Miracle-dz/UniFAR-FTUs huggingface dataset:
Anticodon sequence determines the impact of mistranslating tRNAAla variants

Transfer RNAs (tRNAs) maintain translation fidelity through accurate charging by their cognate aminoacyl-tRNA synthetase and codon:anticodon base pairing with the mRNA at the ribosome. Mistranslation occurs when an amino acid not specified by the genetic message is incorporated into proteins and has applications in biotechnology, therapeutics and is relevant to disease. Since the alanyl-tRNA synthetase uniquely recognizes a G3:U70 base pair in tRNAAla and the anticodon plays no role in charging, tRNAAla variants with anticodon mutations have the potential to mis-incorporate alanine. Here, we characterize the impact of the 60 non-alanine tRNAAla anticodon variants on the growth of Saccharomyces cerevisiae. Overall, 36 tRNAAla anticodon variants decreased growth in single-or multi-copy. Mass spectrometry analysis of the cellular proteome revealed that 52 of 57 anticodon variants, not decoding alanine or stop codons, induced mistranslation when on single-copy plasmids. Variants with G/C rich anticodons resulted in larger growth deficits than A/U rich variants. In most instances, synonymous anticodon variants impact growth differently, with anticodons containing U at base 34 being the least impactful. For anticodons generating the same amino acid substitution, reduced growth generally correlated with the abundance of detected mistranslation events. Differences in decoding specificity, even between synonymous anticodons, resulted in each tRNAAla variant mistranslating unique sets of peptides and proteins. We suggest that these differences in decoding specificity are also important in determining the impact of tRNAAla anticodon variants.
Imaging cyclotron orbits and scattering sites in a high-mobility two-dimensional electron gas

We present experimental images and computer simulations of electron and conduction-band-hole trajectories transmitted between two series constrictions in a two-dimensional electron gas formed at a GaAs/AlGaAs heterojunction. The electric perturbation of a scanning charged probe modified the trajectories to generate the experimental images. In a weak magnetic field, the images revealed cyclotron orbits allowing a measurement of electron and conduction-band-hole energies. Using the same technique, a scattering site caused a 26\ifmmode^\circ\else\textdegree\fi{} change in the trajectories. Computer simulations with localized charge fluctuations in the donor layer, which locally distort the conduction band by $24%$ of the Fermi energy, reproduced structures seen in the experimental images and features in a related magnetic steering experiment. Conduction-band-holes are holelike quasiparticles in the conduction band with an energy less than the Fermi energy, being equivalent to unoccupied electron states.
Electro-optically Q-switched Er:YAG laser

For giant pulse generation in the mid-infrared region LiNbO3 crystal with Brewster angle cut faces was inserted inside the Er:YAG laser oscillator and a specially designed driver ensured the precise time of Pockels cell switching. The optimization of the oscillator and Pockels cell driver parameters was performed to obtain the shortest (60 ns) and stable output pulse with maximum energy (60 mJ). It gives 1 MW output peak power. Laser output dependences on the resonator parameters (resonator length and output mirror reflexivity) were also performed and the output laser characteristics well corresponded to the theoretical calculation results.
Occurrence of aspiration pneumonia in dysphagic children post video fluoroscopy

Summary Introduction: The literature reports that when it comes of instrumental assessment of swallowing in children, undoubtedly, video fluoroscopy of swallow offers great advantages over the endoscopic study. Objective: Check the risk of aspiration pneumonia after the study of swallowing by video fluoroscopy, in children with dysphagia. Method: In a study of prospective cutting, participated 16 children aged between 6 months and 10 years, with an average of 5,2 years, referred for study of swallowing by video fluoroscopy. Were tested 4 consistencies, pudding, nectar, honey and liquid. The presences of signs and/or respiratory symptoms were evaluated pre and post study of deglutition by video fluoroscopy, through history and clinical exam. When necessary was asked chest x-ray. Results: Of 16 children, 5 didn't presented dysphagia. In 11 children the exam showed 4 with mild dysphagia, 2 moderate and 5 severe, as classification of OTT (1996) - Classification of severity of dysphagia to the video fluoroscopy. Of the 7 children who aspirated during the exam, only 1 presented respiratory symptoms after the deglutition study, but without signal of pneumonia to the physical examination. Conclusion: In the studied population there were no occurrences of aspiration pneumonia after the study of deglutition was performed by video fluoroscopy, despite the occurrence of aspiration during the exam in about 50% of cases.
Calculating the equilibrium distribution in level dependent quasi-birth-and-death processes

