June 2024

Research articles

    1. Ecology

    Partitioning changes in ecosystem productivity by effects of species interactions in biodiversity experiments

    Jing Tao, Charles A Nock ... Ji Zheng
    Revised
    Reviewed Preprint v3
    • Inadequate
    1. Neuroscience

    Slow kinesin-dependent microtubular transport facilitates ribbon synapse assembly in developing cochlear inner hair cells

    Roos Anouk Voorn, Michael Sternbach ... Christian Vogl
    Not revised
    Reviewed Preprint v1
    • Important
    • Compelling
    • Incomplete
    1. Neuroscience

    A deep learning framework for automated and generalized synaptic event analysis

    Philipp S. O’Neill, Martín Baccino-Calace ... Igor Delvendahl
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Convincing
    1. Neuroscience

    Pinging the Hidden Attentional Priority Map: Suppression Needs Attention

    Changrun Huang, Dirk van Moorselaar ... Jan Theeuwes
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Convincing
    1. Cell Biology

    Novel Mechanism for Tubular Injury in Nephropathic Cystinosis

    Swastika Sur, Maggie Kerwin ... Minnie M. Sarwal
    Not revised
    Reviewed Preprint v1
    • Important
    • Convincing
    • Incomplete
    1. Developmental Biology
    2. Neuroscience

    Microtubule networks in zebrafish hair cells facilitate presynapse transport and fusion during development

    Saman Hussain, Katherine Pinter ... Katie Kindt
    Not revised
    Reviewed Preprint v1
    • Important
    • Convincing
    1. Neuroscience

    Dynamic Gamma Modulation of Hippocampal Place Cells Predominates Development of Theta Sequences

    Ning Wang, Yimeng Wang ... Dong Ming
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Epidemiology and Global Health
    2. Cancer Biology

    Conditional Survival and Nomogram for Elderly Non-Metastatic Colon Cancer Patients Following Colectomy

    Yadong Gao, Huimin Wang ... Jianwei Qiu
    Not revised
    Reviewed Preprint v1
    • Useful
    • Incomplete
    1. Neuroscience

    GABAergic synaptic scaling is triggered by changes in spiking activity rather than AMPA receptor activation

    Carlos Gonzalez-Islas, Zahraa Sabra ... Peter Wenner
    Chronic perturbations of spiking activity trigger compensatory changes in GABAergic synaptic strength, but not compensatory changes in AMPAergic synaptic strength.
    1. Neuroscience

    Serotonergic and dopaminergic neurons in the dorsal raphe are differentially altered in a mouse model for parkinsonism

    Laura Boi, Yvonne Johansson ... Gilad Silberberg
    Dopaminergic and serotonergic neurons in the dorsal raphe nucleus have distinct electrical and morphological properties, which are differentially altered following dopamine and noradrenaline depletion.
    1. Microbiology and Infectious Disease
    2. Structural Biology and Molecular Biophysics

    Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2

    Ai Nguyen, Huaying Zhao ... Peter Schuck
    Exploration of the phenotype space corresponding to the sequence space of viable SARS-CoV-2 nucleocapsid protein species reveals significant diversity of biophysical characteristics, nonlocal mutation effects, and functional constraints.
    1. Immunology and Inflammation

    Self-inhibiting percolation and viral spreading in epithelial tissue

    Xiaochan Xu, Bjarke Frost Nielsen, Kim Sneppen
    A gene expression data-informed model reveals that a small fraction of interferon-producing cells can effectively constrain early virus spread in epithelial tissue, elucidating connections between critical dynamics and infection heterogeneity.
    1. Neuroscience

    Neural interactions in the human frontal cortex dissociate reward and punishment learning

    Etienne Combrisson, Ruggero Basanisi ... Andrea Brovelli
    Reward and punishment learning is represented in partly overlapping regions of the brain while relying on specific intra- and inter-regional interactions.
    1. Epidemiology and Global Health

    Strong isolation by distance and evidence of population microstructure reflect ongoing Plasmodium falciparum transmission in Zanzibar

    Sean V Connelly, Nicholas F Brazeau ... Jeffrey A Bailey
    Parasite migration between mainland Tanzania and Zanzibar and ongoing transmission clusters within Zanzibar highlight the need for continued preventive measures to reduce malaria transmission in the archipelago.
    1. Neuroscience

    Single neurons and networks in the claustrum integrate input from widespread cortical sources

    Andrew M Shelton, David K Oliver ... Adam M Packer
    Revised
    Reviewed Preprint v2
    • Valuable
    • Incomplete
    1. Computational and Systems Biology

    Accurate prediction of CDR-H3 loop structures of antibodies with deep learning

    Hedi Chen, Xiaoyu Fan ... Boxue Tian
    A deep learning-based toolkit predicting the 3D structures of monoclonal antibodies and nanobodies outperforms other current computational methods.
    1. Immunology and Inflammation

    Elevated glycolytic metabolism of monocytes limits the generation of HIF1A-driven migratory dendritic cells in tuberculosis

    Mariano Maio, Joaquina Barros ... Luciana Balboa
    A newly identified immunometabolic mechanism clarifies the aberrant trafficking of dendritic cells to lymph nodes in tuberculosis.
    1. Genetics and Genomics
    2. Neuroscience

    The neuron-specific IIS/FOXO transcriptome in aged animals reveals regulatory mechanisms of cognitive aging

    Yifei Weng, Shiyi Zhou ... Coleen T Murphy
    Neuron-specific sequencing of aged wild-type, daf-2, and daf-16;daf-2 mutants revealed transcriptomic changes with age, and in longevity mutants, putative neuroprotective genes are upregulated, which are required for prolonged cognitive functions.
    1. Microbiology and Infectious Disease

    RNA polymerase III is involved in regulating Plasmodium falciparum virulence

    Gretchen Diffendall, Aurelie Claes ... Artur Scherf
    RNA polymerase III plays a crucial role in controlling virulence in response to environmental changes and provides a new molecular perspective into the development of asymptomatic malaria.
    Version of Record
    Research Article
    • Important
    • Convincing
    • Incomplete
    1. Cancer Biology

    FAK loss reduces BRAFV600E-induced ERK phosphorylation to promote intestinal stemness and cecal tumor formation

    Chenxi Gao, Huaibin Ge ... Jing Hu
    Mice studies show that the 'just-right' balance optimal for BRAFV600E-induced cecal tumor formation can be achieved through FAK alteration.
    1. Computational and Systems Biology

    Semantical and Geometrical Protein Encoding Toward Enhanced Bioactivity and Thermostability

    Yang Tan, Bingxin Zhou ... Liang Hong
    Revised
    Reviewed Preprint v2
    • Valuable
    • Solid
    1. Genetics and Genomics

    Dimeric R25CPTH(1-34) Activates the Parathyroid Hormone-1 Receptor in vitro and Stimulates Bone Formation in Osteoporotic Female Mice

    Minsoo Noh, Xiangguo Che ... Sihoon Lee
    Revised
    Reviewed Preprint v2
    • Valuable
    • Convincing
    1. Medicine
    2. Computational and Systems Biology

    Identification of type 2 diabetes- and obesity-associated human β-cells using deep transfer learning

    Gitanjali Roy, Rameesha Syed ... Michael A. Kalwat
    Not revised
    Reviewed Preprint v1
    • Useful
    • Solid
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Hybrid immunity from severe acute respiratory syndrome coronavirus 2 infection and vaccination in Canadian adults: A cohort study

    Patrick E Brown, Sze Hang Fu ... Ab-C Study Collaborators
    Population-level hybrid immunity depends substantially on vaccination coverage, including among those previously infected, and dried blood spot collection serves as a practicable biological surveillance platform for these immune responses.
    1. Neuroscience

