bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulatory mechanisms of c‐di‐AMP synthase from Mycobacterium smegmatis revealed by a structure: Function analysis
Authors: Gautam Sudhanshu , Mahapa Avisek , Yeramala Lahari , Gandhi Apoorv , Krishnan Sushma , Kutti R. Vinothkumar , Chatterji Dipankar 
Published: January 2023

AbstractCyclic‐di‐nucleotide‐based secondary messengers regulate various physiological functions, including stress responses in bacteria. Cyclic diadenosine monophosphate (c‐di‐AMP) has recently emerged as a crucial second messenger with implications in processes including osmoregulation, antibiotic resistance, biofilm formation, virulence, DNA repair, ion homeostasis, and sporulation, and has potential therapeutic applications. The contrasting activities of the enzymes diadenylate cyclase (DAC) and phosphodiesterase (PDE) determine the equilibrium levels of c‐di‐AMP. Although c‐di‐AMP is suspected of playing an essential role in the pathophysiology of bacterial infections and in regulating host‐pathogen interactions, the mechanisms of its regulation remain relatively unexplored in mycobacteria. In this report, we biochemically and structurally characterize the c‐di‐AMP synthase (MsDisA) from Mycobacterium smegmatis. The enzyme activity is regulated by pH and substrate concentration; conditions of significance in the homoeostasis of c‐di‐AMP levels. Substrate binding stimulates conformational changes in the protein, and pApA and ppApA are synthetic intermediates detectable when enzyme efficiency is low. Unlike the orthologous Bacillus subtilis enzyme, MsDisA does not bind to, and its activity is not influenced in the presence of DNA. Furthermore, we have determined the cryo‐EM structure of MsDisA, revealing asymmetry in its structure in contrast to the symmetric crystal structure of Thermotoga maritima DisA. We also demonstrate that the N‐terminal minimal region alone is sufficient and essential for oligomerization and catalytic activity. Our data shed light on the regulation of mycobacterial DisA and possible future directions to pursue.
The B domain of protein A retains residual structures in 6 M guanidinium chloride as revealed by hydrogen/deuterium‐exchange NMR spectroscopy
Authors: Yanaka Saeko , Yagi‐Utsumi Maho , Kato Koichi , Kuwajima Kunihiro 
Published: January 2023

AbstractThe characterization of residual structures persistent in unfolded proteins is an important issue in studies of protein folding, because the residual structures present, if any, may form a folding initiation site and guide the subsequent folding reactions. Here, we studied the residual structures of the isolated B domain (BDPA) of staphylococcal protein A in 6 M guanidinium chloride. BDPA is a small three‐helix‐bundle protein, and until recently its folding/unfolding reaction has been treated as a simple two‐state process between the native and the fully unfolded states. We employed a dimethylsulfoxide (DMSO)‐quenched hydrogen/deuterium (H/D)‐exchange 2D NMR techniques with the use of spin desalting columns, which allowed us to investigate the H/D‐exchange behavior of individually identified peptide amide (NH) protons. We obtained H/D‐exchange protection factors of the 21 NH protons that form an α‐helical hydrogen bond in the native structure, and the majority of these NH protons were significantly protected with a protection factor of 2.0–5.2 in 6 M guanidinium chloride, strongly suggesting that these weakly protected NH protons form much stronger hydrogen bonds under native folding conditions. The results can be used to deduce the structure of an early folding intermediate, when such an intermediate is shown by other methods. Among three native helical regions, the third helix in the C‐terminal side was highly protected and stabilized by side‐chain salt bridges, probably acting as the folding initiation site of BDPA. The present results are discussed in relation to previous experimental and computational findings on the folding mechanisms of BDPA.
A super‐resolution proof of concept in a cycloidal coded aperture miniature mass spectrometer
Authors: Aloui Tanouir , Serpa Rafael Bento , Abboud Nabil , Horvath Kathleen L. , Keogh Justin , Parker Charles B. , Stern Jennifer C. , Denton M. Bonner , Sartorelli Maria Luisa , Glass Jeffrey T. , Gehm Michael E. , Amsden Jason J. 
Published: January 2023

