Article
Ecology
Chun-Wei Chang, Takeshi Miki, Masayuki Ushio, Po-Ju Ke, Hsiao-Pei Lu, Fuh-Kwo Shiah, Chih-hao Hsieh
Summary: A novel approach for reconstructing high-dimensional interaction Jacobian networks without specific model assumptions was proposed in this study, which successfully identified important species and revealed mechanisms governing the dynamical stability of a bacterial community. The method overcame the challenge of high dimensionality in large natural dynamical systems.
Article
Multidisciplinary Sciences
Iunio Iervolino, Georgios Baltzopoulos, Antonio Vitale, Antonio Grella, Giovanni Bonini, Antonio Iannaccone
Summary: In the field of structural engineering, the design and assessment of bridges should be based on a probabilistic approach considering the loads. Weigh-in-motion (WIM) systems can provide stochastic models for traffic loads. However, WIM is not widely used, and there is a lack of recent and comprehensive data in the literature. To ensure structural safety, the A3 highway in Italy, which spans 52 km and connects Naples and Salerno, has been equipped with a WIM system since the beginning of 2021. The system's measurements of vehicle weights have prevented overloads on the bridges. As of now, the WIM system has been operational for over a year, collecting more than thirty-six million data points. This paper presents and discusses the WIM measurements, including the empirical distributions of traffic loads, making the original data available for further research and applications.
Article
Genetics & Heredity
Michael H. Guo, Laurent C. Francioli, Sarah L. Stenton, Julia K. Goodrich, Nicholas A. Watts, Moriel Singer-Berk, Emily Groopman, Philip W. Darnowsky, Matthew Solomonson, Samantha Baxter, Grace Tiao, Benjamin M. Neale, Joel N. Hirschhorn, Heidi L. Rehm, Mark J. Daly, Anne O'Donnell-Luria, Konrad J. Karczewski, Daniel G. MacArthur, Kaitlin E. Samocha
Summary: This study developed a strategy to infer the phase for rare variant pairs within genes using genotypes observed in the Genome Aggregation Database. The approach showed high accuracy in determining phase in both trio data and patients with Mendelian conditions, providing a valuable resource for interpreting rare co-occurring variants in the context of recessive diseases.
Article
Computer Science, Information Systems
Xiaoqi Shen, Wenzhong Shi, Zhewei Liu, Anshu Zhang, Lukang Wang, Fanxin Zeng
Summary: This research proposes a novel area extraction framework (ELV) that tackles the challenge of varying densities of large-scale spatial data by using clustering with an adaptive distance parameter and a re-segmentation strategy with noise recovery. Compared with other algorithms, ELV showed better performance on real-life datasets and achieved a significant improvement in the Silhouette coefficient indicator.
ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION
(2022)
Article
Psychology, Multidisciplinary
Tingxuan Li
Summary: In this study, keystroke log data was used to quantify students' writing process and the estimated parameters were found to be meaningful and interpretable across cognitive processes. The mixture model captured details of the writing process and revealed differences between students with different scores.
FRONTIERS IN PSYCHOLOGY
(2021)
Article
Immunology
Martin Corcoran, Mark Chernyshev, Marco Mandolesi, Sanjana Narang, Mateusz Kaduk, Kewei Ye, Christopher Sundling, Anna Farnert, Taras Kreslavsky, Carolina Bernhardsson, Maximilian Larena, Mattias Jakobsson, Gunilla B. Karlsson Hedestam
Summary: Detailed analysis of TCR genes in 45 donors from four human populations revealed 175 additional TCR variable and junctional alleles, with coding changes and different frequencies among populations. The study also identified Neanderthal-derived TCR regions and a highly divergent TRGV4 variant that is frequent in modern Eurasian population groups. These findings highlight the remarkable variation in TCR genes and suggest the inclusion of allelic variation in studies of TCR function.
Article
Chemistry, Physical
Amir Hossein Afsharinejad, Chuanyi Ji, Robert Wilcox
Summary: The study reveals that prioritizing large failures can help the majority of customers to recover quickly from massive power outages induced by natural disasters. However, as the severity of disruptions increases, recovery capability degrades and prolonged small failures dominate the entire recovery processes. Enhancing recovery of a small fraction of large failures through distributed generation and storage shows promise in mitigating the degradation.
