dataesr/scientific-paragraphs-categorization huggingface dataset:
Surface Roughness Measurements The initially polished surfaces and the specimens with different initial roughness prepared on AISI 1045 and Ti-6Al-4V were measured by Wyko NT3300S optical interferometric profiler. Vertical Scanning Interferometry (VSI) mode was used to measure the surfaces. The measurement principle is that unfiltered white light beam is split in two. Half of a beam is directed through a microscope objective and reflected from the surface and half is reflected from the reference mirror. When reflected beams combine together they produce interference fringes, where the best-contrast fringe occurs at best focus. In VSI mode the objective moves vertically to scan the surface at various heights. A 3D surface is reconstructed by analysis of fringes at every pixel. VSI mode uses algorithms to process fringe modulation data from the intensity signal to calculate surface heights.
GERIE protocol The GERIE study consisted of a European multicentre cross-sectional study that collected and integrated information belonging to several different aspects of the interaction between the NH environment and health status. To this extent a semi-individual design with individual health data and ecological environmental exposure data at the NH level was adopted. As a crucial part of health assessment, NH airborne infection control policies and COPD friendliness were appraised. Information on GERIE Study protocol and methods are available at (www. geriestudy. eu).
GERIE Study methods to assess air pollutants and comfort parameters Temperature, relative humidity, and carbon dioxide concentrations were measured during two days by an instrument with data loggers (Q-track) Illumination was measured at 20-30 points in each living room by a conventional lux-meter, in two different days. Acoustics in the living room (reverberation time) was also measured Noise levels were measured in the living room at three different conditions. Empty living room with windows closed and empty living room, windows opened. These measurements were both performed during lunch time. In addition, noise measurements (dBA) during the day were performed by an integrating sound meter. Particles PM 10 , PM 2. 5 and ultra-fine particles (PM 0. 1 ) were measured during two days by portable instruments with data loggers (Dust-track and P-track) In addition, high flow pumps (18 L/min) were used to collect PM 2.
Chemical markers (ergosterol for fungal biomass, muramic acid for bacterial peptidoglycan, and 3-hydroxy fatty acids for endotoxin) were analyzed in settled dust sampled by vacuuming floor and chairs according to a standardized protocol and analyzed by gas chromatography/ tandem mass spectrometry (GC-MSMS)  [11, 12]. Microbial particles by an electrostatic samples (5 L/min flow) were used for viral analysis. Irritants from disinfectants (e. g. chlorine) were determined by classical analysis. Details on constructions, materials, type of ventilation system, signs of building dampness, information on physical space e. g. m 2 /person, m 2 of the living room/ shared rooms were collected using a standardized form. To ensure the quality and reproducibility of data collection, a specialized Environmental Team was established.
Expected confounders include sex, social class, education centre, active and passive smoking, previous exposure to air pollutants, co-morbidities… Past exposures to occupational and environmental hazards were assessed also retrospectively. Exposure to outdoor pollution was modelled using appropriate approaches (proximity models of dispersion of air pollutants). In the long-term, data collected in the GERIE study will be employed in the search for gene*environmental interactions in the response to indoor pollutants and in the expression of the disease.
Descriptive data The total number of the elderly living permanently in the NHs selected in each centre and that participated in the GERIE study was 600, corresponding to a participation rate of 50% among the eligible persons. 2. The objective of targeting elderly was obtained. The GERIE population was aged on average 82 years. 66% of them were aged over 80 years and 74% were women. Mean BMI was 26. 8 kg/m 2. Regarding education, 55 (11%) had never been to school and 173 (34%) attended only primary studies. The highest school level attained was in Poland with 25 (16%) of the elderly in a four year college. 210 (40%) of participants declared that they smoked. Regarding respiratory health status, breathlessness was the most frequently respiratory outcome reported with a prevalence of 46%, the highest prevalence was in Poland with 62% of the participants.
Acknowledgements We are indebted to the participants of the GERIE Study as well as to the health professionals in the NHs and the authorities from which they depend. PhD Malek Bentayeb,  MSc Moran Guo , associate professor  Xin Zang, PhD  student  Sie Sie Siew , and  Franck Vibert  that all participated in the NH measurements. The Geriatric study in Europe on health effects of air quality in NHs has been funded by  European DG-SANCO  (Contract n°2006343 of European DG-SANCO) and  French Agency for Environment and Energy Management (ADEME, France)  (Contract  n°08 62 C 0076 ).
