dataesr/scientific-paragraphs-categorization huggingface dataset:
Results Data collection on career and publication outcomes was initially carried out in 2017 and updated in 2021. Using manual Google searches, we located publicly available information identifying the current role of 89% (2035/2284) of the ECRs in the study (Figure  1A ). These alumni were predominantly based in the European Union (60%, 1224/2035), other European countries including UK and Switzerland (20%), and the US (11%). For 71% of alumni (1626/2284), we were able to reconstruct a detailed career path based on online CVs and biographies. On average, ECRs published 4. 5 publications from their EMBL work, with 1. 6 of those being first author research articles (Supplementary Table  1 ). Overall, 90% of ECRs (2047/2284) authored at least one publication from their EMBL work, and 73% (1666/2284) published at least one first author research article.
PhD cohorts Postdoc cohorts  1997-2004 2005-2012 2013-2020 1997-2004 2005-2012   2 ). For example, the proportion of alumni in PI roles 5-years after EMBL was markedly lower for PhD students and postdocs from the 2005-2012 and 2013-2020 cohorts than the 1997-2004 cohort (Figure  2A ). Other smaller changes were also observed in the less well-represented career areas. Detailed career path indicates alumni for whom we were able to reconstruct a career path from EMBL to their current role with a maximum of two 1-year CV gaps, current position only indicates that we were not able to construct a complete career path but were able to identify their current position, and position unknown indicates that we were not able to identify their current role. The percentage of EMBL alumni becoming PIs is similar to data released by North American institutions for both older and more recent cohorts To assess whether the changes in career outcomes are EMBL-specific, we compared our data with cohort-based data released by other institutions.
We note that there are several limitations in comparing absolute career outcomes between individual studies. Most critically, individual studies often use different data collection methods and role classifications. Furthermore, career outcomes are influenced by the broader scientific ecosystem and the subject focuses of the institution's departments, which may attract ECRs with dissimilar career motivations. Nevertheless, comparing the outcomes with multiple institutions allows us to interrogate whether the changes we observe for the most frequent, well-defined and linear career path, the PhD-postdoc-PI track, reflect a general trend. 4 ). Supplementary Figure  3  contains further examples of other programmes with high overlap of scientific areas. Generally, EMBL and the other institutes have a similar proportion of alumni entering PI roles for comparable cohorts.
This is consistent with our hypothesis that the differences between cohorts are not EMBL-specific, and reflect a wide-spread change in the number of PhDs and postdocs relative to available PI positions. We did not analyse the data for non-PI roles, as smaller numbers of individuals entering these roles make it difficult to identify real trends. Additionally, for postdoc career outcomes, only a small number of institutions have released detailed data on the destinations of recent alumni and we are not aware of any long-term cohort-based data.
While most EMBL ECRs remain in science-related professions, the rate at which they become PIs has decreased with time To estimate the probability of alumni from different cohorts entering each type of role each year after completing an EMBL PhD or postdoc, we used a statistical regression method, the Cox proportional hazards model. This model is commonly used to model time-to-event distributions from observational data with censoring (i. e. , when not all study subjects are monitored until the event occurs, or the event never occurs for some of the subjects). In brief, we fitted the data to a univariate Cox proportional hazards model to calculate hazard ratios, which represent the relative chance of the event considered (here: entering a specific type of role) occurring in each cohort with respect to the oldest cohort.
More collaborative publications Previous reports suggest that more recent biology publications have increased amounts of data and more authors  (40, 50) ; a corresponding decrease in the number of first author publications per PhD student has also been reported. For research articles linked to ECRs in this study, the average number of authors per research article has more than doubled between 1995 and 2020 (Figure  5A ). No statistically significant difference was found for the number of research articles per ECR between cohorts (Figure  5B , average 3. 6 per ECR); however, there was a difference in the number of first author research articles between cohorts. ECRs from the more recent cohorts published fewer firstauthor publications (Figure  5C , Supplementary Table  12 ). Data from Clarivate Analytics InCites databases suggest that increasing collaboration may contribute to the increasing number of authors: 79% of EMBL's publications in 2020 involved international collaboration, compared to 47% in 1995(51).
