Identifying representative sequences of protein families using submodular optimization.

Identifying representative sequences for groups of functionally similar proteins and enzymes poses significant computational challenges. In this study, we applied submodular optimization, a method effective in data summarization, to select representative sequences for thioesterase enzyme families. We introduced and validated two algorithms, Greedy and Bidirectional Greedy, using curated protein sequence data from the ThYme (Thioester-active enzYmes) database.

Predicting Magnetic Barriers in Lanthanide Complexes with Electrostatic Potential Charges.

Single-molecule magnets (SMMs) with slow relaxation of magnetization and blocking temperatures above that of liquid nitrogen are essential for practical applications in high-density data storage devices and quantum computers. A rapid and accurate prediction of the effective magnetic relaxation barrier () is needed to accelerate the discovery of high-performance SMMs. Using density functional theory and multireference calculations, we explored correlations between , partial atomic charges, and the anisotropic barrier for a series of sandwich-type lanthanide complexes containing cyclooctatetraene, substituted cyclopentadiene, phospholyl, boratabenzene, or borane ligands.

exhibits necrotrophic behavior when causing soft rot in ripe fruit.

is known for causing soft rot in fruit and vegetables during postharvest. Although it has traditionally been considered a saprophyte, it appears to behave more like a necrotrophic pathogen. In this study, we propose that invades host tissues by actively killing host cells and overcoming the host defense mechanisms, as opposed to growing saprophytically on decaying plant matter.

Pairing a Global Optimization Algorithm with EXAFS to Characterize Lanthanide Structure in Solution.

-average sampling of structures from molecular dynamics (AIMD) simulations can be used to predict theoretical extended X-ray absorption fine structure (EXAFS) signals that closely match experimental spectra. However, AIMD simulations are time-consuming and resource-intensive, particularly for solvated lanthanide ions, which often form multiple nonrigid geometries with high coordination numbers. To accelerate the characterization of lanthanide structures in solution, we employed the Northwest Potential Energy Surface Search Engine (NWPEsSe), an adaptive-learning global optimization algorithm, to efficiently screen first-shell structures.

De novo whole-genome assembly and annotation of Coffea arabica var. Geisha, a high-quality coffee variety from the primary origin of coffee.

Geisha coffee is recognized for its unique aromas and flavors and, accordingly, has achieved the highest prices in the specialty coffee markets. We report the development of a chromosome-level, well-annotated, genome assembly of Coffea arabica var. Geisha.

Advances in grape and pathogen genomics toward durable grapevine disease resistance.

The future sustainability of viticulture depends on the development of grapevine cultivars with genetic resistance to diseases such as powdery mildew, downy mildew, and Pierce's disease. Recent advances in grape and pathogen genomics have dramatically improved our approach to durable disease resistance. The availability of diploid genome references for wild species, combined with the ability to phase resistance haplotypes and conduct genome-wide association and expression analyses, has greatly enhanced our ability to dissect genetic resistance loci.

An Opportunity for Developing Cancer Prevention Leadership in Mexico.

Cancer in Mexico is a major public burden for which rates are expected to increase over time. In settings like Mexico, much potential for reduction through cancer prevention efforts remains unrealized, due in part, to a lack of formal cancer prevention and control training and career opportunities. We trained a cadre of instructors to deliver a pilot cancer prevention education program for oncology professionals and leaders.

Genome analysis of the esca-associated Basidiomycetes Fomitiporia mediterranea, Fomitiporia polymorpha, Inonotus vitis, and Tropicoporus texanus reveals virulence factor repertoires characteristic of white-rot fungi.

Some Basidiomycete fungi are important plant pathogens, and certain species have been associated with the grapevine trunk disease esca. We present the genomes of 4 species associated with esca: Fomitiporia mediterranea, Fomitiporia polymorpha, Tropicoporus texanus, and Inonotus vitis. We generated high-quality phased genome assemblies using long-read sequencing.

Effect of ion to ligand ratio on the aqueous to organic relative solubility of a lanthanide-ligand complex.

In the solvent extraction of rare earth elements, mechanistic aspects remain unclear regarding where and how extractant molecules coordinate metal ions and transport them from the aqueous phase into the organic phase. Molecular dynamics simulations were used to examine how unprotonated di(2-ethylhexyl)phosphoric acid (DEHP) ligands that coordinate the Gd ion can transfer the ion across the water-organic interface. Using the umbrella sampling technique, potential of mean force profiles were constructed to quantify the relative solubility of the Gd ion coordinated to 0-3 DEHP ligands in either water, 1-octanol, or hexane solvents and at the water-organic interfaces.

Chelator-Assisted Precipitation-Based Separation of the Rare Earth Elements Neodymium and Dysprosium from Aqueous Solutions.

