cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4962809
title: Hypoxia favors the generation of human plasma cells

description: Plasma cells (PCs) generation occurs in hypoxic conditions <i>in vivo</i>, whereas the relevance of O<sub>2</sub> pressure in PC differentiation remains unknown. Using our <i>in vitro</i> PC differentiation model, we investigated the role of hypoxia in PC generation. Hypoxia increases the generation of plasmablasts (PBs) starting from memory B cells, by increasing cell cycle and division number. Reactome analysis demonstrated a significant enrichment of genes involved in HIF1α and HIF2α transcription factor network, metabolism and MYC related pathways in hypoxic compared with normoxic PBs. Hypoxia-induced metabolism alteration and MYC pathway are involved in malignant PC pathophysiology. Therefore, the expression of 28 out of the 74 genes overexpressed in hypoxic PBs compared with normoxic ones was found to be associated with an adverse prognosis (event free survival and overall survival) in newly diagnosed multiple myeloma patients. According to the role of hypoxia in supporting PBs generation through cell cycle induction, c-MYC activation and metabolism alteration, it could be involved in plasma cell tumorigenesis.
DOI: 10.6084/m9.figshare.4962758
title: Data extraction REST-alignment

description: Data extraction sheet for mapping study regarding alignment of requirements engineering and software testing<br>
DOI: 10.6084/m9.figshare.4962809.v1
title: Hypoxia favors the generation of human plasma cells

description: Plasma cells (PCs) generation occurs in hypoxic conditions <i>in vivo</i>, whereas the relevance of O<sub>2</sub> pressure in PC differentiation remains unknown. Using our <i>in vitro</i> PC differentiation model, we investigated the role of hypoxia in PC generation. Hypoxia increases the generation of plasmablasts (PBs) starting from memory B cells, by increasing cell cycle and division number. Reactome analysis demonstrated a significant enrichment of genes involved in HIF1α and HIF2α transcription factor network, metabolism and MYC related pathways in hypoxic compared with normoxic PBs. Hypoxia-induced metabolism alteration and MYC pathway are involved in malignant PC pathophysiology. Therefore, the expression of 28 out of the 74 genes overexpressed in hypoxic PBs compared with normoxic ones was found to be associated with an adverse prognosis (event free survival and overall survival) in newly diagnosed multiple myeloma patients. According to the role of hypoxia in supporting PBs generation through cell cycle induction, c-MYC activation and metabolism alteration, it could be involved in plasma cell tumorigenesis.
DOI: 10.6084/m9.figshare.4962758.v2
title: Data extraction REST-alignment

description: Data extraction sheet for mapping study regarding alignment of requirements engineering and software testing<br>
DOI: 10.6084/m9.figshare.4962758.v1
title: New draft item

description: Data extraction sheet for mapping study regarding alignment of requirements engineering and software testing<br>
DOI: 10.6084/m9.figshare.4962683
title: Dados complementares: Flora herbácea e subarbustiva associada a um ecossistema de butiazal no Bioma Pampa - Rodriguésia vol. 69 - n. 2. 2018.

description: Dados de localização das áreas de estudo do levantamento da flora herbácea e subarbustiva associada ao ecossistema de butiazal no município de Tapes, Rio Grande do Sul, Brasil<br>Trata-se de uma área de 750 hectares, particular, com 70.000 butiazeiros da espécie <i>Butia odorata</i>. Composta por uma vegetação de campo nativo, onde foram registrados 261 táxons herbáceos e subarbustivos durante o levantamento florístico realizado de 2011 a 2013, durante o doutorado da primeira autora.<br><br>
DOI: 10.6084/m9.figshare.4962683.v1
title: Dados complementares: Flora herbácea e subarbustiva associada a um ecossistema de butiazal no Bioma Pampa - Rodriguésia vol. 69 - n. 2. 2018.

description: Dados de localização das áreas de estudo do levantamento da flora herbácea e subarbustiva associada ao ecossistema de butiazal no município de Tapes, Rio Grande do Sul, Brasil<br>Trata-se de uma área de 750 hectares, particular, com 70.000 butiazeiros da espécie <i>Butia odorata</i>. Composta por uma vegetação de campo nativo, onde foram registrados 261 táxons herbáceos e subarbustivos durante o levantamento florístico realizado de 2011 a 2013, durante o doutorado da primeira autora.<br><br>
DOI: 10.6084/m9.figshare.4960580
title: Salmon nasal cartilage proteoglycan enhances growth of normal human dermal fibroblast through Erk1/2 phosphorylation

