Inference and design of antibody specificity: From experiments to models and back.

Exquisite binding specificity is essential for many protein functions but is difficult to engineer. Many biotechnological or biomedical applications require the discrimination of very similar ligands, which poses the challenge of designing protein sequences with highly specific binding profiles. Experimental methods for generating specific binders rely on in vitro selection, which is limited in terms of library size and control over specificity profiles.

Translational symmetry in convolutions with localized kernels causes an implicit bias toward high frequency adversarial examples.

Adversarial attacks are still a significant challenge for neural networks. Recent efforts have shown that adversarial perturbations typically contain high-frequency features, but the root cause of this phenomenon remains unknown. Inspired by theoretical work on linear convolutional models, we hypothesize that together with , and that this is one of the main causes of .

Involvement of , , and genes in breast cancer and muscle cell development.

Patients with breast cancer show altered expression of genes within the pectoralis major skeletal muscle cells of the breast. Through analyses of The Cancer Genome Atlas (TCGA)-breast cancer (BRCA), we identified three previously uncharacterized putative novel tumor suppressor genes expressed in normal muscle cells, whose expression was downregulated in breast tumors. We found that NEDD4 binding protein 2-like 1 (), pleckstrin homology domain-containing family A member 4 (), and brain-enriched guanylate kinase-associated protein () that are normally highly expressed in breast myoepithelial cells and smooth muscle cells were significantly downregulated in breast tumor tissues of a cohort of 50 patients with this cancer.

Gut microbiota depletion delays somatic peripheral nerve development and impairs neuromuscular junction maturation.

Gut microbiota is responsible for essential functions in human health. Several communication axes between gut microbiota and other organs via neural, endocrine, and immune pathways have been described, and perturbation of gut microbiota composition has been implicated in the onset and progression of an emerging number of diseases. Here, we analyzed peripheral nerves, dorsal root ganglia (DRG), and skeletal muscles of neonatal and young adult mice with the following gut microbiota status: a) germ-free (GF), b) gnotobiotic, selectively colonized with 12 specific gut bacterial strains (Oligo-Mouse-Microbiota, OMM12), or c) natural complex gut microbiota (CGM).

Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc.

Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we present CNAqc, an evolution-inspired method to perform the computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing. CNAqc is validated using single-cell data and simulations, is applied to over 4000 TCGA and PCAWG samples, and is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England.

A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing.

Single-cell RNA and ATAC sequencing technologies enable the examination of gene expression and chromatin accessibility in individual cells, providing insights into cellular phenotypes. In cancer research, it is important to consistently analyze these states within an evolutionary context on genetic clones. Here we present CONGAS+, a Bayesian model to map single-cell RNA and ATAC profiles onto the latent space of copy number clones.

Advances in the Diagnosis and Treatment of Enthesitis-Related Arthritis.

Enthesitis-related arthritis (ERA) represents 5-30% of all cases of juvenile idiopathic arthritis (JIA) and belongs to the spectrum of the disorders included in the group of juvenile spondyloarthritis. In the last decade, there have been considerable advances in the classification, diagnosis, monitoring, and treatment of ERA. New provisional criteria for ERA have been recently proposed by the Paediatric Rheumatology INternational Trials Organisation, as part of a wider revision of the International League of Associations for Rheumatology criteria for JIA.

Tissue memory relies on stem cell priming in distal undamaged areas.

Epithelial cells that participated in wound repair elicit a more efficient response to future injuries, which is believed to be locally restricted. Here we show that cell adaptation resulting from a localized tissue damage has a wide spatial impact at a scale not previously appreciated. We demonstrate that a specific stem cell population, distant from the original injury, originates long-lasting wound memory progenitors residing in their own niche.

Robust deep learning object recognition models rely on low frequency information in natural images.

Machine learning models have difficulty generalizing to data outside of the distribution they were trained on. In particular, vision models are usually vulnerable to adversarial attacks or common corruptions, to which the human visual system is robust. Recent studies have found that regularizing machine learning models to favor brain-like representations can improve model robustness, but it is unclear why.

DNMT3B supports meso-endoderm differentiation from mouse embryonic stem cells.

The correct establishment of DNA methylation patterns during mouse early development is essential for cell fate specification. However, the molecular targets as well as the mechanisms that determine the specificity of the de novo methylation machinery during differentiation are not completely elucidated. Here we show that the DNMT3B-dependent DNA methylation of key developmental regulatory regions at epiblast-like cells (EpiLCs) provides an epigenetic priming that ensures flawless commitment at later stages.

Contribution of Ultrasound in Current Practice for Managing Juvenile Idiopathic Arthritis.

