Miracle-dz/UniFAR-FTUs huggingface dataset:
The Active-to-passive Transition of Chalcopyrite

The active-to-passive transition of chalcopyrite is studied using electrochemical techniques and leaching tests to establish the conditions under which chalcopyrite electrodes display active-passive behavior. Results from potentiostatic anodic polarizations are predictive and agree very well with leaching results while potentiodynamic techniques give only erratic values. The critical current and oxidation rate in the active potential range increases with the concentration of acid, but the passivation potential decreases. The corrosion rate of chalcopyrite was studied at various temperatures and concentrations of acid in electrolytes containing only ferric (no ferrous) using electrochemical impedance spectroscopy; the higher the concentration of acid and the lower the temperature, the lower the corrosion rate.
Effect of mutations in DUNC-45 on its activity as a myosin chaperone, using Drosophila as a modelm

Myosin II is an actin-based molecular motor that drives movement and its folding is a critical step in myofibril formation and muscle assembly. Myosin folding is mediated by the muscle specific chaperone UNC-45. UNC-45 has a C-terminal UCS domain that binds to the myosin head. UNC-45 is important for myosin folding and protection against stress conditions. Interaction between the myosin head domain and the UCS domain of UNC-45 is well established. However, the precise residues on each of these proteins that interact with each other are not well known. The UCS domain is a highly conserved region across all isoforms of UNC-45. In this study, three residues in the UCS domain: arginine 864, asparagine 786 and serine 747, were chosen to test for their importance in myosin interaction and were mutated to alanine, arginine and arginine, respectively. These three residues lie in the conserved cleft of Drosophila melanogaster UNC-45 (DUNC-45) and they are oriented outwards on the protein surface. We hypothesized that these residues mediate interactions of the DUNC-45 chaperone with the myosin head. Molecular cloning of the constructs in bacteria permitted induction of mutant protein expression and these were purified using affinity and size exclusion chromatography. They were tested for chaperone function and stability using biochemical assays. Aggregation kinetics showed the mutant proteins were quite heat-sensitive, suggesting that the amino acid residues may be important for DUNC-45 function. Myosin-binding assays showed no difference in the ability of the mutant UNC-45 molecules to bind myosin compared to WT-DUNC-45. The R864A-DUNC-45 mutation was also expressed in D. melanogaster using P element-mediated germline transformation. Ten viable fly lines were obtained. Protein was expressed in the DUNC-45 null background, to ensure that only the mutant DUNC-45 is expressed in the transgenic flies. Functional tests were performed to analyze the effect of this mutation on the function of the myosin protein in vivo. Flight testing of one-day-old flies revealed no significant difference between the transgenic mutant flies and the control. No change in myosin heavy chain accumulation during adult thoracic muscle development was observed in the presence of the mutated chaperone by SDS-PAGE gel analysis. Thus, flies grown at room temperature were unaffected by the mutant DUNC-45. The effect of increased temperature on development was also tested. Even though the lethality of heat-shocked embryos was slightly higher for the mutant transgenic lines compared to control, the difference was not statistically significant. Overall, in vitro studies suggested that the R864A DUNC-45 was prone to aggregation but did not significantly affect myosin accumulation or function in vivo. In summary, in vitro aggregation studies revealed that these mutant proteins could be important for regulating chaperone function, however binding studies of all three mutants and in vivo studies of the R864A-DUNC45 mutant did not reveal a significant effect of the…
Morphologies Controlled Synthesis of MnO2 Nanostructures

Spherical MnO2 nanosheet aggregates have been synthesized by the reaction between MnSO4 and KMnO4 at room temperature. After the resulting products are treated under hydrothermal conditions, MnO2 nanorods and tower‐like crystals have been prepared in the absence/presence of cetyltrimethylammonium bromide, respectively. The products are characterized by field‐emission scanning electron microscopy and x‐ray diffractometer, respectively.
Lipase-based in vitro release assays for pharmaceutical lipid formulations

