cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.8839784
title: Additional file 4 of DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

description: RMarkdown for reproducibility. The additional file 4 includes the different scripts used to test all HVR primers (for single HVR and HVR pairs), scripts used to customize the different database in order to use them in the different assignation tools, and scripts used for DAIRYdb validation. We mainly used bash and R scripts [101, 102]. The file is in html format and was generated starting from a Rmarkdown file. (HTML 1012 kb)
DOI: 10.6084/m9.figshare.8839784.v1
title: Additional file 4 of DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

description: RMarkdown for reproducibility. The additional file 4 includes the different scripts used to test all HVR primers (for single HVR and HVR pairs), scripts used to customize the different database in order to use them in the different assignation tools, and scripts used for DAIRYdb validation. We mainly used bash and R scripts [101, 102]. The file is in html format and was generated starting from a Rmarkdown file. (HTML 1012 kb)
DOI: 10.6084/m9.figshare.8839754
title: Additional file 2 of DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

description: Krona diagram. Additional file 2 is an html file with a Krona diagram showing the complete diversity present in the DAIRYdb can be interactively inspected in a webbrowser. (HTML 872 kb)
DOI: 10.6084/m9.figshare.8839754.v1
title: Additional file 2 of DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

description: Krona diagram. Additional file 2 is an html file with a Krona diagram showing the complete diversity present in the DAIRYdb can be interactively inspected in a webbrowser. (HTML 872 kb)
DOI: 10.6084/m9.figshare.8839736
title: Additional file 1 of DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

description: Species list. The additional file 1 is a text file with all species included in the DAIRYdb in alphabetical order. Can be opened with any text editor or spreadsheet software. (TXT 100 kb)
DOI: 10.6084/m9.figshare.8839736.v1
title: Additional file 1 of DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

description: Species list. The additional file 1 is a text file with all species included in the DAIRYdb in alphabetical order. Can be opened with any text editor or spreadsheet software. (TXT 100 kb)
DOI: 10.6084/m9.figshare.8839586
title: Additional file 2: of Multimorbidity states associated with higher mortality rates in organ dysfunction and sepsis: a data-driven analysis in critical care

description: Supplementary methods. Figure S1. Graph summary of ROC curves depicting predictive performance of LCA input variables at differentiating a given subgroup from the remaining subgroups. Table S2. Table summary of classifier performance (assessed using area under the receiver operating curve, AUC) at predicting subgroup membership based on the input variables used in the LCA (age, sex, type of admission, and morbidities). Figure S2. Violin plot summary of organ systems impairment in the multimorbidity subgroups. Figure S3. Network summary of the multimorbidity subgroups with lower rates of sepsis and death. (ZIP 524 kb)
DOI: 10.6084/m9.figshare.8839586.v1
title: Additional file 2: of Multimorbidity states associated with higher mortality rates in organ dysfunction and sepsis: a data-driven analysis in critical care

description: Supplementary methods. Figure S1. Graph summary of ROC curves depicting predictive performance of LCA input variables at differentiating a given subgroup from the remaining subgroups. Table S2. Table summary of classifier performance (assessed using area under the receiver operating curve, AUC) at predicting subgroup membership based on the input variables used in the LCA (age, sex, type of admission, and morbidities). Figure S2. Violin plot summary of organ systems impairment in the multimorbidity subgroups. Figure S3. Network summary of the multimorbidity subgroups with lower rates of sepsis and death. (ZIP 524 kb)
DOI: 10.6084/m9.figshare.8839310
title: Additional file 2: of Test equating sleep scales: applying the Leunbachâ s model

description: Raw score conversion tables among sleep instruments. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.8839310.v1
title: Additional file 2: of Test equating sleep scales: applying the Leunbachâ s model

description: Raw score conversion tables among sleep instruments. (XLSX 28 kb)
DOI: 10.6084/m9.figshare.8839235
title: Additional file 1: of Comparison of time-series models for monitoring temporal trends in endemic diseases sero-prevalence: lessons from porcine reproductive and respiratory syndrome in Danish swine herds

description: R code used for a Dynamic Linear Model (DLM) and a Dynamic Generalized Linear Model (DGLM), both with a linear trend component. (TXT 5 kb)
DOI: 10.6084/m9.figshare.8839235.v1
title: Additional file 1: of Comparison of time-series models for monitoring temporal trends in endemic diseases sero-prevalence: lessons from porcine reproductive and respiratory syndrome in Danish swine herds

