dataesr/scientific-paragraphs-categorization huggingface dataset:
DFT calculations The unit-cell X-ray structure of [VO(TPP)]  27  was used as starting points for a periodic DFT optimization of a 3 × 3 × 3 supercell with the software CP2K  59  (see Supplementary Table  4 ). Density functional theory (DFT) with the PBE functional  60  , including Grimme's D3 van der Waals corrections  61  , was used together with a double-zeta polarized (DZVP) MOLOPT basis set. A plane-wave cutoff of 1875 Ry was used. Lattice force constants and phonons were computed with the software MolForge  26. Lattice force constants were computed with a two-point numerical differentiation of atomic forces with step of 0. 01 Å. The tensors A and g were computed with the software ORCA  62  using DFT with the hybrid functional PBE0  63  and DKH-def2-SVP basis for C and H atoms and DKH-def2-TZVPP for all other atoms.
(  2 ) with pDFT-calculated phonon energies ω j (q) and normal modes polarization vectors σ d j ðqÞ. A rescaling of about 10% was uniformly applied to all the calculated phonon energies along all the symmetry directions. We then assumed a single-dampedharmonic-oscillator line-shape with the FWHM of the corresponding dataset (for the colour maps we used a FWHM = 0. 1 meV, in order to distinguish the contribution of single phonon branches with a nonzero cross-section within the experimental resolution).
Acknowledgements Dr. Yong Cai  is gratefully acknowledged for useful discussions on IXS experiments. This project has received funding from the  European Union 's  Horizon 2020 Research and Innovation Programme  under grant agreement No  862893  ( FET-OPEN  project  FATMOLS ) (S. C. ) and from the  European Research Council (ERC)  (grant agreement No. [948493]) (A. L. ). It was also supported by the  Italian MIUR  with the  Progetto Dipartimenti di Eccellenza   2018-2022  (ref. B96C1700020008 ) (F. T. , R. S. ), by  Fondazione Cariparma  (S. C. ) and  The National Recovery and Resilience Plan ,  Mission 4 Component 2 -Investment 1. 4 -NATIONAL CENTER FOR HPC ,  BIG DATA AND QUANTUM COMPUTING -funded by the  European Union-NextGeneration   EU -CUP B83C22002830001  (F. T. ). We also acknowledge the  European Synchrotron Radiation Source  for instrument time on the ID28 beamline (proposal number  HC-4312 ) (E.
Eligibility criteria and literature search strategy A systematic and comprehensive search of electronic databases, including Medline database (https://pubmed. ncbi. nlm. nih. gov/), Scopus, ClinicalTrials. gov, Science Direct, Springer Link, Google Scholar, and EMBASE was done from January 2023 to October 2023. The search process was completed using the keywords: "glycans", "glycome", "mucin intestinal tract", "microbiota", and "athletes". The search was not restricted to the type of study (e. g. , case-control, prospective cohort studies, randomized control trial, before-andafter study, cross-over randomized control trial), type of sport, sample size, age, gender, ethnicity, geographic localization, or species. However, editorials, systematic and literature reviews, and letters to the editors were excluded.
Data extraction Complete copies of citations coded as potentially relevant were obtained, and those meeting the inclusion criteria were read in detail and data extracted. The authors pulled information about the species, study aims, population, sample size, dietary records, experimental design and duration of follow-up, individual characteristics, changes in the microbiota composition, mucin characterization, and association or not with gastrointestinal damage. The primary outcome was the microbiota profile and mucin composition or structure changes. If eligibility could be determined, the entire article was retrieved. The extracted data included the year the paper was published, the species, the sample size, protocol, and outcomes. All papers were exported to the reference database Mendeley.
Data synthesis A search conducted in January 2023 resulted in the following list of crucial term combinations (gut microbiota, mucins, gut permeability = 107; mucin glycome and gut microbiota = 14; mucin, exercise, and gut microbiota = 2; mucin, dietary glycans, and gut microbiota = 134. After the removal of duplicates, 81 article titles and abstracts were screened. During the full-text screening, 14 were excluded for not meeting the inclusion criteria or because one or more of the criteria for exclusion were met. Finally, 67 articles met all criteria for inclusion in the current review. Among them, 24 were related to the gut microbiota, mucins, and gut permeability, 13 were associated with glycome and microbiota, 2 with mucin, exercise, and gut microbiota, and 28 with mucin, dietary glycans, and gut microbiota.
