dataesr/scientific-paragraphs-categorization huggingface dataset:
The functional readouts collected following 7 or 14 days in culture include albumin and urea production levels from the liver fraction, observation of cardiac electrical properties, measurement of contractile activity in the cardiac and the skeletal muscle fractions and recordings of action potential firing activity in the cultured neurons. The correlation of observed results from this system with human in vivo data as shown in Table  1  validates the platform as a novel tool for studying and eventually predicting drug efficacy and toxicity. The concentration analyzed for each compound was selected to produce modest toxic effects within 48 hours in the specific organs, and the dosages were based on the available literature. Doxorubicin (DOX) is a widely used chemotherapeutic that impairs replication and transcription, but has a strict dose limit due to its established cardiotoxic side effects  36.
2 mL). After 48 hour of drug incubation, on day 7, systems were disassembled to test organ functionality that same day. For mono-culture conditions, surfaces remained in a 12-well plated with 1 mL of the co-culture defined serum-free medium maintained by daily replacement of half volume. Bright-Field Cell Imaging. Cell morphology and function were studied each day with an inverted bright-field microscope (Carl Zeiss) using a 10X objective. This working distance allowed the imaging of the cells in the specific surfaces inside the housing. Images of each fraction and systems were collected with an Axio Cam and AxioVision AC software to study morphological or functional changes in the co-culture chamber for each organ. Human Serum Albumin quantification. Human Serum Albumin (HSA) production from the liver fraction was tracked throughout the co-culture, by measuring the HSA concentration in the supernatant of the culture as it represents liver protein anabolism.
Samples were collected from the exchanged medium (1. 2 mL) and stored at -20 °C until analysis. One freeze-thaw cycle occurred before samples were analyzed following manufacturers' instructions provided in the ELISA Starter Accessory Kit (Bethyl Laboratories Inc, Cat #: E101). Samples were diluted as necessary in sample conjugate/diluent buffer to ensure readings measured within the range of the standard curve. The standard curve was prepared by serial dilutions of human reference serum in sample conjugate/diluent buffer (0-1600 ng/ml). After the reaction was stopped optical densities (OD) were immediately measured at 450 nm using a Synergy HT plate reader and KC4 software. Final HSA concentrations were calculated in an excel file by first removing the average OD reading measured for blanks from average sample and standard OD readings.
To permeabilize the cells a 0. 2% triton X-100 in 1X PBS was incubated for 15 minutes. Non-specific binding sites were blocked with 5% DS and 0. 5% BSA in 1X PBS for 1 hour at RT. Primary antibodies were incubated on the cells OVN at 4 °C. The following day, primary antibodies were removed and surfaces were rinsed, with 1X PBS, 3 times. Then, the cells were incubated with secondary antibodies, in the dark, for 2 hours at RT. Surfaces were newly rinsed and incubated with 3 mM 4′ -6-Diamidino-2-Phenylindole (DAPI) in 1X PBS for 10 min, in the dark and at RT for nuclei staining. Finally, two more 1X PBS rinses were done before imaging. DAPI incubation was replaced by a Hard Set Mounting with DAPI (Vector laboratories, Inc. ) when the cells were on coverslips. Images were collected with Axioskop 2 mot plus upright spinning disk confocal microscope (Carl Zeiss) with a XCite 120 Fluorescence Illumination system (EXFO) beam and a multi-spectral laser scanning, coupled to Volocity software (Perkin Elmer).
Supernatant removal was followed by the addition of the solubilization reagent (0. 57% acetic acid and 1% SDS in DMSO). Cell viability was measured at 570 nm in a Synergy HT plate reader and KC4 software. The results were expressed as the percentage of cell survival relative to the control (untreated or incubated with vehicle). The neuronal fraction viability was evaluated through morphological analysis throughout the co-culture experiment as the final coverslips were used for patch-clamp electrophysiology. Phase images (10X) where obtained every day of the co-culture. Neuronal viability was evaluated by cell morphology integrity and by cell count from day 1 to day 14.
Strain identification All the colonies were identified using MALDI-TOF MS, as described below. Colonies that exhibited a MALDI-TOF-MS score > 1. 9 were considered as correctly identified, and colonies that exhibited a MALDI-TOF-MS score < 1. 9 with spectra in the database were further characterized using 16S rRNA sequencing as previously described  (Seng et al. 2010). If the similarity value between the 16S rRNA sequence was lower than 98. 7%, we considered a new species without performing DNA-DNA hybridization as suggested by  Stackebrandt and Ebers (2006).
