bluuebunny/crossref_metadata_2025_split huggingface dataset:
How good are comparative models in the understanding of protein dynamics?
Authors: Yazhini Arangasamy , Srinivasan Narayanaswamy 
Published: January 2020

AbstractThe 3D structure of a protein is essential to understand protein dynamics. If experimentally determined structure is unavailable, comparative models could be used to infer dynamics. However, the effectiveness of comparative models, compared to experimental structures, in inferring dynamics is not clear. To address this, we compared dynamics features of ~800 comparative models with their crystal structures using normal mode analysis. Average similarity in magnitude, direction, and correlation of residue motions is >0.8 (where value 1 is identical) indicating that the dynamics of models and crystal structures are highly similar. Accuracy of 3D structure and dynamics is significantly higher for models built on multiple and/or high sequence identity templates (>40%). Three‐dimensional (3D) structure and residue fluctuations of models are closer to that of crystal structures than to templates (TM score 0.9 vs 0.7 and square inner product 0.92 vs 0.88). Furthermore, long‐range molecular dynamics simulations on comparative models of RNase 1 and Angiogenin showed significant differences in the conformational sampling of conserved active‐site residues that characterize differences in their activity levels. Similar analyses on two EGFR kinase variant models highlight the effect of mutations on the functional state‐specific αC helix motions and these results corroborate with the previous experimental observations. Thus, our study adds confidence to the use of comparative models in understanding protein dynamics.
Structure and dynamics at N‐ and C‐terminal regions of intrinsically disordered human c‐Myc PEST degron reveal a pH‐induced transition
Authors: Ansari Mohd. Ziauddin , Swaminathan Rajaram 
Published: January 2020

AbstractWe investigated the structure and Brownian rotational motion of the PEST region (201‐268) from human c‐Myc oncoprotein, whose overexpression/dysregulation is associated with various types of cancer. The 77‐residue PEST fragment revealed a large Stokes radius (~3.1 nm) and CD spectrum highlighting abundance of disordered structure. Changes in structure/dynamics at two specific sites in PEST degron were observed using time‐resolved fluorescence spectroscopy by labeling Cys9 near N‐terminal with dansyl probe and inserting a Trp70 near C‐terminal (PEST M1). Trp in PEST M1 at pH 3 was inaccessible to quencher, showed hindered segmental motion and slow global rotation (~30 ns) in contrast to N‐terminal where the dansyl probe was free, exposed with fast global rotation (~5 ns). Remarkably, this large monomeric structure at acidic pH was retained irrespective of ionic strength (0.03‐0.25 M) and partially so in presence of 6 M Gdn.HCl. With gradual increase in pH, a structural transition (~pH 4.8) into a more exposed and freely rotating Trp was noticeable. Interestingly, the induced structure at C‐terminal also influenced the dynamics of dansyl probe near N‐terminal, which otherwise remained unstructured at pH > 5. FRET measurements confirmed a 11 Å decrease in distance between dansyl and indole at pH 4 compared to pH 9, coinciding with enhanced ANS binding and increase in strand/helix population in both PEST fragments. The protonation of glutamate/aspartate residues in C‐terminal region of PEST is implicated in this disorder‐order transition. This may have a bearing on the role of PEST in endocytic trafficking of eukaryotic proteins.
Treatment of Porphyromonas gulae infection and downstream pathology in the aged dog by lysine‐gingipain inhibitor COR388
Authors: Arastu‐Kapur Shirin , Nguyen Mai , Raha Debasish , Ermini Florian , Haditsch Ursula , Araujo Joseph , De Lannoy Ines A. M. , Ryder Mark I. , Dominy Stephen S. , Lynch Casey , Holsinger Leslie J. 
Published: January 2020

