BMRetriever/BMRetriever-410M
Feature Extraction • 0.4B • Updated • 91 • 2
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10.1101/008326 | PMCE: efficient inference of expressive models of cancer evolution with high prognostic power | MotivationDriver (epi)genomic alterations underlie the positive selection of cancer subpopulations, which promotes drug resistance and relapse. Even though substantial heterogeneity is witnessed in most cancer types, mutation accumulation patterns can be regularly found and can be exploited to reconstruct predictive mo... | bioinformatics |
10.1101/008326 | PMCE: efficient inference of expressive models of cancer evolution with high prognostic power | MotivationDriver (epi)genomic alterations underlie the positive selection of cancer subpopulations, which promotes drug resistance and relapse. Even though substantial heterogeneity is witnessed in most cancer types, mutation accumulation patterns can be regularly found and can be exploited to reconstruct predictive mo... | bioinformatics |
10.1101/010553 | Convergent evolution of primate testis transcriptomes reflects mating strategy | In independent mammalian lineages where females mate with multiple males (multi-male mating strategies), males have evolved larger testicles relative to those lineages where females mate with fewer males (single-male mating strategies). Here we study published bulk testis transcriptomes from humans, chimpanzees, gorill... | evolutionary biology |
10.1101/022459 | A max-margin model for predicting residue-base contacts in protein-RNA interactions | Protein-RNA interactions (PRIs) are essential for many biological processes, so understanding aspects of the sequences and structures involved in PRIs is important for unraveling such processes. Because of the expensive and time-consuming techniques required for experimental determination of complex protein-RNA structu... | bioinformatics |
10.1101/035972 | Engineered acetoacetate-inducible whole-cell biosensors based on the AtoSC two-component system | Whole-cell biosensors hold potential in a variety of industrial, medical and environmental applications. These biosensors can be constructed through the repurposing of bacterial sensing mechanisms, including the common two-component system. Here we report on the construction of a range of novel biosensors that are sens... | synthetic biology |
10.1101/046052 | Association of NQO1 C609T (Pro187Ser) with risk of Oral Submucous Fibrosis in Eastern Indian population | Oral submucous fibrosis (OSF) is a debilitating disease mainly attributed to chewing areca nut with a 7.4-13% malignant transformation rate. Present study explores the role of NADPH quinone oxidoreductase 1 (NQO1) C609T (Pro187Ser) polymorphism in susceptibility to OSF among habitual areca nut chewers in an eastern Ind... | genetics |
10.1101/060012 | Fast gene set enrichment analysis | Gene set enrichment analysis (GSEA) is an ubiquitously used tool for evaluating pathway enrichment in transcriptional data. Typical experimental design consists in comparing two conditions with several replicates using a differential gene expression test followed by preranked GSEA performed against a collection of hund... | bioinformatics |
10.1101/062083 | Immunoecology of species with alternative reproductive tactics and strategies | Alternative reproductive tactics and strategies (ARTS) refer to polymorphic reproductive behaviours in which in addition to the usual two sexes, there are one or more alternative morphs, usually male, that have evolved the ability to circumvent direct intra-sexual competition. Each morph has its own morphological, ecol... | evolutionary biology |
10.1101/067736 | Frameshifts and wild-type protein sequences are always highly similar because the genetic code and genomes were optimized for frameshift tolerance | Frameshift protein sequences encoded by alternative reading frames of coding genes have been considered meaningless, and frameshift mutations have been considered of little importance for the molecular evolution of coding genes and proteins. However, functional frameshifts have been found widely existing. It was puzzli... | genetics |
10.1101/067736 | Frameshift and wild-type proteins are highly similar because the genetic code and genomes were optimized for frameshift tolerance | Frameshift protein sequences encoded by alternative reading frames of coding genes have been considered meaningless, and frameshift mutations have been considered of little importance for the molecular evolution of coding genes and proteins. However, functional frameshifts have been found widely existing. It was puzzli... | genetics |
10.1101/078378 | Estimating the timing of multiple admixture events using 3-locus Linkage Disequilibrium | Estimating admixture histories is crucial for understanding the genetic diversity we see in present-day populations. Allele frequency or phylogeny-based methods are excellent for inferring the existence of admixture or its proportions. However, to estimate admixture times, spatial information from admixed chromosomes o... | bioinformatics |
10.1101/086710 | Revisiting the effect of red on competition in humans | Bright red coloration is a signal of male competitive ability in animal species across a range of taxa, including non-human primates. Does the effect of red on competition extend to humans? A landmark study in evolutionary psychology established such an effect through analysis of data for four combat sports at the 2004... | evolutionary biology |
