dataesr/scientific-paragraphs-categorization huggingface dataset:
Data were acquired in data dependent acquisition (DDA) mode, using a Top20 method. MS1 resolution was set to 70,000 (at 400 m/z), automatic gain control (AGC) to 3e 6 and maximum injection time was set to 20 msec. MS1 isolation window was set to 1. 6 mass units. MS2 resolution was set to 17,500, AGC to 1e 6 and maximum injection time of 60 ms. Protein Identification and Quantification-Raw data were processed using MaxQuant (MQ) version 1. 6. 5. 0 (25) and the embedded Andromeda search engine  (26). Data were searched against the human sequences in Swissprot human proteome version 2017_01 (20299 entries). Precursor mass and fragment mass were searched with mass tolerance of 4. 5 and 20 ppm, respectively. The search included variable modifications of oxidation (methionine) and protein N-terminal acetylation, and fixed modification of carbamidomethyl (cysteine).
Enzyme specificity was set to trypsin, a maximum of two miscleavages were allowed, and a minimal peptide length was set to 7 amino acids. The false discovery rate (FDR) for peptide and protein identifications was 0. 01. For the conventional versus TOP proteome extraction the defaults were kept, except: deamidation (NQ) was added as variable modification, and match between runs was not enabled. The bioinformatics was performed on Perseus suite (version 1. 6. 2. 3). The data were filtered for reverse, contaminants and identified by site. Then the data were filtered such that a protein had to have none-zero LFQ intensity in all 19 samples with 3 or more peptides, unless stated otherwise. Gene Ontology annotation performed using STRING site version 10. 5.
Using permutation-based false detection rate (FDR p-Value , 0. 05, S = 0. 1), we found 67 and 35 proteins to be overexpressed in the MSI-H or MSS group, respectively (Fig. 3A ; supplemental Table  S2 ). Using the STRING v11 database, we investigated the connections of the proteins  (32). We found no statistically significant enrichment in the 35 proteins overexpressed by the MSS tumors. In sharp contrast, the STRING analysis found a highly significant connection enrichment in the MSI-H overexpressed proteins (Fig. 3B ; p-Value , 10 216 ). Furthermore, ;33% of the proteins (22 out of 65) were found to be linked to immune response processes (Fig. 3C ), and specifically to the Interferon-g-mediated signaling pathway (Fig. 3D ) and antigen processing and presentation (FDR 7. 9e 28 ). In agreement, the three top ranked KEGG enrichment pathways were the proteasome (8 proteins), the phagosome (10 proteins) as well as antigen processing and presentation (8 proteins) (FDR p-Value 3.
General Equilibrium Framework We represent the world economy as a network of input-output relationships embedded in a general equilibrium model as in  Acemoglu et al. (2012). The economy consists of K countries, each comprising of the same L industries. The model is calibrated to the world economy using the world input-output database  (Timmer et al. 2015) , which provides inputoutput relationships between L = 56 industries in K = 44 countries. The data set includes all major economies and a composite country representing the rest of the world. Within our model, each industry of each country is represented as one monopolistically competitive firm. Each of the K countries also has two representative households, which are differentiated by the source of their revenues. The workers' representative household receives the labor share of value-added from each domestic sector, while the capitalists' receives the capital share.
Propagation of Impacts Through Supply Chains For a given value of the elasticity parameter θ, we calibrate the parameters (M, α, β) of the model so that the equilibrium input-output flows of the economy correspond to the flows provided in the latest version of the world input-output database  (Timmer et al. 2015). Furthermore, we initialize the output, prices, monetary balances, and inventories of all agents to their equilibrium values. In particular, parameters are normalized such that the equilibrium price of every good is 1. Prior to any simulation, we numerically check that the resulting general equilibrium is a steady-state of the dynamics defined by Eqs. 3 to 9. We then calibrate the direct impact of a COVID-19 lockdown shocks as follows: • For each country k ∈ K, we infer from public sources 3  the start (T s (k) ∈ N) and end dates (T e (k) ∈ N) of COVID-19 related lockdown measures (see Table  1  in the Appendix).