    Reconfigurations of cortical manifold structure during reward-based motor learning

    Qasem Nick, Daniel J Gale ... Jason Gallivan
    Dimensionality reduction approaches on functional MRI data reveal that human reward-based motor learning emerges from dynamic changes in functional brain network interactions among sensorimotor, attention, and default mode networks.
    1. Biochemistry and Chemical Biology
    2. Evolutionary Biology

    Fitness landscape of substrate-adaptive mutations in evolved amino acid-polyamine-organocation transporters

    Foteini Karapanagioti, Úlfur Águst Atlason ... Sebastian Obermaier
    Secondary active transporters can evolve to accommodate a broader range of substrates without losing their original substrate specificities.
    1. Neuroscience

    Precision-based causal inference modulates audiovisual temporal recalibration

    Luhe Li, Fangfang Hong ... Michael S Landy
    Revised
    Reviewed Preprint v2
    • Valuable
    • Convincing
    1. Ecology

    Combining radio-telemetry and radar measurements to test optimal foraging in an aerial insectivore bird

    Itai Bloch, David Troupin ... Nir Sapir
    Revised
    Reviewed Preprint v3
    • Important
    • Solid
    1. Neuroscience

    Fast burst fraction transients convey information independent of the firing rate

    Richard Naud, Xingyun Wang ... Guy Doron
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Neuroscience

    Cingulate cortex shapes early postnatal development of social vocalizations

    Gurueswar Nagarajan, Denis Matrov ... Yogita Chudasama
    Not revised
    Reviewed Preprint v1
    • Important
    • Solid
    1. Neuroscience

    Chromatin regulator Kdm6b is required for the establishment and maintenance of neural stem cells in mouse hippocampus

    Eugene Gil, Sung Jun Hong ... Daniel A. Lim
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Neuroscience

    Cerebellar Purkinje Cells Control Posture in Larval Zebrafish (Danio rerio)

    Franziska Auer, Katherine Nardone ... David Schoppik
    Revised
    Reviewed Preprint v2
    • Important
    • Convincing
    1. Cell Biology

    Eugenol mimics exercise to promote skeletal muscle fiber remodeling and myokine IL-15 expression by activating TRPV1 channel

    Tengteng Huang, Xiaoling Chen ... Zhiqing Huang
    Eugenol has the potential as a novel exercise mimetic, and TRPV1 may represent a promising target for the development of exercise mimetics.
    1. Computational and Systems Biology
    2. Medicine

    The vaginal immunoproteome for the prediction of spontaneous preterm birth: A retrospective longitudinal study

    Zachary Shaffer, Roberto Romero ... Nardhy Gomez-Lopez
    The vaginal immunoproteome in pregnancy is more predictive of spontaneous preterm birth (sPTB) than maternal characteristics alone, with sPTB cases showing heightened pro-inflammatory profiles accompanied by reduced levels of antimicrobial proteins/peptides.
    1. Biochemistry and Chemical Biology

    Mapping the molecular motions of 5-HT3 serotonin-gated channel by voltage-clamp fluorometry

    Laurie Peverini, Sophie Shi ... Pierre-Jean Corringer
    Conformational motions elicited by antagonists, partial agonists, and agonists in serotonin-gated ion channels 5-HT3AR progressively spread from the extracellular to the transmembrane domain.
    1. Neuroscience

    Visuo-motor updating in individuals with heightened autistic traits

    Antonella Pomè, Eckart Zimmermann
    Efference copy dysfunctions in heightened autistic traits impair the use of eye movement information for spatial representation and object localization.
    1. Genetics and Genomics

    Discovering non-additive heritability using additive GWAS summary statistics

    Samuel Pattillo Smith, Gregory Darnell ... Lorin Crawford
    Computational analysis reveals that additive summary statistics from genome-wide association studies can provide evidence of non-additive heritability in complex traits.
    1. Neuroscience

    Medial anterior prefrontal cortex stimulation downregulates implicit reactions to threats and prevents the return of fear

    Eugenio Manassero, Giulia Concina ... Benedetto Sacchetti
    Implicit defensive reactions to a learned threat-predictive cue and novel stimuli may be significantly downregulated through a repetitive transcranial magnetic stimulation procedure over the medial anterior prefrontal cortex in humans.
    1. Structural Biology and Molecular Biophysics

    The αC-β4 loop controls the allosteric cooperativity between nucleotide and substrate in the catalytic subunit of protein kinase A

    Cristina Olivieri, Yingjie Wang ... Gianluigi Veglia
    The αC-β4 loop emerges as a hot spot for tuning allosteric cooperativity in the catalytic subunit of protein kinase A.
    1. Microbiology and Infectious Disease

    Rapid bacterial evaluation beyond the colony forming unit in osteomyelitis

    Qi Sun, Kimberley Huynh ... Dongqing Yang
    This time-shortened work flow improves sensitivity and specificity for the identification of bacteria in bone infections independently of bacterial culturability.
    Version of Record
    Short Report
    • Fundamental
    • Compelling
    1. Cell Biology

    The Kv2.2 channel mediates the inhibition of Prostaglandin E2 on glucose-stimulated insulin secretion in pancreatic β-cells

    Chengfang Pan, Ying Liu ... Changlong Hu
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Immunology and Inflammation

    T follicular helper cell profiles differ by malaria antigen and for children compared to adults

    Catherine S. Forconi, Christina Nixon ... Ann M. Moormann
    Not revised
    Reviewed Preprint v1
    • Useful
    • Incomplete
    1. Computational and Systems Biology

    Balancing reaction-diffusion network for cell polarization pattern with stability and asymmetry

    Yixuan Chen, Guoye Guan ... Chao Tang
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Ecology

    Coordinated molecular and ecological adaptations underlie a highly successful parasitoid

    Lan Pang, Gangqi Fang ... Jianhua Huang
    The parasitoid Trichopria drosophilae has evolved both molecular adaptions (venom proteins and teratocytes) and ecological strategies (tolerance of intraspecific and avoidance of interspecific competition) to successfully parasitize Drosophila suzukii.
    1. Structural Biology and Molecular Biophysics

    Automated multiconformer model building for X-ray crystallography and cryo-EM

    Stephanie A Wankowicz, Ashraya Ravikumar ... James S Fraser
    Creating structural models with multiple conformations of proteins improves the fit of the model to experimental data X-ray crystallography and improve the model geometry.
    1. Neuroscience

    Choline supplementation in early life improves and low levels of choline can impair outcomes in a mouse model of Alzheimer’s disease

    Elissavet Chartampila, Karim S Elayouby ... Helen E Scharfman
    Supplementing the diet in early life with choline improved memory, neuronal morphology, and neuronal activity in mice with a genetic form of Alzheimer's disease, whereas low choline had mixed effects.
    1. Developmental Biology

    Drosophila medulla neuroblast termination via apoptosis, differentiation, and gliogenic switch is scheduled by the depletion of the neuroepithelial stem cell pool

    Phuong-Khanh Nguyen, Louise Y Cheng
    The termination of medulla neuroblasts is specified by the depletion of the neuroepithelium and mediated by apoptosis, differentiation, and gliogenic switch.
    1. Plant Biology

    Arabidopsis transcriptome responses to low water potential using high-throughput plate assays

    Stephen Gonzalez, Joseph Swift ... Joseph R Ecker
    The 'low water' agar assay provides a reliable and practical high-throughput method for studying plant molecular signaling responses to drought stress.
    Version of Record
    Short Report
    • Valuable
    • Solid
    1. Developmental Biology

