Article
Mathematical & Computational Biology
R. Jorquera, C. Gonzalez, P. T. L. C. Clausen, B. Petersen, D. S. Holmes
Summary: Single-exon coding sequences, defined as protein-coding genes without introns, have been linked to various diseases. SinEx DB 2.0, the largest SEG database, provides information from 60 eukaryotic genomes to enhance our understanding of SEG evolution, function, and disease associations.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Environmental Sciences
Dwight Owens, Dilumie Abeysirigunawardena, Ben Biffard, Yan Chen, Patrick Conley, Reyna Jenkyns, Shane Kerschtien, Tim Lavallee, Melissa MacArthur, Jina Mousseau, Kim Old, Meghan Paulson, Benoit Pirenne, Martin Scherwath, Michael Thorne
Summary: The advent of large-scale cabled ocean observatories has led to the development of comprehensive data management systems such as Oceans 2.0 and Oceans 3.0. These systems are designed to handle large amounts of ocean-based data and provide tools for data acquisition, storage, quality control, discovery, and access. Oceans 3.0 is evolving towards cloud-based environments for data processing, analysis, and exchange.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Medicine, General & Internal
Caicun Zhou, Ke-Jing Tang, Byoung Chul Cho, Baogang Liu, Luis Paz-Ares, Susanna Cheng, Satoru Kitazono, Muthukkumaran Thiagarajan, Jonathan W. Goldman, Joshua K. Sabari, Rachel E. Sanborn, Aaron S. Mansfield, Jen-Yu Hung, Michael Boyer, Sanjay Popat, Josiane Mourao Dias, Enriqueta Felip, Margarita Majem, Mahmut Gumus, Sang-we Kim, Akira Ono, John Xie, Archan Bhattacharya, Trishala Agrawal, S. Martin Shreeve, Roland E. Knoblauch, Keunchil Park, Nicolas Girard, PAPILLON Investigators
Summary: Amivantamab plus chemotherapy demonstrated significantly longer progression-free survival and higher response rate in patients with advanced NSCLC with EGFR exon 20 insertions compared to chemotherapy alone. The combination therapy showed superior efficacy as a first-line treatment option.
NEW ENGLAND JOURNAL OF MEDICINE
(2023)
Article
Computer Science, Artificial Intelligence
Hongzong Li, Jun Wang
Summary: This paper presents an upgraded version of the CAPKM++ clustering algorithm, called CAPKM++2.0. It introduces the re-initialization of weights and the iterative minimization of the power-mean sum during annealing. Ablation study results and experimental results on benchmark datasets demonstrate the effectiveness of the power-mean and the collaboration of multiple modules, and the superior clustering performance of the upgraded algorithm.
KNOWLEDGE-BASED SYSTEMS
(2023)
Article
Multidisciplinary Sciences
Nicholas A. Steinmetz, Cagatay Aydin, Anna Lebedeva, Michael Okun, Marius Pachitariu, Marius Bauza, Maxime Beau, Jai Bhagat, Claudia Bohm, Martijn Broux, Susu Chen, Jennifer Colonell, Richard J. Gardner, Bill Karsh, Fabian Kloosterman, Dimitar Kostadinov, Carolina Mora-Lopez, John O'Callaghan, Junchol Park, Jan Putzeys, Britton Sauerbrei, Rik J. J. van Daal, Abraham Z. Vollan, Shiwei Wang, Marleen Welkenhuysen, Zhiwen Ye, Joshua T. Dudman, Barundeb Dutta, Adam W. Hantman, Kenneth D. Harris, Albert K. Lee, Edvard Moser, John O'Keefe, Alfonso Renart, Karel Svoboda, Michael Hausser, Sebastian Haesler, Matteo Carandini, Timothy D. Harris
Summary: The research introduces the Neuropixels 2.0 probe and newly designed analysis algorithms, enabling high-quality recordings for long time scales in small mammals. Automatic post hoc correction for brain movements allows recording from the same neurons for more than 2 months. These probes and algorithms enable stable recordings from thousands of sites during free behavior.
