Miracle-dz/UniFAR-FTUs huggingface dataset:
A biologically oriented algorithm for spatial sound segregation

Listening in an acoustically cluttered scene remains a difficult task for both machines and hearing-impaired listeners. Normal-hearing listeners accomplish this task with relative ease by segregating the scene into its constituent sound sources, then selecting and attending to a target source. An assistive listening device that mimics the biological mechanisms underlying this behavior may provide an effective solution for those with difficulty listening in acoustically cluttered environments (e.g., a cocktail party). Here, we present a binaural sound segregation algorithm based on a hierarchical network model of the auditory system. In the algorithm, binaural sound inputs first drive populations of neurons tuned to specific spatial locations and frequencies. Lateral inhibition then sharpens the spatial response of the neurons. Finally, the spiking response of neurons in the output layer are then reconstructed into audible waveforms via a novel reconstruction method. We evaluate the performance of the algorithm with psychoacoustic measures of normal-hearing listeners. This two-microphone algorithm is shown to provide listeners with perceptual benefit similar to that of a 16-microphone acoustic beamformer in a difficult listening task. Unlike deep-learning approaches, the proposed algorithm is biologically interpretable and does not need to be trained on large datasets. This study presents a biologically based algorithm for sound source segregation as well as a method to reconstruct highly intelligible audio signals from spiking models. Author Summary Animal and humans can navigate complex auditory environments with relative ease, attending to certain sounds while suppressing others. Normally, various sounds originate from various spatial locations. This paper presents an algorithmic model to perform sound segregation based on how animals make use of this spatial information at various stages of the auditory pathway. We showed that the performance of this two-microphone algorithm provides as much benefit to normal-hearing listeners a multi-microphone algorithm. Unlike mathematical and machine-learning approaches, our model is fully interpretable and does not require training with large datasets. Such an approach may benefit the design of machine hearing algorithms. To interpret the spike-trains generated in the model, we designed a method to recover sounds from model spikes with high intelligibility. This method can be applied to spiking neural networks for audio-related applications, or to interpret each node within a spiking model of the auditory cortex.
Molecular characterisation and diversity analysis of Burkina Faso rice landraces using 23 microsatellite markers and establishment of a core collection

Understanding the genetic diversity of rice and its population structure is a key to the sustainable in situ and ex situ management of genetic resources. In this study, the molecular analysis of 330rice varieties collected in 59 villages across Burkina Faso was undertaken, using 23microsatellite markers. These markers were found to be polymorphic with an average allele number of 9.4and a mean PIC per locus of 0.58, ranging from 0.034 (RM338) to 0.838(RM1). The 23 SSR markers were powerful enough to separate the two species (O. sativa and O. glaberrima), and to identify a group of most probably resulting from natural crosses between the two species. The glaberrima group were divided into two subgroups in relation with their cultivation ecosystem, deep-water and lowland while O. sativa japonica accessions were clustered in G2. Accessions of O. s.indica species were clustered in three groups (G3, G4 and G5). G3 was composed of accessions of late maturing cropped in lowland environment. G5 accessions were tall and late maturing adapted to deep water condition.G4accessions were of short stature and early maturing adapted to lowland conditions. Using the molecular data and the framework it provided, a core collection of 52 accessions was established that represents the diversity of rice in Burkina Faso. This core collection represents 16% of the collection and account for 89% of the alleles of the whole collection. A core collection of this size could be easily manageable by the national agricultural research institute for conservation in situ or ex situ.
Baculovirus actin-rearrangement-inducing factor ARIF-1 induces the formation of dynamic clusters of invadosome-like structures

The baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV), a pathogen of lepidopteran insects, has a striking dependence on the host cell actin cytoskeleton. During the delayed-early stage of infection, AcMNPV was shown to induce the accumulation of actin at the cortex of infected cells. However, the dynamics and molecular mechanism of cortical actin assembly remained unknown. Here, we show that AcMNPV induces dynamic cortical clusters of dot-like actin structures that resemble clusters of invadosomes in mammalian cells. Furthermore, we find that the AcMNPV protein actin-rearrangement-inducing factor-1 (ARIF-1), which was previously shown to be necessary and sufficient for cortical actin assembly and efficient viral infection in insect hosts, is both necessary and sufficient for invadosome-like structure formation. We mapped the sequences within the C-terminal cytoplasmic region of ARIF-1 that are required for invadosome-like structure formation and identified individual tyrosine and proline residues that are required for organizing these structures. Additionally, we found that ARIF-1 and the invadosome-associated proteins cortactin and the Arp2/3 complex localize to invadosome-like structures, and Arp2/3 complex is required for their formation. These ARIF-1-induced invadosome-like structures may be important for the function of ARIF-1 in systemic virus spread.
Heterozygous Cell Models of STAT1 Gain-of-Function Reveal a Broad Spectrum of Interferon-Signature Gene Transcriptional Responses

Signal Transducer and Activator of Transcription 1 (STAT1) gain-of-function (GOF) is an autosomal dominant immune disorder marked by wide infectious predisposition, autoimmunity, vascular disease and malignancy. Its molecular hallmark, elevated phospho-STAT1 (pSTAT1) following interferon (IFN) stimulation, is seen consistently in all patients and may not fully account for the broad phenotypic spectrum associated with this disorder. While over 100 mutations have been implicated in STAT1 GOF, genotype-phenotype correlation remains limited, and current overexpression models may be of limited use in gene expression studies. We generated heterozygous mutants in diploid HAP1 cells using CRISPR/Cas9 base-editing, targeting the endogenous STAT1 gene. Our models recapitulated the molecular phenotype of elevated pSTAT1, and were used to characterize the expression of five IFN-stimulated genes under a number of conditions. At baseline, transcriptional polarization was evident among mutants compared with wild type, and this was maintained following prolonged serum starvation. This suggests a possible role for unphosphorylated STAT1 in the pathogenesis of STAT1 GOF. Following stimulation with IFNα or IFNγ, differential patterns of gene expression emerged among mutants, including both gain and loss of transcriptional function. This work highlights the importance of modelling heterozygous conditions, and in particular transcription factor-related disorders, in a manner which accurately reflects patient genotype and molecular signature. Furthermore, we propose a complex and multifactorial transcriptional profile associated with various STAT1 mutations, adding to global efforts in establishing STAT1 GOF genotype-phenotype correlation and enhancing our understanding of disease pathogenesis.
Long-read isoform sequencing reveals survival-associated splicing in breast cancer

Tumors display widespread transcriptome alterations, but the full repertoire of isoform-level alternative splicing in cancer is not known. We developed a long-read RNA sequencing and analytical platform that identifies and annotates full-length isoforms, and infers tumor-specific splicing events. Application of this platform to breast cancer samples vastly expands the known isoform landscape of breast cancer, identifying thousands of previously unannotated isoforms of which ~30% impact protein coding exons and are predicted to alter protein localization and function, including of the breast cancer-associated genes ESR1 and ERBB2. We performed extensive cross-validation with -omics data sets to support transcription and translation of novel isoforms. We identified 3,059 breast tumor-specific splicing events, including 35 that are significantly associated with patient survival. Together, our results demonstrate the complexity, cancer subtype-specificity, and clinical relevance of novel isoforms in breast cancer that are only annotatable by LR-seq, and provide a rich resource of immuno-oncology therapeutic targets.
Disproportionate CH4 Sink Strength from an Endemic, Sub-Alpine Australian Soil Microbial Community