Training in the use of such devices may be conducted by the health providers or technologists through the local clinic hubs or remotely by technologists, through a phone or computer link with the patient, to ensure proper use of the EEG devices. The advantages in terms of diagnostic capabilities are difficult to overstate; because patients may wear the device over extended periods of time, clinicians can effectively review more useful data before, during, and after a seizure event. In addition, the recording takes place in a safe and familiar environment for the patient, which increases the chance of collecting higher yielding data as the patient is in a more "natural" setting. Moreover, data recorded by the device can be sent to physicians or EEG technicians who have experience in reading EEGs, demonstrating the power of a disaggregated team of specialists that collectively form a virtual clinic.
Funding: This work was supported by  Inserm , the  University of Strasbourg , the  European Union  ( ERC-2014-AdG-671231-HEPCIR ,  755460-PRELICAN  and  862551-HEPCAN ) and  Horizon 2020 research and innovation program  under grant agreement  667273-HEPCAR , the  Agence Nationale de Recherches sur le Sida et les Hépatites Virales  ( ANRS 15/1099 ), the  French Cancer Agency  ( ARC IHU201301187  and  IHU201901299 ), the  US National Institutes of Health  ( NIH/NIAID U19AI123862-01 ,  NIH/NIAID   R03AI131066 ,  NIH/NCI   R21CA209940 ), the  ITMO Cancer from AVIESAN  in collaboration with  INCa and Inserm (Plan Cancer  "Single cell" 2018 grant) and the Office of the Assistant Secretary of Defense for Health Affairs through the  PRCRP  under HCC risk after HCV treatment Low risk (<1. 5% per year) No cirrhosis and  FIB4 <3.
Furthermore, studies from the US suggest that the seasonal nature of human WNV cases (with most cases from late summer through to mid-autumn) is associated with a shift in mosquito blood meals from birds to mammals during the high-risk period, which may be driven by birds beginning their southward migration at this time  [13]. To date, similar studies on the transmission dynamics of WNV in Canada are lacking. In this study, we aimed to develop a priority list of bird species likely involved in the circulation of WNV in the region of Montréal in southern Québec, Canada. To do so we scanned the literature and dead bird surveillance data to identify bird species that breed in the region and are known to be competent WNV amplifiers/reservoirs. We also prioritized these species according to field and laboratory data on the feeding preferences of Culex pipiens-restuans (CPR) mosquitoes, while accounting for bird species abundance in the Montréal area.
Identification of Priority List of Wild Bird Reservoir Species To construct the list of bird species that are possible WNV amplifier and reservoir host in our study area, we used an approach by successive augmentation. Starting with a reference list of regional breeding bird species L 0 , the priority list L f of birds that could potentially play a role in the WNV transmission cycle was obtained as, L f = L 0 ∩ [L 1 + L 2 + L 3 -L 1 ∩ L 2 -L 1 ∩ L 3 -L 2 ∩ L 3 + L 1 ∩ L 2 ∩ L 3 ], where ∪ indicates the "union" of data from databases (bringing all species from the databases together), and ∩ indicates the "intersection" of data from the databases (i. e. , where species are in the different databases). L 1 , L 2 and L 3 are, respectively, the "databases" of: (i) species identified as infected by WNV in dead bird surveillance; (ii) species identified as being targets for CPR blood meals on the basis of blood meal analyses; (iii) species identified as WNV reservoirs by literature review.
Identification of Priority List of Wild Bird Reservoir Species To construct the list of bird species that are possible WNV amplifier and reservoir host in our study area, we used an approach by successive augmentation. Starting with a reference list of regional breeding bird species  , the priority list  of birds that could potentially play a role in the WNV transmission cycle was obtained as,  =  ∩  +  +   ⋂  ⋂  ⋂ +  ⋂ ⋂ , where ∪ indicates the "union" of data from databases (bringing all species from the databases together), and ∩ indicates the "intersection" of data from the databases (i. e. , where species are in the different databases). ,  and  are, respectively, the "databases" of: (i) species identified as infected by WNV in dead bird surveillance; (ii) species identified as being targets for CPR blood meals on the basis of blood meal analyses; (iii) species identified as WNV reservoirs by literature review.
In summary,  is the first basic list that is augmented with species from  and  not already in. The comparison with  is a check to ensure that selected bird species are found in the study area. comprised 318 species extracted from the Avibase database  [27] , which includes all breeding species in the Montréal area. Species reported as rare (n = 65) in the Avibase were excluded from. Details on  ,  and  are described in the sub-sections below.
