dataesr/scientific-paragraphs-categorization huggingface dataset:
To investigate if non-bee pollinators in our sampling area were also indicative of the whole region, we conducted a wider search on the ALA (11,500 km 2 ) which also comprised forested and mountainous areas that were not sampled in our study (Table  S2 , Fig. S2 ). Further, species utilise resources at different times of the year, leading to substantial temporal turnover in insect communities within an area  (Lambkin et al. , 2011; Thomsen et al. , 2016; Winfree et al. , 2018). Thus, to help interpret differences in peak activity periods for each fly and wasp family (and thus likelihood of capture during our sampling period), records were taken from the ALA database for the state of Victoria, grouped by month in which individuals were reported on the database (Fig. S3 ).
Statistical analyses We conducted three separate analyses corresponding to our three main questions. First, to determine if vane traps were effective at sampling the non-bee fauna compared with historical records for these groups, we ran generalised linear models in package nlme  (Pinheiro et al. , 2018) , assuming a binomial distribution for presence/absence data. We compared the number of fly and wasp families separately to those recorded on the ALA database. We ran separate models comparing presence of families (pooled richness) in different coloured traps (blue and yellow), and within different habitat types (open and wooded). Sites containing tree cover (roads and creeks with tree cover and scattered tree sites) were classified as 'wooded', whilst sites that lacked tree cover (roads and creeks without tree cover and open farmland) were classified as 'open'.
Overdispersion was checked using Pearson residuals  (Zuur et al. , 2013)  and none was detected in any model. For one model (wasp-colour preference), we fitted a Firth's bias-reduced logistic regression in package logistf  (Heinze et al. , 2018)  due to BVTs containing all wasp families sampled (separation problem,  Heinze & Schemper, 2002). To determine the level of overlap in families between the ALA, BVTs and YVTs, we calculated the Morista-Horn index in package divo  (Pietrzak et al. , 2016). This quantifies the level of overlap in families between sampling methods, giving a value range between zero (no overlap) and one (perfect overlap). Second, to determine if there was a difference in the effectiveness of vane traps when sampling flies and wasps using different colours and/or within open and wooded environments, we ran generalised linear mixed models in package nlme  (Pinheiro et al.
, 2018). We ran separate models to test for differences in the richness and abundance of 'all 14 individuals', 'all fly families' and 'all wasp families'. We assumed a Poisson distribution for richness measures and a negative binomial distribution for abundance data. Due to clustering of sites within 1 km diameter landscapes and pairing of different colour traps at each survey point, landscape and the survey location (pair) were used as random effects in the models. Last, to test if the response of different fly and wasp families were consistent, we tested differences in the abundance of each family with >30 individuals sampled (see Table  S2 ) between trap colours and habitat types, using generalised linear mixed models in the nlme package  (Pinheiro et al. , 2018). We assumed a Poisson distribution for all models, except for where overdispersion was detected (Syrphidae, Tachinidae), where we assigned a negative binomial distribution  (Zuur et al.
DISCUSSION This study demonstrates that vane traps can be used to representatively sample the non-bee pollinator fauna among different habitat types within agricultural landscapes. At the scale of the sampling area, we collected and identified an equal number of families within a short sampling period to that recorded on an historical database. When broadening the scale to encompass the region, we found our sampling to be equal for wasps, but less representative for the fly fauna, potentially due to the inclusion of larger forest patches, waterbodies and altitudinal gradients at this scale. Large numbers of individuals were collected from multiple fly and wasp families across the survey period, with certain families known to be pollinators (e. g. Syrphidae:  Armstrong, 1979.
Sampling effectiveness Whilst many studies have compared different trapping methods and tested colour attraction in pollinating insects  (Kirk, 1984; Campbell & Hanula, 2007; Saunders & Luck, 2013)  At the scale of the sampling area, vane traps sampled an equivalent diversity of fly and wasp families to the ALA database. In fact, the diversity of wasp families captured was greater than that recorded for the study area. The number of fly families sampled was lower than, but comparable to, the ALA and sampled some families not recorded on it. The lower number of fly families sampled in our study is likely due to the short sampling period. We sampled during the austral spring which may not align with the peak activity of certain families, such as Anthomyiidae and Platystomatidae, which may more likely be recorded in early summer or autumn (Fig.