10.1101/092619 | Resolving the Functional Significance of BRCA1 RING Domain Missense Substitutions | Part 1Development and calibration of suitably accurate functional assays for BRCA1 RING domain and BRCT domain missense substitutions could dramatically accelerate clinical classification of rare missense substitutions observed in that gene. Leveraging data from 68,000 full sequence tests of BRCA1 and BRCA2, plus data ... | genetics |
10.1101/092205 | Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software | BackgroundComputational biology provides widely used and powerful software tools for testing and making inferences about biological data. In the face of rapidly increasing volumes of data, heuristic methods that trade software speed for accuracy may be employed. We are have studied these trade-offs using the results of... | bioinformatics |
10.1101/092205 | Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software | BackgroundComputational biology provides widely used and powerful software tools for testing and making inferences about biological data. In the face of rapidly increasing volumes of data, heuristic methods that trade software speed for accuracy may be employed. We are have studied these trade-offs using the results of... | bioinformatics |
10.1101/093237 | Correcting Chimeric Crosstalk in Single Cell RNA-seq Experiments | As part of the process of preparing sequencing libraries that include unique molecular identifiers (UMIs) such as many single cell RNA-seq (scRNA-seq) libraries, a diverse template must be amplified. During amplification, spurious chimeric molecules can be formed between molecules originating in different cells. While ... | bioinformatics |
10.1101/105437 | The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation | Predicting a multicellular organisms phenotype quantitatively from its genotype is challenging, as genetic effects must propagate across scales. Circadian clocks are intracellular regulators that control temporal gene expression patterns and hence metabolism, physiology and behaviour. Here we explain and predict canoni... | plant biology |
10.1101/113449 | Aperiodic neural activity is a better predictor of schizophrenia than neural oscillations | Diagnosis and symptom severity in schizophrenia is associated with irregularities across neural oscillatory frequency bands, including theta, alpha, beta, and gamma. However, electroencephalographic signals consist of both periodic and aperiodic background activity, characterized by the (1/f) slope of the power spectru... | neuroscience |
10.1101/132514 | Population Temporal Structure Supplements The Rate Code During Sensorimotor Transformations | Sensorimotor transformations are mediated by premotor brain networks where individual neurons represent sensory, cognitive, and movement-related information. Such multiplexing poses a conundrum - how does a decoder know precisely when to initiate a movement if its inputs are active at times when a movement is not desir... | neuroscience |
10.1101/135749 | Sexual dimorphism and plasticity in wing shape in three Diptera | The ability of powered flight in insects facilitated their great evolutionary success allowing them to occupy various ecological niches. Beyond this primary task, wings are often involved in various premating behaviors, such as the generation of courtship songs and the initiation of mating in flight. These specific fun... | zoology |
10.1101/121061 | Laser-free super-resolution microscopy | We report that high-density single-molecule super-resolution microscopy can be achieved with a conventional epifluorescence microscope setup and a Mercury arc lamp. The configuration termed as laser-free super-resolution microscopy (LFSM), is an extension of single molecule localisation microscopy (SMLM) techniques and... | biophysics |
10.1101/145896 | The Effects of Central Nervous System Stimulants on Drosophila melanogaster Reproduction | Stimulant drugs are used everyday by people around the world. The effect stimulants have on developing human fetuses is widely unknown. The fruit fly Drosophila melanogaster has become a valuable system to model the complex effects and properties of drugs in mammals. In this study, Drosophila is used to analyze the eff... | developmental biology |
10.1101/145664 | Proteins with prion-like domains can form viscoelastic condensates that enable membrane remodeling and endocytosis | Membrane invagination and vesicle formation are key steps in endocytosis and cellular trafficking. Here, we show that endocytic coat proteins with prion-like domains (PLDs) form hemispherical puncta in the budding yeast, S. cerevisiae. These puncta have the hallmarks of biomolecular condensates and enable membrane remo... | cell biology |
10.1101/156109 | Intestine-to-neuronal signaling alters risk-taking behaviors in food-deprived Caenorhabditis elegans | Animals integrate changes in external and internal environments to generate behavior. While neural circuits detecting external cues have been mapped, less is known about how internal states like hunger are integrated into behavioral outputs. We use the nematode C. elegans to decode how changes in internal nutritional s... | neuroscience |
10.1101/162644 | Distinct C4 Sub-Types and C3 Bundle Sheath Isolation In The Paniceae Grasses | In C4 plants, the enzymatic machinery underpinning photosynthesis can vary, with, for example, three distinct C4 acid decarboxylases being used to release CO2 in the vicinity of RuBisCO. For decades, these decarboxylases have been used to classify C4 species into three biochemical sub-types. However, more recently the ... | plant biology |
