last week in biology

634

new preprints about biology in the last week

bioRxiv

most active server in biology in the last week

gene expression

32 preprints

Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems

Together, this work provides a set of genetic tools that can be used to tune gene expression across various eukaryotic systems.
1 day ago
bioRxiv

Comparison of visceral adipose tissue DNA methylation and gene expression profiles in female adolescents with obesity

Global methylation (n=20) and gene expression (N=30) patterns were profiled via microarray and interrogated for differences between groups by ANCOVA (p
4 days ago
bioRxiv

Prediction of a cell-type specific mouse mesoconnectome using gene expression data

Afterwards, we predicted the strength of axonal projections and their binary form using expression patterns of individual genes and co-expression patterns of spatial gene modules.
4 days ago
bioRxiv

single cell

24 preprints

A Single-Cell Transcriptome Atlas for Zebrafish Development

Our single-cell transcriptome Atlas encompasses transcriptional profiles from 44,102 cells across four days of development using duplicate experiments that confirmed high reproducibility.
3 hours ago
bioRxiv

Expression profiling of the mature C. elegans nervous system by single-cell RNA-Sequencing

We generated single cell transcriptomes for 52,412 neurons that resolve as clusters corresponding to 109 of the canonical 118 neuron classes in the mature hermaphrodite nervous system.
3 days ago
bioRxiv

Time-resolved single-cell transcriptomics uncovers dynamics of cardiac neutrophil diversity in murine myocardial infarction

Conclusion: Altogether, our data provide a time-resolved census of neutrophil diversity and gene expression dynamics in the mouse ischemic heart at the single-cell level, and suggests that temporal neutrophil heterogeneity is in part driven by local transition to a SIGLECFhi state.
3 days ago
bioRxiv

machine learning

22 preprints

Efficient prediction of vitamin B deficiencies via machine-learning using routine blood test results in patients with intense psychiatric episode

Discussion: This study demonstrates that machine-learning can efficiently predict some vitamin deficiencies in patients with active psychiatric symptoms, based on the largest cohort to date with intense psychiatric episode.
6 days ago
medRxiv

Deep Learning and Machine Learning in Hydrological Processes, Climate Change and Earth Systems: A Systematic Review

On the other hand, machine learning methods are already established in the fields, and novel methods with higher performance are emerging through ensemble techniques and hybridization.
5 days ago
Preprints.org

Constrained Multi-Objective Optimization for Automated Machine Learning

Incorporation of multiple objectives and constraints in the model exploration and selection process provides the flexibility needed to satisfy trade-offs necessary in practical machine learning applications.
6 days ago
arXiv

genome wide

18 preprints

Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells

Results: In this study, we performed a genome-wide analysis of transcriptional bursting in mouse embryonic stem cells (mESCs) using single-cell RNA-sequencing.
4 days ago
bioRxiv

A gene-diet interaction-based score predicts response to dietary fat in the Women's Health Initiative

These results lay the foundation for the combination of many genome-wide gene-diet interactions for diet response prediction while highlighting the need for further research and larger samples in order to achieve robust biomarkers for use in personalized nutrition.
2 days ago
medRxiv
6 days ago
bioRxiv

escherichia coli

15 preprints

Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 - 2016) differ in ST distribution, antimicrobial resistance gene and virulence gene content

Background: Knowledge on the molecular epidemiology of Escherichia coli causing E. coli bacteremia (ECB) in the Netherlands is almost exclusively based on extended-spectrum beta-lactamase producing E. coli isolates (ESBL-PEc) that are responsible for about 10% of all ECB episodes.
4 days ago
bioRxiv

Identification of Escherichia coli ClpAP in regulating susceptibility to type VI secretion system-mediated attack by Agrobacterium tumefaciens

In Agrobacterium tumefaciens, T6SS has been shown to kill other bacteria such as Escherichia coli.
5 days ago
bioRxiv

Escherichia coli clonobiome: assessing the strains diversity in feces and urine by deep amplicon sequencing

In order to rapidly assess E. coli clonal diversity, we developed a novel method based on deep sequencing of two loci used for sequence typing, along with an algorithm for analysis of resulting data.
5 days ago
bioRxiv

e coli

14 preprints

A case of mistaken identity: structurally similar ligand inhibits Thymidylate Kinase causing reversible filamentation of E. coli

