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JOURNAL ARTICLE
Saikat Nandi, Axel Stenquist, Asimina Papoulia, Edvin Olofsson, Laura Badano, Mattias Bertolino, David Busto, Carlo Callegari, Stefanos Carlström, Miltcho B Danailov, Philipp V Demekhin, Michele Di Fraia, Per Eng-Johnsson, Raimund Feifel, Guillaume Gallician, Luca Giannessi, Mathieu Gisselbrecht, Michele Manfredda, Michael Meyer, Catalin Miron, Jasper Peschel, Oksana Plekan, Kevin C Prince, Richard J Squibb, Marco Zangrando, Felipe Zapata, Shiyang Zhong, Jan Marcus Dahlström
Quantum entanglement between the degrees of freedom encountered in the classical world is challenging to observe due to the surrounding environment. To elucidate this issue, we investigate the entanglement generated over ultrafast timescales in a bipartite quantum system comprising two massive particles: a free-moving photoelectron, which expands to a mesoscopic length scale, and a light-dressed atomic ion, which represents a hybrid state of light and matter. Although the photoelectron spectra are measured classically, the entanglement allows us to reveal information about the dressed-state dynamics of the ion and the femtosecond extreme ultraviolet pulses delivered by a seeded free-electron laser...
April 19, 2024: Science Advances
#2
JOURNAL ARTICLE
Ryan Lorig-Roach, Melissa Meredith, Jean Monlong, Miten Jain, Hugh Olsen, Brandy McNulty, David Porubsky, Tessa Montague, Julian Lucas, Chris Condon, Jordan M Eizenga, Sissel Juul, Sean McKenzie, Sara E Simmonds, Jimin Park, Mobin Asri, Sergey Koren, Evan Eichler, Richard Axel, Bruce Martin, Paolo Carnevali, Karen Miga, Benedict Paten
Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequencing technologies are often used to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse...
April 16, 2024: Genome Research
#3
JOURNAL ARTICLE
Nisha Gopal, Jeremy Leitz, Chuchu Wang, Luis Esquivies, Richard A Pfuetzner, Axel T Brunger
Synaptic vesicles specific to inhibitory GABA-releasing neurons are critical for regulating neuronal excitability. To study the specific molecular composition, architecture, and function of inhibitory synaptic vesicles, we have developed a new method to isolate and purify GABA synaptic vesicles from mouse brains. GABA synaptic vesicles were immunoisolated from mouse brain tissue using an engineered fragment antigen-binding region (Fab) against the vesicular GABA transporter (vGAT) and purified. Western blot analysis confirmed that the GABA synaptic vesicles were specifically enriched for vGAT and largely depleted of contaminants from other synaptic vesicle types, such as vesicular glutamate transporter (vGLUT1), and other cellular organelles...
2024: Current research in physiology
#4
JOURNAL ARTICLE
Kelvin J Richards, Axel Timmermann
The success of individual species under a change to the environment is dependent on a number of factors, which include the changes to habitat, competition with other species and adaptability. Here we investigate the impact of differing dispersal characteristics of two competing species responding to the change using an idealized spatio-temporal model. The rate of dispersion is given by a combination of the growth term and the form of the diffusion term, which is set to give either normal diffusion or anomalous (super) diffusion...
