cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17188/1202852
title: Materials Data on Nb4Te12I by Materials Project

description: Nb4Te12I crystallizes in the monoclinic C2/c space group. The structure is one-dimensional and consists of four Nb4Te12I ribbons oriented in the (0, 1, 0) direction. there are two inequivalent Nb+4.75+ sites. In the first Nb+4.75+ site, Nb+4.75+ is bonded to five Te+1.50- and one I1- atom to form a mixture of corner and edge-sharing NbTe5I pentagonal pyramids. There are a spread of Nb–Te bond distances ranging from 2.65–2.93 Å. The Nb–I bond length is 3.01 Å. In the second Nb+4.75+ site, Nb+4.75+ is bonded to five Te+1.50- and one I1- atom to form a mixture of corner and edge-sharing NbTe5I pentagonal pyramids. There are a spread of Nb–Te bond distances ranging from 2.65–2.95 Å. The Nb–I bond length is 3.00 Å. There are six inequivalent Te+1.50- sites. In the first Te+1.50- site, Te+1.50- is bonded in a single-bond geometry to one Nb+4.75+ atom. In the second Te+1.50- site, Te+1.50- is bonded in a 2-coordinate geometry to two Nb+4.75+ atoms. In the third Te+1.50- site, Te+1.50- is bonded in a single-bond geometry to one Nb+4.75+ atom. In the fourth Te+1.50- site, Te+1.50- is bonded in a 2-coordinate geometry to two Nb+4.75+ atoms. In the fifth Te+1.50- site, Te+1.50- is bonded in a 2-coordinate geometry to two Nb+4.75+ atoms. In the sixth Te+1.50- site, Te+1.50- is bonded in a 2-coordinate geometry to two Nb+4.75+ atoms. I1- is bonded in a 4-coordinate geometry to four Nb+4.75+ atoms.
DOI: 10.14457/cu.the.2015.1095
title: Characteristics, performance, and greenhouse gas evaluation ofjatropha biodiesohol for agricultural machinery

description: Microemulsion is a proposed technique for biofuel production with simple and low-cost preparation called biodiesohol. For this study, diesel based microemulsion with ethanol, surfactant, and Jatropha oil were studied for their phase behavior focusing on homogeneity of the fuel. Various types of surfactant, ethanol-surfactant ratio (E/S ratio) and ethanol-surfactant content (E/S content) had been investigated and the result showed that LS1, E/S ratio at 3 and E/S content at 5 tend to be the most appropriate for Jatropha biodiesohol preparation. The mixture design was effectively applied to predict or estimate kinematic viscosity in the desired range by {3,3} lattice augmented with interior points and centroid. The property results of biodiesohol showed compatible properties with biodiesel standard except for acid number, flash point, and density. The EHN (ethylhexyl nitrate) was added into biodiesohol as additive to increase the efficiency of engine performance. The engine performance testing using Jatropha biodiesohol (E/S:Jatropha oil:Diesel at 5:20:75 namely JBH20 and 5:25:70 namely JBH25), JME (Jatropha methylester), and diesel as fuel show that forming microemulsion can partially improve power, torque, and brake specific fuel consumption compared to diesel. In addition, exhaust gas emission also decreased. The cradle to gate life cycle inventory based on the Wiangsa agricultural cooperative at Nan Province, which existed the system for JME production show that JME emits 329.42 kgCO2e/GJ. JME showed greater GHG emissions than that of JBH25 approximately 2 times. The waste handling was main emissions for JME, while the maximum emission of JBH25 was combustion process.The results of NER (Net energy ratio) showed that neat JME is the most suitable energy efficiency compared to JME25 (Jatropha biodiesel blended with diesel at 25 %v/v) and JBH25. The energy credits from co-products and wastes significantly cause on increase of NER.
DOI: 10.17188/1202853
title: Materials Data on PtS by Materials Project

description: PtS crystallizes in the tetragonal P4_2/mmc space group. The structure is three-dimensional. Pt2+ is bonded in a square co-planar geometry to four equivalent S2- atoms. All Pt–S bond lengths are 2.34 Å. S2- is bonded to four equivalent Pt2+ atoms to form a mixture of edge and corner-sharing SPt4 tetrahedra.
DOI: 10.17188/1202854
title: Materials Data on LuB2Os3 by Materials Project

