Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulations of atomic and electronic structure of realistic Co and Pt based nanoalloy clusters

The interest in alloys of late transition metals arises from their potential applications in high-density magnetic storage devices where they can be used as supported magnetic nanoparticle arrays and as stable, efficient and selective catalysts. The preparation of materials with optimal properties faces a number of technological and physical restrictions and requires an in-depth knowledge of the interplay between structural features on the atomic level and the desired macroscopic properties. In the thesis, after extensive discussion of Density Functional Theory and Tight Binding approaches the work focused on DFT calculations of bulk systems, surfaces and small clusters. The results allow to conclude on general validity of the method and especially to justify the local neutrality assumption in the case of low-coordinated sites in nanoparticles. Basic structural, magnetic and energetic properties were also studied and compared with the experimental data. Subsequently TB calculations were performed and verified with DFT results. The scope of the calculations was then extended for the case of nanoclusters of realistic sizes, unavailable in DFT. Local Densities of State on sites with different chemical environment and coordination numbers were analyzed. The observations prove that basic features of LDOS (d-band centre and d-band width) can be predicted by simple laws on the basis of two terms: a structural term represented by the linear function of the site coordination and a chemical term as a rigid shift which opens a new way to predict the ordering tendency (mapping of the ordering domains) for any transition metal nanoalloy as a function of its size.
The Effects of Exchange Rates on Macroeconomic Variables: A Study of the Selected Emerging Economies

The exchange rate channel of the monetary transmission mechanism has gained importance through widespread use of the floating exchange rate regime with increased globalization. In this context, this study aims to explore the effectiveness of the exchange rate channel on net exports and thereby total output and price level using vector auto-regression (VAR) models. The sample countries are Turkey and Argentina, which have employed a floating exchange rate regime since 22 February 2001 and 11 February 2002, respectively. The monthly data set consists of five macro-economic variables, which are short-term interest rates, the real effective exchange rate, net exports, the consumer price index, and the industrial production index for the period 2003 to 2010. The impulse-response function outcomes indicate that the operation of the exchange rate channel is effective, both in Turkey and in Argentina.
RNA polymerase mapping in plants identifies enhancers enriched in causal variants

Promoter-proximal pausing and divergent transcription at promoters and enhancers, which are prominent features in animals, have been reported to be absent in plants based on a study of Arabidopsis thaliana. Here, our PRO-Seq analysis in cassava (Manihot esculenta) identified peaks of transcriptionally-engaged RNA polymerase II (Pol2) at both 5’ and 3’ ends of genes, consistent with paused or slowly-moving Pol2, and divergent transcription at potential intragenic enhancers. A full genome search for bi-directional transcription using an algorithm for enhancer detection developed in mammals (dREG) identified many enhancer candidates. These sites show distinct patterns of methylation and nucleotide variation based on genomic evolutionary rate profiling characteristic of active enhancers. Maize GRO-Seq data showed RNA polymerase occupancy at promoters and enhancers consistent with cassava but not Arabidopsis. Furthermore, putative enhancers in maize identified by dREG significantly overlapped with sites previously identified on the basis of open chromatin, histone marks, and methylation. We show that SNPs within these divergently transcribed intergenic regions predict significantly more variation in fitness and root composition than SNPs in chromosomal segments randomly ascertained from the same intergenic distribution, suggesting a functional importance of these sites on cassava. The findings shed new light on plant transcription regulation and its impact on development and plasticity.
Analysis of Capital Flight in Developing Countries: A Study on Turkey between 1980 and 2010

The aim of this study is to determine whether there is a relationship between Capital flight and some macroeconomic variables by using anual data between 1980 and 2010 in Turkey. Capital flight measured by World Bank (1985) method, was used as dependent variable and external debt, foreign direct investment, uncertainty, real GDP growth, exchange rates, trade balance and consumer price index were used as independent variables. Ordinary Least squares estimation method, Johansen-Jeselius cointegration test, Granger causality test and variance decomposition results produced by VEC model were used in the study. After those econometrics and economics analysis, this paper put forward that there is a long run relationship between some macroeconomic variables and capital flight.The results show external debt, foreign direct investment inflows, and foreign reserves to be the major effector of capital flight.
Accumulation of 137Cs in bottom sediments of the Curonian Lagoon

