cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9879278
title: Circulating adiponectin as a biomarker in renal cell carcinoma: a systematic review and meta-analysis

description: <b>Context</b>: Metabolic imbalance in renal cell carcinoma (RCC) can lead to abnormal adiponectin levels. <b>Objective</b>: To evaluate circulating adiponectin as a detection or predictive marker for RCC. <b>Methods</b>: A comprehensive literature search and meta-analysis was performed on studies reporting circulating adiponectin levels and RCC. The meta-analysis was performed using RevMan. <b>Results</b>: Seven studies compared the circulating adiponection levels between RCC cases and controls. Adiponectin level was significantly lower in RCC cases compared to controls at pre-diagnosis and pre-operative time-points. RCC stage, grade and subtype did not affect adiponectin levels. <b>Conclusion</b>: Low circulating adiponectin could be a predictive or risk factor for RCC.
DOI: 10.6084/m9.figshare.9879275
title: Genotype-guided antiplatelet therapy compared with conventional therapy for patients with acute coronary syndromes: a systematic review and meta-analysis

description: To evaluate whether genotype-guided antiplatelet therapy reduces the rates of cardiovascular events and bleeding events in patients with acute coronary syndrome (ACS). We systematically searched Pubmed, Embase and the Cochrane Central Register of Controlled Trials (CENTRAL) (searched in September 2018) for controlled studies evaluating genotype-guided antiplatelet therapy in ACS with percutaneous coronary intervention (PCI) or without PCI. The primary endpoint was a composite of death, myocardial infarction (MI), stroke, targeted vessel revascularization and/or major bleeding. A total of five studies involving 2900 patients were included. Compared with the conventional group, the genotype-guided group had a decreased risk of primary composite outcomes (RR= 0.54; 95% CI: 0.41–0.72; <i>I</i><sup>2</sup> = 30%), death (RR = 0.54; 95% CI: 0.32–0.94; <i>I</i><sup>2</sup> = 21%), MI (RR = 0.52; 95% CI: 0.31–0.88; <i>I</i><sup>2</sup> = 49%), targeted vessel revascularization (RR = 0.59; 95% CI: 0.35–0.98; <i>I</i><sup>2</sup> = 0%), but not for stroke (RR = 0.53; 95% CI: 0.22–1.24; <i>I</i><sup>2</sup> = 0%) and bleeding events (RR = 0.80; 95% CI: 0.51–1.25; <i>I</i><sup>2</sup> = 33%). Genotype-guided strategies could reduce the rates of cardiovascular events without increasing bleeding events compared with conventional treatment in ACS. Future multi<b>-</b>centre genotype-based randomized control trials are required to confirm these findings.
DOI: 10.6084/m9.figshare.9879344.v2
title: System requirements and descriptions

description: System requirements and descriptions
DOI: 10.6084/m9.figshare.9879278.v1
title: Circulating adiponectin as a biomarker in renal cell carcinoma: a systematic review and meta-analysis

description: <b>Context</b>: Metabolic imbalance in renal cell carcinoma (RCC) can lead to abnormal adiponectin levels. <b>Objective</b>: To evaluate circulating adiponectin as a detection or predictive marker for RCC. <b>Methods</b>: A comprehensive literature search and meta-analysis was performed on studies reporting circulating adiponectin levels and RCC. The meta-analysis was performed using RevMan. <b>Results</b>: Seven studies compared the circulating adiponection levels between RCC cases and controls. Adiponectin level was significantly lower in RCC cases compared to controls at pre-diagnosis and pre-operative time-points. RCC stage, grade and subtype did not affect adiponectin levels. <b>Conclusion</b>: Low circulating adiponectin could be a predictive or risk factor for RCC.
DOI: 10.6084/m9.figshare.9879233
title: Supplementary Material for: Expression of the Voltage-Gated Potassium Channel Kv1.3 in Lesional Skin from Patients with Cutaneous T-Cell Lymphoma and Benign Dermatitis

