dataesr/scientific-paragraphs-categorization huggingface dataset:
Study design TOWER (The Titration study in lOWer and uppER limb spasticity; NCT01603459) was a prospective, single-arm, multicenter, non-randomized dose-titration study investigating the safety and efficacy of incobotulinumtoxinA in subjects with upper-and lower-limb spasticity who were deemed by the investigator to require total body doses of 800 U incobotulinumtoxinA. The study was conducted at 30 centers in Europe and North America. To minimize potential bias of subject-rated outcomes, subjects were blinded to which dose they were receiving during which cycle. Study details, safety and results from selected efficacy variables have been published elsewhere  [20]. In brief, the study comprised three consecutive, flexible, 12-16-week injection cycles, in which the following escalating doses of incobotulinumtoxinA (BoNT-A free from complexing proteins, Xeomin®, Merz Pharmaceuticals GmbH) were administered by intramuscular injection in the same body side on the first day of each injection cycle: cycle 1, a fixed total body dose of 400 U into the upper limb or lower limb only, or split between both; cycle 2, a fixed total body dose of 600 U into the upper limb or lower limb only, or split between both; cycle 3, a total body dose of 800 U split between both upper and lower limbs (maximum dose of 600 U per limb) or a lower total dose of between 600 and 800 U, if 800 U was not indicated for clinical or safety reasons.
Acknowledgements The authors wish to thank the subjects and study investigators. This study was supported by  Merz Pharmaceuticals GmbH, Frankfurt am Main, Germany. Medical writing support, under the direction of the authors, was provided by  Claire Cairney, PhD ,  CMC  Connect, McCann Health Medical Communications and  Kirsteen Munn, PhD , on behalf of CMC Connect, funded by  Merz Pharmaceuticals GmbH , in accordance with Good Publication Practice (GPP3) guidelines.
| INTRODUC TI ON The invention and applications of polymerase chain reaction  (PCR)  and DNA sequencing have revolutionized research on wild organisms, including parasites and other pathogens. A few of the services provided by these methods include the unambiguous identification of morphologically difficult species, discoveries of cryptic species, delimitation of parasite host range, and resolution of life cycles. Furthermore, the generated DNA sequences can be used for constructing phylogenetic relationships. The importance of these contributions to the ecology and evolution of parasitic organisms cannot be overestimated. To facilitate data sharing it has become standard to report findings of parasites and pathogens based on DNA sequences in open DNA databases such as NCBI, but also in specialist databases delimited on various taxonomic levels or the organisms they infect, such as EuPathDB  (Aurrecoechea et al.
, 2017)  and PubMLST  (Jolley et al. , 2018). The database MalAvi (http://130. 235. 244. 92/Malav i/index. html) was initiated 10 years ago  (Bensch et al. , 2009)  in order to structure the growing numbers of PCR-based findings of bird blood parasites known as haemosporidians that include malaria parasites. The database presently contains >3,900 unique mitochondrial lineages (based on 478 bp of the cyt b gene) recorded from >1,800 species of birds and 58 species of blood-sucking dipterans. It has become an important resource for analyses of the geographic distribution and host range of these globally distributed parasites  (Rivero & Gandon, 2018) , with 436 citations (web of science 2020-04-30) and steady annual growth of records. Clearly, the value of a database depends on the quality of the data.
Incorrect records may inflate estimates of host species range and geographic distribution of the parasites. In this respect, false positives are more impactful than false negatives. Curated databases such as MalAvi are not resistant to erroneous records. However, as the knowledge of the typical distribution of parasites in host species or in geography are accumulating, unexpected findings can alert us to carefully check and confirm these before publication, and hence keep the database resources as accurate as possible. In the present paper, we evaluate several unexpected findings of haemosporidian parasites in unusual host species or geographical regions that appear to be the results of PCR contamination or mix up of samples. We would like to emphasize that the authors of these papers are no guiltier of publishing records resulting from contamination than other researchers in the field, as the examples highlighted here probably represent only the tip of the iceberg of a widespread problem.