10.1101/165845 | The effects of an 8-week mindful eating intervention on anticipatory reward responses in striatum and midbrain | Obesity is a highly prevalent disease, usually resulting from chronic overeating. Accumulating evidence suggests that increased neural responses during the anticipation of high-calorie food play an important role in overeating. A promising method for counteracting enhanced food anticipation in overeating might be mindf... | neuroscience |
10.1101/111674 | Bromodomains regulate dynamic targeting of the PBAF chromatin remodeling complex to chromatin hubs | Transcriptional bursting involves genes rapidly switching between active and inactive states. Chromatin remodelers actively target arrays of acetylated nucleosomes at select enhancers and promoters to facilitate or shut down the repeated recruitment of RNA Pol II during transcriptional bursting. It is unknown how acety... | cell biology |
10.1101/180273 | cytoNet: Spatiotemporal Network Analysis of Cell Communities | We introduce cytoNet, a cloud-based tool to characterize cell populations from microscopy images. cytoNet quantifies spatial topology and functional relationships in cell communities using principles of network science. Capturing multicellular dynamics through graph features, cytoNet also evaluates the effect of cell-c... | bioengineering |
10.1101/181198 | Plant genetic effects on microbial hubs impact fitness across field trials | Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about whic... | plant biology |
10.1101/191858 | MARS-Net: Deep learning-based segmentation pipeline for profiling cellular morphodynamics from multiple types of live cell microscopy | Quantitative studies of cellular morphodynamics rely on extracting leading-edge velocity time-series based on accurate cell segmentation from live cell imaging. However, live cell imaging has numerous challenging issues about accurate edge localization. Here, we develop a deep learning-based pipeline, termed MARS-Net (... | bioinformatics |
10.1101/193946 | Histone deacetylase inhibition reduces deleterious cytokine release induced by ingenol stimulation | IntroductionLatency reversal agents (LRAs), such as protein kinase C (PKC) agonists, constitute a promising strategy for exposing and eliminating the HIV-1 latent reservoir. PKC agonists activate NF-{kappa}B and, in turn, induce deleterious pro-inflammatory cytokine production. Adjuvant pharmacological agents, such as ... | microbiology |
10.1101/193946 | Histone deacetylase inhibition reduces deleterious cytokine release induced by ingenol stimulation | IntroductionLatency reversal agents (LRAs), such as protein kinase C (PKC) agonists, constitute a promising strategy for exposing and eliminating the HIV-1 latent reservoir. PKC agonists activate NF-{kappa}B and, in turn, induce deleterious pro-inflammatory cytokine production. Adjuvant pharmacological agents, such as ... | microbiology |
10.1101/194266 | Plasma amyloid β levels are driven by genetic variants near APOE, BACE1, APP, PSEN2: A genome-wide association study in over 12,000 non-demented participants | INTRODUCTIONThere is increasing interest in plasma A{beta} as an endophenotype and biomarker of Alzheimers disease (AD). Identifying the genetic determinants of plasma A{beta} levels may elucidate important processes that determine plasma A{beta} measures.
METHODSWe included 12,369 non-demented participants derived fr... | genetics |
10.1101/196105 | Measuring nonapoptotic caspase activity with a transgenic reporter in mice | The protease caspase-3 is a key mediator of apoptotic programmed cell death. But weak or transient caspase activity can contribute to neuronal differentiation, axonal pathfinding, and synaptic long-term depression. Despite the importance of sublethal, or nonapoptotic, caspase activity in neurodevelopment and neural pla... | neuroscience |
10.1101/196105 | Measuring nonapoptotic caspase activity with a transgenic reporter in mice | The protease caspase-3 is a key mediator of apoptotic programmed cell death. But weak or transient caspase activity can contribute to neuronal differentiation, axonal pathfinding, and synaptic long-term depression. Despite the importance of sublethal, or nonapoptotic, caspase activity in neurodevelopment and neural pla... | neuroscience |
10.1101/197780 | Improved management facilitates return of an iconic fish species | Species declines and losses of biota are often associated with shifting baselines in perceived historical abundances, and/or neglect or abandonment of recovery actions aimed at ecological restoration. Such declines are frequently accompanied by contractions in the geographical distribution of the species, with associat... | ecology |
10.1101/205294 | Early urinary candidate biomarkers and clinical outcomes of intervention in a rat model of experimental autoimmune encephalomyelitis | Multiple sclerosis is a chronic autoimmune demyelinating disease of the central nervous system and is difficult to diagnose in early stages. Without homeostatic control, urine was reported to have the ability to accumulate early changes in the body. We expect that urinary proteome can reflect early changes in the nervo... | biochemistry |
