Article
Computer Science, Software Engineering
Alexandre Decan, Tom Mens
Summary: This article empirically compares the SemVer compliance of four software packaging ecosystems and studies how ecosystem-specific characteristics or policies influence the degree of compliance. It also proposes an evaluation method based on the wisdom of the crowds principle to assist package maintainers in deciding which type of version constraints they should impose on their dependencies.
IEEE TRANSACTIONS ON SOFTWARE ENGINEERING
(2021)
Article
Astronomy & Astrophysics
Nat Gopalswamy, Grzegorz Michalek, Seiji Yashiro, Pertti Makela, Sachiko Akiyama, Hong Xie
Summary: The weakened state of the heliosphere during cycle 24 affected the width and occurrence of coronal mass ejections (CMEs). In cycle 25, the occurrence rate and properties of halo CMEs (HCMEs) are found to be intermediate between cycles 23 and 24, but closer to cycle 24. The strength of cycle 25 is expected to be similar to or slightly stronger than cycle 24, as indicated by polar-field precursor methods.
ASTROPHYSICAL JOURNAL LETTERS
(2023)
Review
Chemistry, Inorganic & Nuclear
Yan Peng, Annie K. Powell
Summary: This review focuses on the 3d-4f butterfly systems as examples of single molecule magnets and their coordination cluster counterparts, aiming to facilitate the design and synthesis of polynuclear 3d-4f clusters with improved SMM performance through examining synthetic strategies.
COORDINATION CHEMISTRY REVIEWS
(2021)
Review
Biotechnology & Applied Microbiology
Mayara Mari Murata, Luiz Rodrigo Ito Morioka, Josemeyre Bonifacio Da Silva Marques, Alessandra Bosso, Helio Hiroshi Suguimoto
Summary: Microalgae have various applications in agriculture, including plant growth promotion, biofertilization, plant disease control, weed management, and post-harvest quality improvement. The use of microalgae-derived products in agriculture has been increasing since 2015, particularly in the United States, China, and Europe, indicating a growing interest in innovative agricultural solutions.
Editorial Material
Hematology
Arnold Ganser
Summary: The study demonstrates the impact of comutations on the prognostic significance of isocitrate dehydrogenase (IDH) mutations in adult patients with newly diagnosed acute myeloid leukemia (AML) undergoing intensive chemotherapy (IC) followed by allogeneic hematopoietic stem cell transplantation (allo-HSCT).
Review
Oncology
Wiktoria Blaszczak, Pawel Swietach
Summary: Invasive cancer is a product of somatic evolution, which can be mathematically modelled and demonstrated through therapeutic responses. Altering the chemical microenvironment shared between host and cancer cells is a strategy to drive cancer cell extinction, with acidosis being a key chemical signature of the tumor microenvironment. Research efforts are focused on understanding and exploiting the competitive advantage that cancer cells gain from responses to acidosis.
CANCER AND METASTASIS REVIEWS
(2021)
Article
Reproductive Biology
Sebastian P. Arlt, Iris M. Reichler, Johannes Herbel, Sabine Schaefer-Somi, Lisa Riege, Johanna Leber, Bianca Frehner
Summary: Dog breeders often require breeding soundness evaluations which include andrological examinations, hormone measurements, and semen analyses. However, there is a lack of standardized procedures and reference ranges for specific examinations, making it difficult to compare results from different facilities and draw conclusive findings regarding the health and fertility of male dogs. Conventional semen examination, though, remains useful in identifying abnormalities, especially when confounding factors are considered and the exam is repeated for inconclusive findings.
Article
Geography, Physical
RachelP. Oien, Iestyn D. Barr, Matteo Spagnolo, Robert G. Bingham, Brice R. Rea, John Jansen
Summary: By mapping and analyzing the distribution and altitude variations of cirques in the Scandinavian Peninsula, the study suggests that cirque floor altitude (CFA) may serve as a proxy for paleoclimate. The results reveal close relationships between CFA and factors such as latitude, aspect, and distance to the coastline, indicating potential links to ancient climate conditions.
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2022)
Review
Chemistry, Physical
Connor Davis, Stephanie X. Wang, Lior Sepunaru
Summary: This article provides a critical analysis of the potential and limitations of electrochemistry in investigating single-enzyme catalysis, with a focus on nano-impact electrochemistry (NIE) and electrochemical scanning tunneling microscopy. NIE can report single-enzyme activity, but its future broad applicability for studying freely diffusing individual enzymes is questionable.Recent discoveries indicate that enzyme conductance depends directly on biophysical parameters such as substrate binding, oxidation state of the catalytic center, and structural fluctuations.
CURRENT OPINION IN ELECTROCHEMISTRY
(2021)
Editorial Material
Biochemistry & Molecular Biology
Andrius J. Dagilis
Summary: This study examines the different distributions of inversion sizes under adaptive and nonadaptive scenarios. The results suggest that larger inversions are more likely to evolve under local adaptation scenarios, and smaller inversions are more likely to evolve when they are either underdominant or directly beneficial. Additionally, the study investigates how the presence of deleterious mutations within populations affects the probability of fixing inversions of different types.