Quasi-Birth-and-Death (QBD) processes have been analysed in detail by many authors. This paper considers the calculation of equilibrium distributions in level dependent QBD processes which are an extension of the classical QBD process. In addition to the general case, we consider a number of special cases of level dependent QBD processes, presenting algorithms for computing the equilibrium distribution
Beak morphometry and morphogenesis across avian radiations

Adaptive avian radiations associated with the diversification of bird beaks into a multitude of forms enabling different functions are exemplified by Darwin’s finches and Hawaiian honeycreepers. To elucidate the nature of these radiations, we quantified beak shape and skull shape using a variety of geometric measures that allowed us to collapse the variability of beak shape into a minimal set of geometric parameters. Furthermore, we find that just two measures of beak shape, the ratio of the width to length and the normalized sharpening rate (increase in the transverse beak curvature near the tip relative to that at the base of the beak), are both strongly correlated with diet, and thus indicative of how bite forces are correlated with beak shape. Finally, by considering how transverse sections to the beak centerline evolve with distance from the tip, we show that a simple geometry-driven growth law termed “modified mean curvature flow” captures the beak shapes of Darwin’s finches and Hawaiian honeycreepers. A surprising consequence of the simple growth law is that beak shapes that are not allowed based on the developmental program of the beak are also not observed in nature, suggesting a link between evolutionary morphology and development in terms of growth-driven developmental constraints.
Stochastic within-host dynamics of antibiotic resistance: Resistant survival probability, size at the end of treatment and carriage time after treatment

The use of an antibiotic often leads to the emergence and spread of bacterial strains resistant to this antibiotic. Experimental and theoretical studies have investigated the drug dose that minimizes the risk of resistance evolution over the course of treatment of an individual, showing that the optimal dose will either be the highest or the lowest drug concentration possible to administer; however, no analytical results exist that help decide between these two extremes. To address this gap, we develop a stochastic mathematical model of bacterial within-host dynamics under antibiotic treatment. We explore various scenarios of density regulation (bacterial density affects cell birth or death rates), and antibiotic modes of action (biostatic or biocidal). We derive analytical results for the survival probability of the resistant subpopulation until the end of treatment, the size of the resistant subpopulation at the end of treatment, the carriage time of the resistant subpopulation until it is replaced by a sensitive one after treatment, and verify these results with stochastic simulations. We ﬁnd that the scenario of density regulation and the drug mode of action are important determinants of the survival of a resistant subpopulation. Resistant cells survive best when bacterial competition reduces cell birth and under biocidal antibiotics. Compared to an analogous deterministic model, the population size reached by the resistant type is larger and carriage time is slightly reduced by stochastic loss of resistant cells. Moreover, we obtain an analytical prediction of the antibiotic concentration that maximizes the survival of resistant cells, which may help to decide which drug dosage (not) to administer. Our results are amenable to experimental tests and help link the within and between host scales in epidemiological models.
Ongoing HIV replication in lymph node sanctuary sites in treated patients contributes to the total latent HIV at a very slow rate

