cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5563063
title: <i>Elainella</i> gen. nov.: a new tropical cyanobacterium characterized using a complex genomic approach

description: Cyanobacteria represent an ancient, monophyletic lineage of bacteria with the ability to undertake oxygenic photosynthesis. Although they possess a relatively high degree of morphological variability compared with other prokaryotes and there is a wealth of molecular data, there are still significant gaps in our knowledge of cyanobacterial diversity, especially in tropical areas. Here, we present a novel, filamentous, tropical cyanobacterium, which could be classified as <i>Pseudophormidium</i> based on morphological criteria. A total evidence investigation employing ecological, morphological and genomic data, indicated that our strains form a new and ancient evolutionary lineage among cyanobacteria unrelated to <i>Pseudophormidium</i>. Based on this polyphasic assessment, our strains represent a novel, monospecific genus: <i>Elainella</i>. This new genus represents an example of phenotypic convergence, which seems to be a prevalent macroevolutionary pattern in cyanobacteria, a likely cause of the frequently cited polyphyly within a majority of genera.
DOI: 10.6084/m9.figshare.5563063.v1
title: <i>Elainella</i> gen. nov.: a new tropical cyanobacterium characterized using a complex genomic approach

description: Cyanobacteria represent an ancient, monophyletic lineage of bacteria with the ability to undertake oxygenic photosynthesis. Although they possess a relatively high degree of morphological variability compared with other prokaryotes and there is a wealth of molecular data, there are still significant gaps in our knowledge of cyanobacterial diversity, especially in tropical areas. Here, we present a novel, filamentous, tropical cyanobacterium, which could be classified as <i>Pseudophormidium</i> based on morphological criteria. A total evidence investigation employing ecological, morphological and genomic data, indicated that our strains form a new and ancient evolutionary lineage among cyanobacteria unrelated to <i>Pseudophormidium</i>. Based on this polyphasic assessment, our strains represent a novel, monospecific genus: <i>Elainella</i>. This new genus represents an example of phenotypic convergence, which seems to be a prevalent macroevolutionary pattern in cyanobacteria, a likely cause of the frequently cited polyphyly within a majority of genera.
DOI: 10.6084/m9.figshare.5562964
title: Suitable reference gene selection for gene expression studies in knee osteoarthritis synovium using quantitative PCR analysis

description: Osteoarthritis (OA) is the leading cause of musculoskeletal disability in the elderly. Insights into the biological features of OA are obtained by characterization of the molecular features by gene expression profiling using reverse transcription-quantitative PCR (RT-qPCR). However, it has recently become evident that the use of suitable reference genes is required for appropriate normalization of this technique. Here total RNA was isolated from the synovium of 18 men and 20 women who underwent total knee arthroplasty for knee OA (KOA). We validated the expression stability of 7 candidate housekeeping genes (<i>ACTB, B2M, GAPDH, HPRT1, RPL13A, SDHA</i>, and <i>YWHAZ</i>) in the synovium of KOA with 3 commonly used algorithms (geNorm, NormFinder, and BestKeeper). Additionally, we evaluated expression profiles of the steroid hormone receptor (<i>AR, ESR1, ESR2, GR, MR</i>, and <i>PR</i>) and proinflammatory cytokines (<i>IL1B</i> and <i>IL6</i>) genes in the synovium and their correlations with the risk factors of KOA, using the most and least stable housekeeping genes for comparison. Results showed that <i>HPRT1</i> was the most stable gene, whereas <i>B2M</i> was the least stable. RT-qPCR analysis revealed sexually dimorphic expression of <i>AR, IL1B</i>, and <i>IL6</i>; intercorrelations between steroid hormone receptor expression levels and female-specific correlations of <i>IL1B</i> expression with <i>ESR1</i> and <i>PR</i> expression, <i>IL6</i> expression with <i>ESR1</i> and <i>GR</i> expression, and body mass index with <i>AR</i> and <i>PR</i> expression; and the choice of the least stable reference gene altered several correlations and statistical significances. In conclusion, <i>HPRT1</i> was identified as the suitable reference gene for normalization in the OA synovium.
DOI: 10.6084/m9.figshare.5562964.v1
title: Suitable reference gene selection for gene expression studies in knee osteoarthritis synovium using quantitative PCR analysis