    The Alk receptor tyrosine kinase regulates Sparkly, a novel activity regulating neuropeptide precursor in the Drosophila central nervous system

    Sanjay Kumar Sukumar, Vimala Antonydhason ... Ruth H Palmer
    The newly characterized activity regulating neuropeptide encoding gene Spar is a transcriptional target of the Jeb/Alk receptor tyrosine kinase signaling pathway in the Drosophila nervous system.
    1. Medicine

    Dengue viremia kinetics and effects on platelet count and clinical outcomes: An analysis of 2340 patients from Vietnam

    Nguyen Lam Vuong, Nguyen Than Ha Quyen ... Ronald Geskus
    Higher plasma viremia levels in early dengue and a slower subsequent decline are associated with worse clinical outcomes and provide valuable outcome measures for future therapeutic intervention trials.
    1. Computational and Systems Biology
    2. Genetics and Genomics

    Discovery of runs-of-homozygosity diplotype clusters and their associations with diseases in UK Biobank

    Ardalan Naseri, Degui Zhi, Shaojie Zhang
    ROH-DICE is an efficient method for detecting ROH clusters in biobank data, enabling the study of population history of large cohorts, and providing a new genome-wide association analysis approach for finding disease-causing loci with multi-marker recessive effects.
    1. Cell Biology

    The non-mitotic role of HMMR in regulating the localization of TPX2 and the dynamics of microtubules in neurons

    Yi-Ju Chen, Shun-Cheng Tseng ... Eric Hwang
    The protein hyaluronan-mediated motility receptor interacts with microtubules to enhance their stability and recruits TPX2 to promote microtubule emanation in neurons.
    1. Neuroscience

    A novel method for estimating properties of attentional oscillators reveals an age-related decline in flexibility

    Ece Kaya, Sonja A Kotz, Molly J Henry
    Individual performance in rhythm perception and production is maximized within a range of domain-specific rates and is adversely affected by temporal context, and this effect is amplified with age.
    1. Biochemistry and Chemical Biology

    Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IκBα through a phosphoenzyme intermediate

    Prateeka Borar, Tapan Biswas ... Smarajit Polley
    Not revised
    Reviewed Preprint v1
    • Fundamental
    • Solid
    1. Microbiology and Infectious Disease

    Frequent intertrophic transmission of Wolbachia by parasitism but not predation

    Zhi-Chao Yan, Lan-Da Qi ... Yuan-Xi Li
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Developmental Biology

    E3 ubiquitin ligase Deltex facilitates the expansion of Wingless gradient and antagonizes Wingless signaling through a conserved mechanism of transcriptional effector Armadillo/β-catenin degradation

    Vartika Sharma, Nalani Sachan ... Ashim Mukherjee
    Genetic and molecular analysis shows that Deltex modulates the Wingless gradient and counters Wingless signaling by promoting Armadillo/β-catenin degradation through a conserved regulatory mechanism.
    1. Immunology and Inflammation
    2. Neuroscience

    Spontaneous human CD8 T cell and autoimmune encephalomyelitis-induced CD4/CD8 T cell lesions in the brain and spinal cord of HLA-DRB1*15-positive multiple sclerosis humanized immune system mice

    Irini Papazian, Maria Kourouvani ... Lesley Probert
    Severely immunodeficient B2m-NOG mice transplanted with human peripheral blood mononuclear cells from multiple sclerosis patients partially reproduce disease immunopathology and represent novel experimental models for studying human immune responses to the central nervous system in a rapid and personalized manner.
    1. Biochemistry and Chemical Biology
    2. Cell Biology

    Identification of a third myosin-5a-melanophilin interaction that mediates the association of myosin-5a with melanosomes

    Jiabin Pan, Rui Zhou ... Xiang-dong Li
    In addition to the exon-F-binding domain and the globular tail domain-binding motif, the actin-binding domain of melanophilin interacts with myosin-5a tail region and mediates the association of myosin-5a with melanosomes.
    1. Physics of Living Systems

    Cyclic muscle contractions reinforce the actomyosin motors and mediate the full elongation of C. elegans embryo

    Anna Dai, Martine Ben Amar
    Computational and theoretical biomechanical analysis reveals how actomyosin filaments and axial muscles conjugate their activity to realize a fourfold elongation during C. elegans embryogenesis, 4 hr just before hatching.
    1. Neuroscience

    Stochastic characterization of navigation strategies in an automated variant of the Barnes maze

    Ju-Young Lee, Dahee Jung, Sebastien Royer
    A set of stochastic processes reproduces the mouse exploration patterns in an automated variant of the Barnes maze.
    1. Microbiology and Infectious Disease

    Multimodal HLA-I genotype regulation by human cytomegalovirus US10 and resulting surface patterning

    Carolin Gerke, Liane Bauersfeld ... Anne Halenius
    Analysis of human cytomegalovirus-encoded glycoprotein US10 targeting human leucocyte antigen class I molecules reveals a multimodal strategy, resulting in a geno- and allotypic-dependent effects.
    1. Ecology

    Boosting biodiversity monitoring using smartphone-driven, rapidly accumulating community-sourced data

    Keisuke Atsumi, Yuusuke Nishida ... Shogoro Fujiki
    Integrating an innovative community science platform with statistical modelling advances biodiversity monitoring and improves species habitat estimation across diverse taxa, supporting more effective conservation strategies.
    1. Cell Biology

    Novel autophagy inducers by accelerating lysosomal clustering against Parkinson’s disease

    Yuki Date, Yukiko Sasazawa ... Shinji Saiki
    Lysosomal clustering around the microtubule-organizing centre would be a promising therapeutic strategy for Parkinson's disease.
    1. Cell Biology

    Metabolic regulation of misfolded protein import into mitochondria

    Yuhao Wang, Linhao Ruan ... Rong Li
    The conserved AMP-activated protein kinase inhibits mitochondrial import of misfolded proteins and helps preserve mitochondrial and cellular fitness under proteotoxic stress.
    1. Neuroscience

    Spatial and temporal pattern of structure–function coupling of human brain connectome with development

    Guozheng Feng, Yiwen Wang ... Ni Shu
    Multimodal brain connectome analysis reveals patterns of structure–function coupling and links their developmental changes to cognitive function and transcriptomic architecture.
    1. Ecology
    2. Evolutionary Biology

    The trunk replaces the longer mandible as the main feeding organ in elephant evolution

    Chunxiao Li, Tao Deng ... Shiqi Wang
    The long mandibles were gradually replaced by more flexible trunks in the evolution of proboscideans.
    1. Immunology and Inflammation

    Role of Hepatocyte RIPK1 in Maintaining Liver Homeostasis during Metabolic Challenges

    Weigao Zhang, Hu Liu ... Dan Weng
    Revised
    Reviewed Preprint v2
    • Important
    • Convincing
    1. Physics of Living Systems
    2. Evolutionary Biology

    Changes in wing morphology rather than wingbeat kinematics enabled evolutionary miniaturization of hoverflies

    Camille Le Roy, Nina Tervelde ... Florian T. Muijres
    Not revised
    Reviewed Preprint v1
    • Important
    • Incomplete
    1. Microbiology and Infectious Disease
    2. Neuroscience

    Enteric glia regulate Paneth cell secretion and intestinal microbial ecology

    Aleksandra Prochera, Anoohya N. Muppirala ... Meenakshi Rao
    Not revised
    Reviewed Preprint v1
    • Important
    • Solid
    1. Developmental Biology

    Genetic and physical interactions reveal overlapping and distinct contributions to meiotic double-strand break formation in C. elegans

    Marilina Raices, Fabiola Balmir ... Judith Yanowitz
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Cell Biology
    2. Genetics and Genomics

