dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements The authors thank the patients who participated in the endTB observational study and the clinicians and program staff of participating national TB programs (the full list of the endTB study group is available at http://www. endtb. org/resources/endtbstudy-group-members);our funder, Unitaid, for financing the endTB project, including the observational study; endTB staff at Partners In Health,  Médecins Sans Frontières, Epicentre , and  Interactive Research and Development. The endTB Observational Study was funded by  UNITAID. MFF, CDM ,  MLR , and KJS, and CZ were supported by the  National Institute of Allergy and Infectious Diseases of the National Institutes of Health  under Award Number  R01AI46095. The funders had no role in the conceptualization, analysis or presentation of findings of this study.
Characterisation of Hybrid Cyclodextrin-CaCO3 Particles Scanning electron microscopy (SEM) was performed on a LEO1530 microscope equipped with an InLens and secondary electron detectors using a low accelerating voltage (3 kV) and was used to observe the shape of the obtained materials (in Leo Elektronenmikroskopie GmbH, Oberkochen, Germany). Zeta potential measurements were performed on a Zetasizer Nano-ZS (Zetasizer 4700 Malvern Instruments, Palaiseau, France) with a suspension of CaCO3 particles (suspended in water). Structural characterisation was performed by X-ray diffraction (XRD) using a D8 advance diffractometer (Bruker, Champs sur Marne, France) (Cu Kα radiation). Data were recorded over a 2Ɵ range from 5 to 80°in steps of 0. 02° at an incident wavelength  of 1. 54056 Å. Thermogravimetric analysis (TGA) was performed on a Setaram Setsys Evolution 16 thermobalance (Setaram Instrumentation, Caluire, France) by heating the samples at a rate of 10 °C/min from 30 to 900 °C.
Characterisation of Hybrid Cyclodextrin-CaCO 3 Particles Scanning electron microscopy (SEM) was performed on a LEO1530 microscope equipped with an InLens and secondary electron detectors using a low accelerating voltage (3 kV) and was used to observe the shape of the obtained materials (in Leo Elektronenmikroskopie GmbH, Oberkochen, Germany). Zeta potential measurements were performed on a Zetasizer Nano-ZS (Zetasizer 4700 Malvern Instruments, Palaiseau, France) with a suspension of CaCO 3 particles (suspended in water). Structural characterisation was performed by X-ray diffraction (XRD) using a D8 advance diffractometer (Bruker, Champs sur Marne, France) (Cu Kα radiation). Data were recorded over a 2θ range from 5 to 80 • in steps of 0. 02 • at an incident wavelength λ of 1. 54056 Å. Thermogravimetric analysis (TGA) was performed on a Setaram Setsys Evolution 16 thermobalance (Setaram Instrumentation, Caluire, France) by heating the samples at a rate of 10 • C/min from 30 to 900 • C.
Patients and samples Bio-banked serum samples of adult individuals ≥ 18 years old with CLD were included in this study. These samples were a subset of those described by Stämmler et al. (17) , and were selected from patients with CLD within the validation cohort (i. e. , not part of the development dataset)  (17). A total of 205 samples were included in this analysis, collected from CLD patients in Rochester, MN, USA (n = 155) and Lyon, France (n = 50). Samples were stored at - 80°C and underwent no more than one freeze-thaw cycle before NMR analysis, as previously described  (17). The study was conducted according to the guidelines of the Declarations of Helsinki and Istanbul, and was approved by the relevant Institutional Review Boards (Mayo Clinic IRB# 19-003513, dated 16 May 2019, and Hospital Edouard Herriot IRB# DC-2012-1615, dated 2 July 2012.
Other variables The performance of eGFR equations was also evaluated in terms of correct CKD staging (G1 to G5)  (22) , using mGFR as reference, in the whole population, in preserved versus reduced liver function subgroups, and according to the following liver and renal dysfunction parameters: (i) the severity of liver dysfunction based on the Model of End-stage Liver Disease (MELD) score  (21, 23) , with a threshold of MELD > 15 for liver dysfunction, (ii) the presence or absence of ascites, and (iii) renal dysfunction (mGFR < 60 ml/min/1. 73 m 2 ). Other relevant clinical parameters are listed in Table  1. (30). Descriptive summary tables were created via the gtsummary (Version 1. 3. 5) package  (31). Key performance indicators (KPIs) for performance evaluation were selected as previously described  (17).
