cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3510347
title: Effects of subchronic exposure of silver nanoparticles on intestinal microbiota and gut-associated immune responses in the ileum of Sprague-Dawley rats

description: Silver nanoparticles (AgNP) are widely used for their antibacterial properties. Incorporation of AgNP into food-related products and health supplements represents a potential route for oral exposure to AgNP; however, the effects of such exposure on the gastrointestinal system are mostly unknown. This study evaluated changes in the populations of intestinal-microbiota and intestinal-mucosal gene expression in Sprague-Dawley rats (both male and female) that were gavaged orally with discrete sizes of AgNP (10, 75 and 110 nm) and silver acetate. Doses of AgNP (9, 18 and 36 mg/kg body weight/day) and silver acetate (100, 200 and 400 mg/kg body weight/day) were divided and administered to rats twice daily (∼10 h apart) for 13 weeks. The results indicate that AgNP prompted size- and dose-dependent changes to ileal-mucosal microbial populations, as well as, intestinal gene expression and induced an apparent shift in the gut microbiota toward greater proportions of Gram-negative bacteria. DNA-based analyses revealed that exposure to 10 nm AgNP and low-dose silver acetate caused a decrease in populations of <i>Firmicutes</i> phyla, along with a decrease in the <i>Lactobacillus</i> genus. Analysis of host gene expression demonstrated that smaller sizes and lower doses of AgNP exposure prompted the decreased expression of important immunomodulatory genes, including <i>MUC3, TLR2, TLR4, GPR43</i> and <i>FOXP3</i>. Gender-specific effects to AgNP exposure were more prominent for the gut-associated immune responses. These results indicate that the oral exposure to AgNP alter mucosa-associated microbiota and modulate the gut-associated immune response and the overall homeostasis of the intestinal tract.
DOI: 10.6084/m9.figshare.3510347.v1
title: Effects of subchronic exposure of silver nanoparticles on intestinal microbiota and gut-associated immune responses in the ileum of Sprague-Dawley rats

description: Silver nanoparticles (AgNP) are widely used for their antibacterial properties. Incorporation of AgNP into food-related products and health supplements represents a potential route for oral exposure to AgNP; however, the effects of such exposure on the gastrointestinal system are mostly unknown. This study evaluated changes in the populations of intestinal-microbiota and intestinal-mucosal gene expression in Sprague-Dawley rats (both male and female) that were gavaged orally with discrete sizes of AgNP (10, 75 and 110 nm) and silver acetate. Doses of AgNP (9, 18 and 36 mg/kg body weight/day) and silver acetate (100, 200 and 400 mg/kg body weight/day) were divided and administered to rats twice daily (∼10 h apart) for 13 weeks. The results indicate that AgNP prompted size- and dose-dependent changes to ileal-mucosal microbial populations, as well as, intestinal gene expression and induced an apparent shift in the gut microbiota toward greater proportions of Gram-negative bacteria. DNA-based analyses revealed that exposure to 10 nm AgNP and low-dose silver acetate caused a decrease in populations of <i>Firmicutes</i> phyla, along with a decrease in the <i>Lactobacillus</i> genus. Analysis of host gene expression demonstrated that smaller sizes and lower doses of AgNP exposure prompted the decreased expression of important immunomodulatory genes, including <i>MUC3, TLR2, TLR4, GPR43</i> and <i>FOXP3</i>. Gender-specific effects to AgNP exposure were more prominent for the gut-associated immune responses. These results indicate that the oral exposure to AgNP alter mucosa-associated microbiota and modulate the gut-associated immune response and the overall homeostasis of the intestinal tract.
DOI: 10.6084/m9.figshare.3510345
title: Extracellular HMGB1 regulates multi-walled carbon nanotube-induced inflammation <i>in vivo</i>

