQC, HMBC, APT and DEPT pulse sequences followed technical standards. For EI-MS, mass spectroscopy with a Thermo Scientific ISQ single-quadrupole mass spectrometer was used. For ESI-MS, a mass spectrometer from Thermo Scientific with a triple-quadrupole Access MAX system and Xcalibur 2. 1 software was used. Sephadex LH-20 and silica gel (E. Merck, 70-230 mesh) column chromatography were used for obtaining pure metabolites.
Molecular Docking Studies The binding manners and interactions of the isolates (papaverine and its metabolites 1-7) were demonstrated using molecular docking studies (MOE version 2020. 9010) and the Discovery Studio (DS) visualizer tool. The three crystal structures of the human PTP1B catalytic domain, α-glucosidase and lipase, with resolutions of 1. 80 (PDB ID: 1G7F), 1. 60 (PDB ID: 3A4A) and 2. 46 (PDB ID: 1LPB), respectively, were obtained from the Protein Data Bank. The compounds were predocked with their ligands. There were hydrophilic and hydrophobic amino acids present in each enzyme's ligand-binding site. A redocking approach for each ligand was used to confirm the docking process through establishing a number of docked poses, one of which had an RMSD value less than 1 (0. 85 (with INZ), 0.
We followed the method recommended by the Collaboration for Environmental Evidence (CEE)  (CEE 2018). Adapted to the field of ecology, CEE systematic reviews are based on standardized protocols and provide a transparent, accurate and unbiased reporting of evidence to help practitioners make informed and efficient decisions  (Haddaway et al. 2016; Berger-Tal et al. 2019; Pullin et al. 2022). We used a comprehensive search strategy based on several databases and performed a critical analysis of accepted observations in order to judge the level of confidence which could be granted to the reported impacts of flashing light.
Search for literature We carried out a search for literature on three accessible databases from the Web of Science platform (Clarivate): Web of Science Core Collection, Biological Abstracts, and Zoological Records. These databases were chosen for their functionalities, which enabled an advanced search strategy to be carried out, and because of their wide coverage on biological and ecological matters. For the Web of Science Core Collection search, SCI-EXPANDED, SSCI, A&HCI, CPCI-S, CPCI-SSH, BKCI-S, BKCI-SSH, ESCI and CCR-EXPANDED citation indexes were used. As for Biological Abstracts and Zoological Records, we had access to all indexed databases  (respectively 1969-present and 1864present). In order to achieve the best recovery of citations, several successive search strings were designed by both ecological scientists from the French National Museum of Natural History (MNHN) and physicists from the National Conservatoire of Arts and Crafts (CNAM).
Data extraction Data on the influence of flashing light for a particular species or taxa were extracted by one reviewer (AL) although a test was first conducted on a subsample of observations by two reviewers (RS and AL) to assess agreement between reviewers. Metadata were also extracted for each observation, namely locations, specificities of population (age, sex) and light sources (type, wavelength, power, luminance, correlated colour temperatures and flicker frequency) as well as outcomes (e. g. behaviour, weight, mortality). Each species was associated with its taxonomic class and name updated with the latest taxonomy (GBIF 2021). Critical appraisal risks of bias were also appended to each observation included in the database.
Screening process and critical appraisal A total number of 19,730 citations were extracted from the three databases from which 5,253 citations were kept after title screening. Among them, 2,145 citations had no indexed abstracts and were discarded. After abstract screening, 2,594 citations were kept. With the addition of 68 citations identified through the call for grey literature and 63 identified by the review team, 2,130 PDFs were successfully retrieved and screened on full-texts. The screening process resulted in 32 accepted articles (see Suppl. material 3 for inclusions/exclusions on titles, abstracts and full-texts, Suppl. material 4 for full-text reasons for exclusion and Suppl. material 6 for unobtainable full-texts). All 32 articles accepted after the screening process were then split into 62 observations-an observation corresponding to one species and one outcome-and subjected to critical appraisal.
