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Integrating Genomic & Transcriptomic Features for Noninvasive Detection, Characterization, and Monitoring of T-Cell Lymphomas

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Blood 2024年 144卷 454-454页

作者： Takeshi Sugio Monica Nesselbush Navika Shukla Andrea Garofalo Jurik A. Mutter Mohammad Shahrokh Esfahani Stefan K. Alig Shuyu Shi Troy Noordenbos Mark P. Hamilton Cedric Rossi Feng Tian Chih Long Liu Mari Olsen Xiaoman Kang David A Russler-Germain Steven Horwitz Koji Kato Ayumu Ito Makoto Yamagishi Ash A. Alizadeh Department of Medicine Divisions of Oncology and Hematology Stanford University Stanford CA Program in Cancer Biology Stanford School of Medicine Stanford CA Divisions of Oncology and Hematology Stanford University Stanford CA Department of Radiation Oncology Stanford University Stanford CA Dept. of Bioengineering Schools of Engineering and Medicine Stanford CA Division of Blood and Marrow Transplantation and Cellular Therapy Stanford University School of Medicine Palo Alto CA CHU Dijon DIJON France Department of Medicine Division of Oncology Stanford University Stanford CA Siteman Cancer Center Division of Oncology Washington University School of Medicine Saint Louis MO Lymphoma Service Department of Medicine Memorial Sloan Kettering Cancer Center New York NY Department of Medicine and Biosystemic Science Kyushu University Graduate School of Medicine Fukuoka Japan Department of Hematopoietic Stem Cell Transplantation National Cancer Center Hospital Tokyo Japan Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences The University of Tokyo Tokyo JPN

Background : Mature T-cell lymphoma (TCL) outcomes remain inferior to aggressive B-cell counterparts, and thus represent unmet need. Given high relapse rates after remissions induced by current regimens, more sensitive MRD methods are needed to personalize treatment. We tackled these questions by integrating distinct host and viral molecular features for noninvasive detection, risk profiling, and monitoring of diverse mature TCLs. Methods : We studied 132 patients diagnosed with diverse TCLs (PTCL-NOS n=21, ALCL n=13, TFH lymphoma n=21, ATLL n=54, ENKTL n=6, CTCL n=15, others n=2). 37% of pts had newly diagnosed TCL primarily treated with CHOP-based regimens, while 62% had relapsed/refractory disease treated with salvage chemotherapies (26%), nivolumab (5%), and/or allogeneic HSCT (31%). We molecularly profiled 530 specimens, including serial blood plasma samples drawn before, during, and at the end-of-therapy (EOT) (n=274), baseline tumor tissues (n=128), and matched normal cells (n=128). Plasma cfDNA for all cases were profiled to detect somatic mutations in 259 recurrently mutated TCL genes by CAPP-Seq, genome-wide CNVs by CANARy (Chabon 2020 Nature), clonotypic VDJ at all TCR/BCR loci by SABER, T/B-cell abundance by QUARTZ (Sugio ASH 2024 abstract #193441), and inferred expression of 381 TCL/immune-related genes by EPIC-Seq (Esfahani Nature biotechnology 2022). Viral load and genotyping for EBV and HTLV-1 were assessed by VirCAPP-Seq (Garofalo ASH2022). Plasma cfRNA expression was profiled using RARE-Seq, by targeting 6.8k coding genes (Nesselbush 2024 Cancer Research). Results : We found that mutation-based disease burden measurements in cfDNA by CAPP-Seq were significantly correlated with clonotypic cell-free TCR levels (cfTCR; R=0.95, p<0.001) across all patients and plasma HTLV-1 load in ATLL patients (R=0.84, p<0.001). When considering outcomes after CHOP-based regimens, detection of ctDNA-MRD at EOT predicted significantly higher relapse risk (p= 0.003), i