March 20, 2024: Journal of Theoretical Biology
#5
JOURNAL ARTICLE
Helen M Faddy, Carla Osiowy, Brian Custer, Michael Busch, Susan L Stramer, Melinda M Dean, Jessika Acutt, Elvina Viennet, Thijs van de Laar, Wai-Chiu Tsoi, Claire Styles, Phil Kiely, Angelo Margaritis, So-Yong Kwon, Yan Qiu, Xuelian Deng, Antoine Lewin, Signe Winther Jørgensen, Christian Erikstrup, David Juhl, Silvia Sauleda, Bernardo Armando Camacho Rodriguez, Lisbeth Jennifer Catherine Soto Coral, Paula Andrea Gaviria García, Sineenart Oota, Sheila F O'Brien, Silvano Wendel, Emma Castro, Laura Navarro Pérez, Heli Harvala, Katy Davison, Claire Reynolds, Lisa Jarvis, Piotr Grabarczyk, Aneta Kopacz, Magdalena Łętowska, Niamh O'Flaherty, Fiona Young, Padraig Williams, Lisa Burke, Sze Sze Chua, An Muylaert, Isabel Page, Ann Jones, Christoph Niederhauser, Marion Vermeulen, Syria Laperche, Pierre Gallian, Masahiro Satake, Marcelo Addas-Carvalho, Sebastián Blanco, Sandra V Gallego, Axel Seltsam, Marijke Weber-Schehl, Arwa Z Al-Riyami, Khuloud Al Maamari, Fatma Ba Alawi, Hem Chandra Pandey, Rochele Azevedo França, Richard Charlewood
BACKGROUND AND OBJECTIVES: Nucleic acid-amplification testing (NAT) is used for screening blood donations/donors for blood-borne viruses. We reviewed global viral NAT characteristics and NAT-yield confirmatory testing used by blood operators. MATERIALS AND METHODS: NAT characteristics and NAT-yield confirmatory testing used during 2019 was surveyed internationally by the International Society of Blood Transfusion Working Party Transfusion-Transmitted Infectious Diseases...
March 22, 2024: Vox Sanguinis
#6
JOURNAL ARTICLE
Bruce E Sands, Geert D'Haens, David B Clemow, Peter M Irving, Jordan T Johns, Theresa Hunter Gibble, Maria T Abreu, Scott Lee, Tadakazu Hisamatsu, Taku Kobayashi, Marla C Dubinsky, Severine Vermeire, Corey A Siegel, Laurent Peyrin-Biroulet, Richard E Moses, Joe Milata, Vipin Arora, Remo Panaccione, Axel Dignass
BACKGROUND: Mirikizumab, a p19-directed interleukin-23 monoclonal antibody, is efficacious in inducing clinical remission at week 12 (W12) and maintaining clinical remission at W52 in patients with moderately to severely active ulcerative colitis. Results are presented from the open-label extension study through W104. METHODS: Clinical, symptomatic, quality-of-life, and adverse event outcomes are reported for mirikizumab induction responders and extended induction responders, including biologic-failed patients, who entered LUCENT-3, with data shown for W52 maintenance responders or remitters...
March 9, 2024: Inflammatory Bowel Diseases
#7
JOURNAL ARTICLE
Okyaz Eminaga, Mahmoud Abbas, Christian Kunder, Yuri Tolkach, Ryan Han, James D Brooks, Rosalie Nolley, Axel Semjonow, Martin Boegemann, Robert West, Jin Long, Richard E Fan, Olaf Bettendorf
Prostate cancer pathology plays a crucial role in clinical management but is time-consuming. Artificial intelligence (AI) shows promise in detecting prostate cancer and grading patterns. We tested an AI-based digital twin of a pathologist, vPatho, on 2603 histological images of prostate tissue stained with hematoxylin and eosin. We analyzed various factors influencing tumor grade discordance between the vPatho system and six human pathologists. Our results demonstrated that vPatho achieved comparable performance in prostate cancer detection and tumor volume estimation, as reported in the literature...
March 4, 2024: Scientific Reports
#8
JOURNAL ARTICLE
Pavel Loginovic, Feiyi Wang, Jiang Li, Lauric Ferrat, Uyenlinh L Mirshahi, H Shanker Rao, Axel Petzold, Jessica Tyrrell, Harry D Green, Michael N Weedon, Andrea Ganna, Tiinamaija Tuomi, David J Carey, Richard A Oram, Tasanee Braithwaite
Optic neuritis (ON) is associated with numerous immune-mediated inflammatory diseases, but 50% patients are ultimately diagnosed with multiple sclerosis (MS). Differentiating MS-ON from non-MS-ON acutely is challenging but important; non-MS ON often requires urgent immunosuppression to preserve vision. Using data from the United Kingdom Biobank we showed that combining an MS-genetic risk score (GRS) with demographic risk factors (age, sex) significantly improved MS prediction in undifferentiated ON; one standard deviation of MS-GRS increased the Hazard of MS 1...
