Article
Multidisciplinary Sciences
Ping Han, Maybelle K. Go, Jeng Yeong Chow, Bo Xue, Yan Ping Lim, Michael A. Crone, Marko Storch, Paul S. Freemont, Wen Shan Yew
Summary: This study introduces a semi-automated, kit-free RNA extraction method by adapting a well-established TRIzol-based protocol into a high-throughput format for SARS-CoV-2 detection, demonstrating scalability and cost-effectiveness.
SCIENTIFIC REPORTS
(2021)
Article
Nanoscience & Nanotechnology
Shan Jiang, Junyeob Song, Yujing Zhang, Meitong Nie, Jongwoon Kim, Ana Lopez Marcano, Kelly Kadlec, William A. Mills, Xiaodong Yan, Hefei Liu, Rong Tong, Han Wang, Ian F. Kimbrough, Harald Sontheimer, Wei Zhou, Xiaoting Jia
Summary: The study demonstrates the integration of flexible nano-optoelectrode arrays into multifunctional fiber probes for hybrid optical-electrical sensing modalities. This technology enables simultaneous electrical neural recording and optical biochemical sensing at the single-cell level, providing significant opportunities for multimodal monitoring of brain activities.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Biology
Aude I. Segaliny, Jayapriya Jayaraman, Xiaoming Chen, Jonathan Chong, Ryan Luxon, Audrey Fung, Qiwei Fu, Xianzhi Jiang, Rodrigo Rivera, Xiaoya Ma, Ci Ren, Jan Zimak, Per Niklas Hedde, Yonglei Shang, George Wu, Weian Zhao
Summary: Researchers have developed a high throughput, single-cell functional screening platform for efficient discovery and isolation of rare functional bispecific antibodies (BsAbs). The platform demonstrated high screening efficiency in a CD19xCD3 BiTE model and identified novel BiTEs with unique properties. This single-cell platform has the potential to increase the discovery efficiency of new immunotherapeutics and enable the design of generalizable principles based on an in-depth understanding of sequence, structure, and function relationships.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Lucas Czech, Moises Exposito-Alonso
Summary: grenepipe is an all-in-one workflow that streamlines the data processing from raw high-throughput sequencing data to genotype variant calls. It integrates popular software tools, automatically installs dependencies, and is highly scalable and easy to run.
Article
Chemistry, Multidisciplinary
Yazhi Zheng, Hanxu Chen, Xiang Lin, Minli Li, Yuanjin Zhao, Luoran Shang
Summary: Drug microcarriers were prepared using a microfluidic step emulsification method, which allows for high-throughput production of droplets and hydrogel microparticles. The microparticles encapsulated basic fibroblast growth factor (bFGF) and incorporated black phosphorus (BP) for controllable release via near-infrared (NIR) stimulation. These microparticles serve as drug carriers to induce angiogenesis and collagen deposition, promoting wound repair. These findings suggest that the step emulsification technique has the potential to provide scalable production of drug microcarriers for wound healing and tissue regeneration.
Article
Biophysics
Camila C. Filgueiras, Yongwoon Kim, Kyle G. Wickings, Faheim El Borai, Larry W. Duncan, Denis S. Willett
Summary: Understanding the diversity of soil organisms is difficult due to the scale and substrate. However, the Smart Soil Organism Detector is a high-tech instrument that combines imaging, sensing, flow cytometry, and machine learning to extract, identify, and separate soil organisms in a non-destructive and reproducible manner. It has shown remarkable accuracy in identifying and classifying nematodes and micro-arthropods, making it a valuable tool for studying global soil biodiversity.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Environmental Sciences
Vasileios Sitokonstantinou, Alkiviadis Koukos, Thanassis Drivas, Charalampos Kontoes, Ioannis Papoutsis, Vassilia Karathanassi
Summary: There is an expected 70% increase in the demand for rice production in Asia over the next 30 years, highlighting the importance of a balanced productivity and food security management. This necessitates the timely and accurate mapping of paddy rice extent through the processing of big satellite data of high spatial resolution.
Article
Polymer Science
Fei Li, Xi Liu, Wensheng Wang, Haoyan Xu, Wenlong Song, Zhuangzhi Sun
Summary: In this work, a flexible intelligent probe (FIP) with a top-driven sensing strategy is proposed to accurately localize thrombosis in a liquid flow environment. The FIP shows excellent electrical conductivity and mechanical properties, and has a quasi-linear sensitivity to flow sensing in the low flow velocity range. It is capable of completing specified command actions accurately and has a good response to real-time sensing feedback.