Article
Biotechnology & Applied Microbiology
Ramyar Molania, Momeneh Foroutan, Johann A. Gagnon-Bartsch, Luke C. Gandolfo, Aryan Jain, Abhishek Sinha, Gavriel Olshansky, Alexander Dobrovic, Anthony T. Papenfuss, Terence P. Speed
Summary: Accurate identification and removal of unwanted variation in RNA-seq data are crucial for meaningful downstream analyses. Our PRPS strategy with RUV-III normalization effectively addresses this issue and can be applied to integrate and normalize large transcriptomic datasets from multiple sources.
NATURE BIOTECHNOLOGY
(2022)
Article
Computer Science, Artificial Intelligence
Anthony C. Constantinou, Yang Liu, Kiattikun Chobtham, Zhigao Guo, Neville K. Kitson
Summary: This study investigated the performance of 15 state-of-the-art structure learning algorithms and found that traditional synthetic performance may overestimate real-world performance by 10% to over 50%. It also emphasized that a higher fitting score does not necessarily imply a more accurate causal graph.
INTERNATIONAL JOURNAL OF APPROXIMATE REASONING
(2021)
Article
Paleontology
Jodie L. Murphy, Mark N. Puttick, Joseph E. O'Reilly, Davide Pisani, Philip C. J. Donoghue
Summary: The study investigated 486 tetrapod morphological cladistic datasets to establish an empirical distribution of consistency among characters and datasets. It was found that the consistency between phylogenetic history and individual character histories has a bearing on the evolutionary process, with the most significant decreases resulting from the addition of taxa rather than characters. This research challenges the conjecture that high quality phylogenetic characters are quickly exhausted in the search for phylogenetic resolution.
Article
Environmental Sciences
Eliza S. Deutsch, Jeffrey A. Cardille, Talia Koll-Egyed, Marie-Josee Fortin
Summary: The study used Landsat 8 images and water clarity datasets from southern Canada to evaluate the relationship between in situ Secchi disk depth and Landsat 8 Blue/Red band ratio, finding that a global algorithm effectively represents this relationship across diverse lake types. Improved model fit was achieved by applying a median filter to remove outliers caused by atmospheric artifacts in available imagery. The findings suggest that large datasets and temporal averaging methods can help better elucidate the true relationships between in situ water clarity and satellite reflectance data.
Article
Green & Sustainable Science & Technology
Jing He, Fu Ren, Robert Weibel, Cheng Fu
Summary: China's Photovoltaic Poverty Alleviation Project (PPAP) has been effective in reducing multidimensional poverty, particularly in terms of economic capital, social capital, and human capital. However, its impact on physical and natural capital is limited. The project has been more successful in designated poverty counties and has shown the most substantial poverty alleviation effect in Northwest China.
Review
Biochemical Research Methods
Alba Gutierrez-Sacristan, Carlos De Niz, Cartik Kothari, Sek Won Kong, Kenneth D. Mandl, Paul Avillach
Summary: Precision medicine aims to provide the best diagnosis, treatment, and prognosis for each individual by tailoring therapeutic approaches to their genetic profile, lifestyle, and environmental exposures. However, to achieve this goal, researchers need access to large-scale clinical and genomic data repositories, which can be challenging to locate and obtain.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Computer Science, Artificial Intelligence
Ana Castillo, Laura Ruiz, Jose Benitez, Florian Schuberth, Rafael Reina
Summary: This study provides empirical evidence on the positive impact of IT resource investment on open innovation performance, highlighting the enabling role of IT in the development of open innovation initiatives.
DECISION SUPPORT SYSTEMS
(2023)
Article
Urban Studies
Ling Yin, Nan Lin, Zhiyuan Zhao
Summary: This study proposes a method to mine human activity chains from large-scale mobile phone location data by integrating spatial and temporal features, finding that the frequency distribution of major activity chain patterns agrees well with patterns derived from travel surveys and advanced methods.
