Article
Geriatrics & Gerontology
Samira A. Maboudian, Ming Hsu, Zhihao Zhang
Summary: This study introduces a method for analyzing verbal fluency data using recurrence analysis and proposes a new metric, DfD, to quantify semantic fluency data. The method is applied to compare Alzheimer's disease patients and healthy controls, showing significant differences in DfD between the two groups and complementing existing metrics in diagnostic prediction. Additionally, the visualization method allows for comparison of aggregate recall data at the group level.
FRONTIERS IN AGING NEUROSCIENCE
(2022)
Review
Public, Environmental & Occupational Health
Annett Schulze, Fabian Brand, Johanna Geppert, Gaby-Fleur Boel
Summary: This systematic review examines the current state of research on dashboards in the context of public health risks and diseases. The findings suggest a lack of evaluation of dashboard content and a focus on purely functional evaluations by development teams. The study highlights the need for a theory-based integration of user-specific risk information needs in research on public health intervention tools like dashboards.
FRONTIERS IN PUBLIC HEALTH
(2023)
Article
Multidisciplinary Sciences
Qingyun Li, Hanwei Zhang, Kai Lou, Yabi Yang, Xiaofan Ji, Jintao Zhu, Jonathan L. Sessler
Summary: Issues of molecular weight determination are critical in the development of supramolecular polymer chemistry, as there is often no simple correlation between optical performance and number-average molecular weight. This study reports an anion-responsive supramolecular polymer that exhibits monotonic changes in fluorescence color as a function of molecular weight. The anion-responsive nature of the system allows for regulation of supramolecular polymerization and monitoring of changes in molecular weight.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Vincent F. Scalfani, Vishank D. Patel, Avery M. Fernandez
Summary: This article demonstrates how to create Chemical Space Networks (CSNs) using a Python RDKit and NetworkX workflow, and introduces different CSN visualization features and network analysis calculations.
JOURNAL OF CHEMINFORMATICS
(2022)
Article
Geochemistry & Geophysics
John B. Rundle, Andrea Donnellan, Geoffrey Fox, James P. Crutchfield
Summary: The paper explores two methods of using proxy variables to depict the earthquake cycle in California, and finds that both methods provide almost equivalent information on earthquake correlations in the region. The resulting timeseries are concluded to be proxies for the cycle of stress accumulation and release associated with major tectonic activity.
SURVEYS IN GEOPHYSICS
(2022)
Article
Chemistry, Analytical
Yuan Luo, Shuchen Wang, Zhuowei Feng, Jie Li, Cuiping Mao, Rui Wang, Xingyu Jiang
Summary: Biopolymers are a promising alternative for information storage, and using chemically synthesized DNA to represent binary data has been the most successful implementation. However, the current systems lack the desired system integration and process automation, and rely too much on tubes and vials for DNA storage. This study presents a microfluidic platform that can automate the storage and retrieval of data-encoding oligonucleotide samples using a microvalve network architecture, achieving enhanced function integration and process automation compared to existing microfluidic approaches.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Jiahe Sun, Fang Lu, Yongjiang Luo, Lingzi Bie, Ling Xu, Yi Wang
Summary: Advancements in comparative genomics research have led to a growing interest in studying species evolution and genetic diversity. OrthoVenn3 has been developed as a powerful web-based tool that enables users to efficiently identify and annotate orthologous clusters and infer phylogenetic relationships across a range of species. The latest upgrade of OrthoVenn includes several important new features, enhancing its accuracy, visualization capabilities, and expanding its functionality for gene family analysis and collinearity analysis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Green & Sustainable Science & Technology
Chihli Hung, Wei-Chao Lin
Summary: This study develops a method using information visualization technology for evaluating researchers' research productivity and impact (RPI). Through the introduction of visualization and clustering components, the usefulness of this method in assessing RPI is demonstrated.