0, Bruker) and analyzed by standard pattern matching (with default parameter settings) against the main spectra of 2843 bacteria. The identification method included m/z from 3000 to 15,000 Da. For every spectrum, we compared spectra in the database with a maximum of 100 peaks. From the resulting score, we could identify tested species, where a score ≥ 1. 9 enabled identification at the species level with a validly published species. For strain JC119 T , no significant MALDI-TOF score was obtained against the database, suggesting that this isolate was not a member of a known species. We added the spectrum from strain JC119 T to our database (Fig. 1A ). Finally, the gel view was used to demonstrate the spectral differences with other members of the Methylobacteriaceae family (Fig. 1B ). Table  1.
Genome annotation and comparison Open reading frames (ORFs) were predicted using Prodigal  (Hyatt et al. 2010 ) with default parameters. However, the predicted ORFs were excluded if they were spanning a sequencing gap region (containing N). The predicted bacterial protein sequences were searched against Clusters of Orthologous Groups (COG) databases  (Tatusov et al. 2001 ) using BLASTP  (Altschul et al. 1990 ) (E-value 1e -03 , coverage 70%, and identity percent 30%). If no hit was found, the search was performed against the NR database using BLASTP with the same parameters as before. If the sequence lengths were smaller than 80 amino acids, we used an E-value of 1e -05. The tRNA genes were found by the tRNAScanSE tool  (Lowe and Eddy 1997) , whereas ribosomal RNAs (rRNAs) were found by using RNAmmer  (Lagesen et al.
2007 ). Lipoprotein signal peptides and the number of transmembrane helices were predicted using Phobius  (Käll et al. 2004 ). ORFans were identified if all the BLASTP performed did not give positive results (E-value smaller than 1e -03 for ORFs with a sequence size higher than 80 aa or E-value smaller than 1e -05 for ORFs with sequence lengths smaller than 80 aa). Similar parameter thresholds have already been used in previous work to define ORFans  (Yin and Fischer 2006, 2008). Based on 16S rDNA of M. massiliensis (JF824802) and closely related species, sequences were aligned using CLUSTALW, and phylogenetic tree was obtained using the maximum-likelihood method within the MEGA 6. 06 software  (Tamura et al. 2013 ). Numbers at the nodes are bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree.
We performed a BLASTP  (Altschul et al. 1990 ) against the database of microbial polyketide and nonribosomal peptide gene clusters  (Conway and Boddy 2013)  for the predicted number of polyketide synthase (PKS)-and nonribosomal peptide synthetase (NRPS)-encoding genes, and we keep only the best hit for each protein. For the genomic comparison, we used M. massiliensis strain JC119 T (CDSD00000000), Microvirga aerilata strain BSC39 (JPUG00000000), Microvirga flocculans strain ATCC BAA-817 (JAEA00000000), M. lotononidis strain WSM3557 (AJUA00000000), and Microvirga lupini strain Lut6 (AZYE00000000) genomes. Orthologous proteins were identified using the Proteinortho software, version 1. 4  (Lechner et al. 2011) , using a 30% protein identity and 1e -05 E-value. The average genomic identity of orthologous gene sequences (AGIOS) between compared genomes was determined using the Needleman-Wunsch algorithm global alignment technique.
Genomic characteristics Based on 16S rDNA, the M. massiliensis strain JC119 T (accessory number JF824802) exhibited, among other, 95% sequence identity with M. lotononidis WSM3557 T (accessory number HM362432)  (Ardley et al. 2012). We summarized the closest strains of M. massiliensis based on their sequence identity percentage in Table  S1. The phylogenetic tree highlights the position of M. massiliensis JC119 T (Fig. 3 ) in relation to other type strains within the Microvirga genus and closely related species. The genome of M. massiliensis JC119 T is 9,207,211 bp long with 63. 28% GC content (Fig. 4 ). It is composed of 50 scaffolds (accession number LN811350-LN811399) (composed of 365 contigs) with one plasmid. Table  1  shows the project information and its association with MIGS version 2.
M. massiliensis strain JC119 T is the type strain of M. massiliensis sp. nov. , a new species of the genus Microvirga. The genome of M. massiliensis JC119 T is 9,207,211 bp long, representing the largest genome of a bacteria isolated from a human sample  (Lagier et al. 2012a,b,c,d). It ranks 139th among the largest bacterial genomes according to the Genomes OnLine Database (GOLD)  (Kyrpides 1999). All these bacteria whose genome is larger than M. massiliensis are found in the environment  (soil, ocean, sand, and landfill). Different characteristics of this bacterium can explain a broad genome. The proportion of no detectable homologs (ORFans) from the gene prediction is about 17%, which corresponds to 1500 ORFans. The number of noncoding genes is important. This genome has 77 RNA: 56 tRNA and 21 rRNA.