description: R code used for a Dynamic Linear Model (DLM) and a Dynamic Generalized Linear Model (DGLM), both with a linear trend component. (TXT 5 kb)
DOI: 10.6084/m9.figshare.8839175
title: Additional file 4: of Impact of type 2 diabetes treated with non-insulin medication and number of diabetes-coexisting diseases on EQ-5D-5 L index scores in the Finnish population

description: A Marginal effects estimated with two-part model for the association between NI-T2D and EQ-5D-5 L disutility score (i.e., 1 – EQ-5D-5 L index score) (N = 4998). The marginal effects of the two-part model used in calculating EQ-5D-5 L index scores. 4 B Marginal effects estimated with two-part model for the association between NI-T2D and crosswalk EQ-5D-3 L disutility score (i.e., 1 – crosswalk EQ-5D-3 L index score) (N = 4998). The marginal effects of the two-part model used in calculating EQ-5D-5 L/3 L Crosswalk index scores. (ZIP 34 kb)
DOI: 10.6084/m9.figshare.8839175.v1
title: Additional file 4: of Impact of type 2 diabetes treated with non-insulin medication and number of diabetes-coexisting diseases on EQ-5D-5 L index scores in the Finnish population

description: A Marginal effects estimated with two-part model for the association between NI-T2D and EQ-5D-5 L disutility score (i.e., 1 – EQ-5D-5 L index score) (N = 4998). The marginal effects of the two-part model used in calculating EQ-5D-5 L index scores. 4 B Marginal effects estimated with two-part model for the association between NI-T2D and crosswalk EQ-5D-3 L disutility score (i.e., 1 – crosswalk EQ-5D-3 L index score) (N = 4998). The marginal effects of the two-part model used in calculating EQ-5D-5 L/3 L Crosswalk index scores. (ZIP 34 kb)
DOI: 10.6084/m9.figshare.8834537
title: H NMR bucket data

description: This file contains the intensities of the signals of each bucket. Buckets have a bucket width of 0.04 ppm. The weight for each plant and the damage by <i>Mamestra brassicae</i> are also given.
DOI: 10.6084/m9.figshare.8834144
title: Supplementary Material for: Placenta-Specific 8 Is Overexpressed and Regulates Cell Proliferation in Low-Grade Human Pancreatic Neuroendocrine Tumors

description: <b><i>Background/Aims:</i></b> Many aspects of the biology of pancreatic neuroendocrine tumors (PanNETs), including determinants of proliferative, invasive, and metastatic potential, remain poorly understood. Placenta-specific 8 (<i>PLAC8</i>), a gene with unknown molecular function, has been reported to have tumor-promoting roles in different human malignancies, including exocrine pancreatic cancer. Since preliminary data suggested deregulation of PLAC8 expression in PanNET, we have performed detailed analyses of PLAC8 expression and function in human PanNET. <b><i>Methods:</i></b> Primary tissue from PanNET patients was immunohistochemically stained for PLAC8, and expression was correlated with clinicopathological data. In vitro<i>,</i> PLAC8 expression was inhibited by siRNA transfection in PanNET cell lines and effects were analyzed by qRT-PCR, Western blot, and proliferation assays. <b><i>Results:</i></b> We report that PLAC8 is expressed in the majority of well-differentiated human PanNETs, predominantly in early-stage and low-grade tumors. SiRNA-mediated knockdown of <i>PLAC8</i> in PanNET cells resulted in decreased proliferation and viability, while apoptosis was not induced. Mechanistically, these effects were mediated by attenuation of cell cycle progression, as Western blot analyses demonstrated upregulation of the tumor suppressor p21/CDKN2A and downregulation of the cell cycle regulator Cyclin D1 as well as reduced levels of phosphorylated ribosomal protein s6 and retinoblastoma protein. <b><i>Conclusion:</i></b> Our findings establish PLAC8 as a central mediator of cell growth in a subset of human PanNET, providing evidence for the existence of distinct molecular subtypes within this class of tumors.
DOI: 10.6084/m9.figshare.8834144.v1
title: Supplementary Material for: Placenta-Specific 8 Is Overexpressed and Regulates Cell Proliferation in Low-Grade Human Pancreatic Neuroendocrine Tumors

