dataesr/scientific-paragraphs-categorization huggingface dataset:
 This study used data from the  COURAGE-PD consortium , conducted under a partnership agreement between 35 studies. The  COURAGE-PD consortium  is supported by the  EU   Joint Program for Neurodegenerative Disease  research (JPND; https://www. neurodegenerationresearch. eu/initiatives/annual-calls-for-proposals/closedcalls/risk-factors-2012/risk-factor-call-results/courage-pd/).  CD is the recipient of a doctoral grant from  Université Paris-Saclay, France.  MS  was supported by the grants from the  German Research Council  ( DFG/SH 599/6-1 ),  MSA Coalition , and  Michael J Fox Foundation (USA Genetic Diversity in PD Program: GAP-India  Grant  ID: 17473 ).  ABS, DGH, and CE are funded by the  Intramural Research Program  of the  National Institute on Aging, National Institutes of Health, Department of Health and Human Services , project  ZO1 AG000949.
 ER is funded by the  Canadian Consortium on Neurodegeneration in Aging.  SK is funded by  MSWA.  PT is the recipient of an  Estonian Research Council  Grant  PRG957.  EMV is funded by the  Italian Ministry of Health  ( Ricerca Corrente 2020 ).  SB and JC are supported by grants from the  National Research Foundation of South Africa  (Grant Number:  106052 ); the  South African Medical Research Council  ( Self-Initiated Research Grant ); and  Stellenbosch University , South Africa; they also acknowledge the support of the  NRF-DST Centre of Excellence for Biomedical Tuberculosis Research ;  South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University ,  Cape Town.
Study population and design Data from 105 patients diagnosed with liver-limited CRC metastases harboring BRAF V600E mutations between April 1, 2008, and December 31, 2017, were retrospectively collected from 25 French hospitals. Exclusion criteria were as follows: presence of extra-hepatic metastases, date of CRLM diagnosis not available, and follow-up less than 12 months. Data from the majority of patients who underwent CRLM resection came from databases of the following four French scientific groups: Fédération de Recherche et Chirurgie (FRENCH), Association de Chirurgie Hépato-Bilio-Pancréatique et Transplantation (ACHBT), Association des Gastro-Enterologues Oncologues (AGEO), and the PRODIGE group (Partenariat de Recherche en Oncologie DIGEstive). BRAF V600E mutated-patients were identified from molecular biology platforms and each case was screened in order to identify and include patients with liver-only disease.
Patients with synchronous extra-hepatic resectable disease metastases were excluded. The study was conducted according to the ethical standards in line with the French regulation. French Data Protection Authority (CNIL agreement n° DEC18-409 (2018_01)) provided a waiver of informed consent for this retrospective study and permitted the publication of anonymized data. BRAF and RAS mutational statuses were determined from either primary CRC samples or CRLM tissues-as several studies have demonstrated a high molecular concordance between primary CRC and liver metastases  [14, 15] -using PCR or next-generation sequencing according to the technology available at each hospital. The following clinical, molecular, and pathological characteristics were collected at baseline: age at CRLM diagnosis, sex, KRAS and NRAS mutations, mismatch repair (MMR) status, primary tumor site, surgery of primary tumor, tumor and nodal stages according to the American Joint Committee on Cancer (AJCC), synchronous (<6 months) versus metachronous CRLM diagnosis, CRLM distribution and number, and initial resectability status.
Vasodilatory shock, such as septic shock, requires personalized management which include adequate fluid therapy and vasopressor treatments. While these potent drugs are numerous, they all aim to counterbalance the vasodilatory effects of a systemic inflammatory response syndrome. Their specific receptors include α-and β-adrenergic receptors, arginine-vasopressin receptors, angiotensin II receptors and dopamine receptors. Consequently, these may be associated with severe adverse effects, including acute mesenteric ischemia (AMI). As the risk of AMI depends on drug class, we aimed to review the evidence of plausible associations by performing a worldwide pharmacovigilance analysis based on the World Health Organization database, VigiBase®. Among 24 million reports, 104 AMI events were reported, and disproportionality analyses yielded significant association with all vasopressors, to the exception of selepressin.
