dataesr/scientific-paragraphs-categorization huggingface dataset:
Experiments Following  [11] , we generate molecules that jointly optimize the octanol-water partition coefficient logP and the other two properties: synthetic accessibility  [19]  and ring penalty that penalizes unrealistically large rings. The score of molecule S is described J(S) = logP (S) -SA(S) -RingP enalty(S). (1) The reward function of ChemTS is defined as r(S) = J(S) 1+|J(S)| Valid SMILES -1. 0 otherwise. (2) ChemTS was compared with two existing methods CVAE  [11]  and GVAE  [12]  based on variational autoencoders. Their implementation is available at https://github. com/mkusner/grammarVAE. Both methods perform molecular generation by Bayesian optimization (BO) in a latent space of VAE. RNN, CVAE and GVAE were trained with approximately 250,000 molecules in ZINC database  [20]. All methods were trained for 100 epochs.
DFT+LDA band structure calculations: We computed electronic structures using the projector augmented wave method  31, 32  as implemented in the VASP  33, 34  package within the generalized gradient approximation (GGA)  35. Experimental lattice constants (a = 5. 39 Å, b = 5. 59 Å and c = 11. 77 Å) and a 12 × 10 × 4 Monkhorst-Pack k-point mesh was used in the computations with a cutoff energy of 400 eV. The spin-orbit coupling (SOC) effects are included self-consistently. In order to model Mott physics, we constructed a first-principles tightbinding model Hamiltonian, where the Bloch matrix elements were calculated by projecting onto the Wannier orbitals  36, 37  , which used the VASP2WANNIER90 interface  38. We used Ru t 2g orbitals to construct Wannier functions without using the maximizing localization procedure.
The resulting 24-band spin-orbit coupled model with Bloch Hamiltonian matrix Ĥ0 k reproduces well the first principle electronic structure near the Fermi energy. To model the spectral function, we added a gap with a leading divergent 1/ω term to the self-energy Σ(ω) = Pxz,yz ∆ with the two adjustable parameters ∆ CF and ∆ xz,yz , we obtained the spectral function A(k, ω) by taking the trace over all orbital and spin degrees of freedom. DFT+DMFT band structure calculations: We calculate the electronic structure within DFT+DMFT using the full potential implementation  39  and the TRIQS library  40, 41. In the DFT part of the computation the Wien2k package  42  was used. The LDA is used for the exchange-correlation functional. For projectors on the correlated t 2g orbital in DFT+DMFT, Wannier-like t 2g orbitals are constructed out of Kohn-Sham bands within the energy window [-2,1] eV with respect to the Fermi energy.
Democratic Republic of Congo (DRC). The study was performed on 187 residents of Misaie, a village located in the Bagata territory of Kwilu Province. This village is located in a savanna area on the right bank of the Kwilu River approximately 300 km north-east of Kinshasa. Misaie village is also a study site of the impact of community MDA with ALB on LF. The data reported here come from a survey that was conducted in June 2014, just prior to the first round of MDA. Liberia. Two sites were studied in Liberia. One study was performed in 9 villages in Foya district, Lofa county (681 subjects tested), in the north-western part of the country. This area is also endemic for onchocerciasis, and community-directed treatments with IVM (CDTI) had been irregularly provided there since 2000. A baseline survey completed in September 2012 revealed an antigenemia prevalence (by ICT) of 19.
Post-MDA with DEC+ALB Cohen's κ estimates were based on published results from studies performed in Sri Lanka and Indonesia  [9]. The calculation was done using a model fitted using R package metafor (R software, version 3. 2. 3) [15]. This included a random effect at the village level so that we could estimate heterogeneity (I 2 index)  [16]. We also assessed differences between the distributions of ICT and FTS scores. Lastly, the relationship between ICT prevalence rates and the FTS/ICT ratios was examined using data collected in the study sites listed above and published data from Sri Lanka and Indonesia  [9]. The second series of analyses, performed at the level of individual study subjects, used a three-level logistic random-intercept model to explain the nature of the higher sensitivity of FTS compared to ICT.
