dataesr/scientific-paragraphs-categorization huggingface dataset:
Similarly, introduction of these new data resulted in a decrease in estimated mortality from malaria, so that the GBD 2017 estimate for the year 2016 included 78 200 fewer deaths for Nigeria than were estimated by GBD 2016 for that year. GBD 2017 also included an additional 502 countryyears of cancer registry data and 127 country-years of VR system data compared with GBD 2016; 49•6% of the new cancer registry data came from the newly released Cancer Incidence in Five Continents (CI5 XI) database. 62 or GBD 2017, major changes to the modelling strategy for dementia and Parkinson's disease included reallocating deaths from causes identified in multiple cause of death data in the USA as the likely alternative cause of death if dementia had not been assigned as the underlying cause. This approach allowed for more accurate identification of deaths to be reassigned to dementia and Parkinson's disease, including a sizeable proportion that had been assigned to garbage code categories as well as common, more specific causes of death in people with dementia or Parkinson's disease.
Changes in data sources and methods have led to improved estimates for several causes. Comparing the most recent decade between GBD 2016 and GBD 2017, 2006 to 2016, the estimated increase in deaths from drug use disorders in GBD 2017 (55•9% [95% UI 53•1-58 •8]) was greater than the estimated increase for the same period in GBD 2016 (15•2% [4•8-26•4]), driven by a better fit to most recent years of data in the USA and the use of more appropriate covariates, including sales of prescription opioids by country and the prevalence of injecting drug use. Estimates of HIV/AIDS deaths among children in 2016 were higher in GBD 2017 (84 500 deaths [75 800-94 200]) than those (61 700 deaths [56 000-68 000]) estimated by GBD 2016 for the same year. In countries with high-quality VR data, child incidence was adjusted to produce mortality estimates that better align with recorded HIV/AIDS deaths.
Comparison of GBD 2017 to other estimates The primary comparison dataset for malaria is the World Malaria Report (WMR)  64  produced by WHO. As the Malaria Atlas Project produces results for both GBD and the many countries in the WMR, it is not surprising that these results align closely. WHO hepatitis estimates for 2015 present combined mortality results for different stages of viral hepatitis infection (acute hepatitis, cirrhosis, and liver cancer), but the methods and data sources used to generate these estimates are incompletely described;  65   The estimates from the WHO Maternal Child Epidemiology Estimation (MCEE) for cause-specific under-5 mortality in 2016 at the global level differ from those produced by GBD 2017. Notable differences include the absence of estimates for haemoglobinopathies by WHO-MCEE and estimates of deaths from congenital anomalies (303 000 deaths) that are lower than those estimated by GBD (516 000 deaths [95% UI 446 000-595 000]).
70 The investigators estimated 25 997 deaths (95% CI 17 358-49 096) in 2015 compared with GBD 2017 estimates of 90 700 (95% UI 82 800-97 500). Higher GBD estimates are the result of the garbage code redistribution method used by GBD, although the geo graphical distribution of deaths by country is similar for both studies. In GBD, a substantial number of garbage-coded deaths (eg, heart failure, senility, and atherosclerosis) are redistributed to cardiovascular disease causes, including ischaemic heart disease and alcoholic cardiomyopathy. In this iteration, we estimated that 136 000 deaths were from drug use disorders globally in 2015; by contrast, the 2017 World Drug Report by the UN Office on Drugs and Crime (UNODC) estimated a total of 191 000 drugattributable deaths in 2015. Differences might reflect the fact that UNODC data are reported directly by member states and the definition of drug-related deaths differs between countries; some countries include overdose deaths, whereas others can include deaths for which drug use was considered to be a contributing factor.
Limitations Limitations remain in GBD 2017 despite advances in methodology that addressed some of the difficulties of estimating cause-specific mortality at global, regional, national, and subnational scales. Limitations that primarily affect specific causes-such as identification of covariates to address the non-linearity in the association between some injuries and the SDI or accounting for changes in awareness of NASH as an explanation for estimated increased mortality-are described in detail in appendix 1 (section 3). Here, we identify limitations with applicability across many causes. First, time lags in available data, absence of data from specific regions, age groups, or time periods, or unreliability in the data that are available-as is the case for malaria estimation, where a key limitation is the rare and punctuated nature of nationally representative surveys of parasite rate; or diarrhoea mortality estimation, where data are restricted among adults and for the geographical areas with the highest mortality levels-can affect the precision of estimations.
