A Distributed Workflow Management System with Case Study of Real-life Scientific Applications on Grids

Next-generation scientific applications feature complex workflows comprised of many computing modules with intricate inter-module dependencies. Supporting such scientific workflows in wide-area networks especially Grids and optimizing their performance are crucial to the success of collaborative scientific discovery. We develop a Scientific Workflow Automation and Management Platform (SWAMP), which enables scientists to conveniently assemble, execute, monitor, control, and steer computing workflows in distributed environments via a unified web-based user interface. The SWAMP architecture is built entirely on a seamless composition of web services: the functionalities of its own are provided and its interactions with other tools or systems are enabled through web services for easy access over standard Internet protocols while being independent of different platforms and programming languages. SWAMP also incorporates a class of efficient workflow mapping schemes to achieve optimal end-to-end performance based on rigorous performance modeling and algorithm design. The performance superiority of SWAMP over existing workflow mapping schemes is justified by extensive simulations, and the system efficacy is illustrated by large-scale experiments on real-life scientific workflows for climate modeling through effective system implementation, deployment, and testing on the Open Science Grid.     

Structure-Activity Relationships of Benzamides and Isoindolines Designed as SARS-CoV Protease Inhibitors Effective against SARS-CoV-2

Inhibition of coronavirus (CoV)-encoded papain-like cysteine proteases (PL^pro) represents an attractive strategy to treat infections by these important human pathogens. Herein we report on structure-activity relationships (SAR) of the noncovalent active-site directed inhibitor (R)-5-amino-2-methyl-N-(1-(naphthalen-1-yl)ethyl) benzamide ( 2 b ), which is known to bind into the S3 and S4 pockets of the SARS-CoV PL^pro. Moreover, we report the discovery of isoindolines as a new class of potent PL^pro inhibitors. The studies also provide a deeper understanding of the binding modes of this inhibitor class. Importantly, the inhibitors were also confirmed to inhibit SARS-CoV-2 replication in cell culture suggesting that, due to the high structural similarities of the target proteases, inhibitors identified against SARS-CoV PL^pro are valuable starting points for the development of new pan-coronaviral inhibitors.     

Machine Learning Reduced Gene/Non-Coding RNA Features That Classify Schizophrenia Patients Accurately and Highlight Insightful Gene Clusters

RNA-seq has been a powerful method to detect the differentially expressed genes/long non-coding RNAs (lncRNAs) in schizophrenia (SCZ) patients; however, due to overfitting problems differentially expressed targets (DETs) cannot be used properly as biomarkers. This study used machine learning to reduce gene/non-coding RNA features. Dorsolateral prefrontal cortex (dlpfc) RNA-seq data from 254 individuals was obtained from the CommonMind consortium. The average predictive accuracy for SCZ patients was 67% based on coding genes, and 96% based on long non-coding RNAs (lncRNAs). Machine learning is a powerful algorithm to reduce functional biomarkers in SCZ patients. The lncRNAs capture the characteristics of SCZ tissue more accurately than mRNA as the former regulate every level of gene expression, not limited to mRNA levels.     

Investigation of the Anti-Methicillin-Resistant Staphylococcus aureus Activity of (+)-Tanikolide- and (+)-Malyngolide-Based Analogues Prepared by Asymmetric Synthesis

Herein, we report antibacterial and antifungal evaluation of a series of previously prepared (+)-tanikolide analogues. One analogue, (4S,6S)-4-methyltanikolide, displayed promising anti-methicillin-resistant Staphylococcus aureus activity with a MIC of 12.5 µg/mL. Based on the antimicrobial properties of the structurally related (−)-malyngolide, two further analogues (4S,6S)-4-methylmalyngolide and (4R,6S)-4-methylmalyngolide bearing a shortened n-nonyl alkyl side chain were prepared in the present study using a ZrCl₄-catalysed deprotection/cyclisation as the key step in their asymmetric synthesis. When these were tested for activity against anti-methicillin-resistant Staphylococcus aureus, the MIC increased to 50 µg/mL.     