The first 100 amplification products were visualized by gel electrophoresis on 1. 9% agarose gel, whereas the remaining samples were run on QIAxcel (Qiagen, Toronto, TO, Canada). Positive samples were purified using the Wizard SV Gel and PCR Clean-up system (Promega, Madison, WI, USA), and Sanger sequencing was performed by the NML Genomics Core Facility using Applied Biosystems 3730 xl DNA Analyzer with Big Dye Terminator version 3. 1 and pop7 chemistries. The sequence data were analyzed using DNASTAR Lasergene 9 software and compared to those in the GenBank (NCBI). Since the technology used does not allow for the accurate identification of mixed blood meals, the sequence data from mosquitoes that took multiple host blood meals from different species did not lead to identifiable host species.
Such a p s can be regarded as the relative risk for a given bird species of being bitten by the mosquito in relation to its relative abundance  [32]. Unfortunately, p s gets larger and tends to infinity when a s tends to zero. Therefore, we use the following definition for the preference index  [33, 34] : p s = a s f s / n j=1 a j f j , where n is the total number of bird species identified from CPR blood meals. Likewise, the relative risk for a given bird species of being bitten by the mosquito, relative to homogeneous abundance, is RR s = n × p s. Bird species bitten more or less often than chance are characterized by RR s > 1 and RR s < 1, respectively. Values for a s were obtained from wild bird count data, taken from the EPOQ-ebird database, managed, in part, by the Regroupement Québec Oiseaux (RQO) for the years 2001 to 2016  [35].
Literature Review: List L 3 Literature research was conducted in August 2017 in five electronic databases: Scopus, Pubmed, CAB Abstract, Embase and Medline. The search terms used for searching in all databases were: "(West Nile Fever OR West Nile Virus) AND (Bird* OR Avian) AND (Mortality OR Sero-prevalence OR prevalence OR competence OR capacity OR transmission) AND (USA OR Canada)". All articles published from 1 January 1999 to 16 August 2017 (end of the search) were included in the selection process using criteria on the language, title, and abstract, as shown in Table  1. In short, selected studies had to be written in English or French, dealing with an epidemiological content about bird susceptibility (host competence, WNV-induced mortality, etc. ) to WNV in Canada or the United States.
Data on sero-prevalence and host competence were extracted from the retrieved publications. To rank birds species belonging to L 3 , the standardized WNV sero-positive ratio, or relative ratio, RR s , for each bird species "s" was calculated as, RR s = m s /(λ × n s ), where m s is the number of WNV sero-positive birds of species "s", n s is the sample size of the tested birds and λ = s m s / s n s is the sero-positive rate under the homogeneous hypothesis; (λ × n s ) is the expected number of WNV sero-positive birds of species "s". Migratory status (migratory M, resident R birds or both M and R) and wintering and breeding areas were also added for each bird species. Wintering/breeding areas were defined as the three main regions of the East Atlantic migration corridor: region of Québec QC, North USA and South USA, delimited by the northern border of the states of North Carolina and Tennessee  [38].
All other bird species were associated with a relative feeding preference lower than 1, suggesting that, while very abundant (as with Red-winged blackbirds), these species are not fed upon by CPR mosquitoes, as shown in Figure  4. [20, 50, 51] ; 3 Percentage of dead birds positive for WNV (n = sample size) (CWHC). Data used in the construction of list L 1 ; 4 a s is the density of species s divided by the total density of the avian community-data come from the EPOQ database. The sum of all a s is equal to one; 5 f i is the fraction of total blood meals taken by Cx. pipiens-restuans from host s  [9]. The sum of all f i is equal to one; 6 M: Migratory bird species; R: Resident bird species; 7 S: South USA; N: North USA; QC: Québec. Dashed vertical lines at relative abundance and feeding "1" represent the ratio "1/n" where n = 23 is the bird species diversity.
Literature Review: List 𝐿 The literature search identified a total of 1244 articles, 23 of which met the selection criteria, as shown in Figure  6. As a result, we found a list  = 53 that was sorted based on the relative ratio of sero-positives, as shown in Figure  7 , as follows: 22 bird species were found most often sero-positive for WNV (with the relative ratio of sero-positives ≥ 1) and the top five species were Red-shouldered hawk, Merlin, Green heron, Eastern meadowlark and Cooper's hawk (all with the same ratio of about 4). Conversely, 31 bird species rarely had serological evidence of exposure to WNV with American redstart having the lowest sero-prevalence. + L 2 + L 3 -L 1 ∩ L 2 -L 1 ∩ L 3 -L 2 ∩ L 3 + L 1 ∩ L 2 ∩ L 3 ] = 18 + 23 + 53 -2 -7 -20 + 2, representing 21% of L 0 = 318 species from the Avibase database  [27] , which includes all the species present in the Montréal area.
