dataesr/scientific-paragraphs-categorization huggingface dataset:
Wide-baseline matching In this section we apply our models to the wide-baseline stereo dataset of  [25] , which consists of two multi-view sets of high-resolution images with ground truth depth maps. This allows us to further evaluate the generality of our models across different datasets, and to study how robust the descriptors are against perspective transformations. We pit our descriptor against SIFT, Daisy [27] and VGG  [23]. We consider the 'fountain' set, which contains much wider baselines in terms of angular variation and provides a harder challenge. Fig. 7  (top) shows the images used-we match '3' (the rightmost view) against '4'-'8'. We sample 1000 (non-occluded) points randomly and use the ground truth depth maps to determine their correspondence over the opposite camera. We match every point in one camera with every possible correspondence, and compute PR curves.
The difference in viewpoint across increasing baselines creates perpective transformations, which include scaling, rotation, and partial occlusions. We explore different patch sizes, from 8×8 up to 64×64. Note that our models were trained with patches of size 64×64, and we upscale the patches if required; we expect that better performance can be obtained by training filters of a size commensurate to the patch. The results are shown in Tables  6 7 8 9 10 ; the top perfomer for every setting is highlighted in bold, and the top performer for a given baseline is marked with †. As expected, large patches are more informative across narrow baselines, whereas small patches perform better across wide baselines. Our descriptors outperform the baselines in just about every scenario, proving that they generalize well across datasets.
Deformation and Varying Illumination Dataset Lastly, we evaluate our descriptors on a recent, publicly available dataset featuring challenging non-rigid deformations and very severe illumination changes  [22]. The dataset consists of a series of photographs of 12 deformable ob-     [22]. We evaluate over three different settings, corresponding to deformation changes only (Def. ), illumination changes only (Ill. ), and both simultaneously (Def. +Ill. ). We show the mean accuracy of descriptor matches and highlight the top-performing descriptor for each of setting, in bold. (Def. +Ill. ) settings. This is despite having to upscale the image patches from 41×41 pixels to 64×64 pixels, the fact that the image patches are cropped to be circular while our descriptor relies on square patches, and that we trained our descriptors on datasets of rigid, non-deformable objects.
Conclusions We use Siamese networks to train deep convolutional models for the extraction of image descriptors. Training such models involves small patches, which constraints the network size and discriminative power, and large datasets, which makes exhaustive computations intractable. In this paper we introduce a novel training scheme, based on mining of both positive and negative correspondences, and obtain large performance gains in patch retrieval. Our models generalize well across different datasets and applications, including wide-baseline matching, non-rigid deformations and extreme illumination changes. They can be used as drop-in replacement for traditional descriptors, e. g. SIFT, and are publicly available.
Stereo matching, baseline '3' vs'8'. jects,suchasclothesandnewspapers, which are subjected to four different deformation levels and four different illumination levels, i. e. 16 images per object, for a total of 192 grayscale 640×480 images. Feature points, extracted with Difference-of-Gaussians detectors, are provided for each image. Some examples of the kind of transformations featured in this dataset are shown in Fig. 7(bottom). We pit our descriptor against DaLI, SIFT, Daisy and the VGG descriptor, and show the results in Table11. We evaluate our model trained on three different splits of the MVS dataset, and observe that they all obtain similar performance. We outperform the current state of the art in the deformation (Def. ) and deformation with illumination.
* First two authors contributed equally. This work was partly funded by the  Spanish MINECO  project  RobInstruct   TIN2014-58178-R , by the  ERA-Net Chistera project ViSen   PCIN-2013-047 , by  EU  projects  AEROARMS H2020-ICT-2014-1-644271 ,  ISUP-PORT H2020-ICT-2014-1-643666  and  MOBOT FP7-ICT-2011-600796 , and by the  ERC  project  MicroNano. ' 3' '4' '5' '6' '7' '8 '.
A number of natural history studies and placebo arms from previous trials have shown a decline in the 6MWT over time. However, due to the heterogeneity in the DMD population there is variability across the various studies to date. There are currently a number of natural history studies ongoing. It is hoped data from these studies collected over the coming years will be collated and used as reference information for future studies, particularly those where the study population would be too small for a properly powered placebo-controlled trial. Extrapolating to young patients is an important consideration as the ultimate goal of many therapeutic approaches is dystrophin restoration, which relies on the muscle quality at treatment initiation. As such restoring dystrophin in the very young, where muscle quality is still relatively good, would be expected to give the best opportunity to prevent muscle damage and slow down disease progression.