The rare earth elements (REEs) are critical resources for many clean energy technologies, but are difficult to obtain in their elementally pure forms because of their nearly identical chemical properties. Here, an analogue of macropa, G-macropa, was synthesized and employed for an aqueous precipitation-based separation of Nd and Dy. G-macropa maintains the same thermodynamic preference for the large REEs as macropa, but shows smaller thermodynamic stability constants.

Multiple deletions of candidate effector genes lead to the breakdown of partial grapevine resistance to downy mildew.

Grapevine downy mildew, caused by the oomycete Plasmopara viticola (P. viticola, Berk. & M.

Molecular characterization of a rare case of high-grade B-cell lymphoma with MYC, BCL2, BCL6, and CCND1 rearrangements.

Quadruple-hit lymphomas are extremely rare non-Hodgkin lymphomas with a reported dismal prognosis in the few reported cases. A "quadruple hit" has been defined by the presence of concurrent MYC, BCL2, BCL6, and CCND1 chromosomal rearrangements. We report a new case of a quadruple hit lymphoma in a 73-year-old Hispanic man who presented with an enlarging left-sided neck mass.

Disseminated Anaplastic Lymphoma Kinase (ALK)-Positive T-cell Lymphoma Involving the Uterus and Cervix: A Case Report.

Primary or secondary non-Hodgkin lymphomas (NHLs) involving the female gynecologic tract are rare. T-cell subtypes are further rare and portend a worse prognosis. We present a case of a 23-year-old female presenting with a cervical mass accompanied by constitutional symptoms and abnormal vaginal bleeding.

Efficacy, safety, and tolerability of adjunctive eslicarbazepine acetate in patients with focal to bilateral tonic-clonic seizures.

Objective: To report the efficacy, safety, and tolerability of adjunctive eslicarbazepine acetate (ESL) treatment in reducing focal to bilateral tonic-clonic seizures (FBTCS).

Methods: Data were pooled from 3 randomized clinical trials (RCTs) of adjunctive ESL in patients with focal seizures. Patients treated with 800 or 1200 mg/day ESL and who experienced ≥ 1 FBTCS during baseline were included.

Identification and Pathogenicity of Species Associated with Young Vine Decline in California.

Grapevine trunk diseases are caused by a broad diversity of fungal taxa that have serious impacts on the worldwide viticulture industry due to significant reductions in vineyards yield and lifespan. Field surveys carried out from 2018 to 2022 in California nurseries and young vineyards revealed a high incidence of . Since species are important pathogens of other perennial crops, the present study aimed to identify and determine the pathogenicity of the species on grapevines.

Time to sustained responder status in patients with focal seizures treated with adjunctive eslicarbazepine acetate.

Rapid and sustained clinical responses are critical in improving long-term outcomes in epilepsy. While a 50 % reduction from baseline in standardized seizure frequency (SSF) is often cited as a measure of clinically meaningful efficacy, sustained response (SR) is an alternative method that allows the assessment of onset and durability of the response. Time to sustained response in SSF of ≥ 50 %, ≥ 75 %, ≥ 90 %, and 100 % was assessed for pooled data from 3 similar randomized clinical trials of adjunctive eslicarbazepine acetate (ESL).

Correction: The solution structures and relative stability constants of lanthanide-EDTA complexes predicted from computation.

Correction for 'The solution structures and relative stability constants of lanthanide-EDTA complexes predicted from computation' by Ravi D. O'Brien , , 2022, , 10263-10271, https://doi.org/10.

Long-term quality of life in patients with focal seizures treated with adjunctive eslicarbazepine acetate.

By controlling seizures, anti-seizure medications can improve health-related quality of life (HRQOL). Data from a post-hoc pooled analysis of adjunctive eslicarbazepine acetate (ESL) was used to describe HRQOL measures, including overall quality of life, seizure worry, emotional well-being, energy/fatigue, cognitive functioning, medication effects, social function, and overall score over a period of up to one year. Patients who completed a double-blind treatment phase (Part 1) of these trials were eligible to enter the open label extension (OLE; Part 2).

First Report of Binucleate Rhizoctonia AG-G Causing Grapevine () Trunk Diseases in California Nurseries.

Grapevine Trunk Diseases (GTD) are caused by a consortium of fungal pathogens that affect the biological functions of the vascular system of mature and young grapevines (Gramaje et al. 2018). We conducted surveys to profile GTD pathogens in California grapevine nurseries and collected 784 cuttings of cvs.

Acyltransferase families that act on thioesters: Sequences, structures, and mechanisms.

Acyltransferases (AT) are enzymes that catalyze the transfer of acyl group to a receptor molecule. This review focuses on ATs that act on thioester-containing substrates. Although many ATs can recognize a wide variety of substrates, sequence similarity analysis allowed us to classify the ATs into fifteen distinct families.