Literature sources The majority of accepted observations came from our search on Web of Science Core Collection database (32 observations) while 10 were provided thanks to the work carried out during  Lafitte et al. (2022) 's systematic review on CFF, 8 were extracted thanks to Adams et al. 's systematic map on the effect of ALAN on birds  (Adams et al. 2019 (Adams et al. , 2021)) , three were identified by the review team and finally one was provided thanks to the call for grey literature. No observations from Zoological Records or Biological Abstracts databases were accepted in the end.
Studied taxa Data on the four main taxonomic classes Aves (28 observations), Actinopterygii (10 observations), Insecta (8 observations) and Mammalia (6 observations) were collated (Fig. 3A ). Additionally, two observations investigated the effects of flashing light on plankton (notably on Malacostraca and Polychaeta larvae). While a fraction of observations was conducted in-situ (18 observations), 70% of observations (36 observations) were carried out in laboratories. The starling S. vulgaris was the most investigated species with 13 observations (Fig. 3B ), followed by the brown-headed cowbird Molothrus ater (4 observations) and the cat flea Ctenocephalides felis (3 observations). All other species or taxa were only studied once or twice.
Indeed, a species perception of a flashing light source could theoretically be inferred thanks to the knowledge of its CFF and the flicker frequency of a light source. To that end,  Inger et al. (2014)  first reviewed the actual perception of flashing light by animals by collating one of the first databases on animal CFF. Lafitte et al. (2022)  then updated this work by following the method of systematic reviews recommended by the CEE (CEE 2018) and were able to collate a comprehensive database of 200 CFF values. As they identified that animal CFF ranged from 0. 57 to a maximum of 500 Hz, they argued that outdoor lighting should exceed this upper threshold in order to limit the impacts of ALAN on wild animals. In addition, they reported that some nocturnal animals (e. g. moths and fishes) had CFF higher than the 100 Hz threshold sometimes found in some lighting technologies such as LED.
Review limitations Our methodology comprised some biases which have to be pointed out. First, while the majority of articles found in this review came from our literature search, more than a third was provided by additional sources of literature, indicative that the scope of our search string might have been too limited. In addition, we sometimes had to decide to reduce our requirements compared to CEE guidelines (CEE 2018) due to time limitations and financing constraints. First, we could not request supplementary databases (e. g. Scopus) or include search engines (e. g. Google Scholar) in our search strategy. However, doing so may have increased the number of test list articles indexed in the requested databases which would have probably increased the reliability of our search strategy. In addition, while consistency checks between reviewers were performed for the title and abstract screening stages, we could not do so for full-text screening.
Likewise, CEE guidelines (CEE 2018) call for a double independent assessment by two reviewers during critical appraisal and data extraction. However, in this review, only one reviewer critically appraised and extracted data from all observations accepted after full-text screening. A test between two reviewers on a subsample of articles was still performed before starting critical appraisal and data extraction to check their agreement. In addition, citations for which an appended abstract was not available were discarded during the screening process. Indeed, searching for these additional 2,145 full-texts was deemed to represent an unfeasible additional workload within the scope of our project. We nevertheless made sure to create an additional database which lists these citations without abstract (see Suppl.
material 5). We hope that this database will prove useful for whomever would want to continue this work. Moreover, due to the high level of accepted citations after title and abstract screening and while the initial scope of this review included plants, microorganisms, domesticated animals as well as the impacts of ALAN timing on circadian rhythms, we had to downgrade our expectations and only carry out this systematic review on the sole behavioural and physiological impacts of flashing light on animals. However, if one wishes to disentangle the impacts of flashing on the other identified taxa, we made sure to create easily available categories in Suppl. material 3 to facilitate a potential future full-text screening on these citations. We chose to only consider and report results comparing continuous and flashing lights as we judged they were the only ones to really assess the effect of the flashing characteristic of a light stimulus alone, as opposed to the effect of the light stimulus as a whole.