Article
Multidisciplinary Sciences
Amin Allahyar, Mark Pieterse, Joost Swennenhuis, G. Tjitske Los-de Vries, Mehmet Yilmaz, Roos Leguit, Ruud W. J. Meijers, Robert van der Geize, Joost Vermaat, Arjen Cleven, Tom van Wezel, Arjan Diepstra, Leon C. van Kempen, Nathalie J. Hijmering, Phylicia Stathi, Milan Sharma, Adrien S. J. Melquiond, Paula J. P. de Vree, Marjon J. A. M. Verstegen, Peter H. L. Krijger, Karima Hajo, Marieke Simonis, Agata Rakszewska, Max van Min, Daphne de Jong, Bauke Ylstra, Harma Feitsma, Erik Splinter, Wouter de Laat
Summary: The authors introduced a new method for detecting translocations in preserved samples, which showed high sensitivity and specificity, outperforming traditional methods; FFPE-TLC is a powerful clinical tool for accurate rearrangement detection in FFPE specimens.
NATURE COMMUNICATIONS
(2021)
Article
Nanoscience & Nanotechnology
Haozhi Zhang, Hao Jia, Zao Ni, Ming Li, Ying Chen, Pengcheng Xu, Xinxin Li
Summary: This study demonstrates a new type of MEMS differential thermopile gas sensor for the highly sensitive, rapid detection of trace hydrogen gas in air. The sensor has a high temperature sensitivity, allowing for the detection of miniscule temperature changes due to the catalytic reaction of hydrogen gas. It has a detection limit as low as 1 ppm at an operating temperature of 120 degrees Celsius, and exhibits a wide linear detection range and fast response and recovery times.
MICROSYSTEMS & NANOENGINEERING
(2023)
Article
Biochemical Research Methods
Yang Chen, Shue Chen, Elissa P. Lei
Summary: This study presents a novel differential analysis method (DiffChIPL) based on Limma, which accurately detects differential peaks in ChIP-seq data. The method shows superior performance in simulations and real datasets, and exhibits better differential analysis capability in various applications.
Article
Biochemistry & Molecular Biology
Tingting Fu, Fengcheng Li, Yang Zhang, Jiayi Yin, Wenqi Qiu, Xuedong Li, Xingang Liu, Wenwen Xin, Chengzhao Wang, Lushan Yu, Jianqing Gao, Qingchuan Zheng, Su Zeng, Feng Zhu
Summary: This study describes a major update of the VARIDT database, including experimental resolved structures and structural variability data updates through literature review and homology modeling. The newly collected data are essential for explaining drug sensitivity, revealing drug-drug interaction mechanisms, and more.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Genetics & Heredity
Aqsa Ayoub, Samar Ijaz Gul, Ahmed Murtaza Mehdi, Syed Aoun Ali, Fazeel Majeed, Ali Nisar Ayoub, Ghufran Tariq, Rabat Razia, Sharoon Hanook, Deeba Noreen Baig
Summary: This study conducted a detailed investigation on the expression of ERM genes and the mutations in the Moesin gene in meningioma patients. The results showed that the expression levels of Ezrin and Radixin were upregulated, while Moesin expression was downregulated in meningioma tissues. In addition, several novel mutations in the Moesin gene were identified. These findings provide important insights into the pathogenesis of meningioma and may contribute to the development of targeted therapies in the future.
Article
Oncology
Harshitha Shobha Manjunath, Moza Al Khulaifi, Heba Sidahmed, Adham Ammar, Jayakumar Vadakekolathu, Sergio Rutella, Muneera Jassim Al-Mohannadi, Mamoun Elawad, William Mifsud, Adrian Charles, Cristina Maccalli, Sara Tomei
Summary: The gene expression analysis of FFPE tissues is often limited by poor RNA quality, but FFPE samples are valuable for studying disease progression and prognosis. Advances in genomic technologies have led to the development of reliable and accurate gene expression workflows for samples of poor quality. This study tested two RNA extraction methods and evaluated the impact of RNA degradation and RNA input on gene expression profiles. The nCounter platform was found to be robust and reliable for assessing gene expression in RNA samples with DV200 > 30%.
TECHNOLOGY IN CANCER RESEARCH & TREATMENT
(2022)
Article
Oncology
Laila Salameh, Poorna Manasa Bhamidimarri, Narjes Saheb Sharif-Askari, Youssef Dairi, Sarah Musa Hammoudeh, Amena Mahdami, Mouza Alsharhan, Syed Hammad Tirmazy, Surendra Singh Rawat, Hauke Busch, Qutayba Hamid, Saba Al Heialy, Rifat Hamoudi, Bassam Mahboub
Summary: This study identified a group of transcripts involved in both severe asthma and lung cancer pathogenesis, which may be useful for early diagnosis of lung cancer. Additionally, it is the first study to identify common genes associated with severe asthma and lung cancer.