description: LuOs3B2 crystallizes in the hexagonal P6/mmm space group. The structure is three-dimensional. Lu3+ is bonded to twelve equivalent Os1- atoms to form LuOs12 cuboctahedra that share corners with twelve equivalent LuOs12 cuboctahedra, edges with six equivalent LuOs12 cuboctahedra, edges with twelve equivalent BOs6 pentagonal pyramids, faces with two equivalent LuOs12 cuboctahedra, and faces with six equivalent BOs6 pentagonal pyramids. All Lu–Os bond lengths are 3.15 Å. Os1- is bonded in a distorted square co-planar geometry to four equivalent Lu3+ and four equivalent B atoms. All Os–B bond lengths are 2.20 Å. B is bonded to six equivalent Os1- atoms to form distorted BOs6 pentagonal pyramids that share corners with six equivalent BOs6 pentagonal pyramids, edges with six equivalent LuOs12 cuboctahedra, edges with three equivalent BOs6 pentagonal pyramids, faces with three equivalent LuOs12 cuboctahedra, and faces with two equivalent BOs6 pentagonal pyramids.
DOI: 10.14457/cu.the.2015.1096
title: Conformations and permeation mechanism into lipid bilayer of cyclodextrins

description: Cyclodextrins (CDs) are potent host molecules, which can improve physical and chemical properties of guest compounds through their inclusion complexes. The binding and unbinding between guest ligand and CDs as well as the releasing into cell membrane are key factors that control the CD complex functions. Here, we aim to understand the pre-steps of that CD-ligand formation. Firstly, the conformational diversity of CD6-CD10 and CD14 was studied by the replica exchange molecular dynamics (REMD) simulations. Free CD molecules in solution were performed under the assumption that the CDs structural changes may influence the ligand binding affinity. The large ring CD (LR-CD) systems were tested for the first time with REMD simulations using various carbohydrate force fields. The structural properties and the dynamic behavior of LR-CDs corresponding to temperature changes were newly investigated. Our results indicate that: i) REMD simulation can describe the CDs conformational changes, ii) the glycam06 force field is reliable for describing the flip of glucose subunits, iii) the most probable conformations of CD10 and CD14 are bent-shape like their crystals, however, CD14 is slightly opened in comparison to the X-ray structure, iv) additionally, the various conformations of CDs could be also observed at high temperatures due to their high ring flexibility. Secondly, the pre-step of ligand transportation based on CD inclusion complexes into the membrane was studied. The micro-scale molecular dynamics (MD) simulations were used to investigated the permeation behavior of single beta-cyclodextrin (βCD) into lipid bilayer. Our results show that βCD passively diffuses into the lipid bilayer by pointing its wider rim toward the lipid polar groups and then remains at the phosphate and glycerol-ester groups with hydrogen bond formation. Moreover, the βCD derivatives (methylated- and hydroxypropyl-βCD) showed a somewhat deeper permeation that might be able to explain why these two derivatives offer a faster release of hydrophobic ligands. Our findings in this study might be helpful for the selection of proper CDs for drug transport as well as for further design of higher potent drug carriers.
DOI: 10.14457/cu.the.2015.1097
title: Effects of guttiferone k, oblongifolin c and isojacareubin on expression of p-glycoprotein in caco-2 cells