description: <b><i>Background/Aims:</i></b> Many aspects of the biology of pancreatic neuroendocrine tumors (PanNETs), including determinants of proliferative, invasive, and metastatic potential, remain poorly understood. Placenta-specific 8 (<i>PLAC8</i>), a gene with unknown molecular function, has been reported to have tumor-promoting roles in different human malignancies, including exocrine pancreatic cancer. Since preliminary data suggested deregulation of PLAC8 expression in PanNET, we have performed detailed analyses of PLAC8 expression and function in human PanNET. <b><i>Methods:</i></b> Primary tissue from PanNET patients was immunohistochemically stained for PLAC8, and expression was correlated with clinicopathological data. In vitro<i>,</i> PLAC8 expression was inhibited by siRNA transfection in PanNET cell lines and effects were analyzed by qRT-PCR, Western blot, and proliferation assays. <b><i>Results:</i></b> We report that PLAC8 is expressed in the majority of well-differentiated human PanNETs, predominantly in early-stage and low-grade tumors. SiRNA-mediated knockdown of <i>PLAC8</i> in PanNET cells resulted in decreased proliferation and viability, while apoptosis was not induced. Mechanistically, these effects were mediated by attenuation of cell cycle progression, as Western blot analyses demonstrated upregulation of the tumor suppressor p21/CDKN2A and downregulation of the cell cycle regulator Cyclin D1 as well as reduced levels of phosphorylated ribosomal protein s6 and retinoblastoma protein. <b><i>Conclusion:</i></b> Our findings establish PLAC8 as a central mediator of cell growth in a subset of human PanNET, providing evidence for the existence of distinct molecular subtypes within this class of tumors.
DOI: 10.6084/m9.figshare.8834537.v2
title: H NMR bucket data

description: This file contains the intensities of the signals of each bucket. Buckets have a bucket width of 0.04 ppm. The weight for each plant and the damage by <i>Mamestra brassicae</i> are also given.
DOI: 10.6084/m9.figshare.8832824
title: Supplementary Material for: A Three-Dimensional Musculoskeletal Model of the Western Lowland Gorilla Foot: Examining Muscle Torques and Function

description: Due to difficulty of obtaining accurate quantitative data on foot muscles, relatively little has been done to study foot muscle function in non-human apes. Gorilla feet are known to be similar in bony proportions and mechanics to those of humans, hence are key to understanding human foot evolution and its ecological context. We present the first 3D musculoskeletal computer model of a western lowland gorilla foot, giving muscle torques about the tarsometatarsal, metatarsophalangeal and interphalangeal joints of digits 2–5. Peak flexor torque around the fifth metatarsophalangeal joint occurs at a highly flexed position, suggesting an ability to maintain flexed postures around lateral metatarsophalangeal joints, useful for grasping vertical supports. For distal interphalangeal joints, flexor torques peaked the more medial the digit at relatively flexed postures. We report, for the first time, interossei acting upon proximal and distal interphalangeal joints. All these facilitate maintenance of flexed positions around distal interphalangeal joints, likely used for grasping of small supports/objects. Humans lack these features, suggesting that semi-arboreal early hominins made less use of the peripheral canopy than gorillines. Information here could be used in gorilla enclosure design to encourage wild-type locomotor repertoires in captivity.
DOI: 10.6084/m9.figshare.8834537.v1
title: H NMR bucket data

description: This file contains the intensities of the signals of each bucket. Buckets have a bucket width of 0.04 ppm. The weight for each plant and the damage by <i>Mamestra brassicae</i> are also given.
DOI: 10.6084/m9.figshare.8832506
title: Supplementary Material for: Assessment of Predictors of Sun Sensitivity as Defined by Fitzpatrick Skin Phototype in an Ecuadorian Population and Its Correlation with Skin Damage

