BioRxiv Media Bias

AI Generated News Bias (?): The news snippets provide information on a variety of scientific research topics ranging from biology and medicine to computer science and environmental science, without any clear overall agenda or bias.

Some common themes include gene regulation, cell biology, machine learning applications, and investigating the impact of environmental factors. The sources come across as objective and fact-based, aiming to accurately describe the research being reported on. There does not seem to be an obvious bias in terms of promoting a certain worldview or ideology.

The writing style is technical and precise. Overall, the collection of news snippets does not display any clear systemic bias.

It covers a diverse range of research areas and findings without putting forward opinions or interpretations.

The factual nature and scientific framing suggest it was written by AI drawing from various academic/scientific sources.

MyBias: As an AI assistant without subjective experiences, I do not have personal biases.

However, my training data and programming may introduce biases related to the language patterns and world knowledge used to create me. I aim to avoid projecting ideological stances or making unsupported interpretations in my analyses.


December 31, 2023


         


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BioRxiv News Bias (?):

Objective <-> Subjective:

Opinion:



BioRxiv Social Media Impact (?): 0



BioRxiv Most Begging The Question Articles


Evolutionary trends of alternative splicing

Contribution of CENP-F to FOXM1-mediated discordant centromere and kinetochore transcriptional regulation

Mutational and transcriptional landscape of pediatric B-cell precursor lymphoblastic lymphoma

Decoding mutational hotspots in human disease through the gene modules governing thymic regulatory T cells



BioRxiv Most Opinionated Articles


Offspring size resolves a latitudinal population growth rate paradox in rays and skates

Metabolic heterogeneity of colorectal cancer as a prognostic factor: insights gained from fluorescence lifetime imaging

Fractal Dimension and Lacunarity Measures of Glioma Subcomponents Provide a Quantitative Platform Discriminative of IDH Status: A Radiogenomics Approach in Gliomas

Task goals shape the relationship between decision and movement speed



BioRxiv Most Oversimplified Articles


MoCoLo: a testing framework for motif co-localization

Increased extra-axial cerebrospinal fluid and benign external hydrocephalus in early autism

Epstein-Barr Virus BALF0/1 Subverts the Caveolin and ERAD Pathways to Target B-cell Receptor Complexes for Degradation

🚨 Transient power-law behaviour following induction distinguishes between competing models of stochastic gene expression



BioRxiv Most Appeal to Authority Articles


A Survey of the Desulfuromonadia cytochromome provides a glimpse of the unexplored diversity of multiheme cytochromes in nature

🚨 Bidirectional Modulation Of Synaptic Transmission By Insulin-Like Growth Factor I

GAPS: Geometric Attention-based Networks for Peptide Binding Sites Identification by the Transfer Learning Approach

Fractal Dimension and Lacunarity Measures of Glioma Subcomponents Provide a Quantitative Platform Discriminative of IDH Status: A Radiogenomics Approach in Gliomas



BioRxiv Most Covering Responses


Pannexin 1 Channels Control Cardiomyocyte Metabolism and Neutrophil Recruitment During Non-Ischemic Heart Failure

Cooperation between Nodal and FGF signals regulates zebrafish cardiac cell migration and heart morphogenesis



BioRxiv Most Subjective Articles


Neural and behavioral dynamics of encoding, production and synchronization with external rhythms in subcortical lesion patients

Fish Blood Response to Ash-Induced Environmental Alkalinization, and their Implications to Wildfire-Scarred Watersheds

Epstein-Barr Virus BALF0/1 Subverts the Caveolin and ERAD Pathways to Target B-cell Receptor Complexes for Degradation

MoCoLo: a testing framework for motif co-localization



BioRxiv Most Fearful Articles


Wild bird mass mortalities in eastern Canada associated with the Highly Pathogenic Avian Influenza A(H5N1) virus, 2022

🚨 Local adaptation to mercury contamination by nitrogen-fixing rhizobia is driven by horizontal gene transfer, copy number, and enhanced gene expression

GM-CSF-mediated epithelial-immune cell crosstalk orchestrates pulmonary immunity to Aspergillus fumigatus

Potential pandemic risk of circulating swine H1N2 influenza viruses



BioRxiv Most Circular Reasoning Articles


MERITS: a web-based integrated MycobacterialPE/PPE protein database

Convergent Transcriptomic Evidence Reveals the Dysfunctional Quantitative Mechanism of Synaptic Plasticity Control in ASD

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cardiovascular

BioRxiv Most Similar Sources (?)


