bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative Proteomics for Monitoring Renal Transplant Injury
Authors: Song Lei , Fang Fei , Liu Peng , Zeng Gang , Liu Hongda , Zhao Yang , Xie Xubiao , Tseng George , Randhawa Parmjeet , Xiao Kunhong
Published: January 2020

Purpose

This study is aimed at developing a molecular diagnostics platform to enhance the interpretation of renal allograft biopsies using quantitative proteomic profiling of formalin‐fixed and paraffin‐embedded (FFPE) specimens.

Experimental Design

A quantitative proteomics platform composed of 1) an optimized FFPE protein sample preparation method, 2) a tandem mass tag TMT10‐plex‐based proteomic workflow, and 3) a systematic statistical analysis pipeline to reveal differentially expressed proteins has been developed. This platform is then tested on a small sample set (five samples per phenotype) to reveal proteomic signatures that can differentiate T‐cell mediated rejection (TCMR) and polyomavirus BK nephropathy (BKPyVN) from healthy functionally stable kidney tissue (STA).

Results

Among 2798 quantified proteins, the expression levels of 740 BKPyVN and 638 TCMR associated proteins are significantly changed compared to STA specimens. Principal component analysis demonstrated good segregation of all three phenotypes investigated. Protein detection and quantitation are highly reproducible: replicate comparative analyses demonstrated 71–84% overlap of detected proteins, and the coefficient of variation for protein measurements is <15% in triplicate liquid chromatography‐tandem mass spectrometry runs.

Conclusions and Clinical Relevance

Quantitative proteomics can be applied to archived FFPE specimens to differentiate different causes of renal allograft injury.
Salivary Fingerprinting of Periodontal Disease by Infrared‐ATR Spectroscopy
Authors: Beyer‐Hans Kerstin Meta‐Catherina , Sigrist Markus Werner , Silbereisen Angelika , Ozturk Veli Ozgen , Emingil Gulnur , Bostanci Nagihan
Published: January 2020

Purpose

Periodontal diseases, the most common chronic inflammatory diseases in humans, do not only affect tooth‐supporting tissues but also other body parts by contributing to the development of life‐threatening conditions. Since currently available diagnostic methods in periodontics lack the ability to identify patients at high risk for periodontal disease progression, development of innovative, non‐invasive, rapid detection methods for diagnosing periodontal diseases is needed. This study aims to assess the potential of infrared attenuated total reflection (IR‐ATR) spectroscopy to detect differences in composition of saliva supernatant in non‐periodontitis individuals (control) and patients with generalized aggressive periodontitis (G‐AgP).

Experimental Design

IR‐ATR is performed with a wavelength interval from 1230 to 1180 cm−1, analyzed with a simple subtraction in absorbance data.

Results

Ten samples show in the analysis of variance of the two data sets a true difference (99.8%). A principal component analysis (PCA) is able to discriminate between G‐AgP and control groups.

Conclusion and Clinical Relevance

This study demonstrates for the first time that IR‐ATR spectroscopy is a promising tool for the analysis of saliva supernatant for the diagnosis of periodontitis, and potentially other periodontal conditions. IR‐ATR spectroscopy holds the potential to be miniaturized and utilized as a non‐invasive screening test.
A strong correlation between consensus sequences and unique super secondary structures in leucine rich repeats
Authors: Batkhishig Dashdavaa , Enkhbayar Purevjav , Kretsinger Robert H. , Matsushima Norio
Published: January 2020

Leucine rich repeats (LRRs) are present in over 430 000 proteins from viruses to eukaryotes. The LRRs are 20 to 30 residues long and occur in tandem. Individual LRRs are separated into a highly conserved segment with the consensus of LxxLxLxxNxL or LxxLxLxxNxxL (HCS) and a variable segment (VS). In LRRs parallel stacking of short β‐strands (at positions 3‐5 in HCS) form a super helix arrangement called a solenoid structure. Many classes have been recognized. All three classes of Plant specific, Leptospira‐like, and SDS22‐like LRRs which are 24, 23, and 22 residues long, respectively, form a 3(10)‐helix in the VS part. To get a deeper understanding of sequence, structure correlations in LRR structures, we utilized secondary structure assignment and HELFIT analysis (calculating helix axis, pitch, radius, residues per turn, and handedness) based on the atomic coordinates in crystal structures of 43 LRR proteins. We also defined three structural parameters using the three unit vectors of the helix axes of 3(10)‐helix, β‐turn, and LRR‐domain calculated by HELFIT. The combination of the secondary structure assignment and HELFIT reveals that their LRRs adopt unique super secondary structures consisting of a 3(10)‐helix and one or two Type I β‐turns. We propose one structural parameter as a geometrical invariant of LRR solenoid structures. The common LxxLxxL sequence (where “L” is Leu, Ile, Val, Phe or Cys) in the three classes is an essential determinant for the super secondary structures providing a medium range interaction.
How good are comparative models in the understanding of protein dynamics?
Authors: Yazhini Arangasamy , Srinivasan Narayanaswamy
Published: January 2020