AbstractCOR388, a small‐molecule lysine‐gingipain inhibitor, is currently being investigated in a Phase 2/3 clinical trial for Alzheimer's disease (AD) with exploratory endpoints in periodontal disease. Gingipains are produced by two species of bacteria, Porphyromonas gingivalis and Porphyromonas gulae, typically associated with periodontal disease and systemic infections in humans and dogs, respectively. P. gulae infection in dogs is associated with periodontal disease, which provides a physiologically relevant model to investigate the pharmacology of COR388. In the current study, aged dogs with a natural oral infection of P. gulae and periodontal disease were treated with COR388 by oral administration for up to 90 days to assess lysine‐gingipain target engagement and reduction of bacterial load and downstream pathology. In a 28‐day dose‐response study, COR388 inhibited the lysine‐gingipain target and reduced P. gulae load in saliva, buccal cells, and gingival crevicular fluid. The lowest effective dose was continued for 90 days and was efficacious in continuous reduction of bacterial load and downstream periodontal disease pathology. In a separate histology study, dog brain tissue showed evidence of P. gulae DNA and neuronal lysine‐gingipain, demonstrating that P. gulae infection is systemic and spreads beyond its oral reservoir, similar to recent observations of P. gingivalis in humans. Together, the pharmacokinetics and pharmacodynamics of COR388 lysine‐gingipain inhibition, along with reduction of bacterial load and periodontal disease in naturally occurring P. gulae infection in the dog, support the use of COR388 in targeting lysine‐gingipain and eliminating P. gingivalis infection in humans.
Distance education as socio‐material assemblage: Place, distribution, and aggregation
Authors: Gunter Ashley , Raghuram Parvati , Breines Markus Roos , Prinsloo Paul 
Published: January 2020

AbstractThis paper outlines some of the material assemblages that are formed in international distance education (DE) in Africa. It offers a first exploratory study of materialities in DE and how they potentially distribute and aggregate to form a network to provide education. Through the use of interviews, students lived experiences are explored to unpack the multiplicity of networks needed to overcome the de‐aggregated and distributed institution. The multiplicity of networks that form in DE brings challenges that question how spaces become connected and disconnected and how different materialities shape DE. The materialities in DE produce forces and effects, such as translocal and transmobilites that are more than just the human actor, but extrude materials, networks, and connectives that transform continuously. The interconnectivities of the university and home or institution and students are brought together through enabling technology, but infrastructure does not always have the ability for the facilitation of aggregation.
Optimized wavelet‐based adaptive mesh refinement algorithm for numerical modeling of three‐dimensional global‐scale atmospheric chemical transport
Authors: Semakin A. N. , Rastigejev Y. 
Published: January 2020

AbstractSubstantial numerical difficulties associated with the computational modeling of multiscale global atmospheric chemical transport impose severe limitations on the spatial resolution of nonadaptive fixed grids. The crude spatial discretization introduces a large amount of numerical diffusion into the system, which, in combination with strong flow stretching, causes large numerical errors. To resolve this issue, we have developed an optimized wavelet‐based adaptive mesh refinement (OWAMR) method. The OWAMR is a three‐dimensional adaptive method that introduces a fine grid dynamically only in the regions where small spatial structures occur. The algorithm uses a new two‐parameter adaptation criterion that significantly (by factors between 1.5 and 2.7) reduces the number of grid points compared with the more conventional one‐parameter grid adaptation used by wavelet‐based adaptive techniques and high‐order upwind schemes, which enable one to increase the accuracy of approximation of the advection operator substantially. It has been shown that the method simulates the dynamics of a pollution plume that travels on a global scale, producing less than 3% error. To achieve such accuracy, conventional three‐dimensional nonadaptive techniques would require five orders of magnitude more computational resources. Therefore, the method provides a realistic opportunity to model accurately a variety of the most demanding multiscale problems in the area of atmospheric chemical transport, which are difficult or impossible to simulate on existing computational facilities with conventional fixed‐grid techniques.
Reduced‐precision parametrization: lessons from an intermediate‐complexity atmospheric model
Authors: Saffin Leo , Hatfield Sam , Düben Peter , Palmer Tim 
Published: January 2020