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White Paper on Enabling Global Image Data Sharing in the Life sciences

arXiv

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arXiv 2024年

作者： Bajcsy, Peter Bhattiprolu, Sreenivas Börner, Katy Cimini, Beth A. Collinson, Lucy Ellenberg, Jan Fiolka, Reto Giger, Maryellen Goscinski, Wojtek Hartley, Matthew Hotaling, Nathan Horwitz, Rick Jug, Florian Kreshuk, Anna Lundberg, Emma Mathur, Aastha Narayan, Kedar Onami, Shuichi Plant, Anne L. Prior, Fred Swedlow, Jason Taylor, Adam Keppler, Antje National Institute of Standards and Technology GaithersburgMD20899 United States ZEISS Microscopy Customer Center DublinCA94568 United States Intelligent Systems Engineering Indiana University BloomingtonIN47408 United States Imaging Platform Broad Institute CambridgeMA United States Electron Microscopy Science Technology Platform Francis Crick Institute 1 Midland Road LondonNW1 1AT United Kingdom European Molecular Biology Laboratory Heidelberg Germany Lyda Hill Department of Bioinformatics UT Southwestern Medical Center DallasTX United States Department of Radiology and Committee on Medical Physics University of Chicago ChicagoIL United States National Imaging Facility Brisbane Australia European Molecular Biology Laboratory European Bioinformatics Institute Hinxton Cambridge United Kingdom National Center for Advancing Translational Science National Institutes of Health Rockville United States Allen Institute for Cell Science Seattle United States Fondazione Human Technopole Milan Italy Stanford University California US and SciLifeLab KTH Royal Institute of Technology Stockholm Sweden Center for Molecular Microscopy Center for Cancer Research National Cancer Institute National Institutes of Health BethesdaMD20892 United States Cancer Research Technology Program Frederick National Laboratory for Cancer Research FrederickMD21702 United States RIKEN Center for Biosystems Dynamics Research Kobe Japan Department of Biomedical Informatics Department of Radiology University of Arkansas for Medical Sciences Little RockAR72205 United States Divisions of Computational Biology and Molecular Cell and Developmental Biology University of Dundee United Kingdom Sage Bionetworks SeattleWA United States

Coordinated collaboration is essential to realize the added value of and infrastructure requirements for global image data sharing in the life sciences. In this White Paper, we take a first step at presenting some of the most common use cases as well as critical/emerging use cases of (including the use of artificial intelligence for) biological and medical image data, which would benefit tremendously from better frameworks for sharing (including technical, resourcing, legal, and ethical aspects). In the second half of this paper, we paint an ‘ideal world scenario’ for how global image data sharing could work and benefit all life sciences and beyond. As this is still a long way off, we conclude by suggesting several concrete measures directed toward our institutions, existing imaging communities and data initiatives, and national funders, as well as publishers. Our vision is that within the next ten years, most researchers in the world will be able to make their datasets openly available and use quality image data of interest to them for their research and benefit. This paper is published in parallel with a companion White Paper entitled "Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data", which addresses challenges and opportunities related to producing well-documented and high-quality image data that is ready to be shared. The driving goal is to address remaining challenges and democratize access to everyday practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location. © 2024, CC BY-NC-SA.

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Is there any linkage between interstellar aldehyde and alcohol?

arXiv

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arXiv 2021年

作者： Mondal, Suman Kumar Gorai, Prasanta Sil, Milan Ghosh, Rana Etim, Emmanuel E. Chakrabarti, Sandip K. Shimonishi, Takashi Nakatani, Naoki Furuya, Kenji Tan, Jonathan C. Das, Ankan Indian Centre for Space Physics 43 Chalantika Garia Station Road Kolkata700084 India Department of Space Earth and Environment Chalmers University of Technology GothenburgSE-412 96 Sweden Department of Chemical Sciences Federal University Wukari Katsina-Ala Road P.M.B. 1020 Taraba State Wukari Nigeria Center for Transdisciplinary Research Niigata University Nishi-ku Niigata950-2181 Japan Environmental Science Program Department of Science Faculty of Science Niigata University Nishi-ku Niigata950-2181 Japan Institute for Catalysis Hokkaido University N21W10 Kita-ku Hokkaido Sapporo001-0021 Japan Center for Computational Sciences University of Tsukuba Tsukuba305-8577 Japan Department of Astronomy University of Virginia CharlottesvilleVA22904 United States Department of Chemistry Graduate School of Science and Engineering Tokyo Metropolitan University 1-1 Minami-Osawa Hachioji Tokyo192-0397 Japan National Astronomical Observatory of Japan Tokyo181-8588 Japan

