cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14457/cu.the.2016.247
title: Development of paper-based devices for detection of Vibrio parahaemolyticus DNA from loop-mediated isothermal amplification

description: Vibrio parahaemolyticus (V. parahaemolyticus) is a gram-negative, halophilic marine bacterium and marine seafood-borne pathogen causing gastrointestinal disorders to humans. In this work, colorimetric paper-based device was employed for the determination of V. parahaemolyticus DNA amplified by loop-mediated isothermal amplification (LAMP). LAMP was performed using a set of six specially designed primers which is specific to V. parahaemolyticus DNA. The optimal isothermal amplification was at 65°C for 45 min. After DNA amplifyed by LAMP, colorimetric assay was carried out on paper-based device for DNA determination using silver nanoparticles (AgNPs) as colorimetric agent. It was found that the color of AgNPs did not change in the presence of amplified DNA, whereas color of AgNPs changed from yellow to red in the presence of unamplified DNA. The results of the assay can be easily evaluated by naked eyes. The limit of detection (LOD) was found to be 11.15 CFU mL-1. Therefore, the developed method was used for the determination of V. parahaemolyticus DNA in seafood (shrimps and oysters). Comparison of the results obtained from this proposed method to those obtained by the plate count method (TCBS) and LAMP-gel electrophoresis proved that this developed method has good agreement with the conventional method in terms of accuracy for practical applications. Hence, LAMP-AgNPs on PADs serves as a rapid, inexpensive and simple assay without the need for complicated instrumentation.
DOI: 10.17188/1720641
title: Materials Data on HoAlSi by Materials Project

description: HoAlSi crystallizes in the orthorhombic Cmcm space group. The structure is three-dimensional. Ho is bonded in a 5-coordinate geometry to four equivalent Al and five equivalent Si atoms. All Ho–Al bond lengths are 3.16 Å. There are a spread of Ho–Si bond distances ranging from 2.91–3.02 Å. Al is bonded in a 12-coordinate geometry to four equivalent Ho and four equivalent Si atoms. All Al–Si bond lengths are 2.66 Å. Si is bonded in a 9-coordinate geometry to five equivalent Ho and four equivalent Al atoms.
DOI: 10.14457/cu.the.2016.248
title: Anti-inflammatory activity of peptide from chicken feather meal in macrophage RAW 264.7

description: Inflammation is a defense mechanism in the body induced by foreign chemicals or pathogens. Thus, inflammation is one of the most critical factors implicated in vasodilation, carcinogenesis and other degenerative disorders. However, the study of the anti-inflammatory mechanism of peptides has been limited. So studies on anti-inflammatory peptides from natural sources are increasing in interest. The objective of this study, to investigate the optimal condition of enzymatic hydrolysis to prepare an anti-inflammatory peptide from chicken feather meal by using 3 types of microbial protease (Alcalase®, Flavourzyme®, and Neutrase®) in various concentrations (1% 2.5% and 5%). Peptide hydrolysate with 1% Flavourzyme® produced the best results for inhibition of NO production (IC50 5.48±1.0 µg/ml) when compared with other proteases. These peptide fractions were fractionated by ultrafiltration with 10, 5, 3 and 0.65 kDa membranes and further analyzed for NO scavenging activity. Among the fractions, MW ≤ 0.65 kDa exhibited a high level of antioxidant activity toward the NO radical scavenging assay. The ≤ 0.65 kDa fractions were selected for further fractionation by gel filtration chromatography. The F2 fraction was the strongest in inhibiting nitric oxide production. After that, F2 fraction was selected to study the NO production and cytotoxicity test by MTT assay in LPS-stimulated macrophage RAW 264.7. The result shows that the peptide also inhibited NO production and wasn’t toxic to macrophage RAW 264.7. The peptide fraction was further purified by HPLC and identification by mass spectrometry with amino acid sequence characterized into 4 peptides. In addition, the peptides are suppressed in the expression mRNA of iNOS, COX-2, IL-6 and TNF-α which are responsible for pro-inflammatory cytokine production. The results indicate that bioactive peptide from chicken feather meal can be developed to medical, pharmaceutical and cosmetic products.
DOI: 10.17188/1720642
title: Materials Data on Li3CrN2 by Materials Project