    Assessment of the Epigenomic Landscape in Human Myometrium at Term Pregnancy

    San-Pin Wu, Elvis Quiroz ... Francesco J. DeMayo
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Genetics and Genomics

    Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseases

    Raehoon Jeong, Martha L. Bulyk
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Convincing
    1. Genetics and Genomics

    Poseidon – A framework for archaeogenetic human genotype data management

    Clemens Schmid, Ayshin Ghalichi ... Stephan Schiffels
    Not revised
    Reviewed Preprint v1
    • Important
    • Compelling
    • Exceptional
    1. Neuroscience

    Machine learning of dissection photographs and surface scanning for quantitative 3D neuropathology

    Harshvardhan Gazula, Henry FJ Tregidgo ... Juan E Iglesias
    New open-source software enables, for the first time, extraction of quantitative information from brain dissection photographs that are routinely taken at brain banks for archiving purposes but otherwise not exploited.
    1. Medicine

    Senescence of endplate osteoclasts induces sensory innervation and spinal pain

    Dayu Pan, Kheiria Gamal Benkato ... Xu Cao
    Depleting senescent osteoclasts using the senolytic drug Navitoclax (ABT263) can reduce sensory innervation in the endplate and attenuate low back pain, thus representing a potent therapy for treating spinal pain.
    1. Chromosomes and Gene Expression

    Transcriptional immune suppression and up-regulation of double-stranded DNA damage and repair repertoires in ecDNA-containing tumors

    Miin S Lin, Se-Young Jo ... Vineet Bafna
    Extrachromosomal DNA containing tumors up-regulate DNA damage and repair, cell cycle control, and mitotic processes, but down-regulate global immune regulation pathways, suggesting new avenues for therapeutic intervention.
    1. Computational and Systems Biology
    2. Epidemiology and Global Health

    Reliance on self-reports and estimated food composition data in nutrition research introduces significant bias that can only be addressed with biomarkers

    Javier I Ottaviani, Virag Sagi-Kiss ... Gunter GC Kuhnle
    The reliance on food composition databases for the assessment of dietary intake is unreliable and results in a large bias when investigating the associations between diet and disease risk.
    1. Plant Biology

    Distinct effects of phyllosphere and rhizosphere microbes on invader Ageratina adenophora during its early life stages

    Zhao-Ying Zeng, Jun-Rong Huang ... Han-Bo Zhang
    An inoculation experiment shows phyllosphere microbiome plays an important role in invader Ageratina adenophora population establishment by killing seedlings at very early growth stage.
    1. Neuroscience

    An adaptable, reusable, and light implant for chronic Neuropixels probes

    Célian Bimbard, Flóra Takács ... Philip Coen
    Revised
    Reviewed Preprint v2
    • Valuable
    • Compelling
    1. Plant Biology

    Diurnal rhythmicity in metabolism and salivary effector expression shapes host colonization by aphids

    Jinlong Han, Daniel Kunk ... Vamsi J. Nalam
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Plant Biology

    A dual function of the IDA peptide in regulating cell separation and modulating plant immunity at the molecular level

    Vilde Olsson Lalun, Maike Breiden ... Melinka A Butenko
    A molecular investigation on the role of the peptide ligand inflorescence deficient in abscission (IDA) in regulating immunity and development during cell separation in Arabidopsis thaliana.
    1. Cancer Biology
    2. Cell Biology

    SOD1 is a synthetic-lethal target in PPM1D-mutant leukemia cells

    Linda Zhang, Joanne I Hsu ... Margaret A Goodell
    PPM1D-mutant leukemia cells exhibit a dysregulated redox landscape, a diminished response to oxidative stress, and rely on SOD1 for their survival.
    1. Immunology and Inflammation

    Fine-tuning spatial-temporal dynamics and surface receptor expression support plasma cell-intrinsic longevity

    Zhixin Jing, Phillip Galbo ... David Fooksman
    Enigmatic long-lived plasma cells display an enhanced clustering in bone marrow niches and require CXCR4 for retention, survival, and maintenance of antibody titers.
    1. Physics of Living Systems

    Diffusive lensing as a mechanism of intracellular transport and compartmentalization

    Achuthan Raja Venkatesh, Kathy H Le ... Onn Brandman
    Agent-based modeling of space-dependent diffusivity inside cells reveals potential effects on biomolecule concentration and mesoscale dynamics.
    1. Structural Biology and Molecular Biophysics

    Structural features of heteromeric channels composed of CALHM2 and CALHM4 paralogs

    Katarzyna Drożdżyk, Martina Peter, Raimund Dutzler
    Structural studies revealing the organization of assemblies consisting of CALHM2 and CALHM4 subunits provide insight into the mechanism of heteromerization of large pore channels.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Tribbles1 is host protective during in vivo mycobacterial infection

    Ffion R Hammond, Amy Lewis ... Philip M Elks
    The pseudokinase Tribbles1 is expressed in human monocytes after mycobacterial challenge and can be manipulated to be host protective against mycobacterial infection, due to control of innate immune cell function, in a zebrafish tuberculosis model.
    1. Cell Biology
    2. Structural Biology and Molecular Biophysics

    Structural analysis of the dynamic ribosome-translocon complex

    Aaron JO Lewis, Frank Zhong ... Ramanujan S Hegde
    A combination of cryo-electron microscopy, structure prediction, and evolutionary analyses reveal several functional states of the dynamic protein translocation machinery at the mammalian endoplasmic reticulum.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    ASAR lncRNAs control DNA replication timing through interactions with multiple hnRNP/RNA binding proteins

    Mathew Thayer, Michael B Heskett ... Phillip A Yates
    Molecular genetic analyses of ASARs reveals regulation of large-scale mammalian chromosome structure and function that includes long non-coding RNAs and nuclear RNA binding proteins as essential regulators of chromosome dynamics.
    1. Cancer Biology
    2. Computational and Systems Biology

    Optimal transport for automatic alignment of untargeted metabolomic data

    Marie Breeur, George Stepaniants ... Vivian Viallon
    A computational method based on optimal transport enables state-of-the-art alignment between untargeted metabolomic studies and is evaluated on cord blood and cancer datasets.
    1. Developmental Biology

    Skeletal Muscle Satellite Cells Co-Opt the Tenogenic Gene Scleraxis to Instruct Regeneration

    Yun Bai, Tyler Harvey ... Chen-Ming Fan
    Revised
    Reviewed Preprint v2
    • Important
    • Convincing
    1. Neuroscience

    Sub-type specific connectivity between CA3 pyramidal neurons may underlie their sequential activation during sharp waves

    Rosanna P. Sammons, Stefano Masserini ... Dietmar Schmitz
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Cell Biology
    2. Developmental Biology

    The Drosophila EcR-Hippo component Taiman promotes epithelial cell fitness by control of the Dally-like glypican and Wg gradient

    Colby K. Schweibenz, Victoria C. Placentra, Kenneth H. Moberg
    Not revised
    Reviewed Preprint v1
    • Useful
    • Incomplete
    1. Cell Biology

    ScRNA-seq and scATAC-seq reveal that sertoli cell mediate spermatogenesis disorders through stage-specific communications in non-obstructive azoospermia

    Shimin Wang, Hongxian Wang ... Dong Zhao
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Convincing
    • Incomplete
    1. Neuroscience

    Local, calcium- and reward-based synaptic learning rule that enhances dendritic nonlinearities can solve the nonlinear feature binding problem

    Zahra Khodadadi, Daniel Trpevski ... Jeanette Hellgren Kotaleski
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Immunology and Inflammation

    Expression of modified FcγRI enables myeloid cells to elicit robust tumor-specific cytotoxicity