February 28, 2024: Nature Communications
#9
JOURNAL ARTICLE
Helen M Faddy, Carla Osiowy, Brian Custer, Michael Busch, Susan L Stramer, Opeyemi Adesina, Thijs van de Laar, Wai-Chiu Tsoi, Claire Styles, Phil Kiely, Angelo Margaritis, So-Yong Kwon, Yan Qiu, Xuelian Deng, Antoine Lewin, Signe Winther Jørgensen, Christian Erikstrup, David Juhl, Silvia Sauleda, Bernardo Armando Camacho Rodriguez, Lisbeth Jennifer Catherine Soto Coral, Paula Andrea Gaviria García, Sineenart Oota, Sheila F O'Brien, Silvano Wendel, Emma Castro, Laura Navarro Pérez, Heli Harvala, Katy Davison, Claire Reynolds, Lisa Jarvis, Piotr Grabarczyk, Aneta Kopacz, Magdalena Łętowska, Niamh O'Flaherty, Fiona Young, Padraig Williams, Lisa Burke, Sze Sze Chua, An Muylaert, Isabel Page, Ann Jones, Christoph Niederhauser, Marion Vermeulen, Syria Laperche, Pierre Gallian, Salam Sawadogo, Masahiro Satake, Ahmad Gharehbaghian, Marcelo Addas-Carvalho, Sebastián Blanco, Sandra V Gallego, Axel Seltsam, Marijke Weber-Schehl, Arwa Z Al-Riyami, Khuloud Al Maamari, Fatma Ba Alawi, Hem Chandra Pandey, Dora Mbanya, Rochele Azevedo França, Richard Charlewood
BACKGROUND AND OBJECTIVES: Nucleic acid amplification testing (NAT), in blood services context, is used for the detection of viral and parasite nucleic acids to reduce transfusion-transmitted infections. This project reviewed NAT for screening blood donations globally. MATERIALS AND METHODS: A survey on NAT usage, developed by the International Society of Blood Transfusion Working Party on Transfusion-transmitted Infectious Diseases (ISBT WP-TTID), was distributed through ISBT WP-TTID members...
February 23, 2024: Vox Sanguinis
#10
EDITORIAL
Topun Austin, Daniel Connolly, Kate Dinwiddy, Anthony Richard Hart, Axel Heep, Sundeep Harigopal, Harriet Joy, Karen Luyt, Christina Malamateniou, Nazakat Merchant, Chrysoula Rizava, Mary A Rutherford, Kelly Spike, Brigitte Vollmer, James P Boardman
No abstract text is available yet for this article.
February 23, 2024: Archives of Disease in Childhood. Fetal and Neonatal Edition
#11
JOURNAL ARTICLE
Health Economic Consequences Associated With COVID-19-Related Delay in Melanoma Diagnosis in Europe.
Lara V Maul, Dagmar Jamiolkowski, Rebecca A Lapides, Alina M Mueller, Axel Hauschild, Claus Garbe, Paul Lorigan, Jeffrey E Gershenwald, Paolo Antonio Ascierto, Georgina V Long, Michael Wang-Evers, Richard A Scolyer, Babak Saravi, Matthias Augustin, Alexander A Navarini, Stefan Legge, István B Németh, Ágnes J Jánosi, Simone Mocellin, Anita Feller, Dieter Manstein, Alexander Zink, Julia-Tatjana Maul, Alessandra Buja, Kaustubh Adhikari, Elisabeth Roider
IMPORTANCE: The COVID-19 pandemic resulted in delayed access to medical care. Restrictions to health care specialists, staff shortages, and fear of SARS-CoV-2 infection led to interruptions in routine care, such as early melanoma detection; however, premature mortality and economic burden associated with this postponement have not been studied yet. OBJECTIVE: To determine the premature mortality and economic costs associated with suspended melanoma screenings during COVID-19 pandemic lockdowns by estimating the total burden of delayed melanoma diagnoses for Europe...