description: Proteoglycan (PG) is a heavily glycosylated protein, localized to cell surface and extracellular matrix, and has various functions. Recently, it has been gradually revealed that PG interacts with various growth factors and morphogens and regulates cellular functions. Although salmon nasal cartilage PG (Salmon-PG) increases proliferation of immortalized cells, its mechanism remains unclear. In this study, we confirmed the effect of Salmon-PG on normal human dermal fibroblast (NHDF) and investigated the mechanism of PG action on NHDF. Salmon-PG dose- and time-dependently increased NHDF proliferation. Receptor tyrosine kinase array revealed that Salmon-PG increased only Erk1/2 signaling. Erk1/2 phosphorylation was significantly increased by Salmon-PG in a time-(10 min) and dose-(400 or 800 μg/mL) dependent manner. MEK inhibitor suppressed the enhancement of NHDF proliferation by Salmon-PG. The overall findings indicate that Salmon-PG plays a role as a growth factor in NHDF via Erk1/2 activation, suggesting that Salmon-PG contributes to the maintenance of skin homeostasis. Salmon-PG contributes to the maintenance of skin homeostasis through the enhancement of NHDF proliferation by up-regulating Erk1/2 signaling.
DOI: 10.6084/m9.figshare.4960508
title: Graphs for HPIV2, NDV and HRSV

description: Graphs linking conservation, entropy and DynaMine data for HPIV2, NDV and HRSV.
DOI: 10.6084/m9.figshare.4960406
title: R code for species distribution modeling in "Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion."

description: Zipped R code and necessary data for MaxEnt species distribution modeling used in "Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion." It covers loading of data, model selection, fitting and prediction as well as assessment of variable importances. Included is also the code for plotting of predicted relative occurrence rates (ROR) and for "double density plots" confronting distribution of variable values across background with its ROR-weighted version.
DOI: 10.6084/m9.figshare.4960508.v1
title: Graphs for HPIV2, NDV and HRSV

description: Graphs linking conservation, entropy and DynaMine data for HPIV2, NDV and HRSV.
DOI: 10.6084/m9.figshare.4960406.v2
title: R code for species distribution modeling in "Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion."

description: Zipped R code and necessary data for MaxEnt species distribution modeling used in "Phylogeography of a widespread sub-Saharan murid rodent Aethomys chrysophilus: the role of geographic barriers and paleoclimate in the Zambezian bioregion." It covers loading of data, model selection, fitting and prediction as well as assessment of variable importances. Included is also the code for plotting of predicted relative occurrence rates (ROR) and for "double density plots" confronting distribution of variable values across background with its ROR-weighted version.
DOI: 10.6084/m9.figshare.4960295
title: Visual perception of nature scenes within urban environment

description: Survey on visual perception of natural scenery within urban tropical environment.<br><br>Questionnaire for landscape professionnals:<br>- Material: 54 images of nature scenes, taken within urban tropical environment in Singapore.<br>- Evaluation of each scenery photo is based on the 19 visual criteria, by using a 5 levels likert scale.<br>- Assessment of 19 visual criteria: coherence, legibility, complexity, prospect, stewardship, compatibility, disturbance, risk, refuge, colours, water, cultural identity, naturalness, distinctiveness, mystery, scenic beauty, being away, fascination, extent), related to wellbeing.<br>- Sceneries of urban nature projected on a large screen within a room. High quality photography.<br><br>
DOI: 10.6084/m9.figshare.4960298
title: read_me.txt

description: README for network building PERL algorithms
DOI: 10.6084/m9.figshare.4960298.v1
title: read_me.txt

description: README for network building PERL algorithms
DOI: 10.6084/m9.figshare.4960199
title: PowerPoint Slides for: Pregnancy Outcomes in Patients with Glomerular Disease Attending a Single Academic Center in North Carolina