Article
Public, Environmental & Occupational Health
Mohammad Reza Baneshi, James Eynstone-Hinkins, Paul McElwee, Gita D. Mishra, Lauren Moran, Michael Waller, Annette Dobson
Summary: The prevalence of multimorbidity increases with age and is higher among women than men. The analysis of death records in Australia reveals different patterns of multimorbidity associated with demographic characteristics.
JOURNAL OF EPIDEMIOLOGY AND COMMUNITY HEALTH
(2023)
Article
Biodiversity Conservation
Marina D. A. Scarpelli, Milton Cezar Ribeiro, Camila P. Teixeira
Summary: The ecoacoustics approach is used to analyze environmental recordings and understand big ecological patterns related to different sound sources. The study found that different acoustic indices respond to different scales, and their medians vary according to the amount of surrounding vegetation cover.
ECOLOGICAL INDICATORS
(2021)
Review
Immunology
Asma Hassani, Gulfaraz Khan
Summary: Multiple sclerosis (MS) is a chronic disease of the central nervous system (CNS) characterized by demyelination, inflammation, and neurodegeneration. It is believed that both genetic predisposition and environmental factors contribute to the development of MS, with Epstein-Barr virus (EBV) being one of the possible environmental culprits. However, the mechanism by which EBV induces MS pathogenesis remains unknown. This review highlights the use of animal models, including nonhuman primates (NHP), rodents, and rabbits, to understand the link between EBV and MS and the role of virus-immune interaction disruption in viral pathogenesis and neuroinflammation. The findings from these animal models can provide directions for future studies aimed at unraveling the mechanism(s) by which EBV induces MS and developing preventive and therapeutic interventions for the disease.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Ophthalmology
Ian Flitcroft, Sara Mccullough, Kathryn Saunders
Summary: In young children, small degrees of anisometropia (>= 0.5 D) are associated with impaired emmetropisation. This suggests that anisometropia is a marker for poorly regulated eye growth, indicating that, in addition to environmental and genetic influences on eye growth, stochastic processes contribute to refractive outcomes.
BRITISH JOURNAL OF OPHTHALMOLOGY
(2021)
Article
Clinical Neurology
Alexandre Paim Diaz, Jair C. Soares, Paolo Brambilla, Allan H. Young, Sudhakar Selvaraj
Summary: The study evaluated the rankings of scientific journals in the field of psychiatry and mental health according to different metrics, finding a high correlation among these metrics. However, rankings may vary depending on different subject categories.
JOURNAL OF AFFECTIVE DISORDERS
(2021)
Article
Biology
Mariona Baliu-Pique, Vera van Hoeven, Julia Drylewicz, Lotte E. van der Wagen, Anke Janssen, Sigrid A. Otto, Menno C. van Zelm, Rob J. de Boer, Jurgen Kuball, Jose A. M. Borghans, Kiki Tesselaar
Summary: The study found that in patients after autologous hematopoietic stem cell transplantation (autoHSCT), the production rates of most T- and B-cell subsets increased significantly, but accompanied by an increase in cell loss rates, which persisted even after cell numbers normalized.
Article
Multidisciplinary Sciences
Peter C. de Greef, Rob J. de Boer
Summary: T cells with a diverse T cell receptor (TCR) protect the body from infection, with a substantial proportion of TCR beta rearrangements lacking a D segment. These sequences are more likely to be abundant within individuals and persist during fetal development and in the elderly.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Bettina Weigelin, Annemieke Th den Boer, Esther Wagena, Kelly Broen, Harry Dolstra, Rob J. de Boer, Carl G. Figdor, Johannes Textor, Peter Friedl
Summary: The study demonstrates that sublethal interactions from multiple CTL can accumulate over time and achieve tumor cell killing by additive cytotoxicity. Statistical modeling reveals that delivering three serial hits within decay intervals below 50 minutes can distinguish between tumor cell death or survival after recovery.
NATURE COMMUNICATIONS
(2021)
Article
Oncology
Richard J. Beck, Bettina Weigelin, Joost B. Beltman
Summary: CTLs play a crucial role in controlling tumours, and stimulation of their CD137 receptor enhances their antitumour effects by inhibiting proliferation and prolonging their presence within the tumour.
Article
Immunology
Juliane Schroter, Anet J. N. Anelone, Rob J. de Boer
Summary: In early-treated children with successful viral suppression, the CD4 depletion is typically mild and CD4(+) T cells tend to fully recover in numbers.
JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES
(2022)
Article
Immunology
Mariona Baliu-Pique, Julia Drylewicz, Xiaoyan Zheng, Lisa Borkner, Arpit C. Swain, Sigrid A. Otto, Rob J. de Boer, Kiki Tesselaar, Luka Cicin-Sain, Jose A. M. Borghans
Summary: Memory T cells play a crucial role in providing immune protection against reinfection and their long-term survival is still a subject of debate. This study suggests that memory phenotype CD8(+) T cells maintain themselves through cell division rather than individual cell longevity. CMV infection induces inflationary CD8(+) T cell responses that may result from the accumulation of long-lived CMV-specific memory CD8(+) T cells. The lifespans and production rates of CMV-specific CD8(+) T cells are similar to those of bulk memory-phenotype CD8(+) T cells.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Immunology
Jason Cosgrove, Lucie S. P. Hustin, Rob J. de Boer, Leila Perie
Summary: Hematopoiesis is a dynamic process where stem and progenitor cells give rise to a vast number of blood and immune cells. Quantitative descriptions can help consolidate existing data, identify knowledge gaps, and generate new hypotheses.
