Miracle-dz/UniFAR-FTUs huggingface dataset:
SARS-CoV-2 vaccine-breakthrough infections (VBIs) by Omicron (B.1.1.529) variant and consequences in structural and functional impact

This study investigated the efficacy of existing vaccinations against hospitalization and infection due to the Omicron variant of COVID-19, particularly for those who received two doses of Moderna or Pfizer vaccines and one dose of a vaccine by Johnson & Johnson or who were vaccinated more than five months previously. A total of 36 variants in Omicron’s spike protein, targeted by all three vaccinations, have made antibodies less effective at neutralizing the virus. Genotyping of SARS-CoV-2 viral sequencing revealed clinically significant variants such as E484K in three genetic mutations (T95I, D614G, and del142-144). One woman displayed two of these mutations, indicating a potential risk of infection following successful immunization, as recently reported by Hacisuleyman (2021). We examined the effects of mutations on domains (NID, RBM, and SD2) found at the interfaces of spike domains Omicron B.1. 1529, Delta/B.1. 1529, Alpha/B.1. 1.7, VUM B.1. 526, B.1. 575.2, and B.1. 1214 (formerly VOI Iota). We tested the affinity of Omicron for hACE2 and found that the wild and mutant spike proteins were using atomistic molecular dynamics simulations. According to binding free energies calculated during mutagenesis, hACE2 bound Omicron spike more strongly than SARS-CoV-2 wild strain. T95I, D614G, and E484K are three substitutions that significantly contribute to the RBD, corresponding to hACE2 binding energies and a doubling of Omicron spike proteins’ electrostatic potential. Omicron appears to bind hACE2 with greater affinity, increasing its infectivity and transmissibility. The spike virus was designed to strengthen antibody immune evasion through binding while boosting receptor binding by enhancing IgG and IgM antibodies that stimulate human β-cell, as opposed to the wild strain, which has more vital stimulation of both antibodies.
Genetic analysis of the rice jasmonate receptors reveals specialized functions for OsCOI2

COI1-mediated perception of jasmonate is critical for plant development and responses to environmental stresses. Monocots such as rice have two groups of COI genes due to gene duplication: OsCOI1a and OsCOI1b that are functionally equivalent to the dicotyledons COI1 on one hand and OsCOI2 whose function remains unclear. In order to assess the function of OsCOI2 and its functional redundancy with COI1 genes, we developed a series of rice mutants in the 3 genes OsCOI1a, OsCOI1b and OsCOI2 by CRISPR Cas9 and characterized their phenotype and responses to jasmonate. Characterization of OsCOI2 uncovered important roles in root, leaf and flower development. In particular, we show that crown root growth inhibition by jasmonate relies on OsCOI2 and not OsCOI1a or OsCOI1b in rice, revealing a major function for the non-canonical OsCOI2 in jasmonate-dependent control of rice root growth. Collectively, these results point to a specialized function of OsCOI2 in the regulation of plant development in rice and indicate that sub-functionalisation of jasmonate receptors has occurred in the monocot phylum.
The Arabidopsis Target of Rapamycin (TOR) kinase regulates ammonium assimilation and glutamine metabolism

In Eukaryotes, Target of Rapamycin (TOR) is a well conserved kinase that controls cell metabolism and growth in response to nutrients and environmental factors. Nitrogen (N) is an essential element for plants and TOR functions as a crucial N and amino acid sensor in animals and yeast. However, the knowledge on the connections between TOR and the overall N metabolism and assimilation in plants is still limited. In this study, we investigate the regulation of TOR in Arabidopsis by the N source as well as the impact of TOR deficiency on N metabolism. Inhibition of TOR globally decreases ammonium uptake while triggering a massive accumulation of amino acids such as Gln, but also of polyamines. Coherently, TOR complex mutants were found to be hypersensitive to Gln. We also show that the glutamine synthetase inhibitor glufosinate abolishes Gln accumulation resulting from TOR inhibition and improves the growth of TOR complex mutants. These results suggest that a high level of Gln contributes to the reduction in plant growth resulting from TOR inhibition. Glutamine synthetase activity was reduced by TOR inhibition while the enzyme amount increased. In conclusion our findings show that the TOR pathway is intimately connected to N metabolism and that a decrease in TOR activity results in a glutamine synthetase-dependent Gln and amino acids accumulation. One sentence summary The conserved Target of Rapamycin (TOR) kinase is an important sensor and regulator of the nitrogen metabolism and here we show that inhibiting this kinase affects ammonium uptake and results in Gln accumulation in a glutamine synthetase-dependent manner.
Nonlinear Waves of Vorticity