description: <b><i>Background:</i></b> The Fitzpatrick skin phototype scale (FSPTS) is a widely used instrument to assess skin type. <b><i>Methods:</i></b> A cross-sectional survey collected responses from 254 subjects from Quito regarding self-reported FSPTS, gender, age, education, and tobacco and alcohol consumption. Univariate and multivariate logistic regression analyses were performed to determine if ethnicity, hair color, and eye color significantly predict FSPTS. In addition, we studied the correlation between FSPTS and the SCINEXA scale with Pearson’s correlation coefficient. <b><i>Results:</i></b> Ethnicity, eye color, and hair color are significant independent predictors of FSPTS (<i>p</i> &lt; 0.0001). <b><i>Conclusions:</i></b> Patient self-reported race and pigmentary phenotypes are inaccurate predictors of sun sensitivity as defined by Fitzpatrick skin phototype. Our study does not fully represent the population of the country. There are limitations to using patient-reported race and appearance in predicting individual sunburn risk.
DOI: 10.6084/m9.figshare.8832500
title: Supplementary Material for: Ustekinumab with Intravenous Infusion: Results in Hidradenitis Suppurativa

description: Adalimumab is the only approved biological therapy for hidradenitis suppurativa (HS). The last published recommendations support the use of other off-label biologic therapies. We report on a multicentric retrospective review of patients with HS treated with an ustekinumab dosing schedule of intravenous infusion adjusted by weight, followed by a subcutaneous maintenance dose of 90 mg every 8 weeks, as recently approved for Crohn’s disease. The minimal follow-up period required for inclusion was 16 weeks. A total of 14 patients from six hospitals were included. In 50% of the treated patients, therapeutic outcomes, measured by means of the Hidradenitis Suppurativa Clinical Response (HiSCR) and decrease of Dermatology Life Quality Index (DLQI) and visual analog scale (VAS) of pain, were reached at week 16. In 71.42% of patients DLQI and VAS of pain improved, irrespective of achievement of HiSCR. Two patients abandoned treatment due to lack of efficacy or patient preferences. No ustekinumab-related adverse effects were reported. The results are limited by the retrospective nature of the study, the short follow-up period, and the small patient number. This therapeutic regime proved to be safe and showed moderate efficacy in treating HS with failure to previous biologic therapy. Ideally, the efficacy of ustekinumab in HS should be tested in randomized and controlled clinical trials.
DOI: 10.6084/m9.figshare.8832509.v2
title: Data and R code for "The paleoclimatic footprint in the soil carbon stock of the Tibetan permafrost region"

description: A new estimate of Tibetan soil carbon pool, at a 0.1° spatial resolution, obtained by including paleoclimate, modern climate and landform, soil geochemical properties in multiple machine learning algorithms.
DOI: 10.6084/m9.figshare.8832506.v1
title: Supplementary Material for: Assessment of Predictors of Sun Sensitivity as Defined by Fitzpatrick Skin Phototype in an Ecuadorian Population and Its Correlation with Skin Damage

description: <b><i>Background:</i></b> The Fitzpatrick skin phototype scale (FSPTS) is a widely used instrument to assess skin type. <b><i>Methods:</i></b> A cross-sectional survey collected responses from 254 subjects from Quito regarding self-reported FSPTS, gender, age, education, and tobacco and alcohol consumption. Univariate and multivariate logistic regression analyses were performed to determine if ethnicity, hair color, and eye color significantly predict FSPTS. In addition, we studied the correlation between FSPTS and the SCINEXA scale with Pearson’s correlation coefficient. <b><i>Results:</i></b> Ethnicity, eye color, and hair color are significant independent predictors of FSPTS (<i>p</i> &lt; 0.0001). <b><i>Conclusions:</i></b> Patient self-reported race and pigmentary phenotypes are inaccurate predictors of sun sensitivity as defined by Fitzpatrick skin phototype. Our study does not fully represent the population of the country. There are limitations to using patient-reported race and appearance in predicting individual sunburn risk.
DOI: 10.6084/m9.figshare.8832500.v1
title: Supplementary Material for: Ustekinumab with Intravenous Infusion: Results in Hidradenitis Suppurativa

description: Adalimumab is the only approved biological therapy for hidradenitis suppurativa (HS). The last published recommendations support the use of other off-label biologic therapies. We report on a multicentric retrospective review of patients with HS treated with an ustekinumab dosing schedule of intravenous infusion adjusted by weight, followed by a subcutaneous maintenance dose of 90 mg every 8 weeks, as recently approved for Crohn’s disease. The minimal follow-up period required for inclusion was 16 weeks. A total of 14 patients from six hospitals were included. In 50% of the treated patients, therapeutic outcomes, measured by means of the Hidradenitis Suppurativa Clinical Response (HiSCR) and decrease of Dermatology Life Quality Index (DLQI) and visual analog scale (VAS) of pain, were reached at week 16. In 71.42% of patients DLQI and VAS of pain improved, irrespective of achievement of HiSCR. Two patients abandoned treatment due to lack of efficacy or patient preferences. No ustekinumab-related adverse effects were reported. The results are limited by the retrospective nature of the study, the short follow-up period, and the small patient number. This therapeutic regime proved to be safe and showed moderate efficacy in treating HS with failure to previous biologic therapy. Ideally, the efficacy of ustekinumab in HS should be tested in randomized and controlled clinical trials.
DOI: 10.6084/m9.figshare.8832509.v1
title: Data and R code for "The paleoclimatic footprint in the soil carbon stock of Tibetan permafrost region"

