Correlation between the binding affinity and the conformational entropy of nanobody SARS-CoV-2 spike protein complexes.

Camelid single-domain antibodies, also known as nanobodies, can be readily isolated from naïve libraries for specific targets but often bind too weakly to their targets to be immediately useful. Laboratory-based genetic engineering methods to enhance their affinity, termed maturation, can deliver useful reagents for different areas of biology and potentially medicine. Using the receptor binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and a naïve library, we generated closely related nanobodies with micromolar to nanomolar binding affinities. By analyzing the structure-activity relationship using X-ray crystallography, cryoelectron microscopy, and biophysical methods, we observed that higher conformational entropy losses in the formation of the spike protein-nanobody complex are associated with tighter binding. To investigate this, we generated structural ensembles of the different complexes from electron microscopy maps and correlated the conformational fluctuations with binding affinity. This insight guided the engineering of a nanobody with improved affinity for the spike protein.

Genome-wide association and polygenic risk score estimation of type 2 diabetes mellitus in Kinh Vietnamese-A pilot study.

A genome-wide association study (GWAS) is a powerful tool in investigating genetic contribution, which is a crucial factor in the development of complex multifactorial diseases, such as type 2 diabetes mellitus. Type 2 diabetes mellitus is a major healthcare burden in the Western Pacific region; however, there is limited availability of genetic-associated data for type 2 diabetes in Southeast Asia, especially among the Kinh Vietnamese population. This lack of information exacerbates global healthcare disparities. In this study, 997 Kinh Vietnamese individuals (503 with type 2 diabetes and 494 controls) were prospectively recruited and their clinical and paraclinical information was recorded. DNA samples were collected and whole genome genotyping was performed. Standard quality control and genetic imputation using the 1000 Genomes database were executed. A polygenic risk score for type 2 diabetes was generated in different models using East Asian, European, and mix ancestry GWAS summary statistics as training datasets. After quality control and genetic imputation, 107 polymorphisms reached suggestive statistical significance for GWAS (≤5 × 10-6) and rs11079784 was one of the potential markers strongly associated with type 2 diabetes in the studied population. The best polygenic risk score model predicting type 2 diabetes mellitus had AUC = 0.70 (95% confidence interval = 0.62-0.77) based on a mix of ancestral GWAS summary statistics. These data show promising results for genetic association with a polygenic risk score estimation in the Kinh Vietnamese population; the results also highlight the essential role of population diversity in a GWAS of type 2 diabetes mellitus.

Determination of the Structure and Dynamics of the Fuzzy Coat of an Amyloid Fibril of IAPP Using Cryo-Electron Microscopy.

In recent years, major advances in cryo-electron microscopy (cryo-EM) have enabled the routine determination of complex biomolecular structures at atomistic resolution. An open challenge for this approach, however, concerns large systems that exhibit continuous dynamics. To address this problem, we developed the metadynamic electron microscopy metainference (MEMMI) method, which incorporates metadynamics, an enhanced conformational sampling approach, into the metainference method of integrative structural biology. MEMMI enables the simultaneous determination of the structure and dynamics of large heterogeneous systems by combining cryo-EM density maps with prior information through molecular dynamics, while at the same time modeling the different sources of error. To illustrate the method, we apply it to elucidate the dynamics of an amyloid fibril of the islet amyloid polypeptide (IAPP). The resulting conformational ensemble provides an accurate description of the structural variability of the disordered region of the amyloid fibril, known as fuzzy coat. The conformational ensemble also reveals that in nearly half of the structural core of this amyloid fibril, the side chains exhibit liquid-like dynamics despite the presence of the highly ordered network backbone of hydrogen bonds characteristic of the cross-ß structure of amyloid fibrils.

A PTER-dependent pathway of taurine metabolism linked to energy balance.

