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10.1101/341008 | Network Reconstruction from Perturbation Time Course Data | Networks underlie much of biology from subcellular to ecological scales. Yet, understanding what experimental data are needed and how to use them for unambiguously identifying the structure of even small networks remains a broad challenge. Here, we integrate a dynamic least squares framework into established modular re... | systems biology |
10.1101/341008 | Network Inference from Perturbation Time Course Data | Networks underlie much of biology from subcellular to ecological scales. Yet, understanding what experimental data are needed and how to use them for unambiguously identifying the structure of even small networks remains a broad challenge. Here, we integrate a dynamic least squares framework into established modular re... | systems biology |
10.1101/342030 | Rapid adaptation of endocytosis, exocytosis and eisosomes after an acute increase in membrane tension in yeast cells | During clathrin-mediated endocytosis in eukaryotes, actin assembly is required to overcome large membrane tension and turgor pressure. However, the molecular mechanisms by which the actin machinery adapts to varying membrane tension remain unknown. In addition, how cells reduce their membrane tension when they are chal... | cell biology |
10.1101/342030 | Rapid adaptation of endocytosis, exocytosis and eisosomes after an acute increase in membrane tension in yeast cells | During clathrin-mediated endocytosis in eukaryotes, actin assembly is required to overcome large membrane tension and turgor pressure. However, the molecular mechanisms by which the actin machinery adapts to varying membrane tension remain unknown. In addition, how cells reduce their membrane tension when they are chal... | cell biology |
10.1101/342261 | Evolutionary forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens | Experimental evolution with microbes is often highly repeatable under identical conditions, suggesting the possibility to predict short-term evolution. However, it is not clear to what degree evolutionary forecasts can be extended to related species in non-identical environments, which would allow testing of general pr... | evolutionary biology |
10.1101/344499 | KChIP4a selectively controls mesolimbic dopamine neuron inhibitory integration and learning from negative prediction errors | Midbrain dopamine (DA) neurons are essential for multiple behaviors. DA neurons that project to different regions also have unique biophysical properties, and it is thought that this diversity reflects specializations to particular computational functions. If this is true, there should be specific genetic determinants ... | neuroscience |
10.1101/344200 | A pragmatic approach to make theoretical syntheses in ecology | Theoretical syntheses have the role of describing and guiding knowledge generation, and are usually done by enunciating the conceptual bases that guide research in a given field. In fields that develop axiomatically, the conceptual basis can be easily identified in the set of axioms guiding model building. However, eco... | ecology |
10.1101/348433 | Microbial adaptation to venom is common in snakes and spiders | Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane disrupting activity against multi-drug resistant bacteria. However, bite wound infections are common in developing nations. Investigating the oral and venom microbiome of five snake and two spider species, we evidence viable mi... | microbiology |
10.1101/348383 | The Goldilocks Effect: Female geladas in mid-sized groups have higher fitness | The cost-benefit ratio of group-living is thought to vary with group size: individuals in "optimally-sized" groups should have higher fitness than individuals in groups that are either too large or too small. However, the relationship between group size and individual fitness has been difficult to establish for long-li... | evolutionary biology |
10.1101/348383 | The Goldilocks Effect: Female geladas in mid-sized groups have higher fitness | The cost-benefit ratio of group-living is thought to vary with group size: individuals in "optimally-sized" groups should have higher fitness than individuals in groups that are either too large or too small. However, the relationship between group size and individual fitness has been difficult to establish for long-li... | evolutionary biology |
10.1101/348391 | Joint inference of species histories and gene flow | When populations become isolated, members of these populations can diverge genetically over time. This leads to genetic differences between these populations that increase over time if the isolation persists. This process can be counteracted by gene flow, i.e. when genes are exchanged between populations. In order to s... | evolutionary biology |
10.1101/348391 | Joint inference of species histories and gene flow | When populations become isolated, members of these populations can diverge genetically over time. This leads to genetic differences between these populations that increase over time if the isolation persists. This process can be counteracted by gene flow, i.e. when genes are exchanged between populations. In order to s... | evolutionary biology |
10.1101/354480 | 5' Modifications Improve Potency and Efficacy of DNA Donors for Precision Genome Editing | Nuclease-directed genome editing is a powerful tool for investigating physiology and has great promise as a therapeutic approach to correct mutations that cause disease. In its most precise form, genome editing can use cellular homology-directed repair (HDR) pathways to insert information from an exogenously supplied D... | molecular biology |
10.1101/358986 | Structure-aware M. tuberculosis functional annotation uncloaks resistance, metabolic, and virulence genes | Accurate and timely functional genome annotation is essential for translating basic pathogen research into clinically impactful advances. Here, through literature curation and structure-function inference, we systematically update the functional genome annotation of Mycobacterium tuberculosis virulent type strain H37Rv... | genomics |
