Miracle-dz/UniFAR-FTUs huggingface dataset:
New aryloxy-quinone derivatives as potential anti-Chagasic agents: synthesis, trypanosomicidal activity, electrochemical properties, pharmacophore elucidation and 3D-QSAR analysis

A set of new aryloxy-quinones were synthesized and evaluated in vitro against the epimastigote form of Trypanosoma cruzi and their unspecific cytotoxicity was tested on murine macrophages J-774 cells. Most of these novel compounds were found to be much more potent and selective than the standard drug nifurtimox. Interestingly, 2-phenoxy-naphthoquinone 3b displayed a remarkable nanomolar inhibitory activity, IC50 = 20 nM, and a high selectivity index, SI = 625. The Epc1 was determined for the most interesting compounds and no correlation with the trypanosomicidal effect was found. Therefore, an in silico study was carried out to obtain a pharmacophoric model and quantitative structure–trypanosomicidal activity relationship. The designed pharmacophore recognized the more potent and selective molecules, exhibiting five pharmacophoric features. A correlation coefficient R2 of 0.99 of pIC50 plotted against the predicted values indicated that the 3D-QSAR equation could be applied to further predictions of newly designed trypanosomicidal compounds.
A Unified Sample Selection Framework for Output Noise Filtering: An Error-Bound Perspective

The existence of output noise will bring difficulties to supervised learning. Noise filtering, aiming to detect and remove polluted samples, is one of the main ways to deal with the noise on outputs. However, most of the filters are heuristic and could not explain the filtering influence on the generalization error (GE) bound. The hyper-parameters in various filters are specified manually or empirically, and they are usually unable to adapt to the data environment. The filter with an improper hyper-parameter may overclean, leading to a weak generalization ability. This paper proposes a unified framework of optimal sample selection (OSS) for the output noise filtering from the perspective of error bound. The covering distance filter (CDF) under the framework is presented to deal with noisy outputs in regression and ordinal classification problems. Firstly, two necessary and sufficient conditions for a fixed goodness of fit in regression are deduced from the perspective of GE bound. They provide the unified theoretical framework for determining the filtering effectiveness and optimizing the size of removed samples. The optimal sample size has the adaptability to the environmental changes in the sample size, the noise ratio, and noise variance. It offers a choice of tuning the hyper-parameter and could prevent filters from overcleansing. Meanwhile, the OSS framework can be integrated with any noise estimator ∗. Corresponding author. c ©2021 Gaoxia Jiang, Wenjian Wang, Yuhua Qian and Jiye Liang. License: CC-BY 4.0, see https://creativecommons.org/licenses/by/4.0/. Attribution requirements are provided at http://jmlr.org/papers/v22/19-498.html. Jiang, Wang, Qian and Liang and produces a new filter. Then the covering interval is proposed to separate low-noise and high-noise samples, and the effectiveness is proved in regression. The covering distance is introduced as an unbiased estimator of high noises. Further, the CDF algorithm is designed by integrating the cover distance with the OSS framework. Finally, it is verified that the CDF not only recognizes noise labels correctly but also brings down the prediction errors on real apparent age data set. Experimental results on benchmark regression and ordinal classification data sets demonstrate that the CDF outperforms the state-of-the-art filters in terms of prediction ability, noise recognition, and efficiency.
Tracking the transformations of mesoporous microspheres of calcium silicate hydrate at the nanoscale upon ibuprofen release: a XANES and STXM study

Drug release and the accompanying biomineralization of the drug carrier, mesoporous calcium silicate hydrate (CSH) microspheres, are monitored with X-ray absorption near edge structures and scanning transmission X-ray microscopy (STXM). The in vitro biomineralization of hydroxyapatite (HAp) on CSH microspheres is investigated by tracking specimens soaked in simulated body fluid (SBF) for various time periods; the study is complemented with X-ray powder diffraction. We clarified the presence of amorphous CaCO3 at the early stage of biomineralization with solid evidence, which is still controversial from previous studies. More importantly, the observations from the STXM images and microscopy spectra directly demonstrated that amorphous SiO2 from the hydrolysis of silicate ions provide the preferential sites for the aggregation of HAp. These results demonstrate that XANES and STXM are sensitive techniques which can be used to analyze various bioceramics for medical applications.
ATOMIC CHARGES OF THE WATER MOLECULE AND THE WATER DIMER