BACKGROUND Vasodilatory shock, among which the first cause is septic shock, rank first in the causes of mortality in intensive care units  (1). Upkeeping organs perfusion is one of the main goals of shock management, and to that end, volume resuscitation and vasopressors administration are key to maintaining adequate blood pressure  (1). Yet, the variety of molecules which may be used as vasopressors has been increasing over the years, and their efficacy and drawbacks have been compared in numerous meta-analyses and reviews. Among adverse effects related to use of vasopressors, acute mesenteric ischemia (AMI) is an uncommon (with a below than 1% incidence) but lethal  (2, 3)  and its diagnosis difficult  (4). In this review, we especially focused on AMI related to vasopressors use. In the first part, we performed a worldwide pharmacovigilance analysis based on the World Health Organization database, VigiBase R to assess the potential association between the different vasopressors and AMI.
Study Design This is a worldwide observational case-non-case cross-sectional study focusing on AMI related to vasopressors use, from the international pharmacovigilance database, VigiBase R  (5). VigiBase R is the WHO global individual case safety reports (ICSR) deduplicated database, managed by the Uppsala-Monitoring-Centre (Uppsala, Sweden, accessible at www. vigiaccess. org). It contains over 23 million ICSR received from over 130 countries since 1967 with over 25,000 drugs and vaccines. ICSR originate from different sources, such as healthcare professionals, patients, and pharmaceutical companies, and are generally notified post-marketing. ICSR include administrative information (country, type of report and reporter), patient data (age, sex) and nature of the outcome, using the latest version (currently v22.
e. , full database with all drugs). The denominator in these analyses is the total number of ADR reported for each group of drugs. If the proportion of cases associated with a specific drug is greater than in patients without this ADR (non-cases), there is a disproportionality association (signal identification) between the ADR and the drug. In the present work, the calculated Bayesian disproportionality estimate was the information component (IC)  (8). Herein, we also performed for selected previously unknown liable drugs a sensitivity analysis excluding from full database the ICSR in which drugs already known to be associated with AMI were reported. Calculation of the IC using a Bayesian confidence propagation neural network was developed and validated by the Uppsala Monitoring Centre as a flexible, automated indicator value for disproportionate reporting that compares observed and expected ADR associations to find new drug-ADR signals with identification of probability difference from the background data (full database)  (9).
Probabilistic reasoning in intelligent systems (information theory) has proved to be effective for the management of large datasets, is robust in handling incomplete data, and can be used with complex variables. The information theory tool is ideal for finding drug-ADR combinations with other variables that are highly associated compared with the generality of the stored data  (9). Several examples of validation with the IC exist, showing the power of the technique to find signals sooner after drug approval than by a regulatory agency, and to avoid false positives, whereby an association between a common drug and a common ADR occurs in the database only because the drug is widely used and the ADR is frequently reported (i. e. , between digoxin and rash)  (9, 10). Like others, our team published several studies using VigiBase R and disproportional reporting calculation to characterize and identify new drug-ADR associated signals, which were subsequently corroborated by preclinical mechanistic studies or prospective cohorts  (8, (11) (12) (13) (14).
This later element requires to be emphasized, as IC value should be interpreted only as means to perform clinical reviews of plausible associations and do not signify causality in any way. The IC 025 is the lower end of the 95% credibility interval for the IC. A positive value of the IC 025 is deemed significant  (8, 15). For description of ICSR, continuous data were reported in median (interquartile range). All data were available, otherwise specified. Data management was performed using Python software v3. 0 (Python software foundation, Wilmington, Delaware, USA).