The mobility and fate of radionuclides in the environment to a great extent depend on the speciation and on their transformation. Removal processes of portion of water-soluble radionuclides released to the environment are usually related to their sorption onto soil and sediment particles. Natural sediments are usually a sink for various contaminants but they may become a source, for example, under drastically changing environmental conditions in the fresh and saline waters mixing zone. Caesium is one of the most important anthropogenic radionuclides, which was introduced into the environment through nuclear weapons testing and nuclear accidents at Chernobyl; its inventories in radioactive waste are significant as well. Caesium harmful effects on animate nature are evident taking into account its properties: unlimited solubility, potential mobility and high bioavailability. The sorption-desorption processes of radiocaesium on various minerals have been the subjects of many recent studies [2, 5, 7, 11, 12]. The numerous publications concerning the binding of Cs by clays reflect the importance of this radionuclide relevant to safety assessment, and on the other hand, the search for low-cost barriers for isolation of radioactive wastes Accumulation of Cs in bottom sediments of the Curonian Lagoon Galina Lujaniene , Beata Vilimaite -Šilobritiene , Kęstutis Jokšas
INFLUENCE OF DRIP IRRIGATION MANAGEMENT ON SUGAR BEET YIELD AND SOME WATER RELATIONS AT NORTH NILE DELTA

Two field experiments have been conducted at the experimental farm of Agriculture Faculty, Kafr El-Sheikh University, Kafr El-Sheikh Governorate (31° 05’ N latitude and 30° 56’ E longitude) during the two successive growing seasons of 2009/2010 and 2010/2011 to study the overall effect of drip irrigation management on sugar beet productivity, its components and some water relations in clay soil in North Nile Delta. The treatments were arranged in a split plot design with four replicates. The main plots were assigned to three types emitters of drip irrigation system namely: built-in, simple orifice and long-path. Three irrigation regimes i.e. 10 minutes daily, 20 minutes every two days and 30 minutes every three days were allocated in the sub plots. The main results in this study can be summarized in the following points: 1-The drip irrigation with long-path emitters (Turbo) had been achieved the highest average values of root length (34.54 and 34.20 cm), root diameter (14.43 and 14.29 cm), sucrose percentage (20.77 and 20.71%), root yield (25.93 and 26.26 ton fed.-1), sugar yield (5.39 and 5.44 ton fed.-1), water productivity (18.74 and 18.84 kg root m-3 water consumptive use) and irrigation of water productivity (15.33 and 15.32 kg root m-3 applied water) during 2009/2010 and 2010/2011 growing seasons, respectively. 2-The highest average values of root yield (26.16 and 26.51 ton fed.-1), sugar yield (5.0 and 5.05 ton fed.-1), water productivity (17.56 and 17.64 kg root m-3 water consumptive use) and irrigation of water productivity (14.82 and 14.87 kg root m-3 applied water) had been obtained at irrigation sugar beet 20 minutes every two days in the 1st and 2nd seasons, respectively. 3-The highest average values of root yield (27.76 and 28.0 ton fed.-1) and sugar yield (5.81 and 5.85 ton fed.-1) were obtained with interaction between irrigation 20 minutes every two days and the Turbo emitter (long–path) in the 1st and 2nd seasons, respectively, while, the lowest average values of root yield (20.79 and 21.08 ton fed.-1) and sugar yield (3.70 and 3.73 ton fed.-1) had been obtained with irrigation 30 minutes every three days using the Metalic emitter (simple-orifice) in the same growing seasons, respectively.
Liquid Chromatography Column Theory

Introduction to the liquid chromatography column the plate theory the column dead volume extensions of the plate theory applications of the plate theory introduction to the rate theory the Van Deemter equation alternative equations for peak dispersion validation of the Van Deemter equation extra column dispersion LC column design - the design protocol LC column design - the design process for packed columns LC column design - the design process for open tubular columns preparative liquid chromatography columnn. Appendices: the diffusion coefficients of some low molecular weight substances the diffusion coefficients of some selected peptides the physical properties of some LC solvents.
A simple model of a quadruped discovers single-foot walking and trotting as energy optimal strategies