The purpose of this project was to develop and test lipase-based in vitro release (IVR) assays for model and active pharmaceutical ingredients (API) entrapped in lipid formulations based on mixtures of phosphatidylcholine (PC) and glycerol dioleate (GDO). Two dyes, Fluorescein disodium salt and Patent Blue V sodium salt, functioning as model drug compounds, were investigated separately in the PC/GDO formulation. As the lipid formulation containing one of the two dyes was injected in vitro into a buffered saline solution, the lipids self-assembled into liquid crystal (LC) phases which trap the dye inside a nearly spherical LC depot. The dye was then released slowly over time. In the presence of lipases, the dye release was accelerated by biodegradation of the lipids. The IVR rate was followed by spectrophotometric measurements of the dye concentration in the aqueous release medium. This thesis describes the investigation of many parameters such as the suitability of the two dyes as model APIs, the effect of two different triacyl glycerol lipases (TGL) and a phospholipase, different concentrations of lipases as well as mixtures of different lipases, different lipid formulation types, the difference between a single vial experimental setup and a 96 well plate setup, as well as an overall evaluation of the project. It was shown that the addition of lipases dramatically increases the IVR rate, even at low concentrations. The effect on IVR was much higher for the phospholipase than for the TGLs. This research is of interest to the research- and development based pharmaceutical company Camurus AB in Lund, Sweden, currently developing pharmaceutical products based on the lipid liquid crystal formulation technology. The results will be used in the assessment and development of in vitro in vivo correlation (IVIVC) assays which are useful for formulation development and for regulatory purposes in conjunction with post registration changes related to Chemistry, Manufacturing and Controls (CMC).
Mutation-based Compliance Testing for RISC-V

Compliance testing for RISC-V is very important. Essentially, it ensures that compatibility is maintained between RISC-V implementations and the ever growing RISC-V ecosystem. Therefore, an official Compliance Test-suite (CT) is being actively developed. However, it is very difficult to achieve that all relevant functional behavior is comprehensively tested.In this paper, we propose a mutation-based approach to boost RISC-V compliance testing by providing more comprehensive testing results. Therefore, we define mutation classes tailored for RISC-V to assess the quality of the CT and provide a symbolic execution framework to generate new test-cases that kill the undetected mutants. Our experimental results demonstrate the effectiveness of our approach. We identified several serious gaps in the CT and generated new tests to close these gaps.
Thermal pretreatment of lignocellulosic biomass

Torrefaction is a process to convert diverse lignocellulosic biomass feedstocks into an energy dense homogeneous solid, a pretreatment for subsequent thermochemical conversion. Loblolly pine was treated by wet torrefaction (hot compressed water, 200–260°C) and dry torrefaction (nitrogen, 250–300°C), with mass yield of solid product ranging between 57 and 89%, and energy densification to 108–136% of the original feedstock. The solid product has been characterized, including proximate analysis, fiber analysis, ultimate analysis, and equilibrium moisture. In both dry and wet torrefaction, increasing temperature results in decreased mass yield and increased energy densification, and results in a solid with increased carbon content, decreased oxygen content, and decreased volatiles. The biomass is transformed into a fuel similar to a low‐rank coal. Generally, the wet torrefaction process produces a solid with greater energy density than dry torrefaction, with the same mass yield. The fiber analysis indicates that hemicellulose is quickly removed during wet torrefaction, and the solid product contains substantial quantities of aqueous soluble compounds. The equilibrium moisture content of solids produced by both processes is somewhat decreased from that of the biomass feedstock, indicating a hydrophobic solid suitable for storage and transportation. © 2009 American Institute of Chemical Engineers Environ Prog, 2009
Conservation tillage systems: a review of its consequences for greenhouse gas emissions

Conservation tillage (CT) is an umbrella term encompassing many types of tillage and residue management systems that aim to achieve sustainable and profitable agriculture. Through a global review of CT research, the objective of this paper was to investigate the impacts of CT on greenhouse gas (GHG) emissions. Based on the analysis presented, CT should be developed within the context of specific climates and soils. A number of potential disadvantages in adopting CT practices were identified, relating mainly to enhanced nitrous oxide emissions, together with a number of advantages that would justify its wider adoption. Almost all studies examined showed that the adoption of CT practices reduced carbon dioxide emissions, while also contributing to increases in soil organic carbon and improvements in soil structure.
Lipid Oxidation: Measurement Methods

Numerous analytical methods are routinely used for measuring lipid oxidation in foods. However, there is no uniform and standard method for detecting all oxidative changes in all food systems. Therefore, it is necessary to select a proper and adequate method for a particular application. The available methods to monitor lipid oxidation in foods can be classified into five groups based on what they measure: the absorption of oxygen, the loss of initial substrates, the formation of free radicals, and the formation of primary and secondary oxidation products. A number of physical and chemical tests, including instrumental analyses, have been employed in laboratories and the industry for measurement of various lipid oxidation parameters. These include the weight-gain and headspace oxygen uptake method for oxygen absorption: chromatographic analysis for changes in reactants; iodometric titration, ferric ion complexes, and Fourier transform infrared (FTIR) method for peroxide value; spectrometry for conjugated dienes and trienes, 2-thio-barbituric acid (TBA) value, p-anisidine value (p-AnV), and carbonyl value; Rancimat and Oxidative Stability Instrument method for oil stability index; and electron spin resonance (ESR) spectrometric assay for free-radical type and concentration. Other techniques based on different principles, such as differential scanning calorimetry (DSC) and nuclear magnetic resonance (NMR), have also been used for measuring lipid oxidation. In addition, sensory tests provide subjective or objective evaluation of oxidative deterioration, depending on certain details. Keywords: lipid oxidation; dietary lipids; food quality; differential scanning calorimetry; nuclear magnetic resonance; electron spin resonance; sensory analysis; Fourier transform infrared method
Chemical Durability Studies of Perfluorinated Sulfonic Acid Polymers and Model Compounds under Mimic Fuel Cell Conditions