Here we report that several destabilizing mutations in E. coli Dihydrofolate Reductase (DHFR) enzyme result in pronounced yet reversible filamentation of bacterial cells.
1 hours ago
bioRxiv

Redesigned upstream processing enables a 24 hour workflow from E. coli cells to cell-free protein synthesis

The Escherichia coli cell extract-based platform, being one of the most affordable and versatile CFPS platforms, has been broadly adopted.
6 days ago
bioRxiv

stem cells

13 preprints

Aging induces aberrant state transition kinetics in murine muscle stem cells

Murine muscle stem cells (MuSCs) experience a transition from quiescence to activation that is required for regeneration, but it remains unclear if the transition states and rates of activation are uniform across cells, or how features of this process may change with age.
1 hours ago
bioRxiv

Release of stem cells from quiescence reveals multiple gliogenic domains in the adult brain

Quiescent neural stem cells (NSCs) in the adult ventricular-subventricular zone (V-SVZ) have a regional identity and undergo activation to generate neurons.
3 days ago
bioRxiv

Lysosomal perturbations in dopaminergic neurons derived from induced pluripotent stem cells with PARK2 mutation

In addition, we found perturbed autophagic flux and decreased lysosomal enzyme activity suggesting an impairment of the autophagy-lysosomal pathway in parkin-deficient cells.
6 days ago
bioRxiv

high throughput

13 preprints

New method for high-throughput measurements of viscosity in submicrometer-sized membrane systems

Our approach, which is suitable for high-throughput screening, is based on the simultaneous measurements of absorbance and fluorescence emission of a viscosity-sensitive fluorescent dye DCVJ incorporated into a lipid membrane.
4 days ago
bioRxiv

High-throughput multicolor 3D localization in live cells by depth-encoding imaging flow cytometry

Imaging flow cytometry replaces the canonical point-source detector of flow cytometry with a camera, unveiling subsample details in 2D images while maintaining high-throughput.
5 days ago
bioRxiv

Improved detection of differentially represented DNA barcodes for high-throughput lineage phenomics

Building on the reliable statistical methodology, we illustrate how multidimensional phenotypic profiling (or high-throughput lineage phenomics) enables one to deconvolute phenotypically distinct cell subpopulations within a cancer cell line.
5 days ago
bioRxiv

cell types

12 preprints

Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation

Probe-Seq should enable RNA profiling of specific cell types from any organism.
4 days ago
bioRxiv

A Single-Cell Transcriptome Atlas for Zebrafish Development

The resulting Atlas is a resource of biologists to generate hypotheses for genetic (mutant) or functional analysis, to launch an effort to define the diversity of cell-types during zebrafish organogenesis, and to examine the transcriptional profiles that produce each cell type over developmental time.
3 hours ago
bioRxiv

Prediction of a cell-type specific mouse mesoconnectome using gene expression data

We analysed the ability of gene expression patterns to predict cell-type and laminar specific projection patterns and analyzed the biological context of the most predictive groups of genes.
4 days ago
bioRxiv

transcription factors

11 preprints

Leptin promotes expression of EMT-related transcription factors and invasion in a Src and FAK-dependent pathway in MCF10A mammary epithelial cells

For instance, we tested the expression and subcellular localization of the EMT-related transcription factors Twist and beta-catenin, by western blot and immunofluorescence.
1 day ago
bioRxiv

The transcription factor E2A drives neural differentiation in pluripotent cells

In pluripotent mouse cells, BMP blocks entry into the neural lineage via transcriptional upregulation of Inhibitor of Differentiation (Id) factors.
5 days ago
bioRxiv

Evolution of p38 MAP Kinases in Drosophila

We further find that the p38Kb genomic locus includes conserved binding sites for the AP-1 and lola-PT transcription factors.
4 days ago
bioRxiv

deep learning

11 preprints

Deep Learning and Machine Learning in Hydrological Processes, Climate Change and Earth Systems: A Systematic Review

The paper concludes that deep learning is still in the first stages of development, and the research is still progressing.
5 days ago
Preprints.org

SHIFT: speedy histological-to-immunofluorescent translation of whole slide images enabled by deep learning

We show that deep learning-extracted feature representations of histological images can guide representative sample selection, which improves SHIFT generalizability.
4 days ago
bioRxiv

Deep learning brain conductivity mapping using a patch-based 3D U-net

Results: High quality of reconstructions from networks trained on simulations with and without noise confirms the potential of deep learning for EPT.
7 days ago
arXiv