10.1101/364042 | Distracting Linguistic Information Impairs Neural Tracking of Attended Speech | Listening to speech is difficult in noisy environments, and is even harder when the interfering noise consists of intelligible speech as compared to unintelligible sounds. This suggests that the competing linguistic information interferes with the neural processing of target speech. Interference could either arise from... | neuroscience |
10.1101/365825 | Extracellular histones, a new class of inhibitory molecules of CNS axonal regeneration | Axonal regeneration in the mature CNS is limited by extracellular inhibitory factors. Triple knockout mice lacking the major myelin-associated inhibitors do not display spontaneous regeneration after injury, indicating the presence of other inhibitors. Searching for such inhibitors we have detected elevated levels of h... | neuroscience |
10.1101/370692 | Dispensing a synthetic green leaf volatile to two plant species in a common garden differentially alters physiological responses and herbivory | Herbivore-induced plant volatile (HIPV)-mediated eavesdropping by plants is a well-documented, inducible phenomenon that has practical agronomic applications for enhancing plant defense and pest management. However, as with any inducible phenomenon, responding to volatile cues may incur physiological and ecological cos... | ecology |
10.1101/373332 | The taxonomic and functional biogeographies of phytoplankton and zooplankton communities across boreal lakes | AO_SCPLOWBSTRACTC_SCPLOWStrong trophic interactions link primary producers (phytoplankton) and consumers (zooplankton) in lakes. However, the influence of such interactions on the biogeographical distribution of the taxa and functional traits of planktonic organisms in lakes has never been explicitly tested. To better ... | ecology |
10.1101/373332 | The taxonomic and functional biogeographies of phytoplankton and zooplankton communities across boreal lakes | AO_SCPLOWBSTRACTC_SCPLOWStrong trophic interactions link primary producers (phytoplankton) and consumers (zooplankton) in lakes. However, the influence of such interactions on the biogeographical distribution of the taxa and functional traits of planktonic organisms in lakes has never been explicitly tested. To better ... | ecology |
10.1101/380162 | Predicting subclinical psychotic-like experiences on a continuum using machine learning | Previous studies applying machine learning methods to psychosis have primarily been concerned with the binary classification of chronic schizophrenia patients and healthy controls. The aim of this study was to use electroencephalographic (EEG) data and pattern recognition to predict subclinical psychotic-like experienc... | neuroscience |
10.1101/384024 | Individuals with ventromedial frontal damage have more unstable but still fundamentally transitive preferences | The ventromedial frontal lobes (VMF) are important for decision-making, but the precise causal role of the VMF in the decision process has not yet fully been established. Previous studies have suggested that individuals with VMF damage violate transitivity, a hallmark axiom of rational decisions. However, these prior s... | neuroscience |
10.1101/384834 | De Novo Mutational Signature Discovery in Tumor Genomes using SparseSignatures | Cancer is the result of mutagenic processes that can be inferred from tumor genomes by analyzing rate spectra of point mutations, or "mutational signatures". Here we present SparseSignatures, a novel framework to extract signatures from somatic point mutation data. Our approach incorporates a user-specified background ... | bioinformatics |
10.1101/385591 | GranatumX: A community engaging, modularized and flexible software environment for single-cell analysis | We present GranatumX, a next-generation software environment for single-cell data analysis. GranatumX is inspired by the interactive web tool Granatum. It enables biologists to access the latest single-cell bioinformatics methods in a web-based graphical environment. It also offers software developers the opportunity t... | bioinformatics |
10.1101/385591 | GranatumX: A community engaging, modularized and flexible webtool for single-cell analysis | We present GranatumX, a next-generation software environment for single-cell data analysis. GranatumX is inspired by the interactive web tool Granatum. It enables biologists to access the latest single-cell bioinformatics methods in a web-based graphical environment. It also offers software developers the opportunity t... | bioinformatics |
10.1101/388447 | High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur). | The Src homology-2 domain containing phosphatase SHP2 is a critical regulator of signal transduction, being implicated in cell growth and differentiation. Activating mutations cause developmental disorders and act as oncogenic drivers in hematologic cancers. SHP2 is activated by phosphopeptide binding to the N-SH2 doma... | evolutionary biology |
10.1101/388447 | High-quality SNPs from genic regions highlight introgression patterns among European white oaks (Quercus petraea and Q. robur). | The Src homology-2 domain containing phosphatase SHP2 is a critical regulator of signal transduction, being implicated in cell growth and differentiation. Activating mutations cause developmental disorders and act as oncogenic drivers in hematologic cancers. SHP2 is activated by phosphopeptide binding to the N-SH2 doma... | evolutionary biology |
10.1101/391896 | Eye movements during text reading align with the rate of speech production | Across languages, the speech signal is characterized by a predominant modulation of the amplitude spectrum between about 4.3-5.5Hz, reflecting the production and processing of linguistic information chunks (syllables, words) every [~]200ms. Interestingly, [~]200ms is also the typical duration of eye fixations during re... | neuroscience |
