cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4543435.v3
title: A public data set of running biomechanics and the effects of running speed on lower extremity kinematics and kinetics

description: The data set comprises raw and processed lower extremity gait kinematics and kinetics signals of 28 subjects in different file formats (c3d and txt). A file of metadata (in txt and xls formats), including demographics, running characteristics, foot-strike patterns, and muscle strength and flexibility measurements is provided. In addition, a model file (mdh) and a pipeline file (v3s) for the Visual 3D software program are also provided.The data were collected using a three-dimensional (3D) motion-capture system and an instrumented treadmill while the subjects ran at 2.5 m/s, 3.5 m/s, and 4.5 m/s wearing standard neutral shoes.<br>
DOI: 10.6084/m9.figshare.4543303.v1
title: Theoretical study of Si<sup>+</sup>(<sup>2</sup><i>P<sub>J</sub></i>)–RG complexes and transport of Si<sup>+</sup>(<sup>2</sup><i>P<sub>J</sub></i>) in RG (RG = He–Ar)

description: We calculate accurate interatomic potentials for the interaction of a singly charged silicon cation with a rare gas atom of helium, neon or argon. We employ the RCCSD(T) method, and basis sets of quadruple-ζ and quintuple-ζ quality; each point is counterpoise-corrected and extrapolated to the basis set limit. We consider the lowest electronic state of the silicon atomic cation, Si<sup>+</sup>(<sup>2</sup><i>P</i>), and calculate the interatomic potentials for the terms that arise from this: <sup>2</sup>Π and <sup>2</sup>Σ<sup>+</sup>. We additionally calculate the interatomic potentials for the respective spin-orbit levels, and examine the effect on the spectroscopic parameters; we also derive effective ionic radii for C<sup>+</sup> and Si<sup>+</sup>. Finally, we employ each set of potentials to calculate transport coefficients, and compare these to available data for Si<sup>+</sup> in He.
DOI: 10.6084/m9.figshare.4543240
title: Overexpression of TIFY genes promotes plant growth in rice through jasmonate signaling

description: Because environmental stress can reduce crop growth and yield, the identification of genes that enhance agronomic traits is increasingly important. Previous screening of full-length cDNA overexpressing (FOX) rice lines revealed that OsTIFY11b, one of 20 TIFY proteins in rice, affects plant size, grain weight, and grain size. Therefore, we analyzed the effect of <i>OsTIFY11b</i> and nine other TIFY genes on the growth and yield of corresponding TIFY-FOX lines. Regardless of temperature, grain weight and culm length were enhanced in lines overexpressing TIFY11 subfamily genes, except <i>OsTIFY11e.</i> The TIFY-FOX plants exhibited increased floret number and reduced days to flowering, as well as reduced spikelet fertility, and <i>OsTIFY10b</i>, in particular, enhanced grain yield by minimizing decreases in fertility. We suggest that the enhanced growth of TIFY-transgenic rice is related to regulation of the jasmonate signaling pathway, as in <i>Arabidopsis.</i> Moreover, we discuss the potential application of TIFY overexpression for improving crop yield.
DOI: 10.6084/m9.figshare.4543246
title: Supplementary Materials bioRxiv 097261

description: Supplementary Materials preprint <b>Esteve-Altava B</b>. 2017. <i>Challenges in identifying and interpreting organizational modules in morphology</i>. bioRxiv 097261; doi: https://doi.org/10.1101/097261
DOI: 10.6084/m9.figshare.4543243
title: Natural selection accounts for differences in dizygotic twinning rates at the worldwide scale

description: 22pop_random0.1sorted_neutral.map - plink map file for Bayenv; reference dataset<br>22pop_random0.1sorted_neutral.ped - plink ped file for Bayenv; reference dataset<br>22pop_random0.1sorted_neutral_bayenv - Input file for Bayenv; reference dataset<br>22pop_continental_maf0.005_83genes.map - plink map file for Bayenv; candidate dataset<br>22pop_continental_maf0.005_83genes.ped - plink ped file for Bayenv; candidate dataset<br>22pop_continental_maf0.005_83genes_bayenv - Input file for Bayenv; candidate datasetrandom0.1sorted_neutral.map - plink map file for BayeScan; reference dataset<br>random0.1sorted_neutral.ped - plink ped file for BayeScan; reference dataset<br>random0.1sorted_neutral_bayescan - Input file for Bayescan; reference dataset continental_maf0.005_83genes.map - plink map file for BayeScan; candidate dataset<br>continental_maf0.005_83genes.ped - plink ped file for BayeScan; candidate dataset<br>continental_maf0.005_83genes_bayescan - Input file for Bayescan; candidate dataset <br>twins_rate_22pop_Oct2016 - Values of the environmental variable (twins rate) used as input for Bayenv<br>
DOI: 10.6084/m9.figshare.4543255.v1
title: Nmin_Data.csv