RNA seq

10 preprints

Comparison of RNA Isolation Methods on RNA-Seq: Implications for Differential Expression and Meta-Analyses

Based on the different chemistries of "classic" phenol extraction of RNA compared to common commercial RNA isolation kits, we hypothesized that specific mRNAs may be preferentially extracted depending upon method, which could masquerade as differential expression in downstream RNA-seq analyses.
7 days ago
bioRxiv

The evaluation of RNA-Seq de novo assembly by PacBio long read sequencing

By comparing the de novo assemblies generated by RNA-Seq short reads with the real-time transcriptome from the same biological sample, we find that Trinity is best at the completeness by generating more assemblies than the alternative assemblers, but less continuous and having more misassemblies; Oases is best at the...
4 days ago
bioRxiv

Interpretable factor models of single-cell RNA-seq via variational autoencoders

Single cell RNA-seq makes possible the investigation of variability in gene expression among cells, and dependence of variation on cell type.
3 days ago
bioRxiv

systematic review

9 preprints

Applications of qualitative grounded theory methodology to investigate hearing loss: Protocol for a qualitative systematic review

The International Prospective Register of Systematic Reviews (http://www crd.york.ac.uk/PROSPERO) holds the registration record of this systematic review.
6 days ago
medRxiv

Prevalence of diabetic foot ulcer and its association with duration of illness and residence in Ethiopia: a systematic review and meta-analysis.

Hence, the objective of this systematic review and meta-analysis was to estimate the national prevalence of diabetic foot ulcer and investigate the association with duration of illness and patient residence among diabetic patients.
6 days ago
medRxiv

From Mind to Picture: A Systematic Review on Children’s and Adolescents’ Understanding of the Link between Artists and Pictures

The aim of this article was to conduct a systematic review on children’s and adolescents’ understanding of the relation between artists and pictures.
4 hours ago
PsyArXiv

cell death

9 preprints

Genetically encoded cell-death indicators (GEDI) to detect an early irreversible commitment to neurodegeneration

GEDI specifically detects an intracellular Ca2+ level that cells achieve early in the cell death process and marks a stage at which cells are irreversibly committed to die.
5 days ago
bioRxiv

The ZIKA Virus Controls Cell Death through the Anti-Apoptotic Bcl-2 Family Proteins

Finally, our work highlights an important role for anti-apoptotic Bcl-2 family protein in the ability of ZIKV to control apoptotic pathways, avoiding premature cell death and thereby promoting virus replication in the host-cell.
5 days ago
Preprints.org

Effect of systemic treatment with Tauroursodeoxycholic Acid (TUDCA) on retinal ganglion cell death following optic nerve crush

One week after ONC, immunofluorescencing cell counts were 100+/-4.5 cells/per field in the PBS-injected control group and 177+/-19 cells/per field in the TUDCA-injected group according to Brn3a labeling (P
6 days ago
bioRxiv

amino acid

9 preprints

Probability of Change in Life: amino acid changes in single nucleotide substitutions

Our calculations allow us to uncover an in-built self-preservation organization of the genetic code that steers away from disruptive changes at the amino acid level, away from start, aromatic, negative charged amino acids and stop codons.
6 days ago
bioRxiv

Reporter system architecture affects measurements of noncanonical amino acid incorporation efficiency and fidelity

The ability to genetically encode noncanonical amino acids (ncAAs) within proteins supports a growing number of applications ranging from fundamental biological studies to enhancing the properties of biological therapeutics.
4 days ago
bioRxiv

Defects in the assembly of ribosomes selected for β-amino acid incorporation

Mutant ribosomes have been developed that improve the incorporation of several non-standard monomers including D-amino acids, dipeptides, and {beta}-amino acids into polypeptide chains.
6 days ago
bioRxiv

learning models

8 preprints

Building Energy Information: Demand and Consumption Prediction with Machine Learning Models for Sustainable and Smart Cities

Through a systematic review and a comprehensive taxonomy, the advances of machine learning are carefully investigated and promising models are introduced.
3 days ago
Preprints.org

Benchmarking machine learning models for the analysis of genetic data using FRESA.CAD Binary Classification Benchmarking

Machine learning models have proven to be useful tools for the analysis of genetic data.
6 days ago
bioRxiv

State of the Art Survey of Deep Learning and Machine Learning Models for Smart Cities and Urban Sustainability

Deep learning (DL) and machine learning (ML) methods have recently contributed to the advancement of models in the various aspects of prediction, planning, and uncertainty analysis of smart cities and urban development.
6 days ago
Preprints.org

meta analysis

8 preprints

Meta-analysis of problematic alcohol use in 435,563 individuals identifies 29 risk variants and yields insights into biology, pleiotropy and causality

In summary, this large PAU meta-analysis identified novel risk loci and revealed genetic relationships with numerous other outcomes.
3 days ago
bioRxiv

Prevalence of diabetic foot ulcer and its association with duration of illness and residence in Ethiopia: a systematic review and meta-analysis.