It is widely held that quadrupeds choose steady gaits that minimize their energetic cost of transport, but it is difficult to explore the entire range of possible footfall sequences empirically. We present a simple model of a quadruped that can spontaneously produce any of the 2500+ planar footfall sequences available to quadrupeds. Through trajectory optimization of a work and force-rate cost, and a large sample of random initial guesses, we provide stronger evidence towards the global optimality of symmetrical four-beat walking at low speeds and two beat running (trotting) at intermediate speeds. Using input parameters based on measurements in dogs, the model predicts the correct phase offset in walking. It also spontaneously reproduces the double-hump ground reaction force profile observed in walking, and the half-sine profile observed in trotting, despite the model’s lack of springs. However, the model incorrectly predicts duty factor at the slowest speeds, and does not choose galloping as globally optimal at high speeds. These limitations might point to missing levels of complexity that could be added to future quadrupedal models, but the present results suggest that massive legs, elastic components, head-neck oscillations and even multi-linked legs are not critical determiners for the optimality of natural quadrupedal walking and trotting. Author summary
T cell regulation of acute and chronic viral infection

Regulatory T cells play a critical role in maintaining tissue homeostasis and preventing the development of immunopathology. DEREG mice express a DTRenhanced green fluorescent protein (eGFP) transgene under the control of the Foxp3 promoter allowing for Treg depletion following DT administration. DEREG mice have been utilized to investigate the role of Tregs in a wide range of disease settings. Administration of DT to naïve DEREG mice resulted in the rapid depletion of Foxp3 Tregs from the peripheral blood. However, by day 4 post-DT administration, a GFP Foxp3 Treg population emerged that lacked expression of the DTR transgene and was resistant to further depletion by additional DT treatment. I further evaluated the impact of Treg depletion during both acute and chronic viral infections. Similar to naïve mice, Treg numbers rapidly rebounded during an inflammatory setting following an acute viral infection. DT treatment of both WT and DEREG mice following both acute and chronic viral infections induced exacerbated disease as compared to PBS-treated controls. Furthermore, following a chronic systemic viral infection, DT treatment resulted in nearly 100 percent mortality in both WT and DEREG mice while the PBS-treated controls survived. My results demonstrate that Treg depletion in DEREG mice is transient and that DT administration can have adverse effects during virus-induced
Reduction of iron ore fines in the Ifcon furnace

This work involved an investigation into the mechanisms governing the reduction of material in the solids bed of the Ifcon® process. Thermo gravimetric analyses were done to investigate the influence of various operational parameters on the rate of solid state reduction. The experiments were modeled, and model predictions were compared to experimental results. Kinetic data was analised and the reduction rate constants were calculated. The rate constants were used as inputs to a model, which describes the reduction behaviour and temperature profile in a composite solids bed (similar to that in the Ifcon® process). High temperature reductionand melting tests were done in an 150 kW induction furnace, to simulate final reduction in a solids bed. The temperature profile through the solids bed was measured and results were compared to model predictions. Finall y the extent to which so lid state reduction occurs in the solids bed was estimated as a function of production rate .
Genetic discontinuity of Digenea (Rhodomelaceae, Rhodophyta) from Mexico supports recognition of two new species, D. mexicana and D. rafaelii

Copyright © 2018 The Korean Society of Phycology 231 http://e-algae.org pISSN: 1226-2617 eISSN: 2093-0860 Genetic discontinuity of Digenea (Rhodomelaceae, Rhodophyta) from Mexico supports recognition of two new species, D. mexicana and D. rafaelii Ga Hun Boo, Daniel Robledo, Gabriella Andrade-Sorcia and Sung Min Boo* University Herbarium, University of California Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, CA 94720, USA Department of Marine Resources, Centro de Investigación y Estudios Avanzados Unidad Mérida, Yucatán, CP 97310, Mexico Programa de Investigación en Botánica Marina, Departamento de Biología Marina, Universidad Autónoma de Baja California Sur, Carretera al sur 5.5 km, P.C. 23080, 19-B, La Paz, Baja California Sur, México Department of Biology, Chungnam National University, Daejeon 34134, Korea
Mian: Interactive Web-Based 16S rRNA Operational Taxonomic Unit Table Data Visualization and Discovery Platform

