cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5524/100744
title: Supporting data for "Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy"

description: Infinium Human Methylation BeadChip is an array platform for complex evaluation of DNA methylation at an individual CpG loci in the human genome based on Illuminas bead technology and it is one of the most common techniques used in epigenome-wide association studies (EWAS). Finding associations between epigenetic variation and phenotype is a significant challenge in biomedical research. The newest version, HumanMethylationEPIC, quantifies the DNA methylation level of 850k CpG sites, while the previous versions, HumanMethylation450 and HumanMethylation27, measured over 450k and 27k loci, respectively. Although a number of bioinformatics tools have been developed to analyse this assay, they require some programming skills and experience in order to be usable.<br> We have developed a pipeline for the Galaxy platform for those without experience aimed at DNA methylation analysis using the Infinium Human Methylation BeadChip. Our tool is integrated into Galaxy, a web based platform. This allows users to analyse data from the Infinium Human Methylation BeadChip in the easiest possible way. <br>The pipeline provides a group of integrated analytical methods wrapped into an easy to use interface. Our tool is available from the Galaxy toolshed, GitHub repository and also as a Docker image. The aim of this project is to make Infinium Human Methylation BeadChip analysis more flexible and accessible to everyone.
DOI: 10.5524/100746
title: Supporting data for "Genomic consequences of dietary diversification and parallel evolution due to nectarivory in Leaf-nosed bats"

description: The New World Leaf-Nosed bats (Phyllostomids) exhibit a diverse spectrum of feeding habits and innovations in their nutrient acquisition and foraging mechanisms. However, the genomic signatures associated with their distinct diets are unknown. <br>We conducted a genomic comparative analysis to study the evolutionary dynamics related to dietary diversification and specialization. We sequenced, assembled and annotated the genomes of five Phyllostomid species: one insect-feeder (<i>Macrotus waterhousii</i>), one fruit-feeder (<i>Artibeus jamaicensis</i>), and three nectar-feeders from the Glossophaginae subfamily (<i>Leptonycteris yerbabuenae</i>, <i>Leptonycteris nivalis</i> and <i>Musonycteris harrisoni</i>), also including the previously sequenced Desmodus rotundus. Our phylogenomic analysis based on 22,388 gene families displayed differences in expansion and contraction events across the Phyllostomid lineages. Independently of diet, genes relevant for feeding strategies and food intake experienced multiple expansions and signatures of positive selection. We also found adaptation signatures associated with specialized diets: the vampire exhibited traits associated with a blood diet (i.e., coagulation mechanisms), whereas the nectarivore clade shares a group of positively selected genes involved in sugar, lipid, and iron metabolism. Interestingly, in fruit-nectar feeding Phyllostomid and Pteropodids bats, we detected positive selection in two genes: AACS and ALKBH7, which are crucial in sugar and fat metabolism. Moreover, in these two proteins we found parallel amino-acid substitutions in conserved positions exclusive to the tribe Glossophagini and to Pteropodids. <br>Our findings illuminate the genomic and molecular shifts associated with the evolution of nectarivory and shed light on how nectar-feeding bats can avoid the adverse effects of diets with high glucose content.
DOI: 10.5524/100750
title: Supporting data for "Trans-NanoSim characterizes and simulates nanopore RNA-seq data"

description: Compared to second-generation sequencing technologies, third-generation single-molecule RNA sequencing has unprecedented advantages; the long reads it generates facilitate isoform-level transcript characterization. In particular, the Oxford Nanopore Technology sequencing platforms have become more popular in recent years due to their relatively high affordability and portability compared to other third-generation sequencing technologies. To aid the development of analytical tools that leverage the power of this technology, simulated data provides a cost-effective solution with ground truth. However, nanopore sequence simulator targeting transcriptomic data is not available yet. We introduce Trans-NanoSim, a tool that simulates reads with technical and transcriptome-specific features learnt from nanopore RNA-seq data. We comprehensively benchmarked Trans-NanoSim on direct RNA and cDNA datasets describing human and mouse transcriptomes. Through comparison against other nanopore read simulators, we show the unique advantage and robustness of Trans-NanoSim in capturing the characteristics of nanopore cDNA and direct RNA reads. As a cost-effective alternative to sequencing real transcriptomes, Trans-NanoSim will facilitate the rapid development of analytical tools for nanopore RNA-seq data.
DOI: 10.5524/100752
title: Genome data for the draft assembly of the Chinese tertiary relict tree, <i>Nyssa yunnanensis</i>.