The 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

We 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

COR388, 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

This 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.
A Comparative Study of the γ‐Ray Radiation Effect on Zr‐Doped and Al‐Doped HfO2‐Based Ferroelectric Memory
Authors: Zhang Wanli , Li Gang , Long Xiaojiang , Cui Lian , Tang Minghua , Xiao Yongguang , Yan Shaoan , Li Yadong , Zhao Wenxi
Published: January 2020

The γ‐ray total dose radiation effects on Zr‐doped HfO2 (HfZrO) and Al‐doped HfO2 (HfAlO) ferroelectric thin films are comparatively studied. The J–E, P–E, C–V, εr–f curves and fatigue characteristics of both HfZrO and HfAlO thin films are measured and analyzed with the increasing total dose from 0 to 5 Mrad (Si). The remnant polarization (Pr) values of both HfZrO and HfAlO thin films first decrease and then increase with the increasing total dose. A competitive mechanism between the pinned domains and increasing polarization switching charges induced by radiation is proposed to explain this phenomenon. This work presents doped HfO2 film with great radiation tolerance for nuclear and aerospace applications.
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

Substantial 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

Reducing 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

This 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

Dams 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 fair comparison of tree‐based and parametric methods in multiple imputation by chained equations
Authors: Slade Emily , Naylor Melissa G.
Published: January 2020

Multiple imputation by chained equations (MICE) has emerged as a leading strategy for imputing missing epidemiological data due to its ease of implementation and ability to maintain unbiased effect estimates and valid inference. Within the MICE algorithm, imputation can be performed using a variety of parametric or nonparametric methods. Literature has suggested that nonparametric tree‐based imputation methods outperform parametric methods in terms of bias and coverage when there are interactions or other nonlinear effects among the variables. However, these studies fail to provide a fair comparison as they do not follow the well‐established recommendation that any effects in the final analysis model (including interactions) should be included in the parametric imputation model. We show via simulation that properly incorporating interactions in the parametric imputation model leads to much better performance. In fact, correctly specified parametric imputation and tree‐based random forest imputation perform similarly when estimating the interaction effect. Parametric imputation leads to slightly higher coverage for the interaction effect, but it has wider confidence intervals than random forest imputation and requires correct specification of the imputation model. Epidemiologists should take care in specifying MICE imputation models, and this paper assists in that task by providing a fair comparison of parametric and tree‐based imputation in MICE.
Analysis of counts for cluster randomized trials: Negative controls and test‐negative designs
Authors: Dufault Suzanne M. , Jewell Nicholas P.
Published: January 2020

In cluster randomized trials (CRTs), the outcome of interest is often a count at the cluster level. This occurs, for example, in evaluating an intervention with the outcome being the number of infections of a disease such as HIV or dengue or the number of hospitalizations in the cluster. Standard practice analyzes these counts through cluster outcome rates using an appropriate denominator (eg, population size). However, such denominators are sometimes unknown, particularly when the counts depend on a passive community surveillance system. We consider direct comparison of the counts without knowledge of denominators, relying on randomization to balance denominators. We also focus on permutation tests to allow for small numbers of randomized clusters. However, such approaches are subject to bias when there is differential ascertainment of counts across arms, a situation that may occur in CRTs that cannot implement blinded interventions. We suggest the use of negative control counts as a method to remove, or reduce, this bias, discussing the key properties necessary for an effective negative control. A current example of such a design is the recent extension of test‐negative designs to CRTs testing community‐level interventions. Via simulation, we compare the performance of new and standard estimators based on CRTs with negative controls to approaches that only use the original counts. When there is no differential ascertainment by intervention arm, the count‐only approaches perform comparably to those using debiasing negative controls. However, under even modest differential ascertainment, the count‐only estimators are no longer reliable.
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

An 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

A 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

Android 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

Paratuberculosis (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

ChemML 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

In 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.
Adapting urban best management practices for resilience to long‐term environmental changes
Authors: Job Scott C. , Harris Maureen , Julius Susan , Butcher Jonathan B. , Kennedy Joseph Todd
Published: January 2020