In recent years, there has been strong interest in examining the microbiome and its impact on human health and the environment. By leveraging modern sequencing technologies, investigators can quickly determine the composition of a given microbial sample. At the same time, the same investigations often yield an array of categorical and numerical metadata derived from the sequenced samples such as immunohistochemical measures or locality information. Understanding how the microbiome data is associated with this external metadata is essential in developing targeted treatments for chronic diseases or proposing bacteria-modulated host responses. While many R or Python libraries and command-line tools have been developed for specific analysis purposes, there are still relatively few tools to facilitate open-ended data exploration and hypothesis generation. Here we introduce Mian, an open-source web framework to interactively visualize or run a suite of statistical and feature selection tools on the microbiome to identify important taxonomic groups in the context of any provided categorical or numerical metadata. Visualizations include boxplots, correlation networks, and PCA or NMDS scatterplots. Tools include Fisher’s Exact Test, Boruta feature selection, alpha and beta diversity, and differential and correlational analysis. Mian supports multiple standard representations of the OTU table as input and optionally subsamples the data during the upload process. Users can also filter and aggregate the OTU table at different taxonomic levels and dynamically adjust analysis parameters to see how the visualizations, results, and statistical measures change in real-time. Mian is freely available at: miandata.org
Mating system complexity and cryptic speciation in the seed bank pathogen Pyrenophora semeniperda

Mating strategies contributing to a balance between inbreeding and outcrossing are understudied in all but a few model fungal pathogens. This study examined factors that influence the occurrence of the sexual state of Pyrenophora semeniperda. It was consistently found to have functional copies of the MAT1-1 and MAT1-2 idiomorphs essential for sexual reproduction, despite considerable polymorphism in both single nucleotide polymorphisms (SNPs) and number of 18base minisatellite repeats. The two idiomorphs occurred at approximately equal frequencies across 25 populations on Bromus tectorum seeds in the western United States, suggesting maintenance of sexual reproduction. The putative mating system is described as facultative pseudohomothallism, with only one of the two MAT1 idiomorphs found in a nucleus. Unikaryotic strains of opposite mating type can potentially mate, as can nuclei of opposite mating type in a thallus that results from anastomosis between vegetatively compatible unikaryotic strains. Strains shown to be dikaryotic using simple sequence repeat (SSR) markers may contain either or both MAT1 idiomorphs. Most populations consist of a mixture of MAT1-1, MAT1-2 and MAT1-1/MAT1-2 genotypes. A possible constraint on recombination is the presence of multiple strain groups characterized by ITS haplotype. These are apparently vegetatively incompatible, as even dikaryotic strains are invariably composed of a single ITS haplotype. Different ITS haplotypes also have unique combinations of MAT1-1 and MAT1-2 allelic variants, suggesting that perhaps these strain groups are also sexually incompatible. Phylogenetic analysis using both genome-wide SNP/indel polymorphisms and SSR markers demonstrated genetic divergence among ITS haplotypes, supporting the hypothesis that these strain groups may represent cryptic species.
Inactivation of Protein Tyrosine Phosphatase 1B (PTP1B) Activity by the Aqueous Partition of Guava Leaf Extract