description: Two benzophenones, guttiferone K (GK) and oblongifolin C (OC), and a xanthone, isojacaruebin (ISO), were phytochemicals isolated from the wood of Garcinia schomburgkiana (Thai name: Ma-dan). These three compounds exhibited cytotoxic activity against several cancer cell lines. However, the capability of these compounds to increase chemo-resistance in cancer cells was not reported. The objective of this study was to investigate the effects of these compounds on the oxidative stress-mediated up-regulation of MDR1 mRNA in the Caco-2 cells, and the involvement of MAPK pathway. The cells treated with each of these compounds (50 µM) for 24 h had the amount of MDR1 mRNA increased significantly, as measured by qRT-PCR assay. The up-regulation of MDR1 in this study was related to oxidative stress generated from cellular exposure to these compounds. Addition of n-acetyl cysteine (NAC; a ROS scavenger) in the culture was able to abolish the inductive effect of GK, OC and ISO on MDR1 mRNA level. Moreover, MAPK inhibitors including U0126 (an inhibitor of ERK1/2/MAPK activity) and SB202190 (an inhibitor of p-38/MAPK activity) were able to suppress an increase of MDR1 mRNA levels in the cells treated with benzophenones and xanthone, respectively. These findings were in agreement with the increase of phosphorylated form of either ERK1/2 (p-ERK1/2) or p38 (p-p38) upon treatment of the cells with these three compounds. In addition, OC and ISO, but not GK, increased mRNA of c-JUN/AP-1 level. These results suggested that GK, OC and ISO were able to up-regulate MDR1 mRNA in Caco-2 cells via the activation of oxidative stress-mediated mitogen-activated kinase (MAPK) signaling pathway. Further determination of their inductive effect on P-gp protein level might be pursued.
DOI: 10.17188/1202856
title: Materials Data on La5Ti4O15 by Materials Project

description: La5Ti4O15 crystallizes in the trigonal P-3c1 space group. The structure is three-dimensional. there are three inequivalent La3+ sites. In the first La3+ site, La3+ is bonded in a 6-coordinate geometry to six equivalent O2- atoms. There are three shorter (2.51 Å) and three longer (2.55 Å) La–O bond lengths. In the second La3+ site, La3+ is bonded to twelve O2- atoms to form distorted LaO12 cuboctahedra that share corners with nine equivalent LaO12 cuboctahedra, faces with three equivalent LaO12 cuboctahedra, and faces with seven TiO6 octahedra. There are a spread of La–O bond distances ranging from 2.52–3.01 Å. In the third La3+ site, La3+ is bonded to twelve O2- atoms to form LaO12 cuboctahedra that share corners with six equivalent LaO12 cuboctahedra, faces with six equivalent LaO12 cuboctahedra, and faces with eight TiO6 octahedra. There are six shorter (2.74 Å) and six longer (2.78 Å) La–O bond lengths. There are two inequivalent Ti+3.75+ sites. In the first Ti+3.75+ site, Ti+3.75+ is bonded to six O2- atoms to form TiO6 octahedra that share corners with three equivalent TiO6 octahedra and faces with four LaO12 cuboctahedra. The corner-sharing octahedral tilt angles are 14°. There is three shorter (1.90 Å) and three longer (2.06 Å) Ti–O bond length. In the second Ti+3.75+ site, Ti+3.75+ is bonded to six O2- atoms to form TiO6 octahedra that share corners with six TiO6 octahedra and faces with seven LaO12 cuboctahedra. The corner-sharing octahedra tilt angles range from 0–14°. There is three shorter (1.97 Å) and three longer (1.98 Å) Ti–O bond length. There are three inequivalent O2- sites. In the first O2- site, O2- is bonded in a distorted linear geometry to four La3+ and two equivalent Ti+3.75+ atoms. In the second O2- site, O2- is bonded in a 1-coordinate geometry to three La3+ and one Ti+3.75+ atom. In the third O2- site, O2- is bonded in a 2-coordinate geometry to three La3+ and two Ti+3.75+ atoms.
DOI: 10.14457/cu.the.2015.1098
title: Study of cytoprotective effect of glutaraldehyde erythropoietin on HEK293 kidney cell after silver nanoparticle exposure