Atomic charges in the water molecule and the water dimer have been calculated by two different schemes for partitioning the total charge distribution: Mulliken charges and atomic polar tensor-based charges. Large-scale calculations have been carried out where the basis set has been increased systematically toward the basis-set limit. The Mulliken charges are highly sensitive to the choice of basis, and no convergence is observed. In contrast, atomic charges obtained from the trace of the atomic polar tensor exhibit rapid basis-set convergence. We have also investigated the effects of electron correlation on the atomic charges of the water molecule. Finally, the polarization and charge-transfer effects on the atomic charges have been calculated for the water dimer. The importance of such terms in a water potential used in molecular dynamics simulations of aqueous solutions is discussed.
Development of models for segregation of infrastructure project management elements using a mono-template in safety-oriented management

The impact of a turbulent environment of dynamic changes in human life, the growing number of emergencies and events form and exert a critical load on critical infrastructure systems and infrastructure projects. In particular, over the last decade, a number of large infrastructure projects have been realized and are being implemented in Ukraine alone. Among them: “Construction of a new Beskidy tunnel”; “Building of a new safe confinement”; “GO Highway”; “Liquid radioactive waste processing plant”; “3G and 4G technology implementation projects in Ukraine” and others. Today there are various standards of project management, models and methods of project planning and implementation are developed and tested. However, the state of affairs indicates that existing standards, models and methods can no longer fully balance the quality, safety and viability of the environment and project stakeholders. Therefore, there is a need for synergy of existing knowledge in order to develop a new paradigm for detailed structuring of infrastructure projects, develop mono-templates and segregate elements in the planning, implementation and operation of such projects at different levels and stages. There is a need to take into account the dynamics and imCopyright © 2020, D. Kobylkin, O. Zachko, N. Korogod, D. Tymchenko
How representative are social partners in Europe ? The role of dissimilarity GLO Discussion

Social partners (trade unions and employers’ associations) shape labour institutions and economic and social outcomes in many countries. In this paper, we argue that, when examining social partners’ representativeness, it is important to consider both affiliation and dissimilarity measures. The latter concerns the extent to which affiliated and nonaffiliated firms or workers are distributed similarly across relevant dimensions, including firm size. In our analysis of European Company Survey data, we find that affiliation and dissimilarity measures correlate positively across countries, particularly in the case of employers’ associations. This result also holds across employers’ associations when we use firm population data for Portugal. Overall, we conclude that higher affiliation rates do not necessarily equate to more representative social partners as they can involve greater dissimilarity between affiliated and non-affiliated firms.
The dissolution mechanisms of water in silicate melts; a synthesis of recent data

Abstract Dissolved water has significant effects on the physical and chemical properties of silicate melts. Some of the different approaches towards understanding these effects are reviewed here. Spectroscopic measurements on hydrous glasses quenched from melts provide good models for the structure of the melts at the glass transition temperature (Tg). Such measurements suggest that the mechanism of dissolution of water in silicate melts varies strongly with the bulk composition. In particular framework aluminosilicate compositions seem to have very different dissolution mechanisms from Al-free compositions. The water speciation reactions are temperature dependent, with some of the molecular water which is present in glasses at room temperature being converted to hydroxyl at high temperatures. This conversion probably occurs only above Tg. Data on the kinetics of the speciation reaction and the dynamics of microscopic processes in hydrous silicate melts are also discussed. Finally some important aims of future work on hydrous silicate melts are suggested.
A CGM-Based Parallel Algorithm Using the Four-Russians Speedup for the 1-D Sequence Alignment Problem

