last week in biology

765

new preprints about biology in the last week

bioRxiv

most active server in biology in the last week

gene expression

30 preprints

Digital nuclear morphometry correlates to BAP-1 expression, gene expression class and metastasis-free survival in uveal melanoma

We conclude that digital morphometry can be fast and highly reproducible, that for the first time, morphometry parameters can be objectively quantitated in thousands of cells at a time, and that variables describing the shape and size of the nuclei correlate to nBAP-1 expression, gene expression class and prognosis...
1 day ago
medRxiv

An integrated platform for genome engineering and gene expression perturbation in Plasmodium falciparum

Overall, this molecular toolkit enables P. falciparum genetics broadly and facilitates deeper interrogation of parasite genes involved in diverse biological processes.
2 days ago
bioRxiv

Wnt signaling activates gene expression in the absence of the C. elegans DREAM repressor complex in somatic cells

We propose a model whereby a set of embryonically expressed transcription factors, and the Wnt/PCP pathway, act opportunistically to activate DREAM complex target genes in somatic cells of DREAM complex mutants at 26{degrees}C.
5 days ago
bioRxiv

genome wide

21 preprints

Genome-wide association study of gastrointestinal disorders reinforces the link between the digestive tract and the nervous system

We conducted genome-wide association analyses based on 456,414 individuals and identified 27 independent and significant loci for GORD, PUD and IBS, including SNPs associated with PUD at or near genes MUC1, FUT2, PSCA and CCKBR, for which there are previously established roles in Helicobacter pylori infection, response...
5 days ago
bioRxiv

Finding genetic variants in plants without complete genomes

Structural variants and presence/absence polymorphisms are common in plant genomes, yet they are routinely overlooked in genome-wide association studies (GWAS).
1 day ago
bioRxiv

Attacks on genetic privacy via uploads to genealogical databases

In databases that detect IBS segments using unphased genotypes, approximately 100 uploads of falsified datasets can reveal enough genetic information to allow accurate genome-wide imputation of every person in the database.
4 days ago
bioRxiv

single cells

17 preprints

Single-cell dissection of a rare human prostate basal cell carcinoma

Interestingly, at single-cell resolution the gene expression patterns of prostate BCC tumor cells show uniqueness compared with that of common prostate cancer-derived circulating tumor cells.
2 days ago
bioRxiv

Spatially-mapped single-cell chromatin accessibility

We apply sciMAP-ATAC in the adult mouse cortex to discriminate cortical layering of glutamatergic neurons and establish the spatial ordering of single cells within intact tissue.
5 days ago
bioRxiv

Protein Phosphatase 1 activity controls a balance between collective and single cell modes of migration

Inhibition of Pp1 causes border cells to round up, dissociate, and move as single cells with altered motility.
6 days ago
bioRxiv

high throughput

17 preprints

High-throughput, temporal and dose dependent, effect of vitamins and minerals on chondrogenesis

This high-throughput platform was used to assess the effect of vitamins and minerals, alone and in combination with TGF{beta}1, on type II collagen expression.
5 days ago
bioRxiv

Bayesian modelling of high-throughput sequencing assays with malacoda

High-throughput screens powered by NGS have greatly increased the rate of variant functionalization, but the development of comprehensive statistical methods to analyze screen data has lagged behind.
1 day ago
bioRxiv

Third-Generation Method for High Throughput Quantification of Trace Palladium by Color or Fluorescence

We previously reported a colorimetric method for trace palladium quantification, the only high throughput method implemented in the pharmaceutical industry.
30 hours ago
chemRxiv

machine learning

14 preprints

Distinguishing between paediatric brain tumour types using multi-parametric magnetic resonance imaging and machine learning: a multi-site study

The results show that diffusion and perfusion weighted imaging of both the tumour and whole brain provide significant features which differ between tumour types, and that combining these features gives the optimal machine learning classifier with greater than 80 percent predictive precision.
5 days ago
arXiv

Machine Learning for Inferring CO2 Fluxes: The New Metaphysics of Neural Nets

A non-intuitive machine learning metaphysical result was observed by the omission of CO2 concentrations as an input variable.
2 days ago
EarthArXiv

Multi-omics-based pan-cancer prognosis prediction using an ensemble of deep-learning and machine-learning models

We introduce DeepProg, a new computational framework that robustly predicts patient survival subtypes based on multiple types of omic data, using an ensemble of deep-learning and machine-learning models.
1 day ago
medRxiv

mass spectrometry

12 preprints

Identifying Sialylation Linkages at the Glycopeptide Level by Glycosyltransferase Labeling Assisted Mass Spectrometry (GLAMS)