Acknowledgments We also wish to thank  Françoise Viénot ,  Christophe Martinsons ,  Jack Falcón ,  Christian Kerbiriou ,  Léa Mariton  and  Matthieu Iodice  for providing us with literature. We also sincerely thank  Dakis-Yaoba Ouédraogo  and  Marie-Pierre Alexandre  for their support and advice all along our study.
There are two types of structures in bone with different densities: cortical bone, a denser region, and trabecular bone, a porous part. Poly(lactic acid) -PLA, a biopolymer widely used in additive manufacturing (AM), can be applied for fabricate products for medical and dental applications since it is biodegradable and biocompatible to several mammalian cell lines. This article proposes a methodology for generating STL to produce by AM a structure with geometry similar to that of trabecular bone using a mathematical model that describes the population dynamics of bone cells. Bone density values obtained by solving the differential equations model with finite differences are used to develop a mesh surface. This surface is converted into a binarized mesh using a binary algorithm and, finally, the STL file is obtained by applying the multidimensional arrays tool from Matlab® software.
Methodology for STL surface using cells models Two strategies (S1) and (S2) were developed in this article to produce the three-dimensional surfaces based on the presented models. The same cubic envelop was used for both strategies wherein bone and porous regions were produced, so a Basic Multicellular Unit, BMU. The first strategy used a 2D methodology for each layer and the second one calculated the regions in all envelop. The surfaces were transformed in STL file format for allowing 3D printing. The application of Matlab's tool stlwrite was used to export the surface volume produced with the two strategies. Strategy 1 (S1). This strategy is based on solving differential equations in two dimensions and applying the isosurface tool. Bone density values obtained by solving the differential equations model with finite differences are used to develop a mesh surface.
This surface is converted into a binarized mesh using a binary algorithm and, finally, the STL file is obtained by applying the multidimensional arrays tool from Matlab® software. Strategy 2 (S2) solves the differential equations in three dimensions, and with the obtained three-dimensional matrix, an isosurface similar to the one produced in S1 is created. For two dimensions (x and y), applying finite differences in Eq. (  5 ) and (  6 ), Eq. (  8 ) and (  9 ) represents the model used for this strategy: These meshes at different times can be "stacked" using the Marching cubes algorithm (isosurface tool from Matlab®) to obtain a three-dimensional surface. Using these meshes in Eq. 6, also a mesh is produced for bone mass. This strategy, called here as Strategy 1, would correspond to cell migration in the z direction that would continuously produce an extracellular matrix.
1d , 1e and 1f. The initial value problem for this ODE system can exemplify the bone remodeling mechanism. However, the bone mass distribution is only for a single BMU. Ayati et al. [6] , Valério et al. [7]  and Fernández-Cervantez et al. [9]  solved the presented model by adding a diffusive term for cell population and bone mass shown in Eqs. 7-10. Different BMUs were evaluated at each point of a given mesh or solid block. The approach of Valério et al. [7, 9]  and Fernandez-Cervantez et al. [9]  were replicated below, in the respective Strategies 1 and 2. While in Strategy 1 the cell distribution is solved in x and y, in Strategy 2 it is solved in x, y and z. In order to obtain a three-dimensional block with the structure of trabecular bone, in the first form, therefore, it was necessary to apply the Multidimensional Matrices technique and the application of the isosurface tool after binarizing the data of each mesh x and y.
In this figure we can see the distribution of cells in different areas, that is, where there are osteoclasts there is less population of osteoblasts, Figs. 2a  and 2b. Also, denser regions could be seen in Fig. 2c  areas with presence of osteoblasts, and less dense regions could be in populated osteoclasts areas. A loop was used in this case, with dt = 0. 01 days The distributions of cell populations and bone mass can be obtained as shown in Fig. 3. This figure shows the threedimensional distribution of cells and bone mass. As consideration of isosurfaces produced: the marching cubes algorithm connects areas with the same value (defined as isovalue). For this, the data was binarized (a 3D Matrix of zeros and ones) to produce the isosurface in Fig. 3c. The stlwrite algorithm in Matlab was applied in order to export the STL files.