description: Osteoarthritis (OA) is the leading cause of musculoskeletal disability in the elderly. Insights into the biological features of OA are obtained by characterization of the molecular features by gene expression profiling using reverse transcription-quantitative PCR (RT-qPCR). However, it has recently become evident that the use of suitable reference genes is required for appropriate normalization of this technique. Here total RNA was isolated from the synovium of 18 men and 20 women who underwent total knee arthroplasty for knee OA (KOA). We validated the expression stability of 7 candidate housekeeping genes (<i>ACTB, B2M, GAPDH, HPRT1, RPL13A, SDHA</i>, and <i>YWHAZ</i>) in the synovium of KOA with 3 commonly used algorithms (geNorm, NormFinder, and BestKeeper). Additionally, we evaluated expression profiles of the steroid hormone receptor (<i>AR, ESR1, ESR2, GR, MR</i>, and <i>PR</i>) and proinflammatory cytokines (<i>IL1B</i> and <i>IL6</i>) genes in the synovium and their correlations with the risk factors of KOA, using the most and least stable housekeeping genes for comparison. Results showed that <i>HPRT1</i> was the most stable gene, whereas <i>B2M</i> was the least stable. RT-qPCR analysis revealed sexually dimorphic expression of <i>AR, IL1B</i>, and <i>IL6</i>; intercorrelations between steroid hormone receptor expression levels and female-specific correlations of <i>IL1B</i> expression with <i>ESR1</i> and <i>PR</i> expression, <i>IL6</i> expression with <i>ESR1</i> and <i>GR</i> expression, and body mass index with <i>AR</i> and <i>PR</i> expression; and the choice of the least stable reference gene altered several correlations and statistical significances. In conclusion, <i>HPRT1</i> was identified as the suitable reference gene for normalization in the OA synovium.
DOI: 10.6084/m9.figshare.5562886
title: HEMOBPHEMOBP

description: a hemodialysis database to build a BP predictive model and real-time decision suggestion system
DOI: 10.6084/m9.figshare.5562886.v1
title: HEMOBP

description: a hemodialysis database to build a BP predictive model and real-time decision suggestion system
DOI: 10.6084/m9.figshare.5562793.v1
title: Data_Dept

description: PRj for 503
DOI: 10.6084/m9.figshare.5562886.v3
title: HEMOBP

description: a hemodialysis database to build a BP predictive model and real-time decision suggestion system
DOI: 10.6084/m9.figshare.5562730
title: Supplementary Material for: Online Self-Help as an Add-On to Inpatient Psychotherapy: Efficacy of a New Blended Treatment Approach

description: <b><i>Background:</i></b> Depression is one of the most frequent and costly mental disorders. While there is increasing evidence for the efficacy of online self-help to improve depression or prevent relapse, there is little evidence in blended care settings, especially combined with inpatient face-to-face psychotherapy. Therefore, we evaluated whether an evidence-based online self-help program improves the efficacy of inpatient psychotherapy. <b><i>Methods:</i></b> A total of 229 depressed patients were randomly allocated either to an online self-help program (intervention group [IG]; Deprexis) or an active control group (CG; weekly online information on depression) in addition to inpatient psychodynamic psychotherapy. Both groups had access to their respective experimental intervention for 12 weeks, regardless of inpatient treatment duration. Reduction of depressive symptoms, as measured with the Beck Depression Inventory-II, was the primary outcome at the end of the intervention (T2). <b><i>Results:</i></b> Depressive symptoms were statistically significantly lower in the IG compared to the active CG at T2 with a moderate between-group effect size of <i>d</i> = 0.44. The same applied to anxiety (<i>d</i> = 0.33), quality of life (<i>d</i> = 0.34), and self-esteem (<i>d</i> = 0.38) at discharge from inpatient treatment (T1). No statistically significant differences were found regarding dysfunctional attitudes (<i>d</i> = 0.14) and work ability (<i>d</i> = 0.08) at T1. <b><i>Conclusions:</i></b> This is the first evidence for blended treatment combining online self-help with inpatient psychotherapy. The study opens new and promising avenues for increasing the efficacy of inpatient psychotherapy. Future studies should determine how integration of online self-help into the therapeutic process can be developed further.
DOI: 10.6084/m9.figshare.5562778.v1
title: Data_Corp.xlsx

description: prj for 503
DOI: 10.6084/m9.figshare.5562886.v2
title: HEMOBP

description: a hemodialysis database to build a BP predictive model and real-time decision suggestion system
DOI: 10.6084/m9.figshare.5562664
title: Datasets on which the conclusions of the paper entitled "Female mound-building mice prefer males who invest more in building behavior, even when this behavior is not observed" relies.

