cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3951861
title: Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å

description: These are the molecular dynamics (MD) data that are analyzed, in Flores et al. 2020. Each trajectory file (.dcd) has an associated structure file (.psf), which can be analyzed in VMD. Each gap junction system, Cx46 & Cx50, were simulated with either KCl or NaCl in the intracellular space: Cx46_KCl/NaCl, Cx50_KCl/NaCl. All four systems were equilibrated for 30ns and then followed up with 2 separate 100ns production runs. For MD lipid-densities the Cx50_KCl system was used as the representative dataset. Lipid densities from all other systems can be calculated with the provided TCL script <em>calc-density.tcl</em>. <strong>In VMD TK-Console:</strong> &gt; mol new &lt;system&gt;.psf<br> &gt; mol addfile &lt;system&gt;.dcd waitfor all<br> &gt; source /path/to/scripts/LipNetwork.tcl<br> &gt; align<br> &gt; source /path/to/scripts/calc-density.tcl<br> &gt; dmpcdensity &lt;outname&gt;<br> [output] outname_ltailden.dx<br> <br> Convert from .dx to .mrc using <em>UCSF-Chimera Volume_Viewer</em> plugin.<br> [output] outname_ltailden.mrc<br> <br> <strong>Using Relion:</strong><br> <br> $ relion_image_handler --i outname_ltailden.mrc --o outname_ltailden_D6-Sym.mrc --sym D6<br> [output] outname_ltailden_D6-Sym.mrc All trajectory files (.dcd) are 100ns longs (1,000 frames x 100ps/frame). For questions regarding MD-data analysis and full trajectory files (2ps/frame), please contact Dr. Steve Reichow (reichow@pdx.edu).
DOI: 10.6084/m9.figshare.6832886
title: Production of Nanometric Bi4Ti3O 12 Powders: from Synthesis to Optical and Dielectric Properties

description: This paper aims to evaluate the synthesis and annealing parameters for production of nanometric Bi4Ti3O12 and its properties. The powders were obtained through the solution combustion route and the impacts of annealing temperature on the materials’ physicochemical features as well as their optical and electrical properties were investigated. Thus, the prepared powders were annealed at 600ºC, 700ºC and 800ºC and then characterized by several techniques. The results demonstrated that the combustion method was effective for production of nanocrystalline powders with high levels of purity. A trend for particle and crystallite growth was observed as the calcination temperature increased. X-Ray, HRTEM and Raman spectroscopy confirmed the crystalline nature of the powders, whereas impedance spectroscopy demonstrated a reduction of electrical resistance according to the calcination temperature applied. Optical properties were not highly influenced by annealing. The temperature of 600ºC was appropriate to produce crystalline particles with desirable low sizes for application.
DOI: 10.6084/m9.figshare.6832886.v1
title: Production of Nanometric Bi4Ti3O 12 Powders: from Synthesis to Optical and Dielectric Properties

description: This paper aims to evaluate the synthesis and annealing parameters for production of nanometric Bi4Ti3O12 and its properties. The powders were obtained through the solution combustion route and the impacts of annealing temperature on the materials’ physicochemical features as well as their optical and electrical properties were investigated. Thus, the prepared powders were annealed at 600ºC, 700ºC and 800ºC and then characterized by several techniques. The results demonstrated that the combustion method was effective for production of nanocrystalline powders with high levels of purity. A trend for particle and crystallite growth was observed as the calcination temperature increased. X-Ray, HRTEM and Raman spectroscopy confirmed the crystalline nature of the powders, whereas impedance spectroscopy demonstrated a reduction of electrical resistance according to the calcination temperature applied. Optical properties were not highly influenced by annealing. The temperature of 600ºC was appropriate to produce crystalline particles with desirable low sizes for application.
DOI: 10.6084/m9.figshare.6832883
title: Eastern extension of the geographic range of Mico emiliae

description: ABSTRACT The distribution of the callitrichids inhabiting the Tapajós-Xingu interfluvium is still poorly understood, probably because of the limited number of studies in this remote region. Mico emiliae is a callitrichid endemic to Brazil, occurring between the Jamanxim and Teles Pires rivers, and Serra do Cachimbo in the west and Iriri River in the east, in the states of Pará and Mato Grosso. However, its current distribution is still uncertain. After ca. 430-km surveys in Serra do Pardo National Park, we successfully confirmed the occurrence of this species for the first time approximately 180 km east of its previously known eastern limit in Pará. Our records expand the distribution of M. emiliae to the left bank of the Xingu River, increasing the known extent of its occurrence by 83%.
DOI: 10.6084/m9.figshare.6832880
title: Description of amino acid and fatty acid content during initial development of Lophiosilurus alexandri (Siluriformes: Pseudopimelodidae), a carnivorous freshwater catfish

