Fully automated cellular-resolution vertebrate screening platform with parallel animal processing

The zebrafish larva is an optically-transparent vertebrate model with complex organs that is widely used to study genetics, developmental biology, and to model various human diseases. In this article, we present a set of novel technologies that significantly increase the throughput and capabilities of our previously described vertebrate automated screening technology (VAST). We developed a robust multi-thread system that can simultaneously process multiple animals. System throughput is limited only by the image acquisition speed rather than by the fluidic or mechanical processes. We developed image recognition algorithms that fully automate manipulation of animals, including orienting and positioning regions of interest within the microscope's field of view. We also identified the optimal capillary materials for high-resolution, distortion-free, low-background imaging of zebrafish larvae.National Institutes of Health (U.S.) (Director's New Innovator Award DP2 OD002989)National Institutes of Health (U.S.) (Transformative Research Award R01 NS073127)David & Lucile Packard Foundation (Award in Science and Engineering)Broad Institute of MIT and Harvard (SPARC Award)Foxconn International Holdings Ltd.Athinoula A. Martinos Center for Biomedical Imaging (Training Grant

Evaluation of Phytoavailability of Heavy Metals to Chinese Cabbage ( Brassica chinensis

This study compared the extractability of Cd, Cu, Ni, Pb, and Zn by 8 extraction protocols for 22 representative rural soils in Taiwan and correlated the extractable amounts of the metals with their uptake by Chinese cabbage for developing an empirical model to predict metal phytoavailability based on soil properties. Chemical agents in these protocols included dilute acids, neutral salts, and chelating agents, in addition to water and the Rhizon soil solution sampler. The highest concentrations of extractable metals were observed in the HCl extraction and the lowest in the Rhizon sampling method. The linear correlation coefficients between extractable metals in soil pools and metals in shoots were higher than those in roots. Correlations between extractable metal concentrations and soil properties were variable; soil pH, clay content, total metal content, and extractable metal concentration were considered together to simulate their combined effects on crop uptake by an empirical model. This combination improved the correlations to different extents for different extraction methods, particularly for Pb, for which the extractable amounts with any extraction protocol did not correlate with crop uptake by simple correlation analysis

High-throughput vertebrate total analysis/screening platform

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2012.Cataloged from PDF version of thesis.Includes bibliographical references.High-throughput screening (HTS) is seen as one of the most promising technologies to facilitate biomedical studies and pharmaceutical discoveries. Although large varieties of in vitro HTS technologies have opened great opportunities, the speed of improvement has been limited by lack of advanced tools for in vivo screening on whole complex organisms, such as vertebrates. To address this issue, a high-throughput platform as a vertebrate total analysis/screening system (V-TAS) is proposed. This platform consists of two independent parts: an automated imaging system and an automated microinjection system. These two systems are designed for general high-content high-throughput pharmaceutical and genetic screens on whole zebrafish larvae, and therefore, are well-modularized for adapting different situations. Furthermore, to demonstrate the capability of V-TAS, a screen of lipidoid library for biologics delivery on thousands of animals was conducted. Very limited damage to the larvae was shown during the screening. In the end, the author also validated the hits discovered by V-TAS can be applied to more advanced animal models such as rats, and be more predictable than cell-based assays.by Tsung-Yao Chang.Ph.D

Analysis of Resistance to Clarithromycin and Virulence Markers in Helicobacter pylori Clinical Isolates from Eastern Taiwan