description: Endotoxin is often used to activate NF-κB <i>in vitro</i> when assessing NLRP3 inflammasome activation by various exogenous particles including nanoparticles. However, the endogenous source of this signal 1 is unknown. High-mobility group box 1 (HMGB1) is known to play a critical role in acute lung injury, however the potential contribution of the alarmin HMGB1 to NLRP3 Inflammasome activation has not been determined in response to nanoparticles <i>in vivo</i>. In this study, the ability of multi-walled carbon nanotubes (MWCNT) to cause release of HMGB1 <i>in vitro</i> and <i>in vivo</i>, as well as the potential of HMGB1 to function as signal 1 <i>in vitro</i> and <i>in vivo</i>, was determined. HMGB1 activity <i>in vivo</i> was assessed by administration of HMGB1 neutralization antibodies following MWCNT exposure. <i>Caspase-1</i><sup><i>−/−</i></sup> mice were utilized to elucidate the dependence of HMGB1 secretion on NLRP3 inflammasome activity. MWCNT exposure increased extracellular HMGB1 levels in primary alveolar macrophages from C57Bl/6 mice and C10 mouse epithelial cell culture supernatants, and in C57Bl/6 mouse lung lavage fluid. MWCNT-induced HMGB1 secretion was dependent upon caspase-1. HMGB1 increased MWCNT-induced IL-1β release from macrophages <i>in vitro</i>, and neutralization of extracellular HMGB1 reduced MWCNT-induced IL-1β secretion <i>in vivo</i>. HMGB1 neutralization was accompanied with overall decreased inflammation. In summary, this study suggests extracellular HMGB1 participates in NLRP3 inflammasome activity and regulates IL-1β associated sterile inflammation induced by MWCNT.
DOI: 10.6084/m9.figshare.3510345.v1
title: Extracellular HMGB1 regulates multi-walled carbon nanotube-induced inflammation <i>in vivo</i>

description: Endotoxin is often used to activate NF-κB <i>in vitro</i> when assessing NLRP3 inflammasome activation by various exogenous particles including nanoparticles. However, the endogenous source of this signal 1 is unknown. High-mobility group box 1 (HMGB1) is known to play a critical role in acute lung injury, however the potential contribution of the alarmin HMGB1 to NLRP3 Inflammasome activation has not been determined in response to nanoparticles <i>in vivo</i>. In this study, the ability of multi-walled carbon nanotubes (MWCNT) to cause release of HMGB1 <i>in vitro</i> and <i>in vivo</i>, as well as the potential of HMGB1 to function as signal 1 <i>in vitro</i> and <i>in vivo</i>, was determined. HMGB1 activity <i>in vivo</i> was assessed by administration of HMGB1 neutralization antibodies following MWCNT exposure. <i>Caspase-1</i><sup><i>−/−</i></sup> mice were utilized to elucidate the dependence of HMGB1 secretion on NLRP3 inflammasome activity. MWCNT exposure increased extracellular HMGB1 levels in primary alveolar macrophages from C57Bl/6 mice and C10 mouse epithelial cell culture supernatants, and in C57Bl/6 mouse lung lavage fluid. MWCNT-induced HMGB1 secretion was dependent upon caspase-1. HMGB1 increased MWCNT-induced IL-1β release from macrophages <i>in vitro</i>, and neutralization of extracellular HMGB1 reduced MWCNT-induced IL-1β secretion <i>in vivo</i>. HMGB1 neutralization was accompanied with overall decreased inflammation. In summary, this study suggests extracellular HMGB1 participates in NLRP3 inflammasome activity and regulates IL-1β associated sterile inflammation induced by MWCNT.
DOI: 10.6084/m9.figshare.3510342
title: Inhibition of autophagy protects against PAMAM dendrimers-induced hepatotoxicity

description: Toxicity of nanomaterials is one of the biggest challenges in their medicinal applications. Although toxicities of nanomaterials have been widely reported, the exact mechanisms of toxicities are still not well elucidated. Consequently, the exploration of approaches to attenuate toxicities of nanomaterials is limited. In this study, we reported that poly-amidoamine (PAMAM) dendrimers, a widely used nanomaterial in the pharmaceutical industry, caused toxicity of human liver cells by inducing cell growth inhibition, mitochondria damage, and apoptosis. Meanwhile, autophagy was activated in PAMAM dendrimers-induced toxicity and inhibition of autophagy-rescued viability of hepatic cells, indicating that autophagy played a key role in PAMAM dendriemrs-induced hepatotoxicity. To further explore approaches to attenuate PAMAM dendrimers-induced liver injury, effects of autophagic inhibitors on PAMAM dendrimers’ hepatotoxicity were investigated in an <i>in vivo</i> model. Autophagy blockage in PAMAM dendrimers-administered mice led to weight restoration, damage reversion of liver tissue, and protection against changes of serum biochemistry parameters. Moreover, inhibition of Akt/mTOR and activation of Erk1/2 signaling pathways were involved in PAMAM dendrimers-induced autophagy. Collectively, these findings indicated that autophagy was associated with PAMAM dendrimers-induced hepatotoxicity, and supported the possibility that autophagy inhibitors could be used to reduce hepatotoxicity of PAMAM dendrimers.
DOI: 10.6084/m9.figshare.3510342.v1
title: Inhibition of autophagy protects against PAMAM dendrimers-induced hepatotoxicity