Peroxide radical treatments of a perfluorinated ionomer used in polymer electrolyte membrane (PEM) fuel cells and its small molecule analogues were carried out, along with analysis of the resultant products. Molecules containing terminal carboxylic acids degraded at least 1 order of magnitude faster than noncarboxylate materials; all of the systems did show peroxide-initiated degradation nonetheless. Product analysis suggests that terminal carboxylic acids react according to a sequential chain shortening, consistent with previous studies. Cleavage of side chains from both polymer and model compounds was also observed to be important and in fact may be the dominate pathway in low carboxyl content commercial PEM membranes, based on the following comparison of reactivity and concentration. The relative reactivities of carboxylic chain ends and ether linkages is approximately 500, as calculated using model compounds fluoride generation rates. Commercial perfluorosulfonic acid (PFSA) products contain minimal c.
Arsenic accumulation and speciation in freshwater fish living in arsenic-contaminated waters

Environmental context. Inorganic arsenic, a well-known human carcinogen, represents a major worldwide environmental problem because contaminated water supplies have lead to widespread human exposure. This study investigates the arsenic content of freshwater fish from arsenic-contaminated and non-contaminated sites in Thailand, and reports high arsenic concentrations and significant amounts of inorganic arsenic in the edible muscle tissue. The data suggest that freshwater fish may represent a significant source of inorganic arsenic to some human populations. Abstract. Striped snakehead (Channa striata), carnivorous freshwater fish that serve as popular food in Thailand, were collected from a reference site (1.4 µg As L–1) and from two arsenic-contaminated ponds (Pond A, 550 µg As L–1; Pond B, 990 µg As L–1) in southern Thailand and analysed for arsenic by inductively coupled plasma mass spectrometry (ICPMS) and for arsenic species by HPLC-ICPMS performed on aqueous methanol extracts of muscle, liver and gill (n = 3 fish from each site). Mean total arsenic concentration in muscle tissue of C. striata collected from the reference site was 1.9 µg As g–1 (dry mass) while fish from the contaminated sites contained 13.1 µg As g–1 (Pond A) and 22.2 µg As g–1 (Pond B). Liver and gill tissues showed similar increasing arsenic concentrations on going from the reference site to Ponds A and B, with Pond B showing the highest levels. Speciation analysis on the three tissues showed that, although arsenate was the major extractable arsenical in reference fish (e.g. 0.73 µg As g–1 in muscle tissue), dimethylarsinate was by far the dominant arsenic species in fish from the two contaminated sites. Three non-carnivorous fish species (Danio regina, Rasbora heteromorpha and Puntius orphoides), collected from Pond B only, had lower arsenic concentrations (7.9–11.3 µg As g–1 in muscle tissue) than did C. striata, and contained appreciable amounts of trimethylarsine oxide together with two other major arsenicals, arsenate and dimethylarsinate, and smaller quantities of arsenite and methylarsonate. The study shows for the first time a clear effect of water arsenic concentrations on natural fish tissue arsenic concentrations, and is the first report of a freshwater fish species attaining arsenic concentrations comparable with those found in marine fish species. Furthermore, the high concentrations of toxic inorganic arsenic (predominantly arsenate) in the muscle tissue of the edible fish C. striata have human health implications and warrant wider investigations.
On the apparent spectroscopic rigidity of floppy molecular systems

There has been a wealth of recent infrared experimental data on van der Waals and hydrogen bonded complexes obtained under cooled, supersonic jet conditions where only a small fraction of the total bound quantum states can be elucidated. This partial set of data can often be well fit to a traditional Watson Hamiltonian derived from a rigid rotor perspective with low order centrifugal distortion effects included. In this paper we show that even in extremely floppy molecular systems with wide amplitude vibrational motion, the quantum term values are very well fit by a rigid or semirigid rotor Hamiltonian over the limited range of energy states accessible in a cooled beam. We provide explicit examples of this behavior by full quantum solutions in two extremes of floppy motion: (1) a symmetric triatomic with a square well bending potential (‘‘hinge’’) and (2) a nearly free internal rotor (‘‘pinwheel’’). These results show that potentials with fundamentally different topologies can be consistent with same data.
Project survey

