Miracle-dz/UniFAR-FTUs huggingface dataset:
Model-based anti-HIV therapy

Modern combination drug therapy has substantially improved the clinical management of HIV-1 infection. Still, the emergence of drug-resistant variants eventually leads to therapy failure in most patients. The selection of an optimal follow-up regimen is complicated by an ever-increasing range of possible drug combinations. In this thesis, we present foundations for rational, model-based treatment strategies. Firstly, we study viral evolution. In a simulation study, we establish a general link between the shape of a fitness landscape and population dynamics, using an idealized population undergoing mutation, recombination and selection at three biallelic loci as an example. Using techniques from survival analysis, a model of mutation dynamics in the absence of drug is proposed. Differently from mutation accumulation, mutations are found to disappear independently from each other, but with individual survival probabilities. A Fisher kernel for mixtures of mutagenetic trees is derived, quantifying the similarity of evolutionary escape from drug pressure between two viral sequence samples. Kernel-based prediction of drug resistance leads to significant improvements over an evolution-agnostic approach. Secondly, the controversial interplay between genotypic, phenotypic, and clinical resistance is analyzed. Methods for identifying resistance mutations from either in vitro or in vivo data, and for characterizing mutational covariation patterns are described. A case study focusing on reverse transcriptase inhbitors yields over 20 previously undescribed mutations, most of them extending classical resistance pathways. Finally, the widely held view of an ill-defined relation between phenotypic and clinical resistance is challenged, and a hybrid model incorporating both genotypic and inferred phenotypic information is shown to outperform its components in predictivity. Surprisingly, the incorporation of viral fitness does not lead to any further improvements. Thirdly, genotypic, clinical, host-specific, and structural determinants of viral cell entry via the human receptors CCR5 and CXCR4 are investigated. Previously undescribed mutations in the third hypervariable region of the viral envelope protein, CD4 cell counts, host heterozigosity for the CCR5-∆32 allele, number of sequence ambiguities arising from population sequencing, and presence of indels are shown to be predictive of coreceptor choice alone and in combination, as are changes in the predicted side-chain conformation in a three-dimensional model of the V3 loop.
Thermal treatment effect on dynamics of luminescent states in oxyfluoride glass-ceramics doped with Pr3+ and Tb3+

The 50GeO2–(50–x–y)PbO–yPbF2–xLnF3 glass single doped with Pr3+ and Tb3+ ions was studied. The composition of the material was modified by varying the content of both PbF2 ( y = 5, 10, 15 mol%) and LnF3 (x = 0.2 and 2 mol%). The differential thermal analysis (DTA) of as-melted samples was used to determine thermal characteristics. Optical techniques and kinetics measurements were used to monitor the effect of thermal treatment on spectroscopic properties and dynamics of luminescent states of optically-active ions in amorphous and two-phase systems. It was found that non-exponential decays of praseodymium luminescence in as-melted material become exponential or nearly exponential with corresponding longer lifetimes in thermally-treated samples. This effect was not so strong in the Tb3+-doped glass. The influence of the PbF2 content on luminescence dynamics was studied for samples doped with 2 mol% of Pr3+. It was observed that the increase of PbF2 content leads to lengthening of luminescence lifetime, e.g., the D2 lifetime increases from 4.1 to 45 μs in 5 and 15 mol% of PbF2 as-melted samples, respectively.
Performance of different varieties of mango under sub-montane zone of Maharashtra

Sixteen Mango varieties studied at Zonal Agricultural Research Station, Sub-montane Zone, Shenda Park Farm, Kolhapur from 2015-16 to 2017 - 2018 on fourteen years old mango garden having cultivars like Karel, Ratna, Vellai Kolamban, Amrapalli, Alphanso, Dudhpedha, Sindhu, Kokan Ruchi, Kesar, Fernandin, Vanraj, Goa Mankur, Suvarnarekha, Pairi, Mallika and Creeping planted at spacing of 10 x 10 m to evaluate their performance for growth and yield parameters. Analysis of three years pooled data revealed that Pairi has significantly highest plant height (7.5m) and maximum tree spread in E-W (6.3 m) and N-S directions (7.6 m) amongst all the varieties of mango. The variety Keshar recorded highest number of fruits/ tree (201) and maximum yield of 43.28 kg/tree amongst all the varieties of mango. During early productive phase it can be concluded that among varieties Keshar was found to perform better than the rest of the varieties for better production.
Absorption in packed towers with concurrent downward high-velocity flows: II - Mass transfer

