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+Here we present 3DSim ( 3D Structural Implication of Mutations ) , a database and web application facilitating the localization and visualization of single amino acid polymorphisms ( SAAPs ) mapped to protein structures even where the structure of the protein of interest is unknown .
+The server is publicly available at http://www.biomedcentral.com/content/pdf/1471-2105-10-S8-info.pdf .
+Here we present 3DSim ( 3D Structural Implication of Mutations ) , a system mapping single amino - acid polymorphisms onto structures of CATH domains .
+This provides a comprehensive overview of the distribution of mutations in structural space , as well as a visualization tool for pinpointing the locations of mutations on individual structures rendered in Jmol http://www.biomedcentral.com/content/pdf/1471-2105-10-S8-info.pdf , as well as links to detailed information on each sequence , structure and mutation .
+The 3DSim application , which was designed with the aim of being very intuitive , easy to use and user - friendly , is publicly available at http://www.biomedcentral.com/content/pdf/1471-2105-10-S8-info.pdf .
+For each of the 11904 Gene3D domain sequences mapped to CATH structural superfamilies for which there is information about mutations in SAAPdb ( see previous section ) , a BLAST [ 26 ] search was run against the corresponding superfamily database .
+The groups ( including the sequence of the representative structure ) were then aligned using MUSCLE [ 27 ] and the resulting alignments used to transfer the mutations from Gene3D sequences to CATH domain representative structures .
+Once the user has selected a CATH domain , 3DSim displays both an interactive Jmol plug - in that allows the visualization of the mutations projected onto the three - dimensional structure of the representative CATH domain and a table displaying all the information available for that given domain in terms of available mutations , sequence and structure positions of the mutations , pathogenicity information , and similarity ( BLAST sequence identity ) between the sequences in Gene3D and the representative CATH domain sequence .
+In order to allow remote programmatic access to the information contained in the database , we have developed a total of nine SOAP web services , powered by the Perl SOAP :: Lite toolkit http://www.biomedcentral.com/content/pdf/1471-2105-10-S8-info.pdf .
+We have presented 3DSim ( 3D Structural Implication of Mutations ) , a system that enables the localization and visualization of single amino acid polymorphisms projected onto protein structures based on homologous relationships captured in the CATH and Gene3D databases .
+The server has been running internally since we started working on the analysis of point mutations in protein families [ 31 , 32 ] and is accessible at http://3DSim.bioinfo.cnio.es/ .
+Some proteins that are not available in HSSP [ 33 ] and DSSP [ 34 ] programs are also omitted .
+The surface residues are defined based on their relative solvent accessible surface area ( RASA ) , which is calculated by the DSSP program [ 34 ] .
+Following the method used by ConSurf [ 36 ] , amino acid sequences similar to each other in the PDB [ 37 ] are collected by using PSI - BLAST [ 38 ] and then multiple aligned by using MUSCLE [ 39 ] .
+The evolutionary conservation of each amino acid position in the alignment is calculated by using the Rate 4Site algorithm [ 40 ] .
+Sequence entropy values for residues are extracted from the HSSP database [ 33 ] .
+PSSMs are taken from multiple sequence alignment obtained by PSI - BLAST [ 38 ] searching against NCBI non - redundant database ftp://ftp.ncbi.nih.gov/blast/db/ , with parameters j = 3 and e = 0 . 001 .
+ASA features represent the relative accessible surface areas , which are calculated by using DSSP program [ 34 ] for each residue in the unbound state .
+Here the LIBSVM package 2 . 8 http://www.csie.ntu.edu.tw/~cjlin/libsvm/ is used with radial basis function as the kernel .
+Finally , a test on protein complex 1IAI ( PDB code ) is conducted as an example to further illustrate the effectiveness of our approach by using the RasMol software [ 49 ] .
+Availability : The Swiss Var portal is available at www.expasy.org/swissvar .
+In this article , we present the SwissVar portal ( www.expasy.org/swissvar ) , which provides access to a comprehensive collection of single amino acid polymorphisms ( SAPs ) and diseases in the UniProtKB / Swiss - Prot knowledgebase via a unique search engine .
+The databases are implemented in PostgreSQL 8 . 1 . 9 and are updated at each UniProt release .
+The SwissVar portal can be accessed via www.expasy.org/swissvar .
+We have been developing a semantic interpreter , SemRep [ 19 ] , which extracts content from biomedical text in the form of semantic predications .
+While the UMLS Semantic Network has not been designed as an ontology in a strict sense , the extended version that SemRep uses [ 21 ] serves as an ontological resource:itdefinesadomainmodelconsistingofconcepttypes ( semantic types ) , relation types ( ontological predicates ) and the relationships that can hold between concept types ( ontological predications ) .
+SemRep processing is supported by an underspecified syntactic analysis based on the UMLS SPECIALIST Lexicon [ 22 ] and the MedPost part - of - speech tagger [ 23 ] .
+MetaMap [ 24 ] is used to map simple noun phrases to UMLS Metathesaurus concepts .
+Entrez Gene [ 25 ] serves as a supplementary source to the UMLS Metathesaurus with respect to gene / protein terms , which are identified using ABGene [ 26 ] , in addition to MetaMap .
+To lighten the burden of finding an appropriate UMLS Metathesaurus concept corresponding to a textual mention , UMLS Metathesaurus concepts were extracted from these sentences using MetaMap [ 24 ] and were provided to the annotators ( an average of 9 . 86 concepts per sentence ) .
+When in doubt , the annotator should try to find a concept that better matches the text ( a UMLS Metathesaurus concept or an Entrez Gene term ) using the UMLS Terminology Services ( UTS [ 35 ] ) or Entrez Gene [ 36 ] , keeping in mind that SemRep currently uses the 2006AA version of the UMLS knowledge sources .
+In fact , we have extended the UMLS Semantic Network to create the SemRep ontology in prior work [ 21 , 38 ] specifically to redress this gap .
+There are multiple mature , open source tools for 16S rRNA gene analyses , that are well maintained and widely used within the scientific community , such as QIIME ( Quantitative Insights Into Microbial Ecology ) [ 4 ] and mothur [ 5 ] .
+We have integrated those tools within the Genboree Microbiome Toolset and deployed them through the Genboree Workbench [ 6 ] using the Software - as - a - Service model .
+The output of RDP Classifier 2 . 1 ( and newer ) assigns each sequence to the most specific taxon level ( from the Domain to the Genus levels ) .
+The QIIME package [ 4 ] performs multi - step chained OTU picking using multiple third party tools , including cd - hit [ 11 ] , mothur [ 5 ] , and uclust [ 12 ] .
+Chimeric sequences , which can be falsely detected as novel organisms , resulting in the artificial inflation of diversity are detected and removed using Chimera Slayer [ 13 ] .
+Phylogenetic differences may be visualized using tools such as the interactive Tree Of Life ( iTOL ) , which supports upload , display , and manipulation of phylogenetic trees [ 15 ] .
+The phylogenetic - based UniFrac [ 14 ] algorithm enables the analysis of different microbiomes by providing both a quantitative measurement , using weighted UniFrac , and a qualitative measurement , using unweighted UniFrac .
+The pipeline utilizes the R package randomForest [ 20 ] for supervised learning and Boruta [ 21 ] for feature selection .
+Because randomForest does not inherently provide for feature selection [ 22 ] , we employed the R package Boruta , a feature selection algorithm built around the randomForest algorithm .
+A visualization of the phylogenetic tree , along with the sample metadata input ( Fig [ 6 ] . ) was produced using the Interactive Tree of Life ( iTOL ) [ 15 ] API from input generated by the Microbiome Toolset .
+The Genboree Microbiome Toolset is part of the Genboree Workbench and can be accessed at the address http://genboree.org/java-bin/workbench.jsp .
+Supported browsers are Internet Explorer versions 8 and above , Mozilla Firefox versions 7 and above .
+It is available at http://it.inf.uni-tuebingen.de/software/reveal/ .
+Furthermore , we integrated Reveal into our visual analytics software Mayday ( Battke et al . , 2010 ) , allowing for combined and highly interactive analyses of genotypic and expression data as well as meta - data ( e . g . disease phenotype ) .
+A popular stand - alone tool is WGAViewer ( Ge et al . , 2008 ) which offers an interactive Manhattan plot embedded into an annotation environment in order to help identify those associations with large biological relevance .
+Genevar ( Yang et al . , 2010 ) combines a database and a visualization of SNPs associated with gene expression using Manhattan plots .
+Two examples for this approach are eQTL Explorer ( Mueller et al . , 2006 ) and the AssociationViewer ( Martin et al . , 2009 ) .
+eQTL Viewer ( Zou et al . , 2007 ) is a web - based tool that visualizes the relationships between the expression traits and candidate genes in the eQTL regions .
+A specialized application to visualize all HapMap genotypes together with gene expression levels is SNPexp ( Holm et al . , 2010 ) .
+A visual analytics approach is followed with GenAMap ( Curtis et al . , 2011 ) .
+Among the commercial tools for this type of data , the SNP and Variation Suite ( SVS 7 ) by ( Golden Helix , 2012 ) offer various statistical tests and visualization within an integrated genome browser .
+Agilent ' s GeneSpring ( Agilent , 2012 ) has a number of statistical and visualization methods for GWASs , however , no specific eQTL analysis methods are offered .
+Illumina GenomeStudio [UNK] ( Illumina , 2012 ) also offers an integrated use of PLINK as well as a QTL viewer .
+On these data , statistical methods such as the PLINK tool ( Purcell et al . , 2007 ) can be used to compute the significance of the association between any SNP ( or pair of SNPs ) and differences in gene expression .
+User interaction further includes panning , rotating and zooming , as well as rearranging nodes either manually or using layout algorithms ( provided by the Jung library ( O ' Madadhain et al . , 2005 ) ) .
+Here , we use the same aggregation strategy as iHat ( Heinrich et al . , 2012 ) , our previously published prototype tool for visual analytics of GWASs .
+Further interactions include scrolling , zooming and interactive selection of SNPs of interest , which can then be used for example to be displayed in Mayday ' s genome browser . 3 . 3 eQTL expression .
+To illustrate how Reveal can be used to analyze eQTL data , we applied it to the data provided for the BioVis 2011 Contest ( http://it.inf.uni-tuebingen.de/software/reveal ) .