Stormwater best management practices (BMPs) help mitigate the adverse effects of urban development on stream hydrology and water quality, and are widely specified in development requirements and watershed management plans. However, design of stormwater BMPs largely relies on experience with historic climate, which may not be a reliable guide to the future. To inform BMP design that is robust to future conditions, it is important to examine how potential changes in precipitation, temperature, and potential evapotranspiration will affect the performance of BMPs. We use continuous simulation modeling to examine BMP performance under current and potential future climatic conditions and determine the changes needed in site configuration to address future impacts. We perform modeling for five development types in five different regions of the United States and explore both conventional (“gray”) and green infrastructure (GI) stormwater management approaches. If stormwater designs are adapted to address potential future climate conditions, this study suggests that the most cost‐effective approaches may use both gray and green BMPs. If the magnitude of extreme weather events increases dramatically, then gray practices that provide detention storage may have better cost‐effectiveness. Incorporating risk of future climate impacts into stormwater design may help communities become more resilient.

Practitioner points

There is a risk that projected changes in meteorological forcing will negatively affect stormwater BMP performance.

Under projected future climate conditions, this study suggests the most cost‐effective approaches may use both gray and green BMPs.

If the magnitude of extreme weather events increases dramatically, gray practices that provide detention storage may have better cost‐effectiveness.

Flexibility is beneficial in adaptation and resilience planning due to uncertainty in projected precipitation volume and intensity changes.
Application of eco‐friendly multifunctional porous graphene oxide for adsorptive sequestration of chromium in aqueous solution
Authors: Nkutha Cynthia S. , Diagboya Paul N. , Mtunzi Fanyana M. , Dikio Ezekiel D.
Published: January 2020

Graphene oxide (GO) was functionalized using two silanes ((3‐aminopropyl)‐triethoxysilane and (3‐mercaptopropyl)‐triethoxysilane) to obtain, separately, the eco‐friendly amine‐functionalized GO (GONH) and thiol‐functionalized GO (GOSH). Both silanes were also used together to obtain the amine–thiol dual‐functionalized GO (GOSN). Various physicochemical characterizations were obtained including spectra from using Fourier‐transform infrared (FTIR) spectrometer, thermogravimetric analyzer, and X‐ray diffractometer. The adsorbents were used for a comparative study of Cr adsorption from aqueous solution. The obtained data were fitted to pseudo‐first order (PFO) and pseudo‐second order (PSO) models, the homogeneous fractal pseudo‐second order (FPSO), and the Weber–Morris intraparticle diffusion (IPD) kinetics models. Model parameters of the Langmuir and Freundlich adsorption isotherm models, as well as the thermodynamics, were calculated. Characterization results showed successful functionalizations. The GONH, GOSH, and GOSN exhibited alkaline, acidic, and neutral pH, respectively, in water. Amine and thiol functional groups were observed in the new adsorbents, as well as reduced orderliness. The adsorbents had higher density per unit weight and better thermal stability than pristine GO. Equilibrium Cr adsorption was attained within 60 min for all adsorbents. The PSO and FPSO described the rate data better. The Cr adsorption decreased as solution pH increased; optimum adsorption was recorded at pH 2. Equilibrium adsorption data fitted the Langmuir adsorption isotherm model for the GONH, while it fitted the Freundlich for both GOSH and GOSN. The adsorption process was theoretically exothermic process that was spontaneous processes. The Cr adsorption capacities of these adsorbents are 114, 89.6, and 173 mg/g for GONH, GOSH, and GOSN, respectively, and these were better than several reported graphene‐based adsorbents and suggest the potential of these adsorbents for water treatment.

Practitioner points

Graphene oxide was mono and dual‐functionalized with amine and thiol groups for Cr adsorption.

The adsorption capacities of these adsorbents were better than several earlier reported.