These analyses only considered data from Africa, and the work focused on subjects with a negative ICT result and a positive FTS result ("ICT-miss"). We considered three variables for participants (age [five categories: 5-10, 11-20, 21-40, 41-60, >60 y. o. ], sex, and W. bancrofti Mf presence [negative vs. positive] and two contextual variables, namely ICT prevalence by village of residence (four categories: <5, 5-10, 11-25, >25%), and a history of recent MDA in the past 5 years (yes vs. no). The choice of ICT prevalence over FTS for this analysis was because we were comparing the new test (FTS) to the older, reference test. The model also considered the effect of district (5 groups) and village (28 groups). Because of a high negative correlation between the ICT prevalence rates and the variable "history of MDA" (polychoric correlation coefficient = -0.
T he purpose of this study was to identify the incidence, causes and impact of non-adherence to oral and subcutaneous chronic treatments for patients with polycythemia vera or essential thrombocythemia. Patients receiving cytoreductive drugs for polycythemia vera or essential thrombocythemia were recruited at our institution (Observatoire Brestois des Néoplasies Myéloprolifératives registry). They completed a one-shot questionnaire designed by investigators (Etude de l'Observance Thérapeutique et des Effets Secondaires des Traitements study). Data about complications (thrombosis, transformation and death) at any time in the patient's life (before diagnosis, up until consultation and after the completion of the questionnaire) were collected. Sixty-five (22. 7%) of 286 patients reported poor adherence (<90%) to their treatment with cytoreductive drugs and 46/255 /18%) also declared non-adherence to antithrombotic drugs.
Recruitment of patients Between December 2014 and December 2015, adult patients followed for PV or ET at the Institut de Cancéro-Hématologie (CHRU of Brest, France) and treated with oral (group 1) or subcutaneous (group 2) cytoreductive therapies for more than 6 months were enrolled in the OUEST study (NCT02893410). All patients signed informed consent to participation in the study, which was approved by the regional authorities of the Ethics Committee "CPP Ouest V" dated 04/09/2014, pursuant to Article L. 1121-1 of the Code of Public Health, and has been declared to the Commission Nationale Informatique et Libertés (CNIL) (N. 13809*03). We excluded patients treated for other MPN, patients who did not receive any treatment and those with physical or mental disabilities who were unable to consent and complete the questionnaire.
Questionnaire and data collected This single-center prospective study was based on a closed questionnaire (with simple and multiple-choice questions) given to the patient at the end of a consultation or sent by e-mail. The questionnaire varied according to the route of administration of the cytoreductive drugs (oral or subcutaneous) (Online Supplementary Figure  S1 ). The questionnaires were validated by both the Scientific and Ethical Committees of our hospital. A complete blood count was also performed at the time the questionnaire was administered. The questionnaire was filled in by patients, the results of complete blood counts were collected and sent directly to the data analyzers. Consultants were not allowed to know which patients were or were not adherent to treatment. Non-adherence to drug prescription was defined by at least three omissions of medication during the preceding month (representing ≥10% of the dose) for the group treated orally (group 1) and omission of at least one injection during the two preceding months for the subcutaneously treated group (group 2).
Statistical methods The responses were analyzed using conventional descriptive parameters. The response items were described in terms of frequency for qualitative responses and as the median ± the extreme values for quantitative answers. Statistical analyses were performed by the Clinical Investigation Center of Brest Hospital (INSERM CIC 1412) using SAS software (SAS, Brie Comte Robert, France). The data were compared using the chi-square test for qualitative parameters and non-parametric tests for quantitative parameters. A P value <0. 05 was considered statistically significant. The risks of thrombosis and transformation were analyzed by calculating the hazard ratios between treatment-adherent and non-adherent patients.
Discussion 4] [15] [16]  These studies typically demonstrate that poor adherence has a negative impact on clinical evolution. However, to the best of our knowledge, no such data were previously available regarding patients with Philadelphia-negative MPN. Yet, these chronic disorders have very variable clinical evolution and are prone to complications. We, therefore, decided to assess MPN patients' compliance with cytoreductive and antithrombotic treatments. Many ways of assessing patients' adherence to treat-ment have been described, including pill counts, drug plasma levels, various microelectronic monitoring systems and dispensation by a third party. All methods have their pros and cons. We chose to assess patients' adherence using a single questionnaire. The self-evaluation method using a questionnaire is easier and less expensive to implement, even though patients' reluctance to admit omitting drug intake could theoretically bias the results.
