cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/v3av6-ks350
title: H. pylori 26695 / Hs.746T

description: Grid box YWC057
description: <strong>Tilt Series Date:</strong> 2013-12-16</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.5°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> H.pylori 26695 from ATCC, prepared by Lee Rettberg</p>
<strong>Purification / Growth Conditions / Treatment:</strong> H.pylori cells grown in BLBB + 10% heat inactivated fetal bovine serum at 37 degrees in microaerobic chamber with GasPak EZ Campy Sachets for 2 days, OD600=0.4 Hs.746T cells cultivated on QF Au finder grid for 2 day in RPMI + 10% FBS. Infect by pylori for 3 hr.</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 37 C, 3µl BSA treated 20 nm gold (0.8 ml gold resuspent in 30 ul RPMI+10% FBS). Manual blot by Whatman 40 filter paper. Ethane/propane mix.</p>
  ycw2013-12-16-34_slicer9841.jpg: Chemoreceptors .  Helicobacter pylori
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-16-34/rawdata/</p>20131216_YWC057_10028.mrc,  Tilt Series (Pixel Size 0.48 nm), 2.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-16-34/rawdata/20131216_YWC057_10028.mrc"
        > <i class="download icon"></i> Download </a></p>

        20131216_YWC057_10028_part87_3.rec,  Reconstruction (Pixel Size 1.92 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-16-34/3dimage_36174/20131216_YWC057_10028_part87_3.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qmpz6-cje08
title: Bdellovibrio/E. coli minicell

description: Sample box: YWC053Bdellovibrio invasion complex with E. coli WM3433 minicell, early stage of invasion: mixing time 36 min
description: <strong>Tilt Series Date:</strong> 2013-12-06</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Bdellovibrio bacteriovorus</p>
<strong>Strain:</strong> HD100</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Bdellovibrio Strain from Liz Sockett, WM3433 E. coli minicell from Jun Liu & William Margolin, Sample prepared by Lee Rettberg</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Bdellovibrio cells grown in S17-1 prey solution at 30 degrees, then filtered by 0.45 um filter, concentrated by centrifugation. WM3433 E. coli minicells were enriched by 2 step centrifugation (3,000 rcf, 3 min --> 9,000 rcf, 5 min). Invasion complex were made by mixing them for 36 min. Pellet of 10 nm gold beads were first resuspent thoroughly and 20 ul cells were then gently mixed in by tapping the tube</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 nm BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix. Grid: QF Cu R2/2 200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-06-34/rawdata/</p>montage_25x250026.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-06-34/rawdata/montage_25x250026.mrc"
        > <i class="download icon"></i> Download </a></p>

        montage_25x250026_full.rec,  Reconstruction (Pixel Size 1.68 nm), 688.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-06-34/3dimage_35774/montage_25x250026_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/7n4gs-4v946
title: H.pylori 26695 delta-cagH / AGS

description: grid box: YWC087Hp cell were scraped from agar plate, grown few more hours in BLBB, not happy
description: <strong>Tilt Series Date:</strong> 2014-02-16</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 210.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> H.pylori & AGS cells from Carrie Shaffer</p>
<strong>Purification / Growth Conditions / Treatment:</strong> H.pylori cells grown in BLBB + 5% heat inactivated fetal bovine serum at 37 degrees in 5% CO2 chamber to OD600=~0.5. AGS cells cultivated on QF Au finder grid for 1 day in RPMI + 10% FBS. Infect by pylori for 4 hr.</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 37 C, 3µl BSA treated 20 nm gold (100 ul gold+ 25 ul BSA, pellets from 6 tubes merged into ~30 ul final solution). Manual blot by Whatman 40 filter paper for 3 sec. Ethane/propane mix.</p>
  ycw2014-02-16-1_slicer9863.jpg: Helicobacter pylori .  flat vesicle
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-02-16-1/rawdata/</p>20140216_YWC087_10001.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-02-16-1/rawdata/20140216_YWC087_10001.mrc"
        > <i class="download icon"></i> Download </a></p>

        20140216_YWC087_10001_full.rec,  Reconstruction (Pixel Size 1.92 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-02-16-1/3dimage_38990/20140216_YWC087_10001_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.5f5hsy
title: Occurrence Download

description: A dataset containing 42779 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Inula salicina"
 ]
}