description: Toxicity of nanomaterials is one of the biggest challenges in their medicinal applications. Although toxicities of nanomaterials have been widely reported, the exact mechanisms of toxicities are still not well elucidated. Consequently, the exploration of approaches to attenuate toxicities of nanomaterials is limited. In this study, we reported that poly-amidoamine (PAMAM) dendrimers, a widely used nanomaterial in the pharmaceutical industry, caused toxicity of human liver cells by inducing cell growth inhibition, mitochondria damage, and apoptosis. Meanwhile, autophagy was activated in PAMAM dendrimers-induced toxicity and inhibition of autophagy-rescued viability of hepatic cells, indicating that autophagy played a key role in PAMAM dendriemrs-induced hepatotoxicity. To further explore approaches to attenuate PAMAM dendrimers-induced liver injury, effects of autophagic inhibitors on PAMAM dendrimers’ hepatotoxicity were investigated in an <i>in vivo</i> model. Autophagy blockage in PAMAM dendrimers-administered mice led to weight restoration, damage reversion of liver tissue, and protection against changes of serum biochemistry parameters. Moreover, inhibition of Akt/mTOR and activation of Erk1/2 signaling pathways were involved in PAMAM dendrimers-induced autophagy. Collectively, these findings indicated that autophagy was associated with PAMAM dendrimers-induced hepatotoxicity, and supported the possibility that autophagy inhibitors could be used to reduce hepatotoxicity of PAMAM dendrimers.
DOI: 10.6084/m9.figshare.3510318
title: Supplementary Material for: Pain Intensity and Pain Interference in Older Adults: Role of Gender, Obesity and High-Sensitivity C-Reactive Protein

description: <strong><em>Background</em></strong><strong><em>:</em></strong> Among older adults, pain intensity and pain interference are more common in women than men and associated with obesity and inflammatory markers. <b><i>Objective:</i></b> We examined whether the obesity and pain relationship is mediated by the high-sensitivity C-reactive protein (hsCRP), a nonspecific marker of systemic inflammation, and whether this relationship differs by sex. <b><i>Methods:</i></b> Items from Medical Outcomes Study Short Form-36 were used to measure pain intensity and pain interference in daily life. Ordinal logistic regression was used to assess the cross-sectional association among body mass index (BMI), hsCRP levels, pain intensity and pain interference using gender-stratified models adjusted for demographic variables. <b><i>Results:</i></b> Participants included 667 community-residing adults over the age of 70 years, free of dementia, enrolled in the Einstein Aging Study (EAS). In women (n = 410), pain intensity was associated with obesity [BMI ≥30 vs. normal, odds ratio (OR) = 2.29, 95% confidence interval (CI) 1.43-3.68] and higher hsCRP (OR = 1.28, 95% CI 1.08-1.51). In a model with obesity and hsCRP, both remained significant, but the association between hsCRP and pain intensity was somewhat attenuated. Obesity (OR = 3.04, 95% CI 1.81-5.11) and higher hsCRP levels (OR = 1.30, 95% CI 1.08-1.56) were also independently associated with greater pain interference in women. After adjustment for pain intensity and BMI, hsCRP was no longer associated with pain interference in women. Greater pain intensity and being overweight or obese continued to be significantly associated with pain interference in women. In men (n = 257), obesity and hsCRP were not associated with pain intensity or pain interference. <b><i>Conclusions:</i></b> In women, the relationship between obesity and higher levels of pain intensity or interference may be accounted for by factors related to hsCRP.
DOI: 10.6084/m9.figshare.3510318.v1
title: Supplementary Material for: Pain Intensity and Pain Interference in Older Adults: Role of Gender, Obesity and High-Sensitivity C-Reactive Protein

description: <strong><em>Background</em></strong><strong><em>:</em></strong> Among older adults, pain intensity and pain interference are more common in women than men and associated with obesity and inflammatory markers. <b><i>Objective:</i></b> We examined whether the obesity and pain relationship is mediated by the high-sensitivity C-reactive protein (hsCRP), a nonspecific marker of systemic inflammation, and whether this relationship differs by sex. <b><i>Methods:</i></b> Items from Medical Outcomes Study Short Form-36 were used to measure pain intensity and pain interference in daily life. Ordinal logistic regression was used to assess the cross-sectional association among body mass index (BMI), hsCRP levels, pain intensity and pain interference using gender-stratified models adjusted for demographic variables. <b><i>Results:</i></b> Participants included 667 community-residing adults over the age of 70 years, free of dementia, enrolled in the Einstein Aging Study (EAS). In women (n = 410), pain intensity was associated with obesity [BMI ≥30 vs. normal, odds ratio (OR) = 2.29, 95% confidence interval (CI) 1.43-3.68] and higher hsCRP (OR = 1.28, 95% CI 1.08-1.51). In a model with obesity and hsCRP, both remained significant, but the association between hsCRP and pain intensity was somewhat attenuated. Obesity (OR = 3.04, 95% CI 1.81-5.11) and higher hsCRP levels (OR = 1.30, 95% CI 1.08-1.56) were also independently associated with greater pain interference in women. After adjustment for pain intensity and BMI, hsCRP was no longer associated with pain interference in women. Greater pain intensity and being overweight or obese continued to be significantly associated with pain interference in women. In men (n = 257), obesity and hsCRP were not associated with pain intensity or pain interference. <b><i>Conclusions:</i></b> In women, the relationship between obesity and higher levels of pain intensity or interference may be accounted for by factors related to hsCRP.
DOI: 10.6084/m9.figshare.3510288
title: FBAP monsoon measurement data