This is a review of solutions of the vorticity equation for two‐dimensional flow of an inviscid incompressible fluid that represent nonlinear waves. Geophysical applications are emphasized. Some of the solutions are valid in the beta‐plane of Rossby. Some are related to weakly nonlinear perturbations of basic parallel flows and axisymmetric flows, to initial‐value problems of hydrodynamic instability and to variational principles of minimal enstrophy or maximal entropy. Some have been found by exploiting well‐known ideas of the theory of solitons. In addition to listing known solutions and presenting a synthesis of their relationship to other fluid dynamic results, we report a few new ideas and new solutions for strongly nonlinear waves.
Candidate genes associated with economically important traits in dairy goats

Abstract Goats are important livestock species worldwide, due to their valuable commodities, including meat, milk, dairy products, fleece, and skin. Most of the economically important traits in dairy goats are complex quantitative traits, greatly influenced by polygenes and environmental factors. Hence, direct selection of these traits based on phenotypic data will not resulted a remarkable improvements in phenotypes of the traits, rather it needs to understand and include the molecular mechanisms controlling the traits in dairy goat breeding and trait selection. Consequently, following the advancement of molecular genetics and genotyping techniques, great quantities of candidate genes associated with economically important traits in different dairy goat breeds have been investigated by several scholars in the world. This review quantify candidate genes associated with the major economically important traits, including milk production, milk composition, reproduction, body conformation, environmental adaptations, and disease resistance traits in dairy goats by searching the available literature from different databases. As evidenced from literature, candidate genes have different functions on economically important traits, including regulating gene expression, protein functions, metabolism, physiological process, and expression of phenotype of the traits in dairy goats. The search of candidate genes associated with economically important traits, recognizing their genomic region, and physiological functions help breeders to identify marker-genes linked with economic traits used to attain faster selection response in dairy goat breeding. Therefore, quantifying candidate genes and their association with economically important traits will enhance the genetic improvement of dairy goats, which will improve nutritional security and the livelihoods of smallholder farmers.
Rice landraces from haor areas of Bangladesh possess greater genetic diversity as revealed by morpho-molecular approaches along with grain quality traits

Abstract Haors are slightly depressed bowl or saucer-shaped wetland ecosystems, between the natural levees of rivers flowing into sea. Landraces are locally adapted germplasms, often with and have valuable traits. Genetically diverse germplasm is a valuable resource for the crop improvement programme. Therefore, the genetic diversity of 40 rice landraces from haor areas in Bangladesh was assessed through phenotyping and genotyping. Significant variability was found for several agronomic traits at p ≤ 0.01. Lal paijam was the earliest maturing genotype (130 days) with the lowest yield (8 g/plant). Lal kumri was the best genotype suited to haor lands due to its medium earliness (144 days) and the highest yield (30 g/plant). The genotypes were grouped using phenotypic or genotypic traits into five clusters. The first five principal components with eigenvalue of >1.0 were responsible for a cumulative variance of 72.9% in which principal components (PC); PC1, PC2, PC3, PC4, and PC5 contributed 25.7%, 19.2%, 10.9%, 8.8%, and 8.3%, respectively. A sum of 80 alleles was observed at 6 Simple Sequence Repeat (SSR) loci specifying the range of allele number from 11 (RM 169) to 16 (RM 25) with an average of 14.17. The mean values of polymorphism information content and gene diversity were 0.859 and 0.871, respectively. Most of the genotypes exhibited medium grain size and shape, intermediate gelatinization temperature, and intermediate amylose content. The findings of this study can be exploited to develop early, high-yielding rice varieties with premium grain quality.
Event-triggered output feedback dissipative control of nonlinear systems under DoS attacks and actuator saturation