With the help of the SME HANKAMP (Netherlands), we have reproduced one of their industrial processes in our Laboratory. Participants had to replicate the process, without and with the help of the robot. During the task, we monitored the participants' biomechanical activity. After the task, the participants completed a survey with usability and acceptability measures; 7 workers of the SME had completed the same survey. The experiments mentioned above are shown in the video available at: https://gite. lirmm. fr/humar/research-projects/sophia_dataset_example/-/blob/ main/videos/rgbd_dataset_overview. mp4 The contributions of our work with respect to the state of art are the following. • For the first time, Potvin technique  [14, 15] , commonly used in ergonomics to quantify physical effort in repetitive tasks, is applied to assess a collaborative robot.
All participants, after being introduced to data privacy issues and voluntariness of the participation, gave their written consent to participate in the study. The individuals in this manuscript have given written informed consent (as outlined in PLOS consent form) to publish these case details. Participants' exclusion criteria included inability to give informed written consent, history of musculoskeletal disorders, limb or trunk surgery, orthopedic or neurological diseases, disorders of the vestibular system, visual impairments or back pain, current pregnancy, current pharmacological treatment, and obesity. Each participant completed the task six times: three times without (denoted woB) and three times with (wB) BAZAR. We randomly ordered the two conditions (w and wo BAZAR), for each participant.
Measuring physical effort To evaluate the participants' biomechanical effort, we relied on a Xsens (Xsens, Enschede, The Netherlands) MVN Link suit with inertial measurement units (IMU) and on Wi-Fi surface electromyographs (FreeEMG300 System, BTS, Milan, Italy) at 1000 Hz, as sEMG. We used Xsens MVN Analyze software (v2018. 0. 0) to record IMU data at 60 Hz, and 16-channel. The IMU and sEMG data were acquired simultaneously, synchronizing the two devices. MVN Awinda system motion analysis system includes a protocol comprising 17 IMUs placed all over the body to measure the orientation of body segments  [50] , hence the whole-body kinematics. We acquired sEMG signals via bipolar Ag/AgCl surface electrodes (diameter 2 cm, H124SG Kendall ARBO, Tyco healthcare, Neustadt/Donau, Germany), placed with electroconductive gel over the muscle belly, in the direction of the muscle fibers, and with 2 cm between the electrodes' centers.
If a worker does multiple tasks that are each more than 2 hours long, none of the tasks should exceed the TLV. Static exertions of the hand, elbow or shoulder should not exceed 20 minutes. The recommended limits apply specifically to the upper limb. The statistical analyses were performed using SPSS 20. 0 (IBM SPSS). For each participant and each condition (wB and woB), the data of the three trials were averaged. Preliminarily, we applied the Shapiro-Wilk normality test, to check whether the data had a normal distribution. A two-way repeated measures ANOVA was performed to determine if there was any significant effect on the Potvin results, among the %MVC and between wB and woB. Wherever the ANOVA test had shown a main effect, we carried out the post hoc analysis, with Bonferroni's correction.
Measuring the robot performance BAZAR  [48]  is a dual arm mobile robot, equipped with two 7-DOF Kuka LWR4 arms attached to a Neobotix MPO-700 omnidirectional mobile base. A Microsoft Kinect camera is mounted on BAZAR's head, and an ATI Mini 45 force/torque sensor is mounted on each of its wrists. We equipped each wrist with a 3D printed concave part, designed to fit the gear, and denoted 'hand' in the paper. We used the camera to detect the spots on the tables for lifting/placing the gear, and the force sensors both to regulate the grasp and to make BAZAR comply with the participants' manual guidance. BAZAR's framework is programmed in C++ within RKCL  [58] , a hierarchical quadratic programming library that applies task prioritization. The framework is executed on a computer with an Intel(R) Xeon(R) E5-2620 v3 CPU running Linux with the PREEMPT-RT patch.
a4) Move gear: for this action, we use the cooperative task representation  [62]. Instead of controlling each arm independently, we consider them as a unique entity and define their motion via an absolute task (which controls the pose of the gear in the workspace), and a relative task (which regulates the pose of one hand with respect to the other). When there is no human interaction, the absolute task is pose controlled, whereas during 'brushing' we control the gear vertical translation and tilt angle with damping control. By compensating gravity  [58] , only the human forces guide the robot. This allows him/her to move the gear with minimal effort. We recorded data from the robot at 20 Hz. To measure joint repeatability, we proceeded as follows. • We computed the median duration (across all experiments) of each of the three tasks, to obtain: 30.