Microtomography analyses. The application of microtomography (microCT) of the printed pieces allowed the complete geometry of the manufactured workpieces. Fig. 4  shows the microCT images of the S1 (Fig. 4a ), S2 (Fig. 4b ) and of real bone (femoral head (FH) gently provided by the National Institute of Technology (INT-Brazil), Fig. 4c ). The Bone J (ImageJ software plugin) was used in these analysis to obtain the parameters: trabecular thickness (TbTh, usually a mean value of thickness of the trabecula), trabecular separation (TbSp, the mean distance between the trabecula, it is similar to pore size), bone volume fraction (BV/TV, the fraction of material in the sample), degree of anisotropy (DA, it estimates how geometrically non-isotropic is the bone fraction), and connectivity (Conn, it gives an estimate of the number of connected trabeculae in the image)  [11] ,  [13].
M E T H O D S 2. 1 Study population and data sources For the modelling analysis, we included 12 metropolitan regions which are in mainland France (hereafter France) and excluded the metropolitan region of Corse and the five French overseas regions (DOM-TOM). To conduct our analysis, we drew on data from three different sources. We first retrieved 2017 self-reported data on newly diagnosed HIV among MSM from the French subsample of the European-MSM-Internet-Survey (EMIS-2017, www. emis2017. eu). EMIS-2017 recruited 10,385 MSM living in mainland France between  19  October 2017 and 30 January 2018  [16]. Ethical approval and informed consent for EMIS-2017 was obtained from the Observational Research Ethics Committee at the London School of Hygiene & Tropical Medicine (review reference 14421/RR/8805).
Our approach can be based on survey-and surveillance-based data of newly diagnosed HIV among MSM, and does not require more complex and potentially more costly general populationbased survey such as CSF  [31]  to estimate the MSM proportion among adult males. In turn, scarce HIV prevention resources can be targeted more efficiently. In addition, using EMIS-2017 data, we further estimated the number of PrEP-eligible MSM regionally across France. We acknowledge that, compared to the French PrEP guideline  [26]  and the estimations by Annequin et al. [8] , our eligibility criteria also included bacterial STI diagnosis in the preceding 5 years. Therefore, our estimated proportions are higher than the estimations by Annequin et al. (around 35% nationwide in France). However, given the sexual health profiles of men who acquire sexually transmitted infections (STIs) and the established links to HIV  [32, 33] , the inclusion of STI histories is useful to estimate PrEP eligibility under financially constrained conditions (e.
We prioritized homogeneity over incidentally higher data quality, thus our estimations for HIV-negative or PrEP-eligible MSM populations can be seen as underestimates. Third, we applied the EMIS-2017-based psychosocial determinants for all periods included, assuming these determinants were stable and comparable between 2016S1 and 2021S1. Given the established increasing trends of some of the included determinants, such as the STIs incidence  [39] , CAI  [40]  and chemsex  [41] , our estimations may be underestimated. Finally, due to a wording issue in the French-language version (possible confound between STI testing and diagnosis) of EMIS-2017, we extrapolated the proportion of MSM with an STI diagnosis in the preceding 5-year from participants in France completing the survey in languages other than French  [27].
A U T H O R S ' C O N T R I B U T I O N S HW, DVDV and KJJ conceptualized this research; HW, JMM, RDS, AJS, FH and KJJ collected the data for this research; HW analysed the data; HW and KJJ drafted the manuscript; all authors critically revised the manuscript for intellectual content; AJS and FH edited the manuscript. All authors read and approved the final version of the manuscript.
Comparing with the HLA-C*05:01:01:02 sequence, the novel allele, C*05:278N carries one nucleotide mismatch G > A at position 1767 in exon 4 (Figure  1 ), making residue 244 encoded by TGG (Tryptophan) become TGA (stop codon). Thus the introduction of this premature stop codon is predicted to render this allele null with no cell surface expression of this allele. We were unable to perform serological typing using micro-lymphocyte cytotoxicity assay due to the lack of reagents for HLA-C typing. The nucleotide sequence of the exons 1-8 of this new allele was submitted to the GenBank database (Accession no. OP297268) and to the IPD-IMGT/HLA Database 2 (Submission no. HWS10062728). The name HLA-C*05:278N has been officially assigned by the WHO Nomenclature Committee for Factors of the HLA System 3 in January 2023.
