dataesr/scientific-paragraphs-categorization huggingface dataset:
Not all Species Benefit Equally from Conservation Actions The dominance of type D species (targeted threats, collateral conservation) in our data set was not surprising considering that ungulates are a prime target for hunters and therefore subject to over-exploitation. It would perhaps be expected that the overall impact of conservation on such species would not be very high given that, in general, the right threats are not being addressed and species only benefit in a collateral sense from conservation (e. g. , through habitat protection or anti-poaching efforts targeting type A species). However, our results (Fig. 3 ) suggest that non-targeted conservation can make a big difference. Many African duikers (tribe Cephalophini), for example, although able to adapt to disturbed habitats, are subject to high rates of off-take for bushmeat markets (through cable snares or with shotguns at night  [Newing 2001] ).
3 ) and ungulates are dominated by species types that are unlikely to be representative of broader mammalian diversity. Whereas type D species (targeted threats, collateral conservation actions) were the most common in our data set, it is likely that most mammal groups are dominated by type B species (collateral threats, collateral conservation). On one hand, habitat loss is the dominant threat among mammals  (Schipper et al. 2008) , and most species are collaterally covered by existing protected areas  (Rodrigues et al. 2004 ). On the other hand, species in the most speciose mammalian orders (e. g. , Chiroptera, Erinaceomorpha, Soricomorpha, Rodentia) are (with a few exceptions) neither specifically persecuted nor specifically targeted by conservation actions and so most are likely to be type B.
Acknowledgments We are grateful to the following individuals for reviewing data and providing expert inputs into the determination of the counterfactual red-list categories (although possible errors in our estimation remain our own):  K. Aune ,  R. Baldi ,  J. Burton ,  B. Franklin ,  B. Gonzalez ,  S. Gonzalez ,  R. Harris ,  S. Hedges ,  C. Jackson ,  G. Lichtenstein ,  N. Maddison ,  E. Meijaard , the late  W. Oliver , and  R. Sarno. We remain grateful to the many hundreds of experts contained in the African Rhino, Antelope,  Asian Rhino ,  Asian Wild Cattle, Bison, Caprinae, Deer, Equid, Giraffe and Okapi, Hippo, Peccary, South American Camelid, Tapir , and  Wild Pig Specialist Groups of the IUCN Species Survival Commission , all of whom who devote their knowledge, intellect, and time voluntarily to the compilation of data on the IUCN Red List.
Sample and data collection Rainfall, stream and overland flow waters were sampled during a flood on 23 May 2012. Rainfall intensity (I ) was monitored with an automatic weather station (elevation: 536 m a. s. l. ; Fig. 1 ) and stream discharge was calculated from water level continuous records and rating curves. Estimates of event water discharge (EWD), defined here as the total water volume exported from each sub-catchment during the event minus the base flow discharge, were calculated by adding sequential water volumes corresponding to the average discharge between two successive water level measurements. Specific runoff (SR, in mm) was obtained by dividing EWD by the corresponding sub-catchment area  (Chow et al. , 1988). Rainfall was sampled with three cumulative collectors located: in the village near the confluence between the Houay Pano and Houay Xon streams, near a teak plantation on the hillslopes located just upstream of the village and within the upstream Houay Pano catchment (Fig.
On average, 97 ± 3 % of the total organic matter recovered during the flood was particulate. Our results are therefore very likely to reflect the composition and behaviour of particle-bound organic matter, as the dissolved fraction was negligible. To expand the topsoil data set available for the catchment  (Huon et al. , 2013) , additional soil cores were collected on hillslopes connected to the Houay Pano stream and the Houay Xon River (Fig. 1 ) in May and December 2012. Several gully (n = 5) and riverbank (n = 6) samples were also collected in December 2012 to document the characteristics of the potential subsurface sources of sediment to the river. Cumulated suspended sediment yields (SSY) were calculated at each station by summing the total suspended sediment (TSS) exports between successive samples.