RationaleHigher resolution in fieldable mass spectrometers (MS) is desirable in space flight applications to enable resolving isobaric interferences at m/z < 60 u. Resolution in portable cycloidal MS coupled with array detectors could be improved by reducing the slit width and/or by reducing the width of the detector pixels. However, these solutions are expensive and can result in reduced sensitivity. In this paper, we demonstrate high‐resolution spectral reconstruction in a cycloidal coded aperture miniature mass spectrometer (C‐CAMMS) without changing the slit or detector pixel sizes using a class of signal processing techniques called super‐resolution (SR).MethodsWe developed an SR reconstruction algorithm using a sampling SR approach whereby a set of spatially shifted low‐resolution measurements are reconstructed into a higher‐resolution spectrum. This algorithm was applied to experimental data collected using the C‐CAMMS prototype. It was then applied to synthetic data with additive noise, system response variation, and spatial shift nonuniformity to investigate the source of reconstruction artifacts in the experimental data.ResultsExperimental results using two ½ pixel shifted spectra resulted in a resolution of ¾ pixel full width at half maximum (FWHM) at m/z = 28 u. This resolution is equivalent to 0.013 u, six times better than the resolution previously published at m/z = 28 for N2+ using C‐CAMMS. However, the reconstructed spectra exhibited some artifacts. The results of the synthetic data study indicate that the artifacts are most likely caused by the system response variation.ConclusionsThis paper demonstrates super‐resolution spectral reconstruction in C‐CAMMS without changing the slit or detector pixel sizes using a sampling SR approach. With improvements, this technique could be used to resolve isobaric interferences in a portable cycloidal MS for space flight applications.
Solution Behavior of Bovine Skin Gelatin in the Presence of Cationic Gemini Surfactants
Authors: Ansari Farah , Lal Hira , Osama Mohammad , Akram Mohd. , Kabir‐ud‐Din  
Published: January 2023

AbstractThe biophysical interaction between gelatin and cationic biodegradable Cm−E2O−Cm gemini surfactants (Cm represents alkyl chain where m=12, 14 and 16; E2 and O denote two ester groups and ethylene oxide, respectively) was analyzed utilizing a multi‐technique approach. The electronic absorption spectroscopy, far‐UV CD and pyrene micropolarity data evinced the formation of a complex between the concerned geminis and the biopolymer. Interestingly, the intrinsic fluorescence spectra do not exhibit concentration dependent behavior with respect to the surfactants giving an impression of poor interaction of gelatin with the geminis. Thereafter, the bulk solution properties, viz. foaming stabilities, viscosities and emulsion stabilities were measured to analyze the effect of binding. All the results combined together led to the inference of significant interaction between gelatin and the gemini surfactants which influence their physicochemical properties.
Photocatalytic and Protective Thin Films for Enhanced Self‐cleaning Activity and Durability of Painted Steel Roofings
Authors: Fernando T. Lakshini D. , Ray Sudip , Perera Janesha , Swift Simon , Simpson M. Cather 
Published: January 2023

AbstractFouling of painted steel roofings over time due to biological organisms and other pollutants is a well‐known aesthetic, functional and environmental problem that highlights the importance of developing greener self‐cleaning technologies for roofing applications. Accordingly, a series of novel photocatalytic coating systems have been developed in this study by introducing a copolymer of tetratethyl orthosilane and methyltrimethoxysilane as the photochemically stable binder and intermediate protective layer. Visible light active carbon doped titanium dioxide and surface modified nano titanium dioxide with anatase‐rutile hetero junctions were used as the semiconductor photocataysts. The concentration of titanium dioxide was set as 10 %, 25 % and 40 % by weight of the dried photocatalytic film. Methylene blue photoderadation reaction kinetics and antimicrobial assays were used as the key measures of assessing the self‐cleaning performance. The morphological and chemical composition changes were analyzed as a function of time using scanning electron microscopic and spectroscopic techniques as a measure of service life of these putative photocatalytic coating systems. According, a high degree of self‐cleaning activity was observed in these novel photocatalytic coating systems having 10 % (w/w) to 40 % (w/w) titanium dioxide loading compared to the painted steel roofing control sample. A complete eradication and 2–3 orders of log reduction were achieved respectively against E.coli bacteria and A.niger and Cladosporium fungies. The introduction of the intermediate polysiloxane protective layer has significantly enhanced both the self‐cleaning activity and service life, minimizing the diffusion of photogenerated reactive oxygen species into subsequent underneath paint layers. The photocatalytic self‐cleaning activity and the rate of photodegradation have been increased with titanium dioxide concentration. The coating system with 10 % (w/w) surface modified nano titanium dioxide loading having the intermediate protective layer was found to be the optimum coating formulation to obtain a high degree of self‐cleaning activity at a minimum rate of photodegradation in this study.
Zn‐Doped CeO2 Nanorods: a Highly Efficient Heterogeneous Catalyst for the Direct Synthesis of Dimethyl Carbonate from CO2 and Methanol
Authors: Liu Na , Xue Yun , Yu Zairan , Li Yuanyuan , Xu Yang , Xu Jie , Xue Bing , Luo Jun , Wang Fei 
Published: January 2023

