Evaluation of Reusable Thermal Protection System Materials Using a High-Velocity Oxygen Fuel Torch.

We studied a candidate TPS (thermal protection system) material for reusable re-entry space vehicle applications. The material was based on a high-temperature-resistant material called Cerakwool. A total of six specimens were fabricated with substrate densities of 0.

GPCR-BERT: Interpreting Sequential Design of G Protein-Coupled Receptors Using Protein Language Models.

With the rise of transformers and large language models (LLMs) in chemistry and biology, new avenues for the design and understanding of therapeutics have been opened up to the scientific community. Protein sequences can be modeled as language and can take advantage of recent advances in LLMs, specifically with the abundance of our access to the protein sequence data sets. In this letter, we developed the GPCR-BERT model for understanding the sequential design of G protein-coupled receptors (GPCRs).

PeptideBERT: A Language Model Based on Transformers for Peptide Property Prediction.

Recent advances in language models have enabled the protein modeling community with a powerful tool that uses transformers to represent protein sequences as text. This breakthrough enables a sequence-to-property prediction for peptides without relying on explicit structural data. Inspired by the recent progress in the field of large language models, we present PeptideBERT, a protein language model specifically tailored for predicting essential peptide properties such as hemolysis, solubility, and nonfouling.

Recent advances in utilization of ferredoxins for biosynthesis of valuable compounds.

Ferredoxin (Fd) is a small metalloprotein holding one or two Fe-S clusters in its inner shell. Like many other metalloproteins, Fd is redox active and involved in electron transfer during cellular metabolism. The electrons from reduced Fd are mostly used to regenerate NADPH under physiological conditions.

mutations in hiPSCs inform mechanisms for maldevelopment of the heart, pancreas, and diaphragm.

Damaging variants cause cardiac outflow tract defects, sometimes with pancreatic and diaphragmic malformations. To define molecular mechanisms for these diverse developmental defects, we studied transcriptional and epigenetic responses to loss of function (LoF) and missense variants during cardiomyocyte differentiation of isogenic human induced pluripotent stem cells. We show that GATA6 is a pioneer factor in cardiac development, regulating that activates and that with orchestrates outflow tract formation.

The response of the melanized yeast Exophiala dermatitidis to gamma radiation exposure.

The melanized yeast Exophiala dermatitidis is resistant to many environmental stresses and is used as a model for understanding the diverse roles of melanin in fungi. Here, we describe the extent of resistance of E. dermatitidis to acute γ-radiation exposure and the major mechanisms it uses to recover from this stress.

Misdiagnosis of ameloblastoma in a patient with clear cell odontogenic carcinoma: a case report.

Clear cell odontogenic carcinoma (CCOC), a rare tumor in the head and neck region, displays comparable properties with other tumors clinically and pathologically. In consequence, an incorrect diagnosis may be established. A 51-year-old male patient who was admitted to the Department of Oral and Maxillofacial Surgery at Pusan National University Dental Hospital was initially diagnosed with ameloblastoma via incisional biopsy.

Transcriptomic analysis reveals the relationship of melanization to growth and resistance to gamma radiation in Cryptococcus neoformans.

The pathogenic fungus Cryptococcus neoformans produces melanin within its cell wall for infection and resistance against external stresses such as exposure to UV, temperature fluctuations and reactive oxygen species. It has been reported that melanin may also protect cells from ionizing radiation damage, against which C. neoformans is extremely resistant.

Complete Genome Sequences of Two Bioluminescent Vibrio campbellii Strains Isolated from Biofouling Communities in the Bay of Bengal.

is a pathogen of aquatic animals and has been proposed as a bacterial partner in the formation of bioluminescent milky seas. We present here the complete genome sequences assembled from Illumina and Oxford Nanopore data for two bioluminescent strains (BoB-53 and BoB-90) isolated from biofouled moorings in the Bay of Bengal.

Biofilm community structure and the associated drag penalties of a groomed fouling release ship hull coating.

Grooming is a proactive method to keep a ship's hull free of fouling. This approach uses a frequent and gentle wiping of the hull surface to prevent the recruitment of fouling organisms. A study was designed to compare the community composition and the drag associated with biofilms formed on a groomed and ungroomed fouling release coating.

Corrigendum: Relationship between disease stage and renal function in bisphosphonate-related osteonecrosis of the jaw.

[This corrects the article on p. 16 in vol. 43, PMID: 28280705.

Relationship between disease stage and renal function in bisphosphonate-related osteonecrosis of the jaw.

Objectives: Bisphosphonate is the primary cause of bisphosphonate-related osteonecrosis of the jaw (BRONJ). Bisphosphonates are eliminated from the human body by the kidneys. It is anticipated that bisphosphonate levels in the body will increase if the kidney is in a weak state or if there is systemic disease that affects kidney function.

Large-scale analysis of branchpoint usage across species and cell lines.

The coding sequence of each human pre-mRNA is interrupted, on average, by 11 introns that must be spliced out for proper gene expression. Each intron contains three obligate signals: a 5' splice site, a branch site, and a 3' splice site. Splice site usage has been mapped exhaustively across different species, cell types, and cellular states.

Effect of La2O3 addition on interface chemistry between 4YSZ top layer and Ni based alloy bond coat in thermal barrier coating by EB PVD.

The effect of a 5 mol% La2O3 addition on the forming behavior and compositional variation at interface between a 4 mol% Yttria (Y2O3) stabilized ZrO2 (4YSZ) top coat and bond coat (NiCrAlY) as a thermal barrier coating (TBC) has been investigated. Top coats were deposited by electron beam physical vapor deposition (EB PVD) onto a super alloy (Ni-Cr-Co-Al) substrate without pre-oxidation of the bond coat. Top coats are found to consist of dense columnar grains with a thin interdiffusion layer between metallic bond coats.