Acknowledgements. The authors would like to thank the  Lao NAFRI (National Agriculture and Forestry Research Institute in Vientiane)  and the  MSEC  project ( Multi-Scale Environment Changes ) for their support. They are also grateful to  Keo Oudone Latsachack ,  Bounsamai Soulileuth  and  Chanthamousone Thammahacksa  for their help in the field, to  Véronique Vaury  ( iEES Paris ) for organic matter composition measurements, and to  Patricia Richard  ( iEES Thiverval-Grignon ) for δ 18 O measurements of water samples. Elian Gourdin  received a PhD fellowship from  Paris-Sud University, Orsay, France. This work received financial support from the  French CNRS EC2CO/BIOHEFECT program  ( Belcrue  project). The authors are grateful for the constructive comments of two anonymous referees who helped improve a previous draft of the manuscript.
The serum sample was subsequently tested for the presence of hantavirus RNA. The assay was negative using a real-time reverse transcriptionpolymerase chain reaction (RT-PCR) targeting part of the small (S) genome segment of PUUV, but positive using a pan-hantavirus nested RT-PCR targeting part of the large (L) segment, and a Arvicolinae-borne hantavirus nested RT-PCR targeting part of the S segment, PUUV being used as positive control  [1] [2] [3]. Amplicons were sequenced and an analysis by basic local alignment search tool indicated that both sequences were very similar to those of Tula virus (TULV) strains, especially to that of the south-east German rodent strain GER/152/Arv (GenBank accession numbers: HQ728459 and HQ697350). Compared to this strain, the patient strain had 89. 5% and 90.
L (n = 347 nt) and S segments (n=307 nt). This corresponded, at the amino acid (aa) level, to 99. 1% (n=115) and 100% (n=102) aa identity (partial L sequence deposited in GenBank database under accession number: KU297981). The complete S coding DNA sequence (CDS) (GenBank accession number: KT946591) was recovered via three nested RT-PCRs using primers reported elsewhere  [4] , producing three overlapping amplicons. The aa sequence (n=429 aa) was similar to those of TULV strains reported in GenBank (divergence 0. 2 to 4. 9%), and presented highest similarity at the nt and aa levels with the sequence of the rodent Bavarian German strain g20 (GenBank accession number: AF164093). Using molecular evolutionary genetics analysis (MEGA) version 5. 1  [5] , a phylogenetic analysis based on the S segment coding domain sequence confirmed that the strain -named CHEVRU/Hu/FRA/2015/15.
00453belonged to TULV species, and was most closely related to the g20 south-east German strain  (Figure). Sequence comparison was also performed with a reduction of the S CDS dataset to 297 nt (positions 865-1,161 according to the numbering of our sequence) in order to include the only two TULV partial sequences reported from France and detected in Microtus arvalis  [6]. Divergence at the aa level was 4. 0% with these two sequences (compared to only 1. 0% with the g20 sequence). The phylogenetic analysis was also performed with this dataset. The French human and animal strains were not closely related but the statistical support was low (data not shown).
It should be noted that Paganin's algorithm can potentially lead to a small sacrifice in spatial resolution, which could be overcome by the application of a more sophisticated phase retrieval method  29. CT reconstruction was performed with FBP and in "half tomography" mode since the sample slightly moved out of the field of view during its rotation  30. Images were processed using the ESRF in-house software PyHST, and analyzed and displayed with ImageJ 31 and 3DSlicer. Small intestine specimens were imaged with an "analyzer-based" PC-CT setup implemented at the SYRMEP (SYnchrotron Radiation for Medical Physics) beamline of the Elettra synchrotron (Trieste, Italy). A schematic of the method is shown in Fig. 1(b) : it comprises a (quasi) parallel synchrotron beam, an object rotation stage, a double crystal analyzer and a pixelated detector.