All measures showed an acceptable internal reliability (0. 7 or higher, see  [64] ) for the workers, but for the participants some measures showed questionable to poor reliability, namely for Performance Expectancy (ɑ = 0. 568), Facilitating Conditions (ɑ = 0. 426) and Attitude (ɑ = 0. 520). We calculated a single score for each concept for both groups, by adding all items per concept and calculating their mean. The statistical analyses were performed using SPSS version 28 (IBM SPSS). P-values lower than 0. 05 were considered statistically significant.
Life History Analyses of Neoplasia Prevalence Evolutionary life history theory provides a framework for understanding the tradeoffs governing species' survival and reproduction  (19, 20). Life history theory can be used to explain how species level traits shape organismal cancer risk based on trade-offs between investment in somatic maintenance (e. g. , cancer suppression) and reproduction or growth. Several smaller studies have shown that specific life history traits can serve as prognostic indicators of neoplasia prevalence in animals managed under human care  (17, 21). We tested for relationships between life history factors and neoplasia or malignancy prevalence, controlling for phylogenetic relatedness, and weighting species data points by the number of necropsies in our dataset. In contrast to previous studies  (16) (17) (18) , we found an increase in neoplasia prevalence with increases in body mass (2.
Analysis of Veterinary Necropsy Records We collected necropsy records with permission from 99 zoological institutions, aquariums, and other facilities that house animals under managed care. Gross necropsies had all been conducted by veterinary pathologists who specialize in nondomestic species and neoplasia was identified histologically by board-certified pathologists. Cases where suspect neoplasms were not examined histologically were excluded from the dataset. We used a terminology dictionary (Supplemental table  3 ) to distinguish benign from malignant neoplasms based on the diagnoses in the necropsy reports. We excluded neonatal records to reduce bias from high levels of neonate and infant mortality that is common in many species. Because only common names were recorded for most records, we developed a tool, kestrel, to translate common names into scientific names which is available at https://pkg.
go. dev/github. com/icwells/kestrel. All of the institutions that provided prior approval for the use of their data in these analyses are Association of Zoos and Aquariums (AZA) accredited. AZA accreditation encourages the institution to perform a necropsy on all animals that die under their care to determine cause of death and to monitor morbidity and mortality of each species. Furthermore, each institution had IACUC approval with the Exotic Species Cancer Research Alliance (ESCRA) and the Arizona Cancer and Evolution Center (ACE) for the use of their deceased animal's records of animals with neoplasia for use in this study. Previous analyses included both necropsies for animals diagnosed with neoplasia and animals that were still alive  (18). In this study, we restricted our analyses to only necropsies -for both cancer and non-cancer diagnosed animals, because alive animals may harbor undetected cancer or might be eventually diagnosed with cancer, thus skewing estimates in cancer prevalence.
Testing for relationships with life history factors We extracted data for maximum lifespan, adult body weight, basal metabolic rate, gestation length, litter size, time to sexual maturity, and growth rate from PanTHERIA  (36). We used a weighted phylogenetic regression to control for non-independence of phenotypes (e. g. neoplasia prevalence) in closely related species. We report the phylogenetic signal, lambda, for each analysis, along with the p-value and R 2. A single phylogenetic tree encompassing the three clades was collected from timetree. org. We pruned the tree to the 292 species in our data set using the setdiff and keep. tip/drop. tip functions in the APE R package. Estimates for neoplasia and malignancy prevalence are more accurate in species with more necropsies. To address the differences in number of necropsies, and to limit the noise from prevalence estimates based on few individuals, we weighted the species data points by the square-root of the number of necropsies records we have.