description: One dataset with raw data of the preferences tests. One dataset with raw data of the pup retrieval procedure measuring paternal care.
DOI: 10.6084/m9.figshare.5562640
title: PRG GS Crown Rust Data

description: Conditional modes (BLUPs) for crown rust infection generated in lme4 from data collected over two years and multiple time points in a replicated field trial. Sequencing data from these genotypes is available on NCBI (PRJNA352789).
DOI: 10.6084/m9.figshare.5562640.v1
title: PRG GS Crown Rust Data

description: Conditional modes (BLUPs) for crown rust infection generated in lme4 from data collected over two years and multiple time points in a replicated field trial. Sequencing data from these genotypes is available on NCBI (PRJNA352789).
DOI: 10.6084/m9.figshare.5562664.v2
title: Datasets on which the conclusions of the paper entitled "Female mound-building mice prefer males who invest more in building behavior, even when this behavior is not observed" relies.

description: One dataset with raw data of the preferences tests. One dataset with raw data of the pup retrieval procedure measuring paternal care.
DOI: 10.6084/m9.figshare.5562538
title: Mentions of webby words in WWW2018 conference submissions

description: Analysing 250 PDFs 250 PDFs submitted to WWW2018 Web Content Analysis, Semantics, and Knowledge track Raw, counting webby words like "http" or "Web". Extracted using pdf2text and grep. See also https://gist.github.com/stain/8ce77dc74d2a86b4d772ba5f4403ad8a
DOI: 10.6084/m9.figshare.5562664.v1
title: Datasets on which the conclusions of the paper entitled "Females prefer cooperative males even when cooperative behavior is unobserved: evidence from the mound-building mouse, Mus spicilegus" rely.

description: One dataset with male building behaviors, including the results of the PCA implemented with them. One dataset with raw data of the preferences tests. One dataset with raw data of the pup retrieval procedure measuring paternal care.
DOI: 10.6084/m9.figshare.5562508
title: AE, VP, CWI data

description: Details in README.txt<br>
DOI: 10.6084/m9.figshare.5562538.v1
title: Mentions of webby words in WWW2018 conference submissions

description: Analysing 250 PDFs 250 PDFs submitted to WWW2018 Web Content Analysis, Semantics, and Knowledge track Raw, counting webby words like "http" or "Web". Extracted using pdf2text and grep. See also https://gist.github.com/stain/8ce77dc74d2a86b4d772ba5f4403ad8a
DOI: 10.6084/m9.figshare.5562484
title: Acute <i>in vitro</i> and <i>in vivo</i> toxicity of a commercial grade boron nitride nanotube mixture

description: Boron nitride nanotubes (BNNTs) are an emerging engineered nanomaterial attracting significant attention due to superior electrical, chemical and thermal properties. Currently, the toxicity profile of this material is largely unknown. Commercial grade BNNTs are composed of a mixture (BNNT-M) of ∼50–60% BNNTs, and ∼40–50% impurities of boron and hexagonal boron nitride. We performed acute <i>in vitro</i> and <i>in vivo</i> studies with commercial grade BNNT-M, dispersed by sonication in vehicle, in comparison to the extensively studied multiwalled carbon nanotube-7 (MWCNT-7). THP-1 wild-type and NLRP3-deficient human monocytic cells were exposed to 0–100 µg/ml and C57BL/6 J male mice were treated with 40 µg of BNNT-M for <i>in vitro</i> and <i>in vivo</i> studies, respectively. <i>In vitro</i>, BNNT-M induced a dose-dependent increase in cytotoxicity and oxidative stress. This was confirmed <i>in vivo</i> following acute exposure increase in bronchoalveolar lavage levels of lactate dehydrogenase, pulmonary polymorphonuclear cell influx, loss in mitochondrial membrane potential and augmented levels of 4-hydroxynonenal. Uptake of this material caused lysosomal destabilization, pyroptosis and inflammasome activation, corroborated by an increase in cathepsin B, caspase 1, increased protein levels of IL-1β and IL-18 both <i>in vitro</i> and <i>in vivo</i>. Attenuation of these effects in NLRP3-deficient THP-1 cells confirmed NLRP3-dependent inflammasome activation by BNNT-M. BNNT-M induced a similar profile of inflammatory pulmonary protein production when compared to MWCNT-7. Functionally, pretreatment with BNNT-M caused suppression in bacterial uptake by THP-1 cells, an effect that was mirrored in challenged alveolar macrophages collected from exposed mice and attenuated with NLRP3 deficiency. Analysis of cytokines secreted by LPS-challenged alveolar macrophages collected after <i>in vivo</i> exposure to dispersions of BNNT-M showed a differential macrophage response. The observed results demonstrated acute inflammation and toxicity <i>in vitro</i> and <i>in vivo</i> following exposure to sonicated BNNT-M was in part due to NLRP3 inflammasome activation.
DOI: 10.6084/m9.figshare.5562508.v2
title: AE, VP, CWI data