February 5, 2024: JAMA Network Open
#12
LETTER
Jacob S Appelbaum, Andrew H Wei, Sumithra J Mandrekar, Ing S Tiong, Chong Chyn Chua, Tse-Chieh Teh, Chun Yew Fong, Stephen B Ting, Daniela Weber, Axel Benner, Hannah Hill, Maral Saadati, Jun Yin, Richard M Stone, Guillermo Garcia-Manero, Harry P Erba, Geoffrey L Uy, Guido Marcucci, Richard A Larson, Abin Thomas, Sylvie D Freeman, Nuria Marquez Almuina, Konstanze Döhner, Ian Thomas, Nigel H Russel, Hartmut Döhner, Megan Othus, Elihu H Estey, Roland B Walter
No abstract text is available yet for this article.
February 2024: Leukemia
#13
JOURNAL ARTICLE
Ruba Hammad, Jamal Alzubi, Manuel Rhiel, Kay O Chmielewski, Laura Mosti, Julia Rositzka, Marcel Heugel, Jan Lawrenz, Valentina Pennucci, Birgitta Gläser, Judith Fischer, Axel Schambach, Thomas Moritz, Nico Lachmann, Tatjana I Cornu, Claudio Mussolino, Richard Schäfer, Toni Cathomen
The CRISPR-Cas12a platform has attracted interest in the genome editing community because the prototypical Acidaminococcus Cas12a generates a staggered DNA double-strand break upon binding to an AT-rich protospacer-adjacent motif (PAM, 5'-TTTV). The broad application of the platform in primary human cells was enabled by the development of an engineered version of the natural Cas12a protein, called Cas12a Ultra. In this study, we confirmed that CRISPR-Cas12a Ultra ribonucleoprotein complexes enabled allelic gene disruption frequencies of over 90% at multiple target sites in human T cells, hematopoietic stem and progenitor cells (HSPCs), and induced pluripotent stem cells (iPSCs)...
January 12, 2024: International Journal of Molecular Sciences
#14
JOURNAL ARTICLE
Romain Cohen, Morteza Raeisi, Benoist Chibaudel, Takayuki Yoshino, Qian Shi, John R Zalcberg, Richard Adams, Chiara Cremolini, Axel Grothey, Robert J Mayer, Eric Van Cutsem, Josep Tabernero, Hideaki Bando, Toshihiro Misumi, Michael J Overman, Thierry André, Aimery de Gramont
PURPOSE: Immune checkpoint inhibitors (ICIs) appeared active in single-arm trials for patients with chemoresistant metastatic colorectal cancer (mCRC) harboring microsatellite instability (MSI). Given the paucity of randomised controlled trials (RCTs) in this setting, we evaluated the effect size of ICIs using intra-patients comparison and ARCAD database as historical controls. PATIENTS AND METHODS: Individual-patient data from NIPICOL and CheckMate 142 phase II trials that evaluated a combination of ICIs for MSI mCRC patients (N = 176) and from five non-ICI mCRC historical RCTs in second-line or latter (N = 4026) were analyzed...