Our R code for all analyses and figures included in this manuscript is freely available at https://github. com/zacharycompton/cancerAcrossVertebrates. git. In addition, we only analyzed species for which we had at least 20 necropsy results (previous studies had used  10 (16)  or 20  (17, 18)  for the lower bound number of individuals). The main pglsSEyPagel analyses were done with all species together, including mammals, sauropsids and amphibians. In the analyses of litter size and gestation time, we also tested for a relationship with neoplasia prevalence in mammals alone. We carried out a total of 28 pglsSEyPagel analyses. To control for multiple testing, we used a false discovery rate (FDR) of 10%.
The following day, doxorubicin was added at one of four concentrations (0μM [DMSO vehicle control], 0. 11μM, 0. 33μM, and 1μM). Each condition was tested in triplicate in three separate experiments. Cell proliferation and apoptosis were measured by real-time fluorescence microscopy (IncyCyte, Sartorius) at two-hour intervals for three days. Apoptosis was measured using a fluorescent cell death marker, Annexin V Dye (Sartorius). Images were processed and analyzed using IncuCyte software. The number of dead or dying cells were identified by counting Annexin V positive cells. In addition, cell count overtime was calculated using IncuCyte cell-by-cell software. To measure response to radiation-induced DNA damage, cells were irradiated with one of four doses: 0Gy, 0. 4Gy, 2Gy, and 10 Gy. Radiation dose was delivered using an RS-2000 X-Ray Irradiator (Radsource).
We had hoped to discover species that are able to prevent malignant transformation by finding species that get a fair number of benign neoplasms, but few to no malignant neoplasms. The common paradigm in understanding the evolution of cancer suppression emphasizes the importance of protecting against tumor initiation. However, mechanisms that suppress malignant transformation could be similarly important in maintaining an organism's fitness. Unfortunately, only a few species in our dataset fit that description. The species with the lowest proportion of malignant to benign neoplasms was the common squirrel, with only 12% of their tumors being malignant.
These animals were generally protected from predators, provided with veterinary care, had different diets and exercise from their wild counterparts, many lived in an urban environment, and interacted with different species and microbes than a free-ranging animal. It is striking to us that four of the species with the lowest prevalence of neoplasias in our dataset, the gray squirrel, the common dormouse, the striped grass mouse, and the common field vole are all from wild, urban populations. These necropsies come from the London Zoo which has a policy of performing a necropsy on any animal they recover that dies on its grounds, not just the animals under its care. This is a hint that cancer may well be less common in the wild. If the "gross" cause of death was obvious for an animal, an institution may not have submitted the animal's samples for histopathology, and would not be included in our data collection.
Acknowledgements We would like to thank our dear colleague  Drury Reavill  who passed away prior to the preparation of this manuscript. We are forever grateful to her contribution to the field of veterinary science and her dedication to the health and survival of all animals. Many thanks to our continued collaboration with  Michael Garner  and  Northwest Zoo Pathology  who provided the annotated veterinarian pathology database. Liam Revell , the developer of the R software package "phytools", was extremely helpful in providing input for the application of his methods in novel ways. We would also like to thank the zoos and aquaria who cared for these animals and gave us permission to analyze their data. These discoveries could not have been made without them. Among these contributing institutions we would like to specifically thank these zoos:  Akron Zoo, Atlanta Zoo, Audubon Nature Institute, Bergen County Zoo, Birmingham Zoo, Buffalo Zoo, Capron Park Zoo ,  Central Florida Zoo, Dallas Zoo, El Paso Zoo, Elmwood Park Zoo, Fort Worth Zoo, Gladys Porter Zoo, Greensboro Science Center, Henry Doorly Zoo, Utah's Hogle Zoo, Jacksonville Zoo ,  John Ball Zoo ,  Los Angeles Zoo, Louisville Zoo ,  Mesker Park Zoo, Miami Zoo, Oakland Zoo, Oklahoma City Zoo, Philadelphia Zoo, Phoenix Zoo, Pueblo Zoo ,  San Antonio Zoo ,  Santa Ana Zoo ,  Santa Barbara Zoo ,  Sedgwick County Zoo, Seneca Park Zoo , The  Brevard Zoo, The Detroit Zoo, The Oregon Zoo , and  Toledo Zoo.
