The effects of incretin-based therapies on weight reduction and metabolic parameters in children with obesity: A systematic review and meta-analysis.

Background: Growing evidence indicates that incretin-based therapies (IBTs), glucagon-like peptide-1 receptor agonists (GLP-1 RAs), and dipeptidyl peptidase-4 inhibitors (DPP4is) are effective and safe for treating pediatric obesity patients with or without type 2 diabetes. Therefore, we aimed to perform a systematic review and meta-analysis for updating current evidence.

Methods: We searched the PubMed, the Cochrane Library, and the EMBASE database for articles published until September 15, 2023, and limited to randomized control trials.

Opportunities and challenges in Taiwan for implementing the learning health system.

Due to the low ratio of medical decisions made upon solid scientific evidence (4%) and the low efficiency of deploying knowledge in practice (17 years), the concept of a learning health system (LHS) was initiated to speed up knowledge generation and adoption and systematically approach continuous improvement in clinical practice. This concept can be illustrated by a so-called learning health cycle. This cycle, the first version as well as its variants, provides a framework for discussion on a common basis and has been well-accepted by the medical communities.

Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms.

Predicting ligand binding sites (LBSs) on protein structures, which are obtained either from experimental or computational methods, is a useful first step in functional annotation or structure-based drug design for the protein structures. In this work, the structure-based machine learning algorithm ISMBLab-LIG was developed to predict LBSs on protein surfaces with input attributes derived from the three-dimensional probability density maps of interacting atoms, which were reconstructed on the query protein surfaces and were relatively insensitive to local conformational variations of the tentative ligand binding sites. The prediction accuracy of the ISMBLab-LIG predictors is comparable to that of the best LBS predictors benchmarked on several well-established testing datasets.

Predominant structural configuration of natural antibody repertoires enables potent antibody responses against protein antigens.

Humoral immunity against diverse pathogens is rapidly elicited from natural antibody repertoires of limited complexity. But the organizing principles underlying the antibody repertoires that facilitate this immunity are not well-understood. We used HER2 as a model immunogen and reverse-engineered murine antibody response through constructing an artificial antibody library encoded with rudimentary sequence and structural characteristics learned from high throughput sequencing of antibody variable domains.

Sequence-motif detection of NAD(P)-binding proteins: discovery of a unique antibacterial drug target.

Many enzymes use nicotinamide adenine dinucleotide or nicotinamide adenine dinucleotide phosphate (NAD(P)) as essential coenzymes. These enzymes often do not share significant sequence identity and cannot be easily detected by sequence homology. Previously, we determined all distinct locally conserved pyrophosphate-binding structures (3d motifs) from NAD(P)-bound protein structures, from which 1d sequence motifs were derived.

Antibody variable domain interface and framework sequence requirements for stability and function by high-throughput experiments.

Protein structural stability and biological functionality are dictated by the formation of intradomain cores and interdomain interfaces, but the intricate sequence-structure-function interrelationships in the packing of protein cores and interfaces remain difficult to elucidate due to the intractability of enumerating all packing possibilities and assessing the consequences of all the variations. In this work, groups of β strand residues of model antibody variable domains were randomized with saturated mutagenesis and the functional variants were selected for high-throughput sequencing and high-throughput thermal stability measurements. The results show that the sequence preferences of the intradomain hydrophobic core residues are strikingly flexible among hydrophobic residues, implying that these residues are coupled indirectly with antigen binding through energetic stabilization of the protein structures.

Hidden relationship between conserved residues and locally conserved phosphate-binding structures in NAD(P)-binding proteins.

A one-dimensional (1D) motif usually comprises conserved essential residues involved in catalysis, ligand binding, or maintaining a specific structure. However, it cannot be easily detected in proteins with low sequence identity because it is difficult to (1) identify protein sequences suspected to contain the motif, and (2) align sequences with little sequence identity to spot the conserved residues. Here, we present a strategy for discovering phosphate-binding 1D motifs in NAD(P)-binding proteins sharing low sequence identity that overcomes these two hurdles by determining all distinct locally conserved pyrophosphate-binding structures and aligning the same-length sequences comprising each of these structures to identify the conserved residues.