Article
Multidisciplinary Sciences
Steve Sweet, David Chain, Wen Yu, Philip Martin, Marlon Rebelatto, Andrew Chambers, Fabiola Cecchi, Yeoun Jin Kim
Summary: Mass spectrometry-based targeted proteomics allows objective protein quantitation of clinical biomarkers. The use of high-field asymmetric waveform ion mobility spectrometry and parallel reaction monitoring improves assay sensitivity and enables quantitation of proteins in clinical samples.
SCIENTIFIC REPORTS
(2022)
Article
Astronomy & Astrophysics
C. B. Adams, W. Benbow, A. Brill, J. H. Buckley, M. Capasso, J. L. Christiansen, A. J. Chromey, M. K. Daniel, M. Errando, A. Falcone, K. A. Farrell, Q. Feng, J. P. Finley, L. Fortson, A. Furniss, A. Gent, C. Giuri, D. Hanna, T. Hassan, O. Hervet, J. Holder, G. Hughes, T. B. Humensky, W. Jin, P. Kaaret, M. Kertzman, D. Kieda, S. Kumar, M. J. Lang, M. Lundy, G. Maier, C. E. McGrath, P. Moriarty, R. Mukherjee, D. Nieto, M. Nievas-Rosillo, S. O'Brien, R. A. Ong, A. N. Otte, N. Park, S. Patel, K. Pfrang, M. Pohl, R. R. Prado, E. Pueschel, J. Quinn, K. Ragan, P. T. Reynolds, D. Ribeiro, E. Roache, J. L. Ryan, M. Santander, G. H. Sembroski, R. Shang, A. Weinstein, D. A. Williams, T. J. Williamson, I Bartos, K. R. Corley, S. Marka, Z. Marka, D. Veske
Summary: The article describes a new method that uses sub-threshold event candidates to search for transient events using archival very-high-energy gamma-ray data from IACTs. This method has the potential to be applied to future LIGO/Virgo data releases and other sub-threshold studies for multimessenger transients.
ASTROPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Tobias Fehlmann, Fabian Kern, Omar Lahaml, Christina Backes, Jeffrey Solomon, Pascal Hirsch, Carsten Volz, Rolf Mueller, Andreas Keller
Summary: miRMaster is a tool for analyzing small non-coding RNA sequencing data, with a wide range of features and updates that support analysis of multiple species and non-coding RNA classes. It includes new downstream analysis modules, sample embeddings, batch effect analysis, and support for new output formats and single cell small-RNA sequencing data analysis.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Cardiac & Cardiovascular Systems
Peter A. Henriksen, Peter Hall, Olga Oikonomidou, Iain R. MacPherson, Morag Maclean, Steff Lewis, Heather McVicars, Angus Broom, Fiona Scott, Pam McKay, Annabel Borley, Clare Rowntree, Simon Lord, Graham Collins, John Radford, Amy Guppy, John R. Payne, David E. Newby, Nick L. Mills, Ninian N. Lang
Summary: The Cardiac CARE trial aims to investigate the effects of cardiac biomarker monitoring and combination drug therapy on patients receiving anthracycline chemotherapy. By monitoring the impact of beta-adrenergic receptor blockers and renin-angiotensin-system inhibitors on cardiac function, the trial seeks to find a treatment strategy to mitigate the cardiotoxicity of anthracycline drugs.
CIRCULATION-HEART FAILURE
(2022)
Article
Medicine, General & Internal
Stephen M. Ansell, John Radford, Joseph M. Connors, Monika Dlugosz-Danecka, Won-Seog Kim, Andrea Gallamini, Radhakrishnan Ramchandren, Jonathan W. Friedberg, Ranjana Advani, Martin Hutchings, Andrew M. Evens, Piotr Smolewski, Kerry J. Savage, Nancy L. Bartlett, Hyeon-Seok Eom, Jeremy S. Abramson, Cassie Dong, Frank Campana, Keenan Fenton, Markus Puhlmann, David J. Straus
Summary: The study found that using A+AVD for the treatment of stage III or IV Hodgkin's lymphoma provides a survival advantage over ABVD.