AbstractReducing numerical precision can save computational costs which can then be reinvested for more useful purposes. This study considers the effects of reducing precision in the parametrizations of an intermediate complexity atmospheric model (SPEEDY). We find that the difference between double‐precision and reduced‐precision parametrization tendencies is proportional to the expected machine rounding error if individual timesteps are considered. However, if reduced precision is used in simulations that are compared to double‐precision simulations, a range of precision is found where differences are approximately the same for all simulations. Here, rounding errors are small enough to not directly perturb the model dynamics, but can perturb conditional statements in the parametrizations (such as convection active/inactive) leading to a similar error growth for all runs. For lower precision, simulations are perturbed significantly. Precision cannot be constrained without some quantification of the uncertainty. The inherent uncertainty in numerical weather and climate models is often explicitly considered in simulations by stochastic schemes that will randomly perturb the parametrizations. A commonly used scheme is stochastic perturbation of parametrization tendencies (SPPT). A strong test on whether a precision is acceptable is whether a low‐precision ensemble produces the same probability distribution as a double‐precision ensemble where the only difference between ensemble members is the model uncertainty (i.e., the random seed in SPPT). Tests with SPEEDY suggest a precision as low as 3.5 decimal places (equivalent to half precision) could be acceptable, which is surprisingly close to the lowest precision that produces similar error growth in the experiments without SPPT mentioned above. Minor changes to model code to express variables as anomalies rather than absolute values reduce rounding errors and low‐precision biases, allowing even lower precision to be used. These results provide a pathway for implementing reduced‐precision parametrizations in more complex weather and climate models.
Prozac for depressed states? Effect of mood on local economic recessions
Authors: Chhaochharia Vidhi , Korniotis George M. , Kumar Alok 
Published: January 2020

AbstractThis paper examines whether people's mood and optimism affect economic activity. We consider two sets of exogenous proxies for optimism that are unrelated to the economic environment: (1) weather (average temperature and cloud cover) and (2) sports and political optimism. We show that economic recessions are weaker and expansions are stronger in the United States where local individuals are more optimistic. Further, local optimism has a stronger impact on state‐level business cycles of smaller states and regions with low levels of risk sharing. In contrast, the incremental effects of local optimism are weaker in states where people are younger, more educated and sophisticated, and socially more connected. States with larger concentration of minority and urban population also exhibit lower sensitivity to variations in mood and optimism. Alternative explanations based on the state's industrial composition, tax environment, migration, seasonal affective disorder (SAD), oil shocks, and direct economic impact of weather cannot explain these findings.
Fish trophic guild responses to damming: Variations in abundance and biomass
Authors: Dias Rosa Maria , Ortega Jean Carlo Gonçalves , Strictar Larissa , dos Santos Natália Carneiro Lacerda , Gomes Luiz Carlos , da Luz‐Agostinho Karla Danielle Gaspar , Agostinho Carlos Sérgio , Agostinho Angelo Antonio 
Published: January 2020

AbstractDams and associated reservoirs cause drastic changes in the composition and structure of ichthyofauna. Therefore, functional groups within a fish assemblage may respond distinctly to such human interventions in rivers. The objective of this study was to evaluate how fluctuations in fish abundance and biomass differ among trophic guilds. Fish were sampled before and after damming four reservoirs, in their inner areas (more heavily impacted areas) and upstream (less impacted areas). To evaluate possible changes, we used a before–after and control‐impact experimental design. Fish were classified into trophic guilds through diet analysis and based on information available from the literature. Six trophic guilds were identified. The effect of periods (before and after damming) and sites (more and less impacted) on abundance and biomass differed among the trophic guilds. Highly specialized trophic guilds, such as herbivores and detritivores, were negatively affected by damming. Invertivores were negatively affected in the impacted area and increased in abundance and biomass in the less impacted sites. The findings of this study show that modifications imposed by damming are reflected in the abundance and biomass of fish trophic guilds, but the degree of such impacts vary according to characteristics of the considered trophic guild.
A Sustainable and Eco‐Friendly Polymer Based Graphene Oxide Nanocomposite Anti‐Corrosion Coating on Mild Steel
Authors: Hegde Mahesh B. , Mohana Kikkeri N. 
Published: January 2020