All statistical analyses were done using STATA version 14 software for Windows, and meta-analysis was carried out using a random-effects method.
6 days ago
medRxiv

What difference do retractions make? An estimate of the epistemic impact of retractions on recent meta-analyses.

However, our results also suggest that retractions due to issues with data, methods or results should be accompanied by a revision of relevant meta-analyses, and by extension a downwards revision of prior scientific beliefs.
6 days ago
bioRxiv

t cells

8 preprints

Coordinated Postnatal Trajectories of T Cells and Microbiota in Preterm and Full- term Newborns

These results together suggest that microbiota and T cell maturation are coordinated during infant development.
4 days ago
bioRxiv

Classifying T cell activity in autofluorescence intensity images with convolutional neural networks

One specific objective is assessing antigen-induced T cell activation because only functionally active T cells are capable of killing the desired targets.
4 days ago
bioRxiv

Predicting antigen-specificity of single T-cells based on TCR CDR3 regions

It has recently become possible to assay T-cell specificity with respect to large sets of antigens as well as T-cell receptor sequence in high-throughput single-cell experiments.
5 days ago
bioRxiv

oxidative stress

8 preprints

Translational Regulation Promotes Oxidative Stress Resistance in the Human Fungal Pathogen Cryptococcus neoformans

Our results illustrate translational suppression as a key determinant of select mRNA decay, gene expression, and subsequent survival in response to oxidative stress.
4 days ago
bioRxiv

A molecular switch for Cdc48 activity and localization during oxidative stress and aging

We have thus identified a unique redox switch in Cdc48, which may provide a clearer picture of the importance of the Cdc48 localization in maintaining a healthy proteome during oxidative stress and chronological aging in yeast.
7 days ago
bioRxiv

Cholinergic-like neurons carrying PSEN1 E280A mutation from familial Alzheimers disease reveal intraneuronal Abeta42 accumulation, hyperphosphorylation of TAU, oxidative stress, apoptosis and Ca2+ flux dysregulation: Therapeutic implications

Furthermore, PSEN1 E280A ChLNs presented oxidative stress (OS) as evidenced by the oxidation of DJ-1Cys106-SH into DJ-1Cys106-SO3 and the detection of DCF-positive cells and apoptosis markers such as activated pro-apoptosis proteins p53, c-JUN, PUMA and CASPASE-3 and the concomitant loss of the mitochondrial membrane...
5 days ago
bioRxiv

neural networks

7 preprints

Muon Identification Using Deep Neural Networks with the Muon Telescope Detector at STAR

The installation of the muon telescope detector opened new possibilities for studying dimuon production at STAR.
4 days ago
arXiv

Incorporating human and learned domain knowledge into training deep neural networks: A differentiable dose volume histogram and adversarial inspired framework for generating Pareto optimal dose distributions in radiation therapy

We propose a novel domain specific loss, which is a differentiable loss function based on the dose volume histogram, and combine it with an adversarial loss for the training of deep neural networks to generate Pareto optimal dose distributions.
3 days ago
arXiv

Differentiable Soft Quantization: Bridging Full-Precision and Low-Bit Neural Networks

Hardware-friendly network quantization (e.g., binary/uniform quantization) can efficiently accelerate the inference and meanwhile reduce memory consumption of the deep neural networks, which is crucial for model deployment on resource-limited devices like mobile phones.
5 days ago
arXiv

machine learning models

7 preprints

Building Energy Information: Demand and Consumption Prediction with Machine Learning Models for Sustainable and Smart Cities

Through a systematic review and a comprehensive taxonomy, the advances of machine learning are carefully investigated and promising models are introduced.
3 days ago
Preprints.org

Benchmarking machine learning models for the analysis of genetic data using FRESA.CAD Binary Classification Benchmarking