Herein, an innovative strategy of glycosyltransferase labeling assisted mass spectrometry (GLAMS) were developed.
5 days ago
bioRxiv

MitoPlex: A Targeted Multiple Reaction Monitoring Assay for Quantification of a Curated Set of Mitochondrial Proteins

Here, we present a high throughput, reproducible and quantitative mass spectrometry multiple reaction monitoring based assay of 37 proteins critical to central carbon chain metabolism and overall mitochondrial function termed MitoPlex.
27 hours ago
bioRxiv

Encapsulation of a Ruthenium(II) Complex in Polylactide Nanoparticles: A Route to Remarkable Cellular Uptake for Photodynamic Therapy of Cancer

Finally, their photo-therapeutic activity (λexc = 480 nm, 3.21 J cm-2) in cancerous human cervical carcinoma (HeLa) and non-cancerous retinal pigment epithelium (RPE-1) cells was tested alongside that of RuOH and their cellular uptake in HeLa cells was assessed by confocal microscopy and inductively coupled plasma - mass spectrometry...
5 days ago
chemRxiv

decision making

10 preprints

Autonomous Industrial Management via Reinforcement Learning: Self-Learning Agents for Decision-Making -- A Review

We then introduce self-play scenarios and how they can be used to teach self-learning agents through a supportive environment which focuses on how the agents can adapt to different real-world environments.
6 days ago
arXiv

Decommissioning of offshore man-made installations: Taking an ecosystem approach

We are entering a legacy era for the offshore oil and gas industry.
5 days ago
MarXiv

Disruption of Nrxn1α within excitatory forebrain circuits drives value-based dysfunction

By relating deficits in value-based decision-making to region-specific Nrxn1 disruption and changes in reward-associated neural activity, we reveal potential neural substrates for the pathophysiology of neuropsychiatric disease-associated cognitive dysfunction.
1 day ago
bioRxiv

state of the art

10 preprints

Zero-Shot Multi-Speaker Text-To-Speech with State-of-the-art Neural Speaker Embeddings

We investigate multi-speaker modeling for end-to-end text-to-speech synthesis and study the effects of different types of state-of-the-art neural speaker embeddings on speaker similarity for unseen speakers.
3 days ago
arXiv

Self-Attention for Raw Optical Satellite Time Series Classification

Finally, we look into the self-attention transformer model and visualize attention scores as bipartite graphs in the context of the input time series and a low-dimensional representation of internal hidden states using t-distributed stochastic neighborhood embedding (t-SNE).
3 days ago
arXiv

Stain Style Transfer using Transitive Adversarial Networks

Compared with the state-of-the-art methods, our method yields an improvement of 0.87dB in terms of PSNR, demonstrating the effectiveness of the proposed TAN method in stain style transfer.
4 days ago
arXiv

protein coding

10 preprints

Pwas: proteome-wide association study

We compared PWAS to existing methods, proving its capacity to recover causal protein-coding genes and highlighting new associations with plausible biological mechanism.
5 days ago
bioRxiv

Genetic control of the human brain proteome

We identified 28,211 SNVs that were significantly associated with the abundance of 864 proteins (i.e. pQTLs), and the complete results are searchable at http://brainqtl.org.
2 days ago
bioRxiv

Exploring the overlap between rheumatoid arthritis susceptibility loci and long non-coding RNA annotations

This is especially true for the majority of variants that do not affect protein-coding regions. lncRNA represent a group of molecules that have been shown to be enriched amongst variants associated with RA and other complex diseases, compared to random variants.
5 days ago
bioRxiv

genetic variants

9 preprints

Finding genetic variants in plants without complete genomes

Our results demonstrate the power of performing GWAS before linking sequence reads to specific genomic regions, which allow detection of a wider range of genetic variants responsible for phenotypic variation.
1 day ago
bioRxiv

PheWAS-ME: A web-app for interactive exploration of multimorbidity patterns in PheWAS

The Phenome-wide association study (PheWAS) is a widely used technique for high-throughput evaluation of relationships between a set of genetic variants and a large collection of clinical phenotypes recorded in EHRs.
2 days ago
medRxiv

An integrated platform to systematically identify causal variants and genes for polygenic human traits.