The range of temperature growth is 28-55°C (with an optimum at 37°C). The potential pathogenicity of the type strain JC119 T (=CSUR P153 = DSM 26813) is unknown but was isolated from the stool specimen from a Senegalese male, in Marseille (France), using culturomics  (Lagier et al. 2012a,b,c,d; Dubourg et al. 2014). The G+C content of the genome is 63. 28%. The partial 16S rRNA sequence of M. massiliensis was deposited in GenBank under the accession number JF824802. The whole-genome sequence of Microvirga massiliensis strain JC119 T (=CSUR P153 = DSM 26813) has been deposited in EMBL under accession numbers CDSD01000001-CDSD01000365 for contigs and LN811350-LN811399 for scaffolds.
1 Latitude 13. 71667 IDA MIGS-4. 1 Longitude -16. 41667 IDA MIGS-4. 3 Depth Surface IDA MIGS-4. 4 Altitude 34 m above sea level IDA MIGS-31 Finishing quality Noncontiguous finished MIGS-28 Libraries used Six paired-end and two Shotgun 454; mate pair MiSeq MIGS-29 Sequencing platform 454 GS FLX Titanium and Illumina MIGS-31. 2 Fold coverage 77× MIGS-30 Assemblers Newbler 2. 8 MIGS-32 Gene calling method Prodigal GenBank Date of Release November, 2014 NCBI project ID PRJEB8433 EMBL accession CDSD00000000.
All traits were tested for deviations from normality by determining whether a frequency histogram of trait values across all 286 full grown individuals (14 of the originally planted individuals died early in development, but at least 12 individuals for each population were analyzed (Table  1 )) was significantly different from a normal distribution with the Shapiro-Wilk test in JMP 11 (SAS Institute, Cary, NC) and trait values were transformed using a Box-Cox transformation  [33]  as necessary. Restricted maximum likelihood was used with region as a fixed effect (blocks and a block-by-region interaction were included as random effects) to test for regional differences in trait values. For fatty acid traits, the date of fatty acid extraction was used as a blocking factor instead of greenhouse block because an inspection of the raw data indicated clear variation in extraction efficiency across days.
e. , minor allele frequency < 0. 05), and/or large amounts of missing data (i. e. , fraction of missing data > 0. 05) were removed prior to population genetic analysis. A total of 246 loci (average = 14. 5 per LG; range = 11-20 per LG) were retained for further analysis (http://dx. doi. org/10. 5061/dryad. 6p1c4).
Population genetic analyses Measures of genetic diversity, including the percentage of polymorphic loci, observed heterozygosity (H o ), and Nei's unbiased expected heterozygosity (UH e ;  [35] ) were calculated at the population level using GenAlEx (version 6. 501;  [36] ). We also used GenAlEx to investigate genetic differentiation amongst populations by performing an analysis of molecular variance (AMOVA) with 999 permutations to determine the level of population structure in our dataset. Finally, the program STRUC-TURE (version 2. 3. 4) [37]  was used to investigate population genetic structure across the species range. Specifically, STRUCTURE was run using the admixture model from K = 1 to 17 population genetic clusters with a burn-in of 100,000 and 1,000,000 MCMC iterations (with 20 replicates for each K value).
2 ). The STRUCTURE bar plot for K = 2 revealed a north-south divide with the east-central portion of Region 3 corresponding to a transition zone (Fig. 2 ). An additional STRUCTURE run containing only the southernmost six populations also indicated that K = 2. For this level of K, TX1 was separated from the remaining five populations found in Texas and Oklahoma, although K = 6 showed a secondary peak (Additional files 2, 3, and 4). When the northernmost six populations were analyzed by STRUCTURE, K = 2 was again the most well-supported number of genetic groups. Similar to the result for the southern portion of the range, only a single population (ND1) in the northern portion of the range was separated from the other five populations at K = 2 (Additional files 5 and 6). Additionally, since the initial full dataset STRUC-TURE analysis suggested that two of the three middle latitude populations were more southern while the other population appeared more northern we performed more STRUCTURE analyses to explore differentiation within the middle of the range.