Guava leaf tea has been used as a folk medicine for treating hyperglycemic conditions in Asia and Africa. The hypoglycemic efficacy of guava leaf has been documented by many scientists in these regions, but the hypoglycemic mechanism is poorly understood. Guava leaves were extracted with methanol and the crude extract was partitioned against hexane, ethyl acetate, and butanol in sequence. The leftover in water is defined as the aqueous partition. A second smaller batch was extracted with hot water directly. Oral glucose tolerance test was carried out on healthy mice instead of diabetic mice that lack endogenous insulin. Glucose uptake was examined with 3T3-L1 adipocytes. Oxidative effect on PTP1B (protein tyrosine phosphatase 1b) was carried out with real-time PTP1B enzymatic assay. The aqueous partition of guava leaf extract possesses a potent inhibitory effect on PTP1B enzymatic activity and this PTP1B inhibition is through a slow oxidative but reversible inactivation on the enzyme. The reversible inactivation would suggest guava leaf extract may augment PTP1B inhibition alongside the endogenous H2O2 which itself is induced by insulin. In addition, our study confirmed the hypoglycemic efficacy being associated with guava leaf and found the most effective molecules reside in the aqueous partition which is also less cytotoxic to Chinese hamster ovary cells when compared to other less polar partitions. The guava leaf extract can modulate insulin activity through a redox regulation on PP1B enzymatic activity. It is speculated that a compound similar to gallocatechin in the aqueous partition can reduce an oxygen molecule to hydrogen peroxide which in turn oxidizes the catalytic residue Cys in PTP1B. Therefore, the guava leaf tea can serve as a functional hypoglycemic drink that is suitable for either healthy or diabetic subjects.
Enhancing the Irish NFI usingk-nearest neighbors and a genetic algorithm

This paper presents a nationwide application of k-nearest neighbors (k-NN) to estimate growing stock volume per hectare for the Irish National Forest Estate using optical satellite imagery and field inventory data from the second National Forest Inventory (NFI). Two approaches are tested: an unweighted k-NN and an improved version (ik-NN) that is optimised using a genetic algorithm. The performance of the models is assessed in terms of the root mean square error (RMSE) and prediction error. From the simulations, it was found that the optimal value of k was 3, and the smallest pixel-level RMSE for growing stock was 126 m3·ha–1 when ik-NN was used. Comparisons with estimates from the NFI show that the ik-NN technique can enhance the Irish NFI. These improvements include a total estimate of growing stock volume of 102 million m3 with a confidence interval of ±3%, which is smaller than the NFI-reported confidence interval of ±5%. In addition, while total county-level estimates of growing volume estimated usin.
Desulphurization of petroleum coke

The sulphur content in coal and petroleum coke varies from traces to 10% or more by weight. The exists in two forms inorganic and organic. Sulfur in coal and rocks associated with coal mines like petroleum wastes can occur as organic sulfur, surfate sulfur and pyritic sulfur. On combustion of coal / coke, sulphur gets released into the atmosphere and contributes to the air pollution in the form of acid rain. Organic sulphur occurs as an intergral part of the molecular coal and the petroleum waste matrix and is not readily accessible for microbial attack. So, the removal of organic sulphur from coal/coke/petcoke while retaining its fuel value is most difficult, Chemical processes need a very lengthy and tedious process involving elevated temperature and pressure, which is not feasible on a technical scale. On the other hand, biological processes occur under very mild reaction conditions. Hence, the desulphurization of petroleum waste by microbial technique can be achieved in an economical and simpler way. In the presnt paper, a biological process using Thiobacillus thiooxidans has been described for the removal of total sulphur from Navanagar5 petcoke sample. The results have shown that the mean total sulphur content in the metcoke sample was 6.32%. After first bacterial leaching with T.thiooxidans 13.5% sulphur was removed by the bacteria and the remaining sulphur content in the metcoke was 5.46%. The second leaching of the previously leached petcoke sample, using T.thiooxidands resulted in to sulphur removal up to 93%.
Could the growth of Litopenaeus vannamei be compensated by long-term cyclic feed deprivation and following refeeding?

ABSTRACT The effects of long-term cyclic feed deprivation and refeeding on compensatory growth and body composition of Litopenaeus vannamei were assessed for five different feeding protocols (i.e., 0, 1, 2, 4, 7 days fasting/days feeding) during 15 study weeks. Shrimp in each tank were weighed to calculate growth parameters. The control group has shown the highest specific growth rate (SGR) and the highest final weight compared to the cycling-feeding groups during the first 8 weeks (P < 0.05). On the other hand, during the realimentation period (9–15 weeks), SGR of the cycling feeding groups and the control group are equivalent (P < 0.05). It has been concluded that long-term cycling starvation and feeding treatment lead to compensatory growth of L. vannamei. Final survival rates ranged between 64.4% and 79.9% in all the groups (P > 0.05).