This paper presents a novel event-triggered dynamic output feedback dissipative control of nonlinear systems under intermittent denial-of-service (DoS) attacks and actuator saturation. Firstly, based on attack information, a secure event-triggered mechanism (ETM) is introduced, which not only saves systems resources but also is Zeno-free and resilient to DoS attacks. Secondly, a switched T–S fuzzy closed-loop system model is built, which unifies the parameters of nonlinear plant, noises, ETM, DoS attacks, switched output feedback fuzzy controller, and actuator saturation all in one framework. Thirdly, low conservative exponential stability criteria are derived while guaranteeing strict , , -dissipativity, and hence the relationships between system performance and factors such as DoS attacks, secure ETM, noises and actuator saturation are established. Further, sufficient conditions are given for the co-design of the switched output-based fuzzy controller and the secure ETM. Finally, the effectiveness of the proposed method is confirmed by numerical examples, achieving over 92% system resources.
Magnetic Structure of NiCr2O4 Studied by Neutron Scattering and Magnetization Measurements

The magnetic ordering of the normal spinel ferrimagnet NiCr 2 O 4 below T C = 74 K was reinvestigated by neutron scattering and magnetization measurements on a powder specimen. We found another magnetic transition at T S = 31 K besides T C in both experiments. The ordering of a ferrimagnetic (longitudinal) component and that of an antiferromagnetic (transverse) component occur at T C and T S , separately. A new magnetic structure model of NiCr 2 O 4 below T S with a spontaneous magnetization of about 0.3 µ B /formula is proposed based on experimental neutron scattering intensity.
Combination of LCA and circularity index for assessment of environmental impact of recycled aggregate concrete

Multidisciplinary approach is used to evaluate concrete with recycled concrete aggregates (RCA) from technical, environmental impacts and product circularity perspectives. Two RCA replacements investigated, RAC50: fine aggregates; RAC100: both coarse, fine aggregates. Reference, recycled concretes have same cement content, similar workability and compressive strength requirement, proven experimentally. RCA is sourced from pre-fab element discards of a Swedish plant, the logistical alternatives requiring environmental impact analysis. Alternatives are RCA crushing at plant and crushing at a different location including transportation. LCA shows transportation is second largest contributor after cement in all impact categories. RAC alternatives show lower total impact than reference concrete due to RCA replacement. A circularity index for concrete based on economic value of recirculated aggregates; supplements LCA for sustainability reporting. Circularity index results: RAC100 > RAC50 > RC. Combining circularity index with LCA helps optimize recycling process with regard to amount of recycled material and logistics respectively.
HR-Specific NLP for the Homogeneous Classification of Declared and Inferred Skills

ABSTRACT The use of natural language processing in human resource management has become of paramount importance in order to provide support for recruiting and corporate population management. This paper proposes a heuristic algorithm to solve two problems: (i) semantic matching among heterogeneous datasets storing the hard skills possessed by the company’s employees to obtain a homogeneous catalog, according to the O*NET and ESCO competence dictionaries, and (ii) inferring the employee’s soft skills with respect to his/her own declaration of interests, work experience, certifications, etc., given his/her curriculum vitae. Empirical results demonstrate that the proposed approach yields improved performance results by comparison with baseline methods available in the literature.
The Absolute Value of The Chern-Simons-Witten Invariants of Lens Spaces

An explicit formula for the absolute value of the Witten invariants is derived. We discuss the relation between homotopy equivalence and the absolute value of Witten invariants for lens spaces. We also give examples of arbitrarily finitely many lens spaces which have the same Witten invariants for any level r.
Correlation based system to assess the completeness and correctness of cognitive stimulation activities of elders