Article
Multidisciplinary Sciences
Kazumasa Muta, Ravinder K. Mittal, Ali Zifan
Summary: Patients with unexplained dysphagia show abnormalities in the distension phase of esophageal peristalsis, with faster bolus transit, smaller luminal cross-sectional area, and fragmented bolus flow compared to normals. These abnormalities are sensitive and specific markers of dysphagia, suggesting that the cause of dysphagia sensation may be due to esophageal contraction forcing the bolus through a narrow lumen esophagus.
Article
Computer Science, Information Systems
Maria Frasca, Genoveffa Tortora
Summary: The paper discusses the integration of computer science and medical research, focusing on analyzing PPMI data for Parkinson's disease. Information Retrieval and Machine Learning techniques are used to correlate data and classify patients, with a visualization system aiding in early diagnosis by supporting doctors in analyzing chronological data.
MULTIMEDIA TOOLS AND APPLICATIONS
(2022)
Review
Chemistry, Analytical
Zhirong He, Kun Xu, Yongming Li, Han Gao, Tingting Miao, Rui Zhao, Yanyan Huang
Summary: This article introduces the recent progress in fluorescent sensors for molecularly targeted imaging and real-time tracking of cellular senescence, and summarizes their molecular design, sensing mechanisms, biological activities, and fluorescent performance towards senescence biomarkers.
Article
Multidisciplinary Sciences
Ali Bahari Malayeri, Mohammad Bagher Khodabakhshi
Summary: This study investigates the cuffless estimation of blood pressure using deep neural networks and fuzzy recurrence plot. The proposed model combines 1-D and 2-D convolutional neural networks to capture the temporal and spatial dependencies of peripheral signals. The performance of the model is evaluated on a public dataset and it meets the requirements set by AAMI and achieves a grade of A according to BHS standard. The results demonstrate the feasibility and accuracy of the proposed approach.
SCIENTIFIC REPORTS
(2022)
Article
Materials Science, Multidisciplinary
Shanshan Zhao, Guangen Li, Qi Guo, Yaxin Wang, Mingjiang Zhang, Yajie Zhou, Shan Jin, Manzhou Zhu, Taotao Zhuang
Summary: Creating security materials with distinct optical characteristics, such as circularly polarized long afterglow (CPLA), is important for enhancing anticounterfeiting levels. A cementation-coupling strategy is designed to combine chiral photonic membranes with phosphor films, creating full-colored CPLA architectures. These CPLA systems achieve desired performance and can be used as optical labels in security fields.
ADVANCED OPTICAL MATERIALS
(2023)
Article
Biology
Federico Claudi, Adam L. Tyson, Luigi Petrucco, Troy W. Margrie, Ruben Portugues, Tiago Branco
Summary: The study introduces brainrender, an open-source Python package for interactive visualization of multidimensional datasets registered to brain atlases. This tool facilitates the creation of complex renderings with different data types in the same visualization, accelerating the analysis, interpretation, and dissemination of brain-wide multidimensional data.
Review
Chemistry, Inorganic & Nuclear
Siyue Ma, Guang Chen, Jie Xu, Yuxia Liu, Guoliang Li, Tao Chen, Yulin Li, Tony D. James
Summary: Alzheimer's disease is a common form of dementia that has seen significant advancements in early diagnosis research, leading to the development of novel fluorescent molecular probes suitable for modern clinical applications. Emerging concepts and strategies include increasing permeability, enhancing specificity, and improving optical properties.