description: The toxic effects from exposure to silver nanoparticles (AgNPs), which are broadly present in many consumer products, have long raised concerns. Many studies have focused on the mechanisms of nanosilver, which cause toxicity in human cells, but little is known about prevention of this type of injury. This study investigated the in vitro effects of glutaraldehyde erythropoietin (GEPO), a cytoprotective compound derived from erythropoietin, in terms of cell protection against AgNP-induced-injury. HEK293 cells were pre-treated with or without GEPO before administration of AgNPs. The protective effects of GEPO in this cell line were assessed by the percentage of viable cells, alterations of cell morphology, and the proliferative capability of the cells. In addition, we assessed the role of GEPO in lowering cellular oxidative stress and regulating expression of the anti-apoptotic protein Bcl2. The results showed rescue effects on the percentage of viable and proliferative cell cells among GEPO pre-treated cells. Pre-treatment with GEPO maintained the normal cell shape and ultrastructural morphology. Moreover, GEPO reduced the generation of reactive oxygen species in cells and activated expression of Bcl2, which are the major mechanisms in protection against cellular toxicity induced by AgNPs. In conclusion, our study showed that the cytotoxic effects from exposure to AgNPs can be prevented by GEPO.
DOI: 10.17188/1202857
title: Materials Data on Sr4Zn3F14 by Materials Project

description: Sr4Zn3F14 crystallizes in the trigonal P31m space group. The structure is three-dimensional. there are three inequivalent Sr2+ sites. In the first Sr2+ site, Sr2+ is bonded in a 9-coordinate geometry to nine F1- atoms. There are a spread of Sr–F bond distances ranging from 2.57–2.72 Å. In the second Sr2+ site, Sr2+ is bonded in a 9-coordinate geometry to nine F1- atoms. There are a spread of Sr–F bond distances ranging from 2.50–2.70 Å. In the third Sr2+ site, Sr2+ is bonded in a 9-coordinate geometry to nine F1- atoms. There are a spread of Sr–F bond distances ranging from 2.50–2.71 Å. Zn2+ is bonded to five F1- atoms to form distorted corner-sharing ZnF5 trigonal bipyramids. There are a spread of Zn–F bond distances ranging from 1.99–2.05 Å. There are five inequivalent F1- sites. In the first F1- site, F1- is bonded in a 3-coordinate geometry to two Sr2+ and one Zn2+ atom. In the second F1- site, F1- is bonded in a distorted single-bond geometry to three Sr2+ and one Zn2+ atom. In the third F1- site, F1- is bonded in a trigonal planar geometry to three equivalent Zn2+ atoms. In the fourth F1- site, F1- is bonded to four Sr2+ atoms to form a mixture of distorted edge and corner-sharing FSr4 tetrahedra. In the fifth F1- site, F1- is bonded in a 1-coordinate geometry to three Sr2+ and one Zn2+ atom.
DOI: 10.14457/cu.the.2015.1099
title: Structure and dynamics properties involved with the transport of ions across lipid membrane by ion channels using molecular dynamics simulations

description: Ion channels are integral membrane proteins that select and transport ions across biological membranes. They are activated by a variety of stimuli. The molecular mechanism underlying ion selectivity and gating of ion channels has been a subject of intense research since the first crystal structure of potassium channel had been published in 1998. The aim of this thesis is to investigate the structure-function relationship of two ion channels, potassium (KvAP) channel and magnesium (TmCorA) channel, using molecular modeling and molecular dynamics simulations. The first part of the thesis is a molecular dynamics (MD) study of voltage sensor domain (VSD) of KvAP channel in two functional states, Up and Down. The MD simulations of Down-conformation conducted in two different lipid types, phospholipid and non-phospholipid bilayer, revealed higher accessible water molecules at the intracellular side of the VSD core than that of the Up-conformation. The results showed a change in the shape of water-crevice of the Down conformation with respect to that of the Up structure to accommodate the charged arginines moving towards the intracellular side of the bilayer. The second part of this thesis is the investigation of the ion selectivity of TmCorA channel. MD simulations and quantum chemical calculations were carried out to explore coordination chemistry and solvation structure of Mg2+ and other cations in the selectivity filter containing the conserved Gly-Met-Asn (GMN) sequence of TmCorA. The results showed that the GMN residues act as the second shell ligands for Mg2+. The first-shell structure of Mg2+ has six water molecules in an octahedral arrangement. The removal of Mg2+ at the Divalent Cation Sensor (DCS) site caused a weaker binding of Mg2+ to the filter. Moreover, the QM/MM results revealed the stabilization energy ordered from Co3+-hex &gt; Al3+ &gt; Ni2+-hex, Co2+, Ni2+, Mg2+, Ca2+ &gt; K+ &gt; Li+ &gt; Na+ which is consistent with the experimental selective trend of metal ions in CorA proteins supporting the selectivity property of binding with the octahedral metal complex.
DOI: 10.17188/1202859
title: Materials Data on Tl2Pt5S6 by Materials Project

