dataesr/scientific-paragraphs-categorization huggingface dataset:
However, ice freezing and consolidation pushed the collar upward so that the collar was not properly sealed. After the fifth day of the experiment, the chamber was therefore moved to mesocosm 11 and was properly sealed. A pump within the LI-COR Multiplexer (LI-8150) circulated the air in the chamber at a flow rate of 2. 1 L min -1. When the pCO 2 of ice is higher than atmospheric pCO 2 , CO 2 is transferred from the ice to the atmosphere and the automated chamber records a positive flux. A negative flux is observed in the opposite case. Water-corrected CO 2 flux was computed automatically with LI-8100 File Viewer 3. 1. 0 package provided by LI-COR Biosciences. The flux was either calculated with a linear or an empirical exponential regression depending on which method provided the best fit (assessed from the normalized sums of the squares of the residuals).
Acknowledgments The authors would like to thank the  Hamburg Ship Model Basin (HSVA) , and the ice tank crew, for the hospitality, technical and scientific support and the professional execution of the test program in the  Research Infrastructure ARC-TICLAB. We are grateful to  Michael Fischer  for his help with the deployment of the automated chambers and treatment of flux data, to Nicolas-Xavier Geilfus, one anonymous reviewer, the Editor  Jody Deming  and the associate editor for their comments that improve the overall quality of the manuscript.
Funding information This study was supported by the  European Community 's  7th Framework Programme  through the grant to the budget of the  Integrated Infrastructure Initiative HYDRALAB-IV , Contract no. 261520. The work was supported by a  FiDiPro award  by the  Academy of Finland , the  Walter and Andree Nottbeck Foundation , and the  BIGSOUTH  project funded by the  Belgian Science Federal Policy Office. MK and JZ, SM and BD are respectively research fellows, postdoctoral researcher and research associate of the  Fonds de la Recherche Scientique -FNRS. MV acknowledges support from the  EU, through BISICLO  ( FP7 CIG  grant no  321938 ). This is a MARE contribution.
Statistical analysis Experiments were carried out for two years. However, year has no significant effect on competitive indices and yield of crop. Thus, the data of both years were combined for statistical analysis. Mean values and standard deviations were calculated for each of the six competitive indices with respect to variety and densities. Combined multivariate analysis of variance (MANOVA) appropriate to three factors (bottle gourd, cassava and density) and several independent variables was performed to compare gourd, cassava and density effect, as well as the interaction. This allowed the identification of significant factors based on a vector of dependent variables. The general linear models procedure of the SAS statistical package version 9. 1 (SAS 2004) was used to identify traits contributing to differences when MANOVA revealed significant difference for a factor.
Background: Mucormycosis has emerged as a rare but frequently fatal invasive fungal disease. Current knowledge on paediatric mucormycosis is based on case reports and small series reported over several decades. Contemporary data on a large cohort of patients is lacking. Methods: Two large international registries (Zygomyco. net and FungiScope™) were searched for mucormycosis cases in ≤19 year-old patients. Cases enrolled between 2005 and 2014 were extracted, and dual entries in the two databases merged. Epidemiology, clinical characteristics, diagnostic procedures, therapeutic management and final outcome were recorded and analysed with SPSS v. 12. Results: Sixty-three unique cases (44 proven and 19 probable) were enrolled from 15 countries (54 in European and 9 in non-European countries).
In paediatric reviews, prematurity has also been a risk factor for invasive mucormycosis, and age <12 months was an independent risk factor for mortality  [1, 11, 12]. While some investigators have shown an increasing incidence in adults  [13] , the epidemiological data in children are too limited as to provide epidemiological trends  [2]. Due to the rarity of the disease and the limited awareness of physicians to diagnose and record these cases, the true burden in the paediatric setting is difficult to be estimated. The aim of this study was to collect and analyse data of paediatric mucormycosis cases from two international case registry databases to update and broaden our knowledge on epidemiology, clinical characteristics, diagnostic procedures, microbiology, treatment and outcome of mucormycosis in children.
