dataesr/scientific-paragraphs-categorization huggingface dataset:
For all PCRs we used the following conditions in a 25 µl PCR reaction; input cDNA 2 µl cDNA, 1x Accuprime buffer II (Invitrogen), supplemented with 0. 2 mM 7-Deaza-2'-deoxyguanosine, 0. 2 μM of each primer and 0,5 µl AccuPrime Taq Polymerase. The PCR conditions consisted of an initial denaturation step at 95 °C for 2 min. , followed by 40 cycles of denaturation at 94 °C for 30 s, annealing at 58 °C for 30 s, and extension at 68 °C for 2 min. 30 s. The final extension time was 10 min. at 72 °C. All the primers used were designed using Primer 3 software. To study biallelic expression in FSHD2 we used the following PCR conditions. For the 4A161S amplicon (164 bp) we used forward primer DUX4RT-F2 5′-CCC AGG TAC CAG CAG ACC-3′ and reverse primer pLAMR4 5‵-TCC AGG AGA TGT AAC TCT AAT CCA-3‵. In a 15 µl PCR reaction we used 5 microliter cDNA, 1× Sybrgreen PCR mix (buffer and dNTP and Polymerase) and 0.
Acknowledgements We thank all FSHD families for participating in our studies. This study was supported by funds from the  National Institute of Neurological Disorders and Stroke  award number  P01 NS069539  to SJT, RT and SMvdM, the  Prinses Beatrix Spierfonds  (award numbers W. OP14-01  and W. OB17-01 ) to SMvdM,  Spieren voor Spieren  to  BvE and SMvdM , and the  European Union   Framework Programme 7  (agreement 2012-305121, NEUROMICS) to SMvdM.
Genbank accession numbers DUX4 transcript accession numbers MF422078 (DUX4La) and MF422079 (DUX4Lb) and for D4Z4 genomic accession numbers KQ983258. 1, MF693913, MF503833, MF503834, MF503835, MF503836, MF741677, MF741678 (4A161L); MF776830, MF776831, MF776832, MF776833, MF776834, MF776835 (4A161S); MF776826, MF776827, MF776828, MF776829 (4A166) and MF776824, MF776825 (4A166H1).
Mutational analysis. Mutation analysis of the GDAP1 gene (NM_018972. 2) was performed mostly in the same center as previously described using an Applied Biosystems 3730xl DNA analyzer (Foster City, CA, USA) 1. To investigate the novelty of the identified variants, the following databases were consulted: dbSNP (http://www. ncbi. nlm. nih. gov/SNP), ESP6500 (http://evs. gs. washington. edu/EVS/), ExAC (http://exac. broadinstitute. org/), and CSVS (http://csvs. babelomics. org/). In silico analysis was performed to predict the pathogenicity of the novel variants, using SIFT (http://sift. bii. a-star. edu. sg/) and PolyPhen-2 (http://genetics. bwh. harvard. edu/pph2/) algorithms for missense changes and NNSPLICE v0. 9 (http://www. fruitfly. org/seq_tools/splice. html) for splicing alterations.
Sural nerve biopsy was performed before the genetic diagnosis was confirmed, or for investigational reasons after specific informed consent. Sections were evaluated under a light microscope, and morphometric data was analyzed when available  18. Statistical studies. Patient characteristics, data from clinical examination, electrophysiological, examination and physical disability were analyzed using descriptive statistics with the program R (version 3. 3. 3), the ordinal package (version 2015. 6-28) and brglm (0. 5-9). A logistic regression model was developed to determine the co-variables that could predict a higher CMTNS score.
Acknowledgements This collaborative joint project is awarded by  IRDiRC  and funded by the  Instituto de Salud Carlos III (ISCIII) -Subdirección General de Evaluación y Fomento de la Investigación  within the framework of the  National R + D + I Plan  [Grants no. IR11/TREAT-CMT, PI12/00453 ,  PI12/00946 ,  PI15/00187 ], co-funded with FEDER funds. Dr Espinos  has a "Miguel Servet" contract funded by the  ISCIII and CIPF  [Grant no. CPII14/00002 ]. Roberto Fernandez-Torron  recieved a  Rio Hortega Grant  from  Instituto de Salud Carlos III. The  Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)  is an initiative from the  ISCIII. National Registry of Hereditary Neuropathy  ( NMD-ES  Project) is partially funded by  Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER).
