cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.23452895.v1
title: The complete mitochondrial genome of <i>Stibochiona nicea</i> (Gray, 1846) (Lepidoptera: Nymphalidae) and phylogenetic analysis

description: In this study, the complete mitochondrial genome (mitogenome) of <i>Stibochiona nicea</i> (Gray, 1846) (Lepidoptera: Nymphalidae) was first reported with 15,298 bp in size, containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes (<i>rrnL</i> and <i>rrnS</i>), and one control region. The nucleotide composition of the entire mitogenome is highly A + T biased (81.5%). The gene content and arrangement of the newly sequenced mitogenome are identical to those of the other available mitogenomes of Nymphalidae. All PCGs start with the conventional ATN codons, except for <i>cox1</i> initiating with atypical CGA(R). Nine PCGs (<i>atp8</i>, <i>atp6</i>, <i>cox3</i>, <i>nad1</i>, <i>nad2</i>, <i>nad3</i>, <i>nad4l</i>, <i>nad6</i>, and <i>cob</i>) utilize a typical stop codon TAA, whereas the remaining PCGs (<i>cox1</i>, <i>cox2</i>, <i>nad4</i>, and <i>nad5</i>) end with an incomplete stop codon T–. Phylogenetic analysis revealed that <i>S. nicea</i> is closely related to <i>Dichorragia nesimachus</i> within Pseudergolinae, which further forms the sister group to the grouping of (Nymphalinae + (Cyrestinae + (Biblidinae + Apaturinae))). The complete mitogenome of <i>S. nicea</i> will provide useful genetic information for improving the taxonomic system and phylogenetics of Nymphalidae.
DOI: 10.6084/m9.figshare.12448871
title: Optimal Sampling for Generalized Linear Models Under Measurement Constraints

description: Under “measurement constraints,” responses are expensive to measure and initially unavailable on most of records in the dataset, but the covariates are available for the entire dataset. Our goal is to sample a relatively small portion of the dataset where the expensive responses will be measured and the resultant sampling estimator is statistically efficient. Measurement constraints require the sampling probabilities can only depend on a very small set of the responses. A sampling procedure that uses responses at most only on a small pilot sample will be called “response-free.” We propose a response-free sampling procedure optimal sampling under measurement constraints (OSUMC) for generalized linear models. Using the A-optimality criterion, that is, the trace of the asymptotic variance, the resultant estimator is statistically efficient within a class of sampling estimators. We establish the unconditional asymptotic distribution of a general class of response-free sampling estimators. This result is novel compared with the existing conditional results obtained by conditioning on both covariates and responses. Under our unconditional framework, the subsamples are no longer independent and new martingale techniques are developed for our asymptotic theory. We further derive the A-optimal response-free sampling distribution. Since this distribution depends on population level quantities, we propose the OSUMC algorithm to approximate the theoretical optimal sampling. Finally, we conduct an intensive empirical study to demonstrate the advantages of OSUMC algorithm over existing methods in both statistical and computational perspectives. We find that OSUMC’s performance is comparable to that of sampling algorithms that use complete responses. This shows that, provided an efficient algorithm such as OSUMC is used, there is little or no loss in accuracy due to the unavailability of responses because of measurement constraints. Supplementary materials for this article are available online.
DOI: 10.6084/m9.figshare.19783039
title: Application of an improved hollow fiber liquid phase microextraction technique coupled to LC-MS/MS to studying migration of fluorescent whitening agents from plastic food contact materials

description: In this paper, a new hollow fiber liquid-phase microextraction method was developed to improve the extraction of five fluorescent whitening agents that migrated from plastics food contact materials. Influencing factors, such as the types of membrane, the extraction solvent, the stirring speed, the addition of salt ion, and extraction time, were investigated in detail. Under the optimal conditions, high enrichment factors (71–205) can be obtained with 15 μL extraction solvent. The new method is advantageous; the polypropylene hollow fiber membrane modified by sepiolite nanoparticles had excellent solvent binding force and mass transfer effect compared with the conventional extraction technique. The extracts were analyzed by high performance liquid chromatography–tandem mass spectrometry, the limits of detection were 0.3 or 0.9 ng kg<sup>−1</sup> with good correlation coefficients (<i>r</i><sup>2</sup> ≥ 0.9940) for the five fluorescent whitening agents. The intra-day and inter-day recoveries ranged between 82.6% and 112%, with a relative standard deviation of less than 12%. The established method was successfully applied to the analysis of fluorescent whitening agent migration from four types of plastic food contact materials immersed in three food simulants.
DOI: 10.6084/m9.figshare.20307329.v1
title: Differential Regulation of Integrin α5 and β4 in Normal and Psoriatic Epidermal Keratinocytes

