cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.24209088
title: Additional file 5 of Establishment and validation of an immune infiltration predictive model for ovarian cancer

description: Additional file 5: Table S1. Clinical information of TCGA-OV patients. Table S2. Immune-related genesets enriched in TP53 MUT OVs. Table S3. Differentially expressed immune-related genes between TP53 WT and TP53 MUT OVs.Table S4. Univariate Cox regression analysis of differentially expressed immune-related genes. Table S5. Analysis of correlations between risk score and immune checkpoints. Table S6. Top 20 clusters with their representative enriched terms by Metascape.
DOI: 10.6084/m9.figshare.24209088.v1
title: Additional file 5 of Establishment and validation of an immune infiltration predictive model for ovarian cancer

description: Additional file 5: Table S1. Clinical information of TCGA-OV patients. Table S2. Immune-related genesets enriched in TP53 MUT OVs. Table S3. Differentially expressed immune-related genes between TP53 WT and TP53 MUT OVs.Table S4. Univariate Cox regression analysis of differentially expressed immune-related genes. Table S5. Analysis of correlations between risk score and immune checkpoints. Table S6. Top 20 clusters with their representative enriched terms by Metascape.
DOI: 10.6084/m9.figshare.12219092
title: Additional file 2 of Milk exosome-derived miRNAs from water buffalo are implicated in immune response and metabolism process

description: Additional file 2. Predicted targets of top 10 expressed miRNAs in buffalo milk exosome. Query represented for miRNA candidates; Ref represented for reference genes.
DOI: 10.6084/m9.figshare.12219101
title: Additional file 3 of Milk exosome-derived miRNAs from water buffalo are implicated in immune response and metabolism process

description: Additional file 3. The KEGG analysis of top 10 expressed miRNAs’ targets
DOI: 10.6084/m9.figshare.8025353.v2
title: A systematic review of the approaches to multi-level learning in the general practice context, using a realist synthesis approach: BEME Guide No. 55

description: <b>Background:</b> Recent global increases in medical student numbers and shifts in medical education from teaching hospitals to community settings call for effective strategies to meet the demand for general practice teaching placements. It has been proposed that “multi-level learning” (MLL), in which learning and teaching are shared across different levels of learners, may provide teaching efficiencies and valuable experiences for learners and teachers. <b>Aims:</b> To identify, evaluate and synthesize the evidence related to the types, benefits, challenges, and facilitators of MLL in community-based general practice, and the underlying mechanisms and associated contexts to explain the reported outcomes. <b>Method:</b> A realist synthesis approach guided the systematic review. <b>Results</b>: Fifteen papers were identified, providing primary evaluation data predominantly from interviews with or surveys of key stakeholders. Generally, all levels of learners reported overall satisfaction with their MLL experiences. Medical students appreciated learning from prevocational doctors and registrars due to social and cognitive congruence. Mechanisms and contexts that supported our hypotheses regarding successful MLL outcomes were identified, with “a strong teaching culture” being a major mechanism. <b>Conclusions:</b> The findings can help inform practices considering the implementation or enhancement of MLL initiatives in general practice. Further research should include measuring defined learning outcomes.
DOI: 10.6084/m9.figshare.12219125
title: Additional file 7 of Milk exosome-derived miRNAs from water buffalo are implicated in immune response and metabolism process

description: Additional file 7. The KEGG analysis of the down-regulated miRNAs’ targets
DOI: 10.6084/m9.figshare.12744160.v1
title: Additional file 1 of Mapping quantitative trait loci for disease resistance to false smut of rice

description: Additional file 1 Table S1. Evaluation criteria for resistance to false smut of rice
DOI: 10.6084/m9.figshare.12219107.v1
title: Additional file 4 of Milk exosome-derived miRNAs from water buffalo are implicated in immune response and metabolism process

description: Additional file 4. Predicted targets of significantly up-regulated miRNAs in buffalo milk exosome
DOI: 10.6084/m9.figshare.12219119.v1
title: Additional file 5 of Milk exosome-derived miRNAs from water buffalo are implicated in immune response and metabolism process

description: Additional file 5. Predicted targets of significantly down-regulated miRNAs in buffalo milk exosome
DOI: 10.6084/m9.figshare.12219092.v1
title: Additional file 2 of Milk exosome-derived miRNAs from water buffalo are implicated in immune response and metabolism process