description: This contains the data of atmospheric bioaerosol number size distribution measured at a high altitude site of Munnar in southern India using UV-APS. The measurements were carried out during the 2014 monsoon season.
DOI: 10.6084/m9.figshare.3510288.v1
title: FBAP monsoon measurement data

description: This contains the data of atmospheric bioaerosol number size distribution measured at a high altitude site of Munnar in southern India using UV-APS. The measurements were carried out during the 2014 monsoon season.
DOI: 10.6084/m9.figshare.3510267
title: Supplementary.xlsx

description: List of pentapeptide sequences which have a Glutathionylation Likelihood Score (G-Score) of equal to or above 1.25, as scored by GluP tool for prediction of glutathionylation sites. These pentapeptides are expected to be hotspots of protein S-glutathionylation and can serve as potential candidates to identify such proteins.<br>
DOI: 10.6084/m9.figshare.3510267.v1
title: Supplementary.xlsx

description: List of pentapeptide sequences which have a Glutathionylation Likelihood Score (G-Score) of equal to or above 1.25, as scored by GluP tool for prediction of glutathionylation sites. These pentapeptides are expected to be hotspots of protein S-glutathionylation and can serve as potential candidates to identify such proteins.<br>
DOI: 10.6084/m9.figshare.3510258
title: 5507_9085_400_magsquarew_1.jpg

description: Founded by industry veterans with 60+ years of experience, Industrial Components Group provides high quality inch and metric size operating and control elements to companies throughout the United States, Canada, Europe and Asia. In addition to providing standard parts for industry such as: hand wheels, crank handles, adjustable clamping levers, ratchet handles, adjustable handles, pull handles, hand knobs, toggle clamps, and leveling devices, ICG prides itself in offering complete in house CAD services to help customers develop non-standard products needed for their special applications. These include, but are not limited to, custom precision stampings, castings, injection molding, screw machine products, secondary machining services and contract assembly and kit operations.
DOI: 10.6084/m9.figshare.3510258.v1
title: 5507_9085_400_magsquarew_1.jpg

description: Founded by industry veterans with 60+ years of experience, Industrial Components Group provides high quality inch and metric size operating and control elements to companies throughout the United States, Canada, Europe and Asia. In addition to providing standard parts for industry such as: hand wheels, crank handles, adjustable clamping levers, ratchet handles, adjustable handles, pull handles, hand knobs, toggle clamps, and leveling devices, ICG prides itself in offering complete in house CAD services to help customers develop non-standard products needed for their special applications. These include, but are not limited to, custom precision stampings, castings, injection molding, screw machine products, secondary machining services and contract assembly and kit operations.
DOI: 10.6084/m9.figshare.3510251
title: Schizophrenia Patients Demonstrate Both Inter-voxel Level and Intra-voxel Level White Matter Alterations

description: The dataset are the TBSS results for this manuscript, which including the inter-group differnces in MD, FA and LDH.
DOI: 10.6084/m9.figshare.3510251.v1
title: Schizophrenia Patients Demonstrate Both Inter-voxel Level and Intra-voxel Level White Matter Alterations

description: The dataset are the TBSS results for this manuscript, which including the inter-group differnces in MD, FA and LDH.
DOI: 10.6084/m9.figshare.3510233
title: Postoperative pain treatment after vascular surgical procedures

description: This study was conducted at the Department of Surgery of the University Hospital Split, Croatia. The following data on 501 patients who underwent vascular surgical procedures during year 2013 were collected from patients’ medical records: age, gender, type and dosage of premedication, preoperative patient's physical status, type of procedure, duration of procedure – surgical and anesthesia time, type and dosage of anesthesia, the type and dosage of postoperative analgesia for each postoperative day, the need for intensive care. Departmental procedures were examined to assess adherence to guidelines for perioperative pain management.
DOI: 10.6084/m9.figshare.3510221
title: Improved lower bounds &gt; 0 for Riemann Zeta function off the critical line using derivatives of Re(Riemann Siegel Z) function.