Data collection & analysis The study includes individuals who graduated from the EMBL International PhD Programme (n=969) between 1997 and 2020 or who left the EMBL postdoc programme between 1997 and 2020 after spending at least one year as an EMBL postdoctoral fellow (n=1315). Each person is included only once in the study: where a PhD student remained at EMBL for a bridging or longer postdoc, they were included as PhD alumni only, with the postdoc position listed as a career outcome. For each alumnus or alumna, we retrieved demographic information from our internal records and identified publicly available information about each person's career path (see supplementary methods). Where possible, this information was used to reconstruct a detailed career path for each ECR. An individual was classified as having a "detailed career path" if an online CV or biosketch was found that accounted for their time since EMBL excluding a maximum of two 1-calendar-year career breaks (which may, for example, reflect undisclosed sabbaticals or parental leave).
Each position was classified using a detailed taxonomy, based on a published schema  (42) , and given a broad overall classification (see Supplementary Methods). The country of the position was also recorded. For the most recent position, we noted whether the job title was indicative of a senior or management level role (included "VP", "chief","cso","cto";"ceo";"head;"principal";"president";"manager"; "leader"; "senior"), or if they appeared to be running a scientific service or core facility in academia. We use calendar years for all outcome data -for example, for an ECR who left EMBL in 2012, the position one calendar year after EMBL would be the position held in 2013. If multiple positions were held in that year, we take the most recent position. We use calendar years, as the available online information often only provides the start and end year of a position (rather than exact date).
An EMBL publication record was also reconstituted for each person in the study. Each of their publications linked to EMBL in Clarivate Analytics' Web of Science and InCites databases in June 2021 were recorded. The data included publication year and -for those indexed in InCites-crude metrics, such as category normalised citation impact and percentile in subject area (measures of citations) as well as journal impact factor. EMBL publications were assigned to individuals in the study based on matching name and publication year (see Supplementary Methods for full description). When an individual was the second author on a publication, we manually checked for declarations of co-first authorship. Aggregate publication statistics for ECRs with the same primary supervisor were also calculated. The names and other demographic information that would allow easy identification of individuals in the case of a data breach were pseudonymised.
For example, EMBL has strong scientific overlap with Stanford University bioscience departments. Stanford has reported that 34% of its 2000-2005 bioscience PhD alumni and 13% of its 2011-2015 bioscience PhD alumni were in research-focussed faculty roles in 2018(45). The equivalent data for EMBL is similar -with 37% of its 2000-2005 alumni and 11% of its 2011-2015 PhD alumni known to be in PI roles in 2018 (Figure 2B / Supplementary Table.
Acknowledgements We would like to thank  Monika Lachner  and  Anne Ephrussi  for their critical reading of the manuscript and strong support of this project. We also acknowledge the instrumental support of  EMBL's Alumni Relations, HR, SAP, Library ,  International PhD Programme and Postdoc Programme  teams providing the initial information that allowed this study to be completed. Finally, we thank  Edith Heard ,  Brenda Stride ,  Jana Watson-Kapps  (FMI), and  EMBL 's Directorate, SAC, SSMAC and  Council for discussion. Rachel Coulthard-Graf  is employed by  EMBL 's  Interdisciplinary Postdoc Programme , which has received funding from the  European Union 's  Horizon 2020 research and innovation programme  under  Marie Skłodowska-Curie  grant agreements  664726  ( 2016-2020 ) and 847543 (2019-present).
Data availability, and data protection The data were collated for the provision of statistics, and are stored in a manner compliant with EMBL's internal policy on data protection (https://www. embl. org/documents/document/internal-policy-no-68-on-general-data-protection/). The nature of the data precludes sufficient anonymisation to provide a public data-release. Summary statistics for the data table used to generate the figures can be found in Supplementary Table  1. Code availability Rmarkdown documentation of the analysis and figures (except 1A, created in adobe illustrator) can be found at: https://www. huber. embl. de/users/jlu/EMBLcareer/analysis. html Source code is available at: https://github. com/Huber-group-EMBL/EMBL-Career-Analysis.