Acknowledgements The authors want to thank  John Venz  (numares  AG ) for statistical consultation and  Jochen H. Ehrich  for valuable clinical discussions on metabolite physiology in liver disease. The authors thank  Anne Rascle  of  AR Medical Writing (Regensburg, Germany ) for providing medical writing support, which was funded by numares  AG (Regensburg, Germany) , in accordance with Good Publication Practice (GPP3) guidelines (http://www. ismpp. org/gpp3).
6 to 4. 9 GeV, thereby providing access to charmed baryon thresholds. J/ψ ηη ′ J P C = 1 -+ J/ψ X(1835) → π + π - η ′ pp η(1405) → f 0 (980)π 0 a 0 (980) ↔ f 0 (980) CP J/ψ → Λ Λ J/ψ → Ξ - Ξ- In 2019, BESIII achieved one of its main data-taking goals with the successful accumulation of 10 billion events for studies of light hadron physics. An early payoff from this unprecedentedly large data sample was the discovery of an isospin-singlet meson resonance with manifestly exotic quantum numbers  [19, 20]. This is best explained as a "smoking-gun" candidate for a quantum chromodynamics (QCD) hybrid meson comprising a quark-antiquark pair plus a valence gluon, a hadronic substructure that was predicted over forty years ago  [21]  but has only recently started to emerge experimentally thanks to the availability of enormous datasets such as the BESIII 10 billion event sample.
[66, 67 ] , respectively. Both of these experiments can produce more leptons and charmed hadrons and mesons than the STCF. However, STCF data samples will have distinctly lower backgrounds, near-100% detection efficiencies, almost full detector-acceptance, better full-event reconstruction rates, well-controlled systematic uncertainties, etc. The STCF will also have several unique features that are not available at Belle II and LHCb, including the direct production of resonances such as charmonium  ( , and )  and Y (4260) Y (4320) Y (4660) K L nonstandard charmonium-like mesons, such as , and , as well as operation near particleantiparticle thresholds, thus providing the ability to fully reconstruct events with final-state neutrinos, neutrons/antineutrons or mesons with high efficiency. To achieve these goals, a sophisticated, machinecompatible detector will be required to maximize the physics potential.
Advanced data acquisition (DAQ) and trigger systems are required to handle a high event rate in the range from 60 kHz to 400 kHz. The rest of the document is organized as follows: The physics opportunities at the STCF are discussed in Section 2. In Section 3, the conceptual designs of the STCF detector system are described. In Section 4, performances of several benchmark physics processes are introduced, and Section 5 is the future plans and R&D prospects.
Among the three CKM angles, is of particular importance because it is the only -violating observable that can be determined using tree-level decays. Currently, the world-best single measurement of is from LHCb:  [162]. The precision measurement of will be one of the top priorities for the LHCb upgrade(s) and the Belle II experiment. γ B + → D0 K + B + → D 0 K + B D γ D γ The most precise method of measuring is based on the interference between the and decays  [163] [164] [165] [166] [167]. In the future, the statistical uncertainties of these measurements will be greatly reduced by using the large meson samples collected by LHCb and Belle II. Hence, limited knowledge of the strong phases of the decays will systematically restrict the overall sensitivity. A 20 fb -1 dataset collected at 3. 773 GeV at BESIII would lead to a systematic uncertainty of ~0.
Hadron production via collisions with ISR [297] plays an important role. Current and future experiments present a real opportunity for a dramatic improvement in our knowledge of the spectrum. J/ψ ψ(3686) f 0 (1710) f 0 (1500) J/ψ ψ(3686) q q γγ J P C At present, BESIII remains unique in its ability to study and search for QCD exotics and new excited baryons  [298] , as its high-statistics data sets of charmonia provide a gluon-rich environment with clearly defined initial-and final-state properties  [71]. At the STCF, many more data sets of charmonia will be obtained. The expected high-statistics data samples for and decays, including both hadronic and radiative decay channels, will provide an unprecedented opportunity to obtain a better understanding of the spectrum of light hadrons, their properties and their couplings to all the channels in which they appear and, from these, to learn about the composition of these states, including glueballs and hybrid states.