description: This file contains data on inorganic nitrogen availability, soil moisture, soil organic matter, and soil pH across sites. Data were collected in summer 2014.
DOI: 10.6084/m9.figshare.4543243.v1
title: Natural selection accounts for differences in dizygotic twinning rates at the worldwide scale

description: 22pop_random0.1sorted_neutral.map - plink map file for Bayenv; reference dataset<br>22pop_random0.1sorted_neutral.ped - plink ped file for Bayenv; reference dataset<br>22pop_random0.1sorted_neutral_bayenv - Input file for Bayenv; reference dataset<br>22pop_continental_maf0.005_83genes.map - plink map file for Bayenv; candidate dataset<br>22pop_continental_maf0.005_83genes.ped - plink ped file for Bayenv; candidate dataset<br>22pop_continental_maf0.005_83genes_bayenv - Input file for Bayenv; candidate datasetrandom0.1sorted_neutral.map - plink map file for BayeScan; reference dataset<br>random0.1sorted_neutral.ped - plink ped file for BayeScan; reference dataset<br>random0.1sorted_neutral_bayescan - Input file for Bayescan; reference dataset continental_maf0.005_83genes.map - plink map file for BayeScan; candidate dataset<br>continental_maf0.005_83genes.ped - plink ped file for BayeScan; candidate dataset<br>continental_maf0.005_83genes_bayescan - Input file for Bayescan; candidate dataset <br>twins_rate_22pop_Oct2016 - Values of the environmental variable (twins rate) used as input for Bayenv<br>
DOI: 10.6084/m9.figshare.4543246.v1
title: Supplementary Materials bioRxiv 097261

description: Supplementary Materials preprint <b>Esteve-Altava B</b>. 2017. <i>Challenges in identifying and interpreting organizational modules in morphology</i>. bioRxiv 097261; doi: https://doi.org/10.1101/097261
DOI: 10.6084/m9.figshare.4543108
title: Supplementary Material for: The P2X7 Receptor Contributes to the Development of the Exacerbated Inflammatory Response Associated with Sepsis

description: <b><i>Background:</i></b> Sepsis is associated with high mortality rates in intensive care units worldwide and represents a systemic inflammatory response to infection. P2X7 is an ionotropic purine receptor with known proinflammatory activity. Here, we investigated the role of the P2X7 receptor in sepsis induced by cecal ligation and puncture (CLP). <b><i>Methods:</i></b> Wild-type (WT) and P2X7KO (P2X7 null) mice were subjected to CLP and their survival was monitored for 7 days. Blood, peritoneal wash and lungs were collected 24 h after CLP and used to measure bacterial load, immune cell infiltration, nitric oxide (NO), cytokine levels, and peritoneal cell death and to assess lung injury. <b><i>Results:</i></b> P2X7KO mice showed significantly increased survival 7 days after CLP (30% compared to 60% in WT animals) accompanied by an overall attenuated inflammatory response, with decreased cell recruitment to the peritoneum, no or limited increases in the levels of NO and proinflammatory cytokines (IL-1β, IL-6, IL-12, IL-17, and IL-4), reduced peritoneal cell apoptosis, and less pronounced lung infiltration and morphological changes. <b><i>Conclusions:</i></b> Our data show the P2X7 receptor is required for the development of the inflammatory response associated with sepsis and support the notion that P2X7 receptor is a valid therapeutic target against inflammatory diseases.
DOI: 10.6084/m9.figshare.4543255.v2
title: Nmin_Data.csv

description: This file contains data on inorganic nitrogen availability, soil moisture, soil organic matter, and soil pH across sites. It also contains data on soil d15N before and after prescribed burns. Data were collected in summer 2014.
DOI: 10.6084/m9.figshare.4543240.v2
title: Overexpression of TIFY genes promotes plant growth in rice through jasmonate signaling