10.1101/207357 | Majority of choice-related variability in perceptual decisions is present in early sensory cortex | While performing challenging perceptual tasks such as detecting a barely visible target, our perceptual reports vary across presentations of identical stimuli. This perceptual variability is presumably caused by neural variability in our brains. How much of the neural variability that correlates with the perceptual var... | neuroscience |
10.1101/214361 | Removing unwanted variation between samples in Hi-C experiments | Hi-C data is commonly normalized using single sample processing methods, with focus on comparisons between regions within a given contact map. Here, we aim to compare contact maps across different samples. We demonstrate that unwanted variation, of likely technical origin, is present in Hi-C data with replicates from d... | genomics |
10.1101/215590 | A bacterial GW-effector directly targets Arabidopsis Argonaute 1 to suppress PAMP-triggered immunity and cause disease | Pseudomonas syringae (P. syringae) type-III effectors were previously found to suppress the Arabidopsis microRNA (miRNA) pathway through unknown mechanisms. Here, we first show that the P. syringae HopT1-1 effector promotes pathogenicity by suppressing the Arabidopsis Argonaute 1 (AGO1)-dependent miRNA pathway. We furt... | plant biology |
10.1101/211466 | Differential and defective expression of Koala Retrovirus indicate complexity of host and virus evolution | Koala retrovirus (KoRV) is unique amongst endogenous (inherited) retroviruses in that its incorporation to the host genome is still active, providing an opportunity to study what drives this fundamental process in vertebrate genome evolution. Animals in the southern part of the natural range of koalas were previously t... | microbiology |
10.1101/219931 | Experimental evidence of non-classical brain functions | Exploring unknown quantum systems is an experimental challenge. Recent proposals exploring quantum gravity have suggested circumventing this problem by considering the unknown system as a mediator between two known systems. If such a mediation can locally generate entanglement in the known systems, then the mediator mu... | bioinformatics |
10.1101/202523 | A GenoChemetic strategy for derivatization of the violacein natural product scaffold | Natural products and their analogues are often challenging to synthesise due to their complex scaffolds and embedded functional groups. Solely relying on engineering the biosynthesis of natural products may lead to limited compound diversity. Integrating synthetic biology with synthetic chemistry allows rapid access to... | synthetic biology |
10.1101/225151 | Proof of concept continuous event logging in living cells | Cells must detect and respond to molecular events such as the presence or absence of specific small molecules. To accomplish this, cells have evolved methods to measure the presence and concentration of these small molecules in their environment and enact changes in gene expression or behavior. However, cells dont usua... | synthetic biology |
10.1101/225318 | Modeling Dynamic Transcriptional Circuits with CRISPRi | Targeted transcriptional repression with catalytically inactive Cas9 (CRISPRi) promises to reproduce the functions of traditional synthetic transcriptional circuits, but with better orthogonality, programmability, and extensibility. However, CRISPRi lacks obvious cooperativity-a feature classically considered critical ... | synthetic biology |
10.1101/229617 | Scanning along a compressed timeline of the future | Several authors have suggested a deep symmetry between the psychological processes that underlie our ability to remember the past and make predictions about the future. The judgment of recency (JOR) task measures temporal order judgments for the past by presenting pairs of probe stimuli; participants choose the probe t... | animal behavior and cognition |
10.1101/231548 | Single-cell characterization of step-wise acquisition of carboplatin resistance in ovarian cancer | Acquired resistance to carboplatin is a major obstacle to the cure of ovarian cancer, but its molecular underpinnings are still poorly understood and often inconsistent between in vitro modeling studies. Using sequential treatment cycles, multiple clones derived from a single ovarian cancer cell reached similar levels ... | cancer biology |
10.1101/231209 | System drift and speciation | Even if a species phenotype does not change over evolutionary time, the underlying mechanism may change, as distinct molecular pathways can realize identical phenotypes. Here we use linear system theory to explore the consequences of this idea, describing how a gene network underlying a conserved phenotype evolves, as ... | evolutionary biology |
10.1101/241752 | The effectiveness of glass beads for plating cell cultures | Cell plating, the spreading out of a liquid suspension of cells on a surface followed by colony growth, is a common laboratory procedure in microbiology. Despite this, the exact impact of its parameters on colony growth has not been extensively studied. A common protocol involves the shaking of glass beads within a pet... | biophysics |
10.1101/228056 | Iron oxidation by a fused cytochrome-porin common to diverse iron-oxidizing bacteria | Iron (Fe) oxidation is one of Earths major biogeochemical processes, key to weathering, soil formation, water quality, and corrosion. However, our understanding of microbial contribution is limited by incomplete knowledge of microbial iron oxidation mechanisms, particularly in neutrophilic iron-oxidizers. The genomes o... | microbiology |
