Pore Network Modeling of Intraparticle Transport Phenomena Accompanied by Chemical Reactions.

In this work, a 3D pore network model (PNM) is introduced for modeling reaction-diffusion phenomena, with and without coupled heat transfer, in a spherical porous catalyst particle. The particle geometry is generated by packing thousands of microspheres inside a large sphere to represent the 3D geometry, porosity, and tortuosity of a spherical catalyst particle. A pore-network representation is extracted from this geometry, and a PNM for diffusion-reaction and heat conduction is constructed.

Functional profiling of CHAP domain-containing peptidoglycan hydrolases of Staphylococcus aureus USA300 uncovers potential targets for anti-staphylococcal therapies.

The bacterial pathogen Staphylococcus aureus employs a thick cell wall for protection against physical and chemical insults. This wall requires continuous maintenance to ensure strength and barrier integrity, but also to permit bacterial growth and division. The main cell wall component is peptidoglycan.

CFD-DEM Fluidized Bed Drying Study Using a Coarse-Graining Technique.

Fluidized beds are commonly applied to industrial drying applications. Modeling using the computational fluid dynamics-discrete element method (CFD-DEM) can be employed to increase the fundamental understanding of solids drying. A large drawback of CFD-DEM is the computational requirements, leading to a limitation regarding the system size.

Modeling the Drying Process of Porous Catalysts: Impact of the Pore Size Distribution.

The distribution of catalytically active species in heterogeneous porous catalysts strongly influences their performance and durability in industrial reactors. A drying model for investigating this redistribution was developed and implemented using the finite volume method. This model embeds an analytical approach regarding the permeability and capillary pressure from arbitrary pore size distributions.

CFD-DEM Evaluation of the Clustering Behavior in a Riser-the Effect of the Drag Force Model.

Riser reactors are frequently applied in catalytic processes involving rapid catalyst deactivation. Typically heterogeneous flow structures prevail because of the clustering of particles, which impacts the quality of the gas-solid contact. This phenomenon results as a competition between fluid-particle interaction (i.

Mutation order in acute myeloid leukemia identifies uncommon patterns of evolution and illuminates phenotypic heterogeneity.

Acute myeloid leukemia (AML) has a poor prognosis and a heterogeneous mutation landscape. Although common mutations are well-studied, little research has characterized how the sequence of mutations relates to clinical features. Using published, single-cell DNA sequencing data from three institutions, we compared clonal evolution patterns in AML to patient characteristics, disease phenotype, and outcomes.

Effect of a tunnel barrier on time delay statistics.

We develop a semiclassical approach for the statistics of the time delay in quantum chaotic systems in the presence of a tunnel barrier, for broken time-reversal symmetry. Results are obtained as asymptotic series in powers of the reflectivity of the barrier, with coefficients that are rational functions of the channel number. Exact expressions, valid for arbitrary reflectivity and channel number, are conjectured and numerically verified for specific families of statistical moments.

COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data.

Reconstructing the history of somatic DNA alterations can help understand the evolution of a tumor and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, most existing phylogenetic methods for scDNAseq data are designed either for single nucleotide variants (SNVs) or for large copy number alterations (CNAs), or are not applicable to targeted sequencing.

Host-device interactions: exposure of lung epithelial cells and fibroblasts to nickel, titanium, or nitinol affect proliferation, reactive oxygen species production, and cellular signaling.

Endoscopic implantation of medical devices for the treatment of lung diseases, including airway stents, unidirectional valves and coils, is readily used to treat central airway disease and emphysema. However, granulation and fibrotic tissue formation impairs treatment effectiveness. To date little is known about the interaction between implanted devices, often made from metals, such as nickel, titanium or nitinol, and cells in the airways.

Sexual abuse and psychotic phenomena: a directed acyclic graph analysis of affective symptoms using English national psychiatric survey data.

