dataesr/scientific-paragraphs-categorization huggingface dataset:
These features were examined to select the genes encoding putative homologous PRAC enzymes in trypanosome genomes. Amino-acid and nucleotide sequences of whole TcPRAC-homologous genes (~1062 bp) from the various trypanosome species were obtained from genome data banks, aligned using Clustal X v2. 0 and manually adjusted. In addition, partial (~1015 bp) PRAC nucleotide sequences obtained by PCR-sequencing were used for polymorphism analysis within T. cruzi by comparing sequences from TcI-TcVI and Tcbat isolates. An alignment was created with partial PRAC amino acid sequences from T. rangeli isolates of lineages A-E and T. conorhini as outgroup. Maximum-likelihood (ML) and maximum-parsimony (MP) analyses were performed respectively with RAxML v7. 2. 8 and PAUP*v4b10 based on nucleotide and amino acid alignments.
PCR amplification and sequencing of PRAC gene sequences from T. cruzi and T. rangeli isolates PCR amplification of partial TcPRAC sequences (~1015 bp comprising all essential motifs and residues of TcPRAC enzyme) from large number of isolates from T. cruzi and T. rangeli (Additional file 1) was conducted as previously described  [8]  using the primers PRAC1 (5'-CTTCCCATGG GGCAGGAAAAGCTTCTG-3') and PRAC2 (5'-CTGA GCTCGACCAGATCTATCTGC-3'). The PCR-amplified products were cloned, and 3-5 clones from each isolate were sequenced, whereas ~10 clones were sequenced from each of the hybrid isolates. The PRAC sequences representing the genetic diversity within T. cruzi and T. rangeli were deposited in GenBank and the access numbers are listed in Additional file 2.
Phylogenetic analysis based on gGAPDH gene sequences Phylogenetic tree of Euglenozoa species based on gGAPDH gene sequences was inferred by ML and MP as described above for PRAC genes. The alignment created for this analysis was done using for guidance a comprehensive alignment of kinetoplastid gGAPDH genes  [3]  and included sequences from 32 trypanosome species, non-trypanosome trypanosomatids of seven genera, and five bodonids and euglenids as outgroups. Bootstrap support was estimated with 100 pseudoreplicates in RAxML using GTRGAMMA. The Genbank access numbers of all gGAPDH genes included in the phylogenetic trees are listed in Additional file 1.
Horizontal-gene-transfer analysis The horizontal-gene-transfer (HGT) analysis includes a comprehensive dataset of 2,530 PRAC-like protein sequences from prokaryotes and eukaryotes in the non redundant (NR) database. A BLASTp search was performed with a maximum-expected-value threshold of 1e-20, using the TcPRACA and TcPRACB sequences as queries. The retrieved sequences were checked for PRAC-like domains using the Batch search tool in the Conserved Domain Database (http://www. ncbi. nlm. nih. gov/ Structure/bwrpsb/bwrpsb. cgi). Multiple-sequence alignment was performed using MUSCLE v3. 8, and edited using Gblocks v0. 91b  [45]  to eliminate poorly aligned positions. The final phylogenetic tree was obtained by ML analysis with 2,530 sequences under the WAG substitution model with gamma-distributed heterogeneity rate categories, and estimated empirical residue frequencies (model PROTGAMMAWAG) as implemented in RAxMLv7.
2. 8. One hundred different best tree searches were performed, and the tree with best likelihood found was kept. RAxML rapid bootstrap was performed with 100 pseudoreplicates. The tree was also visualized using Dendroscope v3. 2. 4  [46]  with further cosmetic adjustments done using the Inkscape vector image editor (http://inkscape. org). To better resolve and visualize the putative HGT donor lineages, a ML analysis was performed using a subset of 303 PRAC-like sequences from NR database and 39 TryPRAC aligned with the nearest neighbor taxons identified in the analysis using 2,530 sequences. The tree search and bootstrap were conducted using the same parameters for both datasets.