AbstractThe direct synthesis of dimethyl carbonate from methanol and CO2 is a green and sustainable processes. In this paper, a new type of Zn‐doped CeO2 nanorods catalyst was successfully prepared by a facile hydrothermal process, and characterized by a combination of techniques including XRD, Raman, HRTEM, SEM, N2‐sorption, CO2‐TPD, NH3‐TPD, XPS. The catalyst was employed as a catalyst for the synthesis of dimethyl carbonate from methanol and CO2. Catalytic results revealed that the Ce1Zn0.1Oδ nanorods catalyst demonstrated superior catalytic activity, affording a high DMC yield of 24.2 mmolDMC/gcat, which compared favorably to other previously reported catalysts. According to the XPS and CO2‐TPD measurements, in comparison with the pure CeO2 nanorods, the surface oxygen vacancies and weak basic sites can be systemically enriched by introducing optimal amount of Zn dopants into CeO2 to improve the catalytic activity for the reaction. This work establishes an efficient catalyst for the direct synthesis of dimethyl carbonate from CO2 and methanol.
Propitious Indazole Compounds as β‐ketoacyl‐ACP Synthase Inhibitors and Mechanisms Unfolded for TB Cure: Integrated Rational Design and MD Simulations
Authors: Adewumi Adeniyi T. , Oluyemi Wande M. , Adekunle Yemi A. , Adewumi Nonhlanhla , Alahmdi Mohamed Issa , Soliman Mahmoud E. S. , Abo‐Dya Nader E. 
Published: January 2023

AbstractMycobacterium tuberculosis β‐ketoacyl‐ACP synthase I (KasA) involves in mycolic acid biosynthesis for cell wall maintenance; hence, it is a critical target in TB drug design. Thiolactomycin (TLM) and derivatives are the known standard KasA enzyme activity inhibitors. However, TLM analogues have poor activity against KasA protein. Indazole sulphonamide chemotype (JSF‐3285/JFX) was recently reported as a promising KasA enzyme inhibitor. JSF‐3285 mechanism is unclear; thus, it provides a means for designing KasA inhibitors. This study unfolds six hits as unprecedented KasA inhibitors. The inhibitory mechanisms of the screened compounds were investigated and compared with a standard inhibitor (TLM) using integrated molecular informatics and dynamics. JFX, M1, M2, and M5 molecules showed stronger interactions with KasA, having binding energy (kcal/mol) of −44.05, −41.52, −39.51, and −35.9, respectively, against −11.69 for TLM. Molecules showed good predicted inhibitory constants, drug‐likeness, ADME, and synthetic accessibility. KasA complex C‐α atoms RMSD and RMSF showed stable and erratic fluctuations compared to apo KasA. The findings provide potential antimycobacterial lead‐like molecules for future TB drugs.
In Silico Predictability of Toxicity Parameters Using the OECD QSAR Toolbox of Some Components of Cannabis sativa
Authors: Vázquez‐Valadez Víctor Hugo , Oliva‐Arellano María Virginia , Martínez‐Soriano Pablo Arturo , Hernández‐Serda Manuel Alejandro , Velázquez‐Sánchez Ana María , Concepción Rodríguez‐Maciel José , Angeles Enrique 
Published: January 2023