NEW ENGLAND JOURNAL OF MEDICINE
(2022)
Review
Hematology
Georg Hess, Martin Dreyling, Lucie Oberic, Eva Gine, Pier Luigi Zinzani, Kim Linton, Adam Vilmar, Mats Jerkeman, Jenny M. H. Chen, Anke Ohler, Stephan Stilgenbauer, Catherine Thieblemont, Jonathan Lambert, Vittorio Ruggero Zilioli, Juan-Manuel Sancho, Ana Jimenez Ubieto, Luca Fischer, Toby A. Eyre, Sam Keeping, Julie E. Park, James J. Wu, Rubina Siddiqi, John Reitan, Sally Wade, Gilles Salles
Summary: Relapsed Mantle cell lymphoma (MCL) has a poor prognosis and there is no standard treatment. This study examined the outcomes of salvage therapy in MCL patients who failed Bruton tyrosine kinase inhibitor (BTKi) therapy, showing shorter overall survival in this group compared to those who received post-BTKi therapy.
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Article
Hematology
Paola Ghione, Maria Lia Palomba, Herve Ghesquieres, Sabela Bobillo, Anik R. Patel, Myrna Nahas, Steve Kanters, Kevin Deighton, Anthony Hatswell, Long Ma, Eve H. Limbrick- Oldfield, Julia Thornton Snider, Sally W. Wade, Maria Teresa Riberio, John Radford, Sara Beygi, John Gribben
Summary: The SCHOLAR-5 study examines the treatment patterns and outcomes of real-world follicular lymphoma (FL) patients who are in the 3rd line of treatment or higher, where existing data are limited. The study found that the most common regimen in each line of treatment was chemoimmunotherapy, but experimental drugs were increasingly used at later lines of treatment. The overall response rate decreased with each line of treatment, and the duration of response and survival diminished with each subsequent line.
Article
Hematology
Kate Cwynarski, Thomas Cummin, Wendy Osborne, Joanne Lewis, Sridhar Chaganti, Jeff Smith, Kim Linton, Paul Greaves, Pam McKay, Christopher P. Fox
BRITISH JOURNAL OF HAEMATOLOGY
(2023)
Article
Oncology
M. Lia Palomba, Paola Ghione, Anik R. Patel, Myrna Nahas, Sara Beygi, Anthony J. Hatswell, Steve Kanters, Eve H. Limbrick-Oldfield, Sally W. Wade, Markqayne D. Ray, Jessica Owen, Sattva S. Neelapu, John Gribben, John Radford, Sabela Bobillo
Summary: In the ZUMA-5 trial, axicabtagene ciloleucel (axi-cel) showed high rates of durable response in relapsed/refractory follicular lymphoma (FL) patients and clear superiority compared to the SCHOLAR-5 external control cohort. This study provides an updated analysis using 24-month data from ZUMA-5.
EXPERT REVIEW OF ANTICANCER THERAPY
(2023)
Article
Archaeology
K. N. White, D. Chiasserini, R. Loynes, A. R. David, B. E. van Dongen, K. Drosou, R. Forshaw, S. Fraser, P. Causey-Freeman, J. Metcalfe, E. Murphy, M. Regan, P. J. Reimer, D. G. Tosh, A. Whetton, A. J. Freemont
Summary: Scientific examination of mummies provides insights into human ancestry, diet, disease, cultures, and societies. However, invasive methods have raised concerns. A minimally invasive approach using imaging techniques and biopsy sampling allows for the collection of valuable data without significant disturbance to the mummy. This study on Takabuti demonstrates the potential of such methods.
JOURNAL OF ARCHAEOLOGICAL SCIENCE-REPORTS
(2023)
Article
Medicine, General & Internal
Radhakrishnan Ramchandren, Peter Johnson, Nilanjan Ghosh, Jia Ruan, Kirit M. Ardeshna, Roderick Johnson, Gregor Verhoef, David Cunningham, Sven de Vos, Shireen Kassam, Luis Fayad, John Radford, Sarah Bailly, Fritz Offner, David Morgan, Javier Munoz, Jerry Ping, Edith Szafer-Glusman, Karl Eckert, Jutta K. Neuenburg, Andre Goy
Summary: This study evaluated the efficacy and safety of the combination of ibrutinib, lenalidomide, and rituximab in patients with relapsed/refractory DLBCL ineligible for stem cell transplantation. The results showed that the combination therapy demonstrated durable antitumor activity in DLBCL patients.