Lymph nodes (LNs) serve as a sanctuary site for HIV viruses due to the heterogeneous distribution of the antiretrovirals (ARVs) inside the LNs. There is an ongoing debate whether this represents ongoing cycles of viral replication in the LNs or merely residual virus production by latently infected cells. Previous work has claimed that the measured levels of genetic variation in proviruses sampled from the blood were inconsistent with ongoing replication. However, it is not clear what rate of variation is consistent with ongoing replication in small sanctuary sites. In this study, we used a spherically symmetric compartmental ODE model to track the HIV viral dynamics in the LN and predict the contribution of ongoing replication within the LN to the wholebody proviral pool in an ARV-suppressed patient. This model tracks the reaction-diffusion dynamics of uninfected, actively infected, and latently infected T-cells as well as free virus within the LN parenchyma and the blood, and distinguishes between latently infected cells created before ARV therapy and during ARV therapy. We simulated suppressive therapy beginning in year 5 post-infection. Each LN sanctuary site had a volume of 1 ml, and we considered cases of 1ml, 30ml, and 250ml total volume, which represent a single active sanctuary site, moderate systemic involvement, and involvement of the total lymphoid tissue. Viral load in the blood rapidly dropped and remained below the limit of detection in all cases but remained high in the LN sanctuary sites. Novel latent cells increased systemically over time but very slowly, taking between 25 and 50 years to reach 5% of the total latent pool, depending on the volume of lymphoid tissue involvement. Putative sanctuary sites in LNs are limited in volume and produce novel latent cells slowly. Assays to detect genetic drift due to such sites would require very deep sequencing if sampling only from the blood. Previous studies showing a lack of genetic drift are consistent with the expected contribution of ongoing replication in lymph node sanctuary sites.
Astrocyte-like subpopulation of NG2 glia in the adult mouse cortex exhibits characteristics of neural progenitor cells and is capable of forming neuron-like cells after ischemic injury

Glia cells expressing neuron-glial antigen 2 (NG2) play a critical role as oligodendrocyte precursor cells (OPCs) in the healthy brain; however, their differentiation potential after ischemic injury remains an unresolved question. Here, we aimed to elucidate the heterogeneity and role of NG2 glia in the ischemic brain. We used transgenic mice to label NG2-expressing cells and their progeny with red fluorescent protein tdTomato in the healthy brains and those after focal cerebral ischemia (FCI). Based on single-cell RNA sequencing, the labeled glial cells were divided into five distinct subpopulations. The identity of these subpopulations was determined based on gene expression patterns. In addition, membrane properties were further analyzed using the patch-clamp technique. Three of the observed subpopulations represented OPCs, whereas the fourth group exhibited characteristics of cells destined for oligodendrocyte fate. The fifth subpopulation of NG2 glia carried astrocytic markers. Importantly, we detected features of neural progenitors in these cells. This subpopulation was present in both healthy and post-ischemic tissue; however, its gene expression changed after ischemia, with genes related to neurogenesis being more abundant. Neurogenic gene expression was monitored over time and complemented by immunohistochemical staining, which showed increased numbers of Purkinje cell protein 4-positive NG2 cells at the edge of the ischemic lesion 12 days after FCI, and NeuN-positive NG2 cells 28 days after injury, indicating the existence of neuron-like cells that develop from NG2 glia in the ischemic tissue. Our results provide further insight into the differentiation plasticity and neurogenic potential of NG2 glia after stroke. Main Points Different subpopulations of NG2 glia in the healthy and ischemic adult cortex were identified based on their gene expression and membrane properties. Astrocyte-like NG2 glia exhibit neurogenic gene expression and are more abundant in post-ischemic tissue. Progeny of NG2-positive cells carrying neuronal marker NeuN was observed at the edge of the ischemic lesion.
Evolutionary changes in germ granule mRNA content are driven by multiple mechanisms in Drosophila

