dataesr/scientific-paragraphs-categorization huggingface dataset:
COI-5P and psbA phylogenies and secondary species hypothesis The phylogeny inferred from the mitochondrial COI-5P gene was well resolved (15 nodes with posterior. 0. 95 out of 26 nodes) and four major lineages could be distinguished (Fig. 1 ). Regardless of the approach used for species delineation, all the PSHs that included more than one COI-5P haplotype always coincided with clades with high statistical support (posterior. 0. 9) with the exception of PSH 7. The chloroplastic psbA gene was sequenced for fifteen of the sixteen PSHs defined with COI-5P data. A fragment of 892 bp generated for 29 specimens produced 15 haplotypes. The phylogeny inferred from psbA data was remarkably congruent with the one inferred from the COI-5P gene (Fig. 2 ). Again, four major lineages could be recognized, one of them separated from the others at an earlier time.
As a result, 16 initial PSHs were converted to 13 SSHs (Fig. 2 ; see also Table  S2b  for average COI-5P sequence divergence between and within SSHs). Two pairs of PSHs alternatively recognized as either a single PSH or as two different PSHs by ABGD and GMYC were turned in a single SSH each (SSH 4+5, SSH 6+7). Unfortunately, we did not manage to obtain a psbA sequence for PSH 9, a PSH supported by only one of the partitions derived from the GMYC model. Since its COI-5P sequence was very close to the haplotypes found in PSH 8, we opted for a conservative inclusive approach and considered these two PSHs as a single SSH (8+9). The final partition into SSHs matched the delineation obtained with the single-threshold alternative of GMYC applied to COI-5P data only and was nearly identical to the less inclusive partition generated by ABGD.
Matches in public data bases Based on the literature and on the magnitude of intra-SSH variability found in our study, we used ad-hoc cutoff values (. 98% identity for COI-5P,. 99% for psbA) to determine which GenBank searches had returned hits for potential conspecifics. Only 9 out of our 29 COI-5P haplotypes (4 SSHs) and 3 out of the 15 psbA haplotypes (2 SSHs) resulted in a relevant match in either GenBank or BOLD (Table  S3 ). Altogether, we obtained hits for 4 out of our 13 SSHs: SSH4+5, SSH6+7, SSH12, and SSH16. Only SSH4+5 resulted in a match to an identified species, L. glaciale: our COI-5P sequences were 98. 6-99. 9% similar to, and shared the same Barcode Index Number (BOLD:AAA6958), 39 accessions uploaded to BOLD for plants collected in Northeast USA and Canada. Also from OSPAR region I, SSH6+7 was conspecific with plants (BIN BOLD: ABA9580) from the Pacific (British Columbia) which, according to pictures logged in BOLD, have a branched morphology typical of maerl-forming plants.
Attribution of available species names Six SSHs could be assigned to a species name using a body of proofs. In two cases, name assignment rested on comparisons with molecular data obtained from type material. SSH 12 was identical to COI-5P sequences obtained from neotype material of P. calcareum from BM. Likewise, our collections of SSH 1 included the holotype of M. sphaericum. For the second most widespread and common species in our study (SSH 8+9), we tentatively attributed the species name L. corallioides because the latter, together with P. calcareum, is typically regarded as a common component of maerl beds in Atlantic Europe. Furthermore, samples from the type locality of L. corallioides (Rade de Brest, Finistere, France)  [34]  were resolved in the SSH 8+9. In light of the morphological traits observed by SEM together with the existence of previous records from the same area, we temporarily attributed the names L.
However, it is likely that most, if not all, of the species that we left unnamed in this study may have already been described elsewhere. We did not dare to identify SSH 6+7 (Lithothamnion sp. 2) to species level. Its confinement to OSPAR region I and to northernmost sites of region II suggests that L. tophiforme could be a plausible name but our sequences did not match two collections from New Foundland, Canada lodged in BOLD as L. tophiforme. However, the identity of these collections in BOLD has not been confirmed with sequence data from type material and should be considered with caution. Lithothamion tophiforme is mainly reported as an Arctic species that, in European waters, is confined to very high latitudes  [47]. Somewhat unexpectedly, however, L. tophiforme went unrecorded in a detailed recent investigation of the northernmost maerl communities currently known, discovered in 2006 at 80u31'N in the Svalbard Archipelago  [36].