MRI data acquisition All data were acquired with a 3 T scanner (MR 750, General Electric Healthcare, Little Chalfont, UK). The anatomical scan used an inversion recovery 3-D T1-weighted gradientecho sequence images (TE = 4. 3 ms, TR = 11. 2 ms, TI = 400 ms, matrix = 384 × 384, slice thickness = 1. 2 mm). Functional images were acquired using a gradient-echo echoplanar (EPI) sequence (TE = 30 ms, TR = 2000 ms, flip angle = 90˚, matrix = 64 × 64, slice thickness = 3 mm, 42 contiguous sections). The first four volumes of each functional run were discarded in order to allow longitudinal magnetization to approach equilibrium.
ACKNOWLEDGMENTS The present study was supported by the  National Hospital Clinical Research Program (PHRC NEMAUVI)  allotted to  Thierry Gallarda  and  Pascale Piolino , the  Institut Universitaire de France  (postdoc funding for  Marco Sperduti  and  Sandrine Kalenzaga ) and the  Ministry of Higher Education and Research of France (Ph. D. funding of Pénélope Martinelli). We thank all volunteers for their participation in this study and the clinical and neuroimaging staff of the  Center of Psychiatry and Neuroscience at Sainte Anne Hospital , especially  Marion Delhommeau  and  Adèle Anssens. We would like greatly to thank  Angela Carpenter  and  Todd Lubart  for the language corrections of the manuscript.
Acknowledgements The senior author wishes to acknowledge the  Australian Leadership Awards-AusAID  for the financial support to undertake this study. Thanks are also extended to the  NSW Department of Primary Industries at Wagga Wagga and at Yanco  for providing the seeds and growth rooms used for the study and to their staff who helped maintain the growth environments used here. Special appreciation is extended to  Dr. David Luckett  and  Dr. Raymond Cowley  for their help during the initial stage of the experimental set-up in Wagga Wagga and to  Mr. Bill Hardy  of  IRRI  for editing the manuscript.
Data selection and event reconstruction The data sample was collected in 2010, in low instantaneous luminosity conditions, allowing a less restrictive selection at the trigger level in comparison to subsequent data taking periods. Data are included in the analysis for all periods where the silicon tracker, the muon detectors, and the trigger were performing well and the luminosity information was available. In the first data-taking period, the trigger requires the detection of two muons without an explicit p μ T requirement. The minimum distance between each reconstructed muon trajectory and the average proton-proton interaction point in the transverse plane must be less than 2 cm. In the second data-taking period, characterized by higher LHC instantaneous luminosities, additional requirements are imposed at trigger level: the two muons must have opposite charge and an invariant mass in the mass range 1.
(  1 ). The (p Υ T , y Υ ) values represent the generated and reconstructed values, respectively in the denominator and the numerator, thus accounting also for the effect of detector resolution in the definition of A. In addition the numerator requires the two tracks to be reconstructed with opposite charges and have an invariant mass within the Υ mass-fit range of 7-14 GeV/c 2. The acceptance is evaluated with a signal MC simulation sample in which the Υ decay to two muons is generated with the evtgen  [19]  package, including FSR. There are no particles in the event besides the Υ , its daughter muons, and the FSR photons. The Υ mesons are generated uniformly in p Υ T and y Υ. This sample is then simulated and reconstructed with the CMS detector simulation software to assess the effects of multiple scattering and finite resolution of the detector.
The efficiency that an identified muon satisfies the trigger is denoted by ε trig. The track quality, muon trigger, and muon identification efficiencies are determined using the tag-and-probe (T&P) technique. The T&P implementation follows Ref. [6] , and utilizes a J/ψ data sample as it provides a statistically independent, largeyield dimuon sample. The Υ efficiency is estimated from the product of the singlemuon efficiencies. A factor, ρ, is used as a correction to this factorization hypothesis, and to account for possible biases introduced by the T&P efficiency measurement with the J/ψ sample. We define ρ as ρ p Υ T , y Υ = (Υ ) (μ + J/ψ ) • (μ - J/ψ ) , (5) where (Υ ) is the efficiency for a Υ to pass the trigger and muon identification selections, and (μ + J/ψ ) and (μ - J/ψ ) are the corresponding efficiencies for positively and negatively charged muons from a J/ψ decay with the same p T and η as a muon in the Υ decay.