Soil-to-atmosphere methane (CH4) fluxes are dependent on opposing microbial processes of production and consumption. Here we use a soil-vegetation gradient in an Australian sub-alpine ecosystem to examine links between composition of soil microbial communities, and the fluxes of greenhouse gases they regulate. For each soil-vegetation type (forest, grassland, and bog), we measured carbon dioxide (CO2) and CH4 fluxes and their production/consumption at 5-cm intervals to a depth of 30 cm. All soils were sources of CO2, ranging from 49-93 mg CO2 m−2 h−1. Forest soils were strong net sinks for CH4 at rates up to −413 μg CH4 m−2 h−1. Grassland soils varied with some soils acting as sources and some as sinks, but overall averaged −97 μg CH4 m−2 h−1. Bog soils were net sources of CH4 (+340 μg CH4 m−2 h−1). Methanotrophs were dominated by USCα in forest and grassland soils, and Candidatus Methylomirabilis sp. in the bog soils. Methylocystis were also detected at relatively low abundance. The potential disproportionately large contribution of these ecosystems to global CH4 oxidation, and poorly understood microbial community regulating it, highlight our dependence on soil ecosystem services in remote locations can be driven by a unique population of soil microbes.
Costly induction of defense reduces plant growth and alters reproductive traits in mixed-mating Datura stramonium

Herbivory shapes plant trait evolution by altering allocation to growth and defense in ways that affect plant reproduction and fitness. Initiation of these trade-offs may be particularly strong in juvenile plants with high phenotypic plasticity. Herbivory costs are often measured in terms of plant size or flower numbers, but other herbivore-induced floral changes can alter interactions with pollinators and have important implications for mating systems. In mixed-mating plants that can both self-fertilize and outcross, herbivory can maintain mating system variation if herbivore damage and defensive induction change a plant’s likelihood of selfing versus outcrossing. Here, I use mixed-mating Datura stramonium to evaluate how early defensive induction and herbivory result in trade-offs among plant defense, growth and reproduction. I used a 2×2 factorial manipulation of early chemical defense induction and season-long insecticide in the field. Growth costs of chemical induction were seen even before plants received damage, indicating an inherent cost of defense. Induction and herbivory changed multiple aspects of floral biology associated with a plant’s selfing or outcrossing rate. This including reduced floral allocation, earlier flowering, and reduced anther-stigma separation (herkogamy). Although these floral changes are associated with decreased attractiveness to pollinators, plants exposed to natural herbivory did not have decreased seed set. This is likely because their floral morphologies became more conducive to selfing (via reduced herkogamy). These vegetative and floral changes following damage and defensive induction can impact interactions among plants (by altering mating environment) and interactions with pollinators (via changes in floral allocation and floral phenology).
First report in France of Caenoplana decolorata, a recently described species of alien terrestrial flatworm (Platyhelminthes, Geoplanidae)

Alien land flatworms (family Geoplanidae) are invading many countries in the world. Some can easily be identified by their morphology and colour pattern, but some are more cryptic and necessitate a molecular approach. Caenoplana decolorata Mateos et al., 2020 was recently described, from specimens found in Spain, as a sibling species to C. coerulea Moseley, 1877. We found that one specimen collected in Nantes, France in 2014 had a 100% identity of its COI sequence with one specimen of the original description of C. decolorata, and thus we record here the species for the first time in France.
Evolution of the complex transcription network controlling biofilm formation in Candida species

