Distribution-free uncertainty quantification for kernel methods by gradient perturbations

Machine Learning - We propose a data-driven approach to quantify the uncertainty of models constructed by kernel methods. Our approach minimizes the needed distributional assumptions, hence,...     

Pull-Down of Metalloproteins in Their Native States by Using Desthiobiotin-Based Probes

One-third of all proteins are estimated to require metals for structural stability and/or catalytic activity. Desthiobiotin probes containing metal binding groups can be used to capture metalloproteins with exposed active-site metals under mild conditions so as to prevent changes in metallation state. The proof-of-concept was demonstrated with carbonic anhydrase (CA), an open active site, Zn²⁺-containing protein. CA was targeted by using sulfonamide derivatives. Linkers of various lengths and structures were screened to determine the optimal structure for capture of the native protein. The optimized probes could selectively pull down CA from red blood cell lysate and other protein mixtures. Pull-down of differently metallated CAs was also investigated.     

Carbon-based TiO2-x heterostructure nanocomposites for enhanced photocatalytic degradation of dye molecules

Application of brown titanium dioxide (TiO_2-x) and its modified composite forms in the photocatalytic decomposition of organic pollutants in the environment is a promising way to provide solutions for environmental redemption. Herein, we report the synthesis of effective and stable TiO_2-x nanoparticles with g-C₃N₄, RGO, and multiwalled carbon nanotubes (CNTs) using a simple hydrothermal method. Among all the as-synthesized samples, excellent photocatalytic degradation activity was observed for RGO-TiO_2-x nanocomposite with high rate constants of 0.075 min^?1_, 0.083 min^?1 and 0.093 min^?1 for methylene blue, rhodamine-B, and rosebengal dyes under UV–Visible light irradiation, respectively. The altered bandgap (1.8 eV) and the large surface area of RGO-TiO_2-x nanocomposite impacts on both absorption of visible light and efficiency of photogenerated charge electron (e^?)/hole (h⁺) pair separation. This resulted in enhanced photocatalytic property of carbon-based TiO_2-x nanocomposites. A systematic study on the influence of different carbon nanostructures on the photocatalytic activity of brown TiO_2-x is carried out.     

An automated treatment planning strategy for highly noncoplanar radiotherapy arc trajectories

Radiation therapy is a technology-driven cancer treatment modality that has experienced significant advances over the last decades, due to multidisciplinary contributions that include engineering and computing. Recent technological developments allow the use of noncoplanar volumetric modulated arc therapy (VMAT), one of the most recent photon treatment techniques, in clinical practice. In this work, an automated noncoplanar arc trajectory optimization framework designed in two modular phases is presented. First, a noncoplanar beam angle optimization algorithm is used to obtain a set of noncoplanar irradiation directions. Then, anchored in these directions, an optimization strategy is proposed to compute an optimal arc trajectory. The computational experiments considered a pool of twelve difficult head-and-neck tumor cases. It was possible to observe that, for some of these cases, the optimized noncoplanar arc trajectories led to significant treatment planning quality improvements, when compared with coplanar VMAT treatment plans. Although these experiments were done in a research environment treatment planning software (matRad), the conclusions can be of interest for a clinical setting: automated procedures can simplify the current treatment workflow, produce high-quality treatment plans, making better use of human resources and allowing for unbiased comparisons between different treatment techniques.     

Impact of high-intensity ultrasound on physical properties and degree of oxidation of lipase modified menhaden oil with caprylic acid and/or stearic acid

The purpose of this research was to determine the effect of high-intensity ultrasound (HIU) on physical properties, degree of oxidation, and oxidative stability of structured lipids (SLs). Caprylic acid (C) and stearic acid (S) were incorporated into menhaden oil using Lipozyme® 435 lipase to obtain five samples: (1) LC 20 (menhaden oil with 20% of C), (2) LC 30 (menhaden oil with 30% C), (3) LS 20 (menhaden oil with 20% S), (4) LS 30 (menhaden oil with 30% S), and (5) Blend C (menhaden oil with 16.24% C and 13.04% S). Samples were crystallized for 90 min at the following temperatures: (1) LC 20 at 15.5°C, (2) LC 30 at 17.5°C, (3) LS 20 at 24°C, (4) LS 30 at 30°C, and (5) Blend C at 18.0°C, and HIU was applied at the onset of crystallization. Physical properties, degree of oxidation, and oxidative stability were evaluated in sonicated and nonsonicated samples. All SLs had statistically higher G′ after sonication. Sonicated LS 30, LC 30, and Blend C had a higher melting enthalpy than the nonsonicated ones, while enthalpy values in sonicated LS 20 and LC 20 samples were not statistically different than the nonsonicated ones. No significant difference between sonicated and nonsonicated samples was observed in peroxide values (1.2 ± 0.1 meq/kg, p > 0.05) and in the oxidative stability index (6.3 ± 0.2 h, p > 0.05). These results showed that HIU was effective at changing physical properties without affecting the oxidation of the samples.     

Alteration of the Route to Menaquinone towards Isochorismate-Derived Metabolites

Chorismate and isochorismate constitute branch-point intermediates in the biosynthesis of many aromatic metabolites in microorganisms and plants. To obtain unnatural compounds, we modified the route to menaquinone in Escherichia coli. We propose a model for the binding of isochorismate to the active site of MenD ((1R,2S, 5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxycyclohex-3-ene-1-carboxylate (SEPHCHC) synthase) that explains the outcome of the native reaction with α-ketoglutarate. We have rationally designed variants of MenD for the conversion of several isochorismate analogues. The double-variant Asn117Arg–Leu478Thr preferentially converts (5S,6S)-5,6-dihydroxycyclohexa-1,3-diene-1-carboxylate (2,3-trans-CHD), the hydrolysis product of isochorismate, with a >70-fold higher ratio than that for the wild type. The single-variant Arg107Ile uses (5S,6S)-6-amino-5-hydroxycyclohexa-1,3-diene-1-carboxylate (2,3-trans-CHA) as substrate with >6-fold conversion compared to wild-type MenD. The novel compounds have been made accessible in vivo (up to 5.3 g L⁻¹). Unexpectedly, as the identified residues such as Arg107 are highly conserved (>94 %), some of the designed variations can be found in wild-type SEPHCHC synthases from other bacteria (Arg107Lys, 0.3 %). This raises the question for the possible natural occurrence of as yet unexplored branches of the shikimate pathway.