Article
Biochemical Research Methods
Eran Elhaik, Desmond M. Ryan
Meeting Abstract
Hematology
Linda B. Baughn, Zhou Li, Kathryn E. Pearce, Celine M. Vachon, Mei-Yin Polley, Jonathan J. Keats, Eran Elhaik, Michael L. Baird, Terry Therneau, James R. Cerhan, P. Leif Bergsagel, Angela Dispenzieri, Vincent Rajkumar, Yan Asmann, Shaji K. Kumar
Letter
Oncology
Linda B. Baughn, Zhuo Li, Kathryn Pearce, Celine M. Vachon, Mei-Yin Polley, Jonathan Keats, Eran Elhaik, Michael Baird, Terry Therneau, James R. Cerhan, P. Leif Bergsagel, Angela Dispenzieri, S. Vincent Rajkumar, Yan W. Asmann, Shaji Kumar
BLOOD CANCER JOURNAL
(2020)
Article
Medicine, General & Internal
Linda B. Baughn, Neeraj Sharma, Eran Elhaik, Aleksandar Sekulic, Alan H. Bryce, Rafael Fonseca
MAYO CLINIC PROCEEDINGS
(2020)
Article
Biochemistry & Molecular Biology
Kern Rei Chng, Chenhao Li, Denis Bertrand, Amanda Hui Qi Ng, Junmei Samantha Kwah, Hwee Meng Low, Chengxuan Tong, Maanasa Natrajan, Michael Hongjie Zhang, Licheng Xu, Karrie Kwan Ki Ko, Eliza Xin Pei Ho, Tamar Av-Shalom, Jeanette Woon Pei Teo, Chiea Chuen Khor, Swaine L. Chen, Christopher E. Mason, Oon Tek Ng, Kalisvar Marimuthu, Brenda Ang, Niranjan Nagarajan, David Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Sofia Ahsanuddin, Chandrima Bhattacharya, Daniel J. Butler, Francesca De Filippis, Jochen Hecht, Andre Kahles, Mikhail Karasikov, Nikos C. Kyrpides, Marcus H. Y. Leung, Dmitry Meleshko, Harun Mustafa, Beth Mutai, Russell Y. Neches, Amanda Ng, Marina Nieto-Caballero, Olga Nikolayeva, Tatyana Nikolayeva, Eileen Png, Jorge L. Sanchez, Heba Shaaban, Maria A. Sierra, Xinzhao Tong, Ben Young, Josue Alicea, Malay Bhattacharyya, Ran Blekhman, Eduardo Castro-Nallar, Ana M. Canas, Aspassia D. Chatziefthimiou, Robert W. Crawford, Youping Deng, Christelle Desnues, Emmanuel Dias-Neto, Daisy Donnellan, Marius Dybwad, Eran Elhaik, Danilo Ercolini, Alina Frolova, Alexandra B. Graf, David C. Green, Iman Hajirasouliha, Mark Hernandez, Gregorio Iraola, Soojin Jang, Angela Jones, Frank J. Kelly, Kaymisha Knights, Pawel P. Labaj, Patrick K. H. Lee, Levy Shawn, Per Ljungdahl, Abigail Lyons, Gabriella Mason-Buck, Ken McGrath, Emmanuel F. Mongodin, Milton Ozorio Moraes, Houtan Noushmehr, Manuela Oliveira, Stephan Ossowski, Olayinka O. Osuolale, Orhan Ozcan, David Paez-Espino, Nicolas Rascovan, Hugues Richard, Gunnar Raetsch, Lynn M. Schriml, Torsten Semmler, Osman U. Sezerman, Leming Shi, Le Huu Song, Haruo Suzuki, Denise Syndercombe Court, Dominique Thomas, Scott W. Tighe, Klas Udekwu, Juan A. Ugalde, Brandon Valentine, Dimitar Vassilev, Elena Vayndorf, Thirumalaisamy P. Velavan, Maria M. Zambrano, Jifeng Zhu, Sibo Zhu
Review
Microbiology
Jake M. Robinson, Zohar Pasternak, Christopher E. Mason, Eran Elhaik
Summary: The rise of microbiomics and metagenomics in forensic investigations is driven by advances in technology and methods, offering great potential, yet facing challenges such as limited sample sizes, low model accuracies, and overly idealized environmental settings.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Emma B. Johannsen, Linda B. Baughn, Neeraj Sharma, Nicolina Zjacic, Mehdi Pirooznia, Eran Elhaik
Summary: SIDS is a syndrome of unexplained sudden death in infants under one year old, with genetic studies showing uncertainty and limited supporting evidence for candidate genes.
