rbm 10

We present here an approach to protein design that combines (i) scarce functional information such as experimental data (ii) evolutionary information learned from a natural sequence variants and (iii) physics-grounded modeling. Using a Restricted Boltzmann Machine (RBM), we learn a sequence model of a protein family. We use semi-supervision to leverage available functional information during the RBM training. We then propose a strategy to explore the protein representation space that can be informed by external models such as an empirical force-field method (FoldX)...

This study investigated the effect of anti-autotaxin (ATX) aptamers on the development of proliferative vitreoretinopathy (PVR) in both in vivo and in vitro PVR swine models. For the in vitro study, primary retinal pigment epithelial (RPE) cells were obtained from porcine eyes and cultured for cell proliferation and migration assays. For the in vivo study, a swine PVR model was established by inducing retinal detachment and injecting cultured RPE cells (2.0 × 106 ). Concurrently, 1 week after RPE cell injection, the anti-ATX aptamer, RBM-006 (10 mg/mL, 0...

The COVID pandemic fueled by emerging SARS-CoV-2 new variants of concern remains a major global health concern, and the constantly emerging mutations present challenges to current therapeutics. The spike glycoprotein is not only essential for the initial viral entry, but is also responsible for the transmission of SARS-CoV-2 components via syncytia formation. Spike-mediated cell-cell transmission is strongly resistant to extracellular therapeutic and convalescent antibodies via an unknown mechanism. Here, we describe the antibody-mediated spike activation and syncytia formation on cells displaying the viral spike...

Applications of generative models for genomic data have gained significant momentum in the past few years, with scopes ranging from data characterization to generation of genomic segments and functional sequences. In our previous study, we demonstrated that generative adversarial networks (GANs) and restricted Boltzmann machines (RBMs) can be used to create novel high-quality artificial genomes (AGs) which can preserve the complex characteristics of real genomes such as population structure, linkage disequilibrium and selection signals...

With hundreds of coronaviruses (CoVs) identified in bats that can infect humans, it is essential to understand how CoVs that affected the human population have evolved. Seven known coronaviruses have infected humans, of which three CoVs caused severe disease with high mortality rates: SARS-CoV emerged in 2002, MERS-CoV in 2012, and SARS-CoV-2 in 2019. SARS-CoV and SARS-CoV-2 belong to the same family, follow the same receptor pathway, and use their receptor binding domain (RBD) of spike protein to bind to the ACE2 receptor on the human epithelial cell surface...

The vaccination campaign against SARS-CoV-2 relies on the world-wide availability of effective vaccines, with a potential need of 20 billion vaccine doses to fully vaccinate the world population. To reach this goal, the manufacturing and logistic processes should be affordable to all countries, irrespective of economical and climatic conditions. Outer membrane vesicles (OMVs) are bacterial-derived vesicles that can be engineered to incorporate heterologous antigens. Given the inherent adjuvanticity, such modified OMVs can be used as vaccines to induce potent immune responses against the associated proteins...

The highly glycosylated S protein plays a vital role in host cell invasion, making it the principal target for vaccine development. Differences in mutations observed on the spike (S) protein of SARS-CoV-2 variants may result in distinct glycosylation patterns, thus influencing immunological evasion, infectivity, and transmissibility. The glycans can mask key epitopes on the S1 protein and alter its structural conformation, allowing the virus to escape the immune system. Therefore, we comprehensively characterize O -glycosylation in eleven variants of SARS-CoV-2 S1 subunits to understand the differences observed in the biology of the variants...

Mitochondrial dysfunction is thought to be a key component of neurodevelopmental disorders such as autism, intellectual disability, and ADHD. However, little is known about the molecular mechanisms that protect against mitochondrial dysfunction during neurodevelopment. Here, we address this question through the investigation of rbm-26 , the C. elegans ortholog of the RBM27 autism candidate gene, which encodes an RNA-binding protein whose role in neurons is unknown. We report that RBM-26 (RBM26/27) protects against neurodevelopmental defects by negatively regulating expression of the MALSU-1 mitoribosomal assembly factor...

We propose a high-order stochastic-statistical moment closure model for efficient ensemble prediction of leading-order statistical moments and probability density functions in multiscale complex turbulent systems. The statistical moment equations are closed by a precise calibration of the high-order feedbacks using ensemble solutions of the consistent stochastic equations, suitable for modeling complex phenomena including non-Gaussian statistics and extreme events. To address challenges associated with closely coupled spatiotemporal scales in turbulent states and expensive large ensemble simulation for high-dimensional systems, we introduce efficient computational strategies using the random batch method (RBM)...

Considering that cancer is resulting from the comutation of several essential genes of individual patients, researchers have begun to focus on identifying personalized edge-network biomarkers (PEBs) using personalized edge-network analysis for clinical practice. However, most of existing methods ignored the optimization of PEBs when multimodal biomarkers exist in multi-purpose early disease prediction (MPEDP). To solve this problem, this study proposes a novel model (MMPDENB-RBM) that combines personalized dynamic edge-network biomarkers (PDENB) theory, multimodal optimization strategy and latent space search scheme to identify biomarkers with different configurations of PDENB modules (i...

