bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allosterism and Drug Discovery
Authors: Bell John E. , Bell Jessica K. 
Published: April 2021

AbstractInterest in allostery and drug development has significantly expanded with increasingly broad ranges of targets and diseases. Experimental and computational approaches have led to advances in understanding of the mechanisms and roles of protein dynamics and conformational states, and come together in the concept of conformational selection. The models of Monod, Wyman, and Changeux and Koshland, Nemethy, and Filmer provide conceptual explanations of homotropic cooperativity and heterotropic allostery, while conformational selection provides realistic detail that can be exploited in drug design. Distinction between allostery and cooperativity and development of approaches to identify cryptic sites on proteins significantly expands the range of targets for allosteric drug design. High‐throughput screening and SAR optimization remain a staple of drug design, however, increased understanding of the thermodynamics of protein–ligand interactions and conformational changes, and the mechanisms of information flow between existing allosteric sites and across subunit interfaces or between allosteric and active sites, rational design of ligands to interact with a cryptic “allosteric” site on any protein becomes possible. Recent “omics” approaches to identify druggable targets both genome wide andin vivofurther enhance the range of targets for drug design, both covalent and noncovalent, exploiting allosteric and cooperative properties of proteins.
Confronting theCOVID‐19 Pandemic: December 2019–May 2020
Authors: Dolle Roland E. , J. Abraham Donald , Norman Bryan , Kinch Michael 
Published: April 2021

AbstractThe SARS‐CoV‐2 (COVID‐19) pandemic was officially declared by the World Health Organization on 11 March, 2020. From the initial public reports from China in December 2019, the contagion blazed its way from ground zero in Wuhan, China into 165 countries. The health disaster caught the planet by surprise. At the time of this writing, 6.6 million COVID‐19 cases were confirmed worldwide. Central and South America are the latest hotspots. Utilizing state‐of‐the‐art science and technology, industry, government, and academic enterprises internationally are engaged in a monumental campaign to combat and eliminate the viral threat. Small‐molecule therapeutics discovery largely by way of drug repurposing and accelerated vaccine development are at the forefront of this campaign. Within five months time, 500 unique therapeutic agents have advanced into development, >150 clinical trials initiated, and seven agents authorized for emergency use. This article presents a snapshot of these activities as of 29 May 2020.
Evolution of
V1R
Repertoires in Subterranean Rodents
Authors: Zhao Huabin 
Published: April 2021

Abstract

Pheromones are chemicals released and perceived by members of the same species, triggering sexual and social behaviours or physiological changes in diverse animals. Although rodents are the first mammals in which vomeronasal receptors and their major roles in pheromonal olfaction were identified, little is known about the evolution of vomeronasal receptor gene repertoires in subterranean rodents. Recent genome‐wide surveys in rodents have shown that the number of functional vomeronasal type 1 receptor (
V1R
) genes was markedly reduced in phylogenetically distinct subterranean rodents compared with their superterranean relatives, possibly due to confined pheromonal signals in underground burrows. Interestingly, population genetic analysis proved that many
V1R
genes may have undergone positive selection rather than relaxed selection in one species of subterranean rodent. Exploration of functional roles of the reduced number of
V1R
genes would help to uncover the importance of pheromonal olfaction in subterranean rodents.

Key Concepts

Pheromones are odour molecules that elicit sexual and social behaviours or physiological changes in conspecific individuals.

Subterranean rodents live in underground burrows with confined pheromonal signals, which represent a contrasting lifestyle compared with their superterranean relatives.

Genome‐wide surveys have shown that convergent reduction in vomeronasal type 1 receptor (V1R) repertoires in multiple lineages of subterranean rodents was significantly associated with their lifestyle.

Population genetic analysis revealed that many
V1R
genes may have undergone positive selection rather than relaxed selection in one species of subterranean rodent.