description: A new estimate of Tibetan soil carbon pool, at a 0.1° spatial resolution, obtained by including paleoclimate, modern climate and landform, soil geochemical properties in multiple machine learning algorithms.
DOI: 10.6084/m9.figshare.8832458
title: ASV counts and taxonomic assignments PRJNA507590/SRP171602

description: This table contains the bacterial 16S rRNA amplicon sequence variant (ASV) count data and taxonomic assignment after bioinformatic processing used in the data descriptor: "Bacterial succession along a sediment porewater gradient at Lake Neusiedl in Austria". Further information on the bioinformatic processing can be found in the material and methods section of the paper.
DOI: 10.6084/m9.figshare.8832458.v1
title: ASV_counts_and_taxonomic_assignments

description: This table contains the bacterial 16S rRNA amplicon sequence variant (ASV) count data and taxonomic assignment after bioinformatic processing used in the data descriptor: "Bacterial succession along a sediment porewater gradient at Lake Neusiedl in Austria". Further information on the bioinformatic processing can be found in the material and methods section of the paper.
DOI: 10.6084/m9.figshare.8832458.v3
title: ASV counts and taxonomic assignments PRJNA507590/SRP171602

description: This table contains the bacterial 16S rRNA amplicon sequence variant (ASV) count data and taxonomic assignment after bioinformatic processing used in the data descriptor: "Bacterial succession along a sediment porewater gradient at Lake Neusiedl in Austria". Further information on the bioinformatic processing can be found in the material and methods section of the paper.
DOI: 10.6084/m9.figshare.8832458.v2
title: ASV_counts_and_taxonomic_assignments_PRJNA507590

description: This table contains the bacterial 16S rRNA amplicon sequence variant (ASV) count data and taxonomic assignment after bioinformatic processing used in the data descriptor: "Bacterial succession along a sediment porewater gradient at Lake Neusiedl in Austria". Further information on the bioinformatic processing can be found in the material and methods section of the paper.
DOI: 10.6084/m9.figshare.8832326
title: Impact of social support on psychosocial symptoms and quality of life in cancer patients: results of a multilevel model approach from a longitudinal multicenter study

description: <b>Background:</b> This prospective multicenter study aimed to investigate the courses of positive support (PS) and detrimental interaction (DI), two different aspects of social support, and the relation between social support and psychosocial distress and/or health-related quality of life (HRQOL) in a large sample of patients with different cancers. <b>Methods:</b> For this observational study, we enrolled adult patients with cancer from 13 comprehensive cancer centers (CCCs) in Germany. We included a total of 1087 patients in our analysis. We assessed the outcomes via standardized self-report questionnaires at three measurement points: at admission for acute care (T1), 6 (T2) and 12 months (T3) thereafter. Our outcome variables included PS and DI, depression and anxiety symptoms, distress, mental quality of life (MQoL) and physical QoL (PQoL). Data were analyzed using three-level hierarchical linear modeling (HLM) and group-based trajectory modeling. <b>Results:</b> During the first year after the cancer diagnosis, both PS and DI decreased in our sample. Baseline depression symptom severity was a significant predictor of PS and DI. Further analyses revealed significant associations between PS, DI and the course of depression and anxiety symptoms, and MQoL. PS buffered the negative effects of DI with regards to these variables. Low DI was associated with better PQoL, whereas PS was not. In general, the impact of social support on psychosocial outcomes was weak to moderate. <b>Conclusions:</b> Our findings provide evidence for the influence of PS and DI on psychosocial symptoms and HRQOL, and emphasize the importance of psycho-oncological interventions that strengthen PS and prevent or reduce DI for patients with cancer and their relatives.