+All samples were sequenced with the Illumina technology ( http://www.illumina.com ) , which is now the most commonly used NGS platform for RNA - seq [ 32 ] .
+In the second phase , paired - ends and singletons were mapped with TopHat [ 33 ] in a two - steps procedure .
+Alignment files from paired - end and singleton reads were finally merged in a single BAM file using the merge utility of samtools [ 34 ] .
+Totcounts were computed using bedtools [ 35 ] .
+We implemented the method for computing maxcounts in a new patch for bedtools that can be downloaded from http://www.dei.unipd.it/~finotell/maxcounts/ ( see additional details in " Additional file [ 1 ] " ) .
+Within - lane full - quantile normalization of counts on exon length was performed using EDASeq [ 24 ] .
+Further biological processes can be described using cause - and - effect relationships from the OpenBEL framework [ 29 ] .
+Raw RNA expression data were analyzed using the affy and gcrma packages of the Bioconductor suite of microarray analysis tools available in the R statistical environment ( version 2 . 14 . 0 ) .
+The fold - changes and their moderated t - statistics were computed using limma [ 42 ] .
+This paradigm is becoming increasingly popular [ 21 , 23 , 43 , 44 ] and among others , “ backward - causal ” features have been introduced recently in Ingenuity Pathway Analysis software [ 43 ] .
+To facilitate this task , the study data is manually entered into the OpenClinica Clinical Data Management System ( CDMS ) by study staff [ 13 ] .
+OpenClinica [ 14 ] is an open - source CDMS for collecting and managing clinical data .
+These queries have been executed on a Virtuoso 6 . 1 instance running on a virtual machine with an AMD Opteron Processor 62xx CPU , 8GB of DDR 3 RAM and running Ubuntu 13 . 04 LTS ( Raring Ringtail ) .
+ECC2comp , presented in [ 16 ] and illustrated in Fig [ 1 ] . , is a further reduction of EColiCore 2 derived by exploiting NetworkReducer [ 17 ] , i . e . , an algorithm able to automatically compress metabolic models by lumping linear chains of reactions in a single cumulative equation and by removing elements ( metabolites and reactions ) that are non essential to represent key metabolic functions referred to as “ protected functions ” .
+The numerical integration of the ODEs system has been realized exploiting the software library LSODA ( Livermore solver for ODEs with automatic method ) [ 19 .
+efficiently implemented in SciPy [ 20 ] .
+In particular here we exploited PyTables [ 21 ] , a package for managing hierarchical datasets designed to efficiently and easily cope with extremely large amounts of data .
+In addition , we also estimated the D . silvatica genome size from the distribution of k - mers ( from short reads ) with Jellyfish v . 2 . 2 . 3 ( Jellyfish , https://scicrunch.org/resolver/RRID:SCR_005491 ) [ 28 ] .
+The distribution of k - mers of size 17 , 21 , and 41 ( GenomeScope ( GenomeScope , https://scicrunch.org/resolver/RRID:SCR_017014 ) [ 29 ] ) resulted in a haploid genome size of ∼ 1 . 23 Gb ( Supplementary Fig . S1 ) .
+We downloaded all genomes of all these kinds available in the GenBank database ( Supplementary Table S1 - 3 ) and used BLASTN v 2 . 4 . 0 ( BLASTN , https://scicrunch.org/resolver/RRID:SCR_001598 ) [ 31 ] to detect and filter all contaminant reads ( E - value < 10 ; > 90 % alignment length ; > 90 % identity ) .
+We preprocessed raw reads using PRINSEQ v . 0 . 20 . 3 ( PRINSEQ , https://scicrunch.org/resolver/RRID:SCR_005454 ) [ 32 ] .
+For the short - insert 100 PE library , we used Trimmomatic v 0 . 36 ( Trimmomatic , https://scicrunch.org/resolver/RRID:SCR_011848 ) [ 33 ] with specific lists of adapters of the TruSeq v 3 libraries to filter all reads shorter than 36 bp or with minimum quality scores < 30 along 4 - bp sliding windows .
+Long - insert MP libraries were preprocessed using NxTrim v 0 . 4 . 1 [ 34 ] with default parameters ( Supplementary Table S1 - 4a and b ) .
+We preprocessed the raw PacBio reads using the SMRT Analysis Software ( SMRT Analysis Software , https://scicrunch.org/resolver/RRID:SCR_002942 ) [ 35 ] , by generating circularized consensus sequence to further perform a polishing analysis with Pilon v 1 . 22 ( Pilon , https://scicrunch.org/resolver/RRID:SCR_014731 ) [ 36 ] based on short reads ( Supplementary Table S1 - 4c ) .
+We used MaSuRCA v 3 . 2 . 9 ( MaSuRCA , https://scicrunch.org/resolver/RRID:SCR_010691 ) [ 37 ] for a hybrid de novo assembly of the D . silvatica genome ( Supplementary Fig . S2 ) .
+Additionally , we performed a scaffolding phase using AGOUTI ( minimum number of joining reads pairs support , k = 3 ) [ 38 ] , and the raw reads from a D . silvatica RNA sequencing ( RNAseq ) experiment [ 39 ] ( Supplementary Table S1 - 5 and S1 - 6 ) .
+Particularly , we used 5 datasets , BUSCO v 3 ( BUSCO , https://scicrunch.org/resolver/RRID:SCR_015008 ) with genome option [ 40 ] using ( i ) the Arthropoda or ( ii ) the Metazoa dataset , ( iii ) the 457 core eukaryotic genes ( CEGs ) of Drosophila melanogaster [ 41 ] , ( iv ) the 58 , 966 transcripts in the D . silvatica transcriptome [ 39 ] , and ( v ) the 9 , 473 1:1orthologsacross5Dysderaspecies , D . silvatica ; D . gomerensis Strand , 1911 ; D . verneaui Simon , 1883 ; D . tilosensis Wunderlich , 1992 ; and D . bandamae Schmidt , 1973 obtained from the comparative transcriptomics analysis of these species [ 42 ] .
+We determined the average genome coverage for each sequencing library with SAMtools v 1 . 3 . 1 ( SAMtools , https://scicrunch.org/resolver/RRID:SCR_002105 ) [ 43 ] , by mapping short reads ( using bowtie 2 v 2 . 2 . 9 [ bowtie 2 , https://scicrunch.org/resolver/RRID:SCR_005476 ] [ 44 ] ) or long reads ( using minimap 2 [ 45 ] ) to the final draft assembly ( Table [ 1 ] ; Supplementary Table S1 - 8 ; Supplementary Fig . S3 ) .
+We analyzed the distribution of repetitive sequences in the genome of D . silvatica , using either a de novo with RepeatModeler v 1 . 0 . 11 ( RepeatModeler , https://scicrunch.org/resolver/RRID:SCR_015027 ) [ 46 ] , or a database - guided search strategy with RepeatMasker v . 4 . 0 . 7 ( RepeatMasker , https://scicrunch.org/resolver/RRID:SCR_012954 ) [ 47 ] .
+We used 3 different databases of repetitive sequences , ( i ) D . silvatica - specific repetitive elements generated with RepeatModeler v 1 . 0 . 11 [ 46 ] , ( ii ) the Dfam _ Consensus [ 48 ] ( version 20170127 ) , and ( ii ) the RepBase ( version 20170127 ) [ 49 , 50 ] .
+We used HISAT 2 v 2 . 1 . 0 ( HISAT 2 , https://scicrunch.org/resolver/RRID:SCR_015530 ) [ 51 ] to map the RNAseq reads to the reference and Trinity v 2 . 4 . 0 . ( Trinity , https://scicrunch.org/resolver/RRID:SCR_013048 ) [ 52 ] ( genome - guided bam , max intron = 50 kb , min coverage = 3 ) to assemble the transcriptome ( named " Dsil - RefGuided transcriptome " ; Supplementary Table S1 - 10 ) .
+We used the MAKER 2 v 2 . 31 . 9 ( MAKER 2 , https://scicrunch.org/resolver/RRID:SCR_005309 ) [ 53 ] genome annotation pipeline for the structural annotation of D . silvatica genes ( Supplementary Fig . S2 ) , using both ab initio gene predictions and annotation evidences from D . silvatica and other sources .
+For the ab initio gene predictions we initially trained Augustus v 3 . 1 . 0 ( Augustus , https://scicrunch.org/resolver/RRID:SCR_008417 ) [ 54 ] and SNAP ( SNAP , https://scicrunch.org/resolver/RRID:SCR_002127 ) [ 55 ] softwares using scaffolds longer than 20 kb , and BUSCO gene models generated from completeness searches .
+After several iterative training rounds , we applied MAKER 2 , Augustus , and SNAP , adding other sources of evidence: ( i ) transcript evidence ( Dsil - RefGuided transcriptome ) , ( ii ) RNAseq reads exon junctions generated with HISAT 2 [ 51 ] and regtools [ 57 ] , and ( iii ) proteins annotated in other arthropods , especially chelicerates ( Fig [ 2 ] . ; Supplementary Table S1 - 11 ) .
+We searched for the presence of protein domain signatures in annotated protein - coding genes using InterProScan v 5 . 15 - 54 ( InterProScan , https://scicrunch.org/resolver/RRID:SCR_005829 ) [ 60 , 61 ] , which includes information from public databases ( see additional details in Supplementary Table S1 - 7 ) .
+Additionally , we used NCBI BLASTP v . 2 . 4 . 0 ( BLASTP , https://scicrunch.org/resolver/RRID:SCR_001010 ) [ 31 ] ( E - value cutoff < 10 ; > 75 % alignment length ) against the Swiss - Prot database to annotate D . silvatica genes .
+We searched for homologs of the functionally annotated peptides ( 36 , 398 ) ( i ) among CEG genes of Drosophila melanogaster [ 41 ] ; ( ii ) among the predicted peptides of Parasteatoda tepidariorum , a spider with a well - annotated genome [ 62 ] ; ( iii ) among the 9 , 473 1:1orthologsacross5Dysderaspecies ; and ( iv ) among the 2 , 198 single - copy genes identified in all spiders and available in OrthoDB v 10 [ 56 ] .