LIMITATIONS We acknowledge several and important biases due to the nature of the pharmacovigilance database. The first being underreporting, associated with halo bias and lack of information on the exposed population for calculation of incidence, which would require sales data from the industry. Indeed, acute mesenteric ischemia may be caused by shock, which is a major confusion bias. Moreover, as mesenteric ischemia remains a rare entity, true incidence remains elusive, due to numerous factors. The lack of consensual definition, with multiple criteria possible, as well as hardship to have definite diagnosis makes underreporting plausible. Moreover, not being able to return to each report to ensure that an exhaustive search for etiologies and concomitant drugs intake has been carried out leads to an information bias, which leads to the fact that the likelihood of a causal relationship is not the same in all reports.
It is of importance to underline that the association we found between vasopressors and acute mesenteric ischemia is not necessarily synonymous with causality and, given the low quality of evidence that can be inferred from the analysis of large databases such as the pharmacovigilance database, our results should be interpret with caution. Yet, with all these elements, disproportionality analysis methodology allows to focus the attention of clinical physicians, and to assess plausibility of the incrimination of a drug toward a singular adverse effect. Although all vasopressors except Dopamine do not have dose-dependent physiological effects and were used in the same indications in the different studies included in our literature review, it should be kept in mind that the incidence of acute mesenteric ischemia may be influenced by the dose of vasopressors administered, especially in patients with impaired vascularity (elderly patients, smokers.
Data Collection Data were collected using a cross-sectional study design with an online survey. The survey was implemented via mobile phones using the survey platform Pollfish  [39]  and was limited to individuals aged ≥ 18 across all regions in Italy. We aimed at a sample size of 1000 individuals based on a previous study  [40]  where approximately 20% of the population manifested hesitancy. This fraction was determined as sufficient to explore the association with socio-demographic and other factors. In addition, eligible participants in this study were identified using a screening question to limit the sample to those who were not vaccinated at all, and those who had received only one dose of a COVID-19 vaccine requiring two doses at the time of the survey. The Pollfish platform uses random device engagement (RDE), an approach like Random Device Dialing (RDD), to reach users engaged in using mobile applications (rather than calling them).
Users are identified only by a unique device ID. Compared to RDD, RDE results in a higher response rate and avoids the potential bias of interviewer-respondent interactions. For this survey, a random sample of 1000 users who fit the study's eligibility criteria was selected and data were collected between 21-28 May 2021. Only 16% of the Italian population had been fully vaccinated when the survey was launched  [41]. All respondents were asked to consent to participate in the survey before proceeding to answer the survey questions. The study protocol and survey instrument were approved by the Harvard T. H. Chan School of Public Health Institutional Review Board (IRB) on 8 December 2020 (protocol #20-203) and were granted a checklist-based self-assessment exempt status at Bocconi University on 22 April 2021 (protocol #31146).
Socio-Demographics and Comorbidities Data were collected on socio-demographic factors such as age, education, sex, citizenship, and region of residence. The region of residence was categorized into: "North" (Emilia-Romagna region and further north) and "South/Central (Tuscany and further south)". The respondents experience with economic stress was measured by asking respondents "In the past 12 months (1 year) have there been occasions in which you were worried about not having enough money or resources to be able to have enough food to eat?" with responses coded as "No" (0) and "Yes"  (1). Respondents were also asked to report if they were at high risk due to a health condition from a list of options of diseases or conditions associated with the risk of severity in case of COVID-19 infection such as diabetes, cancers, hypertension, and auto-immune diseases.
Study Selection and Search Results On 28 July 2021, following the search strategy defined in Section 4. 1, a total of 1360 publications were found in the PubMed database, 1246 papers were rejected based on the abstract reading by the two independent reviewers. The screening phase resulted in 114 records selected. Four publications could not be accessed, and 42 more articles were rejected after reviewing the entire article. Figure  1  summarizes the bibliographic search strategy and the reasons for excluding articles. The complete list of publications reviewed is provided in the additional file Table  S1. However, concerning human co-infection, the situation is more complex. Indeed, the term 'co-infection' mixes several different concepts. 'Co-infection' is more frequently used to refer to multiple seropositivity without an associated disease.