description: <b><i>Background:</i></b> Contemporary data regarding pregnancy outcomes in US patients with primary glomerular diseases are lacking. We aimed to report fetal and maternal outcomes among women with biopsy-proven primary glomerular disease who received obstetric care at a single large academic US center. <b><i>Methods:</i></b> All women with a biopsy-confirmed primary glomerular disease diagnosis and without end-stage kidney disease who received obstetric care at the University of North Carolina (UNC) Hospitals (1996-2015) were identified using the Glomerular Disease Collaborative Network registry and the UNC Hospitals Perinatal Database. The primary study outcome was perinatal death (stillbirth at &gt;20 weeks or neonatal death). Secondary outcomes included premature birth (&lt;37 weeks), birth weight, preeclampsia, and kidney function changes (postpartum vs. baseline). Demographics, clinical characteristics, and outcomes were compared across glomerular disease subtypes. <b><i>Results:</i></b> Among 48 pregnancies in 43 women (IgA nephropathy <i>n</i> = 17, focal segmental glomerulosclerosis [FSGS] <i>n</i> = 16, membranous nephropathy <i>n</i> = 6, minimal change disease <i>n</i> = 4), 13% of pregnancies resulted in perinatal death and 48% of babies were born prematurely. From a maternal perspective, 33% of pregnancies were complicated by preeclampsia, 39% by a doubling of urinary protein, and 27% by a ≥50% increase in serum creatinine. Outcome differences across glomerular disease subtypes were not statistically significant, although decline in kidney function appeared most frequent in FSGS. <b><i>Conclusion:</i></b> Adverse pregnancy outcomes are frequently observed in women with glomerular disease. The independent influence of glomerular disease subtype on outcomes requires further study. More widespread reporting and analysis of pregnancy outcomes in women with glomerular disease are urgently needed.
DOI: 10.6084/m9.figshare.4960178
title: PowerPoint Slides for: Use of Phosphorus Binders among Non-Dialysis Chronic Kidney Disease Patients and Mortality Outcomes

description: <b><i>Background:</i></b> Whether the benefits of phosphorus binders extend to those without end stage renal disease is uncertain. Among a large diverse non-dialysis chronic kidney disease (CKD) population with hyperphosphatemia, we sought to evaluate phosphorus binder use and compare mortality risk between patients prescribed and not prescribed binders. <b><i>Methods:</i></b> A retrospective cohort study within an integrated health system (January 1, 1998 - December 31, 2012) among CKD patients (age ≥18) was performed. Non-dialysis CKD patients with 2 separate estimated glomerular filtrate rate (eGFR) &lt;30 mL/min/1.73 m<sup>2</sup> and serum phosphorus ≥5.0 mg/dL within 180 days of eGFR were included. Multivariable cox proportional hazards and inverse probability of treatment-weighted models were used to estimate mortality hazard ratios (HRs) for patients who received phosphorus binders compared to no binders. <b><i>Results:</i></b> Among 10,165 study patients, 2,733 subjects (27%) received phosphorus binders. Compared to the no-phosphorus-binder group, the binder group had mortality HRs (95% CI) of 0.86 (0.79-0.94) and 0.86 (0.80-0.93) using traditional multivariable and inverse probability of treatment-weighted models respectively. Sensitivity analyses removing patients who were prescribed binders &gt;180 days after index date revealed no difference in mortality between those with binders and with no binders. <b><i>Conclusion:</i></b> Our findings from a real-world clinical environment revealed that 27% of hyperphosphatemic non-dialysis CKD patients were prescribed binders. They also had lower risk of mortality compared to those not prescribed phosphorus binders. However, the lower mortality risk was not observed when we accounted for immortal time bias. Whether phosphorus binder use in CKD improves survival remains to be determined.
DOI: 10.6084/m9.figshare.4960178.v1
title: PowerPoint Slides for: Use of Phosphorus Binders among Non-Dialysis Chronic Kidney Disease Patients and Mortality Outcomes

description: <b><i>Background:</i></b> Whether the benefits of phosphorus binders extend to those without end stage renal disease is uncertain. Among a large diverse non-dialysis chronic kidney disease (CKD) population with hyperphosphatemia, we sought to evaluate phosphorus binder use and compare mortality risk between patients prescribed and not prescribed binders. <b><i>Methods:</i></b> A retrospective cohort study within an integrated health system (January 1, 1998 - December 31, 2012) among CKD patients (age ≥18) was performed. Non-dialysis CKD patients with 2 separate estimated glomerular filtrate rate (eGFR) &lt;30 mL/min/1.73 m<sup>2</sup> and serum phosphorus ≥5.0 mg/dL within 180 days of eGFR were included. Multivariable cox proportional hazards and inverse probability of treatment-weighted models were used to estimate mortality hazard ratios (HRs) for patients who received phosphorus binders compared to no binders. <b><i>Results:</i></b> Among 10,165 study patients, 2,733 subjects (27%) received phosphorus binders. Compared to the no-phosphorus-binder group, the binder group had mortality HRs (95% CI) of 0.86 (0.79-0.94) and 0.86 (0.80-0.93) using traditional multivariable and inverse probability of treatment-weighted models respectively. Sensitivity analyses removing patients who were prescribed binders &gt;180 days after index date revealed no difference in mortality between those with binders and with no binders. <b><i>Conclusion:</i></b> Our findings from a real-world clinical environment revealed that 27% of hyperphosphatemic non-dialysis CKD patients were prescribed binders. They also had lower risk of mortality compared to those not prescribed phosphorus binders. However, the lower mortality risk was not observed when we accounted for immortal time bias. Whether phosphorus binder use in CKD improves survival remains to be determined.
DOI: 10.6084/m9.figshare.4960157
title: BDNF cleavage sites by elastase-2a and chymotrypsin

