biorxiv.org Media Bias

AI Generated News Bias (?): Based on the limited news snippets provided, I do not have enough information to make an empirically grounded assessment of the source's general bias, agenda, or worldview.

Most of the snippets seem to be summaries of scientific studies on specialized topics like biology, medicine, and technology.

Without more context or a representative sample of the source's overall coverage, it would be speculative for me to draw conclusions about its objectivity or impartiality.

I aimed to avoid making assumptions and instead focused my response on noting the lack of information to make an informed assessment. As an AI assistant without personal biases, beliefs, or ideological stances, I do not have inherent limitations that affected my analysis.

However, my training data and methods do shape my capabilities.

I was designed by Anthropic to be helpful, harmless, and honest using a technique called constitutional AI. But I have limits in understanding nuanced texts or judging the impartiality of sources without sufficient evidence.

I tried providing a transparent response explaining these limitations.


January 13, 2024


Show Historical Bias


         


Customize Your AI News Feed. No Censorship. No Ads.





biorxiv.org News Cycle (?):



Rats rely on airflow cues for self-motion perception

Self-motion perception is a vital skill for all species. It is an inherently multisensory process, that combines inertial (body-based) and relative (with respect to the environment) motion cues. While extensively studied in human and non-human primates, there is currently no paradigm to test self-motion perception in rodents using both inertial and relative self-motion cues. We developed a novel rodent motion simulator using two synchronized robotic arms to generate inertial, relative or combined (inertial and relative) cues of self-motion. Eight rats were trained to perform a task of heading-discrimination, similar to the popular primate paradigm. Strikingly, the rats relied heavily on airflow for relative self-motion perception, with little contribution from optic flow (performance in the dark was almost ...

biorxiv.org     Dec 19, 2023


Machine learning of brain-specific biomarkers from EEG

Electroencephalography (EEG) has a long history as a clinical tool to study brain function, and its potential to derive biomarkers for various applications is far from exhausted. Machine learning (ML) can guide future innovation by harnessing the wealth of complex EEG signals to isolate relevant brain activity. Yet, ML studies in EEG tend to ignore physiological artifacts, which may cause problems for deriving biomarkers specific to the central nervous system (CNS). We present a framework for conceptualizing machine learning from CNS versus peripheral signals measured with EEG. A common signal representation across the frequency spectrum based on Morlet wavelets allowed us to define traditional brain activity features (e.g.

biorxiv.org     Dec 19, 2023


UVAE: Integration of Heterogeneous Unpaired Data with Imbalanced Classes

We introduce the Unbiasing Variational Autoencoder (UVAE), a novel computational framework developed for the integration of unpaired biomedical data streams, with a particular focus on clinical flow cytometry. UVAE effectively addresses the challenges of batch effect correction and data alignment by training a semi-supervised model on partially labeled datasets. This approach enables the simultaneous normalisation and integration of diverse data within a shared latent space. The framework is implemented in Python with a descriptive interface for the specification and incorporation of multiple, partially overlapping data series. UVAE employs a probabilistic model for batch effect normalisation, with a generative capacity for unbiased data reconstruction and inference from heterogeneous samples.

biorxiv.org     Dec 19, 2023


A compendium of Amplification-Related Gain Of Sensitivity (ARGOS) genes in human cancer

Chromosomal gains are among the most frequent somatic genetic alterations occurring in cancer. While the effect of sustained oncogene expression has been characterized, the impact of copy-number gains affecting collaterally-amplified "bystander" genes on cellular fitness remains less understood. To investigate this, we built a comprehensive map of dosage compensation across human cancers by integrating expression and copy number profiles from over 8,000 TCGA tumors and CCLE cell lines. Further, we analyzed the effect of gene overexpression across 17 human cancer ORF screens to provide an overview of genes that prove toxic to cancer cells when overexpressed. Combining these two independent approaches we propose a class of 'Amplification-Related Gain Of Sensitivity' (ARGOS) genes.

biorxiv.org     Dec 19, 2023


Fertilisation of agricultural soils with municipal biosolids: Part 1- Glyphosate and aminomethylphosphonic acid inputs to Quebec field crop soils

Municipal biosolids (MBS) are suggested to be abundant, sustainable, inexpensive fertilisers, rich in phosphorus and nitrogen. However, MBS can also contain glyphosate and phosphonates that can degrade to AMPA. Glyphosate-based herbicides (HBG) are used in field crops all over the world. Most glyphosate generally degrades within a few weeks, mainly as aminomethylphosphonic acid (AMPA). AMPA is more persistent than glyphosate, and can accumulate from one crop year to the next. AMPA is phytotoxic even to glyphosate-resistant crops. The aims of this study were to assess whether applications of MBS significantly contribute to: 1) glyphosate and AMPA contents of agricultural soils, 2) trace metal elements contents, and 3) partial replacement of mineral fertilisation while maintaining similar yields.