10.1101/386920 | Basal ganglia and cortical control of thalamic rebound spikes | Movement-related decreases in firing rate have been observed in basal ganglia output neurons. They may transmit motor signals to the thalamus, but the effect of these firing rate decreases on downstream neurons in the motor thalamus is not known. One possibility is that they lead to thalamic post-inhibitory rebound spi... | neuroscience |
10.1101/396036 | Reduction in CD11c+ microglia correlates with clinical progression in chronic experimental autoimmune demyelination | Multiple sclerosis (MS) is a chronic autoimmune demyelinating disease with high variability of clinical symptoms. In most cases MS appears as a relapsing-remitting disease course that at a later stage transitions into irreversible progressive decline of neurologic function. The mechanisms underlying MS progression rema... | neuroscience |
10.1101/410803 | Dimerisation of APOBEC1 is dispensable for its RNA/DNA editing activity and modulates its availability | The AID/APOBECs are DNA/RNA deaminases whose mutagenic activity has been linked to cancer. Among them, APOBEC1 physiologically partakes into a complex that edits a CAA codon into UAA Stop codon in the transcript of Apolipoprotein B (APOB), a protein crucial in the transport of lipids in the blood. Catalytically inactiv... | molecular biology |
10.1101/410803 | Dimerisation of APOBEC1 is dispensable for its RNA/DNA editing activity and modulates its availability | The AID/APOBECs are DNA/RNA deaminases whose mutagenic activity has been linked to cancer. Among them, APOBEC1 physiologically partakes into a complex that edits a CAA codon into UAA Stop codon in the transcript of Apolipoprotein B (APOB), a protein crucial in the transport of lipids in the blood. Catalytically inactiv... | molecular biology |
10.1101/412213 | Diversity and composition of cave methanotrophic communities | Methane oxidizing bacteria (methanotrophs) are a ubiquitous group of microorganisms that represent a major sink for the greenhouse gas methane (CH4). Recent studies have demonstrated that methanotrophs are abundant and contribute to CH4 dynamics in caves. However, very little is known about what controls the distributi... | microbiology |
10.1101/412924 | Genetic characterization of outbred Sprague Dawley rats and utility for genome-wide association studies | Sprague Dawley (SD) rats are among the most widely used outbred laboratory rat populations. Despite this, the genetic characteristics of SD rats have not been clearly described, and SD rats are rarely used for experiments aimed at exploring genotype-phenotype relationships. In order to use SD rats to perform a genome-w... | genetics |
10.1101/413153 | Nuclear envelope budding is a response to cellular stress | Nuclear envelope budding (NEB) is a recently discovered alternative pathway for nucleocytoplasmic communication distinct from the movement of material through the nuclear pore complex. Through quantitative electron microscopy and tomography, we demonstrate how NEB is evolutionarily conserved from early protists to huma... | cell biology |
10.1101/415992 | Tension suppresses Aurora B kinase-triggered release of reconstituted kinetochore-microtubule attachments | Chromosome segregation requires kinetochores to attach to microtubules from opposite spindle poles. Proper attachments come under tension and are stabilized, but defective attachments lacking tension are released, giving another chance for correct attachments to form. This error correction process requires the Aurora B... | cell biology |
10.1101/417972 | Human cortical dynamics during full-body heading changes | The retrosplenial complex (RSC) plays a crucial role in spatial orientation by computing heading direction and translating between distinct spatial reference frames based on multi-sensory information. While invasive studies allow investigating heading computation in moving animals, established non-invasive analyses of ... | neuroscience |
10.1101/422063 | Paternal knockdown of tRNA (cytosine-5-)-methyltransferase (Dnmt2) increases offspring susceptibility to infection in flour beetles | Intergenerational effects from fathers to offspring are increasingly reported from diverse organisms, but the underlying mechanisms remain speculative. Paternal trans-generational immune priming (TGIP) was demonstrated in the red flour beetle Tribolium castaneum: non-infectious bacterial exposure of fathers protects th... | evolutionary biology |
10.1101/422063 | Paternal knockdown of tRNA (cytosine-5-)-methyltransferase (Dnmt2) increases offspring susceptibility to infection in red flour beetles | Intergenerational effects from fathers to offspring are increasingly reported from diverse organisms, but the underlying mechanisms remain speculative. Paternal trans-generational immune priming (TGIP) was demonstrated in the red flour beetle Tribolium castaneum: non-infectious bacterial exposure of fathers protects th... | evolutionary biology |
10.1101/423467 | An epi-evolutionary model to predict spore-producing pathogens adaptation to quantitative resistance in heterogeneous environments | We model the evolutionary epidemiology of spore-producing plant pathogens in heterogeneous environments sown with several cultivars carrying quantitative resistances. The model explicitly tracks the infection-age structure and genetic composition of the pathogen population. Each strain is characterized by pathogenicity... | evolutionary biology |
10.1101/427864 | Subcutaneous neurotrophin-3 infusion induces corticospinal neuroplasticity and improvements in dexterity and walking in elderly rats after large cortical stroke | There is an urgent need for a therapy which reverses disability after stroke when initiated in a time frame suitable for the majority of new victims. Neurotrophin-3 (NT3) is a growth factor made by muscle spindles and skin which is required for the survival, development and function of locomotor circuits involving affe... | neuroscience |