Examples of widespread generalists are the lineages SGS1 and GRW04 of the morphospecies Plasmodium relictum, recorded in 132 and 82 host species, respectively (MalAvi database, October 2019). However, pinpointing records, if any, as being due to contamination will remain speculative. A report of GRW04 from one single greylag goose Anser anser in Germany  (Musa et al. , 2018)  is indicative of contamination as both the host species and the transmission area are surprising. Also, the lineage GRW04 was amplified in a parallel project carried out in the same laboratory  (Musa et al. , 2019). Whereas the lineage SGS1 is widespread and common in Eurasia and Africa, there are only two published records from the Americas; in a single tree swallow from Canada  (Turcotte et al. , 2018)  and from several species of hummingbirds and passerines at two sites in Peru  (Marzal et al.
We expect that these are just the tip of the problem because for most of the >3,900 lineages found to date, we know far too little of haemosporidian natural occurrence to be alerted if a record is improbable. Errors assigning parasites to host species is a problem that goes beyond the study itself, because when entered to common databases, the records will repeat the errors in global analyses of parasite host and distribution ranges  (Clark et al. , 2014). A relevant question to ask is whether PCR contaminations in publications, and as a consequence falsely assigned host species, have contributed to the general conclusion that haemosporidian parasites mainly evolve by frequent host switching rather than co-speciation  (Fecchio et al. , 2018). We think this is unlikely because switching between host species  (Ricklefs et al.
highly infected samples increases the risk of generating PCR contaminants that may carry over to other samples in the same experiment or form background contamination in the laboratory which could affect later projects. The ignorance of positive controls being the potential source of contamination dominates studies of avian haemosporidians; <5% of the papers included in the MalAvi database have reported the lineage(s) of the sample(s) used as positive controls. Insightful selection of samples for positive controls may also highlight cases of potential contamination. For example, it would be more informative to use samples from a known host-specific parasite when screening samples from other bird species than using a sample from known generalist parasites. The finding of the former in an unexpected host species would call for checking the sample again, using a new DNA extract or primers from a different region of the parasite's genome.
Objective: To define the role of ureteroscopy for treatment of staghorn calculi. Methods: A systematic review was conducted using the Scopus and Medline databases. Original articles and systematic reviews were selected according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Only studies relating to the role of ureteroscopy for treatment of staghorn calculi were included. Results: In five studies on ureteroscopic monotherapy, stone-free rate (SFR) ranged from 33% to 93%, with a maximum four ureteroscopy sessions per patient and no major complications. Endoscopic combined intrarenal surgery (ECIRS) was compared with percutaneous nephrolithotomy (PNL) in two studies and reached significantly higher SFR (88%e91% vs. 59%e65%) and lower operative times (84e110 min vs.
Methods A systematic review was conducted using the Scopus and Medline databases, updated to March 2019 with no time period restriction. The search terms ("ureteroscopy" OR "ureterorenoscopy" OR "retrograde intrarenal surgery") AND ("staghorn calculi" OR "staghorn stone") were used and the filters "English" and "humans" were applied. Original articles and systematic reviews were selected according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines (Fig. 2 ). Reference lists of selected manuscripts were checked manually for eligible articles. Only studies relating to the role of ureteroscopy for treatment of staghorn calculi were included. Case reports, editorials and letters were excluded. A narrative synthesis for analysis of the studies was used.
These studies differ in their methodology and their findings for policy effectiveness. Popp et al. (43)  analysed the influence of the ratification (or not) of the Kyoto Protocol. According to the authors, although ratification is not in itself a direct incentive for investment, it can serve to signal a country's commitment to climate policy and, hence, to future carbon prices. Their model, that included data from the OECD countries between 1991 and 2004, showed a positive and significant relationship between the ratification of the Kyoto Protocol and investment, but no significant influence of direct support policies. Marques and Fuinhas  (23)  included a broader range of policy variables to evaluate RE effectiveness in a set of 23 European countries from 1990 to 2007. First, the authors constructed a variable for the number of policy measures in each country (the accumulated Number of RE Policies and Measures).