description: Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations
DOI: 10.14457/cu.the.2016.249
title: Molecular modeling on 3C protease/inhibitor complexes involving hand foot mouth disease

description: Hand, foot and mouth disease (HFMD) outbreaks frequently occur with children during the rainy season even becoming epidemic in some case. In general, HFMD patients have mild symptoms, that clear quickly. The enterovirus A71 (EV-A71) is a variant of the virus that causes severe pathogenic HFMD and may lead to death. In 2012, over 100000 HFMD cases were reported in Vietnam with 166 deaths due to EV-71 infection. HFMD occurrs in many countries e.g. Malaysia, China, Singapore, Vietnam, Brunei, Cambodia, and Great Britain. No vaccine or drug against HFMD is available. Rupintrivir, a broad-spectrum inhibitor, is a drug candidate for HFMD treatment, Another candidate is SG85, which is reported to have a better binding affinity than rupintrivir against CV-A16. Both inhibitors exhibit a comparable affinity against EV-A71 3C protease (3Cpro). In this work, the molecular information in term of the binding of the two inhibitors to the proteases will be elucidated. We aimed to investigate the inhibitory mechanisms of some potent compounds (e.g. rupintrivir) against the 3Cpro of the virus CV-A16, EV-A71 and EV-D68 in order to understand their biological activity and to develop procedures to improve their inhibitory potency. Molecular Docking and Molecular Dynamics simulation (MD simulation) are used as computational tools. The second part of this study is search for other potent HFMD inhibitors this was performed by screening several compound libraries (ZINC database, DrugBank and ChemBL) against the CV-A16 and EV-A71 3C proteases using steered molecular dynamic (SMD) simulations. Based on the hypothesis that a higher force is needed for pulling a more effective ligand from the protein target, the two analogs of rupintrivir containing the hydroxyl methyl at -meta and -para positions of the P2 side chain required an averaged rupture force higher than rupintrivir and SG85. The obtained information could be useful for the further development of anti-HFMD drugs.
DOI: 10.17188/1720644
title: Materials Data on TlIn(PS3)2 by Materials Project

description: TlIn(PS3)2 crystallizes in the monoclinic P2_1 space group. The structure is three-dimensional. Tl1+ is bonded in a 9-coordinate geometry to nine S2- atoms. There are a spread of Tl–S bond distances ranging from 3.12–4.05 Å. In1+ is bonded in a square pyramidal geometry to five S2- atoms. There are a spread of In–S bond distances ranging from 2.56–2.81 Å. There are two inequivalent P5+ sites. In the first P5+ site, P5+ is bonded in a trigonal non-coplanar geometry to three S2- atoms. There are a spread of P–S bond distances ranging from 1.98–2.08 Å. In the second P5+ site, P5+ is bonded in a trigonal non-coplanar geometry to three S2- atoms. There are a spread of P–S bond distances ranging from 2.04–2.07 Å. There are six inequivalent S2- sites. In the first S2- site, S2- is bonded in a 2-coordinate geometry to one Tl1+, one In1+, and one P5+ atom. In the second S2- site, S2- is bonded in a distorted single-bond geometry to three equivalent Tl1+ and one P5+ atom. In the third S2- site, S2- is bonded in a distorted L-shaped geometry to one In1+ and one P5+ atom. In the fourth S2- site, S2- is bonded in a 2-coordinate geometry to two equivalent Tl1+, one In1+, and one P5+ atom. In the fifth S2- site, S2- is bonded in a 2-coordinate geometry to two equivalent Tl1+, one In1+, and one P5+ atom. In the sixth S2- site, S2- is bonded in a 3-coordinate geometry to one Tl1+, one In1+, and one P5+ atom.
DOI: 10.14457/cu.the.2016.250
title: Preparation of fish oil nanospheres for shrimp feeds

