Miracle-dz/UniFAR-FTUs huggingface dataset:
Formatting biological big data for modern machine learning in drug discovery

Biological data is accumulating at an unprecedented rate, escalating the role of data‐driven methods in computational drug discovery. This scenario is favored by recent advances in machine learning algorithms, which are optimized for huge datasets and consistently beat the predictive performance of previous art, rapidly approaching human expert reasoning. The urge to couple biological data to cutting‐edge machine learning has spurred developments in data integration and knowledge representation, especially in the form of heterogeneous, multiplex and semantically‐rich biological networks. Today, thanks to the propitious rise in knowledge embedding techniques, these large and complex biological networks can be converted to a vector format that suits the majority of machine learning implementations. Here, we explain why this can be particularly transformative for drug discovery where, for decades, customary chemoinformatics methods have employed vector descriptors of compound structures as the standard input of their prediction tasks. A common vector format to represent biology and chemistry may push biological information into most of the existing steps of the drug discovery pipeline, boosting the accuracy of predictions and uncovering connections between small molecules and other biological entities such as targets or diseases.
The Effects of Chronic Ethanol Exposure of the Dopaminergic System of the Rat Brain

Pellegrino SM and Druse MJ. (1989) Brain D1 receptors in rats chronically fed ethanol. Research Society of Alcoholism Meeting. Alcoholism: Clinical and Experimental Research 13:317. Druse MJ and Pellegrino SM. (1990) Dopamine 02 receptors in the nucleus accumbens and striatum of alcohol-fed rats. Neuroscience Abs. 16:532.
Progress and prospects in low‐dimensional multiferroic materials

Functional materials with ferroelectricity or multiferroicity based on two‐dimensional (2D) materials have been a fast developing field which attracts intensive investigations due to their potential applications and underlying new science. In this study, we review recent progress in theoretical simulation and experimental observation of low‐dimensional multiferroic materials, including exploring 2D van der Waals ferroelectrics, designing ferroelectrics or multiferroics by various manipulations such as chemical functionalization or external strain. The reported new physical mechanisms are also provided to explain the low‐dimensional multiferroics. We also discuss several exciting possibilities for design of devices based on these materials in novel applications.
Interaction of Streptococcus suis with neutrophil extracellular traps (NETs)

Streptococcus (S.) suis causes as infectious agent suppurative meningitis in humans and piglets, which is characterized by a pleocytosis in the cerebrospinal fluid (CSF). In neutrophils, a novel fundamental innate immune defense mechanism against different pathogens has been identified: the formation of neutrophil extracellular traps (NETs). NETs are formed by neutrophils following extracellular ejection of DNA in combination with antimicrobial molecules and bind, disarm and kill pathogens. Different pathogens express NET evasion factors like DNases. NETs might play different roles in diseases and the mechanisms leading to NET release are only poorly understood. In this study, the interaction of S. suis and NETs was investigated using immunofluorescence microscopy. Especially the function of two DNases was investigated. Phenotypic analysis was conducted using in frame deletion mutants, which were investigated comparatively to the wildtype under various conditions. Important phenotypes in the pathogen-host interaction were identified. In the first part of this thesis [Chapter 3.1] it was demonstrated for the first time that S. suis induces NETs, is entrapped in NETs and degrades NETs. Furthermore, this work revealed that the known secreted nuclease A (SsnA) is involved in NET degradation and that this nuclease protects S. suis against the antimicrobial activity of NETs. The second part [Chapter 3.2] includes the identification of a novel endonuclease A of S. suis (EndAsuis), which is involved in NET degradation during the exponential growth phase. EndAsuis was shown to require Mg2+ for activity whereas SsnA needed Mg2+ and Ca2+. In the third part [Chapter 3.3] NET formation in the S. suis-infected CSF compartment was examined. In an inverse transwell model, human neutrophils followed S. suis by transmigration through the epithelium formed by choroid plexus papilloma cells in the lower compartment, which represents the CSF-compartment. Importantly, NETs were detected in the CSF compartment by immunofluorescence microscopy and biochemical determination of dsDNA. Furthermore, it was visualized that streptococci were entrapped in NETs. However, the number of detectable NETs and the bacterial survival did not depend on the expression of the bacterial nucleases SsnA and EndAsuis. The detected induction of the NET protecting factor LL-37 might explain this result. These in vitro results were corroborated by the detection of NETs in CSF samples of S. suis infected piglets. In conclusion, the results suggest that NET formation and degradation might play a role in the pathogenesis of S. suis meningitis.
Effect of iso-energetic exchange of dietary fat and starch on growth performance and body composition of broilers: Experiment 2

