Article
Biotechnology & Applied Microbiology
Ahmed Arslan, Zhuoqing Fang, Meiyue Wang, Yalun Tan, Zhuanfen Cheng, Xinyu Chen, Yuan Guan, Laura J. Pisani, Boyoung Yoo, Gill Bejerano, Gary Peltz
Summary: Long read sequencing is a useful method for identifying structural variants causing human genetic diseases. In this study, the genomes of six inbred strains were sequenced using long read sequencing, and it was found that structural variants are abundant and cannot be accurately detected using short read sequencing. The advantage of a more complete map of genetic variation was demonstrated by analyzing the genomic sequence of BTBR mice and identifying a unique deletion contributing to neuroanatomic abnormalities.
Article
Plant Sciences
Long Chen, Matthias Daub, Hans-Georg Luigs, Marcus Jansen, Martin Strauch, Dorit Merhof
Summary: This study introduces a high-throughput system based on computer vision for quantifying beet cyst nematode infestation and measuring cyst phenotypic traits. The computer vision approach accurately counts and segments nematode cysts, allowing for the identification of phenotypic differences between nematode populations in different soils and planting periods.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Robert D. Hall, John C. D'Auria, Antonio C. Silva Ferreira, Yves Gibon, Dariusz Kruszka, Puneet Mishra, Rick van de Zedde
Summary: High-throughput plant phenotyping approaches are rapidly developing and helping bridge the genotype-phenotype gap. Metabolites play a crucial role in defining key physiological and agronomic traits in plants. Despite challenges, novel technological innovations have the potential to fully integrate metabolomics approaches into plant phenotyping pipelines in the near future.
TRENDS IN PLANT SCIENCE
(2022)
Article
Computer Science, Information Systems
Hossein Estiri, Zachary H. Strasser, Shawn N. Murphy
Summary: This study aimed to develop a high-throughput phenotyping method leveraging temporal sequential patterns from electronic health records. Using temporal sequences for phenotyping resulted in superior classification performance compared to standard representations, and transitive sequences offered more accurate phenotype characterization.
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2021)
Review
Plant Sciences
Rupesh Tayade, Jungbeom Yoon, Liny Lay, Abdul Latif Khan, Youngnam Yoon, Yoonha Kim
Summary: This article provides an overview of various VIs used in agricultural research, focusing on those often employed for crop or vegetation evaluation, as they have a linear relationship to crop output and are frequently used for crop chlorophyll, health, moisture, and production predictions. In addition, the importance of VIs in crop research and precision agriculture, their utilization in high-throughput phenotyping, recent photogrammetry technology, mapping, and geographic information system software integrated with unmanned aerial vehicles and its key features are described.
Review
Plant Sciences
Alebel Mekuriaw Abebe, Younguk Kim, Jaeyoung Kim, Song Lim Kim, Jeongho Baek
Summary: Plant phenotyping plays a vital role in plant breeding programs by selecting genotypes with desirable traits. The current techniques for phenotyping are time-consuming and destructive. However, the development of imaging platforms and sensors has revolutionized high-throughput phenotyping studies. This review focuses on the trends and applications of image-based phenotyping methods in horticultural crops, highlighting the advantages and limitations of different imaging platforms and techniques. It also emphasizes the potential of high-throughput phenotyping in discovering new phenotypic traits for future exploration.
Article
Biochemical Research Methods
Diane Gleeson, Debarati Sethi, Radka Platte, Jonathan Burvill, Daniel Barrett, Shaheen Akhtar, Michaela Bruntraeger, Joanna Bottomley, James Bussell, Edward Ryder
Summary: Genotyping of knockout alleles in mice can be performed using endpoint PCR, qPCR, or NGS, with NGS being highly scalable and applicable to various allele types. One challenge is locating unique areas of the genome, especially when dealing with gene families or regions of high homology.
Article
Environmental Sciences
Lukas Roth, Christoph Barendregt, Claude-Alain Betrix, Andreas Hund, Achim Walter
Summary: This study demonstrates the importance of high-throughput field phenotyping in the context of physiological and breeding-related analyses of crops using the example of soybean production in Switzerland. The results show that analyzing the dynamics of vegetative growth from remote sensing imagery can predict yield and protein content in soybean genotypes adapted to a temperate oceanic climate.