Our understanding of the importance of pheromonal olfaction and its receptor genes appears to be incomplete in animals.
Microviridae
Authors: Breitbart Mya , Fane Bentley A 
Published: April 2021

Abstract

Members of the
Microviridae
comprise at least two subfamilies (
Bullavirinae
and
Gokushovirinae
), with divergent sequences from many uncultured representatives yet to be formally classified. Bullaviruses (canonical species φX174), which infect free‐living bacteria, are among the fastest known replicating viruses. Gokushoviruses were originally thought to occupy a unique niche, infecting obligate intracellular bacteria; however, genomic analyses suggest that this group infects free‐living hosts as well. Some gokushoviruses, unlike other members of the family, can undergo both lytic and lysogenic replication cycles.
Microviridae
contain small (4000–6000 bases), circular and single‐stranded deoxyribonucleic acid (ssDNA) genomes of positive polarity, which are packaged inside small (∼25 nm diameter)
T
= 1 icosahedral capsids. The most well‐known member of the
Microviridae
, φX174, has been fundamental in uncovering the mechanisms of DNA replication and capsid assembly and become a model system for experimental evolution. In contrast, little is known about the replication, structure and host range of gokushoviruses despite viromics indicating their ubiquity throughout the biosphere.

Whilst overlapping reading frames increase the amount of genetic information encoded in small genomes, they do not appear to significantly impact the ability of the virus to genetically adapt to selective pressures.

Due to the genome's positive polarity, DNA replication must commence before viral genes can be transcribed.

Microvirus DNA replication occurs in three distinct stages: (1) ssDNA is first converted to a double‐stranded molecule, (2) amplification of the double‐stranded molecule and (3) single‐stranded genomic DNA synthesis and packaging.

Genomic DNA synthesis and packaging are concurrent processes; thus, a genome is not synthesised unless there exists a capsid in which to package it.

Gene expression is controlled by the finely tuned interplay of
cis
‐acting genetic elements: promoters, ribosome‐binding sites, mRNA stability sequences and transcription terminators.

Bullaviruses (φX174, G4 and α3) are distinguished by their two‐scaffolding protein system, whereas gokushoviruses utilise a single scaffolding protein. Scaffolding proteins induce conformational switches in the viral coat protein to control the timing and fidelity of morphogenesis.

Cell lysis is achieved by inhibiting host cell‐wall biosynthesis, a mechanism reminiscent of some antibiotics.

Viromics has revealed the ubiquity of
Microviridae
genomes throughout the biosphere, with gokushoviruses and uncharacterised divergent lineages being the most common.

Hosts are unknown for the vast majority of environmental
Microviridae
, leading to a dearth of knowledge on their gene functions, replication strategies, virion structures or even absolute abundance in the environment.

Although the
Microviridae
were traditionally thought to be purely lytic, genomic studies have demonstrated that some gokushoviruses are capable of lysogeny.
Catalytic RNA
Authors: Kent Alexandra D , Burke Cassandra R , Lupták Andrej 
Published: April 2021

Abstract

RNA molecules have diverse roles in biological systems. While some code for proteins or act to translate codons to amino acids, others fold into specific shapes that endow them with the ability to catalyse specific chemical transformations. These catalytic RNAs, ribozymes, are responsible for protein synthesis, tRNA processing, self‐splicing of certain introns, self‐scission during rolling circle replication of some single‐stranded RNA viruses and cofactor‐dependent gene regulation in bacteria. Other ribozymes have been evolved
in vitro
to perform a wide variety of transformations. Two of these, tRNA aminoacylase and RNA polymerase ribozymes, are featured here because molecules with such capabilities are thought to have existed on early Earth, before proteins took over as the dominant biological catalysts. Most of the ribozymes have been shown to perform multiturnover catalysis and thus act as true enzymes, either in their natural, biological form or as engineered constructs.

Key Concepts

RNA molecules can fold into specific conformations and accelerate chemical transformations, thus acting as catalytic biomacromolecules, ribozymes.

Ribozymes can accelerate chemical reactions by many orders of magnitude.

Many ribozymes are capable of multiturnover catalysis, acting as enzymes.

Protein synthesis templated by mRNA is catalysed by ribosomal RNA.

Most ribozymes are phosphoryl transferases.

In vitro
selected ribozymes have been shown to catalyse a wide variety of reactions.