Complete Genome Sequence of the Bioluminescent Marine Bacterium Vibrio harveyi ATCC 33843 (392 [MAV]).

Vibrio harveyi is a Gram-negative marine γ-proteobacterium that is known to be a formidable pathogen of aquatic animals and is a model organism for the study of bacterial bioluminescence and quorum sensing. In this report, we describe the complete genome sequence of the most studied strain of this species: V. harveyi ATCC 33843 (392 [MAV]).

Large area and depth-profiling dislocation imaging and strain analysis in Si/SiGe/Si heterostructures.

We demonstrate the combined use of large area depth-profiling dislocation imaging and quantitative composition and strain measurement for a strained Si/SiGe/Si sample based on nondestructive techniques of electron beam-induced current (EBIC) and X-ray diffraction reciprocal space mapping (XRD RSM). Depth and improved spatial resolution is achieved for dislocation imaging in EBIC by using different electron beam energies at a low temperature of ~7 K. Images recorded clearly show dislocations distributed in three regions of the sample: deep dislocation networks concentrated in the "strained" SiGe region, shallow misfit dislocations at the top Si/SiGe interface, and threading dislocations connecting the two regions.

Binding to the lipid monolayer induces conformational transition in Aβ monomer.

Using implicit solvent atomistic model and replica exchange molecular dynamics, we study binding of Aβ monomer to zwitterionic dimyristoylphosphatidylcholine (DMPC) lipid monolayer. Our results suggest that Aβ binding to the monolayer is governed primarily by positively charged and aromatic amino acids. Lysine residues tend to interact with surface choline and phosphorous lipid groups, whereas aromatic amino acids penetrate deeper into the monolayer, reaching its hydrophobic core.

Explicit solvent molecular dynamics simulations of Aβ peptide interacting with ibuprofen ligands.

Using all-atom explicit water model and replica exchange molecular dynamics, we study the interactions between Aβ monomer and nonsteroidal anti-inflammatory drug ibuprofen, which is known to reduce the risk of Alzheimer's disease. Ibuprofen binding to Aβ is largely governed by hydrophobic effect, and its binding site in Aβ peptide is entirely composed of hydrophobic amino acids. Electrostatic interactions between negatively charged ibuprofen ligands and positively charged side chains make a relatively small contribution to binding.

Changes in sensitization rate to weed allergens in children with increased weeds pollen counts in Seoul metropolitan area.

The prevalence of allergic diseases in children has increased for several decades. We evaluated the correlation between pollen count of weeds and their sensitization rate in Seoul, 1997-2009. Airborne particles carrying allergens were collected daily from 3 stations around Seoul.

The revised edition of korean calendar for allergenic pollens.

The old calendar of pollens did not reflect current pollen distribution and concentrations that can be influenced by changes of weather and environment of each region in South Korea. A new pollen calendar of allergenic pollens was made based on the data on pollen concentrations obtained in eight regions nationwide between 1997 and 2009. The distribution of pollen was assessed every day at 8 areas (Seoul, Guri, Busan, Daegu, Jeonju, Kwangju, Kangneung, and Jeju) for 12 years between July 1, 1997 and June 30, 2009.

Does amino acid sequence determine the properties of Aβ dimer?

The effect of random reshuffling of amino acids on the properties of dimers formed by Aβ peptides is studied using replica exchange molecular dynamics and united atom implicit solvent model. We show that thermodynamics of dimer assembly and the dimer globule-like state are not affected by sequence permutation. Furthermore, sequence reshuffling does not change the distributions of non-local interactions and, to a large extent, amino acids in the dimer volume.

Naproxen interferes with the assembly of Aβ oligomers implicated in Alzheimer's disease.

Experimental and epidemiological studies have shown that the nonsteroidal antiinflammatory drug naproxen may be useful in the treatment of Alzheimer's disease. To investigate the interactions of naproxen with Aβ dimers, which are the smallest cytotoxic aggregated Aβ peptide species, we use united atom implicit solvent model and exhaustive replica exchange molecular dynamics. We show that naproxen ligands bind to Aβ dimer and penetrate its volume interfering with the interpeptide interactions.

The effect of Er:YAG laser irradiation on the surface microstructure and roughness of hydroxyapatite-coated implant.

Purpose: The present study was performed to evaluate the effect of erbium:yttrium-aluminium-garnet (Er:YAG) laser irradiation on the change of hydroxyapatite (HA)-coated implant surface microstructure according to the laser energy and the application time.

Methods: The implant surface was irradiated by Er:YAG laser under combination condition using the laser energy of 100 mJ/pulse, 140 mJ/pulse and 180 mJ/pulse and application time of 1 minute, 1.5 minutes and 2 minutes.

Mapping conformational ensembles of aβ oligomers in molecular dynamics simulations.

Although the oligomers formed by Aβ peptides appear to be the primary cytotoxic species in Alzheimer's disease, detailed information about their structures appears to be lacking. In this article, we use exhaustive replica exchange molecular dynamics and an implicit solvent united-atom model to study the structural properties of Aβ monomers, dimers, and tetramers. Our analysis suggests that the conformational ensembles of Aβ dimers and tetramers are very similar, but sharply distinct from those sampled by the monomers.

Globular state in the oligomers formed by Abeta peptides.

Replica exchange molecular dynamics and implicit solvent model are used to study two oligomeric species of Abeta peptides, dimer and tetramer, which are typically observed in in vitro experiments. Based on the analysis of free energy landscapes, density distributions, and chain flexibility, we propose that the oligomer formation is a continuous transition occurring without metastable states. The density distribution computations suggest that Abeta oligomer consists of two volume regions-the core with fairly flat density profile and the surface layer with rapidly decreasing density.