    Leen Farhat-Younis, Manho Na ... Yaron Carmi
    Genetic engineering of murine myeloid cells reveals the challenges in ectopic expression of chemiric receptors and provides a novel framework to endow them with tumor-specific cytotoxic ability.
    1. Neuroscience

    Homeostatic regulation of rapid eye movement sleep by the preoptic area of the hypothalamus

    John J Maurer, Alexandra Lin ... Shinjae Chung
    Preoptic area of the hypothalamus is important for the homeostatic regulation of rapid eye movement sleep.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

    Roberto Efraín Díaz, Andrew K Ecker ... James S Fraser
    Biochemical and structural investigations of the pH adaptability of mouse Acidic Mammalian Chitinase offer insights for designing enhanced enzyme variants that can function in both lung and gut.
    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    MftG is crucial for ethanol metabolism of mycobacteria by linking mycofactocin oxidation to respiration

    Ana Patrícia Graça, Vadim Nikitushkin ... Gerald Lackner
    Revised
    Reviewed Preprint v3
    • Fundamental
    • Compelling
    1. Neuroscience
    2. Computational and Systems Biology

    A common alteration in effort-based decision-making in apathy, anhedonia, and late circadian rhythm

    Sara Z. Mehrhof, Camilla L. Nord
    Revised
    Reviewed Preprint v3
    • Important
    • Convincing
    1. Cell Biology
    2. Genetics and Genomics

    Temporally controlled nervous system-to-gut signaling bidirectionally regulates longevity in C. elegans

    Lingxiu Xu, Chengxuan Han ... Jianfeng Liu
    Not revised
    Reviewed Preprint v1
    • Important
    • Incomplete
    1. Chromosomes and Gene Expression

    Srs2 binding to PCNA and its sumoylation contribute to RPA antagonism during the DNA damage response

    Jiayi Fan, Nalini Dhingra ... Xiaolan Zhao
    Revised
    Reviewed Preprint v2
    • Valuable
    • Solid
    1. Developmental Biology

    Identification and characterization of intermediate states in mammalian neural crest cell epithelial to mesenchymal transition and delamination

    Ruonan Zhao, Emma L Moore ... Paul A Trainor
    Epithelial to mesenchymal transition (EMT) is a continuous process, in which the transition or intermediate states can be molecularly and spatially defined, shedding new light on development and disease EMT.
    1. Cancer Biology

    A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma

    Haley R Noonan, Alexandra M Thornock ... Leonard I Zon
    An in vivo reporter of TGFb signaling in zebrafish reveals that melanoma cells undergoing chronic TGFb signaling up-regulate extracellular matrix genes, down-regulate IFN, and are preferentially phagocytosed by macrophages compared to non-TGFb responsive melanoma cells.
    1. Neuroscience

    Distance and grid-like codes support the navigation of abstract social space in the human brain

    Zilu Liang, Simeng Wu ... Chao Liu
    New data provides partial evidence that abstract social knowledge adopts a similar encoding scheme as spatial cognitive maps in the human brain.
    1. Plant Biology

    The Rhizobial effector NopT targets Nod factor receptors to regulate symbiosis in Lotus japonicus

    Hanbin Bao, Yanan Wang ... Yangrong Cao
    Revised
    Reviewed Preprint v2
    • Important
    • Solid
    1. Neuroscience

    Sleep need driven oscillation of glutamate synaptic phenotype

    Kaspar E Vogt, Ashwinikumar Kulkarni ... Robert W Greene
    Revised
    Reviewed Preprint v2
    • Important
    • Incomplete
    1. Medicine
    2. Neuroscience

    Cold induces brain region-selective cell activity-dependent lipid metabolism

    Hyeonyoung Min, Yale Y Yang, Yunlei Yang
    Revised
    Reviewed Preprint v2
    • Useful
    • Incomplete
    1. Neuroscience

    Three-photon excited fluorescence microscopy enables imaging of blood flow, neural structure and inflammatory response deep into mouse spinal cord in vivo

    Yu-Ting Cheng, Kawasi M. Lett ... Chris B. Schaffer
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Neuroscience

    ElectroPhysiomeGAN: Generation of Biophysical Neuron Model Parameters from Recorded Electrophysiological Responses

    Jimin Kim, Qiang Liu, Eli Shlizerman
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Neuroscience
    2. Evolutionary Biology

    Investments in photoreceptors compete with investments in optics to determine eye design

    Francisco JH Heras, Simon B Laughlin
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Neuroscience

    An image-computable model of speeded decision-making

    Paul I. Jaffe, Gustavo X. Santiago-Reyes ... Russell A. Poldrack
    Not revised
    Reviewed Preprint v1
    • Important
    • Incomplete
    1. Neuroscience

    Nonlinear feedback modulation contributes to the optimization of flexible decision-making

    Xuanyu Wu, Yang Zhou
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Genetics and Genomics

    Base editing strategies to convert CAG to CAA diminish the disease-causing mutation in Huntington’s disease

    Doo Eun Choi, Jun Wan Shin ... Jong-Min Lee
    Uninterrupted CAG repeat length determines onset age in Huntington's disease, and therefore, base editing strategies to generate CAA interruption offer new therapeutic opportunities as they diminish the disease-causing mutation.
    1. Neuroscience

    Brain age has limited utility as a biomarker for capturing fluid cognition in older individuals

    Alina Tetereva, Narun Pat
    When used to capture fluid cognition, Brain Age likely fails to add substantially more information over and above chronological age and could miss up to around one-third of the variation.
    1. Cell Biology
    2. Developmental Biology

    A CDK1 phosphorylation site on Drosophila PAR-3 regulates neuroblast polarisation and sensory organ formation

    Nicolas Loyer, Elizabeth KJ Hogg ... Jens Januschke
    PAR-3/Baz function is regulated by CDK1 in asymmetrically dividing cells in the central and peripheral nervous system of Drosophila revealing direct regulation of cell polarity by the cell cycle machinery in the context of cell fate specification.
    1. Evolutionary Biology

    Sex-biased regulatory changes in the placenta of native highlanders contribute to adaptive fetal development

    Tian Yue, Yongbo Guo ... Bing Su
    Comparative transcriptome analyses of human placenta reveal regulatory divergence between native highlanders and lowland immigrants living at high altitude, and a sex-biased pattern of genetic adaptation.
    1. Developmental Biology
    2. Neuroscience

    A microRNA that controls the emergence of embryonic movement

    Jonathan AC Menzies, André Maia Chagas ... Claudio R Alonso
    A novel behavioural pipeline enables the quantitative analysis of the onset of movement in Drosophila embryos revealing that a microRNA modulates this process through regulatory effects in the sensory system.
    1. Computational and Systems Biology
    2. Evolutionary Biology

    Evolutionary trends of alternative splicing

    Rebeca de la Fuente, Wladimiro Díaz-Villanueva ... Andrés Moya
    Not revised
    Reviewed Preprint v1
    • Important
    • Inadequate
    1. Cancer Biology
    2. Cell Biology

    RAPSYN-mediated neddylation of BCR-ABL alternatively determines the fate of Philadelphia chromosome-positive leukemia

    Mengya Zhao, Beiying Dai ... Yijun Chen
    Scaffolding protein RAPSYN can exert its NEDD8 E3 ligase activity to neddylate and stabilize oncogenic BCR-ABL by competing proteasomal degradation in Ph+ leukemia.
    1. Medicine

    Phosphate as an adjunct to calcium in promoting coronary vascular calcification in chronic inflammatory states

    Gordon L Klein
    Phosphate and calcium from resorbing bone can find their way to the coronary circulation and contribute to atherosclerotic calcification of the blood vessels.
    1. Cell Biology
    2. Genetics and Genomics