Hence, further sequence data from type material will be required to assign a species name to SSH13. Lastly, our results clearly indicate that the maerl-forming algae that colonize Macaronesia deserve further study with appropriate sampling design and molecular tools. To our knowledge, this is the first barcoding study focused on maerl-forming algae. Previous DNA barcode studies on coralline algae mostly focused on geniculate forms  [13, 22, 46, 54]  or were intended to resolve infra-ordinal phylogenetic relationships among the Corallinales  [55]. Nevertheless, Bittner et al. [56]  sequenced geniculated and non-geniculated coralline algae, mainly from South Pacific Islands, for psbA and COI-5P, and used ABGD and GYMC to delineate species. As the authors found very divergent numbers of 'genetic species' depending on the criteria and the marker, they concluded that DNA-barcoding was non-accurate for assessing the species diversity in this group (but see  [33]  for alternative explanations when GMYC has a highly divergent outcome).
Contrarily, we are in favor of an integrative systematic approach to investigate the diversity of maerl-forming red algae. We propose the use of the mitochondrial COI-5P barcode as the first marker and the plastidial psbA gene as a secondary marker along with other lines of evidence. In this regard, we follow other authors that already noted the intrinsic limitations of delimiting species from single-locus studies and advocate the incorporation of multiple lines of evidence (biogeographical, biological, additional gene sequences) in this studies  [10, 32, 33]. Despite considerable efforts to identify specimens collected in this study based on their morpho-anatomical characters, sequence data were incomparably more efficient. In fact, our Fig. 2  shows that even maerl assigned to different morphogenera turned out to belong to the same molecular entity.
Finally, the congruence between partitions recovered with analyses based on radically different criteria (coalescence vs. distribution of pairwise differences between sequences) indicates that there is a strong signal in the COI-5P data set. If any, the only shortcoming encountered in the course of that study was the erratic amplification of the COI-5P fragment that failed on 1/3 of the specimens at the first attempt, although repeated amplifications and/or re-extracting DNA from the same individual often solved this issue. The remarkable coincidence between the patterns revealed by our psbA and COI-5P sequence data indicates that the plastidial marker, which is easier to amplify than COI-5P, could be a useful alternative for the identification of maerl-forming species (but see  [54]  for a intrageneric study where the gene trees produced by COI-5P and by another plastidencoded gene, rbcL, were not always congruent).
Acknowledgments Many colleagues collected material:  Alfonso Ramos-Espla ,  Carlos Sangil ,  Daniel Pritchard ,  Estı ´baliz Berecı ´bar ,  Francis Bunker ,  Halldor Halldorsson ,  Jan Buedenbender ,  Jacques Grall ,  Jason M. Hall-Spencer ,  Jerome Jourde ,  Jan Rueness ,  Ken Collins ,  Louise Kregting ,  Meadhbh Moriarty ,  Miguel Rodrigues ,  Nick Kamenos ,  Niamh Nolan ,  Pedro Neves ,  Peter Wirtz ,  Rui Santos ,  Thomas Wilfried ,  Veronica Garcı ´a Redondo ,  Vivian Husa , and  Yann Fontana. We also thank  Jo Wilbraham  (BM) and  Nicolien Sol  (L) for assistance with obtaining type material on loan for molecular work.
This work was funded by  Ministerio de Ciencia e Innovacion of Spain  (grant  CTM2010-18787 , partially co-founded by  FEDER ,  Fondo Europeo de Desarrollo Regional) , and  Xunta de Galicia  (grant  10MMA103003PR ). Samples from  French Brittany  were collected with the support of a  European Community-Research Infrastructure Action  under the  FP7 ''Capacities'' Specific Programme  ( ASSEMBLE grant  agreement no. 227799 ). Several authors were supported by fellowships:  CP (Xunta de Galicia  Axudas aetapa predoutoral do Plan I2C-2011, and  Spain's Ministerio de Educacion Programa FPU-2010) ,  LL  ( Universidade da Corun ˜a Contratos Predoutorais-2012 ), and  VP (Xunta de Galicia Axudas posdoutorais do Plan   I2C-2012 ). VP acknowledges support for examining type material ( Action Transversale du Museum National d'Histoire Naturelle , project " Taxonomie moleculaire: DNA Barcode et gestion durable des collections ").