5% of treatment non-adherent patients. These frequencies are slightly higher than those reported for patients with PV (26. 4% versus 9. 3-19%) and in accordance with the scientific literature for patients with ET (18. 2% versus 7. 6-22%). 17 egarding the events that occurred during the prospective follow-up, the median time was shorter (1. 8 years). However, events were recorded in 35 (12. 2%) patients. No differences were noted between the treatment adherent and non-adherent groups regarding thrombotic events or death, but phenotypic evolution was more frequent in the treatment non-adherent patients, especially in group 1. Although this result must be interpreted with caution given the small number of affected patients (n=7), the impact of adherence on phenotypic evolution of MPN is reminiscent of data reported for chronic myeloid leukemia or acute lymphoblastic leukemia, confirming the importance of constant therapeutic pressure for the control of malignant clones.
Acknowledgments The authors would like to thank all the patients who took the time to complete the questionnaire as a mark of interest in this study. The authors would also like to thank the  France Intergroup of Myeloproliferative neoplasms (FIM)  for its help with this study: RLC, VU, SG, EL and JCI are members of this cooperative group. MPN patients' non-adherence to treatment haematologica | 2018; 103 (4).
Culture Collection and Strains Identification The Banyuls Bacterial Culture Collection (BBCC) is referenced in the World Data Center for Microorganisms as WDCM911 and harbors more than 2000 bacterial strains isolated from different geographical sites which are mostly heterotrophic marine bacteria identified on the 16S rRNA gene sequence  [45]. Genomic DNA of each of the strains was extracted with the Wizard Genomic DNA purification kit (Promega, Charbonnières-les-Bains, France) as previously described  [46]. PCR was performed using the universal primers targeting bacteria, 27Fmod (AGRGTTTGATC-MTGGCTCAG)  [47]  and 1492Rmod (TACGGYTACCTTGTTAYGACTT)  [48]. PCR products were purified using the Agencourt AMPureXp purification kit (Beckman Coulter, Villepinte, France) and sequenced as described previously with an AB3130xl genetic analyzer (Applied Biosystems, Courtaboeuf, France).
All molecular biology instrumentation was available through the Bio2Mar platform at the Observatoire Oceanologique de Banyuls-sur-Mer. The 16S rRNA gene sequences were compared to sequences within the NCBI nt database using the Basic Local Alignment Search Tool-2 sequences  [49, 50]. For the QS screening we selected all strains in the BBCC Culture Collection with a similarity percent above 98% to known Vibrio species (i. e. , Table  1 ). The List of the 87 tested strains with their origin, their identification by 16S rRNA gene sequence and their GenBank accession numbers can be found in Table  S1  of the Supplementary Material.
AHL Detection by UHPLC-HRMS/MS Prior to injection, fractions were diluted at 1 mg•mL -1 and 5 µL were injected. UHPLC-MS analyses were performed with a Dionex Ultimate 3000 UHPLC-HESI HRMS Q-Exactive focus system (Thermo Scientific) controlled by the Xcalibur software. The column was a Hypersil GOLD C18 (2. 1 mm × 150 mm) with 1. 9 µm particle size (Thermo Scientific). The column oven was set to 50 • C. The flow rate was maintained at 0. 8 mL•min -1. The mobile phase was composed of 0. 1% formic acid in water (eluent A) and 0. 1% formic acid in acetonitrile (B). A gradient profile was used, starting with 100% of A, and keeping this composition constant for 5 min. The proportion of B was linearly increased to 100% in 5 min, and was left at 100% for 5 min. Settings for the ion source were: 20 aux gas flow rate, 75 sheath gas flow rate, 4 µA spray current, 3 kV spray voltage, 350 • C capillary temperature, 450 • C heater temperature, and 40 S-lens RF and nitrogen was used as nebulizing gas by the ion trap source.