+Furthermore , the analysis based on the putative homologs of the single - copy genes included in the BUSCO dataset ( BUSCO , https://scicrunch.org/resolver/RRID:SCR_015008 ) [ 40 ] , applying the default parameters for the genome and protein mode , also demonstrated the high completeness of the genome draft .
+We assembled the mitochondrial genome of D . silvatica ( mtDsil ) from 126 , 758 reads identified in the 100PE library by the software NOVOPlasty [ 63 ] .
+CGVIEW ( CGVIEW , https://scicrunch.org/resolver/RRID:SCR_011779 ) [ 64 ] was used to generate a genome visualization of the annotated mtDsil genome ( Supplementary Fig . S10 ) .
+AED : annotation edit distance ; AGOUTI : Annotated Genome Optimization Using Transcriptome Information ; BLAST : Basic Local Alignment Tool ; bp : base pair ; BUSCO : Benchmarking Universal Single Copy Orthologs ; CEG : core eukaryotic gene ; Cz : Cretaceous period ; Dsil : Dysdera silvatica ; Gb : gigabase pairs ; GC : guanine cytosine ; GO : Gene Ontology ; HCR : high - coverage regions ; Isca : Ixodes scapularis ; kb : kilobase pairs ; LINE : long interspersed nuclear element ; LTR : long terminal repeats ; MaSuRCA : Maryland Super - Read Celera Assembler ; Mb : megabase pairs ; MP : mate pair ; Mya : million years ago ; NCBI : National Center for Biotechnology Information ; PacBio : Pacific Biosciences ; PE : paired - end ; PRINSEQ : PReprocessing and INformation of SEQuence data ; Ptep : Parasteatoda tepidariorum ; RNAseq : RNA sequencing ; SINE : short interspersed nuclear element ; Smim : Stegodyphus mimosarum ; SMRT : .
+For PacBio library construction , the genomic DNA of C . mollissima was sheared to 20 kb , and fragments shorter than 7 kb were filtered using BluePippin ( Sage Science , Beverly , MA , USA ) .
+The filtered DNA was then used to prepare a proprietary SMRTbell library using the PacBio DNA Template Preparation Kit ( Pacific Biosciences , Menlo Park , CA , USA ) .
+The PacBio data quality control standard of RQ > 0 . 75 was used , and the minimum subread length was 500 bp using SMRT Link 6 . 0 software .
+The assembled sequence was then polished using Quiver ( SMRT Analysis version 2 . 3 . 0 ) with the default parameters .
+Both RepeatModeler and RepeatMasker ( RepeatMasker , https://scicrunch.org/resolver/RRID:SCR_012954 ) [ 26 ] were used for the de novo identification and masking of repeats .
+The ab initio gene prediction was conducted with Augustus ( Augustus , https://scicrunch.org/resolver/RRID:SCR_008417 ; version 3 . 2 . 2 ) , GeneMark - ET ( version 4 . 29 ) , and SNAP 15 to predict coding genes .
+Then , Exonerate ( Exonerate , https://scicrunch.org/resolver/RRID:SCR_016088 ; version 2 . 47 . 3 ) [ 27 ] was used to generate gene structures based on the homology alignments .
+For the transcriptome - based prediction , transcriptome data were generated from mixed samples of flowers , buds , leaves , nuts , and roots on the Illumina HiSeq 2500 platform ( a total of 20 . 84 Gb raw data ) and mapped to the genome assembly using TopHat ( TopHat , https://scicrunch.org/resolver/RRID:SCR_013035 ; version 2 . 1 . 1 ) .
+Cufflinks ( Cufflinks , https://scicrunch.org/resolver/RRID:SCR_014597 ; version 2 . 1 . 1 ) [ 28 ] was then used to identify spliced transcripts in the gene models .
+All the gene evidence predicted by the aforementioned 3 approaches was integrated by EVidenceModeler ( EVM version 1 . 1 . 1 ) .
+The obtained gene set was functionally analyzed using BLASTP ( BLASTP , https://scicrunch.org/resolver/RRID:SCR_001010 ) with an E - value of 1e against the NCBI - NR , Swiss - Prot , and euKaryotic Orthologous Groups ( KOG ) databases .
+Protein domains were annotated by mapping genes to the InterPro and Pfam databases using InterProScan ( InterProScan , https://scicrunch.org/resolver/RRID:SCR_005829 ) [ 29 ] and HMMER ( Hmmer , https://scicrunch.org/resolver/RRID:SCR_005305 ) [ 30 ] .
+To evaluate the completeness and coverage of the assembly , we aligned Illumina DNA and RNA reads to the C . mollissima assembly using BWA ( BWA , https://scicrunch.org/resolver/RRID:SCR_010910 ) [ 31 ] and HISAT [ 32 ] , respectively .
+In the core gene estimation using BUSCO ( BUSCO , https://scicrunch.org/resolver/RRID:SCR_015008 ) [ 33 ] , 1 , 392 of the 1 , 440 core genes ( 96 . 7 % ) were found to be complete in the assembled genome , and 1 , 412 ( complete BUSCOs and fragmented BUSCOs ) ( 98 . 1 % ) of the 1 , 440 core genes had at least partial matches ( Table S5 ) .
+To gain greater insights into the evolutionary dynamics of the genes , we determined the expansion and contraction of the orthologous gene clusters in these 8 species with CAFE software ( CAFE , https://scicrunch.org/resolver/RRID:SCR_005983 ) [ 42 ] .
+To examine the evolutionary relationships of Chinese chestnut with other plants , we applied RAxML software ( RAxML , https://scicrunch.org/resolver/RRID:SCR_006086 ; version 8 . 0 . 0 ; substitution model PROTGAMMAJTT , bootstrap value 100 ) [ 43 ] to perform a maximum - likelihood genome - wide phylogenetic analysis of 540 single - copy genes from the 9 plant genomes ( Fig . 2b ) .
+To estimate the insertion times of the LTR elements , we identified complete LTRs using a combination of de novo searches and manual inspection with LTR _ Finder ( LTR _ Finder , https://scicrunch.org/resolver/RRID:SCR_015247 ) [ 44 ] .
+GO enrichment analysis of genes from the TAGs was performed using OmicShare Tools [ 48 ] .
+BAC : bacterial artificial chromosome ; BLAST : Basic Local Alignment Search Tool ; bp : base pairs ; BUSCO : Benchmarking Universal Single - Copy Orthologs ; BWA : Burrows - Wheeler Aligner ; Gb : gigabase pairs ; GO : Gene Ontology ; kb : kilobase pairs ; KEGG : Kyoto Encyclopedia of Genes and Genomes ; KOG : euKaryotic Orthologous Groups ; LTR : long terminal repeat ; Mb : megabase pairs ; Mya : million years ago ; NCBI : National Center for Biotechnology Information ; PacBio : Pacific Biosciences ; PE : paired - end ; QTL : quantitative trait locus ; RAxML : Randomized Axelerated Maximum Likelihood ; TAG : tandemly arrayed genes .
+To enhance compliance with the FAIR principles ( findability , accessibility , interoperability , and reusability ) for scholarly digital objects [ 17 ] , we designed a Reproducible Epigenomic Analysis ( REA ) pipeline for ChIP - seq and RNA - seq using Galaxy [ 18 ] , an open web - based platform where each analytical step is formally documented and can be shared and reproduced .
+These workflows were executed on a locally administered Galaxy server via a Docker container image [ 19 ] .
+Analytical steps that could not be integrated within a Galaxy workflow were captured and documented in Jupyter notebooks [ 20 ] , an open - source interactive computing environment that allows sharing of code , documentation , and results .
+The REA pipeline is available in the GitHub repository [ 21 ] and in the associated Zenodo release [ 22 ] .
+We used well - established tools including Bowtie 2 [ 23 ] for short - read sequence alignment , HTSeq [ 24 ] for feature mapping quantification , epic 2 [ 25 ] for ChIP - seq peak calling , MAnorm [ 26 ] for quantitative comparison of ChIP - seq data , and DESeq 2 [ 27 ] for differential gene expression analysis .
+Two of the most commonly used aligners for ChIP - seq analysis are Burrows - Wheeler Aligner ( BWA ) [ 28 ] and Bowtie 2 , which carry out fast mapping of DNA sequences using the Burrows - Wheeler transform method .
+Mapping with Bowtie 2 against the B . rapa v 3 . 0 genome [ 16 ] yielded an average 82 % mapping rate , where 42 - 61 % of the reads mapped to multiple locations ( Table S1 ) , likely reflecting the mesopolyploid nature of the B . rapa genome or the abundance of repeated DNA elements .
+After mapping , duplicated reads were removed and ChIP - seq signal distribution over B . rapa genome was visualized and inspected using the Integrative Genomics Viewer ( IGV ) [ 29 ] .
+We compared 2 widely used but different peak - calling algorithms : MACS 2 [ 30 ] , an algorithm initially designed to identify sharp peaks but extended to detect broad peaks such as those arising from this analysis ; and epic 2 , a highly performant implementation of SICER [ 31 ] , an algorithm designed for noisy and diffuse ChIP - seq data such as histone methylation .
+These gene lists were used as input for singular enrichment analysis ( SEA ) of Gene Ontology ( GO ) terms using agriGO [ 33 ] .
+The resulting GO term list was summarized and reduced in complexity using REVIGO [ 34 ] .
+The pipeline was constructed using a set of well - established genomic tools and approaches , using a combination of a Galaxy environment and Jupyter notebooks [ 20 ] .
+Jupyter Lab ' s R and bash kernels were installed using Anaconda 3 ( Anaconda Software Distribution , 2018 ) .
+The REA pipeline was implemented as a series of steps distributed within a Docker container [ 52 ] that includes all required software dependencies .
+To be able to download and use a Dockerized version of Galaxy [ 53 ] , Docker version 18 . 09 . 3 was first installed following the documentation on Docker - CE for Ubuntu .
+Next , Galaxy version 18 . 05 was locally installed with the following commands: .
+This local Galaxy server can be accessed and administered on http://localhost:8080/ .
+Most tools were installed from the Galaxy Tool Shed , with the exception of epic 2 v 0 . 0 . 14 [ 25 ] , which we manually installed inside the Docker container via an interactive session using Python pip and wrapped as a Galaxy tool .
+Our wrapped epic 2 tool has been successfully integrated into Galaxy and published into the Galaxy Tool Shed [ 54 ] .