Taurine is a conditionally essential micronutrient and one of the most abundant amino acids in humans1-3. In endogenous taurine metabolism, dedicated enzymes are involved in biosynthesis of taurine from cysteine as well as the downstream derivatization of taurine into secondary taurine metabolites4,5. One such taurine metabolite is N-acetyltaurine6. Levels of N-acetyltaurine are dynamically regulated by diverse physiologic perturbations that alter taurine and/or acetate flux, including endurance exercise7, nutritional taurine supplementation8, and alcohol consumption6,9. While taurine N-acetyltransferase activity has been previously detected in mammalian cells6,7, the molecular identity of this enzyme, and the physiologic relevance of N-acetyltaurine, have remained unknown. Here we show that the orphan body mass index-associated enzyme PTER (phosphotriesterase-related)10 is the principal mammalian taurine N-acetyltransferase/hydrolase. In vitro, recombinant PTER catalyzes bidirectional taurine N-acetylation with free acetate as well as the reverse N-acetyltaurine hydrolysis reaction. Genetic ablation of PTER in mice results in complete loss of tissue taurine N-acetyltransferase/hydrolysis activities and systemic elevation of N-acetyltaurine levels. Upon stimuli that increase taurine levels, PTER-KO mice exhibit lower body weight, reduced adiposity, and improved glucose homeostasis. These phenotypes are recapitulated by administration of N-acetyltaurine to wild-type mice. Lastly, the anorexigenic and anti-obesity effects of N-acetyltaurine require functional GFRAL receptors. Together, these data uncover enzymatic control of a previously enigmatic pathway of secondary taurine metabolism linked to energy balance.

AI-clinician collaboration via disagreement prediction: A decision pipeline and retrospective analysis of real-world radiologist-AI interactions.

Clinical decision support tools can improve diagnostic performance or reduce variability, but they are also subject to post-deployment underperformance. Although using AI in an assistive setting offsets many concerns with autonomous AI in medicine, systems that present all predictions equivalently fail to protect against key AI safety concerns. We design a decision pipeline that supports the diagnostic model with an ecosystem of models, integrating disagreement prediction, clinical significance categorization, and prediction quality modeling to guide prediction presentation. We characterize disagreement using data from a deployed chest X-ray interpretation aid and compare clinician burden in this proposed pipeline to the diagnostic model in isolation. The average disagreement rate is 6.5%, and the expected burden reduction is 4.8%, even if 5% of disagreements on urgent findings receive a second read. We conclude that, in our production setting, we can adequately balance risk mitigation with clinician burden if disagreement false positives are reduced.

Wavelet radiomics features from multiphase CT images for screening hepatocellular carcinoma: analysis and comparison.

Early detection of liver malignancy based on medical image analysis plays a crucial role in patient prognosis and personalized treatment. This task, however, is challenging due to several factors, including medical data scarcity and limited training samples. This paper presents a study of three important aspects of radiomics feature from multiphase computed tomography (CT) for classifying hepatocellular carcinoma (HCC) and other focal liver lesions: wavelet-transformed feature extraction, relevant feature selection, and radiomics features-based classification under the inadequate training samples. Our analysis shows that combining radiomics features extracted from the wavelet and original CT domains enhance the classification performance significantly, compared with using those extracted from the wavelet or original domain only. To facilitate the multi-domain and multiphase radiomics feature combination, we introduce a logistic sparsity-based model for feature selection with Bayesian optimization and find that the proposed model yields more discriminative and relevant features than several existing methods, including filter-based, wrapper-based, or other model-based techniques. In addition, we present analysis and performance comparison with several recent deep convolutional neural network (CNN)-based feature models proposed for hepatic lesion diagnosis. The results show that under the inadequate data scenario, the proposed wavelet radiomics feature model produces comparable, if not higher, performance metrics than the CNN-based feature models in terms of area under the curve.

C-Glycosylcrotylboronates for the Synthesis of Glycomimetics.

The stereoselective synthesis of E- and Z- isomers of a C- mannosyl crotylpinacolboronate via Ni-promoted reactions on an allylic acetate and a diene precursor, respectively, is described. The E- and Z- isomers reacted with 1,2-O-isopropylidene glyceraldehyde in the presence or absence of (R)- and (S)- TRIP catalysts, to give predominantly 3,4-anti and 3,4-syn crotylation products, respectively, with moderate to high facial selectivity. These products were transformed to biologically relevant C-manno-disaccharides.

Oxocarbenium ion cyclizations for the synthesis of disaccharide mimetics of 2-amino-2-deoxy-pyranosides: Application to the carbasugar of ß-galactosamine-(1,4)-3-O-methyl-D-chiro-inositol.