description: Because environmental stress can reduce crop growth and yield, the identification of genes that enhance agronomic traits is increasingly important. Previous screening of full-length cDNA overexpressing (FOX) rice lines revealed that OsTIFY11b, one of 20 TIFY proteins in rice, affects plant size, grain weight, and grain size. Therefore, we analyzed the effect of <i>OsTIFY11b</i> and nine other TIFY genes on the growth and yield of corresponding TIFY-FOX lines. Regardless of temperature, grain weight and culm length were enhanced in lines overexpressing TIFY11 subfamily genes, except <i>OsTIFY11e.</i> The TIFY-FOX plants exhibited increased floret number and reduced days to flowering, as well as reduced spikelet fertility, and <i>OsTIFY10b</i>, in particular, enhanced grain yield by minimizing decreases in fertility. We suggest that the enhanced growth of TIFY-transgenic rice is related to regulation of the jasmonate signaling pathway, as in <i>Arabidopsis.</i> Moreover, we discuss the potential application of TIFY overexpression for improving crop yield.
DOI: 10.6084/m9.figshare.4543093
title: Supplementary Material for: HLA-B Alleles B*15:01 and B*15:02: Opposite Association with Hepatitis C Virus Infection in Chinese Voluntary Blood Donors

description: <b><i>Background:</i></b> Although human leukocyte antigens (HLA) have been shown in association with the outcomes of hepatitis C virus (HCV) infection among different ethnic groups, such studies remain absent in China, where the HCV prevalence is higher than the global average. <b><i>Methods:</i></b> In this study, 426 HCV-infected and 709 uninfected blood donors were analyzed, among whom the HLA alleles were sequenced using a high-resolution genotyping method. <b><i>Results:</i></b> At the 2-digit level, none of the alleles showed a statistical difference between the HCV-infected and uninfected groups. However, at the 4-digit level, the HLA-B alleles B*15:01 and B*15:02 showed an opposite association with HCV infection, i.e. B*15:01 was significantly higher in the HCV-infected group (odds ratio, OR = 1.561, p = 0.010), while B*15:02 was significantly higher in the uninfected group (OR = 0.778, p = 0.016). We also identified a higher frequency of B*13:02 in the HCV-infected group (OR = 1.515, p = 0.009) and a higher frequency of B*07:05 in the uninfected group (OR = 0.299, p = 0.001). <b><i>Conclusions:</i></b> The frequencies of four HLA alleles, B*07:05, B*13:02, B*15:01, and B*15:02, were found to be significantly different between the HCV-infected and uninfected blood donors in China, revealing an inverse relation of B*15:01 and B*15:02 with HCV infection. This finding suggests that the ethnic genetic variations of HLA may greatly affect the host immune responses against HCV.
DOI: 10.6084/m9.figshare.4543108.v1
title: Supplementary Material for: The P2X7 Receptor Contributes to the Development of the Exacerbated Inflammatory Response Associated with Sepsis

description: <b><i>Background:</i></b> Sepsis is associated with high mortality rates in intensive care units worldwide and represents a systemic inflammatory response to infection. P2X7 is an ionotropic purine receptor with known proinflammatory activity. Here, we investigated the role of the P2X7 receptor in sepsis induced by cecal ligation and puncture (CLP). <b><i>Methods:</i></b> Wild-type (WT) and P2X7KO (P2X7 null) mice were subjected to CLP and their survival was monitored for 7 days. Blood, peritoneal wash and lungs were collected 24 h after CLP and used to measure bacterial load, immune cell infiltration, nitric oxide (NO), cytokine levels, and peritoneal cell death and to assess lung injury. <b><i>Results:</i></b> P2X7KO mice showed significantly increased survival 7 days after CLP (30% compared to 60% in WT animals) accompanied by an overall attenuated inflammatory response, with decreased cell recruitment to the peritoneum, no or limited increases in the levels of NO and proinflammatory cytokines (IL-1β, IL-6, IL-12, IL-17, and IL-4), reduced peritoneal cell apoptosis, and less pronounced lung infiltration and morphological changes. <b><i>Conclusions:</i></b> Our data show the P2X7 receptor is required for the development of the inflammatory response associated with sepsis and support the notion that P2X7 receptor is a valid therapeutic target against inflammatory diseases.
DOI: 10.6084/m9.figshare.4543240.v1
title: Overexpression of TIFY genes promotes plant growth in rice through jasmonate signaling