Study Selection and Search Results On 28 July 2021, following the search strategy defined in Section 4. 1, a total of 1360 publications were found in the PubMed database, 1246 papers were rejected based on the abstract reading by the two independent reviewers. The screening phase resulted in 114 records selected. Four publications could not be accessed, and 42 more articles were rejected after reviewing the entire article. Figure  1  summarizes the bibliographic search strategy and the reasons for excluding articles. The complete list of publications reviewed is provided in the additional file Table  S1. A total of 68 articles were included in this systematic review encompassing 28 case reports (41. 2%), 18 prospective studies (26. 5%), 17 retrospective studies (25%), and 5 case series (7.
Studies' Analysis and Data Collection Potentially eligible articles were selected and screened using their title and abstract. The articles were included or not according to the inclusion or exclusion criteria. The final inclusion was done by analyzing the full texts of the included articles. A consensus between the two readers was used to resolve any disagreement. Information regarding the authors, location, study design, characteristics and size of the explored cohort, clinical picture(s) described, diagnostic tests used, treatment, outcome, data on severity, and specific results was extracted and entered into an Excel sheet. In order to compare studies, the initial diagnosis made by the authors was reviewed, and an imputability scoring system was established using clinical data and microbiological documentation.
Statistical Analysis The experiments were replicated at least 5 times. Mean and standard deviation of the data were calculated. The Fisher's least significant difference (LSD) tests were applied for analysis of the effects of PEF treatment, level of dehydration and frying temperature. For each analysis, the significance level of 5% was assumed. All statistical analyses were performed with a 95% confidence interval. For the derivation of frying rates constant, the software package TableCurve 2D, version 5. 01 (Systat Software, San Jose, CA, United States) was used.
The empirical Henderson and Pabis equation (Eq. 4) was used to fit the curve of moisture ratio as a function of frying time (Figure  1 , solid and dashed lines). Software package, TableCurve 2D, version 5. 01 (Systat Software, San Jose, CA, United States) was used to obtain the relevant correlation coefficients (R 2 ) and the frying rates constant, k. The R 2 were rather high for untreated and PEF pre-treated samples at all temperatures (R 2 = 0. 978-0. 901). The values of frying rate constant, k, as a function of frying temperature ranged from 2. 06 × 10 -3 s -1 to 6. 07 × 10 -3 s -1 and 2. 17 × 10 -3 s -1 to 6. 74 × 10 -3 s -1 for untreated and PEF pre-treated samples, respectively (insert to Figure  1 ). The results demonstrated that the increase in frying temperature and application of PEF pre-treatment caused a significant increase in frying rate constant (p < 0.
A. Data Description The data includes the three parts: 1) Picture: Pictures were taken during driving and their shooting time. 2) Camera: Camera calibration data, which includes intrinsic parameters, extrinsic parameters, and distortion parameters. Distortion parameters are used to restore the distortion in pictures. Intrinsic parameters are used to establish the camera shooting model, and it contains the focal length of the lens, the offset between the lens center and the image center, the size of the imaging unit, etc. [4]. The extrinsic parameter here is the relative spatial relationship between the camera and the vehicle. Since these two devices are always relatively stationary, we just need relative rotation between them and the installation height of the camera  [5]. 3) GPS: GPS position of the driving recorder during driving and the corresponding accurate time.
3) Result of Overall Accuracy: In order to evaluate the accuracy of the method in this article, we select 6 traffic signs of different sizes for measurement. Their specific specifications are shown in Fig. 3. b. According to the characteristics of traffic signs, as long as the lengths of the sides are right, the shape and size are correct. Therefore, we choose the perimeter to evaluate the measurement error. Table  II  is the measurement error analysis. We selected 227 pairs of images, and this dataset contains all the six kinds of traffic signs above. From this table, we can see that most of the data's (about 88. 5%) errors are ¡10%. We list all those errors inside 10%, and their distribution is shown in Fig. 3. b and Fig. 3. d. For traffic signs of different sizes, we count their error separately, and the result is shown in Table  III.