We examine how a complex transcription network composed of seven “master” regulators and hundreds of target genes evolved over a span of approximately 70 million years. The network controls biofilm formation in several Candida species, a group of fungi that are present in humans both as constituents of the microbiota and as opportunistic pathogens. The ability to form biofilms is crucial for microbial colonization of different host niches, particularly when an implanted medical device is present. We examined and compared the network underlying biofilm formation across four Candida species (C. albicans, C. dubliniensis, C. tropicalis, and C. parapsilosis), all of which form biofilms composed of multiple cell types. To describe the salient features of the network across different species, we employed four approaches: (1) we phenotypically characterized the biofilms formed by these species using a variety of methods; (2) we knocked out — one by one — the master regulators identified in C. albicans in the four species and monitored their effect on biofilm formation; (3) we identified the target genes of 18 master regulator orthologs across the four species by performing ChIP-seq experiments; and (4) we carried out transcriptional profiling across each species during biofilm formation. Additional network information was obtained by analyzing an interspecies hybrid formed between the two most closely related species, C. albicans and C. dubliniensis. We observed two major types of changes that have occurred in the biofilm circuit since the four species last shared a common ancestor. Master regulator “substitutions” occurred over relatively long evolutionary times, resulting in different species having overlapping, but different sets of master regulators of biofilm formation. Second, massive changes in the connections between the master regulators and their target genes occurred over much shorter timescales. Both types of change are crucial to account for the structures of the biofilm networks in extant species. We believe this analysis is the first detailed, empirical description of how a complex transcription network has evolved.
Full species-wide leaf and seed ionomic diversity of Arabidopsis thaliana

Soil is a heterogenous reservoir of essential elements needed for plant growth and development. Plants have evolved mechanisms to balance their nutritional needs based on availability of nutrients. This has led to genetically-based variation in the elemental composition ‘ionome’, of plants, both within and between species. We explore this natural variation using a panel of wild-collected, geographically widespread Arabidopsis thaliana accessions from the 1001 Genomes Project including over 1,135 accessions, and the 19 parental accessions of the Multi-parent Advanced Generation Inter-Cross (MAGIC) panel, all with full-genome sequences available. We present an experimental design pipeline for high-throughput ionomic screenings and analyses with improved normalisation procedures to account for errors and variability in conditions often encountered in large-scale, high-throughput data collection. We report quantification of the complete leaf and seed ionome of the entire collection using this pipeline and a digital tool-IonExplorer to interact with the dataset. We describe the pattern of natural ionomic variation across the A. thaliana species and identify several accessions with extreme ionomic profiles. It forms a valuable resource for exploratory QTL, GWA studies to identify genes underlying natural variation in leaf and seed ionome and genetic adaptation of plants to soil conditions.
Beta and Theta Oscillations Correlate With Subjective Time During Musical Improvisation in Ecological and Controlled Settings: A Single Subject Study

In this paper, we describe the results of a single subject study attempting at a better understanding of the subjective state during musical improvisation. In a first experiment, we setup an ecological paradigm measuring EEG on a musician in free improvised concerts with an audience, followed by retrospective rating of the mental state of the improviser. We introduce Subjective Temporal Resolution (STR), a retrospective rating assessing the instantaneous attention of the musician towards short or long musical events. We identified high and low STR states using Hidden Markov Models in two performances, and were able to decode those states using supervised learning on instantaneous EEG power spectrum, showing increases in theta and alpha power with high STR values. In a second experiment, we found an increase of theta and beta power when experimentally manipulating STR in a musical improvisation imagery experiment. These results are interpreted with respect to previous research on flow state in creativity, as well as with the temporal processing literature. We suggest that a component of the subjective state of musical improvisation may be reflected in an underlying mechanism responsible for modulating subjective temporal processing of musical events.
Assembly of higher-order SMN oligomers is essential for metazoan viability and requires an exposed structural motif present in the YG zipper dimer

Protein oligomerization is one mechanism by which homogenous solutions can separate into distinct liquid phases, enabling assembly of membraneless organelles. Survival Motor Neuron (SMN) is the eponymous component of a large macromolecular complex that chaperones biogenesis of eukaryotic ribonucleoproteins, and localizes to distinct membraneless organelles in both the nucleus and cytoplasm. SMN forms the oligomeric core of this complex, and missense mutations within its YG box domain are known to cause Spinal Muscular Atrophy (SMA). The SMN YG box utilizes a variation of the glycine zipper motif to form dimers, but the mechanism of higher-order oligomerization remains unknown. Here, we use a combination of molecular genetic, bioinformatic, biophysical, and computational approaches to show that formation of higher-order SMN oligomers depends on a set of YG box residues that are not involved in dimerization. Mutation of key residues within this new structural motif restricts assembly of SMN to dimers and causes locomotor dysfunction and viability defects in animal models.
An End-to-end Oxford Nanopore Basecaller Using Convolution-augmented Transformer