description: <b><i>Background:</i></b> The voltage-gated potassium channel Kv1.3 (KCNA3) is expressed by effector memory T cells (T<sub>EM</sub>) and plays an important role in their activation and proliferation. Mycosis fungoides (MF), the most common subtype of cutaneous T-cell lymphoma (CTCL), was recently proposed to be a malignancy of skin-resident T<sub>EM</sub>. However, the expression of Kv1.3 in CTCL has not been investigated. <b><i>Objectives:</i></b> This study aims to examine the expression of Kv1.3 in situ and in vitro in CTCL. <b><i>Methods:</i></b> The expression of Kv1.3 was examined by immunohistochemistry in skin lesions from 38 patients with MF, 4 patients with Sézary syndrome (SS), and 27 patients with benign dermatosis. In 4 malignant T-cell lines of CTCL (Myla2059, PB2B, SeAx, and Mac2a) and a non-malignant T-cell line (MyLa1850), the expression of Kv1.3 was determined by flow cytometry. The proliferation of those cell lines treated with various concentrations of Kv1.3 inhibitor ShK was measured by <sup>3</sup>H-thymdine incorporation. <b><i>Results:</i></b> Half of the MF patients (19/38) displayed partial Kv1.3 expression including 1 patient with moderate Kv1.3 positivity, while the other half (19/38) exhibited Kv1.3 negativity. An almost identical distribution was observed in patients with benign conditions, that is, 44.4% (12/27) were partially positive for Kv1.3 including 1 patient with moderate Kv1.3 positivity, while 55.6% (15/27) were Kv1.3 negative. In contrast, 3 in 4 SS patients displayed partial Kv1.3 positivity including 2 patients with weak staining and 1 with moderate staining, while 1 in 4 SS patients was Kv1.3 negative. In addition, all malignant T-cell lines, and a non-malignant T-cell line, displayed low Kv1.3 surface expression with a similar pattern. Whereas 2 cell lines (PB2B and Mac2a) were sensitive to Kv1.3 blockade, the other 2 (Myla2059 and SeAx) were completely resistant. <b><i>Conclusions:</i></b> We provide the first evidence of a heterogeneous Kv1.3 expression in situ in CTCL lesions.
DOI: 10.6084/m9.figshare.9879233.v1
title: Supplementary Material for: Expression of the Voltage-Gated Potassium Channel Kv1.3 in Lesional Skin from Patients with Cutaneous T-Cell Lymphoma and Benign Dermatitis

description: <b><i>Background:</i></b> The voltage-gated potassium channel Kv1.3 (KCNA3) is expressed by effector memory T cells (T<sub>EM</sub>) and plays an important role in their activation and proliferation. Mycosis fungoides (MF), the most common subtype of cutaneous T-cell lymphoma (CTCL), was recently proposed to be a malignancy of skin-resident T<sub>EM</sub>. However, the expression of Kv1.3 in CTCL has not been investigated. <b><i>Objectives:</i></b> This study aims to examine the expression of Kv1.3 in situ and in vitro in CTCL. <b><i>Methods:</i></b> The expression of Kv1.3 was examined by immunohistochemistry in skin lesions from 38 patients with MF, 4 patients with Sézary syndrome (SS), and 27 patients with benign dermatosis. In 4 malignant T-cell lines of CTCL (Myla2059, PB2B, SeAx, and Mac2a) and a non-malignant T-cell line (MyLa1850), the expression of Kv1.3 was determined by flow cytometry. The proliferation of those cell lines treated with various concentrations of Kv1.3 inhibitor ShK was measured by <sup>3</sup>H-thymdine incorporation. <b><i>Results:</i></b> Half of the MF patients (19/38) displayed partial Kv1.3 expression including 1 patient with moderate Kv1.3 positivity, while the other half (19/38) exhibited Kv1.3 negativity. An almost identical distribution was observed in patients with benign conditions, that is, 44.4% (12/27) were partially positive for Kv1.3 including 1 patient with moderate Kv1.3 positivity, while 55.6% (15/27) were Kv1.3 negative. In contrast, 3 in 4 SS patients displayed partial Kv1.3 positivity including 2 patients with weak staining and 1 with moderate staining, while 1 in 4 SS patients was Kv1.3 negative. In addition, all malignant T-cell lines, and a non-malignant T-cell line, displayed low Kv1.3 surface expression with a similar pattern. Whereas 2 cell lines (PB2B and Mac2a) were sensitive to Kv1.3 blockade, the other 2 (Myla2059 and SeAx) were completely resistant. <b><i>Conclusions:</i></b> We provide the first evidence of a heterogeneous Kv1.3 expression in situ in CTCL lesions.
DOI: 10.6084/m9.figshare.9878978
title: Genome annotation of Neurospora species