Since no phase retrieval procedure has been applied, CT images showed attenuation in addition to "edge contrast" due to refraction within the sample. Moreover, some propagation-based phase contrast may have been present in the images due to uni-directional sensitivity of crystal analyzer and the non-negligible propagation distance (90 cm) between the sample and the detector. Images were processed using the PITRE software package  34  , and analyzed and displayed in ImageJ and OsiriX. Laboratory-based PC-CT. One esophagus specimen was also imaged using an "edge illumination" PC-CT setup implemented with a commercially available x-ray tube in the radiation physics laboratory at University College London. Although this PC-CT implementation was initially developed at synchrotrons  35, 36  , it does not rely on beam coherence  37, 38  ; hence, its working principle is not violated when implemented with x-ray tubes with relatively large focal spots.
If the pixel level resolution is sufficient, a significantly reduced exposure time can be expected. We would also like to highlight that the total exposure could be reduced by an additional factor of two through the use of a recently published phase retrieval procedure which is based on the acquisition of one image at each angle only  44. Following phase retrieval  39  , CT reconstruction was performed with FBP. A specialized filter function was used to account for the differential nature of edge illumination images, converting the "edge contrast" that is due to refraction into phase-based area contrast  45. A MATLAB routine was written to perform the image processing. Images were analyzed and displayed using ImageJ and 3DSlicer.
Results Results are presented and discussed individually for each organ (esophagus, lung, liver and small intestine). Esophagus. Rabbit esophagi were successfully decellularized after three cycles of DET, as evident by histology and DNA quantification (data not shown). Images of an esophageal scaffold acquired with synchrotron-based PC-CT are shown in Fig. 2(a, b ) in form of a transverse cross section through the reconstructed volume and a three-dimensional rendering, respectively. The corresponding images acquired with laboratory-based PC-CT are shown in Fig. 2(c, d ). All images revealed intact scaffold microarchitecture, allowing the identification of all layers of the native tissue, namely: mucosa, sub-mucosa, muscularis propria (MP), and adventitia. Intact blood vessels were detected in the submucosa and a clear demarcation was seen between the inner circular and outer longitudinal layers of the MP.
Acknowledgements This work was supported by the  UK Engineering and Physical Sciences Research Council  (Grant Nos. EP/ L001381/1  and  EP/I021884/1 ). PCD and ME are supported by  Marie   Curie Career Integration Grant  Nos. PCIG12-GA-2012-333990  and  PCIG12-GA-2012-334056  within the  Seventh Framework Programme  of the  European Union. The authors also acknowledge support by grants from the  Medical Research Council , the  Royal College of Surgeons of England , the  Sparks Children Medical Charity , the  British Foreign Office for the UK/USA Stem Cell Collaboration Award and the Mittal Research Fund. PDC is supported by  Great Ormond Street Hospital Children's Charity. We would also like to thank the  Royal Society/Wolfson Foundation  for the tissue engineering laboratory refurbishment grant obtained for the  Pediatric Surgery Department at University College London (UCL) Institute of Child Health.
The apo form of vDHBPS (E-Apo) crystals were grown in 0. 2 M Na 2 HPO 4 , pH 9. 1 and 20% PEG 3350, and phosphate-bound (E-PO 4 ) crystals were grown in 0. 2 M NaH 2 PO 4 , pH 4. 5 and 20% PEG 3350. The Ru5P and 4PEH complex crystals were obtained by mixing vDHBPS with 10 mM Ru5P (E-Ru5P) and 4PEH (E-4PEH) separately and incubated for 30 min at 20 °C. The crystals were grown in 0. 2 M Na 2 HPO 4 , pH 9. 1 and 20% PEG 3350. Finally, the E-Ru5P-Zn 2ϩ and E-4PEH-Zn 2ϩ complex crystals were obtained by soaking the E-Ru5P and E-4PEH crystals with 100 mM zinc chloride (ZnCl 2 ) for 12 h at 20 °C. Data Collection and Processing-The x-ray diffraction data set for the E-PO 4 complex crystal was collected at 100 K using synchrotron radiation at BM14 beamline (European Synchrotron Radiation Facility, Grenoble, France) equipped with a MAR Mosaic charge-coupled device detector.