During a cognitive stimulation session where elders with cognitive decline perform stimulation activities, such as solving puzzles, we observed that they require constant supervision and support from their caregivers, and caregivers must be able to monitor the stimulation activity of more than one patient at a time. In this paper, aiming at providing support for the caregiver, we developed a vision-based system using an Phase-SDF filter that generates a composite reference image which is correlated to a captured wooden-puzzle image. The output correlation value allows to automatically verify the progress on the puzzle solving task, and to assess its completeness and correctness.
Quorum Sensing How Bacteria Talk to Each Other

Traditionally, social cooperation has been considered the preserve of higher organisms. Only in relatively recent times have biologists begun to appreciate that bacteria are also highly interactive creatures. They exhibit complex coopera-tive behaviours, such as conjugal plasmid transfer, biofilm maturation and virulence. Many of these behaviours are regulated by a process known as quorum sensing.
Aerosol–cloud impacts on aerosol detrainment and rainout in shallow maritime tropical clouds

Abstract. This study investigates how aerosol-induced changes to cloud properties subsequently influence the overall aerosol budget through changes to detrainment and rainout. We simulated an idealized field of shallow maritime tropical clouds using the Regional Atmospheric Modeling System (RAMS) and varied the aerosol loading and type between 16 simulations. The full aerosol budget was tracked over the course of the 48 h simulation, showing that increasing the aerosol loading leads to an increase in aerosol regeneration and detrainment aloft at the expense of aerosol removal via rainout. Under increased aerosol loadings, cloud droplets are smaller and more likely to evaporate before they form precipitation-sized hydrometeors. As a result, the aerosol particles contained inside these droplets are released into the environment rather than being removed to the surface via rainout. However, the few raindrops which do happen to form under increased aerosol loadings tend to be larger, since the cloud water available for collection is divided among fewer raindrops, and thus raindrops experience less evaporation. Thus, in contrast to previous work, we find that increases in aerosol loading lead to decreases in aerosol rainout efficiency, even without a decrease in the overall precipitation efficiency. We further used tobac, a package for tracking and identifying cloud objects, to identify shifts in the overall cloud population as a function of aerosol loading and type, and we found contrasting aerosol effects in shallow cumulus and congestus clouds. Shallow cumulus clouds are more sensitive to the increase in cloud edge and/or top evaporation with increased aerosol loading and thereby tend to rain less and remove fewer aerosols via rainout. On the other hand, larger congestus clouds are more protected from evaporation and are thereby able to benefit from warm-phase invigoration. This leads to an increase in rain rates but not in domain-wide aerosol rainout, as the domain total rainfall becomes concentrated over a smaller horizontal area. Trends as a function of aerosol loading were remarkably consistent between the different aerosol types tested. These results represent a pathway by which a polluted environment not only has higher aerosol loadings than a pristine one but is also less able to regulate those loadings by removal processes, instead transporting aerosols to the free troposphere where they remain available for reactivation and further aerosol–cloud interactions.
Current Executive

Second, in addition to several insightful book reviews, this issue also contains an article on scientific misconduct that builds on the commentary by Montgomerie and Birkhead published in the previous Newsletter (ISBE Newsletter 17: 16-24). In his article “Improving the processing of scientific misconduct charges: an eyewitness perspective”, Anders Pape Møller uses his own experience on this subject to review and recommend policies for handling accusations of misconduct. Due to the serious consequences on individuals’ careers that can stem from charges of misconduct, it is imperative that judicious reviews of the allegations are conducted. I applaud Anders for sharing his experiences, and moreover for using these to analytically assess and provide recommendations for how such cases should be conducted.
Study of interface roughness dependence of electron mobility in Si inversion layers using the Monte Carlo method

The electron mobility in the inversion layer of a metal–oxide semiconductor field effect transistor formed on the (100) silicon surface is calculated by using a Monte Carlo approach which takes into account size quantization, acoustic phonon scattering, intervalley phonon scattering and surface roughness scattering. Degeneracy is also considered because it is important at higher normal effective fields (high gate voltages). The main emphasis is placed on the influence of the specific autocovariance function, used to describe the surface roughness, on the electron mobility. Here we compare the mobilities obtained using exponential and Gaussian autocovariance functions. It is found that the electron mobility calculated with roughness scattering rates based on the exponential function shows good agreement with experiments. The effect of the degeneracy and screening on the roughness scattering is also discussed.
Implementation of Stereo Vision for Depth Calculation