Graphs are ubiquitous in the real world, e.g., social networks, molecular structures, and world wide webs. Recent years, the machine learning community has made substantial efforts on many graph-based learning tasks, such as node classification and link prediction. Unlike Convolutional Neural Networks (CNN) which perform the end-toend learning on grid-structured images, graph-based models have to face the data where nodes are arbitrarily connected with others. There have been several works that generalize convolutional networks on graphs, e.g., Burna et al. (2014); Duvenaud et al. (2015); Kearnes et al. (2016); Defferrard et al. (2016). Graph Convolutional Networks (GCN) (Kipf & Welling, 2016) apply the adjacency matrix of the graph as a filter that directs information to propagate over the edges. The feedforward process is formulated as
Evaluation of genetic diversity among chickpea (Cicer arietinum) genotypes using PCR based simple sequence repeats markers

To assess genetic diversity a set of 50 germplasm accessions of chickpea (Cicer arietinum) were screened for polymorphism using 102 simple sequence repeat (SSR) primers. All the 102 primers produced amplification with a total number of 219 alleles. One hundred and eighty four alleles were polymorphic whereas 35 monomorphic. The number and size of alleles amplified ranged from 1to 7 and 50 to 1500bp respectively. The PIC values of the primers ranged from 0.20 to 1.00. Primers H1O01, H1O09, H5E05 and P74 produced a unique band in genotypes H91-47, FG-711, H00-256 and CSG-8962 respectively which can be used for genotype identification. Two of the genotypes, HC-1 and HC-3, showed the maximum genetic similarity value of 0.91. HK99-27 and CSG-8962 are most diverse genotypes at a minimum value of similarity coefficient i.e. 0.68. This information may be further utilized in the identification of the genotypes.
The effect of organ preservation solutions on short‐term outcomes after liver transplantation: a single‐center retrospective study

The effect of preservation solutions on outcomes has been subject of many debates but the relative benefits of the various solutions remain unclear. We retrospectively compared short‐term outcomes of 885 liver transplantations performed between 1/2000 and 12/2017 and preserved with either Histidine–Tryptophan–Ketoglutarate (HTK, n = 190), University of Wisconsin (UW, n = 557), or Institute George Lopez 1 preservation solution (IGL‐1, n = 139). Inverse probability of treatment weighting (IPTW) was performed to account for baseline differences between groups and analyses were adjusted for confounders. In the IPTW analyses, peak AST within 7 days was 44% higher (95% CI 15–81%, P < 0.001) in HTK than in UW. Mean model of early allograft function (MEAF) score was 0.61 points (95% CI 0.12–1.10, P = 0.01) higher in HTK than in UW. Early allograft dysfunction (EAD) was more likely to occur with HTK compared to IGL‐1 (IPTW OR = 2.87, 95% CI = 1.00–8.19, P = 0.049) and UW (IPTW OR = 1.75, 95% CI = 1.06–2.88, P = 0.023). The type of preservation solution had no impact on hospital stay, ICU stay, incidence of biliary strictures, or graft and recipient survival. HTK was the least effective on reducing graft injury and increased the probability of graft dysfunction after transplantation. UW and IGL‐1 were equally effective in reducing graft injury and dysfunction.
Long-term survival of thoracoscopic surgery compared with open surgery for clinical N0 adenocarcinoma

Background Early stage non-small cell lung cancer (NSCLC) is good candidate for video-assisted thoracoscopic surgery (VATS). Long-term outcome compared between VATS and open surgery remains unclear. The aim of this study was to assess the long-term outcome of VATS in early stage adenocarcinoma. Methods A retrospective study was performed in 546 patients which were operated between January 2006 and December 2010 in our institute and of those, 240 (220 lobectomies, and 20 segmentectomies) were clinical N0 adenocarcinoma. One hundred and thirty-five patients underwent VATS and 105 patients for open surgery. Long-term oncological outcomes were compared in both groups. Results There were significant differences in age, gender, Blinkman index, clinical T factor and tumor size between two groups. VATS group showed statistically longer operation time (P=0.01), less blood loss (P=0.005), shorter length of stay (P=0.001), and less dissected number of lymph nodes (P<0.001) compared with open surgery. Disease-free survival in VATS was significantly better than open surgery (5- and 10-year survival; VATS, 91.4%, 79.0%; open, 85.1%, 73.6%; respectively, P=0.04). Overall survival in VATS was not different from open (P=0.58). Propensity matched disease-free and overall survival was not significantly different between two groups. Multivariate Cox regression analysis showed that age [P=0.04, 95% confidence interval (CI): (1.02–6.81)] in overall and T factor [P=0.01, 95% CI: (1.41–17.3)] in disease-free survival was prognostic significant after propensity matching. Conclusions Our study demonstrated that long-term outcome in VATS for early stage adenocarcinoma was equivalent to open surgery. VATS may be a treatment of choice for promising long-term prognosis.