dataesr/scientific-paragraphs-categorization huggingface dataset:
Diffraction data were processed using the HKL3000 suit of programs  78  , and structural statistics is summarized in Supplementary Table  S4. The MGS0169 structure was determined by the single-wavelength anomalous diffraction (SAD) method using phasing, density modification, and initial protein model building as implemented in the HKL3000 software package  [79] [80] [81] [82] [83] [84]. Several cycles of manual corrections of the model were carried out using the programs COOT  85  and REFMAC of the CCP4 86 and finalized using Phenix  87. The final model was refined against all reflections except for 5% randomly selected reflections, which were used for monitoring R free. The final refinement statistics are presented in Supplementary Table  S4.
Acknowledgements We thank all members of the  Centre for Structural Proteomics in Toronto  for help in conducting these experiments. This work was supported by the  Government of Canada through Genome Canada , the  Ontario Genomics Institute  ( 2009-OGI-ABC-1405 ),  Ontario Research Fund  ( ORF-GL2-01-004 ), and the  NSERC Strategic Network  grant IBN. Structural results shown in this manuscript are derived from work performed at  Argonne National Laboratory, Structural Biology Center at the Advanced Photon Source  operated by  UChicago Argonne, LLC , for the  U. S. Department of Energy, Office of Biological and Environmental Research  under contract  DE-AC02-06CH11357. The work was also supported by  European Community  project  MAMBA  ( FP7-KBBE-2008-226977 ),  MAGIC-PAH  ( FP7-KBBE-2009-245226 ),  ULIXES  ( FP7-KBBE-2010-266473 ),  MicroB3  ( FP7-OCEAN.
2011-2-287589 ),KILL-SPILL ( FP7-KBBE-2012-312139 ),  EU Horizon 2020  Project  INMARE  (Contract Nr 634486) and  ERA   Net IB2  Project MetaCat through  UK Biotechnology and Biological Sciences Research Council (BBSRC)  Grant  BB/M029085/1. This work was further funded by grants  BIO2011-25012 ,  PCIN-2014-107  and  BIO2014-54494-R  from the  Spanish Ministry of Economy and Competitiveness , the  UK Biotechnology and Biological Sciences Research Council (BBSRC) , and the  German Federal Ministry of Education and Research (BMBF)  within the  ERA NET-IB2 program  (grant number  ERA-IB-14-030 ). The authors gratefully acknowledge the financial support provided by the  European Regional Development Fund (ERDF).
For the PEU, losses are more directly measured by voltage and current (and thus power) measured on the input and the output sides. In order to balance coulombs in battery round-trips, the ampsecond flow on the DC bus was monitored in real time by using the DC meter. When the desired number of amp-seconds was reached, a python script automatically changed the charging AC current to discharging and vice versa by communicating with the VSL (see 2. 2). In order to obtain losses as a function of the SOC, the SOC should not change substantially within an experiment. The SOC deviation remained less than 1%. These round-trips were performed for various steady AC current values and battery SOC values. Measurements were conducted for different combinations of current rates in the range of 10e70Amps and SOCs in the range of 20e80%.
Based on both general principles and on the cursory comparison of other charger specifications, the general findings should hold over many or most EVs. with ĨDC the measured current and I DC the actual one. A very precise DC current source, Keithley Source Meter 2600, was used. The values measured by the couple probe/meter for several current values were recorded from 5Amps to 30Amps. In the end, the error parameters m and s for each current value were evaluated such that: ε IDC $ N m IDC ; s 2 IDC (C. 2) with m IDC and s IDC respectively the mean and standard-deviation of the errors. It was observed that the standard deviations were rather low and steady. On the contrary, mean errors can reach up to 0. 7Amps for 30Amps, which triggers a 2. 3% error. Matlab curve   By using the interpolation function and the real-time communication ability of the AcuDC meter, the probe measures were corrected in real time in order to monitor the Coulomb cycles properly.