The synthesis of the carbasugar of ß-galactosamine-(1,4)-3-O-methyl-D-chiro-inositol (INS-2), a potential tool for studying glucose metabolism, is described. The synthetic strategy, entails an oxocarbenium ion cyclization on a chiro-inositol derived, thioacetal-enol ether to give a carbocyclic enol ether, which is elaborated to the 2-amino-2-deoxy carbasugar framework via a 2-oximo derivative.

Australian Consensus Statements for the Assessment and Management of Non-radiographic Axial Spondyloarthritis.

BACKGROUND: The understanding of non-radiographic axial spondyloarthritis (nr-axSpA) has accelerated over the last decade, producing a number of practice-changing developments. Diagnosis is challenging. No diagnostic criteria exist, no single finding is diagnostic, and other causes of back pain may act as confounders. AIM: To update and expand the 2014 consensus statement on the investigation and management of non-radiographic axial spondyloarthritis (nr-axSpA). METHODS: We created search questions based on our previous statements and four new topics then searched the MEDLINE and Cochrane databases. We assessed relevant publications by full-text review and rated their level of evidence using the GRADE system. We compiled a GRADE evidence summary then produced and voted on consensus statements. RESULTS: We identified 5145 relevant publications, full-text reviewed 504, and included 176 in the evidence summary. We developed and voted on 22 consensus statements. All had high agreement. Diagnosis of nr-axSpA should be made by experienced clinicians, considering clinical features of spondyloarthritis, blood tests, and imaging. History and examination should also assess alternative causes of back pain and related conditions including non-specific back pain and fibromyalgia. Initial investigations should include CRP, HLA-B27, and AP pelvic radiography. Further imaging by T1 and STIR MRI of the sacroiliac joints is useful if radiography does not show definite changes. MRI provides moderate-to-high sensitivity and high specificity for nr-axSpA. Acute signs of sacroiliitis on MRI are not specific and have been observed in the absence of spondyloarthritis. Initial management should involve NSAIDs and a regular exercise program, while TNF and IL-17 inhibitors can be used for high disease activity unresponsive to these interventions. Goals of treatment include improving the frequent impairment of social and occupational function that occurs in nr-axSpA. CONCLUSIONS: We provide 22 evidence-based consensus statements to provide practical guidance in the assessment and management of nr-axSpA.

Association of ADIPOQ Single-Nucleotide Polymorphisms with the Two Clinical Phenotypes Type 2 Diabetes Mellitus and Metabolic Syndrome in a Kinh Vietnamese Population.

PURPOSE: Genetic factors play an important role in the development of type 2 diabetes mellitus (T2DM) and metabolic syndrome (MetS). However, few genetic association studies related to these disorders have been performed with Vietnamese subjects. In this study, the potential associations of ADIPOQ single nucleotide polymorphisms (SNPs) with T2DM and MetS in a Kinh Vietnamese population were investigated. PATIENTS AND METHODS: A study with 768 subjects was conducted to examine the associations of four ADIPOQ SNPs (rs266729, rs1501299, rs3774261, and rs822393) primarily with T2DM and secondarily with MetS. The TaqMan SNP genotyping assay was used to determine genotypes from subjects' DNA samples. RESULTS: After statistical adjustment for age, sex, and body mass index, the ADIPOQ SNP rs266729 was found to be associated with increased risk of T2DM under multiple inheritance models: codominant (OR = 2.30, 95% CI = 1.16-4.58), recessive (OR = 2.17, 95% CI = 1.11-4.26), and log-additive (OR = 1.32, 95% CI = 1.02-1.70). However, rs1501299, rs3774261, and rs822393 were not associated with risk for T2DM. Additionally, rs266729, rs3774261, and rs822393 were statistically associated with MetS, while rs1501299 was not. Haplotype analysis showed a strong linkage disequilibrium between the SNP pairs rs266729/rs822393 and rs1501299/rs3774261, and the haplotype rs266729(G)/rs822393(T) was not statistically associated with MetS. CONCLUSION: The results show that rs266729 is a lead candidate SNP associated with increased risk of developing T2DM and MetS in a Kinh Vietnamese population, while rs3774261 is associated with MetS only. Further functional characterization is needed to uncover the mechanism underlying the potential genotype-phenotype associations.