Genomic organization, GC content and codon pressure analyses of trypanosome PRAC genes The comparison of PRAC genomic organization in the analyzed genomes was performed with the bl2seq BLASTX algorithm using the flanking downstream and upstream regions (~10,000 bp) previously reported for T. cruzi and T. vivax  [8, 9]  in all trypanosome genomes investigated in this study. Codon-selection analysis was performed using the HyPhy v2. 2 package  [47]  with a threshold p-value < 0. 05. The GC content comparison between TryPRAC homologs and both flanking genes and whole genomes were conducted using the mfsizes v. 1. 8. 3 software (http://sourceforge. net/projects/mfsizes/).
rangeli. The arrows on the gGAPDH tree (B) indicate the places hypothesised for the horizontal transference of bacterial PRAC gene to a common ancestor of Trypanosoma, and the gene loss in a common ancestor of T. brucei ssp. and T. congolense. Genbank accession numbers of PRAC and gGAPDH gene sequences are respectively showed in Table  1  and Additional file 1. sequences. Compared to divergence among TryPRAC sequences, the species of the subgenus Schizotrypanum were separated by much smaller gGAPDH sequence divergences (~8. 0% between T. cruzi and T. dionisii), whereas ~15% and ~17. 5% of gGAPDH sequence divergence separated T. cruzi from T. rangeli and T. vivax, respectively. Divergences of gGAPDH and the more conserved SSU rRNA genes, which are the traditional genes employed for phylogenetic inferences of the Trypanosomatidae, were previously reported for the trypanosome species included in PRAC phylogeny  [5, 39, 40].
The complete list of putative donor lineages currently available on NCBI NR protein database included in the phylogenetic analysis is presented in Additional file 6. Considering the presence/absence of PRAC genes and the congruence of all species in phylogenies based on PRAC and gGAPDH genes (Figure  2 ), we hypothesised gains and losses of PRAC genes during trypanosome evolution. In the most parsimonious evolutionary scenario, one prokaryotic PRAC gene was transferred through a single HGT to the root of the genus Trypanosoma in a common ancestor of this genus, which gave origin to all extant trypanosome species with respective TryPRAC homologs. The absence in T. brucei and T. congolense suggested the loss of PRAC gene by a common ancestor of the subclade comprising these species (Figure  2B ).
Synteny analysis revealed highly conserved gene order around TryPRAC homologs Our findings demonstrated that TryPRAC homologs are ubiquitous in the genus Trypanosoma (Figure  2A ). Previous studies revealed high conservation of gene segments containing the PRAC locus from T. cruzi and T. vivax  [8, 10]. To verify the genome organisation of PRAC genes in the different trypanosome species, we performed BLAST searches in genome databases for orthologous genes in PRAC loci. The results showed a syntenic block shared by all species (Figure  6 ). The adjacent regions of PRAC genes exhibited high synteny in T. cruzi, T. c. marinkellei, T. erneyi, T. dionisii, T. vivax and T. grayi, with at least 8 genes arranged in the same order: K39 kinesin, WD domain-containing protein, cold shock domain-containing protein, PRAC, hypothetical protein, zinc-finger protein, poly (A) polymerase, carbohydrate kinase and phosphatidyl serine.
Acknowledgements We are grateful to The  Wellcome Trust (TriTrypDB)  and to the  Kinetoplastid Genome Sequencing  and  Analysis Consortium NIH/NHGRI/NIAID  (project  ID   59941 ) of the  Genome Institute at Washington University School of Medicine (USA)  for making genomes of trypanosomatids freely available. Additional draft and ongoing genomes were obtained within ATOL (Assembling the tree of  Life -Phylum Euglenozoa ) program sponsored by the  National Science Foundation, USA (PI Gregory Buck :  DEB-0830056 ), and by projects supported by  CNPq ,  CAPES  and  USP  to MMGT. ZEC is recipient of a PhD fellowship from  SENACYT (Panamá). AGCM, RCF and JMPA are recipients of fellowships from Brazilian agencies  CNPq ,  CAPES  and  FAPESP  (grant # 2013/14622-3 ,  São Paulo Research Foundation ), respectively.
After cells were washed twice in PBS, secondary antibody solution (goat anti-mouse Alexa 488, Life Technologies, A11001) was added over 45 min at RT in the dark in 150 ml PBS (10% Goat Serum) with the appropriate concentration (usually 1:500). Slides were visualized on an Axioimager microscope and fluorescence quantification and cell diameter measurements were performed with ImageJ software. Cell cycle analysis assay, xenotransplantation, the derivation of cell cycle parameters, modeling, transcriptome studies, bioinformatics, qPCR, lentiviral transduction, and mitochondrial mass measurements are reported in the Supplemental Experimental Procedures.
