Miracle-dz/UniFAR-FTUs huggingface dataset:
Computer simulation of lipids and DNA using a coarse grain methodology

The nucleus of the eukaryotic cell contains a large pool of lipids together with structural proteins and genomic DNA. The project aim was to develop simple and robust lipid and DNA models that will allow for these complex molecules to be mixed together in order to elucidate the possible interactions. The large percentage of lipids found within the nucleus makes it likely that they exist in aggregates, although the actual role and structure in which they exist is unknown. While there has not been substantial work done to model such interactions between lipids and DNA in order to better understand the interactions within the nucleus, a substantial body of work exists on lipid/DNA complexes in relation to gene therapy. These simulations in many cases however, are too simple and the structures formed are pre-imposed to a certain degree. Our model would attempt to simulate these interactions without such pre-imposed conditions relying solely on interactions between the particles to drive the structures being formed. A coarse graining approach in which several groups of atoms are subsumed into single interaction sites was deemed suitable given the complexity of modelling a mixture of DNA and lipids, together with the solvent and ion environment. In this regard new models of lipids, DNA, ion and solvent models were developed in a purpose built molecular dynamics package called LANKA-Lipid And Nucleic acid Komputer Algorithm. The lipids in the model are represented as polar ellipsoids and the solvent as spheres with dipoles embedded within them. The interactions between the lipids and solvent are modelled using the Gay Berne potential. The developed lipid model was able to self assemble into a stable bilayer phase and reproduce many bilayer properties of a liquid crystal phase. The model was then extended to capture some of the other lipid phases seen in nature, including lyotropic phase transitions. A simple study of lipid mixtures has also been undertaken during this period. The importance of considering multicomponent lipid systems has increasingly been highlighted in the literature to make the lipid models more realistic. The developed lipid models are simple enough to extend and attempt to simulate the formation of lipid rafts and domain formation. Simulation of DNA in the past has largely focused on atomistic studies. While these have proved valuable they do not consider the macroscopic length scales of the molecule. Simplified models trying to capture long length scales have had to compromise on the molecular level detail. Coarse grain models while trying to bridge the gap have also remained largely idealistic in nature.
Phytophthora genus pathogens isolated from rhododendrons in Lithuania

Rhododendron spp. plants were surveyed for Phytophthora infection in Lithuania during 2010 – 2016. This study aims to identify Phytophthora genus pathogen which infects rhododendrons in Lithuania. Samples were taken from young sick plants with visible infection symptoms. Soil sampling was performed from the rhizosphere of sick plants. DNA from soil and plant was tested for the presence of Phytophthora genus pathogens. Data showed positive results of Phytophthora genus specific probe during real-time PCR. All tested diseased leaves and soil samples have indicated Phytophthora sp. infection during Alert-LF® Phytophthora spp. analysis. The extracted DNA concentrations were not very high for Phytophthora species identification, but in most cases, it was high enough for further researches.
In vitro antioxidant activity of methanolic extracts of Ageratum conyzoides and Ageratina adenophora leaves

Characterization of natural products based on the antioxidant activity gains tremendous interest in the past decade. In the current work, the antioxidant activity of the methanolic extract of Ageratina adenophora and Ageratum conyzoides leaves were determined. Both plants belong to the family Asteraceae and are invasive species in many tropical and subtropical countries, including northeastern India, China, Sri lanka, Nigeria. A. conyzoides is an annual herbaceous plant having a number of bioactive compounds. A. conyzoides is typically found in cultivated fields and other disturbed ecosystems; and is known for its medicinal use in the treatment of burns and wounds, arthritis, asthma, dermatitis, leprosy, malaria, and as an insecticide. Notable compounds include toxic pyrrolizidine alkaloids, phenolic acids, cumarin and polymethoxyflavones. In this study, antioxidant activity of the plant leaves was characterized for DPPH (2, 2-diphenyl-1-picrylhydrazy) and hydrogen peroxide radical scavenging activity. Antioxidant activity determines the potential of a compound to scavenge a free radical generated during oxidative stress in the body. The result suggests that A. adenophora and A. conyzoides leaves extracts showed potential antioxidant activity in terms of both DPPH and hydrogen peroxide scavenging activity.
A bipartite transcription factor module controlling expression in the bundle sheath of Arabidopsis thaliana

