cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.9255587
title: Supplementary Material for: Effectiveness of Stress-Reducing Interventions on the Response to Challenges to the Immune System: A Meta-Analytic Review

description: <b><i>Background:</i></b> There is consistent evidence showing an interplay between psychological processes and immune function in health and disease processes. <b><i>Objectives:</i></b> The present systematic review and meta-analysis aims to provide a concise overview of the effectiveness of stress-reducing psychological interventions on the activation of immune responses in both healthy subjects and patients. <b><i>Methods:</i></b> Included are 3 types of challenges: in vivo, in vitro, and psychophysiological. Such challenges are designed to mimic naturally occurring immune-related threats. <b><i>Results:</i></b> A systematic literature search was conducted using PubMed, EMBASE, and PsychInfo, resulting in 75 eligible studies. The risk of bias was assessed with the Cochrane risk-of-bias tool. Across all studies, a small-to-medium effect size was found for the effects of psychological interventions on optimization of the immune function (<i>g</i> = 0.33; 95% CI 0.22–0.43). While the largest effects were found for in vivo immune-related challenges (<i>g</i> = 0.61; 95% CI 0.34–0.88; especially on studies that incorporated skin tests and wound healing), studies incorporating psychophysiological challenges and in vitro immune-related stimulations similarly suggest more optimal immune responses among those receiving stress-reducing interventions (<i>g</i> = 0.28; 95% CI 0.15–0.42). <b><i>Conclusion:</i></b> These findings showed substantial heterogeneity depending on the type of challenge, the study populations, and the intervention types. These data demonstrate support for the effectiveness of stress-reducing psychological interventions in improving immunity in studies that tested immune function by means of incorporating an in vivo<i>,</i>in vitro, or psychophysiological challenge. Future research should more consistently incorporate challenges into the study design to gather more insights in the mechanisms underlying the optimized immune function following a psychological intervention. This is also relevant for clinical practice, as psychological interventions can possibly supplement, or at least partially replace, current drug treatments in various somatic conditions to reduce side effects.
DOI: 10.6084/m9.figshare.9255587.v1
title: Supplementary Material for: Effectiveness of Stress-Reducing Interventions on the Response to Challenges to the Immune System: A Meta-Analytic Review

description: <b><i>Background:</i></b> There is consistent evidence showing an interplay between psychological processes and immune function in health and disease processes. <b><i>Objectives:</i></b> The present systematic review and meta-analysis aims to provide a concise overview of the effectiveness of stress-reducing psychological interventions on the activation of immune responses in both healthy subjects and patients. <b><i>Methods:</i></b> Included are 3 types of challenges: in vivo, in vitro, and psychophysiological. Such challenges are designed to mimic naturally occurring immune-related threats. <b><i>Results:</i></b> A systematic literature search was conducted using PubMed, EMBASE, and PsychInfo, resulting in 75 eligible studies. The risk of bias was assessed with the Cochrane risk-of-bias tool. Across all studies, a small-to-medium effect size was found for the effects of psychological interventions on optimization of the immune function (<i>g</i> = 0.33; 95% CI 0.22–0.43). While the largest effects were found for in vivo immune-related challenges (<i>g</i> = 0.61; 95% CI 0.34–0.88; especially on studies that incorporated skin tests and wound healing), studies incorporating psychophysiological challenges and in vitro immune-related stimulations similarly suggest more optimal immune responses among those receiving stress-reducing interventions (<i>g</i> = 0.28; 95% CI 0.15–0.42). <b><i>Conclusion:</i></b> These findings showed substantial heterogeneity depending on the type of challenge, the study populations, and the intervention types. These data demonstrate support for the effectiveness of stress-reducing psychological interventions in improving immunity in studies that tested immune function by means of incorporating an in vivo<i>,</i>in vitro, or psychophysiological challenge. Future research should more consistently incorporate challenges into the study design to gather more insights in the mechanisms underlying the optimized immune function following a psychological intervention. This is also relevant for clinical practice, as psychological interventions can possibly supplement, or at least partially replace, current drug treatments in various somatic conditions to reduce side effects.
DOI: 10.6084/m9.figshare.9255575
title: Supplementary Material for: Advanced Cutaneous Squamous Cell Carcinoma Is Associated with Suboptimal Initial Management in a Cohort of 109 Patients