description: The aim of this work is to fabricate the encapsulated fish oil particles for shrimp feed. The co-encapsuted fish oil with BHT (Butylated hydroxytoluene as the antioxidant) particles size is 1.00 ± 0.74 mm prepared solvent displacement method using ethylcellulose as the polymeric material. The morphology of these particles were characterized by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The encapsulated fish oil-BHT particles were tested to investigate the stability properties. The results indicate that encapsulated fish oil-BHT processes better thermal stability, oxidative stability and shelf life stability than unencapsulated fish oil. Moreover, encapsulated fish oil-BHT particles were added into the shrimp feed to increase the content of unsaturation of polyunsaturated fatty acids (PUFAs) in shrimp diet. The shrimp feeds were prepared with two different methods: 1) mixing encapsulated fish oil-BHT particle to shrimp feed paste for pelting machine before pelleting, 2) spraying encapsulated fish oil-BHT particle suspension onto the shrimp feed pellets. Both methods gave feed with minimal degradation of unsaturation functionality. In addition, Litopenaeus vannamei fed with feed containing the encapsulated fish oil-BHT particle shows better health such as, growth, weight, length and immunity index than those fed with unencapsulated fish oil containing feed.
DOI: 10.17188/1720645
title: Materials Data on CdRe2C6(N6O7)2 by Materials Project

description: Re2CdC6(N6O7)2 crystallizes in the monoclinic P2_1/c space group. The structure is two-dimensional and consists of one Re2CdC6(N6O7)2 sheet oriented in the (-1, 0, 2) direction. Re7+ is bonded in a tetrahedral geometry to four O2- atoms. There are a spread of Re–O bond distances ranging from 1.75–1.77 Å. Cd2+ is bonded in an octahedral geometry to six O2- atoms. There are a spread of Cd–O bond distances ranging from 2.26–2.36 Å. There are three inequivalent C4+ sites. In the first C4+ site, C4+ is bonded in a 1-coordinate geometry to two N1- and one O2- atom. There is one shorter (1.37 Å) and one longer (1.38 Å) C–N bond length. The C–O bond length is 1.22 Å. In the second C4+ site, C4+ is bonded in a 1-coordinate geometry to two N1- and one O2- atom. There is one shorter (1.37 Å) and one longer (1.38 Å) C–N bond length. The C–O bond length is 1.21 Å. In the third C4+ site, C4+ is bonded in a 1-coordinate geometry to two N1- and one O2- atom. There is one shorter (1.36 Å) and one longer (1.38 Å) C–N bond length. The C–O bond length is 1.23 Å. There are six inequivalent N1- sites. In the first N1- site, N1- is bonded in a 1-coordinate geometry to one C4+ and one N1- atom. The N–N bond length is 1.33 Å. In the second N1- site, N1- is bonded in a 1-coordinate geometry to one C4+ and one N1- atom. The N–N bond length is 1.33 Å. In the third N1- site, N1- is bonded in a 1-coordinate geometry to one C4+, one N1-, and one O2- atom. The N–N bond length is 1.34 Å. The N–O bond length is 2.60 Å. In the fourth N1- site, N1- is bonded in a 1-coordinate geometry to one C4+ and one N1- atom. In the fifth N1- site, N1- is bonded in a distorted single-bond geometry to one C4+ and one N1- atom. In the sixth N1- site, N1- is bonded in a 1-coordinate geometry to one C4+, one N1-, and one O2- atom. The N–O bond length is 2.96 Å. There are seven inequivalent O2- sites. In the first O2- site, O2- is bonded in a single-bond geometry to one Re7+ atom. In the second O2- site, O2- is bonded in a distorted single-bond geometry to one Re7+ and one N1- atom. In the third O2- site, O2- is bonded in a bent 120 degrees geometry to one Cd2+ and one C4+ atom. In the fourth O2- site, O2- is bonded in a distorted bent 120 degrees geometry to one Cd2+ and one C4+ atom. In the fifth O2- site, O2- is bonded in a single-bond geometry to one Re7+ and one N1- atom. In the sixth O2- site, O2- is bonded in a single-bond geometry to one Re7+ atom. In the seventh O2- site, O2- is bonded in a distorted bent 120 degrees geometry to one Cd2+ and one C4+ atom.
DOI: 10.14457/cu.the.2016.251
title: Coal petrography and associated stratigraphy in central part of Mae Moh Basin, Changwat Lampang