description: Tl2Pt5S6 crystallizes in the monoclinic P2_1/c space group. The structure is three-dimensional. there are three inequivalent Pt2+ sites. In the first Pt2+ site, Pt2+ is bonded to one Tl1+ and four S2- atoms to form distorted PtTlS4 square pyramids that share corners with two equivalent PtTl2S4 octahedra, edges with two equivalent PtTl2S4 octahedra, and edges with two equivalent PtTlS4 square pyramids. The corner-sharing octahedra tilt angles range from 62–65°. The Pt–Tl bond length is 3.16 Å. There are a spread of Pt–S bond distances ranging from 2.33–2.38 Å. In the second Pt2+ site, Pt2+ is bonded to two equivalent Tl1+ and four S2- atoms to form distorted PtTl2S4 octahedra that share corners with two equivalent PtTlS4 square pyramids, edges with two equivalent PtTl2S4 octahedra, and edges with two equivalent PtTlS4 square pyramids. There are one shorter (3.14 Å) and one longer (3.22 Å) Pt–Tl bond lengths. There are a spread of Pt–S bond distances ranging from 2.32–2.39 Å. In the third Pt2+ site, Pt2+ is bonded in a distorted square co-planar geometry to four S2- atoms. There are two shorter (2.34 Å) and two longer (2.40 Å) Pt–S bond lengths. Tl1+ is bonded in a 6-coordinate geometry to three Pt2+ and three S2- atoms. There are a spread of Tl–S bond distances ranging from 3.13–3.39 Å. There are three inequivalent S2- sites. In the first S2- site, S2- is bonded in a 3-coordinate geometry to three Pt2+ and two equivalent Tl1+ atoms. In the second S2- site, S2- is bonded to four Pt2+ atoms to form distorted corner-sharing SPt4 tetrahedra. In the third S2- site, S2- is bonded in a 4-coordinate geometry to three Pt2+ and one Tl1+ atom.
DOI: 10.14457/cu.the.2015.1100
title: Antimicrobial and antibiofilm formation activities of chrysazin on bacillus species in vitro and in vivo using Thai silkworm model

description: Bacillus species cause food poisoning, localized infections and systemic infections. They also can become more resistant to antibiotic by forming of biofilms. The aim of this study, therefore was to investigate antimicrobial and antibiofilm activities of chrysazin, a major bioactive compound in Xyris indica L. on Bacillus cereus and Bacillus subtilis using both in vitro studies and in vivo studies using Thai silkworm model. From broth microdilution method, we observed that B. cereus was more susceptible to chrysazin than B. subtilis with MIC value of 7.81 and 15.63 µg/ml, respectively. Furthermore, results from Time-Kill Assay indicated that chrysazin was bacteriostatic agent against both microorganisms. In addition chrysazin also exerted antibiofilm formation activity against both B. cereus and B. subtilis in a concentration-dependent manner with maximum % inhibition of 85.15 and 73.86, for B. cereus and B. subtilis, respectively at concentration 500 µg/ml. Chrysazin demonstrated antibacterial activity in Thai silkworm infection model on both B. cereus and B. subtilis with the maximum % survival of 60.33±0.33 and 50.67±0.33, respectively at concentration 1,000 µg/ml. In conclusion this study showed that chrysazin has its potential for developing as an antibacterial drug and antibiofilm agent against B. cereus and B. subtilis.
DOI: 10.17188/1202861
title: Materials Data on TlReO4 by Materials Project