The interest and application of musculoskeletal ultrasound (MSUS) in juvenile idiopathic arthritis (JIA) are increasing. Numerous studies have shown that MSUS is more sensitive than clinical examination for detecting subclinical synovitis. MSUS is a well-accepted tool, easily accessible and non-irradiating.

FOXA1 regulates alternative splicing in prostate cancer.

Dysregulation of alternative splicing in prostate cancer is linked to transcriptional programs activated by AR, ERG, FOXA1, and MYC. Here, we show that FOXA1 functions as the primary orchestrator of alternative splicing dysregulation across 500 primary and metastatic prostate cancer transcriptomes. We demonstrate that FOXA1 binds to the regulatory regions of splicing-related genes, including HNRNPK and SRSF1.

Understanding Robustness and Generalization of Artificial Neural Networks Through Fourier Masks.

Despite the enormous success of artificial neural networks (ANNs) in many disciplines, the characterization of their computations and the origin of key properties such as generalization and robustness remain open questions. Recent literature suggests that robust networks with good generalization properties tend to be biased toward processing low frequencies in images. To explore the frequency bias hypothesis further, we develop an algorithm that allows us to learn highlighting the needed for preserving a trained network's performance.

Machine learning algorithms on eye tracking trajectories to classify patients with spatial neglect.

Background And Objective: Eye-movement trajectories are rich behavioral data, providing a window on how the brain processes information. We address the challenge of characterizing signs of visuo-spatial neglect from saccadic eye trajectories recorded in brain-damaged patients with spatial neglect as well as in healthy controls during a visual search task.

Methods: We establish a standardized pre-processing pipeline adaptable to other task-based eye-tracker measurements.

Shallow Univariate ReLU Networks as Splines: Initialization, Loss Surface, Hessian, and Gradient Flow Dynamics.

Understanding the learning dynamics and inductive bias of neural networks (NNs) is hindered by the opacity of the relationship between NN parameters and the function represented. Partially, this is due to symmetries inherent within the NN parameterization, allowing multiple different parameter settings to result in an identical output function, resulting in both an unclear relationship and redundant degrees of freedom. The NN parameterization is invariant under two symmetries: permutation of the neurons and a continuous family of transformations of the scale of weight and bias parameters.

Hematemesis in Infants: The First Evidence-Based Score to Predict the Need for Timely Endoscopy.

Objectives: Infantile acute upper gastrointestinal bleeding involves a decision for therapeutic intervention that most pediatricians first coming into contact with the patient are, not unreasonably, unable to objectively provide. Therefore, some objective tools of individual risk assessment would seem to be crucial. The principal aim of the present study was to investigate the anamnestic and clinical parameters of infants with hematemesis, together with laboratory and instrumental findings, to create a scoring system that may help identify those infants requiring an appropriate and timely application of upper gastrointestinal (GI) endoscopy.

The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7.

The histone acetyltransferase p300 (also known as KAT3B) is a general transcriptional coactivator that introduces the H3K27ac mark on enhancers triggering their activation and gene transcription. Genome-wide screenings demonstrated that a large fraction of long non-coding RNAs (lncRNAs) plays a role in cellular processes and organ development although the underlying molecular mechanisms remain largely unclear (1,2). We found 122 lncRNAs that interacts directly with p300.

Genome-Wide Analysis of Smad7-Mediated Transcription in Mouse Embryonic Stem Cells.

Smad7 has been identified as a negative regulator of the transforming growth factor TGF-β pathway by direct interaction with the TGF-β type I receptor (TβR-I). Although Smad7 has also been shown to play TGF-β unrelated functions in the cytoplasm and in the nucleus, a comprehensive analysis of its nuclear function has not yet been performed. Here, we show that in ESCs Smad7 is mainly nuclear and acts as a general transcription factor regulating several genes unrelated to the TGF-β pathway.

[Cardiopulmonary exercise testing: an essential tool for a tailored exercise prescription in patients with cardiac disease].

Cardiovascular diseases are the leading cause of death in high-income countries. Exercise prescription is an effective tool for primary and secondary cardiovascular prevention and the cardiovascular benefits of physical activity are well established, ranging from improving the quality of life to reducing mortality. A tailored approach based on patient's personal and clinical characteristics represents a cornerstone for the benefits of exercise prescription.

Risk stratification in cardiogenic shock: a focus on the available evidence.

Cardiogenic shock is a clinical syndrome which is defined as the presence of primary cardiac disorder that results in hypotension together with signs of organ hypoperfusion in the state of normovolaemia or hypervolaemia. It represents a complex life-threatening condition, characterized by a high mortality rate, that requires urgent diagnostic assessment as well as treatment; therefore, it is of paramount important to advocate for a thorough risk stratification. In fact, the early identification of patients that could benefit the most from more aggressive and invasive approaches could facilitate a more efficient resource allocation.