To study the middle latitude populations we added NE1 and NE2 to the southern dataset, and WY1 to the northern dataset for further testing. When we performed STRUCTURE analyses of these larger groupings, we found that K = 3 for the northern cluster. The three clusters corresponded to ND1, WY1, and the remaining populations. Additionally, we found that K = 2 for the southern cluster with the one cluster corresponding to NE2 individuals, and the other contained the remaining seven populations.
Population genetic structure The STRUCTURE analysis of the full dataset revealed an overall north/south division in the natural range of wild sunflower, with a transitional zone occurring in the vicinity Nebraska and Wyoming. Previous sampling of H. annuus genetic diversity had hinted at a similar north/south division  [51] , and our analysis builds on this finding by increasing the marker density and sampling density within each population. Historically, this latitudinal transect has seen similar patterns of genetic differentiation. For example, using transplant gardens, McMillian  [52]  showed that multiple grassland species exhibited heritable differences in flowering time in which northern populations flowered significantly earlier. When further STRUCTURE analyses were performed on northern and southern subsets of individuals, it was discovered that hierarchical structure exists in our dataset.
Acknowledgements We thank  Scott Jackson 's laboratory in the  Institute of Plant Breeding Genetics and Genomics at the University of Georgia  for greenhouse space and access to lab equipment, and  Ben Blackman  for providing HaFT sequences for probe design. We thank members of the  Burke lab  for comments on an earlier version of this manuscript. Special thanks to  Caitlin Ishibashi  and  Jeff Roeder  for assisting with the DNA extractions and to  Shannon Ritter ,  Michael Cherry , and  Shreyas Vangala  for assistance in phenotyping.
The optimal conditions resulted from the treatment in H 2 /N 2 (5/95) atmosphere at 1200 C for 12 h. The rate of heating and cooling was 5 C min À1. Thermal treatments longer than 12 h did not produce changes in the obtained samples, suggesting that the new samples reached equilibrium with the atmosphere before this treatment time. The initial identification and characterization of the samples was carried out by X-ray powder diffraction (XRPD). The crystallographic study was carried out from XRPD patterns collected at RT. The experimental XRPD patterns were obtained on a diffractometer Rigaku D-MAX-IIIC with Cu Ka (l ¼ 1. 5418 Å) radiation. The data were collected over a range of 10-120 (2q) with a step of 0. 02 ; the effective counting time was 5 s per step. For the structural refinements, neutron powder diffraction (NPD) pattern was collected at RT in the D2B neutron diffractometer, with l ¼ 1.
594 Å, belonging to Institute Laue Langevin (ILL), Grenoble, France. The patterns were refined by the Rietveld method  [16]  using the FullProf refinement program  [17]. A pseudo-Voigt function was chosen to generate the line shape of the diffraction peaks. In the final runs, the following parameters were refined: scale factors for the main and impurity phases, background coefficients, zero-point error, unit cell parameters, pseudo-Voigt corrected for asymmetry parameters, positional coordinates, anisotropic thermal factors, and antisite disorder of Mn/Mo and occupancy factors for oxygen atoms. Thermogravimetric analysis was performed in a Shimadzu TG-50H thermal analyzer apparatus using flowing air at 50 mL/min from 25 C to 1000 C, at a heating rate of 5 C/min. About 18 mg of the sample was used in the experiment.
Crystallographic structure The XRPD patterns of SMM and BMM (Fig. 1 ) are characteristic of perovskite structures, cubic for BMM, and showing the splitting of certain high-angle reflections for SMM, typical of a monoclinic symmetry. Minor amounts of BaMoO 3 in BMM were detected from XRPD and NPD data. The structural refinement was performed from XRPD and NPD data at RT. For BMM, the Fm3 m space group (No. 225), Z ¼ 4, was considered, with unitecell parameter related to a 0 (ideal cubic perovskite, a 0 z 3. 9 Å) as a ¼ 2a 0. Ba atoms were located at 8c (¼,¼,¼) positions and oxygen atoms at 24e (x,0,0) sites. In this space group there are two possible sites for B-type cations, namely, 4a and 4b. We placed Mn/Mo at random at 4a (0,0,0) and 4b (½,½,½) sites, and refined the long-range ordering as described below.