biorxiv.org     Dec 19, 2023


Emotion Dynamics in Reciprocity: Deciphering the Role of Prosocial Emotions in Social Decision-making

To date, the relevance of prosocial emotions in social decisions based on reciprocity remains poorly understood. Expected and experienced emotions in interoceptive-social dimension, expected offers, and actual acceptance were measured in 476 participants during an ultimatum game consisting of fair, moderate, and unfair offers. We investigated whether participants adjust social decisions according to prediction errors on prosocial emotions and reciprocity. Participants' acceptance trajectories were explained by prediction errors in dominance, valence, and reward. Participants were categorized into 4 distinct subgroups based on their patterns of reward expectation, acceptance, and emotional experiences before and after the offer. Furthermore, the relationships between prosocial emotions, social decisions, and reciprocity varied across these subgroups.

biorxiv.org     Dec 19, 2023


Within-subject changes in DNA-methylome profile identify individual signatures of early-life adversity, with a potential to predict neuropsychiatric outcome.

Background: Adverse early-life experiences (ELA), including poverty, trauma and neglect, affect a majority of world children. Whereas the impact of ELA on cognitive and emotional health throughout the lifespan is well-established, it is not clear how distinct types of ELA influence child development, and there are no tools to predict for an individual child their vulnerability or resilience to the consequences of ELAs. Epigenetic markers including DNA-methylation profiles of peripheral cells may encode ELA and provide a predictive outcome marker. However, the rapid dynamic changes in DNA methylation in childhood and the inter-individual variance of the human genome pose barriers to identifying profiles predicting outcomes of ELA exposure.

biorxiv.org     Dec 19, 2023


Hofbauer cells and fetal brain microglia share transcriptional profiles and responses to maternal diet-induced obesity

Maternal immune activation is associated with adverse offspring neurodevelopmental outcomes, many mediated by in utero microglial programming. As microglia remain inaccessible throughout development, identification of noninvasive biomarkers reflecting fetal brain microglial programming could permit screening and intervention. We used lineage tracing to demonstrate the shared ontogeny between fetal brain macrophages (microglia) and fetal placental macrophages (Hofbauer cells) in a mouse model of maternal diet-induced obesity, and single-cell RNA-seq to demonstrate shared transcriptional programs. Comparison with human datasets demonstrated conservation of placental resident macrophage signatures between mice and humans. Single-cell RNA-seq identified common alterations in fetal microglial and Hofbauer cell gene expression induced by maternal obesity, as well as sex differences in these alterations.

biorxiv.org     Dec 19, 2023


How Clustering Promotes Biodiversity: A Solution to the Plankton Paradox

It is known that a species-saturated ecological community driven by competitive Lotka-Volterra equations, following a path of competitive exclusion, lingers in a long-term state with species congregated in niche space into well-separated clusters. Characterizing the topology of the niche structure of this state as a hierarchical one, we put forward a generalization of the Lotka-Volterra multi-resource competition model, which recognizes this topology at the basis of its own network structure of interrelated differential equations. This kind of generalization substantially reduces the competitive constraints on species coexistence, offering promising potential for a conceptual resolution of the plankton paradox.

biorxiv.org     Dec 19, 2023


Agonism between family groups of cooperative breeding smooth-coated otters (Lutrogale perspicillata)

Intraspecific agonistic interactions are common in the animal kingdom and have significant consequences for animals. With a growing population and limited resources, these interactions have been observed more frequently among smooth-coated otters in Singapore. However, little is known about the behavioral patterns of these interactions and the factors that may affect their outcomes. To address this, we analyzed intraspecific agonistic interactions through publicly available videos from citizen scientists. Our analysis revealed different behavioral patterns and typical behaviors between winning and losing family groups in different environments. We also found suggestive evidence that larger family groups with more individuals than opponents have an advantage in these interactions.

biorxiv.org     Dec 19, 2023


Understanding Genome Structure Facilitates the Use of Wild Lentil Germplasm for Breeding: A Case Study with Shattering Loci

