cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8305925.v1
title: Supplementary Material for: Adult Atopic Dermatitis in Hospitalized Patients: Comparison between Those with Childhood-Onset and Late-Onset Disease

description: Atopic eczema is one of the most prevalent diseases worldwide. It is a common dermatological disorder that affects 17.8 million individuals in the USA, up to 20% of children and up to 3% of adults. Recent data show that the incidence of the disease is still rising, both in children and adults, especially in low-income countries. Atopic dermatitis in adults consists of childhood-onset (COAD) and adult or late-onset types (LOAD). Prior research has described differences in clinical features, laboratory data, and response to treatment between COAD and LOAD. Most studies have been done on an ambulatory population that mostly contains patients with mild to moderate disease. <b><i>Objective:</i></b> The aim of the study was to describe the differences between adults hospitalized with COAD and LOAD. <b><i>Methods:</i></b> Data were analyzed from a retrospective cohort of 107 adult AD patients who were hospitalized from 2009 to 2017. Analysis of data included epidemiology, clinical and laboratory characteristics, and response to treatment. <b><i>Results:</i></b> Of the total sample, 87 (81%) patients were diagnosed with LOAD, and 20 (19%) patients were diagnosed with COAD. The median age was 66 years for all patients, 42 years for COAD patients, and 77 years for LOAD patients. The prevalence of atopy was lower in the LOAD group than in the COAD group (33.8 vs. 68.8% for family history, 35.5 vs. 84.8% for personal history). A higher incidence of head, neck, and flexural involvement was found in COAD patients. LOAD patients had lower immunoglobulin E levels and responded better to phototherapy. <b><i>Conclusions:</i></b> Elderly patients with LOAD constitute the majority of adults hospitalized with AD. As in ambulatory AD patients, there are significant differences in medical background, clinical picture, laboratory characteristics, and response to treatment between hospitalized LOAD and COAD patients. There is a need to determine diagnostic criteria and treatment guidelines for these patients.
DOI: 10.6084/m9.figshare.8305880
title: Supplementary Material for: Mass Cytometry Reveals the Immaturity of Circulating Neutrophils during SIV Infection

description: The infected host fails to eradicate HIV-1, despite significant control of viral replication by combinational antiretroviral therapy. Here, we assessed the impact of HIV infection on immune-cell compartments in a SIVmac251 nonhuman primate infection model, which allowed the choice of contamination route, time of infection, and treatment follow-up. We performed high-throughput multiparameter single-cell phenotyping by mass cytometry to obtain a global vision of the immune system in blood and bone marrow. Circulating polymorphonuclear neutrophils (PMNs) with impaired phagocytosis had altered surface expression of CD62L and CD11b during early chronic infection. The initiation of combinational antiretroviral treatment during primary infection did not restore PMN function. The maturation state of PMNs was highly altered during late chronic SIV infection, showing a primarily immature phenotype. Our results provide new insights into PMN involvement in the pathogenesis of HIV infection and may play a role in the establishment and maintenance of chronic immune activation.
DOI: 10.6084/m9.figshare.8305874
title: Dataset for: ZNF384-fusion proteins have high affinity for the transcriptional co-activator EP300 and aberrant transcriptional activities

description: ZNF384 fusion (Z-fusion) genes have recently been identified as recurrent fusion genes of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) and have been detected in 7-17% of Philadelphia chromosome-negative BCP-ALL cases. We selected SALL4 and ID2 as potential Z-fusion-specific transcriptional targets that might lead to differentiation disorder of Z-fusion-positive ALL. The introduction of EP300-ZNF384 and SYNRG-ZNF384 induced the expression of these genes. Z-fusion proteins exhibited stronger transcriptional activities on the promoter or enhancer region of these genes than Wild-Z. Furthermore, GST pull-down assay revealed that Z-fusion proteins associated more strongly with EP300 than Wild-Z. Co-expression of EP300 specifically enhanced the transcriptional activities of Z-fusion proteins. We propose the increased EP300-binding of Z-fusion proteins as a mechanism for their increased transcriptional activities.
DOI: 10.6084/m9.figshare.8305862
title: Supplementary Material for: Men Have a Stronger Monocyte-Derived Cytokine Production Response upon Stimulation with the Gram-Negative Stimulus Lipopolysaccharide than Women: A Pooled Analysis Including 15 Study Populations