Oxford Nanopore sequencing is fastly becoming an active field in genomics, and it’s critical to basecall nucleotide sequences from the complex electrical signals. Many efforts have been devoted to developing new basecalling tools over the years. However, the basecalled reads still suffer from a high error rate and slow speed. Here, we developed an open-source basecalling method, CATCaller, by simultaneously capturing global context through Attention and modeling local dependencies through dynamic convolution. The method was shown to consistently outper-form the ONT default basecaller Albacore, Guppy, and a recently developed attention-based method SACall in read accuracy. More importantly, our method is fast through a heterogeneously computational model to integrate both CPUs and GPUs. When compared to SACall, the method is nearly 4 times faster on a single GPU, and is highly scalable in parallelization with a further speedup of 3.3 on a four-GPU node.
Potential of in vivo- and in vitro-cultured entomopathogenic nematodes to infect Lobesia vanillana (Lepidoptera: Tortricidae) under laboratory conditions

The in vivo- and in vitro-cultured South African entomopathogenic nematodes (EPNs), Steinernema yirgalemense and Steinernema jeffreyense (Rhabditida: Steinernematidae), were evaluated against larvae and pupae of Lobesia vanillana in laboratory bioassays. For larvae, high mortality was observed for all treatments: In vitro-cultured S. yirgalemense (98%) performed better than S. jeffreyense (73%), while within in vivo cultures, there was no difference between nematode species (both 83%). No significant difference was detected between in vivo- and in vitro cultures of the same nematode species. The LD50 of the in vitro-cultured S. yirgalemense, the best performing species, was 7.33 nematodes per larva. Mortality by infection was established by dissecting cadavers and confirming the presence of nematodes, which was > 90% for all treatments. Within in vitro cultures, both S. yirgalemense and S. jeffreyense were able to produce a new cohort of infective juveniles from L. vanillana larvae. Pupae, however, were found to be considerably less susceptible to EPN infection. The relative success of local in vivo- and in vitro-cultured EPN species against a tortricid species in laboratory assays is encouraging for further research and development of this technology.
Synapses from the high-order thalamic nucleus and motor cortex are co-clustered in the distal tuft dendrites of the mouse somatosensory cortex

The posterior medial nucleus of the thalamus (POm) and vibrissal primary motor cortex (vM1) convey essential information to the barrel cortex (S1BF) regarding whisker position and movement. Therefore, understanding the relative spatial relationships of these two inputs is critical prerequisites to acquire insight into how S1 synthesizes information to interpret the location of an object. Using array tomography, we identified the locations of synapses from vM1 and POm on distal tuft dendrites of L5 pyramidal neurons. We found that synapses from vM1 and POm are spatially clustered on the same set of dendrites with unusually high density. Furthermore, the clusters of vM1 and POm synapses colocalize each other. These findings suggest that synaptic clusters, but not dendritic branches, act as functional units and cooperatively contribute to nonlinear dendritic responses.
Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences

Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2,770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ranging from 7 bp to 126 bp, and with array lengths up to 230 bp. We detected 35,638 VNTR loci and classified 5,676 as common (occurring in >5% of the population). Common VNTR loci were found to be enriched in genomic regions with regulatory function, i.e., transcription start sites and enhancers. Investigation of the common VNTRs in the context of population ancestry revealed that 1,096 loci contained population-specific alleles and that those could be used to classify individuals into super-populations with near perfect accuracy. Comparison of genotyping results with proximal genes indicated that in 120 cases (118 genes), expression differences correlated with VNTR genotype. We validated our predictions in several ways, including experimentally, through identification of predicted alleles in long reads, and by comparisons showing consistency between sequencing platforms. This study is the most comprehensive analysis of minisatellites VNTRs in the human population to date.