Miracle-dz/UniFAR-FTUs huggingface dataset:
Developing a Multi-Platform Speech Recording System Toward Open Service of Building Large-Scale Speech Corpora

This paper briefly reports our ongoing attempt at the development of a multi-platform browser-based speech recording system. We designed the system toward a service of providing open service of building large-scale speech corpora at a low-cost for any researchers and developers related to speech processing. The recent increase in the use of crowdsourcing services, e.g., Amazon Mechanical Turk, enable us to reduce the cost of collecting speakers in the web, and there have been many attempts to develop the automated speech collecting platforms or application that is designed for the use the crowdsourcing. However, one of the major problems in the previous studies and developments for the attempts is that most of the systems are not a form of common service of speech recording and corpus building, and each corpus builder is necessary to develop the system in their own environment including a web server. For this problem, we develope a new platform where both the corpus builders and recording participants can commonly use a single system and service by creating their user accounts. A brief introduction of the system is given in this paper as the start of this challenge.
Title : Scaling up freshwater macrozoobenthos metabarcoding with new BF 2 + BR 2 fusion 1 primer sets in 96-well format 2

Title: Scaling up freshwater macrozoobenthos metabarcoding with new BF2+BR2 fusion 1 primer sets in 96-well format 2 Running Title (45 char max): Metabarcoding with fusion primer sets 3 Word count: _____ 4 Authors: Vasco Elbrecht, Dirk Steinke 5 6 Affiliations: 7 1) Centre for Biodiversity Genomics, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada 8 2) Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada 9 *Corresponding author: Vasco Elbrecht (elbrecht@uoguelph.ca), 10 11 Abstract: 12 The viability of DNA metabarcoding for assessment of freshwater macrozoobenthos has been demonstrated over the past 13 years. It matured to a stage where it can be applied to monitoring at a large scale, keeping pace with increased high 14 throughput sequencing (HTS) capacity. However, workflows and sample tagging need to be optimized to accommodate for 15 hundreds of samples within a single sequencing run. We here conceptualize a streamlined metabarcoding workflow, in 16 which samples are processed in 96-well plates. Each sample is replicated starting with tissue extraction. Negative and 17 positive controls are included to ensure data reliability. With our newly developed fusion primer sets for the BF2+BR2 18 primer pair up to three 96-well plates (288 samples) can be uniquely tagged for a single Illumina sequencing run. By 19 including Illumina indices tagging can by extended to thousands of samples. We hope that our metabarcoding workflow 20 will be used as practical guide for future large-scale biodiversity assessments involving freshwater invertebrates. However, 21 we also want to acknowledge that this is just one approach, and that we hope this article will stimulate discussion and 22 publication of alternatives and extensions. 23 24
Fall 2019 CSE 534 Project Report Adaptive Video Streaming

Adaptive video streaming is critical for video websites to provide smooth and high-quality videos streaming experience to their customers. In a typical setup, the server encodes the video with different bitrate settings, then split each of the output videos into short chunks. The video streaming client fetches those chunks and puts them into its local buffer, then the player plays the chunk to the viewer. At each boundary between two chunks, the client needs to select among different bitrates according to current network condition. When the bandwidth is limited, it fetches low bitrate chunks to make sure the buffer is not drained so viewer will not have a pause. When network condition is good, it fetches high bitrate chunks to have high-quality video. The overall goal is to provide highest quality video without smoothness being compromised. It is not trivial to develop efficient adaptive bitrate (ABR) selection algorithms, because the network condition is highly varied, and the choice of selection has long-term consequences. The algorithm needs to predict what the network condition will be in the near future, then make decision based on such predictions and the number of chunks in the buffer. Also the metrics to evaluate the performance are conflicting, some of them value video quality while others prefer smoothness. Most adaptive video streaming clients use hand-crafted bitrate selection functions. These methods perform well under designated conditions, but can fail under unseen networks. Also each of them is usually fixed to improving only one certain user-experience metric.
BANDWIDTH BASED PHO ALGORITHM FOR B 4 G HETEROGENEOUS WIRELESS NETWORKS

