Modeling the Transmission of the SARS-CoV-2 Delta Variant in a Partially Vaccinated Population

In a population with ongoing vaccination, the trajectory of a pandemic is determined by how the virus spreads in unvaccinated and vaccinated individuals that exhibit distinct transmission dynamics based on different levels of natural and vaccine-induced immunity. We developed a mathematical model that considers both subpopulations and immunity parameters, including vaccination rates, vaccine effectiveness, and a gradual loss of protection. The model forecasted the spread of the SARS-CoV-2 delta variant in the US under varied transmission and vaccination rates. We further obtained the control reproduction number and conducted sensitivity analyses to determine how each parameter may affect virus transmission. Although our model has several limitations, the number of infected individuals was shown to be a magnitude greater (~10×) in the unvaccinated subpopulation compared to the vaccinated subpopulation. Our results show that a combination of strengthening vaccine-induced immunity and preventative behavioral measures like face mask-wearing and contact tracing will likely be required to deaccelerate the spread of infectious SARS-CoV-2 variants.

Analysis of LINE1 Retrotransposons in Huntington’s Disease

Transposable elements (TEs) are mobile genetic elements that made up about half the human genome. Among them, the autonomous non-LTR retrotransposon long interspersed nuclear element-1 (L1) is the only currently active TE in mammals and covers about 17% of the mammalian genome. L1s exert their function as structural elements in the genome, as transcribed RNAs to influence chromatin structure and as retrotransposed elements to shape genomic variation in somatic cells. L1s activity has been shown altered in several diseases of the nervous system. Huntington disease (HD) is a dominantly inherited neurodegenerative disorder caused by an expansion of a CAG repeat in the HTT gene which leads to a gradual loss of neurons most prominently in the striatum and, to a lesser extent, in cortical brain regions. The length of the expanded CAG tract is related to age at disease onset, with longer repeats leading to earlier onset. Here we carried out bioinformatic analysis of public RNA-seq data of a panel of HD mouse models showing that a decrease of L1 RNA expression recapitulates two hallmarks of the disease: it correlates to CAG repeat length and it occurs in the striatum, the site of neurodegeneration. Results were then experimentally validated in HttQ111 knock-in mice. The expression of L1-encoded proteins was independent from L1 RNA levels and differentially regulated in time and tissues. The pattern of expression L1 RNAs in human HD post-mortem brains showed similarity to mouse models of the disease. This work suggests the need for further study of L1s in HD and adds support to the current hypothesis that dysregulation of TEs may be involved in neurodegenerative diseases.

Fleeting: a Novel Ultrasonic Vocalization in Mice That Allows to Define Altered Developmental Milestones in Autism Spectrum Disorder

A major mode of rodent communication occurs through ultrasonic vocalizations (USVs), which are influenced by environmental factors, mouse strain or genetic background and, importantly, by developmental stage. However, few studies have looked into the age-dependent evolution of spectral features of mouse USVs. Here, we report the existence of a novel vocalization, previously unreported, which we named “Fleeting” consisting of two acoustic elements produced with a narrow silent temporal interval between them. Strikingly, this vocalization pattern was extinguished after the second postnatal week, and this temporal pattern was associated with increased emission of Complex vocalizations, by gradual loss of the inter-element interval, suggesting a maturation process occurring at this time point. Importantly, the Fleeting vocalization was analyzed in a mouse model (Tsc2+/-) of Autism Spectrum Disorder (ASD), and showed an abnormal persistence, in particular in females which presented delayed conversion of Fleeting into Complex vocalizations compared with males. The identification of this novel vocalization represents an important insight into the maturation of mouse vocal repertoire and may be used as a developmental milestone in studies on neurodevelopmental disorders with communication impairments.

Post-Symbolic Images in Platform Capitalism

Platform capitalism brings several processes to completion that were already apparent during post-industrial capitalism. One of these involves images and their gradual loss of a symbolic dimension. The mechanisms that platforms employ to direct the production of media content reduce images to objects of immediate use and consumption. Consequently, images fail to synthetise the multiplicity of the social reality: instead of inscribing it within a horizon of meaning, they simply reflect it. This article reconstructs the “de-symbolising” process of images during the various phases of capitalism and explains why a post-symbolic aesthetics should also be viewed as “impolitical”. If the political is indeed symbolic, since the giving of meaning and direction to society (a political task par excellence) also takes place through the construction of symbolic systems, the post-symbolic aesthetic is instead imposed by platforms for purely economic reasons.