description: <b><i>Background:</i></b> Little is known about the epidemiological characteristics of patients with advanced cutaneous squamous cell carcinoma (A-cSCC). <b><i>Objective and Method:</i></b> A retrospective study was conducted on a routine care cohort of 109 patients to identify the epidemiological factors associated with A-cSCC. <b><i>Results:</i></b> The median age was 83 years (IQR: 73.9–89.8), and the median ECOG was 1 (IQR: 1–2). Sixty percent of the patients had a history of cardiac disease and 22% had cognitive disorders. Seventy-four percent of patients were from rural/semi-rural areas (towns of &lt;15,000 residents) and 17% were living in nursing homes. The cSCC lesions were on the head and neck in 72% of cases. Thirty-seven percent of patients were not diagnosed until the disease was in an advanced stage, indicating a lack of cSCC identification. In the remaining 69 patients, 7% did not received treatment within 3 months of the cSCC being identified, 62% had an incomplete histological report, and 37% had incomplete treatment. <b><i>Conclusion:</i></b> A-cSCC is associated with incomplete initial treatment in an elderly and rural population with good general condition. We hypothesize that a lack of access to good dermatological expertise may have led to underestimation of the aggressiveness of cSCC and/or therapeutic mismanagement.
DOI: 10.6084/m9.figshare.9255593.v1
title: gDNA Sequencing

description: ab1 files for gDNA ASS1 mutation sequencing
DOI: 10.6084/m9.figshare.9255575.v1
title: Supplementary Material for: Advanced Cutaneous Squamous Cell Carcinoma Is Associated with Suboptimal Initial Management in a Cohort of 109 Patients

description: <b><i>Background:</i></b> Little is known about the epidemiological characteristics of patients with advanced cutaneous squamous cell carcinoma (A-cSCC). <b><i>Objective and Method:</i></b> A retrospective study was conducted on a routine care cohort of 109 patients to identify the epidemiological factors associated with A-cSCC. <b><i>Results:</i></b> The median age was 83 years (IQR: 73.9–89.8), and the median ECOG was 1 (IQR: 1–2). Sixty percent of the patients had a history of cardiac disease and 22% had cognitive disorders. Seventy-four percent of patients were from rural/semi-rural areas (towns of &lt;15,000 residents) and 17% were living in nursing homes. The cSCC lesions were on the head and neck in 72% of cases. Thirty-seven percent of patients were not diagnosed until the disease was in an advanced stage, indicating a lack of cSCC identification. In the remaining 69 patients, 7% did not received treatment within 3 months of the cSCC being identified, 62% had an incomplete histological report, and 37% had incomplete treatment. <b><i>Conclusion:</i></b> A-cSCC is associated with incomplete initial treatment in an elderly and rural population with good general condition. We hypothesize that a lack of access to good dermatological expertise may have led to underestimation of the aggressiveness of cSCC and/or therapeutic mismanagement.
DOI: 10.6084/m9.figshare.9255596.v1
title: cDNA Sequencing

description: ab1 files cDNA sequencing
DOI: 10.6084/m9.figshare.9255566
title: Supplementary Material for: Involvement of Plasma Endocannabinoids and the Hypothalamic Endocannabinoid System in Increasing Feed Intake after Parturition of Dairy Cows

description: The endocannabinoids (ECs) N-arachidonylethanolamide (anandamide; AEA) and 2-arachidonoylglycerol (2-AG) participate in the control of feed intake and energy metabolism. Most mammals increase their feed intake after parturition to cope with the increased energy and nutrient requirements for milk synthesis, thereby increasing their metabolic rate. Here we investigated in experiment 1 the regulation of plasma AEA and 2-AG concentrations during the transition from late pregnancy to early lactation in dairy cows, and analyzed in experiment 2 the expression of the EC system in the paraventricular nucleus (PVN) and the arcuate nucleus (ARC) of the hypothalamus of late and early lactating cows using immunohistochemistry. Cows in experiment 1 were retrospectively grouped based on peak plasma fatty acid concentrations to a high (H) or low (L) group. Feed intake was not different between groups before parturition, but was lower in H than L cows during early lactation. Plasma AEA and 2-AG concentrations increased 2.2- to 2.4-fold during early lactation, in which time plasma AEA concentrations rose faster in H cows than in L cows postpartum. Upregulation of N-acyl phosphatidylethanolamine-specific phospholipase D together with tending increased cannabinoid receptor 1 (CB1) expression, and downregulation of fatty acid amide hydrolase in early lactating cows suggested an increased PVN AEA tone. The abundance of CB1 in the ARC and diacylglycerol lipase-alpha was not different between late and early lactating cows, but PVN monoacylglycerol lipase expression was 30% higher in early lactating cows, indicating diminished PVN 2-AG concentrations. The results show a potential involvement of AEA in stimulating feed intake and of 2-AG in regulating energy metabolism of early lactating cows.
DOI: 10.6084/m9.figshare.9255566.v1
title: Supplementary Material for: Involvement of Plasma Endocannabinoids and the Hypothalamic Endocannabinoid System in Increasing Feed Intake after Parturition of Dairy Cows