Acknowledgment The empirical work reported in this paper was funded by a joint venture between an  NRG Energy EV group  and the  University of Delaware ; the NRG EV group is now a separate spinoff called EVgo Services, LLC. Part of the research was also financially supported by the  U. S. Department of Energy  via the  National Renewable Energy Laboratory (NREL) , as " Open V2X  at  ESIF 00  , Subcontract No. NCS-5-42326-05 , which also paid for open access. The authors thank the  NREL  staff, including  Andrew Meintz  and  Mike Simpson  from the  Energy Systems Integration Facility (ESIF)  for support of some of the vehicle efficiency measurements reported here. Also, the authors are grateful to  Matthias Kluck  and  AutoPort, Inc  for the advice and assistance with the MiniE and to BMW AG, including  Peter Krams  and  Xaver Pfab  for making the  BMW MiniE 's available for this project.
A C T In Europe, Defitelio (defibrotide) has a Market Authorization in curative treatment of severe sinusoidal obstruction syndrome (SOS) but not in prophylaxis (2013). In France, defibrotide has had a compassionate-use program since 2009. Today, the high cost of defibrotide remains a major hurdle for hospital budgets. Medicine and economic issues were evaluated for the 39 hospitals of the French Public Assistance-Hospitals of Paris (AP-HP). We analyzed literature reviews, consumption, and expenditures through AP-HP data in 2014 and patient profiles with defibrotide in the corresponding diagnostic-related groups (DRGs) and consulted a board of hematologists. Finally, 18 publications were selected. Between 2011 and 2014 consumption increased to €5. 2M. In 2014, 80 patients receiving defibrotide were mainly ascribed to the DRG "hematopoietic stem cell transplantation" levels 3 or 4.
Assessment of Therapeutic Need in Prophylaxis and SOS Curative Treatment Benefice-to-risk balance and therapeutic interest of defibrotide were assessed, taking into account evidence-based medicine standards and the latest recommendations regarding SOS treatments. The first part of this work needs to describe efficacy and safety outcomes from the published literature about defibrotide. A literature review was conducted using a PubMed, EMBASE, and Google Scholar search. The terms and key words "defibrotide AND hepatic veno-occlusive disease AND haematopoietic stem cell transplantation" were used. Because existing clinical data are very little (low prevalence of the disease, inclusion difficulties in the studies), we chose wide inclusion criteria. The inclusion criteria considered for our work were adult and pediatric populations, indications in curative and prophylaxis SOS treatment, the route of administration (i.
AP-HP Economic and Demographic Data The cost of a cure with defibrotide was calculated for the treatment of an adult and a child according to the posology described in the MA of Defitelio. The cost for a prophylactic treatment by defibrotide was estimated from the posology described in learned societies guidelines. To determine therapeutic indications of patients treated by defibrotide and their DRGs, an extraction of the French medical information system program for 2014 was performed (medical information available from the Medicalization Program of the Information Systems the AP-HP database). Extracted data provided information about the number of patients receiving defibrotide, their age, the duration of hospitalization, and the main diagnosis associated with the corresponding DRGs this same year for AP-HP hospitals.
Expert Opinion of AP-HP Hospitals A total of 17 experts in hematology were solicited for opinions. Finally, the board of experts, representing AP-HP, was composed of 6 physicians (3 of them represented the larger pediatric hospitals of Paris) and 4 pharmacists. All experts declared to have no major links with the company commercializing Defitelio. Concerning the SOS curative treatment, the experts agreed that the indications described in the MA should be respected, and defibrotide should be reserved for the curative treatment of severe SOS in HSCT therapy. In case of mild or moderate stages of SOS, the experts could not recommend its use because of the lack of clinical data but symptoms of seriousness must be detected. In prophylaxis, to take into account the interest of patients and the economic impact of defibrotide, a regulation of defibrotide use was necessary and a consensus was reached.
Main and Associated Diagnosis for Patients Receiving Defibrotide in 2014 According to the Classification of Diseases (ICD-10) Defined by the World Health Organization These data were issued by the Medicalization Program of the Information Systems database. ICD-10 indicates International Classification of Diseases, 10th Revision. The DRG tariff was extracted by the Official Journal dated 11/03/2015. The part attributed to drugs was extrapolated by the National Cost Survey in 2012.