It is speculated that there might be some linkage between interstellar aldehydes and their corresponding alcohols. Here, an observational study and astrochemical modeling are coupled together to illustrate the connection between them. The ALMA cycle 4 data of a hot molecular core, G10.47+0.03 is utilized for this study. Various aldehydes (acetaldehyde, propanal, and glycolaldehyde), alcohols (methanol and ethylene glycol), and a ketone (acetone) are identified in this source. The excitation temperatures and the column densities of these species were derived via the rotation diagram method assuming LTE conditions. An extensive investigation is carried out to understand the formation of these species. Six pairs of aldehyde-alcohol: i) methanal and methanol;ii) ethanal and ethanol;iii) propanal and 1-propanol;iv) propenal and allyl alcohol;v) propynal and propar gyl alcohol;vi) glycolaldehyde and ethylene glycol;vii) along with one pair of ketone-alcohol (acetone and isopropanol) and viii) ketene-alcohol (ethenone and vinyl alcohol) are considered for this study. Two succes sive hydrogenation reactions in the ice phase are examined to form these alcohols from aldehydes, ketone, and ketene, respectively. Quantum chemical methods are extensively executed to review the ice phase formation route and the kinetics of these species. Based on the obtained kinetic data, astrochemical modeling is employed to derive the abundances of these aldehydes, alcohols, ketone, and ketene in this source. It is seen that our model could successfully explain the observed abundances of various species in this hot molecular core. Copyright © 2021, The Authors. All rights reserved.

关键词： Acetone

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Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer's disease

npj metabolic health and disease

引用

npj metabolic health and disease 2024年第1期2卷 15页

作者： Annalise Schweickart Richa Batra Bryan J Neth Cameron Martino Liat Shenhav Anru R Zhang Pixu Shi Naama Karu Kevin Huynh Peter J Meikle Leyla Schimmel Amanda Hazel Dilmore Kaj Blennow Henrik Zetterberg Colette Blach Pieter C Dorrestein Rob Knight Suzanne Craft Rima Kaddurah-Daouk Jan Krumsiek Tri-Institutional Program in Computational Biology & Medicine Weill Cornell Medicine New York NY USA. Department of Physiology and Biophysics Weill Cornell Medicine Institute for Computational Biomedicine Englander Institute for Precision Medicine New York NY USA. Department of Neurology Mayo Clinic Rochester MN USA. Department of Pediatrics University of California San Diego La Jolla CA USA. Department of Microbiology New York University Grossman School of Medicine New York NY USA. Department of Biostatistics and Bioinformatics Duke University Durham NC USA. Tasmanian Independent Metabolomics and Analytical Chemistry Solutions (TIMACS) Hobart TAS Australia. Baker Heart and Diabetes Institute 75 Commercial Road Melbourne VIC Australia. Baker Department of Cardiovascular Research Translation and Implementation La Trobe University Bundoora VIC Australia. Department of Psychiatry and Behavioral Sciences Duke University Durham NC USA. Department of Psychiatry and Neurochemistry University of Gothenburg Gothenburg Sweden. Duke Molecular Physiology Institute Duke University Durham NC USA. Skaggs School of Pharmacy and Pharmaceutical Sciences University of California San Diego La Jolla CA USA. Departments of Pediatrics Computer Science and Engineering Bioengineering University of California San Diego La Jolla CA USA. Department of Gerontology and Geriatric Medicine Wake Forest University School of Medicine Winston Salem NC USA. Duke Institute of Brain Sciences Duke University Durham NC USA. Department of Medicine Duke University Durham NC USA.