2 ). Additional data have been collected on cardiac, respiratory, gastrointestinal, behavioural and other organ functions. Both DMD and BMD are complex multisystem diseases that have only fairly recently attracted the attention of pharmaceutical companies. Despite the fact that there is still no licensed drug with a specific indication for DMD and BMD and that the results from recent interventional trials have been somewhat disappointing, the improved understanding of the natural history of dystrophin deficiency and the wealth of the recently collected outcome measure data forms a very good foundation to inform new trials and drug development programmes. Linking positive findings of clinical trials to novel biomarkers such as those derived from omics technologies and MRI/MRS should both reduce the future need for invasive monitoring and also allow investigators to assess response in smaller cohorts of DMD patients, which will be essential when experimental approaches such as exon skipping move to rarer exons for which large studies will never be feasible.
Acknowledgements We would like to express our thanks to the  Muscular Dystrophy Campaign , the  Parent Project Muscular Dystrophy , the  United Parent Projects Muscular Dystrophy , the  AFM Telethon  and the  BMBS COST Action BM1207  for kindly funding the workshop, which was held at the  Wellcome Trust in London. Thanks also go to the secretariat of the  TREAT-NMD Alliance at Newcastle University  for organising the meeting.
Invisible Higgs Decays If the lightest LSP neutralino has a mass M χ < M h /2, then the h → χχ decay channel is kinematically open and the Higgs boson may acquire a non-zero invisible width. However, since the hχχ coupling also controls the χp scattering cross section and may contribute to the neutralino annihilation cross section there is a correlation between the rate of h → χχ, the scattering cross section and the neutralino relic density, where the current bounds place some non-trivial constraints. Figure  3  shows this correlation. SUSY points with neutralino relic density compatible with that extracted from the analysis of CMB data may have a large Higgs branching fraction into neutralino pair, even larger than the limit already obtained by the analysis of the Higgs properties at the LHC.
One-three E. crystallarophias, five C. acutus or five M. gerlachei were placed in separate, triplicate chambers for each species and incubated for 6-12 hours. After the incubation was terminated, the fecal pellets collected at the bottom of the jars were counted, photographed digitally, and preserved at -80°C for future molecular analyses. ImageJ Software was used to measure pellet length and width to calculate volumes of the fecal pellets based on the volumes of ovoid and cylinder shapes and converted into carbon values as measured in  (Gleiber et al. , 2012). We calculated potential POC fluxes for target species from these measurements and MOCNESS tows at ASPIRE sampling stations 13, 25, 35, 50 and 57 (Figure  1 ) for depth-integrated zooplankton abundance data to 150 m. Flux values from the sediment trap covering the period of zooplankton sampling were used for this comparison.
Other measurements and observations A number of other quantities were used in our analysis of particle flux in the Amundsen Sea Polynya, as described briefly here. Details of the measurements and derivations are given in other papers in this Special Feature, as cited. Net primary production rates were measured by 24-hour shipboard incubations of seawater samples with 14 C-bicarbonate. Net community production and export, were derived from changes in nutrient and carbon inventories  (Yager et al. , 2014). Bacterial production and community respiration rates, measured using 3 H-leucine incorporation and CO 2 production during 24-48 hour dark incubations, were obtained from  Williams et al. (2015). ASP sediment trap data are available at the BCO-DMO website (BCO-DMO ASPIRE site, http://www. bco-dmo.
org/project/2132). Palmer LTER data are available at: (http://oceaninformatics. ucsd. edu/datazoo/data/pallter/datasets; Dataset number 26, "Offshore sediment trap fluxes". In the results and discussion below, we define the particulate carbon flux departing the upper 100 m as the export flux to discriminate it from that captured by sediment traps at 350 m, termed as the trap flux, when needed for clarity.
Seasonality and evolution of the annual flux events Particle flux in Antarctic waters, especially in the sea ice zone, is emphatically seasonal  (Fischer et al. , 1988). Ducklow et al. (2008) , using the long-term  (1993) (1994) (1995) (1996) (1997) (1998) (1999) (2000) (2001) (2002) (2003) (2004) (2005) (2006) (2007)  WAP dataset, showed that on average 85% of the annual particle flux was contained in the annual flux peaks. "Peaks" were defined as periods when the flux exceeded 0. 2 mmol C m -2 d -1 , a criterion that resulted in long 'tails' on the flux profiles. For the ASP, this low threshold would place the entire year in the peak, so we used a more stringent value of 0. 8 mmol C m -2 d -1 , which makes the peak events shorter. Even so, the average peak in the LTER dataset  contributed 59% of the annual flux in just 52 days, or 14% of the year, a 4.