AbstractAn eco‐friendly polymer‐based nanocomposite coating on mild steel (MS) surface was prepared using Garcinia indica vegetable oil (GIVO). Graphene oxide (GO) was synthesized by the modified Hummers method and used to prepare Garcinia indica vegetable oil‐Graphene oxide (GIVO‐GO) dispersion. The anti‐corrosion coating of GIVO and GIVO‐GO dispersion was studied by electrochemical methods. GO, GIVO and GIVO‐GO are characterized by X‐ray diffraction (XRD), Fourier‐transform infrared spectroscopy (FTIR) and Raman spectral studies. The coated MS samples are examined by scanning electron microscopy (SEM), atomic force microscopy (AFM), XRD and water contact angle measurement. Electrochemical investigations revealed that incorporation of GO into GIVO reduced the corrosion rate of MS to around 600 times with 0.4 wt % of GO compared to the GIVO coated sample. The enhancement of the corrosion prevention behavior of GO incorporated coating is discussed based on the impermeable action of GO to the corrosive ions and also the reduction of pores in the polymer that are formed during the curing of the coating.
A Hybrid Electrochemical Energy Storage Device Using Sustainable Electrode Materials
Authors: Minakshi Manickam , Mitchell David R. G. , Jones Robert T. , Pramanik Nimai Chand , Jean‐Fulcrand Annelise , Garnweitner Georg 
Published: January 2020

AbstractA new electrochemical energy storage device, comprising a faradaic rechargeable pseudo‐capacitor type electrode with a non‐faradaic rechargeable capacitor electrode, is successfully developed for potential applications in smart electric grids. Mapping new electrodes possessing both high energy and power densities as well as long cycle life is vital for the sustainable energy management. In this work, we present a new approach to design electrodes, fabricated from sustainable resources by hybridizing calcined eggshell capacitor anode with a mixed binary metal oxide pseudo‐capacitor cathode. Calcium carbonate (calcite), obtained from the biowaste‐derived eggshell, is an effective electrode material and operates via accumulation of ions on the electrode surface, providing a high discharge capacitance of 100 F/g through a non‐faradaic process. The calcite present in eggshells is found to be a valuable renewable resource which can be utilized for energy storage through suitable process design. Otherwise, such potentially useful materials (eggshells) are generally discarded as landfill. The mixed binary metallic oxide (NiO/Co3O4) showed a typical pseudocapacitive behaviour associated with both charge transfer reactions and electrostatic means provided a high discharge capacitance of 225 F/g. The fabricated prototype hybrid device provides an energy density 35 Wh/Kg at a power density 420 W/Kg. The charge storage characteristics of the hybrid device depend heavily on the current rate employed. The design and fabrication of new sustainable electrode materials provides an understanding of materials and their electrochemical performance in the high‐voltage window.
All about activity injection: Threats, semantics, detection, and defense
Authors: Hwang Sungjae , Lee Sungho , Ryu Sukyoung 
Published: January 2020

SummaryAndroid supports seamless user experience by maintaining activities from different applications (apps) in the same activity stack. Although such close inter‐app communication is essential in the Android framework, the powerful inter‐app communication contains vulnerabilities that can inject malicious activities into a victim app's activity stack to hijack user interaction flows. In this article, we demonstrate activity injection attacks with a simple malware, and formally specify the activity activation mechanism using operational semantics. Based on the operational semantics, we develop a static analysis tool, which analyzes Android apps to detect activity injection attacks. Our tool is fast enough to analyze real‐world Android apps in 6 seconds on average, and our experiments found that 1761 apps out of 129,756 real‐world Android apps inject their activities into other apps' tasks. Moreover, we propose a defense mechanism, dubbed signature‐based activity access control (SAAC), which completely prohibits activity injection attacks. The defense mechanism is general enough to keep the current Android multitasking features intact, and it is simple enough to be independent of the complex activity activation semantics, which does not increase activity activation time noticeably. With the extension of the formal semantics for SAAC, we prove that SAAC correctly mitigates activity injection attacks without any false alarms.
Seroprevalence of anti‐Mycobacterium aviumsubsp.paratuberculosisantibodies in female sheep in Tunisia
Authors: Khamassi Khbou Médiha , Romdhane Rihab , Sassi Limam , Amami Amira , Rekik Mourad , Benzarti M’hammed 
Published: January 2020