All tests were done in triplicates. Two allergic patients with reaction after remoulade sauce consumption entered the clinic for a diagnostic work-up. Remoulade sauce, a typical French sauce, is based on mayonnaise, vinegar, mustard, pickles, and celery. Clinical data of the patients (Table  1 ) indicated that celery could be the trigger of the reactions. Patient number 1, a 64 year-old male, was suffering from pollinosis and allergy to parsley and both raw (urticaria) and cooked celery (oral allergy syndrome). SPT was positive to raw/cooked celery, parsley, raw carrot, dandelion, fennel, cumin, artemisia, ambrosia, grass, and birch pollen. ImmunoCAP tests were positive for Ambrosia (19. 6 kU/l), Artemisia (19. 7 kU/l) and Art v 1 (15. 2 kU/I), respectively. Patient number 2, a 55 year-old female also experienced urticaria upon consumption of raw celery but she did not report any symptoms to cooked celery.
She was also suffering from spring pollinosis and oral syndrome with raw carrot. SPT was positive for raw celery, Artemisia, grass and birch pollen. ImmunoCAP was positive for nArt v 1 (1. 52 kU/l), rApi g 1 (1. 40 kU/l), and rPhl p 1 (80 kU/ l), respectively. Based on the clinical data we decided to investigate the IgE binding patterns of both sera for celery tuber and seed extracts. Celery tuber and seed extracts revealed different patterns of proteins in Coomassie stained 15% SDS-PAGE analysis (Fig. 1 ). Tuber extract contained more proteins in the high molecular mass range (HMW) as compared to the seed extract with more intense protein bands in the low molecular mass range. IgE immunoblots performed with celery seed extract provided a similar pattern when testing both sera. Specific IgE antibodies bound to 2 HMW proteins of 55 kDa and 90 kDa, respectively.
Integrated Method To assess the risk of chemical mixtures, we propose application of an integrated approach composed of the following steps (Figure  1 ). Step 0: Before Starting the Risk Assessment This part aims to provide a number of pointers for practical issues commonly encountered when working with data sets for risk assessment. One issue is the analytical quality of the available contaminant concentration or biomonitoring data and the presence of censored data [i. e. , when the concentrations were reported below the limit of reporting (LR)]. EFSA (2010) proposed a substitution method with three options: the lower bound (LB) option, which replaces censored data by zero when nondetected and by the limit of detection when nonquantified, the upper bound (UB) and the middle bound (MB) options, which replace censored values by LR or LR/2, respectively.
Step 4: Component-Based Risk Assessment under Dose-Addition and Uncertainty Analysis Several component-based risk metrics related to dose addition have been published (EFSA 2013a; EFSA Scientific Committee 2019;  Kortenkamp et al. 2009; Meek et al. 2011; Sarigiannis and Hansen 2012; Vejdovszky et al. 2019; WHO 2009b WHO , 2017)). To select one of them, we propose to consider the heterogeneity of the collected data (human, animal, in vitro), heterogeneity of UF values, and the type of collected end points (most sensitive effect, specific effect, mode of action, etc. ). For example, in the case of a CAG established by EFSA for a specific effect of pesticides on the basis of animal experiments, for a substance s, a relative potency factor (RPF s ) can be calculated by dividing the NOAEL of the index compound (NOAEL index ) by the NOAEL of the substance s (NOAEL s ): RPF s = NOAEL index =NOAEL s.
Selected participants were healthy mothers over 18 years of age, living in France, breastfeeding a healthy child no older than 6 months of age, and having donated their milk to a milk bank. Donors provided a pool of breast milk samples collected at home over a period of 2-3 wk. Milk samples from a single mother were pasteurized at 62. 5°C for 30 min, cooled down at 40°C, and then frozen at -20 C before analysis. The breast milk samples used in this work were the ones declared unsuitable for consumption by newborns due to a total aerobic flora after 24 h incubation at 37 o C ≥ 10 6 bacteria per milliliter. Analyzed substances were selected from a first estimate of the risk calculated using published data. For that, breast milk contamination data were searched using the search engine PubMed and the following keywords "contaminated breastmilk" or "breastmilk contamination," or "name of substance AND contaminated breastmilk," or "name of substance AND breastmilk contamination.