10.1101/430744 | Ratio-based sensing of two transcription factors regulates the transit to differentiation | Cell state transitions are usually thought to be triggered by changes in the absolute concentrations of relevant transcription factors. In the Drosophila eye, the transcription factor Yan maintains cells in a progenitor state by repressing gene expression, while the Pointed transcription factor activates gene expressio... | developmental biology |
10.1101/432328 | Pink Cedar (Acrocarpus fraxinifolius): its prophylactic role against APAP induced organs toxicity in rats and its antiviral activity against Herpes simplex virus type 1 | The possible protective effects of methanolic extract Acrocarpus fraxinifolius leaves (MEAFL) were assessed against the APAP-induced organ toxicity in male rats. Also, the content of polyphenols extracted from AFL was studied, and their relationship with antioxidant activity was investigated. MEAFL was tested for cytot... | physiology |
10.1101/432328 | Pink Cedar (Acrocarpus fraxinifolius): its prophylactic role against APAP induced organs toxicity in rats and its antiviral activity against Herpes simplex virus type 1 | The possible protective effects of methanolic extract Acrocarpus fraxinifolius leaves (MEAFL) were assessed against the APAP-induced organ toxicity in male rats. Also, the content of polyphenols extracted from AFL was studied, and their relationship with antioxidant activity was investigated. MEAFL was tested for cytot... | physiology |
10.1101/432328 | Pink Cedar (Acrocarpus fraxinifolius): its prophylactic role against APAP induced organs toxicity in rats and its antiviral activity against Herpes simplex virus type 1 | The possible protective effects of methanolic extract Acrocarpus fraxinifolius leaves (MEAFL) were assessed against the APAP-induced organ toxicity in male rats. Also, the content of polyphenols extracted from AFL was studied, and their relationship with antioxidant activity was investigated. MEAFL was tested for cytot... | physiology |
10.1101/432328 | Pink Cedar (Acrocarpus fraxinifolius): its prophylactic role against APAP induced organs toxicity in rats and its antiviral activity against Herpes simplex virus type 1 | The possible protective effects of methanolic extract Acrocarpus fraxinifolius leaves (MEAFL) were assessed against the APAP-induced organ toxicity in male rats. Also, the content of polyphenols extracted from AFL was studied, and their relationship with antioxidant activity was investigated. MEAFL was tested for cytot... | physiology |
10.1101/430306 | Dual brain cortical calcium imaging reveals social interaction-specific wide-spread correlated cortical activity in mice. | We employ cortical mesoscale calcium-imaging to observe brain activity in two head-fixed mice in a staged social touch-like interaction. Using a rail system, mice are brought together to a distance where macrovibrissae of each mouse make contact. Cortical signals were recorded from both mice simultaneously before, duri... | neuroscience |
10.1101/436634 | RegTools: Integrated analysis of genomic and transcriptomic data for the discovery of splicing variants in cancer | Somatic mutations in non-coding regions of the genome and even exonic mutations may have unidentified non-coding consequences which are often overlooked in analysis workflows. Here we present RegTools (www.regtools.org), a free, open-source software package designed to integrate analysis of somatic variant calls from g... | bioinformatics |
10.1101/436634 | RegTools: Integrated analysis of genomic and transcriptomic data for the discovery of splicing variants in cancer | Somatic mutations in non-coding regions of the genome and even exonic mutations may have unidentified non-coding consequences which are often overlooked in analysis workflows. Here we present RegTools (www.regtools.org), a free, open-source software package designed to integrate analysis of somatic variant calls from g... | bioinformatics |
10.1101/436758 | Sensory experience controls dendritic structure and behavior by distinct pathways involving degenerins | Dendrites are crucial for receiving information into neurons. Sensory experience affects the structure of these tree-like neurites, which, it is assumed, modifies neuronal function, yet the evidence is scarce, and the mechanisms are unknown. To study whether sensory experience affects dendritic morphology, we use the C... | neuroscience |
10.1101/437327 | The best of both worlds: A new lipid complex has micelle and bicelle-like properties | Bicelles have been demonstrated to be a valuable tool for studying membrane protein interactions and structure in vitro. They are distinguished by a distinct lipid bilayer that mimics the plasma membrane of cells making it more native-like than its detergent micelle counter-part. Bicelles are typically comprised of a l... | biophysics |
10.1101/437335 | Inferring the heritability of large-scale functional networks with a multivariate ACE modeling approach | Recent evidence suggests that the human functional connectome is stable at different time scales and unique. These characteristics posit the functional connectome not only as an individual marker but also as a powerful discriminatory measure characterized by high intersubject variability. Among distinct sources of inte... | neuroscience |
10.1101/437228 | BIN1 genetic risk factor for Alzheimer is sufficient to induce early structural tract alterations in entorhinal cortex-dentate gyrus pathway and related hippocampal multi-scale impairments | Genetic factors are known to contribute to Late Onset Alzheimers disease (LOAD) but their contribution to pathophysiology, specially to prodomic phases accessible to therapeutic approaches are far to be understood.
