Review
Multidisciplinary Sciences
Lloyd M. Smith, Jeffrey N. Agar, Julia Chamot-Rooke, Paul O. Danis, Ying Ge, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin, Neil L. Kelleher
Summary: Understanding the structure and properties of proteins is crucial in deciphering biological functions. The concept of defining the human proteome as a reference set of proteoforms is proposed, with a call for improved technologies in a two-pronged strategy.
Article
Neurosciences
Jennifer Stine Elam, Matthew F. Glasser, Michael P. Harms, Stamatios N. Sotiropoulos, Jesper L. R. Andersson, Gregory C. Burgess, Sandra W. Curtiss, Robert Oostenveld, Linda J. Larson-Prior, Jan-Mathijs Schoffelen, Michael R. Hodge, Eileen A. Cler, Daniel M. Marcus, Deanna M. Barch, Essa Yacoub, Stephen M. Smith, Kamil Ugurbil, David C. Van Essen
Summary: The Human Connectome Project (HCP) aims to accelerate advances in human neuroimaging by studying a large number of healthy young adults and sharing data and tools. The WU-Minn-Ox consortium has achieved its core objectives and emerged as a set of best-practice strategies for optimizing data acquisition and analysis.
Review
Biochemical Research Methods
Gilbert S. Omenn
Summary: The HUPO Human Proteome Project celebrates its 10th anniversary by achieving the milestone of confident detection of proteins from 90% of predicted protein-coding genes. This global project has influenced data-sharing, quality assurance, and issued stringent guidelines for detecting missing proteins. The project's impact is highlighted in special issues of Nature Communications and Journal of Proteome Research.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Optics
Libor Nozka, Giulio Avoni, Elzbieta Banas, Andrew Brandt, Karel Cerny, Paul M. Davis, Serge Duarte Pinto, Vjaceslav Georgiev, Miroslav Hrabovsky, Tomas Komarek, Krzysztof Korcyl, Ivan Lopez-Paz, Marko Milovanovic, Goran Mladenovic, Dmitry A. Orlov, Michael Rijssenbeek, Petr Schovanek, Tomas Sykora, Maciej Trzebinski, Vladimir Urbasek, Jan Zich
Summary: This study presents the performance results of the upgraded Cherenkov time-of-flight (ToF) detector for the AFP project. The improved detector, consisting of solid L-shaped fused silica bars, customized ALD-coated micro-channel plate photomultipliers (MCP-PMTs), and updated construction, aims to enhance efficiency, lifetime, and radiation hardness. Testing at the CERN-SPS facility confirmed that the detector maintained a timing resolution of 20 ps despite low gain and reduced optical throughput.
Article
Neurosciences
Caroline Demro, Bryon A. Mueller, Jerillyn S. Kent, Philip C. Burton, Cheryl A. Olman, Michael-Paul Schallmo, Kelvin O. Lim, Scott R. Sponheim
Summary: This paper describes an investigation within the Human Connectome Project focusing on psychotic psychopathology, with data collected from clinical assessments, cognitive assessments, motor assessments, blood specimens, and MRI data. The goal is to provide information on data acquisition process for researchers planning to use the publicly available data, with a companion paper detailing the study's 7 Tesla image acquisition protocol.
Review
Biochemistry & Molecular Biology
Ewan Birney
Summary: The Human Genome Project was an international effort, resulting in the freely available human genome for researchers worldwide. In the future, the reference human genome may evolve into a graph genome and incorporate more diverse global sequences. An international mindset is also key in data analysis for interpreting the human genome in both basic and clinical research.
HUMAN MOLECULAR GENETICS
(2021)
Article
Computer Science, Theory & Methods
Mario Jose Divan, Maria Laura Sanchez-Reynoso, Silvio Miguel Gonnet
Summary: The Internet-of-Things devices have improved the Spatiotemporal resolution in Real-time Data Gathering Systems. However, the heterogeneity of sensors has increased the complexity. This work presents a strategy for defining and communicating measurement projects using a conceptual hierarchy derived from a measurement ontology. It also introduces a data interchange format called BriefPD.
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF ESCIENCE
(2022)
News Item
Multidisciplinary Sciences
Mitch Leslie
Summary: This article introduces a major effort by an agency to explore the importance of accumulating mutations in somatic cells.
Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: According to the 2022 metrics of the HUPO Human Proteome Project (HPP), protein expression has been detected for 93.2% of the predicted proteins in the human genome. The number of missing proteins has been reduced, indicating experimental progress and reclassification. Proteomics continues to yield significant findings in biological and clinical studies and integrates with other omics platforms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Computer Science, Interdisciplinary Applications
David Sayah
Summary: This paper reviews compact continuous-time formulations for the multi-mode resource-constrained project scheduling problem. It identifies flaws in existing formulations and proposes alternatives to address the inconsistencies in mode choices. The paper also compares different models and concludes that network flow formulations are more effective in multi-mode settings compared to event-based models.