+All of these files are also available in the associated Zenodo snapshot release [ 22 ] .
+A first step of trimming was performed with Trimmomatic ( v 0 . 36 . 5 ) ( Trimmomatic , https://scicrunch.org/resolver/RRID:SCR_011848 ) [ 55 ] .
+Trimmed reads were mapped to the B . rapa Chiifu v 3 . 0 genome using Bowtie 2 v 2 . 3 . 4 . 2 ( Bowtie , https://scicrunch.org/resolver/RRID:SCR_005476 ) or BWA v 0 . 7 . 17 . 3 ( BWA , https://scicrunch.org/resolver/RRID:SCR_010910 ) , and the results were compared with SAMtools Flagstat [ 56 ] .
+BAM files were filtered with SAMtools v 1 . 8 ( SAMTOOLS , https://scicrunch.org/resolver/RRID:SCR_002105 ) by mapping quality ( including concordance of mates ) and by duplication state ( possible duplicate reads that may arise during library preparation ) , marked by Picard MarkDuplicates v 2 . 18 . 2 . 0 ( Picard , https://scicrunch.org/resolver/RRID:SRC_006525 ) [ 57 ] .
+The set of deduplicated reads was used for ChIP - seq peak calling on pooled replicates using epic 2 v 0 . 0 . 14 or MACS 2 v 2 . 1 . 1 ( MACS 2 , https://scicrunch.org/resolver/RRID:SRC_013291 ) for comparison to one another ; the epic 2 output was then used for downstream processes .
+Additional steps in the workflow are aimed at collecting quality metrics using MultiQC [ 58 ] , as well as producing bigwig files using DeepTools 3 . 1 . 2 ( Deeptools , https://scicrunch.org/resolver/RRID:SCR_016366 ) [ 59 ] with the coverage of filtered alignments on bin sizes of 50 bp .
+Differential levels of H3K 27me 3 histone mark intensities were computed by comparison of read abundances on our curated list of peaks with MAnorm v 1 . 2 . 0 ( MAnorm , https://scicrunch.org/resolver/RRID:SCR_010869 ) [ 26 ] , which uses MA plot methods to normalize read density levels on provided peaks and calculate P - values .
+Peaks from either epic 2 or MAnorm were annotated according to overlap of B . rapa gene models using ChIPpeakAnno ( ChIPpeakAnno , https://scicrunch.org/resolver/RRID:SCR_012828 ) [ 60 ] , and the distribution of ChIP signal over genes was visualized with ngs . plot ( ngs . plot , https://scicrunch.org/resolver/RRID:SCR_011795 ) [ 61 ] .
+The obtained counts were used for mRNA differential expression analysis with DESeq 2 1 . 18 . 1 ( DESeq 2 , https://scicrunch.org/resolver/RRID:SCR_015687 ) to infer gene expression changes of leaves compared to inflorescences .
+Gene Ontology analysis was performed using agriGO v 2 . 0 ( agriGO , https://scicrunch.org/resolver/RRID:SCR_006989 ) [ 33 ] ( Fisher statistical test method ; Yekutieli Multi _ test adjustment method ; P < 0 . 05 ; and Plant GO slim ontology type ) ; data were visualized reduced in complexity and redundant GO terms using REViGO ( REViGO , https://scicrunch.org/resolver/RRID:SCR_005825 ) [ 34 ] with default parameters ( allowed similarity = 0 . 7 ; semantic similarity measure = SimRel ) .
+We curated BraA . AG . a gene structure using AUGUSTUS ( Augustus , https://scicrunch.org/resolver/RRID:SCR_008417 ) [ 63 ] and Bra 013364 ( B . rapa genome V 1 . 5 ) gene information at the B . rapa database [ 46 ] .
+Latest versions of the components of the REA pipeline , and instructions to deploy the Galaxy / Jupyter containers and run the analysis , can be found in the GitHub repository https://github.com/wilkinsonlab/epigenomics_pipeline ; this is associated with a Zenodo release to match the configuration used in this publication [ 22 ] .
+The REA pipeline is registered as https://scicrunch.org/resolver/RRID:SCR_017544 and biotools : Epigenomics _ Workflow _ on _ Galaxy _ and _ Jupyter at SciCrunch and bio . tools databases , respectively .
+3 ′ RNA - seq : 3 ′ - end mRNA high - throughput sequencing ; AG : AGAMOUS ; bp : base pairs ; cDNA : complementary DNA ; ChIP : chromatin immunoprecipitation ; ChIP - seq : ChIP followed by high - throughput sequencing ; ChIP - qPCR : ChIP followed by real - time quantitative PCR ; CLF : CURLY LEAF ; DAG : days after germination ; DEG : differentially expressed genes ; FAIR : findability , accessibility , interoperability , and reusability ; FC : fold change ; FDR : false discovery rate ; GO : gene ontology ; H3K 27me 3 : histone H3 lysine 27 trimethylation ; IGV : integrative genomics viewer ; kb : kilobase pairs ; LOWESS : Locally Weighted Scatterplot Smoothing ; M : log fold - change of the normalized H3K 27me 3 read densities in leaves relative to inflorescences calculated by MAnorm ; MACS : Model - based Analysis of ChIP - Seq ; mRNA : messenger RNA ; NCBI : National Center for Biotechnology Information ; PRC 2 : Polycomb repressive complex 2 ; REA : Reproducible Epigenomic Analysis ; RNA - seq : RNA sequencing ; RT - qPCR : .
+The method of batch correction used for TCGA microarray data was based on median and standard deviation correction , following Hsu et al . [ 16 ] , and for TCGA RNA - seq data , a linear model using limma [ 17 ] .
+Second , we considered a Gaussian splitting method in which the central mode is fit by a Gaussian density function using the R package mclust [ 18 ] .
+Additionally , these sets of genes were also used to query several GO pathway analysis tools ( Gorilla [ 21 ] , PantherDB [ 22 ] ) .
+R version 3 . 2 . 3 was used for all analysis .
+All five datasets contain samples from primary solid tumour and recurrent solid tumour collected at UNC using Illumina HiSeq 2000 RNA Sequencing Version 2 Analysis , were log 2 - transformed and reported as fragments per kilobase of transcript per million ( FPKM ) mapped reads via RSEM [ 33 ] .
+These data were collected using an Illumina HiSeq 2000 , processed with GEM mapper 1 . 349 , and log 2 - transformed .
+Summary intensities were extracted by the methylumi R package ( v . 2 . 10 . 0 run in R v . 3 . 1 . 0 ) .
+A variable standard deviation Gaussian mixture model from the R / Bioconductor package mclust ( version 5 . 0 . 2 run on R version 3 . 1 . 2 ) was used to cluster genes by skew difference .
+We used tools from the Bioconductor package GOstats ( version 1 . 7 . 4 , run on R version 3 . 1 . 2 ) [ 36 ] and the Bioconductor package KEGG . db ( version 2 . 1 run on R version 3 . 1 . 2 ) [ 37 ] .
+The identified proteins and phosphoproteins in all three cell lines were grouped based on their class using the PANTHER system [ 17 ] as presented in supplementary Figure S1 .
+We have examined the differentially expressed proteins and phosphoproteins and their involvement in pathway enrichment analysis using DAVID software [ 19 ] .
+Peptide / protein identification and quantification were performed using Integrated Proteomics Pipeline - IP 2 ( Integrated Proteomics Applications ) .
+The MS raw data files were converted into mzXML format using RawConverter [ 50 ] .
+For protein identification , tandem mass spectra were searched against a database including the Uniprot human database , reversed sequences , and contaminate using ProLuCID [ 51 ] .
+Identified proteins were further filtered with 1 % false discovery rate ( FDR ) using DTASelect [ 52 ] .
+Protein quantitative analysis was achieved by Census tool [ 53 ] .
+The statistical analysis for the quantitative results was done by quantitative COMPARE tool , part of IP 2 .
+Go enrichment analysis for protein classification was performed using Protein Analysis THrough Evolutionary Relationships ( PANTHER ) system .
+The pathway enrichment analysis was generated using the Database for Annotation , Visualization , and Integrated Discovery ( DAVID ) software .
+For treemap and Volcano plots visualization , Tableau software was used ( v . 2018 . 1 . 1 , Tableau , WA , USA ) .
+Analysing the optimised azole ligands ( Gaussian 16 C . 01 program [ 25 ] ) docked to the protein ( PDB code:3ewh.pdb , AutoDock Vina [ 26 ] ) , we noticed that ligands 1 - 6 and 9 nearly overlapped ( Figure 1 ) .
+For the analysis , we used the Psi 4 1 . 3 . 2 software [ 37 ] treating the complexes ligand - amino acid as a closed - shell system [ 38 , 39 ] and utilizing the recommended jun - cc - pVDZ basis set [ 40 ] .
+For this purpose , we applied the polarizable continuum ( PCM ) solvation model [ 45 ] with water as solvent on the MP 2 / 6 - 31G * level of theory using the GAMESS program [ 46 ] .
+In this evaluation , we considered values of the final heat of formation ( HOF ) under standard conditions using the Mopac 2016 program and its implemented module Mozyme [ 47 ] .
+For this purpose , the Desmond software from Schrodinger Suite [ 49 ] was employed to simulate the solvated complexes .
+Next , all the resulting conformations were optimized with PM 7 ( Mopac 2016 ) [ 47 , 51 ] , then each from the four most energetically stable conformers of hetarenes 1 - 9 , i . e . , with the lowest HOF , was optimized using density functional theory formalism [ 52 ] in the gaseous phase .
+On this account , DFT calculations were executed , and geometries of each previously pre - optimized conformers of 1 - 9 ( Scheme 1 ) were further optimized using the Gaussian 16 C . 01 program [ 25 ] at the B3LYP / 6 - 31G ( d , p ) level of theory ( very tight criteria ) [ 53 ] .
+The molecular electrostatic potential ( MEP ) was determined by the B3LYP / 6 - 311 + + G ( 2d , 3p ) approach for the conformers of azoles 1 - 9 ( 1st poses ) with geometry previously optimized at B3LYP / 6 - 31G ( d , p ) level of theory in the gaseous phase ( Gaussian 16 C . 01 program [ 25 ] , key - word , pop = esp ” ) .