description: Because environmental stress can reduce crop growth and yield, the identification of genes that enhance agronomic traits is increasingly important. Previous screening of full-length cDNA overexpressing (FOX) rice lines revealed that OsTIFY11b, one of 20 TIFY proteins in rice, affects plant size, grain weight, and grain size. Therefore, we analyzed the effect of <i>OsTIFY11b</i> and nine other TIFY genes on the growth and yield of corresponding TIFY-FOX lines. Regardless of temperature, grain weight and culm length were enhanced in lines overexpressing TIFY11 subfamily genes, except <i>OsTIFY11e.</i> The TIFY-FOX plants exhibited increased floret number and reduced days to flowering, as well as reduced spikelet fertility, and <i>OsTIFY10b</i>, in particular, enhanced grain yield by minimizing decreases in fertility. We suggest that the enhanced growth of TIFY-transgenic rice is related to regulation of the jasmonate signaling pathway, as in <i>Arabidopsis.</i> Moreover, we discuss the potential application of TIFY overexpression for improving crop yield.
DOI: 10.6084/m9.figshare.4543045
title: Supplementary Material for: Trepanation or Complete Removal of the Outer Table of the Calvarium for Granulation Induction: The Erbium:YAG Laser as an Alternative to the Rose Head Burr

description: <b><i>Background:</i></b> Large scalp defects devoid of periosteum following tumor excisions are a surgical challenge. In this case, drilling the outer table of the calvarium with a rose head burr is a standard method to induce granulation tissue. <b><i>Objectives:</i></b> We describe<b> </b>an alternative for trepanation or complete removal of the outer table of the calvarium. <b><i>Methods:</i></b> We demonstrate the use of an erbium:yttrium-aluminum-garnet (erbium:YAG) laser for the induction of granulation tissue, compare this technique with the standard procedure and evaluate the benefits and limitations. <b><i>Results:</i></b> The erbium:YAG laser is an excellent method for trepanation or complete removal of the outer table of the calvarium and induction of granulation tissue. <b><i>Conclusion:</i></b> The use of the laser for trepanation of the calvarium gives results comparable to those of the rose head burr for inducing granulation tissue but has its benefits. Therefore, this method should become a standard alternative to the known procedure.
DOI: 10.6084/m9.figshare.4543093.v1
title: Supplementary Material for: HLA-B Alleles B*15:01 and B*15:02: Opposite Association with Hepatitis C Virus Infection in Chinese Voluntary Blood Donors

description: <b><i>Background:</i></b> Although human leukocyte antigens (HLA) have been shown in association with the outcomes of hepatitis C virus (HCV) infection among different ethnic groups, such studies remain absent in China, where the HCV prevalence is higher than the global average. <b><i>Methods:</i></b> In this study, 426 HCV-infected and 709 uninfected blood donors were analyzed, among whom the HLA alleles were sequenced using a high-resolution genotyping method. <b><i>Results:</i></b> At the 2-digit level, none of the alleles showed a statistical difference between the HCV-infected and uninfected groups. However, at the 4-digit level, the HLA-B alleles B*15:01 and B*15:02 showed an opposite association with HCV infection, i.e. B*15:01 was significantly higher in the HCV-infected group (odds ratio, OR = 1.561, p = 0.010), while B*15:02 was significantly higher in the uninfected group (OR = 0.778, p = 0.016). We also identified a higher frequency of B*13:02 in the HCV-infected group (OR = 1.515, p = 0.009) and a higher frequency of B*07:05 in the uninfected group (OR = 0.299, p = 0.001). <b><i>Conclusions:</i></b> The frequencies of four HLA alleles, B*07:05, B*13:02, B*15:01, and B*15:02, were found to be significantly different between the HCV-infected and uninfected blood donors in China, revealing an inverse relation of B*15:01 and B*15:02 with HCV infection. This finding suggests that the ethnic genetic variations of HLA may greatly affect the host immune responses against HCV.
DOI: 10.6084/m9.figshare.4543021
title: Supplementary Material for: Interleukin-17A Promotes Arginase-1 Production and 2,4-Dinitrochlorobenzene-Induced Acute Hyperinflammation in Human Papillomavirus E7 Oncoprotein-Expressing Skin

description: Human papillomaviruses (HPVs) have evoked numerous mechanisms to subvert host innate immunity and establish a local immunosuppressive environment to facilitate persistent virus infection. Topical application of 2,4-dinitrochlorobenzene (DNCB) was speculated to overcome this immunosuppressive environment and was employed in the immunotherapy of HPV-associated lesions. We have previously shown that DNCB treatment of skin expressing HPV16.E7 protein, the major oncogenic protein expressed in HPV-associated premalignant cervical epithelium, results in a hyperinflammatory response, with an associated induction of Th2 cytokines and infiltration of myeloid cells producing arginase-1, which also contributes to the hyperinflammation. However, the molecular mechanisms underlying arginase-1 induction and arginase-mediated hyperinflammation in K14.E7 skin have not been elucidated. Here, we show that HPV16.E7 protein expression as a transgene in skin is associated with enhanced IL-17A production by macrophages exposed to DNCB. Interestingly, induction of arginase-1 by DNCB is not seen in K14.E7 animals unable to express IL-17A. Further, blockade of either IL-17A or arginase activity alleviates DNCB-induced hyperinflammation through reduced recruitment of neutrophils, as a consequence of decreased CXCL1 and CXCL5 chemokine production. Thus, our findings suggest that increased IL-17A expression by macrophages in E7-expressing skin exposed to DNCB promotes arginase-1 induction and contributes directly to the observed hyperinflammation.
DOI: 10.6084/m9.figshare.4543045.v1
title: Supplementary Material for: Trepanation or Complete Removal of the Outer Table of the Calvarium for Granulation Induction: The Erbium:YAG Laser as an Alternative to the Rose Head Burr