The other output is connected to a FC connectorized fiber that we fusion splice to Fibercore SM800 fiber. We then place the SM800 fiber in the fiber puller and record the intensity of light through the fiber at the output of the fiber puller using another DET36A for the duration of the pull. We record data on a DPO7054 Tektroniks oscilloscope in high resolution mode set to collect 10 7 samples. We normalize the signal through the fiber puller to the laser drift throughout the pull.
ACKNOWLEDGMENTS Work supported by  National Science Foundation of the USA  through the  Physics Frontier Center  at the  Joint Quantum Institute, Army Research Office Atomtronics MURI , and S. R. thanks the  Fulbright Foundation  for support. We acknowledge the support of the  Maryland NanoCenter  and its NispLab. We would like to thank  Fredrik Fatemi  and  Guy Beadie  for their major contributions to the higher-order mode studies and  Prof. A. Rauschenbeutel  for his support and interest in this project.
An additional 5 ml of whole blood from febrile patients was immediately incubated in an aerobic blood culture bottle (Pharmaceutical Factory No. 2, Vientiane, Lao PDR), sent to Phnom Penh in an insulated box (with an electronic temperature monitor), and incubated and monitored at 37uC, for 5 days. The patient's data and the specimens were anonymized on site. Clinical data forms were sent to CNM where translation and data entry were performed.
Electrophoregrams were visualized and analyzed with CEQ2000 genetic analysis system software (Beckman Coulter, Villepinte, France). Nucleotide sequences were compared to the P. falciparum 3D7 sequence (GenBank accession number AY282930), Leptospira interrogans 16sRNA sequence (GenBank accession number EU581713), Orientia tsutsugamushi 47 kDa sequence (GenBank accession number L11697) and Rickettsia sp. OmpB and GltA sequences (GenBank accession numbers EF219461 and AB444098). Plasma and throat swab samples were processed for RNA extraction using the QIamp Viral RNA Mini Kit (Qiagen, Hilden, Germany) on 200 ml of plasma and from 140 ml of throat swab-sample, according to the manufacturer's instructions. In-house multiplex Reverse-Transcriptase (RT) PCR assays were performed on plasma and throat swab RNA extracts, for detection of Dengue (PrM/E gene  [25] ) and Influenza-Virus (M gene  [26] ), respectively  [27].
Statistical Analysis Data were entered and verified using Microsoft Excel software and analyzed using XLSTAT (Addinsoft, France) and MedCalc (MedCalc 9. 1. 0. 1, Belgium). The Mann-Whitney U test or Kruskal-Wallis method were used for non-parametric compari-sons, and Student's t test or one-way analysis of variance for parametric comparisons. For categorical variables, Chi-squared or Fisher's exact tests were used to assess significant differences in proportions. Odd ratios (OR) and their 95% confidence intervals (CI) were measured to compare prevalence of pathogens between case and control groups. The Attributable Fraction among case (AFe) was assessed for each pathogen using the following formula: [(OR-1)/OR]6100. Hypothesis testing was made using risk differences, exact 95% confidence intervals, and p-values.
Accessory information such as a full blood cell count and other biomarkers could provide additional useful diagnostic clues that may help to refine decision-making. This first NMFI study conducted in Cambodia provides highly valuable information for the planning and design of further investigations. Further studies where district hospitals and HCs are compared for disease burden and diagnosis of severe infections should also be considered. Seasonality of fever cases as demonstrated in this study should also be considered to target resources and increase cost-effectiveness. Paired serum samples should be collected from all patients to define previous or recent exposure to pathogens and guide epidemiological studies. Based on the results of this study, future studies should also collect data on: (i) regional disease burden and seasonality of infectious diseases, (ii) clinical condition of patients and severity of disease (case fatality rates with and without treatment), and (iii) availability and level of health care facilities and services.