One possible solution would be to sample for a shorter period but to increase the number of sampling periods to capture seasonal changes (turnover) in the pollinator community  (Thomsen et al. , 2016; Winfree et al. , 2018). This would further increase the effectiveness of this trapping method in sampling a representative pollinator insect community. A further limitation is the general dearth of knowledge of insect pollinators, which makes it difficult to draw meaningful ecological conclusions, given even basic distributional data is often lacking for Australia. This highlights the importance of using historical datasets as a baseline comparison to determine how representative sampling is for an area  (Bartomeus et al. , 2018). Taxonomic keys to the region are also limiting in that they only go as far as family-level, and expertise on pollinators is hard to come by  (Batley & Hogendoorn, 2009).
, few have directly compared results to the known insect fauna of the study region in question. Here, we not only compare two colours of vane traps (blue and yellow), but also measure the effectiveness of this sampling method compared to a baseline of insect diversity within the same study area. The ALA is a comprehensive repository of environmental and biological information for Australia (Atlas of Living Australia, 2019). It has been used to inform plant suitability under climate-change(Booth et al. , 2012; Belbin & Williams, 2016), but such databases are still rarely used as a reference point for insect communities within a geographic area (but see Godefroid et al. , 2015;  De Palma et al. , 2017; Young et al. , 2017  for examples of effective use of historical data obtained through databases and museum specimens).
Materials and methods The articles included in this review were selected using research engines such as PubMed, Ovid, Cochrane, Elsevier/ScienceDirect, Research Gate, and Google Scholar. Keywords such as POPs, PCBs, OCPs, dichlorodiphenyltrichloroethane (DDT), and hexachlorobenzene (HCB) were used with the word Lebanon, as well as names of matrices and other words of interest: environment, water, groundwater, sediments, abiotic, soil, biomonitoring, animal, marine, serum, and breast milk, among others. Google Scholar was used to find geographical information about Lebanon. Data related to OCPs in rainwater and drinking water networks were excluded since they did not identify contamination or unsafe levels. Articles published prior to 1999 and those related to the validation of analytical techniques for measuring OCPs were also excluded.
Human serum In Lebanon, the first human serum biomonitoring of PCBs and OCPs was reported in 2017  (Harmouche-Karaki et al. , 2017a , 2017b). From 2013 to 2015, 133 men and 181 women between the ages of 18 and 65 were recruited from students and employees of the Saint-Joseph University of Beirut; 97. 5% of the subjects were from Beirut and the Mount Lebanon Governorate. Data collection included samples of blood, anthropometric measures, blood pressure measurements, 24 h dietary recall, and food frequency and sociodemographic questionnaires. Four OCPs were screened e HCB, b-HCH, DDT, and DDE eand six of the seven PCBs were screened e PCB28, PCB52, PCB101, PCB138, PCB153, and PCB180. These analytes were measured using targeted analytical methods: SPE followed by GC-MS/MS.
Subjects and ethics The estimate of G 4 C 2 repeats number on the expanded allele was done in 125 C9orf72 carriers, including 73 symptomatic patients and 52 presymptomatic (PS) carriers. Genetic status has been established for all of them by repeat-primed PCR before, as previously described (Le  Ber et al. , 2013). Clinical data and blood samples were obtained after written informed consent for clinic-genetic studies was signed. Local ethic committee approvals were obtained for studies of symptomatic (IRB: CPP Ile de France II, project #RBM 02-59) and presymptomatic carriers (RCB: 2015-A00856-43 CPP 68-15 Ile-de-France VI, for PrevDemAls and FTLD-exome studies, respectively). A brief description of patients and PS cohorts is provided in Table  1. Among the patients (62 were French, 11 Italian), 42 presented isolated FTD, 12 had isolated ALS, and 19 had FTD and secondarily developed ALS.
05). Consequently, Spearman's rho (r) was used to estimate correlation levels with associated 2tailed p value. A 2-tailed Mann-Whitney U test was performed for all statistical comparisons of means. Since a previous study showed that gender can influence AO in patients with C9orf72 mutations (Le  Ber et al. , 2013) , correlations between C9orf72 repeats number and AO were calculated using residual values of AO after adjusting for sex. In some analyses, repeats number was adjusted for the age at collection or AO. Residual values of repeats number were then used in correlation or in group comparisons analyses. GraphPad Prism Software v5. 00 was used for data visualization.