description: The endocannabinoids (ECs) N-arachidonylethanolamide (anandamide; AEA) and 2-arachidonoylglycerol (2-AG) participate in the control of feed intake and energy metabolism. Most mammals increase their feed intake after parturition to cope with the increased energy and nutrient requirements for milk synthesis, thereby increasing their metabolic rate. Here we investigated in experiment 1 the regulation of plasma AEA and 2-AG concentrations during the transition from late pregnancy to early lactation in dairy cows, and analyzed in experiment 2 the expression of the EC system in the paraventricular nucleus (PVN) and the arcuate nucleus (ARC) of the hypothalamus of late and early lactating cows using immunohistochemistry. Cows in experiment 1 were retrospectively grouped based on peak plasma fatty acid concentrations to a high (H) or low (L) group. Feed intake was not different between groups before parturition, but was lower in H than L cows during early lactation. Plasma AEA and 2-AG concentrations increased 2.2- to 2.4-fold during early lactation, in which time plasma AEA concentrations rose faster in H cows than in L cows postpartum. Upregulation of N-acyl phosphatidylethanolamine-specific phospholipase D together with tending increased cannabinoid receptor 1 (CB1) expression, and downregulation of fatty acid amide hydrolase in early lactating cows suggested an increased PVN AEA tone. The abundance of CB1 in the ARC and diacylglycerol lipase-alpha was not different between late and early lactating cows, but PVN monoacylglycerol lipase expression was 30% higher in early lactating cows, indicating diminished PVN 2-AG concentrations. The results show a potential involvement of AEA in stimulating feed intake and of 2-AG in regulating energy metabolism of early lactating cows.
DOI: 10.17045/sthlmuni.9255452
title: Expression of genes involved in nodule development in Datisca glomerata

description: The dataset shows the statistical analysis organized in a spreadsheet (Microsoft Excel, 2016) with tabs linking to the Figures present in the manuscript. Differences in gene expression were assessed by analysis of variance (ANOVA). Equality of variances was checked by Levene’s test. For equal variances, one-way ANOVA was fitted to log2-transformed 2^(-ΔΔCq) with treatments as fixed term and biological repeats as random effects accounting for dependencies between treatments. To estimate and adjust for pairwise multiple comparisons, a non-parametric post-hoc Tukey HSD test was applied. For unequal variances, a Welch’s pairwise t-test with Holm’s correction was used. For the assay involving the interaction of two factors, a two-way ANOVA was fitted to the data with “treatments” as a fixed factor in the model. Biological repeats accounted for random effects nested under the interaction term. Statistics were calculated in RStudio (R studio team, 2017).
DOI: 10.6084/m9.figshare.9255425
title: The effect of ego depletion or mental fatigue on subsequent physical endurance performance: a meta-analysis

description: - Ego depletion and mental fatigue impair subsequent endurance performance- The duration of the depletion task doesn't predict the magnitude of impairment- The depletion effect is higher on isolation than whole-body tasks- The depletion effect is higher when the person-situation fit is low- This effect should not be seen only through the "fatigue" prism but also as "value"<br>
DOI: 10.6084/m9.figshare.9255449
title: Supplementary Material for: Visit-to-Visit Variability in Total Cholesterol Correlates with the Progression of Renal Function Decline in a Chinese Community-Based Hypertensive Population