description: Abstract Psoriasis is a chronic skin inflammation, characterized by impaired differentiation, hyperproliferation of keratinocytes involving pro-inflammatory factors interleukin (IL)-13/17A, tumor necrosis factor (TNF)-α, interferon (IFN)-γ. Among the integrin family, α5 is important for blood vessel formation, and β4 for proliferation, differentiation of keratinocytes. To investigate the expression and regulation of integrin α5 and β4 in psoriatic keratinocytes. Skin biopsies were obtained from 14 psoriatic patients and 12 normal volunteers. We compared the immunolocalization and regulation of α5 and β4 between the psoriatic and normal ones, before and after incubation with MEK/ERK pathway inhibitor U0126 by immunohistochemistry and western blot separately. Immunohistochemistry showed psoriatic keratinocytes had higher α5 than normal ones. According to western blot, IL-17A and IL-13 increased normal keratinocytes’ α5 and β4 respectively, but psoriatic keratinocytes were the exact opposite. Incubated with U0126, normal keratinocytes’ α5 was enhanced by the 5 cytokines ; while IL-13/17A, IFN-γ suppressed β4. Psoriatic keratinocytes’ α5 was increased by IL-13/17A, decreased by IFN-γ; but β4 increased by IL-17A, IFN-γ. IL-13/17A, TNF-α, IFN-γ regulate α5 and β4 through ERK pathway whether normal or psoriasis. The normal and psoriatic keratinocytes respond to the same cytokines differently.
DOI: 10.6084/m9.figshare.19783039.v1
title: Application of an improved hollow fiber liquid phase microextraction technique coupled to LC-MS/MS to studying migration of fluorescent whitening agents from plastic food contact materials

description: In this paper, a new hollow fiber liquid-phase microextraction method was developed to improve the extraction of five fluorescent whitening agents that migrated from plastics food contact materials. Influencing factors, such as the types of membrane, the extraction solvent, the stirring speed, the addition of salt ion, and extraction time, were investigated in detail. Under the optimal conditions, high enrichment factors (71–205) can be obtained with 15 μL extraction solvent. The new method is advantageous; the polypropylene hollow fiber membrane modified by sepiolite nanoparticles had excellent solvent binding force and mass transfer effect compared with the conventional extraction technique. The extracts were analyzed by high performance liquid chromatography–tandem mass spectrometry, the limits of detection were 0.3 or 0.9 ng kg<sup>−1</sup> with good correlation coefficients (<i>r</i><sup>2</sup> ≥ 0.9940) for the five fluorescent whitening agents. The intra-day and inter-day recoveries ranged between 82.6% and 112%, with a relative standard deviation of less than 12%. The established method was successfully applied to the analysis of fluorescent whitening agent migration from four types of plastic food contact materials immersed in three food simulants.
DOI: 10.6084/m9.figshare.16632882
title: Additional file 3 of Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR

description: Additional file 3: Table S2: Enrichment P-values according to Fisher’s exact test for validation of the identified methQTLs in independent samples (monocytes, transverse colon) and independent studies (blood and fetal brain).
DOI: 10.6084/m9.figshare.21351346.v1
title: Additional file 1 of Genetic diversity in the transmission-blocking vaccine candidate Plasmodium vivax gametocyte protein Pvs230 from the China–Myanmar border area and central Myanmar

description: Additional file 1: Table S1. Primers used in Pvs230 amplification and sequencing.
DOI: 10.6084/m9.figshare.21351349.v1
title: Additional file 2 of Genetic diversity in the transmission-blocking vaccine candidate Plasmodium vivax gametocyte protein Pvs230 from the China–Myanmar border area and central Myanmar

description: Additional file 2: Table S2. The diversity pattern of the N-terminal repeat region in IVP of Pvs230 from global isolates. Related to Fig. 2.
DOI: 10.6084/m9.figshare.17157078
title: Additional file 5 of Genome-wide identification and expression analysis of the bZIP transcription factors, and functional analysis in response to drought and cold stresses in pear (Pyrus breschneideri)