Acknowledgements The authors thank the DNA and cell bank of the  ICM, Hopital Pitié-Salpêtrière, Paris. The authors are very grateful to the  Adrian Isaac's team (UCL, London)  for their technical advices. Funding sources: The research leading to these results has received funding from the program " Investissements d'avenir "  ANR-10-IAIHU-06. This work was partially funded by the  Program Hospitalier de Recherche Clinique FTLD-exome  (to ILB. , promotion  Assistance PubliqueeHôpitaux de Paris ) and by the  ANR-PRTS   PREV-DEMALS  project (to ILB, promotion by  Assistance PubliqueeHôpitaux de Paris ). The  French Clinical and Genetic Research Network on FTLD/ FTLD-ALS  includes:  Alexis Brice  ( Hôpital de la Salpêtrière, Paris ),  Sophie Auriacombe  ( CHU Pellegrin, Bordeaux ),  Serge Belliard  ( CHU Rennes ),  Frédéric Blanc  ( Hôpitaux Civils, Strasbourg ),  Claire Bouteleau-Bretonnière  ( CHU Laennec, Nantes ),  Mathieu Ceccaldi  ( CHU.
Phenotypic Analysis and Genotype-Phenotype Correlation Charts from the 14 subjects harboring a deep-intronic variant were reviewed and all clinical data available collected. These data are presented in Table  3. IV II Present Yes No I - - - F - - - - - - - - - - - - 2. 2. 1. c. 4253+43G>A Subjects CIC03648, CIC08281, CIC09117, and CIC09817 harbor the variant c. 4253+43G>A on intron 28 (pedigrees shown in Figure  S3 ). CIC09117, CIC08281 and CIC09817 show a milder phenotype with a later age of onset, peripapillary sparing, and intact photoreceptor function as assessed by the full-field electroretinogram (ff-ERG). Instead, CIC03648 shows a more severe phenotype with an earlier age of onset, presence of diffused flecks, and impairment of the cone responses on the ff-ERG. Based on these data, overall, a mild or hypomorphic effect of c.
Patients and Preliminary Results Patients with a presumed diagnosis of STGD1 disease were recruited at the Reference Center for rare diseases, Referet, of the Quinze-Vingts hospital, Paris. Informed consent was obtained from each patient after explanation of the study and its potential outcome. The study protocol adhered to the tenets of the Declaration of Helsinki and was approved by a national ethics committee (CPP Ile de France V, Project number 06693, N•EUDRACT 2006-A00347-  44, 11 December 2006). All the patients and available family members were asked to donate a blood sample for genetic screening for ABCA4 mutations. There were a total of 1012 blood samples (528 index patients and 484 affected and unaffected family members). DNA samples incorporated in this study were obtained from the NeuroSensCol DNA bank, for research in neuroscience (PI: JA Sahel, co-PI I Audo, partner with CHNO des Quinze-Vingts, Inserm and CNRS).
Literature Review Literature search was performed using Pubmed (https://www. ncbi. nlm. nih. gov/pubmed/), with a last check on January 30th, 2019, in order to collect all reported and validated deep-intronic variants on ABCA4 in association with STGD1. Additional databases were queried such as The Human Gene Mutation Database (HGMD Professional 2017. 4, http://www. hgmd. cf. ac. uk/ac/index. php) last queried on January 30th, 2019 and Leiden Open Variation Database (LOVD V. 3. 0, https://www. lovd. nl/) last queried on January 30th, 2019. In particular, we included all variants located more than ± 15 pb from the exonic borders, with at least one of the following characteristics: (1) in vitro assays were performed to demonstrate an effect of the variant on the transcript; (2) in silico analysis, as well as segregation analysis and MAF were suggestive of a disease causing variant.
hgvs. org/ mutnomen). Novel variants, distinct from those enlisted in the Table  S1 , were further investigated. First, the MAF was determined using the Genome Aggregation Database (gnomAD, data available at: https://gnomad. broadinstitute. org/). Only variants with a MAF ≤ 0. 01 were included in a more detailed analysis: (1) Evolutionary conservation was investigated using the 46-way Vertebrate Multiz Alignment and Conservation of the University of California Santa Cruz (UCSC, http://genome. ucsc. edu/) genome browser. A nucleotide was considered highly conserved if it was present in all species or was different in just one species among fishes or reptiles, moderately conserved if different in 2 to 5 species (included), and not conserved if different in more than 5 species or in at least one primate (out of 9 included).