Review
Biotechnology & Applied Microbiology
Hannah Carress, Daniel John Lawson, Eran Elhaik
Summary: The over-representation of Europeans in genomic studies restricts global understanding of disease risk and inhibits research into genomic differences between carriers and patients. To address this, more diverse samples are needed, with diversity quantified, compared and annotated for insight.
Article
Genetics & Heredity
Eran Elhaik, Dan Graur
Summary: Soft selective sweep mechanisms have gained significant importance in evolutionary studies, but caution should be taken when interpreting results involving the use of supervised machine learning techniques due to the lack of legitimate training datasets, potentially leading to misleading conclusions.
Article
Microbiology
Eran Elhaik, Sofia Ahsanuddin, Jake M. Robinson, Emily M. Foster, Christopher E. Mason
Summary: Advancements in metagenomic technology and computational prediction have the potential to weaken individual privacy rights by allowing the inference of personal details from microbiome data. There is a need for thorough ethical and legal scrutiny to ensure the protection of genetic privacy rights in the face of these developments.
Article
Cell Biology
Helen Eachus, Lara Oberski, Jack Paveley, Irina Bacila, John-Paul Ashton, Umberto Esposito, Fayaz Seifuddin, Mehdi Pirooznia, Eran Elhaik, Marysia Placzek, Nils P. Krone, Vincent T. Cunliffe
Summary: This article investigates glucocorticoid resistance commonly observed in depression, which has been linked to reduced expression and/or function of the glucocorticoid receptor (GR). By comparing the brain methylomes and transcriptomes of wild-type and GR-mutant zebrafish, the authors identify 249 differentially methylated regions (DMRs) regulated by GR. They also find GR-regulated genes associated with chaperone-mediated protein folding, circadian rhythm regulation, metabolism regulation, and behavior, which are known to be related to unipolar depression and anxiety. The findings provide insights into the molecular mechanisms through which GR mediates stress responses in the adult zebrafish brain and support the use of the zebrafish GR mutant as a model for studying affective disorders.
DISEASE MODELS & MECHANISMS
(2023)
Article
Biochemical Research Methods
Sara Behnamian, Umberto Esposito, Grace Holland, Ghadeer Alshehab, Ann M. Dobre, Mehdi Pirooznia, Conrad S. Brimacombe, Eran Elhaik
Summary: Radiocarbon dating is commonly used in archaeology to estimate the age of skeletons, but it has limitations in providing reliable dates. Researchers developed a new DNA-based dating method called TPS and applied it to ancient and modern Eurasian samples, resolving conflicting reports and improving the study of phenotypic traits over time.
CELL REPORTS METHODS
(2022)
Article
Genetics & Heredity
Laurence Freeman, Conrad Stephen Brimacombe, Eran Elhaik
NAR GENOMICS AND BIOINFORMATICS
(2020)
Meeting Abstract
Biochemistry & Molecular Biology
U. Esposito, G. Holland, E. Elhaik
EUROPEAN JOURNAL OF HUMAN GENETICS
(2019)
Meeting Abstract
Hematology
Linda B. Baughn, Dirk Larson, Mei-Yin Polley, Kathryn E. Pearce, Eran Elhaik, Michael L. Baird, Colin Colby, Joanne Benson, Zhou Li, Yan Asmann, Terry Therneau, James R. Cerhan, Celine M. Vachon, A. Keith Stewart, P. Leif Bergsagel, Angela Dispenzieri, Shaji K. Kumar, S. Vincent Rajkumar