Acknowledgments We acknowledge the following individuals and organizations for assistance in our study: the captains, officers and crews of  RVIB NB Palmer  ( NBP10-05 ) and  RVIB Araon ; the  Korean Polar Research Institute (KOPRI) ;  P. Abrahamson  ( UK-BAS ) and  R. Guerrero  for able support deploying (NBP) and recovering ( KOPRI, Araon ) our mooring;  Raytheon Polar Services  for science support during the entire  ASPIRE  project; and  M. Conte  and  J. C. Weber  ( MBL Ecosystems Center ) for help with sample analysis. A. Bausch  and  J-E. Tesdal  ( LDEO ) recovered the  WAP Chl data. B. Hönisch (LDEO)  kindly loaned her dissecting microscope and digital camera for Figure 7. Thanks also to all our colleagues in ASPIRE for fruitful and stimulating discussion and support throughout the project.
Acknowledgements This work has been partially financially supported by  Laboratory of Excellency 'GaNeX' and 'NanoSaclay' , by  ANR-14-CE26-0020-01  project 'PLATOFIL' and by  EU ERC  project " NanoHarvest " (grant no. 639052 ). The device processing has been performed at  CTU-IEF-Minerve technological platform , member of the  Renatech RTB network.
Micromonas Clades Distinguished by Cultured Isolates and Environmental Clones The first goal of our study was to evaluate the presence and distribution of IEs in Clade D isolates apart from CCMP1545 (representing the species M. pusilla), as well as in other Micromonas clades. Because this effort relies on robust clade discrimination, Micromonas isolates were analyzed using new and existing 18S rRNA gene data from cultured strains and environmental clone libraries. The phylogenetic reconstruction established the existence of seven clades (fig. 1a ) designated here largely according to a previously established lettered naming system for cultured clades and Clade -. IV for the uncultured clade  (Slapeta et al. 2006; Worden 2006 ) (table 1, supplementary table S1, Supplementary Material online).
In the 18S rRNA gene phylogeny the key node separating Micromonas Clades A and B did not acquire bootstrap support (fig. 1a ); however, these clades were distinguished using a concatenation of four protein-encoding genes (supplementary fig. S1 , Supplementary Material online, see below). Different from prior phylogenies, Clade E members formed two distinct clades due to incorporation of new data (fig. 1a  and supplementary fig. S1 , Supplementary Material online). We termed these Clades E1 and E2, with the latter containing the Arctic isolate CCMP2099. We next evaluated prasinophyte orthologs of four genes carrying IEs in CCMP1545. The selected genes were   1a ). The genes encode a putative Calcium ATPase (hereafter the gene is referred to as ATPase), a putative NADH dehydrogenase [ubiquinone] flavoprotein 1 (hereafter Dehydrogenase), Actin, and an ATP-binding cassette transporter (hereafter Transporter).
PCR primers were designed against available genome sequenced prasinophytes to amplify gene regions spanning one or more known IE in CCMP1545 (supplementary table S2, Supplementary Material online). Micromonas clade representatives from each cultured clade were then selected, grown, and these regions examined using PCR-based sequence data (table  1 ). Micromonas Clade D representative CCMP490, isolated in the western North Atlantic, had IEs at the same insertion positions and phases as in the CCMP1545 orthologs (fig. 1b-e ). Identities for IEs at homologous positions were 100% and 99% for the two Actin IE1s and 100% (IE2), 98% (IE1) and 97% (IE3) for those in the ATPase, Transporter and Dehydrogenase, respectively. Three of these were phase-0 (i. e. , introns located between two codons), whereas the 5 0 -most IE in the Actin gene fragment was phase-1 and the Transporter IE was phase-2.