10.1101/242875 | Novel Integrative Modeling of Molecules and Morphology Pinpoints Caninae Evolution across Timescales | Evolutionary models account for either population- or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-de... | evolutionary biology |
10.1101/242875 | Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales | Evolutionary models account for either population- or species-level processes, but usually not both. We introduce a new model, the FBD-MSC, which makes it possible for the first time to integrate both the genealogical and fossilization phenomena, by means of the multispecies coalescent (MSC) and the fossilized birth-de... | evolutionary biology |
10.1101/245076 | Dynamic Flux Balance Analysis Models in SBML | Computational models in systems biology and systems medicine are typically simulated using a single formalism such as ordinary differential equations (ODE). However, more complex models require the coupling of multiple formalisms since different biological phenomena are better described by different methods. For exampl... | bioinformatics |
10.1101/250696 | Seidr: Efficient Calculation of Robust Ensemble Gene Networks | Gene regulatory and gene co-expression networks are powerful research tools for identifying biological signal within high-dimensional gene expression data. In recent years, research has focused on addressing shortcomings of these techniques with regard to the low signal-to-noise ratio, non-linear interactions and datas... | bioinformatics |
10.1101/253724 | High-throughput microcolony growth analysis from suboptimal low-magnification micrographs | New technological advances have enabled high-throughput phenotyping at the single-cell level, yet analyzing the large amount of data generated by high throughput phenotyping experiments automatically and accurately is a considerable challenge. Here we introduce Processing Images Easily (PIE), software that automaticall... | bioinformatics |
10.1101/254961 | Visual and auditory brain areas share a representational structure that supports emotion perception | Emotionally expressive music and dance occur together across the world. This may be because features shared across the senses are represented the same way even in different sensory brain areas, putting music and movement in directly comparable terms. These shared representations may arise from a general need to identif... | neuroscience |
10.1101/257162 | Bayesian model comparison for rare variant association studies | Whole genome sequencing studies applied to large populations or biobanks with extensive phenotyping raise new analytic challenges. The need to consider many variants at a locus or group of genes simultaneously and the potential to study many correlated phenotypes with shared genetic architecture provide opportunities f... | genetics |
10.1101/257162 | Bayesian model comparison for rare variant association studies | Whole genome sequencing studies applied to large populations or biobanks with extensive phenotyping raise new analytic challenges. The need to consider many variants at a locus or group of genes simultaneously and the potential to study many correlated phenotypes with shared genetic architecture provide opportunities f... | genetics |
10.1101/266429 | Nanoscale colocalization of NK cell activating and inhibitory receptors controls signal integration | NK cell responses depend on the balance of signals from inhibitory and activating receptors. However, how the integration of antagonistic signals occurs upon NK cell-target cell interaction is not fully understood. Here, we provide evidence that NK cell inhibition via the inhibitory receptor Ly49A is dependent on its r... | immunology |
10.1101/266429 | Nanoscale colocalization of NK cell activating and inhibitory receptors controls signal integration | NK cell responses depend on the balance of signals from inhibitory and activating receptors. However, how the integration of antagonistic signals occurs upon NK cell-target cell interaction is not fully understood. Here, we provide evidence that NK cell inhibition via the inhibitory receptor Ly49A is dependent on its r... | immunology |
10.1101/268672 | Genie: An interactive real-time simulation for teaching genetic drift | Neutral evolution is a fundamental concept in evolutionary biology but teaching this and other non-adaptive concepts is specially challenging. Here we present Genie, a browser-based educational tool that facilitates demonstration of concepts such as genetic drift, population isolation, gene flow, and genetic mutation. ... | scientific communication and education |
10.1101/268862 | The effect of mutational robustness on the evolvability of multicellular organisms | Canalization involves mutational robustness, the lack of phenotypic change as a result of genetic mutations. Given the large divergence in phenotype across species, understanding the relationship between high robustness and evolvability has been of interest to both theorists and experimentalists. Although canalization ... | evolutionary biology |
10.1101/276683 | The importance of semantic network brain regions in integrating prior knowledge with an ongoing dialogue | To understand a dialogue we need to know the specific topics that are being discussed. This enables us to integrate our knowledge of what was said previously, in order to interpret the current dialogue. Here, we selectively manipulated knowledge about the narrative content of dialogues between two people, presented in ... | neuroscience |