Discussion In this study, we constructed a priority list of bird species potentially involved in the transmission of WNV in the greater Montréal region. We constructed this list by combining three sources of data: (i) results from WNV surveillance in wild (dead) birds in the province (2002-2015); (ii) evidence from molecular blood meal analysis that selected bird species are fed upon by CPR, the primary enzootic vectors of WNV in the region, collected in mosquito surveillance in the study area in 2008 and 2014; and (iii) a literature review on evidence for exposure to WNV (sero-prevalence) and the host competence of resident bird species. There were 67 breeding species identified by these data sources, which highlights the potential complexity of WNV transmission cycles in Québec. Out of the 67 bird species, host competences were documented for 22 bird species, including eight highly competent (competence > 1) bird species ranked as follows (from the most to the least competent): Blue jay, Common grackle, House finch, House sparrow, Song sparrow, American robin, American crow and Ring-billed gull.
Final List:  The distribution of the species we identified among the lists is as follows:  = 18 (mortality data of wild birds),  = 23 (blood meal analysis of the CPR) and  = 53 (literature review) with the number of common species,  ⋂ = 2 ,  ⋂ = 7 and  ⋂ = 20 , and  ⋂ ⋂ = 2 species (American crow and Cooper's hawk) belonging to all three lists. The final list of 67 bird species was obtained as, 67 =  +  +   ⋂  ⋂  ⋂ +  ⋂ ⋂ = 18 + 23 + 53 2 7 20 + 2, representing 21% of  = 318 species from the Avibase database.
Acknowledgments: The authors thank all the workers from  MSSS, RQO  and  CWHC  who collected and reported the data used in this study. This study was funded by the  Public Health Agency of Canada, ComUE-UGA  and  IDEX "Université Grenoble Alpes :  Université de l'innovation". CRIPA is a research center financially supported by the  Fonds de recherche Québec Nature et Technologies (FRQNT).
3. 4. 4 Final List:  The distribution of the species we identified among the lists is as follows:  = 18 (mortality data of wild birds),  = 23 (blood meal analysis of the CPR) and  = 53 (literature review) with the number of common species,  ⋂ = 2 ,  ⋂ = 7 and  ⋂ = 20 , and  ⋂ ⋂ = 2 species (American crow and Cooper's hawk) belonging to all three lists. The final list of 67 bird species was obtained as, 67 =  +  +   ⋂  ⋂  ⋂ +  ⋂ ⋂ = 18 + 23 + 53 2 7 20 + 2, representing 21% of  = 318 species from the Avibase database.
Finally, Fig. 4d  shows the THz energy scaling with pump intensity using the FWHM pulse duration as for comparison with Bach et al. 40. Here two data sets are used, one with constant pulse duration and one with a constant pump energy which is shown in Fig. 5  (263 mJ). THz energy production decreases at large pump intensities and, as discussed above, is mainly attributed to redshifting effects which reduce pump beam transmission through the AR-coated surfaces and can also produce phase mismatching from dispersive effects. The drop off behavior for the constant pump energy data set could reasonably be attributed to other nonlinear processes like self-phase modulation in the stack. THz conversion efficiencies generally scale linearly with the pump intensity up to the saturation level. However, as is well discussed and derived in ref.
Data acquisition and error analysis. The IR laser pulses were measured with an Ophir power meter with 2% rms uncertainty. The employed THz detectors had a measurement uncertainty of 3% rms. The shot-to-shot energy fluctuations of the IR laser was 0. 5% rms corresponding to 1% rms shot-to-shot energy fluctuations of the measured THz energies. The measurements were averaged over 100 shots with an oscilloscope. The error bars on our figures reflect the square root of the sum of the squares for these uncorrelated errors. Processing techniques for acquired data. The Fourier transform is essential to understand the bandwidth or frequency content of a signal. In essence, a signal in time, s(t) can be transformed into the frequency domain (F ðωÞ) via, F ðf Þ ¼ Z 1 À1 sðtÞ Àiωt dt; ð7Þ note here, the angular frequency used here is defined as ω = 2πf.