Alzheimer's disease (AD) is influenced by a variety of modifiable risk factors, including a person's dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only a few studies have explored KD's metabolic impact, especially on blood and cerebrospinal fluid (CSF). Our study involved participants at risk for AD, either cognitively normal or with mild cognitive impairment. The participants consumed both a modified Mediterranean Ketogenic Diet (MMKD) and the American Heart Association diet (AHAD) for 6 weeks each, separated by a 6-week washout period. We employed nuclear magnetic resonance (NMR)-based metabolomics to profile serum and CSF and metagenomics profiling on fecal samples. While the AHAD induced no notable metabolic changes, MMKD led to significant alterations in both serum and CSF. These changes included improved modifiable risk factors, like increased HDL-C and reduced BMI, reversed serum metabolic disturbances linked to AD such as a microbiome-mediated increase in valine levels, and a reduction in systemic inflammation. Additionally, the MMKD was linked to increased amino acid levels in the CSF, a breakdown of branched-chain amino acids (BCAAs), and decreased valine levels. Importantly, we observed a strong correlation between metabolic changes in the CSF and serum, suggesting a systemic regulation of metabolism. Our findings highlight that MMKD can improve AD-related risk factors, reverse some metabolic disturbances associated with AD, and align metabolic changes across the blood-CSF barrier.

关键词： Diseases Metabolomics

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Assessing the Potential of GPT-4 to Annotate Medical Notes Across Different Languages and Countries: A Model Evaluation Study

SSRN

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SSRN 2024年

作者： Saad Menezes, Maria Clara Hoffman, Alexander F. Tan, Amelia L.M. Nalbandyan, Mariné Omenn, Gilbert S. Mazzotti, Diego R. Hernández-Arango, Alejandro Visweswaran, Shyam Venkatesh, Shruthi Mandl, Kenneth D. Bourgeois, Florence T. Lee, James W.K. Makmur, Andrew Hanauer, David A. Semanik, Michael G. Kerivan, Lauren T. Hill, Terra Forero, Julian Restrepo Castro, Carlos Andrés C.R. Vigna, Matteo Ceriana, Piero Abu-El-rub, Noor Avillach, Paul Bellazzi, Riccardo Callaci, Thomas Gutiérrez-Sacristán, Alba Malovini, Alberto Mathew, Jomol P. Morris, Michele Murthy, Venkatesh Parimbelli, Enea Patel, Lav P. Sáez, Carlos Samayamuthu, Malarkodi Jebathilagam Thompson, Jeffrey A. Tibollo, Valentina Xia, Zongqi Kohane, Isaac S. Harvard Medical School Department of Biomedical Informatics 10 Shattuck Street BostonMA02115 United States School of Medicine and Public Health University of Wisconsin-Madison Office of Informatics and Information Technology 750 Highland Ave MadisonWI53705 United States University of Michigan Department of Computational Medicine & Bioinformatics Internal Medicine Human Genetics Environmental Health 100 Washtenaw Avenue Ann ArborMI48109 United States University of Kansas Medical Center Division of Medical Informatics Division of Pulmonary Critical Care and Sleep Medicine Department of Internal Medicine 3901 Rainbow Blvd Kansas CityKS66160 United States University of Antioquia Hospital Alma Máter de Antioquia Department of Internal Medicine Calle 64 N°51 D - 154 Medellín Colombia University of Pittsburgh Department of Biomedical Informatics 5607 Baum Blvd PittsburghPA15206 United States University of Pittsburgh Department of Neurology 3501 5th Avenue PittsburghPA15206 United States Boston Children's Hospital Computational Health Informatics Program 300 Longwood Avenue BostonMA02115 United States Boston Children's Hospital Department of Pediatrics 300 Longwood Avenue BostonMA02115 United States National University Health System Department of Surgery 1E Kent Ridge Rd Singapore119228 Singapore National University Health System Department of Diagnostic Imaging 1E Kent Ridge Rd Singapore119228 Singapore University of Michigan Department of Learning Health Sciences NCRC 100 2800 Plymouth Road Ann ArborMI48109 United States University of Kansas Medical Center Department of Surgery 3901 Rainbow Blvd Kansas CityKS66160 United States Istituti Clinici Scientifici Maugeri IRCCS Respiratory rehabilitation unit Via Maugeri 10 Pavia27100 Italy University of Kansas Medical Center 3901 Rainbow Blvd Kansas CityKS66160 United States University of Pavia Department of Electrical Computer and Biomedical Engineering via Ferrata 5 Pavia2710