— The object detection using stereovision is a process to identify a specific object in sequence of different images. In many years it receives a much more attention due to huge number of applications like navigation, automated inspection, wildlife analysis etc. The detection of actual object with different shapes is a difficult task; due to some issues like external environment, fast movement of object, shadows, noises etc., so there is requirement to choose appropriate methods/algorithms with respect to it. So this paper specifies depth analysis with stereo vision using appropriate algorithm.
Dispersion analysis and element‐free Galerkin solutions of second‐ and fourth‐order gradient‐enhanced damage models

Gradient-dependent damage formulations incorporate higher-order derivatives of state variables in the constitutive equations. Different formulations have been derived for this gradient enhancement, comparison of which is difficult in a finite element context due to higher-order continuity requirements for certain formulations. On the other hand, the higher-order continuity requirements are met naturally by element-free Galerkin (EFG) shape functions. Thus, the EFG method provides a suitable tool for the assessment of gradient enhanced continuum models. Dispersion analyses have been carried out to compare different gradient enhanced models with the non-local damage model. The formulation of the additional boundary conditions is addressed. Numerical examples show the objectivity with respect to the discretization and the differences between various gradient formulations with second- and fourth-order derivatives. It is shown that with the same underlying internal length scale, very different results can be obtained. Copyright © 2000 John Wiley & Sons, Ltd.
The therapeutic effects of low-intensity pulsed ultrasound in musculoskeletal soft tissue injuries: Focusing on the molecular mechanism

Musculoskeletal soft tissue injuries are very common and usually occur during both sporting and everyday activities. The intervention of adjuvant therapies to promote tissue regeneration is of great importance to improving people’s quality of life and extending their productive lives. Though many studies have focused on the positive results and effectiveness of the LIPUS on soft tissue, the molecular mechanisms standing behind LIPUS effects are much less explored and reported, especially the intracellular signaling pathways. We incorporated all research on LIPUS in soft tissue diseases since 2005 and summarized studies that uncovered the intracellular molecular mechanism. This review will also provide the latest evidence-based research progress in this field and suggest research directions for future experiments.
Mycorrhiza governs plant-plant interactions through preferential allocation of shared nutritional resources: A triple (13C, 15N and 33P) labeling study

Plant-plant interactions and coexistence can be directly mediated by symbiotic arbuscular mycorrhizal (AM) fungi through asymmetric resource exchange between the plant and fungal partners. However, little is known about the effects of AM fungal presence on resource allocation in mixed plant stands. Here, we examined how phosphorus (P), nitrogen (N) and carbon (C) resources were distributed between coexisting con- and heterospecific plant individuals in the presence or absence of AM fungus, using radio- and stable isotopes. Congeneric plant species, Panicum bisulcatum and P. maximum, inoculated or not with Rhizophagus irregularis, were grown in two different culture systems, mono- and mixed-species stands. Pots were subjected to different shading regimes to manipulate C sink-source strengths. In monocultures, P. maximum gained more mycorrhizal phosphorus uptake benefits than P.bisulcatum. However, in the mixed culture, the AM fungus appeared to preferentially transfer nutrients (33P and 15N) to P.bisulcatum compared to P. maximum. Further, we observed higher 13C allocation to mycorrhiza by P.bisulcatum in mixed- compared to the mono-systems, which likely contributed to improved competitiveness in the mixed cultures of P.bisulcatum vs. P. maximum regardless of the shading regime. Our results suggest that the presence of mycorrhiza influenced competitiveness of the two Panicum species in mixed stands in favor of those with high quality partner, P. bisulcatum, which provided more C to the mycorrhizal networks. However, in mono-species systems where the AM fungus had no partner choice, even the lower quality partner (i.e., P.maximum) could also have benefitted from the symbiosis. Future research should separate the various contributors (roots vs. common mycorrhizal network) and mechanisms of resource exchange in such a multifaceted interaction.