description: Annotations were produced using MAKER and functions were assigned to predict proteins using an all-to-all BLAST search against a <i>Neurospora</i> database assembled using available proteins sequences from UniProt. The resulting gff file is located here.<br>Strain list:<br><br>FGSC # | Species<br>-------+----------------------<br>2489 | Neurospora crassa<br>5940 | Neurospora sitophila<br>5941 | Neurospora sitophila<br>9033 | Neurospora tetrasperma L1<br>9034 | Neurospora tetrasperma L1<br>10707 | Neurospora tetrasperma L10<br>10708 | Neurospora tetrasperma L10<br>2508 | Neurospora tetrasperma L6<br>2509 | Neurospora tetrasperma L6<br><br>For further information on the strains and the genome assemblies, please see:<br>Hosseini et al., (2020) "Comparative analysis of genome-wide DNA methylation in Neurospora": https://www.epigenetics.com/articles/xxx (DOI: 10.1080/15592294.2020.1741758)<br><br><br>
DOI: 10.6084/m9.figshare.9878849
title: Metadata record for: Time series of heat demand and heat pump efficiency for energy system modeling

description: This dataset contains key characteristics about the data described in the Data Descriptor Time series of heat demand and heat pump efficiency for energy system modeling. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format<br><br>Versioning Note:Version 2 was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9878849.v1
title: Metadata record for: Time series of heat demand and heat pump efficiency for energy system modeling

description: This dataset contains key characteristics about the data described in the Data Descriptor Time series of heat demand and heat pump efficiency for energy system modeling. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format<br><br>
DOI: 10.6084/m9.figshare.9878786
title: Dataset from Plant-mediated interactions between a vector and a non-vector herbivore promote the spread of a plant virus

description: Herbivores that transmit plant pathogens often share hosts with non-vector herbivores. These co-occurring herbivores can affect vector fitness and behaviour through competition and by altering host plant quality. However, few studies have examined how such interactions may both directly and indirectly influence the spread of a plant pathogen. Here, we conducted field and greenhouse trials to assess whether a defoliating herbivore (<i>Sitona lineatus</i>) mediated the spread of a plant pathogen, <i>Pea enation mosaic virus</i> (PEMV), by affecting the fitness and behaviour of <i>Acrythosiphon pisum</i>, the PEMV vector. We observed higher rates of PEMV spread when infectious <i>A. pisum</i> individuals shared hosts with <i>S. lineatus</i> individuals. Using structural equation models, we showed that herbivory from <i>S. lineatus</i> increased <i>A. pisum</i> fitness, which stimulated vector movement and PEMV spread. Moreover, plant susceptibility to PEMV was indirectly enhanced by <i>S. lineatus</i>, which displaced <i>A. pisum</i> individuals to the most susceptible parts of the plant. Subsequent analyses of plant defence genes revealed considerable differences in plant phytohormones associated with anti-herbivore and anti-pathogen defence when <i>S. lineatus</i> was present. Given that vectors interact with non-vector herbivores in natural and managed ecosystems, characterizing how such interactions affect pathogens would greatly enhance our understanding of disease ecology.
DOI: 10.6084/m9.figshare.9878786.v1
title: Dataset from Plant-mediated interactions between a vector and a non-vector herbivore promote the spread of a plant virus