The CGM model is one of the most widely used models for the design of parallel algorithms. It has shown its efﬁciency in solving several problems modeled by dynamic programming such as the longest common subsequence problem, which is a special case of the one-dimensional sequence alignment problem. This problem consists in aligning two strings of length n to measure their similarity. It is widely used in many ﬁelds, particularly in Bioinformatics where n is usually very large. Brubach and Ghurye proposed a sequential solution based on the Four-Russians speed-up that requires O ( n 2 / log n ) execution time. To the best of our knowledge, there are not yet parallel solutions on the CGM model to solve this problem. This paper is exclusively dedicated to this task. Our solution applies to both local and global similarity computations and is based on Brubach and Ghurye’s sequential algorithm. It requires O ( n 2 /p log n ) execution time with O ( p ) communication rounds on p processors.
Effects of Egg Yolk and Egg Yolk Plasma Tris-Base Extenders on Beetal Buck Semen Preservation

Livestock Census (Anonymous, 2019). However, the recognized breeds of Indian goat population are facing a greater threat due to lack of enforcement of proper breeding policy, inadequate number of breeding bucks, indiscriminate crossbreeding and intermixing among breeds with local animals etc. Furthermore, the population of male bucks in the country in 2019 is 37.62 million is also showing a decrease of 14.65% over the previous census. To improve the productive potential of goat, the incorporation of superior International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 9 Number 11 (2020) Journal homepage: http://www.ijcmas. com
Family status and women’s career mobility during urban China’s economic transition

BACKGROUND In contrast to the historical experience of Western welfare states, where social and family policies help create more integrated public–private spheres, marketization in China has presented a case of sphere separation. This phenomenon has important implications for the dynamics of gender inequality in economic transition. OBJECTIVE This article examines how family status is associated with women’s career mobility in reform-era urban China and the impact of family on women’s career choices across different reform stages. METHOD Based on retrospective data from the Chinese General Social Survey (CGSS) in 2008, we adopt discrete-time logit models to examine the effects of marriage and childbearing on women’s upward mobility, the risk of labor market exit, and how the effects vary over time. RESULTS Chinese women in the workforce are adversely affected by marriage and having dependent children. They are more likely than men to experience (involuntary, in particular) job exit to fulfill their roles as wives and mothers and less likely to move up in the career ladder. This pattern is more prominent as the economic reform proceeds. CONCLUSION Marketization has adversely affected Chinese women’s career outcomes by increasing work–family tension after the work unit (danwei) system and socialist programs that supported working women were scrapped. CONTRIBUTION This study is one of the few empirical studies to attempt to explain the widening gender gap in China’s job market from the perspective of family using the two-sphere separation framework. The framework originated in Western family studies but has been adapted to suit the context of urban China.
Prognostic Significance of Preoperative Serum Alpha-fetoprotein in Hepatocellular Carcinoma in China

Hepatocellular carcinoma (HCC) is the sixth most common cancer worldwide and the third most frequent cause of cancer-related death. Half of these cases and deaths are estimated to occur in China (Ferlay et al., 2010; Jemal et al., 2011). Although there is substantial geographical variation, the greatest burden of the disease is in East Asia, Eastern Europe and sub-Saharan Africa, where hepatitis B virus (HBV) infection is highly prevalent (Yuen et al., 2009). HBV infection is the predominant cause of HCC development, associated with approximately half of all cases of HCC, and almost all cases of HCC in children (El-Serag et al., 2011). By contrast, in North America, Europe, and Japan, infection with hepatitis C virus (HCV) is the main risk factor. In addition to HBV and HCV infections, increasing age, male sex and chronic alcohol consumption are significant risk
A General Method for the Preparation of Chiral TREN Derivatives