description: Details in README.txt<br>
DOI: 10.6084/m9.figshare.5562484.v2
title: Acute <i>in vitro</i> and <i>in vivo</i> toxicity of a commercial grade boron nitride nanotube mixture

description: Boron nitride nanotubes (BNNTs) are an emerging engineered nanomaterial attracting significant attention due to superior electrical, chemical and thermal properties. Currently, the toxicity profile of this material is largely unknown. Commercial grade BNNTs are composed of a mixture (BNNT-M) of ∼50–60% BNNTs, and ∼40–50% impurities of boron and hexagonal boron nitride. We performed acute <i>in vitro</i> and <i>in vivo</i> studies with commercial grade BNNT-M, dispersed by sonication in vehicle, in comparison to the extensively studied multiwalled carbon nanotube-7 (MWCNT-7). THP-1 wild-type and NLRP3-deficient human monocytic cells were exposed to 0–100 µg/ml and C57BL/6 J male mice were treated with 40 µg of BNNT-M for <i>in vitro</i> and <i>in vivo</i> studies, respectively. <i>In vitro</i>, BNNT-M induced a dose-dependent increase in cytotoxicity and oxidative stress. This was confirmed <i>in vivo</i> following acute exposure increase in bronchoalveolar lavage levels of lactate dehydrogenase, pulmonary polymorphonuclear cell influx, loss in mitochondrial membrane potential and augmented levels of 4-hydroxynonenal. Uptake of this material caused lysosomal destabilization, pyroptosis and inflammasome activation, corroborated by an increase in cathepsin B, caspase 1, increased protein levels of IL-1β and IL-18 both <i>in vitro</i> and <i>in vivo</i>. Attenuation of these effects in NLRP3-deficient THP-1 cells confirmed NLRP3-dependent inflammasome activation by BNNT-M. BNNT-M induced a similar profile of inflammatory pulmonary protein production when compared to MWCNT-7. Functionally, pretreatment with BNNT-M caused suppression in bacterial uptake by THP-1 cells, an effect that was mirrored in challenged alveolar macrophages collected from exposed mice and attenuated with NLRP3 deficiency. Analysis of cytokines secreted by LPS-challenged alveolar macrophages collected after <i>in vivo</i> exposure to dispersions of BNNT-M showed a differential macrophage response. The observed results demonstrated acute inflammation and toxicity <i>in vitro</i> and <i>in vivo</i> following exposure to sonicated BNNT-M was in part due to NLRP3 inflammasome activation.
DOI: 10.6084/m9.figshare.5562508.v1
title: Data for JGR submission

description: Details in README.txt<br>
DOI: 10.6084/m9.figshare.5562460
title: Dataset for: Recurrence-associated gene signature optimizes recurrence free survival prediction of colorectal cancer

description: High throughput gene expression profiling has showed great promise in providing insight into molecular mechanisms. Metastasis-related mRNAs may potentially enrich genes with the ability to predict cancer recurrence，therefore we attempted to build a recurrence-associated gene signature to improve prognostic prediction of colorectal cancer (CRC). We identified 2848 differentially expressed mRNAs by analyzing CRC tissues with or without metastasis. For the selection of prognostic genes, a LASSO Cox regression model was employed. Using this method, a 13-mRNA signature was identified and then validated in two independent Gene Expression Omnibus (GEO) cohorts. This classifier could successfully discriminate the high-risk patients in discovery cohort (HR = 5.27, 95%CI= 2.30-12.08, P &lt; 0.0001). Analysis in two independent cohorts yielded consistent results (GSE14333: HR=4.55, 95%CI=2.18 – 9.508, P&lt;0.0001) (GSE33113: HR=3.26, 95%CI=2.16 – 9.16, P=0.0176). Further analysis revealed that the prognostic value of this signature was independent of tumor stage, postoperative chemotherapy and somatic mutation. Receiver operating characteristic (ROC) analysis showed that the area under receiver operating characteristic curve (AUC) of this signature was 0.8861 and 0.8157 in the discovery and validation cohort, respectively. A nomogram was constructed for clinicians, which did well in the calibration plots. Furthermore, this 13-mRNA signature outperformed other known gene signatures, including oncotypeDX colon cancer assay. Single-sample gene-set enrichment analysis (ssGSEA) revealed that a group of pathways related to drug resistance, cancer metastasis and stemness were significantly enriched in the high-risk patients. In conclusion, this 13-mRNA signature may be a useful tool for prognostic evaluation and will facilitate personalized management of CRC patients.
DOI: 10.6084/m9.figshare.5562457
title: R code and data used in Aadrean and Usio (2017)