Genome-wide association studies (GWAS) have identified over 150,000 links between common genetic variants and human traits or complex diseases.
2 days ago
bioRxiv

cell cycle

9 preprints

Investigating the Central Dogma of Molecular Biology in the Context of Nuclear Architecture and Cell Cycle

We show that, across the cell cycle, the expression of a CCNA2 gene copy is stochastic and depends neither on its sub-nuclear position - which usually lies close to nuclear lamina - nor on the expression from the other copies.
6 days ago
bioRxiv

Evolution of multiple CDK1 paralogs towards specializations in late cell cycle events in a lineage with fast developing planktonic embryos.

In an intriguing twist on the general rule that it is Cyclin B oscillations on a background of stable CDK1 levels that regulate M-phase MPF activity, it is the CDK1d protein levels that oscillate, rather than Cyclin Ba levels, to drive rapid, early embryonic cell cycles.
2 days ago
bioRxiv

Pan-cancer single cell RNA-seq uncovers recurring programs of cellular heterogeneity

These programs of heterogeneity are associated with diverse biological processes, including cell cycle, senescence, stress and interferon responses, epithelial-to-mesenchymal transition (EMT), and protein maturation and degradation.
5 days ago
bioRxiv

cell types

9 preprints

Fully-automated cell-type identification with specific markers extracted from single-cell transcriptomic data

Using a compendium of 7 scRNA-seq datasets from various human and mouse tissues, we demonstrate how ScType enables unbiased, accurate and fully-automated single-cell type annotation by guaranteeing the specificity of marker genes both across cell clusters and cell types.
5 days ago
bioRxiv

Unifying single-cell annotations based on the Cell Ontology

Here, we present OnClass, an algorithm and accompanying software for automatically classifying cells into cell types represented by a controlled vocabulary derived from the Cell Ontology.
7 days ago
bioRxiv

Pathological modeling of TBEV infection reveals differential innate immune responses in human neurons and astrocytes that correlate with their susceptibility to infection.

Our results thus reveal that cell type-specific innate immunity is likely to contribute to shaping TBEV tropism for human brain cells.
1 day ago
bioRxiv

high resolution

9 preprints

Divide-and-Conquer Adversarial Learning for High-Resolution Image and Video Enhancement

Both quantitative and qualitative results clearly demonstrate that the proposed DACAL achieves the state-of-the-art performance for high-resolution image and video enhancement.
3 days ago
arXiv

High Resolution Photoelectron Spectroscopy of Cryogenically-Cooled NO3ˉ

High-resolution anion photoelectron spectra of cryogenically cooled NO3ˉ anions obtained using slow photoelectron velocity-map imaging are presented and provide new insight into the vibronic structure of the corresponding neutral radical.
5 days ago
chemRxiv

Amino and PEG-Amino Graphene Oxide Grids Enrich and Protect Samples for High-resolution Single Particle Cryo-electron Microscopy

By introducing a PEG spacer, particles are kept away from both the GO surface and the air-water interface, protecting them from potential denaturation.
4 days ago
bioRxiv

extracellular matrix

9 preprints

Three-dimensional Structural Interrelations between Cells, Extracellular Matrix and Mineral in Vertebrate Mineralization

The spatial-temporal relationship between cells, extracellular matrices and mineral deposits is fundamental for understanding mineralization mechanisms in vertebrate tissues.
4 days ago
bioRxiv

Cell based strain stiffening of a non-fibrous matrix as organizing principle for morphogenesis

Here, we identify a mechanism that allows cells to form networks by mechanically reorganizing and stiffening their extracellular matrix, independent of chemical guidance cues.
3 days ago
bioRxiv

Matrix mechanotransduction mediated by thrombospondin-1/integrin/YAP signaling pathway in the remodeling of blood vessels

Rationale: The extracellular matrix (ECM) initiates mechanical cues and transduces intracellular signaling through matrix-cell interactions.
5 days ago
bioRxiv

deep learning

8 preprints

Applying deep learning to teleseismic phase detection and picking: PcP and PKiKP cases

In this study, we detect and pick the PcP and PKiKP phases from a Hinet dataset with 7386 seismograms by applying a deep-learning-based scheme.
6 days ago
arXiv

Test-time augmentation for deep learning-based cell segmentation on microscopy images

Deep learning network architectures have a large number of parameters, thus, in order to reach high accuracy, they require massive amount of annotated data.
4 days ago
bioRxiv

Multi-omics-based pan-cancer prognosis prediction using an ensemble of deep-learning and machine-learning models

Furthermore, models built on closely related cancer types using DeepProg are predictive of the subtypes of some other cancers, demonstrating the utility of DeepProg for transfer learning.
1 day ago
medRxiv

genome sequence

8 preprints

Rice Bean (Vigna umbellata) draft genome sequence: unravelling the late flowering and unpalatability related genomic resources for efficient domestication of this underutilized crop.