In this paper we expand on the methods presented in  [7, 12] , reconstructing the wave-front using Fourier filters derived from discrete models of the measurement process, as developed in  [8]. We include additional constraints, specifically enforcing periodicity on the WFS data and demonstrate the improvements offered by this routine using open and closed loop end-to-end simulations of an adaptive optics system using a Shack-Hartmann WF sensor. The specific motivation is to provide a robust reconstruction in the Fourier domain in order to investigate anti-aliasing filters developed in  [8]. To observe the anticipated gains in contrast we require accurate reconstructors which perform well across the correction band, and particularly avoid errors at high spatial frequencies.
Limitations of Fourier analysis for non-rectangular domains The Fourier transform decomposes a function into Fourier modes, with these modes satisfying the conditions of an orthonormal basis over an infinite cartesian space. Analysis of discrete data defined over a finite space, such as slope measurements from a WFS, requires the Fast Fourier Transform (FFT). The Fourier modes used in the FFT are defined by the interval and sampling of the data. The FFT requires data defined over a rectangular space and assumes that the data is periodic. In this way the data can be completely described by the FFT modes. If either of these two conditions are not full-filled errors can occur in the Fourier analysis. In the case of adaptive optics systems the data is the slope measurements from a wave-front sensor.
End-to-end simulation results In order to test the performance of the Gerchberg extension we compare the results of end-to-end simulations using our extension method and the Hudgin extension. Particularly we aim to investigate the number of iterations required to achieve a comparable performance, the impact of enforcing periodicity with the Gerchberg extension and the effect of the extension window (number of pixels either side of the aperture). The results presented here are for a SPHERE-like case  [18]  and the parameters used are summarised in table 1. The simulations are carried out using OOMAO (Object Oriented Matlab Table  1. Summary of simulation parameters used in end-to-end simulations of a full AO loop. The atmospheric properties (the Fried parameter r 0 and outer scale L 0 ) are both given, as well as the telescope properties and wavelengths for the wave-front sensing and science star.
This avoids introducing additional features to the reconstructed phase, leading to errors particularly at high spatial frequency. Here we have presented results as applied to apertured data, but this method is potentially applicable to other obstructions. For example segmented telescopes, such as future ELTs, will produce spatially discontinuous WFS data. We foresee the use of the Gerchberg method to extend the slope data between the segments, thus allowing for reconstruction using Fourier methods. In addition the Gerchberg formalism should be directly applicable to other types of wave-front sensor, such as the Pyramid, whose signals are not pure gradient measurements and so do not conform to previously derived constraints. Further investigations into this method may also prove useful for the application of Fourier reconstruction over non-cartesian grids, such as the actuator geometry proposed for the European Extremely Large Telescope system HARMONI  [23].
Funding The research leading to these results received the support of the A* MIDEX  project (no. ANR-11-IDEX-0001-02 ) funded by the  Investissements d'Avenir French Government program  and managed by the  French National Research Agency (ANR). This research was co-funded by the  People Programme  ( Marie Curie Actions ) of the European Union's  Seventh Framework Programme  ( FP7/2007-2013)  under  REA  grant agreement n. PCOFUND-GA-2013-609102, through the  PRESTIGE programme  coordinated by  Campus France.
Methods We conducted literature searches in multiple databases (EMBASE, Scopus, PubMed, ProQuest, and Google Scholar; articles published before August 2015) and included clinical studies that used MIP as either a primary or secondary clinical endpoint outcome measure and reported a relationship between MIP and survival, QoL, pulmonary, and/or nonpulmonary functional endpoints. BioMarin Pharmaceutical Inc. provided funding for this analysis and for medical writing and editorial support during manuscript development. BioMarin Pharmaceutical Inc. was not involved in the collection, analysis, or interpretation of data. All authors had full access to study data and were solely responsible for the decision to submit for publication. Search terms included the following key words: ("maximal inspiratory pressure" or "nasal inspiratory pressure" or "negative inspiratory force" or "MIP" or "PImax") AND ("outcome" or "endpoint" or "efficacy" or "treatment effectiveness" or "sleep-disordered breathing" or "nocturnal hypoventilation" or "mortality" or "survival" or "death").