An interesting example is the study of the glueball nature of some states using data from the STCF. The production properties suggest a prominent glueball nature of and a flavor octet structure of  [71 ]. However, the scalar meson sector is the most complex one, and the interpretation of the states' natures and their nonet assignments are still very controversial. There is no question that more states than can be accommodated by a single meson nonet have been found. However, the nature of all of these states is still open for discussion. At the STCF, a year of operation will provide ~3T and ~500B events at their peak cross sections for exploring light hadron physics. Traces of glueballs and hybrid states may be found in some more confirmed ways. Measurements of electromagnetic couplings to glueball candidates would be extremely useful for the clarification of the nature of these states.
In addition, more precise study on the isoscalar , combined with previous and also future measurements of the isovector states, will provide critical clue of searching for other partners of exotic supermultiplets. Nevertheless, the extraction of resonance properties from experimental data is far from straightforward; the resonances tend to be broad and plentiful, leading to intricate interference patterns, or buried under a background in the same and other waves. The key to success lies in high statistical precision complemented by sophisticated analysis methods. Partial wave or amplitude analysis (PWA) techniques  [299]  are the state-of-the-art way to disentangle the contributions from individual, even small, resonances and to determine their quantum numbers. Nevertheless, the extremely high statistics at the STCF will present new challenges for data handling and processing.
Deviations of measured quantities from their QED predictions are usually described in terms of a time-like transition form factor, which, in addition to being an important probe into the meson's structure  [307] , has an important role in the evaluation of the hadronic light-by-light contribution to the muon anomalous magnetic moment (see the nice review in Ref. [310]  for details). In addition, using the expected large data sample to be collected at a center-ofmass energy above the peak at the STCF, measurements of the space-like transition form factors in the decay via interactions in the transfer momentum ( ) range of GeV/c 2 will be feasible. The measured space-like transition form factors will uniquely cover the range that is relevant to the hadronic light-by-light correction for the evaluation of the muon anomalous moment.
By exploiting the spin entanglement between the baryon and its antiparticle , BESIII has enabled a direct determination of the weak-phase difference, rad  [28]. A Ξ A Λ A ΞΛ 3. 4 × 10 12 J/ψ A ΞΛ A Ξ A Λ -3 × 10 -5 ≤ A Λ ≤ 4 × 10 -5 -2 × 10 -5 ≤ A Ξ ≤ 1 × 10 -5 The sensitivities for the , and asymmetries with a data sample of events at the STCF (see Table  2. 10) are given in Table  2. 11. The statistical uncertainty for the asymmetry from the dedicated HyperCP experiment will be surpassed at the STCF. The SM predictions for the and asymmetries are and  [323]. 0. 037 ϕ Ξ 3. 1 × 10 5 Ξ -Ξ+ 1. 4 × 10 5 J/ψ → Ξ -Ξ+ 114 × 10 6 ϕ Ξ 0 3 × 10 2 Ξ 0 Ξ0 Under the assumption of a value of for the parameter, five-sigma significance would require exclusive events. Reaching a statistical uncertainty of 0.
CP The sensitivities for the weak phase difference [321 ] using the two independent methods are also given in Table  2. 11. The SM estimate for is. However, it should be stressed that the SM predictions for all asymmetries need to be updated in view of the recent and forthcoming BESIII results on hyperon decay parameters using the collected events. A wide range of precision tests can be conducted based on a single measurement. Thus, the spin-entangled cascade-anticascade system is a promising probe for testing fundamental symmetries in the strange baryon sector. J/ψ, ψ(3686) → B B 3. 4 × 10 12 J/ψ 3. 2 × 10 9 ψ(3686) Λ → pπ - Ξ → Λπ Table  2. 10 Branching fractions for some decays and the estimated sizes of the data samples from the full data set of and to be collected by the STCF. The approximate detection efficiencies for the final states reconstructed using the and decay modes are based on the published BESIII analyses using partial data sets  [325] [326] [327].