Background: Sexual abuse and bullying are associated with poor mental health in adulthood. We previously established a clear relationship between bullying and symptoms of psychosis. Similarly, we would expect sexual abuse to be linked to the emergence of psychotic symptoms, through effects on negative affect.

Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees.

Cancer progression is an evolutionary process shaped by both deterministic and stochastic forces. Multi-region and single-cell sequencing of tumors enable high-resolution reconstruction of the mutational history of each tumor and highlight the extensive diversity across tumors and patients. Resolving the interactions among mutations and recovering recurrent evolutionary processes may offer greater opportunities for successful therapeutic strategies.

What Do You Do When You Can Do No More? Limited Resources, Unimaginable Environments, Personal Danger: What Have Previous Disasters Taught Us About Moral and Ethical Challenges?

Historically, natural and manmade disasters create many victims and impose pressures on health-care infrastructure and staff; potentially hampering the provision of patient care and overloading clinician capacity. Throughout the course of history, clinicians have performed heroics to work well above their required duty, despite limitations, even putting their own health and safety at risk. In times when clinicians needed to either physically abandon patients or consider abandoning active treatment, we have seen extreme hesitancy to do so, fearing that they may be giving up too soon, that undue harm may come to patients, or even feeling unsure of legal or moral burdens that may ensue.

The chaperone DNAJB6 surveils FG-nucleoporins and is required for interphase nuclear pore complex biogenesis.

Biogenesis of nuclear pore complexes (NPCs) includes the formation of the permeability barrier composed of phenylalanine-glycine-rich nucleoporins (FG-Nups) that regulate the selective passage of biomolecules across the nuclear envelope. The FG-Nups are intrinsically disordered and prone to liquid-liquid phase separation and aggregation when isolated. How FG-Nups are protected from making inappropriate interactions during NPC biogenesis is not fully understood.

Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model.

Comprehensive molecular characterization of cancer subtypes is essential for predicting clinical outcomes and searching for personalized treatments. We present bnClustOmics, a statistical model and computational tool for multi-omics unsupervised clustering, which serves a dual purpose: Clustering patient samples based on a Bayesian network mixture model and learning the networks of omics variables representing these clusters. The discovered networks encode interactions among all omics variables and provide a molecular characterization of each patient subgroup.

Loss of hepatic SMLR1 causes hepatosteatosis and protects against atherosclerosis due to decreased hepatic VLDL secretion.

Background And Aims: The assembly and secretion of VLDL from the liver, a pathway that affects hepatic and plasma lipids, remains incompletely understood. We set out to identify players in the VLDL biogenesis pathway by identifying genes that are co-expressed with the MTTP gene that encodes for microsomal triglyceride transfer protein, key to the lipidation of apolipoprotein B, the core protein of VLDL. Using human and murine transcriptomic data sets, we identified small leucine-rich protein 1 ( SMLR1 ), encoding for small leucine-rich protein 1, a protein of unknown function that is exclusively expressed in liver and small intestine.

Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence.

Motivation: Tumours evolve as heterogeneous populations of cells, which may be distinguished by different genomic aberrations. The resulting intra-tumour heterogeneity plays an important role in cancer patient relapse and treatment failure, so that obtaining a clear understanding of each patient's tumour composition and evolutionary history is key for personalized therapies. Single-cell sequencing (SCS) now provides the possibility to resolve tumour heterogeneity at the highest resolution of individual tumour cells, but brings with it challenges related to the particular noise profiles of the sequencing protocols as well as the complexity of the underlying evolutionary process.

Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks.

Dynamic Bayesian networks (DBNs) can be used for the discovery of gene regulatory networks (GRNs) from time series gene expression data. Here, we suggest a strategy for learning DBNs from gene expression data by employing a Bayesian approach that is scalable to large networks and is targeted at learning models with high predictive accuracy. Our framework can be used to learn DBNs for multiple groups of samples and highlight differences and similarities in their GRNs.