" The names of the substances were the ones targeted in the infant French Total Diet Study  (Hulin et al. 2014). From the 131 obtained surveys, we selected human studies conducted from 2000 to 2011 in Europe, North America, Japan, and Australia, and with at least 30 subjects. For the 79 selected studies we reported the following information: the date, the country, the number of women with their age, body weight (BW), number of children, dietary and smoking habits, the sampling period, the sample size, the analytical method, and the quantity taken. All information on the distribution of contamination was also collected (mean, median, standard error (SE), minimum, maximum, P95th percentiles). The mean and the P95th (or when not available the mean+2 × SE) were combined with the mean and the P95th of the breast milk consumption data from the Child-Specific Exposure Factors handbook (U.
This approach resulted in null concentrations for all individuals for 16 substances that were removed. We obtained a final data set containing 32 substances or sum of substances (Excel Table  S1 ). Step 1: Mixture selection for exposure through breast milk. Breast milk exposure estimates. We estimated exposure to the s = 32 selected substances for 180 infants using consumption and standard BW values proposed by EFSA (2017b) for infants under 6 months of age. To this end, we multiplied each concentration C s in the breast milk by a mean consumption of 763 mL and divided by a mean BW of 6:1 kg: E s = C s x 0:763 6:1 : The combined exposure expressed in micrograms per kilogram BW per day formed a matrix E of 32 × 180 size. Statistical method to define mixtures from combined exposure. We applied the sparse nonnegative matrix underapproximation (SNMU)  (Gillis and Plemmons 2013)  to the exposure matrix E to define mixtures from the 32 substances in the ContaLait data set.
The search focusing on these two end points was performed for each substance up to December 2019. In parallel with this selection, effects for which institutional HBGVs have been established were screened from the reports and databases of ATSDR  (2002, 2007, 2017) ; U. S. EPA (1992 EPA ( , 2012)) ;  WHO (2003) ; EFSA (2012); and ANSES (2007). It was found that the available HBGVs were established on diverse critical effects, hindering the selection of a common toxicological effect. Regarding the targeted population of children, we selected the thyroid and neurodevelopmental. Thyroid disruption may underlie certain neurodevelopmental alterations because thyroid hormones play a vital role in brain development  (Williams 2008; Zoeller and Rovet 2004). They regulate several processes, such as neuronal proliferation and migration or myelination  (Zoeller and Rovet 2004).
2004 ), PCBs and PBDEs  (Eriksson et al. 2006) , or PBDEs and MeHg  (Fischer et al. 2008)  suggested additive effects on motor coordination. Altogether, these observations led us to use dose additivity to predict the mixture effects on the thyroid and neurodevelopment. Step 3: TTs for thyroid and neurodevelopmental effects. We conducted a new literature review for each substance of mixture 1 to collect toxicity data related to the thyroid and neurodevelopmental end points using the PubMed search engine up to December 2019. For thyroid effects, the keywords "name of substance AND thyroid" were used. The data reporting effects on thyroid hormone levels were chosen primarily to a) have a homogeneity in the effects compared between the studied substances and b) establish a link between the thyroid and nervous systems.
We prioritized the available HBGVs for the considered end points (thyroid and neurodevelopmental effects) from the reports and database of  ATSDR 2002 ATSDR , 2007 ATSDR , 2017;; U. S. EPA 1992 U. S. EPA , 2012;; WHO 2003; EFSA 2012; and ANSES 2007. HBGVs were taken as such without any change of the UFs applied for their determination. Otherwise, we used the results of the literature search, as described above in step 3, to identify the key experimental studies that made it possible to construct toxicological thresholds (TT) based on each of the two selected end points. Particular attention was paid to the experimental studies addressing exposure effects either on thyroid hormone levels or sensorimotor or motor and behavioral responses as a priority during gestational and/or lactational periods of exposure.