They then tested the influence of different types of policies according to the general classification proposed by the IEA Global Renewable Energy Policies and Measures Database: Information and Education Policies, Economic Instruments (including FIT, FIP, etc. ), R&D, Regulatory Instruments (including quotas, standards, etc. ), Voluntary Approaches and Policy Support. Their results showed a positive and significant impact of public policies in general. However, if considered individually, only subsidies and policy support (e. g. , strategic planning and creation of institutional frameworks) showed a major influence. Overall, Marques and Fuinhas found that regulatory instruments and all other types of policies were not significant for promoting RE. Aguirre & Ibikunle  (44)  whose approach was similar to that followed by  Marques & Fuinhas (2012) , analysed the OECD and BRIC countries from 1990 to 2010.
Polzin et al. (22) used ordinal variables to represent the different policies in place in the OECD countries between 2000 and 2011. They highlighted the importance of a reliable policy framework with clear medium-and long-term objectives and found that tax and economic incentives (FIT, FIP) are the most relevant measures for investors based on an evident reduced risk associated with such projects. Other indirect instruments, including tradable CO2 emissions permit systems, seem to have a positive impact, but only for the most mature technologies. The Kilinc-Ata  (21)  study used data from 1990 to 2008 from Europe and the US. They showed that FITs, tenders and tax incentives are effective for boosting the deployment of RE, while quotas are not. Finally, Kim and Park (33) included a single policy variable: FIT.
Data and method. Our dataset covers 50 countries (i=1,…,i=50) and 20 years (t=1995,…,t=2014) and is balanced  5. In this section, we explain our choices concerning the explained variable (3. 1), the explanatory variables, including a brief description of RE policy in Europe and Latin America (3. 2 and 3. 3), and the econometric model (3. 4).
Support policies in Europe and Latin America The main explanatory variables included in our model are Ex_pol, which denotes the existence or not of support policy, and four variables for the type of instrument. We consider the main support instruments: Feed-in Tariff and Feed-in Premium (FIT), the auction system (AUC), the quota obligations with negotiable green certificates or Renewable Portfolio Standards (RPS), and the fiscal -tax-incentives (FIS). We do not include instruments implemented for short periods, such as voluntary agreements or green pricing. The selected variables reflect the intensity and diversity of the policies implemented in the two regions studied. We exploited several data sources: IRENA/IEA (Joint Policies and Measures database), European RE-Shaping projects  (54) , and data from (  55 ) and (  56 )Since we are interested in investments in new technologies for electricity generation, we focus on policies specific to the electricity sector.
Our database contains 1,000 observations indicating the existence or not of a policy in the country i in the year t, and the type of instrument. These observations were transformed into binary variables. In Latin America, promotion policies have followed a different logic. These countries were much less concerned about climate policies in the 1990s and 2000s: per capita emissions were significantly lower due to lower energy consumption and the existence of high levels of hydroelectric production in most countries. Figure  1  shows that the first policies were put in place only in the late 1990s and early 2000s. They seek to diversify electricity production by attracting private investment needed to meet growing demand. There is also no coordinated planning of the energy sector in this region.
Acknowledgements To the memory of our friend and colleague  Pete Burnard  with whom we have had many discussions about the origin of noble gases on Earth. We would like to thank  Steve Parman  and an anonymous reviewer for comments and suggestions that help us to improve our manuscript. MAB acknowledges the support of a  NERC  and the  PNP-CNRS program. This work was also supported by  NERC  grants to APJ. This is Laboratory of Excellence ClerVolc contribution number  429. Editor:  Helen Williams.