Acknowledgements We congratulate our colleagues in the CERN accelerator departments for the excellent performance of the LHC and thank the technical and administrative staffs at  CERN  and at other  CMS institutes  for their contributions to the success of the CMS effort. In addition, we gratefully acknowledge the computing centres and personnel of the Worldwide LHC Computing Grid for delivering so effectively the computing infrastructure essential to our analyses. Finally, we acknowledge the enduring support for the construction and operation of the LHC and the CMS detector provided by the following funding agencies:  BMWF  and  FWF (Austria) ;  FNRS  and  FWO (Belgium) ;  CNPq ,  CAPES ,  FAPERJ , and  FAPESP (Brazil) ;  MEYS (Bulgaria) ;  CERN ;  CAS, MoST , and  NSFC (China) ;  COLCIENCIAS (Colombia) ;  MSES (Croatia) ;  RPF (Cyprus) ;  MoER ,  SF0690030s09  and  ERDF (Estonia) ;  Academy of Finland ,  MEC , and  HIP (Finland) ;  CEA  and  CNRS/IN2P3  (France);  BMBF ,  DFG , and  HGF (Germany) ;  GSRT (Greece) ;  OTKA  and  NKTH (Hungary) ;  DAE  and  DST (India) ;  IPM (Iran) ;  SFI (Ireland) ;  INFN (Italy) ;  NRF  and  WCU (Republic of Korea) ;  LAS (Lithuania) ;  CINVESTAV ,  CONACYT ,  SEP , and  UASLP-FAI (Mexico) ;  MSI (New Zealand );  PAEC (Pakistan) ;  MSHE  and  NSC (Poland) ;  FCT (Portugal) ;  JINR (Armenia, Belarus, Georgia, Ukraine, Uzbekistan) ;  MON, RosAtom, RAS  and  RFBR (Russia) ;  MSTD (Serbia) ;  SEIDI  and  CPAN (Spain) ;  Swiss Funding Agencies (Switzerland) ;  NSC (Taipei) ;  ThEPCenter, IPST  and  NSTDA (Thailand) ;  TUBITAK  and  TAEK (Turkey) ;  NASU (Ukraine) ;  STFC  ( United Kingdom );  DOE  and  NSF (USA).
3% in models of focal cerebral ischaemia (95% CI, 28. 6% to 46. 0%, 41 comparisons), and reduced neurobehavioural data by 40. 5% (33. 4% to 47. 7%, 30 comparisons). Overall study quality was low (median=4, interquartile range 3-5) and measures to reduce bias were seldom reported. Publication bias was prevalent and associated with a substantial overstatement of efficacy for lesion size. Conclusions: RhoA and ROCK inhibitors appear to be effective in animal models of stroke. However the low quality score, publication bias and limited number of studies are areas which need attention prior to conducting clinical trials.
However, this trial was limited in sample size and outcomes were assessed at just 1-month follow-up. The evidence of safety and potential efficacy makes fasudil and other ROCK inhibitors ideal candidates for further investigation. Systematic review and meta-analysis of preclinical data are becoming increasingly common. They provide useful summaries which can be used to inform clinical trial design, highlight areas which may benefit from further preclinical research, and provide insights into the reasons for translational failures  [11, 12]. Prior to conducting a clinical trial, these techniques should be used to assess whether efficacy has been achieved in high quality, pragmatically designed studies which adequately reflect the human sample (for example, aged population with comorbidities) and the treatment paradigm which can be achieved (for example, later times to treatment)  [13].