We initially screened literature records on the basis of title and abstract and excluded records not meeting the inclusion criteria (eg, no MIP results reported, disease and/or natural history focused). To identify open, ongoing clinical trials that are using MIP as an endpoint (primary or secondary), we searched the ClinicalTrials. gov database (www. clinicaltrials. gov). The search was conducted on July 12, 2015; search terms included maximal inspiratory pressure, PImax, and negative inspiratory force.
MIP as an endpoint in clinical trials We identified 8 publications in which MIP was used as a primary or secondary endpoint in a randomized controlled trial (RCT) of a pharmacologic therapy in a broad spectrum of conditions (Table  1 )  [26, [30] [31] [32] [33] [34] [35] [36]. One of these studies was in patients with Duchenne muscular dystrophy  [36]. Across the studies, the MIP endpoint was reported to be a sensitive and specific clinical measure for evaluation of the pharmacologic interventions, all of which directly targeted the respiratory musculature. A search of the clinical trials database revealed 31 open trials where MIP was cited as either a primary or secondary endpoint (Table  2 ). The trials reflected a range of clinical conditions; approximately 1 in 3 were in individuals with a NMD (including ALS, Duchenne muscular dystrophy, myasthenia gravis, Pompe disease, and X-linked myotubular myopathy).
The most efficient uses for digital health are still being explored in malaria, but integrating diagnostic results generated from malaria case management into elimination programme surveillance efforts offer a near-term opportunity to fill critical data gaps in mapping malaria prevalence  [2, 7]. For example, 1 study combined a globally accessible database with mobile phone-based imaging of RDTs to provide an objective diagnostic readout and automated collection of surveillance data  [74]. A similar approach in Kenya used digital RDT readers with upload to a cloud database  [75]. However, lessons learned from digital health applied to the eradication programme for tuberculosis suggest that attaining a population-level impact are undermined by insufficient scale, coordination, and end-user engagement  [76].
Acknowledgments The  Malaria Eradication Research Agenda (malERA) Refresh Consultative Panel on Tools for Malaria Elimination  was chaired by  David C. Kaslow ,  PATH Essential Medicines and PATH Center for Vaccine Innovation and Access, Seattle , Washington, US; and co-chaired by  Fredros Okumu ,  Ifakara Health Institute, Tanzania ; and  Timothy N. C. Wells ,  Medicines for Malaria Venture, Geneva, Switzerland. The paper was written based on consultations during a malERA meeting held in Washington, DC, US, on 12-13 October 2015 plus additional literature searches and methods detailed in the introduction paper to this series [11]. Mahamadou Ali Thera ,  European Vaccine Institute , participated in the panel discussion. Authors thank  Dan Strickman  ( Bill & Melinda Gates Foundation ) for providing expert information on dormancy and mosquitoes as parasitic reservoirs.
The prevalence study is detailed in Molla et al. (  [32] ), but briefly, data on health and socioeconomic status was gathered from a house-to-house survey of 611 individuals that had been selected by a case-control protocol. Samples of soil were taken from a randomised selection of cases and controls, and of the 103 soils collected initially, we categorised 81 samples by disease endemicity status-40 from areas regarded as 'endemic' and 41 from areas regarded as 'non-endemic' (  [9] ) to enable comparison of soil characteristics and haemolytic potential. Of the 103 soil samples, 22 were from areas of unknown endemicity, and were included in the study to increase the sample size in the multivariate analyses on the data without considering endemicity. Once in the laboratories at Addis Ababa University, the soil was air dried, homogenised and aliquots were separated.
This is the recommended methodology for comparing response data across multiple materials (  [37] ,  [38] ). Furthermore, the slopes were normalized to that of quartz DQ12, a well understood haemolytic material. Data analysis was performed using non-parametric statistical tests, Student's t-test, Spearman's Rho correlation coefficient, multivariate linear regression and principal component analysis (PCA) in IBM1 SPSS statistics program (versions 20 and 21). A value of p <0. 05 was considered significant.