The co-packaging of mRNAs into biomolecular condensates called germ granules is a conserved strategy to post-transcriptionally regulate mRNAs that function in germline development and maintenance. In D. melanogaster, mRNAs accumulate in germ granules by forming homotypic clusters, aggregates that contain multiple transcripts from a specific gene. Nucleated by Oskar (Osk), homotypic clusters in D. melanogaster are generated through a stochastic seeding and self-recruitment process that requires the 3’ UTR of germ granule mRNAs. Interestingly, the 3’ UTR belonging to germ granule mRNAs, such as nanos (nos), have considerable sequence variations among Drosophila species. Thus, we hypothesized that evolutionary changes in the 3’ UTR influences germ granule development. To test our hypothesis, we investigated the homotypic clustering of nos and polar granule component (pgc) in four Drosophila species and concluded that homotypic clustering is a conserved developmental process used to enrich germ granule mRNAs. Additionally, we discovered that the number of transcripts found in nos and/or pgc clusters could vary significantly among species. By integrating biological data with computational modeling, we determined that multiple mechanisms underlie naturally occurring germ granule diversity, including changes in nos, pgc, osk levels, and/or homotypic clustering efficacy. Finally, we found that the nos 3’ UTR from different species can alter the efficacy of nos homotypic clustering, resulting in germ granules with reduced nos accumulation. Our findings highlight the impact that evolution has on the development of germ granules and may provide insight into processes that modify the content of other classes of biomolecular condensates.
Flute instability in the presence of non-uniform electric fields

A general equation describing the flute instability in a low-β plasma, in the presence of a non-uniform electric field perpendicular to the magnetic field, is derived from guiding centre equations. The equations obtained by Rosenbluth and Simon and by Damm et al. correspond to two different limiting cases of this more general equation. The physical significance of various stabilizing terms is discussed. In the high density, zero gyro-radius limit, the shear flow resulting from the non-uniform electric field has a de-stabilizing effect. At low densities the imbalance between the equilibrium ion and electron densities has a significant stabilizing effect.
Complex chemical signals dictate Ah receptor activation through the gut-lung axis

The aryl hydrocarbon receptor (AHR) mediates intestinal barrier homeostasis. Many AHR ligands are also CYP1A1/1B1 substrates, which can result in the rapid clearance within the intestinal tract, limiting AHR activation. This led us to the hypothesis that there are dietary substrates of CYP1A1/1B1 that increase the half-life of potent AHR ligands. We examined the potential of urolithin A (UroA) as a CYP1A1/1B1 substrate to enhance AHR activity in vivo. UroA is a competitive substrate for CYP1A1/1B1 in an in vitro competition assay. A broccoli-containing diet promotes the gastric formation of the potent hydrophobic AHR ligand and CYP1A1/1B1 substrate, 5,11-dihydroindolo[3,2-b]carbazole (ICZ). Dietary exposure to UroA in a broccoli diet led to a coordinated increase in duodenal, cardiac, and pulmonary AHR activity, but no increase in activity in liver. Thus, CYP1A1 dietary competitive substrates can lead to intestinal “escape”, likely through the lymphatic system, increasing AHR activation in key barrier tissues.
Comparison between Canine and Porcine Models of Chronic Deep Venous Thrombosis

Venous thromboembolism(VTE) refers to deep venous thrombosis(DVT) and pulmonary embolism(PE), which is a worldwide problem and has very high morbidity and mortality. The research of venous thrombosis involves pathogenesis, pathophysiology, and therapeutic attempt. Alternative experimental animal models have changed dramatically over the past 20 years, from small murine models to large ones. Larger animal models offer more options and are more consistent with human physiology. This article aims to induce chronic deep venous thrombosis in the left iliac vein in canine and porcine models and compare these two models. We think that feasible large animal models can better translate the results of therapeutic research into clinical application.
Evolution of Degree Metrics in Large Temporal Graphs

: Graph metrics, such as the simple but popular vertex degree and others based on it, are well defined for static graphs. However, adapting static metrics for temporal graphs is still part of current research. In this paper, we propose a set of temporal extensions of four degree-dependent metrics, as well as aggregations like minimum, maximum, and average degree of (i) a vertex over a time interval and (ii) a graph at a specific point in time. We show why using the static degree can lead to wrong assumptions about the relevance of a vertex in a temporal graph and highlight the need to include time as a dimension in the metric. We propose a baseline algorithm to calculate the degree evolution of all vertices in a temporal graph and show its implementation in a distributed in-memory dataflow system. Using real-world and synthetic datasets containing up to 462 million vertices and 1.7 billion edges, we show the scalability of our algorithm on a distributed cluster achieving a speedup of around 12 on 16 machines.
Anticipating change: the impact of simulated seasonal heterogeneity on heat tolerances along a latitudinal cline