The present study aims to quantify the potential of hyperspectral thermal infrared sounders such as the Infrared Atmospheric Sounding Interferometer (IASI) and the future IASI next generation (IASI-NG) for retrieving the ice cloud layer altitude and thickness together with the ice water path. We employed the radiative transfer model Radiative Transfer for TOVS (RTTOV) to simulate cloudy radiances using parameterized ice cloud optical properties. The radiances have been computed from an ice cloud profile database coming from global operational short-range forecasts at the European Center for Medium-range Weather Forecasts (ECMWF) which encloses the normal conditions, typical variability, and extremes of the atmospheric properties over one year  (Eresmaa and McNally (2014) ). We performed an information content analysis based on Shannon's formalism to determine the amount and spectral distribution of the information about ice cloud properties.
Based on this analysis, a retrieval algorithm has been developed and tested on the profile database. We considered the signal-to-noise ratio of each specific instrument and the non-retrieved atmospheric and surface parameter errors. This study brings evidence that the observing system provides information on the ice water path (IWP) as well as on the layer altitude and thickness with a convergence rate up to 95% and expected errors that decrease with cloud opacity until the signal saturation is reached (satisfying retrievals are achieved for clouds whose IWP is between about 1 and 300 g/m 2 ).
NWP Database and the Measurement Vector To assess the information content of the IASI and IASI-NG measurements and test the retrieval algorithm against realistic case studies, the measurement vector is computed from a representative ensemble profile dataset from the global operational 137-level shortrange forecasts of the European Center for Medium-range Weather Forecasts (ECMWF) (see https://www. nwpsaf. eu/site/software/atmospheric-profile-data/-last accessed on 15 December 2020). These profiles have been chosen to capture the normal conditions, variability, and extremes of the model behavior for different atmospheric properties over one year  [64]. The selection process samples key atmospheric variables (temperature, humidity, ozone, cloud condensate, and precipitation) in a subset of profiles chosen among the 10 8 reanalysis profiles generated from 1 September 2013 to 31 August 2014.
An iterative process ensures the variability of the sampled variable by comparing the squared distance between all the chosen profiles, a statistical procedure is used to ensure that the database accounts for a realistic amount of frequently-occurring atmospheric states and a filter is applied to prevent from non-physical profiles. The details of the selection procedure can be found in reference  [64]. The geographical position of the profiles that make up the database is given in Figure  1. We have split them into three cloud scene categories depending on the cloud layer position and water thermodynamical phase. The first category (called IC in the following) is composed of 1424 atmospheric conditions corresponding to single-layer ice clouds. The second one, composed of 821 cases, corresponds to multi-layer cases (ice above liquid) with no mixture between layers (labeled as LIC-SEP in the following).
The third category, the largest one with 2330 cases, corresponds to atmospheric columns with ice and liquid clouds that have some mixed layers (labeled as LIC-MIX). Figure  2  summarizes the characteristics of the cloud condensed water profiles for the three cloud configurations given by the database. The measurement vector is built from those profiles. We used them as an input of the radiative transfer model and calculated the synthetic radiances as would be measured by IASI and IASI-NG at the top of the atmosphere by adding a random noise from the radiometric noise of each instrument  [40].
This climatology, built from 6 years of measurements, allows one to express CGT as a function of CTH and IWP. We have built this climatology by differentiating lands and oceans as well as day and night. Examples of daytime climatologies are depicted in Figure  6. The CGT increases with IWP with a relatively small standard deviation for CTH which varies between about 2. 5 and 18 km. We have compared the cloud geometric thickness (CGT) from the database with that obtained from the climatology. This comparison led us to apply a shift of 0. 5 km to the climatology to compensate for the bias found in the profile database. The previously defined climatology introduces some dependencies between CGT and the two others parameters we want to retrieve, that is CTH and IWP. If the optimal estimation method allows one to take into account any correlation between retrieved variables, this correlation has to be mathematically well known, which is not the case here.
Retrieval Results from Synthetic Radiances The performance of the retrieval algorithm is tested against IASI and IASI-NG synthetic measurements generated from the vertically inhomogeneous diverse profile database with a randomly added noise from the radiometric noise of each instrument  [40]. The corresponding IASI and IASI-NG pixel is considered to be overcast (cloud fraction equal to 1). This assumption underestimates the model error accounted for in S F by ignoring the uncertainty due to the spatial inhomogeneity that would be encountered in a real retrieval. Indeed, the IASI field of view is quite large compared to cloud formations (from 12 km in diameter for nadir viewing to 39 km for maximum off-nadir field of view for a satellite altitude of 840 km). In this study, we did not introduce any bias between atmospheric profiles used to generate the synthetic observations and the one used in the retrieval process.
