Miracle-dz/UniFAR-FTUs huggingface dataset:
Psychoacoustic evaluation of a fast HRTF measurement system

To accurately simulate sound sources from arbitrary directions, a stimuli can be convoluted with the headrelated transfer function (HRTF) of the desired direction [1]. The HRTF represents the influence of the listeners head on the sound field. A convolution of a stimuli with a HRTF will reproduce this same effect in a virtual scene. To simulate sound sources in a room, a HRTF with sufficiently high resolution is needed as reflections will arrive at the subjects ears from every directions. To reduce measurement effort so called artificial heads can be constructed which have a HRTF that fits reasonably good on many listeners. The perceived sound direction of virtual sources auralized with dummy-head HRTF will vary in between subjects depending on the geometric properties of the subjects head. The use of individual HRTFs always improves the subjects localization ability of the sources [2] and are thus needed for simulations with high accuracy and in simulations where realism of the simulation is an important factor. To measure individual HRTFs with high resolution, fast measurement techniques need to be applied to reduce measurement time. These techniques often result in a trade-of between measurement accuracy and measurement time.
Direct numerical simulation of interaction between a stationary crossflow instability and forward-facing steps

Abstract The interaction between forward-facing steps of several heights and a pre-existing critical stationary crossflow instability of a swept-wing boundary layer is analysed. Direct numerical simulations (DNS) are performed of the incompressible three-dimensional laminar base flow and the stationary distorted flow that arise from the interaction between an imposed primary stationary crossflow perturbation and the steps. These DNS are complemented with solutions of the linear and the nonlinear parabolised stability equations, used towards identifying the influence of linearity and non-parallelism near the step. A fully stationary solution of the Navier–Stokes equations is enforced numerically, in order to isolate the mechanisms pertaining to the interaction of the stationary disturbance with the step. Results provide insight into the salient modifications of the base laminar boundary layer due to the step, and the response of the incoming crossflow instability to these changes. The fundamental spanwise Fourier mode of the disturbance field gradually lifts up as it approaches the step and passes over it. The flow environment around the step is characterised by a sudden spanwise modulation of the base-flow streamlines. Additional stationary perturbation structures are induced at the step, which manifest in the form of spanwise-aligned velocity streaks near the wall. Shortly downstream of the step, the fundamental component of the crossflow perturbation maintains a rather constant amplification for the smallest steps studied. For the largest step, however, the fundamental crossflow perturbation is stabilised significantly shortly downstream of the largest step. This surprising result is ascribed to a modulation of the kinetic energy transfer between the base flow and the fundamental perturbation field, which is brought forward as a new step interaction mechanism. Possible non-modal growth effects at the step are discussed. Furthermore, the results from DNS indicate significant amplification of the high-order harmonic crossflow components downstream of the step.
Epidemiology and Pathophysiology of Intracranial Large Artery Stenosis

Intracranial stenosis due to atherosclerosis is a disease of significant prevalence worldwide and is responsible for a significant economic burden due to stroke-related disability. Known risk factors including age, race, sex, and medical co-morbidities contribute to its incidence. While ischemic stroke and transient ischemic attack can develop from myriad mechanisms in patients with intracranial stenosis, it is likely that an interplay of hemodynamic failure, in-situ thrombosis, and distal embolism results in brain ischemia. Knowledge of disease prevalence, risk factors, and pathophysiology is critical to development of better medical and interventional treatments for this grave condition.
Paired echo suppression algorithm in helicopter-borne SAR imaging

A helicopter may vibrate at high frequencies during its flight, which can give rise to paired echoes in the helicopter-borne synthetic aperture radar (SAR) imagery. This phenomenon substantially degrades the quality of SAR images since it may generate unwanted ghost targets in the images. In this study, the authors propose a method consisting of three steps to suppress paired echoes in helicopter-borne SAR imagery based on the characteristics of the helicopter vibration. The proposed method can suppress paired echoes with high efficiency and accuracy in the case of vibrations with varying amplitude. Furthermore, this method does not require the presence of isolated or strong points in a range cell. Both simulated and acquired data are processed to demonstrate the effectiveness of the proposed algorithm.
Dose-dependent disruption of hepatic zonation by 2,3,7,8-tetrachlorodibenzo-p-dioxin in mice: integration of single-nuclei RNA sequencing and spatial transcriptomics