C4 photosynthesis evolved repeatedly from the ancestral C3 state, improving photosynthetic efficiency by ∼50%. In most C4 lineages photosynthesis is compartmented between mesophyll and bundle sheath cells but how gene expression is restricted to these cell types is poorly understood. Using the C3 model Arabidopsis thaliana we identified cis-elements and transcription factors driving expression in bundle sheath strands. Upstream of the bundle sheath preferentially expressed MYB76 gene we identified a region necessary and sufficient for expression containing two cis-elements associated with the MYC and MYB families of transcription factors. MYB76 expression is reduced in mutant alleles for each. Moreover, down-regulated genes shared by both mutants are preferentially expressed in the bundle sheath. Our findings are broadly relevant for understanding the spatial patterning of gene expression, provide specific insights into mechanisms associated with evolution of C4 photosynthesis and identify a short tuneable sequence for manipulating gene expression in the bundle sheath.
New Records of Hoverflies (Diptera, Syrphidae) from Ukraine. III. Pipizinae and Syrphinae

Abstract Five species of hoverflies of the subfamilies Pipizinae and Syrphinae: Pipiza accola Violovitsh, 1985, Platycheirus nielseni Vockeroth, 1990, P. occultus Goeldlin, Maibach and Speight, 1990, Epistrophe olgae Mutin, 1990, and Xanthogramma laetum (Fabricius, 1794) are recorded from Ukraine for the first time. Distributions of these species are summarized and diagnoses of the species are provided.
Performance and Characterization of U.S. Naval Observatory Clocks

Abstract : Six years of U.S. Naval Observatory clock data are analyzed to determine the optimal data filter length and the amplitude and frequency of occurrence of statistically significant changes in the frequencies and frequency drifts of cesium-beam frequency standards and hydrogen masers by means of relative and correlation-corrected N-cornered-hat analyses of the frequency stabilities of postprocessed mean timescales. The effects of temperature and humidity on cesium and maser frequencies and drifts are also investigated.
The aerodynamic effect of fillet radius in a low speed compressor cascade. Thesis - Von Karman Inst. for Fluid Dynamics

The aerodynamic effects of fillet size in a low speed compressor cascade were experimentally studied. Two blade profiles were used during the experiment, namely a controlled diffusion blade and a double circular arc blade. Cascades were tested with three fillet radii and two boundary layer thicknesses over a large range of incidence angles. The cascade performance was determined by extensive downstream flow measurements using a two head, 5 hole pressure probe. Results differ significantly between the two types of blades tested. As fillet radius increases secondary flows and total pressure losses were found to increase for the controlled diffusion blades; whereas, for the double circular arc blades the losses decrease, particularly at high incidence angles.
X-ray diffraction line profile analysis of acid-resistant goethite in Western Australian nickel laterite ore

The goethite peaks in synchrotron and laboratory X-ray powder diffraction (XRPD) patterns of an acid-resistant nickel laterite ore sample from a site in Western Australia exhibit a `super-Lorentzian' shape. The method for extracting the coherently scattering domain size distribution published by Leoni & Scardi [J. Appl. Cryst. (2004), 37, 629–634] is adapted to fit the asymmetric goethite peak profiles, allowing the refinement of lattice parameters for multiple goethite structural models while maintaining their relationships. The anisotropic peak broadening due to the acicular shape of the goethite crystals is addressed using spherical harmonics predefined from an XRPD pattern of a synthetic goethite sample. A bimodal coherently scattering domain size distribution of goethite crystals is predicted from the goethite profile fitting and agrees with previous transmission electron microscopy findings that two goethite populations with different domain sizes and metal substitutions exist in the ore sample. The small goethite size fraction dissolved slowly during atmospheric acid leaching, while the large goethite fraction barely dissolved. Caustic pre-treatment by KOH digestion significantly enhanced the acid-leaching performance of the small goethite fraction, but had no effect on the large goethite fraction. This study demonstrates that quantitative phase analysis on designated goethite size fractions can successfully fit the super-Lorentzian shaped line profiles of natural goethite crystals with a confirmed bimodal domain size distribution.
Nitric oxide regulates photosynthetic performance and stomatal behaviour supplemented with nitrogen and sulfur in mustard under salt stress.