Haemodynamic and functional outcomes Postoperative haemodynamics become normal or near normal in most patients after PEA. From the University of California, San Diego (UCSD; CA, USA) and international CTEPH databases, improvements from PVR 700-800 dyn•s•cm -5 to 250 dyn•s•cm -5 have been experienced  [15, 23]  following surgery, a fall of ∼65%. Other parameters that have been shown to improve markedly following PEA include mPAP (from 46 to 26 mmHg)  [15]  and median 6-min walking distance (from 362 to 459 m)  [23]. Many patients may experience a shift towards improved New York Heart Association (NYHA) functional class after PEA  [23] , as well as improvements in other measures of exercise capacity, such as the Bruce protocol  [24] , and quality of life  [7]. Reverse remodelling of the right ventricle, with improvement of structure and function, also occurs  [25].
3% and 0. 9% in those with (>500 dyn•s•cm -5 ) and without (<500 dyn•s•cm -5 ) persistent pulmonary hypertension, respectively  [15]. Data from the UK national cohort showed that higher mPAP, right atrial pressure and PVR, and lower cardiac index were negatively correlated with long-term survival in multivariate analyses  [8]. An mPAP ⩾36 mmHg and a PVR ⩾416 dyn•s•cm -5 (as time-varying measures) were the optimal thresholds correlated with a higher risk of death from any cause, whereas an mPAP ⩾38 mmHg and a PVR ⩾425 dyn•s•cm -5 identified those patients at higher risk of death because of CTEPH. Recurrent pulmonary hypertension after PEA Generally, the early haemodynamic benefits of PEA remain unchanged over the medium term  [34]. However, occasionally, patients can re-present with CTEPH or pulmonary hypertension, which can be proximal or distal, many years after successful PEA.
In addition to centre experience, the clinical status (World Health Organization class) of the patient before PEA is a critical determinant of outcome, with mortality being significantly higher in patients with worse clinical status before surgery, independently of other considerations [9]. This illustrates the importance of early referral of patients with suspected CTEPH to an expert centre for evaluation and management. International networks could be important for communication and sharing of information to improve the standards of all CTEPH centres. International registries with prospective data on risk factors and early and late outcome after PEA or other treatments will help expand our knowledge. Registries provide a wealth of data on real-world clinical experience, supplement data from randomised clinical trials and may be useful in validating the criteria for identifying centres of excellence.
Some centres may be unable to share their data because of local or national regulations. This could hamper categorisation. Another potential barrier is that there is no current method for standardising operability or surgical risk, which to a large extent is a subjective decision of surgeons based on their experience  [12, 39]. The relatively small number of patients with CTEPH and difficulty of objectively measuring disease distribution and surgeon expertise hinder the development of a statistically reliable scoring system along the lines of the EuroSCORE system for cardiac surgery, which was developed and validated from tens of thousands of patients. An attempt to develop a simple ranking system based on operative mortality, number of interventions performed and ability to operate on distal/segmental disease is proposed in table  3.
For this population (technically operable but with nonacceptable risk:benefit ratio) the guideline recommends targeted medical therapy and suggests that BPA may be considered, but technically operable patients with CTEPH were excluded from the clinical trials of pharmacological treatments, and data to support the use of BPA in this setting are sparse. BPA should not currently be offered as a substitute for PEA. For technically inoperable patients, the algorithm suggests BPA or targeted medical therapy. However, this does not fully reflect the written recommendations. BPA is less invasive than PEA and it has been reported to improve haemodynamics with low procedural risk  [40] , but more data are required before it becomes established, and it has a IIb/C recommendation  [1]. Targeted medical therapy with riociguat has a IB recommendation for the treatment of patients with inoperable CTEPH and those with persistent or recurrent pulmonary hypertension after PEA  [1].
Developments in PEA may also demand more refined definitions of CTEPH. More distal segmental and subsegmental disease may be considered inoperable CTEPH at less experienced centres, but an experienced surgeon may consider this patient group operable. It is our opinion that all patients who have evidence of thromboembolic disease, including those with distal disease, should be considered for PEA. The specific role of BPA in CTEPH remains uncertain; we await longer-term follow-up data and the current CTEPH registry should provide this. The role of drug treatment in the algorithm will need to be established further. Currently, riociguat is approved for inoperable CTEPH or the treatment of persistent/ recurrent CTEPH after PEA, but other pulmonary arterial hypertension vasodilator drugs have not been proven to benefit patients with CTEPH in randomised controlled trials.