In wireless communications, accessing the world wide information by the end user is being a challenge due to seamless mobility among different networks. In order to provide wireless access for the end user moving from one network to another network handover between the networks is very much essential. Bandwidth is the one of most important metric used for analyzing the handover. In this paper, the bandwidth based probability of handover (PHO) algorithm has been implemented for Beyond Fourth Generation (B4G) heterogeneous wireless networks. The probability of handover relies on the traffic load, bandwidth and threshold. Probability of handover analysis has been done for different configurations such as the variation of probability of handover with respect to traffic load, threshold and bandwidth. It is noticed from the results that with increase in threshold, the probability of handover is reduced for constant traffic load. It is also observed that even though network traffic load increases, the probability of handover does not vary much for the equal bandwidth network configuration.
Statistical theory of turbulence-II

The methods described in Part I have been used by Mr. L. F. G. Simmons, of the National Physical Laboratory, to find experimentally the correlation between the turbulent components of velocity u0 and uy at two points distant y apart in a direction transverse to the stream. The measurements were made at mean speed U = 25 feet per second in a wind tunnel behind a honeycomb with 0·9-inch square mesh. The results are shown in fig. 1 where the ordinates are Ry = ¯¯uouy/ ¯¯u2 and the abscissae are the corresponding values of y. It will be seen that the Ry curve is apparently rounded at the top and that Ry falls to 0·08 at y = 0·38 inches. No measurements were made beyond this point, but extrapolation seems to show that Ry = 0 when y is about 0·5 inches, i.e., when y is slightly greater than 1/2M. Integrating the curve of fig. 1 the value of l2 = ∫0 0.5" Ry = 0·175 inch, so that l2/M = 0·175/0·9 = 0·195.
Single-Nucleotide Polymorphism Analysis to Select Conserved Regions for an Improved Real-Time Reverse Transcription–PCR Test Specific for Newcastle Disease Virus

SUMMARY. A bioinformatics approach using single-nucleotide polymorphism (SNP) analysis was performed to improve the current real-time reverse transcription–PCR (RRT-PCR) tests for the rapid detection of Newcastle disease virus (NDV). In total, 422 NDV complete genomes were analyzed using the Virus Pathogen Resource to compare the conservation of the primer and probe sequences and to select regions to develop new RRT-PCR tests. The sensitivity and specificity of the three new RRT-PCR tests targeting the nucleoprotein (NP) and polymerase (L) genes were optimized and were compared with established tests for NDV detection. The SNP analysis was also used to identify the number of mismatches between selected primers/probes and the NDV complete genome sequences. The SNP analysis, averaged over the entire primer or probe, showed the primer/probe sequences of three new tests were more conserved than the primer/probe sequences of the commonly used test targeting the matrix (M) gene. The M RRT-PCR test was compared with the new tests on a panel of 46 viruses, comprising 31 NDV isolates. Limit of detection (LOD) varied from 1.3 to 3.7 log 50% egg-infective doses using five isolates from different genotypes by all tests. The two RRT-PCR tests targeting the L and M genes detected three out of five isolates with the lowest LOD. The NP and M RRT-PCR tests had the lowest and highest rates of genetic variants, respectively, among all probes. Because currently used tests are likely to miss some isolates, the availability of validated alternative tests provides alternatives for detection of viral variants that can be rapidly deployed to diagnostic laboratories.
Research Progress of the Liquid-Phase Exfoliation and Stable Dispersion Mechanism and Method of Graphene