 The dataset includes 42779 records from 676 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0011961-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6084/m9.figshare.11769582
title: Additional file 2 of Comparative proteomic analysis reveals that exogenous 6-benzyladenine (6-BA) improves the defense system activity of waterlogged summer maize

description: Additional file 2. GO term level2 classification of differentially abundant proteins.
DOI: 10.6084/m9.figshare.11769582.v1
title: Additional file 2 of Comparative proteomic analysis reveals that exogenous 6-benzyladenine (6-BA) improves the defense system activity of waterlogged summer maize

description: Additional file 2. GO term level2 classification of differentially abundant proteins.
DOI: 10.6084/m9.figshare.11769591
title: Additional file 3 of Comparative proteomic analysis reveals that exogenous 6-benzyladenine (6-BA) improves the defense system activity of waterlogged summer maize

description: Additional file 3. Details of differentially abundant proteins.
DOI: 10.6084/m9.figshare.11769591.v1
title: Additional file 3 of Comparative proteomic analysis reveals that exogenous 6-benzyladenine (6-BA) improves the defense system activity of waterlogged summer maize

description: Additional file 3. Details of differentially abundant proteins.
DOI: 10.6084/m9.figshare.19619495.v1
title: Additional file 2 of Small HSPs play an important role in crosstalk between HSF-HSP and ROS pathways in heat stress response through transcriptomic analysis in lilies (Lilium longiflorum)

description: Additional file 2. DEGs for GO and KEGG enrichment analysis.
DOI: 10.6084/m9.figshare.22779645.v1
title: Isolation and identification of pigment-producing filamentous fungus DBFL05 and its pigment characteristics and chemical structure

description: Natural pigments derived from microorganisms have many advantages and are widely studied in the food industry. A filamentous fungus, DBFL05, was identified as <i>Aspergillus ustus</i>, which produces a bright and abundant brown pigment. This extracellular, water-soluble pigment is highly polar and slightly soluble in alcohol but insoluble in other organic solvents. The pigment is stable under sunlight, at pH 2–10, and below 100°C. However, it is sensitive to Zn<sup>2+</sup>, Fe<sup>3+</sup>, Fe<sup>2+</sup>, and Cu<sup>2+</sup>. The pigment is mainly composed of two chemical components, pyrropyrazine diketone and dianthrone, and is classified as a polyketone pigment. Both components of the pigment exhibit inhibitory effects on bacteria and scavenging abilities for •OH and DPPH. The pigment showed no significant toxicity to plants and low toxicity to brine shrimp larvae. These findings indicate that the easily obtainable <i>A. ustus</i> pigment is a polyketone with attractive colour, stability, safety, and bioactivity.
DOI: 10.6084/m9.figshare.8099642.v1
title: Additional file 5: of Mitochondrial genome and transcriptome analysis of five alloplasmic male-sterile lines in Brassica juncea

description: Table S4. Gene content of each mitochondrial genome and RNA editing number of each gene. (XLSX 13â kb)
DOI: 10.6084/m9.figshare.25125773
title: <b>Dental disease in companion rabbits under UK primary veterinary care: frequency and risk factors</b>

description: Objectives Some prior evidence has suggested rabbits with lop ear and brachycephalic skull conformations have higher dental disease risk. This retrospective cohort study reports the frequency and conformational risk factors for primary-care veterinary diagnosis with dental disease in companion rabbits in the UK. MethodsAnonymised VetCompass clinical records were manually reviewed to confirm dental disease cases. Risk factor analysis used multivariable binary logistic regression modelling. Results From 161,979 rabbits under primary veterinary care in 2019, the one-year period prevalence of dental disease overall was 15.36% (95% confidence interval [CI]: 14.78-15.96). Prevalence of dental disease affecting incisors was 3.14% (95% CI: 2.87-3.44) and cheek teeth was 13.72% (95% CI: 13.17-14.29). Neither lop ear conformation or brachycephalic skull conformation were statistically significantly associated with the odds of dental disease . Male rabbits had 1.23 times higher odds of dental disease than females (95% CI: 1.12-1.35). Dental disease odds increased as age increased, and decreased as bodyweight increased. Clinical SignificanceHigh overall prevalence highlights dental disease as a major welfare concern for all companion rabbits, regardless of conformation. This information can be used to encourage regular routine dental assessment of rabbits of all conformations to promote earlier diagnosis, paying particular attention to males, older rabbits or those with low bodyweight. <br>
DOI: 10.6084/m9.figshare.12285281.v1
title: Additional file 2 of Genomic characterization of high-recurrence risk papillary thyroid carcinoma in a southern Chinese population

description: Additional file 2.
DOI: 10.6084/m9.figshare.12285281
title: Additional file 2 of Genomic characterization of high-recurrence risk papillary thyroid carcinoma in a southern Chinese population

description: Additional file 2.
DOI: 10.6084/m9.figshare.11769732
title: Additional file 2 of Effects of excess sugars and lipids on the growth and development of Caenorhabditis elegans

description: Additional file 2: File S1. Genes significantly up-regulated and down-regulated in nematodes after 400â€‰mM sucrose treatment compared to the untreated group.
DOI: 10.6084/m9.figshare.11769732.v1
title: Additional file 2 of Effects of excess sugars and lipids on the growth and development of Caenorhabditis elegans