ACKNOWLEDGMENTS We thank the obstetrics unit of  Trillium Health Partners (Missisauga and Credit Valley sites ) for cord blood samples;  N. Simard ,  P. A. Penttila  ¨,  A. Khandi ,  L. Jamieson , and  S. Zhao  at the  UHN-SickKids Flow Cytometry Facility  for cell sorting;  V. Voisin  and  G. Bader  for advice on bioinformatics; and  M. Doedens  for help with intrafemoral injections. This work was supported by the  Swiss National Science Foundation  (E. L. ),  Roche  (E. L. ), the  Fondation Suisse pour les Bourses en Medecine et Biologie  (E. L. ), the  Swedish Research Council  (S. Z. ); and a  Canadian Institutes of Health Research (CIHR)  fellowship in partnership with the  Aplastic Anemia and Myelodysplasia Association of Canada  (S. Z. ). Work in J. E. D. 's laboratory is supported by grants from the  CIHR ,  Canadian Cancer Society ,  Terry Fox Foundation ,  Genome Canada  through the  Ontario Genomics Institute ,  Ontario Institute for Cancer Research  with funds from the province of Ontario, a  Canada Research Chair , the  Princess Margaret Hospital foundation , and the  Ontario Ministry of Health and Long Term Care (OMOHLTC).
The Api 20NE strip (bioMérieux) identified B. avium based on the score 0000067 with high percentage (96. 7%) and typicality (T = 1). Routine identification by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (Brucker Daltonik GmbH, Germany) gave B. hinzii with good scores (T = 2. 29 for case-patient 1 and T = 2. 35 for case-patient 2). Final identification for both cases involved amplification and sequencing of 1,480 nt of 16S rRNA gene, then use of the blastn program (http:// www. ncbi. nlm. nih. gov/BLAST/) and the GenBank database. The nucleotide sequences showed the best BLAST hit with B. hinzii (99. 9% homology in both cases). Antimicrobial susceptibility testing was performed on Mueller-Hinton medium by an Etest method (bioMérieux) and MICs determined (Table ).
B. hinzii was isolated 8 times during a 1-year period from the respiratory tract of a cystic fibrosis patient  (5). B. hinzii infections are presumably underdiagnosed because of misidentification by the routine phenotypic identification procedures that are the basis for Phoenix (Phoenix BD Diagnostic Systems, Sparks, MD, USA) and Vitek (bioMérieux) automated systems and for the API 20NE strip manual system (bioMérieux). Indeed, B. hinzii is not referenced in the API 20NE database and often gives the same score as B. avium. The API 20NE database should be updated and the score 0000067 should be referred to as B. avium-B. hinzii complex. The mean score for 6 clinical isolates analyzed with the MALDI-TOF mass spectrometry system (Brucker Daltonik GmbH) by the French National Reference Centre of pertussis and other bordetelloses was T = 2.
The curative doses needed to eliminate B. hinzii appear to be high because B. hinzii was isolated from case-patient 1 despite prophylactic treatment with trimethoprim/sulfamethoxazole, a combination to which the isolate was susceptible. Numerous discrepancies exist between the results of disk diffusion and MIC tests (5), as observed for B. bronchiseptica (A. Le Coustumier, unpub. data). MIC testing should be performed to confirm the sensitivity of any such isolates. We can speculate about possible antimicrobial resistance acquisition, regarding fluoroquinolone resistance in casepatient 1 and his exposure to this pharmacologic class during previous hospitalizations, as described elsewhere (3), but data remain insufficient to prove it. Microbiological tests after the episode are required to evaluate the effectiveness of treatment.
Since tal genes are notoriously difficult to be assembled from short reads due to their repetitive nature, we sequenced the tal genes upon PCR amplification. Surprisingly, the two genome-assembled tal genes turned out to be correctly assembled, probably due to the very high coverage and a significant number of single-nucleotide polymorphisms (on average, 1 per 10 bp) that distinguish all individual repeats from each other. This information opens the way for studying the role of tal genes in the pathogenicity of X. translucens. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. JWHD00000000. The version described in this paper is the first version, JWHD01000000.
ACKNOWLEDGMENTS This work was supported by grant  ANR-2010-GENM-013  from the  French Agence Nationale de la Recherche. C. P. thanks the  Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture  ( 093604 ) for support. The LIPM is part of the  LABEX TULIP  ( ANR-10-LABX-41 ). Strain CFBP 2541 is available at the  CIRM-CFBP, French Collection for Plant-Associated bacteria  (http://www6. inra. fr/cirm_eng/CFBP-Plant-Associated-Bacteria). crossmark Genome Announcements January/February 2015 Volume 3 Issue 1 e01574-14 genomea. asm. org 1.