Acknowledgements J. C. P. thanks  CONICET  (Project  PIP 112-200801-01360 ),  SECyT-UNSL  (Project  PROICO 2-7707-22/Q823 ) and  ANPCYT  (Project  PICT 6/25459 ). R. D. S. thanks  UN Cuyo ,  CONICET and ANPCyT (Argentina)  under grants  06/C389 ,  PIP-490  and  PICT2007-0832/ PICT2011-0752. C. A. L. , M. E. S. , J. C. P. and R. D. S. are members of  CONICET. J. A. A. acknowledges the financial support of the  Spanish Please  provide the grant number for: 1)  Ministry of Education , 2) Brazilian Synchrotron Light Laboratory , if any. Ministry of Education  to the project  MAT2013-41099-R. We are grateful to  ILL  for making all facilities available. Also, the authors thank the  Brazilian Synchrotron Light Laboratory (LNLS)  for the beamtime ( D04B -XAFS1-11681 ), and the staff of the  XAFS1 Beamline  for providing assistance during the experiment.
The material parameters used for the simulations are measured on rammed earth blocks made by the same mason who built the wall, using the same pneumatic rammer and the same manufacturing water content of 19%. The resulting data and the methods used for the measurements are reported in Table  1  and Table  2  and some additional details are provided in the following paragraphs. The thermal conductivity was measured on compressed earth blocks (CEB) of 30 x14x10 cm 3 just after their manufacture (when its water content was equal to 19%), and after a drying period of 48 hours, which results in a water content equal to 17%. To ensure the homogeneity of water content within the samples, they were wrapped in a sealed plastic film at least 48 hours at constant temperature before each measurement of thermal conductivity.
Results and model validation against experimental data The system of partial differential equations (  13 )-(  22 ) is solved with COMSOL Multiphysics® using PDE module. The simulations are made on a 2D prismatic geometry of length L=0. 3m (x direction) and height H=1m (y direction). It represents a lateral cross section of the tested wall. The finite element mesh used is reported in Error! Reference source not found. b (element size of 0. 037m) and the time step used is 1s. Boundary conditions of the simulations are set in accordance with measurements made on both sides of the insulated box. Thus, a null thermal and moisture flow are imposed at the y=0 and y=H boundaries, while thermal and moisture exchanges on the lateral surfaces x=0 and x=L, of normal outward vector n, verify the following equation: ( ) ( ) ( ) ( ) ( ) ( ) ( ) ( ) T sat sat L L V v a a v s s T a s T L T n g g n p T p T T T g Lg n T L L T L n ϕ ϕ ϕ ϕ ρ β ϕ ϕ α λ - Κ ∇ + Κ ∇ ⋅ + ⋅ - = = - - ⋅ -∇ + ∇ + ∇ ⋅ ( 29 ) where n is the outgoing vector at the considered boundary, L g and V g are respectively the liquid water and vapor mass flow vector, T g is the heat flow vector, a As suggested by  [17] , realistic values for β and α are respectively 25.
DNA extraction, amplification and sequencing Parasite DNA was extracted from whole blood samples using the QIAamp DNA Blood Mini Kit (Qiagen, Courtaboeuf, France), following manufacturer's instructions. The pvmdr1 gene was amplified and sequencing using protocol (primers and amplification condition) previously described by Lekweiry et al. [33]  except the polymerase, 0. 025 U/μl of Ampli Taq Gold ™ , 2. 5 mM MgCl 2 , 1× PCR Gold Buffer (Applied Biosystems). The amplification product was loaded on a 1. 5% agarose gel and visualized after electrophoresis. Sequencing of pvmdr1 PCR product was performed by using the nested primers  [33]  generating a product length of 547 bp (region between codon 931 and 1095). These sequence were compared with the reference sequence Sal-1 (Genbank accession number AY571984).
Real-time PCR to quantify the pvmdr1 gene copy number The pvmdr1 gene copy number was measured by performing a qPCR in comparison to the reference gene pvaldolase, using the method previously described by Lekweiry et al. [33]. The reproducibility problems encountered were solved by designing new probes using Primer Express ® software (Applied Biosystems). These primers and probes are listed in Table  1. The qPCR was carried out in a 25 μl reaction volume containing 1 μl of DNA, 300 nM of each primer, 200 nM of probe, 12. 5 μl of TaqMan ® Universal Master Mix II (Applied Biosystems) and water. Real-time PCR was performed under the following conditions: 95 °C for 10 min, then 40 cycles at 95 °C for 15 s and 65 °C for 1 min. Samples were set up in triplicate and experiments were repeated independently twice.
Relationship between copy number and genotype of the pvmdr1 gene The copy number of the pvmdr1 gene was determined for all samples and varied from 1 to 8 (mean 1. 45, CI 95% [1. 35-1. 55]). The majority of the sample, 68. 5%  ). This decrease over time was statistically significant (p < 0. 0001, Chi square test for trend, see Fig. 3 ). Moreover, relationship between epidemiological data and copy number was not observed.