Article
Biology
Budhaditya Chowdhury, Meng Wang, Joshua P. Gnerer, Herman A. Dierick
Summary: Chowdhury et al. developed the Divider Assay, a simplified experimental procedure that allows Drosophila researchers to conduct aggression analysis over a long period of time and in complete darkness. They observed a peak in fighting during the middle of the day. This pipeline is expected to facilitate high-throughput screening for aggression research.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Petar B. Petrov, Luqman O. Awoniyi, Vid Sustar, M. Ozge Balc, Pieta K. Mattila
Summary: Protein-protein interactions play a critical role in cellular processes, but their regulatory networks are still not fully understood. This study introduces AutoCoEv, a computational pipeline that can efficiently search for coevolution between a large number of proteins. By applying this pipeline to investigate proteins involved in lipid rafts of B lymphocytes, novel interactions and clusters of functionally related molecules were predicted. This tool provides a time- and cost-efficient approach for predicting functional interactions from large datasets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
An-Zhe Guo, Li-Hui Chou, Shun-Hsiang Yang, Dan Wang, Xiao-Feng Wang, Itaru Osaka, Hao-Wu Lin, Cheng-Liang Liu
Summary: In this study, spray deposition of mixed halide perovskite was achieved using a ternary channel pumping system, resulting in highly efficient MAPbI(2.91)Br(0.09) film with a champion power conversion efficiency. Vacuum-assisted thermal annealing further improved the optimized PCE to 17.07%, demonstrating the relevance of high-throughput screening of perovskite compositions and the versatility of scalable solution process.
ADVANCED MATERIALS INTERFACES
(2021)
Article
Biochemistry & Molecular Biology
Emma J. Chory, Dana W. Gretton, Erika A. DeBenedictis, Kevin M. Esvelt
Summary: Researchers have developed Pyhamilton, an open-source Python platform for executing complex pipetting patterns required for high-throughput experiments. By integrating a plate reader, they were able to maintain nearly 500 remotely monitored bacterial cultures in log-phase growth without the need for user intervention. Using this technology, they successfully optimized bioreactor protein production and comprehensively sampled the carbon, nitrogen, and phosphorus fitness landscape.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Computer Science, Theory & Methods
Shixiong Zhao, Fanxin Li, Xusheng Chen, Xiuxian Guan, Jianyu Jiang, Dong Huang, Yuhao Qing, Sen Wang, Peng Wang, Gong Zhang, Cheng Li, Ping Luo, Heming Cui
Summary: vPipe is the first system to provide dynamic layer partitioning and memory management for pipeline parallelism, improving training throughput significantly by using an online algorithm to search for near-optimal solutions, and employing a live layer migration protocol to rebalance layer distribution across the training pipeline.
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
(2022)
Article
Genetics & Heredity
Stefano Capomaccio, Michela Ablondi, Daniele Colombi, Cristina Sartori, Andrea Giontella, Katia Cappelli, Enrico Mancin, Vittoria Asti, Roberto Mantovani, Alberto Sabbioni, Maurizio Silvestrelli
Summary: In this study, the current status of the modern Italian gene pool was described. The results show that some native Italian breeds preserve distinct gene pools, potentially due to adaptation to different geographical contexts. However, comparisons with international breeds reveal strong gene flow from renowned breeds into several Italian breeds, likely due to historical introgression. Some breeds also show unique characteristics based on their breeding history. Lastly, certain breeds exist more for cultural, traditional, and geographical reasons rather than genetic distinctiveness.
FRONTIERS IN GENETICS
(2023)
Article
Environmental Sciences
Ying Li, Wei Chen, Xiaoying Zheng, Qiang Liu, Wei Xiang, Jixiang Qu, Chengfang Yang
Summary: The study found that the sludge retention time (SRT) can significantly affect the microbial community structure in a hybrid membrane bioreactor (HMBR), with different trends appearing in the three functional units. The largest number of mutual operational taxonomic units was found in the suspended filler mixture and suspended carrier with SRTs of 20 days and 30 days. Species belonging to Proteobacteria had the greatest contribution to between-group differences in the 10-day SRT group.
Review
Biochemistry & Molecular Biology
Teresita M. Porter, Mehrdad Hajibabaei
Article
Multidisciplinary Sciences
Teresita M. Porter, Mehrdad Hajibabaei
SCIENTIFIC REPORTS
(2018)
Article
Multidisciplinary Sciences
Teresita M. Porter, Mehrdad Hajibabaei
Article
Multidisciplinary Sciences
Victoria Carley Maitland, Chloe Victoria Robinson, Teresita M. Porter, Mehrdad Hajibabaei
Article
Biochemical Research Methods
T. M. Porter, M. Hajibabaei
Summary: This study aims to develop a method to screen for nuMTs in large COI datasets. Results show that introducing a pseudogene filtering step in the processing of marker gene sequences can remove up to 5% of sequences, and using open reading frame length filtering combined with hidden Markov model analysis can effectively screen out apparent pseudogenes from large datasets.
BMC BIOINFORMATICS
(2021)
Article
Ecology
Natalie K. Rideout, Zacchaeus G. Compson, Wendy A. Monk, Meghann R. Bruce, Mehrdad Hajibabaei, Teresita M. Porter, Michael T. G. Wright, Donald J. Baird
Summary: The study examines the relationships among floodplain wetland habitats, invertebrate communities, and ecosystem function. It reveals the importance of environmental filters and traits linked to ecosystem functions in shaping the diversity and stability of floodplain ecosystems.
FUNCTIONAL ECOLOGY
(2022)