description: Figure based on the information obtained in Peptide-cutter (Swiss Institute of Bioinformatics).
DOI: 10.6084/m9.figshare.4960124
title: cela2a mBDNF 90-119 interaction

description: CABS docking-derived interaction between BDNF 91-119aa residues and mCELA2A
DOI: 10.6084/m9.figshare.4960097
title: Mumps Raw Data Files

description: Raw data files for the mumps proteins
DOI: 10.6084/m9.figshare.4960097.v1
title: Mumps Raw Data Files

description: Raw data files for the mumps proteins
DOI: 10.6084/m9.figshare.4960124.v3
title: cela2a mBDNF 90-119 interaction

description: CABS docking-derived interaction between BDNF 91-119aa residues and mCELA2A
DOI: 10.6084/m9.figshare.4960124.v2
title: cela2a mBDNF 90-119 model4.pse

description: CABS docking-derived interaction between BDNF 91-119aa residues and mCELA2A
DOI: 10.6084/m9.figshare.4960052
title: Supplementary Material for: Schizophrenia and Human Self-Domestication: An Evolutionary Linguistics Approach

description: Schizophrenia (SZ) is a pervasive neurodevelopmental disorder that entails social and cognitive deficits, including marked language problems. Its complex multifactorial etiopathogenesis, including genetic and environmental factors, is still widely uncertain. SZ incidence has always been high and quite stable in human populations, across time and regardless of cultural implications, for unclear reasons. It has been hypothesized that SZ pathophysiology may involve the biological components that changed during the recent human evolutionary history, and led to our distinctive mode of cognition, which includes language skills. In this paper we explore this hypothesis, focusing on the self-domestication of the human species. This has been claimed to account for many human-specific distinctive traits, including aspects of our behavior and cognition, and to favor the emergence of complex languages through cultural evolution. The “domestication syndrome” in mammals comprises the constellation of traits exhibited by domesticated strains, seemingly resulting from the hypofunction of the neural crest. It is our intention to show that people with SZ exhibit more marked domesticated traits at the morphological, physiological, and behavioral levels. We also show that genes involved in domestication and neural crest development and function comprise nearly 20% of SZ candidates, most of which exhibit altered expression profiles in the brain of SZ patients, specifically in areas involved in language processing. Based on these observations, we conclude that SZ may represent an abnormal ontogenetic itinerary for the human faculty of language, resulting, at least in part, from changes in genes important for the domestication syndrome and primarily involving the neural crest.
DOI: 10.6084/m9.figshare.4960052.v1
title: Supplementary Material for: Schizophrenia and Human Self-Domestication: An Evolutionary Linguistics Approach

description: Schizophrenia (SZ) is a pervasive neurodevelopmental disorder that entails social and cognitive deficits, including marked language problems. Its complex multifactorial etiopathogenesis, including genetic and environmental factors, is still widely uncertain. SZ incidence has always been high and quite stable in human populations, across time and regardless of cultural implications, for unclear reasons. It has been hypothesized that SZ pathophysiology may involve the biological components that changed during the recent human evolutionary history, and led to our distinctive mode of cognition, which includes language skills. In this paper we explore this hypothesis, focusing on the self-domestication of the human species. This has been claimed to account for many human-specific distinctive traits, including aspects of our behavior and cognition, and to favor the emergence of complex languages through cultural evolution. The “domestication syndrome” in mammals comprises the constellation of traits exhibited by domesticated strains, seemingly resulting from the hypofunction of the neural crest. It is our intention to show that people with SZ exhibit more marked domesticated traits at the morphological, physiological, and behavioral levels. We also show that genes involved in domestication and neural crest development and function comprise nearly 20% of SZ candidates, most of which exhibit altered expression profiles in the brain of SZ patients, specifically in areas involved in language processing. Based on these observations, we conclude that SZ may represent an abnormal ontogenetic itinerary for the human faculty of language, resulting, at least in part, from changes in genes important for the domestication syndrome and primarily involving the neural crest.
DOI: 10.6084/m9.figshare.4959947
title: data_source_publ.zip