+The genetic algorithm ( GA ) method implemented in the program AutoDock Vina [ 26 ] was employed to locate the appropriate binding orientations and conformations of the compounds into the VEGFR 2 binding pocket .
+The outputs ( * . pdbqt files ) after docking procedure were visualized using the Chimera 1 . 13 . 1 package [ 54 ] .
+The projections of the 1st poses of azoles 1 - 9 docked to the kinase pocket were visualised with LigPlot + v . 2 . 2 software [ 55 , 56 ] ( Figure 2a - c ) .
+For semi - empirical calculations with the use of the PM 7 method [ 48 ] , we used the Mopac 2016 software [ 47 ] and Mozyme method [ 50 ] .
+For this purpose , we applied the MP 2 / 6 - 31G * level using the GAMESS program [ 46 ] , as well as the polarizable continuum ( PCM ) solvation model [ 45 ] and water as a solvent .
+For molecular dynamics MD calculations , the Desmond software [ 49 ] was employed to simulate the solvated complexes .
+The output trajectory of indazole 1 was hierarchically clustered , basing on the RMSD matrix , into 15 clusters using trajectory analysis tools from the Maestro ( Schrodinger ) suite .
+The output of CAVER 3 . 0 provided us with the necessary data for CAVERDOCK computational analysis of the time evolution of individual pathways .
+The MS - ESI parameters were as follows:positiveandnegativemode ; ESI interface voltage , 4 . 5 kV and − 3 . 5 kV ; detector voltage , 1 . 15 kV ; nebulizing gas flow , 1 . 5 mL / min ; drying gas flow , 15 mL / min ; heat block temperature , 200 ° C ; temperature of desolvation line pipe , 250 ° C , SCAN mode 300 - 600 m / z ; and chromatograms were analyzed using software LabSolutions ver . 5 . 75 SP 2 ( Shimadzu , Kyoto , Japan ) .
+The spectra were recorded in Orbitrap operated with a resolution of 100 , 000 and processed using Xcalibur software ( Thermo Fisher Scientific ) . 4 . 8 .
+The analysis of the access tunnels was performed by Caver 3 . 0 PyMOL Plugin [ 29 , 38 ] , as described previously [ 39 ] .
+The molecular structure was opened using PyMOL 1 . 7 and the starting point coordinates were set in the position corresponding to 30 . 969 , 29 . 83 , and 38 . 043 A .
+In order to explore the accessibility of substrates rutin and isoquercitrin to the active site of AnRut protein , the CAVERDOCK 1 . 1 [ 40 ] tool was applied .
+The current version of CaverDock uses CAVER for the pathway identification and a modified Autodock Vina ver . 1 . 1 . 2 [ 41 ] as the docking engine .
+The structures of the rutin and isoquercitrin substrates were obtained from the Pubchem database [ 42 ] and their molecular geometry was optimized using Chimera [ 43 ] .
+The involvement of active site residues in the substrate binding was examined by DS Visualizer ver . 20 . 1 . 0 . 19295 [ 44 ] , which provided all types of non - covalent interactions in two - dimensional ( 2D ) diagram . 4 . 10 .
+Before molecular dynamics simulations , rutin and isoquercitrin substrates were docked into the AnRut crystal structure using Autodock Vina tool implemented in Chimera 1 . 3 . 1 ; the size of grid box was as follows:size_x=19.87A , size _ y = 22 . 97 A , and size _ z = 18 . 56 A .
+Then , the protein molecule was consecutively processed using molecular dynamics software Gromacs 2016 . 3 [ 45 , 46 ] with OPLS - AA / L all - atom force field .
+Mutalyzer ( https://mutalyzer.nl/ ) is a Web interface used for constructing , validating , and transforming sequence variant descriptions .
+Variant Validator ( https://variantvalidator.org/ ) is a web - based variant validation tool which provides an interface which allows the validation of genomic variations published in scientific literature or databases .
+Hence , we used 9 tools which consist of standalone molecular modeling packages such as FoldX [ 11 ] , Schrodinger with two differ ( ent force fields , OPLS 2005 [ 12 ] and OPLS 3 [ 13 ] , MOE [ 14 ] and web servers such as CUPSAT [ 15 ] , mCSM [ 16 ] , SDM [ 17 ] , iMutant 2 . 0 [ 18 ] and POPMUSIC [ 19 ] .
+To perform MD simulations , we selected the first structure from the ensembles of solution structures and mutations were introduced using COOT [ 23 ] .
+The variant data is stored in MongoDB v 3 . 4 . 10 .
+The data can be accessed through a web interface running on Apache HTTP server using PHP 7 . 0 .
+The user - friendly web interface for querying the database is coded in PHP 7 . 0 , AngularJS , HTML , Bootstrap 4 and CSS .
+MongoDB v 3 . 4 . 10 was used to keep track of data processing through the web interface .
+A total of four functional protein domains were annotated as per Pfam database using maftools package in r - programming .
+The datasets considered include the 1000 Genomes , ExAC and the gnomAD ( version 2 ) .
+Similarly , when applied to two different force fields , i . e . , OPLS 2005 and OPLS 3 , Schrodinger predicted as ‘ stabilizing ’ for variants R 844C , R 844H , P852L , G876R .
+All analysis was analyzed with Prism 8 . 0 software .
+The ProdMX is a free and publicly available Python package which can be installed with popular package mangers such as PyPI and Conda , or with a standard installer from source code available on the ProdMX GitHub repository at https://github.com/visanuwan/prodmx .
+Pfam [ 5 ] is a popular database started more than two decades ago , that collects a broad set of protein functional domains using the HMMER tool [ 6 ] .
+Early tools for domain architecture comparison , such as CDART [ 7 ] are often implemented as a web - based application , and is limited by the number of inputs .
+The data manipulation in the tool was handled with the Pandas package [ 11 ] .
+The database was implemented to store protein accessions associated with protein functional domains or domain architectures as an option for users with SQlite [ 12 ] .
+The genomes were run through Prodigal [ 16 ] for prediction of proteins ; the proteins were then searched for functional domains using HMMER 3 . 1b 2 with Pfam version 32 [ 17 ] , resulting 4950 protein functional domains and 11 , 574 domain architectures .
+The ProdMX requires an installation of Python 3 . 5 or newer , which is distributed through the Python Software Foundation [ 18 ] .
+Other dependencies can be detected and installed by either the Python Package Index ( PyPI ) or Conda [ 19 ] .
+The test data and extended versions for example 3 . 1 and 3 . 2 in Jupyter Notebook can be downloaded at the ProdMX GitHub repository ( https://github.com/visanuwan/prodmx ) .

test_phase1_texts.txt

@@ -0,0 +1,203 @@
+Data were analysed using Stata V 13 ( StataCorp , Stata Statistical Software : Release 13 , College Station , Texas , USA ) .
+Descriptive statistics were performed using Graphpad Prism 6 .
+Linkage disequilibrium between the two UCP 2 polymorphisms was determined using the online tool CubeX [34] ( http://www.oege.org/software/cubex/ ) .
+All data analysis was performed using IBM SPSS Statistics 18.0 .
+All analyses were performed using STATA 11 ( Stata Corporation , College Station , TX , U.S .A . )
+All statistical calculations , except those pertaining to the Gower calculations , were made using SPSS 18 ( IBM Corp . , Somers , NY , USA ) .
+The search was conducted using PAUP * v. 4.0b 10 [45] with 100 random stepwise additions and TBR branch swapping .
+This was performed using the svyset and svy commands in Stata Version 12.1 ( StataCorp , 4905 Lakeway Drive , College Station , Texas 77845 , USA ) .
+The data were manually entered into a database and analysed using the Statistical Package for the Social Sciences software ( IBM SPSS Statistics 18 ) .
+The normality tests , repeated measures and multivariate ANOVAs , Student t - test ( two - tailed ) and Mann - Withney analysis were done using SPSS statistic 19.0 ( IBM ) .
+Peaking calling of the ChIP samples was conducted by comparison with the reads of input using MACS 2 [21] , with the significance level of p < 0.005 .
+The statistical packages SPSS 15.1 and STATA 11.1 were used to carry out the analyses .
+Regression backward model selection was conducted , using IBM SPSS Statistics v 20.0 package [94] to fit each model .
+Statistical analyses were conducted using SAS software , version 9.3 ( PROC GENMOD , with options REPEATED , CORR = IND , DIST = BINOMIAL , LINK = LOGIT ; SAS Institute , Inc . , Cary , NC ) , and a P < 0.05 was considered statistically significant .
+The GLM procedure of Minitab software , version 16.1 ( Minitab Inc . , 2010 ) was used and with the following model of fixed factors and their interactions :
+The OpenSim software is covered by the Apache License 2.0 , which permits its use for any purpose including both nonprofit and commercial applications .
+Implementation illuminaio is an R package [9] .
+PyMOL software ( DeLano Scientific LLC , San Carlos , CA , 2009 - 10 ) was used to render all the output from InsightII and to calculate the distances of hydrogen bonds as measured between the hydrogen and its assumed binding partner .
+ScoreA and ScoreB were previously reported ( [55] ) and are described in more details in the Supplementary Material .
+All analyses were conducted using SAS version 9.4 ( SAS Institute , Cary , NC ) .
+The following variables were examined using Poisson regression with robust variance estimation to account for clustering of cats within shelters ( Stata 13.1 / IC , StataCorp LP , College Station , Texas ) for possible associations with monthly URI rates between shelters : double compartment housing ( no / yes ) , intake housing floor space ( 3 - 6 ft 2 , 6 - 8 ft 2 , > 8 - 10ft 2 { .28 - .56m 2 , .56 - .74m 2 , > .74 - .93m 2 } ) , hiding space provided in intake housing ( no , sometimes , always ) , mixed - age housing ( no , yes ) , frequency of cat moves in and out of the cage in the first week ( ≤ 2 moves , > 2 moves ) , use of intranasal vaccine ( no , yes ) and monthly shelter intake ( natural log transformation ) .
+Outcomes were analyzed using unweighted linear or logistic regression ( SAS / STAT software , version 9.2 ) .