These adsorbents may be used for real contaminated water treatment.
Synthesis, Crystal Structures, and Properties of Mn(NCS)2 Coordination Compounds with 4‐Picoline as Coligand and Crystal Structure of Mn(NCS)2
Authors: Neumann Tristan , Gallo Gianpiero , Dinnebier Robert E. , Näther Christian
Published: January 2020

Reaction of Mn(NCS)2 with 4‐picoline (4‐methylpyridine) leads to the formation of [Mn(NCS)2(4‐picoline)4]·0.67·4‐picoline·0.33·H2O (1‐Mn) reported in literature, Mn(NCS)2(4‐picoline)2(H2O)2 (2‐Mn/H2O), and of [Mn(NCS)2(4‐picoline)2]n (2‐Mn/I). 1‐Mn and 2‐Mn/H2O consist of discrete complexes, in which the metal cations are octahedrally coordinated, whereas in 2‐Mn/I the metal cations are linked by pairs of μ‐1,3‐bridging thiocyanate anions into corrugated chains. Measurements using thermogravimetry and differential scanning calorimetry as well as temperature dependent X‐ray powder diffraction on 1‐Mn and 2‐Mn/H2O reveal that upon heating both compounds transform into [Mn(NCS)2(4‐picoline)]n (3‐Mn) via 2‐Mn/I as intermediate. 3‐Mn shows a very rare chain topology in which the metal cations are linked by μ‐1,3,3 (N,S,S) coordinating anionic ligands which was never observed before with MnII. From these investigations there is no hint that a further modification of 2‐Mn can be prepared as recently observed for [M(NCS)2(4‐picoline)2]n (M = Fe, Cd) and such a form is also not available if the metastable forms of the FeII or CdII compounds were used as template during thermal decomposition. Magnetic investigations on 2‐Mn/H2O show only paramagnetic behavior, whereas for 2‐Mn/I antiferromagnetic ordering is observed. Finally, the crystal structure of Mn(NCS)2 was determined from XRPD data, which shows that it is strongly related to that of 3‐Mn.
Nonlinear Langevin dynamics via holography
Authors: Chakrabarty Bidisha , Chakravarty Joydeep , Chaudhuri Soumyadeep , Jana Chandan , Loganayagam R. , Sivakumar Akhil
Published: January 2020

Abstract

In this work, we consider non-linear corrections to the Langevin effective theory of a heavy quark moving through a strongly coupled CFT plasma. In AdS/CFT, this system can be identified with that of a string stretched between the boundary and the horizon of an asymptotically AdS black brane solution. We compute the Feynman-Vernon influence phase for the heavy quark by evaluating the Nambu-Goto action on a doubled string configuration. This configuration is the linearised solution of the string motion in the doubled black brane geometry which has been proposed as the holographic dual of a thermal Schwinger-Keldysh contour of the CFT. Our expression for the influence phase passes non-trivial consistency conditions arising from the underlying unitarity and thermality of the bath. The local effective theory obeys the recently proposed non-linear fluctuation dissipation theorem relating the non-Gaussianity of thermal noise to the thermal jitter in the damping constant. This furnishes a non-trivial check for the validity of these relations derived in the weak coupling regime.
Axion-like relics: new constraints from old comagnetometer data
Authors: Bloch Itay M. , Hochberg Yonit , Kuflik Eric , Volansky Tomer
Published: January 2020

Abstract

The noble-alkali comagnetometer, developed in recent years, has been shown to be a very accurate measuring device of anomalous magnetic-like fields. An ultra-light relic axion-like particle can source an anomalous field that permeates space, allowing for its detection by comagnetometers. Here we derive new constraints on relic axion-like particles interaction with neutrons and electrons from old comagnetometer data. We show that the decade-old experimental data place the most stringent terrestrial constraints to date on ultra-light axion-like particles coupled to neutrons. The constraints are comparable to those from stellar cooling, providing a complementary probe. Future planned improvements of comagnetometer measurements through altered geometry, constituent content and data analysis techniques could enhance the sensitivity to axion-like relics coupled to nucleons or electrons by many orders of magnitude.
Jets with electrons from boosted top quarks
Authors: Chatterjee Suman , Godbole Rohini , Roy Tuhin S.
Published: January 2020

Abstract

We propose a method to identify jets consisting of all the visible remnants of a boosted top quark decaying semileptonically with an electron in the final state. An overlap of electron shower with the b quark initiated shower, and the large nontrivial energy-momentum carried by the invisible neutrino in the top quark decay are the two obstacles to achieving this aim. Our method uses the distribution of energy in different parts of the detector to identify a jet containing an energetic electron, involves use of substructure of the jet to determine the momentum associated with the electron and then completes the identification of top jet with the construction of new variables which would reflect the top quark decay kinematics. The last part involves an ansatz of the existence of a massless, invisible four-momentum roughly collimated with the electron, whose four- momentum when combined with that of the the electron and the full jet, reconstructs to the W boson and the top quark respectively. We demonstrate the efficacy of this proposal using simulated data and show that our method not only reduces the backgrounds from light flavor jets, b jets from QCD, and hadronic top jets, it can also tell apart jets rich in electrons but not due to top quark decays.
Gauged supergravity from the Lunin-Maldacena background
Authors: Liu James T. , McPeak Brian
Published: January 2020