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) dose-dependently induces the development of hepatic fat accumulation and inflammation with fibrosis in mice initially in the portal region. Conversely, differential gene and protein expression is first detected in the central region. To further investigate cell-specific and spatially resolved dose-dependent changes in gene expression elicited by TCDD, single-nuclei RNA sequencing and spatial transcriptomics were used for livers of male mice gavaged with TCDD every 4 days for 28 days. The proportion of 11 cell (sub)types across 131,613 nuclei dose-dependently changed with 68% of all portal and central hepatocyte nuclei in control mice being overtaken by macrophages following TCDD treatment. We identified 368 (portal fibroblasts) to 1,339 (macrophages) differentially expressed genes. Spatial analyses revealed initial loss of portal identity that eventually spanned the entire liver lobule with increasing dose. Induction of R-spondin 3 (Rspo3) and pericentral Apc, suggested dysregulation of the Wnt/β-catenin signaling cascade in zonally resolved steatosis. Collectively, the integrated results suggest disruption of zonation contributes to the pattern of TCDD-elicited NAFLD pathologies. SYNOPSIS Single-nuclei RNA sequencing (snRNAseq) and spatial transcriptomics were integrated to investigate cell-specific and spatially resolved dose-dependent changes elicited by TCDD. We show that TCDD causes a loss of zonal characteristics that disrupts spatially defined metabolic functions. - Dose-dependent analyses show higher responsiveness of central hepatocytes despite hepatotoxicity occurring initially in the portal region. - Integration of snRNAseq and spatial transcriptomics demonstrates a loss of hepatocytes with portal characteristics. - TCDD disrupted spatially resolved expression of β-catenin signaling members that are critical in maintaining liver zonation. - Spatial transcriptomics and snRNAseq shows induction of R-spondin3 from nonparenchymal cells which serve as cue for the β-catenin pathway.
MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens

Multilevel genome typing (MGT) enables the genomic characterization of bacterial isolates and the relationships among them. The MGT system describes an isolate using multiple multilocus sequence typing (MLST) schemes, referred to as levels. Thus, for a new isolate, sequence types (STs) assigned at multiple precisely defined levels can be used to type isolates at multiple resolutions. The MGT designation for isolates is stable, and assignment is faster than existing approaches. MGT’s utility has been demonstrated in multiple species. This paper presents a publicly accessible web service called MGTdb, which enables the assignment of MGT sequence types to isolates, along with their storage, retrieval and analysis. The MGTdb web service enables upload of genome data as sequence reads or alleles, which are processed and assigned MGT identifiers. Additionally, any newly sequenced isolates deposited in NCBI Sequence Read Archive are also regularly retrieved (currently daily), processed, assigned MGT and made publicly available in MGTdb. Interactive visualisation tools are presented to assist analysis, along with capabilities to download publicly available isolates and assignments for use with external software. MGTdb is currently available for Salmonella enterica serovars Typhimurium and Enteritidis, and Vibrio cholerae. We demonstrate the usability of MGTdb through three case studies to study the long-term national surveillance of S. Typhimurium, and the local epidemiology and outbreaks of S. Typhimurium, and the global epidemiology of V. cholerae. Thus, MGTdb enables epidemiological and microbiological investigations at multiple levels of resolution for all publicly available isolates of these pathogens. Database URL https://mgtdb.unsw. edu.au
Temporal and spatial frameworks supporting plant responses to vegetation proximity

After perception of vegetation proximity by the phytochrome photoreceptors, shade-avoider plants initiate a set of responses known as the Shade Avoidance Syndrome (SAS). The shade-induced de-repression of active phytochrome B (phyB) releases the repression imposed over the PHYTOCHROME INTERACTING FACTORs (PIFs). In Arabidopsis thaliana seedlings, this mechanism triggers rapid and massive changes in gene expression, increases auxin production in a SHADE AVOIDANCE 3-dependent manner and promotes hypocotyl elongation. Other components, such as phyA and ELONGATED HYPOCOTYL 5 (HY5), also participate in the shade regulation of the hypocotyl elongation response repressing it. However, it is less clear how phyA and HY5 interact with PIFs to regulate this response. Our physiological, genetic, cell biology and transcriptomic analyses showed that these components are organized in two main branches, and incorporate into the model for the regulation of shade-induced hypocotyl elongation the temporal and spatial functional importance of the various SAS regulators analyzed in here. They also indicated that PIFs and HY5, belonging to separate branches, target common genes whose expression is rapidly modulated by shade. This transcriptional relationship, however, changes after longer shade-treatments, suggesting that it is a dynamic convergence point to modulate the hypocotyl elongation.
Simulation of Energy Regeneration in Human Locomotion for Efficient Exoskeleton Actuation