description: Approximate lower bounds &gt; 0, for abs ( ζ ( s )) off the critical line are generated using the real part of the Riemann Siegel function Re(Z(t)) and its first derivative, further supporting the Riemann Hypothesis. An approximation to abs ( ζ ( s )) off the critical line, is then obtained by the rescaled series sum of the Re(Z(t)) and several higher order derivatives.
DOI: 10.6084/m9.figshare.3510221.v2
title: Improved lower bounds &gt; 0 for Riemann Zeta function off the critical line using derivatives of Re(Riemann Siegel Z) function.

description: Approximate lower bounds &gt; 0, for abs ( ζ ( s )) off the critical line are generated using the real part of the Riemann Siegel function Re(Z(t)) and its first derivative, further supporting the Riemann Hypothesis. An approximation to abs ( ζ ( s )) off the critical line, is then obtained by the rescaled series sum of the Re(Z(t)) and several higher order derivatives.
DOI: 10.6084/m9.figshare.3510221.v3
title: Improved lower bounds &gt; 0 for Riemann Zeta function off the critical line using derivatives of Re(Riemann Siegel Z) function.

description: Approximate lower bounds &gt; 0, for abs ( ζ ( s )) off the critical line are generated using the real part of the Riemann Siegel function Re(Z(t)) and its first derivative, further supporting the Riemann Hypothesis. An approximation to abs ( ζ ( s )) off the critical line, is then obtained by the rescaled series sum of the Re(Z(t)) and several higher order derivatives.
DOI: 10.6084/m9.figshare.3510221.v4
title: Improved lower bounds &gt; 0 for Riemann Zeta function off the critical line using derivatives of Re(Riemann Siegel Z) function.

description: Approximate lower bounds &gt; 0, for abs ( ζ ( s )) off the critical line are generated using the real part of the Riemann Siegel function Re(Z(t)) and its first derivative, further supporting the Riemann Hypothesis. An approximation to abs ( ζ ( s )) off the critical line, is then obtained by the rescaled series sum of the Re(Z(t)) and several higher order derivatives.
DOI: 10.6084/m9.figshare.3510221.v5
title: Improved lower bounds &gt; 0 for Riemann Zeta function off the critical line using derivatives of Re(Riemann Siegel Z) function.

description: Approximate lower bounds &gt; 0, for abs ( ζ ( s )) off the critical line are generated using the real part of the Riemann Siegel function Re(Z(t)) and its first derivative, further supporting the Riemann Hypothesis. An approximation to abs ( ζ ( s )) off the critical line, is then obtained by the rescaled series sum of the Re(Z(t)) and several higher order derivatives.
DOI: 10.6084/m9.figshare.3510203
title: iLIR database: A web resource for LIR motif-containing proteins in eukaryotes

description: Atg8-family proteins are the best-studied proteins of the core autophagic machinery. They are essential for the elongation and closure of the phagophore into a proper autophagosome. Moreover, Atg8-family proteins are associated with the phagophore from the initiation of the autophagic process to, or just prior to, the fusion between autophagosomes with lysosomes. In addition to their implication in autophagosome biogenesis, they are crucial for selective autophagy through their ability to interact with selective autophagy receptor proteins necessary for the specific targeting of substrates for autophagic degradation. In the past few years it has been revealed that Atg8-interacting proteins include not only receptors but also components of the core autophagic machinery, proteins associated with vesicles and their transport, and specific proteins that are selectively degraded by autophagy. Atg8-interacting proteins contain a short linear LC3-interacting region/LC3 recognition sequence/Atg8-interacting motif (LIR/LRS/AIM) motif which is responsible for their interaction with Atg8-family proteins. These proteins are referred to as LIR-containing proteins (LIRCPs). So far, many experimental efforts have been carried out to identify new LIRCPs, leading to the characterization of some of them in the past 10 years. Given the need for the identification of LIRCPs in various organisms, we developed the iLIR database (https://ilir.warwick.ac.uk) as a freely available web resource, listing all the putative canonical LIRCPs identified in silico in the proteomes of 8 model organisms using the iLIR server, combined with a Gene Ontology (GO) term analysis. Additionally, a curated text-mining analysis of the literature permitted us to identify novel putative LICRPs in mammals that have not previously been associated with autophagy.