description: 35 coal samples from 3 boreholes in the central part of Mae Moh basin have been investigated for stratigraphy, petrography, and geochemical analyses. Lithostratigraphic of studied boreholes is Na Khaem formation in Mae Moh group, characterized by fine grained sediments with thin to thick coals from bottom to top as Q-, K- and J seams. The Na Khaem formation has been formed by the sedimentation under the alternation of lacustrine and swamp. Na kheam formation is overlaid by Huai Luang formation mainly of fine to coarse grained sediments with thin coal as I seam interbedded, indicated fluviatile environment. Detailed petrographic of individual seam reveals the studied coals consist largely of macerals &gt;70% with small amount of inorganic materials &lt;30%. Huminite group (43-68%) is characterized by gelinite, densinite, and some texto-ulminite. Liptinite group (5-30%) is composed of liptodetrinite, sporinite, cutinite, alginite, and exsudatinite. Inertinite group (4-15%) is fusinite, semifusinite and sclerotinite. The inorganic material (8-30%) is characterized by diatomite, clay mineral, framboidal pyrite, silicate, carbonate, and some volcanic ash in place. Mae Moh coals were plotted in the Diessel's diagram (1986) with TPI (Tissue Preservation Index) and GI (Gelification Index) base on maceral assemblage. The results are low TPI values (0.11-0.52) and moderate to high GI value (3.67-13.50); suggesting coals have originated under limnic condition (lacustrine) of peat formation with vegetation characteristics of marsh and wet forest swamp. Based upon the geochemical analyses, the studied coals can be classified as low rank (lignite A to subbituminous B) and low quality due to high ash and sulphur contents.
DOI: 10.17188/1720647
title: Materials Data on La15CuGe9 by Materials Project

description: La15CuGe9 crystallizes in the hexagonal P6_3mc space group. The structure is three-dimensional. there are four inequivalent La sites. In the first La site, La is bonded to six Ge atoms to form a mixture of distorted corner, edge, and face-sharing LaGe6 octahedra. The corner-sharing octahedra tilt angles range from 35–36°. There are a spread of La–Ge bond distances ranging from 3.22–3.38 Å. In the second La site, La is bonded in a 6-coordinate geometry to one Cu and five Ge atoms. The La–Cu bond length is 2.90 Å. There are a spread of La–Ge bond distances ranging from 3.15–3.76 Å. In the third La site, La is bonded in a 4-coordinate geometry to four Ge atoms. There are a spread of La–Ge bond distances ranging from 3.12–3.32 Å. In the fourth La site, La is bonded in a 5-coordinate geometry to one Cu and four Ge atoms. The La–Cu bond length is 2.93 Å. There are a spread of La–Ge bond distances ranging from 3.13–3.29 Å. Cu is bonded in an octahedral geometry to six La atoms. There are three inequivalent Ge sites. In the first Ge site, Ge is bonded in a 8-coordinate geometry to eight La atoms. In the second Ge site, Ge is bonded in a 8-coordinate geometry to eight La atoms. In the third Ge site, Ge is bonded in a 9-coordinate geometry to nine La atoms.
DOI: 10.14457/cu.the.2016.252
title: ANALYSIS OF ALLERGENS FROM BLACK TIGER SHRIMP (Penaeus monodon) BY COMBINING TWO-DIMENSIONAL GEL ELECTROPHORESIS WITH RS-ATL8 REPORTER CELL LINE