Nitric oxide (NO) is a hormone that connects numerous reactions in plant cells under normal and environmental stress conditions. We found that application of 100 μM NO as sodium nitroprusside (SNP; NO donor) was studied individually or in combination of 100 mg N or 100 mg S applied in different combinations i.e., 100 mg N or S kg-1 soil applied at the time of sowing [100N+100S]0d or with split, 50 mg N or S kg-1 soil at the time of sowing and similar dose at 20 d after sowing [50N+50S]0d +[50N+50S]20d on alleviation of 100 mM NaCl stress in mustard (Brassica juncea L.). Application of 100 μM NO plus split application of N and S more significantly promoted stomatal behavior, photosynthetic and growth performance in the absence of salt stress and maximally alleviated effects of salt stress through increased N- and S-use efficiency, proline and antioxidant system. The combined application of N and S at the time of sowing was lesser effective in promoting photosynthesis and growth under salt or no salt stress conditions in presence or absence of NO. The study suggests that salt stress effects on photosynthetic performance of plants are mitigated more efficiently when NO was applied in the split application of N and S given at two stages, and the photosynthetic activity was promoted under salt stress through increased N and S assimilation and antioxidant system. The strategy may be adopted in agricultural system for overcoming salt stress effects on performance of mustard. This article is protected by copyright. All rights reserved.
PROD and BROD modulation in Nile tilapia after exposure to 17 beta-estradiol

The activities of 7-ethoxyresorufin-O-deetylase (EROD), 7-benzyloxyresorufin-O-debenzylase (BROD), 7-pentoxyresorufin-O-depentilase (PROD), and glutathione S-transferase (GST) were measured in Nile tilapias exposed for 7 days of 5 and 15 μg/L 17 β-estradiol. EROD and GST activities were unchanged. PROD activity increased in animals exposed to the higher dose of the hormone, while BROD was increased after 7 exposure days to both doses of the compound. These results indicate the usefulness of these enzymes as biomarkers for 17 β-estradiol exposure.
An analytical model of multi-particle electric double-layer interaction between identical spherical colloid nanoparticles

The present work is devoted to the theoretical study of the colloid nanoparticle interaction. A simple analytical model for the multi-particle interaction between the amphoteric oxide nanoparticles with low surface potential has been developed. The model utilizes the framework of the DLVO (Derjaguin, Landau, Verwey, Overbeak) theory and accounts for the surface charge regulation during the multi-particle interaction. The results of this study demonstrate a good qualitative agreement with the experimental data and reveal the presence of the orientation effects during nanoparticle aggregation, which may cause the formation of aggregates with different morphologies.
PRINSIP SYARIAH DALAM PENYELENGGARAAN BANK WAKAF MIKRO SEBAGAI PERLINDUNGAN HAK SPIRITUAL NASABAH

ABSTRAK Tujuan : Penelitian ini bertujuan untuk mengetahui pengaturan mengenai prinsip syariah dalam pengelolaan Bank Wakaf Mikro (BWM) sebagai upaya perlindungan hak spiritual nasabah atau masyarakat pada umumnya. Metodologi : Penelitian ini adalah metode yuridis normatif atau metode penelitian hukum yang bersifat doctrinal, dengan menggunakan pendekatan perundang-undangan dan pendekatan konseptual. Temuan : Penelitian ini menunjukan dasar hukum penyelenggaraan BWM di Indonesia sebagai bagian dari LKM diatur dalam UU LKM. UU LKM ini mewajibkan penerapan prinsip syariah dalam pengelolaan bisnis BWM. Kebijakan penerapan prinsip syariah ini dimaksudkan sebagai jaminan perlindungan hak spiritual masyarakat khususnya nasabah dari BWM yang mayoritas beragama Islam. Kegunaan : Kebijakan hadirnya bisnis BWM pada dasarnya untuk memberikan pilihan bagi masyarakat, khususnya umat Islam dalam memilih lembaga keuangan yang menyediakan jasa keuangan seperti pembiayaan. Sedangkan hasil dari penelitian ini diharapkan dapat mengghilangkan sikap “skeptis” masyarakat terhadap lembaga keuangan berbasis Hukum Islam yang masih dianggap sama dengan lembaga keuangan konvensional lainnya. Kebaruan/Orisinalitas : Berbeda dengan penelitian yang telah dilakukan sebelumnya, penelitian ini lebih berfokus pada kebijakan prinsip syariah pada BWM sebagai upaya perlindungan hak spiritual.
Consistent Cooperative Control of Multi-energy Storage in DC Microgrid