Plant breeders are generally reluctant to cross elite crop cultivars with their wild relatives to introgress novel desirable traits due to associated negative traits such as pod shattering. This results in a genetic bottleneck that could be reduced through better understanding of the genomic locations of the gene(s) controlling this trait. We integrated information on parental genomes, pod shattering data from multiple environments, and high-density genetic linkage maps to identify pod shattering QTLs in three lentil (Lens culinaris) interspecific recombinant inbred line (RIL) populations. The broad-sense heritability on a multi-environment basis varied from 0.46 (in LR-70, L. culinaris x L. odemensis) to 0.77 (in LR-68, L. orientalis x L. culinaris).

biorxiv.org     Dec 19, 2023


Identification of methylation markers for age and Bovine Respiratory Disease in dairy cattle

Methylation profiles of animals is known to differ by age and disease status. Bovine respiratory disease (BRD), a complex infectious disease, primarily affects calves and has significant impact on animal welfare and the cattle industry, predominantly from production losses. BRD susceptibility is multifactorial, influenced by both environmental and genetic factors. We investigated the epigenetic profile of BRD susceptibility in calves and age-related methylation differences between healthy calves and adult dairy cows using Reduced Representation Bisulfite Sequencing (RRBS). We identified 3,452 genes within differentially methylated regions between calves and adults. Functional analysis revealed enrichment of developmental pathways including cell fate commitment and tissue morphogenesis.

biorxiv.org     Dec 19, 2023


Arctos: Community-driven innovations for managing biodiversity and cultural collections

Museum collections house millions of objects and associated data records that document biological and cultural diversity. In recent decades, digitization efforts have greatly increased accessibility to these data, thereby revolutionizing interdisciplinary studies in evolutionary biology, biogeography, epidemiology, cultural change, and human-mediated environmental impacts. Curators and collection managers can make museum data as accessible as possible to scientists and learners by using a collection management system. However, selecting a system can be a challenging task. Here, we describe Arctos, a community solution for managing and accessing collections data for research and education. Specific goals are to: (1) Describe the core elements of Arctos for a broad audience with respect to the biodiversity informatics principles that enable high quality ...

biorxiv.org     Dec 19, 2023


Whole-brain modular dynamics at rest predict sensorimotor learning performance

Predictive biomarkers of cognitive performance are informative about the neural mechanisms underlying cognitive phenomena, and have tremendous potential for the diagnosis and treatment of neuropathologies with cognitive symptoms. Among such biomarkers, the modularity (subnetwork composition) of whole-brain functional networks is especially promising, due to its longstanding theoretical foundations and recent success in predicting clinical outcomes. We used functional magnetic resonance imaging to identify whole-brain modules at rest, calculating metrics of their spatio-temporal dynamics before and after a sensorimotor learning task on which fast learning is widely believed to be supported by a cognitive strategy. We found that participants' learning performance was predicted by the strength of dynamic modularity scores (clarity of subnetwork composition), the degree of coordination ...

biorxiv.org     Dec 19, 2023


Age-dependent Powassan Virus Lethality is Directed by Glial Cell Activation and Divergent Neuroinflammatory Cytokine Responses in a Murine Model

Powassan virus (POWV) is an emergent tick-borne flavivirus that causes fatal encephalitis in the elderly and long-term neurologic sequelae in survivors. How age contributes to severe POWV encephalitis remains an enigma and there are currently no animal models that reflect age-dependent POWV neuropathology. Inoculating C57BL/6 mice with a POWV strain (LI9) currently circulating in Ixodes ticks, resulted in age-dependent POWV lethality with overt spongiform brain damage 10-15 dpi. Infection of 50 week old mice resulted in 82% lethality 10-15 dpi that was sequentially reduced by age to 7.1% in 10 week old mice. LI9 encephalitis resulted in early neuronal depletion, with severe CNS damage, persistent inflammatory gliosis and long-term spongiform pathology in survivors (30 dpi).

biorxiv.org     Dec 19, 2023


Interpretable deep learning framework towards understanding molecular changes in human brains with Alzheimer's disease: implication for microglia activation and sex differences in AD

INTRODUCTION: The objective of this study is to characterize the molecular changes associated with AD from gene expression data of brain tissues taking an interpretable deep learning approach which has not been fully exploited. METHODS: We trained multi-layer perceptron (MLP) models for the classification of neuropathologically confirmed AD vs. controls using the transcriptomic data of three brain regions from the ROSMAP study. The whole disease spectrum was then modeled as a progressive trajectory. SHAP (SHapley Additive exPlanations) value was derived to explain model predictions and identify significant implicated genes for subsequent network analysis of key gene modules underlying AD progression. The framework was validated using two external datasets: the Mayo RNA-seq study cohort and the Mount Sinai ...

biorxiv.org     Dec 19, 2023







×

Chat with Helium


 Ask me any question!