The existence of ribozymes supports the RNA World hypothesis.
A minimal sensing and communication control strategy for adaptive platooning
Authors: Yang Kang , Liu Di , Yu Wenwu 
Published: April 2021

SummarySeveral cooperative driving strategies proposed in literature, sometimes known as cooperative adaptive cruise control strategies, assume that both relative spacing and relative velocity with preceding vehicle are available from on‐board sensors (laser or radar). Alternatively, these strategies assume communication of both velocity states and acceleration inputs from preceding vehicle. However, in practice, on‐board sensors can only measure relative spacing with preceding vehicle (since getting relative velocity requires additional filtering algorithms); also, reducing the number of variables communicated from preceding vehicle is crucial to save bandwidth. In this work we show that, after framing the cooperative driving task as a distributed model reference adaptive control problem, the platooning task can be achieved in a minimal sensing and communication scenario, that is, by removing relative velocity measurements with preceding vehicle and by removing communication from preceding vehicle of velocity states. In the framework we propose, vehicle parametric uncertainty is taken into account by appropriately designed adaptive laws. The proposed framework is illustrated and shown to be flexible to several standard architectures used in cooperative driving (one‐vehicle look‐ahead topology, leader‐to‐all topology, multivehicle look‐ahead topology).
Interfacial Engineering of Bifunctional Niobium (V)‐Based Heterostructure Nanosheet Toward High Efficiency Lean‐Electrolyte Lithium–Sulfur Full Batteries
Authors: Shi Haodong , Qin Jieqiong , Lu Pengfei , Dong Cong , He Jian , Chou Xiujian , Das Pratteek , Wang Jiemin , Zhang Liangzhu , Wu Zhong‐Shuai 
Published: April 2021

AbstractHigh‐efficiency lithium–sulfur (Li–S) batteries depend on an advanced electrode structure that can attain high sulfur utilization at lean‐electrolyte conditions and minimum amount of lithium. Herein, a twinborn holey Nb4N5–Nb2O5 heterostructure is designed as a dual‐functional host for both redox–kinetics–accelerated sulfur cathode and dendrite‐inhibited lithium anode simultaneously for long‐cycling and lean‐electrolyte Li–S full batteries. Benefiting from the accelerative polysulfides anchoring–diffusion–converting efficiency of Nb4N5–Nb2O5, polysulfide‐shutting is significantly alleviated. Meanwhile, the lithiophilic nature of holey Nb4N5–Nb2O5 is applied as an ion‐redistributor for homogeneous Li‐ion deposition. Taking advantage of these merits, the Li–S full batteries present excellent electrochemical properties, including a minimum capacity decay rate of 0.025% per cycle, and a high areal capacity of 5.0 mAh cm−2 at sulfur loading of 6.9 mg cm−2, corresponding to negative to positive capacity ratio of 2.4:1 and electrolyte to sulfur ratio of 5.1 µL mg−1. Therefore, this work paves a new avenue for boosting high‐performances Li–S batteries toward practical applications.
Nanotoxoids: Biomimetic Nanoparticle Vaccines against Infections
Authors: Guo Zhongyuan , Kubiatowicz Luke J. , Fang Ronnie H. , Zhang Liangfang 
Published: April 2021

AbstractNanoparticles have been widely explored for vaccine applications based on their ability to elicit potent immune responses. Their advantages include protection of antigen payloads, improved in vivo distribution, enhanced cellular uptake, and codelivery with immunostimulatory adjuvants, among others. Of the various nanoparticulate platform technologies, cell membrane‐coated nanoparticles are an emerging class of nanocarrier that have been utilized for a wide range of biomedical applications. Here, the development and application of nanotoxoids as vaccines against infection are reviewed. Prepared by the complexation of toxins with cell membrane‐coated nanoparticles, nanotoxoids are able to safely deliver virulent proteins in their native conformation, thus generating strong and high avidity immune responses. The synthesis of nanotoxoids leverages the natural affinities of virulence factors with cell membranes, enabling for the rapid development of multiantigenic formulations from unknown mixtures of toxins. Considering their many advantages over conventional toxoids, it is envisioned that continued research on nanotoxoids will lead to new and more effective vaccine formulations against high priority infectious diseases.
Optimal Design and Performance Analysis of Thermoelectric Power Generation Device Based on Multi‐Objective Genetic Algorithm
Authors: Wu Jinmeng , Chen Yan , Dou Yinke , Ma Chunyan , Du Qian , Liu Qiang 
Published: April 2021