COORDINATION CHEMISTRY REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Sylvan C. Baca, Davide Prandi, Michael S. Lawrence, Juan Miguel Mosquera, Alessandro Romanel, Yotam Drier, Kyung Park, Naoki Kitabayashi, Theresa Y. MacDonald, Mahmoud Ghandi, Eliezer Van Allen, Gregory V. Kryukov, Andrea Sboner, Jean-Philippe Theurillat, T. David Soong, Elizabeth Nickerson, Daniel Auclair, Ashutosh Tewari, Himisha Beltran, Robert C. Onofrio, Gunther Boysen, Candace Guiducci, Christopher E. Barbieri, Kristian Cibulskis, Andrey Sivachenko, Scott L. Carter, Gordon Saksena, Douglas Voet, Alex H. Ramos, Wendy Winckler, Michelle Cipicchio, Kristin Ardlie, Philip W. Kantoff, Michael F. Berger, Stacey B. Gabriel, Todd R. Golub, Matthew Meyerson, Eric S. Lander, Olivier Elemento, Gad Getz, Francesca Demichelis, Mark A. Rubin, Levi A. Garraway
Article
Oncology
Jonathan E. Rosenberg, Richard M. Bambury, Eliezer M. Van Allen, Harry A. Drabkin, Primo N. Lara, Andrea L. Harzstark, Nikhil Wagle, Robert A. Figlin, Gregory W. Smith, Levi A. Garraway, Toni Choueiri, Fredrik Erlandsson, Damian A. Laber
INVESTIGATIONAL NEW DRUGS
(2014)
Article
Oncology
Nikhil Wagle, Eliezer M. Van Allen, Daniel J. Treacy, Dennie T. Frederick, Zachary A. Cooper, Amaro Taylor-Weiner, Mara Rosenberg, Eva M. Goetz, Ryan J. Sullivan, Deborah N. Farlow, Dennis C. Friedrich, Kristin Anderka, Danielle Perrin, Cory M. Johannessen, Aaron McKenna, Kristian Cibulskis, Gregory Kryukov, Eran Hodis, Donald P. Lawrence, Sheila Fisher, Gad Getz, Stacey B. Gabriel, Scott L. Carter, Keith T. Flaherty, Jennifer A. Wargo, Levi A. Garraway
Article
Oncology
Eliezer M. Van Allen, Nikhil Wagle, Antje Sucker, Daniel J. Treacy, Cory M. Johannessen, Eva M. Goetz, Chelsea S. Place, Amaro Taylor-Weiner, Steven Whittaker, Gregory V. Kryukov, Eran Hodis, Mara Rosenberg, Aaron McKenna, Kristian Cibulskis, Deborah Farlow, Lisa Zimmer, Uwe Hillen, Ralf Gutzmer, Simone M. Goldinger, Selma Ugurel, Helen J. Gogas, Friederike Egberts, Carola Berking, Uwe Trefzer, Carmen Loquai, Benjamin Weide, Jessica C. Hassel, Stacey B. Gabriel, Scott L. Carter, Gad Getz, Levi A. Garraway, Dirk Schadendorf
Article
Multidisciplinary Sciences
Nora A. Moskowitz, Alexandre B. Roland, Eva K. Fischer, Ndimbintsoa Ranaivorazo, Charles Vidoudez, Marianne T. Aguilar, Sophia M. Caldera, Jacqueline Chea, Miruna G. Cristus, Jett P. Crowdis, Bluye DeMessie, Caroline R. desJardins-Park, Audrey H. Effenberger, Felipe Flores, Michael Giles, Emma Y. He, Nike S. Izmaylov, ChangWon C. Lee, Nicholas A. Pagel, Krystal K. Phu, Leah U. Rosen, Danielle A. Seda, Yong Shen, Santiago Vargas, Andrew W. Murray, Eden Abebe, Sunia A. Trauger, David A. Donoso, Miguel Vences, Lauren A. O'Connell
Review
Biochemistry & Molecular Biology
Tanya E. Keenan, Kelly P. Burke, Eliezer M. Van Allen
Article
Genetics & Heredity
Felix Dietlein, Donate Weghorn, Amaro Taylor-Weiner, Andre Richters, Brendan Reardon, David Liu, Eric S. Lander, Eliezer M. Van Allen, Shamil R. Sunyaev
Article
Cell Biology
Alok K. Tewari, Alexander T. M. Cheung, Jett Crowdis, Jake R. Conway, Sabrina Y. Camp, Stephanie A. Wankowicz, Dimitri G. Livitz, Jihye Park, Rosina T. Lis, Alice Bosma-Moody, Meng Xiao He, Saud H. AlDubayan, Zhenwei Zhang, Rana R. McKay, Ignaty Leshchiner, Myles Brown, Steven P. Balk, Gad Getz, Mary-Ellen Taplin, Eliezer M. Van Allen
Summary: The study conducted whole-exome and transcriptome sequencing on pre-treatment tumor biopsies from prostate cancer patients receiving intensive anti-androgen therapies, identifying distinct molecular features in exceptional responders and non-responders, such as clonal SPOP mutation and TP53 mutation. These findings may inform prospective validation studies to improve patient stratification and treatment strategies in high-risk localized prostate cancer.