MATERIAL AND METHOD The specimen of Youngina capensis (BP/1/2871) (Fig. 1A, B ) was scanned at the ID19 beamline of the European Synchrotron Radiation Facility (ESRF, Grenoble, France) using propagation phase contrast synchrotron radiation x-ray micro-computed tomography (PPC-SRlCT) (see Appendix S1 for full methodology). Our study focusses on the palate and mandible because these structures are incompletely described for Youngina and because both structures are relatively well preserved in BP/1/2871. The right hemimandible is articulated, whereas the right side of the palate is disarticulated and slightly fragmented (Fig. 1C, D ). The right hemimandible and right side of the palate were digitally segmented using Materialise Mimics v19. 0 software (https://www. materialise. com) to produce 3D mesh models of the individual elements, which were then exported as.
ply files into Blender 2. 9 series software (https://www. blender. org). Bones were manipulated in Blender to produce a reconstruction of the right side of the palate and then the model was rendered to produce two-dimensional images. The right hemimandible is fully articulated and did not require reconstruction. All images of the right hemimandible (and some images of the parabasisphenoid) were generated using the Microsoft 'Snipping Tool' application when viewing the 3D models in Materialise Mimics. Our new observations of the palate, mandible and parabasisphenoid allowed us to review and, where appropriate, revise the relevant character scores for Youngina used in a recently published phylogeny of early amniotes  (Ford & Benson 2019a , 2020). We conducted a Bayesian analysis using the modified version of the matrix and the Mkv non-time-calibrated Bayesian script of  Ford & Benson (2019a ) with MrBayes v3.
PHYLOGENETIC RELATIONSHIPS We investigated the impact of our novel observations on the phylogenetic placement of Youngina by incorporating them into the data matrix of  Ford & Benson (2019a). This data matrix consists of 70 taxa and 294 characters, with 41 mandibular characters (including characters concerning marginal dentition) and 33 palatal characters (including characters concerning the parabasisphenoid). We reviewed 41 mandibular and 29 palatal characters, of which 13 mandibular scores and seven palatal scores were either novel or revised information for Youngina capensis. We reanalysed the revised matrix of Ford & Benson (2019a) using Bayesian inference. Our results are expressed as a fully resolved tree (allcompat command in MrBayes), which is based on a 50% majority rule tree with the addition of all compatible groups to such a tree.
DATA ARCHIVING STATEMENT CT data and 3D models are available on MorphoSource: https://www. morphosource. org/projects/000460987. A list of individual MorphoSource DOIs is available in Appendix S2. Data associated with the phylogenetic analysis are available on OSF: https://doi. org/10. 17605/OSF. IO/FBK2Q Editor. Kenneth Angielczyk.
PLoS One, 9 (2), e89165. F L Y N N , J. J. , N E S B I T T , S. J. , P A R R I S H , J. M. , R A N I -V O H A R I M A N A N A , L. and W Y S S , A. R. 2010. A new species of Azendohsaurus (Diapsida, Archosauromorpha) from the Triassic Isalo Group of southwestern Madagascar; cranium and mandible. Palaeontology, 53, 669-688. F O R D , D. P. and B E N S O N , R. B. J. 2019a. The phylogeny of early amniotes and the affinities of Parareptilia and Varanopidae. Dryad Digital Repository. https://doi. org/10. 5061/dryad. t4b8gthx8 F O R D , D. P. and B E N S O N , R. B. J. 2019b. A redescription of Orovenator mayorum (Sauropsida, Diapsida) using highresolution lCT, and the consequences for early amniote phylogeny. Papers in Palaeontology, 5, 197-239. F O R D , D. P. and B E N S O N , R. B. J. 2020.
Parameters evaluated To investigate the impacts of pollen diet and parasite, several parameters in microcolonies were measured  (Tasei & Aupinel, 2008) , namely resource collection, reproductive success, stress response, and individual health through fat body content (i. e. , immunocompetence proxy;  Arrese & Soulages, 2010; Rosales, 2017; Vanderplanck et al. , 2021)  and parasite load measurements. Resource collection was assessed by weighing every two days in each microcolony the syrup container, as well as the recovered pollen candy and the newly introduced one. These data were corrected for evaporation using controls, as well as divided by the total worker mass by microcolony to avoid bias due to worker activity. To evaluate the reproductive success, all microcolonies were dissected at the end of the experiment (Day 35) to weigh the total hatched brood mass, as well as the individual mass of each emerged male used as reference of viable offspring at the end of development  (Goulson, 2010).