To translate genetic risk of Alzheimers disease (AD) into mechanistic insight, we generated transgenic m... | neuroscience |
10.1101/437228 | BIN1 genetic risk factor for Alzheimer is sufficient to induce early structural tract alterations in entorhinal cortex-dentate gyrus pathway and related hippocampal multi-scale impairments | Genetic factors are known to contribute to Late Onset Alzheimers disease (LOAD) but their contribution to pathophysiology, specially to prodomic phases accessible to therapeutic approaches are far to be understood.
To translate genetic risk of Alzheimers disease (AD) into mechanistic insight, we generated transgenic m... | neuroscience |
10.1101/439083 | Single cell variations in expression of codominant alleles A and B on RBC of AB blood group individuals. | One of the key questions in biology is whether all cells of a "cell type" have more or less the same phenotype, especially with relation to non-imprinted autosomal loci. Recent studies point to differential allelic expression of autosomal genes being a prevalent phenomenon responsible to confer phenotypic variability a... | genetics |
10.1101/440321 | A confirmation bias in perceptual decision-making due to hierarchical approximate inference | Making good decisions requires updating beliefs according to new evidence. This is a dynamical process that is prone to biases: in some cases, beliefs become entrenched and resistant to new evidence (leading to primacy effects), while in other cases, beliefs fade over time and rely primarily on later evidence (leading ... | animal behavior and cognition |
10.1101/441246 | Inferring linguistic transmission between generations at the scale of individuals | Historical linguistics strongly benefited from recent methodological advances inspired by phylogenetics. Nevertheless, no available method uses contemporaneous within-population linguistic diversity to reconstruct the history of human populations. Here, we developed an approach inspired from population genetics to perf... | bioinformatics |
10.1101/442822 | I knew that! Response-based Outcome Predictions and Confidence Regulate Feedback Processing and Learning | Influential theories emphasize the importance of predictions in learning: we learn from feedback to the extent that it is surprising, and thus conveys new information. Here we explore the hypothesis that surprise depends not only on comparing current events to past experience, but also on online evaluation of performan... | neuroscience |
10.1101/445304 | A Sparse Additive Model for High-Dimensional Interactions with an Exposure Variable | A conceptual paradigm for onset of a new disease is often considered to be the result of changes in entire biological networks whose states are affected by a complex interaction of genetic and environmental factors. However, when modelling a relevant phenotype as a function of high dimensional measurements, power to es... | bioinformatics |
10.1101/445643 | Decoding locomotion from population neural activity in moving C. elegans | The activity of an animals brain contains information about that animals actions and movements. We investigated the neural representation of locomotion in the nematode C. elegans by recording population calcium activity during unrestrained movement. We report that a neural population more accurately decodes locomotion ... | neuroscience |
10.1101/411702 | Epigenome priming dictates transcription response and white matter fate upon perinatal inflammation | Inflammatory insults accompanying prematurity provokes diffuse white matter injury (DWMI) which is associated with increased risk of neurodevelopmental disorders: pre-term infants have a 10 to 18-fold increased risk of developing autism spectrum disorders, compared to term infants. DWMI is due to maturation arrest in o... | developmental biology |
10.1101/449009 | Reorganization of thalamocortical connections in congenitally blind humans | Evidence of cross-modal plasticity in blind individuals has been reported over the past decades showing that non-visual information is carried and processed by visual brain structures. This feature of the blind brain makes it a pivotal model to explore the limits and mechanisms of brain plasticity. However, despite mu... | neuroscience |
10.1101/452326 | Inference of the worldwide invasion routes of the pinewood nematode Bursaphelenchus xylophilus using approximate Bayesian computation analysis | AO_SCPLOWBSTRACTC_SCPLOWPopulation genetics have been greatly beneficial to improve knowledge about biological invasions. Model-based genetic inference methods, such as approximate Bayesian computation (ABC), have brought this improvement to a higher level and are now essential tools to decipher the invasion routes of ... | genetics |
10.1101/452326 | Inference of the worldwide invasion routes of the pinewood nematode Bursaphelenchus xylophilus using approximate Bayesian computation analysis | AO_SCPLOWBSTRACTC_SCPLOWPopulation genetics have been greatly beneficial to improve knowledge about biological invasions. Model-based genetic inference methods, such as approximate Bayesian computation (ABC), have brought this improvement to a higher level and are now essential tools to decipher the invasion routes of ... | genetics |
10.1101/453746 | Cyclic, condition-independent activity in primary motor cortex predicts corrective movement behavior | Reaching movements are known to have large condition-independent neural activity and cyclic neural dynamics. A new precision center-out task was performed by rhesus macaques to test the hypothesis that cyclic, condition-independent neural activity in the primary motor cortex (M1) occurs not only during initial reaching... | neuroscience |
10.1101/453746 | Cyclic, condition-independent activity in primary motor cortex predicts corrective movement behavior | Reaching movements are known to have large condition-independent neural activity and cyclic neural dynamics. A new precision center-out task was performed by rhesus macaques to test the hypothesis that cyclic, condition-independent neural activity in the primary motor cortex (M1) occurs not only during initial reaching... | neuroscience |
