SciCombinator

Discover the most talked about and latest scientific content & concepts.

Journal: Data in brief

149

In this data article we provide topologies and force field parameters files for molecular dynamics simulations of lipids in the OPLS-aa force field using the GROMACS package. This is the first systematic parameterization of lipid molecules in this force field. Topologies are provided for four phosphatidylcholines: saturated DPPC, mono-cis unsaturated POPC and DOPC, and mono-trans unsaturated PEPC. Parameterization of the phosphatidylcholines was achieved in two steps: first, we supplemented the OPLS force field parameters for DPPC with new parameters for torsion angles and van der Waals parameters for the carbon and hydrogen atoms in the acyl chains, as well as new partial atomic charges and parameters for torsion angles in the phosphatidylcholine and glycerol moieties [1]. Next, we derived parameters for the cis and trans double bonds and the neighboring them single bonds [2]. Additionally, we provide GROMACS input files with parameters describing simulation conditions (md.mdp), which are strongly recommended to be used with these lipids models. The data are associated with the research article “Cis and trans unsaturated phosphatidylcholine bilayers: a molecular dynamics simulation study” [2] and provided as supporting materials.

Concepts: Molecular dynamics, Atom, Chemical bond, Lipid, Lipid bilayer, Lecithin, GROMACS, OPLS

145

This article describes the various chemical components as obtained from the oils in the leaves of Cymbopogon citratus using hydrodistillation and solvent-free microwave extraction methods. Furthermore, extractions of the oils were also carried out with a slight in pH variation and compared, “GC-MS evaluation of C. citratus (DC) Stapf oil obtained using modified hydrodistillation and microwave extraction methods” (Ajayi et al., 2016 [1]). The current article contains one table exhibiting a list of compounds in the four different methods of extraction. Comparative studies amongst the various methods of extraction are highlighted in the table.

Concepts: Chemical compound, Essential oil, Oil, Oils, Cymbopogon, Cymbopogon citratus

143

This article includes data from three prospective longitudinal human cohorts of prenatal marijuana exposure (PME) and offspring outcomes from the fetal period through young adulthood. The table herein contains an overview of the major adverse effects associated with PME from the following human cohorts: (1) The Ottawa Prenatal Prospective Study (OPPS); (2) The Maternal Health Practices and Child Development Study (MHPCD); and (3) The Generation R Study (Gen R). In the OPPS, fetal gestational age was measured and age-appropriate standardized neuropsychological instruments were used to assess neonatal responses, and infant-child and adolescent-young adult cognitive and behavioral skills. In the MHPCD, birth length and weight, neonatal body length, and infant-child sleep, cognition, and behavioral parameters were measured. In the Gen R, birth weight and growth were measured, as were infant-child attention and aggression. The data in this article are in support of our report entitled “Prenatal Cannabis Exposure - The "First Hit” to the Endocannabinoid System" (K.A. Richardson, A.K. Hester, G.L. McLemore, 2016) [13].

Concepts: Psychology, Pregnancy, Infant, Embryo, Prenatal development, Fetus, Obstetrics, Gestational age

141

Cell extracts from A549, H460, and U2OS human cancer cell lines treated with cisplatin and docetaxel were analyzed by mass spectrometry (MS) proteomic analysis. The extracts were enriched for cellular signaling proteins using a mix of three different immobilized kinase inhibitors (Purvalanol B, Bisindolylmaleimide X, and ®-3-(4-((1-Phenylethyl)amino)thieno[2,3-d]pyrimidin-6-yl)benzoic acid (SB6-060-05)) on sepharose bead columns. Raw data is deposited in the PRIDE database [1], project number PXD005286. Data presented () shows changes relative to untreated control for each biological replicate for the three cell lines.

Concepts: DNA, Protein, Gene, Cell nucleus, Enzyme, Cell biology, Chemotherapy, Cell culture

136

The data presented in this article are related to the research article entitled “CuO photocathode-embedded semitransparent photoelectrochemical cell” (Patel et al., 2016) [1]. This article describes the growth of Cu oxides films using reactive sputtering and application of CuO photocathode in semitransparent photoelectrochemical cell (PEC). In this data article, physical, optical and electrical properties, and PEC performances data set of the reactively sputtered semitransparent CuO samples are made publicly available to enable extended analyses.

Concepts: Data, Research, Copper, Oxide, Photoelectrochemical cell

134

We studied morphometric features of the spiral structure of the narwhal tusk and show that angular parameters of the arcs of the cementum layer determine the pattern of the spiral structure of the tusk. Given the straight shape of the tusk and the inclined pattern of the arcs of the cementum layer, the angular characteristics of the spiral were determined through the ratio of the legs of a right triangle, which was a basis for calculating the tangent of the angle of inclination. We found the angle of inclination through the arctangent. The tangent of the angle of inclination of the arcs of the spiral of the narwhal tusk is 2.39 ± 0.07, while the angle of inclination is 66.88 ± 0.61°. The indicators reflect the spiral morphology of the narwhal tusk. Researchers can use the data obtained in morphology practices, as well as in modeling the natural spiral structure in biomimetics.

130

We present the bathymetric dataset of a single beam sounding. Surveys were conducted in 25 expeditions of the Atlantic branch of Shirshov Institute of Oceanology RAS in the Russian EEZ area of the southeastern part of the Baltic Sea in the period from 2004 to 2018. Acoustic data were acquired by echo sounders Simrad EA-400SP and Furuno FS-700. The raw sounding data were filtered and corrected by sound velocity values. The dataset is presented as spreadsheets (*.xslx) and GIS point-class shapes (*.shp). The digital elevation model (DEM) of 1: 500 000 scale has been constructed for the entire Russian EEZ on base of the original array of sounding profiles and an open sources bathymetry [1]. DEM is presented by XYZ-grid (*.txt) and GeoTIFF raster (*.tif).

35

The data presented in this article are related to the research paper entitled “Increased expression of mitochondrial sodium-coupled ascorbic acid transporter-2 (mitSVCT2) as a central feature in breast cancer”, available in Free Radical Biology and Medicine Journal [1]. In this article, we examined the SVCT2 transporter expression in various breast cancer cell lines using RT-PCR and Western blot assays. In addition, we analyzed the subcellular localization of SVCT2 by immunofluorescence colocalization assays and cellular fractionation experiments. Finally, an analysis of different cancer tissue microarrays immunostained for SVCT2 and imaged by The Human Protein Atlas (https://www.proteinatlas.org) is presented.

22

This article has researched role of leaders in developing expertise in teaching and their influence on teachers in secondary school in Kazakhstan. Also, how principles can affect to educators developing to meet needs and challenges of today’s trends of teaching and learning. The following research report has been precisely written to evaluate the exact role of leadership practices in the development of expertise in teaching and in what manner the expert teachers or the principals help to develop expertise across various departments of the schools.

11

The amount of electricity generated by Photovoltaic (PV) systems is affected by factors such as shading, building orientation and roof slope. To increase electricity generation and reduce volatility in generation of PV systems, a portfolio of PV systems can be made which takes advantages of the potential synergy among neighboring buildings. This paper contains data supporting the research article entitled: PACPIM: new decision-support model of optimized portfolio analysis for community-based photovoltaic investment [1]. We present a set of data relating to physical properties of 24 houses in Oregon, USA, along with simulated hourly electricity data for the installed PV systems. The developed Matlab code to construct optimized portfolios is also provided in . The application of these files can be generalized to variety of communities interested in investing on PV systems.

Concepts: Risk, Photovoltaics, Bond, Investment, Construction, Building, House, MATLAB