The DC microgrid contains a large number of distributed power generation units, and energy storage devices with appropriate capacity can smooth the power output of the distributed power supply and provide power support for the microgrid. A distributed cooperative control strategy based on consistency is proposed for multi-energy storage system in DC microgrid. The control strategy consists of two modules: virtual inertial control and consistency control. The virtual inertial control module can realize the power interaction between the energy storage device and the microgrid, and make the energy storage provide the inertial support of voltage for the grid. Consistency control module realizes information exchange between energy storage devices through low-bandwidth communication, and achieves the purpose of compensating grid voltage and reasonably distributing reactive power of energy storage devices. Finally, the correctness and effectiveness of the proposed control strategy are verified in PSCAD/EMTDC software.
Dynamics and interactions of the voltage-dependent anion channel 1 studied by NMR spectroscopy

The voltage-dependent anion channel (VDAC), the most abundant protein in the outer mitochondrial membrane, acts as a gatekeeper for the entry and exit of mitochondrial metabolites and is involved in mitochondrial apoptosis. Recent determination of its high-resolution structure by three independent groups revealed a 19-stranded β-barrel with a differently arranged N-terminal α-helix inside the pore. In this thesis, the NMR resonance assignment of isoform one of human VDAC (VDAC1) in solution is increased. In addition, this study provides evidence for a kinked α-helical structure of the N-terminus, which is compatible with the crystal structure of VDAC1, although other structures cannot be excluded. Furthermore, this study reveals functional dynamics of VDAC1 by a combination of solution NMR spectroscopy, Gaussian network model (GNM) analysis, and molecular dynamics (MD) simulations. Low signal intensities indicate conformational exchange in the second part of the N-terminal α-helix and the linker connecting the α-helix to the first β-strand. In addition, mutation of arginine 15 in the second α-helical part affects the stability of the α-helix and the overall barrel in a complex manner. Micro- to millisecond dynamics are significantly increased in the N-terminal α-helix, the linker, and the N-terminal six β-strands of VDAC1 in micellar solution. In addition, hydrogen bonds are instable in the N-terminal three β-strands. In agreement, the N-terminal β-strands exhibit increased B-factors in the crystal structure of VDAC1 and intrinsic instability predicted by the GNM analysis. Mutation or chemical modification of the membrane facing glutamic acid 73 (E73) strongly reduces the micro- to millisecond dynamics in solution. MD simulations reveal that a charge on E73 accounts for the elevation of N-terminal protein dynamics as well as a thinning of the nearby membrane. Since E73 is necessary for hexokinase-I-induced VDAC1 channel closure and inhibition of apoptosis, these results imply that micro- to millisecond dynamics in the N-terminal part of the β-barrel are essential for VDAC1 interaction and gating. Moreover, the data suggest that dynamics in the α-helix are connected with these processes. Furthermore, this study reveals two binding sites for the pore's most important transport substrate ATP. The location of the ATP binding sites, one of them comprising the N-terminal α-helix, the linker, and nearby β-strands, suggests controlled metabolite flux and ligand-induced stabilization of the open state of the VDAC1 pore. Finally, Ca2+ is found to interact with two distinct N-terminal and C-terminal regions in the β-barrel. These regions overlap with VDAC1 oligomerization sites and dynamic regions, suggesting a connection between Ca2+ interaction, gating, and oligomerization.
Cl−-HCO3− Exchange in Developing Neonatal Rat Cardiac Cells

Abstract The Cl−-HCO3− exchanger is the main anionic exchanger (AE) that alleviates alkaline loads in cardiac cells. We recently identified in adult ventricular cells two membrane proteins (80 and 120 kD) immunologically related to the erythroid band 3 and likely to mediate the anion exchange. In the present study, we further investigated the Cl−-HCO3− exchanger activity concomitantly with the expression and intracellular localization of the band 3–like proteins during the development of neonatal rat cardiac cells maintained in culture for 17 days. Microspectrofluorometric measurements of pHi in single cells show that neonatal rat cardiomyocytes display a fully functional DIDS-sensitive Cl−-HCO3− exchanger at early stages of development. Neither basal pHi nor the anion exchange activity changes with different stages of the culture. In Western blotting with an anti–whole erythroid band 3 antibody, we found both the 80- and the 120-kD band 3–like proteins in whole heart and cultured neonatal cardiac cells.
Advances in molecular structure research