Association of KCNJ11 and ABCC8 single-nucleotide polymorphisms with type 2 diabetes mellitus in a Kinh Vietnamese population.

Type 2 diabetes mellitus (T2DM) is a genetically influenced disease, but few studies have been performed to investigate the genetic basis of T2DM in Vietnamese subjects. Thus, the potential associations of KCNJ11 and ABCC8 single nucleotide polymorphisms (SNPs) with T2DM were investigated in a Kinh Vietnamese population. A cross-sectional study consisting of 404 subjects including 202 T2DM cases and 202 non-T2DM controls was designed to examine the potential associations of 4 KCNJ11 and ABCC8 SNPs (rs5219, rs2285676, rs1799859, and rs757110) with T2DM. Genotypes were identified based on restriction fragment length polymorphism and tetra-primer amplification refractory mutation system polymerase chain reaction. After statistically adjusting for age, sex, and BMI, rs5219 was found to be associated with an increased risk of T2DM under 2 inheritance models: codominant (OR = 2.15, 95% confidence intervals [CI] = 1.09-4.22) and recessive (OR = 2.08, 95%CI = 1.09-3.94). On the other hand, rs2285676, rs1799859, and rs757110 were not associated with an increased risk of T2DM. Haplotype analysis elucidated a strong linkage disequilibrium between the 3 SNPs, rs5219, rs2285676, and rs757110. The haplotype rs5219(A)/rs2285676(T)/rs757110(G) was associated with an increased risk of T2DM (OR = 1.42, 95%CI = 1.01-1.99). The results show that rs5219 is a lead candidate SNP associated with an increased risk of developing T2DM in the Kinh Vietnamese population. Further functional characterization is needed to uncover the mechanism underlying the potential genotype-phenotype associations.

Systematic Review and Meta-Analysis of Inflammatory Bowel Disease Adverse Events with Anti-Interleukin 17A Agents and Tumor Necrosis Factor Inhibitors in Rheumatic Disease and Skin Psoriasis.

INTRODUCTION: The aim of this work is to perform a systematic review and meta-analysis of anti-tumor necrosis factor (anti-TNF) and anti-interleukin-17 (anti-IL-17) trials for spondyloarthritis, psoriatic arthritis, and psoriasis comparing rates of inflammatory bowel disease (IBD) events compared to placebo. METHODS: MEDLINE, EMBASE, and The Cochrane Library were searched for double-blind, randomized placebo-controlled anti-TNF and anti-IL-17 trials of included diseases. Inflammatory bowel disease events from the RCT period were pooled and meta-analyzed using statistical methods suitable for low-event-rate meta-analysis (Peto's, Mantel-Haenszel, hypergeometric-normal model, and Shuster-Guo-Skyler). When observed data were insufficient, we performed an exploratory sensitivity analysis to compare methods. RESULTS: We identified 9551 original papers, and included 96 publications: 65 anti-TNF and 31 anti-IL-17 trials, containing 21 new and 12 flare IBD events in 28,209 participants. New IBD on anti-IL-17 occurred 0.23/100 patient-years (PY) in psoriasis, 0.61/100 PY in PsA and 1.63/100 PY in spondyloarthritis, rates similar to observational cohorts, and less commonly on anti-TNF (0/100 PY, 0/100 PY, 0.32/100 PY, respectively). No evidence of difference between groups was found, with wide CI from many pooled counts of zero, especially in placebo arms. CONCLUSIONS: IBD events were rare, occurring at rates similar to biologic-naive groups. We could not find statistically significant differences in risk of new or recurrent IBD between treatment and control groups using selected meta-analytical methods for low event rate scenarios. Meta-analyses of this topic require more IBD events, ideally without pooling heterogeneous groups. Larger, thoroughly reported trials with systematic and detailed safety reporting are required to improve risk estimation and to make accurate inferences.

Targeted AKT Inhibition in Prostate Cancer Cells and Spheroids Reduces Aerobic Glycolysis and Generation of Hyperpolarized [1-13C] Lactate.