March 2024: European Journal of Cancer
#15
JOURNAL ARTICLE
Laura K Wiley, Jonathan A Shortt, Emily R Roberts, Jan Lowery, Elizabeth Kudron, Meng Lin, David Mayer, Melissa Wilson, Tonya M Brunetti, Sameer Chavan, Tzu L Phang, Nikita Pozdeyev, Joseph Lesny, Stephen J Wicks, Ethan T Moore, Joshua L Morgenstern, Alanna N Roff, Elise L Shalowitz, Adrian Stewart, Cole Williams, Michelle N Edelmann, Madelyne Hull, J Tacker Patton, Lisen Axell, Lisa Ku, Yee Ming Lee, Jean Jirikowic, Anna Tanaka, Emily Todd, Sarah White, Brett Peterson, Emily Hearst, Richard Zane, Casey S Greene, Rasika Mathias, Marilyn Coors, Matthew Taylor, Debashis Ghosh, Michael G Kahn, Ian M Brooks, Christina L Aquilante, David Kao, Nicholas Rafaels, Kristy R Crooks, Steve Hess, Kathleen C Barnes, Christopher R Gignoux
Precision medicine initiatives across the globe have led to a revolution of repositories linking large-scale genomic data with electronic health records, enabling genomic analyses across the entire phenome. Many of these initiatives focus solely on research insights, leading to limited direct benefit to patients. We describe the biobank at the Colorado Center for Personalized Medicine (CCPM Biobank) that was jointly developed by the University of Colorado Anschutz Medical Campus and UCHealth to serve as a unique, dual-purpose research and clinical resource accelerating personalized medicine...
January 4, 2024: American Journal of Human Genetics
#16
JOURNAL ARTICLE
Christoph Seidel, Finn-Ole Paulsen, Tim Nestler, Richard Cathomas, Marcus Hentrich, Pia Paffenholz, Carsten Bokemeyer, Axel Heidenreich, Daniel Nettersheim, Felix Bremmer
Approximately 30% of seminoma (SEM) patients present with moderately elevated human chorionic gonadotropin (hCG) levels at first diagnosis. In case of high hCG serum levels, the presence of a non-SEM component, i.e. choriocarcinoma (CC), may be assumed. To characterize cases described as pure seminoma with high serum hCG levels, tissue samples and DNA were analyzed. Patient files from an international registry were screened for patients with SEM and extraordinarily high hCG serum levels. IHC and qRT-PCR analysis was performed for markers of SEM, embryonal carcinoma (EC) and CC/trophoblast cells...
December 14, 2023: Virchows Archiv: An International Journal of Pathology
#17
JOURNAL ARTICLE
Axel Hochkirch, Melanie Bilz, Catarina C Ferreira, Anja Danielczak, David Allen, Ana Nieto, Carlo Rondinini, Kate Harding, Craig Hilton-Taylor, Caroline M Pollock, Mary Seddon, Jean-Christophe Vié, Keith N A Alexander, Emily Beech, Manuel Biscoito, Yoan Braud, Ian J Burfield, Filippo Maria Buzzetti, Marta Cálix, Kent E Carpenter, Ning Labbish Chao, Dragan Chobanov, Maarten J M Christenhusz, Bruce B Collette, Mia T Comeros-Raynal, Neil Cox, Matthew Craig, Annabelle Cuttelod, William R T Darwall, Benoit Dodelin, Nicholas K Dulvy, Eve Englefield, Michael F Fay, Nicholas Fettes, Jörg Freyhof, Silvia García, Mariana García Criado, Michael Harvey, Nick Hodgetts, Christina Ieronymidou, Vincent J Kalkman, Shelagh P Kell, James Kemp, Sonia Khela, Richard V Lansdown, Julia M Lawson, Danna J Leaman, Joana Magos Brehm, Nigel Maxted, Rebecca M Miller, Eike Neubert, Baudewijn Odé, David Pollard, Riley Pollom, Rob Pople, Juan José Presa Asensio, Gina M Ralph, Hassan Rankou, Malin Rivers, Stuart P M Roberts, Barry Russell, Alexander Sennikov, Fabien Soldati, Anna Staneva, Emilie Stump, Andy Symes, Dmitry Telnov, Helen Temple, Andrew Terry, Anastasiya Timoshyna, Chris van Swaay, Henry Väre, Rachel H L Walls, Luc Willemse, Brett Wilson, Jemma Window, Emma G E Wright, Thomas Zuna-Kratky
Biodiversity loss is a major global challenge and minimizing extinction rates is the goal of several multilateral environmental agreements. Policy decisions require comprehensive, spatially explicit information on species' distributions and threats. We present an analysis of the conservation status of 14,669 European terrestrial, freshwater and marine species (ca. 10% of the continental fauna and flora), including all vertebrates and selected groups of invertebrates and plants. Our results reveal that 19% of European species are threatened with extinction, with higher extinction risks for plants (27%) and invertebrates (24%) compared to vertebrates (18%)...