Screening of AHL-Producing Vibrio Strains A total of 87 Vibrio spp. strains were selected from the BBCC Culture Collection of c. a. 2000 strains. The strains were previously isolated from seawater, crater lake water, sea urchin, green alga, sponge, Rodophyta, macrophytes, Urochordata or jellyfish and from different geographical sites. These strains are closely related to 28 described species, as shown in Table  1. Isolates closely related to the Splendidus clade represented 40% of the strains, the highest number of isolates was related to V. gigantis (16 isolates) mostly isolated from benthic and pelagic macro-organisms followed by V. splendidus (8 isolates) which were rather isolated from seawater. The 26 remaining species varied between 1 and 7 isolates. A 16S rRNA phylogenetic analysis of the strains and the GenBank accession numbers are provided in the Supplementary Material Figure  S2  and Table  S1.
Supplementary Materials: The following are available online at http://www. mdpi. com/1424-8220/17/4/906/s1, Figure  S1 : Fragmentation MS/MS spectra of AHL standards, Figure  S2 : Maximum likelihood tree of 16S rDNA gene sequence (559 bp) of the 87 isolates and 35 type strains of Vibrio using the Kimura 2 parameter (K2+G+I, Mega), Table  S1 : List of the 87 tested strains with their origin, their identification by 16S rRNA gene sequence and their GenBank accession numbers.
Acknowledgments: We thank the  French Ministry of Education , for a PhD fellowship to  Lea Girard  through the  Doctoral School 227 of the University Pierre et Marie Curie  and the  National Museum of Natural History, Paris. We thank the  CNRS  (grant  EC2CO-ROSEOCOM ) and the  Sorbonne Universités  (grant  ENDOQUO ) for funding this research. We are grateful to the BIO2MAR platform (http://bio2mar. obs-banyuls. fr)for access to instrumentation and particularly  Karine Escoubeyrou  for providing support technical aid. We thank  Alice Rodrigues  for her support in analytical chemistry and  Nicole Batailler  for her technical assistance in some steps of the experimental work.
Background: Breeds with small population size are in danger of an increased inbreeding rate and loss of genetic diversity, which puts them at risk for extinction. In Sweden there are a number of local breeds, native breeds which have adapted to specific areas in Sweden, for which efforts are being made to keep them pure and healthy over time. One example of such a breed is the Swedish Gute sheep. The objective of this study was to estimate inbreeding and genetic diversity of Swedish Gute sheep. Results: Three datasets were analysed: pedigree information of the whole population, pedigree information for 100 animals of the population, and microsatellite genotypes for 94 of the 100 animals. The average inbreeding coefficient for lambs born during a six year time period (2007-2012) did not increase during that time period.
Data Pedigree information for all registered Gute sheep in Sweden born from 1960 to 2014 was provided by Elitlamm, the recording program for sheep in Sweden. For the early records only a small proportion of the population were registered in ElitLamm, but in recent years a very large proportion of the Gute sheep population in Sweden has been registered in ElitLamm because animals must be registered in order to be entitled to financial support for the keeping of endangered breeds. Pedigree information included animal identification numbers, year of birth and parent identification numbers. The animal identification numbers were anonymous. Blood samples and phenotypic records (tail length and information about horns) were collected from different parts of Sweden by a trained technician in collaboration with the association "Föreningen Gutefåret", one of the two Gute sheep breed organizations in Sweden.
Analyses Pedigree information of the whole population was used to estimate population parameters. Generation intervals, effective number of founders, effective number of ancestors, effective number of founder genomes and marginal contributions of ancestors were estimated with the software Pedig  [7]. Generation interval for sires of sires, dams of sires, sires of dams and dams of dams were calculated separately. The average was calculated from these four values and used as the overall generation interval. The coefficient of inbreeding by birth year  [8] , pedigree completeness indices, number of complete generation equivalents and average coancestry within birth cohorts were estimated with software, EVA  [9]. Effective population size was calculated as one divided by double the annual rate of inbreeding multiplied by the generation interval  [10].
The pedigree information for each of the 100 sheep with blood samples available were combined into one pedigree. This pedigree was used for calculating average coefficient of inbreeding and pedigree completeness with the software EVA  [9]  for comparison with results for these parameters from the whole pedigree. Diversity within populations (1-Q INTRA ) and between populations (1-Q INTER ), inbreeding in individuals compared with the population inbreeding (F IS ), and Hardy Weinberg tests for heterozygosity deficiency and excess in microsatellite markers were estimated with the program Genepop v. 4. 3  [11]. Inbreeding and relatedness among individuals  [12]  were estimated using the microsatellite genotypes using software Coancestry v. 1. 0. 1. 5 [13]. Multilocus heterozygosity was calculated as the proportion of typed loci at which an individual was heterozygous divided by the population heterozygosity at those same loci  [14].