+" Project name : Pathway analysis tool WPS for high - throughput data ; Project home page : http://www.abcc.ncifcrf.gov/wps/wps_index.php [63] Operating system : Microsoft Window 2000 or XP Programming language : Microsoft Visual Basic 6 Other requirements : Internal databases for different species and a collection of over 1900 PathwayScopeFiles ( PSCP files for mouse ) available on web site ; Additional user - provided PSCP files and those from other sources will be made available as they are collected .
+Preprocessing and statistical analysis of the fMRI data was performed with SPM 8 ( Wellcome Department of Cognitive Neurology , London UK ) software for MATLAB ( Version R 2010a , The MathWorks Inc . , Natick , MA ) .
+We performed all analysis using SAS statistical software , version 9.2 ( SAS Institute Inc , Cary , NC ) .
+In the CellProfiler 3.0 release , we introduced methods for analyzing 3D images , using deep learning architectures and cloud computing resources , and other improvements to CellProfiler ’ s usability and capabilities .
+Imputation and genome wide association analyses : SCOOP , STILTS and UKHLS single - variant association analysis : Genotypes from SCOOP , STILTS and UKHLS controls were phased together with SHAPEITv 2 [61] , and subsequently imputed with IMPUTE 2 [62,63] to the merged UK 10K and 1000G Phase 3 reference panel [64] , containing ~ 91.3 million autosomal and chromosome X sites , from 6,285 samples .
+Mann - Whitney tests were performed for statistical analyses using GraphPad 4.03 ( GraphPad , San Diego , CA ) .
+Leica .xlef files were converted in .lif files and the latter were loaded into Imaris 9.1.2 ( Bitplane , Zurich , Switzerland ) .
+FACS data were analyzed with FlowJo 2 , version 1.1.0 .
+A Virtual Machine for Oracle ' s VirtualBox has also been built to provide easy access to IDEPI for users unfamiliar with the intricacies of Python package management , and is available from the main package distribution page ( http://github.com/veg/idepi/ ) .
+A PCA analysis was conducted using XLSTAT 2015 for Excel .
+We loaded the transcripts into MAXQDA 11 which is a software tool used to analyze qualitative data [88] .
+Table 1 shows that due to its implementation in the R environment , glmnet has a much heftier memory requirement than our C + + implementation and could not load the 1 million SNP dataset .
+At baseline and biennial follow - up evaluations , data collected included demographic characteristics , medical history , cognitive function , memory functioning , blood pressure , depression , and physical functioning .
+The data presented in this article represent mean ± standard deviation and were calculated using Statistical Package for the Social Sciences ( SPSS , IBM ) .
+Full details of the exact procedure are contained in the Bootstrap software used to perform the procedure ( Bootstrap Version 1.0 , http://www.pbarrett.net/Bootstrap/Bootstrap.html ) .
+The statistical analysis was performed using the Statistical Package for Social Sciences ( SPSS for Windows , version 19.0 ; IBM Corp , Armonk , New York , USA ) .
+Linear regression analyses were performed using statistical analyses software ( SAS 9 ) version 9.2 ( SAS Institute , Cary , NC ) .
+All statistical tests were conducted in Stata 11 ( Stata Corp . , College Station , TX [41] ) .
+aLFQ is written in R and freely available under the GPLv 3 from CRAN ( http://www.cran.r-project.org ) .
+Heart rate and RR intervals were obtained using Iox 2.9.5.73 software ( Emka Technologies , Paris , France ) , with an acquisition frequency of 500 Hz .
+All analyses were conducted in Stata v. 12 ( StataCorp , TX , USA ) .
+We generated multilevel logistic regression models with random intercepts to evaluate the impact of patients and trust factors on each dependent variable using MLWin V. 2.31 software ( Rasbash J , Charlton C , Browne W , et al . MLwiN , Version 2.31 . Centre for Multilevel Modelling , University of Bristol ) .
+Stimuli were elaborated using the image processing toolbox on MATLAB ( Mathworks Inc . , Sherborn , MA , USA ) .
+The results of E - β - ocimene influence on honey bee behavioural development were analysed with a two - ways ANOVA ( years and treatments ) followed by Fisher post - hoc test ( STATVIEW 5.0 , SAS Institute , Cary , NC ) .
+Cumulative survival analysis was performed using the Kaplan - Meier method , and the log - rank test was used to compare the curves ( R packages survminer and survival ) .
+We used SAS 9.4 ( SAS Institute , Cary , NC , USA ) for data set - up and analyses .
+Users are welcome to use an instance of PhyloBot available at http://www.phylobot.com , or launch their own instance of PhyloBot using its open - source code .
+All tests were performed using the JMP 5.0 Statistics software package ( SAS Institute Inc . , Cary , NC ) .
+The data were log ( 2 ) transformed and normalized using Partek Genomics Suite ( Partek Inc . , St . Louis , MO ) .
+The internal consistency and reliability of the psychometric tools ( PHQ - 9 , GAD - 7 , PSQI ( 5 ) , BAI , and IES - R ) were determined by computing Cronbach ’ s alpha values [28] .
+In short , there are three advantages for illustrating our results with Pong : i ) the Pong game has a real - time two player mode , ii ) DQNs are good in Pong and iii ) the game is well - known and can be easily understood by the reader .
+We have developed ANDES , a software library and a suite of applications , written in Perl and R , for the statistical ANalyses of DEep Sequencing .
+IDEPI makes use of open source libraries for machine learning ( scikit - learn , scikit-learn.org/ ) , sequence alignment ( HMMER , hmmer.janelia.org/ ) , sequence manipulation ( BioPython , biopython.org ) , and parallelization ( joblib , pythonhosted.org/joblib ) , and provides a programming interface which allows users to engineer sequence features and select machine learning algorithms appropriate for their application .
+All of this analysis was implemented using Matlab , and the code is available for download from a public GitHub repository https://github.com/EmoryUniversityTheoreticalBiophysics/C.-elegans .
+All statistical analyses were performed using the statistical package SAS , version 9.1 ( SAS Institute , Inc . , Cary , North Carolina ) .
+Finally , membranes were developed with enhanced chemiluminescence ( ECL ) western blotting substrate ( ThermoFischer Scientific ) , scanned using a LAS 4000 Biomolecular imager ( GE Healthcare ) and analysed with ImageQuant TL version 7.0 software ( GE Healthcare ) .
+OpenEpi ( Atlanta , GA ) [25] was used to perform t - tests and χ 2 tests of independence , and SAS version 9.2 ( Cary , NC ) was used for descriptive statistics and logistic regression modeling .
+The experiment program was conducted by the E - Prime 1.2 ( Psychology Software Tools , Inc . , Pittsburgh , PA ) .
+Statistical analysis
+The significance level was defined as p < .05 and the data were analyzed using SAS software version 9.1 ( SAS Institute Inc . , 2003 ) .
+For the Maxent model , we used the ‘ dismo ’ R package ( version 0.8 - 17 ) with the Maxent default settings .
+The interval confidence of apparent prevalences were calculated with the “ EpiR ” package , the graphics were performed with the “ ggplot 2 ” package and the GAMs were implemented in the “ mgcv ” statistical package , all from the R statistical software [43] .
+Networks were visualized using the BisoGenet plug - in [27,28,32] within the Cytoscape environment [24,33] .
+Statistical analyses were performed using SAS 9.3 ( SAS Institute INC . Cary , NC , USA ) , R software ( http://www.r-project.org ) , and a web - based PABAK - OS calculator ( http://www.singlecaseresearch.org/calculators/pabak-os ) .
+We used the LiDAR Analyst 5.0 extension [50] of ArcGIS 10.1 [51] to identify biophysical attributes of trees in the study area that are relevant to the estimation of biomass .
+To quantify the evidence in support of the null hypothesis in these two comparisons , we computed the corresponding Bayes factors ( using JASP 0.7.5.6 ; www.jasp-stats.org ) .
+To analyze associations between individual and environmental variables and walking for transportation , we estimated several multilevel logit ordinal regression models using the Dual Quasi - Newton optimization estimation approach of Proc Glimmix in SAS 9.3 ( SAS Institute Inc . , Cary , North Carolina ) .
+" Project name : MicroSyn Project home page : http://fcsb.njau.edu.cn/microsyn Operating system ( s ) : Windows Programming language : C # Requirements : .net framework on Windows "
+We investigated transcriptional regulatory networks consisting of transcription factors and associated induced / repressed target genes using R package RTN [54] .
+A distribution of averages was then used to derive 95 % confidence intervals using the first - order normal approximation as implemented in the boot package for R [114] .
+All analyses were performed using Stata 14.2 [36] .
+Statistical analyzes were performed using the STATA version 13 application ( StataCorp , College Station , Texas , USA ) and the thematic maps were constructed using the QGIS software version 2.12.3 ( OSGeo , Beaverton , OR , USA ) .
+Execution times were similar between glmnet and gpu - lasso , where gpu - lasso was slightly faster .
+The methods of this study have been reported previously [41] .
+" Project name : GenomePop v. 1.0 Project home page : http://webs.uvigo.es/acraaj/GenomePop.htm Operating system ( s ) : Windows and Linux ( the source will be provided to compile for Mac ) Programming language : C + + License : GNU GPL . "
+STATA 12.0 by StataCorp LLC was the statistical software used in the analysis .
+From each PCLS , triplicates of 30 μ m thick 3D stacks were recorded randomly and analyzed using IMARIS 7.4.0 software ( Bitplane Scientific Software , Zurich , Switzerland ) , as described previously [7] .
+The above analyses were performed in Stata 13 statistical software [32] .
+For the purposes of the present study , we linked data from Jan 1 , 2000 to Dec 31 , 2009 .
+For the statistical analysis of the BOLD signal changes , we specified general linear models ( GLM ) with regressors for the experimental conditions defined in SPM 8 ( Welcome Trust Centre for Neuroimaging , UK ) .
+Statistical analysis was performed with the Statistical Package for the Social Sciences ( SPSS , Chicago , IL , USA , version 21.0 ) and SAS 9.2 for Windows 9.2 TS Level 1M 0 ( SAS Institute Inc . Cary , NC , USA ) .
+All recordings were acquired using Scan 4.3 ( Compumedics Neuroscan ) and stored for off - line treatment .
+Effects were evaluated for significance at p < .01 .
+Analysis were conducted using SPSS vs . 20.0 ( IBM Corp . , released 2011 , Armonk , NY ) and GraphPad Prism 7.0 software ( GraphPad Software , Inc . , San Diego , CA ) .