AbstractIn this paper, the quantitative structure‐activity relationship predictive models (QSAR) are presented: the prediction model for some of the main components of cannabis sativa, acute toxicity LD50 (n=45, r2=0.917, q2=0.902), chronic toxicity LOAEL (n=35, r2=0.911, q2=0.868), NOAEL(n=22, r2=0.964, q2=0.937), LOEL (n=26, r2=0.911, q2=0.863) and NOEL (n=25, r2=0.867, q2=0.802), in addition to carcinogenicity and mutagenicity effects. Only for the case of LD50, the values reported in the literature of the delta 9‐THC compound present in Cannabis sativa were taken into account and this model was applied to the other compounds present in the plant, which we consider the most relevant since they fell from the allowed domain for QSAR Toolbox to predict the LD50 of each of them, while the other additional endpoints were established according to the methodology that marks the QSAR Toolbox software. The application of these models and predictions allowed us to predict the permissible daily exposure (PDE) and acceptable daily intake (ADI) values of some of the cannabis components. This work aims to present important elements of the toxicology of some of the components of the plant that serve only as a reference and does not intend to favor or inhibit the use of cannabis for medicinal or recreational use.
Review on influence of nano bubble technology to enhance nanoboiling heat transfer: Environmental perspective
Authors: Senthilkumar Gnanamani , Ismail Rafi Mohamed , Karpagavasan Murughanandham 
Published: January 2023

AbstractThe primary focus of this review article is to investigate the behavior of multi walled carbon nanotubes (MWCNT) suspended in clean water during the boiling heat dispersions (transfer process). With novel nano boiling technique, the convective heat transfer coefficient of nanoparticles in nanofluid, density, viscosity, and thermal conductivity were reviewed. The various research outcomes on MWCNT mixed with water are discussed. Based on various test results, it was evident that adding (MWCNT) raised the boiling heat transfer coefficient of the base fluids.
Postmortem of a juvenile male Ganges River dolphin (Platanista gangetica spp. gangetica) in Bangladesh
Authors: Shil Subrata Kumar , Zahangir Md. Mahiuddin , Rahman Mohammad Mahbubur , Kibria Md. Manzoorul , Das Bhajan Chandra , Yadav Saroj Kumar , Siddiki AMAM Zonaed 
Published: January 2023

AbstractA juvenile male Ganges River dolphin (Platanista gangetica spp. gangetica) was accidentally trapped in a seine net, rescued as dead and brought for postmortem examination to the Chittagong Veterinary and Animal Sciences University Hospital. This endemic species has suffered an expressive population reduction over the last few decades. Therefore, the necropsy aimed to reveal the factors for the dolphin's death. The study revealed a few bruises and scratches in the lateral thoracic region of the skin, including congestion of the lung and liver, both macro‐ and microscopically. Furthermore, we observed that the dolphin's stomach was empty, the intestines were filled with gas and there was a cyst on its wall. The authors concluded that the dolphin died of suffocation from underwater entrapment in the fishing net. These findings may be helpful for veterinarians and conservationists to make strategies to save this endangered species.
RNA‐binding proteins in autoimmunity: From genetics to molecular biology
Authors: Lodde Valeria , Floris Matteo , Zoroddu Enrico , Zarbo Ignazio Roberto , Idda Maria Laura 
Published: January 2023

AbstractAutoimmune diseases (ADs) are chronic pathologies generated by the loss of immune tolerance to the body's own cells and tissues. There is growing recognition that RNA‐binding proteins (RBPs) critically govern immunity in healthy and pathological conditions by modulating gene expression post‐transcriptionally at all levels: nuclear mRNA splicing and modification, export to the cytoplasm, as well as cytoplasmic mRNA transport, storage, editing, stability, and translation. Despite enormous efforts to identify new therapies for ADs, definitive solutions are not yet available in many instances. Recognizing that many ADs have a strong genetic component, we have explored connections between the molecular biology and the genetics of RBPs in ADs. Here, we review the genetics and molecular biology of RBPs in four major ADs, multiple sclerosis (MS), type 1 diabetes mellitus (T1D), systemic lupus erythematosus (SLE), and rheumatoid arthritis (RA). We anticipate that gaining insights into the genetics and biology of ADs can facilitate the discovery of new therapies.This article is categorized under:
RNA in Disease and Development > RNA in Disease
AdS/BCFT from conformal bootstrap: construction of gravity with branes and particles
Authors: Kusuki Yuya , Wei Zixia 
Published: January 2023