Thus, the newly identified CCMP2099 introns do not appear to be similar to IEs in other Micromonas clades with sequenced genomes. Given the lack of additional genome data, it remained unclear whether the new introns were present in other CCMP2099 genes, as expected of an IE family. Therefore, environmental data were searched and multiple copies of the shorter CCMP2099 Transporter intronic sequences (type 1) were recovered in metagenomes from the Antarctic (Ace Lake, Southern Ocean, Ross Sea; fig. 2a ). The detected sequences interrupted multiple different protein-encoding genes according to BLASTx analyses of the metagenomic reads against NCBI's nr database. Those with known functions included an autophagocytosis-associated protein, a putative aminopeptidase, transcriptional repressors, and an early lightinduced protein (ELIP).
1997 ) evaluation against NCBI's nonredundant database and an in-house database of publically available genomes. CCMP1545 and CCMP490 ATPase Clusters O and P (one clone per strain) each had a one nucleotide difference from the CCMP1545 genome sequence  (Worden et al. 2009 ) and PCR-derived sequences from this study (across the entire amplicon, including IE sequence); these were considered PCR artifacts and not analyzed further. CCMP1764 DNA was sequenced using the 454-FLX platform. Clustering, RSI Identities, and Phylogenetics Genomic DNA and cDNA sequences were aligned using ClustalW, or manually in DNAStar or Bioedit. Clustering of environmental clones was performed using BLASTClust  (Altschul et al. 1990 ) with required coverage specified by both a similarity threshold of 100% and minimum length coverage of 1.
Acknowledgments The authors thank  H. M. Wilcox ,  E. Demir-Hilton , and  D. McRose  for assistance. They are grateful to  G. Dick  and  S. Jain  for blasting IEs against their deep sea metagenomes (negative results) and also to  J. Sarmiento  and  L. Talley  for kindly discussing NADW formation and movement with us. Sequences generated in this study have been deposited in NCBI database under accessions  KR089059 - KR089061  for 18S rRNA gene sequences from Micromonas RCC434, RCC472, and  RCC1614 ;  KR089139-KR089205  for the four genes studied using PCR amplification; representative (nonredundant) sequences KR089062-KR089138 (ATPase) and  KR089206-KR089345  (Actin) from environmental clone libraries from the  Eastern Pacific ;  KR152644-KR152649  for the 3,000-m  NADW Transporter clones ; and genomic DNA 454-FLX reads from  CCMP1764  have been deposited in CAMERA under project  CAM_PROJ_CCMP1764.
Materials and methods Materials In this study we used a-PVA-SPION which were synthesized and characterized following a protocol previously described. 51 he mean diameter of the magnetic cores (d core in nm) of the a-PVA-SPION was determined by counting 400 diameters observed in transmission electron microscopy (TEM; CM12 from Philips Electron Optics, Zürich, Switzerland). Hydrodynamic size (d H in nm) and Zeta potential (Z potential in mV) were measured at around pH 7 by dynamic laser scattering using a Malvern NanoZS (Nanosizer 7. 2 software) using the theoretical refractive index of 2. 42 of magnetite. 57 The saturation magnetization (Sat mag in emu/g) was obtained from freeze dried powder of SPION before PVA coatings using a superconducting quantum interference device. 58 tibodies and reagents Lipopolysaccharide (LPS), lectin from Phaseolus vulgaris (PHA), Brefeldin A, Saponin, and carboxyfluorescein diacetate N-succinimidyl ester (CFSE) were from Sigma-Aldrich Co.
The acquired data were analyzed using FlowJo 7. 6. 1 software. For the investigation of survival of positive cells for the surface markers (CD3, CD14, CD19 or CD15), Annexin V-PE/7-AAD staining was performed according to the manufacturer's instructions after cell washing (to determine apoptosis). After data acquisition by flow cytometry, these populations were analyzed for the percentage of Annexin V (apoptotic) or 7-AAD (dead) positive cells.
Whole blood intracellular staining After extracellular antibody staining, cells were fixed with 2% paraformaldehyde and subsequently cell membranes were permeabilized by washing twice with 0. 5% Saponin-PBA (PBS/BSA/Acid). Non-specific binding was blocked with human immunoglobulin (5 mg/mL) for 10 minutes at RT. The washed (Saponin-PBA) cell pellets were resuspended in 10 µL of undiluted anti-human-IL1β-PE antibody and incubated for 15 minutes at RT in the dark. After two final washing steps cells were analyzed by flow cytometry using the MACSQuant analyzer equipped with plate MACSQuant MiniSampler. The acquired data were analyzed using FlowJo 7. 6. 1 software, where positive cells for the according surface marker (CD3, CD14, CD19 or CD15) were selected and these populations were analyzed for the percentage and number of IL1β positive cells.