An understanding of thermal limits and variation across geographic regions is central to predicting how any population may respond to scenarios of global change. Latitudinal clines, in particular, have been used in demonstrating that populations can be locally adapted to their own thermal environment and, as a result, not all populations will be equally impacted by an increase in temperature. But how robust are these signals of thermal adaptation to the other ecological challenges that animals commonly face in the wild? Seasonal changes in population density, food availability, or photoperiod are common ecological challenges that could disrupt patterns of thermal tolerance along a cline if each population differentially used these signals to anticipate future temperatures and adjust their thermal tolerances accordingly. In this study, we aimed to test the robustness of a cline in thermal tolerance to simulated signals of seasonal heterogeneity. Experimental animals were derived from clones of the Australian water flea, Daphnia carinata, sampled from nine populations along a latitudinal transect in eastern Australia. We then factorially combined summer (18h light, 6h dark) and winter (6h light, 18h dark) photoperiods with high (5 million algal cells individual-1 day-1) and low (1 million algal cells individual-1 day-1) food availabilities, before performing static heat shock assays and recording knockdown times as a measure of thermal tolerance. In general, higher food availably led to an increase in thermal tolerances, with the magnitude of increase varying by clone. In contrast, summer photoperiods led to rank order changes in thermal tolerances, with heat resistance increasing for some clones, and other decreasing for others. Heat resistance, however, still declined along the latitudinal cline, irrespective of the manipulation of seasonal signals, with northern clones always showing greater thermal resistance, and that this was most likely driven by adaptation to winter thermal conditions. While photoperiod and food availability can clearly shape thermal tolerances for specific clones or populations, they are unlikely to be used to anticipate future temperatures, and thus observed clines in heat resistance will remained robust to these forms of seasonal heterogeneity.
Integrating simultaneous motor imagery and spatial attention for EEG-BCI control

Objective: EEG-based brain-computer interfaces (BCI) are non-invasive approaches for replacing or restoring motor functions in impaired patients, and direct brain-to-device communication in the general population. Motor imagery (MI) is one of the most used BCI paradigms, but its performance varies across individuals and certain users require substantial training to develop control. In this study, we propose to integrate a MI paradigm simultaneously with a recently proposed Overt Spatial Attention (OSA) paradigm, to accomplish BCI control. Methods: We evaluated a cohort of 25 human subjects’ ability to control a virtual cursor in one- and two-dimensions over 5 BCI sessions. The subjects used 5 different BCI paradigms: MI alone, OSA alone, MI and OSA simultaneously towards the same target (MI+OSA), and MI for one axis while OSA controls the other (MI/OSA and OSA/MI). Results: Our results show that MI+OSA reached the highest average online performance in 2D tasks at 49% Percent Valid Correct (PVC), statistically outperforms MI alone (42%), and was higher, but not statistically significant, than OSA alone (45%). MI+OSA had a similar performance to each subject’s best individual method between MI alone and OSA alone (50%) and 9 subjects reached their highest average BCI performance using MI+OSA. Conclusion: Integrating MI and OSA leads to improved performance over MI alone at the group level and is the best BCI paradigm option for some subjects. Significance: This work proposes a new BCI control paradigm that integrates two existing paradigms and demonstrates its value by showing that it can improve users’ BCI performance.
Measuring clothing image similarity with bundled features

Purpose – Clothing retrieval is very useful to help the clients to efficiently search out the apparel they want. Currently, the mainstream clothing retrieval methods are attribute semantics based, which however are inconvenient for common clients. The purpose of this paper is to provide an easy‐to‐operate apparels retrieval mode with the authors' novel approach of clothing image similarity measurement.Design/methodology/approach – The authors measure the similarity between two clothing images by computing the weighted similarities between their bundled features. Each bundled feature consists of the point features (SIFT) which are further quantified into local visual words in a maximally stable extremal region (MSER). The authors weight the importance of bundled features by the precision of SIFT quantification and local word frequency that reflects the frequency of the common visual words appeared in two bundled features. The bundled features similarity is computed from two aspects: local word frequency; a.