TrimTail: Low-Latency Streaming ASR with Simple but Effective Spectrogram-Level Length Penalty

In this paper, we present TrimTail, a simple but effective emission regularization method to improve the latency of streaming ASR models. The core idea of TrimTail is to apply length penalty (i.e., by trimming trailing frames, see Fig. 1-(b)) directly on the spectrogram of input utterances, which does not require any alignment. We demonstrate that TrimTail is computationally cheap and can be applied online and optimized with any training loss or any model architecture on any dataset without any extra effort by applying it on various end-to-end streaming ASR networks either trained with CTC loss [1] or Transducer loss [2]. We achieve 100 $\sim$ 200ms latency reduction with equal or even better accuracy on both Aishell-1 and Librispeech. Moreover, by using TrimTail, we can achieve a 400ms algorithmic improvement of User Sensitive Delay (USD) with an accuracy loss of less than 0.2.Comment: submitted to ICASSP 202

Selectivity of Monaural Synaptic Inputs Underlying Binaural Auditory Information Integration in the Central Nucleus of Inferior Colliculus

Neurons in the central nucleus of the inferior colliculus (ICC) receive ascending inputs from the ipsilateral and contralateral auditory pathway. However, the contributions of excitatory or inhibitory synaptic inputs evoked by ipsilateral and contralateral stimuli to auditory responses of ICC neurons remain unclear. Using in vivo whole-cell voltage-clamp recordings, we investigated excitatory and inhibitory synaptic currents in neurons of the ICC in response to binaural stimulation by performing an intensity-intensity scan. To systematically analyze the contribution of the ipsilateral and contralateral ear, the sound intensity was randomly delivered to each side from 0 dB sound pressure level (SPL) to 70 dB SPL. Although the synaptic responses were dominated by contralateral inputs at weak sound intensities, they could be increased (or decreased) by additional ipsilateral stimulation at higher intensities. Interestingly, the synaptic responses to contralateral acoustic inputs were not linearly superimposed with the ipsilateral ones. By contrast, the responses showed either a contralateral or ipsilateral profile, depending on which one was more dominant. This change occurred at a certain intensity “switch” point. Thus, the binaural auditory responses of the ICC neurons were not simply mediated by the summation of the inputs evoked by ipsilateral and contralateral stimulations. This suggested that the ICC might inherit the acoustic information integrated at the brainstem, causing the selectivity of monaural excitation and inhibition to underlie the neuronal binaural acoustic response

Laser powder bed fusion-built Ti6Al4V bone scaffolds composed of sheet and strut-based porous structures: Morphology, mechanical properties, and biocompatibility

Laser powder bed fusion (L-PBF)-built triply periodic minimal surface (TPMS) structures are designed by implicit functions and are endowed with superior characteristics, such as adjustable mechanical properties and light-weight features for bone repairing; thus, they are considered as potential candidates for bone scaffolds. Unfortunately, previous studies have mainly focused on different TPMS structures. The fundamental understanding of the differences between strut and sheet-based structures remains exclusive, where both were designed by one formula. This consequently hinders their practical applications. Herein, we compared the morphology, mechanical properties, and biocompatibility of sheet and strut-based structures. In particular, the different properties and in vivo bone repair effects of the two structures are uncovered. First, the morphology characteristics demonstrate that the manufacturing errors of sheet-based structures with diverse porosities are comparable, and semi-melting powders as well as the ball phenomenon are observed; in comparison, strut-based samples exhibit cracks and thickness shrinking. Second, the mechanical properties indicate that the sheet-based structures have a greater elastic modulus, energy absorption, and better repeatability compared to strut-based structures. Furthermore, layer-by-layer fracturing and diagonal shear failure modes are observed in strut-based and sheet-based structures, respectively. The in vivo experiment demonstrates enhanced bone tissues in the strut-based scaffold. This study significantly enriches our understanding of TPMS structures and provides significant insights in the design of bone scaffolds under various bone damaging conditions

Comparative Transcriptomic Profiling in Ovarian Tissues of Lohmann Hens and Chengkou Mountain Chicken