AbstractParatuberculosis (Ptb) is a widespread chronic infection caused byMycobacterium aviumsubsp.paratuberculosis(Map) that affects both domestic and wild ruminants. Most of the studies focused on cattle while, the prevalence of Ptb in sheep in different regions of the world is not well investigated. This study aimed to address this gap of knowledge by screening adult female sheep for paratuberculosis antibodies in different geographical regions of Tunisia. A total number of 338 female sheep from 15 small to middle‐sized, extensively managed sheep farms in six regions across Tunisia were sampled. Animals were clinically examined before blood sampling. Sera were tested for the presence of anti‐Mycobacterium aviumsubsp.paratuberculosisantibodies using a commercial ELISA kit. Six farms out of 15 comprised at least one seropositive animal and 11 female sheep out of 338 tested animals (3.25%; 95% CI = [1.83–5.73]) were seropositive toM. aviumsubsp.paratuberculosis. The seroprevalence was significantly lower in 5‐year‐old females (p = .04) and animals that do not graze (p = .02). Due to its huge economic and social impacts, paratuberculosis represents a health problem in Tunisia and several other countries Further investigations are needed to rank sheep Ptb in Tunisia among other diseases and to assess the main risk factors using a larger nation‐wide survey.
ChemML: A machine learning and informatics program package for the analysis, mining, and modeling of chemical and materials data
Authors: Haghighatlari Mojtaba , Vishwakarma Gaurav , Altarawy Doaa , Subramanian Ramachandran , Kota Bhargava U. , Sonpal Aditya , Setlur Srirangaraj , Hachmann Johannes 
Published: January 2020

AbstractChemML is an open machine learning (ML) and informatics program suite that is designed to support and advance the data‐driven research paradigm that is currently emerging in the chemical and materials domain. ChemML allows its users to perform various data science tasks and execute ML workflows that are adapted specifically for the chemical and materials context. Key features are automation, general‐purpose utility, versatility, and user‐friendliness in order to make the application of modern data science a viable and widely accessible proposition in the broader chemistry and materials community. ChemML is also designed to facilitate methodological innovation, and it is one of the cornerstones of the software ecosystem for data‐driven in silico research.This article is categorized under:
Software > Simulation Methods
Computer and Information Science > Chemoinformatics
Structure and Mechanism > Computational Materials Science
Software > Molecular Modeling
Elucidation of the potential of Moringa oleifera leaves extract as a novel alternate to the chemical coagulant in water treatment process
Authors: Pandey Pratibha , Khan Fahad , Mishra Rashmi , Singh Sujeet Kumar 
Published: January 2020

AbstractIn recent years, several studies have been developed to search for sustainable and eco‐friendly natural coagulants as an alternative to inorganic and synthetic coagulants to obtain drinking water. Despite the performance and cost‐effectiveness of these coagulants, they require pH and alkalinity adjustments, they generate high volumes of sludge, and their residuals in treated water (e.g., aluminum) are linked with neurodegenerative diseases such as Alzheimer's, as well as neurotoxic and carcinogenic effects. Moringa oleifera seeds had shown better coagulation properties but have numerous limitations which have prompted us to find better alternatives. To the best part of my knowledge, utilization of its leaves extract obtained from different organic solvents in water purification has rarely been reported. Our findings clearly revealed that M. oleifera leaves hexane extract has significantly improved the water quality parameters including pH (8.2–7.1), TDS (512–221), hardness (246–138), turbidity (15.6–6.1), fluoride (2.3–1.1), and Escherichia coli count (315–41) whereas alum effectively improved these parameters at a dose of 50 mg/L. Moringa oleifera showed significant removal capability in comparison to alum but slightly at higher dose, thus our results strongly supported the efficacy of M. oleifera leaves extracts as better alternative to chemical coagulant in water purification.Practitioner Points

Chemical coagulants pose severe side effects to humans such as neurodegenerative diseases.

Use of Moringa oleifera leaves as natural coagulants in water purification is a cost‐effective approach due to its easy availability throughout the year.

Moringa oleifera leaves exhibited significant coagulating efficiency by improving water quality parameters including pH, turbidity, total dissolved solids, fluoride, hardness, and E. coli count.