Galaxy as a gateway to bioinformatics: Multi-Interface Galaxy Hands-on Training Suite (MIGHTS) for scRNA-seq.

Background: Bioinformatics is fundamental to biomedical sciences, but its mastery presents a steep learning curve for bench biologists and clinicians. Learning to code while analyzing data is difficult. The curve may be flattened by separating these two aspects and providing intermediate steps for budding bioinformaticians.

Differences in activity and stability drive transposable element variation in tropical and temperate maize.

Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, to de novo annotate TEs in a pangenome context. We then generated a unified TE annotation for a maize pangenome derived from 26 reference-quality genomes, which reveals an excess of 35.

Thrombotic complications after radiofrequency and cyanoacrylate endovenous ablation: Outcomes of a multicenter real-world experience.

Objective: Chronic venous insufficiency (CVI) affects >40% of the U.S. population; thus, intervention for symptomatic venous disease comprises a large portion of many vascular practices.

Using Redox-Active Ligands to Generate Actinide Ligand Radical Species.

Using a redox-active dioxophenoxazine ligand, DOPO (DOPO = 2,4,6,8-tetra--butyl-1-oxo-1-phenoxazine-9-olate), a family of actinide (U, Th, Np, and Pu) and Hf tris(ligand) coordination compounds was synthesized. The full characterization of these species using H NMR spectroscopy, electronic absorption spectroscopy, SQUID magnetometry, and X-ray crystallography showed that these compounds are analogous and exist in the form M(DOPO)(DOPO), where two ligands are of the oxidized quinone form (DOPO) and the third is of the reduced semiquinone (DOPO) form. The electronic structures of these complexes were further investigated using CASSCF calculations, which revealed electronic structures consistent with metals in the +4 formal oxidation state and one unpaired electron localized on one ligand in each complex.

Looking the same, but remembering differently: Preserved eye-movement synchrony with age during movie watching.

Naturalistic stimuli (e.g., movies) provide the opportunity to study lifelike experiences in the lab.

Origin of Bond Elongation in a Uranium(IV) -Bis(imido) Complex.

The activation of U-N multiple bonds in an imido analogue of the uranyl ion is accomplished by using a system that is very electron-rich with sterically encumbering ligands. Treating the uranium(VI) -bis(imido) UI(NDIPP)(THF) (DIPP = 2,6-diisopropylphenyl and THF = tetrahydrofuran) with -butyl(dimethylsilyl)amide (NTSA) results in a reduction and rearrangement to form the uranium(IV) -bis(imido) [U(NDIPP)(NTSA)]K (). Compound features long U-N bonds, pointing toward substantial activation of the N═U═N unit, as determined by X-ray crystallography and H NMR, IR, and electronic absorption spectroscopies.

Conversion of Trivalent Uranium Anilido to Tetravalent Uranium Imido Species via Oxidative Deprotonation.

Two uranium(III) anilido complexes were synthesized, Tp*U(NH-CH--terpyridine) () and Tp*U(NH-CH--CH) (), where Tp* = hydrotris(3,5-dimethylpyrazolyl)borate, by protonation of Tp*UBn (; Bn = benzyl) with 4-[2,6-di(pyridin-2-yl)pyridin-4-yl]benzenamine or -toluidine, respectively. Conversion to the respective uranium(IV) imido species was possible by oxidation and deprotonation, forming Tp*U(N-CH--terpyridine) () and Tp*U(N-CH--CH) (). These compounds were characterized by multinuclear NMR spectroscopy, IR spectroscopy, electronic absorption spectroscopy, and X-ray crystallography.

A centrality based multi-objective approach to disease gene association.

Disease Gene Association finds genes that are involved in the presentation of a given genetic disease. We present a hybrid approach which implements a multi-objective genetic algorithm, where input consists of centrality measures based on various relational biological evidence types merged into a complex network. Multiple objective settings and parameters are studied including the development of a new exchange methodology, safe dealer-based crossover.

To lead or to herd: optimal strategies for 3D collective migration of cell clusters.

Cells migrating in clusters play a significant role in a number of biological processes such as embryogenesis, wound healing, and tumor metastasis during cancer progression. A variety of environmental and biochemical factors can influence the collective migration of cells with differing degrees of cell autonomy and inter-cellular coupling strength. For example, weakly coupled cells can move collectively under the influence of contact guidance from neighboring cells or the environment.

Chronic restraint stress during withdrawal increases vulnerability to drug priming-induced cocaine seeking via a dopamine D1-like receptor-mediated mechanism.

Background: A major obstacle in the treatment of individuals with cocaine addiction is their high propensity for relapse. Although the clinical scenario of acute stress-induced relapse has been well studied in animal models, few pre-clinical studies have investigated the role of chronic stress in relapse or the interaction between chronic stress and other relapse triggers.

Methods: We tested the effect of chronic restraint stress on cocaine seeking in rats using both extinction- and abstinence-based animal relapse models.

Expanding the Library of Uranyl Amide Derivatives: New Complexes Featuring the tert-Butyldimethylsilylamide Ligand.

New uranyl derivatives featuring the amide ligand, -N(SiHMe) Bu, were synthesized and characterized by X-ray crystallography, multinuclear NMR spectroscopy, and absorption spectroscopies. Steric properties of these complexes were also quantified using the computational program Solid-G. The increased basicity of the free ligand -N(SiHMe) Bu was demonstrated by direct comparison to -N(SiMe), a popular supporting ligand for uranyl.

The ability of massive osteochondral allografts from the medial tibial plateau to reproduce normal joint contact pressures after glenoid resurfacing: the effect of computed tomography matching.

Background: Current techniques for resurfacing of the glenoid in the treatment of arthritis are unpredictable. Computed tomography (CT) studies have demonstrated that the medial tibial plateau has close similarity to the glenoid. The purpose of this study was to assess contact pressures of transplanted massive tibial osteochondral allografts to resurface the glenoid without and with CT matching.

Dissecting the dimerization motif of Enterococcus hirae's Zn(II)CopY.

The regulation of the copper homeostasis pathway in Enterococcus hirae is conducted through activity of the zinc metalloprotein Zn(II)CopY, which is a Cu(I)-responsive dimeric repressor (Cobine et al., Biochemistry 41:5822-5829, 2002). Its dimerization domain contains a C-terminal cysteine-rich metal-binding motif used for Cu(I) sensing adjacent to an aliphatic-rich repeating sequence, but it is unclear as to which regions contribute most to the interaction.

Stalking metal-linked dimers.

Protein dimerization is essential for cellular processes including regulation and biosignalling. While protein-protein interactions can occur through many modes, this review will focus on those interactions mediated through the binding of metal ions to the proteins. Selected techniques used to study protein-protein interactions, including size exclusion chromatography, mass spectrometry, affinity chromatography, and frontal zone chromatography, are described as applied to the characterization of the Enterococcus hirae protein CopY.