A structural-alphabet-based strategy for finding structural motifs across protein families.

Proteins with insignificant sequence and overall structure similarity may still share locally conserved contiguous structural segments; i.e. structural/3D motifs.

Comment on 'Electron-phonon scattering in Sn-doped In2O3 FET nanowires probed by temperature-dependent measurements'.

We point out that the recently reported electrical quantities and transport behavior in a Sn-doped indium oxide FET nanowire (Berengue et al 2009 Nanotechnology 20 245706) should require serious reevaluation.

Protein transport in human cells mediated by covalently and noncovalently conjugated arginine-rich intracellular delivery peptides.

Generally, biomacromolecules, such as DNA, RNA, and proteins, cannot freely permeate into cells from outside the membrane. Protein transduction domains (PTDs) are peptides containing a large number of basic amino acids that can deliver macromolecules into living cells. Arginine-rich intracellular delivery (AID) peptides are more effective than other PTD peptides at carrying large molecules across cellular membranes.

The structure and dynamics of microparticles at pickering emulsion interfaces.

We have employed a laser scanning confocal microscope (LSCM) to study the structure and dynamics of microparticles at Pickering emulsion interfaces. The microparticles can have rich morphology at the emulsion interfaces, ranging from an aggregated structure to colloidal lattices, with a possibility of involving heterogeneous particles. With a specific interest in colloidal lattices, we find that although the enhanced electrostatic repulsion explains the formation of colloidal lattices by sulfate-treated polystyrene (S-PS) particles, it fails to interpret the unsuccessfulness of assembling lattices containing single-species carboxylate-treated polystyrene (C-PS) particles.

Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation.

Binding of polyanionic DNA depends on the cluster of electropositive atoms in the binding site of a DNA-binding protein. Such a cluster of electropositive protein atoms would be electrostatically unfavorable without stabilizing interactions from the respective electronegative DNA atoms and would likely be evolutionary conserved due to its critical biological role. Consequently, our strategy for predicting DNA-binding residues is based on detecting a cluster of evolutionary conserved surface residues that are electrostatically stabilized upon mutation to negatively charged Asp/Glu residues.

Dynamics and collapse of two-dimensional colloidal lattices.

One interesting aspect of colloidal particles is the formation of colloidal crystals at the 2D and 3D levels. Here we report the dynamics and collapse of colloidal lattices at liquid-liquid interfaces using Pickering emulsions as an experimental template. The colloidal particles oscillate around their equilibrium positions.

Dynamics of charged microparticles at oil-water interfaces.

Solid-stabilized emulsions have been used as a model system to investigate the dynamics of charged microparticles with diameters of 1.1 microm at oil-water interfaces. Using confocal microscopy, we investigated the influences of interfacial curvature, cluster size, and temperature on the diffusion of solid particles.

Self-assembled structure of nanoparticles at a liquid-liquid interface.

Pickering emulsions are used as a template to investigate the multiphase interactions and self-assembled structure of nanoparticles at a trichloroethylene-water interface. The dodecanethiol-capped silver nanoparticles of 1-5 nm form randomly distributed multilayers at the liquid/liquid interface, with an interparticle distance varying from close contact to approximately 25 nm. This report offers the first direct observation of nanoparticles in a liquid medium using the environmental transmission electron microscope, as well as the first work revealing the detailed self-assembled structure of nanoparticles at a liquid/liquid interface when the size of the nanoparticles is comparable to the molecular dimension of the liquids.

Novel inhibition of cis/trans retinoic acid interconversion in biological fluids--an accurate method for determination of trans and 13-cis retinoic acid in biological fluids.

All-trans retinoic acid (tRA, or tretinoin) can be metabolized through stereoisomerization to 13-cis retinoic acid (13-cRA) in vivo. We have developed a simple, sensitive and accurate method for analyzing tRA and 13-cRA in plasma with the addition of N-ethylmaleimide (NEM) and Vitamin C (Vit. C) to prevent the interconversion of cis/trans retinoic acid.