Dietary factors such as the concentrations of protein/amino acids, fat, and starch + sugar and their ratio, may affect the post-absorptive metabolism of energy and protein and energy deposition in the body. In a 2x3 factorial block design, the effects of two dietary crude protein (high protein (HP) vs. low protein (LP) concentrations; 200/190 vs. 170/160 g/kg) in grower and finisher phase and three dietary fat/starch concentrations (high fat (HF); fat and starch 120 and 350 g/kg, respectively, medium fat (MF); fat and starch 80 and 425 g/kg and low fat (LF); fat and starch 40 and 500 g/kg, respectively) on growth performance and body composition of Ross 308 broilers were studied (8 to 38 d). From this experiment it can be concluded that dietary energy source and protein level in isoenergetic diets, balanced for first limiting essential amino acids, influence growth performance and body composition of broilers.
Protective Mechanisms of Limonoids from Khaya grandifoliola against Cisplatin-Toxicity in L-02 Hepatocytes: Targeting JNK Activation and Nuclear Translocation of Nrf2

Background: Cisplatin is one of the most effective antineoplastic drugs, but it has undesirable side effects such as hepatotoxicity. This study investigated in vitro the protective activity of three limonoids known as 17-epi-methyl-6-hydroxylangolensate, 7-deacetoxy-7-oxogedunin and deacetoxy-7R-hydroxygedunin, isolated from Khaya grandifoliola (Meliaceae) against cisplatin-induced hepatotoxicity and the possible mechanisms involved in this activity. Methods: Normal human liver L-02 cells line were intoxicated with cisplatin or co-treated with the limonoids for 36h prior to evaluation of biochemical and molecular parameters through spectrophotometric assays, western blots and quantitative real-time polymerase chain reaction analysis. Results: The studied limonoids prevented cisplatin-induced cell death and leakage of alanine aminotransferase (ALT) in the incubation medium in a concentration-dependent manner. Overproduction of intracellular reactive oxygen species (ROS), depletion of glutathione and lipid membrane peroxidation induced by cisplatin were inhibited by the limonoids. Cisplatin-induced phosphorylation of c-Jun N-terminal Kinase (JNK) and mitochondrial translocation of phospho-JNK was abrogated in limonoids co-treated cells. Interestingly, the studied limonoids increased the expression of mitogen-activated protein kinase phosphatase -1, an endogenous inhibitor of JNK phosphorylation, in cisplatin-intoxicated cells. Moreover, these compounds induced the nuclear translocation of nuclear factor erythroid 2-related factor 2 (Nrf2), decreased the expression of kelch-like ECH-associated protein-1, and increased the mRNA levels of Nrf2 target genes: catalase, superoxide dismutase-1 and glutathione-Stransferase. Conclusions: The present findings suggest that limonoids from K. grandifoliola may constitute promising phytochemicals for alleviating cisplatininduced hepatotoxicity.
Role of Charge Density Wave in Monatomic Assembly in Transition Metal Dichalcogenides

The charge density wave (CDW) in transition metal dichalcogenides (TMDs) has drawn tremendous interest due to its potential for tailoring their surface electronic and chemical properties. Due to technical challenges, however, how the CDW could modulate the chemical behavior of TMDs is still not clear. Here, this work presents a study of applying the CDW of NbTe2, with a high transition temperature above room temperature, to generate the assembling adsorption of Sn adatoms on the surface. It is shown that highly ordered monatomic Sn adatoms with a quasi‐1D structure can be obtained under regulation by the single‐axis CDW of the substrate. In addition, the CDW modulated superlattices could in turn change the surface electronic properties from semimetallic to metallic. These results demonstrate an effective approach for tuning the surface chemical properties of TMDs by their CDWs, which could be applied in exploring them for various practical applications, such as heterogeneous catalysis, epitaxial growth of low‐dimensional materials, and future nanoelectronics.
Hypermethylation and Expression of MicroRNA 1285 and Sterol Carrier Proteins 2 in Type 2 Diabetes Mellitus