TRENDS IN IMMUNOLOGY
(2021)
Letter
Biochemical Research Methods
Mario Castro, Rob J. de Boer
Summary: Despite the limitations pointed out by Villaverde and Massonis, the SIM method still holds value due to its applicability to various models, simplicity, and potential role in introducing identifiability issues to investigators with little mathematical training.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Microbiology
Sara P. H. A. van den Berg, Lyanne J. Derksen, Julia Drylewicz, Nening Nanlohy, Lisa Beckers, Josien Lanfermeijer, Stephanie Gessel, Martijn Vos, Sigrid Otto, Rob de Boer, Kiki Tesselaar, Jose A. M. Borghans, Debbie van Baarle
Summary: Cytomegalovirus (CMV) infection has a significant impact on the T-cell pool and is associated with immune system aging. However, the phenotypical differences between CMV-positive and CMV-negative individuals cannot be solely explained by the presence of large CMV-specific CD8(+) T-cell populations. CMV infection seems to have minimal effect on the dynamics of the T-cell pool, and the abundance of CMV-specific CD8(+) T-cells is not attributed to their longer lifespans.
Article
Immunology
Kaspar Bresser, Lianne Kok, Arpit C. Swain, Lisa A. King, Laura Jacobs, Tom S. Weber, Leila Perie, Ken R. Duffy, Rob J. de Boer, Ferenc A. Scheeren, Ton N. Schumacher
Summary: This study investigates the relationship between replicative history and the formation of distinct CD8(+) memory T cell subgroups. The researchers developed a genetic-tracing approach and found that central memory T (T-CM) cell pool has a higher number of prior divisions compared to the effector memory T cell pool. They also discovered that lowly divided T-CM cells display enriched expression of stem-cell-associated genes, exist in a relatively quiescent state, and are superior in eliciting a proliferative recall response upon activation.
Correction
Immunology
Kaspar Bresser, Lianne Kok, Arpit C. Swain, Lisa A. King, Laura Jacobs, Tom S. Weber, Leila Perie, Ken R. Duffy, Rob J. de Boer, Ferenc A. Scheeren, Ton N. Schumacher
Article
Immunology
Arpit C. Swain, Jose A. M. Borghans, Rob J. de Boer
Summary: The paper investigates the impact of resource competition on T-cell receptor diversity in the memory T-cell pool. It shows that cellular aging, along with a small continuous source, can increase TCR diversity and regulate chronic memory responses.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Gerdien Mijnheer, Nila Hendrika Servaas, Jing Yao Leong, Arjan Boltjes, Eric Spierings, Phyllis Chen, Liyun Lai, Alessandra Petrelli, Sebastiaan Vastert, Rob J. de Boer, Salvatore Albani, Aridaman Pandit, Femke van Wijk, Di Chen
Summary: Autoimmune inflammation is characterized by tissue infiltration and expansion of antigen-specific T cells. In this study, the authors used CyTOF analysis and TCR sequencing to investigate the immune cell composition and expansion of specific T cell clones in juvenile idiopathic arthritis (JIA). They found that the infiltrates in different affected joints of the same patient were similar, and dominant T cell clones, including Tregs, persisted over time. These findings suggest the presence of autoantigen-driven expansion of T cell clones in localized autoimmune disease.
Article
Biology
Edward Schrom, Ann Kinzig, Stephanie Forrest, Andrea L. Graham, Simon A. Levin, Carl T. Bergstrom, Carlos Castillo -Chavez, James P. Collins, Rob J. de Boer, Adam Doupe, Roya Ensafi, Stuart Feldman, Bryan T. Grenfell, Alex Halderman, Silvie Huijben, Carlo Maley, Melanie Moses, Alan S. Perelson, Charles Perrings, Joshua Plotkin, Jennifer Rexford, Mohit Tiwari
Summary: Defending against various types of attacks and avoiding self-attacks are the common challenges faced by mammalian immune systems and computer systems. Despite extensive research, there has been limited exchange of information between the fields of biological immunity and cybersecurity. This paper proposes a conceptual framework to compare and evaluate different defensive strategies in both fields, aiming to identify general principles of optimal defense applicable to various defensive realms.
MATHEMATICAL BIOSCIENCES
(2023)
Article
Biophysics
Inge M. N. Wortel, Ioana Niculescu, P. Martijn Kolijn, Nir S. Gov, Rob J. de Boer, Johannes Textor
Summary: Cell migration is diverse, but a universal coupling between speed and persistence exists. An existing cellular Potts model shows how cell shape dynamics and local protrusion dynamics play a role in reproducing this speed-persistence coupling.
BIOPHYSICAL JOURNAL
(2021)