Measurements were made of mass transfer coefficients with gas and liquid phase controlling resistance using a concurrent flow packed column with a wide range of operating conditions and 4 types of packing. Mass transfer coefficients were much larger than those obtainable in countercurrent towers. The results were correlated with dissipated energy values. The correlations obtained can be used to determine absorption efficiency. Experimental results show that the use of a high velocity concurrent flow column is particularly suitable when mass transfer is controlled by the liquid phase resistance with chemical reaction in the liquid. (18 refs.)
Supplemental Materials: Novel Isotypic g/z-Subunits Reveal Three Coatomer Complexes in Mammals

Fig. A 1 shows a Western blot analyzing the specificity of the antibodies against g- and z-isotypes. These antibodies were probed in different mammalian species (Fig. A 2). Coatomer was labeled with [35S]-methionine for different time periods, and the incorporation of [35S]-methionine as well as the corresponding stoichiometries of the coatomer subunits are shown in Fig. A 3. Characterization of anti-coatomer antibody 883 is depicted in Fig. A 4.
3D hierarchically mesoporous Cu-doped NiO nanostructures as high-performance anode materials for lithium ion batteries

We report on the rational design and synthesis of three-dimensional (3D) hierarchically mesoporous Cu-doped NiO architectures with an adjustable chemical component, surface area, and hierarchically porous structure. The effect of Mn doping and calcining temperature on the microstructure, surface area, and porous structure of the 3D mesoporous Cu-doped NiO nano-architectures is investigated using SEM, TEM, XPS, XRD, and nitrogen adsorption–desorption isotherm techniques. The electrochemical performance of the Cu-doped NiO architectures is studied via cyclic voltammetry (CV), galvanostatic charge–discharge and electrochemical impedance spectroscopy (EIS) techniques. The 3D hierarchically mesoporous Cu-doped NiO architectures display greatly enhanced electrochemical performance of high reversible capacity, high rate capability, and excellent cycling performance as LIB anode materials. The improved performance of 3D mesoporous CuxNiO anodes can be attributed to the synergetic effects of an optimal level of Cu doping and the hierarchically porous feature. The doping of Cu greatly improves charge transport kinetics at the interface between the electrode and the electrolyte, and the hierarchically porous structure provides a larger surface area, allows effective electrolyte penetration, and alleviates the strain induced by volume excursion in cycle processes.
Adsorption of Organic Contaminants from Water Using Tailored ACFs

Six activated carbon fibers (ACFs) with different chemical and physical properties were prepared by first curing a phenolic resin-coated glass fiber, followed by activation and post-treatment. Their adsorption properties were investigated to evaluate the removal of benzene, toluene, ethylbenzene, and p-xylene (BTEX) and the chemical warfare simulants dissopropylmethyl phosponate (DIMP) and half mustard (HM) from water. The adsorption isotherms showed that ACF SL-2 (activated with CO2/H2O at 800 °C) has a higher adsorption capacity for BTEX, DIMP, and HM than other ACFs. This suggests that the high adsorption affinity of SL-2 is related to its higher surface area, larger average micropore size of 11.6 A (especially effective for the adsorption of DIMP), and lower oxygen content of the surface. The adsorption isotherms are well represented by the Freundlich equation. For BTEX, the adsorption parameters based on carbon coating showed that, in all cases, ACFs have a higher K value than the best available data.
CLASSIFICATION OF METAL OBJECTS USING DEEP NEURAL NETWORKS IN WASTE PROCESSING LINE