description: <i>Nyssa yunnanensis</i> is a deciduous tree species in the family <i>Nayssaceae</i> within the order <i>Cornales</i>. With only eight individuals across two geographic sites recorded in the Yunnan province of China, this species was listed as a national grade-I protected species in China in 1999. It is also one of the 120 species in the <i>Implementation Plan of Rescuing and Conserving Chinas Plant Species with Extremely Small Populations (PSESP)</i> (2011-2-15). <i>N. yunnanensis</i> has also been evaluated as Critically Endangered in the IUCN red list and Threatened Species List of China's Higher Plants. Hence understanding the genomic characteristics of this highly endangered Tertiary relict tree species is essential, especially for developing conservation strategies.<br>Here we present the draft genome assembly of <i>N. yunnanensis</i>. Using 10X genomics linked-reads sequencing data. We carried out the <i>de novo</i> assembly and annotation analysis. The <i>N. yunnanensis</i> genome assembly is 1475 Mb in length containing 288,519 scaffolds with an scaffold N50 length of 985.59 kb. 799.51 Mb of the assembled genome was identified as repetitive elements, accounting for 54.24% of the sequenced genome and a total of 39,803 protein-coding genes were predicted. <br>The genomic data of <i>N. yunnanensis</i> provided in this study will provide basic information for future genomic and evolutionary studies. With the genomic characteristics of <i>N. yunnanensis</i> available, our study might also facilitate future conservation biology studies to help protect this extremely threatened tree species.
DOI: 10.5524/100754
title: Data from the female urinary microbiota

description: Human urine is traditionally considered to be sterile, and whether the urine harbors distinct microbial communities has been a matter of debate. Potential link between female urine and reproductive tract microbial communities is currently not clear. <br>Here we collected urine samples from 147 Chinese women of reproductive age and explored the nature of colonization by 16S rRNA gene amplicon sequencing, quantitative real-time PCR, and live bacteria culture. To demonstrate the utility of this approach, the intra-individual Spearman's correlation was used to explore the relationship between urine and multiple sites of the female reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. <i>Streptococcus</i>-dominated, <i>Lactobacillus</i>-dominated and diverse type were the three most common urinary bacterial community types in the cohort. Detailed comparison of the urinary microbiota with multiple sites of the female reproductive tract microbiota demonstrated that the urinary microbiota were more similar to the microbiota in the cervix and uterine cavity than to those of the vagina in the same women. <br>Our data demonstrate the potential connectivity among microbiota in the female urogenital system and provide insight and resources for exploring diseases of the urethra and genital tract.
DOI: 10.3535/a4f-4cr-qv9
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qf3-ty6-mpv
title: †Trilobatus quadrilobatus (d'Orbigny, 1846)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yje-t93-vc3
title: †Discocyclina archiaci (Schlumberger, 1903)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/4sz-lr9-jea
title: Semicytherura sella (Sars, 1866)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7aw-2ab-f73
title: Plantae

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/95a-lfa-n5v
title: †Gryphaea Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jlv-w6h-xnt
title: †Orbitoides d'Orbigny, in Lyell, 1848

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9nw-3qh-5s9
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/b1l-d2n-r51
title: Cetacea Brisson, 1762

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/l7j-2a8-q4x
title: Isocrinida Sieverts-Doreck, 1952

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/bdr-s8l-tw8
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/khy-kqe-9xy
title: †Fusulinidae Möller, 1878

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t39-ddh-sbl
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tsz-p6k-gdg
title: Nummulitidae Blainville, 1827

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qpq-dz3-mfz
title: Elphidium excavatum (Terquem, 1875)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/tmj-evg-j3p
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/zkg-zdt-qyy
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/ghe-2r6-ws3
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kf8-bxd-ftg
title: Guttulina d'Orbigny, 1839

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/32l-mg0-j4x
title: Bos taurus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/c5l-m40-exh
title: Equus (Equus) caballus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/an5-1af-glt
title: Equus (Equus) caballus Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/pgp-3ld-j1z
title: Mammalia Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.15468/dl.nqn6m9
title: Occurrence Download

description: A dataset containing 6560 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is CUBA:Herbario del Jardín Botánico Nacional, La Habana, Cuba: HAJB-Pteridophyta"
 ]
}

 The dataset includes 6560 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0018253-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/6tq-6m8-3ws
title: †Lepidocyclina yurnagunensis Cushman, 1919

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7br-kmp-ypn
title: Bryozoa

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/e50-2bh-pab
title: Ostracoda Latreille, 1802

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/f73-4b0-mc2
title: †Gryphaea Lamarck, 1801

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/kej-5l7-ks5
title: †Orbitoides d'Orbigny, in Lyell, 1848

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/m50-cq2-abe
title: †Helicorbitoides longispiralis (Papp & Küpper, 1953)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/1mh-cgj-057
title: †Subbotina triloculinoides (Plummer, 1927)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lsw-vft-krb
title: Porifera Grant, 1836

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3b9-y77-d2s
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/843-dd7-jpe
title: Polymorphinidae d'Orbigny, 1839

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.24403/jp.1383462
title: Orte des Lesens : Queeres Zentrum Erfurt ; Beratung, Bildung, Begegnung in Thüringen / von Sophia Klefisch
DOI: 10.3535/8ae-af4-bk3
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/9h0-wnx-kd1
title: Foraminifera d'Orbigny, 1826

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/vzs-wfw-9ma
title: Sus scrofa Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/k1j-761-5jy
title: Ostracoda Latreille, 1802

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/q9s-ms2-yb0
title: Buliminus H. Beck, 1837

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/qyk-79m-hh3
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/gd5-0zb-jwl
title: Alnus glutinosa (L.) Gaertn.