The Emergence of a Mixed Type Dialect: The Example of the Dialect of the Bani ˁAbbād Tribe (Jordan)

The present article aims at questioning the status of the šāwi dialect of the Bani ʕAbbād tribe by providing a new analysis of the main distinctive phonological, morphological, and syntactical traits which may hint at dialect mixing. The data provided by the field research, based on a functional framework that relies on descriptive linguistics and a typological approach, show that this dialect is deeply affected by a koineizing tendency due to increasing contacts with the populations of the neighboring areas (especially ʕAmmān and Salṭ) which, in turn, leads to the gradual loss of its authentic features. Finally, this paper discusses whether the dialect of the Bani ʕAbbād should still be considered as belonging to the yigūl group (recently renamed Central Bedouin ygūlu) of the Syro-Mesopotamian sheep-raising tribes or if a new typology of mixed type dialects should eventually be adopted for the dialects displaying important markers of both Bedouin and sedentary types.

Multi-year Use of the Standard Gauge Railway Underpasses by Mammals in Tsavo, Kenya: Influence of Underpass Dimensions, Infrastructure and Ecology

Rail and road infrastructure is essential for economic growth and development but can cause a gradual loss in biodiversity and degradation of ecosystem function and services. We assessed influence of underpass dimensions, fencing, proximity to water and roads, Normalized Difference Vegetation Index (NDVI), presence of other species and livestock on underpass use by large and medium-sized mammals. Results revealed hyenas and leopards used the underpasses more than expected whereas giraffes and antelopes used the underpasses less than expected. Generalized linear mixed effects models (GLMMs) revealed that underpass height influenced their use by wildlife, with several species preferring to use taller underpasses. Electric fencing increased underpass use by funneling species towards underpasses, except for elephants and black-backed jackal for which it reduced underpass passage. GLMMs also revealed that the use of underpasses by livestock reduced the probability of their use by nearly 50% of wildlife species. Carnivore species were more likely to cross underpasses used by their prey. Buffalo, livestock, and hyenas used underpasses with higher NDVI and near water sources while baboons, dik-diks and antelope avoided underpasses with high NDVI. The findings suggest a need for diverse, and comprehensive approach for mitigating the negative impacts of rail on African wildlife.

Indirect Routes to Aminoacyl-tRNA: The Diversity of Prokaryotic Cysteine Encoding Systems

Universally present aminoacyl-tRNA synthetases (aaRSs) stringently recognize their cognate tRNAs and acylate them with one of the proteinogenic amino acids. However, some organisms possess aaRSs that deviate from the accurate translation of the genetic code and exhibit relaxed specificity toward their tRNA and/or amino acid substrates. Typically, these aaRSs are part of an indirect pathway in which multiple enzymes participate in the formation of the correct aminoacyl-tRNA product. The indirect cysteine (Cys)-tRNA pathway, originally thought to be restricted to methanogenic archaea, uses the unique O-phosphoseryl-tRNA synthetase (SepRS), which acylates the non-proteinogenic amino acid O-phosphoserine (Sep) onto tRNACys. Together with Sep-tRNA:Cys-tRNA synthase (SepCysS) and the adapter protein SepCysE, SepRS forms a transsulfursome complex responsible for shuttling Sep-tRNACys to SepCysS for conversion of the tRNA-bound Sep to Cys. Here, we report a comprehensive bioinformatic analysis of the diversity of indirect Cys encoding systems. These systems are present in more diverse groups of bacteria and archaea than previously known. Given the occurrence and distribution of some genes consistently flanking SepRS, it is likely that this gene was part of an ancient operon that suffered a gradual loss of its original components. Newly identified bacterial SepRS sequences strengthen the suggestion that this lineage of enzymes may not rely on the m1G37 identity determinant in tRNA. Some bacterial SepRSs possess an N-terminal fusion resembling a threonyl-tRNA synthetase editing domain, which interestingly is frequently observed in the vicinity of archaeal SepCysS genes. We also found several highly degenerate SepRS genes that likely have altered amino acid specificity. Cross-analysis of selenocysteine (Sec)-utilizing traits confirmed the co-occurrence of SepCysE and the Sec-utilizing machinery in archaea, but also identified an unusual O-phosphoseryl-tRNASec kinase fusion with an archaeal Sec elongation factor in some lineages, where it may serve in place of SepCysE to prevent crosstalk between the two minor aminoacylation systems. These results shed new light on the variations in SepRS and SepCysS enzymes that may reflect adaptation to lifestyle and habitat, and provide new information on the evolution of the genetic code.