Results A total of 70 474 Gute sheep births were recorded in our dataset since 1960, with 30 616 recorded births during the last six years (2007 to 2012) (Fig. 1 ). Animals born from 2007 to 2012 had a pedigree completion index for three generations greater than 0. 8. The average generation interval for this cohort was 3. 6 years with generation intervals for sires being longer than for dams (Table  1 ), the total effective population size was 155. 4 (Table  1 ) and the average inbreeding and average coancestry were low (0. 038 and 0. 007) (Fig. 2a  and b ). The distributions of inbreeding coefficients of animals born in 2007 and 2012 are in Fig. 2c. Measures of diversity and changes in population structure including effective number of founders, effective number of ancestors and effective number of founder genomes are reported in Table  1.
Inbreeding estimated based on data from the entire pedigree was more than twice the estimated inbreeding from the sample population (0. 038 versus 0. 018) which could be due to the amount of pedigree information available for each animal. The entire pedigree is more complete and has more depth: the average depth of the entire population pedigree in generations was 6. 06 compared in contrast with 5. 41 for the sample population. The founders of a pedigree are assumed to be unrelated and when information from more generations is available, there could be more relationships accounted for. Nevertheless, both estimates of inbreeding were low and our hypothesis is, that this could be because neither of the datasets could account for bottlenecks occurring earlier in time (ie. Before pedigree information was collected).
Methods: The CAC compiled the National Cancer and Human Immunodeficiency Virus (HIV) administrative registries, which identify unique patients diagnosed with both Cancer and AIDS from 1983 to 2015. For the 736 cases found, we considered only those diagnosed with Cancer five years before a diagnosis of AIDS and all cases after the diagnosis. A final sample of 238 individuals, with age ranging from 17 to 84 years, diagnosed with AIDS between 1998 and 2015, was analyzed using Stata Software to compute Standardized Incidence Ratio (SIR) of cancers. Results: Results show that patients with AIDS display an elevated risk of developing the following specific types of cancer: Kaposi's sarcoma's (male SIR 301. 12; female SIR 252. 67) Invasive cervical cancer (female SIR 5. 09); Non-Hodgkin Lymphoma (male SIR 20.
Materials and Methods To evaluate the risk of cancer among AIDS patients in Colombia, we used the general administrative CAC population-based National Cancer Registry of 2015 [19], matched with the National HIV Registry of the same year  [20] , to create a database of unique patients using STATA software. For analysis, we considered cases with a diagnosis of cancer and AIDS between 1983 and 2015, of which 1325 HIV patients matched with the national cancer database. Neoplasms were stablished in clusters by using International Classification of Diseases, Tenth Version codes. 213 different ICD10 codes were clustered into the most common and relevant pathologies into groups to make the analysis comprehensible and useful. We used the classification and definitions of the Centers for Disease Control and Prevention to determine AIDS and non-AIDS-defining cancers  [21].
Data Analysis This paper was limited to neoplasms diagnosed between 60 months before and any date after a diagnosis of AIDS. This time interval was established, on the one hand, to make our results comparable with other similar studies, and, on the other hand, because there is evidence to support that AIDS tends to occur within the first 60 months after HIV infection  [9, 22]. A diagnosis of a non-AIDS-defining neoplasm did not change the status of HIV-infected patients into AIDS, therefore counting them as in pre-AIDS period. Besides, patients that were diagnosed with AIDS and after that were diagnosed with cancer have no limit of incidence date and were counted as in post-AIDS period. Applying the criteria described above we obtained a sample of 238 patients with AIDS and cancer. Age ranged from 17 to 84 years.
We first calculated the probability of developing a certain type of cancer using the National Cancer Registry Database by a group of age and diagnosis date, to determine the expected number of cases within the population with AIDS reported in the National HIV Registry Database for the same group ages and diagnosis date. Thereafter we computed the odds ratio (OR) for the patients in the Post-AIDS period, obtaining a total sample of 183 of cases diagnosed with AIDS, that also developed specific neoplasms (both related and non-related cancers) between 2008 and 2015 (Figure  1 ).