Background: As a crucial economic characteristic and a major indicator of reproductive performance in layers, egg production is controlled by a series of complex regulatory heredity basis. In particular, the interacting regulatory function between noncoding RNAs (ncRNAs) and coding RNA plays important roles in regulating laying performance. Methods: In this study, the RNA sequencing (RNA-seq) of ovarian tissues from Lohmann hens (n = 3) and Chengkou Mountain chicken (n = 3) under the laying peak period was performed to identify RNA transcriptional differences among different laying-performance populations. Results: Results showed that the expression level of 303 mRNAs, 68 long ncRNAs (lncRNAs), 533 circular RNAs (circRNAs), and 79 microRNAs (miRNAs) was significantly different among the groups. Functional enrichment analysis of these differentially expressed (DE) mRNAs revealed that the laying process was implicated in numerous significantly enriched pathways (p < 0.05), such as the neuroactive ligand-receptor interaction, steroid hormone biosynthesis, and calcium-signaling pathway. Furthermore, the lncRNA/circRNA–miRNA–mRNA regulatory networks related to the regulation of laying performance were constructed. Some randomly selective DE RNAs were verified by Real Time Quantitative (RT-qRCR), indicating that the bioinformatics analysis results of RNA-seq data were credible. Conclusions: This study could increase our understanding of the heredity basis of transcriptome in the laying performance of chicken

Polyploid evolution in Oryza officinalis complex of the genus Oryza

BACKGROUND: Polyploidization is a prominent process in plant evolution, whereas the mechanism and tempo-spatial process remained poorly understood. Oryza officinalis complex, a polyploid complex in the genus Oryza, could exemplify the issues not only for it covering a variety of ploidy levels, but also for the pantropical geographic pattern of its polyploids in Asia, Africa, Australia and Americas, in which a pivotal genome, the C-genome, witnessed all the polyploidization process. RESULTS: Tracing the C-genome evolutionary history in Oryza officinalis complex, this study revealed the genomic relationships, polyploid forming and diverging times, and diploidization process, based on phylogeny, molecular-clock analyses and fluorescent in situ hybridization using genome-specific probes. Results showed that C-genome split with B-genome at ca. 4.8 Mya, followed by a series of speciation of C-genome diploids (ca. 1.8-0.9 Mya), which then partook in successive polyploidization events, forming CCDD tetraploids in ca. 0.9 Mya, and stepwise forming BBCC tetraploids between ca. 0.3-0.6 Mya. Inter-genomic translocations between B- and C-genomes were identified in BBCC tetraploid, O. punctata. Distinct FISH (fluorescent in situ hybridization) patterns among three CCDD species were visualized by C-genome-specific probes. B-genome was modified before forming the BBCC tetraploid, O. malampuzhaensis. CONCLUSION: C-genome, shared by all polyploid species in the complex, had experienced different evolutionary history particularly after polyploidization, e.g., inter-genomic exchange in BBCC and genomic invasion in CCDD tetraploids. It diverged from B-genome at 4.8 Mya, then participated in the tetraploid formation spanning from 0.9 to 0.3 Mya, and spread into tropics of the disjunct continents by transcontinentally long-distance dispersal, instead of vicariance, as proposed by this study, given that the continental splitting was much earlier than the C-genome species radiation. We also find reliable evidence indicated that an extinct BB diploid species in Asia was presumptively the direct genomic donor of their sympatric tetraploids

Polyploid evolution in <it>Oryza officinalis </it>complex of the genus <it>Oryza</it>