description: ReTlO4 crystallizes in the monoclinic P2_1/c space group. The structure is three-dimensional. there are three inequivalent Re7+ sites. In the first Re7+ site, Re7+ is bonded in a tetrahedral geometry to four O2- atoms. There is one shorter (1.75 Å) and three longer (1.76 Å) Re–O bond length. In the second Re7+ site, Re7+ is bonded in a tetrahedral geometry to four O2- atoms. All Re–O bond lengths are 1.76 Å. In the third Re7+ site, Re7+ is bonded in a tetrahedral geometry to four O2- atoms. All Re–O bond lengths are 1.76 Å. There are three inequivalent Tl1+ sites. In the first Tl1+ site, Tl1+ is bonded in a 8-coordinate geometry to eight O2- atoms. There are a spread of Tl–O bond distances ranging from 2.92–3.08 Å. In the second Tl1+ site, Tl1+ is bonded in a 9-coordinate geometry to nine O2- atoms. There are a spread of Tl–O bond distances ranging from 2.89–3.33 Å. In the third Tl1+ site, Tl1+ is bonded in a 8-coordinate geometry to eight O2- atoms. There are a spread of Tl–O bond distances ranging from 2.98–3.14 Å. There are twelve inequivalent O2- sites. In the first O2- site, O2- is bonded in a distorted single-bond geometry to one Re7+ and one Tl1+ atom. In the second O2- site, O2- is bonded in a distorted single-bond geometry to one Re7+ and two equivalent Tl1+ atoms. In the third O2- site, O2- is bonded in a single-bond geometry to one Re7+ and three Tl1+ atoms. In the fourth O2- site, O2- is bonded in a distorted single-bond geometry to one Re7+ and two equivalent Tl1+ atoms. In the fifth O2- site, O2- is bonded in a distorted single-bond geometry to one Re7+ and two equivalent Tl1+ atoms. In the sixth O2- site, O2- is bonded in a distorted single-bond geometry to one Re7+ and two Tl1+ atoms. In the seventh O2- site, O2- is bonded in a distorted single-bond geometry to one Re7+ and two Tl1+ atoms. In the eighth O2- site, O2- is bonded in a distorted single-bond geometry to one Re7+ and two equivalent Tl1+ atoms. In the ninth O2- site, O2- is bonded in a distorted single-bond geometry to one Re7+ and two Tl1+ atoms. In the tenth O2- site, O2- is bonded in a distorted single-bond geometry to one Re7+ and two equivalent Tl1+ atoms. In the eleventh O2- site, O2- is bonded in a distorted single-bond geometry to one Re7+ and two equivalent Tl1+ atoms. In the twelfth O2- site, O2- is bonded in a distorted single-bond geometry to one Re7+ and three equivalent Tl1+ atoms.
DOI: 10.14457/cu.the.2015.1101
title: Error prone pcr mutagenesis of toluene dioxygenase of Pseudomonas putida T57 to enhancedegradation of 4-chloroaniline

description: Chloroanilines are important intermediates for the production of polyurethanes, rubber additives, pesticides and dye. 4-Chloroaniline (4CA) is one of chloroaniline group, which is an aromatic amine ubiquitously detected to accumulate during the growing of agricultural and industrial activities. 4CA is toxic toward human and living organism, so it requires appropriate technique for treatment. Bioremediation is an effective technique using whole-cell microorganisms or enzymes. The recent report demonstrated that Escherichia coli recombinant strain harboring todC1C2BA, the gene encoding toluene dioxygenase from Pseudomonas putida T57, was able to oxidize 4CA, but with limited efficiency. Consequently, this study aimed to enhance the enzyme efficiency toward 4CA using error prone PCR technique to random mutagenesis of todC1C2 gene. The degradation rate of the obtained E. coli recombinant strain (pET21atodC1C2’BA) was determined by the modified Gibbs method. The degradation rate of the mutants was then compared with that of the wild-type. The changing in amino acid residues of the mutated enzyme was identified by nucleotide sequence analysis. After one round of random mutagenesis, the mutants were selected with the higher degradation rate of 4CA or aniline using the modified Gibbs method. The selected mutants were confirmed the degradation rate by HPLC analysis. The kinetics parameter of mutants showed the high catalytic efficiency compared to the wild-type enzyme. The mutated position (E339 and V345) of todC1 revealed to be involved in substrate binding site.