A general procedure for the preparation of C-3-symmetric TREN derivatives with backbone chirality has been developed. Stereo- and regioselective ring opening by ammonia of (S)-N-tosyl-2-isopropylaziridine, obtained starting from either the corresponding amino alcohol or amino acid, followed by deprotection of the amino groups afforded the parent chiral TREN compound in high overall yield. In addition to TREN compounds with primary amino groups, the synthetic method employed provides easy access to a variety of N,N',N-substituted derivatives. ((c) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005).
A CONVENIENT SYNTHESIS OF NEW 5-AMINO-4,5-DIHYDRO-1HPYRAZOL-1-YL PROPANE NITRILE AND 4,5-DIHYDRO [2-(CYANOAMINO)] PYRIMIDINES

An efficient method for the synthesis of 5-amino-4,5-dihydro-1H-pyrazol-1-yl propannitrile derivatives 2 and 4,5-dihydro [2-(cyanoamino)] pyrimidines 3 in good yields by the Treatment of 2-aryllydene malononitriles 1 with dicyanodiamide in n- pentanol or 2- cyanoethyl-hydrazine in methanol respectively. The structure of newly synthesised product was established by spectral data
Microstructure and pseudomorphism in molecular beam epitaxially grown ZnCdS on GaAs(001)

We have carried out an electron‐microscopy‐based microstructural study of molecular beam epitaxially grown ZnxCd1−xS epilayers on GaAs(001) substrates. We find that sulfur attacks bare GaAs substrates, resulting in pits that act as nucleating centers for defects that propagate into the epilayer. Such pitting may be avoided by capping the GaAs substrate with a ZnSe buffer in a sulfur‐free separate growth chamber. We also investigate the pseudomorphic zinc blende to wurtzite crystal structure change in epitaxial ZnxCd1−xS and propose a microstructural model for this structural transition.
Transition state structures and reaction profiles from constrained optimization procedure. Implementation in the framework of density functional theory

A method for finding the transition structures (TS) based on constrained optimization techniques is proposed. The algorithm can be considered as a step‐by‐step walking uphill process along the minimum energy path, followed by a refining procedure of TS parameters in the saddle point vicinity. By accounting for the constraint conditions in a straightforward manner, it is possible to use efficient quasi‐Newton algorithms at every geometry reoptimization step and to manage the moving direction in a reaction valley. This approach may be suitable in the framework of density functional theory. Tests including a potential energy surface model, HNC→HCN and N2H2 trans–cis isomerizations and LiBH4 rearrangements are given. The possible future development of the approach is discussed.
The evolutionary conserved protein CG 9186 is associated with lipid 1 droplets , required for their positioning and for fat storage 2 3 4

3 4 Katharina Thiel, Christoph Heier, Verena Haberl, Peter J. Thul, Monika Oberer, 5 Achim Lass, Herbert Jäckle & Mathias Beller* 6 7 8 1 Department of Molecular Developmental Biology, Max Planck Institute for Biophysical 9 Chemistry, Göttingen, Germany, 2 Institute of Molecular Biosciences, University of Graz, Graz, 10 Austria, 3 Institute for Mathematical Modeling of Biological Systems, Heinrich Heine University 11 Düsseldorf, Düsseldorf, Germany 12 13 * Correspondence: mathias.beller@hhu.de 14 15 16 17 18 19 20 21 22 23 24 Running title: LD regulation by a novel protein family 25 26
Polysaccharide-based scaffold for tissue-regeneration 6