    SCC3 is an axial element essential for homologous chromosome pairing and synapsis

    Yangzi Zhao, Lijun Ren ... Zhukuan Cheng
    SCC3 not only functions as a member of cohesin complex but also participates in homologous pairing and synapsis during rice meiosis.
    1. Structural Biology and Molecular Biophysics

    Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern

    Callum M Ives, Linh Nguyen ... Elisa Fadda
    Viral evolution can lead to mutations that render specific glycosylation sites dispensable for folding and for supporting the protein's function, allowing changes in the shield, and in the immunogenic profile.
    1. Physics of Living Systems

    Quantifying gliding forces of filamentous cyanobacteria by self-buckling

    Maximilian Kurjahn, Antaran Deka ... Stefan Karpitschka
    The self-buckling behavior of filamentous cyanobacteria allowed a quantification of their propulsion forces, indicating that adhesion plays an important role in gliding motility.
    1. Immunology and Inflammation

    The delayed kinetics of Myddosome formation explains why amyloid-beta aggregates trigger Toll-like receptor 4 less efficiently than lipopolysaccharide

    Bing Li, Prasanna Suresh ... David Klenerman
    Amyloid-beta aggregates and lipopolysaccharide differ in their kinetics of Myddosome formation and size of Myddosome formed, providing an explanation for the less efficient triggering of TLR4 observed with aggregates.
    1. Neuroscience

    Synaptic mechanisms modulate the spatiotemporal dynamics of striatal direct pathway neurons and motor output

    John J Marshall, Jian Xu ... Anis Contractor
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Computational and Systems Biology

    Untargeted Pixel-by-Pixel Imaging of Metabolite Ratio Pairs as a Novel Tool for Biomedical Discovery in Mass Spectrometry Imaging

    Huiyong Cheng, Dawson Miller ... Qiuying Chen
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Immunology and Inflammation
    2. Computational and Systems Biology

    PAbFold: Linear Antibody Epitope Prediction using AlphaFold2

    Jacob DeRoo, James S Terry ... Brian J Geiss
    Revised
    Reviewed Preprint v2
    • Useful
    • Incomplete
    1. Developmental Biology
    2. Neuroscience

    A unique multi-synaptic mechanism involving acetylcholine and GABA regulates dopamine release in the nucleus accumbens through early adolescence in male rats

    Melody C Iacino, Taylor A Stowe ... Mark J Ferris
    A circuit within the nucleus accumbens that exists during a specific developmental window through early adolescence male rats may serve as a substrate that underlies heightened reward seeking in this population.
    1. Immunology and Inflammation

    The interferon-rich skin environment regulates Langerhans cell ADAM17 to promote photosensitivity in lupus

    Thomas Morgan Li, Victoria Zyulina ... Theresa T Lu
    Interferon contributes to photosensitivity at least in part by causing Langerhans cell ADAM17 dysfunction, raising the possibility that anifrolumab ameliorates lupus skin disease in part by restoring Langerhans cell function.
    1. Neuroscience

    Cell-autonomous role of leucine-rich repeat kinase in the protection of dopaminergic neuron survival

    Jongkyun Kang, Guodong Huang ... Jie Shen
    LRRK plays an essential, cell-intrinsic role in the protection of dopaminergic neurons during aging, and new genetic findings suggest that LRRK2 mutations may impair its function, leading to dopaminergic neurodegeneration in PD.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    7,8-Dihydroxyflavone is a direct inhibitor of human and murine pyridoxal phosphatase

    Marian Brenner, Christoph Zink ... Antje Gohla
    Direct inhibition of pyridoxal phosphatase activity by 7,8-dihydroxyflavone indicates a pharmacological entry point into brain disorders associated with vitamin B6 deficiency.
    1. Developmental Biology

    Defective mesenchymal Bmpr1a-mediated BMP signaling causes congenital pulmonary cysts

    Yongfeng Luo, Ke Cao ... Wei Shi
    Disrupted mesenchymal Bmpr1a-mediated signaling in fetal mouse lung leads to abnormal airway development and congenital pulmonary cyst formation.
    1. Immunology and Inflammation

    Secreted antigen A peptidoglycan hydrolase is essential for Enterococcus faecium cell separation and priming of immune checkpoint inhibitor therapy

    Steven Klupt, Kyong Tkhe Fam ... Howard C Hang
    The peptidoglycan hydrolase activity of Enterococcus faecium secreted antigen A is crucial for cell wall remodeling during bacterial cell separation and generates muropeptides that stimulate host immunity to enhance immune checkpoint inhibitor anti-cancer therapy.
    1. Developmental Biology

    Obox4 promotes zygotic genome activation upon loss of Dux

    Youjia Guo, Tomohiro Kitano ... Haruhiko Siomi
    Analysis of mouse zygotic genome activation (ZGA) reveals that a mis-annotated multicopy homeobox gene Obox4 functions redundantly with Dux to promote ZGA.
    1. Computational and Systems Biology
    2. Medicine

    Single-cell transcriptome analysis of cavernous tissues reveals the key roles of pericytes in diabetic erectile dysfunction

    Seo-Gyeong Bae, Guo Nan Yin ... Jihwan Park
    Single-cell RNA sequencing analysis of diabetic mouse cavernous tissue revealed that LBH is a novel pericyte marker and may interact with Crystallin Alpha B and Vimentin to promote neurovascular regeneration.
    1. Neuroscience

    Convergence of inputs from the basal ganglia with layer 5 of motor cortex and cerebellum in mouse motor thalamus

    Kevin P Koster, S Murray Sherman
    A detailed physiological characterization of inputs to the motor thalamus adds nuance to the notion that information from the cerebellum and basal ganglia are segregated and provides a mechanism by which the basal ganglia can gate communication between cortical areas.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Rapid, DNA-induced interface swapping by DNA gyrase

    Thomas RM Germe, Natassja G Bush ... Anthony Maxwell
    DNA gyrase, a regulator of bacterial genomes topology, is shown to undergo rearrangements while functioning on DNA in vitro, with important potential consequences for gyrase-targeted antibiotics activity and bacterial evolution.
    1. Computational and Systems Biology
    2. Neuroscience

    Deciphering the genetic code of neuronal type connectivity through bilinear modeling

    Mu Qiao
    A novel bilinear modeling approach reveals genetic code of neuronal connectivity, offering insights for targeted genetic interventions in neural circuits.
    1. Neuroscience

    Establishing synthetic ribbon-type active zones in a heterologous expression system

    Rohan Kapoor, Niko Schwenzer ... Tobias Moser
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Neuroscience

    Rate of brain aging associates with future executive function in Asian children and older adults

    Susan F. Cheng, Wan Lin Yue ... Juan Helen Zhou
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Comparative analysis of multiplexed in situ gene expression profiling technologies

    Austin Hartman, Rahul Satija
    Not revised
    Reviewed Preprint v1
    • Important
    • Incomplete
    1. Neuroscience

    Diffusion MRS tracks distinct trajectories of neuronal development in the cerebellum and thalamus of rat neonates

    Clémence Ligneul, Lily Qiu ... Jason P. Lerch
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Genetics and Genomics

    Enhancing CRISPR prime editing by reducing misfolded pegRNA interactions

    Weiting Zhang, Karl Petri ... Jing-Ruey Joanna Yeh
    Strategic pegRNA designs and other approaches mitigating 5' and 3' interactions within pegRNAs can often lead to substantial improvements in prime editing efficiency.
    1. Genetics and Genomics

    Post-meiotic mechanism of facultative parthenogenesis in gonochoristic whiptail lizard species