Diabetes mellitus (DM) is one of a severe metabolic disease found in all types of people living in developing as well developed countries. Specifically, Type 2 DM accounts for over 90% for older and urban population. It is has been suggesting that the prevalence of diabetes is increasing many countries and most of the cases are type 2 DM, clinical treatments are changed now to manage type 2 DM however, up to date there is no diagnostic, prognostic and therapeutic target for type 2 DM. MicroRNAs (miRNAs) is one of a non-protein coding RNAs have been regulating wide range cellular processes and induce the manifestation of many diseases. Most of the researchers concluding that miRNAs involvement is a important process in a broad range of signaling pathways such as cell proliferation, stem cell maintenance, migration, apoptosis and gene or protein expressions. Expressed sequence Tags (ESTs) are the best source of coding and non-coding sequences for the identification of miRNAs. Although DNA methylation is an important mechanism for microRNA up regulation, this has not been highly explored in type 2 DM. this study may useful to elucidate the molecular mechanism of miR-1285 in type 2 DM and its role in disease progression and we discovered miR-1285 as a novel prognostic, diagnostic and therapeutic target for type 2 DM.
Efecto del contaminante bisfenol A a distintas temperaturas, sobre la microalga marina Tetraselmis suecica

In recent years, the development of new and more sensitive analytical methods has made it possible to alert the presence of emerging contaminants in water. Their impact has caused changes in the composition of individuals in the aquatic community, changes in the dominant organisms of a habitat and impoverishment of species. Many of these pollutants are endocrine disrupters, such as Bisphenol A (BPA). Microalgae play a fundamental role in the equilibrium of the aquatic ecosystem and are a good indicator of medium toxicity. In this paper we study the possible toxic effect exerted by bisphenol A in Tetraselmis suecica. Cultives of these microalgae were carried out at different concentrations of BPA (3, 4, 5 and 6 mg L-1) during 72 h and at two temperatures (18 and 22 o C) respectively. In addition, the cellular content of pigments (chlorophyll a and b and carotenoids) was determined. Cell growth and the amount of pigments show differences in crops exposed to BPA and also vary depending on the temperatures in which they are cultivated. Therefore, it can be determined that T. suecica is sensitive to the toxicity of BPA and that increase in temperature influences negatively. Due to the analyzed parameters, the fact that T. suecica would be a good indicator of environmental quality.
Gd(III)-Grafted Detonation Nanodiamonds for MRI Contrast Enhancement

We report on the first 1H NMR relaxation and magnetic resonance imaging (MRI) study of aqueous suspensions of detonation nanodiamond (DND) grafted by Gd(III) ions. In contrast to Gd(III)–ND conjugates implemented via organic species, Gd(III) ions were directly grafted to the surface of DND particles. Such Gd(III)-grafted DND particles significantly shorten spin–lattice (T1) and spin–spin (T2) relaxation times of water protons providing relaxivities of r1 = 33.4 and r2 = 332 mM–1 s–1, which considerably exceed most of those reported in the literature. It makes the Gd(III)-grafted DND complexes attractive for use as novel MRI contrast agents.
Data retention investigation in Al:HfO2-based resistive random access memory arrays by using high-temperature accelerated tests