Second, the accuracy with which underlying cause of death is assigned is a key limitation for both VR data and VA data sources, which is complicated by multimorbidity at the time of death. GBD 2017 makes substantial efforts to enhance the comparability of results by applying corrections for under-registration and garbage code redistribution algorithms. Levels or estimated time trends might still be affected by systematic problems in selected locations. Third, to separately estimate type 1 and type 2 diabetes we used a regression method to redistribute unspecified diabetes deaths on the basis of the specified type 1 and type 2 deaths. As the proportion of unspecified deaths is high, even in many good-quality VR systems, the type-specific estimates are more uncertain. An additional complication is that many excess deaths in people with diabetes are preferentially coded to macrovascular complications such as stroke and ischaemic heart disease.
assessments At randomization, patients received once-daily tiotropium (Spiriva ® [Boehringer Ingelheim, Ingelheim am Rhein, Germany]) via Respimat 5 μg (two inhalations of 2. 5 μg), Respimat 2. 5 μg (two inhalations of 1. 25 μg), or HandiHaler ® 18 μg, and the parallel HandiHaler or Respimat placebo. They were reviewed at Weeks 0, 6, and 12, and then every 12 weeks. At each visit, data about symptomatic exacerbations, and how these were treated, were collected. An independent mortality adjudication committee attributed the cause of each death. Exacerbations were defined as the worsening of two or more major respiratory symptoms (dyspnea, cough, sputum, chest tightness, or wheezing) for $3 days and requiring specified treatment changes. Following current practice, the severity of exacerbations was defined by the type of treatment received: moderate exacerbations required a prescription for antibiotics, systemic corticosteroids, or both (with no hospitalization) and severe exacerbations required hospitalization (due to COPD).
Discussion In this retrospective analysis of the TIOSPIR dataset, we found that patients with exacerbations who were treated with systemic corticosteroids alone, or together with antibiotics, exacerbated sooner and more frequently than those treated with antibiotics alone, and that an initial hospitalization was a powerful predictor of subsequent hospitalization, mortality, and premature discontinuation. These findings held true even after adjustment for prior ICS use and exacerbation history. While we do not suggest that these findings indicate that lesser treatment benefits the patient, we do believe that the information is of clinical interest both to the analysis of COPD trials and to future clinical management. Time to first COPD exacerbation in the TIOSPIR study was a prespecified outcome, but no specific instructions were given about how exacerbations should be managed.
9] [20] [21]  This increased mortality risk was seen within 60 days of the index event and increased further during the following year. The risk of death compared with that in nonhospitalized patients was broadly similar in the 60-day and 12-month follow-up periods, suggesting that in general the hospitalized patients were intrinsically more likely to die rather than the insult associated with hospitalization being especially severe. Hospitalized patients were less likely to receive antibiotics and/or corticosteroids as outpatients to treat their next exacerbation, which could have been because either they were much more likely to be hospitalized on the next occasion and/or they were more likely to withdraw from the study, or to have died before another event could occur. These data confirm that hospitalized patients pursue a different natural history than nonhospitalized patients, as is suggested from database studies; 21 this has been acknowledged in the current GOLD classification of risk severity.
The fossils are currently stored and exhibited in the new Paleontological Exhibition in the village of Milia, Grevena (Figure  2 ). Upon discovery, one of us (ET) entered each specimen into a digital database in Microsoft Access. The database also included historical (date of collection; collector), anatomical and taxonomic data, updated regularly following the detailed description and study of the various groups over the recent years (see Section 1). This database formed the basis of the analyses herein by the calculation of the Pivot Tables in Microsoft Access and Excel. Preliminary diagrams were created in Microsoft Excel and PAST 3. 03  [13] , and then further edited in Adobe Illustrator for final presentation purposes. For the analyses herein, the following database records have been excluded as not relevant to this study: two well preserved rhino specimens (a mandible and ulna) from the Priporos site, which is an old sandpit between the Milia and Agios Georgios villages (SGP, 40.