Background: Physicians invest hours creating patient notes, which are rich in information but difficult for computers to analyze due to their unstructured format. GPT-4 reshaped our ability to process text, yet it is unknown how well this model can handle medical notes. This project aims to compare GPT-4’s ability to annotate medical notes against experienced physicians across three different languages at multiple institutions and countries. Methods: This study included eight sites from four countries - the United States, Colombia, Singapore, and Italy. Each site contributed seven de-identified notes (admission, progress, or consult) from hospitalized patients. GPT-4 assessed each note by answering 14 questions, including demographic information, clinical judgments, data quality, and patients’ eligibility for a hypothetical study enrollment. For validation, two physicians from each site independently evaluated GPT-4's responses. Findings: Overall, 56 medical notes, written in English, Italian, and Spanish, were analyzed. A total of 784 responses from GPT-4 were generated. Both physicians agreed with GPT-4’s response 79% of the time (622/784, 95%CI 76-82%). Only one of the two physicians agreed with GPT-4’s response 10% of the time (82/784, 95%CI 8-13%). Neither physician agreed with GPT-4’s response 10% of the time (80/784, 95%CI 8-13%). Both physicians agreed with GPT-4 more often in notes written in Spanish and Italian than in English, with agreement rates of 88% (86/98, 95%CI 79-93%), 84% (82/98, 95%CI 75-90%), and 77% (454/588, 95%CI 74-80%), respectively. Hallucinations were rare (10/784, 95%CI 0-2%). GPT-4 correctly selected patients for a hypothetical study enrollment based on three criteria 90% of the time (95%CI 81-98%). Interpretation: The findings indicate that GPT-4 annotations demonstrated a high agreement rate with physicians across all languages. We also demonstrate GPT-4's potential to assist in patient selection for studies. Funding: None. Declarati

关键词： Medical computing

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The Japanese Vision for the Black Hole Explorer Mission

arXiv

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arXiv 2024年

作者： Akiyama, Kazunori Niinuma, Kotaro Hada, Kazuhiro Doi, Akihiro Hagiwara, Yoshiaki Higuchi, Aya E. Honma, Mareki Kawashima, Tomohisa Kolev, Dimitar Koyama, Shoko Masui, Sho Ohsuga, Ken Sano, Hidetoshi Takami, Hideki Tsunetoe, Yuh Uzawa, Yoshinori Akahori, Takuya Akiyama, Yuto Galison, Peter Hayashi, Takayuki J. Hirota, Tomoya Inoue, Makoto Iwata, Yuhei Johnson, Michael D. Kino, Motoki Kofuji, Yutaro Mizuno, Yosuke Moriyama, Kotaro Nagai, Hiroshi Nakamura, Kenta Notsu, Shota Ono, Fumie Oya, Yoko Oyama, Tomoaki Rana, Hannah Saida, Hiromi Saito, Ryo Saito, Yoshihiko Sasada, Mahito Sawada-Satoh, Satoko Takahashi, Mikiya M. Takamura, Mieko Tong, Edward Tsuji, Hiroyuki Yoshioka, Shogo Watanabe, Yoshimasa Massachusetts Institute of Technology Haystack Observatory WestfordMA01886 United States Mizusawa VLBI Observatory National Astronomical Observatory of Japan Iwate023-0861 Japan Black Hole Initiative Harvard University CambridgeMA02138 United States Graduate School of Sciences and Technology for Innovation Yamaguchi University Yamaguchi753-8512 Japan The Graduate School of Science Nagoya City University Aichi467-0001 Japan Institute of Space and Astronautical Science Japan Aerospace Exploration Agency Kanagawa252-5210 Japan Department of Space and Astronautical Science The Graduate University for Advanced Studies SOKENDAI Kanagawa229-8510 Japan Natural Science Laboratory Toyo University Tokyo112-8606 Japan Division of Science School of Science and Engineering Tokyo Denki University Saitama350-0394 Japan Department of Astronomy Graduate School of Science The University of Tokyo Tokyo113-0033 Japan Institute for Cosmic Ray Research The University of Tokyo Chiba277-8582 Japan Space Communication Systems Laboratory Wireless Networks Research Center National Institute of Information and Communications Technology Tokyo184-8795 Japan Graduate School of Science and Technology Niigata University Niigata950-2181 Japan Advanced Technology Center National Astronomical Observatory of Japan Tokyo181-8588 Japan Center for Computational Sciences University of Tsukuba Ibaraki305-8577 Japan Faculty of Engineering Gifu University Gifu501-1193 Japan Harvard University CambridgeMA02138 United States Azabu Junior and Senior High School Tokyo106-0046 Japan Astronomical Science Program The Graduate University for Advanced Studies SOKENDAI Tokyo181-8588 Japan Institute of Astronomy and Astrophysics Academia Sinica Taipei10617 Taiwan Center for Astrophysics Harvard & Smithsonian CambridgeMA02138 United States Kogakuin University of Technology & Engineering Academic Support Center 2665-1 Nakano Hachioji Tokyo192-0015 Japan Tsung-Dao Lee Institut