COMPUTERS & OPERATIONS RESEARCH
(2023)
Article
Neurosciences
Michael-Paul Schallmo, Kimberly B. Weldon, Rohit S. Kamath, Hannah R. Moser, Samantha A. Montoya, Kyle W. Killebrew, Caroline Demro, Andrea N. Grant, Malgorzata Marjanska, Scott R. Sponheim, Cheryl A. Olman
Summary: Visual perception is abnormal in psychotic disorders such as schizophrenia, with differences in fundamental visual processes. The neural basis of abnormal visual perception in people with psychotic psychopathology remains unknown.
Review
Multidisciplinary Sciences
Ting Wang, Lucinda Antonacci-Fulton, Kerstin Howe, Heather A. Lawson, Julian K. Lucas, Adam M. Phillippy, Alice B. Popejoy, Mobin Asri, Caryn Carson, Mark J. P. Chaisson, Xian Chang, Robert Cook-Deegan, Adam L. Felsenfeld, Robert S. Fulton, Erik P. Garrison, Nanibaa' A. Garrison, Tina A. Graves-Lindsay, Hanlee Ji, Eimear E. Kenny, Barbara A. Koenig, Daofeng Li, Tobias Marschall, Joshua F. McMichael, Adam M. Novak, Deepak Purushotham, Valerie A. Schneider, Baergen Schultz, Michael W. Smith, Heidi J. Sofia, Tsachy Weissman, Paul Flicek, Heng Li, Karen H. Miga, Benedict Paten, Erich D. Jarvis, Ira M. Hall, Evan E. Eichler, David Haussler
Summary: The human reference genome, currently in need of a major update, is crucial in human genetics research. The Human Pangenome Reference Consortium is working towards creating a more accurate and comprehensive reference genome to improve gene-disease association studies, expand genomics research, and serve as an important resource for future biomedical research and precision medicine.
Article
Operations Research & Management Science
Manuel A. Nunez, Lynn Kuo, I. Robert Chiang
Summary: In the traditional project crashing problem, the focus is on finding the least expensive way to reduce time in order to complete a project within a given time limit. In this paper, we study a combinatorial probabilistic version of the problem with the objective of minimizing time reduction costs and expected penalty risks. We propose efficient heuristics for this NP-hard problem and extend it to allow for adjustments in resource assignments before the project deadline.
ANNALS OF OPERATIONS RESEARCH
(2022)
Article
Neurosciences
A. David Edwards, Daniel Rueckert, Stephen M. Smith, Samy Abo Seada, Amir Alansary, Jennifer Almalbis, Joanna Allsop, Jesper Andersson, Tomoki Arichi, Sophie Arulkumaran, Matteo Bastiani, Dafnis Batalle, Luke Baxter, Jelena Bozek, Eleanor Braithwaite, Jacqueline Brandon, Olivia Carney, Andrew Chew, Daan Christiaens, Raymond Chung, Kathleen Colford, Lucilio Cordero-Grande, Serena J. Counsell, Harriet Cullen, John Cupitt, Charles Curtis, Alice Davidson, Maria Deprez, Louise Dillon, Konstantina Dimitrakopoulou, Ralica Dimitrova, Eugene Duff, Shona Falconer, Seyedeh-Rezvan Farahibozorg, Sean P. Fitzgibbon, Jianliang Gao, Andreia Gaspar, Nicholas Harper, Sam J. Harrison, Emer J. Hughes, Jana Hutter, Mark Jenkinson, Saad Jbabdi, Emily Jones, Vyacheslav Karolis, Vanessa Kyriakopoulou, Gregor Lenz, Antonios Makropoulos, Shaihan Malik, Luke Mason, Filippo Mortari, Chiara Nosarti, Rita G. Nunes, Camilla O'Keeffe, Jonathan O'Muircheartaigh, Hamel Patel, Jonathan Passerat-Palmbach, Maximillian Pietsch, Anthony N. Price, Emma C. Robinson, Mary A. Rutherford, Andreas Schuh, Stamatios Sotiropoulos, Johannes Steinweg, Rui Pedro Azeredo Gomes Teixeira, Tencho Tenev, Jacques-Donald Tournier, Nora Tusor, Alena Uus, Katy Vecchiato, Logan Z. J. Williams, Robert Wright, Julia Wurie, Joseph V. Hajnal
Summary: The Developing Human Connectome Project is an open science resource that provides researchers with data on typical and atypical brain development during the perinatal period. With a collection of MRI brain datasets and collateral data from fetal and neonatal participants, this project offers valuable insights into brain development.