10.1101/285429 | Y chromosomal noncoding RNAs regulate autosomal gene expression via piRNAs in mouse testis | Majority of the genes expressed during spermatogenesis are autosomal. Mice with different deletions of Yq show sub-fertility, sterility and sperm abnormalities. The connection between Yq deletion and autosomal gene regulation is not well understood. We describe a novel mouse Yq-derived long noncoding RNA, Pirmy, which ... | genomics |
10.1101/285429 | Y chromosomal noncoding RNAs regulate autosomal gene expression via piRNAs in mouse testis | Majority of the genes expressed during spermatogenesis are autosomal. Mice with different deletions of Yq show sub-fertility, sterility and sperm abnormalities. The connection between Yq deletion and autosomal gene regulation is not well understood. We describe a novel mouse Yq-derived long noncoding RNA, Pirmy, which ... | genomics |
10.1101/285429 | Y chromosomal noncoding RNAs regulate autosomal gene expression via piRNAs in mouse testis | Majority of the genes expressed during spermatogenesis are autosomal. Mice with different deletions of Yq show sub-fertility, sterility and sperm abnormalities. The connection between Yq deletion and autosomal gene regulation is not well understood. We describe a novel mouse Yq-derived long noncoding RNA, Pirmy, which ... | genomics |
10.1101/290460 | Effects of adaptive harvesting on fishing down processes and resilience changes in predator-prey systems | Many world fisheries display a declining mean trophic level of catches. This "fishing down the food web" is often attributed to reduced densities of high-trophic-level species. We show here that the fishing down pattern can actually emerge from the adaptive harvesting of a predator-prey community, where changes in fish... | ecology |
10.1101/290882 | Does deterministic coexistence theory matter in a finite world? | Contemporary studies of species coexistence are underpinned by deterministic models that assume that competing species have continuous (i.e. non-integer) densities, live in infinitely large landscapes, and coexist over infinite time horizons. By contrast, in nature species are composed of discrete individuals subject t... | ecology |
10.1101/292458 | Splicing motifs are organized within global structural scaffold of a pre-mRNA | The specific recognition of splice signals at or near exon-intron junctions is not explained by their weak conservation and instead is postulated to require a multitude of features embedded in the pre-mRNA strand. We explored the possibility of three-dimensional structural scaffold of AdML - a model pre-mRNA substrate ... | biochemistry |
10.1101/292458 | Discovery of a pre-mRNA structural scaffold as a contributor to the mammalian splicing code | The specific recognition of splice signals at or near exon-intron junctions is not explained by their weak conservation and instead is postulated to require a multitude of features embedded in the pre-mRNA strand. We explored the possibility of three-dimensional structural scaffold of AdML - a model pre-mRNA substrate ... | biochemistry |
10.1101/292979 | Manipulation of the unfolded protein response: a pharmacological strategy against coronavirus infection | Coronavirus infection induces the unfolded protein response (UPR), a cellular signalling pathway composed of three branches, triggered by unfolded proteins in the endoplasmic reticulum (ER) due to high ER load. We have used RNA sequencing and ribosome profiling to investigate holistically the transcriptional and transl... | microbiology |
10.1101/302349 | Dissecting indirect genetic effects from peers in laboratory mice | The phenotype of one individual can be affected not only by the individuals own genotypes (direct genetic effects, DGE) but also by genotypes of interacting partners (indirect genetic effects, IGE). IGE have been detected using polygenic models in multiple species, including laboratory mice and humans. However, the und... | genetics |
10.1101/305623 | Spatial distribution of private gene mutations in clear cell renal cell carcinoma | Intra-tumour heterogeneity is the molecular hallmark of renal cancer, and the molecular tumour composition determines the treatment outcome of renal cancer patients. In renal cancer tumourigenesis, in general, different tumour clones evolve over time. We analysed intra-tumour heterogeneity and subclonal mutation patter... | cancer biology |
10.1101/310169 | DsbA is a redox-switchable mechanical chaperone | DsbA is a ubiquitous bacterial oxidoreductase that associates with substrates during and after translocation, yet its involvement in protein folding and translocation remains an open question. Here we demonstrate a redox-controlled chaperone activity of DsbA, on both cysteine-containing and cysteine-free substrate, usi... | biophysics |
10.1101/310169 | DsbA is a redox-switchable mechanical chaperone | DsbA is a ubiquitous bacterial oxidoreductase that associates with substrates during and after translocation, yet its involvement in protein folding and translocation remains an open question. Here we demonstrate a redox-controlled chaperone activity of DsbA, on both cysteine-containing and cysteine-free substrate, usi... | biophysics |
10.1101/310169 | DsbA is a redox-switchable mechanical chaperone | DsbA is a ubiquitous bacterial oxidoreductase that associates with substrates during and after translocation, yet its involvement in protein folding and translocation remains an open question. Here we demonstrate a redox-controlled chaperone activity of DsbA, on both cysteine-containing and cysteine-free substrate, usi... | biophysics |