(  2 ) In silico prediction with algorithms capable to predict effects of variants on splicing: SpliceSiteFinder-like (SSF  [47] ), NNSplice (  [48] , http://www. fruitfly. org/seq_tools/splice. html), MaxEntScan (  [49] , http://hollywood. mit. edu/burgelab/maxent/Xmaxentscan_scoreseq. html, Gene Splicer (  [50] , http://www. cbcb. umd. edu/), ESE finder 3. 0 (  [51] , http://rulai. cshl. edu/tools/ESE). All these algorithms are integrated in the Alamut Visual software (v. 2. 11-0, Biointeractive Software, France). For all algorithms' outcomes, changes <10% were considered as having no effects; changes between 10% and 30% were considered mild; changes between 30% and 60% were considered moderate; changes >60% were considered strong.
Phenotypic Analysis A phenotypic analysis was performed on patients whose screening revealed the presence of a deep-intronic variant. Clinical charts were reviewed, and the following data collected: demographic data (i. e. , date of birth, ethnicity, family history, smoking history); age of onset (defined as the age when symptoms related to the disease first occurred); symptoms at onset; age at the last visit and duration of the disease. When possible, the results of the clinical examination were also included from the last most comprehensive visit available: best corrected visual acuity (BCVA) with the Early Treatment Diabetic Retinopathy Study (ETDRS) chart, kinetic and static perimetry, and color vision with the desaturated Farnsworth Panel D-15, full-field and multifocal electroretinography (ff-ERG and mf-ERG; Espion E2; for full field ERG; Diagnosys, Lowell, MA, USA; and Veris II for multifocal ERG; EDI, Redwood City, CA, USA), color fundus photograph (FP; Topcon, Tokyo, Japan), short-wavelength fundus autofluorescence (SW-AF), near-infrared fundus autofluorescence (NIR-AF), spectral domain optical coherence tomography (OCT; Heidelberg retina angiograph [HRA] II or Spectralis HRA+OCT; Heidelberg Engineering, Dossenheim, Germany).
In-silico analysis and conservation study of variants found during our screening, which were never associated with Stargardt disease and with a minor allele frequency (MAF) ≤ 0. 01. MAF data were obtained from the gnomAD database (https://gnomad. broadinstitute. org/). In bold, the two novel variants with moderate to strong predicted changes by the analysis. MAF: Minor allele frequency, SNP: single nucleotide polymorphism.
Funding: LABEX  LIFESENSES  [reference  ANR-10-LABX-65 ] supported by  French  state funds managed by the  Agence Nationale de la Recherche  within the  Investissements d'Avenir program  [ ANR-11-IDEX-0004-0 ],  Foundation Fighting Blindness center  grant  [C-C-CL-0912-0600-INSERM01  and  GE-0912-0601-INSERM02  and  CD-CL-0619-0759-INSERM]  and  Programme Investissements d'Avenir IHU FOReSIGHT  ( ANR-18-IAHU-01 )  Prix de la Fondation de l'OEil (IA) ,.
Statistical analysis Statistical analyses were performed using SAS® software version 9. 4. Descriptive statistics were used for this phase I/Ib study, and descriptive statistics were done by cohort (SD, MD), treatment arm (TG1050 or placebo) and TG1050 dose. Continuous variables were summarized using number of observations (N), arithmetic mean (Mean) and standard deviation (SD). Categorical variables were presented using the number of observations (N) and percentages (%). All the safety analyses were performed on the study population. Adverse Events (AE) were collected from the first treatment administration and up to 28 days after the last TG1050 administration or after the safety follow-up visit. AEs were graded using CTCAE version 4. 03. The number of events, number, and percentage of patients were summarized by preferred terms (PT) as per MedDRA dictionary version 21.
TG1050 induces HBV-specific cellular immune responses In order to analyze HBV-specific T-cell responses during the course of the study, a 10-day in vitro stimulation IFN-γ ELISPOT assay was performed. Such assay characterized by a rather long stimulation time is a standard in HBV immunology as the high tolerogenic environment found in CHB typically precludes (unless cell enrichment is performed) detection of responses. 21 Assay was successfully performed for patients of SD cohort. In contrast, a strong background signal was observed in several MD patients exhibiting higher levels of pre-existing anti-Ad5 NA, precluding interpretation of analysis (data not shown). High baseline levels of anti-Ad5 NA have been in some studies shown to be associated with a reduction of vaccine immunogenicity;  19, 20  yet no consensus exists on a putative inhibiting antibody threshold.