description: Individual-based simulation of the evolution of punishment and cautiousness in a population of floaters and territory owners competing for resources in territories.<br>Data files and sources as published in:<br>M. Hinsch & J. Komdeur (2017): "Punish the thief - coevolution of defense and cautiousness stabilizes ownership" Behavioral Ecology and Sociobiology<br>
DOI: 10.6084/m9.figshare.4959938
title: O and Hf isotope data. Zircon O- and Hf-isotope constraints on the genesis and tectonic significance of Permian magmatism in Patagonia

description: Summary of the O and Hf isotope data from zircon spot analyses
DOI: 10.6084/m9.figshare.4959947.v1
title: data_source_publ.zip

description: Individual-based simulation of the evolution of punishment and cautiousness in a population of floaters and territory owners competing for resources in territories.<br>Data files and sources as published in:<br>M. Hinsch & J. Komdeur (2017): "Punish the thief - coevolution of defense and cautiousness stabilizes ownership" Behavioral Ecology and Sociobiology<br>
DOI: 10.6084/m9.figshare.4959932
title: SHRIMP U–Pb results. Zircon O- and Hf-isotope constraints on the genesis and tectonic significance of Permian magmatism in Patagonia

description: Summary of SHRIMP U–Pb results for zircon from sample CAT50–1905
DOI: 10.6084/m9.figshare.4959932.v1
title: SHRIMP U–Pb results. Zircon O- and Hf-isotope constraints on the genesis and tectonic significance of Permian magmatism in Patagonia

description: Summary of SHRIMP U–Pb results for zircon from sample CAT50–1905
DOI: 10.6084/m9.figshare.4959908
title: Quaternary radiolarian biostratigraphy in the subarctic northeastern Pacific (IODP Expedition 341, Site U1417) and synchroneity of bioevents across the North Pacific

description: Raw data of the counts of biostratigraphic taxa
DOI: 10.6084/m9.figshare.4959908.v1
title: Quaternary radiolarian biostratigraphy in the subarctic northeastern Pacific (IODP Expedition 341, Site U1417) and synchroneity of bioevents across the North Pacific

description: Raw data of the counts of biostratigraphic taxa
DOI: 10.6084/m9.figshare.4959869
title: The entire OCC triplestore data dump, made on April 26, 2017

description: This archive contains the dump of the OpenCitation Corpus (OCC, http://opencitations.net) triplestore (Blazegraph, https://www.blazegraph.com/, licensed in GPLv2) containing all the data of the corpus, and created regularly every month.<br><br>After unzipping the archive, Disk ARchive (DAR, http://dar.linux.free.fr/, a multi-platform archive tool for managing huge amount of data) is needed for recreating the whole structure. For extracting the DAR archive, please run the command<br><br>dar -x [archive-name]<br><br>Where "[archive-name"] is the name of the DAR file without final package number and extension. E.g.:<br><br>dar -x 2016-09-23-triplestore<br><br>Please execute "run.sh" for running the triplestore, and use "stop.sh" for stopping it.<br><br>For further questions, comments, and suggestions please don't hesitate to contact Silvio Peroni at essepuntato@opencitations.net.
DOI: 10.6084/m9.figshare.4959872
title: Selected contaminant and non-contaminant organisms - (Item F)

description: Interactive version of Figure 3. in Kirstahler <i>et al.</i> (2018):<br> Contaminant organisms (light grey) were present in higher abundance in DNA extraction controls (green) compared to the endophthalmitis-positive samples (red). The contaminant organisms were detected in similar abundance in the endophthalmitis-negative (yellow) and basal salt solution samples (blue) as in the DNA extraction control samples. Organisms that were detected in higher abundance in patient samples (dark grey), compared to their respective DNA extraction control samples, were not regarded as sample contaminants. Read counts are presented as counts per million in relation to the total non-human read counts per sample, respectively. The interactive version of this figure has incorporated individual sample information, including read counts. For a detailed list of contaminant organisms, see Supplementary Table S5.<br><br><b>Reference</b> <b>Kirstahler P, Bjerrum SS, Friis-Møller A, </b><b>la Cour M, Aarestrup FM, Westh H., and Pamp SJ. (2018) </b>Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid.<b> </b><b>Scientific Reports</b>, doi:10.1038/s41598-018-22416-4.