10.1101/453746 | Cyclic, condition-independent activity in primary motor cortex predicts corrective movement behavior | Reaching movements are known to have large condition-independent neural activity and cyclic neural dynamics. A new precision center-out task was performed by rhesus macaques to test the hypothesis that cyclic, condition-independent neural activity in the primary motor cortex (M1) occurs not only during initial reaching... | neuroscience |
10.1101/452581 | Understanding population history of range expansion and environmental adaptation by visualizing gene-environment-trait associations | During the history of range expansion, the populations encounter with variety of environments. They respond to the local environments by modifying the mutually interacting traits. Therefore, to understand the whole life history of the populations, it is ideal to capture the history of their range expansion with referen... | bioinformatics |
10.1101/452581 | Exploratory analysis of multiple traits co-adaptations in the population history | During the history of range expansion, the populations encounter with variety of environments. They respond to the local environments by modifying the mutually interacting traits. Therefore, to understand the whole life history of the populations, it is ideal to capture the history of their range expansion with referen... | bioinformatics |
10.1101/457614 | The molecular pH-response mechanism of the plant light-stress sensor PsbS | Plants need to protect themselves from excess light, which causes photo-oxidative damage and lowers the efficiency of photosynthesis. Photosystem II subunit S (PsbS) is a pH sensor protein that plays a crucial role in plant photoprotection by detecting thylakoid lumen acidification in excess light conditions via two lu... | biophysics |
10.1101/460048 | Paradoxical changes in brain reward status during oxycodone self-administration in a novel test of the negative reinforcement hypothesis | Background and PurposeThe extra-medical use of, and addiction to, prescription opioid analgesics is a growing health problem. To characterize how prescription opioid abuse develops, this study investigated the affective consequences of escalating prescription opioid use using intracranial self-stimulation (ICSS) reward... | neuroscience |
10.1101/461129 | From predictive models to cognitive models: Separable behavioral processes underlying reward learning in the rat | Cognitive models are a fundamental tool in computational neuroscience, embodying in software precise hypotheses about the algorithms by which the brain gives rise to behavior. The development of such models is often a hypothesis-first process, drawing on inspiration from the literature and the creativity of the individ... | animal behavior and cognition |
10.1101/458992 | Brain X chromosome inactivation is not random and can protect from paternally inherited neurodevelopmental disease. | Non-random (skewed) X chromosome inactivation (XCI) in the female brain can ameliorate X-linked phenotypes, though clinical studies typically consider 80-90% skewing favoring the healthy allele as necessary for this effect1-10. Here we quantify for the first time whole-brain XCI at single-cell resolution and discover a... | neuroscience |
10.1101/461442 | Timing polymerase pausing with TV-PRO-seq: dissecting the interplay of pausing duration and location, and gene expression | Transcription of many genes in metazoans is subject to polymerase pausing, which is the transient stop of transcriptionally-engaged polymerases. This is known to mainly occur in promoter proximal regions but it is not well understood. In particular, a genome-wide measurement of pausing times at high resolution has been... | systems biology |
10.1101/461707 | A thermodynamic chemical reaction network drove autocatalytic prebiotic peptides formation | The chemical reaction networks (CRNs), which led to the transition on early Earth from geochemistry to biochemistry remain unknown. We show that under mild hydrothermal circumstances, a thermodynamic chemical reaction network including sulfite/sulfate coupled with anaerobic ammonium oxidation (Sammox), might have drive... | biochemistry |
10.1101/463760 | Inferring causal connectivity from pairwise recordings and optogenetics | To study how the brain works mechanistically, neuroscientists want to quantify causal interactions between neurons, typically requiring perturbations. When using optogenetic interventions, multiple neurons are usually perturbed which produces a confound - any of the stimulated neurons can have affected the postsynaptic... | neuroscience |
10.1101/464388 | In for a pound, in for a penny: How the opportunity to gain reward influences the competition for memory resources | When people encounter items that they believe will help them gain reward, they later remember them better than others. A recent model of emotional memory, the emotional Context Maintenance and Retrieval model (eCMR), predicts that these effects would be stronger when stimuli that predict high and low reward can compete... | neuroscience |
10.1101/464388 | In for a pound, in for a penny: How the opportunity to gain reward influences the competition for memory resources | When people encounter items that they believe will help them gain reward, they later remember them better than others. A recent model of emotional memory, the emotional Context Maintenance and Retrieval model (eCMR), predicts that these effects would be stronger when stimuli that predict high and low reward can compete... | neuroscience |
10.1101/464388 | In for a pound, in for a penny: How the opportunity to gain reward influences the competition for memory resources | When people encounter items that they believe will help them gain reward, they later remember them better than others. A recent model of emotional memory, the emotional Context Maintenance and Retrieval model (eCMR), predicts that these effects would be stronger when stimuli that predict high and low reward can compete... | neuroscience |
10.1101/465005 | Ownership, Coverage, Utilisation and Maintenance of Long-lasting insecticidal nets in Three Health Districts in Cameroon: A Cross-Sectional Study | IntroductionThe Bamenda, Santa and Tiko Health Districts are in the highest malaria transmission strata of Cameroon. The purpose of this study was to explore the indicators of ownership and utilisation as well as maintenance of long-lasting insecticidal nets (LLINs) in three health districts in Cameroon.