+Data analyses were conducted using the SAS software version 9.1 ( SAS , 2004 ) and SUDAAN ( Research Triangle Institute , 2004 ) .
+The FragIt source code is distributed under an open source license ( GPL , version 2 or later ) and users of the FragIt code are encouraged to submit changes and additions , especially for their own ( fragmentation ) methods .
+SPSS 23 ( IBM , Armonk , New York ) was used for all analyses .
+SPSS software , version 18.0 ( SPSS Inc . , Chicago , IL , USA ) was used for all analyses .
+The analyses were done using SAS ( Version 9.1.3 . SAS Institute Inc . , Cary , NC , USA ) .
+" Project name : Pathomx Project home page : http://pathomx.org Platform : Binaries are available for download on Windows and MacOS X .
+Statistical analyses were conducted using the Statistical Package for the Social Science ( SPSS ) version 19.0 and a p - value of less than 0.05 was used to define statistical significance .
+These data collection procedures have been described in an earlier study [17] .
+Data were analyzed using Statistical Parametric Mapping 5 ( SPM 5 , Wellcome Department of Cognitive Neurology , London , UK ) software implemented in Matlab 7.8 ( Mathworks , Sherborn , MA , USA ) .
+All statistical analyzes were performed with GraphPad Prism 5.0 for MacOS X ( GraphPad Software Inc , La Jolla CA ) and all data are expressed as mean ± SEM .
+PyPhi is open - source and licensed under the GPLv 3 ; the source code is hosted on GitHub at https://github.com/wmayner/pyphi .
+Statistical analysis was performed using Excel ( Microsoft ) and OriginPro ver 7.5 ( OriginLab ) .
+Statistical analyses were performed using PASW Statistics version 18 for Windows ( SPSS Inc . ) .
+Data were analysed using SPSS 15.0 for Windows .
+Google ’ s deep learning framework TensorFlow [40] was used to train , tune , and test the CNN .
+As such , all figures pertaining to these analyses are presented in the Supporting Information section ( S1 - S4 Figs ) to permit better focus on the principal results of the paper .
+All further statistical analyses ( t - tests for dependent samples ) were calculated using the software package SPSS 11.5 ( SPSS Inc . , Chicago , USA ) .
+To this end , we developed scPipe , an R / Bioconductor package that integrates barcode demultiplexing , read alignment , UMI - aware gene - level quantification and quality control of raw sequencing data generated by multiple protocols that include CEL - seq , MARS - seq , Chromium 10X , Drop - seq and Smart - seq .
+Twenty eight predictors recorded by TEDS - D were included in the analysis .
+The alignment of raw reads was conducted by Bowtie 2 ( [53] ) in end - to - end mode .
+We carried out meta - analyses using standardized betas and standard errors from each of the studies .
+Recombination in our nuclear genes was tested using the PHI test implemented in SPLITSTREE 4.11.3 [35] and the tree - based SBP and GARD methods [36] implemented online via the Datamonkey webserver [37] .
+Imaging data were analysed using BrainVoyager QX ( Brain Innovation , Maastricht , the Netherlands ) .
+STATA SE .9 software was used for all statistical analysis .
+The Open Meta - Analyst ( Center for Evidence Synthesis in Health , Brown University , Providence , RI , USA [9] ) was used for all analyses .
+CloVR - ITS is made available as a pre - installed , automated , and portable software pipeline for cloud - friendly execution as part of the CloVR virtual machine package ( http://clovr.org ) .
+Then , the hypotheses were tested with OLS Ordinary Least Square through the PROCESS macro for SPSS , which assesses the conditional indirect effects [38] .
+Gene correlation analysis and feature correlation heatmaps were performed on the PIVOT platform , developed by the Kim Lab ( http://kim.bio.upenn.edu/software/pivot.shtml ) [65] .
+Figure generated using clam for R [53] .
+All analyses were performed using SPSS software ( version 17.0 , IBM , China ) for Windows 7.0 .
+Data are presented as ( Mean ± SEM ) and were analysed with IBM SPSS 22.0 software .
+All analyses were performed using SAS , release 9.4 ( SAS Inc . Cary , NC , USA ) and SUDAAN , release 11.0.1 ( Research Triangle Institute , Research Triangle Park , NC , USA ) .
+All statistical analyses were conducted using the SPSS version 17.0 ( IBM Inc . , Armonk , NY , USA ) .
+Multilevel regression analyses were performed in SAS software version 9.2 ( SAS Institute Inc . , 2009 ) .
+The Statistical Analysis System for Windows , version 9.4 ( SAS Institute , Cary , NC , USA ) , was used for analysis .
+We checked returned sequences using the RDP Classifier v 2.2 [25] , and discarded a single sequence from the Snodgrassella set not matching Betaproteobacteria .
+Confirmatory factor analysis with Mplus version 7.3 [51] was used to estimate the degree of fit for each grooming measure ( TTM , SP and NB ) .
+Pearson statistics were used for correlational analyses .
+Strawberry was written in C + + 14 and utilizes features such as threading library for parallelization .
+All analyses were done using Stata version 9.2 and ESRI ArcGIS version 9.2 .
+OHM ( OligoHeatMap ) is an online tool able to provide estimates of T for a set of oligomers and a set of aligned sequences , not only as text files of complete results but also in a graphical way : T values are translated into colors and displayed as a heat map image , either stand alone or to be used by softwares such as TreeDyn to be included in a phylogenetic tree .
+Statistical analysis was performed using a one - way ANOVA followed by Bonferroni multiple comparison tests ( Statistical Package for the Social Sciences software , SPSS version 13.0 ) .
+Images were imported into Adobe Photoshop 8.0.1 ( Adobe Systems ) .
+To identify statistical significant differences between the control and IUGR fetal brain tissue samples the processed data files were imported into Agilent Mass Profiler Professional software version 12.1 ( Agilent Technologies , Santa Clara , CA ) for statistical analysis .
+The statistical tests were performed using the Statistical Package for Social Sciences ( SPSS ) for Windows ( Version 13.0 , Chicago , IL , USA ) .
+Models were run using the MATLAB routine REGRESSIONv 2.m described in [54] .
+Studies were exported to remove the duplicates in Refworks ™ and then exported to Microsoft Excel .
+Statistical analysis was carried out using the Statistical Package for the Social Sciences , Release 17.0 ( SPSS Inc . , Chicago , IL ) .
+Data analysis was conducted using SPSS version 14 for windows .
+All statistical analyses were performed using the SAS software version 9.4 ( SAS Institute , Cary , NC , USA ) .
+All estimations were performed by MLwiN within STATA 12 MP ( Stata , Corp . ) and MLWiN 2.26 through runmlwin procedure [30] .
+MIiSR is an open - source project licensed under the GNU General Public License and is available as S1 - MIiSR Program in this paper , with updated versions published at http://www.phagocytes.ca/miisr/ .
+We built a generalized linear mixed model ( GLMM ) using the GLIMMIX procedure [43] in SAS v 9.3 to identify factors associated with the occurrence of groups .
+Data were cleaned in Access and then analyzed using SAS 9.3 ( SAS Institute Inc . ) .
+Predicted targets of known miRNAs were then analyzed with the TargetScan software v 7.0 [102] .
+Furthermore , we performed power calculations for case - control genetic association analyses using PGA v 2.0 [45] .
+All analyses were performed using SAS version 9.2 ( SAS Institute Inc . USA ) .
+Statistical analyses were performed using JAGS Gibbs - sampling environment [43] and R 3.0.3 [44] .
+All statistical analyses were conducted using IBM SPSS Statistics 21 .
+NFTsim is distributed under the Apache 2.0 license .
+The statistical analyses were performed using SPSS software ( version 19.0 ; IBM Corp , New York ) .
+A validated algorithm [14] was used to automatically classify 1 - min actigraphy epochs into active wake , sleep , or waking rest ( Respironics Actiware , Version 5.59.0015 , standard settings ) .
+The raw reads of each sample were mapped to the closed reference genome , CFSAN 001339 , using Novoalign V 2.08.02 ( http://www.novocraft.com ) , and the variants were called using SAMtools and stored in a VCF file [43] .
+For questions for which answers could be “ yes , ” “ I don ' t know ” or “ no , ” ( e.g. , “ Did any of the field sites have a code of conduct ? ” ) , KH and JR conservatively bifurcated responses into “ yes ” and “ not yes . ” Chi - square , t - test , and regression models were constructed in JMP 9.0 ( SAS , Inc ) .
+Correlation of geographic and genetic distances was determined using Mantel ’ s permutation test with 10,000 permutations executed by IBDWS v. 3.15 [52] .
+Spatial preprocessing and statistical analysis of functional images were performed using SPM 8 ( Welcome Department of Cognitive Neurology ) .
+MRI data was analyzed using SPSS Statistics ( IBM , version 19 ) using a generalized linear model fitted to a gamma distribution , with MAM treatment , enrichment , and gender as factors .
+We carried out data analysis in R v. 3.2.1 ( R Development Core Team , 2013 ) .
+Analyses were performed using Stata version 13.0 ( Stata Corp , College Station , Texas ) .
+All statistical analyses were carried out using GraphPad Prism version 5.04 for Windows , GraphPad Software , San Diego , CA , www.graphpad.com.
+All data were analyzed using SPSS statistical software ( version 21.0J ; IBM SPSS Japan , Tokyo , Japan ) .
+Small - for - gestational age was defined as an infant being below the 10th weight centile for gestational age as determined by the INTERGROWTH - 21st Newborn Size Application Tool using standards derived from births in eight ethnically distinct countries ( http://intergrowth21.ndog.ox.ac.uk/ ) .
+Potential trade - offs were identified using radar plots in R ( version 3.2.2 [30] ) and the fmsb package [31] .
+MAGPIE was implemented in Ruby on Rails 5 .
+All regression analyses were conducted using Proc Glimmix in SAS 9.3 ( SAS Institute , Cary , NC , USA ) .
+Data analyses were performed in SPSS ( SPSS Statistics for Windows , Version 20.0 . Armonk , NY : IBM Corp ) and confirmed in R ( Version 3.0.1 , The R Foundation for Statistical Computing , Vienna , Austria ) .