Study design The study was a combined analysis of prospectively collected cases enrolled in two international invasive fungal disease (IFD) registries: Zygomyco. net and FungiScope™. Both databases were searched for invasive infections due to Mucorales in paediatric (≤19 years) patients. Cases diagnosed between 2005 and 2014 were extracted from the registries and analysed. The selection of the study period was based on the availability of data in the two registries. Zygomyco. net was created in 2004 as a European registry and later became a global registry for invasive mucormycosis of the European Confederation of Medical Mycology/International Society for Human and Animal Mycology (ECMM/ISHAM) Working Group on Zygomycosis. For this database, a national coordinator in each participating European country was appointed to prospectively collect and record confirmed cases in standardized case report forms (CRFs) at www.
zygomyco. net, which were then sent either by e-mail or fax to the general study coordinator (GP). The national coordinators were internationally recognized experts in the field of fungal infections, and in most cases they were appointed by the respective national mycology societies. Diagnosis of cases was based on standard mycological tools and when isolate was available by molecular methods in two central laboratories  [9]. FungiScope™ -Global Emerging Fungal Infection Registry (ClinicalTrials. gov NCT01731353) was created in 2003 as an international university-based case registry that collects data of patients with rare IFD, using a webbased electronic case form at www. fungiscope. net. The survey was hosted by ClinicalSurveys. net, an internetbased survey software. For both databases case registration was on a voluntary, non-systematic basis.
Data sets were submitted in a pseudonymized form and regularly checked for completeness with queries made in written form for missing data. Follow-up information was repeatedly requested regarding treatment response, survival or death. If follow-up could not be continued at all requests, outcome at last contact was used. The final analysis of the dataset was performed after checking for and deleting overlapping cases enrolled in both registries. The final combined database included the following variables: gender, age, diagnostic procedures for documenting infection, anatomic location, underlying conditions, microbiology, management and outcome.
Statistical analysis Statistical analysis was conducted using SPSS v. 12. Differences between the qualitative variables in two or more groups were analysed by chi-square test. A two-sided p value of <0. 05 was considered significant. For the estimation of predictors of outcome univariate analysis was performed using logistic regression for each variable separately. The variables for which a statistically significant relationship was shown (p <0. 05) were used to construct a new multivariate model using the logistic regression approach. In the final regression analysis lost-to-follow up cases were excluded.
Ethics Recording patients' data in the zygomyco. net and analysing them was approved by the Ethics Committee of the National and Kapodistrian University Attikon General Hospital located in Athens, Greece, the institution of the registry principal investigator (reference 9/30-8-2011). Informed consent was obtained if required by local laws or regulations. Ethics Committees that approved data collection and use for this registry are in Additional file 1. Similarly, to record patients' data in FungiScope™ informed consent was obtained if required by local laws or regulations. The ethics committee at University of Cologne, Germany, confirmed the data protection and privacy policy (reference-ID 05-102)  [17]. Ethics Committees that approved the protocol for data collection and use in the Fungiscope registry are in Additional file 2.
It is probable that the number of mucormycosis cases in each country in the present study does not necessarily reflect the country-specific rates of the disease, but the awareness of the investigators to report the cases in the two databases. Additionally, several countries reported only one to two cases during the study period therefore a statistical analysis between the variables and the specific counties was not feasible. In an attempt to detect differences in pediatric mucormycosis cases between EU and non-EU countries our analysis showed that there was no statistical difference reported as far as age, causative pathogens and survival is concerned. This result should be interpreted with caution since the number of non-EU cases was small to draw conclusions. On the other hand, due to the rarity of the disease, previous data from the literature until now were mainly extracted from i) mixed adult-children population databases with a limited number of paediatric cases, ii) very small paediatric case series or iii) literature review analyses  [1, 2, 9, 10, 12].
In that sense, this is a first time of prospectively collecting and analysing global contemporary cases of mucormycosis in children. One of the major strengths of the present study is the "merging" of data in order to obtain a satisfactory pediatric sample. This is prerequisite in order to obtain results with sufficient statistical power and to draw conclusions for rare fungal diseases. Beyond the limitations mentioned, the present study increases the degree of awareness of this potentially fatal disease among physicians and offers further important information enriching our knowledge on epidemiology and current management of invasive mucormycosis in the paediatric setting from two international databases.