OBJECTIVES: We evaluated autoencoders as a feature engineering and pretraining technique to improve major depressive disorder (MDD) prognostic risk prediction. Autoencoders can represent temporal feature relationships not identified by aggregate features. The predictive performance of autoencoders of multiple sequential structures was evaluated as feature engineering and pretraining strategies on an array of prediction tasks and compared to a restricted Boltzmann machine (RBM) and random forests as a benchmark...

Amidst the ongoing higher education reforms in China, the escalated investments in colleges and universities underscore the need for an effective assessment of their performance to ensure sustainable development. However, traditional evaluation methods have proven time-consuming and labor-intensive. In response, a novel approach called CS-RBM (Crow Search Restricted Boltzmann Machine) prediction algorithm has been proposed for the educational management of these institutions. By integrating the CS algorithm and an enhanced RBM algorithm, this method facilitates the scoring of project performance indicators, bolstered by insights from user evaluation form reports...

BACKGROUND: Airway remodeling is a prominent feature of asthma, including increased airway smooth muscle (ASM) mass and altered extracellular matrix (ECM) composition. Bronchial thermoplasty (BT), a bronchoscopic treatment for severe asthma, targets this airway remodeling. OBJECTIVE: To investigate the effect of BT on ECM composition and its association with clinical outcomes. METHODS: This is a sub-study of the TASMA trial. Thirty severe asthma patients were BT treated, of which 13 patients prior to BT were treated by six months of standard therapy (control group)...

BACKGROUND: Over the last decade, there has been an increasing interest in risk-based monitoring (RBM) in clinical trials, resulting in a number of guidelines from regulators and its inclusion in ICH GCP. However, there is a lack of detail on how to approach RBM from a practical perspective, and insufficient understanding of best practice. PURPOSE: We present a method for clinical trials units to track their metrics within clinical trials using descriptive statistics and visualisations...

PURPOSE/OBJECTIVE(S): We commissioned the Brainlab Monte Carlo Dose Calculation Algorithm for VMAT SRS planning and verified it by measurements and comparisons with two other algorithms: Pencil beam and Eclipse Acuros. The end-to-end verification and dosimetric comparative study results are reported in this abstract. MATERIALS/METHODS: Brainlab Elements Cranial SRS (v3.0) provides single lesion planning using VMAT optimization, thus allowing dose modulation with MLC leaf positioning, dose rate, and gantry speed...

RATIONALE: In the healthy lung, the pseudostratified conducting airway epithelium is anchored to the reticular basement membrane (RBM) via hemidesmosome junction complexes formed between basal cells and the extracellular matrix (ECM). The RBM within the healthy lung is composed of the ECM proteins laminin and collagen-IV. In patients with asthma, the RBM is remodeled with collagen-I, -III and fibronectin deposition. The goal of this study was to assess the effect of RBM ECM proteins on basal airway epithelial cell attachment, spreading and barrier formation using real-time electrical cell-substrate impedance sensing (ECIS)...

Predictive models play a crucial role in RBMs to analyze performance indicator results to manage unexpected events and make timely decisions to resolve them. Their use in Mexico is deficient, and monitoring and evaluation are among the weakest pillars of the model. In response to these needs, the aim of this study was to perform a comparative analysis of three predictive models to analyze 10 medical performance indicators and cancer data related to children with cancer. To accomplish these purposes, a comparative and retrospective study with nonprobabilistic convenience sampling was conducted...

Melatonin is an endogenous indoleamine that plays a significant role in various physiological processes, including the sleep-wake cycle, anxiety, immunity, and circadian rhythms. However, it is important to clarify that melatonin does not directly control circadian rhythms. Circadian rhythms are primarily synchronized by light, which acts on the suprachiasmatic nucleus (SCN) and subsequently regulates melatonin production. This light-mediated synchronization of circadian rhythms is essential for maintaining the alignment of the body with the light-dark cycle...

As an active substance isolated from the root of Morinda officinalis How., rubiadin-1-methyl ether (RBM), can improve osteoporosis due to its inhibition on osteoclastogenesis. Autophagy plays a key role in osteoclastogenesis. Our research aims to explore the relationship between RBM, autophagy, and osteoclastogenesis. Our results showed that RBM not only inhibited the differentiation level of osteoclasts and the proliferation ability of osteoclast precursors (OCPs), but also repressed the autophagic activity in OCPs (LC3 transformation and the number of autophagosomes observed by transmission electron microscopy)...

Helicity-dependent Raman spectra of an isolated, chiral, single-wall carbon nanotube (SWNT) are reported using circularly polarized light. A polar plot of polarized Raman intensity for the radial breathing mode (RBM), which is excited by left-handed or right-handed circularly polarized light, shows asymmetric angle dependence relative to the nanotube axis direction, which reflects the axial chirality of a SWNT. The asymmetry in the polar plot of the RBM can be analyzed by a complex Raman tensor. The complex phase of each component of the Raman tensor has a maximum at chiral angle θ = 15° of a SWNT which is between two achiral SWNTs, that is, zigzag (θ = 0°) and armchair (θ = 30°) SWNTs...