AbstractThe combined use of flue gas waste heat resources and thermoelectric generators (TEGs) is considered to be a relatively reliable method to generate electricity. The focus of this study is on the optimization and improvement of the hot‐end heat collection pipe. This paper aims to increase the temperature difference between hot and cold ends of TEG and enhance uniformity of temperature distribution, thereby improving the output power of the TEG system. To balance the temperature difference between the cold and hot ends of the TEG, the pressure drop from the inlet to the outlet and the mass of TEG hot end pipes, a finite element simulation model is constructed. Meanwhile, a multi‐objective genetic algorithm is applied to optimize the structure of four dimensions: fin bottom length, fin height, fin thickness, and outlet diameter. Three optimization objectives, namely, average temperature difference, total pressure drop from inlet to outlet, and pipeline mass are globally optimized to determine the best size, based on which the accuracy of the simulation model is verified by conducting experiments.
Evaluation of biosolids‐enriched ammonium sulfate vs. ammonium sulfate in soils and for plant growth
Authors: Chien Sen H. , Singh Upendra , Ruiz Diaz Dorivar A. 
Published: April 2021

AbstractNitrogen (N) and sulfur (S) are essential nutrients for optimum plant growth. A commercial‐grade biosolid‐enriched ammonium sulfate (Bio/AMS) was evaluated and compared with a conventional, commercial‐grade ammonium sulfate (AMS) to investigate the release patterns of N and S in soils. The laboratory‐based studies included (a) characterization of fertilizer sources, (b) soil leaching columns with 0.01% citric acid in an acid soil, (c) soil incubation followed by 1 M KCl extraction in a neutral soil, and (d) NH3 volatilization measurements in an alkaline soil. With one exception, the results showed no significant difference in the amount or the rate of N or S released from each between the two products in all the studies. In that one exception, the Bio/AMS leached significantly less N after 56 d, but not before 14 d, than the conventional AMS application. In greenhouse‐based evaluations, the Bio/AMS and AMS performed comparably at providing S nutrient to the biomass yield and S uptake by canola (Brassica napus L.) at maturity in neutral and alkaline soils. The studies also showed no significant N uptake differences between Bio/AMS and AMS by wheat (Triticum aestivum L.) biomass at maturity in acid and neutral soils. The results from these laboratory and greenhouse studies demonstrated that the Bio/AMS product is a simple physical mixture of biosolids with AMS.
Data‐driven modeling of mesoscale solids stress closures for filtered two‐fluid model in gas–particle flows
Authors: Ouyang Bo , Zhu Li‐Tao , Luo Zheng‐Hong 
Published: April 2021

AbstractThis study performs data‐driven modeling of mesoscale solids stress closures for filtered two‐fluid model (fTFM) in gas–particle flows via an artificial neural network (ANN) based machine learning method. The data used for developing the ANN‐based predictive data‐driven modeling framework is systematically filtered from fine‐grid simulations. The loss function optimization result reveals that coupling two loss functions promotes more accurate predictions of the mesoscale solids stresses than using a single loss function. Further comprehensive assessments of closure markers demonstrate a systematic dependence of the mesoscale solids stresses on the filtered particle velocity and its gradient as additional anisotropic markers, instead of using the conventional isotropic filtered rate of solid phase deformation as a closure marker. An optimal three‐marker mesoscale closure is thus proposed. Comparative analysis of the conventional filtered model and present three‐marker model shows that the data‐driven model can substantially enhance the prediction accuracy.
Using conjugated system from natural sources for the synthesis of sulfur copolymers by bi‐function catalysts at mild temperatures
Authors: Lyu Ya , Hu Qing , Chen Long , Luo Tianxiang , Liu Jianghui , Yin Xiaoxiao 
Published: April 2021