Data (Table  S1 ) were analysed in two ways. First, a comparison was made of the frequency of long and short styles having zero or more than zero germinated pollen grains on their stigmas. Second, a comparison was made of the mean number of germinated pollen grains present on stigmas of long and short styles. In the second form of analysis, data were subjected to analysis of variance (ANOVA) using the generalised linear model procedure (Proc GLM) of the SAS statistical software v. 93  (SAS 2011).
In radiate capitula, both ray and disc florets were subjected to the same pollination treatment. Following pollination, capitula were rebagged and left to set seed. Data (Table  S3 ) in the form of the proportion of pollinated florets per capitulum to set seed with self-or cross-pollen across the three pollination treatments and five plants per variant were subjected to ANOVA using the generalised linear model procedure (Proc GLM) of the SAS statistical software v. 93  (SAS 2011).
Effect of self-pollination on style length At the time when pollen was either removed from florets or florets were left to self-pollinate (0 h), styles remained inserted in florets that had just opened (mean style score equalled ca. 1 across both variants, Figures  1  and 3 ). After 6 h, mean style length (across both variants) had increased to 3. 91 and 3. 96 in non-pollinated and self-pollinated (1) = 85. 12 (P < 0. 001) Frequencies were estimated after pooling data over populations. N equals number of styles sampled. χ 2 values are for 2×2 tests of independence of style length and frequency of stigmas with either 0 or >0 germinated pollen grains on them. P equals probability of independence. (1) = 0. 0335 (P = 0. 855) Frequencies are presented for long-and short-styled florets located in the outer and inner whorls of capitula produced by the radiate and non-radiate variants.
9 after 24 h. Over the next 24 h, style length remained unchanged in non-pollinated florets (mean style length score equalling 4. 35 after 48 h), while styles in self-pollinated florets continued to shrink in length (mean style length score = 2. 31, with only stigma tips protruding from the corolla apex). The same effect of self-pollination on style length development was exhibited in both variants (Figure  S1 ). Linear mixed-effect model analysis using lmer in the lme4 package for R showed no significant effect for variant, but highly significant effects for pollination treatment and time (χ 2 (1) = 24. 68, P < 0. 0001; χ 2 (4) = 97. 29, P < 0. 0001, respectively) and the interaction between pollination treatment and time (χ 2 (4) = 30. 96, P < 0. 0001).
MAXI The Monitor of All-sky X-ray Image (MAXI;  Matsuoka et al. 2009 ) has been deployed aboard the International Space Station since August 2009. We use publicly available data 3 from MAXI/GSC to examine the long-term 2-20 keV intensity of GS 1826-24. We converted the observed GSC count-rate to mCrab units adopting 3. 3 ± 0. 1 count cm -2 s -1 for 1 Crab 4 , as obtained from the average GSC count-rate over the same time interval between October 2013-October 2014.
5 ks. All these XRT observations (see Table  1  for details) were executed in window timing (WT) mode. The raw data were first reduced using the online XRT products tool  (Evans et al. 2009 ) provided by the Swift team at the University of Leicester 7  , and with our own analyses, which gave consistent results with the former. Our analyses, which are used in the present paper, were performed with standard software within HEASOFT v6. 16 and CALDB files from 2014 June 10.
Time-resolved spectral analysis We extracted time-resolved spectra covering each burst observed with Swift and NuSTAR and carried out spectroscopy on these data as follows. We first defined time bins using full-energy range light curves at 0. 25-s time resolution. We subtracted the pre-burst level, and defined time bins forward and backward from the time of peak count-rate such that each bin had approximately the same number of detected counts. For Swift, the aim was 350 counts; for NuSTAR, the aim was 200 counts each in FPMA/B. The shortest time bin for the Swift burst was 3 s; for the NuSTAR bursts, 1 s. Half of the time bins for the NuSTAR bursts were 3 s or shorter. Trial-and-error suggests that shorter bins offer no improvement on the spectral fit parameters. The NuSTAR burst data were significantly affected by dead time, as is commonly the case when observing bright objects  (Harrison et al.