description: The incidence of bacterial infections and sepsis, as well as the mortality risk from sepsis, is sex specific. These clinical findings have been attributed to sex differences in immune responsiveness. The aim of the present study was to investigate sex differences in monocyte-derived cytokine production response upon stimulation with the gram-negative stimulus lipopolysaccharide (LPS) using cytokine data from 15 study populations. Individual data on ex vivo cytokine production response upon stimulation with LPS in whole blood were available for 4,020 subjects originating from these 15 study populations, either from the general population or from patient populations with specific diseases. Men had a stronger cytokine production response than women to LPS for tumour necrosis factor-α, interleukin (IL)-6, IL-12, IL-1β, IL-1RA, and IL-10, but not for interferon-γ. The granulocyte-macrophage colony-stimulating factor production response was lower in men than in women. These sex differences were independent of chronological age. As men had higher monocyte concentrations, we normalized the cytokine production responses for monocyte concentration. After normalization, the sex differences in cytokine production response to LPS disappeared, except for IL-10, for which the production response was lower in men than in women. A sex-based approach to interpreting immune responsiveness is crucial.
DOI: 10.6084/m9.figshare.8305874.v1
title: Dataset for: ZNF384-fusion proteins have high affinity for the transcriptional co-activator EP300 and aberrant transcriptional activities

description: ZNF384 fusion (Z-fusion) genes have recently been identified as recurrent fusion genes of B-cell precursor acute lymphoblastic leukemia (BCP-ALL) and have been detected in 7-17% of Philadelphia chromosome-negative BCP-ALL cases. We selected SALL4 and ID2 as potential Z-fusion-specific transcriptional targets that might lead to differentiation disorder of Z-fusion-positive ALL. The introduction of EP300-ZNF384 and SYNRG-ZNF384 induced the expression of these genes. Z-fusion proteins exhibited stronger transcriptional activities on the promoter or enhancer region of these genes than Wild-Z. Furthermore, GST pull-down assay revealed that Z-fusion proteins associated more strongly with EP300 than Wild-Z. Co-expression of EP300 specifically enhanced the transcriptional activities of Z-fusion proteins. We propose the increased EP300-binding of Z-fusion proteins as a mechanism for their increased transcriptional activities.
DOI: 10.6084/m9.figshare.8305862.v1
title: Supplementary Material for: Men Have a Stronger Monocyte-Derived Cytokine Production Response upon Stimulation with the Gram-Negative Stimulus Lipopolysaccharide than Women: A Pooled Analysis Including 15 Study Populations

description: The incidence of bacterial infections and sepsis, as well as the mortality risk from sepsis, is sex specific. These clinical findings have been attributed to sex differences in immune responsiveness. The aim of the present study was to investigate sex differences in monocyte-derived cytokine production response upon stimulation with the gram-negative stimulus lipopolysaccharide (LPS) using cytokine data from 15 study populations. Individual data on ex vivo cytokine production response upon stimulation with LPS in whole blood were available for 4,020 subjects originating from these 15 study populations, either from the general population or from patient populations with specific diseases. Men had a stronger cytokine production response than women to LPS for tumour necrosis factor-α, interleukin (IL)-6, IL-12, IL-1β, IL-1RA, and IL-10, but not for interferon-γ. The granulocyte-macrophage colony-stimulating factor production response was lower in men than in women. These sex differences were independent of chronological age. As men had higher monocyte concentrations, we normalized the cytokine production responses for monocyte concentration. After normalization, the sex differences in cytokine production response to LPS disappeared, except for IL-10, for which the production response was lower in men than in women. A sex-based approach to interpreting immune responsiveness is crucial.
DOI: 10.6084/m9.figshare.8305850
title: MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation

description: The linker of nucleoskeleton and cytoskeleton (LINC) complex is an essential multi-protein structure spanning the eukaryotic nuclear envelope. The LINC complex functions to maintain nuclear architecture, positioning, and mobility, along with specialized functions in meiotic prophase and chromosome segregation. Members of the LINC complex were recently identified in maize, an important scientific and agricultural grass species. Here we characterized <i>Maize LINC KASH AtSINE-like2, MLKS2</i>, which encodes a highly conserved SINE-group plant KASH protein with characteristic N-terminal armadillo repeats (ARM). Using a heterologous expression system, we showed that actively expressed GFP-MLKS2 is targeted to the nuclear periphery and colocalizes with F-actin and the endoplasmic reticulum, but not microtubules in the cell cortex. Expression of GFP-MLKS2, but not GFP-MLKS2ΔARM, resulted in nuclear anchoring. Genetic analysis of transposon-insertion mutations, <i>mlks2-1</i> and <i>mlks2-2</i>, showed that the mutant phenotypes were pleiotropic, affecting root hair nuclear morphology, stomatal complex development, multiple aspects of meiosis, and pollen viability. In male meiosis, the mutants showed defects for bouquet-stage telomere clustering, nuclear repositioning, perinuclear actin accumulation, dispersal of late prophase bivalents, and meiotic chromosome segregation. These findings support a model in which the nucleus is connected to cytoskeletal F-actin through the ARM-domain, predicted alpha solenoid structure of MLKS2. Functional conservation of MLKS2 was demonstrated through genetic rescue of the misshapen nuclear phenotype of an Arabidopsis (triple-<i>WIP</i>) KASH mutant. This study establishes a role for the SINE-type KASH proteins in affecting the dynamic nuclear phenomena required for normal plant growth and fertility. <b>Abbreviations</b>: FRAP: Fluorescence recovery after photobleaching; DPI: Days post infiltration; OD: Optical density; <i>MLKS2: Maize LINC KASH AtSINE-like2;</i> LINC: Linker of nucleoskeleton and cytoskeleton; NE: Nuclear envelope; INM: Inner nuclear membrane; ONM: Outer nuclear membrane
DOI: 10.6084/m9.figshare.8305850.v2
title: MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation

description: The linker of nucleoskeleton and cytoskeleton (LINC) complex is an essential multi-protein structure spanning the eukaryotic nuclear envelope. The LINC complex functions to maintain nuclear architecture, positioning, and mobility, along with specialized functions in meiotic prophase and chromosome segregation. Members of the LINC complex were recently identified in maize, an important scientific and agricultural grass species. Here we characterized <i>Maize LINC KASH AtSINE-like2, MLKS2</i>, which encodes a highly conserved SINE-group plant KASH protein with characteristic N-terminal armadillo repeats (ARM). Using a heterologous expression system, we showed that actively expressed GFP-MLKS2 is targeted to the nuclear periphery and colocalizes with F-actin and the endoplasmic reticulum, but not microtubules in the cell cortex. Expression of GFP-MLKS2, but not GFP-MLKS2ΔARM, resulted in nuclear anchoring. Genetic analysis of transposon-insertion mutations, <i>mlks2-1</i> and <i>mlks2-2</i>, showed that the mutant phenotypes were pleiotropic, affecting root hair nuclear morphology, stomatal complex development, multiple aspects of meiosis, and pollen viability. In male meiosis, the mutants showed defects for bouquet-stage telomere clustering, nuclear repositioning, perinuclear actin accumulation, dispersal of late prophase bivalents, and meiotic chromosome segregation. These findings support a model in which the nucleus is connected to cytoskeletal F-actin through the ARM-domain, predicted alpha solenoid structure of MLKS2. Functional conservation of MLKS2 was demonstrated through genetic rescue of the misshapen nuclear phenotype of an Arabidopsis (triple-<i>WIP</i>) KASH mutant. This study establishes a role for the SINE-type KASH proteins in affecting the dynamic nuclear phenomena required for normal plant growth and fertility. <b>Abbreviations</b>: FRAP: Fluorescence recovery after photobleaching; DPI: Days post infiltration; OD: Optical density; <i>MLKS2: Maize LINC KASH AtSINE-like2;</i> LINC: Linker of nucleoskeleton and cytoskeleton; NE: Nuclear envelope; INM: Inner nuclear membrane; ONM: Outer nuclear membrane
DOI: 10.6084/m9.figshare.8305850.v1
title: MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation

description: The linker of nucleoskeleton and cytoskeleton (LINC) complex is an essential multi-protein structure spanning the eukaryotic nuclear envelope. The LINC complex functions to maintain nuclear architecture, positioning, and mobility, along with specialized functions in meiotic prophase and chromosome segregation. Members of the LINC complex were recently identified in maize, an important scientific and agricultural grass species. Here we characterized <i>Maize LINC KASH AtSINE-like2, MLKS2</i>, which encodes a highly conserved SINE-group plant KASH protein with characteristic N-terminal armadillo repeats (ARM). Using a heterologous expression system, we showed that actively expressed GFP-MLKS2 is targeted to the nuclear periphery and colocalizes with F-actin and the endoplasmic reticulum, but not microtubules in the cell cortex. Expression of GFP-MLKS2, but not GFP-MLKS2ΔARM, resulted in nuclear anchoring. Genetic analysis of transposon-insertion mutations, <i>mlks2-1</i> and <i>mlks2-2</i>, showed that the mutant phenotypes were pleiotropic, affecting root hair nuclear morphology, stomatal complex development, multiple aspects of meiosis, and pollen viability. In male meiosis, the mutants showed defects for bouquet-stage telomere clustering, nuclear repositioning, perinuclear actin accumulation, dispersal of late prophase bivalents, and meiotic chromosome segregation. These findings support a model in which the nucleus is connected to cytoskeletal F-actin through the ARM-domain, predicted alpha solenoid structure of MLKS2. Functional conservation of MLKS2 was demonstrated through genetic rescue of the misshapen nuclear phenotype of an Arabidopsis (triple-<i>WIP</i>) KASH mutant. This study establishes a role for the SINE-type KASH proteins in affecting the dynamic nuclear phenomena required for normal plant growth and fertility. <b>Abbreviations</b>: FRAP: Fluorescence recovery after photobleaching; DPI: Days post infiltration; OD: Optical density; <i>MLKS2: Maize LINC KASH AtSINE-like2;</i> LINC: Linker of nucleoskeleton and cytoskeleton; NE: Nuclear envelope; INM: Inner nuclear membrane; ONM: Outer nuclear membrane
DOI: 10.6084/m9.figshare.8305811
title: A systematic review and meta<b>-</b>analysis of the efficacy and adverse events of azacitidine<b>-</b>plus<b>-</b>lenalidomide treatment for patients with acute myeloid leukemia, myelodysplastic syndromes and chronic myelomonocytic leukemia<sup>1</sup>

description: The addition of lenalidomide (LEN) to azacitidine (AZA) may further improve the outcomes of acute myeloid leukemia (AML) patients as well as patients with high-risk myelodysplastic syndrome (MDS) and chronic myelomonocytic leukemia (CMML) patients although the evidence for this combination treatment is still relatively limited. This meta-analysis aimed to evaluate efficacy and adverse effects of AZA plus LEN for the treatment of patients with high-risk MDS, AML or CMML. The current study systematically identified all cohort studies of patients with AML and/or MDS and/or CMML who received AZA in combination with LEN that reported the overall complete remission (CR) rate and/or overall response rate (ORR). A DerSimonian–d random–effects model with double arcsine transformation was used for the pooled rates and 95% confidence interval (CI) of the all outcomes. A total of 10 studies with 406 patients were identified and included into the meta-analysis. The pooled CR rate after the treatment with AZA-plus-LEN regimen was 33.0% (95% CI, 27.7%–38.7%, I<sup>2</sup> = 18%) while the pooled ORR was 49.9% (95% CI, 38.4%–61.5%, I<sup>2</sup> = 72%). Nonetheless, adverse events including grade 3–4 neutrophil toxicity events, platelet toxicity events and febrile neutropenia were common with AZA-plus-LEN regimen. The current study may serve as a preliminary data to suggest that the addition of LEN may offer incremental benefit to patients with high-risk MDS, AML and CMML. However, randomized-controlled studies that directly compare the efficacy and adverse events of AZA-plus-LEN regimen versus AZA monotherapy are still needed.
DOI: 10.6084/m9.figshare.8305811.v1
title: A systematic review and meta<b>-</b>analysis of the efficacy and adverse events of azacitidine<b>-</b>plus<b>-</b>lenalidomide treatment for patients with acute myeloid leukemia, myelodysplastic syndromes and chronic myelomonocytic leukemia<sup>1</sup>