description: <b><i>Background:</i></b> Studies have demonstrated that cholesterol variability is an independent predictor of cerebrovascular and cardiovascular events. <b><i>Objective:</i></b> This study aimed to investigate the association of visit-to-visit variability in total cholesterol (TC) with kidney decline in a Chinese community-based population. <b><i>Methods:</i></b> We assessed intraindividual variability in TC among 6,465 hypertensive participants and correlated the results with endpoints. TC variability was measured using standard deviation (SD), average successive variability (ASV), coefficient of variation (CV), and variability independent of the mean (VIM). The endpoint of this study was progression of renal function decline defined as a decrease in estimated glomerular filtration rate (eGFR) ≥30% and to a level &lt;60 mL/min/1.73 m<sup>2</sup> during follow-up if the baseline eGFR was ≥60 mL/min/1.73 m<sup>2</sup>, or a decrease in eGFR ≥50% during follow up if the baseline eGFR was &lt;60 mL/min/1.73 m<sup>2</sup>. <b><i>Results:</i></b> After a median follow-up of 27 months, 13.5% (<i>n</i> = 877) of the participants experienced progression of renal function decline. In the multivariable-adjusted Cox model, each 1-SD increase in TC variability (by SD) increased the risk of renal function decline by 11% (HR = 1.11; 95% CI 1.034–1.197; <i>p</i> = 0.004); this was independent of the baseline eGFR, mean follow-up TC levels, and the lipid-lowering therapy. Similar results were found for the 3 other measures of variability, i.e., ASV, CV, and VIM. <b><i>Conclusion:</i></b> In subjects with hypertension, visit-to-visit variability in TC is an independent predictor of renal function decline.
DOI: 10.17045/sthlmuni.9255452.v1
title: Expression of genes involved in nodule development in Datisca glomerata

description: The dataset shows the statistical analysis organized in a spreadsheet (Microsoft Excel, 2016) with tabs linking to the Figures present in the manuscript. Differences in gene expression were assessed by analysis of variance (ANOVA). Equality of variances was checked by Levene’s test. For equal variances, one-way ANOVA was fitted to log2-transformed 2^(-ΔΔCq) with treatments as fixed term and biological repeats as random effects accounting for dependencies between treatments. To estimate and adjust for pairwise multiple comparisons, a non-parametric post-hoc Tukey HSD test was applied. For unequal variances, a Welch’s pairwise t-test with Holm’s correction was used. For the assay involving the interaction of two factors, a two-way ANOVA was fitted to the data with “treatments” as a fixed factor in the model. Biological repeats accounted for random effects nested under the interaction term. Statistics were calculated in RStudio (R studio team, 2017).
DOI: 10.6084/m9.figshare.9255449.v1
title: Supplementary Material for: Visit-to-Visit Variability in Total Cholesterol Correlates with the Progression of Renal Function Decline in a Chinese Community-Based Hypertensive Population

description: <b><i>Background:</i></b> Studies have demonstrated that cholesterol variability is an independent predictor of cerebrovascular and cardiovascular events. <b><i>Objective:</i></b> This study aimed to investigate the association of visit-to-visit variability in total cholesterol (TC) with kidney decline in a Chinese community-based population. <b><i>Methods:</i></b> We assessed intraindividual variability in TC among 6,465 hypertensive participants and correlated the results with endpoints. TC variability was measured using standard deviation (SD), average successive variability (ASV), coefficient of variation (CV), and variability independent of the mean (VIM). The endpoint of this study was progression of renal function decline defined as a decrease in estimated glomerular filtration rate (eGFR) ≥30% and to a level &lt;60 mL/min/1.73 m<sup>2</sup> during follow-up if the baseline eGFR was ≥60 mL/min/1.73 m<sup>2</sup>, or a decrease in eGFR ≥50% during follow up if the baseline eGFR was &lt;60 mL/min/1.73 m<sup>2</sup>. <b><i>Results:</i></b> After a median follow-up of 27 months, 13.5% (<i>n</i> = 877) of the participants experienced progression of renal function decline. In the multivariable-adjusted Cox model, each 1-SD increase in TC variability (by SD) increased the risk of renal function decline by 11% (HR = 1.11; 95% CI 1.034–1.197; <i>p</i> = 0.004); this was independent of the baseline eGFR, mean follow-up TC levels, and the lipid-lowering therapy. Similar results were found for the 3 other measures of variability, i.e., ASV, CV, and VIM. <b><i>Conclusion:</i></b> In subjects with hypertension, visit-to-visit variability in TC is an independent predictor of renal function decline.
DOI: 10.21942/uva.9255398
title: Phylogenetic tree phsA genes and transcripts

description: Phylogenetic tree (FastTree) based on a protein alignment of partial polysulfide/thiosulfate reductases (encoded by phsA) encoded in MAGs from hypersaline soda lakes and transcribed in a metatranscriptome from the sediment of Cock Soda lake. References were obtained from the NCBI protein database.
DOI: 10.21942/uva.9255395
title: Phylogenetic tree ttrA genes and transcripts