In the last 10 years, the field of transplantation has dramatically improved, increasing patient life expectations and graft survival, but the demand for tissue and organs continues to exceed supply. Currently, every 10 min, someone is added to the national transplant waiting list (United States) that consists of 115,000 people, but only 30% can be treated [1]. The synergy between regenerative medicine and tissue engineering represents an innovative strategy to lighten this demand. The focus of regenerative medicine is the body’s intrinsic tissue repair, but that is not enough. Tissue engineering was introduced by Vacanti and Langer in the 1980s; and the widespread belief is represented as the well-known image of the “human ear on the mouse back. ” The goal of this modern technology is to create a substitute tissue, which supplies an individual therapy for patients with regeneration, remodeling, and growth potential [2]. That is possible thanks to three fundamental components: cells, biomaterial scaffold, and signals (Fig. 6.1). The classic paradigm relies on a combination of these three factors to orchestrate tissue formation and integration within the host environment. An important avenue of tissue engineering is the development of biomaterials that can promote regenerative processes by effectively transporting cell populations and therapeutic agents, as well as providing structural scaffolding that confers sufficient mechanical properties to tissues. Moreover, the biomaterial should ideally degrade at a comparable rate to growth of new tissue at the site of implantation [3]. Focusing on biomaterials, the polysaccharides are valid candidates to synthesize scaffold for cell supporting (e.g., three-dimensional hydrogels), drug delivery (e.g., microgels/nanogels), and self-assembly micelles for gene therapy. Polysaccharides are carbohydrates whose molecules consist in a number of sugar moieties linked together and are abundant in nature, renewable, nontoxic, and intrinsically biodegradable. They are naturally occurring polymers or biopolymers. Typical examples of polysaccharides include: dextran (DeX), starch (AmY), glycogen (Gly), cellulose (CeL), chitosan (CS), hyaluronic acid (HA), alginate (ALG), and many others [4].
Stochastic social behavior coupled to COVID-19 dynamics leads to waves, plateaus, and an endemic state

It is well recognized that population heterogeneity plays an important role in the spread of epidemics. While individual variations in social activity are often assumed to be persistent, that is, constant in time, here we discuss the consequences of dynamic heterogeneity. By integrating the stochastic dynamics of social activity into traditional epidemiological models, we demonstrate the emergence of a new long timescale governing the epidemic, in broad agreement with empirical data. Our stochastic social activity model captures multiple features of real-life epidemics such as COVID-19, including prolonged plateaus and multiple waves, which are transiently suppressed due to the dynamic nature of social activity. The existence of a long timescale due to the interplay between epidemic and social dynamics provides a unifying picture of how a fast-paced epidemic typically will transition to an endemic state.
Machine learnt approximations to the bridge function yield improved closures for the Ornstein-Zernike equation.

A key challenge for soft materials design and coarse-graining simulations is determining interaction potentials between components that give rise to desired condensed-phase structures. In theory, the Ornstein-Zernike equation provides an elegant framework for solving this inverse problem. Pi-oneering work in liquid state theory derived analytical closures for the framework. However, these analytical closures are approximations, valid only for speciﬁc classes of interaction potentials. In this work, we combine the physics of liquid state theory with machine learning to infer a closure directly from simulation data. The resulting closure is more accurate than commonly used closures across a broad range of interaction potentials. We show for two examples of a prototypical inverse design problem, ﬁtting a coarse-grained simulation potential, that our approach leads to improved one-step inversion.
Analysis of 11,430 recombinant protein production experiments reveals that protein yield is tunable by synonymous codon changes of translation initiation sites

Recombinant protein production is a key process in generating proteins of interest in the pharmaceutical industry and biomedical research. However, about 50% of recombinant proteins fail to be expressed in a variety of host cells. Here we show that the accessibility of translation initiation sites modelled using the mRNA base-unpairing across the Boltzmann’s ensemble significantly outperforms alternative features. This approach accurately predicts the successes or failures of expression experiments, which utilised Escherichia coli cells to express 11,430 recombinant proteins from over 189 diverse species. On this basis, we develop TIsigner that uses simulated annealing to modify up to the first nine codons of mRNAs with synonymous substitutions. We show that accessibility captures the key propensity beyond the target region (initiation sites in this case), as a modest number of synonymous changes is sufficient to tune the recombinant protein expression levels. We build a stochastic simulation model and show that higher accessibility leads to higher protein production and slower cell growth, supporting the idea of protein cost, where cell growth is constrained by protein circuits during overexpression.