Graphene is a honeycomb hexagonal 2D crystal nanomaterial with a thickness of only 0.334 nm. It has been widely used and studied because of its ultra-thin 2D nano-characteristics and excellent electrical, thermal, optical and mechanical properties. With the continuous in-depth study of graphene, the liquid phase dispersion of graphene has also achieved breakthroughs. This review summarises the research progress of the liquid phase exfoliation mechanism, exfoliation method, stable dispersion mechanism and dispersion method of graphene in recent years. The research situations of Hamaker constant theory in exfoliation mechanism and Hansen solubility coefficient theory in stable dispersion mechanism are mainly discussed. The shortcomings of the research are summarised, and analyses the graphene liquid phase dispersed in the important challenge in the future. The stable dispersion method of graphene is also summarised. In the future, the π-π interaction is the most potential method for studying graphene stabilization.
Consequences of Making the Inactive Active Through Changes in Antisense Oligonucleotide Chemistries

Antisense oligonucleotides are short, single-stranded nucleic acid analogues that can interfere with pre-messenger RNA (pre-mRNA) processing and induce excision of a targeted exon from the mature transcript. When developing a panel of antisense oligonucleotides to skip every dystrophin exon, we found great variation in splice switching efficiencies, with some antisense oligonucleotides ineffective, even when directed to canonical splice sites and transfected into cells at high concentrations. In this study, we re-evaluated some of these ineffective antisense oligonucleotide sequences after incorporation of locked nucleic acid residues to increase annealing potential. Antisense oligonucleotides targeting exons 16, 23, and 51 of human DMD transcripts were synthesized as two different chemistries, 2′-O-methyl modified bases on a phosphorothioate backbone or mixmers containing several locked nucleic acid residues, which were then transfected into primary human myotubes, and DMD transcripts were analyzed for exon skipping. The ineffective 2′-O-methyl modified antisense oligonucleotides induced no detectable exon skipping, while all corresponding mixmers did induce excision of the targeted exons. Interestingly, the mixmer targeting exon 51 induced two unexpected transcripts arising from partial skipping of exon 51 with retention of 95 or 188 bases from the 5′ region of exon 51. These results indicated that locked nucleic acid/2′-O-methyl mixmers are more effective at inducing exon skipping, however, this improvement may come at the cost of activating alternative cryptic splice sites and off-target effects on gene expression.
Model-Free RL or Action Sequences?

The alignment of habits with model-free reinforcement learning (MF RL) is a success story for computational models of decision making, and MF RL has been applied to explain phasic dopamine responses (Schultz et al., 1997), working memory gating (O'Reilly and Frank, 2006), drug addiction (Redish, 2004), moral intuitions (Crockett, 2013; Cushman, 2013), and more. Yet, the role of MF RL has recently been challenged by an alternate model—model-based selection of chained action sequences—that produces similar behavioral and neural patterns. Here, we present two experiments that dissociate MF RL from this prominent alternative, and present unconfounded empirical support for the role of MF RL in human decision making. Our results also demonstrate that people are simultaneously using model-based selection of action sequences, thus demonstrating two distinct mechanisms of habitual control in a common experimental paradigm. These findings clarify the nature of habits and help solidify MF RL's central position in models of human behavior.
Quantitation and Comparison of Phenotypic Heterogeneity Among Single Cells of Monoclonal Microbial Populations

