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. Though the idea attracted major attention widely, very little has been done in way of actual adoption in real practices in the past 10 years. Nevertheless, as one of the pioneers in Taiwan, we have been involved in the effort to implement the LHS locally since 2016. In this article, we systematically summarize the evolution of the learning health cycle, review cases of its applications and briefly introduce the work we have done for promoting LHSs in Taiwan. Based on the experience we have gained, we try to identify the challenges and opportunities in Taiwan. While full-scale electronic medical records powered by the National Health Insurance system give Taiwan a special advantage in achieving a nationwide LHS, the medical community is not yet ready for a dramatic change. The lack of infrastructure for this use and motivation to take action right away makes the implementation of a LHS in Taiwan challenging.

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. The primary outcomes were changed from baseline in weight metrics and the cardiometabolic profile. A random effects model will be used, as high heterogeneity is expected. All analyses were performed using STATA 17.0. RESULTS: Fifteen trials with a total number of 1286 participants were included in our meta-analysis. Overall, the mean difference in weight change between the IBTs group and the control group was -2.89 kg (95% confidence interval, -5.12 to -0.65, p = 0.011). Additionally, IBTs significantly reduced the HbA1c level and fasting plasma glucose by 0.37% and 6.99 mg/dl, compared with control groups. IBTs showed a little increased risk of GI side effects and hypoglycemia events, but none of the severe hypoglycemia events were occurred in IBTs group. CONCLUSIONS: Our study results have proved that GLP-1 RAs are safe, acceptable, and effective in weight reduction and sugar control for children with obesity. In addition, DPP-4is seems to have no effect on glycemic control and weight loss in childhood obesity. Further research is needed to confirm these findings, especially in younger children.

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. Most methods for finding 3D motifs require a known motif to search for other similar structures or functionally/structurally crucial residues. Here, without requiring a query motif or essential residues, a fully automated method for discovering 3D motifs of various sizes across protein families with different folds based on a 16-letter structural alphabet is presented. It was applied to structurally non-redundant proteins bound to DNA, RNA, obligate/non-obligate proteins as well as free DNA-binding proteins (DBPs) and proteins with known structures but unknown function. Its usefulness was illustrated by analyzing the 3D motifs found in DBPs. A non-specific motif was found with a 'corner' architecture that confers a stable scaffold and enables diverse interactions, making it suitable for binding not only DNA but also RNA and proteins. Furthermore, DNA-specific motifs present 'only' in DBPs were discovered. The motifs found can provide useful guidelines in detecting binding sites and computational protein redesign.

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.

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. A small percentage of C-PS particles in the colloidal mixture does not disturb the formation of lattices made of S-PS particles. The LSCM also provides a meaningful way to probe dynamic information. The diffusion of single particles at the emulsion interfaces depends strongly on the oil phase viscosity, particle size, and particle wettability. A highly curved emulsion interface slows the motion of microparticles at oil-water interfaces but the interface curvature effect decreases with increasing oil phase viscosity. Although the confocal microscope was originally used as an imaging tool, we find that the thermodynamic equilibrium of colloidal lattices can be disturbed and even destroyed when increasing the output laser intensity.

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. The method requires as input the protein structure and sufficient sequence homologs to define each residue's relative conservation, and it yields as output experimentally testable residues that are predicted to bind DNA. By incorporating characteristic DNA-binding site features (i.e., electrostatic strain and amino acid conservation), the new method yields a prediction accuracy of 83%, which is much higher than methods based on only electrostatic strain (57%) or conservation alone (50%). It is also less sensitive to protein conformational changes upon DNA binding than methods that mainly depend on the 3D protein structure.

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. More importantly, the ISMBLab-LIG algorithm has substantial tolerance to the prediction uncertainties of computationally derived protein structure models. As such, the method is particularly useful for predicting LBSs not only on experimental protein structures without known LBS templates in the database but also on computationally predicted model protein structures with structural uncertainties in the tentative ligand binding sites.