FRONTIERS IN NEUROSCIENCE
(2022)
Review
Behavioral Sciences
Howard C. Cromwell, Leroy J. Lowe
Summary: Jaak Panksepp aimed to map the neural basis of the Affectome, contributing significantly to the field of affective science and providing a foundation for modern research.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2022)
Article
Geriatrics & Gerontology
John M. Felt, Karra D. Harrington, Nilam Ram, Kieran J. O'Donnell, Martin J. Sliwinski, Lizbeth Benson, Zhenyu Zhang, Michael J. Meaney, Frank W. Putnam, Jennie G. Noll, Chad E. Shenk
Summary: Deviation from normative trajectories of receptive language abilities after early life adversity may indicate an increased risk for advanced cognitive aging. Accelerated epigenetic aging at midlife may identify those at greatest risk for advanced cognitive aging following early life adversity. This study examines whether midlife epigenetic age acceleration can identify individuals with the greatest change in receptive language abilities after early life adversity.
JOURNALS OF GERONTOLOGY SERIES B-PSYCHOLOGICAL SCIENCES AND SOCIAL SCIENCES
(2023)
Article
Psychology, Multidisciplinary
Denis Gerstorf, Nilam Ram, Johanna Drewelies, Sandra Duezel, Peter Eibich, Elisabeth Steinhagen-Thiessen, Stefan Liebig, Jan Goebel, Ilja Demuth, Arno Villringer, Gert G. Wagner, Ulman Lindenberger, Paolo Ghisletta
Summary: Increases in older adults' levels of cognitive performance over time have been documented in history, but there is little information about historical shifts in within-person cognitive decline and onset of decline. A study comparing data from two independent samples recruited in 1990 and 2010 found that although cognitive functioning has shifted to higher levels, there was no evidence of cohort differences in the amount or rate of decline and the onset of decline. This suggests that cognitive decline in old age proceeds similarly to two decades ago.
PSYCHOLOGICAL SCIENCE
(2023)
Article
Psychology, Social
Naemi D. Brandt, Johanna Drewelies, Sherry L. Willis, K. Warner Schaie, Nilam Ram, Denis Gerstorf, Jenny Wagner
Summary: This study investigates personality stability and change across midlife and old age using four waves of data. Results show substantial rank-order stabilities across facets, while the exact pattern varies between traits and facets. The mean-level change of facets largely mirrors the mean-level change observed for the broader traits from midlife to old age.
JOURNAL OF PERSONALITY
(2023)
Article
Psychology, Multidisciplinary
Markus Wettstein, Hans-Werner Wahl, Johanna Drewelies, Susanne Wurm, Oliver Huxhold, Nilam Ram, Denis Gerstorf
Summary: Based on the analysis of data from the German Ageing Survey, it was found that individuals born later in historical time tend to feel younger, with a 2% decrease in subjective age every birth-year decade. Women reported feeling younger than men, and this gender gap widened over time. The association between higher education and younger subjective age weakened across cohorts. Potential reasons for the subjective-rejuvenation effect across cohorts are discussed in the article.
PSYCHOLOGICAL SCIENCE
(2023)
Article
Computer Science, Software Engineering
Daniel Reimann, Nilam Ram, Robert Gaschler
Summary: Scatterplots overlayed with a nonlinear model enable visual estimation of model-data fit. Although statistical fit is calculated using vertical distances, viewers' subjective fit is often based on shortest distances. Our results suggest that adding vertical lines (lollipops) supports more accurate fit estimation in the steep area of model curves (https://osf.io/fybx5/).
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Mathematics, Interdisciplinary Applications
Nilam Ram, Nick Haber, Thomas N. Robinson, Byron Reeves
Summary: In this paper, the advances in comprehensive recording of individuals' digital lives and AI modeling are discussed in terms of new possibilities for behavioral processes. The potential of transfer learning, self-supervision, and new deep neural network architectures in super-intensive longitudinal data analysis is explored. The authors suggest reevaluating the concerns about generalizability by focusing on transferability and propose adding a statement to the person-specific Manifesto.
MULTIVARIATE BEHAVIORAL RESEARCH
(2023)
Article
Endocrinology & Metabolism
Chang Liu, Jenae M. Neiderhiser, Nilam Ram, Leslie D. Leve, Daniel S. Shaw, Misaki N. Natsuaki, David Reiss, Jody M. Ganiban
Summary: This study aimed to investigate whether child genetic risk for obesity and temperament contribute to stability versus lability in children's weight status over time. The findings showed that higher levels of negative affectivity were associated with greater variability in BMI scores, while higher levels of effortful control and mean-level BMI scores were related to less variability. Additionally, within the group of children with a healthy weight status, better effortful control was associated with more stable BMI scores, whereas genetic risk for higher BMI was associated with more variability in BMI scores.