description: ABSTRACT Samples of eggs, newly hatched larvae (NHL), and larvae at the end of the lecithotrophic period (eight days after hatching) (LPL) of Lophiosilurus alexandri were collected to determine the amino acid and fatty acid profiles. Crude protein did not change throughout initial development and the concentration of lipids was highest in NHL. The content of the indispensable amino acids (IAA) isoleucine, leucine, and valine decreased in LPL, while in eggs and NHL they remained high and similar in value. The dispensable amino acids (DAA), such as aspartic acid, tyrosine, and glycine, increased in LPL, while alanine decreased. The percentage of neutral lipids increased in LPL. The saturated fatty acid content decreased during ontogeny, while monounsaturated fatty acids decreased only in LPL. The polyunsaturated fatty acid content was highest in LP. Polar fatty acids were found in higher percentages in eggs and NHL, but lower in LPL. Saturated fatty acid content decreased during ontogenetic development, while that of monounsaturated fatty acids decreased only in LPL. Polyunsaturated fatty acid content was highest in LPL. Protein content was maintained during ontogenetic development, while amino acid classes experienced changes. Lophiosilurus alexandri preferentially uses saturated and monosaturated fatty acids as an energy source during its early development.
DOI: 10.6084/m9.figshare.6832883.v1
title: Eastern extension of the geographic range of Mico emiliae

description: ABSTRACT The distribution of the callitrichids inhabiting the Tapajós-Xingu interfluvium is still poorly understood, probably because of the limited number of studies in this remote region. Mico emiliae is a callitrichid endemic to Brazil, occurring between the Jamanxim and Teles Pires rivers, and Serra do Cachimbo in the west and Iriri River in the east, in the states of Pará and Mato Grosso. However, its current distribution is still uncertain. After ca. 430-km surveys in Serra do Pardo National Park, we successfully confirmed the occurrence of this species for the first time approximately 180 km east of its previously known eastern limit in Pará. Our records expand the distribution of M. emiliae to the left bank of the Xingu River, increasing the known extent of its occurrence by 83%.
DOI: 10.5281/zenodo.3951860
title: Connexin-46/50 in a dynamic lipid environment resolved by CryoEM at 1.9 Å

description: These are the molecular dynamics (MD) data that are analyzed, in Flores et al. 2020. Each trajectory file (.dcd) has an associated structure file (.psf), which can be analyzed in VMD. Each gap junction system, Cx46 & Cx50, were simulated with either KCl or NaCl in the intracellular space: Cx46_KCl/NaCl, Cx50_KCl/NaCl. All four systems were equilibrated for 30ns and then followed up with 2 separate 100ns production runs. For MD lipid-densities the Cx50_KCl system was used as the representative dataset. Lipid densities from all other systems can be calculated with the provided TCL script <em>calc-density.tcl</em>. <strong>In VMD TK-Console:</strong> &gt; mol new &lt;system&gt;.psf<br> &gt; mol addfile &lt;system&gt;.dcd waitfor all<br> &gt; source /path/to/scripts/LipNetwork.tcl<br> &gt; align<br> &gt; source /path/to/scripts/calc-density.tcl<br> &gt; dmpcdensity &lt;outname&gt;<br> [output] outname_ltailden.dx<br> <br> Convert from .dx to .mrc using <em>UCSF-Chimera Volume_Viewer</em> plugin.<br> [output] outname_ltailden.mrc<br> <br> <strong>Using Relion:</strong><br> <br> $ relion_image_handler --i outname_ltailden.mrc --o outname_ltailden_D6-Sym.mrc --sym D6<br> [output] outname_ltailden_D6-Sym.mrc All trajectory files (.dcd) are 100ns longs (1,000 frames x 100ps/frame). For questions regarding MD-data analysis and full trajectory files (2ps/frame), please contact Dr. Steve Reichow (reichow@pdx.edu).
DOI: 10.6084/m9.figshare.6832880.v1
title: Description of amino acid and fatty acid content during initial development of Lophiosilurus alexandri (Siluriformes: Pseudopimelodidae), a carnivorous freshwater catfish