MethodsA cros... | epidemiology |
10.1101/465005 | Ownership, Coverage, Utilisation and Maintenance of Long-lasting insecticidal nets in Three Health Districts in Cameroon: A Cross-Sectional Study | IntroductionThe Bamenda, Santa and Tiko Health Districts are in the highest malaria transmission strata of Cameroon. The purpose of this study was to explore the indicators of ownership and utilisation as well as maintenance of long-lasting insecticidal nets (LLINs) in three health districts in Cameroon.
MethodsA cros... | epidemiology |
10.1101/465393 | Healthy Choice depends on the latency and rate of information accumulation | The drift diffusion model (DDM) provides a parsimonious explanation of decisions across neurobiological, psychological, and behavioral levels of analysis. Although most DDM implementations assume that only a single value guides decisions, choices often involve multiple attributes that could make separable contributions... | neuroscience |
10.1101/470682 | Consistency of non-cognitive skills and their relation to educational outcomes in a UK cohort | Non-cognitive skills have previously been associated with a range of health and socioeconomic outcomes, though there has been considerable heterogeneity in published research. Many studies have used cross sectional data and therefore the longitudinal consistency of measures designed to capture non-cognitive skills is p... | genetics |
10.1101/469809 | Predictiveness and Reward Effects on Attention can be Explained by a Single Mechanism | The authors have withdrawn their manuscript because of a failure to replicate its main empirical result. Therefore, the authors do not wish this work to be cited as a reference. If you have any questions, please contact the corresponding author. | neuroscience |
10.1101/471201 | Combined use of Candida Utilis and Idesia polycarpa var. Vestita Fruit Improve the Production Performance of Laying Quail | Although Idesia polycarpa oil has been wildly explored as a raw material for biodiesel, the reports studying the by-product Idesia polycarpa fruit residues (IPR) are few. This study aimed to evaluate the effect of the Idesia polycarpa fruit residues fermented feed additive (IPFF) on the egg production of laying quails.... | microbiology |
10.1101/475673 | EEG-based detection of the locus of auditory attention with convolutional neural networks | In a multi-speaker scenario, the human auditory system is able to attend to one particular speaker of interest and ignore the others. It has been demonstrated that it is possible to use electroencephalography (EEG) signals to infer to which speaker someone is attending by relating the neural activity to the speech sign... | neuroscience |
10.1101/480418 | Mismatch repair disturbs meiotic class I crossover control | Sequence divergence, mediated by the anti-recombinogenic activity of mismatch repair (MMR), forms a barrier to meiotic recombination and in turn the formation of viable gametes. However, rather than MMR acting as a non-specific impediment to meiotic recombination, here we provide evidence that at regions of greater seq... | genetics |
10.1101/478347 | Neural Basis Of The Sound-Symbolic Crossmodal Correspondence Between Auditory Pseudowords And Visual Shapes | Sound symbolism refers to the association between the sounds of words and their meanings, often studied using the crossmodal correspondence between auditory pseudowords, e.g. takete or maluma, and pointed or rounded visual shapes, respectively. In a functional magnetic resonance imaging study, participants were prese... | neuroscience |
10.1101/479956 | Uncovering Network Architecture Using an Exact Statistical Input-Output Relation of a Neuron Model | Using observed neuronal activity, we try to unveil hidden microcircuits. A key requirement is the knowledge of statistical input-output relation of single neurons in vivo. We use a recent exact solution of spike-timing for leaky integrate-and-fire neurons under noisy inputs balanced near threshold, and construct a fram... | neuroscience |
10.1101/483263 | A learned embedding for efficient joint analysis of millions of mass spectra | Computational methods that aim to exploit publicly available mass spectrometry repositories primarily rely on unsupervised clustering of spectra. Here, we propose to train a deep neural network in a supervised fashion based on previous assignments of peptides to spectra. The network, called "GLEAMS," learns to embed sp... | bioinformatics |
10.1101/483263 | A learned embedding for efficient joint analysis of millions of mass spectra | Computational methods that aim to exploit publicly available mass spectrometry repositories primarily rely on unsupervised clustering of spectra. Here, we propose to train a deep neural network in a supervised fashion based on previous assignments of peptides to spectra. The network, called "GLEAMS," learns to embed sp... | bioinformatics |