The PI3K/AKT/mTOR (PAM) signaling pathway is frequently mutated in prostate cancer. Specific AKT inhibitors are now in advanced clinical trials, and this study investigates the effect of MK2206, a non-ATP-competitive inhibitor, on the cellular metabolism of prostate cancer cells. We observed a reduction in cell motility and aerobic glycolysis in prostate cancer cells with treatment. These changes were not accompanied by a reduction in the ratio of high-energy phosphates or a change in total protein levels of enzymes and transporters involved in glycolysis. However, a decreased ratio of NAD+/NADH was observed, motivating the use of hyperpolarized magnetic resonance spectroscopy (HP-MRS) to detect treatment response. Spectroscopic experiments were performed on tumor spheroids, 3D structures that self-organize in the presence of an extracellular matrix. Treated spheroids showed decreased lactate production with on-target inhibition confirmed using IHC, demonstrating that HP-MRS can be used to probe treatment response in prostate cancer spheroids and can provide a biomarker for treatment response. Mol Cancer Res; 16(3); 453-60. ©2018 AACR.

Vitrectomy for stage 1 macular holes identified by optical coherence tomography.

BACKGROUND AND OBJECTIVE: To describe a series of patients with decreased vision secondary to stage 1 macular hole confirmed by optical coherence tomography (OCT) that failed to spontaneously resolve with observation. To determine whether current surgical techniques can prevent progression to a full-thickness macular hole and lead to improved visual acuity. PATIENTS AND METHODS: Retrospective, comparative case series presenting patient demographics, duration of symptoms, timing of surgery, preoperative and postoperative vision, and clinical outcome based on examination and OCT. RESULTS: Five eyes of five patients with stage 1 macular holes identified on OCT required surgical repair. All eyes showed anatomic closure and lack of progression to a full-thickness hole confirmed by OCT after one procedure. Mean preoperative visual acuity was 20/102 (range, 20/50 to 20/200) and mean postoperative visual acuity was 20/52 (range, 20/25 to 20/200). Average improvement for all five eyes was 3 Snellen lines, with four of the five (80%) improving 5 lines each. CONCLUSION: In symptomatic eyes with stage 1 macular holes that fail to spontaneously resolve with observation, vitrectomy with intraocular gas tamponade may prevent progression to a full-thickness hole and lead to improved visual acuity.

Sampling Hyperpolarized Molecules Utilizing a 1 Tesla Permanent Magnetic Field.

Hyperpolarized magnetic resonance spectroscopy (HP MRS) using dynamic nuclear polarization (DNP) is a technique that has greatly enhanced the sensitivity of detecting (13)C nuclei. However, the HP MRS polarization decays in the liquid state according to the spin-lattice relaxation time (T1) of the nucleus. Sampling of the signal also destroys polarization, resulting in a limited temporal ability to observe biologically interesting reactions. In this study, we demonstrate that sampling hyperpolarized signals using a permanent magnet at 1 Tesla (1T) is a simple and cost-effective method to increase T1s without sacrificing signal-to-noise. Biologically-relevant information may be obtained with a permanent magnet using enzyme solutions and in whole cells. Of significance, our findings indicate that changes in pyruvate metabolism can also be quantified in a xenograft model at this field strength.

The comparative histologic effects of subthreshold 532- and 810-nm diode micropulse laser on the retina.

PURPOSE: Therapeutic retinal laser photocoagulation can damage the neurosensory retina and cause iatrogenic visual impairment. Subthreshold micropulse photocoagulation may decrease this risk by selective tissue treatment. The aim of this study was to compare subthreshold 810-nm diode micropulse laser and subthreshold 532-nm micropulse laser on the retina by histologic examination and differential protein expression. METHODS: Fourteen Dutch-belted rabbits received subthreshold 810-nm diode micropulse laser photocoagulation in their right eye and subthreshold 532-nm micropulse laser photocoagulation in their left eye. Histology and immunohistochemical detection of stromal cell-derived factor-1 (SDF-1), ß-actin, vascular endothelial growth factor (VEGF), glial fibrillary acidic protein (GFAP), and insulin-like growth factor 1 (IGF-1) were analyzed 12 hours, 3 days, 14 days, and 28 days post-laser photocoagulation. RESULTS: Histologically, all time points produced a similar degree of retinal disruption in both wavelengths. Immunohistochemically, SDF-1 expression was greatest at the 12-hour time point and decreased thereafter. SDF-1, VEGF, and ß-actin up-regulation was detected at early time points in both the 810- and 532-nm micropulse laser-treated animals. CONCLUSIONS: Subthreshold micropulse retinal laser photocoagulation caused equivalent histologic changes from both 532- and 810-nm diode lasers. Differential protein expression was not evident between the different laser conditions.