description: Additional file 2: File S1. Genes significantly up-regulated and down-regulated in nematodes after 400â€‰mM sucrose treatment compared to the untreated group.
DOI: 10.6084/m9.figshare.11769738
title: Additional file 3 of Effects of excess sugars and lipids on the growth and development of Caenorhabditis elegans

description: Additional file 3: File S2. Genes significantly up-regulated and down-regulated in nematodes after 500 μg/mL stearic acid treatment compared to the untreated group.
DOI: 10.6084/m9.figshare.11769738.v1
title: Additional file 3 of Effects of excess sugars and lipids on the growth and development of Caenorhabditis elegans

description: Additional file 3: File S2. Genes significantly up-regulated and down-regulated in nematodes after 500 μg/mL stearic acid treatment compared to the untreated group.
DOI: 10.6084/m9.figshare.11769744
title: Additional file 4 of Effects of excess sugars and lipids on the growth and development of Caenorhabditis elegans

description: Additional file 4: File S3. Genes significantly up-regulated and down-regulated in nematodes after 400 mM sucrose- 500 μg/mL stearic acid treatment compared to the untreated group.
DOI: 10.6084/m9.figshare.11769744.v1
title: Additional file 4 of Effects of excess sugars and lipids on the growth and development of Caenorhabditis elegans

description: Additional file 4: File S3. Genes significantly up-regulated and down-regulated in nematodes after 400 mM sucrose- 500 μg/mL stearic acid treatment compared to the untreated group.
DOI: 10.6084/m9.figshare.11769747
title: Additional file 1 of Characterising avenin-like proteins (ALPs) from albumin/globulin fraction of wheat grains by RP-HPLC, SDS-PAGE, and MS/MS peptides sequencing

description: Additional file 1. Peptide sequencing results of albumin/globulin extracts proteins.
DOI: 10.6084/m9.figshare.11769747.v1
title: Additional file 1 of Characterising avenin-like proteins (ALPs) from albumin/globulin fraction of wheat grains by RP-HPLC, SDS-PAGE, and MS/MS peptides sequencing

description: Additional file 1. Peptide sequencing results of albumin/globulin extracts proteins.
DOI: 10.6084/m9.figshare.11769750.v1
title: Additional file 5 of Effects of excess sugars and lipids on the growth and development of Caenorhabditis elegans

description: Additional file 5: File S4. Genes significantly up-regulated and down-regulated in nematodes after 3.29 μM resveratrol treatment compared to the 400 mM sucrose- 500 μg/mL stearic acid treated group.
DOI: 10.6084/m9.figshare.11769756
title: Additional file 2 of Characterising avenin-like proteins (ALPs) from albumin/globulin fraction of wheat grains by RP-HPLC, SDS-PAGE, and MS/MS peptides sequencing

description: Additional file 2. PF00234 and PF13016 domain sequences of albumin/globulin extracts proteins.
DOI: 10.6084/m9.figshare.11769756.v1
title: Additional file 2 of Characterising avenin-like proteins (ALPs) from albumin/globulin fraction of wheat grains by RP-HPLC, SDS-PAGE, and MS/MS peptides sequencing

description: Additional file 2. PF00234 and PF13016 domain sequences of albumin/globulin extracts proteins.
DOI: 10.6084/m9.figshare.11769768
title: Additional file 1 of Differential expression of matrix metalloproteinases and miRNAs in the metastasis of oral squamous cell carcinoma

description: Additional file 1: The raw data of Microarray analysis.
DOI: 10.6084/m9.figshare.23828397
title: 3-D Vp and Vs models of southern Mariana Margin

description: res -----&gt; The 3-D P and S wave velocity modelsforward_res -----&gt; the arrival-time data residuals<br>
DOI: 10.6084/m9.figshare.23828400
title: PFGLiuData.xlsx

description: 1. Global climate warming threatens biodiversity. The loss of plant functional groups (PFG) accompanying climate warming changes the composition and diversity of litter mixtures, affecting decomposition processes. No consensus has been reached regarding the effect of PFG loss on different microbial groups during the decomposition process. The decomposition effects of different microbial taxa are also unpredictable.2. To explored the response of microbial communities to single-PFG loss during litter mixture decomposition in subalpine coniferous forests. We evaluated the compositions of bacterial and fungal communities by high-throughput sequencing, and the communities were further classified into abundant taxa and rare taxa to assess the subcommunity structure.3. We found that bacteria were more sensitive to single-PFG loss, while the fungal community structure was stable between loss treatments and the total mixture (Tot.Mix.). The changes in rare taxa between single-PFG loss and Tot.Mix. were more significant than those in abundant taxa. K content increased the diversity of total bacterial and total and abundant fungal communities, and Ca content increased the diversity of rare bacterial community, while Mn decreased the diversity of total and abundant bacterial communities.. Additionally, the chemistry of the litter mixture was the most important direct driver determining mixture decomposition, and the microbial decomposition pathway was dominated by abundant fungal taxa. However, litter chemistry and fungal communities among different litter mixtures showed the same convergence in the late decomposition stage, resulting in no difference in litter mass loss among different treatments.4. Overall, microbial community were influenced by the metallic elements that regulate litter degradability. And different microbial taxa showed unique responses to single-PFG loss, the decomposition of litter mixtures was regulated by these responses. Litter mixtures controlled by abundant fungi rather than bacteria and rare taxa, and abundant fungal subcommunity maintained stability after single PFG loss, which is conducive to maintaining the stability of carbon and nutrient cycling in alpine ecosystem after PFG loss.
DOI: 10.6084/m9.figshare.18585542
title: Transcriptome profiling and RNA interference reveals relevant detoxification genes in Monochamus alternatus response to (+)-α-pinene