description: Herbivores that transmit plant pathogens often share hosts with non-vector herbivores. These co-occurring herbivores can affect vector fitness and behaviour through competition and by altering host plant quality. However, few studies have examined how such interactions may both directly and indirectly influence the spread of a plant pathogen. Here, we conducted field and greenhouse trials to assess whether a defoliating herbivore (<i>Sitona lineatus</i>) mediated the spread of a plant pathogen, <i>Pea enation mosaic virus</i> (PEMV), by affecting the fitness and behaviour of <i>Acrythosiphon pisum</i>, the PEMV vector. We observed higher rates of PEMV spread when infectious <i>A. pisum</i> individuals shared hosts with <i>S. lineatus</i> individuals. Using structural equation models, we showed that herbivory from <i>S. lineatus</i> increased <i>A. pisum</i> fitness, which stimulated vector movement and PEMV spread. Moreover, plant susceptibility to PEMV was indirectly enhanced by <i>S. lineatus</i>, which displaced <i>A. pisum</i> individuals to the most susceptible parts of the plant. Subsequent analyses of plant defence genes revealed considerable differences in plant phytohormones associated with anti-herbivore and anti-pathogen defence when <i>S. lineatus</i> was present. Given that vectors interact with non-vector herbivores in natural and managed ecosystems, characterizing how such interactions affect pathogens would greatly enhance our understanding of disease ecology.
DOI: 10.6084/m9.figshare.9878723
title: A MYC/GCN2/eIF2a negative feedback loop limits protein synthesis to prevent MYCdependent apoptosis in colorectal cancer_Fig.5a

description: Fig. 5a MS-Data<br>
DOI: 10.6084/m9.figshare.9878723.v1
title: A MYC/GCN2/eIF2a negative feedback loop limits protein synthesis to prevent MYCdependent apoptosis in colorectal cancer_Fig.5a

description: Fig. 5a MS-Data<br>
DOI: 10.6084/m9.figshare.9878717
title: A MYC/GCN2/eIF2a negative feedback loop limits protein synthesis to prevent MYCdependent apoptosis in colorectal cancer_Fig. 5c

description: Raw Data of Fig. 5c<br>
DOI: 10.6084/m9.figshare.9878717.v1
title: A MYC/GCN2/eIF2a negative feedback loop limits protein synthesis to prevent MYCdependent apoptosis in colorectal cancer_Fig. 5c

description: Raw Data of Fig. 5c<br>
DOI: 10.6084/m9.figshare.9878612
title: A survey on the occurrence of Brachyspira pilosicoli and Brachyspira hyodysenteriae in growing-finishing pigs

description: Data obtained from testing by PCR 401 samples of pig feces collected between January 2017 and August 2019 form 95 different Polish pig herds for presence of B. hyodysenteriae, Lawsonia intracellularis, B. pilosicoli.
DOI: 10.6084/m9.figshare.9878594
title: Metadata record for: Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress

description: This dataset contains key characteristics about the data described in the Data Descriptor Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format3. machine readable metadata file in ISA-Tab format (zipped folder)<br><br>Versioning Note:A revised version was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9878582
title: Willow gene family

description: The latest <i>Salix suchowensis</i> genome (version5_2.fa), annotation information (version5_2.gff3), coding sequences (Willow.gene.cds) and protein sequences (Willow.gene.pep).
DOI: 10.6084/m9.figshare.9878594.v1
title: Metadata record for: Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress

description: This dataset contains key characteristics about the data described in the Data Descriptor Transcriptomic profiling of cotton Gossypium hirsutum challenged with low-temperature gradients stress. <br> Contents: <br> 1. human readable metadata summary table in CSV format 2. machine readable metadata file in JSON format3. machine readable metadata file in ISA-Tab format (zipped folder)<br><br>Versioning Note:A revised version was generated when the metadata format was updated from JSON to JSON-LD. This was an automatic process that changed only the format, not the contents, of the metadata.<br>
DOI: 10.6084/m9.figshare.9878612.v1
title: A survey on the occurrence of Brachyspira pilosicoli and Brachyspira hyodysenteriae in growing-finishing pigs

description: Data obtained from testing by PCR 401 samples of pig feces collected between January 2017 and August 2019 form 95 different Polish pig herds for presence of B. hyodysenteriae, Lawsonia intracellularis, B. pilosicoli.
DOI: 10.6084/m9.figshare.9878492
title: RCP_emis.zip

description: emission data sets
DOI: 10.6084/m9.figshare.9878513
title: Supplementary Material for: Distinct Association of Serum Vitamin D Concentration with Disease Activity and Trough Levels of Infliximab and Adalimumab during Inflammatory Bowel Disease Treatment

description: <b><i>Background:</i></b> Studies of serum vitamin D (Vit-D) levels in patients with inflammatory bowel disease (IBD) treated with anti-tumor necrosis factor-alpha (anti-TNF-α) agents are scarce. The conjunction of Vit-D as well as zinc levels and anti-TNF-α-trough concentrations (TC) has not yet been explored. <b><i>Objectives:</i></b> To determine the association of serum Vit-D, zinc and C-reactive protein (CRP) levels with clinical and biochemical remission and a possible correlation with serum TC and antibody levels of anti-TNF-α. <b><i>Methods:</i></b> Serum Vit-D and zinc levels as well as Infliximab (IFX) and Adalimumab (ADA) TC during the maintenance phase of treatment were measured in 112 IBD patients. Statistical analysis were performed for clinical and biochemical remission. <b><i>Results:</i></b> Vit-D and zinc deficiency were detected in 58 and 4.5% of the patients respectively. In IFX-treated patients, IFX-TC, Vit-D and CRP levels were associated independently with clinical remission with an OR of 20 (95% CI 1.3–333, <i>p</i> = 0.03), 1.3 (95% CI 1.1–1.7, <i>p</i> = 0.02) and 0.4 (95% CI 0.2–0.8, <i>p</i> = 0.01) respectively. Serum IFX-TC and Vit-D levels correlated positively (<i>r</i> = 0.39, <i>p</i> = 0.001), while serum IFX-TC and CRP levels showed an inverse correlation (<i>r</i> = –0.43, <i>p</i> &lt; 0.001). Only ­IFX-TC associated independently with biochemical remission with a threshold of 3.1 µg/mL. In ADA-treated patients, ADA-TC associated independently with clinical and biochemical remission with an OR of 2.5 (95% CI 1.1–5.0, <i>p</i> = 0.04) and 1.3 (95% CI 1.1–1.4, <i>p</i> = 0.03) respectively. The serum zinc level was associated neither with clinical nor with biochemical remission in either cohort. <b><i>Conclusions:</i></b> Our results indicate that serum Vit-D level may be a predictive marker in addition to drug trough levels in IBD patients treated with IFX. Furthermore, due to the correlation between serum IFX and Vit-D levels, Vit-D substitution should be conducted in patients with low Vit-D levels.
DOI: 10.6084/m9.figshare.12833762
title: Stop codon readthrough contexts influence reporter expression differentially depending on the presence of an IRES.