Figures  7 8 9 illustrate the distribution of the retrieved ice cloud properties with respect to the truth considering IASI characteristics. The convergence rate reached by the algorithm (the convergence is achieved when the normalized cost function falls below 1) is satisfactory with 1386 converged profiles over 1424 for IC (97%), 785 over 821 for LIC-SEP (95%), and 2218 over 2330 for LIC-MIX (95%). We have also added to these figures the goal and threshold requirements laid out by the Global Climate Observing System (GCOS) Implementation Plan and the Word Meteorological Organization (WMO) Observing Systems Capability Analysis and Review Tool (OSCAR, see https://www. wmo-sat. info/oscar/last accessed on 15 December 2020). This database is an official repository of requirements for observations of physical variables in support of WMO programs.
For the CBH variable, the OSCAR threshold is 1 km. According to the ECMWF 137-levels dataset selected using the cloud condensate sample (i. e. , representative of the total amount of condensed water in the atmospheric column), the LIC-MIX category, which is the one that leads to the poorer results, is the most frequent in the atmosphere (50% of the cloudy skies). The LIC-SEP and IC cases represent 17. 5% and 4. 5%, respectively. The retrieval of IWP and CTH are rather encouraging, whereas the retrieval of CBH appears to be more difficult especially when there is a mixed liquid cloud layer underneath. Those results are in good agreement with the information content analysis. Again, as expected from the information content analysis, using IASI-NG instead of IASI slightly improves the retrieval accuracy but not the overall performance (not shown).
Discussion and Conclusions In this paper, which deals with the capability of thermal hyperspectral measurements for the study of ice clouds, we have shown the potential of instruments like IASI and IASI-NG to retrieve parameters such as the integrated ice water content, layer position, and vertical extent of these clouds. The use of information theory applied to a database that is representative of the diversity of the cloud column and an accurate description of the errors introduced by the forward model as well as the measurement, allowed us to obtain the limits of this type of observation to get accurate information on cloud parameters in terms of opacity (given by the total amount of ice or IWP) of the observed cloudy layer. We were able to show that the IWP should be adequately retrieved for a range of IWPs between about 1 and 300 g/m 2 , and for a single-layer ice cloud with no liquid cloud beneath or when a clear separation exists between the ice cloud and water cloud.
At a concentration of 200 mM, cation specificity was more evident, with specific activity decreasing according to the sequence: LiCl ~ NaCl ~ KCl > CsCl > GnCl > No Salt. The kinetic parameters of ADH at pH 8. 30 (10 mM Tris buffer) in the absence of any background electrolyte were measured initially. Figure  4A  shows the Michaelis-Menten plot of the initial reaction rate, V0, as a function of ethanol concentration. Values of 5. 5 mM and 11. 3 µmol mL -1 min -1 were obtained for Km and Vmax, respectively (Figure  4B-C ). Hofmeister effects on the kinetic parameters of ADH were investigated. Michaelis-Menten plots in the presence of different 150 mM sodium salts are shown in Figure  4. In agreement with the results obtained in Figure  2 , the addition of salts resulted in an increased rate of reaction in comparison with the data obtained with no added salt.
Outcomes and Measurements Primary outcome was the evolution of FEV1 from the index date. Secondary outcome was that of FVC. Demographic and clinical data were collected at baseline. PFT were collected at the time of skin cGVHD diagnosis, and in the follow-up period. PFT data included FEV1 (ml), FVC (ml), FEV1/FVC ratio (%), and predictive values were determined as previously described  [25]. Other treatments received for cGVHD were also collected. The evolution of skin sclerosis following ruxolitinib initiation was evaluated by dermatologists (C. H. and J. D. B).