description: R code and data used in paper Aadrean and Usio (2017).<br>
DOI: 10.6084/m9.figshare.5562457.v1
title: R code and data used in Aadrean and Usio (2017)

description: R code and data used in paper Aadrean and Usio (2017).<br>
DOI: 10.6084/m9.figshare.5562460.v2
title: Dataset for: Recurrence-associated gene signature optimizes recurrence free survival prediction of colorectal cancer

description: High throughput gene expression profiling has showed great promise in providing insight into molecular mechanisms. Metastasis-related mRNAs may potentially enrich genes with the ability to predict cancer recurrence，therefore we attempted to build a recurrence-associated gene signature to improve prognostic prediction of colorectal cancer (CRC). We identified 2848 differentially expressed mRNAs by analyzing CRC tissues with or without metastasis. For the selection of prognostic genes, a LASSO Cox regression model was employed. Using this method, a 13-mRNA signature was identified and then validated in two independent Gene Expression Omnibus (GEO) cohorts. This classifier could successfully discriminate the high-risk patients in discovery cohort (HR = 5.27, 95%CI= 2.30-12.08, P &lt; 0.0001). Analysis in two independent cohorts yielded consistent results (GSE14333: HR=4.55, 95%CI=2.18 – 9.508, P&lt;0.0001) (GSE33113: HR=3.26, 95%CI=2.16 – 9.16, P=0.0176). Further analysis revealed that the prognostic value of this signature was independent of tumor stage, postoperative chemotherapy and somatic mutation. Receiver operating characteristic (ROC) analysis showed that the area under receiver operating characteristic curve (AUC) of this signature was 0.8861 and 0.8157 in the discovery and validation cohort, respectively. A nomogram was constructed for clinicians, which did well in the calibration plots. Furthermore, this 13-mRNA signature outperformed other known gene signatures, including oncotypeDX colon cancer assay. Single-sample gene-set enrichment analysis (ssGSEA) revealed that a group of pathways related to drug resistance, cancer metastasis and stemness were significantly enriched in the high-risk patients. In conclusion, this 13-mRNA signature may be a useful tool for prognostic evaluation and will facilitate personalized management of CRC patients.
DOI: 10.6084/m9.figshare.5562436
title: From Memories to Memorial: Healing Grief through Moving Image Creation

description: <strong>Abstract:</strong>Mourning is a period of our life that affects us deeply, and could be very traumatic in some cases. Art has been and still is a great way to express non-verbally our deeper feelings, finding meaning to our condition and in the case of mourning, our loss. Photography and Moving images are both medium that have a strong connection with death by embalming time, they can also be used as tools to ease the pain during mourning, and to move forward in our life. This study summarizes first some basic psychology concepts about bereavement and art therapy before focusing on the use of moving images as a healing tool for grief. This study compared the creation of moving images as a tool for healing grief both in art therapy and as a creative process by practitioners who experienced grief. The last part is a case study based on the author's own experience with dealing with grief through the making of an animation in memory of his lost partner. Through the case study, the author explores the process of making the animation and its positive effect on his grief.
DOI: 10.6084/m9.figshare.5562433
title: A decision support system to investigate dynamic last-mile distribution facilitating cargo-bikes

description: This work presents a decision support system to facilitate efficient urban last-mile distribution. Orders are collected and delivered by a fleet of both conventional vehicles owned by a logistics provider and cargo-bikes operated by freelancers. Additionally, micro-hubs are operated to perform transshipments between multiple vehicles. To investigate the corresponding problem setting, an agent-based simulation is developed, which uses dynamic optimisation procedures to generate and select vehicle routes and transshipment points. Experiments motivated by dynamic real-world urban restaurant delivery services investigate the impact of cargo-bikes, urban consolidation and guaranteed delivery times. Potentials are discussed and implications for successful implementations are provided. Results highlight the importance of having a sufficient number of active cargo-bikes available and benefits of incorporating consolidation strategies to guarantee timely deliveries.