Abstract Background Polyploidization is a prominent process in plant evolution, whereas the mechanism and tempo-spatial process remained poorly understood. Oryza officinalis complex, a polyploid complex in the genus Oryza, could exemplify the issues not only for it covering a variety of ploidy levels, but also for the pantropical geographic pattern of its polyploids in Asia, Africa, Australia and Americas, in which a pivotal genome, the C-genome, witnessed all the polyploidization process. Results Tracing the C-genome evolutionary history in Oryza officinalis complex, this study revealed the genomic relationships, polyploid forming and diverging times, and diploidization process, based on phylogeny, molecular-clock analyses and fluorescent in situ hybridization using genome-specific probes. Results showed that C-genome split with B-genome at ca. 4.8 Mya, followed by a series of speciation of C-genome diploids (ca. 1.8-0.9 Mya), which then partook in successive polyploidization events, forming CCDD tetraploids in ca. 0.9 Mya, and stepwise forming BBCC tetraploids between ca. 0.3-0.6 Mya. Inter-genomic translocations between B- and C-genomes were identified in BBCC tetraploid, O. punctata. Distinct FISH (fluorescent in situ hybridization) patterns among three CCDD species were visualized by C-genome-specific probes. B-genome was modified before forming the BBCC tetraploid, O. malampuzhaensis. Conclusion C-genome, shared by all polyploid species in the complex, had experienced different evolutionary history particularly after polyploidization, e.g., inter-genomic exchange in BBCC and genomic invasion in CCDD tetraploids. It diverged from B-genome at 4.8 Mya, then participated in the tetraploid formation spanning from 0.9 to 0.3 Mya, and spread into tropics of the disjunct continents by transcontinentally long-distance dispersal, instead of vicariance, as proposed by this study, given that the continental splitting was much earlier than the C-genome species radiation. We also find reliable evidence indicated that an extinct BB diploid species in Asia was presumptively the direct genomic donor of their sympatric tetraploids.</p

Polyploid evolution in Oryza officinalis complex of the genus Oryza

BACKGROUND: Polyploidization is a prominent process in plant evolution, whereas the mechanism and tempo-spatial process remained poorly understood. Oryza officinalis complex, a polyploid complex in the genus Oryza, could exemplify the issues not only for it covering a variety of ploidy levels, but also for the pantropical geographic pattern of its polyploids in Asia, Africa, Australia and Americas, in which a pivotal genome, the C-genome, witnessed all the polyploidization process. RESULTS: Tracing the C-genome evolutionary history in Oryza officinalis complex, this study revealed the genomic relationships, polyploid forming and diverging times, and diploidization process, based on phylogeny, molecular-clock analyses and fluorescent in situ hybridization using genome-specific probes. Results showed that C-genome split with B-genome at ca. 4.8 Mya, followed by a series of speciation of C-genome diploids (ca. 1.8-0.9 Mya), which then partook in successive polyploidization events, forming CCDD tetraploids in ca. 0.9 Mya, and stepwise forming BBCC tetraploids between ca. 0.3-0.6 Mya. Inter-genomic translocations between B- and C-genomes were identified in BBCC tetraploid, O. punctata. Distinct FISH (fluorescent in situ hybridization) patterns among three CCDD species were visualized by C-genome-specific probes. B-genome was modified before forming the BBCC tetraploid, O. malampuzhaensis. CONCLUSION: C-genome, shared by all polyploid species in the complex, had experienced different evolutionary history particularly after polyploidization, e.g., inter-genomic exchange in BBCC and genomic invasion in CCDD tetraploids. It diverged from B-genome at 4.8 Mya, then participated in the tetraploid formation spanning from 0.9 to 0.3 Mya, and spread into tropics of the disjunct continents by transcontinentally long-distance dispersal, instead of vicariance, as proposed by this study, given that the continental splitting was much earlier than the C-genome species radiation. We also find reliable evidence indicated that an extinct BB diploid species in Asia was presumptively the direct genomic donor of their sympatric tetraploids

Comparative RNA-Seq Analysis Uncovers a Complex Regulatory Network for Soybean Cyst Nematode Resistance in Wild Soybean (Glycine soja)

Abstract Soybean cyst nematode (SCN) is the most damaging pest of soybean worldwide. The molecular mechanism of SCN resistance remains largely unknown. We conducted a global RNA-seq comparison between a resistant genotype (S54) and a susceptible genotype (S67) of Glycine soja, the wild progenitor of soybean, to understand its regulatory network in SCN defense. The number of differentially expressed genes (DEGs) in S54 (2,290) was much larger than that in S67 (555). A number of defense-related genes/pathways were significantly induced only in S54, while photosynthesis and several metabolic pathways were affected in both genotypes with SCN infection. These defense-associated DEGs were involved in pathogen recognition, calcium/calmodulin-mediated defense signaling, jasmonic acid (JA)/ethylene (ET) and sialic acid (SA)-involved signaling, the MAPK signaling cascade, and WRKY-involved transcriptional regulation. Our results revealed a comprehensive regulatory network involved in SCN resistance and provided insights into the complex molecular mechanisms of SCN resistance in wild soybean