As an initiative to compose rice bean (Vigna umbellata) genomic resource, the size of 414 mega-base pairs with an estimate of 31276 highly confidential genes from 15521 scaffolds and functional coverage of 96.08% was sequenced from 30X coverage data from Illumina and PacBio platform.
2 days ago
bioRxiv

Elucidation of the Draft Genome Sequence of Ideonella azotifigens DSMZ21438 A Novel Aerobic Diazotroph of the Betaproteobacteria Isolated from Grass Rhizosphere Soil

Here, we report the draft genome sequence of the type strain of Ideonella azotifigens DSMZ21438T (formally 1a22T = JCM15503T).
5 days ago
Preprints.org

Genome Sequence of Segmented Filamentous Bacteria Present in the Human Intestine

By screening human faecal metagenomic datasets, we identified individuals carrying sequences identical to the new SFB-genome.
5 days ago
bioRxiv

transcription factors

8 preprints

Absolute quantification of transcription factors reveals principles of gene regulation in erythropoiesis

Dynamic cellular processes such as differentiation are driven by changes in the abundances of transcription factors (TFs).
5 days ago
bioRxiv
2 days ago
bioRxiv

Targeting AKT elicits tumor suppressive functions of FOXO transcription factors and GSK3 kinase in Multiple Myeloma

Among the various downstream AKT targets are Forkhead box O (FOXO) transcription factors, and we demonstrate that they are crucial for changes in gene expression upon AKT inhibition.
2 days ago
bioRxiv

follow up

7 preprints

Radiographic and clinical risk factors of total knee arthroplasty in asymptomatic knees; a 15-year follow-up study

Results At follow-up, 40 % had received a TKA in their non-symptomatic knee.
4 days ago
bioRxiv

Whole-Food Plant-Based Lifestyle Program and Decreased Obesity: A 10-Year Follow-up

There were no differences in relative body-composition changes (BMI, body fat percentage and muscle mass index (MMI)) between the three groups.
3 days ago
Preprints.org

Evaluation of a brief intervention to reduce cell phone use in college students

The intervention group agreed or strongly-agreed more than the comparison group on five of the seven areas of cell phone beliefs and behaviors ( p 0.05, item Cohens d = .32 to .47, total d = .50) at one-week following receipt of informational materials.
4 days ago
medRxiv

cancer cells

7 preprints

The kinase inhibitor AT9283 selectively kills colorectal cancer cells with hyperactive NRF2

We identified AT9283, an Aurora kinase inhibitor, for its selectivity towards killing cancer cells with hyperactive NRF2 as a consequence to either genetic or pharmacological activation.
5 days ago
bioRxiv

Cancer Cells Possess Different Isotopic Enrichment

The prior theory and current data are consistent also with a recently observed non-uniform methylation in DNA of cancer cells relative to more uniform methylation in DNA of normal cells.
5 days ago
chemRxiv

Prostate-Derived ETS Factor (PDEF) Regulates Yes Associated Protein 1 (YAP1) in Prostate Cancer Cells: A Potential Cross-Talk between PDEF and Hippo Signaling

In the present studies, we evaluated the effects of PDEF on total and phospho (Ser-127)YAP1 protein(a downstream effector of the Hippo pathway) levels in PC3 cells, a line of castrate resistant prostate cancer.
6 days ago
Preprints.org

electron microscopy

7 preprints

Correlating surface plasmon resonance microscopy of living and fixated cells with electron microscopy allows for investigation of potential preparation artifacts

Due to its unique resolution and the prevalence of instruments, electron microscopy (EM) is used as one of the standard techniques for the analysis of the cell-substrate interface.
2 days ago
bioRxiv

Deep Learning Supersampled Scanning Transmission Electron Microscopy

Building on a history of successful deep learning applications in compressed sensing, we have developed a two-stage multiscale generative adversarial network to supersample scanning transmission electron micrographs with point-scan coverage reduced to 1/16, 1/25, ..., 1/100 px.
3 days ago
arXiv

Amino and PEG-Amino Graphene Oxide Grids Enrich and Protect Samples for High-resolution Single Particle Cryo-electron Microscopy

By introducing a PEG spacer, particles are kept away from both the GO surface and the air-water interface, protecting them from potential denaturation.
4 days ago
bioRxiv

magnetic resonance

7 preprints

Distinguishing between paediatric brain tumour types using multi-parametric magnetic resonance imaging and machine learning: a multi-site study