description: Additional file 5 : Table S2. Sequence information of 20 detected motifs in MEME analysis.
DOI: 10.6084/m9.figshare.21351352.v1
title: Additional file 3 of Genetic diversity in the transmission-blocking vaccine candidate Plasmodium vivax gametocyte protein Pvs230 from the China–Myanmar border area and central Myanmar

description: Additional file 3: Table S3. Codon-based tests for selection on Pvs230 in China–Myanmar border and Myanmar isolates.
DOI: 10.6084/m9.figshare.17157081.v1
title: Additional file 6 of Genome-wide identification and expression analysis of the bZIP transcription factors, and functional analysis in response to drought and cold stresses in pear (Pyrus breschneideri)

description: Additional file 6 : Table S3. Duplication type of PbrbZIP genes in pear (Pyrus bretschneideri).
DOI: 10.6084/m9.figshare.6681740
title: TNFAIP3-DEPTOR complex regulates inflammasome secretion through autophagy in ankylosing spondylitis monocytes

description: Ankylosing spondylitis (AS) is a chronic autoimmune inflammatory disease with severe inflammatory symptoms in the axial skeleton. The cause of ankylosing spondylitis is unknown. TNFAIP3, also named A20, uses ubiquitin-related functions to regulate immune activation, deficiency of which is highly related to autoimmune disease. However, the role of TNFAIP3 in human AS has not been reported. Our objective was to study the role and mechanism of TNFAIP3 in ankylosing spondylitis. TNFAIP3 expression on different types of immunocytes from AS peripheral blood was measured by flow cytometry. In vitro, monocytes were transfected with a <i>TNFAIP3</i> shRNA lentivirus, and IL6 and IL1B activation was tested using real-time PCR and ELISA. The novel interaction complex TNFAIP3-DEPTOR was determined through GST pull-down, yeast two-hybrid system, confocal microscopy, and co-immunoprecipitation. Transmission electron microscopy, the RFP-GFP-LC3 adenovirus, and LC3 expression were used for autophagy detection. Here, we show that TNFAIP3 expression in AS peripheral blood non-classical monocytes was decreased. In normal monocytes, TNFAIP3 induced autophagy, which restricted inflammasome activation to the early stage of LPS stimulation. Zinc-finger domains of TNFAIP3 were able to interact and stabilize DEPTOR. TNFAIP3 and DEPTOR together rapidly promoted autophagy after LPS treatment to prevent NLRP3 inflammasome formation. Finally, TNFAIP3 and DEPTOR deficiency in AS non-classical monocytes facilitated inflammasome activation. Our study indicates that TNFAIP3-DEPTOR complex-induced early-onset autophagy is vital for immune inhibition in autoimmune disease.
DOI: 10.6084/m9.figshare.17157087.v1
title: Additional file 8 of Genome-wide identification and expression analysis of the bZIP transcription factors, and functional analysis in response to drought and cold stresses in pear (Pyrus breschneideri)

description: Additional file 8 : Table S5. Primers of PbrbZIPs for qRT-PCR and vector construction.
DOI: 10.6084/m9.figshare.6681740.v1
title: TNFAIP3-DEPTOR complex regulates inflammasome secretion through autophagy in ankylosing spondylitis monocytes

description: Ankylosing spondylitis (AS) is a chronic autoimmune inflammatory disease with severe inflammatory symptoms in the axial skeleton. The cause of ankylosing spondylitis is unknown. TNFAIP3, also named A20, uses ubiquitin-related functions to regulate immune activation, deficiency of which is highly related to autoimmune disease. However, the role of TNFAIP3 in human AS has not been reported. Our objective was to study the role and mechanism of TNFAIP3 in ankylosing spondylitis. TNFAIP3 expression on different types of immunocytes from AS peripheral blood was measured by flow cytometry. In vitro, monocytes were transfected with a <i>TNFAIP3</i> shRNA lentivirus, and IL6 and IL1B activation was tested using real-time PCR and ELISA. The novel interaction complex TNFAIP3-DEPTOR was determined through GST pull-down, yeast two-hybrid system, confocal microscopy, and co-immunoprecipitation. Transmission electron microscopy, the RFP-GFP-LC3 adenovirus, and LC3 expression were used for autophagy detection. Here, we show that TNFAIP3 expression in AS peripheral blood non-classical monocytes was decreased. In normal monocytes, TNFAIP3 induced autophagy, which restricted inflammasome activation to the early stage of LPS stimulation. Zinc-finger domains of TNFAIP3 were able to interact and stabilize DEPTOR. TNFAIP3 and DEPTOR together rapidly promoted autophagy after LPS treatment to prevent NLRP3 inflammasome formation. Finally, TNFAIP3 and DEPTOR deficiency in AS non-classical monocytes facilitated inflammasome activation. Our study indicates that TNFAIP3-DEPTOR complex-induced early-onset autophagy is vital for immune inhibition in autoimmune disease.
DOI: 10.6084/m9.figshare.6681740.v2
title: TNFAIP3-DEPTOR complex regulates inflammasome secretion through autophagy in ankylosing spondylitis monocytes