10.1101/483362 | Somatic uniparental disomy mitigates the most damaging EFL1 allele combination in Schwachman-Diamond syndrome | Shwachman-Diamond syndrome (SDS; OMIM: #260400) is caused by variants in SBDS (Shwachman-Bodian-Diamond syndrome gene), which encodes a protein that plays an important role in ribosome assembly. Recent reports suggest that recessive variants in EFL1 are also responsible for SDS. However, the precise genetic mechanism t... | genetics |
10.1101/483362 | Somatic uniparental disomy mitigates the most damaging EFL1 allele combination in Shwachman-Diamond syndrome | Shwachman-Diamond syndrome (SDS; OMIM: #260400) is caused by variants in SBDS (Shwachman-Bodian-Diamond syndrome gene), which encodes a protein that plays an important role in ribosome assembly. Recent reports suggest that recessive variants in EFL1 are also responsible for SDS. However, the precise genetic mechanism t... | genetics |
10.1101/483362 | Somatic uniparental disomy mitigates the most damaging EFL1 allele combination in Shwachman-Diamond syndrome | Shwachman-Diamond syndrome (SDS; OMIM: #260400) is caused by variants in SBDS (Shwachman-Bodian-Diamond syndrome gene), which encodes a protein that plays an important role in ribosome assembly. Recent reports suggest that recessive variants in EFL1 are also responsible for SDS. However, the precise genetic mechanism t... | genetics |
10.1101/488445 | Effects of long-lasting insecticide net (LLINs) ownership/utilisation indicators on annual household malaria episodes (AHMEs) in three Health Districts in Cameroon | IntroductionHousehold residents in malaria endemic areas are at high risk of multiple malaria episodes per year. This study investigated the annual household malaria episodes (AHMEs) in three health districts in Cameroon.
MethodsA community-based cross-sectional household survey using a multi-stage cluster design was ... | epidemiology |
10.1101/487157 | Cell fitness is an omniphenotype | Moores law states that computers get faster and less expensive over time. In contrast in biopharma, there is the reverse spelling, Erooms law, which states that drug discovery is getting slower and costing more money every year. At the current pace, we estimate it costing $9.9T and it taking to the year 2574 to find dr... | systems biology |
10.1101/487157 | Cell fitness is an omniphenotype | Moores law states that computers get faster and less expensive over time. In contrast in biopharma, there is the reverse spelling, Erooms law, which states that drug discovery is getting slower and costing more money every year. At the current pace, we estimate it costing $9.9T and it taking to the year 2574 to find dr... | systems biology |
10.1101/487157 | Cell fitness is an omniphenotype | Moores law states that computers get faster and less expensive over time. In contrast in biopharma, there is the reverse spelling, Erooms law, which states that drug discovery is getting slower and costing more money every year. At the current pace, we estimate it costing $9.9T and it taking to the year 2574 to find dr... | systems biology |
10.1101/498352 | Non-random sister chromatid segregation mediates rDNA copy number maintenance in Drosophila | Although considered to be exact copies of each other, sister chromatids can segregate non-randomly in some cases. For example, sister chromatids of the X and Y chromosomes segregate non-randomly during asymmetric division of male germline stem cells (GSCs) in D. melanogaster. Here we identify that the ribosomal DNA (rD... | developmental biology |
10.1101/498352 | Non-random sister chromatid segregation mediates rDNA copy number maintenance in Drosophila | Although considered to be exact copies of each other, sister chromatids can segregate non-randomly in some cases. For example, sister chromatids of the X and Y chromosomes segregate non-randomly during asymmetric division of male germline stem cells (GSCs) in D. melanogaster. Here we identify that the ribosomal DNA (rD... | developmental biology |
10.1101/498469 | A novel mechanosensitive channel controls osmoregulation, differentiation and infectivity in Trypanosoma cruzi | Trypanosoma cruzi, the causative agent of Chagas disease, undergoes drastic morphological and biochemical modifications as it passes between hosts and transitions from extracellular to intracellular stages. The osmotic and mechanical aspects of these cellular transformations are not understood. Here we identify and cha... | microbiology |
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