+CIBERSORT analyses were performed on RNAseq data by using the analytical tool developed by Newman et al . ( http://cibersort.stanford.edu ) [30] .
+All the processing , analyses , and machine learning were conducted using the MATLAB software package ( version R 2009a and R 2015a , Mathworks Inc . , Natick , MA , USA ) .
+This example file runs on BEAST 2.1.0 with the MultiTypeTree package ( http://compevol.github.io/MultiTypeTree/ ) .
+The software and documentation for M - Track are freely available for download from the Scimemi lab website ( https://sites.google.com/site/scimemilab2013/software ) or from the GitHub repository ( https://github.com/scimemia/M-Track ) .
+The SPS contains eight factors covering impairment and symptom severity .
+Excel , Prism 5 ( GraphPad Software Inc . ) , and Adobe Illustrator CS 5 ( version 15.0.0 ) were used to create graphical representations of data ( depicted as mean ± s.e .m ) .
+In order to determine a relationship between biological aspects and behavioral problems statistical analyses were done using IBM SPSS 20 ( IBM SPSS 20 , Chicago , USA ) .
+SCOTTI is implemented as an open - source package for the Bayesian phylogenetic software BEAST 2 [28] , and as such , it can be freely installed and used .
+All statistical analysis was performed using the Stata / SE software ( release 13.1 ) ( Stata Corp LP , College Station , TX , USA ) , and the statistical significance level was set at P = 0.05 in all statistical inferences .
+All statistical analyses were performed using SAS 9.3 ( SAS , Cary , NC , USA ) , with the significance level set to 0.05 , two - tailed .
+A comparison of FSAs that were included in the analyses to those excluded indicated that they were comparable ( e.g. , 51.0 % versus 50.4 % for the % women in the FSAs ) .
+Statistical analysis was performed using GraphPad Prism ( version 4.0 ) and SPSS ( version 20 ) .
+Upon reaching adulthood , individuals were photographed and their head width and pronotum width measured to the nearest 0.01cm using ImageJ 1.48 [45] , with sex being determined by examination of the sexually dimorphic subgenital plates .
+Sperm concentration and motility were assayed using a computer - aided sperm analyses ( CASA ) system coupled to a phase contrast microscope ( Nikon Eclipse model 50i ; Nikon Instruments Europe B.V . , Izasa S.A . ; negative contrast ) and employing Sperm Class Analyzer ( SCA , Barcelona , Spain ) v. 4.0 . software ( Microptic S.L . , Barcelona , Spain ) [35] .
+The reaction network consists of 173 chemical species and 6,581 unidirectional reactions . ( The size of the reaction network reflects the number of protein phosphoforms and protein complexes that can arise from the interactions represented by the rules of the model . ) BioNetGen ’ s built - in ODE solver , CVODE from the SUNDIALS package [69] , was then used to numerically integrate the ODEs , using default settings .
+The present study included follow up data from baseline to October 9 , 2011 .
+This map was generated using ArcGIS 10.2.2 ( www.esri.com ) .
+All images were acquired through the Matlab Image Acquisition Toolbox ( Mathworks , Matlab v 2011b ) at 2 frames / s ( 500 ms exposure ) at 360x 260 pixel ( px ) resolutions ( using 4x 4 hardware binning ) .
+The user - written ice commands [35] - [41] in Stata v 11.2 ( Stata Corp , TX , USA ) were used to complete five imputations with ten cycles in each imputation .
+Age and gender were added as covariates in all analyses but the ones performed on standardized data .
+Sum projection of 2 Z - stacks separated 2 μ m from each other was done with the freeware ImageJ v 1.51 u by Wayne Rasband ( National Institutes of Health , Bethesda , MD , USA ) and images were next automatically quantified with the NIS - Elements Microscope Imaging Software ( Nikon ) .
+We used Microsoft Office Excel 2010 and Stata software ( Stata / SE 13.1 ) for all analyses .
+We conducted all statistical analyses in Stata version 13.1 ( StataCorp , Texas , USA ) .
+All relevant data are within the paper and its Supporting Information files .
+The resampling procedures were conducted in Microsoft Excel 2010 using VBA code written by FAC ( Appendix S2 ) .
+SPSS 22.0 for Windows ( SPSS Inc . , Chicago , IL ) was used for the analyses .
+Reads were mapped to the Genome Reference Consortium GRCm 38 mouse assembly using Tophat 2 ( v 2.0.8 ) [17] with the Illumina iGenomes package ( mm 10 ; http://support.illumina.com/sequencing/sequencing_software/igenome.html ) .
+Novoalign was used to align the sequencing data to the human reference genome [ NCBI build 37 ] and the Genome Analysis Toolkit ( GATK ) [49] was used for post - processing and variant calling according to GATK Best Practices recommendations [50,51] .
+The statistical analysis was performed using the Statistical Package for Social Sciences ( SPSS for windows , version 19.0 ; Chicago , Illinois , USA ) .
+SNPdetector was implemented in C and Perl .
+Table identifier and caption : 10.1371/journal.pmed.1001414.t002 Characteristics of included studies .
+Analyses were conducted using STATA Version 13 for Windows ( College Station , TX , USA ) .
+Data were processed with GraphPad Prism ( GraphPad Software , San Diego , CA ) .
+All statistical analyses were conducted using SPSS Statistics 22 ( Dynelytics , Zurich , Switzerland ) .
+Preprocessing and statistical analysis were performed in SPM 8 ( www.fil.ion.ucl.ac.uk/spm/software/spm8 ) .
+The sample size was calculated using the G * Power 3.1 software ( release 3.1.9.2 ; available from : http://www.gpower.hhu.de/ ) [27] to assess the null hypothesis of no difference in parasite load levels between different sampling sites within the CL ulcer .
+All statistical analyses were conducted with SPSS ( v. 20.0.0.2 ) and R ( v. 3.1.3 ) .
+ImageJ [17] is a public domain , Java - based image - processing program developed at the National Institutes of Health .
+All statistical analysis was undertaken in Stata , version 13.1 [41] .
+The entire sequence of touches for each participant that contains the special runs was then entered into a Monte Carlo program ( TouchStat 3.0 ) [41] to determine if they were likely to have occurred by chance .
+These procedures were performed using the SPSS 11.5 software package [40] .

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+
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+
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+
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+
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+
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+
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+
+
+
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+
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+
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+
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+
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+
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+
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+Version_of	22	20
+
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+
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+
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+
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+Version_of	39	38; Citation_of	40	38
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+Version_of	7	6; Developer_of	12	6
+Version_of	19	18; Citation_of	20	18
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+
+Abbreviation_of	12	5; Citation_of	37	5
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+Developer_of	5	6; Version_of	7	6; Developer_of	9	6
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+
+URL_of	8	1
+Version_of	28	26; Citation_of	29	26
+Version_of	9	6; Citation_of	10	6
+Version_of	10	7; Extension_of	9	7
+
+Version_of	7	5; Developer_of	10	5
+URL_of	28	24; URL_of	41	38
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+
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+URL_of	75	72; Version_of	73	72
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+
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+
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+
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+
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+
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+
+Version_of	8	6; Citation_of	9	6
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+Version_of	9	8; Citation_of	10	8
+
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+Abbreviation_of	18	14; URL_of	21	14; Specification_of	27	14; Version_of	29	27; Citation_of	30	27; Citation_of	32	27
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+
+PlugIn_of	25	29; Citation_of	30	29
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+
+Version_of	11	10; Developer_of	13	10
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+
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+
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+
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+Citation_of	13	12; PlugIn_of	12	9
+Version_of	7	3; Developer_of	8	3
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+
+
+PlugIn_of	25	7
+Version_of	9	7; Abbreviation_of	17	11; Version_of	20	11
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+
+Version_of	14	13; Version_of	5	4
+
+URL_of	6	3; URL_of	20	17
+Version_of	7	4; Developer_of	9	4; Release_of	19	18; Developer_of	21	18
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+
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+Citation_of	13	11; PlugIn_of	11	18; Version_of	19	18
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+Citation_of	5	4; Citation_of	15	14; Citation_of	18	17; Citation_of	21	20; Citation_of	25	24
+Citation_of	8	6; Version_of	10	6; Citation_of	13	12; PlugIn_of	6	12
+Developer_of	10	7; Version_of	8	7
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+Developer_of	6	7; Extension_of	8	7; Version_of	10	7; Extension_of	14	13; Version_of	16	13
+
+Version_of	11	6; Developer_of	13	6; URL_of	39	37; Release_of	44	42; Developer_of	47	42
+Version_of	18	14; Developer_of	32	25
+Version_of	10	9; Developer_of	12	9; Version_of	33	25; Developer_of	35	25
+Version_of	6	5; Developer_of	8	5
+
+Version_of	10	8; Citation_of	11	8; Developer_of	17	14; URL_of	27	14; Version_of	15	14
+Developer_of	13	6; Version_of	25	6
+PlugIn_of	20	18; Citation_of	21	20
+
+
+Abbreviation_of	10	6; Version_of	14	6; Developer_of	16	6
+Version_of	26	25; Citation_of	27	25
+Citation_of	9	7; URL_of	11	7
+Version_of	35	30; Developer_of	37	30
+Version_of	8	5; Developer_of	10	5; Version_of	16	14; Developer_of	18	14
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+Abbreviation_of	7	3; URL_of	10	3
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+Developer_of	6	9; Citation_of	13	12
+
+Developer_of	6	4; Release_of	7	4
+Version_of	7	6; Developer_of	9	6
+Developer_of	14	12; Citation_of	23	21
+PlugIn_of	5	3; Citation_of	7	5
+Developer_of	11	12; Version_of	22	19; Developer_of	24	19; Specification_of	19	12
+Specification_of	18	14; Developer_of	11	14; Developer_of	20	18; URL_of	24	18
+Version_of	10	5; Developer_of	12	5
+Version_of	15	10; URL_of	17	10
+Version_of	19	14; Developer_of	21	14
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+Citation_of	15	12; Citation_of	21	18
+Citation_of	13	11; Citation_of	13	9
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+
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+
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+
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+
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+
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+
+
+Developer_of	7	8; Version_of	12	8
+
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+
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+
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+
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+
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+
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+
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+
+
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+
+Version_of	12	8
+
+URL_of	16	3
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