Article
Multidisciplinary Sciences
Kenneth L. Kehl, Wenxin Xu, Alexander Gusev, Ziad Bakouny, Toni K. Choueiri, Irbaz Bin Riaz, Haitham Elmarakeby, Eliezer M. Van Allen, Deborah Schrag
Summary: By training natural language processing models, researchers have successfully extracted outcome information for participants in precision oncology studies, accelerating research on the correlation between cancer-related biomarkers and clinical endpoints.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Felix Dietlein, Alex B. Wang, Christian Fagre, Anran Tang, Nicolle J. M. Besselink, Edwin Cuppen, Chunliang Li, Shamil R. Sunyaev, James T. Neal, Eliezer M. Van Allen
Summary: We established a comprehensive map of somatic mutation events in the whole cancer genomes, representing 19 tumor types. We found that protein-coding events and noncoding events play different roles in tumors, and noncoding events may be potential drivers. We also discovered that XBP1 mutations primarily accumulate outside the gene's promoter and impact gene expression.
Editorial Material
Oncology
Andrew Hantel, Dillon D. Clancy, Kenneth L. Kehl, Jonathan M. Marron, Eliezer M. Van Allen, Gregory A. Abel
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Oncology
Seyram A. Doe-Tetteh, Sabrina Y. Camp, Dalicia Reales, Jett Crowdis, Anne Marie Noronha, Bernadette Wolff, Tina Alano, Jesse Galle, S. Duygu Selcuklu, Agnes Viale, Nicholas D. Socci, Ying L. Liu, William P. Tew, Carol Aghajanian, Marc Ladanyi, Meng Xiao He, Saud H. AlDubayan, Roei David Mazor, Ofer Shpilberg, Oshrat Hershkovitz-Rokah, Jose A. Riancho, Jose L. Hernandez, M. Carmen Gonzalez-Vela, Justin J. Buthorn, Manda Wilson, Amy E. Webber, Mariko Yabe, Kseniya Petrova-Drus, Marc Rosenblum, Benjamin H. Durham, Omar Abdel-Wahab, Michael F. Berger, Mark T. A. Donoghue, Andrew L. Kung, Julia Glade Bender, Neerav N. Shukla, Samuel A. Funt, Ahmet Dogan, Robert A. Soslow, Hikmat Al-Ahmadie, Darren R. Feldman, Eliezer M. Van Allen, Eli L. Diamond, David B. Solit
Summary: To overcome barriers to genomic testing for rare cancer patients, a program providing free clinical tumor genomic testing was initiated. Patients with specific rare cancers were recruited through social media outreach and engagement with advocacy groups. Tumors were analyzed using next-generation sequencing assay, with results reported to patients and local physicians. Whole-exome sequencing was performed for female patients with germ cell tumors to define the genomic landscape of this rare cancer subtype.
CLINICAL CANCER RESEARCH
(2023)
Article
Genetics & Heredity
Jonathan S. Berg, Laura M. Amendola, Christine Eng, Eliezer Van Allen, Stacy W. Gray, Nikhil Wagle, Heidi L. Rehm, Elizabeth T. DeChene, Matthew C. Dulik, Fuki M. Hisama, Wylie Burke, Nancy B. Spinner, Levi Garraway, Robert C. Green, Sharon Plon, James P. Evans, Gail P. Jarvik
GENETICS IN MEDICINE
(2013)