171834 N, 021. 437836 E) of the former Municipality of Herakleotes  [6]  and 30 fossilized wood specimens from MIL 1, 5, 6, and broader MIL sites. Rarefaction curves are calculated following Lyman  [14]  and references therein. The minimum number of individuals is estimated based on Badgley  [15] , utilizing a range between the Number of Identified Specimens (NISP) and the Minimum Number of Upon discovery, one of us (ET) entered each specimen into a digital database in Microsoft Access. The database also included historical (date of collection; collector), anatomical and taxonomic data, updated regularly following the detailed description and study of the various groups over the recent years (see Section 1). This database formed the basis of the analyses herein by the calculation of the Pivot Tables in Microsoft Access and Excel.
Preliminary diagrams were created in Microsoft Excel and PAST 3. 03  [13] , and then further edited in Adobe Illustrator for final presentation purposes. For the analyses herein, the following database records have been excluded as not relevant to this study: two well preserved rhino specimens (a mandible and ulna) from the Priporos site, which is an old sandpit between the Milia and Agios Georgios villages (SGP, 40. 171834 N, 021. 437836 E) of the former Municipality of Herakleotes  [6]  and 30 fossilized wood specimens from MIL 1, 5, 6, and broader MIL sites. Rarefaction curves are calculated following Lyman  [14]  and references therein. The minimum number of individuals is estimated based on Badgley  [15] , utilizing a range between the Number of Identified Specimens (NISP) and the Minimum Number of Individuals (MNI) counting techniques.
At the same time, there is also clear evidence of moderate fluvial transport and the further modification of the original assemblages. Thus, we can argue with considerable evidence that the collections made in the various localities around Milia represent a single assemblage; as the majority of the localities are surface collections of small extension, both horizontally and vertically, we conclude that most likely the Milia assemblage had a short temporal distribution. In any case, this conclusion should be backed by more stratigraphical, sedimentological, and chronological data in the ongoing research in Grevena. The abundance of the rhino S. jeanvireti and the mastodon M. borsoni confirms the MN16 character of the Milia fauna, further corroborated by the solitary findings of Tapirus a. arvernensis and Sus a.
Acknowledgments: We would like to deeply thank all people that have participated in the excavations and research in Milia, Grevena, Greece. Special thanks to  V. Makridis  for providing the GPS data presented herein, to  H. Wildschut  and  W. van Logchem  for providing photos used herein, and to  R. Bakker  for the wonderful drawings and reconstructions of the extinct animals of Milia that appear in the photographs. We deeply thank three anonymous reviewers and the editorial team for constructive comments that improved this manuscript.
Remark: Platelet transfusion may be an option for patients with active bleeding or at high risk of bleeding. Summary of the evidence. We found 4 nonrandomized studies of patients with HIT receiving platelet transfusions. One nationally representative inpatient database analyzed 6332 patients with HIT International Classification of Diseases, Ninth Revision (ICD-9) codes, of whom 450 received a platelet transfusion. 71 3] [74]  The EtD framework is shown online at https://dbep. gradepro. org/profile/0B5351AD-4CFF-7A8F-8E7E-F9B9307A1441. Benefits. There may be situations of substantial bleeding or high risk of bleeding in which platelet transfusions would provide a benefit to the patient. In the inpatient database study, platelet transfusion was associated with an adjusted odds ratio (OR) for venous thrombosis of 0.
8 (95% CI, 0. 4-0. 7). 71 In the 37-patient cohort, no thrombotic events at 30 days were reported. 72 In the 4-patient cohort, no thrombotic events were reported. 73 One HIT patient with a positive serotonin release assay (SRA) tested SRA negative after platelet transfusion. 74 rms and burden. There may be increased harms of arterial thrombotic events with the addition of platelet transfusion. In the inpatient database study, those receiving platelet transfusions experienced 3. 8% more arterial thromboses than patients not receiving platelet transfusions. 71 The adjusted OR for arterial thrombosis was 3. 4 (95% CI, 1. 2-9. 5). The adjusted OR for venous thrombosis was 0. 8 (95% CI, 0. 4-0. 7). The adjusted OR for any bleeding event was 5. 5 (95% CI, 2. 3-12. 9), although the panel recognized that increased bleeding among patients who received platelet transfusion was likely the result of confounding by indication.