REMOTE SENSING OF ENVIRONMENT
(2022)
Article
Plant Sciences
Hendrik Poorter, Gregoire M. Hummel, Kerstin A. Nagel, Fabio Fiorani, Philipp von Gillhaussen, Olivia Virnich, Ulrich Schurr, Johannes A. Postma, Rick van de Zedde, Anika Wiese-Klinkenberg
Summary: Automated high-throughput plant phenotyping (HTPP) allows for non-invasive and standardized assessments of plant size, development, and physiological variables. Before purchasing or using such equipment, users need to consider financial and time investments, machine constraints, the benefits and drawbacks of non-destructive measurements, the information provided by proxy traits, and the utilization of calibration curves. Despite possible pitfalls, HTPP systems have become valuable tools for plant biologists.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Jiri Lindovsky, Marcela Palkova, Viktoriia Symkina, Miles Joseph Raishbrook, Jan Prochazka, Radislav Sedlacek
Summary: The study aims to use coherent optical tomography and electroretinography techniques to assess the morphology and function of the mouse retina in a high-throughput phenotyping environment. It presents normal range data of retinal parameters in wild-type mice of different age groups and shows examples of pathologies caused by knocking out a single gene. Additionally, it discusses the feasibility of these techniques in high-throughput approaches such as those used by the International Mouse Phenotyping Consortium.
Article
Plant Sciences
Francisco Pinto, Mainassara Zaman-Allah, Matthew Reynolds, Urs Schulthess
Summary: Recent advances in sensors, image-processing technology, and data analysis have provided opportunities for multiple scales phenotyping methods and systems, including satellite imagery. However, the low spatial resolution of satellite images has limited their deployment in breeding trials. The new generation of high-resolution satellites, such as the SkySat constellation, offers potential solutions to overcome these limitations. In this study, we used time series SkySat images to estimate NDVI and evaluated its reliability and capacity to detect seasonal changes and genotypic differences in wheat and maize breeding plots. We discuss the advantages, limitations, and perspectives of this approach for high-throughput phenotyping in breeding programs.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Cell Biology
Uma P. Arora, Beth A. Sullivan, Beth L. Dumont
Summary: This study investigates the interplay between centromere variation and kinetochore protein sequence association in mice, and reveals strain-level differences in both CENP-A positioning and sequence preference along the core centromere satellite.
Review
Biochemistry & Molecular Biology
Minsu Kim, Chaewon Lee, Subin Hong, Song Lim Kim, Jeong-Ho Baek, Kyung-Hwan Kim
Summary: Understanding plant responses to drought stress is crucial, and high-throughput phenotyping (HTP) has emerged as a promising method to address the limitations in genomic and phenomic studies. HTP provides researchers with a non-destructive and accurate way to analyze large-scale phenotypic data, making it an increasingly popular tool in studying plant traits.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Joshua C. O. Koh, German Spangenberg, Surya Kant
Summary: Automated machine learning (AutoML) is considered the next wave in artificial intelligence, showing promise in delivering high-performance machine learning pipelines with minimal user effort. This study compared the performance of AutoML and transfer learning in image-based plant phenotyping, demonstrating that AutoML achieved satisfactory results in a short amount of time.
Article
Environmental Sciences
Tian Gao, Feiyu Zhu, Puneet Paul, Jaspreet Sandhu, Henry Akrofi Doku, Jianxin Sun, Yu Pan, Paul Staswick, Harkamal Walia, Hongfeng Yu
Summary: This study aims to address the challenges of building high-quality, low-cost imaging systems, introducing two new plant imaging systems and a process for generating high-quality 3D data. The results suggest that these systems can be used for 3D reconstruction of plants.
Article
Clinical Neurology
Yoon Hee A. Chang, Robert L. Folmer, Becky Shasha, Judy A. Shea, Kathleen Sarmiento, Carl J. Stepnowsky, Diane Lim, Allan Pack, Samuel T. Kuna
Summary: The study found that the implementation of REVAMP was facilitated by leadership support, staff dedication, perceived usefulness of the program, and positive feedback from Veterans. However, challenges remained in supporting Veterans to create login credentials and integrating REVAMP into existing workflows.