description: ABSTRACT Samples of eggs, newly hatched larvae (NHL), and larvae at the end of the lecithotrophic period (eight days after hatching) (LPL) of Lophiosilurus alexandri were collected to determine the amino acid and fatty acid profiles. Crude protein did not change throughout initial development and the concentration of lipids was highest in NHL. The content of the indispensable amino acids (IAA) isoleucine, leucine, and valine decreased in LPL, while in eggs and NHL they remained high and similar in value. The dispensable amino acids (DAA), such as aspartic acid, tyrosine, and glycine, increased in LPL, while alanine decreased. The percentage of neutral lipids increased in LPL. The saturated fatty acid content decreased during ontogeny, while monounsaturated fatty acids decreased only in LPL. The polyunsaturated fatty acid content was highest in LP. Polar fatty acids were found in higher percentages in eggs and NHL, but lower in LPL. Saturated fatty acid content decreased during ontogenetic development, while that of monounsaturated fatty acids decreased only in LPL. Polyunsaturated fatty acid content was highest in LPL. Protein content was maintained during ontogenetic development, while amino acid classes experienced changes. Lophiosilurus alexandri preferentially uses saturated and monosaturated fatty acids as an energy source during its early development.
DOI: 10.6084/m9.figshare.6832862
title: Prognostic Impact of Iron Metabolism Changes in Patients with Acute Coronary Syndrome

description: Abstract Background: Iron metabolism disorders have been associated with an increased risk of cardiovascular events. However, the prognostic impact on patients (pts) with acute coronary syndrome (ACS) has yet to be clarified. Objective: To determine the prognostic value of serum iron and ferritin levels in pts with ACS in the short and long-term. Methods: Consecutive pts admitted to a coronary care unit with a diagnosis of ACS, for a period of 2 years, were evaluated. The population was divided into tertiles of serum iron and ferritin distribution. The primary adverse events were the occurrence of in-hospital death or heart failure (HF) and death or HF at 1 year of follow-up. Results: We studied 280 pts (73% males; mean age 68 ± 13 years). The mean levels of serum iron and ferritin were 59 ± 34 mcg/dL and 205 ± 185 ng/mL, respectively. Patients included in the 1st tertile of serum iron (≤ 40 mcg/dL) had a higher rate of adverse events, in-hospital and after 1 year. Lower and higher levels of ferritin (1st and 3rd tertiles, ≤ 110; &gt;219 ng/ml, respectively) were associated with a higher incidence of HF during hospitalization and death at 1 year. A ferritin value &gt;316 ng /mL was an independent risk factor for death at 1 year (adjusted OR: 14; 95%CI: 2.6 to 75.9). Conclusion: In this population, iron metabolism alterations were associated with a higher rate of adverse events and higher ferritin levels constituted an independent mortality predictor in the long-term.
DOI: 10.6084/m9.figshare.6832859
title: Persistent Inflammatory Activity in Blood Cells and Artery Tissue from Patients with Previous Bare Metal Stent

description: Abstract Background: Studies have pointed out a higher mortality after coronary artery bypass surgery (CABG) in patients with stent. Objective: To evaluate inflammatory markers in peripheral blood cells and in coronary artery tissue samples obtained during CABG in patients with stent compared to controls. Methods: The case series consisted of two groups, one with previous stent implantation (n = 41) and one control (n = 26). The expression of the LIGHT, IL-6, ICAM, VCAM, CD40, NFKB, TNF, IFNG genes was analyzed in peripheral blood cells collected preoperatively. The coronary artery was evaluated for: interleukin-6, ICAM, VCAM, CD40, NFKB, TNF-alpha and IFN-gamma by immunohistochemistry. A total of 176 tissue samples were grouped for analysis in: A1- arteries with stent (n = 38); A2- native arteries from patients with stent in another artery (n = 68); and A3- arteries without stent from controls undergoing routinely CABG surgery (n = 70). A significance level of 0.05 was adopted. Results: Patients with stent showed higher TNF (p = 0.03) and lower CD40 gene expression (p = 0.01) in peripheral blood cells than controls without stent. In coronary artery samples, the TNF-alpha protein staining was higher in the group A1, not only in the intima-media layer (5.16 ± 5.05 vs 1.90 ± 2.27; p = 0.02), but also in the adipose tissue (6.69 ± 3.87 vs 2.27 ± 4.00; p &lt; 0.001). Furthermore, group A1 had a higher interleukin-6 protein staining in adipose tissue than group A3 (p = 0.04). Conclusion: We observed a persistently higher systemic TNF expression associated with exacerbated TNF-alpha and interleukin-6 local production in patients with stents. This finding may contribute to a worse clinical outcome.
DOI: 10.6084/m9.figshare.6832862.v1
title: Prognostic Impact of Iron Metabolism Changes in Patients with Acute Coronary Syndrome