    David V Ho, Duncan Tormey ... Peter Baumann
    Facultative parthenogenesis in whiptail lizards produces genome-wide homozygosity in offspring.
    1. Biochemistry and Chemical Biology
    2. Stem Cells and Regenerative Medicine

    Targeted protein degradation systems to enhance Wnt signaling

    Parthasarathy Sampathkumar, Heekyung Jung ... Yang Li
    A novel targeted protein degradation system to achieve cell-type-specific enhancement of Wnt signaling.
    1. Developmental Biology

    A-to-I RNA editing of CYP18A1 mediates transgenerational wing dimorphism in aphids

    Bin Zhu, Wei Rui ... Pei Liang
    Not revised
    Reviewed Preprint v1
    • Important
    • Incomplete
    • Inadequate
    1. Neuroscience

    Neuroestrogens facilitate male-typical behaviors by potentiating androgen receptor signaling in medaka

    Yuji Nishiike, Shizuku Maki ... Kataaki Okubo
    Not revised
    Reviewed Preprint v1
    • Important
    • Convincing
    1. Developmental Biology
    2. Stem Cells and Regenerative Medicine

    Endothelial cell signature in muscle stem cells validated by VEGFA-FLT1-AKT1 axis promoting survival of muscle stem cell

    Mayank Verma, Yoko Asakura ... Atsushi Asakura
    Bulk and single-cell RNA-seq data demonstrated that muscle stem cells express low levels of canonical endothelial cell markers, including VEGFA receptors, and VEGFA-FLT1 pathway has a drastic effect on muscle stem cell survival through AKT1 in vitro and in vivo.
    1. Developmental Biology

    Scaling between cell cycle duration and wing growth is regulated by Fat-Dachsous signaling in Drosophila

    Andrew Liu, Jessica O’Connell ... Richard W Carthew
    Two atypical cadherins regulate organ growth by tuning the coupling of cell cycle duration to organ size.
    1. Neuroscience

    Rule-based modulation of a sensorimotor transformation across cortical areas

    Yi-Ting Chang, Eric A Finkel ... Daniel H O'Connor
    Preparatory states within the motor cortex play a critical role in selecting an appropriate action in response to sensory input, dependent on the context.
    1. Developmental Biology

    The autophagy protein, ATG14 safeguards against unscheduled pyroptosis activation to enable embryo transport during early pregnancy

    Pooja Popli, Arin K Oestreich ... Ramakrishna Kommagani
    Revised
    Reviewed Preprint v2
    • Valuable
    • Solid
    1. Neuroscience

    Altered visual cortex excitatory/inhibitory ratio following transient congenital visual deprivation in humans

    Rashi Pant, Kabilan Pitchaimuthu ... Brigitte Röder
    Revised
    Reviewed Preprint v2
    • Valuable
    • Incomplete
    1. Neuroscience

    Compressed sensing based approach identifies modular neural circuitry driving learned pathogen avoidance

    Timothy Hallacy, Abdullah Yonar ... Sharad Ramanathan
    Revised
    Reviewed Preprint v2
    • Important
    • Solid
    1. Developmental Biology

    Mechanical forces pattern endocardial Notch activation via mTORC2-PKC pathway

    Yunfei Mu, Shijia Hu ... Hongjun Shi
    Revised
    Reviewed Preprint v2
    • Important
    • Convincing
    1. Immunology and Inflammation
    2. Cancer Biology

    Unraveling the Power of NAP-CNB’s Machine Learning-enhanced Tumor Neoantigen Prediction

    Almudena Méndez-Pérez, Andrés M. Acosta-Moreno ... Esteban Veiga
    Not revised
    Reviewed Preprint v1
    • Important
    • Compelling
    1. Cancer Biology

    Reduced mitochondrial transcription sensitizes acute myeloid leukemia cells to BCL-2 inhibition

    Laleh S. Arabanian, Jenni Adamsson ... Claes M. Gustafsson
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    1. Neuroscience
    2. Computational and Systems Biology

    Visual information is broadcast among cortical areas in discrete channels

    Yiyi Yu, Jeffery N Stirman ... Spencer LaVere Smith
    Revised
    Reviewed Preprint v2
    • Important
    • Solid
    1. Microbiology and Infectious Disease

    Widespread Horizontal Gene Transfer Among Animal Viruses

    Christopher B. Buck, Nicole Welch ... Gabriel J. Starrett
    Not revised
    Reviewed Preprint v1
    • Fundamental
    • Solid
    1. Neuroscience

    Spatial periodicity in grid cell firing is explained by a neural sequence code of 2-D trajectories

    Rebecca R.G., Giorgio A. Ascoli ... Holger Dannenberg
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Solid
    • Incomplete
    1. Developmental Biology
    2. Evolutionary Biology

    Single Cell Sequencing Provides Clues about the Developmental Genetic Basis of Evolutionary Adaptations in Syngnathid Fishes

    Hope M Healey, Hayden B Penn ... William A Cresko
    Revised
    Reviewed Preprint v2
    • Valuable
    • Solid
    1. Developmental Biology
    2. Physics of Living Systems

    Spectral decomposition unlocks ascidian morphogenesis

    Joel Dokmegang, Emmanuel Faure ... Madhav Mani
    Not revised
    Reviewed Preprint v1
    • Important
    • Convincing
    1. Cell Biology
    2. Physics of Living Systems

    Partitioning to ordered membrane domains regulates the kinetics of secretory traffic

    Ivan Castello-Serrano, Frederick A Heberle ... Ilya Levental
    Direct measurements of trafficking kinetics between organelles of the secretory pathway suggest that lipid-driven membrane domains laterally sort proteins during membrane traffic.
    1. Structural Biology and Molecular Biophysics

    A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery

    Zhuang Liu, Thomas G Gillis ... Qiang Cui
    A combined theoretical and experimental study revealed the mechanistic and structural basis of mutational effects on allostery and provided insights into the intrinsic connection of intra- and inter-domain properties.
    1. Immunology and Inflammation

    G protein subunit Gγ13-mediated signaling pathway is critical to the inflammation resolution and functional recovery of severely injured lungs

    Yi-Hong Li, Yi-Sen Yang ... Liquan Huang
    Conditional abolishment of a G protein subunit in a subset of ectopic tuft cells engenders severer injury, slower recovery, and increased fatality following the infection of the influenza viruses.
    1. Developmental Biology

    Loss of ninein interferes with osteoclast formation and causes premature ossification

    Thierry Gilbert, Camille Gorlt ... Andreas Merdes
    It is shown that the absence of the centrosome protein ninein provokes premature ossification during mouse development, due to a defect in the fusion of precursor cells into syncytial osteoclasts.
    1. Cancer Biology

    Single-cell profiling reveals the intratumor heterogeneity and immunosuppressive microenvironment in cervical adenocarcinoma

    Yang Peng, Jing Yang ... Liang Weng
    Revised
    Reviewed Preprint v2
    • Useful
    • Incomplete
    1. Cell Biology
    2. Chromosomes and Gene Expression

    Live imaging of Alu elements reveals non-uniform euchromatin dynamics coupled to transcription

    Yi-Che Chang, Sofia A. Quinodoz, Clifford P. Brangwynne
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Cell Biology
    2. Microbiology and Infectious Disease

    High-content high-resolution microscopy and deep learning assisted analysis reveals host and bacterial heterogeneity during Shigella infection

    Ana T. López-Jiménez, Dominik Brokatzky ... Serge Mostowy
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Compelling
    1. Neuroscience

    Tracking the neurodevelopmental trajectory of beta band oscillations with optically pumped magnetometer-based magnetoencephalography