AbstractObjectiveLittle information is available concerning the relationships between clarithromycin resistance and virulence marker genes (iceA, cagA and vacA) in Helicobacter pylori isolated in Taiwan. The aim of this study was to evaluate the possible association between clarithromycin resistance and genotypes of the virulence markers on clarithromycin-resistant H. pylori isolates obtained in eastern TaiwanMaterials and MethodsThe genotypes of the virulence marker genes (iceA, cagA and vacA) were analyzed by PCR, and the 23S rDNA region from 18 clarithromycin-resistant clinical isolates of H. pylori was amplified by PCR and sequenced.ResultsPoint mutations were found to occur in all isolates. Two isolates had A2143G, six had T2182C, one had C2227T, six had A2143G plus T2182C, and three had heterozygous alleles. The latter included a wild-type allele (A2143) plus (i) an A2143G, (ii) an A2143G plus an A2223G, and (iii) an A2143G plus a T2182C. The prevalence of the marker genes cagA, iceA1, iceA2, and both iceA1 and iceA2, in the isolates was 95.5%, 66.9%, 7.5%, and 25.6%, respectively. The vacAs1 allele was detected in all isolates, whereas the m1 and m2 alleles were found in 44.4% and 55.6% of the isolates, respectivelyConclusionThere were no significant associations between clarithromycin resistance and the presence of the cagA gene, vacA allele mosaicism, and the iceA genotypes. The most notable finding of our study was that the C2227T single mutation in 23S rDNA could also be related to the high clarithromycin minimal inhibitory concentrations in clinical isolates from eastern Taiwan

Compressing Transformer-based self-supervised models for speech processing

Despite the success of Transformers in self- supervised learning with applications to various downstream tasks, the computational cost of training and inference remains a major challenge for applying these models to a wide spectrum of devices. Several isolated attempts have been made to compress Transformers, but the settings and metrics are different across studies. Trade-off at various compression rates are also largely missing in prior work, making it difficult to compare compression techniques. In this work, we aim to provide context for the isolated results, studying several commonly used compression techniques, including weight pruning, head pruning, low-rank approximation, and knowledge distillation. We report trade- off at various compression rate, including wall-clock time, the number of parameters, and the number of multiply-accumulate operations. Our results show that compared to recent approaches, basic compression techniques are strong baselines. We further present several applications of our results, revealing properties of Transformers, such as the significance of diagonal attention heads. In addition, our results lead to a simple combination of compression techniques that improves trade-off over recent approaches. We hope the results would promote more diverse comparisons among model compression techniques and promote the use of model compression as a tool for analyzing models. Our code of compressing speech self-supervised model is available at https://github.com/nervjack2/Speech-SSL-Compression/.Comment: Submitted to IEEE Transactions on Audio, Speech and Language Processing (TASLP

Organ-targeted high-throughput in vivo biologics screen identifies materials for RNA delivery

Therapies based on biologics involving delivery of proteins, DNA, and RNA are currently among the most promising approaches. However, although large combinatorial libraries of biologics and delivery vehicles can be readily synthesized, there are currently no means to rapidly characterize them in vivo using animal models. Here, we demonstrate high-throughput in vivo screening of biologics and delivery vehicles by automated delivery into target tissues of small vertebrates with developed organs. Individual zebrafish larvae are automatically oriented and immobilized within hydrogel droplets in an array format using a microfluidic system, and delivery vehicles are automatically microinjected to target organs with high repeatability and precision. We screened a library of lipid-like delivery vehicles for their ability to facilitate the expression of protein-encoding RNAs in the central nervous system. We discovered delivery vehicles that are effective in both larval zebrafish and rats. Our results showed that the in vivo zebrafish model can be significantly more predictive of both false positives and false negatives in mammals than in vitro mammalian cell culture assays. Our screening results also suggest certain structure–activity relationships, which can potentially be applied to design novel delivery vehicles.National Institutes of Health (U.S.) (Transformative Research Award R01 NS073127)National Institutes of Health (U.S.) (Director's Innovator Award DP2 OD002989)David & Lucile Packard Foundation (Award in Science and Engineering)Sanofi Aventis (Firm)Foxconn International Holdings Ltd.Hertz Foundation (Fellowship)University Grants Committee (Hong Kong, China) (Early Career Award 125012)National Natural Science Foundation (China) (81201164)ITC (ITS/376/13)Chinese University of Hong Kong (Grant 9610215)Chinese University of Hong Kong (Grant 7200269