One RCT evaluated 13 patients with end-stage renal disease without HIT who received argatroban during intermittent hemodialysis. 128 Two RCTs compared danaparoid and heparin or LMWH during hemodialysis in patients without HIT. 129, 130 These studies reported on the outcomes of bleeding, thromboembolic events, serious adverse events, and laboratory measures. The EtD framework is shown online at https://dbep. gradepro. org/profile/948a7b63-bf96-41ec-8e18-ae25298b9836. Benefits. There may be moderate benefits associated with the treatment of patients with HIT undergoing renal replacement therapy with selected non-heparin anticoagulants (eg, argatroban, danaparoid, or bivalirudin) compared with others (eg, fondaparinux and rivaroxaban) for which there is little data and greater dependence on the kidneys for clearance.
Acknowledgments The authors thank  Housne Ara ,  Vahid Ashoorion ,  Nina Martinez , and  Stephanie Ross  for supporting the systematic reviews;  Itziar Etxeandia  and  Yuan Zhang  for other assistance; and  Robby Nieuwlaat ,  Wojtek Wiercioch , and  Holger Sch  ünemann for being coordinators of the systematic review team. Holger Sch ünemann prepared a template of these guidelines for all panels, which was critically reviewed by  Adam Cuker ,  Rob Kunkle , the  ASH Guideline Oversight Subcommittee , the Methods Group supporting the guidelines, and editors of Blood Advances.
Briefly, PCR reactions were performed in 50 μL final volumes and consisted of 0. 5 μL Taq DNA Polymerase (Qiagen 5 U/μL), 10 μL PCR Buffer (10 ×), 2. 5 μL dNTP Mixture (dATP, dCTP, dGTP, dTTP; 10 mM), 2 μL MgCl 2 (25 mM), 2. 5 μL of each primer (10 μM), 1 μL genomic DNA extract (80 ng/mL) and 34 μL distilled-deionised water. PCR products were visualised under UV light (BIO-RAD Universal Hood II) on 1. 5 % agarose electrophoresis gels stained with ethidium bromide. Macrogen, Inc. (Seoul, South Korea) Europe Lab carried out the purification and sequencing of PCR products. Taxonomic assignments were based both on high percentage homologies with sequences available in public databases (GenBank -NCBI database and CBS-KNAW Collection, Westerdijk Fungal Biodiversity Institute) and the consistency of morphological features with available literature descriptions.
The taxonomic position of doubtful strains (low homologies with sequences available in public databases) or sterile mycelia (i. e. not showing morphological features useful to confirm taxonomical assignments) were inferred via molecular phylogenetic analyses based on DNA sequences from the large ribosomal subunit LSU,  (Vilgalys & Hester 1990). Separate alignments were created for the orders Pleosporales, Capnodiales and Chaetothyriales and two for the classes Leotiomycetes and Sordariomycetes. Alignments were generated using MEGA v. 7. 0 and manually refined. Phylogenetic analyses were performed using a Bayesian Inference (BI; MrBayes v. 3. 2. 2 four incrementally heated simultaneous Monte Carlo Markov Chains (MCMC), run over 10 M generations, (under GTR + Γ + I evolutionary model approach).
BPP values are reported in the resulting trees. A full alignment of the dataset was submitted to TreeBASE (submission number 21746). Representative strains of each species isolated in pure culture during this work are preserved at Mycotheca Universitatis Taurinensis (MUT-www. mut. unito. it) of the Department of Life Sciences and Systems Biology, University of Turin (Italy). The Accession numbers of the sequences deposited in GenBank are available in the supplementary material 1. 2 ), (  5 ), (  7 ), (  19 ), (  21 ), (  22 ), (34) (9), (  12 ), (  14 ), (  15 ), (  18 ), (  27 ) Cladosporium halotolerans 5. 4 10. 8 (5), (  11 ), (  22 ) FR.
Thelebolus spp. growth conditions and molecular study Thelebolus spp. MUT 2357 and MUT 2359 were pre-grown on Potato Dextrose Agar -PDA (Potato extract 4 g, dextrose 20 g, agar 15 g, up to 1 L dH 2 O) at 25 °C and then inoculated in triplicate onto Petri dishes (9 cm Ø) containing MEA, PDA and Carrot Agar (grated carrot 20 g boiled and filtered, agar 20 g, up to 1 L dH 2 O) alone and with different concentration of NaCl (2. 5 %, 5 %, 10 %, 15 %) and incubated at 4 °C, 15 °C and 25 °C. The fungal growth, as well as macroscopic and microscopic features, were evaluated at three, seven, 10, 14, 17, 21 d after the inoculum. Mature reproductive structures were observed and photographed with an optical microscope (LEICA DM4500 B) equipped with a camera (LEICA DFC320). Morphological data (micro-and macroscopic) were compared with the available description of Thelebolus species.