Environmental Health Perspectives 035001-6 130(3) March 2022 Studies of the Faroe Islands cohorts indicated an association between prenatal exposure and auditory function, one of the thyroid regulated processes during development  (Grandjean et al. 1997; Murata et al. 2004 ). 2007). When necessary, an extra factor of 2 or 10 for database insufficiency was added when human and animal surveys were used, respectively  (IPCS 2009; WHO 1994 WHO , 2009a)). In the case of short-term exposure (single exposure, for example) occurring during a critical period of development, no supplementary UF was applied, considering that it is sufficient to cause an adverse effect. The TT was thus calculated by dividing the retained NOAEL or LOAEL dose by the final UF.
Applying this method to other types of data, for example on human biomonitoring to account for all sources of exposure, or in ecotoxicology, will reinforce its relevance for risk assessment. This work also highlighted the importance of improving the efficiency of mixture risk assessment and of continuing the efforts to collect and structure toxicological data. HBGVs are already part of national (www. anses. fr), European (OpenFoodTox data), and American (ATSDR) initiatives. These data sets provide information about critical effects but reveal nothing about other toxicological effects. There is an urgent need for mixtures assessments to also gather reference points on main toxicological issues and make them available to risk assessors.
Acknowledgments The authors express special thanks to the donors and the milk banks involved in the survey, as well as to the  LSA/ANSES  for providing contamination data on trace elements, LABERCA / Oniris  for providing contamination data on persistent organic pollutants (PCDD/F, PCB, BFR, PFAS, OCPs), and  UT2A  for providing contamination data on mercury and methylmercury. The authors also thank  V. Sirot  for her help on the ContaLait survey. The ContaLait survey was funded by a grant from the  Assistance Publique Hôpitaux de Paris (Contrat de Recherche Clinique CRC  No. 12014 ), a grant from  LABERCA/Oniris  (No. 2012-CED-22 ), and two grants from  ANSES  (No. 2012-CED-22  and No. 2014-CED-11 ).
, Canoga Park, CA) by the Luminex technique and the anti-HPA antibodies by MAIPA (Monoclonal Antibody-specific Immobilization of Platelet Antigens, ApDia, Turnhout, Belgium) were negative. Surprisingly, anti-CD36 iso-antibodies (iso-Abs) using a beadbased multiplex assay PakLx (Immucor, Waukesha, WI) were detected with an MFI (mean fluorescence intensity) of 5236. A reference laboratory (HPA/HLA Laboratory, EFS Bretagne, Rennes, France) confirmed the detection of CD36 iso-Abs using MAIPA with clone FA6. 152 anti-CD36 Moab. Homemade sequencing highlighted a mutation in exon 12 of the CD36 gene, NM_000072. 3:c. 975T > G, inducing a stop codon at position 325 of the mature protein, already recorded as rs567787470 in the international database. To limit inefficiency platelet transfusion, three strategies were developed during his treatment.
The different strategies and platelet concentrates transfused following the chronological order of the treatment sequences are described in Table  1. The first strategy was based on searching for CD36-blood donors. These donors were selected from the French registry based on their erythrocyte phenotype of African origin D + C À E À c + e + Fya À Fyb. Three hundred thirtyfour donors were called to be included in the screening program. Among the 27 donors tested (7% of contacted donors) using the MAIPA method, only one (4%) was CD36 negative. CD36 gene sequencing revealed a mutation in exon 12, already described and recorded as rs3211938 in the international database. Platelet collection of this donor was performed only before the second consolidation cure. T A B L E 1 Unfortunately, this donor no longer agreed to donate.
Ordering of the structure and increase of conductivity were additionally confirmed by the increasing sp 2 /sp 3 ratio determined by EELS. The presence of ultramicroporosity was determined by SWAXS, while N 2 gas adsorption provided complementary data on a micro-/mesoscale. The increase of the specific surface area of micropores determined from SWAXS data is in correlation with the iCEs, a larger surface area leading to lower efficiencies. The capacity contributions show a clear dependence between the structural properties of carbons and the ratio between the sloping and plateau regions. Furthermore, parameters determined by SWAXS imply that the contribution of the plateau region increases with the increasing temperature of carbonization. Meanwhile, Raman spectroscopy, EELS, and the parameter w L from SWAXS indicate the presence of defects in the carbon matrix, suggesting a higher contribution of the sloping region in the galvanostatic curves at lower temperatures of carbonization.