Backdriveable actuators with energy regeneration can improve the efficiency and extend the battery-powered operating times of robotic lower-limb exoskeletons by converting some of the otherwise dissipated energy during negative mechanical work into electrical energy. However, previous related studies have focused on steady-state level-ground walking. To better encompass real-world community mobility, here we developed a feedforward human-exoskeleton energy regeneration system model to simulate energy regeneration and storage during other daily locomotor activities. Data from inverse dynamics analyses of 10 healthy young adults walking at variable speeds and slopes were used to calculate the negative joint mechanical power and work (i.e., the mechanical energy theoretically available for electrical energy regeneration). These human joint mechanical energetics were then used to simulate backdriving a robotic exoskeleton and regenerating energy. An empirical characterization of the exoskeleton device was carried out using a joint dynamometer system and an electromechanical motor model to calculate the actuator efficiency and to simulate energy regeneration. Our performance calculations showed that regenerating energy at slower walking speeds and decline slopes could significantly extend the battery-powered operating times of robotic lower-limb exoskeletons (i.e., up to 99% increase in total number of steps), therein improving locomotor efficiency.
Dietary polyphenols drive alterations in behavior, transcriptional regulation, and commensal microbiota in models of opioid use

Opioid Use Disorder (OUD) is a neuropsychiatric condition associated with tremendous medical and social consequences. Despite this burden, current pharmacotherapies for OUD are ineffective or intolerable for many patients. As such, interventions aimed at promoting overall health and resilience against OUD are of immense clinical and societal interest. Recently, treatment with a Bioactive Dietary Polyphenol Preparation (BDPP) was shown to promote behavioral resilience and adaptive neuroplasticity in multiple models of neuropsychiatric disease. Here, we assessed effects of BDPP treatment on behavioral and molecular responses to repeated morphine treatment. We find that BDPP pre-treatment alters responses across the dose range for both locomotor sensitization and conditioned place preference. Most notably, polyphenol treatment consistently reduced formation of preference at low dose (5mg/kg) morphine but enhanced it at high dose (15mg/kg). In parallel, we performed transcriptomic profiling of the nucleus accumbens, which again showed a dose x polyphenol interaction. At high dose morphine, BDPP pre-treatment potentiated gene expression changes induced by morphine particularly for genes related to synaptic function. We also profiled microbiome composition and function, as polyphenols are metabolized by the microbiome and can act as prebiotics. The profile revealed polyphenol treatment markedly altered microbiome composition and function, particularly in the low dose morphine group. Finally, we investigated involvement of the SIRT1 histone deacetylase, and the role of specific polyphenol metabolites in these behavioral phenotypes. Taken together, these results demonstrate that polyphenols have robust dose-dependent effects on behavioral and physiological responses to morphine and lay the foundation for future translational work.
Neither kin selection nor familiarity explain affiliative biases towards maternal siblings in wild mountain gorillas

Evolutionary theories predict that sibling relationships will reflect a complex balance of cooperative and competitive dynamics. In most mammals, dispersal and death patterns mean that sibling relationships occur in a relatively narrow window during development, and/or only with same-sex individuals. Besides humans, one notable exception are mountain gorillas, in which non-sex biased dispersal, relatively stable group composition, and the long reproductive tenures of alpha males mean that animals routinely reside with both same and opposite-sex, and full and half siblings, throughout their lives. Using nearly 40,000 hours of observation data collected over 14 years on 699 sibling and 1258 non-sibling pairs of wild mountain gorillas, we demonstrate that individuals have strong affiliative preferences for full and maternal siblings over paternal siblings or unrelated animals, consistent with an inability to discriminate paternal kin. Intriguingly, however, aggression data imply the opposite. Aggression rates were statistically indistinguishable among all types of dyads except one: in mixed-sex dyads, non-siblings engaged in substantially more aggression than siblings of any type. This pattern suggests mountain gorillas may be capable of distinguishing paternal kin, but nonetheless choose not to affiliate with them over non-kin. A preference for maternal kin occurs despite gorillas not possessing low male reproductive skew, the key characteristic believed to underlie such biases. These results call into question reasons for strong maternal kin biases when paternal kin are identifiable, familiar, and similarly likely to be long-term social partners, and suggest behavioral mismatches at play during a transitional period in mountain gorilla society.
Compositional shifts associated with major evolutionary transitions in plants

Heterogeneity in gene trees, morphological characters, and composition has been associated with several major clades across the plant tree of life. Here, we examine heterogeneity in composition across a large transcriptomic dataset of plants in order to better understand whether locations of shifts in composition are shared across gene regions and whether directions of shifts within clades are shared across gene regions. We estimate mixed models of composition for both DNA and amino acids across a recent large scale transcriptomic dataset for plants. We find shifts in composition across both DNA and amino acid datasets, with more shifts detected in DNA. We find that Chlorophytes and lineages within experience the most shifts. However, many shifts occur at the origins of land, vascular, and seed plants. While genes in these clades do not typically share the same composition, they tend to shift in the same direction. We discuss potential causes of these patterns. Compositional heterogeneity has been highlighted as a potential problem for phylogenetic analysis, but the variation presented here highlights the need to further investigate these patterns for the signal of biological processes. Plain language summary We demonstrate that many nucleotide and amino acid compositional shifts in plants occur at the origins of major clades and while individual genes do not share the same composition they often shift in the same direction. We suggest that these patterns warrant further exploration as the signal of important biological processes during the evolution of plants.
Understanding the genome-wide transcription response to varying cAMP levels using phenomenological models in bacteria