2023: PloS One
#18
RANDOMIZED CONTROLLED TRIAL
David E Kandzari, Raymond R Townsend, Kazuomi Kario, Felix Mahfoud, Michael A Weber, Roland E Schmieder, Stuart Pocock, Konstantinos Tsioufis, Dimitrios Konstantinidis, James Choi, Cara East, Lucas Lauder, Debbie L Cohen, Taisei Kobayashi, Axel Schmid, David P Lee, Adrian Ma, Joachim Weil, Tolga Agdirlioglu, Markus P Schlaich, Sharad Shetty, Chandan M Devireddy, Janice Lea, Jiro Aoki, Andrew S P Sharp, Richard Anderson, Martin Fahy, Vanessa DeBruin, Sandeep Brar, Michael Böhm
BACKGROUND: Renal denervation (RDN) reduces blood pressure (BP) in patients with uncontrolled hypertension in the absence of antihypertensive medications. OBJECTIVES: This trial assessed the safety and efficacy of RDN in the presence of antihypertensive medications. METHODS: SPYRAL HTN-ON MED is a prospective, randomized, sham-controlled, patient- and assessor-blinded trial enrolling patients from 56 clinical centers worldwide. Patients were prescribed 1 to 3 antihypertensive medications...
November 7, 2023: Journal of the American College of Cardiology
#19
JOURNAL ARTICLE
Jacob Marcus Egebjerg, Maria Szomek, Katja Thaysen, Alice Dupont Juhl, Suzana Kozakijevic, Stephan Werner, Christoph Pratsch, Gerd Schneider, Sergey Kapishnikov, Axel Ekman, Richard Röttger, Daniel Wüstner
During starvation in the yeast Saccharomyces cerevisiae vacuolar vesicles fuse and lipid droplets (LDs) can become internalized into the vacuole in an autophagic process named lipophagy. There is a lack of tools to quantitatively assess starvation-induced vacuole fusion and lipophagy in intact cells with high resolution and throughput. Here, we combine soft X-ray tomography (SXT) with fluorescence microscopy and use a deep-learning computational approach to visualize and quantify these processes in yeast. We focus on yeast homologs of mammalian NPC1 (NPC intracellular cholesterol transporter 1; Ncr1 in yeast) and NPC2 proteins, whose dysfunction leads to Niemann Pick type C (NPC) disease in humans...
October 31, 2023: Autophagy
#20
JOURNAL ARTICLE
Maximilian Schmutz, Manuela Zucknick, Richard F Schlenk, Daniel Mertens, Axel Benner, Dieter Weichenhan, Oliver Mücke, Konstanze Döhner, Christoph Plass, Lars Bullinger, Rainer Claus
BACKGROUND: Acute myeloid leukemia (AML) is a heterogeneous disease with a poor prognosis. Dysregulation of the epigenetic machinery is a significant contributor to disease development. Some AML patients benefit from treatment with hypomethylating agents (HMAs), but no predictive biomarkers for therapy response exist. Here, we investigated whether unbiased genome-wide assessment of pre-treatment DNA-methylation profiles in AML bone marrow blasts can help to identify patients who will achieve a remission after an azacytidine-containing induction regimen...
October 26, 2023: Clinical Epigenetics
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