description: Food allergy is an immediate hypersensitivity reaction. Specific IgE is generated against allergens, and binds to the specific IgE receptor on the surface of basophils and mast cells. Allergen binding induces IgE cross-linking that triggers these cells to release chemical mediators such as histamine, prostaglandins and leukotrienes. Symptoms of allergic reactions vary from mild irritation to anaphylaxis and life-threatening. Black tiger shrimp (Penaeus monodon) is an important aquaculture species in Asia and is the common cause of food allergy in Thailand. One of the important problems in management of shellfish allergy is the lack of accurate diagnostic assay because the biological and immunological properties of allergens in the black tiger shrimps have not been well characterized. This study aims to investigate the reactive pattern of serum IgE from shrimp allergic patients to raw and cooked protein extract from black tiger shrimps and to identify shrimp allergens that can trigger IgE crosslinking by combining two-dimensional gel electrophoresis (2-DE) and RS-ATL8 reporter cell line. ELISA using sera from 24 shrimp allergic subjects, indicated that there were significant differences in reactivity to the raw and cooked shrimp extracts (P= 0.0093). Allergic serum IgE reacted stronger to raw shrimp extract than cooked shrimp extract. Consistent with these results, in SDS-PAGE, raw shrimp extract contained more protein bands than in the cooked extract. Western blot demonstrated that there was the major IgE reactivity area at 32-39 kDa in both raw and cooked shrimp extract. Eighteen of 24 patients (75%) and all patients (100%) had specific IgE to proteins in the range of 32-39 kDa in cooked and raw shrimp, respectively. The minimum concentration of crude shrimp extract to induce IgE cross-linking as measured by RS-ATL8 cell line were 10 fg/ml and 100 fg/ml in raw and cooked shrimp extract, respectively. The ten spots excised from 2-DE did not induce IgE cross-linking in RS-ATL8 cell line. The eluted protein from one-dimensional gel electrophoresis at the 115 and 38 kDa bands from raw shrimp extract induced an IgE cross-linking and the proteins were analysed by mass spectrometry. Some novel proteins were identified with the possibility of novel allergen. These results may be useful for shrimp allergy diagnostic test in the future.
DOI: 10.17188/1720648
title: Materials Data on Mn5(Bi2Rh)2 by Materials Project

description: Mn5Rh2Bi4 crystallizes in the cubic F-43m space group. The structure is three-dimensional. there are two inequivalent Mn sites. In the first Mn site, Mn is bonded in a 10-coordinate geometry to two equivalent Mn, two equivalent Rh, and six Bi atoms. Both Mn–Mn bond lengths are 3.00 Å. Both Mn–Rh bond lengths are 2.70 Å. There are a spread of Mn–Bi bond distances ranging from 3.07–3.11 Å. In the second Mn site, Mn is bonded in a 6-coordinate geometry to three equivalent Mn, three equivalent Rh, and four Bi atoms. All Mn–Rh bond lengths are 2.65 Å. There are three shorter (2.91 Å) and one longer (3.42 Å) Mn–Bi bond lengths. Rh is bonded in a 10-coordinate geometry to six Mn and four Bi atoms. There are one shorter (2.75 Å) and three longer (2.95 Å) Rh–Bi bond lengths. There are three inequivalent Bi sites. In the first Bi site, Bi is bonded in a distorted octahedral geometry to ten Mn atoms. In the second Bi site, Bi is bonded in a 10-coordinate geometry to six equivalent Mn and four equivalent Rh atoms. In the third Bi site, Bi is bonded in a 8-coordinate geometry to six Mn and two equivalent Rh atoms.
DOI: 10.14457/cu.the.2016.253
title: ANALYSIS OF ANCIENT STORM DEPOSITS IN CHANGWAT PRACHUAP KHIRI KHAN