10.1101/310300 | A constraints-based theory of senescence: imbalance of epigenetic and non-epigenetic information in histone crosstalk | Cellular aging has been progressively elucidated by science. However, the fundamental cause of senescence--i.e., why organisms age at the multicellular-individual level--remains unclear. A recent theory of individuated multicellularity describes the emergence and growth of crucial information content for cell different... | developmental biology |
10.1101/310300 | A constraints-based theory of the primary cause of senescence: imbalance of epigenetic and non-epigenetic information in histone crosstalk | Cellular aging has been progressively elucidated by science. However, the fundamental cause of senescence--i.e., why organisms age at the multicellular-individual level--remains unclear. A recent theory of individuated multicellularity describes the emergence and growth of crucial information content for cell different... | developmental biology |
10.1101/310219 | Cargo-Loading of Misfolded Proteins into Extracellular Vesicles: The CSPα-EV Export Pathway | Extracellular vesicles (EVs) are secreted vesicles of diverse size and cargo that are implicated in the cell-to-cell transmission of disease-causing-proteins in several neurodegenerative diseases. Mutant huntingtin, the disease-causing entity in Huntingtons disease, has an expanded polyglutamine track at the N terminus... | neuroscience |
10.1101/310938 | Structurally Constrained Effective Brain Connectivity | The relationship between structure and function is of interest in many research fields involving the study of complex biological processes. In neuroscience in particular, the fusion of structural and functional data can help understanding the underlying principles of the operational networks in the brain. To address th... | neuroscience |
10.1101/311241 | Characterization of Animal Movement Patterns using Information Theory: a Primer | Understanding the movement patterns of animals across different spatio-temporal scales, conditions, habitats and contexts is becoming increasingly important for addressing a series of questions in animal behaviour studies, such as mapping migration routes, evaluating resource use, modelling epidemic spreading in a popu... | ecology |
10.1101/314708 | Sperm morphology differences associated with pig fertility | Artificial insemination is routine in commercial pig breeding, and as such, the use of high-quality semen samples is imperative. Here, we have developed a novel, semi-automated, software-based approach to assess pig sperm nucleus morphology in greater detail than was previously possible. This analysis identified subtle... | developmental biology |
10.1101/314658 | Direct programming of human mammary self-organised organoids by miR-106a-3p | Organoids development relies on the self-organizing properties of adult stem cells to create structures which recapitulate the architecture, functionality, and genetic signature observed in original tissues. Little is known about of the exact nature of the intrinsic cell properties at the origin of organoid generation,... | cell biology |
10.1101/316141 | Polymer brush bilayers at thermal equilibrium: A density functional theory approach | By means of the density functional theory (DFT) framework, the longstanding problem of the polymer brush bilayers at thermal equilibrium is studied. The calculated density profiles reveal that the brushes balance compression and interpenetration when they come into contact. The equation of state of the polymer brush bi... | biophysics |
10.1101/316141 | Polymer brush bilayers at thermal equilibrium: A density functional theory approach | By means of the density functional theory (DFT) framework, the longstanding problem of the polymer brush bilayers at thermal equilibrium is studied. The calculated density profiles reveal that the brushes balance compression and interpenetration when they come into contact. The equation of state of the polymer brush bi... | biophysics |
10.1101/319525 | Empirical single-cell tracking and cell-fate simulation reveal dual roles of p53 in tumor suppression | The tumor suppressor p53 regulates various stress responses via increasing its cellular levels. The lowest p53 levels occur in unstressed cells; however, the functions of these low levels remains unclear. To investigate the functions, we used empirical single-cell tracking of p53-expressing (Control) cells and cells in... | cell biology |
10.1101/319525 | Empirical single-cell tracking and cell-fate simulation reveal dual roles of p53 in tumor suppression | The tumor suppressor p53 regulates various stress responses via increasing its cellular levels. The lowest p53 levels occur in unstressed cells; however, the functions of these low levels remains unclear. To investigate the functions, we used empirical single-cell tracking of p53-expressing (Control) cells and cells in... | cell biology |
10.1101/319525 | Empirical single-cell tracking and cell-fate simulation reveal dual roles of p53 in tumor suppression | The tumor suppressor p53 regulates various stress responses via increasing its cellular levels. The lowest p53 levels occur in unstressed cells; however, the functions of these low levels remains unclear. To investigate the functions, we used empirical single-cell tracking of p53-expressing (Control) cells and cells in... | cell biology |