The Black Hole Explorer (BHEX) is a next-generation space very long baseline interferometry (VLBI) mission concept that will extend the ground-based millimeter/submillimeter arrays into space. The mission, closely aligned with the science priorities of the Japanese VLBI community, involves an active engagement of this community in the development of the mission, resulting in the formation of the Black Hole Explorer Japan Consortium. Here we present the current Japanese vision for the mission, ranging from scientific objectives to instrumentation. The Consortium anticipates a wide range of scientific investigations, from diverse black hole physics and astrophysics studied through the primary VLBI mode, to the molecular universe explored via a potential single-dish observation mode in the previously unexplored 50-70 GHz band that would make BHEX the highest-sensitivity explorer ever of molecular oxygen. A potential major contribution for the onboard instrument involves supplying essential elements for its high-sensitivity dual-band receiving system, which includes a broadband 300 GHz SIS mixer and a space-certified multi-stage 4.5K cryocooler akin to those used in the Hitomi and XRISM satellites by the Japan Aerospace Exploration Agency. Additionally, the Consortium explores enhancing and supporting BHEX operations through the use of millimeter/submillimeter facilities developed by the National Astronomical Observatory of Japan, coupled with a network of laser communication stations operated by the National Institute of Information and Communication Technology. Copyright © 2024, The Authors. All rights reserved.

关键词： Radio astronomy

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Data quality measures and data cleansing for research information systems

arXiv

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arXiv 2019年

作者： Azeroual, Otmane Saake, Gunter Abuosba, Mohammad Berlin10117 Germany Otto-Von-Guericke University Magdeburg Department of Computer Science Institute for Technical and Business Information Systems Database Research Group P.O. Box 4120 Magdeburg39106 Germany University of Applied Sciences Htw Berlin Study Program Computational Science and Engineering Wilhelminenhofstrasse 75a Berlin12459 Germany

The collection, transfer and integration of research information into different research information systems can result in different data errors that can have a variety of negative effects on data quality. In order to detect errors at an early stage and treat them efficiently, it is necessary to determine the clean-up measures and the new techniques of data cleansing for quality improvement in research institutions. Thereby an adequate and reliable basis for decision-making using an RIS is provided, and confidence in a given dataset increased. In this paper, possible measures and the new techniques of data cleansing for improving and increasing the data quality in research information systems will be presented and how these are to be applied to the research information. Copyright © 2019, The Authors. All rights reserved.