description: <b><i>Background:</i></b> Large scalp defects devoid of periosteum following tumor excisions are a surgical challenge. In this case, drilling the outer table of the calvarium with a rose head burr is a standard method to induce granulation tissue. <b><i>Objectives:</i></b> We describe<b> </b>an alternative for trepanation or complete removal of the outer table of the calvarium. <b><i>Methods:</i></b> We demonstrate the use of an erbium:yttrium-aluminum-garnet (erbium:YAG) laser for the induction of granulation tissue, compare this technique with the standard procedure and evaluate the benefits and limitations. <b><i>Results:</i></b> The erbium:YAG laser is an excellent method for trepanation or complete removal of the outer table of the calvarium and induction of granulation tissue. <b><i>Conclusion:</i></b> The use of the laser for trepanation of the calvarium gives results comparable to those of the rose head burr for inducing granulation tissue but has its benefits. Therefore, this method should become a standard alternative to the known procedure.
DOI: 10.6084/m9.figshare.4542988
title: Supplementary Material for: Effects of Food-Derived Collagen Peptides on the Expression of Keratin and Keratin-Associated Protein Genes in the Mouse Skin

description: Oral ingestion of collagen peptides (CP) has long been suggested to exert beneficial effects on the skin, but the molecular events induced by CP on the skin remain unclear. Here, we investigated the effects of oral CP administration on gene expression in hairless mouse skin and of prolyl-hydroxyproline (Pro-Hyp), a collagen-derived dipeptide, on gene expression in a coculture of mouse skin keratinocytes and fibroblasts. Using microarray analysis, we found that oral administration of CP to hairless mice for 6 weeks induced increased expression of Krtap and Krt genes in the skin. Annotation analysis using DAVID revealed that a group of the up-regulated genes, Gprc5d, Sprr2a1, Krt27 and Krtap16-7, is associated with the development of the epidermis and the hair cycle. In addition, the presence of Pro-Hyp (200 μM) induced an increase in the expression of Krtap16-7, Krtap15, Krtap14 and Krtap8-2 in keratinocytes in coculture, partially resembling the in vivo result. The Pro-Hyp-induced up-regulation of these genes was not observed when keratinocytes were cultured without fibroblasts, suggesting that the presence of fibroblasts is essential for the effects of Pro-Hyp. Our study presents new insights into the effects of CP on the skin, which might link to the hair cycle.
DOI: 10.6084/m9.figshare.4542985
title: Supplementary Material for: Generating Conditionally Immortalised Podocyte Cell Lines from Wild-Type Mice

description: <b><i>Background:</i></b> Understanding podocyte biology is key to deciphering the pathogenesis of numerous glomerular diseases. However, cultivation of primary podocytes results in de-differentiation with loss of specialised architecture. Human conditionally immortalised podocytes partly overcome this problem, utilising a temperature-sensitive transgene. Conditionally immortalised murine podocytes exist, but are derived from the Immortomouse. <b><i>Methods:</i></b> Using retroviral temperature-sensitive SV40 transfection, we created a conditionally immortalised podocyte cell line from wild-type mice. <b><i>Results:</i></b> These cells develop characteristic mature podocyte morphology and robustly express slit diaphragm proteins. Functionally, these cells demonstrate comparable responses in motility and glucose uptake to human conditionally immortalised podocytes. <b><i>Conclusion:</i></b> Podocyte-specific transgenic mice are extensively used to study glomerular disease and this technique could be used to make podocyte cell lines from any mouse, allowing study at the cellular level. This will help characterise these disease models and add to the laboratory resources used to study podocytopathies and glomerular disease.
DOI: 10.6084/m9.figshare.4542961
title: Jupyter Notebook: Dipteran ortholog search for selected Anopheles stephensi proteins

description: Dipteran ortholog search for selected Anopheles stephensi proteins using orthoDB.