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/lzv-ern-3nf
title: †Orbitoides d'Orbigny, in Lyell, 1848

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.25549/uschist-c104-283584
title: Mark Ridley-Thomas 50th birthday party, Calif., 2004

description: 67 photographs of event celebrating the fiftieth birthday of California state senator Mark Ridley-Thomas, 2004 December 21. Pictured are Will Ali (#217), Lee Baca (#233), James Hahn (#233), Reba Long (#222), Harry McElroy (#244), Mark Ridley-Thomas (#210-#213, #215-#216, #218-#221, #223-#225, #227-#233, #235, #237, #242, #244-#246, #251-#255, #257, #265, #268-#269, #270-#275), John Sincken (#213), Sara Thomas (#214), Carolyn Webb de Macias (#240, #246, #252, #256, #263), Yaroslavsky, Zev, 1948- (#233), and many unidentified women and men.
DOI: 10.25549/uschist-c104-283591
title: Mark Ridley-Thomas 50th birthday party, Calif., 2004

description: 67 photographs of event celebrating the fiftieth birthday of California state senator Mark Ridley-Thomas, 2004 December 21. Pictured are Will Ali (#217), Lee Baca (#233), James Hahn (#233), Reba Long (#222), Harry McElroy (#244), Mark Ridley-Thomas (#210-#213, #215-#216, #218-#221, #223-#225, #227-#233, #235, #237, #242, #244-#246, #251-#255, #257, #265, #268-#269, #270-#275), John Sincken (#213), Sara Thomas (#214), Carolyn Webb de Macias (#240, #246, #252, #256, #263), Yaroslavsky, Zev, 1948- (#233), and many unidentified women and men.
DOI: 10.25549/uschist-c104-283595
title: Mark Ridley-Thomas 50th birthday party, Calif., 2004

description: 67 photographs of event celebrating the fiftieth birthday of California state senator Mark Ridley-Thomas, 2004 December 21. Pictured are Will Ali (#217), Lee Baca (#233), James Hahn (#233), Reba Long (#222), Harry McElroy (#244), Mark Ridley-Thomas (#210-#213, #215-#216, #218-#221, #223-#225, #227-#233, #235, #237, #242, #244-#246, #251-#255, #257, #265, #268-#269, #270-#275), John Sincken (#213), Sara Thomas (#214), Carolyn Webb de Macias (#240, #246, #252, #256, #263), Yaroslavsky, Zev, 1948- (#233), and many unidentified women and men.
DOI: 10.25549/uschist-c104-283599
title: Mark Ridley-Thomas 50th birthday party, Calif., 2004

description: 67 photographs of event celebrating the fiftieth birthday of California state senator Mark Ridley-Thomas, 2004 December 21. Pictured are Will Ali (#217), Lee Baca (#233), James Hahn (#233), Reba Long (#222), Harry McElroy (#244), Mark Ridley-Thomas (#210-#213, #215-#216, #218-#221, #223-#225, #227-#233, #235, #237, #242, #244-#246, #251-#255, #257, #265, #268-#269, #270-#275), John Sincken (#213), Sara Thomas (#214), Carolyn Webb de Macias (#240, #246, #252, #256, #263), Yaroslavsky, Zev, 1948- (#233), and many unidentified women and men.
DOI: 10.25549/uschist-c104-283601
title: Mark Ridley-Thomas 50th birthday party, Calif., 2004

description: 67 photographs of event celebrating the fiftieth birthday of California state senator Mark Ridley-Thomas, 2004 December 21. Pictured are Will Ali (#217), Lee Baca (#233), James Hahn (#233), Reba Long (#222), Harry McElroy (#244), Mark Ridley-Thomas (#210-#213, #215-#216, #218-#221, #223-#225, #227-#233, #235, #237, #242, #244-#246, #251-#255, #257, #265, #268-#269, #270-#275), John Sincken (#213), Sara Thomas (#214), Carolyn Webb de Macias (#240, #246, #252, #256, #263), Yaroslavsky, Zev, 1948- (#233), and many unidentified women and men.
DOI: 10.25549/uschist-c104-283602
title: Mark Ridley-Thomas 50th birthday party, Calif., 2004