Each year, a factory releases a lot of metal debris which is normally used in a recycling phase. In order to be eﬀectively recycled, it is necessary to classify the debris into diﬀerent classes. The sorting by hand takes a lot of times and eﬀort. Other classiﬁcation approaches which use color, size, weight, electrostatic, or magnetic features may not obtain high accuracy. It has a lack of technique to classify the metal debris. Thus, this paper proposes a framework for classiﬁcation of metal debris which is spread on a conveyor belt. The framework employs deep neural networks. Four diﬀerent deep neural network models were investigated and compared in our framework called the AlexNet model, the GoogleNet model, the VGGNet model, and the ResNet model to choose a suitable model for the framework. In addition, the experiments can also investigate and compare the operation of diﬀerent deep neural network models in a practical application instead of using conventional academic benchmarks. Experimental results demonstrated that the proposed framework could be one solution to separate the metal debris. Especially, the AlexNet model had the highest accuracy among the four models.
Investigating photoluminescence quantum yield of silicon nanocrystals formed in SiOx with different initial Si excess

Optical properties of silicon nanocrystals dispersed in SiO2 matrix were investigated in terms of photoluminescence quantum yield at room temperature. Two multilayer samples, prepared from substoichiometric silicon oxide layers by annealing at 1150°C were used to investigate the influence of Si concentration. Significant reduction of photoluminescence quantum yield and a very specific change of its excitation energy dependence upon variation of silicon excess are concluded from the experimental data. Possible mechanisms leading to these changes are discussed.
Government Expenditure Composition and Economic Growth: Empirical Evidence from Pakistan

Like other developing countries, in Pakistan, government expenditure composition always remained a challenging issue because of its direct and indirect consequences for macroeconomic performance of the country. This study aims to observe the effect of various elements of the government expenditures on economic growth of Pakistan for the period1973 to 2018. Based on the ADF test results, Autoregressive Distributive Lag has been employed to analyze the data. This study found that effect of public expenditure components namely expenditure on research and developmental, subsidies and other transfers, education, compensation to employees on per capita GDP remained positive and significant. While the expenditure on interest payment on loans and military have noteworthy and unhelpful effect on per capita output of Pakistan. This study suggested that the government should boost expenditure on research and development, education and employment to accelerate the economic growth in the country.
Comparative toxicity of nine metals to two Malaysian aquatic dipterian larvae with reference to sediment composition

A study was conducted on the effects of sediment type in modifying the toxicity of heavy metals to chironomus and culicoides larvae. Three types of sediment were obtained from three locations within the University Malaysia Terengganu compound and analyzed for sediment type. Based on the analysis, the sediment samples were classified as silt loam, silty–clay loam, and loam. Sediment toxicity tests were conducted following the standard methods of ASTM (2005). Toxicity studies using the three sediment samples were conducted to determine if sediment type affected the toxicity of heavy metals to the two dipterian larvae. The LC50 of the different heavy metals was observed to vary between the three sediment types. In the case of zinc, the LC50 value was observed to be 38.53 mg L−1 for silt loam, 42.22 mg L−1 for silty-clay loam and 70.99 mg L−1 for loam, in the case of Chironomus plumosus. This trend was observed for all nine heavy metals tested, as well as for both dipterian larvae. The data indicate that sediment type plays a role in the manner in which these organisms react to pollutants entering their habitat.
Application of Gamma Irradiation on Manufacturing Changran Jeotgal (aged and seasoned intestine of Alaska pollack) : Microbiological and Sensory Characteristics

Changran Jeotgal (aged and seasoned intestine of Alaska pollack) was prepared as the same method as commercial one and irradiated at 0, 2.5, 5.0 and 10 k㏉ by gamma ray for industrial application. Changran Jeotgal using 10 k㏉-irradiated red pepper powder was also prepared to compare with control (0 k㏉). Commercial red pepper powder was already contaminated at 3.810 CFU/ level by total plate count and 10k㏉ of irradiation reduced the number about 4 log cycles. Gamma irradiated Changran Jeotgal at 2.5,5.0, and 10k㏉ showed 3 6, and 7 log cycles of reduction compared to the non-irradiated control in the total plate count after 12 weeks of storage at 1. Using irradiated (10k㏉) red pepper powder reduced the microbial contamination significantly by 2 log cycles compared to the control. Sensory evaluation showed that the sample irradiated at 2.5 k㏉ was the most acceptable, followed by the sample using irradiated red pepper powder and non-irradiated control. Thus, 2.5 k㏉ of irradiation of Changran Jeotgal was effective to improve safety during distribution and storage without change of sensory quality. Furthermore, using the irradiated red pepper powder is also recommended for safety enhancement of the products.
Massive Preparation of Reduced-Sensitivity Nano CL-20 and Its Characterization