Search strategy We electronically searched three online databases (Pubmed, Web of Knowledge and EMBASE) in September 2012, using the following search terms: ((C3) OR (C3-transferase) OR (Y27632) OR (Y-27632) OR (nonsteroidal anti-inflammatory) OR (NSAID) OR (ibuprofen) OR (Rho kinase) OR (rho-kinase) OR (rho) OR (ROCK) OR (RhoA) OR (Fasudil) OR (HA-1077) OR (HA 1077) OR (HA1077) OR (cethrin) OR (BA-210)) AND ((stroke) OR (ischemia) or (ischaemia) OR (middle cerebral artery) OR (cerebrovascular) OR (MCA) OR (ACA) OR (anterior cerebral artery) OR (MCAO)) NOT (coronary) OR (myocardia*)). Results were limited to animals. Additionally, the Web of Knowledge search was also refined by excluding reviews, books, letters, clinical trials, case reports, patents and editorials. Abstracts were independently screened by two reviewers (GC and ES) to identify those meeting our inclusion criteria (see below), with differences resolved by discussion with a third reviewer (HV and RW).
Inclusion criteria and data extraction We included studies which reported the effects of inhibitors known to directly inhibit RhoA or ROCK in an in-vivo animal model of focal cerebral ischemia. We did not include studies which reported the effects of drugs known to inhibit molecules in the Rho pathway upstream of RhoA and ROCK. We included studies that reported the number of animals per group, outcome as a lesion size (infarct volume or infarct area; primary outcome) or a neurobehavioural score (secondary outcome) or both, and the mean and its variance (standard error of the mean (SEM) or standard deviation (SD)). Experiments with co-treatments were excluded. Data were extracted to the CAMARADES data manager.
Data extraction We extracted data on study design including the time, route and dose of the drug administration, the species, sex and strain of the animal, the type of ischaemia (permanent, temporary or thrombotic), the anaesthetic and ventilation method used during the induction of injury and the method of quantification of lesion size. For each comparison on drug efficacy we extracted data on the number of animals per group, the mean outcome and the variance for both the control and treatment group. When a single control group was used for multiple treatment groups this was adjusted by dividing by the number of treatment groups served. Where data were not reported we made efforts to contact authors. Where data were reported graphically we used digital ruler software (Universal Desktop Ruler) and where data were expressed serially we extracted the final time point.
Data analysis We deemed infarct volume and area to be sufficiently similar to be grouped into the same meta-analysis which we refer to as lesion size. We calculated a normalised mean difference effect size for each comparison (Vesterinen et al. , manuscript in preparation) and combined these in a weighted mean difference meta-analysis using the random effects model  [14]. Where different measures of neurobehavioural outcome were reported from the same cohort of animals we combined individual effect sizes (pre-nested comparisons) using fixed effects meta-analysis (nesting) and used this summary estimate in the random effects model. We used stratified meta-analysis to assess for the impact of drug dose, time of administration, blinded assessment of outcome, random allocation to group, the overall study quality score, type of ischaemia, the sex and species of animal used, anaesthetic used and use of mechanical ventilation; and for infarct volume we additionally analysed the method of quantification.
Results We identified 3,286 publications in our electronic search of which 3,237 were excluded in the first instance (513 duplicates and 2,724 publications which did not meet our inclusion criteria). We screened 49 publications in detail from which we excluded a further 24 publications (16 had no relevant outcome measures; four only reported outcomes measured outside the brain; two were abstracts later published in full; one did not use a relevant intervention; and one was a review). Our systematic review therefore included 25 articles published between 1992 and 2011 which met our inclusion criteria (24 full publications and one conference abstract; Additional file 1). We extracted data for 41 comparisons describing infarct volume from 23 publications and 30 nested comparisons (32 pre-nested) were extracted for neurobehavioural scores from 18 publications (Figure  1 ).
Study quality Our study quality checklist assesses aspects of both internal and external validity, and we have frequently observed studies of poorer methodological quality tending to overstate effect sizes  [2, 18]. Here we found that studies were generally of low quality (median 4 out of 10). Specifically, measures to reduce bias including blinded induction of ischaemia, random allocation to group and blinded assessment of outcome were all seldom reported in this dataset. The overall quality score accounted for a significant proportion of between study heterogeneity; however, a correlation between the aggregate quality score and effect was not clear.
Therefore it is conceivable that this class of intervention would be of no benefit in permanent ischaemia. Across several datasets on preclinical models of stroke, roughly 10% of studies use animals with co-morbidities relevant to stroke patients, such as hypertension and diabetes  [12]. In our dataset, one publication used spontaneously hypertensive rats; no other publication out of 25 used animals with a co-morbidity. This may limit the predictive value of these studies for clinical trials. Furthermore co-morbidities can affect efficacy in animal models  [21].