Practical importance of anti-predatory behavior research in keeping farm animals

The care and livestock management requires knowledge of the behavioral reactivity of the kept species. Domestic ungulates have evolved as prey, so their survival in the wild depended on early detection of a potential threat and then taking a quick response. There are numerous studies into antipredatory behavior concerning a wide range of animal taxa. They predominantly focus on conflict between innate and acquired predator recognition and the influence of various factors on the retain or gradual loss of defense mechanisms against predators. The authors of multiple studies suggest the practical use of research results in areas such as medicine, agriculture and conservancy. The promising effects of these experiments should encourage the research development in this field among farm animals. The aim of the article is to introduce the research findings of antipredatory behavior and to determine their implications in farm animals breeding.

A Cutting-Edge Survey of Tribological Behavior Evaluation Using Artificial and Computational Intelligence Models

Any metal surface’s usefulness is essential in various applications such as machining and welding and aerospace and aerodynamic applications. There is a great deal of wear in metals, used widely in machines and appliances. The gradual loss of the upper metal layers in all metal parts is inevitable over the machine or component’s lifetime. Artificial intelligence implementations and computational models are being studied to evaluate different metals’ tribological behavior, as technological progress has been made in this field. Different neural networks were used for different metals. They are classified in this paper, together with a description of their benefits and inconveniences and an overview and use of the different types of wear. Artificial intelligence is a relatively new term that uses mechanical engineering. There is still no scientific progress to examine various metal wear cases and compare AI and computational models’ accuracy in wear behavior.

Neural stemness unifies cell tumorigenicity and pluripotent differentiation potential

Tumorigenicity and pluripotent differentiation potential are kernel cell properties for tumorgenesis and embryogenesis. A growing number of studies have demonstrated that neural stemness is the source of the two cell properties, because neural stem cells and cancer cells share cell features and regulatory networks and neural stemness has an evolutionary advantage. However, it needs to validate whether neural stemness is a cell property that would unify tumorigenicity and pluripotent differentiation potential. SETDB1/Setdb1 is an epigenetic factor that is upregulated in cancer cells and promotes cancers, and correspondingly, is enriched in embryonic neural cells during vertebrate embryogenesis. We show that knockdown of SETDB1/Setdb1 led to neuronal differentiation in neural stem and cancer cells, concomitant with reduced tumorigenicity and pluripotent differentiation potential in these cells; whereas overexpression caused an opposite effect. On one hand, SETDB1 maintains a regulatory network comprised of proteins involved in developmental programs and basic cellular functional machineries, including epigenetic modifications (EZH2), ribosome biogenesis (RPS3), translation initiation (EIF4G), spliceosome assembly (SF3B1), etc., all of which play active roles in cancers. On the other, it represses transcription of genes promoting differentiation and cell cycle and growth arrest. Moreover, neural stemness, tumorigenicity and pluripotent differentiation potential were simultaneously enhanced during serial transplantation of cancer cells. Expression of proteins involved in developmental programs and basic cellular functional machineries, including SETDB1 and other proteins above, was gradually increased. In agreement with increased expression of spliceosome proteins, alternative splicing events also increased in tumor cells derived from later transplantations, suggesting that different machineries should work concertedly to match the status of high proliferation and pluripotent differentiation potential. The study presents the evidence that neural stemness unifies tumorigenicity and differentiation potential. Tumorigenesis represents a process of gradual loss of original cell identity and gain of neural stemness in somatic cells, which might be a distorted replay of neural induction during normal embryogenesis.