description: The mechanism of how insects defend against toxic effects of phytochemicals provides an interesting insight
for the study of interactions in plant-herbivore. <i>Monochamus
alternatus</i> Hope, as the main vector of pine wood nematode, prefers masson
pine as host and causes huge economic and environmental losses every year. α-Pinene is the primary component of resin from
masson pine and plays a key role in resisting invasive pests, but little is known about the
effects of α-pinene against <i>M. alternatus</i>. Here, bioassays and an
RNA-Seq approach were used to explore the physiological metabolism in larvae
after (+)-α-pinene fumigation treatment.
DOI: 10.6084/m9.figshare.19625390
title: Additional file 1 of Treatment outcome of tardy ulnar nerve palsy associated with traumatic cubitus valgus by supracondylar shortening wedge rotary osteotomy and ulnar nerve in situ tension release

description: Additional file 1.
DOI: 10.6084/m9.figshare.19625390.v1
title: Additional file 1 of Treatment outcome of tardy ulnar nerve palsy associated with traumatic cubitus valgus by supracondylar shortening wedge rotary osteotomy and ulnar nerve in situ tension release

description: Additional file 1.
DOI: 10.6084/m9.figshare.23819794
title: Additional file 1 of Identification of ancient glass categories based on distance discriminant analysis

description: Additional file 1. Chemical composition ratio data set of different glasses.
DOI: 10.6084/m9.figshare.19625411
title: Additional file 2 of One Cell At a Time (OCAT): a unified framework to integrate and analyze single-cell RNA-seq data

description: Additional file 2 Supplementary Tables S1-S9.
DOI: 10.6084/m9.figshare.12285311
title: Additional file 2 of Knowledge-based analyses reveal new candidate genes associated with risk of hepatitis B virus related hepatocellular carcinoma

description: Additional file 2: Excel table of canonical pathways of MSigDB with p &lt; 0.05 by gene-set based association tests.
DOI: 10.6084/m9.figshare.12285311.v1
title: Additional file 2 of Knowledge-based analyses reveal new candidate genes associated with risk of hepatitis B virus related hepatocellular carcinoma

description: Additional file 2: Excel table of canonical pathways of MSigDB with p &lt; 0.05 by gene-set based association tests.
DOI: 10.6084/m9.figshare.11769891
title: Colistin-resistance gene <i>mcr</i> in clinical carbapenem-resistant <i>Enterobacteriaceae</i> strains in China, 2014–2019

description: To investigate whether introduction of colistin into the clinical settings selected colistin-resistant CRE, we performed molecular epidemiological study of 1868 CRE strains collected from different geographical locales in China during the period 2014–2019. 1755 (96.18%) isolates carried the carbapenemase genes <i>bla</i><sub>KPC</sub> and <i>bla</i><sub>NDM</sub>; 14 <i>Escherichia coli</i> isolates (0.75%) carrying <i>mcr-1</i> and <i>bla</i><sub>NDM</sub> (MCR-CREC) were also identified. Importantly, the number and relative prevalence of MCR-CREC isolates increased from 5 (0.41%) to 9 (1.38%) after introduction of polymyxin into clinical practice. Consistently, results of genetic analysis indicated that MCR-CREC strains collected before December 2017 were genetically diverse, yet those collected after that date exhibited more closely related genetic profiles, indicating that specific MCR-CREC strains were rapidly selected as a result of increased usage of colistin in clinical settings. The resistance level of MCR-CREC isolates to colistin increased after the introduction of polymyxin into clinical use with the MIC to colistin from &lt;2 mg/L in 80% strains to 2 mg/L in 100% strains. Further dissemination of MCR-CREC strains, which exhibit resistance to the last-line drugs of carbapenems and colistin, is expected to pose a severe threat to human health.
DOI: 10.6084/m9.figshare.23819794.v1
title: Additional file 1 of Identification of ancient glass categories based on distance discriminant analysis

description: Additional file 1. Chemical composition ratio data set of different glasses.