The diffraction data sets for all other crystals (E-Apo, E-Ru5P, E-Ru5P-Zn 2ϩ , E-4PEH, and E-4PEH-Zn 2ϩ ) were collected using a MAR345 image plate detector (MAR Research, Germany) mounted on a MicroMax-007HF (Rigaku) rotating anode x-ray generator operated at 40 kV and 30 mA. The data sets were collected at 100 K using an Oxford Cryostream. Before diffraction, each crystal was soaked for 10 s in a cryoprotectant solution consisting of 30% glycerol mixed with their corresponding mother liquor  (44). The diffraction images of all the data sets were indexed, integrated, and scaled using the XDS suite of programs  (45). The scaled intensities were converted into structure factors using CTRUNCATE  (46)  as implemented in CCP4 (Collaborative Computational Project Number 4)  (47). Structure Determination and Refinement-The structure of vDHBPS in the apo form was solved by a molecular replacement method using PHASER  (48)  with one subunit of E.
coli DHBPS as the search model (Protein Data Bank code 1G57). The Matthews' coefficient (V M ϭ 2. 1) (49) and solvent content (42%) as calculated by CCP4 (47) indicated two molecules per asymmetric unit. The PHASER with default parameters gave a single solution with two DHBPS molecules in the asymmetric unit. The initial model was refined as a rigid body followed by restraint refinement using REFMAC5  (50). To calculate the free R factor (51), 5% of total reflection data were excluded from the refinement for each structure. The vDHBPS model was further refined using PHENIX (52) and built using the program COOT  (53). During the initial stages of refinement, the model was subjected to simulated annealing refinement  (54)  to minimize the model bias. Moreover, composite omit maps (55) were calculated intermittently during refinements and used to improve the model.
Furthermore, in the apo (E-Apo) and phosphate (E-PO 4 ) complexes, residues from 83 to 97 were not traceable in the electron density map due to their known flexibility and were not included in the model. The refinement and statistical parameters for all crystal structures are within the allowed limits and are shown in Table  3. The coordinates and structure factors for all the crystal structures are deposited in the Protein Data Bank and corresponding Protein Data Bank codes are given in Table  3. Overall Structure of vDHBPS-The overall three-dimensional structure of vDHBPS shows an ␣ ϩ ␤ fold (Fig. 3A ) similar to other reported DHBPS structures (Table  1 ) (28, 30 -36). 3B ). The PISA server  (59)  predicts that the two molecules of vDHBPS in the asymmetric unit form a stable homodimer (Fig.
74 Å for Zn 2ϩ and 0. 72 Å for Mg 2ϩ. Moreover, superposition of the E-Ru5P-Zn 2ϩ complex with the Mg 2ϩ -bound structure of M. grisea (Protein Data Bank code 1K4I)  (32)  revealed that both Zn 2ϩ and Mg 2ϩ occupy the same position. Despite such similarity with Mg 2ϩ and the ability to mediate native-like binding, it is predicted that a zinc ion is unable to initiate the reaction as it is not a strong enough Lewis acid  (33). The crystal structure of the E-Ru5P-Zn 2ϩ complex clearly shows binding of two zinc ions at each active site, and both Loop1 and Loop2 are observed in a closed and ordered conformation (Fig. 4 ). The first zinc ion at position M1 is hexacoordinated and interacts with O3 and O4 of Ru5P, one oxygen from phosphate moiety of Ru5P, N␦1 of His-154, O⑀2 of Glu-39, and O⑀1 of Glu-41 through a water molecule (Fig.