To determine whether fluoxetine acted by affecting ephrinB2a levels, we measured levels of ephrinB2a levels in the TCPTc axons as they crossed the midline at 36 hpf. We found that fluoxetine decreased ephrinB2a levels in the crossing TCPT axons under both control and hypoxia conditions (Fig. 8M ). Hypoxia did not affect the overall distribution of raphe 5-HT axon projections. These data show that raphe neurons can respond to environmental hypoxia and modulate 5-HT expression, thereby altering neural circuit development.
Acknowledgments The authors gratefully acknowledge funding from  Wellcome Trust  ( 094143/Z/10/Z ) and  British Heart Foundation  ( RG/12/11/ 29815 ) (VBO, VJH),  National Institutes of Health  Grant  HD058577 (KK ) and  Grants-in-Aid 26840017  from the  Ministry of Education, Culture, Sports, Science, and Technology (MN).
Expression values were quantile-normalized between experiments and a differential analysis was performed using the Limma R package  [66]. P-values were corrected for multiple testing using the Bonferroni-Holm method. Genes with adjusted p-value <0. 05 were considered differentially expressed in the Δhfq mutant relative to wild-type. The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus  [67]  and are accessible through GEO Series accession number GSE66893 (http://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE66893).
Acknowledgments We thank  Anne Aucouturier  for strain constructions. We thank  Chantal Bohn ,  Annick Jacq  and  R. MacGregor  for technical assistance, helpful discussions, and warm support. We thank  Cyprien Guérin  for his help with tiling arrays signal processing, and  Pierre Nicolas  and  Ulrike Mäder  for the transition from  Nimblegen-based BaSysBio Bsub   T2  design to new BaSysBio Bsub T3 design using Agilent microarrays.
This work was supported by the  Agence Nationale pour la Recherche  (http://www. agencenationale-recherche. fr/)( ANR-2010-BLAN-1602-01  ' Duplex-Omics ' and  ANR-12-BSV6-0008  ' ReadRNA ') to PB and by the  European Commission -funded  BaSysBio  project (http://ec. europa. eu/research/fp6/index_en. cfm)( LSHG-CT-2006-037469 ) to PN. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
A simplified version of the Human Dynamic Clamp is available free on Git-Hub: https://github. com/crowd-coordination/web-vpi. The velocity of the human finger was numerically computed using a 3-point differentiation algorithm and, together with position data plugged into the VT equation. The differential equation returned instantaneous VT acceleration which was integrated using a 4 th order Runge-Kutta method at 500 Hz to provide VT velocity and position. A maximum delay of 2 ms occurred between data acquisition and computation of the model output. To create the animation of VT finger movement, a high-speed camera recorded a human male producing flexion-extension finger motion in the horizontal plane. A complete cycle of movement provided 119 images (17 × 13 cm) indexed by their position. The instantaneous position of the VT was used to select one of the 119 position-indexed images, which was displayed in the center of the screen (59 cm diagonal).
Highlights on hydrologic processes included: Global comparison of SMOS, ASCAT and ERA soil moisture data products; Relative deviations evaluated by climate zone; Soil moisture data products improved with ancillary data; Assimilation of FY -, TRMM and GPM precipitation data products in WRF; Improved algorithm and data products on fractional snow cover; Improvement of MODIS ET with assimilation of LST; TRMM data products evaluated in the Yangtze; Calibration of river basin models using LST; System to calibrate, correct and normalize (spatial, spectral) data collected by imaging spectral radiometers; Integration of data acquired by different sensors, e. g. ET Monitor with optical and microwave (SMOS, FY -3) data; Hydrological data products used both for forcing and evaluation of Qinghai -Tibet Plateau hydrological model; Wetlands vulnerability assessed through changes in land cover 1987 -2013; Multi incidence angle and multi -temporal SAR to monitor water extent.
Water Cycle & River Basins The overall objective of the Water Cycle and River Basins project is to close the water cycle at the river basin scale. Water budget components including precipitation, evapotranspiration (ET), soil moisture (SM), snow water equivalent (SWE), runoff, and groundwater storage will be estimated using multisource remote sensing observations and corresponding time series products of these variables will be generated. These products, in combination with hydrology and land surface modelling will be integrated by data assimilation methods to precisely close the land water budget at the river basin scale. The detailed implementation of the project includes the identification of the 6 key experimental areas (KEAs) in the Heihe River Basin, China and the Ruhr Catchment, Germany.