Article
Clinical Neurology
Atul Malhotra, Indu Ayappa, Najib Ayas, Nancy Collop, Douglas Kirsch, Nigel Mcardle, Reena Mehra, Allan Pack, Naresh Punjabi, David P. White, Daniel J. Gottlieb
Summary: Obstructive sleep apnea (OSA) affects nearly 1 billion people globally with established cardiovascular and neurocognitive consequences. The apnea-hypopnea index (AHI) is a widely studied metric of OSA severity, but alternative metrics like hypoxic burden and arousal intensity are being explored. Future research should focus on capturing clinically meaningful OSA endophenotypes using genetics, blood biomarkers, machine learning, and wearable technologies.
Letter
Clinical Neurology
Allan Pack, Ulysses J. Magalang, Bhajan Singh, Samuel T. Kuna, Brendan T. Keenan, Greg Maislin
Editorial Material
Medicine, General & Internal
Allan I. Pack
Letter
Critical Care Medicine
Brendan T. Keenan, Ulysses J. Magalang, Diego R. Mazzotti, Nigel McArdle, Thorarinn Gislason, Bhajan Singh, Greg Maislin, Allan I. Pack
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2022)
Editorial Material
Clinical Neurology
Allan I. Pack
Article
Clinical Neurology
Brian Geuther, Mandy Chen, Raymond J. Galante, Owen Han, Jie Lian, Joshy George, Allan Pack, Vivek Kumar
Summary: This study explores the use of modern computer vision methods to directly classify sleep substages from video data, avoiding the need for invasive surgery and expert scoring. The visual sleep classifier proved to be highly accurate in classifying wake, non-rapid eye movement sleep (NREM), and rapid eye movement sleep (REM) states, enabling noninvasive high-throughput sleep studies. Additionally, the study discovers video features that correlate with breathing rates and detects sleep stage disturbances induced by amphetamine administration. This research provides a viable alternative to EEG/EMG-based scoring and significantly reduces the barrier to screening mutant mice for sleep abnormalities.
Article
Clinical Neurology
Magdy Younes, Bethany Gerardy, Allan Pack, Samuel T. Kuna, Cecilia Castro-Diehl, Susan Redline
Summary: Conventional metrics for measuring sleep quantity/depth have limitations. An ORP-based approach provides additional information on sleep disorders that is not captured by traditional metrics. The ORP histogram offers unique insights into the neurophysiological characteristics of sleep disorders, potentially advancing diagnosis and management.
Editorial Material
Critical Care Medicine
Allan I. Pack, Brendan T. Keenan
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2022)
Editorial Material
Clinical Neurology
Allan Pack, Antoine Adamantidis, Katie L. Stone, David Gozal
Article
Critical Care Medicine
Jaejin An, Henry A. Glick, Amy M. Sawyer, Jessica Arguelles, Charles J. Bae, Brendan T. Keenan, Samuel T. Kuna, Greg Maislin, Diego R. Mazzotti, Allan I. Pack, Jiaxiao M. Shi, Alexa J. Watach, Dennis Hwang
Summary: This study investigated the association between adherence to positive airway pressure (PAP) therapy and healthcare costs in participants with obstructive sleep apnea (OSA) over a 3-year period. The results showed that higher adherence to PAP therapy was associated with significantly lower healthcare costs.
Article
Clinical Neurology
Jennifer R. Goldschmied, Samuel T. Kuna, Greg Maislin, Pongsakorn Tanayapong, Allan Pack, Magdy Younes
Summary: This study used delta power and ORP as measures to investigate the effects of acute sleep deprivation on sleep depth and to assess the heritability of sleep homeostasis in humans. The results showed that during recovery sleep, ORP decreased and delta power increased, indicating deeper sleep. Furthermore, both ORP and delta power demonstrated a certain level of heritability of sleep homeostasis.
Article
Clinical Neurology
Elin H. Thorarinsdottir, Thorarinn Gislason, Allan Pack, Samuel T. Kuna, Thomas Penzel, Fang Han, Qing Yun Li, Peter A. Cistulli, Ulysses J. Magalang, Nigel McArdle, Bhajan Singh, Brendan T. Keenan
Editorial Material
Clinical Neurology
Allan Pack
Article
Clinical Neurology
Bethany Gerardy, Samuel T. Kuna, Allan Pack, Clete A. Kushida, James K. Walsh, Bethany Staley, Grace W. Pien, Magdy Younes
Summary: This study proposes a new approach to evaluate inter-scorer variability in sleep staging. By recognizing the existence of equivocal sleep epochs, the proposed method provides a more accurate assessment of scorer's competence and reduces disagreements among scorers.