description: 67 photographs of event celebrating the fiftieth birthday of California state senator Mark Ridley-Thomas, 2004 December 21. Pictured are Will Ali (#217), Lee Baca (#233), James Hahn (#233), Reba Long (#222), Harry McElroy (#244), Mark Ridley-Thomas (#210-#213, #215-#216, #218-#221, #223-#225, #227-#233, #235, #237, #242, #244-#246, #251-#255, #257, #265, #268-#269, #270-#275), John Sincken (#213), Sara Thomas (#214), Carolyn Webb de Macias (#240, #246, #252, #256, #263), Yaroslavsky, Zev, 1948- (#233), and many unidentified women and men.
DOI: 10.25549/uschist-c104-284116
title: Carolyn Webb de Macias with USC public relations staff, USC, 2008

description: 9 photographs of USC public relations staff, upstairs in University Commons building, 830 Childs Way, University of Southern California, Los Angeles, California, USA, 2008 April 16. Carolyn Webb de Macias (in green) is in most of the pictures.
DOI: 10.15468/dl.ak83sy
title: Occurrence Download

description: A dataset containing 612 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Plants Diversity and Structure Under different Land Uses of Bale Mountains National Park and its surroundings, South Western Ethiopia"
 ]
}

 The dataset includes 612 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030338-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/uschist-c104-287953
title: Awards & commendations for Carolyn Webb de Macias, 1984-2008

description: 15 photographs of 13 awards for Carolyn Webb de Macias: USC Resolution of Commendation, 2008 March 28; City of Los Angeles for Board of Directors appointment to California African-American Museum, 2003 June 30; City of Los Angeles resolution on her service to Los Angeles, 1997 August 26; County of Los Angeles for her service to Hoover Intergenerational Care Child Development Center "Leave no child behind" program, 2002 October 23; City of Los Angeles commendation for her service to Los Angeles, 1997 August 27; California State Rules Committee Resolution commending her for her service to Los Angeles, 1984 June 6; State of California Senate Rules Committee resolution commending her service to California, 1989 March 28; State of California appointing her to the Board of Directors of the California African-American Museum, 2003 June 2 (2 copies, one mounted with clipping from Daily Trojan, 2003 October 7); USC Women in Management for her honorary membership, [s.d.]; "Each one, reach one, teach one" for her service to Los Angeles African American Women's Public Policy Institute, 2006 May 25; Alpha Delta Chapter of Alpha Phi Alpha Fraternity honoring her at the 4th annual African-American Women Program of "Womenhood in Educatioin", 2001; Los Angeles African American Women's Public Policy Institute for her contributions, 2004 August 26; Alpha Phi Alpha Fraternity award of honor at the 57th Western Region Convention for her contributions, 2005 March 17; USC Black Alumni Association "Barbara Solomon Faculty/Staff Award for her contributions, 2004 April 24.
DOI: 10.25549/uschist-c104-289232
title: Good Neighbors Campaign fliers, USC, 2003-2007

description: 5 fliers announcing the University of Southern California's annual Good Neighbors Campaign, 2003, 2004, 2005, 2006, 2007, each year October 1-31.
DOI: 10.15468/dl.j246bk
title: Occurrence Download

description: A dataset containing 88530 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Campylorhynchus turdinus",
 "Year is greater than or equal to 2000",
 "Year is less than or equal to 2026",
 "HasCoordinate is true"
 ]
}

 The dataset includes 88530 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030316-260208012135463/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/uschist-c104-289233
title: Good Neighbors Campaign fliers, USC, 2003-2007

description: 5 fliers announcing the University of Southern California's annual Good Neighbors Campaign, 2003, 2004, 2005, 2006, 2007, each year October 1-31.
DOI: 10.25549/uschist-c104-289236
title: Good Neighbors Campaign fliers, USC, 2003-2007

description: 5 fliers announcing the University of Southern California's annual Good Neighbors Campaign, 2003, 2004, 2005, 2006, 2007, each year October 1-31.
DOI: 10.25549/uschist-c104-282450
title: Views of Bovard Administration Building & Physical Education building from Public Relations offices, USC, 2008

description: 7 photographs of views from USC Public Relations Office, upstairs University Commons (830 Childs Way), of Bovard Administration Building (3551 Trousdale Parkway) (#078, #084, #100-#103) and the Physical Education Building (3560 Hoover Street) (#104), University of Southern California, Los Angeles, California, USA, 2008 April 16.
DOI: 10.25549/uschist-c104-282861
title: USC president Sample with Nobel prize winner chemist George Olah, 1994

description: Photograph of University of Southern California president Steven Sample, with USC professor of chemistry George Olah at an informal event celebrating Olah's winning of the 1994 Nobel prize in chemistry, USC, 1994. Also pictured are many others.