Yangtze River Basin Hydrology The main objective of the Yangtze River Basin Hydrology project is to assess water quantity and quality under natural and human pressure on the Yangtze River basin, by using two distributed hydrological models (FEST-EWB & XAJ) coupled with satellite and ground data. The detailed sub-objectives were designed to reach the main goal, which leads to the deliverables including GIS database of satellite and ground data, flow duration curves of different river cross-sections for hydropower and agricultural potential use, evapotranspiration product, soil moisture product used for flood forecast and irrigation time management, flooded area map, soil erosion map, and maps of suspended solid sediments, chlorophyll and turbidity and surface water temperature.
Hydrology Products The overall objective of the Hydrology Products project is to generate hydrological data products by merging broadly similar radiometric data collected by satellite systems operated by ESA and the China National Space Administration, with generic algorithms. To support monitoring of the terrestrial water cycle, a suite of land surface biophysical variables will be generated using largely automated procedures with multi-source remotely sensed data. Those variables include LST, LAI, FVC, FAPR, Albedo, ET, SM, Snow Cover, SWE and so on. To facilitate this aim, a software system is being developed, named Multi-Source Remote Sensing Production System (MSRSPS), to realize the functions for batch production of land surface variables. The MSRSPS is composed of three subsystems including multi-source remote sensing data preprocessing sub-system (M-RSPPS), land surface variables batch production sub-system (LSV-BPS), and data and task management sub-system (D&T-MSS).
Dongting Lake Flood Dynamics The aim of this project is to depict the potential of remote sensing for the support of spatial planning for the wetland of Dongting Lake, to assess its dynamics, including flood pulse dynamics, wetland development, the quantification of wetland degradation and the derivation of landuse changes in the direct surroundings of the lake. Based on Envisat ASAR data at different resolution (mapping of inundation extent and frequency), the project is going to derive inundation time series for the three consecutive years of the DRAGON 3 project, as well as for past years based on different modes of different special and temporal resolution. In addition, MERIS data and optical data of multi-spectral data of the Environmental Monitoring Constellation and Beijing-1 and 2 data were used to investigate wetland composition and biodiversity wetland degradation, land use dynamics in the direct lakes surrounding, mapping and change detection of agricultural crops etc.
SMOS Cal-Val and Soil Moisture To quantify and remediate the uncertainties in SMOS and SARbased soil moisture products, regional soil moisture monitoring networks have been established around the world. The project will focus on two of these initiatives, which focus on the Tibetan Plateau and Taklamakhan. Su et al. (  2011 ) describe a Plateau-scale soil moisture/temperature observatory consisting of three regional soil moisture calibration/validation sites. Each site holds a network of at least 20 stations and data records starting from 2006, 2008 and 2010 for the three sites, respectively. Similarly, a comprehensive soil moisture/temperature network has been installed in the Taklamakhan desert, where the ground instrument for measuring L-band brightness temperatures is installed as well.
This project makes use of these in-situ data sets to validate the SMOS and the experimental SAR soil moisture products from ASAR, Sentinel-1 and PALSAR-2. The specific target is to reduce soil moisture retrieval uncertainties related to surface roughness and vegetation effects. The discrete scatter modeling suite developed at the Tor Vergata University in Rome  (Bracaglia et al. 1995)  will be utilized as a theoretical reference and for the advanced interpretation of the observations.
Himalayan Glacier Dynamics Melting of the Himalayan Glaciers has direct consequences for the sea level worldwide, and also has direct consequences for regional hydrology, which directly affects the water supply providing to over 1. 4 billion people and the risk of flooding events. To understand and quantify the changes affecting the Himalayan Glaciers, the project aims to quantify the degree of mass imbalance of the Himalayan Glaciers by exploiting Earth Observation dataset, which can help understand the mechanisms by which mass is being lost and how the Himalayan Glaciers responds to the forcing of heat transport by the atmosphere. The project is going to deliver glacier elevation change, flow divergence, and improve the determination of mass imbalance at the scale of the Himalayan range.
Glaciers & Hydrological Dynamics The goal of this project is to use Earth Observation to support the needs for the monitoring, mapping, and water resource potential evaluating of glacier change in the Yigong Zangbo and Parlung Zangbo catchments. Some key glacier variables will be retrieved using ESA and other satellite data. Finally the applicability of quantitative remote sensing in cryosphere applications and glacier water resource potential evaluation will be promoted. The scope of this project is to illustrate the capabilities of multisource remote sensing data for an assessment of glacier change and its hydrological effects in the Yigong Zangbo & Parlung Zangbo Catchments. The project will investigate the use of multi-temporal and synergistic use of EO data to accurately identify and monitor dynamics of glaciers and how they are changing over time.