Abstract

We show how to expand the Lunin-Maldacena solution to the full bosonic sector of gauged

$$ \mathcal{N} $$

N

= 2 supergravity. In particular, we construct a consistent truncation of IIB supergravity on a β-deformed AdS5 × S
5 background retaining a dynamical metric and graviphoton in five dimensions. We comment on the relation between this solution and similar constructions on Sasaki-Einstein manifolds, as well as the possibility of further consistent truncations which generalize the Lunin-Maldacena solution.
Probing non-standard neutrino interactions with supernova neutrinos at Hyper-K
Authors: Lei Minjie , Steinberg Noah , Wells James D.
Published: January 2020

Abstract

Non-standard neutrino self interactions (NSSI) could be stronger than Fermi interactions. We investigate the ability to constrain these four-neutrino interactions by their effect on the flux of neutrinos originating from a galactic supernova. In the dense medium of a core collapse supernova, these new self interactions can have a significant impact on neutrino oscillations, leading to changes at the flavor evolution and spectra level. We use simulations of the neutrino flux from a 13 solar mass, core collapse supernova at 10 kpc away, and numerically propagate these neutrinos through the stellar medium taking into account vacuum/MSW oscillations, SM ν − ν scattering as well as ν − ν interactions that arise from NSSI. We pass the resulting neutrino flux to a simulation of the future Hyper-Kamiokande detector to see what constraints on NSSI parameters are possible when the next galactic supernova becomes visible. We find that these constraints depend strongly on the neutrino mass hierarchy and if the NSSI is flavor-violating or preserving. Sensitivity to NSSI in the normal hierarchy (NH) at Hyper-K is limited by the experiment’s ability to efficiently detect ν

e
, but deviations from no NSSI could be seen if the NSSI is particularly strong. In the inverted hierarchy (IH) scenario, Hyper-K can significantly improve constraints on flavor-violating NSSI down to

$$ \mathcal{O} $$

O

(10
−1)G

F
.
Hidden monopole dark matter via axion portal and its implications for direct detection searches, beam-dump experiments, and the H0 tension
Authors: Daido Ryuji , Ho Shu-Yu , Takahashi Fuminobu
Published: January 2020

Abstract

Hidden monopole is a plausible dark matter candidate due to its stability, but its direct experimental search is extremely difficult due to feeble interactions with the standard model particles in the minimal form. Then, we introduce an axion, a, connecting the hidden monopole and the standard model particles and examine the current limits and future prospects of direct dark matter searches and beam-dump experiments. We find two parameter regions around m

a
=

$$ \mathcal{O} $$

O

(10) MeV, f

a
=

$$ \mathcal{O} $$

O

(105) GeV and m

a
=

$$ \mathcal{O} $$

O

(100) MeV, f

a
=

$$ \mathcal{O} $$

O

(104) GeV where monopole dark matter and the axion are respectively within the reach of the future experiments such as PICO-500 and SHiP. We also note that the hidden photons mainly produced by the axion decay contribute to dark radiation with ∆N
eff ≃ 0.6 which can relax the H
0 tension.
Chaos in the butterfly cone
Authors: Mezei Márk , Sárosi Gábor
Published: January 2020

Abstract

A simple probe of chaos and operator growth in many-body quantum systems is the out of time ordered four point function. In a large class of local systems, the effects of chaos in this correlator build up exponentially fast inside the so called butterfly cone. It has been previously observed that the growth of these effects is organized along rays and can be characterized by a velocity dependent Lyapunov exponent, λ(v). We show that this exponent is bounded inside the butterfly cone as λ(v) ≤ 2πT (1 − |
v
|/v

B
), where T is the temperature and v

B
is the butterfly speed. This result generalizes the chaos bound of Maldacena, Shenker and Stanford. We study λ(v) in some examples such as two dimensional SYK models and holographic gauge theories, and observe that in these systems the bound gets saturated at some critical velocity v
*
< v

B
. In this sense, boosting a system enhances chaos. We discuss the connection to conformal Regge theory, where λ(v) is related to the spin of the leading large N Regge trajectory, and controls the four point function in an interpolating regime between the Regge and the light cone limit. Finally, we comment on the generalization of the chaos bound to boosted and rotating ensembles and clarify some recent results on this in the literature.