description: The addition of lenalidomide (LEN) to azacitidine (AZA) may further improve the outcomes of acute myeloid leukemia (AML) patients as well as patients with high-risk myelodysplastic syndrome (MDS) and chronic myelomonocytic leukemia (CMML) patients although the evidence for this combination treatment is still relatively limited. This meta-analysis aimed to evaluate efficacy and adverse effects of AZA plus LEN for the treatment of patients with high-risk MDS, AML or CMML. The current study systematically identified all cohort studies of patients with AML and/or MDS and/or CMML who received AZA in combination with LEN that reported the overall complete remission (CR) rate and/or overall response rate (ORR). A DerSimonian–d random–effects model with double arcsine transformation was used for the pooled rates and 95% confidence interval (CI) of the all outcomes. A total of 10 studies with 406 patients were identified and included into the meta-analysis. The pooled CR rate after the treatment with AZA-plus-LEN regimen was 33.0% (95% CI, 27.7%–38.7%, I<sup>2</sup> = 18%) while the pooled ORR was 49.9% (95% CI, 38.4%–61.5%, I<sup>2</sup> = 72%). Nonetheless, adverse events including grade 3–4 neutrophil toxicity events, platelet toxicity events and febrile neutropenia were common with AZA-plus-LEN regimen. The current study may serve as a preliminary data to suggest that the addition of LEN may offer incremental benefit to patients with high-risk MDS, AML and CMML. However, randomized-controlled studies that directly compare the efficacy and adverse events of AZA-plus-LEN regimen versus AZA monotherapy are still needed.
DOI: 10.6084/m9.figshare.8305688.v1
title: Additional file 15: of Full-length transcriptome sequencing and methyl jasmonate-induced expression profile analysis of genes related to patchoulol biosynthesis and regulation in Pogostemon cablin

description: Table S10. Primers used for qPCR analysis. (XLSX 9 kb)
DOI: 10.6084/m9.figshare.8305667
title: Additional file 2: of Methylation analysis for postpartum depression: a case control study

description: Table S1 Result of DAVID 6.8 analysis of the 711 genes associated with the 1000 sites. It shows a result of DAVID 6.8 analysis of the 711 genes associated with the 1000 sites with the lowest p values of association analysis. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.8305667.v1
title: Additional file 2: of Methylation analysis for postpartum depression: a case control study

description: Table S1 Result of DAVID 6.8 analysis of the 711 genes associated with the 1000 sites. It shows a result of DAVID 6.8 analysis of the 711 genes associated with the 1000 sites with the lowest p values of association analysis. (XLSX 99 kb)
DOI: 10.6084/m9.figshare.8305643
title: Additional file 2: of Training opportunities and the increase in the number of nurses in home-visit nursing agenciesÂ in Japan: a panel data analysis

description: Full model for fixed effect panel regression model for the % change in number of FTE nurses and scheduled training programs for new employees. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8305637
title: Additional file 1: of Training opportunities and the increase in the number of nurses in home-visit nursing agenciesÂ in Japan: a panel data analysis

description: Full model for fixed effect panel regression model for the % change in number of FTE nurses and scheduled training programs for all employees. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8305637.v1
title: Additional file 1: of Training opportunities and the increase in the number of nurses in home-visit nursing agenciesÂ in Japan: a panel data analysis

description: Full model for fixed effect panel regression model for the % change in number of FTE nurses and scheduled training programs for all employees. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8305643.v1
title: Additional file 2: of Training opportunities and the increase in the number of nurses in home-visit nursing agenciesÂ in Japan: a panel data analysis

description: Full model for fixed effect panel regression model for the % change in number of FTE nurses and scheduled training programs for new employees. (XLSX 15 kb)
DOI: 10.6084/m9.figshare.8305631
title: MOESM2 of Whole exome sequencing of patients who resolved Crohnâ s disease and complex regional pain syndrome following treatment for paratuberculosis

description: Additional file 2. Search for shared genes and associated disease states in this extended family.
DOI: 10.6084/m9.figshare.8305631.v1
title: MOESM2 of Whole exome sequencing of patients who resolved Crohnâ s disease and complex regional pain syndrome following treatment for paratuberculosis

description: Additional file 2. Search for shared genes and associated disease states in this extended family.
DOI: 10.6084/m9.figshare.8305544
title: MOESM3 of Phenotyping multiple subsets in Sjögren’s syndrome: a salivary proteomic SWATH-MS approach towards precision medicine

description: Additional file 3: Table S3. Differentially expressed proteins found in common between High Focus/Normal Flow, High Focus/ Low Flow and Low Focus/Low Flow groups. Fold changes were showed per each protein.
DOI: 10.6084/m9.figshare.8305544.v1
title: MOESM3 of Phenotyping multiple subsets in Sjögren’s syndrome: a salivary proteomic SWATH-MS approach towards precision medicine

description: Additional file 3: Table S3. Differentially expressed proteins found in common between High Focus/Normal Flow, High Focus/ Low Flow and Low Focus/Low Flow groups. Fold changes were showed per each protein.