ProtoMD: A Prototyping Toolkit for Multiscale Molecular Dynamics

ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates `GROMACS wrapper' to initiate MD simulations, and `MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md

MEASURING WORKING HOURS INPUT IN VINE GROWING AT WORK ORGANIZATION BASED ON PHENOLOGICAL PHASES

Research was based on phenological phases of Italian Riesling, involving differences in labour and financial input for dry, optimal and wet weather. Worktime demand for certain operations in vine growing was determined with an analytic method, work day survey and We worked out alternatives for dry, optimum and wet weather on the basis of phenological phaseses. The worktime demand for the phenological phases with all their operations were analysed and planned in an itemized way based on our findings. We used them to work out the worktime demand for the given vine land for each operation. To analyse differences coming from diverse methods of cultivation and spacing, the material, operational and total costs of hand and mechanized labour were projected for 1 hectare and variance analysis was made

Mineral content of three several muscles from six cattle genotypes

The aim of this study was to determine the effect of genotype and type of muscle on the mineral content of beef. Altogether 62 young bulls from Angus, Charolais, Holstein, Hungarian Simmental, Hungarian Grey, and Charolais×Hungarian Grey were used. The calcium content varied between 26–46 mg kg−1, in longissimus muscle of Hungarian Simmental it was significantly higher than for other genotypes except for Angus. Psoas major of Holstein had the highest phosphorus content, it significantly differed from the longissimus of Angus. Longissimus muscle of Angus was the poorest for magnesium, and the richest was the psoas major of Holstein and Hungarian Grey. Charolais had higher level of potassium in psoas major than Angus and Charolais×Hungarian Grey. Sodium content of semitendinosus in Charolais×Hungarian Grey was lower than in Holstein. Present data showed that levels were detected in the longissimus of Angus and semitendinosus of Holstein. Concerning zinc, a higher level was found in longissimus, especially for Holstein. The results confirmed that beef mineral content depends on genotype, and is related to muscle type, too

Can variability in the effect of opioids on refractory breathlessness be explained by genetic factors?

© 2015, BMJ Publishing Group. All rights reserved. Objectives: Opioids modulate the perception of breathlessness with a considerable variation in response, with poor correlation between the required opioid dose and symptom severity. The objective of this hypothesis-generating, secondary analysis was to identify candidate single nucleotide polymorphisms (SNP) from those associated with opioid receptors, signalling or pain modulation to identify any related to intensity of breathlessness while on opioids. This can help to inform prospective studies and potentially lead to better tailoring of opioid therapy for refractory breathlessness. Setting: 17 hospice/palliative care services (tertiary services) in 11 European countries. Participants: 2294 people over 18 years of age on regular opioids for pain related to cancer or its treatment. Primary outcome measures: The relationship between morphine dose, breathlessness intensity (European Organisation for Research and Treatment of Cancer Core Quality of Life Questionnaire; EORTCQLQC30 question 8) and 112 candidate SNPs from 25 genes (n=588). Secondary outcome measures: The same measures for people on oxycodone (n=402) or fentanyl (n=429). Results: SNPs not in Hardy-Weinberg equilibrium or with allele frequencies ( < 5%) were removed. Univariate associations between each SNP and breathlessness intensity were determined with Benjamini-Hochberg false discovery rate set at 20%. Multivariable ordinal logistic regression, clustering over country and adjusting for available confounders, was conducted with remaining SNPs. For univariate morphine associations, 1 variant on the 5-hydroxytryptamine type 3B (HTR3B) gene, and 4 on the β-2-arrestin gene (ARRB2) were associated with more intense breathlessness. 1 SNP remained significant in the multivariable model: people with rs7103572 SNP (HTR3B gene; present in 8.4% of the population) were three times more likely to have more intense breathlessness (OR 2.86; 95% CIs 1.46 to 5.62; p=0.002). No associations were seen with fentanyl nor with oxycodone. Conclusions: This large, exploratory study identified 1 biologically plausible SNP that warrants further study in the response of breathlessness to morphine therapy

An ab initio study of the rovibronic spectrum of sulphur monoxide (SO): diabatic vs. adiabatic representation

We present an ab initio study of the rovibronic spectra of sulphur monoxide (32S16O) using internally contracted multireference configuration interaction (ic-MRCI) method and aug-cc-pV5Z basis sets. It covers 13 electronic states X3Σ-, a1Δ, b1Σ+, c1Σ-, A''3Σ+, A'3Δ, A3Π, B3Σ-, C3Π, d1Π, e1Π, C'3Π, and (3)1Π ranging up to 66 800 cm-1. The ab initio spectroscopic model includes 13 potential energy curves, 23 dipole and transition dipole moment curves, 23 spin-orbit curves, and 14 electronic angular momentum curves. A diabatic representation is built by removing the avoided crossings between the spatially degenerate pairs C3Π-C'3Π and e1Π-(3)1Π through a property-based diabatisation method. We also present non-adiabatic couplings and diabatic couplings for these avoided crossing systems. All phases for our coupling curves are defined, and consistent, providing the first fully reproducible spectroscopic model of SO covering the wavelength range longer than 147 nm. Finally, an ab initio rovibronic spectrum of SO is computed