Nano 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) was produced massively by ball milling. One thousand grams of the raw CL-20 were used per batch. The product was characterized using laser granularity measurement, scanning electron microscopy (SEM), and differential scanning calorimetry (DSC). The results show that the pulverized particles were pseudo-spheres with an average particle size (d50) of 200 nm, and the thermal decomposition peak temperature of the nano CL-20 was 239.61°C lower than that of the micrometer-sized CL-20 at a heating rate of 15°C · min−1. Furthermore, compared with the raw CL-20, the impact and friction sensitivities of the nano CL-20 were considerably reduced by 116.2 and 22%, respectively, indicating the great improvement in safety of CL-20.
Application of atomic absorption spectrometry in the elements and heavy metals determination in biological media - human hair

Hair analysis is used in assessment of the body mineral status, and environmental or occupational exposures. This study was undertaken to compare the elements concentrations [calcium (Ca), magnesium (Mg), zinc (Zn), copper (Cu), iron (Fe), lead (Pb), and cadmium (Cd)] in hair from 995 persons taken in the years 2007-2010. The measurements were performed by atomic absorption spectrometry (AAS). The average values for concentrations were as follows (in μg/g): Ca – 414, Mg – 19, Zn – 160, Cu – 13, Fe – 10, Pb – 1.0, Cd – 0.07. The contents of Ca, Mg, Zn, Cu were statistically higher in the hair of females in comparison with males and the concentrations of Pb and Cd were lower. Significant correlations were found to exist between age of volunteers and the amounts of Ca, Mg, Zn, Fe and Pb. Both in case of correlations between age and elements contents and the correlating metals pairs, the variations between females and males hair were stated.
Identifying difficulties in rapeseed root penetration in farmers’ fields in northern European conditions

Tap‐rooted rapeseed is generally considered sensitive to soil compaction. We examined 473 Finnish rapeseed fields sown in 2007 to 2009 to both spring turnip rape Brassica rapa L. (dominant crop) and oilseed rape Brassica napus L. Roots were rated late in the growing season according to penetration capacity. Roots in each field were rated from G1 (no problems with root penetration) to G5 (failure to penetrate deeper soil layers). There were significant effects of year, crop species, soil type, special soil properties and soil cultivation methods on frequency of G1 and G4+5 roots. Restricted root penetration was a common phenomenon. Typically, fields had <30% G3 and G4+5 roots, however, some fields had >70% G4+5 roots and were cases for serious concern. Yield loss was linearly related to the incidence of G4+5 plants in 2007, but there was no relationship with the other years. Oilseed rape had a greater proportion of G4+5 roots than turnip rape and twice the proportion of G4+5 roots occurred in direct‐drilled fields than in reduced or fully tilled fields. Rapeseed yield decline may at least partly be related to poor root penetration and it is a useful indicator crop to demonstrate the degree of soil compaction and should be cultivated in fields where sufficient root penetration is possible.
Plant responses to long term elevated ozone in a British upland semi-natural grassland