关键词： Standardization

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Using physical features of protein core packing to distinguish real proteins from decoys

arXiv

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arXiv 2020年

作者： Grigas, Alex T. Mei, Zhe Treado, John D. Levine, Zachary A. Regan, Lynne O'Hern, Corey S. Graduate Program in Computational Biology and Bioinformatics Yale University New HavenCT06520 United States Integrated Graduate Program in Physical and Engineering Biology Yale University New HavenCT06520 United States Department of Chemistry Yale University New HavenCT06520 United States Department of Mechanical Engineering and Materials Science Yale University New HavenCT06520 United States Department of Pathology Yale University New HavenCT06520 United States Department of Molecular Biophysics and Biochemistry Yale University New HavenCT06520 United States Institute of Quantitative Biology Biochemistry and Biotechnology Centre for Synthetic and Systems Biology School of Biological Sciences University of Edinburgh Department of Physics Yale University New HavenCT06520 United States Department of Applied Physics Yale University New HavenCT06520 United States

The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical features that specify a real protein. For example, it has long been appreciated that the hydrophobic cores of proteins contribute signifficantly to their stability. As a dataset of decoys to compare with real protein structures, we studied submissions to the bi-annual CASP competition (speciffically CASP11, 12, and 13), in which researchers attempt to predict the structure of a protein only knowing its amino acid sequence. Our analysis reveals that many of the submissions possess cores that do not recapitulate the features that define real proteins. In particular, the model structures appear more densely packed (because of energetically unfavorable atomic overlaps), contain too few residues in the core, and have improper distributions of hydrophobic residues throughout the structure. Based on these observations, we developed a deep learning method, which incorporates key physical features of protein cores, to predict how well a computational model recapitulates the real protein structure without knowledge of the structure of the target sequence. By identifying the important features of protein structure, our method is able to rank decoys from the CASP competitions equally well, if not better than, state-of-the-art methods that incorporate many additional features. Copyright © 2020, The Authors. All rights reserved.

关键词： Proteins

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Correction to: Authors’ Reply to Letter to the Editor: Continued improvement to genetic diversity indicator for CBD

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Conservation Genetics 2021年第4期22卷 537-539页

作者： Laikre, Linda Hohenlohe, Paul A. Allendorf, Fred W. Bertola, Laura D. Breed, Martin F. Bruford, Michael W. Funk, W. Chris Gajardo, Gonzalo González-Rodríguez, Antonio Grueber, Catherine E. Hedrick, Philip W. Heuertz, Myriam Hunter, Margaret E. Johannesson, Kerstin Liggins, Libby MacDonald, Anna J. Mergeay, Joachim Moharrek, Farideh O’Brien, David Ogden, Rob Orozco-terWengel, Pablo Palma-Silva, Clarisse Pierson, Jennifer Paz-Vinas, Ivan Russo, Isa-Rita M. Ryman, Nils Segelbacher, Gernot Sjögren-Gulve, Per Waits, Lisette P. Vernesi, Cristiano Hoban, Sean Division of Population Genetics Department of Zoology Stockholm University Stockholm Sweden Institute for Bioinformatics and Evolutionary Studies Department of Biological Sciences University of Idaho Moscow USA Division of Biological Sciences University of Montana Missoula USA City College of New York New York USA College of Science and Engineering Flinders University Bedford Park Australia School of Biosciences Cardiff University Cardiff Wales UK Graduate Degree Program in Ecology Department of Biology Colorado State University Fort Collins USA Universidad de Los Lagos Lab Genetics Aquaculture & Biodiversity Osorno Chile Instituto de Investigaciones en Ecosistemas y Sustentabilidad Universidad Nacional Autónoma de México Morelia Mexico School of Life and Environmental Sciences Faculty of Science The University of Sydney Sydney Australia School of Life Sciences Arizona State University Tempe USA INRAE Univ. Bordeaux Biogeco Cestas France U.S. Geological Survey Wetland and Aquatic Research Center Gainesville USA Department of Marine Sciences University of Gothenburg Tjärnö Strömstad Sweden School of Natural and Computational Sciences Massey University Auckland New Zealand The John Curtin School of Medical Research/Research School of Biology The Australian National University Acton Australia Research Institute for Nature and Forest Geraardsbergen Belgium Aquatic Ecology Evolution and Conservation KULeuven Leuven Belgium Novo Nordisk Foundation Center for Basic Metabolic Research Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Faculty of Biological Sciences Tarbiat Modares University Tehran Iran Scottish Natural Heritage Inverness UK Royal (Dick) School of Veterinary Studies and the Roslin Institute University of Edinburgh Midlothian UK Department of Plant Science Institute of Biology University of Campinas Campinas Brazil Australian Wildlife Conservancy Subiaco East Australia Laboratoire Evolution & Div