The shake flasks were inoculated from precultures to a starting OD 600 of 0. 05 and incubated at 28 • C on a rotary shaker at 180 rpm for 72 h. For the determination of extracellular metabolites, biomass, glycogen and lipid content samples from C-lim media were harvested in exponential phase and in stationary phase, and from N-lim media after 24, 48 and 72 h of cultivation. For the determination of survival in stationary phase, cultures were grown in C-lim medium containing 5 g L -1 glucose. Diluted aliquots were plated onto YPD plates (1% yeast extract, 2% peptone, 2% glucose, 2% agar) to determine viability of the cultures. The data for the analysis of chronological lifespan are derived from two independent experiments.
Flux balance analysis The Y. lipolytica iMK735 genome scale metabolic model  (Kavš ček et al. 2015)  was used to predict changes in fluxes for a strain deleted for glycogen synthesis. An optimization was done in the MATLAB environment using the COBRA toolbox  (Schellenberger et al. 2011). The glycogen production rate and glycerol uptake rates were calculated from the experimental data and used as constraints in optimization for lipid production in the wildtype model. For the calculation of the effects of gsy deletion, the glycogen production rate was set to zero and the same glycerol uptake rate as in the wild-type model was used. A dynamic FBA calculation with 3 g L -1 cell dry weight was made to calculate the final TAG content.
The chronological lifespan of Yarrowia lipolytica is affected by a loss of storage metabolism The mutant strains of Y. lipolytica overexpressing glycogen synthase or deleted for this gene did not show any measurable differences to the wild-type with regard to growth rate, biomass yield or cell morphology. Furthermore, like in the wild-type, we did not observe any detectable amounts of metabolites excreted into the medium during growth in carbon-limited media (data not shown). Because storage metabolism is often assumed to play a role in survival during stationary phase, we also assessed the chronological lifespan of the deletion mutant. These experiments indicated that the inability to store glycogen does not affect viability of Y. lipolytica over 20 days of starvation (Fig. 4 ). A similar behavior was demonstrated by Os ório et al.
2  MBF is measured during rest (rMBF) and stress (sMBF), which is achieved through pharmacological vasodilatory hyperaemia. With this measurements, the sMBF/rMBF ratio can be calculated, which is known as the coronary perfusion reserve, myocardial perfusion reserve, coronary flow reserve, or myocardial flow reserve (MFR). 3 Both MFR and sMBF have demonstrated utility in the identification of significant CAD and performance superiority of the latter over the former has been suggested. 4 ecently, a number of publications have explored the added prognostic value that full quantitative PET perfusion can offer. 5, 6 owever, this data has not yet been systematically analysed,  7  and sources of heterogeneity are suspected. Moreover, whether MFR or sMBF might be better suited for prognostic evaluation is still uncertain.
Data extraction and quality assessment Data extraction was conducted according to the following subheadings: study characteristics, population description, predictor measurement (i. e. detailed description of the technique employed), index test (i. e. MFR and sMBF measurement and operationalization) and outcome measure (events description), and quantitative results (multivariate modelling and estimators). Data on the (comparative) performance of both quantitative perfusion estimates (MFR and sMBF) were also extracted when available. Discrepancies or uncertainties were resolved by consensus (R. T. ). If study data were used in multiple publications (i. e. articles that referred a similar number of patients or from the same inclusion period and the same medical centre evaluated through the same imaging protocol), only the results from that with the largest number of patients in the quantitative analysis were included.
Search results and study selection The results of the database search and study selection process are summarized in Figure  1. Our search identified 3196 potentially relevant studies. Twenty-five full-text articles were reviewed from which 17 studies were eligible, and eight were ultimately included in the quantitative description and analysis  [13] [14] [15] [16] [17] [18] [19] [20]  (see Supplementary data online, Table  S2  for individual study characteristics). Two publications studied a population with a majority of subjects with evidence of a previous MI and were performed with  13  N-ammonia,  13, 17  while six others studied mainly subject without previous MI, three using 82 Rb,  15, 16, 18  one using 13 N-ammonia,  14  one using 82 Rb and  13  N-ammonia,  20  and one using  15  O-water.