description: The analysis of ancient storm deposits in Changwat Prachuap Khiri Khan along the Gulf of Thailand is aimed to analyze the sedimentological characteristics and to define depositional age of ancient storm. Ancient storm sediments were found within a distance of 350 m landward from the present shoreline. Thickness of ancient storm deposits varies from 0.5 to 50 cm. The numbers of ancient storm layers possibly indicate the numbers of storm occurrences through time. In this research, ancient storm layers were found up to twenty-seven layers. Grain size of ancient storm sediments ranges from coarse- to very fine-grained sand. Sedimentary structures of ancient storm deposits contain sharp upper and lower contact, normal and reverse grading, parallel lamination and mud rip-up clasts. The thicknesses and grain size of deposit are thinner and finer landward. Furthermore, ancient storm layers contain several microfossils (foraminifera and ostracod) and macrofossils (gastropod and bivalve). The ancient storm sediments contain mostly quartz, heavy minerals and shell fragments. The results of Optically Stimulated Luminescence ages from beach ridges and the correlation of AMS radiocarbon age from a wood fragment from the adjacent area indicate that there are four ancient storm layers occurred in the late-Holocene to the mid-Holocene. There are twenty-three ancient storm layers older than the mid-Holocene. The variability in number of ancient storm deposit during two periods may due to several controlling factors including potential preservation of the area, storm characteristic, the intensity of storm, wind speed, surge height, and climatic condition in the past.
DOI: 10.17188/1720649
title: Materials Data on YbSi3Ni5 by Materials Project

description: YbNi5Si3 crystallizes in the orthorhombic Pnma space group. The structure is three-dimensional. Yb2+ is bonded to six Si4- atoms to form distorted YbSi6 pentagonal pyramids that share corners with twelve NiSi4 tetrahedra, edges with ten NiSi4 tetrahedra, and faces with two equivalent YbSi6 pentagonal pyramids. There are two shorter (2.92 Å) and four longer (2.93 Å) Yb–Si bond lengths. There are five inequivalent Ni2+ sites. In the first Ni2+ site, Ni2+ is bonded to four Si4- atoms to form NiSi4 tetrahedra that share corners with two equivalent YbSi6 pentagonal pyramids, corners with thirteen NiSi4 tetrahedra, edges with three equivalent YbSi6 pentagonal pyramids, and edges with three equivalent NiSi4 tetrahedra. There are a spread of Ni–Si bond distances ranging from 2.26–2.35 Å. In the second Ni2+ site, Ni2+ is bonded to four Si4- atoms to form NiSi4 tetrahedra that share corners with two equivalent YbSi6 pentagonal pyramids, corners with thirteen NiSi4 tetrahedra, edges with three equivalent YbSi6 pentagonal pyramids, and edges with three equivalent NiSi4 tetrahedra. There are a spread of Ni–Si bond distances ranging from 2.35–2.38 Å. In the third Ni2+ site, Ni2+ is bonded to four Si4- atoms to form NiSi4 tetrahedra that share corners with two equivalent YbSi6 pentagonal pyramids, corners with eight NiSi4 tetrahedra, edges with three equivalent YbSi6 pentagonal pyramids, and edges with four NiSi4 tetrahedra. There are one shorter (2.31 Å) and three longer (2.42 Å) Ni–Si bond lengths. In the fourth Ni2+ site, Ni2+ is bonded to four Si4- atoms to form NiSi4 tetrahedra that share corners with six equivalent YbSi6 pentagonal pyramids, corners with eight NiSi4 tetrahedra, an edgeedge with one YbSi6 pentagonal pyramid, and edges with four NiSi4 tetrahedra. There are a spread of Ni–Si bond distances ranging from 2.27–2.31 Å. In the fifth Ni2+ site, Ni2+ is bonded in a 5-coordinate geometry to five Si4- atoms. There are a spread of Ni–Si bond distances ranging from 2.30–2.49 Å. There are three inequivalent Si4- sites. In the first Si4- site, Si4- is bonded in a 9-coordinate geometry to two equivalent Yb2+ and seven Ni2+ atoms. In the second Si4- site, Si4- is bonded in a 9-coordinate geometry to two equivalent Yb2+ and seven Ni2+ atoms. In the third Si4- site, Si4- is bonded in a 9-coordinate geometry to two equivalent Yb2+ and seven Ni2+ atoms.