description: Abstract Background: Iron metabolism disorders have been associated with an increased risk of cardiovascular events. However, the prognostic impact on patients (pts) with acute coronary syndrome (ACS) has yet to be clarified. Objective: To determine the prognostic value of serum iron and ferritin levels in pts with ACS in the short and long-term. Methods: Consecutive pts admitted to a coronary care unit with a diagnosis of ACS, for a period of 2 years, were evaluated. The population was divided into tertiles of serum iron and ferritin distribution. The primary adverse events were the occurrence of in-hospital death or heart failure (HF) and death or HF at 1 year of follow-up. Results: We studied 280 pts (73% males; mean age 68 ± 13 years). The mean levels of serum iron and ferritin were 59 ± 34 mcg/dL and 205 ± 185 ng/mL, respectively. Patients included in the 1st tertile of serum iron (≤ 40 mcg/dL) had a higher rate of adverse events, in-hospital and after 1 year. Lower and higher levels of ferritin (1st and 3rd tertiles, ≤ 110; &gt;219 ng/ml, respectively) were associated with a higher incidence of HF during hospitalization and death at 1 year. A ferritin value &gt;316 ng /mL was an independent risk factor for death at 1 year (adjusted OR: 14; 95%CI: 2.6 to 75.9). Conclusion: In this population, iron metabolism alterations were associated with a higher rate of adverse events and higher ferritin levels constituted an independent mortality predictor in the long-term.
DOI: 10.6084/m9.figshare.6832859.v1
title: Persistent Inflammatory Activity in Blood Cells and Artery Tissue from Patients with Previous Bare Metal Stent

description: Abstract Background: Studies have pointed out a higher mortality after coronary artery bypass surgery (CABG) in patients with stent. Objective: To evaluate inflammatory markers in peripheral blood cells and in coronary artery tissue samples obtained during CABG in patients with stent compared to controls. Methods: The case series consisted of two groups, one with previous stent implantation (n = 41) and one control (n = 26). The expression of the LIGHT, IL-6, ICAM, VCAM, CD40, NFKB, TNF, IFNG genes was analyzed in peripheral blood cells collected preoperatively. The coronary artery was evaluated for: interleukin-6, ICAM, VCAM, CD40, NFKB, TNF-alpha and IFN-gamma by immunohistochemistry. A total of 176 tissue samples were grouped for analysis in: A1- arteries with stent (n = 38); A2- native arteries from patients with stent in another artery (n = 68); and A3- arteries without stent from controls undergoing routinely CABG surgery (n = 70). A significance level of 0.05 was adopted. Results: Patients with stent showed higher TNF (p = 0.03) and lower CD40 gene expression (p = 0.01) in peripheral blood cells than controls without stent. In coronary artery samples, the TNF-alpha protein staining was higher in the group A1, not only in the intima-media layer (5.16 ± 5.05 vs 1.90 ± 2.27; p = 0.02), but also in the adipose tissue (6.69 ± 3.87 vs 2.27 ± 4.00; p &lt; 0.001). Furthermore, group A1 had a higher interleukin-6 protein staining in adipose tissue than group A3 (p = 0.04). Conclusion: We observed a persistently higher systemic TNF expression associated with exacerbated TNF-alpha and interleukin-6 local production in patients with stents. This finding may contribute to a worse clinical outcome.
DOI: 10.6084/m9.figshare.6832847
title: Mass Spectrometry Study of Ammonia Formed During Plasma Nitrocarburizing and Nitriding Processes