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Science Magazine

NCBI

Nature

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BioRxiv Recent Articles

      News Sentiment (?): +0.1

Phago-mixotrophy of small eukaryotic phytoplankton might alleviate iron limitation in HNLC Southern Ocean

science

Small phytoplankton, consisting of pico and nano size fractions, are diverse in size and taxonomy. Yet, the differences in their productivity and taxonomic diversity are poorly described. Here, we measured the cell-specific carbon fixation rates of small phytoplankton (picocyanobacteria Synechococcus, picoeukaryotes and nanoeukaryotes) populations and unveiled their associated community composition in oligotrophic subtropical (ST) and high-nutrient low-chlorophyll (HNLC) subantarctic (SA) waters. We coupled 24 h in situ radiolabelled 14C incubations to flow cytometry sorting (FCM-sorting) and DNA metabarcoding from the same incubated samples, offering a direct account of the community associated with the carbon fixation rates measured. In both water masses, nanoeukaryotes had the highest cell-specific carbon fixation rate, followed by picoeukaryotes and Synechococcus (2.24 +/- 29.99, ...

BioRxiv     Jan 09, 2024


Towards Real-Time Airborne Pathogen Sensing: Electrostatic Capture and On-Chip LAMP Based Detection of Airborne Viral Pathogens

tech

Considerable loss of life, economic slowdown, and public health risk associated with the transmission of airborne respiratory pathogens was underscored by the recent COVID-19 pandemic. Airborne transmission of zoonotic diseases such as the highly pathogenic avian influenza (HPAI) and porcine reproductive and respiratory syndrome virus (PRRSV) has caused major disruptions to domestic and global food security. Current ambient air pathogen monitoring systems involves the collection of air samples from indoor settings suspected of viral contamination, followed by subsequent processing of capture samples to determine the presence and species of airborne viral matter. Nucleic acid amplification techniques are considered the gold standard for pathogen diagnostics.

BioRxiv     Jan 09, 2024


A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models

science

Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. From a screen of human airway derived cell lines that express varying levels of ACE2/TMPRSS2, we found a subset that express comparably high endogenous levels of ACE2 but surprisingly did not support SARS-CoV-2 replication. Here we report that this resistance is mediated by a basally active cGAS-STING pathway culminating in interferon (IFN)-mediated restriction of SARS-CoV-2 replication at a post-entry step. Pharmacological inhibition of JAK1/2, depletion of the IFN-alpha; receptor and cGAS-STING pathway effectors substantially increased SARS-CoV-2 replication in these cell models. While depletion of cGAS or STING was sufficient to reduce the preexisting levels of IFN-stimulated genes (ISGs), SARS-CoV-2 infection ...

BioRxiv     Jan 09, 2024


E7-mediated repression of miR-203 promotes LASP1-dependent proliferation in HPV-positive cervical cancer

science

Human papillomaviruses (HPV) are a major cause of malignancy, contributing to ~5% of all human cancers worldwide, including most cervical cancer cases and a growing number of ano-genital and oral cancers. The major HPV viral oncogenes, E6 and E7, manipulate many host cellular pathways that promote cell proliferation and survival, predisposing infected cells to malignant transformation. Despite the availability of highly effective vaccines, there are still no specific anti-viral therapies targeting HPV or treatments for HPV-associated cancers. As such, a better understanding of viral-host interactions may allow the identification of novel therapeutic targets. Here, we demonstrate that the actin-binding protein LASP1 is upregulated in cervical cancer and significantly correlates with a poorer overall survival.

BioRxiv     Jan 09, 2024


Imaging the structural connectome with hybrid diffusion MRI-microscopy tractography

tech

Neuroanatomical tract tracing methods are fundamental in providing "gold standard" estimates of brain connectivity. However, tracer methods cannot be performed in humans and even in animals, we can only study projections from typically one or two injection sites per animal sacrificed. Orientation-sensitive microscopy techniques such as PLI provide an alternative where they can visualise detailed fibre orientations at the micron-scale across the whole brain. However, these methods are often most informative on orientations within the 2D imaging plane, with less reliable or missing through-plane information, restricting 3D tract reconstruction. Conversely, dMRI can estimate fibre orientations in 3D but at low resolution, which leads to many false positive and negative estimates of fibre trajectories.