TeM analysis Human monocytes (2×10 6 cells/mL) and MDMs (1×10 6 cells/mL) were incubated for 24 hours with PVA-SPION (1,000 µg/mL) or left untreated. Cells were prepared for TEM analysis as previously described. 60 Ultrathin sections were analyzed using routine TEM (EM 906; Carl Zeiss AG Oberkochern, Germany) techniques; micrographs were prepared and further processed using Adobe Photoshop CS software.
statistical analysis Statistical tests for the flow cytometry were performed using Graph Pad Prism Software. Data are presented as box and whiskers, whiskers from minimum to maximum or mean with standard deviation of at least four independent experiments. Multiple comparisons were analyzed by one-way or two-way analysis of variance (ANOVA) as indicated with Bonferroni's multiple comparison post hoc tests for normally distributed data. Probability values of P0. 05 were considered to be statistically significant (***P0. 001; **P0. 01; *P0. 05).
Acknowledgments We would like to thank  Manuela Jakstadt  for outstanding technical assistance,  Barbara Szostak  and  Heide Boeth  for sample collection and archiving,  Sebastian Bachmann  and  Petra Schrade  for their guidance in TEM analysis (all  Charité Berlin ) and  Marie-Gabrielle Beuzelin  ( EPFL Switzerland ) and  Usawadee Sakulkhu  for their support.
Pharmacological treatment Bisphosphonates and teriparatide have been assessed in prevention and treatment of GIOP. There are a number of issues regarding their efficacy. Fracture incidence has not been a primary end point of any study (the end point being BMD), the duration of the studies is low (1 year on average) and the number of men and premenopausal women in these studies is low. Thus the efficacy on fractures is mainly based on bridging data between the shortterm change in BMD in patients with GCs, and the longterm change in BMD and reduction of fracture risk in patients with postmenopausal osteoporosis. Bisphosphonates are the more popular antiosteoporotic drugs. Alendronate (oral 5 or 10 mg once daily, or 70 mg once weekly), risedronate (oral 5 mg daily or 35 mg one weekly) and zoledronate (intravenous infusion 5 mg once yearly) prevent bone loss at the spine and hip in patients initiating GCs, and increase BMD in patients on long-term GCs.
The use of administrative databases offers the opportunity to assess a huge number of patients, taking into account the methodological issues related to these studies (retrospective design, lack of details in patient characteristics, absence of confirmation of the diagnosis of fractures, etc). Two well-designed studies with such an approach, suggest the efficacy of bisphosphonates in reducing fractures and a better efficacy when the antiosteoporosis medication is initiating within 90 days of chronic GC use, reaching a 48% reduction rate of fracture. 72 73 However, not all studies support these conclusions, and there is still a disconnect between GIOP care and improvement of outcomes. 74 here is so far no study of denosumab on GIOP. In a subgroup analysis of a 12-month study of patients with RA (still active although they were receiving methotrexate) treated with denosumab, BMD increases were similar in patients with and without GCs.
The contents of the Code of Conduct and its purpose The Code of Conduct consists of four Chapters (for the text of BNE's Code of Conduct for brain banking see supplementary material). The first Chapter sets out the objectives, general principles and the scope of the Code of Conduct, as well as defining key terminology (indicated in the text by Capital Letters). The second Chapter deals with different aspects of Material procurement (e. g. Informed Consent, Authorization, Incompetent persons, Autopsy). The third Chapter states the principles that should govern the processing of the Material (e. g. financial aspects, confidentiality, data protection measures). The fourth Chapter is concerned with distribution and the use of the Material for research. It also contains articles on research results and guidelines on how to deal with information on hereditary diseases.
The Code of Conduct for brain banking states the principles that should govern brain banking in general. Detailed regulations concerning the local governance of a Brain Bank are to be laid down in a different document such as a Brain Bank Regulations, which should be in concordance with the principles described in the code of conduct. Furthermore to support the daily practice of the Brain Bank documents such as a Material Transfer Agreements, Confidentiality Agreements, Tissue application forms and Personal Data Protection measures should be in place. Examples of these documents are provided on the BNE website (http://www. brainnet-europe. org/index. php?option=com_content&view=article&id=103&Itemid= 103). The scope of the Code of Conduct could be widened to cover all post-mortem tissue donations for research purposes, whether of CNS origin or not (for instance peripheral lymph nodes or dorsal root ganglia), since the same principles apply.