2. 10 and Ref. [75]. AΞ AΛ AΞΛ (ζp -ζs)Ξ (ζp -ζs)Ξ Eq. (  2. 24) Eq. (  2. 26) J/ψ → Λ Λ - 1. 7 × 10 -4 - - - J/ψ → Ξ -Ξ+ ∆Φ = 0 ( ) 2. 2 × 10 -4 2. 1 × 10 -4 2. 5 × 10 -4 2. 4 × 10 -3 6. 5 × 10 -4 Λ Λ J/ψ Λ Λ ∆(B -L) = 2 Λ Λ J/ψ → Λ Λ J/ψ Λ Λ δm Λ Λ < 10 -15 10 -7 δm Λ Λ 10 -17 Λ A large data sample of from decays can also be used to study -oscillations. The seesaw mechanism, as an explanation for the small neutrino masses  [331] , predicts the existence of interactions and baryon-antibaryon oscillations. To date, searches for processes that violate the baryon number by two units have been performed only in neutron-antineutron oscillation experiments  [332]. Searches for -oscillations in the decay at BESIII have been proposed  [333]. With 10 billion decay events at BESIII, the expected sensitivity of the measurement ofoscillation is MeV at the 90% confidence level.
In addition to the server nodes mentioned above, there are some other servers in the SL. The LOG/DB server (LOG) provides the system database for recording the system log information, including the system topology, running status, working parameters, and warning and error messages. The online/control server (OLC) is the command hub of the whole system and can receive, process, and forward the commands sent by the remote control server (RCS). It is also an online information controller that can merge the status stream, extract the online information for each detector system, and decimate the event data. All of this online information is processed in the remote online server (ROL) and the remote event analysis server (REA).
SNiPER framework SNiPER  [462]  is the foundation of the STCF software system and determines the performance, flexibility and extensibility of the system. It provides common functionalities for offline data processing and the standard interfaces for developing different applications via Task, Algorithm, Service and Tool. An algorithm provides a specific procedure for data processing. A sequence of algorithms forms the whole data processing chain. A service provides certain useful features, such as access to the detector geometry or database, which are necessary during data processing. Both algorithms and services are plugged in and executed dynamically, and they can be flexibly selected and combined to perform certain data processing tasks. All applications in terms of algorithms request event data from a Data Store and push new event data back to the Data Store, finally all event data in the Data Store will be automatically written into files via the File Output System.
Acknowledgements We would like to thank  Sergey Barsuk  ( IN2P3-CNRS & Université Paris 11, France ),  Alexander Bonder  ( Novosibirsk State University & Budker Institute of Nuclear Physics, Russia ),  Oliver Callot  ( IN2P3/CNRS & Université Paris 11, France ),  Wolfgang Kühn  ( Justus-Liebig-Universitaet Giessen, II. Physikalisches Institut, Germany ),  Cheng Li  ( University of Science and Technology of China, China ),  Jin Li  ( Institute of High Energy Physics, China ),  Weiguo Li  ( Institute of High Energy Physics, China ),  Alexey Petrov  ( University of South Carolina, USA ),  Yuri Tikhonov  ( Budker Institute of Nuclear Physics, Russia ), and  Changzheng Yuan  ( Institute of High Energy Physics, China; University of Chinese Academy of Sciences, China ) for their reviewing of this report.
We would like to thank  Andrzej Kupsc  ( National Centre for Nuclear Research, Poland; Uppsala University, Sweden ) for his contribution to this report. We thank the  University of Science and Technology of China , the  Hefei Comprehensive National Science Center, State Key Laboratory of Particle Detection and Electronics , and  National Synchrotron Radiation Laboratory  for their strong support. The research work leading to this report was supported by the  National Key R&D Program of China  under Contract No. 2022YFA1602200 , the  International Partnership Program of the Chineses Academy of Sciences  under Grant No. 211134KYSB20200057  and the  STCF Key Technology Research and Development Project.
Ethics Clinical Trial The study was conducted in accordance with the Declaration of Helsinki of 1975 (https://www. wma. net/what-we-do/medical-ethics/declaration-of-helsinki (accessed on 20 May 2021)) revised in 2013. The human study was approved by the French Ethical Committee (2021-071 RIPH2 HPS/N • SI RIPH: 21. 05. 18. 40345/N • EudraCT/ID RCB: 2021-A01211-40/Comité de Protection des Personnes CPP Sud-Est I; approved 18 June 2021). The volunteers were informed of the objectives and the potential risks of the present study and provided their written informed consent before they participated in the study.