A novel free-air gas concentration enrichment (FACE) experiment exposed a species rich semi-natural upland grassland to ozone at average levels of ambient + 75 ppb, + 25 ppb and + 15 ppb over a 6 year period in the North Pennines. In addition to this, high exposures lasting 4 days of up to 309 ppb occurred in June 2012. Three main factors were investigated over the growing season of 2012 in relation to exposure to elevated ozone: the flowering behaviour of 11 species; the nectar volume and composition of the hemi-parasite Rhinanthus minor; and the CO2 exchange of the ecosystem. Dactylis glomerata flower abundance significantly increased over ambient levels with exposure to + 15 ppb ozone, but not ambient + 25 ppb. Conopodium majus also exhibited significant increases in flower abundance, though the effect was seen in ambient + 25 ppb when compared to ambient air, but not ambient + 15 ppb. However, Ranunculus acris flower abundance reduced sharply in both ozone elevations. Peak flowering dates were shown to be two weeks later in two grass species, Festuca pratensis and Trisetum flavescens, when exposed to a long term background of ambient + 25 ppb, and short term exposure to a mean 140 ppb. Short term exposure to 77 ppb and 52 ppb ozone did not significantly affect nectar volume or composition in R. minor flowers; however there may have been an effect on sugar composition at 77 ppb exposure. There was no significant effect of long term ozone exposure at ambient + 75 ppb, ambient + 25 ppb and ambient + 15 ppb on ecosystem respiration, net ecosystem exchange (NEE), or gross primary production (GPP) relating to CO2; however data suggest NEE and GPP may have been reduced through foliar injury relating to acute ozone exposure to an average 309 ppb. The findings have wider implications for conservation of upland grassland species diversity, and also indicate the potential for implications for the wider grassland carbon sink during peak ozone episodes.
Cointegration and Causality between Stock Market Development and Economic Growth in Bangladesh

In this study, we emply Johansen cointegration, Vector Error Correction Model (VECM) and Granger causality Wald test based on VECM to investigate the linkage between stock market development and real economic growth in Bangladesh for the period from 1981 to 2014. Cointegration test confirms that there is a long run positive relationship exists between real economic growth and stock market development in Bangladesh. The empirical result based on the VECM estimate indicates that long run causality is running from stock market development to economic growth. The result also implies that real GDP growth in Bangladesh takes only eight and half months to converge to its long run equilibrium. The Granger causality Wald tests suggest that there is bidirectional causality running between real GDP growth and stock market development in the short run. Therefore, real economic growth and stock market development in Bangladesh are seemingly dependent as economic growth leads to stock market development (market capitalization ratio and turnover ratio) and turnover ratio leads to economic growth.
EFFECTS OF WATER ACTIVITY ON TEXTURAL CHARACTERISTICS OF PUFFED RICE CAKE

The moisture sorption isotherm of puffed whole-grain brown rice cakes was established by equilibrating dehydrated whole cakes over saturated salt solutions and found to be sigmoid-shaped. The effects of water activity (a w ) on textural characteristics of rice cakes were determined using a breaking test. The textural characteristics (first peak force, maximum peak force and work done) of rice cakes can be separated into two groups: a w 0.23-0.44 and 0.57-0.84. a w 0.44 was a critical point as far as rice cake texture is concerned
Effects of Nigella sativa L. and Cinnamomum zeylanicum Blume oils on some physiological parameters in streptozotocin-induced diabetic rats.

The effects of Nigella sativa L. and Cinnamomum zeylanicum Blume oils on some physiological parameters were investigated in streptozotocin (STZ)-induced diabetic male Wistar rats. STZ-induced diabetic rats showed significant increases in the levels of blood glucose, triglycerides, cholesterol, low density lipoprotein LDL-cholesterol, urea, alanine aminotransferase (ALT) and aspartate aminotransferase (AST) while body weight, high density lipoprotein HDL-cholesterol, total protein and uric acid levels were significantly decreased compared to normal rats. Administration of the tested oils to diabetic rats resulted in a significant decrease in blood glucose, triglycerides, cholesterol, LDL–cholesterol and ALT while HDL–cholesterol level was markedly increased after three weeks compared to untreated diabetic rats. In addition, treating diabetic rats with N. sativa plus C. zeylanicum oils showed significant increases in the levels of total protein, uric acid and creatinine. In contrast, administration of C. zeylanicum oil to diabetic rats resulted in a significant decrease in ALT level compared to the untreated diabetic rats. The results of this study indicate that the tested oils possess hypoglycemic, hypolipidemic and antioxidant effects in STZ-induced diabetic rats.