    Lukas Rier, Natalie Rhodes ... Matthew J Brookes
    The first neurodevelopmental study using a novel, wearable brain imaging system based on optically pumped magnetometers, shows age-related changes in neural oscillatory task responses and cortical functional connectivity.
    1. Evolutionary Biology
    2. Genetics and Genomics

    Copy number variation and population-specific immune genes in the model vertebrate zebrafish

    Yannick Schäfer, Katja Palitzsch ... Jaanus Suurväli
    As a result of frequent gene duplication and haplotypic variation, a family of immune genes in the model vertebrate zebrafish has thousands of gene copies that are population- or individual-specific.
    1. Neuroscience

    Ingestible pills reveal gastric correlates of emotions

    Giuseppina Porciello, Alessandro Monti ... Salvatore Maria Aglioti
    Direct measures of inner gastrointestinal signals via ingestible capsules highlight the role of stomach pH in shaping human feelings of disgust, fear and happiness.
    1. Cell Biology

    Syntaxin 17 recruitment to mature autophagosomes is temporally regulated by PI4P accumulation

    Saori Shinoda, Yuji Sakai ... Noboru Mizushima
    The autophagosomal membrane becomes negatively charged during maturation due to the accumulation of PI4P, leading to the recruitment of syntaxin 17, which is required for autophagosome-lysosome fusion.
    1. Computational and Systems Biology

    Statistical and computational methods for integrating microbiome, host genomics, and metabolomics data

    Rebecca A Deek, Siyuan Ma ... Hongzhe Li
    Advanced statistical and computational methods are reviewed and compared for integrating microbiome, host genomics, and metabolomics data, together with future research directions.
    1. Neuroscience

    Adult-born granule cells modulate CA2 network activity during retrieval of developmental memories of the mother

    Blake J Laham, Isha R Gore ... Elizabeth Gould
    Adult-born granule cell projections are necessary for CA2 network activity and retrieval of developmental social memories.
    1. Microbiology and Infectious Disease
    2. Physics of Living Systems

    Potassium-mediated bacterial chemotactic response

    Chi Zhang, Rongjing Zhang, Junhua Yuan
    Escherichia coli exhibits sensitive chemotaxis to potassium, mediated by differential responses of Tar and Tsr chemoreceptors to intracellular pH changes induced by potassium concentration gradients.
    1. Evolutionary Biology

    The evolution of olfactory sensitivity, preferences, and behavioral responses in Mexican cavefish is influenced by fish personality

    Maryline Blin, Louis Valay ... Sylvie Rétaux
    Individual olfactory-driven behaviors, odor preferences, and olfactory sensitivity have rapidly evolved in blind Mexican cavefish, as a quantitative genetic trait.
    1. Evolutionary Biology

    Evolutionary druggability for low-dimensional fitness landscapes toward new metrics for antimicrobial applications

    Rafael F Guerrero, Tandin Dorji ... C Brandon Ogbunugafor
    Inspired by notions of 'druggability' from medicinal chemistry, two new metrics, drug applicability and variant vulnerability, utilize evolutionary perspectives and methods to improve attempts to treat infectious diseases.
    1. Cancer Biology

    TAK1-mediated phosphorylation of PLCE1 represses PIP2 hydrolysis to impede esophageal squamous cancer metastasis

    Qianqian Ju, Wenjing Sheng ... Cheng Sun
    Revised
    Reviewed Preprint v2
    • Valuable
    • Solid
    1. Neuroscience

    Cyclin-dependent kinase 5 (Cdk5) activity is modulated by light and gates rapid phase shifts of the circadian clock

    Andrea Brenna, Micaela Borsa ... Urs Albrecht
    Revised
    Reviewed Preprint v2
    • Important
    • Convincing
    1. Cancer Biology

    In vivo targeted and deterministic single cell malignant transformation

    Pierluigi Scerbo, Benjamin Tisserand ... Bertrand Ducos
    Not revised
    Reviewed Preprint v1
    • Valuable
    • Incomplete
    1. Cell Biology

    Quantitative intra-Golgi transport and organization data suggest the stable compartment nature of the Golgi

    Hieng Chiong Tie, Haiyun Wang ... Lei Lu
    Not revised
    Reviewed Preprint v1
    • Important
    • Convincing
    1. Neuroscience

    Glutamatergic supramammillary nucleus neurons respond to threatening stressors and promote active coping

    Abraham Escobedo, Salli-Ann Holloway ... Aaron J Norris
    Activation of a population of glutamatergic neurons in supramammillary nucleus enhances active coping behaviors in response to threats, offering new insights for therapeutic strategies against anxiety and mood disorders.
    1. Epidemiology and Global Health

    The impact of surgery and oncological treatment on risk of type 2 diabetes onset in patients with colorectal cancer: nationwide cohort study in Denmark

    Caroline Krag, Maria Saur Svane ... Tinne Laurberg
    Treatment of colorectal cancer with colonic resection compared with rectal resection results in sligthly increased T2D risk, whereas chemotherapy treatment does not impact risk of developing T2D.
    1. Cancer Biology
    2. Genetics and Genomics

    DUX4 is a common driver of immune evasion and immunotherapy failure in metastatic cancers

    Jose Mario Bello Pineda, Robert K Bradley
    DUX4 expression is a common feature of metastatic tumors, where it is significantly associated with immune cell exclusion, decreased objective response to immune checkpoint blockade, and reduced patient survival.
    1. Stem Cells and Regenerative Medicine

    Near-perfect precise on-target editing of human hematopoietic stem and progenitor cells

    Fanny-Mei Cloarec-Ung, Jamie Beaulieu ... David JHF Knapp
    Precision genome editing in human hematopoietic stem and progenitor cells can achieve near-perfect efficiency with tunable zygosity, thus enabling isogenic disease modeling for monogenic blood disorders and improving therapeutic applications.
    1. Neuroscience

    The archerfish uses motor adaptation in shooting to correct for changing physical conditions

    Svetlana Volotsky, Opher Donchin, Ronen Segev
    The archerfish adapts with egocentric reference frame to correct for different conditions during shot above water level.
    1. Neuroscience

    Physiological roles of endocytosis and presynaptic scaffold in vesicle replenishment at fast and slow central synapses

    Satyajit Mahapatra, Tomoyuki Takahashi
    Physiologically, vesicle replenishment at the fast calyx synapse requires both fast-endocytosis and scaffold machinery to support rapid neurotransmission, whereas at the slow hippocampal CA1 synapse only endocytosis is necessary.
    1. Developmental Biology

    Styxl2 regulates de novo sarcomere assembly by binding to non-muscle myosin IIs and promoting their degradation

    Xianwei Chen, Yanfeng Li ... Zhenguo Wu
    Styxl2, a sarcomeric muscle-specific pseudophosphatase in vertebrates, functions in sarcomere assembly by promoting protein degradation of non-muscle myosin IIs.
    1. Cell Biology
    2. Computational and Systems Biology

    Agent-based model demonstrates the impact of nonlinear, complex interactions between cytokines on muscle regeneration

    Megan Haase, Tien Comlekoglu ... Silvia S Blemker
    A computational model of skeletal muscle regeneration reveals complex interplay of cytokines, angiogenesis, and cell behaviors, predicting that synergistic cytokine perturbations enhance skeletal muscle regeneration beyond individual cytokine interventions.
    1. Structural Biology and Molecular Biophysics

    Structures of wild-type and a constitutively closed mutant of connexin26 shed light on channel regulation by CO2

    Deborah H Brotherton, Sarbjit Nijjar ... Alexander David Cameron
    The mutation of Lys125 in connexin26 to glutamate, a carbamylation mimetic, pushes the equilibrium of the gap junction channel seen in cryo-EM towards a more closed conformation.