In this work, the feasibility of using accelerated tests at high temperatures to assess the data retention on resistive random access memory devices was evaluated on Al : HfO 2-based 1-transistor-1-resistor 4 kbit arrays. By annealing the samples at four different temperatures (190, 210, 230, and 260 ° C) for 10 h, different distributions of retention failure times were obtained and modeled by using Weibull distributions. Based on the temperature dependency of these distributions, the Arrhenius activation energy of the degradation process was calculated (1.09 eV). In addition, the maximum temperature that guarantees a retention time to failure of a 10 year lifetime was extrapolated ( 105 ° C ). In this work, the feasibility of using accelerated tests at high temperatures to assess the data retention on resistive random access memory devices was evaluated on Al : HfO 2-based 1-transistor-1-resistor 4 kbit arrays. By annealing the samples at four different temperatures (190, 210, 230, and 260 ° C) for 10 h, different distributions of retention failure times were obtained and modeled by using Weibull distributions. Based on the temperature dependency of these distributions, the Arrhenius activation energy of the degradation process was calculated (1.09 eV). In addition, the maximum temperature that guarantees a retention time to failure of a 10 year lifetime was extrapolated ( 105 ° C ).
Production and Analysis of Recycled Ammonium Perrhenate from CMSX-4 superalloys

Abstract The process to extract rhenium from a superalloy is an immense technical challenge due the complex chemistry involved. Being one of the rarest elements in the earth’s crust the scarcity and cost of rhenium makes it advantageous to recover the element from scrap superalloy. In this research the separation and monitoring of the different stages of the recycling process to extract rhenium from CMSX-4 superalloys using a distillation process were performed. This novel method combining distillation and use of exchange resins was used to separate rhenium from a complex mixture of metals in the CMSX-4 superalloy. The identification and quantitation of perrhenate and contaminants were performed by atomic absorption spectroscopy (AAS), Fourier transform infrared spectroscopy (FTIR), ion chromatography (IC) and Scanning Electron Microscopy- Energy Dispersive X-Ray (SEM-EDX). Perrhenate ions were extracted with purity close to 93%. The analytical characteristics for a novel infrared method to quickly identify perrhenate anions from CMSX-4 are presented. The main characteristics of the analytical validation were: LoD: 0.5% w/w; LoQ: 1.5% w/w; linear range 1.5-100% w/w; correlation coefficient R2 = 0.9905; precision (%RSD) for 10%w/w = 6.6 and 75%w/w = 4.1, respectively; accuracy (%) for 10% w/w 99.6% and 75% w/w=101.1, respectively.
Protection of alloxan monohydrate-induced testicular toxicity by Gundelia tournefortii aerial parts aqueous extract in male mice.

For a long period, ethno medicinal plants have been a valuable source of natural products for maintaining human health, especially in the last decade, with more intensive studies for natural therapies. The use of ethno medicinal plant for pharmaceutical purposes has gradually increased in Iran. Gundelia tournefortii has been used as an antibacterial, anti-fungal, antipyretic, anti-inflammatory, and antioxidant agent in Iran. In the recent examination, the testicular protective effect of G. tournefortii aerial parts aqueous extract on diabetic mice has been evaluated. Seventy mice were used and diabetes was induced by administration of 150 mg/kg of alloxan monohydrate intraperitoneally in 60 mature male mice and they were randomly divided into six groups. The treatment groups received glibenclamide 10 mg/kg and 5, 10, 20 and 40 mg/kg of G. tournefortii through gavage for 20 days. Also, one group was considered as the non-diabetic control. At 20 day, the mice were killed, dissected, then blood and testis samples were collected for biochemical and stereological parameters analysis. The data were analyzed by SPSS-21 software. G. tournefortii at all doses (especially GT40) and glibenclamide significantly (p≤0.05) ameliorated the concentrations of fasting blood glucose, testosterone, superoxide dismutase, catalase, glutathione reductase, and glutathione peroxidase. Also, multiple doses of G. tournefortii (especially GT40) and glibenclamide increased the weight and volume of the testis, the volumes of the tubule and interstitial tissue, the length and diameter of the tubule, the height of the germinal epithelium, and the number of the Leydig cell compared to the diabetic untreated group. According to the obtained results, G. tournefortii aerial parts aqueous extract can regulate the concentrations of biochemical parameters and inhibit testicular damages in alloxan monohydrate induced diabetic mice. It seems that G. tournefortii can be offered as a testicular protective supplement or drug for prevention, control, and treatment of testicular toxicity in diabetic patients. Conflicts of Interest: Declared None Funding: None
Informed Trading in the Options Market around CEO Turnover Announcements