The majority of the fungi associated with P. johnstonia were only isolated on GASW (38 %) or on CMASW (33 %); no exclusive taxa were reported on SWA. Interestingly, 66 %, 56 % and 38 % of taxa from S. ciliatum, D. fragilis and P. johnstonia, respectively, not only were recovered in one condition but were isolated only from one plate. A total of 87 taxa were isolated: 54 taxa from D. fragilis, 32 from S. ciliatum and 21 from P. johnstonia; 79 % of the taxa were recognised at species level, 13 % at genus level, 5 % at family level, 2 % at order level, and 1 % at class level (Table  2 ). About one third of taxa were sterile despite the attempt to stimulate the production of reproductive structures using different culture media and incubation under near-UV light. Several sterile mycelia (Table  2 ) showed the same similarity percentages with different species and/or low homology with sequences deposited in public databases.
2005). At present, the genus Thelebolus includes 16 species and two varieties, most of which described at the end of the 19 th or in the first half of the 20 th century. For this reason, many of the described species, are lacking of: i) original exhaustive descriptions (i. e. microscopic characters poorly described); ii) DNA barcode sequences available in public databases; iii) ex-type strains preserved in culture collections. Since the two Thelebolus species isolated in this study presented unique morphological and molecular features, we performed a deep bibliographic search to define the main characters for each described Thelebolus species (Table  3 ) and for those available in culture collections, we obtained comparable sequences, which are now available to the scientific community. The two new marine species can be easily distinguished because they form well-defined lineages within the genus (Fig.
More generally, iORFsT1 tend to be smaller compared to iORFsT0 of the same age, especially for those present at N2 and on terminal branches (Fig. S4C ). Note that the absence of effect at N1 may be attributed to a low detection power due to less iORFsT1 detected at N1 in our dataset (Table  2 ). Translation does not influence the distribution of iORF size changes, which are on average similar for iORFsT0 and iORFsT1 (NS T-test, Fig. S4B ). In addition, longer iORFsT1 tend to be less submitted to size changes compared to iORFsT0 of the same size range (Chi-square test p-value = 0. 005, Fig. S4A ). By comparison with the fitness effect distribution of new mutations, characterized by a large number of mutations of neutral or small effects and few mutations of large effect (Bataillon and Bailey 2014), we hypothesized that only a small fraction of iORFsT1 size changes may be of strong effects and could influence the retention pattern compared to most nearly neutral iORFsT0.
Genome assemblies New genomes assemblies were performed using high-coverage sequencing data from 5, 10 and 9 North American strains belonging to lineages SpA, SpB and SpC respectively 1 (Fig. S1 )  (Leducq et al. 2016 ) using IDBA_UD  (Peng et al. 2012). For strain YPS128, raw reads were kindly provided by J. Schacherer from the 1002 Yeast Genomes project  (Peter et al. 2018). We used the default option for IDBA-UD parameters: a minimum k-mer size of 20 and maximum k-mer size of 100, with 20 increments in each iteration. Scaffolds were then ordered and orientated along a reference genome using ABACAS  (Assefa et al. 2009 ), using the -p nucmer parameter. S. paradoxus and S. cerevisiae scaffolds were respectively aligned along the reference genome of the CBS432  (Liti et al. 2009 ) and S288C (version R64-2-1 from the Saccharomyces Genome Database (https://www.
iORF annotation and conservation Orthologous regions identified between each pair of conserved genes in contemporary strains and their ancestral sequence reconstructions were aligned using Muscle  (Edgar 2004 ) with default parameters. Intergenic regions with a global alignment of less than 50% of identity among strains (including gaps) were removed. We annotated iORFs defined as any sequence between canonical start and stop codons, in the same reading frame and with a minimum size of 3 codons, using a custom Python script. Because we are working on homologous aligned regions, the presenceabsence pattern does not suffer from limitation alignment bias occurring when we are working with short sequences. We extracted a presence/absence matrix based on the exact conservation of the start and the stop codon in the same reading frame (Fig.