Association of adult-onset asthma with specific cardiovascular conditions.

BACKGROUND: While asthma is known to be associated with cardiovascular disease (CVD), the relation to specific manifestations of CVD has not been previously described. Our objective was to explore the relation of child and adult-onset asthma with specific CVD conditions. METHODS: We examined data from 16,943 (projected 178 million) U.S. adults aged 18-90 years old with relevant information on asthma and CVD. The study was a cross-sectional analysis of the National Health and Nutrition Examination Survey 1999-2006. We determined the prevalence of CVD risk factors and likelihood of CVD conditions according to gender and asthma status using multiple logistic regression adjusted for age, gender and other CVD risk factors. RESULTS: The proportions of subjects with child and adult-onset asthma were 4.8% (n=702) and 3.3% (n=534), respectively. Adult-onset asthma was significantly associated with total CVD (OR=2.07, CI=1.2-3.7), but child-onset asthma was not associated with any CVD conditions. Of the four specific CVD endpoints, adult-onset asthma overall was only associated with coronary heart disease (CHD) (OR=2.26, CI=1.2-4.2) in the total population. CONCLUSIONS: Our data suggests that CHD is the major cardiovascular condition associated with asthma; a prospective study must be done to confirm a causal relationship.

Evidence of lung function for stratification of cardiovascular disease risk.

Among adults in the United States, the prevalence of reduced lung function including obstructive and restrictive lung disease is about 20%, representing an over 40 million adults. Persons with reduced lung function often demonstrate chronic systemic inflammation, such as from elevated levels of C-reactive protein. Substantial data suggests that inflammation may have a significant role in the association between reduced lung function and cardiovascular disease (CVD); however, how reduced lung function predicts CVD as risk modification remains largely unknown. Poor lung function has been shown to be a better predictor of all-cause and cardiac-specific mortality than established risk factors such as serum cholesterol, and CVD is the leading cause of mortality among those with impaired lung function. The exact mechanism of atherosclerosis is not clear, but persistent low grade inflammation is considered as one of the culprits in clot formation. The initial presentation of coronary heart disease is either myocardial infarction or sudden death in approximately half of the individuals. Unfortunately, conventional risk factor assessment predicts only 65-80% of future cardiovascular events, leaving many middle-aged and older individuals to manifest a major cardiovascular event despite being classified low risk by the Framingham risk estimates.

High-resolution Fourier-domain optical coherence tomography of choroidal neovascular membranes associated with age-related macular degeneration.

PURPOSE: To investigate the use of high-resolution Fourier-domain optical coherence tomography (Fd-OCT) to image choroidal neovascular membranes (CNVMs) associated with exudative age-related macular degeneration (eAMD). METHODS: An Fd-OCT instrument with axial resolution of 4 to 4.5 microm and transverse resolution of 10 to 15 microm was used to image 21 eyes (19 subjects) with newly diagnosed eAMD. A raster series of 100 B-scans separated by 60 microm was used to study the growth pattern of CNVM and associated morphologic changes. CNVM size was determined using 250 to 300 serial virtual C-scans of reconstructed three-dimensional macular volume. RESULTS: A highly reflective subretinal and/or subretinal pigment epithelial (RPE) lesion that co-localized with the CNVM seen on fluorescein angiography was detected in all eyes by Fd-OCT. Although a combined subretinal and sub-RPE growth pattern of various degrees was noted in 15 (71%) eyes, a statistically significant difference in the distribution of growth pattern was noted when classic CNVM was compared with occult CNVM (chi(2) = 10.4, df = 2, P < 0.005). Classic lesions had >90% subretinal growth pattern, whereas occult lesions had a more variable growth pattern. Angiographic CNVM size correlated with size on Fd-OCT but correlation was better for classic CNVM (classic, r = 0.99, P < 0.0001; nonclassic, r = 0.78, P < 0.001). CONCLUSIONS: Fd-OCT is a promising potential alternative modality to visualize CNVM with AMD. Angiographic lesion size and type correlated with growth pattern and size of CNVM on Fd-OCT, with correlation being stronger for classic lesions.