For example,  Tedersoo et al. (2014)  found the Agaricomycotina to be dominating the fungal communities in their Neotropical forests sites and that Yeasts comprised less than 1% of their operational taxonomic units (OTUs). Likewise,  Kivlin and Hawkes (2016)  sampling of monoculture plots and secondary forests in La Selva Biological Station, Costa Rica, and  Peay et al. (2013)  sampling of forests in Amazonian Peru found the Agaricomycotina to be dominating. Peay et al. did note they found many Yeasts, which accounted for almost 25% of their sequencing reads. To more thoroughly analyse Neotropical rainforest soil fungal communities, we extensively sampled three Central and South American forests and deeply sequenced using Illumina MiSeq. The hyperdiverse protist communities were recently analysed from these same samples, and a large proportion of OTUs were found to be highly dissimilar to those in reference sequence databases, to be dominated by parasites, and to exhibit extremely high heterogeneity between spatially disjunct samples even within the same forests  (Mahé et al.
, 2014) using default parameters and converted to fasta format. Paired-end reads with both primers and no ambiguous nucleotides were retained with Cutadapt v1. 9  (Martin, 2011). Reads were dereplicated into strictly-identical amplicons (that is, reads were merged at 100% similarity and to which an abundance value can be attached) with VSEARCH v1. 6. 0  (Rognes et al. , 2016) , and clustered into OTUs with Swarm v2. 1. 5 (Mahé et al. , 2015b)  using d = 1 with the fastidious option on. Chimeric OTUs were identified and removed with VSEARCH (de novo search). Low abundant OTUs were discarded only if they included 2 reads, and were sequenced from only one sample, and were <99% similar to accessions in the Protist Ribosomal Reference (PR2) database v203  (Guillou et al. , 2013). Following  Adl et al.
(b) Analyses Stampa plots  (Mahé, 2016)  were made to show the distribution of the number of reads and OTUs per similarity value to their best match in the PR2 database. Taxonomic assignment of the amplicons and OTUs used VSEARCH's global pairwise alignments with the PR2 database. Assignment used the best hit, or co-best hits, in the reference database as reported by VSEARCH. The R package Vegan  (Oksanen et al. , 2013)  was used to analyse frequency count data derived from OTU clustering. Different functions of Vegan were called to randomly subsample our samples (rrarefy function) and to estimate and compare species compositions, using Bray-Curtis distance and NMDS ordination (monoMDS function). Figures were made using the R Statistical Environment (R Core Team, 2016) and ggplot2  (Wickham, 2009).
q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q q stress: 0. 2191 but also enormous fermentation tanks anaerobically processing carbon because of the fungi. Data accessibility. The data analysed in this study are available at GenBank's Sequence Read Archive under BioProject number SUB582348. Authors' contributions. M. D. and F. M. conceived the project. M. D. , J. M. , and F. M. collected the data. M. D. , H. K. , D. B. , J. M. , and F. M. performed the analyses and wrote the paper. Competing interests. We have no competing interests.
Yeasts dominate soil fungal communities in three lowland Neotropical rainforests Taxonomic identity and relative abundances of fungi reads and OTUs. Each taxa shown represent at least >0. 1% of the total data. Taxonomic assignment is to the fifth level in PR2 reference database, except for Archaeorhizomyces. clade Costa Rica (La Selva) Agaricomycotina Archaeorhizomyces Chytridiomycotina Cryptomycotina Entomophthoromycotina Glomeromycotina forests Panama (Barro Colorado) Kickxellomycotina Mucoromycotina Pezizomycotina Pucciniomycotina Saccharomycotina Taphrinomycotina Ecuador Unknown (Tiputini) Ustilaginomycotina Zoopagomycotina 0% 25% 50% 75% 100% percentage of observed reads clade Costa Rica (La Selva) Agaricomycotina Archaeorhizomyces Chytridiomycotina Cryptomycotina Entomophthoromycotina Glomeromycotina forests Panama (Barro Colorado) Kickxellomycotina Mucoromycotina Pezizomycotina Pucciniomycotina Saccharomycotina Taphrinomycotina Ecuador Unknown (Tiputini) Ustilaginomycotina Zoopagomycotina 0% 25% 50% 75% 100% percentage of observed OTUs Fig.