Article
Hematology
Philippe Armand, Pier Luigi Zinzani, Hun Ju Lee, Nathalie A. Johnson, Pauline Brice, John Radford, Vincent Ribrag, Daniel Molin, Theodoros P. Vassilakopoulos, Akihiro Tomita, Bastian von Tresckow, Margaret A. Shipp, Alex F. Herrera, Jianxin Lin, Eunhee Kim, Samhita Chakraborty, Patricia Marinello, Craig H. Moskowitz
Summary: This study demonstrates that Pembrolizumab provides durable antitumor activity in patients with relapsed or refractory classical Hodgkin lymphoma, and a second course of treatment can reinduce sustained responses after relapse from initial complete response.
Article
Oncology
Hoa Van Le, Kim Van Naarden Braun, Grzegorz S. Nowakowski, David Sermer, John Radford, William Townsend, Herve Ghesquieres, Tobias Menne, Edit Porpaczy, Christopher P. Fox, Claudia Schusterbauer, Fei Fei Liu, Lihua Yue, Marc De Benedetti, Jens Hasskarl
Summary: This study compared the efficacy of lisocabtagene maraleucel (liso-cel) with conventional therapies in relapsed/refractory large B-cell lymphoma patients. The study used a real-world population as the comparator and matched patients' characteristics with those in a clinical trial. Results showed that liso-cel had significantly better overall response rate, complete response rate, overall survival, and progression-free survival compared to conventional therapies.
LEUKEMIA & LYMPHOMA
(2023)
Article
Multidisciplinary Sciences
Thomas S. Georgi, Lars Kurch, Dirk Hasenclever, Victoria Warbey, Lucy Pike, John F. Radford, Osama Sabri, Regine Kluge, Sally Barrington
Summary: The aim of this study was to evaluate the causes of interobserver variability in assigning the Deauville score (DS) for interim PET (iPET) scans in Hodgkin lymphoma (HL) patients and propose suggestions for improvement. The results showed that a concordant visual DS result was achieved in 56% of the iPET scans, with a minor discrepancy of one DS level in 33% and a major discrepancy of more than one DS level in 11%. The main reasons for major discrepancies were different interpretation of PET-positive lymph nodes, missed lesions, and different assessment of lesions in activated brown fat tissue. In 51% of minor discrepancy scans with residual lymphoma uptake, additional quantification resulted in a concordant quantitative DS result.
Article
Hematology
Greg Hapgood, Monica Civallero, Yana Stepanishyna, Julie Vose, Monica Elena Cabrera, Ranjana H. Advani, Stefano A. Pileri, Martina Manni, Steven M. Horwitz, Francine M. Foss, Felicitas Hitz, John Radford, Ivan Dlouhy, Carlos Chiattone, Won Seog Kim, Tetiana Skrypets, Arnon Nagler, Judith Trotman, Stefano Luminari, Int T Cell Project
Summary: This study investigated the natural history and prognostic factors of limited-stage peripheral T-cell lymphomas (PTCLs) and developed a predictive model for overall survival (OS), which showed good discriminatory power and was validated in an independent cohort.
Proceedings Paper
Computer Science, Artificial Intelligence
H. Chamberlin, E. Henderson, R. Cowan, C. Anandadas, C. Hague, F. Wilson, J. Radford, S. Howell, S. Astley, M. Aznar, E. Vasquez Osorio
Summary: The performance of commercially available segmentation tools (deep learning and atlas-based) was evaluated for breast contouring in young lymphoma patients. Deep learning segmentation performed better in most patients, while atlas-based segmentation was best in a few patients. Variation in breast densities and arm positions may affect auto-contouring performance.
2023 IEEE 20TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING, ISBI
(2023)
Meeting Abstract
Oncology
Tycel Phillips, Wojciech Jurczak, Vincent Ribrag, Kim Linton, Graham P. Collin, Javier Lopez-Jimenez, Nishitha Reddy, Andrea Mengarelli, Gerardo Musuraca, Oonagh Sheehy, Weiming Xu, Michel Azoulay, Richard G. Ghalie, Pier Luigi Zinzani, Andrew D. Zelenetz
CLINICAL LYMPHOMA MYELOMA & LEUKEMIA
(2022)
Meeting Abstract
Oncology
Lorenzo Falchi, Fritz Offner, David Belada, Joshua Brody, Kim M. Linton, Yasmin Karimi, Raul Cordoba, Sylvia Snauwaert, Aqeel Abbas, Liwei Wang, Jun Wu, Brian Elliott, Michael Roost Clausen
CLINICAL LYMPHOMA MYELOMA & LEUKEMIA
(2022)