description: In this work, we used mass spectrometry to investigate ammonia (NH3) formed during the nitrocarburizing and nitriding processes of α-Fe sintered and low alloy steel by using d.c. glow discharges in different N2/H2/CH4 gas concentration mixtures. Experiments were conducted using two different configurations: one to collect and analyze species probed primarily in the bulk of the plasma, at a position distant from the heated sample; and the other to collect and analyze species very close to the reactive surface of the heated sample in such a way as to allow the analysis of lower concentration or residence time species, formed at the plasma/sample surface interface. Use of these configurations contributed to the investigation of the physical chemistry involved in the above plasma processes. An exchange the expected stoichiometry in ammonia formation in N2/H2/CH4 mixtures, with a shift towards higher nitrogen consumption, is observed and is interpreted an indication of nitrogen removal from the surface associated with ammonia and carbonitrides/nitrides formation. The present results point to the existence of a correlation between the nitrocarburizing and nitriding processes with respect to the formation of non-stoichiometric ammonia as a product.
DOI: 10.6084/m9.figshare.6832835
title: De novo transcriptome assembly of the lobster cockroach Nauphoeta cinerea (Blaberidae)

description: Abstract The use of Drosophila as a scientific model is well established, but the use of cockroaches as experimental organisms has been increasing, mainly in toxicology research. Nauphoeta cinerea is one of the species that has been studied, and among its advantages is its easy laboratory maintenance. However, a limited amount of genetic data about N. cinerea is available, impeding gene identification and expression analyses, genetic manipulation, and a deeper understanding of its functional biology. Here we describe the N. cinerea fat body and head transcriptome, in order to provide a database of genetic sequences to better understand the metabolic role of these tissues, and describe detoxification and stress response genes. After removing low-quality sequences, we obtained 62,121 transcripts, of which more than 50% had a length of 604 pb. The assembled sequences were annotated according to their genes ontology (GO). We identified 367 genes related to stress and detoxification; among these, the more frequent were p450 genes. The results presented here are the first large-scale sequencing of N. cinerea and will facilitate the genetic understanding of the species' biochemistry processes in future works.
DOI: 10.6084/m9.figshare.6832835.v1
title: De novo transcriptome assembly of the lobster cockroach Nauphoeta cinerea (Blaberidae)

description: Abstract The use of Drosophila as a scientific model is well established, but the use of cockroaches as experimental organisms has been increasing, mainly in toxicology research. Nauphoeta cinerea is one of the species that has been studied, and among its advantages is its easy laboratory maintenance. However, a limited amount of genetic data about N. cinerea is available, impeding gene identification and expression analyses, genetic manipulation, and a deeper understanding of its functional biology. Here we describe the N. cinerea fat body and head transcriptome, in order to provide a database of genetic sequences to better understand the metabolic role of these tissues, and describe detoxification and stress response genes. After removing low-quality sequences, we obtained 62,121 transcripts, of which more than 50% had a length of 604 pb. The assembled sequences were annotated according to their genes ontology (GO). We identified 367 genes related to stress and detoxification; among these, the more frequent were p450 genes. The results presented here are the first large-scale sequencing of N. cinerea and will facilitate the genetic understanding of the species' biochemistry processes in future works.
DOI: 10.6084/m9.figshare.6832847.v1
title: Mass Spectrometry Study of Ammonia Formed During Plasma Nitrocarburizing and Nitriding Processes

description: In this work, we used mass spectrometry to investigate ammonia (NH3) formed during the nitrocarburizing and nitriding processes of α-Fe sintered and low alloy steel by using d.c. glow discharges in different N2/H2/CH4 gas concentration mixtures. Experiments were conducted using two different configurations: one to collect and analyze species probed primarily in the bulk of the plasma, at a position distant from the heated sample; and the other to collect and analyze species very close to the reactive surface of the heated sample in such a way as to allow the analysis of lower concentration or residence time species, formed at the plasma/sample surface interface. Use of these configurations contributed to the investigation of the physical chemistry involved in the above plasma processes. An exchange the expected stoichiometry in ammonia formation in N2/H2/CH4 mixtures, with a shift towards higher nitrogen consumption, is observed and is interpreted an indication of nitrogen removal from the surface associated with ammonia and carbonitrides/nitrides formation. The present results point to the existence of a correlation between the nitrocarburizing and nitriding processes with respect to the formation of non-stoichiometric ammonia as a product.