description: Ankylosing spondylitis (AS) is a chronic autoimmune inflammatory disease with severe inflammatory symptoms in the axial skeleton. The cause of ankylosing spondylitis is unknown. TNFAIP3, also named A20, uses ubiquitin-related functions to regulate immune activation, deficiency of which is highly related to autoimmune disease. However, the role of TNFAIP3 in human AS has not been reported. Our objective was to study the role and mechanism of TNFAIP3 in ankylosing spondylitis. TNFAIP3 expression on different types of immunocytes from AS peripheral blood was measured by flow cytometry. In vitro, monocytes were transfected with a <i>TNFAIP3</i> shRNA lentivirus, and IL6 and IL1B activation was tested using real-time PCR and ELISA. The novel interaction complex TNFAIP3-DEPTOR was determined through GST pull-down, yeast two-hybrid system, confocal microscopy, and co-immunoprecipitation. Transmission electron microscopy, the RFP-GFP-LC3 adenovirus, and LC3 expression were used for autophagy detection. Here, we show that TNFAIP3 expression in AS peripheral blood non-classical monocytes was decreased. In normal monocytes, TNFAIP3 induced autophagy, which restricted inflammasome activation to the early stage of LPS stimulation. Zinc-finger domains of TNFAIP3 were able to interact and stabilize DEPTOR. TNFAIP3 and DEPTOR together rapidly promoted autophagy after LPS treatment to prevent NLRP3 inflammasome formation. Finally, TNFAIP3 and DEPTOR deficiency in AS non-classical monocytes facilitated inflammasome activation. Our study indicates that TNFAIP3-DEPTOR complex-induced early-onset autophagy is vital for immune inhibition in autoimmune disease.
DOI: 10.6084/m9.figshare.17157078.v1
title: Additional file 5 of Genome-wide identification and expression analysis of the bZIP transcription factors, and functional analysis in response to drought and cold stresses in pear (Pyrus breschneideri)

description: Additional file 5 : Table S2. Sequence information of 20 detected motifs in MEME analysis.
DOI: 10.6084/m9.figshare.17161703
title: Additional file 2 of Immune landscape of advanced gastric cancer tumor microenvironment identifies immunotherapeutic relevant gene signature

description: Additional file 2.
DOI: 10.6084/m9.figshare.6681770
title: Silica nanoparticles induce autophagosome accumulation via activation of the EIF2AK3 and ATF6 UPR pathways in hepatocytes

description: Autophagy dysfunction is a potential toxic effect of nanoparticles. Previous studies have indicated that silica nanoparticles (SiNPs) induce macroautophagy/autophagy dysfunction, while the precise mechanisms remain uncertain. Hence, the present study investigated the molecular mechanisms by which SiNPs enhanced autophagosome synthesis, which then contributed to autophagy dysfunction. First, the effects of SiNPs on autophagy and autophagic flux were verified using transmission electron microscopy, laser scanning confocal microscopy, and western blot assays. Then, the activation of endoplasmic reticular (ER) stress was validated to be through the EIF2AK3 and ATF6 UPR pathways but not the ERN1-XBP1 pathway, along with the upregulation of downstream ATF4 and DDIT3. Thereafter, the ER stress inhibitor 4-phenylbutyrate (4-PBA) was used to verify that SiNP-induced autophagy could be influenced by ER stress. Furthermore, specialized lentiviral shRNA were employed to determine that autophagy was induced via specific activation of the EIF2AK3 and ATF6 UPR pathways. Finally, the 2 autophagic genes <i>LC3B</i> and <i>ATG12</i> were found to be transcriptionally upregulated by downstream ATF4 and DDIT3 in ER stress, which contributed to the SiNP-enhanced autophagosome synthesis. Taken together, these data suggest that SiNPs induced autophagosome accumulation via the activation of the EIF2AK3 and ATF6 UPR pathways in hepatocytes, which offers a new insight into detailed molecular mechanisms underlying SiNP-induced autophagy dysfunction, and specifically how UPR pathways regulate key autophagic genes. This work provides novel evidence for the study of toxic effects and risk assessment of SiNPs.
DOI: 10.6084/m9.figshare.6681770.v1
title: Silica nanoparticles induce autophagosome accumulation via activation of the EIF2AK3 and ATF6 UPR pathways in hepatocytes