Article
Urology & Nephrology
Necole M. Streeper, Jason D. Fairbourn, James Marks, Edison Thomaz, Nilam Ram, David E. Conroy
Summary: This study investigated the feasibility and acceptability of a context-sensitive reminder system called mini sip(IT) for kidney stone patients with poor adherence to increasing fluid intake. The study found that the intervention, which incorporated a connected water bottle and mobile app with text messaging, was well-received and led to significant increases in 24-hour urine volume.
Article
Neurosciences
John M. Felt, Natan Yusupov, Karra D. Harrington, Julia Fietz, Zhenyu Zach Zhang, Martin J. Sliwinski, Nilam Ram, Michael J. Become Working Grp, Michael J. Meaney, Frank W. Putnam, Jennie G. Noll, Elisabeth B. Binder, Chad E. Shenk
Summary: This study found that accelerated epigenetic aging is associated with neurocognitive decline in adults with a history of early life adversity or psychiatric disorders. Estimating epigenetic aging could help identify individuals at risk and facilitate early neurocognitive screening.
NEUROBIOLOGY OF STRESS
(2023)
Article
Psychology
Maia L. Rocklin, Anna Angelina Torres, Byron Reeves, Thomas N. Robinson, Nilam Ram
Summary: So far, there has been no effective way to observe and track the emotional impacts of complex visual stimuli that people encounter in their digital lives. This paper proposes a method that utilizes AI-trained deep neural networks to analyze long sequences of screenshots from participants' smartphones. By obtaining affective valence and arousal ratings from a large number of images, the computational pipeline developed in this study can provide detailed maps of individuals' emotional experiences on their smartphones. This opens up opportunities for large-scale studies on the influence of digital experiences on individuals' well-being.
Article
Psychology, Multidisciplinary
Christine Blech, Daniel Reimann, Nilam Ram, Robert Gaschler
Summary: Data visualization can help detect unexpected aspects of the data. Two experiments were conducted to examine the classification accuracy and confidence of scatterplots depicting different types of mathematical functions. The results showed that continuous linear and negative exponential functions had an advantage in classification over the discontinuous step function. Therefore, scientists and practitioners need to be cautious when developing theories and making decisions based on raw data visualizations.
AMERICAN JOURNAL OF PSYCHOLOGY
(2023)
Proceedings Paper
Computer Science, Artificial Intelligence
Mark Roman Miller, Cyan DeVeaux, Eugy Han, Nilam Ram, Jeremy N. Bailenson
Summary: Scholars have focused on proxemics and mutual gaze in the study of nonverbal behavior, and there has been a correlation between gaze and distance. Virtual reality scholars have also studied these constructs for theoretical and methodological reasons. However, most studies in VR have been conducted in lab settings for short periods of time. This field study analyzed the behaviors of 232 participants over two experimental studies, finding that interpersonal distance and mutual gaze increased over time.
2023 IEEE CONFERENCE VIRTUAL REALITY AND 3D USER INTERFACES, VR
(2023)
Article
Psychology, Clinical
Steffany J. Fredman, Melanie S. Fischer, Donald H. Baucom, Yunying Le, Emily C. Taverna, Sy-Miin Chow, Nilam Ram, Amy D. Marshall
Summary: This study examined the relationship between momentary emotion dynamics and posttraumatic stress disorder (PTSD) symptoms. The findings suggest that higher reexperiencing symptoms are associated with greater emotional inertia, while higher avoidance symptoms are associated with less emotional inertia. Additionally, individuals also respond to their partners' arousal during intimate conversations. The results highlight the importance of considering the interpersonal context of emotion dynamics in PTSD treatment.
Article
Psychology, Social
Timon Elmer, Nilam Ram, Andrew T. Gloster, Laura F. Bringmann
Summary: This study examines the association between the quantity and quality of social interactions and changes in depressive symptoms, finding that the quality of social interactions may play an important role in the progression of individuals' depressive symptoms.
PERSONALITY AND SOCIAL PSYCHOLOGY BULLETIN
(2023)
Article
Computer Science, Software Engineering
Daniel Reimann, Andre Schulz, Nilam Ram, Robert Gaschler
Summary: Node-link diagrams allow for visual assessment of homophily by identifying and evaluating the relative number of intra-cluster and inter-cluster links. Our online experiment demonstrates that a design utilizing link type encoded edge color leads to more accurate perception of homophily compared to a design with same-color edges.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