Limitations The present study provides a useful summary of the preclinical data on RhoA and ROCK inhibitors. However there are limitations to our approach and the results should therefore be interpreted with caution. First, although our search strategy was designed to be robust, we cannot rule out the possibility of missing studies. Furthermore, this may also be due to publication bias. Similar to our previous findings  [24] , we found that publication bias was prevalent in this dataset. Although our dataset was relatively small, we used three approaches to minimise the risk of confounding; indeed the more conservative trim and fill approach did not identify any theoretical missing studies for neurobehavioral outcomes. Taking into account theoretical missing studies, our estimates of efficacy are likely to be overstated.
The well-documented re-colonisation of the French large river basins of Loire and Rhone by European otter and beaver allowed the analysis of explanatory factors and threats to species movement in the river corridor. To what extent anthropogenic disturbance of the riparian zone influences the corridor functioning is a central question in the understanding of ecological networks and the definition of restoration goals for river networks. The generalist or specialist nature of target species might be determining for the responses to habitat quality and barriers in the riparian corridor. Detailed datasets of land use, human stressors and hydro-morphological characteristics of river segments for the entire river basins allowed identifying the habitat requirements of the two species for the riparian zone.
Where on a local scale some species may appear to be functioning as specialists, across their entire geographic range they often have generalised ecologies  [30]. The beaver is much more restricted in mobility (home range 0. 5 -2km) and reliant on the presence of softwood riparian forests for foraging. For this reason, human stressors to the riparian corridor are expected to play a more important role in its colonization. Data of presences were gathered for the otter in the Loire Basin by a network of associations' volunteers gathered under the Loire Basin Mammal Network, and for beaver in the Rhone basin by the field workers of the National Wildlife Office (ONCFS). Harmonised protocols in data collection were adopted following the internationally agreed otter census protocol  [24]  and for the beaver a similar standardised protocol was developed.
At the basis of the metrics for the river segment is finer scaled information on the land use of the riparian corridor that was gathered from the national geographical database of BDTOPO IGN®. Riparian forest cover in different buffers is derived from national aerial sensed data (BDORTHO IGN®). From the SYRAH database, a set of 22 metrics at the river segment scale (Table  1 ), potentially influencing species presence, was selected:.
Analysis of distribution in relation to environmental data To assess the contribution of the different aspects of the riparian corridor functioning and compare them for the otter and beaver datasets, a similar approach for the two investigated river basins is followed. A habitat qualification approach for species distribution by PCA and PLS-R regression  [35]  is used to explore the determining 'habitat' factors, followed by a network analysis integrating the 'ecological niche factor analysis' framework  [36]. The first step is the analysis of the species presences in relationship to the environmental data for the river segments. After a first exploratory PCA analysis, to retain only the relevant variables for the habitat and stressors, a Partial Least Square (PLS) regression is carried out on the selected set of variables.
as possible the number of predictors to improve AUC values as advocated by "ensemble modelling"  [18, 41] , in our approach we try to conserve as many as possible predictors, to increase the mechanistic understanding of the complex interaction between the corridor's habitat quality and connectivity in relation to the network structure and anthropogenic stressors present. The integration of environmental data from different scale levels, collated to the river segment and to a fi ne-scale level of land use in different buffer widths offers a unique and pertinent dataset to the analysis of riparian corridor functioning. The long year colonization observations for the two species over the entire river basins strengthen this large geographic scale network analysis. Most studies interpreting semi-aquatic species distribution start from a landscape pixel approach  [22, 29, 40].
Including spatial and climatic parameters would significantly improve the predictive power of the regression function, but as these variables would be significantly biased by the spatial autocorrelation  [40, 47] , and furthermore fall out of the scope of our study, we did not integrate them. Secondly, the lack of abundance data deters strong responses to habitat factors. The use of presence observations of these mobile species in this large dataset poses risks in discriminating habitat factors, as also in marginal or even unfavourable habitat individuals can be detected during dispersal events or in the vicinity of highly occupied sites according to the source-sink dynamics  [32]. Furthermore expansion in range is much faster than expansion in population  [26] , increasing the risk of over-representing the observations of migrating individuals  [23].