Attempts to understand gene regulation by global transcription factors (TF) have largely been limited to expression studies under binary conditions of presence and absence of the TF. Studies addressing genome-wide transcriptional responses to changing TF concentration at high resolution are lacking. Here, we create a dataset containing the entire E.coli transcriptome as it responds to 10 different cAMP concentrations spanning the biological range. We use the Hill’s model to accurately summarise individual gene responses into 3 intuitively understandable parameters - k, n and Emax reflecting the midpoint of dynamic range, non-linearity and sensitivity of a gene. cAMP-regulated genes show a small dynamic range with midpoints centred around wild-type cAMP concentrations, with genes activating in a switch-like fashion. Using this approach we show that cAMP-CRP affinity at promoters is well correlated to the sensitivity(Emax) of genes but not to the midpoints of dynamic range(k). Finally, genes belonging to different functional classes are tuned to different k, n and Emax. We show phenomenological models to be a better alternative for studying gene expression trends compared to classical clustering methods with the phenomenological constants providing greater insights into how genes are tuned in a regulatory network.
Single cell preparations of Mycobacterium tuberculosis damage the mycobacterial envelope and disrupt macrophage interactions

For decades, investigators have studied the interaction of Mycobacterium tuberculosis (Mtb) with macrophages, which serve as a major cellular niche for the bacilli. Because Mtb are prone to aggregation, investigators rely on varied methods to disaggregate the bacteria for these studies. Here, we examined the impact of routinely used preparation methods on bacterial cell envelop integrity, macrophage inflammatory responses, and intracellular Mtb survival. We found that both gentle sonication and filtering damaged the mycobacterial cell envelope and markedly impacted the outcome of macrophage infections. Unexpectedly, sonicated bacilli were hyperinflammatory, eliciting dramatically higher TLR2-dependent gene expression and elevated secretion of IL-1β and TNF-α. Despite evoking enhanced inflammatory responses, sonicated bacilli replicated normally in macrophages. In contrast, Mtb that had been passed through a filter induced little inflammatory response, and they were attenuated in macrophages. Previous work suggests that the mycobacterial cell envelope lipid, phthiocerol dimycocerosate (PDIM), dampens macrophage inflammatory responses to Mtb. However, we found that the impact of PDIM depended on the method used to prepare Mtb. In conclusion, widely used methodologies to disaggregate Mtb may introduce experimental artifacts in Mtb-host interaction studies, including alteration of host inflammatory signaling, intracellular bacterial survival, and interpretation of bacterial mutants.
Life cycle exposure to cyhalofop-butyl induced reproductive toxicity toward zebrafish

Cyhalofop-butyl (CyB) is an herbicide widely used in paddy fields, which may transfer to aquatic ecosystems and cause harm to aquatic organisms. In this study, zebrafish (Danio rerio) were exposed to CyB (0.1, 1 and 10 ug/L) related to the environment throughout its adult life cycle from embryo to sexual maturity. The effects of CyB on zebrafish growth, reproduction and offspring development were studied. It was found that female spawning was inhibited and adult male fertility decreased. In addition, we detected the expression of sex steroid hormones and genes related to hypothalamus-pituitary-gonad-liver (HPGL) axis. After 150days of exposure, the hormone balance of parent zebrafish (F0) was disturbed and the concentrations of 17β-estradiol (E2) and vitellogenin (VTG) in zebrafish were decreased. F1 embryos showed abnormal developmental results, including decreased heart rate, decreased body length, spontaneous motor inhibition, while the developmental abnormalities of F1 embryos were relieved when exposed to CyB-free clear water. The change of sex hormone is regulated by gene expression related to HPGL axis. These results confirmed that long-term exposure to CyB in the environmental concentrations can damage the reproductive capacity of F0 generation zebrafish by disrupting the transcription of genes related to HPGL axis, which may lead to abnormal development of F1. Overall, these data may provide a new understanding of the reproductive toxicity of zebrafish parents and offspring after long-term exposure to CyB. Highlights Environmental level of CyB exposure caused gonadal impairment. CyB exposure suppressed spawning ability of zebrafish. CyB exposure changed the plasma hormone level of zebrafish and altered HPGL axis in both genders. Parental CyB exposure led to abnormal development of F1.