We examine the informed trading in the options market for firms announcing CEO turnover and their suppliers and find that pre-announcement options trading in both announcing firms and the suppliers have predictive power for abnormal returns around forced CEO turnover events. This effect is stronger with outside successions. However, we do not find any evidence of options trading prior to voluntary CEO turnover events for announcers and their suppliers. Overall, our study suggests that forced CEO turnover events with outside successions have significant information along the supply chain and that informed traders exploit the options markets to trade in the announcing firms and their suppliers surrounding these events.
Can One Laptop per Child Reduce Digital Inequalities? ICT Diffusion Patterns under Plan Ceibal

The study of information and communications technology (ICT) adoption signals that diffusion processes within highly unequal societies produces a stratification in the access to digital technologies and thus, maintains or even increases previous socio-economic disparities. Whereas technological utopians believed that One Laptop Per Child (OLPC)-like programs could reduce societal inequalities, the economic literature studying their consequences mostly focused on student's human capital. Results found no impacts, even for successful programs such as Uruguay's own OLPC-inspired Plan Ceibal. We use an event-study approach to difference-in-differences to identify the impact of Plan Ceibal on the household demand for technological goods across income quintiles. Our results show that Plan Ceibal helped to bridge domestic digital disparities in terms of access to PC for low-income households and favored the demand for internet services. We argue that two diverse mechanisms are behind these results. Regarding PC access, whereas Plan Ceibal was conceived as a universal program targeting primary level students attending public schools, both poverty infantilization and dual-system educational stratification made the policy to exhibit heterogenous impact across different income groups. Regarding household connectivity, we argue that Plan Ceibal reduced the cost of the bundle required to consume internet services at the time of the study, impacting on those households with both reasonable shares of children attending a public school and sufficient income to afford the monthly internet charges.
Unemployment in Sri Lanka

Many researchers as well as policy makers have been identified that Sri Lanka is a dual economic country. In one side, it is concerned that Sri Lanka has an independent, participative democratic and social development. In other side, Sri Lanka is a war-torn country which have a higher unemployment while having a slow growth economy when compared with other Asian countries. The most critical dilemma in Sri Lankan economic system is the structural unemployment in educated youth which might a reason of high level of education wait for a longer period of time before entering to the workforce actively (Aggestam & Hallberg, 2004). Before moving to the further discussions, it is important to review some definitions of key terms which come up with the concept of unemployment.
Entrepreneurial Theories

This paper builds on the theory-based view and the theory of the entrepreneur in economics to describe three archetypal value-creating theories that economic actors can possess and shows that each theory implies a set of prescriptions for how entrepreneurs can organize and govern the process of value creation. These patterns for value creation reveal important insights about the entrepreneurial process, influencing (among other things) entrepreneurial experimentation, economic organization, intellectual property protection, and financing.
Construction of Nafion/Hb/Au/ZIF-8/CILE and its application as electrochemical sensor for determination of bromate and nitrite

In this paper zinc-based metal organic framework material (ZIF-8) modified carbon ionic liquid electrode (CILE) was prepared and electrodeposited with gold nanoparticles to get a composite modified electrode, which was used as the sensing interface for the immobilization of hemoglobin (Hb) with Nafion to prepare a modified electrode (Nafion/Hb/Au/ZIF-8/CILE). Electrochemical behaviors of Hb on the modified electrode were checked by cyclic voltammetry with a pair of well-defined redox peaks appeared. The effects of pH and scan rate on direct electrochemistry of Hb were studied with electrochemical parameters calculated. The prepared electrochemical enzyme sensor showed good catalytic activity to the electroreduction of bromate and nitrite with the linear ranges from 0.5 to 10.0 mmol/L and from 0.1 to 0.8 mmol/L, respectively. The detection limits were calculated as 0.83 mmol/L and 0.03 mmol/L, and the water samples were analyzed to prove the practical application.