description: Extended data - sequences
DOI: 10.6084/m9.figshare.9878477
title: Fig.S1 無価値なエクセルデータ

description: ここに説明を書きます。これのデータは無価値です。
DOI: 10.6084/m9.figshare.9878513.v1
title: Supplementary Material for: Distinct Association of Serum Vitamin D Concentration with Disease Activity and Trough Levels of Infliximab and Adalimumab during Inflammatory Bowel Disease Treatment

description: <b><i>Background:</i></b> Studies of serum vitamin D (Vit-D) levels in patients with inflammatory bowel disease (IBD) treated with anti-tumor necrosis factor-alpha (anti-TNF-α) agents are scarce. The conjunction of Vit-D as well as zinc levels and anti-TNF-α-trough concentrations (TC) has not yet been explored. <b><i>Objectives:</i></b> To determine the association of serum Vit-D, zinc and C-reactive protein (CRP) levels with clinical and biochemical remission and a possible correlation with serum TC and antibody levels of anti-TNF-α. <b><i>Methods:</i></b> Serum Vit-D and zinc levels as well as Infliximab (IFX) and Adalimumab (ADA) TC during the maintenance phase of treatment were measured in 112 IBD patients. Statistical analysis were performed for clinical and biochemical remission. <b><i>Results:</i></b> Vit-D and zinc deficiency were detected in 58 and 4.5% of the patients respectively. In IFX-treated patients, IFX-TC, Vit-D and CRP levels were associated independently with clinical remission with an OR of 20 (95% CI 1.3–333, <i>p</i> = 0.03), 1.3 (95% CI 1.1–1.7, <i>p</i> = 0.02) and 0.4 (95% CI 0.2–0.8, <i>p</i> = 0.01) respectively. Serum IFX-TC and Vit-D levels correlated positively (<i>r</i> = 0.39, <i>p</i> = 0.001), while serum IFX-TC and CRP levels showed an inverse correlation (<i>r</i> = –0.43, <i>p</i> &lt; 0.001). Only ­IFX-TC associated independently with biochemical remission with a threshold of 3.1 µg/mL. In ADA-treated patients, ADA-TC associated independently with clinical and biochemical remission with an OR of 2.5 (95% CI 1.1–5.0, <i>p</i> = 0.04) and 1.3 (95% CI 1.1–1.4, <i>p</i> = 0.03) respectively. The serum zinc level was associated neither with clinical nor with biochemical remission in either cohort. <b><i>Conclusions:</i></b> Our results indicate that serum Vit-D level may be a predictive marker in addition to drug trough levels in IBD patients treated with IFX. Furthermore, due to the correlation between serum IFX and Vit-D levels, Vit-D substitution should be conducted in patients with low Vit-D levels.
DOI: 10.6084/m9.figshare.9878492.v1
title: RCP_emis.zip

description: emission data sets
DOI: 10.6084/m9.figshare.12824483
title: Stop codon readthrough contexts influence reporter expression differentially depending on the presence of an IRES.

description: raw and extended data
DOI: 10.6084/m9.figshare.12824483.v1
title: Stop codon readthrough contexts influence reporter expression differentially depending on the presence of an IRES.

description: raw and extended data
DOI: 10.6084/m9.figshare.12833762.v1
title: Stop codon readthrough contexts influence reporter expression differentially depending on the presence of an IRES.

description: Extended data - sequences
DOI: 10.6084/m9.figshare.9878477.v2
title: Fig.S1 無価値なエクセルデータ

description: ここに説明を書きます。これのデータは無価値です。
DOI: 10.6084/m9.figshare.9878438
title: CoZ_dialogues_stress - Copy.docx

description: This data set was emerged from experiments where we used a Softbank's Pepper robot to interact with a confederate for handling complex conversation. The Pepper robot was remotely controlled by anonymous crowd workers from Amazon Mechanical Turk. We named this system as CoZ. Our main goal was to use CoZ as a life coach for the student who is experiencing stress. For ethical reasons, we opted to employ professional actress (confederate) to improvise all dialogues because this was our first investigation in a laboratory settings. The confederate interacted with the CoZ in different conditions. In each condition, we vary the number of crowd workers who interacted with the confederate via Pepper robot. The purpose of using different number of workers was to observe some performance measures (Latency, quality of conversations). In the data set, we only shared raw conversations. We used 1, 2, 4 and 8 crowd workers in each condition and each condition was repeated 5 times, so total of 20 interactions. In the word document, we named these conditions as 1-worker, 2-worker...