description: Additional file 2. Predicted targets of top 10 expressed miRNAs in buffalo milk exosome. Query represented for miRNA candidates; Ref represented for reference genes.
DOI: 10.5281/zenodo.10645041
title: Examples of sequence alignment with contiguous, binary and ternary seeds

description: Classical sequence alignment algorithms use contiguous chunks of symbols to pre-align short sequences (reads) obtained for a studied organism to a long reference sequence. The use of spaced seeds (when we ignore possible differences between two sequences at some positions) allows researchers to improve the sensitivity of alignment algorithms.

In genetics, point mutations have different probabilities. Therefore, it may be reasonable to consider transitional (A <-> G, C <-> T) and transversional (all other) mutations separately.

In perlotSeeds, we consider the alignment of paired-end reads (Han Chinese South, sequence data, ERR016118) with respect to the Human Reference Genome (Human genome assembly GRCh38.p14).

We consider various contiguous seeds, e.g. C32 for the length of 32, and ternary seeds for the given read’s length (76), e.g. T1V2 is a seed to allow one transitional and two transversional mismatches. Then, generate a library of records corresponding to a chosen seed. This library is used to find candidate alignments of all reads.

We provide statistics (InputStat.zip) related to each library generated, i.e. the number of records having the same signature (generated by the seed). There are also output statistics for all reads and chosen seeds, e.g. outputStatT1V3.zip, when we know how many signatures are generated for each read, how many successful alignments can be done and the best score. More detailed information related to several groups of reads can be found in the ExampleOutput.zip file.
DOI: 10.5281/zenodo.10645042
title: Examples of sequence alignment with contiguous, binary and ternary seeds

description: Classical sequence alignment algorithms use contiguous chunks of symbols to pre-align short sequences (reads) obtained for a studied organism to a long reference sequence. The use of spaced seeds (when we ignore possible differences between two sequences at some positions) allows researchers to improve the sensitivity of alignment algorithms.

In genetics, point mutations have different probabilities. Therefore, it may be reasonable to consider transitional (A <-> G, C <-> T) and transversional (all other) mutations separately.

In perlotSeeds, we consider the alignment of paired-end reads (Han Chinese South, sequence data, ERR016118) with respect to the Human Reference Genome (Human genome assembly GRCh38.p14).

We consider various contiguous seeds, e.g. C32 for the length of 32, and ternary seeds for the given read’s length (76), e.g. T1V2 is a seed to allow one transitional and two transversional mismatches. Then, generate a library of records corresponding to a chosen seed. This library is used to find candidate alignments of all reads.

We provide statistics (InputStat.zip) related to each library generated, i.e. the number of records having the same signature (generated by the seed). There are also output statistics for all reads and chosen seeds, e.g. outputStatT1V3.zip, when we know how many signatures are generated for each read, how many successful alignments can be done and the best score. More detailed information related to several groups of reads can be found in the ExampleOutput.zip file.
DOI: 10.6084/m9.figshare.5928256.v2
title: Antitumor efficacy of liposome-encapsulated NVP-BEZ 235 in combination with irreversible electroporation

description: Irreversible electroporation (IRE) is an emerging minimally invasive tumor ablation technique that delivers short pulses of strong electric fields and kills cancer cells by disrupting their cell membranes with the electric pulses. However, clinical studies report that more than 10% of local tumor recurrences occur at the original ablated site. NVP BEZ-235 (BEZ) is a dual PI3K/mTOR inhibitor that has substantial anticancer effects. However, the clinical trials of BEZ was not satisfactory because of its low bioavailability and high toxicity, which stemmed from the use of oral administration of high doses over a long period of time. In this research, we prepared a liposomal formulation of BEZ (L-BEZ) for intratumoral injection and studied its antitumor efficacy alone and in combination with IRE. We hypothesized that IRE could release BEZ from the liposomes and that the combination could decrease tumor viability. Our results show that IRE released BEZ from its liposomal encapsulation. The combination of L-BEZ and IRE killed more Hep3B tumor cells <i>in vitro</i> than did L-BEZ or IRE alone and also inhibited cancer cell proliferation in nude mice bearing Hep3B xenografts. Combination of chemotherapeutic agent loaded nanoparticles could enhance the antitumor efficacy of IRE.
DOI: 10.13012/b2idb-6453957_v2
title: Soybean seed quality response to eCO2 data files

description: This data set is related to a SoyFACE experiment conducted in 2004, 2006, 2007, and 2008 with the soybean cultivars Loda and HS93-4118. The experiment looked at how seed elements were affected by elevated CO2 and yield.