description: Autophagy dysfunction is a potential toxic effect of nanoparticles. Previous studies have indicated that silica nanoparticles (SiNPs) induce macroautophagy/autophagy dysfunction, while the precise mechanisms remain uncertain. Hence, the present study investigated the molecular mechanisms by which SiNPs enhanced autophagosome synthesis, which then contributed to autophagy dysfunction. First, the effects of SiNPs on autophagy and autophagic flux were verified using transmission electron microscopy, laser scanning confocal microscopy, and western blot assays. Then, the activation of endoplasmic reticular (ER) stress was validated to be through the EIF2AK3 and ATF6 UPR pathways but not the ERN1-XBP1 pathway, along with the upregulation of downstream ATF4 and DDIT3. Thereafter, the ER stress inhibitor 4-phenylbutyrate (4-PBA) was used to verify that SiNP-induced autophagy could be influenced by ER stress. Furthermore, specialized lentiviral shRNA were employed to determine that autophagy was induced via specific activation of the EIF2AK3 and ATF6 UPR pathways. Finally, the 2 autophagic genes <i>LC3B</i> and <i>ATG12</i> were found to be transcriptionally upregulated by downstream ATF4 and DDIT3 in ER stress, which contributed to the SiNP-enhanced autophagosome synthesis. Taken together, these data suggest that SiNPs induced autophagosome accumulation via the activation of the EIF2AK3 and ATF6 UPR pathways in hepatocytes, which offers a new insight into detailed molecular mechanisms underlying SiNP-induced autophagy dysfunction, and specifically how UPR pathways regulate key autophagic genes. This work provides novel evidence for the study of toxic effects and risk assessment of SiNPs.
DOI: 10.6084/m9.figshare.7200005
title: MOESM1 of No association of TP53 codon 72 and intron 3 16-bp duplication polymorphisms with breast cancer risk in Chinese Han women: new evidence from a population-based caseâ control investigation

description: Additional file 1: Table S1. Distributions of the genotype frequencies of codon 72 and intron 3 16-bp duplication polymorphisms in breast cancer patients with different clinicopathological features.
DOI: 10.6084/m9.figshare.17157081
title: Additional file 6 of Genome-wide identification and expression analysis of the bZIP transcription factors, and functional analysis in response to drought and cold stresses in pear (Pyrus breschneideri)

description: Additional file 6 : Table S3. Duplication type of PbrbZIP genes in pear (Pyrus bretschneideri).
DOI: 10.6084/m9.figshare.17157084
title: Additional file 7 of Genome-wide identification and expression analysis of the bZIP transcription factors, and functional analysis in response to drought and cold stresses in pear (Pyrus breschneideri)

description: Additional file 7 : Table S4. Differentially expressed genes after stress treatments.
DOI: 10.15468/dl.xykj22
title: Occurrence Download

description: A dataset containing 1942 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "BasisOfRecord is Observation",
 "BasisOfRecord is Machine Observation",
 "BasisOfRecord is Human Observation",
 "BasisOfRecord is Literature Occurrence"
 ]
 },
 "Country is Finland",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Agriopis aurantiaria (Hübner)"
 ]
}

 The dataset includes 1942 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0250942-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.b97qu8
title: Occurrence Download

description: A dataset containing 148 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Liolaemus coeruleus Cei & Ortiz-Zapata, 1983"
 ]
}

 The dataset includes 148 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049759-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.uxbecr
title: Occurrence Download

description: A dataset containing 482 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Phaenicophilus poliocephalus (Bonaparte, 1851)"
 ]
}

 The dataset includes 482 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0409873-210914110416597/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.avk6bk
title: Occurrence Download

description: A dataset containing 620 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Woodwardia radicans (L.) Sm.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 620 records from 40 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001354-150410134957023/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.