W148 strains are the main contributors to the MDR epidemic in Russia and Eastern Europe, and since the USSR's fall, have also propagated to Western Europe, likely driven by economic or medical migrations of TB patients. As such, this strain dataset represents a unique resource to study the longitudinal and geographical spread, transmission efficacy and drug resistance evolution of Mtbc strains under treatment pressure. Whole genome sequencing (WGS) and Bayesian demographic approaches were combined to infer the phylogenetic structure and origin, as well as bacterial demographic changes and evolutionary steps driving the rise and spread of M/(pre-)XDR-TB in Eurasia over the last decades.
W148 phylogeography and spatio-temporal dispersion We included a total of 731 clinical isolates of L2 for WGS analysis. Of those, 720 belonged to the previously defined W148 European/Russian outbreak based on specific single nucleotide polymorphisms (SNPs)  11. The majority of the collection was sampled during the 21st century and originated from 23 countries, which were later grouped to 14 geographical regions (Fig. 1a , Supplementary Fig. 1 , Supplementary Data 1). Eleven non-W148 modern lineage 2 isolates were used as outgroup in subsequent phylogenetic analysis. To avoid the inclusion of homoplastic sites, mainly due to independent acquisition of identical resistance conferring mutations in our phylogenetic reconstructions, we removed 610 variants located in genes and intergenic regions associated with drug resistance and bacterial fitness (Supplementary Data 1).
A concatenated sequence alignment of 3508 SNPs differentiating the isolates was used to build a maximum-likelihood tree in order to unravel the geographic pattern present in the dataset (Fig. 1 ). The tree revealed a distinction between two major W148 sublineages, bifurcating from the most basal node in the phylogeny, at the extremity of the branch derived from the root (Fig. 1b ). Most Belarus and Estonian strains clustered in a single subclade, indicating local epidemic spread. This pattern of local epidemics was also apparent from a minimum spanning tree (Supplementary Fig. 2 ) where central nodes, containing several identical strain genomes from Estonia or Belarus, are surrounded by numerous variants differing only by 2-5 SNPs. In contrast, strains from Western Europe were randomly distributed in the network suggesting the importation of W148 strains from multiple different regions.
Targets of positive selection and hypervirulence-associated mutation Lastly, we screened the W148 phylogeny for homoplasy, i. e. , identical mutations occurring independently on different branches of the phylogeny and which cannot be explained by transmission events. Their independent evolution in the otherwise strongly clonal and genetically homogenous W148 outbreak would be a strong indication for positive selection. As a proof of principle, we re-introduced mutations in resistance mediating genes in the sequence alignment, which were previously excluded to calculate the ML tree. With the homoplasy analysis, we retrieved 77 such mutations in genes canonically implicated in drug resistance and compensatory effects (Supplementary Data 2). The remaining 82 mutations occurred in 47 genes with noncanonical or (as yet) unknown link with drug resistance or fitness compensation (Supplementary Data 2).
Our analysis confirmed the presence of such ppe38 configuration in all 731 dataset strains. Moreover, the W148 clade additionally underwent two large scale genomic re-arrangements  40  , and has a characteristic frameshift mutation in the two component regulatory system KdpD and KdpE  11  , implicated in the response to oxidative stress  41. A KdpDE deletion mutant of M. tuberculosis was shown to cause higher virulence in a mouse model  42. Furthermore, we detected recurrent instances of emergence of prpR mutations mediating multidrug tolerance  25  in terminal branches of our W148 phylogeny, corresponding in most cases to (pre-)XDR strains carrying both compensatory mutations and resistance mutations to up to 10 anti-TB drugs. Thus, the genetic make-up of the W148 clade may represent a unique "perfect storm" providing extended resistance with little to no fitness cost and incipient additional multidrug tolerance, on top of hypervirulence likely favoring rapid disease progression and enhanced infectiousness.