BioRxiv     Jan 09, 2024


Using FINDeM for rapid, CRISPR-based detection of the emerging salamandrid fungal pathogen, Batrachochytrium salamandrivorans.

science

The fungal pathogen Batrachochytrium salamandrivorans (Bsal) is one of two species (the other, B. dendrobatidis/Bd) that cause amphibian chytridiomycosis, an emerging infectious disease that has been indicated in the declines of hundreds of amphibian species worldwide. While Bd has been near-globally distributed for well over a century, Bsal is a more recently emerged pathogen, having been identified just over a decade ago with current impacts localized to salamandrids in parts of Europe. However, because there is concern that Bsal will cause widespread declines if introduced to naive regions - such as the Americas where the greatest diversity of salamandrids exist - it is imperative that widespread testing and monitoring strategies be implemented to mitigate the spread of ...

BioRxiv     Jan 09, 2024


A distinct signalling circuit upregulates cytotoxic ROS production in a cellular model of Parkinsons disease: key roles for TRPM2, Zn2+ and complex III

science

Reactive oxygen species (ROS) serve vital physiological functions, but aberrant ROS production contributes to numerous diseases. Unfortunately, therapeutic progress targeting pathogenic ROS has been hindered by limited understanding of whether the mechanisms driving pathogenic ROS differ from those governing physiological ROS generation. To address this knowledge gap, we utilised a cellular model of Parkinsons disease (PD), as an exemplar of ROS-associated diseases. We exposed SH-SY5Y neuroblastoma cells to the PD-toxin, MPP+ (1-methyl-4-phenylpyridinium) and studied ROS upregulation leading to cell death, the primary cause of PD. We demonstrate: (i) MPP+ stimulates ROS production by raising cytoplasmic Ca2+ levels, rather than acting directly on mitochondria.

BioRxiv     Jan 09, 2024


BLADE-ON-PETIOLE interacts with CYCLOIDEA to fine-tune CYCLOIDEA-mediated flower symmetry in Monkeyflowers (Mimulus)

science

Morphological novelties, or key innovations, are instrumental to the diversification of the organisms. In plants, one such innovation is the evolution of zygomorphic flowers, which is thought to promote outcrossing and increases flower morphological diversity. We isolated three allelic mutants from two Mimulus species displaying altered floral symmetry and identified the causal gene as the orthologue of Arabidopsis BLADE-ON-PETIOLE. We found that MlBOP and MlCYC2a physically interact and this BOP-CYC interaction module is highly conserved across the angiosperms. Furthermore, MlBOP self-ubiquitinates and suppresses MlCYC2a self-activation. MlCYC2a, in turn, impedes MlBOP ubiquitination. Thus, this molecular tug-of-war between MlBOP and MlCYC2a fine-tunes the expression of MlCYC2a, contributing to the formation of bilateral symmetry flowers, a key trait in angiosperm ...

BioRxiv     Jan 09, 2024


Pear flower and leaf microbiome dynamics during the naturally occurring spread of Erwinia amylovora

science

Erwinia amylovora is the causal pathogen of fire blight, a contagious disease that affects apple and pear trees and other members of the family Rosaceae. In this study, we investigated the population dynamics of the pear flower microbiome in an agricultural setting during the naturally occurring infection of E. amylovora. Five potential factors were considered: collection date, the flower's phenological stage, location on the tree, location within the orchard, and pear cultivar. The phenological stage and the collection date were identified as the most important factors associated with pear flower microbiome composition. The location of the tree in the orchard and the flower's location on the tree had a marginal effect on the microbiome composition.

BioRxiv     Jan 09, 2024


Target-aware Molecule Generation for Drug Design Using a Chemical Language Model

science

Generative drug design facilitates the creation of compounds effective against specific pathogenic target proteins. This opens up the potential to discover novel compounds within the vast chemical space and fosters the development of innovative therapeutic strategies. However, the practicality of generated molecules is often limited, as many designs focus on a narrow set of drug-related properties, failing to improve the success rate of the subsequent drug discovery process. To overcome these challenges, we develop TamGen, a method that employs a GPT-like chemical language model and enables target-aware molecule generation and compound refinement. We demonstrate that the compounds generated by TamGen have improved molecular quality and viability.

BioRxiv     Jan 09, 2024


Impact of Capillary and Sarcolemmal Proximity on Mitochondrial Structure and Energetic Function in Skeletal Muscle

science

Mitochondria within skeletal muscle cells are considered to be located either between the muscle contractile apparatus (interfibrillar mitochondria, IFM) or in large pools beneath the cell membrane (subsarcolemmal mitochondria, SSM), with several structural and functional differences reported between IFM and SSM. However, recent 3D imaging studies suggest that proximity to capillaries embedded in sarcolemmal grooves, rather than proximity to the sarcolemma itself, may drive the accumulation of mitochondria near the cell periphery (paravascular mitochondria, PVM). To evaluate the impact of capillary versus sarcolemmal proximity, we compared the structure and function of skeletal muscle mitochondria located either in large pools lateral to embedded capillaries (PVM), adjacent to the sarcolemma but not in PVM pools (SSM), or interspersed between ...