Phenotypic heterogeneity within microbial populations arises even when the cells are exposed to putatively constant and homogeneous conditions. The outcome of this phenomenon can affect the whole function of the population, resulting in, for example, new “adapted” metabolic strategies and impacting its fitness at given environmental conditions. Accounting for phenotypic heterogeneity becomes thus necessary, due to its relevance in medical and applied microbiology as well as in environmental processes. Still, a comprehensive evaluation of this phenomenon requires a common and unique method of quantitation, which allows for the comparison between different studies carried out with different approaches. Consequently, in this study, two widely applicable indices for quantitation of heterogeneity were developed. The heterogeneity coefficient (HC) is valid when the population follows unimodal activity, while the differentiation tendency index (DTI) accounts for heterogeneity implying outbreak of subpopulations and multimodal activity. We demonstrated the applicability of HC and DTI for heterogeneity quantitation on stable isotope probing with nanoscale secondary ion mass spectrometry (SIP–nanoSIMS), flow cytometry, and optical microscopy datasets. The HC was found to provide a more accurate and precise measure of heterogeneity, being at the same time consistent with the coefficient of variation (CV) applied so far. The DTI is able to describe the differentiation in single-cell activity within monoclonal populations resolving subpopulations with low cell abundance, individual cells with similar phenotypic features (e.g., isotopic content close to natural abundance, as detected with nanoSIMS). The developed quantitation approach allows for a better understanding on the impact and the implications of phenotypic heterogeneity in environmental, medical and applied microbiology, microbial ecology, cell biology, and biotechnology.
A New High Throughput Sequencing Assay for Characterizing the Diversity of Natural Vibrio Communities and Its Application to a Pacific Oyster Mortality Event

The Vibrio genus is notable for including several pathogens of marine animals and humans, yet characterization of Vibrio diversity using routine 16S rRNA sequencing methods is often constrained by poor resolution beyond the genus level. Here, a new high throughput sequencing approach targeting the heat shock protein (hsp60) as a phylogenetic marker was developed to more precisely discriminate members of the Vibrio genus in environmental samples. The utility of this new assay was tested using mock communities constructed from known dilutions of Vibrio isolates. Relative to standard and Vibrio-specific 16S rRNA sequencing assays, the hsp60 assay delivered high levels of fidelity with the mock community composition at the species level, including discrimination of species within the Vibrio harveyi clade. This assay was subsequently applied to characterize Vibrio community composition in seawater and delivered substantially improved taxonomic resolution of Vibrio species compared to 16S rRNA analysis. Finally, this assay was applied to examine patterns in the Vibrio community within oysters during a Pacific oyster mortality event. In these oysters, the hsp60 assay identified species-level Vibrio community shifts prior to disease onset, pinpointing V. harveyi as a putative pathogen. Given that shifts in the Vibrio community can precede, cause, and follow disease onset in numerous marine organisms, there is a need for an accurate high throughput assay for defining Vibrio community composition in natural samples. This Vibrio-centric hsp60 sequencing assay offers the potential for precise high throughput characterization of Vibrio diversity, providing an enhanced platform for dissecting Vibrio dynamics in the environment.
All-Dielectric Nanoresonators for χ(2) Nonlinear Optics

Metal-less nanophotonics offers new opportunities for nonlinear optics with respect to waveguides, and advancements in nanofabrication enabled the development of dielectric subwavelength Mie-type structures. Here we review recent results on second harmonic generation with semiconductor nanoresonators, focusing on their Mie-scattering features in terms of efficiency and control over radiation pattern. Firstly, two theoretical models are comparatively discussed, with a view to possible improvements in analysis and design. Then some relevant experiments are reported, and the origin of χ(2) generation is discussed, outlining the main open topics to investigate in the next future and the advantages offered by these nanostructures to develop novel photonic devices.
One, No One, and One Hundred Thousand: T Regulatory Cells' Multiple Identities in Neuroimmunity