Characteristics of the soil The soils collected from the Ethiopian Volcanic Plateau were fully characterized, in terms of their mineralogy and chemistry, as part of a concurrent study (see supplementary information). The summary statistics for the samples are shown in Table  1 , where data are presented as the geometric mean, geometric standard deviation (GSD = 84 th %-ile/50 th %-ile of the cumulative number distribution) and range, for all of the soil samples, and divided into the endemic and non-endemic categories (indicating the presence or absence of podoconiosis, respectively). For comparison, the mean (arithmetic) soil compositions for major oxides and elements from soils sampled in Sub-Saharan Africa, are also shown in Table  1  (from  [39] ). The majority of the major oxides and elements found within the soil in this study are similar to the reported median or within the range of values documented for soils in Sub-Saharan Africa.
The exception is aluminium oxide, which is higher than the reported range (at 19. 5 wt. %, geometric mean), where the reported range for Al 2 O 3 in Sub-Saharan Africa is up to 16. 8 wt. %. The content of silicon dioxide is lower in the samples of soil analyzed here than that from Sub-Saharan Africa. The low SiO 2 content in our soils maybe due to a combination of several factors, including underlying geology (predominantly mafic), and altitude (where there is little detrital input, wind-derived or riverine, which would increase the quartz content of the soil). The data between the endemic and non-endemic regions were compared, and the results are shown in Table  1. The elevation at which soil samples were collected was statistically significantly different for endemic areas (averaging ~2220 m above sea level (asl)) and non-endemic areas (~2850 m asl).
Sample https://doi. org/10. 1371/journal. pone. 0177219. t003 When the soil samples were analysed, without the addition of RBCs, the average readings from the spectrometer were not above that of the blanks analysed (data not shown). There was, however, limited correlation between the normalised HA and the iron oxide determined by mineralogy and that determined by chemical analysis (r = 0. 34 and r = 0. 37, respectively). As the mineralogy of the soil samples and the HA activity of the individual mineral phases (PPRMs) are known, a prediction of the HA for the soils can be made by multiplying the known HA of the PPRMs by the proportion of each mineral within each sample. The experimental normalised HA was then compared to the calculated HA, and the Spearman's Rho correlation was low (r = 0.
Hence, when kaolinite and smectite were added, the correlation with normalised HA was stronger than with either kaolinite or smectite phases alone; r = 0. 35 (p < 0. 001). Multivariate analysis was used to assess the relationship between normalised HA and particle characteristics. The characteristics were divided into chemistry, that uses the chemical composition of the samples with the other variables (major oxides, minor elements, total carbon and particle size for both <1 μm from water and deflocculant) and mineralogy, which uses the mineralogy of the samples rather than their major chemical composition (minerals, minor elements, total carbon and particle size for both <1 μm from water and deflocculant). The variables were standardized before analysis to produce z scores (calculated as the variable value minus the mean, divided by the standard deviation, which results in a set of z scores for each variable with a mean of 0 and a standard deviation of 1) to enable direct comparison between the variable datasets.
Acknowledgments This work was funded by a  Wellcome Trust   Enhancement Award  ( WT091956MA ; GD), and a  Junior Research Fellowship  (JL). The authors acknowledge  Chris Rolfe in the Geography Department at the University of Cambridge  for access to the Malvern Mastersizer laser diffractometer and  Dr Emma Humphreys-Williams  in the Imaging and Analysis Centre at the  NHM  for assistance with the  ICP-AES.
Presence/absence data For the North American native range, we assembled Douglas-fir occurrence data from forest inventories in British Columbia, Alberta, the United States, and Mexico (see Appendix S1). Absence data was compiled from vegetated areas where Douglas-fir was not observed. The presence and absence layers from the three countries were then merged to obtain a presence raster of 24 599 cells and an absence raster of 47 664 cells for the whole North American range, with a 2. 5-arcminute resolution. Presence cells were classified as interior (P. menziesii var. glauca) or coastal (P. menziesii var. menziesii) based on the zonation presented in  Snajberk and Zavarin (1976). The native presence/absence data set had a broad extent and a relatively coarse resolution. It was not only derived from herbaria records, but also from photo-interpreted data, and some of the plot coordinates had been fuzzed.