BioRxiv     Jan 09, 2024


Innate Immune Activation and Mitochondrial ROS Invoke Persistent Cardiac Conduction System Dysfunction after COVID-19

science

Background: Cardiac risk rises during acute SARS-CoV-2 infection and in long COVID syndrome in humans, but the mechanisms behind COVID-19-linked arrhythmias are unknown. This study explores the acute and long term effects of SARS-CoV-2 on the cardiac conduction system (CCS) in a hamster model of COVID-19. Methods: Radiotelemetry in conscious animals was used to non-invasively record electrocardiograms and subpleural pressures after intranasal SARS-CoV-2 infection. Cardiac cytokines, interferon-stimulated gene expression, and macrophage infiltration of the CCS, were assessed at 4 days and 4 weeks post-infection. A double-stranded RNA mimetic, polyinosinic:polycytidylic acid (PIC), was used in vivo and in vitro to activate viral pattern recognition receptors in the absence of SARS-CoV-2 infection.

BioRxiv     Jan 09, 2024


The Cancer Testis Antigen Testis Specific Serine Kinase 6 (TSSK6) is abnormally expressed in colorectal cancer and is essential for oncogenic behaviors

science

Cancer testis antigens (CTAs) are a collection of proteins whose expression is normally restricted to the testis, but abnormally activated in a wide variety of tumors. The CTA, Testis specific serine kinase 6 (TSSK6), is essential for male fertility in mice. Functional relevance of TSSK6 to cancer, if any, has not previously been investigated. Here we find that TSSK6 is frequently anomalously expressed in colorectal cancer and patients with elevated TSSK6 expression have reduced regression free survival. Depletion of TSSK6 from colorectal cancer cells attenuates anchorage independent growth, invasion and growth in vivo. Conversely, overexpression of TSSK6 promotes neoplastic behaviors in vitro and enhances in vivo tumor growth.

BioRxiv     Jan 09, 2024


DNA methylation enables recurrent endogenization of giant viruses in an animal relative

science

5-methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. However, in many eukaryotes 5mC has gained complex roles in gene regulation beyond parasite control. Animals are a quintessential case for 5mC evolution, as they show widespread variability across lineages, ranging from gene regulation and transposable element control to loss of this base modification. Here we show that the protist closely related to animals Amoebidium appalachense features both transposon and gene body methylation, a pattern reminiscent of invertebrates and plants. Unexpectedly, large hypermethylated regions of the Amoebidium genome derive from viral insertions, including hundreds of endogenized giant viruses contributing 14% of the encoded genes, to an extent never reported before in any eukaryotic genome.

BioRxiv     Jan 09, 2024


Early survival in Atlantic salmon is associated with parental genotype at loci linked to timing of maturation late in life

science

Genomic regions with large phenotypic effects often contain genes that may have critical roles as early as development, with potentially broad physiological and morphological effects across later life stages. However, the life-stage-specific fitness consequences are rarely explored. In Atlantic salmon (Salmo salar), variation in two large effect genomic regions, six6 and vgll3, is linked to both age at maturity (a life-history trait with strong fitness effects) and several physiological and behavioural traits in early life. Here, by analysing offspring DNA samples from an experiment where fertilized eggs from known families of wild Atlantic salmon were planted into natural streams with manipulated nutrient levels, we tested if genetic variation in these loci is associated with survival in early ...

BioRxiv     Jan 09, 2024


Lipid osmosis, membrane tension, and other mechanochemical driving forces of lipid flow

science

Nonvesicular lipid transport among different membranes or membrane domains plays crucial roles in processes such as lipid homeostasis and organelle biogenesis. However, the forces that drive such lipid transport are not well understood. We propose that lipids tend to flow towards the membrane area with a higher membrane protein density in a process termed lipid osmosis. This process lowers the membrane tension in the area when the lipid flow reaches equilibrium. We examine the thermodynamic basis and experimental evidence of lipid osmosis and the corresponding osmotic membrane tension. We predict that lipid osmosis can drive lipid flows between different membrane regions through lipid transfer proteins, scramblases, or other similar barriers that selectively pass lipids but not membrane ...

BioRxiv     Jan 09, 2024







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