description: Phylogenetic tree (FastTree) based on a protein alignment of partial tetrathionate reductases (encoded by ttrA) encoded in MAGs from hypersaline soda lakes and transcribed in a metatranscriptome from the sediment of Cock Soda lake. References were obtained from the EggNog database.
DOI: 10.21942/uva.9255395.v1
title: Phylogenetic tree ttrA genes and transcripts

description: Phylogenetic tree (FastTree) based on a protein alignment of partial tetrathionate reductases (encoded by ttrA) encoded in MAGs from hypersaline soda lakes and transcribed in a metatranscriptome from the sediment of Cock Soda lake. References were obtained from the EggNog database.
DOI: 10.21942/uva.9255371
title: Phylogenetic tree tsdA genes and transcripts

description: Phylogenetic tree (FastTree) based on a protein alignment of partial thiosulfate dehydrogenases (encoded by tsdA) encoded in MAGs from hypersaline soda lakes and transcribed in a metatranscriptome from the sediment of Cock Soda lake. References were obtained from the EggNog database.
DOI: 10.6084/m9.figshare.9255425.v1
title: The effect of ‘ego depletion’ or ‘mental fatigue’ on subsequent physical endurance performance: A commentary and meta-analysis

description: - Ego depletion and mental fatigue impair subsequent endurance performance- The duration of the depletion task doesn't predict the magnitude of impairment- The depletion effect is higher on isolation than whole-body tasks- The depletion effect is higher when the person-situation fit is low- This effect should not be seen only through the "fatigue" prism but also as "value"<br>
DOI: 10.21942/uva.9255371.v1
title: Phylogenetic tree tsdA genes and transcripts

description: Phylogenetic tree (FastTree) based on a protein alignment of partial thiosulfate dehydrogenases (encoded by tsdA) encoded in MAGs from hypersaline soda lakes and transcribed in a metatranscriptome from the sediment of Cock Soda lake. References were obtained from the EggNog database.
DOI: 10.21942/uva.9255398.v1
title: Phylogenetic tree phsA genes and transcripts

description: Phylogenetic tree (FastTree) based on a protein alignment of partial polysulfide/thiosulfate reductases (encoded by phsA) encoded in MAGs from hypersaline soda lakes and transcribed in a metatranscriptome from the sediment of Cock Soda lake. References were obtained from the NCBI protein database.
DOI: 10.6084/m9.figshare.9255425.v2
title: The effect of ego depletion or mental fatigue on subsequent physical endurance performance: a commentary and meta-analysis

description: - Ego depletion and mental fatigue impair subsequent endurance performance- The duration of the depletion task doesn't predict the magnitude of impairment- The depletion effect is higher on isolation than whole-body tasks- The depletion effect is higher when the person-situation fit is low- This effect should not be seen only through the "fatigue" prism but also as "value"<br>
DOI: 10.21942/uva.9255347
title: Phylogenetic tree soxB genes and transcripts

description: Phylogenetic tree (FastTree) based on a protein alignment of soxB proteins encoded in MAGs from hypersaline soda lakes and transcribed in a metatranscriptome from the sediment of Cock Soda lake. References were obtained from the EggNog database.
DOI: 10.21942/uva.9255332
title: Phylogenetic tree dsrB genes and transcripts

description: Phylogenetic tree (FastTree) based on a protein alignment of a partial dissimilatory sulfite reductase (encoded by dsrB) encoded in MAGs from hypersaline soda lakes and transcribed in a metatranscriptome from the sediment of Cock Soda lake. References were obtained from the EggNog database.
DOI: 10.21942/uva.9255332.v1
title: Phylogenetic tree dsrB genes and transcripts

description: Phylogenetic tree (FastTree) based on a protein alignment of a partial dissimilatory sulfite reductase (encoded by dsrB) encoded in MAGs from hypersaline soda lakes and transcribed in a metatranscriptome from the sediment of Cock Soda lake. References were obtained from the EggNog database.
DOI: 10.21942/uva.9255302
title: Phylogenetic tree archaeal MAGs 16 ribosomal proteins

description: Phylogenetic tree of all archaeal MAGs analyzed in this study based on 16 ribosomal proteins. References included in the tree were obtained from Hug et al. (2016, Nature Microbiology) and Vavourakis et al. (2018, Microbiome).
DOI: 10.21942/uva.9255311
title: Phylogenetic tree doxD genes and transcripts

description: Phylogenetic tree (FastTree) based on a protein alignment of a partial thiosulfate:quinone oxidoreductases (encoded by doxD) encoded in MAGs from hypersaline soda lakes and transcribed in a metatranscriptome from the sediment of Cock Soda lake. References were obtained from the EggNog database.