Acknowledgments-We thank  Dr. Hassan Belhrali  for help during data collection at  European Synchrotron Radiation Facility, Grenoble, France. We also grateful for the help of  Dr. Balvinder Singh  in improving the manuscript. Dr. Emmanuel Burgos , currently at the  Albert Einstein College of Medicine (Bronx, NY)  is gratefully acknowledged for the synthesis of 4PEH during his Ph. D. thesis at Orsay (France). We also thank  Dr. Saumya Raychaudhuri  for providing genomic DNA of V. cholerae.
* This work was supported in part by  CSIR Network Projects BSC-210  and  BSC-104  and by the  Department of Biotechnology, Government of India  (for synchrotron data collection in France). The atomic coordinates and structure factors (codes  4P8J ,  4P6D ,  4P77 ,  4P8E ,  4P6C , and  4P6P ) have been deposited in the Protein Data Bank (http://wwpdb. org/). 2 Supported by the  CSIR, Government of India. 3Supported by  University Grant Commission Government of India doctoral fellowships.
80 13. 97 29. 43 22. 35 13. 40 14. 50 Average B for Loop1 (for A and B, Å 2 ) 24. 54 18. 66 30. 17 25. 35 13. 13 15. 35 Average B for Loop2 (for A and B, Å 2 ) 36. 80 25. 35 42. 68 28. 12 20. 39 21. 06 Average B for Solvents (Å 2 ) 30. 43 23. 76 36. 49 26. 84 19. 92 23. 30 Ligands (in active site) Average B for ligands (Å 2 ) PO 4 (2) 19. 87 Ru5P (2) 43. 06 Ru5P (2) 25. 41 4PEH (2) 20. 59 4PEH (2) 12. 59 Average occupancy for ligands 0. 64 1. 00 1. 00 1. 00 1. 00 No. of Zn 2؉ (in active site) 10 (4) 11 (4) Average B for Zn 2؉ (in active site) (Å 2 ) 24. 63 (21. 85) 19. 34 (12. 65) Average occupancy for Zn 2؉ (in active site) 0. 75 (1. 00) 0. 70 (0. 91) Protein Data Bank code 4P8J 4P6D 4P77 4P8E 4P6C 4P6P a R cryst ϭ ⌺ hkl ʈF obs ͉ Ϫ ͉F calc ʈ/⌺͉F obs ͉. b R free is the cross-validation R-factor computed for the test set of 5% of unique reflections.
, clinicaltrials. gov]. Many of the gene products involved in the inflammatory response are regulated by the transcription factor activator protein-1 (AP-1) and the c-Jun NH2-terminal kinase (JNK) pathways: TNF-α, IFN-γ, IL-2, membrane cofactor protein-1 (MCP-1), macrophage in-flammatory protein-1 alpha (MIP-1α), cyclooxygenase-2 (COX-2), inducible nitric oxide synthase (iNOS)… Among all the anti-inflammatory strategies in development, JNK inhibitors have been shown effective in various models of inflammation [Error! Reference source not found. , Error! Reference source not found. ] and could therefore be an interesting alternative to corticosteroid treatments in AAU. XG-102 is a TAT-coupled dextrogyre peptide which selectively inhibits the c-Jun Nterminal kinase in vitro. This peptide contains a 20-amino acid sequence of the JNK binding domain of islet-brain-1 (IB-1)/JNK-interacting protein-1 (JIP-1), a scaffold protein, combined to a 10-amino acid TAT sequence of the HIV TAT protein, allowing its intracellular penetration.
Bands were visualized using the ECL Western Blotting Detection Reagents Kit (Amersham Biosciences, Orsay, France). Blots were then dehybridized and rehybridized successively with a mouse monoclonal anti α-tubulin primary antibody (1:400; Serotec, Düsseldorf, Germany) and a HRP conjugated goat anti-mouse IgG secondary antibody (1:5000; Santa Cruz Biotechnology, Tebu-bio, Le Perray en Yvelines, France). The relative band intensity for phospho c-Jun was calculated in comparison to that for α-tubulin after densitometry analysis (on ImageJ software).