Other existing methods, based on meta-data feedback (e. g. , depth-budget  [4, 15] ) are not easy to read and lack deformation information. In this paper, we present a Dynamic Stereoscopic Previz (DSP) system which overcomes the above limitations. On the one hand, DSP allows a real-time, direct interaction in a game engine, which makes it suitable for use by directors, cinematographers and stereographers. In single user mode, DSP allows camera parameters to be recorded one by one, within a dedicated multi-track recording system. In multi-user mode, DSP allows camera parameters to be recorded from multiple devices. On the other hand, we propose a novel method for simulating a virtual projection room (Sec. 4) that allows seeing, not only a volume, but also the arrangement of the 3D elements of the scene as they will be perceived in the specified projection room.
Those tools do not allow to set different objects on the acquisition space, and see their relative position and deformation as they would be perceived in the projection room. In the area of 3D previz, a virtual environment allows to create simple computer-generated shots. Among existing previz tools, we can find different approaches depending on the target user. A first approach focuses in the ease of use of the creation of the 3D world, by providing big databases of presets for actors, decors, and cameras. FrameForge Previz studio  [12]  with its Stereo Edition is a commercially available previz tool allowing to easily plan stereoscopic shots  [5]. This environment is also able to handle dynamic shots. The user can configure the scene at different keyframes and the program will automatically create the animations.
REAL TIME CAMERA CONTROL DSP consists of python scripts and OpenGL shaders running in the Blender Game Engine, which is multiplatform (Linux, Windows and OsX), and makes it easy to create 3D models for the sets, characters and props required in a movie previsualization. Moreover, a large online community provides free access to a large database of online models and animations. An additional benefit of the Blender Game Engine is that a large majority of USB devices, e. g. , commercially available focus and aperture pullers, can be connected with the real-time OSC protocol  [14]. In our implementation we used a USB game-pad controller.
Search strategy and study selection We searched all controlled trials on disulfiram use with alcohol dependent patients using the PubMed database (last search date June 2012), EMBASE (last search date July 2012), the Cochrane Central Register (last search November 2012), and a manual search. The details of the search strategies can be found in Search Strategies S1. Three investigators (MS, PL, HJA) independently read the abstracts in order to select the publications of interest. Included in this study were original, randomized controlled trials (RCTs) comparing the efficacy of orally administered disulfiram to any control group. All studies included subjects with a diagnosis of alcohol abuse or dependence, whatever the classification system. In some studies, the primary inclusion criterion was cocaine dependence.
Data extraction The data extraction was performed by two independent investigators (MS, HJA). Discrepancies were confronted and a consensus was agreed upon. When possible, authors were contacted by e-mail or personally to retrieve missing data, with a special emphasis on the primary endpoint. We extracted the primary outcome as defined by the authors in their articles (Table  1 ). Additional variables were extracted for subgroup analysis: blind or open-label, with or without supervision, cocaine study or not, and type of control. We also included meta-regressions to explain heterogeneity (treatment duration, disulfiram dosage, and publication year, with a risk of bias score)  [28].
Data analysis Efficacy outcomes were analyzed by calculating the Hedge's g effect-size for each trial with the uncertainty of each result being expressed by their 95% confidence intervals (CI). An effect-size of 0. 2 to 0. 3 is thought to be a ''small'' effect, around 0. 5 a ''medium'' effect, and 0. 8 to infinity, a ''large'' effect  [28]. Effects were summarized using a random-effects model. The random-effects model was chosen because of the high heterogeneity between trial estimates in each meta-analysis. The underlying assumption of a random-effects model is that the true effect could vary between studies based on characteristics of the study population or intervention. In this case, for example, the primary outcomes may differ as a function of alcohol use disorder severity, intervention duration, comparator type, and associated psychosocial intervention intensity.
Included studies Systematic searches resulted in 178 references from PubMed, 42 from Embase, and 93 from the Cochrane Central Register. Of these 313 references, 100 were duplicates. A manual search resulted in 3 additional articles bringing the total to 216. After cross-referencing between investigators, 35 were then selected for a detailed review and analysis. From these, 23 were chosen for inclusion in the meta-analysis. In five of these studies, additional   data were needed on the primary outcome of a subset of the participants. We obtained additional data from the authors in four of these studies. Because we did not obtain a response from the fifth author  [30] , we were unable to include their trial. The final selection procedure thus allowed us to analyze 22 studies (Figure  1 ).