Thermonuclear bursts We detected seven type-I (thermonuclear) bursts during our ToO observations in 2014 June, the first by Swift on MJD 56832. 99124, and the remaining six detected by NuSTAR as shown in Fig. 2. As mentioned above, one more burst appears in the MAXI orbital light curve at MJD 56836. 5224 ± 40s (M. Serino; private communication). We do not have more detailed data for this burst, but we note that its time coincides with a NuSTAR orbital data gap. We number these bursts #1 to 8 based on their chronological order (see also Table  3 ). The bursts we observed were significantly shorter than previous bursts, as determined by the duration over which the count-rate exceed 25% of the maximum. The typical timescales are ≈ 12 s (see Table  3 ), compared to 35. 9 ± 0. 4 s for the RXTE bursts in the MINBAR sample (Fig.
6b ). The presence of PRE in other sources is strongly correlated with the source being in a soft state  (Muno et al. 2004). NuSTAR from GS 1826-24. The smooth curve overplotted is the expected distribution assuming the adopted model (an absorbed blackbody with fixed neutral column density) is correct. The smooth curve is calculated for the average number of degrees of freedom in the fit (50). The peak flux reached during this burst was (40 ± 3) × 10 -9 erg cm -2 s -1. This value is a factor of 1. 42 higher than the mean peak flux of the non-PRE bursts observed by RXTE since 2000, of (28. 4 ± 1. 2) × 10 -9 erg cm -2 s -1 , and a factor of 1. 24 higher than the peak flux of the brightest burst yet observed from the source: (32. 6 ± 1. 0) × 10 -9 erg cm -2 s -1 as qutoed from the MINBAR database.
a Measured from the count-rate burst light curve from 25% to 90% of the peak value in the relevant energy band. b Extrapolated peak bolometric flux in units of 10 -9 erg cm -2 s -1. c Integrated burst bolometric fluence in units of 10 -6 erg cm -2. d As every burst interval was interrupted by at least one data gap, the α-values must formally be considered upper limits. e This burst is recorded from the public MAXI orbital light curve.
Acknowledgements JC would like to thank  Niels Jørgen Westergaard  for useful discussions. JC acknowledges financial support from  ESA/PRODEX  Nr. 90057. PR acknowledges financial contribution from contract  ASI-INAF I/004/11/0  and  ASI-INAF I/037/12/0. This work made use of data from the NuSTAR mission, a project led by the  California Institute of Technology , managed by the  Jet Propulsion Laboratory , and funded by the  National Aeronautics and Space Administration. We thank the  NuSTAR and Swift Operations teams  for executing the ToO observations, and the Software and Calibration teams for analysis support. This research has used the NuSTAR Data Analysis Software (NuSTARDAS) jointly developed by the  ASI Science Data Center (ASDC, Italy)  and the  California Institute of Technology (USA).
Histopathological analysis of muscle from subject 1 revealed evidence of subsarcolemmal mitochondrial accumulation (ragged red fibers) and a mosaic pattern of cytochrome c oxidase (COX) deficiency (Figures  1A-1F ). Analysis of muscle DNA from both subjects excluded mtDNA abnormalities (mtDNA rearrangements and point mutations) and mtDNA copy number was shown to be normal in each case (data not shown). Whole-exome sequencing via previously described methodologies and bioinformatic filtering pipelines  2, 15  identified biallelic variants in TRMT10C (MIM: 615423; GenBank: NM_ 017819. 3; also known as MRPP1 and RG9MTD1). Com-pound heterozygous c. 542G>T (p. Arg181Leu) (ClinVar: SCV000264779. 0) and c. 814A>G (p. Thr272Ala) (ClinVar: SCV000264780. 0) variants were identified in subject 1, whereas subject 2 was homozygous for the c.
542G>T (p. Arg181Leu) variant, also identified in subject 1. Sanger sequencing was undertaken to validate the variants and confirm that these segregated with disease in each family (Figure  1G ). Both identified TRMT10C variants are predicted to result in amino acid substitutions affecting evolutionarily conserved residues (Figure  1H ) and are rare: the c. 542G>T (p. Arg181Leu) variant is present on the ExAC database (10/120,324 alleles) and ESP6500 (1/11,824 alleles) whereas the c. 814A>G (p. Thr272Ala) TRMT10C variant is absent on ExAC, ESP6500, and COSMIC. In silico predictions via SIFT, PolyPhen-2, and aGVGD suggest that the biophysico impact of the p. Arg181Leu substitution are relatively benign but that the proximity of the Arg181 residue to the TRM10type domain (predicted from Met191) could hint at a crucial structural role that only an arginine residue can perform.