CYP154C5 Regioselectivity in Steroid Hydroxylation Explored by Substrate Modifications and Protein Engineering**

CYP154C5 from Nocardia farcinica is a P450 monooxygenase able to hydroxylate a range of steroids with high regio- and stereoselectivity at the 16α-position. Using protein engineering and substrate modifications based on the crystal structure of CYP154C5, an altered regioselectivity of the enzyme in steroid hydroxylation had been achieved. Thus, conversion of progesterone by mutant CYP154C5 F92A resulted in formation of the corresponding 21-hydroxylated product 11-deoxycorticosterone in addition to 16α-hydroxylation. Using MD simulation, this altered regioselectivity appeared to result from an alternative binding mode of the steroid in the active site of mutant F92A. MD simulation further suggested that the entrance of water to the active site caused higher uncoupling in this mutant. Moreover, exclusive 15α-hydroxylation was observed for wild-type CYP154C5 in the conversion of 5α-androstan-3-one, lacking an oxy-functional group at C17. Overall, our data give valuable insight into the structure–function relationship of this cytochrome P450 monooxygenase for steroid hydroxylation.     

Quantification of secondary structure prediction improvement using multiple alignments

The use of multiple sequence alignments for secondary structurepredictions is analysed. Seven different protein families, containingonly sequences of known structure, were considered to providea range of alignment and prediction conditions. Using alignmentsobtained by spatial superposition of main chain atoms in knowntertiary protein structures allowed a mean of 8% in secondarystructure prediction accuracy, when compared to those obtainedfrom the individual sequences. Substitution of these alignmentsby those determined directly from an automated sequence alignmentalgorithm showed variations in the prediction accuracy whichcorrelated with the quality of the multiple alignments and distanceof the primary sequence. Secondary structure predictions canbe reliably improved using alignments from an automatic alignmentprocedure with a mean increase of 6.87percnt;, giving an overallprediction accuracy of 68.5%, if there is a minimum of 25% sequenceidentity between all sequences in a family.     

Some aspects of the role of coal thermoplasticity and coke structure in coal gasification. 2. The effects of pressure and heating rate on dilatometric parameters and optical anisotropy development

An examination of the influence of pressure and heating rate on the thermoplastic properties of a weakly coking coal and of coal with various pitch-like additives was carried out using a high pressure dilatometer. Pressure up to 4 MPa markedly increased the swelling properties and increased the plastic range by decreasing the softening temperature, but the effects of pressure were strongly influenced by rate of heating with high heating rates enhancing the effects. Additions of tar or pitch also enhanced swelling at low pressure. The solid carbonization residues from the dilatometer were examined by polarized light microscopy to determine the content and composition of optically anisotropic species. The anisotropic content was increased by increases in pressure and heating rate and pitch additives enhanced the anisotropic content, especially at low pressure, without affecting the composition of the anisotropy. No direct correlations exist between the dilatometric parameters and the optical anisotropy but their dependence on the conditions emphasizes that when considering high pressure gasification of coal, it is necessary to obtain data under appropriate conditions.     

Characterizing electrocatalytic surfaces: Electrochemical and NMR studies of methanol and carbon monoxide on Pt/C

We use cyclic voltammetry (CV) on fuel cell electrodes to elucidate the important differences between adsorbates resulting from carbon monoxide adsorption and methanol adsorption onto commercial Pt/C electrocatalysts in a sulfuric acid electrolyte. Under open circuit conditions, methanol was found to adsorb preferentially onto the Pt sites associated with “strongly bound” hydrogen. The sites associated with “weakly bound” hydrogen adsorbed methanol more slowly. In the case of CO adsorption, which requires no adsorbate dehydrogenation, all adsorption sites showed similar affinity towards the adsorbate. Electrochemical oxidation of the adsorbates derived from both methanol and CO exposure exhibit slower oxidation when the adsorbate is associated with cubic-packed-like sites than from close-packed-steps and other sites. NMR of a ¹³CO-adlayer prepared by electrochemical adsorption from low concentration ¹³CH₃OH shows a lower NMR shift and smaller linewidth than the previously reported values for electrochemically adsorbed ¹³CO gas. These results are interpreted in terms of adsorbate motion on the electrocatalyst surface.     

RF MEMS continuous reversible variable inductor based on a microfluidic network

In this work, RF MEMS continuous reversible variable inductor has been fabricated by using microelectronic technology and lamination process. We review, evaluate and compare this variable inductor with other work. The proposed inductor is a dual circular coil and has an inductance of few nH. The fundamental idea is to place a liquid droplet between the metal turns of a coil in order to modify the capacitive/resistive coupling between metal tracks and hence to change the stored magnetic energy. The SU-8 resin was used to realize the microfluidic channels and Au as metallic tracks. To prove the reversibility of the inductor, two cases were studied: filling and emptying of channels. The tuning range of the inductance is approximately 107 % at 1.6 GHz, making these devices very suitable as building blocks in many RF applications.