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. All-trans RA, 9-cRA, and 13-cRA were well separated from each other in plasma by using a C18 precolumn and a column with a gradient solvent system of mobile phases A and B at a flow rate of 1.0 ml/min. In addition, thermal stability of tRA and cRA in plasma during the sample preparation under the temperature of 0 and 25 degrees C were studied. Our results showed that (1) the interconversion ratios (%) (cRA/tRA and tRA/cRA) were decreased with the addition of NEM and Vit. C and the minimum concentrations of NEM and Vit. C to inhibit the interconversion were 50 and 150 microM, respectively, (2) higher concentrations of NEM and Vit. C were required to prevent the interconversion at higher temperature, (3) the precision and accuracy of calibration curve with various concentration of tRA (1-1000 ng/ml) and 13-cRA (5-800 ng/ml) in plasma showed good linearity (r(2)=0.9992 and 0.9994), and between-day errors expressed by coefficient of variation (CV, %) for tRA and 13-cRA which were both less than 5.6%, (4) the mean recovery of the analytes were 78-94% for tRA and 80-92% for 13-cRA at concentration range from 1 to 1000 ng/ml and 5 to 800 ng/ml, respectively, and (5) the limit of quantitation of tRA and 13-cRA were 1 and 5 ng/ml, respectively. In addition, the HPLC method had been successfully applied to the tRA pharmacokinetic study in two hepatoma patients after receiving 45 mg/m(2) per day orally. Thus, our results suggest that the HPLC method for analyzing tRA and 13-cRA in plasma with the addition of NEM and Vit. C is a simple, sensitive and accurate method.

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. Here, we aim to establish the precision of these 3d and 1d motifs to annotate NAD(P)-binding proteins. We show that the pyrophosphate-binding 3d motifs are characteristic of NAD(P)-binding proteins, as they are rarely found in nonNAD(P)-binding proteins. Furthermore, several 1d motifs could distinguish between proteins that bind only NAD and those that bind only NADP. They could also distinguish between NAD(P)-binding proteins from nonNAD(P)-binding ones. Interestingly, one of the pyrophosphate-binding 3d and corresponding 1d motifs was found only in enoyl-acyl carrier protein reductases, which are enzymes essential for bacterial fatty acid biosynthesis. This unique 3d motif serves as an attractive novel drug target, as it is conserved across many bacterial species and is not found in human proteins.

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 ß 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. By contrast, the interdomain interface residues are directly coupled with antigen binding. The interdomain interface should be treated as an integral part of the antigen-binding site.

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. We show that the sequence motifs derived from the distinct pyrophosphate-binding structures yield different numbers/spacing of conserved Gly residues. We also show that they depend on the side chain orientations and cofactor type (NAD or NADP). Thus, sequence motifs derived from local similarity of backbone structures without consideration of the cofactor type and/or side chain orientations would reduce their reliability in annotating protein function from sequence alone. The three-dimensional (3D) and 1D motifs comprising conserved residues in nonredundant proteins reveal hidden relationships between the protein structure/function and sequence as well as protein-cofactor interactions.

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. In the present study, we demonstrated that AID peptides are able to deliver cargo proteins into living cells in both covalent and noncovalent protein transductions (CNPT) synchronously. Human A549 cells were treated with a fluorescent protein (FP) that was noncovalently premixed with another AID-conjugated FP, which emitted a different color. After the delivery of carrier AID-FP and cargo FP into cells, the emission and merge of fluorescence were observed and recorded with a confocal microscope, while the internalization efficiency was quantitatively analyzed with a flow cytometer. The optimal molecular ratio between carrier AID-FP and cargo FP for CNPT is about 1:1/3. Fluorescence resonance energy transfer (FRET) assay further confirmed AID-conjugates can physically interact with its cargo FPs in CNPT in cells. Potential uptake mechanisms of CNPT may involve a combination of multiple internalization pathways. After delivery, intracellular distributions of AID-conjugates and FPs may possibly colocalize with lysosomes. These results will facilitate the understanding of multiple mechanisms of PTDs, and provide a powerful tool for simultaneously delivering several proteins or compounds in protein internalization.

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. Our work suggests that a highly curved emulsion interface slows the motion of solid particles. This qualitatively supports the theoretical work by Danov et al. (Danov, K. D.; Dimova, R.; Pouligny, B. Phys. Fluids 2000, 12, 2711); however, the interfacial curvature effect decreases with increasing oil-phase viscosity. The diffusion of multiparticle clusters at oil-water interfaces is a strong function of cluster size and oil-phase viscosity and can be quantitatively related to fractal dimension. Finally, we report the influence of temperature and quantify the diffusion activation energy and friction factor of the particles at the investigated oil-water interfaces.

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. The short-time diffusion constant (<10 s) of single particles increases with increasing lattice spacing; the oil-phase viscosity has an effect on diffusion only at large interparticle distances. Strikingly, we observe that the equilibrium structure can be disturbed when increasing the output laser intensity in a confocal laser scanning microscope, which leads to the collapse of colloidal lattices in the presence of small laser powers.

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.