A correction to this paper has been published: https://***/10.1007/s10592-021-01376-9

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The bulk van der Waals layered magnet CrSBr is a quasi-1D material

arXiv

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arXiv 2022年

作者： Klein, Julian Pingault, Benjamin Florian, Matthias Heißenbüttel, Marie-Christin Steinhoff, Alexander Song, Zhigang Torres, Kierstin Dirnberger, Florian Curtis, Jonathan B. Weile, Mads Penn, Aubrey Deilmann, Thorsten Dana, Rami Bushati, Rezlind Quan, Jiamin Luxa, Jan Sofer, Zdenek Alù, Andrea Menon, Vinod M. Wurstbauer, Ursula Rohlfing, Michael Narang, Prineha Lončar, Marko Ross, Frances M. Department of Materials Science and Engineering Massachusetts Institute of Technology CambridgeMA02139 United States John A. Paulson School of Engineering and Applied Sciences Harvard University CambridgeMA02138 United States QuTech Delft University of Technology Delft2600 GA Netherlands Department of Electrical and Computer Engineering Department of Physics University of Michigan Ann ArborMI48109 United States Institut für Festkörpertheorie Westfälische Wilhelms-Universität Münster Münster48149 Germany Institut für Theoretische Physik Universität Bremen P.O. Box 330 440 Bremen28334 Germany Bremen Center for Computational Materials Science University of Bremen Bremen28359 Germany Department of Physics City College of New York New YorkNY10031 United States College of Letters and Science UCLA Los AngelesCA90095 United States Department of Physics Technical University of Denmark Kgs. LyngbyDK-2800 Denmark MIT.nano Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics The Graduate Center City University of New York New YorkNY10016 United States Photonics Initiative CUNY Advanced Science Research Center New YorkNY10031 United States Physics Program Graduate Center City University of New York New YorkNY10026 United States Department of Inorganic Chemistry University of Chemistry and Technology Prague Technická 5 Prague 6166 28 Czech Republic Institute of Physics Center for Nanotechnology University of Münster Münster48149 Germany

Correlated quantum phenomena in one-dimensional (1D) systems that exhibit competing electronic and magnetic order are of strong interest for studying fundamental interactions and excitations, such as Tomonaga-Luttinger liquids and topological orders and defects with properties completely different from the quasiparticles expected in their higher-dimensional counterparts. However, clean 1D electronic systems are difficult to realize experimentally, particularly magnetically ordered systems. Here, we show that the van der Waals layered magnetic semiconductor CrSBr behaves like a quasi-1D material embedded in a magnetically ordered environment. The strong 1D electronic character originates from the Cr-S chains and the combination of weak interlayer hybridization and anisotropy in effective mass and dielectric screening with an effective electron mass ratio of meX/meY ∼ 50. This extreme anisotropy experimentally manifests in strong electron-phonon and exciton-phonon interactions, a Peierls-like structural instability and a Fano resonance from a van Hove singularity of similar strength of metallic carbon nanotubes. Moreover, due to the reduced dimensionality and interlayer coupling, CrSBr hosts spectrally narrow (1 meV) excitons of high binding energy and oscillator strength that inherit the 1D character. Overall, CrSBr is best understood as a stack of weakly hybridized monolayers and appears to be an experimentally attractive candidate for the study of exotic exciton and 1D correlated many-body physics in the presence of magnetic order. Copyright © 2022, The Authors. All rights reserved.

关键词： Excitons

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