Disulfiram also showed its efficacy as compared to a control condition in the studies primarily enrolling alcoholics. The cocaine studies comprised 152 subjects from three studies. We did not include the results of three other cocaine studies because of their blind design  [10, 14, 26]. The subgroup condition by control group categories showed efficacy of disulfiram when compared to (1) the no disulfiram condition (eight studies), (  2 ) naltrexone (nine studies), and (3) acamprosate (three studies). These three studies had a combined total of 403 subjects. Other evidence outside of this meta-analysis in favor of disulfiram compared to acamprosate comes from retrospective data from 2002-2007 with 353 alcoholic patients  [60]. In the present study, disulfiram was also superior to topiramate and showed no difference with GHB in these single trial categories, thus providing less useful information as only one study was available.
Data collection Questionnaires. At the enrollment visit, HIM study participants completed a comprehensive self-administered questionnaire with information on demographics (age, race, education, and marital status), socioeconomic status, medical history, smoking status, alcohol consumption, and sexual history. Additional questions on risk factors for skin cancer (skin's reaction to season's first sun exposure, history of blistering sunburn, etc. ) were added to the cutaneous HPV sub-study. Eyebrow hairs and swabs of normal skin. Although, in the parent HIM study, swabs from both sun exposed and unexposed skin were collected, only swabs from sun-exposed skin were used for HPV DNA measurement in the present sub-study due to limited funding. A 565 cm area of normal, sun exposed skin, from the top of forearm, was pre-wetted (0.
). Variables that were significantly associated with b HPV prevalence in an age-adjusted model were further evaluated after stratification by b HPV species. Logistic regression was conducted to estimate the association between risk factors and incidence as well as persistence of HPV infection, after adjusting for age. Logistic regression analyses were conducted separately for HPV infection in eyebrow hairs and normal skin swabs. Kaplan-Meier curves were derived for incidence and clearance of any HPV infection. An alpha level of 0. 05 was considered statistically significant. Adjustment for multiple comparisons was not conducted. All analyses were conducted using SAS software, version 9. 3 (SAS Institute Inc. , Cary, NC, USA) and R software, version 2. 13. 1.
Flags S type thermocouple + / -1 • C in the range 0-1000 • C and + /-[1+0. 003(T-1100)] in the range 1100-1600 • C. Two different methods were used to measure the total strain of the sample. On the one hand, an optical micrometer was used to follow the displacement of flags welded on the sample as illustrated in Fig. 5. On the other hand, a strain measurement method based on markers tracking has been implemented. As it can be observed in Fig. 6 , those markers are small wires welded on the sample surface which generate a sufficient optical contrast during the tests. To track the markers position, a python script developed at the Institut Pprime was used to locate the  markers and to find their centroid position from pictures taken with a camera. 20001-p. 2 The strength applied to the sample was also continuously measured using a 5 kN load cell.
ASMET test The results obtained during the ASMET test are presented in Fig. 14. The evolution of plastic strain is here calculated from total strain measured with optical markers tracking method. The absence of strain measurement between 75 and 100 h is due to a computer data overflow. Moreover, strain measurements was not possible during the overheatings, due to a too large radiation of the sample, avoiding any possibility of markers localization. The optical markers tracking method seemed however to give good results during the 75 first hours, with a good correspondence with a mechanical micrometer measurement after sample removal from the testing section. Indeed, the sample had to be removed from the test bench because of a thermocouple failure.
Comparison with Polystar model A new crystal plasticity model called Polystar  [3, 4]  has been used to simulate the two previous tests. Polystar was particularly developed for complex non-isothermal loadings. This model takes into account microstructural changes which can occur in the material such as γ precipitation/dissolution and dislocation recovery processes induced by the temperature history seen by the material, especially close to the γ solvus temperature  [7]. The model was calibrated using isothermal and nonisothermal creep tests performed on MC2 samples having a stress axis close to the [001] crystallographic direction (deviation less than 8 degrees). The real testing temperatures and stresses recorded during the 150 h and ASMET tests have been used as input data for the simulation.