Measuring symmetry in structural chemistry, Hagit Zabrosdsky and David Avnir some perspectives in molecular structure research - an introduction, Istvan Hargittai accurate molecular structure from microwave rotational spectroscopy, Heinz Dieter Rudolph gas-phase NMR studies of conformational processes, Nancy S. True and Cristina Suarez Fourier transform spectroscopy of radicals, Henry W. Rohrs et al the interplay between x-ray, crystallography and "Ab initio" calculations, Ronald Boese et al computational and spectroscopic studies on hydrated molecules, Alfred H. Lowrey and Robert W. Williams experimental electron densities of molecular crystals and calculation of electrostatic properties from high resolution x-ray diffraction, Claude Lecomte order in space - packing of atoms and molecules, Laura E. Depero.
Volumetric heat capacity enhancement in ultrathin fluorocarbon polymers for capacitive thermal management

Capacitive thermal management in electronics requires an enhancement in the volumetric storage density of compatible materials to approximately 1 GJ/m. We investigate potential enhancement in sensible storage density arising from size effects in thin polymer films. We design and fabricate a micro-calorimeter to measure the volumetric heat capacity of nanometer scale thin fluorocarbon polymer films. The storage density increases approximately three times as the film thickness decreases from 27 nm to 12 nm. Using the Debye theory of phonons, we relate this behavior to an increase in the Grüneisen parameter with decreasing film thickness. This work advances the understanding of size dependence in the heat capacity of amorphous polymers as well as highlights their potential for capacitive thermal management.
INFORMATION FLOW MODELING IN WIRELESS SELF-ORGANIZING NETWORK

The technology of the wireless self-organizing network has good application prospects for information exchange provision to search and rescue operations and to perform the operations preventing natural and man-made emergency situations. The article presents the models of information flows transfer through the channels of a wireless self-organizing network. They are based on the representation of the simulated process current states with the help of package identifiers and confirmations related to the transmission of information flows through the channels of a given contour. Mathematical models are presented that take into account the dynamism of network topology and allow to estimate the efficiency of data delivery in the conditions of subscriber mobility and destructive influences.
Predicting Mushroom Productivity from Long-Term Field-Data Series in Mediterranean Pinus pinaster Ait. Forests in the Context of Climate Change

Long-term field-data series were used to fit a mushroom productivity model. Simulations enabled us to predict the consequences of management and climate scenarios on potential mushroom productivity. Mushrooms play an important ecological and economic role in forest ecosystems. Human interest in collecting mushrooms for self-consumption is also increasing, giving forests added value for providing recreational services. Pinus pinaster Ait. is a western Mediterranean species of great economic and ecological value. Over 7.5% of the total European distribution of the species is found on the Castilian Plateau in central Spain, where a great variety of mushrooms can be harvested. The aim of this study was to model and simulate mushroom productivity in Maritime pine (Pinus pinaster Ait.) ecosystems in northern Spain under different silvicultural and climatic scenarios. A mixed model was fitted that related total mushroom productivity to stand and weather variables. The model was uploaded to the SiManFor platform to study the effect of different silvicultural and climatic scenarios on mushroom productivity. The selected independent variables in the model were the ratio between stand basal area and density as a stand management indicator, along with precipitation and average temperatures for September and November. The simulation results also showed that silviculture had a positive impact on mushroom productivity, which was higher in scenarios with moderate and high thinning intensities. The impact was highly positive in wetter scenarios, though only slightly positive and negative responses were observed in hotter and drier scenarios, respectively. Silviculture had a positive impact on mushroom productivity, especially in wetter scenarios. Precipitation had greater influence than temperature on total mushroom productivity in Maritime pine stands. The results of this paper will enable forest managers to develop optimal management approaches for P. pinaster forests that integrate Non-Wood Forest Products resources.