PCR fragments (162 bp for GAPDH,53 bp for CINC and 657 bp for iN-OS) were analyzed by 2. 5% agarose gel electrophoresis and visualized by ethidium bromide staining under ultraviolet light. The relative bands intensity for CINC-1 and iNOS were calculated in comparison to that for GAPDH after densitometry analysis using ImageJ software.
[22, 23, 24]. This is to our knowledge the first study evaluating the effect of sub-conjunctival injection of a peptide for the treatment of uveitis. We have performed a first phase IIa clinical trial (EudraCT Number: 2012-001510-14) to evaluate the safety and tolerance of XG-102 injected subconjunctivally in patients with post-operative inflammation. XG-102 injected either sub-conjunctivally or direclty in the eye could be used in many ocular diseases, associated with intraocular inflammation and/ or excitotoxicity.
Network activity The previous measures analysed spiking data independently on each electrode. As a first approximation to assessing network activity, we used the concept of network spikes  [13]  to define the degree to which activity is coordinated across the entire array. At any time t we count the number of active electrodes; when this count exceeds a threshold, we say that a network spike has occurred. We measured three properties of these network spikes: their rate (per minute), their duration and their peak amplitude. Hippocampal networks tend to have more network spikes than cortical networks (Figure  3G ) and the network spikes involve more electrodes across development (Figure  3H ). The hippocampal network spikes tend to last  slightly longer, although this is not consistent across development (Figure  3I ).
Conclusions We report key differences in the developmental spontaneous activity patterns of cultured networks of hippocampal and cortical neurons. We have proposed a quantitative framework for evaluating these patterns. Our database of recordings and computer programs are all freely available for others to build upon. Future work in this area could be to dissect the cellular or network mechanisms driving the differences in network activity. For example, the differences between the cortical and hippocampus cultures could reflect molecular differences in cells or synapse or cellular differences in the populations of cells. Alternatively, differences in functional connectivity might partially account for these results  [10]. Dissecting these differences will require a detailed understanding of the diversity of cell types defined by singlecell transcriptomes in these brain regions, which is still lacking.
Multielectrode array recording MEAs and all data acquisition hardware and software were from MultiChannel Systems (Reutlingen, Germany). Pairs of MEAs were interfaced with duplex 60 channel amplifiers and 15-minute recordings of spontaneous action potentials were made twice per week during the 4 weeks following plating. MEAs were heated and kept under a light flow of 5% CO 2 /95% air during recordings. Signals were digitised with a 128-channel analogue/digital converter card at a rate of 25 kHz and filtered (100 Hz high pass) to remove low-frequency events and baseline fluctuations. Action potentials were detected by the crossing of a threshold set to a fixed level of -20 μV, which typically approximated to 6 to 8 standard deviations from the baseline noise level. Record samples (1 ms pre-and 2 ms post-crossing of threshold) confirmed the characteristic action potential waveform.
Application of tetrodotoxin (1 μM) totally abolished spiking activity, confirming the absence of false positive event detection using these methods. Spikes were not sorted to distinguish signals generated by individual neurons, so represent multiunit activity. Action potential timestamps were extracted using batch scripts written for NeuroExplorer  [29]  and analysed using software developed in the R statistical programming environment to compute parameters that quantitatively describe network activity. In total, 214 recordings were taken from 32 arrays of cultured cortical neurons, and 329 recordings from 61 arrays of cultured hippocampal neurons.
Acknowledgements Thanks to  Diana Hall ,  Johannes Hjorth  and  Ole Paulsen  for comments on this work. PC and AM were supported by the  Wellcome Trust Genes  to Cognition programme. PC received additional support from the  Biotechnology and Biological Sciences Research Council  ( BB/H008608/1 ). EC was supported by a  Wellcome Trust  PhD studentship and  Cambridge Biomedical Research Centre  studentship. SJE was supported by an  Engineering and Physical Sciences Research Council  grant ( EP/E002331/1 ).