In this V2, 2 new files were added per journal requirement. Total there are 5 data files in text format within the digrado_et_al_gcb_data_V2 and 1 readme file. The name of files are listed below. Details about headers are explained in the readme.txt file.

<b>1. ionomic_data.txt file</b> contains the ionomic data (mg/kg) for the two cultivars. The file contains all six technical replicates for each plot. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry.
<b>2. yield_data.txt file</b> contains the yield data for the two cultivars (seed yield in kg/ha, seed yield in bu/a, Protein (%), Oil (%)). The file contains yield data for every plot. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry.
<b>3. mineral_pro_oil_yield.txt file</b> contains the yield per hectare for each mineral (g/ha) along with the yield per hectare for protein and oil (t/ha). This was obtained by multiplying the seed content of each element (minerals, protein, and oil) by the total seed yield. The file contains yield data for every plots. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry.
<b>4. economic_assessment.txt file</b> contains data used to assess the financial impact of altered seed oil content on soybean oil production. 
<b>5. meteorological_data.txt file</b> contains the meteorological data recorded by a weather station located ~ 3km from the experimental site (Willard Airport Champaign). Data covering the period between May 28 and September 24 were used for 2004; between May 25 and September 24 were used in 2006; between May 23 and September 17 in 2007; and between June 16 and October 24 in 2008.
DOI: 10.6084/m9.figshare.20081144
title: Additional file 1 of Proteome analysis of urinary biomarkers in a cigarette smoke-induced COPD rat model

description: Additional file 1: Table S1. All identification and quantitation details in COPD rats. Table S2. The details of the nodes in PPI.
DOI: 10.6084/m9.figshare.14316834.v1
title: Citronellal-induced disruption of membrane homeostasis in Candida albicans and attenuation of its virulence attributes

description: Abstract: INTRODUCTION There is an increasing burden of multidrug resistance. As a result, deciphering the mechanisms of action of natural compounds with antifungal activity has gained considerable prominence. We aimed to elucidate the probable mechanism of action of citronellal, a monoterpenoid found in the essential oil extracted from Cymbopogon plants, against Candida albicans. METHODS Drug susceptibility was measured by broth microdilution and spot assays. Ergosterol levels were estimated using the alcoholic potassium hydroxide method and H+ extrusion was assessed by monitoring the glucose-induced acidification of the external medium. Virulence traits were studied by hyphal morphogenesis and biofilm formation, along with fungal cell adherence to polystyrene surface and human oral epithelial cells. RESULTS Citronellal showed anticandidal activity against C. albicans and non-albicans species of Candida at a minimum inhibitory concentration of 1 mg/ml. Citronellal interfered with membrane homeostasis, which is the major target of known antifungal drugs, by increasing the hypersensitivity of the fungi to membrane-perturbing agents, reducing ergosterol levels, and diminishing glucose-induced H+ extrusion. In addition, oxidative and genotoxic stresses were induced via an increased production of reactive oxygen species. Furthermore, citronellal inhibited the virulent attributes of yeast-to-hypha transition and biofilm formation. It also reduced cell adherence to polystyrene surface and the human oral epithelial cells. CONCLUSIONS This is the first study to propose the cell membrane, morphogenetic switching, biofilm formation, and cell adherence of Candida albicans as potential targets for the anticandidal activity of citronellal. However, clinical investigations on the therapeutic applications of citronellal are required.
DOI: 10.6084/m9.figshare.20081144.v1
title: Additional file 1 of Proteome analysis of urinary biomarkers in a cigarette smoke-induced COPD rat model

description: Additional file 1: Table S1. All identification and quantitation details in COPD rats. Table S2. The details of the nodes in PPI.
DOI: 10.6084/m9.figshare.12744151.v1
title: Additional file 2 of GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing

description: Additional file 2 Supplementary tables
DOI: 10.6084/m9.figshare.20081147.v1
title: Additional file 10 of Gene fusion as an important mechanism to generate new genes in the genus Oryza

description: Additional file 10. Gene structure re-annotation of species-specific fusion gene in four focus species.
DOI: 10.6084/m9.figshare.20081159.v1
title: Additional file 3 of Gene fusion as an important mechanism to generate new genes in the genus Oryza

description: Additional file 3. Fixation frequency of species-specific fusion gene included in four focus species.
DOI: 10.6084/m9.figshare.20081162
title: Additional file 4 of Gene fusion as an important mechanism to generate new genes in the genus Oryza

description: Additional file 4. FPKM of fusion gene and short copy homologs in O. sativa v.g. japonica, O. barthii, O. glaberrima, O. punctate, O. branchyantha and Leersia.
DOI: 10.6084/m9.figshare.20081171.v1
title: Additional file 6 of Gene fusion as an important mechanism to generate new genes in the genus Oryza

description: Additional file 6. Correlation of O. japonica fusion gene and its short copies FPKM value in different tissues.
DOI: 10.6084/m9.figshare.20081180
title: Additional file 9 of Gene fusion as an important mechanism to generate new genes in the genus Oryza

description: Additional file 9. Transposable element retrieved from O. sativa v.g. japonica fusion genes.
DOI: 10.15468/dl.c8q5vn
title: Occurrence Download

description: A dataset containing 67 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polyalthia flagellaris (Becc.) Airy Shaw"
 ]
}

 The dataset includes 67 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075184-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.4w4zuf
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phlyctidocarpa flava Cannon & W.L.Theob."
 ]
}

 The dataset includes 14 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075185-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vwqx8n
title: Occurrence Download

description: A dataset containing 58 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Planchonella pronyensis Guillaumin"
 ]
}

 The dataset includes 58 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075186-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qhnwtk
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pleioluma lamprophylla (K.Krause) Swenson"
 ]
}

 The dataset includes 22 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075188-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.j54xnr
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus xylorrhizus Thulin"
 ]
}

 The dataset includes 6 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075189-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ebrc2q
title: Occurrence Download

description: A dataset containing 57 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phoebe angustifolia Meisn."
 ]
}

 The dataset includes 57 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075191-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hdg3gv
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polyalthia gracilipes Merr."
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075190-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tx2kjy
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Planchonella pullenii (Vink) Swenson"
 ]
}

 The dataset includes 29 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075193-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hys4sc
title: Occurrence Download

description: A dataset containing 20 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pleioluma lanatifolia (P.Royen) Swenson"
 ]
}

 The dataset includes 20 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075194-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hkkdnp
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus yangambiensis Jean F.Brunel"
 ]
}

 The dataset includes 8 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075195-240321170329656/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.25516261
title: Supplementary Figures and Tables.tif

description: NPWT upregulates IL-17 to promote wound healing by altering chromatin accessibility, which is a novel mechanism for NPWT’s efficacy in wound healing.
DOI: 10.6084/m9.figshare.25516261.v1
title: Supplementary Figures and Tables.tif

description: NPWT upregulates IL-17 to promote wound healing by altering chromatin accessibility, which is a novel mechanism for NPWT’s efficacy in wound healing.
DOI: 10.15468/dl.jea9zb
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polyalthia guabatuensis I.M.Turner & Utteridge"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075196-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.3dg7bj
title: Occurrence Download

description: A dataset containing 116 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phoebe attenuata (Nees) Nees"
 ]
}

 The dataset includes 116 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075197-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cafhfe
title: Occurrence Download

description: A dataset containing 49 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Planchonella pyrulifera (A.Gray) H.J.Lam ex P.Royen"
 ]
}

 The dataset includes 49 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075198-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cpnnh8
title: Occurrence Download

description: A dataset containing 101 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pleioluma lasiantha (Baill.) Swenson & Munzinger"
 ]
}

 The dataset includes 101 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075199-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.8wj4nz
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phyllanthus yaouhensis Schltr."
 ]
}

 The dataset includes 79 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075200-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2sa8cr
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Polyalthia guamusangensis I.M.Turner & Utteridge"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0075201-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.