Generally, however, detectors cannot measure signals continuously, i. e. , they have a limited sampling rate, this detail leads to the requirement of a discrete Fourier transform (DFT) or the fast Fourier transform (FFT) to analyze the spectral content of the signal. Figure  4b  shows the resulting power spectrum of the FFT of Fig. 4a , and is equivalent to the FFT of Fig. 4c. For details behind the FFT algorithm, see ref. 44. The THz absorption factor g is determined by fitting the measured pulse energy vs. the number of wafers against the theoretical model as described above. The leastsquares method is employed for this purpose, where the sum of squared residuals S ¼ X N i r 2 i ð8Þ with r i = y sim,iy mes,i is minimized. Here N refers to the number of measured data points and sim and mes correspond to the simulated and measured values, respectively.
Acknowledgements The authors thank  M. Kellermeier ,  C. Bosch , and  P. Altmann  ( DESY ) for engineering support. We thank  C. Bruni  (PHIL) and  B. Schmidt  ( DESY ) for useful discussions,  K. Floettmann  ( DESY ) and  P. Piot  ( NIU/ANL ) for useful comments of the manuscript. We especially thank the referees for their time, thorough comments and suggestions which improved the manuscript. The authors are indebted to initial simulations, preliminary experiments, and many discussions that were carried out with  K. Ravi ,  M. Hemmer ,  H. Olgun ,  N. Matlis , and  F. X. Kärtner  within the AXSIS collaboration. This project was funded by the  Laserlab-Europe  Grant Agreement No. 654148 ,  European Union 's  Horizon 2020 Research and Innovation programme  under Grant Agreement No. 730871 , and also supported by the  European Research Council (ERC)  under the European Union's  Seventh Framework Programme  (FP/2007-2013)/ ERC AXSIS  Grant agreement No.
Acknowledgments Rémi Vicente thanks the french  National Association for Research and Technology (ANRT) ,  Air Liquide Advanced Technologies and Institut Néel  for his PhD funding under CIFRE contract number  2018-0065. This work was conducted following a pre-study made by  Arnaud Gardelein ,  Jean-Michel Niot  and  Pierre Contini , funded thanks to  Air Liquide Advanced Technology innovation comity.
These CD4 effector T cells elicited by anti-CTLA-4 mAb improved anti-tumor responses by enhancing CD8 T cell infiltration, and cytolytic CD8 activity, demonstrating that PD-1 and CTLA-4 attenuate T cell activation though distinct molecular and cellular mechanisms. Building on these observations, it is tempting to hypothesize that patients developing PCD carry polymorphisms, or that tumors harbor alterations, in genes related to the immune regulation pathway. A detailed next-generation sequencing analysis of ovarian or breast tumors associated with PCD-related to anti-Yo antibodies and in circulating T cells could explore whether there are alterations in immune regulation, either locally or systemically, in patients with PCD. In that respect, the transcriptomic profile of 12 ovarian cancers from anti-Yo PCD was compared with public data of 733 control ovarian tumor transcriptomes from The Cancer Genome Atlas database.
Biodiversity data This subsection should contain all relevant information on the biodiversity data (Table  1 ). First, authors should provide the taxon name(s) and information on the taxonomic reference system (e. g. APG IV, GBIF Backbone Taxonomy), the latter being of particular importance if multiple species or taxa are being modelled (e. g. all known migratory birds,  Zurell et al. 2018). Then, the focal taxonomic units being modelled should be defined. Although species are the most often used focal taxonomic unit, biodiversity models could also focus on: populations, demographic traits, supraspecific taxa, operationally defined taxa (e. g. OTUs or ASVs from barecoding), functional types, functional traits, ecological communities, community traits or species richness, among others. Likewise, studies modelling community-level properties need to specify how the community is being defined (e.
g. trophic levels). Next, the data source needs to be described. If the data do not stem from one's own field surveys, then proper reference to the data source needs to be given. If the data stem from online data repositories such as GBIF (<http://data. gbif. org>) or OBIS (<http://iobis. org>), then information on accession date and/or of the source should be provided. Generally, authors should follow good data citation practices, for example as laid out by GBIF (<www. gbif. org/citation-guidelines>). Authors should also describe the underlying (spatial and temporal) sampling design and any details regarding temporal replications or nestedness of the data. This point applies to all types of biodiversity data, not only on one's own field data. If the biodiversity data stem from a standardised monitoring programme, then authors should detail here how the monitoring was carried out, e.