10.1101/319525 | Empirical single-cell tracking and cell-fate simulation reveal dual roles of p53 in tumor suppression | The tumor suppressor p53 regulates various stress responses via increasing its cellular levels. The lowest p53 levels occur in unstressed cells; however, the functions of these low levels remains unclear. To investigate the functions, we used empirical single-cell tracking of p53-expressing (Control) cells and cells in... | cell biology |
10.1101/332965 | Identification and design of vinyl sulfone inhibitors against Cryptopain1-a cysteine protease from cryptosporidiosis-causing Cryptosporidium parvum | Cryptosporidiosis, a disease marked by diarrhea in adults and stunted growth in children, is associated with the unicellular protozoan pathogen Cryptosporidium; often the species parvum. Cryptopain-1, a cysteine protease characterized in the genome of Cryptosporidium parvum, had been earlier shown to be inhibited by a ... | bioinformatics |
10.1101/334417 | Spatial RNA sequencing identifies robust markers of vulnerable and resistant human midbrain dopamine neurons and their expression in Parkinson's Disease | Defining transcriptional profiles of substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) dopamine neurons is critical to understanding their differential vulnerability in Parkinsons Disease (PD). Here, we determine transcriptomes of human SNc and VTA dopamine neurons using LCM-seq on a large sample co... | neuroscience |
10.1101/336123 | Dissociating Language and Thought in Human Reasoning | What is the relationship between natural language and complex thought? In the context of complex reasoning, there are two main views. Under the first, language is central to the syntax-like combinatorial operations necessary for complex reasoning. Under the second, these operations are independent of the mechanisms of ... | neuroscience |
10.1101/337543 | Broad geographic sampling reveals predictable, pervasive, and strong seasonal adaptation in Drosophila | To advance our understanding of adaptation to temporally varying selection pressures, we identified signatures of seasonal adaptation occurring in parallel among Drosophila melanogaster populations. Specifically, we estimated allele frequencies genome-wide from flies sampled early and late in the growing season from 20... | evolutionary biology |
10.1101/340232 | 3D Reconstruction of Bird Flight Using a Single Video Camera | Video cameras are finding increasing use in the study and analysis of bird flight over short ranges. However, reconstruction of flight trajectories in three dimensions typically requires the use of multiple cameras and elaborate calibration procedures. We present an alternative approach that uses a single video camera ... | animal behavior and cognition |
10.1101/340232 | 3D Reconstruction of Bird Flight Trajectories Using a Single Video Camera | Video cameras are finding increasing use in the study and analysis of bird flight over short ranges. However, reconstruction of flight trajectories in three dimensions typically requires the use of multiple cameras and elaborate calibration procedures. We present an alternative approach that uses a single video camera ... | animal behavior and cognition |
10.1101/341636 | The interspecific fungal hybrid Verticillium longisporum displays sub-genome-specific gene expression | Hybridization is an important evolutionary mechanism that can enable organisms to adapt to environmental challenges. It has previously been shown that the fungal allodiploid species Verticillium longisporum, causal agent of Verticillium stem striping in rape seed, has originated from at least three independent hybridiz... | microbiology |
10.1101/340430 | Ecological Network assembly: how the regional meta web influence local food webs | O_LILocal food webs result from a sequence of colonisations and extinctions by species from the regional pool or metaweb, i.e., the assembly process. Assembly is theorised to be a selective process: whether or not certain species or network structures can persist is partly determined by local processes including habita... | ecology |
10.1101/340430 | Ecological Network assembly: how the regional meta web influence local food webs | O_LILocal food webs result from a sequence of colonisations and extinctions by species from the regional pool or metaweb, i.e., the assembly process. Assembly is theorised to be a selective process: whether or not certain species or network structures can persist is partly determined by local processes including habita... | ecology |
10.1101/340430 | Ecological Network assembly: how the regional meta web influence local food webs | O_LILocal food webs result from a sequence of colonisations and extinctions by species from the regional pool or metaweb, i.e., the assembly process. Assembly is theorised to be a selective process: whether or not certain species or network structures can persist is partly determined by local processes including habita... | ecology |
10.1101/340430 | Ecological Network assembly: how the regional meta web influence local food webs | O_LILocal food webs result from a sequence of colonisations and extinctions by species from the regional pool or metaweb, i.e., the assembly process. Assembly is theorised to be a selective process: whether or not certain species or network structures can persist is partly determined by local processes including habita... | ecology |
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