Methodology Data sets were collected at the "T3" site (3. 2133 • S, 60. 5987 • W) located 70 km to the west of Manaus, Brazil, in central Amazonia  (Martin et al. , 2016a). The site was situated in a pasture (2. 5 km × 2 km) surrounded by forest. The analysis herein focuses on data sets collected during the wet season period of 1 February to 31 March 2014, corresponding to the first Intensive Operating Period (IOP1) of the GoA-mazon2014/5 experiment. A High-Resolution Time-of-Flight Aerosol Mass Spectrometer (HR-ToF-AMS, hereafter AMS; Aerodyne, Inc. , Billerica, Massachusetts, USA) recorded the primary data set of this study. The AMS provided quantitative bulk characterization of the atmospheric PM. The design principles and capabilities of this instrument are described in the literature  (DeCarlo et al.
, 2006; Canagaratna et al. , 2007). The instrument was housed within a temperature-controlled research container, and the inlet to the instrument sampled from 5 m above ground level. Detailed aspects of AMS operation are presented in the Supplement (Sect. S1). In brief, ambient measurements were obtained every other 4 min. Organic, sulfate, ammonium, nitrate, and chloride PM mass concentrations were obtained from "V-mode" data. The choice of ions to fit was aided by the "W-mode" data, which were collected for 1 day every 5 days. Data analysis was performed using SQUIRREL (1. 56D) and PIKA (1. 14G) of the AMS software suite. Positive-matrix factorization was applied to the time series of the organic component of the high-resolution mass spectra  (Ulbrich et al. , 2009). The present study focuses on one of the resolved statistical factors, referred to as the IEPOX-SOA factor  (Hu et al.
, 2015). Diagnostics of the PMF analysis, especially as related to the resolved IEPOX-SOA factor, are presented in the Supplement (Sect. S2). A separate account is forthcoming to present the other PMF factors (de Sá, 2017). Herein, "factor profile" and "factor loading" refer to the mathematical products of the multivariate statistical analysis, whereas "mass spectrum" and "mass concentration" refer to measurements. Complementary to the AMS data sets, mass concentrations of molecular and tracer organic species were measured using a semivolatile thermal desorption aerosol gas chromatograph (SV-TAG) at a time resolution of 1 h. The instrument collected gas and particle samples, followed by thermal desorption, derivatization, and gas chromatography coupled to mass spectrometry  (Isaacman et al.
, 2014). A summary of operational details for GoAmazon2014/5 is presented in the Supplement (Sect. S1), and the main account is presented in  Isaacman-VanWertz et al. (2016). Additional data sets used in the analysis were collected at the T3 site by instruments housed in the research container of the Mobile Aerosol Observing System (MAOS) of the ARM Climate Research Facility (ACRF) operated by the USA Department of Energy  (Mather and Voyles, 2013; Martin et al. , 2016a). A temperature-controlled inlet was mounted at 10 m above ground level. Measurements of nitrogen oxides were made using a chemiluminescence-based instrument (Air Quality Design). The measured odd-nitrogen family "NO y ", meaning NO x plus reservoir species, included NO, NO 2 , HNO 3 , organonitrates, particle nitrate, and peroxyacetyl nitrates.
1 µg m -3 ) and high (> 0. 3 µg m -3 ) sulfate mass concentration and grouped into five levels of NO y concentration (Fig. 6 ). Squares represent medians of each group. Interquartile ranges are represented by whiskers along the abscissa and shading along the ordinate. The plotted data sets were recorded during local afternoon (12:00-16:00 local time; 16:00-20:00 UTC). trend in M org was less steep. The factor loadings decreased by 60 % whereas the M org increased by 25 % for 0. 5 to 2 ppb NO y (Fig. 7a  and b ). Increases in M org can include contributions from secondary PM produced by enhanced concentrations of hydroxyl radicals and ozone in the pollution plume as well as from primary PM emitted from the Manaus urban region  (Martin et al. , 2017; de Sá, 2017). For higher NO y concentrations (> 2 ppb), however, Fig.
Acknowledgements. Institutional support was provided by the  Central Office of the Large Scale Biosphere Atmosphere Experiment in Amazonia (LBA) , the  National Institute of Amazonian Research (INPA) , and  Amazonas State University (UEA). We acknowledge support from the  Atmospheric Radiation Measurement (ARM) Climate Research Facility , a user facility of the  United States Department of Energy (DOE), Office of Science , sponsored by the  Office of Biological and Environmental Research , and support from the  Atmospheric System Research (ASR) program  of that office. Additional funding was provided by the  Amazonas State Research Foundation (FAPEAM) , the  São Paulo State Research Foundation (FAPESP) , the  USA National Science Foundation (NSF) , and the  Brazilian Scientific Mobility Program (CsF/CAPES).