The imaging and subsequent accurate diagnosis of paediatric brain tumours presents a radiological challenge, with magnetic resonance imaging playing a key role in providing tumour specific imaging information.
5 days ago
arXiv

Context-endcoding for neural network based skull stripping in magnetic resonance imaging

Skull stripping is usually the first step for most brain analysisprocess in magnetic resonance images.
3 days ago
arXiv

Functional MRI connectivity accurately distinguishes cases with psychotic disorders from healthy controls, based on cortical features associated with neurodevelopment

Background: Machine learning (ML) can distinguish cases with psychotic disorder from healthy controls based on magnetic resonance imaging (MRI) data, with reported accuracy in the range 60-100%.
29 hours ago
medRxiv

cell death

7 preprints

Vibrio pore-forming leukocidin activates pyroptotic cell death via the NLRP3 inflammasome

Since PTFs of other pathogens were shown to induce cell death by activating the inflammasome pathway, we hypothesized that VPRH-induced cell death is mediated by direct activation of the inflammasome in mammalian immune host cells.
2 days ago
bioRxiv

A novel method to detect intracellular metabolite alterations in MCF-7 cells by doxorubicin induced cell death

Here, these identified intracellular metabolites corroborate to caspase 3 independent and mitochondria induced apoptotic cell death in MCF-7 cells.
5 days ago
bioRxiv

Mechanotransduction activity facilitates hair cell toxicity caused by the heavy metal cadmium

Disrupting hair cell mechanotransduction genetically or pharmacologically significantly reduces the amount of hair cell death seen in response to cadmium, suggesting a role for mechanotransduction in this cell death process, possibly as a means for cadmium uptake into the cells.
5 days ago
bioRxiv

plasma membrane

7 preprints

Transduction of mechanical cellular oscillation by the plasma-membrane mechanosensitive channel MSL10

Here we show that the plasma membrane mechanosensitive channel MscS-LIKE 10 (MSL10) from the model plant Arabidopsis thaliana responds to pulsed membrane stretching with rapid activation and relaxation kinetics in the range of one second.
2 days ago
bioRxiv

AP-1B facilitates endocytosis during cell migration

Importantly, immuno-electron microscopy (EM) showed AP-1B in clathrin-coated pits and budding vesicles at the plasma membrane during cell migration.
27 hours ago
bioRxiv

Midbody remnant inheritance is regulated by the ESCRT subunit CHMP4C

We demonstrate: (1) that MBRs are physically connected to the plasma membrane, (2) how CHMP4C helps maintain the integrity of the connection, and (3) the functional importance of the connection.
6 days ago
bioRxiv

colorectal cancer

5 preprints

Association Between Blood Circulating Vitamin D and Colorectal Cancer Risk in Asian Countries: A Systematic Review and Dose-Response Meta-analysis

Conclusions: The results of this meta-analysis indicated that blood circulating Vitamin D level is associated with decreased risk of colorectal cancer in Asian countries.
1 day ago
medRxiv

The kinase inhibitor AT9283 selectively kills colorectal cancer cells with hyperactive NRF2

Exploiting the CRISPR/Cas9 technology, we generated colorectal cancer cell lines with hyperactive NRF2, and used them to perform a drug screen.
5 days ago
bioRxiv

Colibactin DNA damage signature indicates causative role in colorectal cancer

A survey of somatic mutations at the colibactin target sites of several thousand cancer genomes revealed significant enrichment of the identified motifs in colorectal cancers.
27 hours ago
bioRxiv

machine learning models

3 preprints

Multi-omics-based pan-cancer prognosis prediction using an ensemble of deep-learning and machine-learning models

We introduce DeepProg, a new computational framework that robustly predicts patient survival subtypes based on multiple types of omic data, using an ensemble of deep-learning and machine-learning models.
1 day ago
medRxiv

Improve Protein Solubility and Activity based on Machine Learning Models

Here, we demonstrate that an optimization methodology based on machine learning prediction model can effectively predict which peptide tags can improve protein solubility quantitatively.
2 days ago
bioRxiv

Machine Learning for Inferring CO2 Fluxes: The New Metaphysics of Neural Nets

We present evaluations of two deep machine learning models for estimating CO2 flux or NEE using station tower data acquired from the DOE Atmospheric Radiation Measurement (ARM), AmeriFlux and Fluxnet2015 station datasets.
2 days ago
EarthArXiv