As the Nobel laureate Luigi Pirandello wrote in his novels, identities can be evanescent. Although a quarter of a century has passed since regulatory T cells (Treg) were first described, new studies continue to reveal surprising and contradictory features of this lymphocyte subset. Treg cells are the core of the immunological workforce engaged in the restraint of autoimmune or inflammatory reactions, and their characterization has revealed substantial heterogeneity and complexity in the phenotype and gene expression profiles, proving them to be a most versatile and adaptive cell type, as exemplified by their plasticity in fine-tuning immune responses. Defects in Treg function are associated with several autoimmune diseases, including multiple sclerosis, which is caused by an inappropriate immune reaction toward brain components; conversely, the beneficial effects of immunomodulating therapies on disease progression have been shown to partly act upon the biology of these cells. Both in animals and in humans the pool of circulating Treg cells is a mixture of natural (nTregs) and peripherally-induced Treg (pTregs). Particularly in humans, circulating Treg cells can be phenotypically subdivided into different subpopulations, which so far are not well-characterized, particularly in the context of autoimmunity. Recently, Treg cells have been rediscovered as mediators of tissue healing, and have also shown to be involved in organ homeostasis. Moreover, stability of the Treg lineage has recently been addressed by several conflicting reports, and immune-suppressive abilities of these cells have been shown to be dynamically regulated, particularly in inflammatory conditions, adding further levels of complexity to the study of this cell subset. Finally, Treg cells exert their suppressive function through different mechanisms, some of which—such as their ectoenzymatic activity—are particularly relevant in CNS autoimmunity. Here, we will review the phenotypically and functionally discernible Treg cell subpopulations in health and in multiple sclerosis, touching also upon the effects on this cell type of immunomodulatory drugs used for the treatment of this disease.
Next-Generation Liver Medicine Using Organoid Models

“Liver medicine” refers to all diagnostic and treatment strategies of diseases and conditions that cause liver failure directly or indirectly. Despite significant advances in the field of liver medicine in recent years, improved tools are needed to efficiently define the pathophysiology of liver diseases and provide effective therapeutic options to patients. Recently, organoid technology has been established as the state-of-the-art cell culture tool for studying human biology in health and disease. In general, organoids are simplified three-dimensional (3D) mini-organ structures that can be grown in a 3D matrix where the structural and functional aspects of real organs are efficiently recapitulated. The generation of organoids is facilitated by exogenous factors that regulate multiple signaling pathways and promote the self-renewal, proliferation, and differentiation of the cells to promote spontaneous self-organization and tissue-specific organogenesis. Newly established protocols suggest that liver-specific organoids can be derived from either pluripotent stem cells or liver-specific stem/progenitor cells. Today, robust and long-term cultures of organoids with the closest physiology to in vivo liver, in terms of cellular composition and function, open a new era in studying and understanding the disease pathology as well as high-throughput drug screening. Of note, these next-generation cell culture systems have immense potential to be further improved by genome editing and bioengineering technologies to foster the development of patient-specific therapeutic options for clinical applications. Here, we will discuss recent advances and challenges in the generation of human liver organoids and highlight emerging concepts for their potential applications in liver medicine.
Editorial: Resilience Resources in Chronic Pain Patients: The Path to Adaptation

1 Andalucía Tech, Facultad de Psicología, Instituto de Investigación Biomédica de Málaga, Universidad de Málaga, Málaga, Spain, Center for Child Health, Behavior and Development, Seattle Children’s Research Institute, Seattle, WA, United States, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, WA, United States, Department of Clinical Psychological Science, Faculty of Psychology and Neuroscience, Maastricht
Tool-Use Training Induces Changes of the Body Schema in the Limb Without Using Tool

Previous studies have shown that tool use affects the plasticity of the body schema. In other words, people will perceive the tool as a part of their body, and thus feel like they have “longer limbs” after using tools. However, it is unclear whether tool embodiment could spread to a limb that is not using the tool, and whether other limbs could utilize the proprioception of a limb. In Experiment 1, blindfolded participants were asked to search with a cane (Condition 1) or to walk with a cane (Condition 2). The results in Condition 1 illustrated that the tactile distance perception on the forearm was lengthened after tool use, while other body parts did not significantly change. In Condition 2, the tactile distance perception on the hand and forearm extended significantly after using tools. Additionally, tool-use training even induced an increased perception of the calf that was not using the tool. Possible interference from the difference between walking and standing was excluded in Experiment 2. These results demonstrate that the proprioception information of one limb could be exploited by another limb to extend the body schema even though that limb was not using a tool. It was also observed that the effect of direction was task-dependent in the tactile perception task.