AbstractSulfur‐rich polymers are promising materials to cover several applications including mercury capture adsorbents. Tung oil, a natural conjugated triene triglyceride oil, were selected to prepare sulfur‐rich copolymers. The unique second monomer made reaching the gel point possible at a mild temperature of 130°C in 2.5 h. The reaction accomplishment was confirmed by the depletion of double bonds in tung‐oil‐sulfur copolymers measured by1H NMR, FTIR, XRD, and DSC. A bi‐function catalyst calcium hydroxide accelerates the reactions between triglyceride and sulfur before it is removed to increase the surface area and achieve the aims of preparing adsorbents, which has zero free sulfur, high crosslinking degree, and efficient mercury capture. Newly developed tung‐oil‐sulfur copolymers catalyzed by calcium hydroxide offer the possibility to synthesize sulfur‐rich copolymers that combine the advantages of the high performance and the utility of greener and more environmental friendly raw materials.
Enhanced mechanical and thermal properties of nanodiamond reinforced low density polyethylene nanocomposites
Authors: Morimune‐Moriya Seira , Hashimoto Taiki , Haga Ryohei , Tanahashi Hiroaki 
Published: April 2021

AbstractIn this study, the reinforcement effects of low‐content hydrophilic nanodiamond (ND) on linear low‐density polyethylene (PE) nanocomposites were investigated. ND was incorporated in PE via simple solution blending. The obtained PE/ND nanocomposites were characterized using scanning electron microscopy, ultraviolet–visible spectra, X‐ray diffraction, tensile test, thermogravimetry, and differential scanning calorimetry. Generally, PE/ND nanocomposites with poor interfacial interaction cause large agglomerates, resulting in brittle and poor mechanical properties. Owing to the different natures of non‐polar PE and polar ND, the higher the ND content, the larger the agglomerates formed in the nanocomposites. However, PE/ND nanocomposites show unique mechanical properties, that is, the Young's modulus, tensile strength, elongation at break, and toughness increased upon the incorporation of ND. The Young's modulus of the PE/ND nanocomposites exceeded the theoretical value calculated using the Halpin–Tsai model. In addition, the toughness increased by 18% at only 0.5 wt% ND loading. Furthermore, there was an increase in the thermal degradation temperature, melting temperature, and crystallization temperature.
Applied anatomy and surgical technique of the lateral single‐position L5–S1 fusion
Authors: Bodon Gergely , Kiraly Kristof , Baksa Gabor , Barany Laszlo , Kiss Mate , Hirt Bernhard , Pussert Arndt , Timothy Jake , Stubbs Lenny , Khajavi Kaveh , Braly Brett 
Published: April 2021

AbstractThe latest development in the anterior lumbar interbody fusion (ALIF) procedure is its application in the lateral position to allow for simultaneous posterior percutaneous screw placement. The technical details of the lateral ALIF technique have not yet been described. To describe the surgical anatomy relevant to the lateral ALIF approach we performed a comprehensive anatomical study. In addition, the preoperative imaging, patient positioning, planning of the skin incision, positioning of the C‐arm, surgical approach, and surgical technique are discussed in detail. The technique described led to the successful use of the lateral ALIF technique in our clinical cases. No lateral ALIF procedure needed to be aborted during these cases. Our present work gives detailed anatomical background and technical details for the lateral ALIF approach. This teaching article can provide readers with sufficient technical and anatomical knowledge to assist them in performing their first lateral ALIF procedure.
General histological woes: Definition and classification of tissues
Authors: Neumann Paul E. , Neumann Eve E. 
Published: April 2021

AbstractThe modern view that the human body is composed of tissues and body fluids, and that there are four basic tissue types, may be a more significant departure from Artistotle's homoeomeres, and from Bichat's membranes and tissues, than commonly appreciated. The older concepts described these body parts as structural and functional parts of organs, whereas it is now commonplace to consider a tissue to be a grouping of similar cells with a variable amount of extracellular matrix. The development of the microscope as a useful tool in human anatomy shifted focus from tissues to cells and led to changes in the definition of tissue and the classification of tissues. Not all of these changes have been consistent with observable facts: many tissues contain diverse cell types, not all “connective tissues” are proper connective tissues, and some specialized tissues are not easily classified as subtypes of one of the four basic types. Here we propose corrective measures, including re‐recognition of compound tissues, cataloging all adult human tissue types, and increasing the emphasis on function during the construction of a complete taxonomy of human adult tissues. Specific problems in the current scheme and a preliminary reclassification of human adult tissues are discussed.