To fill this gap, we present an R package named rcontroll, which integrates the TROLL individual-based model into R to simulate forest ecosystem processes and species dynamics. The TROLL model was originally developed for tropical forests, with the aim of simulating ecological succession from bare ground and the spatial patterns emerging from tree falls and gap dynamics  (Chave, 1999). Species-specific parameters are based on plant functional traits allowing the joint simulation of carbon and tree diversity  (Maréchaux & Chave, 2017). TROLL has been applied to the study of tropical forest resilience  (Schmitt et al. , 2020) , tree allometry and how it can be inferred from remote sensing  (Fischer et al. , 2019) , and forest responses to wind-throw  (Rau et al. , 2022).
The combination of these processes at the individual level leads to realistic community-level dynamics, including successional patterns in species composition, self-thinning and gradual saturation of stand biomass on decadal to centennial timescales even with minimal calibration  (Maréchaux & Chave, 2017; Rau et al. , 2022). The minimal set of input files required for a TROLL run include (i) climate data for the focal location, (ii) functional traits for the list of species at the focal location and (iii) global parameters, that is parameters that do not depend on species identity. All these input files and simulation parameters can be easily configured and run using rcontroll. a typical personal computer). The rcontroll R package is a wrapper of TROLL that comprises the model and facilitates its access to users.
rcontroll currently calls version 3. 1. 7 of TROLL using the Rcpp package  (Eddelbuettel & François, 2011). rcontroll includes functions that generate inputs for simulations and run simulations. Finally, it is possible to analyse the TROLL outputs through tables, figures and maps taking advantage of other R visualisation packages. rcontroll also offers the possibility to generate a virtual LIDAR point cloud that corresponds to a snapshot of the simulated forest.
| Construction and manipulation of input files As stated above, three types of input data are needed for a typi- and their uncertainties reported. Therefore, rcontroll users only need to input the species-specific trait data to run TROLL simulations, irrespective of the site. TROLL was originally developed for tropical and subtropical forests, so certain assumptions must be critically examined when applying it outside the tropics. The input files can be used to start a TROLL simulation run within the rcontroll environment (see below) or saved so that the TROLL simulation can be started as a command line tool.
| Sensitivity of TROLL parameters As a first example, we performed a sensitivity analysis of 12 parameters (Table  1 ), the results of which could be used for effective model calibration. Calibration of TROLL consists of adjusting the parameter values so that the model behaves as closely as possible to the empirical data. We simulated an undisturbed forest plot located in French Guiana based on the inventory data from the Paracou research station  (Gourlet-Fleury et al. , 2004). We retained only the species provided as defaults in rcontroll. We sampled the parameter space using the Latin hypercube sampling (LHS) method, using the a priori parameter ranges (Table  1 ). LHS was modified to account for the expected correlation between parameters (Fischer, 2019) using the Huntington-Lyrintzis algorithm  (Huntington & Lyrintzis, 1998)  implemented in the pse R package  (Chalom & Prado, 2017).
To convert the discrete response into a continuous response function, covering the entire space of the 12 parameters, we derived a Gaussian process model for each ecosystem metric from the repeated samples using the hetGP R package  (Binois & Gramacy, 2021). This surrogate method allows us to generate any number of additional simulations for any parameter combination and yields robust mean estimates of ecosystem metrics with TROLL parameters independent from the noise generated from replications. Finally, a sensitivity analysis was carried out using the sensitivity R package to determine the relative influence of the 12 parameters on the mean estimates of the four ecosystem metrics. We used Morris analysis, a qualitative approach to eliminate noninfluential parameters  (Morris, 1991). Morris analysis is based on a one-step-at-a-time sampling scheme (i.