Abstract
We initiate a conformal bootstrap program to study AdS3/BCFT2 with heavy excitations. We start by solving the bootstrap equations associated with two-point functions of scalar/non-scalar primaries under the assumption that one-point functions vanish. These correspond to gravity with a brane and a non-spinning/spinning particle where the brane and the particle do not intersect with each other. From the bootstrap equations, we obtain the energy spectrum and the modified black hole threshold. We then carefully analyze the gravity duals and find the results perfectly match the BCFT analysis. In particular, brane self-intersections, which are usually considered to be problematic, are nicely avoided by the black hole formation. Despite the assumption to solve the bootstrap equations, one-point functions of scalar primaries can be non-zero in general. We construct the holographic dual for a non-vanishing one-point function, in which the heavy particle can end on the brane, by holographically computing the Rényi entropy in AdS/BCFT. As a bonus, we find a refined formula for the holographic Rényi entropy, which appears to be crucial to correctly reproduce the boundary entropy term. On the other hand, we explain why one-point functions of non-scalar primaries always vanish from the gravity dual. The non-sensitivity of the solution for the bootstrap equation to the boundary entropy helps us to construct gravity duals with negative tension branes. We also find a holographic dual of boundary primaries.
Localization patterns of speech and language errors during awake brain surgery: a systematic review
Authors: Collée Ellen , Vincent Arnaud , Visch-Brink Evy , De Witte Elke , Dirven Clemens , Satoer Djaina 
Published: January 2023

AbstractAwake craniotomy with direct electrical stimulation (DES) is the standard treatment for patients with eloquent area gliomas. DES detects speech and language errors, which indicate functional boundaries that must be maintained to preserve quality of life. During DES, traditional object naming or other linguistic tasks such as tasks from the Dutch Linguistic Intraoperative Protocol (DuLIP) can be used. It is not fully clear which speech and language errors occur in which brain locations. To provide an overview and to update DuLIP, a systematic review was conducted in which 102 studies were included, reporting on speech and language errors and the corresponding brain locations during awake craniotomy with DES in adult glioma patients up until 6 July 2020. The current findings provide a crude overview on language localization. Even though subcortical areas are in general less often investigated intraoperatively, still 40% out of all errors was reported at the subcortical level and almost 60% at the cortical level. Rudimentary localization patterns for different error types were observed and compared to the dual-stream model of language processing and the DuLIP model. While most patterns were similar compared to the models, additional locations were identified for articulation/motor speech, phonology, reading, and writing. Based on these patterns, we propose an updated DuLIP model. This model can be applied for a more adequate “location-to-function” language task selection to assess different linguistic functions during awake craniotomy, to possibly improve intraoperative language monitoring. This could result in a better postoperative language outcome in the future.
Seismic assessment and finite element modeling of traditional vs innovative point fixed glass facade systems (PFGFS)
Authors: D’Amore Simone , Bianchi Simona , Ciurlanti Jonathan , Pampanin Stefano 
Published: January 2023

AbstractIn the last decades, recent earthquakes have further highlighted the high vulnerability of non-structural components. Post-earthquake damage due to building envelope, equipment and building contents can lead to substantial economic losses in terms of repair costs and daily activity interruption (downtime). Moreover, non-structural damage can represent a life-safety threat for both occupants and pedestrians. These considerations confirm the crucial need for developing low-damage systems for either structural or non-structural elements. This paper aims to assess the seismic performance of glazed facade systems, widely adopted in modern buildings, focusing on point fixed glass facade systems (PFGFSs), also referred to as “spider glazing”. In this work, a numerical investigation is developed to study the seismic performance of such systems at both local-connection level through a 3D FEM in ABAQUS as well as at global system level through a simplified lumped plasticity model in SAP 2000 to assess the overall in-plane capacity of the facade. Based on the local connection and global facade system behavior, a novel low-damage connection system is herein proposed, and a parametric study is carried out on the key parameters influencing the facade capacity. The benefits of implementing low-damage connection details are highlighted by an increase of the in-plane capacity of the facade system when compared to a traditional solution. To further investigate the potential of the proposed low-damage details in preserving the integrity of the facade system itself, non-linear time history analyses have been carried out on a case-study building equipped with the innovative PFGFSs.