In silico modeling of the TRMT10C variants via RaptorX and Phyre2 produced disparate predictions of MRPP1 protein structure and thus could not be used to indicate any potential misfolding as a consequence of the variants. To investigate the functional effects of the identified TRMT10C variants, Western blot and mitochondrial protein synthesis assays were performed in fibroblast cell lines derived from both affected individuals and age-matched control subjects. These data showed that the steady-state levels of MRPP1 were markedly decreased in the subject cell lines, suggesting that the variants affect the stability of the protein (Figure  2A ). On the other hand, levels of MRPP2 and MRPP3, the other two subunits of RNase P, were unchanged in fibroblasts from affected individuals (Figure  2A ).
(D) In vitro labeling of de novo synthesized mitochondrial translation products with EasyTag EXPRESS 35 S Protein Labeling Mix (Perkin Elmer) followed by fractionation through a 17% SDS-Polyacrylamide gel and autoradiography (as described previously  32  ). Coomassie brilliant blue staining of the gels was used to demonstrate equal loading. lower steady-state levels in subject fibroblasts relative to controls. To further investigate precursor processing, we carried out RNA-seq analysis of mitochondrial RNA isolated from control and affected individuals. Differential analyses of mt-mRNA and mt-tRNA gene expression in TruSeq library datasets and small RNA library datasets, respectively, revealed no significant differences in mitochondrially encoded mt-mRNA, mt-rRNA, and mt-tRNA levels between the samples (not shown).
Acknowledgments This work was supported by a  Wellcome Trust   Strategic Award  ( 096919/Z/11/Z ) (R. W. T. , R. M. , and P. F. C. );  MRC Centre for Neuromuscular Diseases  ( G0601943 ) (R. W. T. , R. M. , and P. F. C. );  UK NHS Highly Specialised  '' Rare Mitochondrial Disorders of Adults and Children '' Service (R. M. and R. W. T. ), and  The Lily Foundation  (R. W. T. , R. M. , and K. T. ). C. L. A. is supported by a  UK National Institute for Health Research (NIHR) doctoral fellowship  ( NIHR-HCS-D12-03-04 ). P. F. C. is a  Wellcome Trust Senior Fellow in Clinical Science  ( 101876/Z/13/Z ) and a  UK NIHR  Senior Investigator who receives additional support from the  Medical Research Council Mitochondrial Biology Unit  ( MC_UP_1501/2 ),  EU   FP7 TIRCON , the  National Institute for Health Research (NIHR) Biomedical Research Centre based at Cambridge University Hospitals NHS Foundation Trust , and the  University of Cambridge.
Different turns have been excluded for various reasons: β -turns III and III' are too close to the 3 10 -helix and types I and I' , whereas turns V, V' and VII are rare, and their definitions are inaccurate  35. Type VI is divided into 2 sub-types, VI a and VI b. Hutchinson and Thornton  39  have divided type VI a into the 2 sub-types VI a1 and VI a2. Wilmot and Thornton have precisely defined type VIII  40  , which is based on Richardson's type I b and was proposed after the removal of type VII  35. The definitions used by Thornton's group  39, 41  are currently considered to be the standard (see Supplementary Information 1)  42. The β -turn assignment program PROMOTIF assigns β -turns on the basis of these standards  43. Studies have shown that repetitive structure assignment approaches have a direct effect on decreasing or increasing the number of residues associated with β -turns  27, 28.
51. They observed 12 combinations in their dataset. The most frequent turns were easily detected, whereas the two most interesting non-classical turns were β E → γ L (8%) and γ L → α R (4%). The 6 other clusters represented only 1% each  51. More recently, Koch and Klebe have proposed a combination of turns of different lengths ranging from 3 to 6 residues; the turns sometimes overlap, thus leading to complex categorizations  52. Koch and Klebe trained a very large modified Self-Organizing Map  53, 54  and extracted new types from the map. The assignment is provided as part of Secbase, an extension module of Relibase  55. Koch and Klebe have used the identified new types in a second step to perform a prediction from the sequence  56. This approach is innovative, but it has not been implemented as a web tool and is therefore less used.