Machine learning models have proven to be useful tools for the analysis of genetic data.
6 days ago
bioRxiv

Efficient prediction of vitamin B deficiencies via machine-learning using routine blood test results in patients with intense psychiatric episode

Also, the machine-learning models well generalized to predict the deficiency in the future unseen data; areas under the receiver operating characteristic curves for the validation dataset (i.e. dataset not used for training the models) were 0.716, 0.599, and 0.796, respectively.
6 days ago
medRxiv

antibiotic resistance

7 preprints

A prospective role for the rumen in generating antibiotic resistance

Antibiotics were a revolutionary discovery of the 20th century, but the ability of bacteria to spread the genetic determinants of resistance via horizontal gene transfer (HGT) has quickly endangered their use.
7 days ago
bioRxiv

Exploiting epistasis to perturb the evolution of antibiotic resistance

The identified functions provide new targets for adjuvants tailored to block evolutionary paths to resistance when combined with antibiotics.
4 days ago
bioRxiv

Impact of pediatric influenza vaccination on antibiotic resistance in England and Wales

However, by combining published data sources, we predict that pediatric live attenuated influenza vaccination in England and Wales will not have a major impact upon antibiotic consumption or health burdens of resistance.
7 days ago
medRxiv

cell cycle

7 preprints

Single Cell Analysis Reveals Multiple Requirements for Zinc in the Mammalian Cell Cycle

By monitoring single cells after Zn2+ deprivation, we found that depending on where cells were in the cell cycle, they either went quiescent or entered the cell cycle but stalled in S phase.
5 days ago
bioRxiv

A RAD9-dependent cell cycle arrest in response to unresolved recombination intermediates in Saccharomyces cerevisiae

In contrast, Rmi1 depletion resulted in delayed and incomplete joint molecule resolution, and most cells did not divide. rad9{triangleup} mutation restored cell division in Rmi1-depleted cells, indicating that the DNA damage checkpoint caused this cell cycle arrest.
4 days ago
bioRxiv

CHD8 regulates the balance between proliferation and differentiation of human iPSCs in neural development

Results: We observed that, compared to WT, CHD8 KD: (1) increased the number of iPSC colonies formed, (2) suppressed spontaneous differentiation along the edges of iPSC colonies, (3) increased the proliferation of NPCs, (4) delayed the formation of neural rosettes, (5) delayed neurite outgrowth, (6) decreased the percentage of cells...
6 days ago
bioRxiv

cancer cells

6 preprints

p53-Mediated Oxidative Stress Enhances Indirubin-3′-Monoxime-induced Apoptosis in HCT116 Colon Cancer Cells by Upregulating Death Receptor 5 and TNF-related Apoptosis-inducing Ligand Expression

However, HCT116 p53-/- cells were resistant to I3M-mediated apoptosis, suggesting that I3M could be a promising anti-cancer candidate against TRAIL-resistant p53+/+ cancer cells.
3 days ago
Preprints.org

Hexokinase 2 displacement from mitochondria-associated membranes prompts Ca2+-dependent death of cancer cells

The HK2-targeting peptide causes massive death of chronic lymphocytic leukemia B cells freshly isolated from patients, and an actionable form of the peptide reduces growth of breast and colon cancer cells allografted in mice without noxious effects on healthy tissues.
4 days ago
bioRxiv

NADPH consumption by L-cystine reduction creates a metabolic vulnerability upon glucose deprivation

We searched for glycolytic enzymes whose expression is essential for survival of cancer cells with high xCT expression and identified the glucose transporter GLUT1.
6 days ago
bioRxiv

b cells

6 preprints

KLF4 acts as a tumor suppressor in human B-cells and patients' B-cell leukemias growing in mice

Azacitidine upregulated KLF4 levels and knockout of KLF4 in PDX B-ALL cells reduced Azacitidine-induced cell death, suggesting that KLF4, at least in part, mediates the anti-tumor effects of Azacitidine.
3 days ago
bioRxiv

Activation-induced deaminase is critical for the establishment of DNA methylation patterns prior to the germinal center reaction

DNA methylation alterations in HIGM2 naive B cells are related to premature overstimulation of the B-cell receptor prior to the germinal center reaction.
3 days ago
bioRxiv

Berberine delays onset of collagen induced arthritis through T cell suppression.

BBR-treated mice also experienced a significant reduction of CD19+ B cells in LNs at day 28.
4 days ago
bioRxiv