The library was amplified over 9 cycles and purified using Ampure XP beads (Beckman Coulter, Villepinte, France). Library concentrations were measured using a Qubit 2. 0 Fluorometer in combination with a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). The library quality was confirmed by size analysis on a Bioanalyzer 2100 instrument with DNA 1000 Assay reagent kit (Agilent Technologies). This size and quantity information was used for pooling the libraries in equimolar concentrations to normalize each library. Single-end, 75 cycle sequencing was performed using a NextSeq 500/550 High Output v2 kit (75 cycles) (Illumina, Evry, France). The FASTQ files were generated using bcl2fastq software (Illumina). RNA-seq data analysis: Reads were trimmed using Trimmomatic software (version 0. 36) to filter poor quality reads and to cut poor quality bases and adapters.
Filtered reads were then mapped to the reference genome (Homo sapiens, assembly GRCh38, release 107) using STAR (version 2. 7. 10). The STAR software was also used to produce the count matrix, assigning reads to features using transcriptome annotation from GTF file. Quality control statistics were summarized using MultiQC software. Descriptive analysis was performed with DESeq2 R package. Differential analysis was performed with edgeR R package. TMM normalization was applied. Functions glmQLFit and glmQLFTest were used to identify differentially expressed genes between the two groups (To and TP). Genes of interest were selected according to the significance (Benjamini-Hochberg correction, corrected p-value less than 0. 05) and the effect size (foldchange). Gene lists were annotated using the WebGestalt tool (http://www.
Statistics Prism V. 7. 0, 8. 0 and V. 9. 4. 1 (GraphPad Software) were used to run statistic tests and draw figures. The following statistic plan was applied: a Shapiro-Wilk normality test was used to determine whether the data was consistent with a Gaussian distribution. If the data was not distributed according to the normal distribution, a Kruskal-Wallis nonparametric test was used followed by Dunn test for post hoc comparison. When normal distribution and equal variance was assumed, measures were subjected to one-way or two-way ANOVA with Tukey's test for multiple comparisons. In the case of a measurement repeated over time, differences between groups and time points were tested using a repeated-measure two-way ANOVA followed by Sidak's post hoc test for multiple comparisons. If a piece of data was missing making it impossible to run a repeated-measures 2-way ANOVA, a mixed-effects analysis was used instead.
Acknowledgments: The authors would like to thank  HELIXIO SAS  ( Saint Beauzire-France ) for performing RNAseq. This work was supported by the  Bordeaux Metabolome Facility  and the  Metabo-HUB  ( ANR11-INBS-0010 ) project. The authors also would like to thank  Marie De Antonio  ( Biostat Unit University Hospital-Clermont Ferrand, France ) for her advice during statistical analyses.
After extraction, the organic phase was transferred to an infusion plate and dried in a speed vacuum concentrator. 1st step dry extract was resuspended in 7. 5 mM ammonium acetate in chloroform/methanol/propanol (1:2:4, V:V:V) and 2nd step dry extract in 33% ethanol solution of methylamine in chloroform/methanol (0. 003:5:1; V:V:V). All liquid handling steps were performed using Hamilton Robotics STARlet robotic platform with the Anti Droplet Control feature for organic solvents pipetting. Mass Spectrometry data analysis and post-processing. Data were analyzed with in-house developed lipid identification software based on LipidXplorer  (3, 4). Data post-processing and normalization were performed using an in-house developed data management system. Only lipid identifications with a signal-to-noise ratio >5, and a signal intensity 5fold higher than in corresponding blank samples were considered for further data analysis.
Background:: The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called 'spatial transcriptomics'. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce. Results:: Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 9 human and murine tissues datasets from 4 different technologies.
Introduction The tissue characterization by single cell RNA sequencing (scRNAseq) technology, spatial transcriptomics (ST), unveils information beyond gene expression profiles and revolutionizes biology and medicine. Today, many packages using R or Python can map cells, score gene signatures, infer cell interactions, and detect spatial patterns  [18]. However, computationally frugal visualization of multimodal ST images raises challenges not addressed so far. Most ST platforms  [4, 10, 13, 14, 17]  yield images of million cells and gigabytes of data which multimodal visualization require overlays with thousands cell scores for thousands gene signatures. So despite the current tools for pre-processing ST data and computing scores, producing such multimodal images remains challenging for (1) the joint availability of spatial coordinates and signature scores, (2) the immediate and tunable overlay of image and signature, (3) the user-friendly environment requested by biomedical users.