Environmental data Air pollution data were provided by the French Air Quality Monitoring Association (AASQA) Network and the local AASQA for each study area. NO 2 , O 3 and PM 10 data were collected hourly in each monitoring station. Home address was used to estimate the residential exposure of each subject at the date of PSP. The home address of each subject was geolocated, and the choice of the appropriate monitoring station in relation to each patient address was made by the team of every local AASQA. Since the number of monitoring stations is limited, this choice was optimized taking into account the distance between the patient's home and the station, the geomorphological situation of the subject's residence and the proximity of the major sources of air pollution. Three exposure assessments were retained: quantitative absolute values, fast increase concentration of air pollutants and peak of pollution.
All patients with a diagnosis of pneumothorax (International Classification of Diseases (ICD) 10 th revision code = J93) during the study period were retrospectively identified by medical informatics queries of the emergency unit databases in the participating centers. The diagnosis of PSP (ICD code J93. 11) or SSP (ICD code J93. 12) was checked by research assistants in the medical files of the EDs admissions database. Demographic characteristics of the study subjects were similar to those of the large descriptive study of  Bobbio et al. (2015). Thirdly, air pollution exposure was assessed using measurements provided by the French National AASQA Network, which is accredited by the French Ministry for the Environment and whose quality is guaranteed by ISO/TC146 standard for air quality. Every patient's home was situated at a median distance of station of 6.
ACKNOWLEDGEMENTS We thank the  Official Air Quality Monitoring Associations (AASQA)  and their experts  ATMO Franche-Comté  ( Anaïs Détournay ),  ASPA Alsace (Pierre Robelet), Atmosf'air Bourgogne  ( Shirley Salomon ),  Air Rhône-Alpes  ( Sabrina Pontet ),  ATMO Auvergne (Sabrina Pontet), Atmo Nouvelle-Aquitaine (Agnes Hulin) ,  Atmo Hauts-de-France  ( Aurélie Dapvril ),  ORAMIP ATMO (Pierre-Yves Robic) ,  Air Pays de la Loire  ( Gilles Levigoureux ), for providing data and for the association between home's address and air quality monitoring station.
Purpose: Recent doubts regarding the efficacy may have resulted in a loss of interest for targeted temperature management (TTM) in comatose cardiac arrest (CA) patients, with uncertain consequences on outcome. We aimed to identify a change in TTM use and to assess the relationship between this change and neurological outcome. Methods: We used Utstein data prospectively collected in the Sudden Death Expertise Center (SDEC) registry (capturing CA data from all secondary and tertiary hospitals located in the Great Paris area, France) between May 2011 and December 2017. All cases of non-traumatic OHCA patients with stable return of spontaneous circulation (ROSC) were included. After adjustment for potential confounders, we assessed the relationship between changes over time in the use of TTM and neurological recovery at discharge using the Cerebral Performance Categories (CPC) scale.
Data collection The following variables are collected in the registry: age, gender, location, witnessed status, bystander cardiopulmonary resuscitation, initial cardiac rhythm, cumulative epinephrine dose employed during resuscitation, delays from collapse to start of chest compressions (no flow) and from start of chest compression to ROSC (low flow), characteristics of the post-resuscitation ECG, arterial pH at hospital admission, temperature management, and coronary interventions after hospital admission. The neurological outcome was scored using the level reached on the Cerebral Performance Categories (CPC) scale  [15]  at ICU discharge, assessed by the physician in charge. Patients with a good cerebral performance (CPC1) or a moderate cerebral disability (CPC2) were considered to have a favorable neurological recovery.
We first assessed the relationship between baseline characteristics and the use of TTM. Test for trend and logistic regression were used to evaluate the pattern of neurological recovery over time and the potential explicative factors. We then performed a univariate analysis testing the different parameters associated with good neurological recovery at ICU discharge. Association between TTM and outcome was analyzed in a multivariate model adjusted on Utstein variables including age, gender, location of arrest, provision of bystander CPR, resuscitation intervals, initial rhythm, epinephrine use, arterial pH at admission, occurrence of a post-cardiac arrest shock, early coronary angiogram performance, TTM, and year of arrest as continuous. In order to take into account missing data, we performed multiple imputations using chained equation  [17]  on the dataset restricted to patients with available survival status at hospital discharge (primary outcome), based on M = 10 imputed completed datasets.