Evaluation of novel indices of walking performance taking oxygen desaturation into account during six-minute walk test in cardiovascular disease patients.

In pulmonary disease patients since oxygen desaturation during 6-min walk test (6MWT) affects walk distance (6MWD), some novel indices such as desaturation/distance ratio [DDR, oxygen desaturation area (DAO2)/6MWD] and distance-saturation product [DSP, 6MWD × minimum peripheral oxygen saturation (SpO2)] are evaluated. However, there has been no study examining these indices that consider exercise-induced desaturation (EID) in patients with cardiovascular disease. In 94 cardiovascular disease patients without pulmonary complications, 6MWT and echocardiography were performed at the entry of cardiac rehabilitation. SpO2 was measured during 6MWT using a continuously monitorable pulse oximeter, and DSP and DDR were calculated using minimum SpO2 and DAO2 [sum of (100-SpO2) per second during 6MWT], respectively. EID was defined as SpO2 decrease of ≥ 4% or minimum SpO2 of < 90% during 6MWT. DSP was slightly lower and DDR was markedly higher in patients with EID than in those without. When examining correlations of DSP and DDR with their components, DSP was correlated with 6MWD much closely than minimum SpO2, while DDR was correlated as closely with DAO2 as 6MWD. Furthermore, DAO2, but not minimum SpO2, had a direct correlation with 6MWD. As for associations with cardiac function, DSP was correlated with several cardiac parameters, but DDR was not correlated with any of these parameters. Our findings suggest that oxygen desaturation during 6MWT affects walking distance in cardiovascular disease patients even without pulmonary complications and that DDR is more appropriate than DSP as an index of walking performance that takes EID into consideration, independently of cardiac function.

Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties.

The nucleosome is a fundamental unit of chromatin in which about 150 base pairs of DNA are wrapped around a histone octamer. The overlapping di-nucleosome has been proposed as a product of chromatin remodeling around the transcription start site, and previously found as a chromatin unit, in which about 250 base pairs of DNA continuously bind to the histone core composed of a hexamer and an octamer. In the present study, our genome-wide analysis of human cells suggests another higher nucleosome stacking structure, the overlapping tri-nucleosome, which wraps about 300-350 base-pairs of DNA in the region downstream of certain transcription start sites of actively transcribed genes. We determine the cryo-electron microscopy (cryo-EM) structure of the overlapping tri-nucleosome, in which three subnucleosome moieties, hexasome, hexasome, and octasome, are associated by short connecting DNA segments. Small angle X-ray scattering and coarse-grained molecular dynamics simulation analyses reveal that the cryo-EM structure of the overlapping tri-nucleosome may reflect its structure in solution. Our findings suggest that nucleosome stacking structures composed of hexasome and octasome moieties may be formed by nucleosome remodeling factors around transcription start sites for gene regulation.

Atomistic mechanism of structural and volume relaxation below glass transition temperature in a soda-lime silicate glass revealed by Raman spectroscopy and its DFT calculations.

To elucidate the atomistic origin of volume relaxation in soda-lime silicate glass annealed below the glass transition temperature (Tg), the experimental and calculated Raman spectra were compared. By decomposing the calculated Raman spectra into specific groups of atoms, the Raman peaks at 800, 950, 1050, 1100, and 1150 cm-1 were attributed to oxygen and silicon in Si-O-Si, non-bridging oxygen in the Q2 unit, bridging oxygen in low-angle Si-O-Si, non-bridging oxygen in the Q4 unit, and bridging oxygen in high-angle Si-O-Si, respectively. Based on these attributions, we found that by decreasing the fictive temperature by annealing below Tg - 70 K, a homogenization reaction Q2 + Q4 → 2Q3 and an increase in average Si-O-Si angle occurred simultaneously. By molecular dynamics simulation, we clarified how the experimentally demonstrated increase in average Si-O-Si angle contributes to volume shrinkage; increasing Si-O-Si angles can expand the space inside the rings, and Na can be inserted into the ring center.

Dynamic action of an intrinsically disordered protein in DNA compaction that induces mycobacterial dormancy.

Mycobacteria are the major human pathogens with the capacity to become dormant persisters. Mycobacterial DNA-binding protein 1 (MDP1), an abundant histone-like protein in dormant mycobacteria, induces dormancy phenotypes, e.g. chromosome compaction and growth suppression. For these functions, the polycationic intrinsically disordered region (IDR) is essential. However, the disordered property of IDR stands in the way of clarifying the molecular mechanism. Here we clarified the molecular and structural mechanism of DNA compaction by MDP1. Using high-speed atomic force microscopy, we observed that monomeric MDP1 bundles two adjacent DNA duplexes side-by-side via IDR. Combined with coarse-grained molecular dynamics simulation, we revealed the novel dynamic DNA cross-linking model of MDP1 in which a stretched IDR cross-links two DNA duplexes like double-sided tape. IDR is able to hijack HU function, resulting in the induction of strong mycobacterial growth arrest. This IDR-mediated reversible DNA cross-linking is a reasonable model for MDP1 suppression of the genomic function in the resuscitable non-replicating dormant mycobacteria.

Ultra-high temperature Soret effect in a silicate melt: SiO2 migration to cold side.

The Soret effect, temperature gradient driven diffusion, in silicate melts has been investigated intensively in the earth sciences from the 1980s. The SiO2 component is generally concentrated in the hotter region of silicate melts under a temperature gradient. Here, we report that at ultra-high temperatures above ∼3000 K, SiO2 becomes concentrated in the colder region of the silicate melts under a temperature gradient. The interior of an aluminosilicate glass [63.3SiO2-16.3Al2O3-20.4CaO (mol. %)] was irradiated with a 250 kHz femtosecond laser pulse for local heating. SiO2 migrated to the colder region during irradiation with an 800 pulse (3.2 ms irradiation). The temperature analysis indicated that migration to the colder region occurred above 3060 K. In the non-equilibrium molecular dynamics (NEMD) simulation, SiO2 migrated to the colder region under a temperature gradient, which had an average temperature of 4000 K; this result supports the experimental result. On the other hand, SiO2 exhibited a tendency to migrate to the hotter region at 2400 K in both the NEMD and experimental study. The molar volume calculated by molecular dynamics simulation without a temperature gradient indicates two bends at 1650 and 3250 K under 500 MPa. Therefore, the discontinuous (first order) transition with coexistence of two phases of different composition could be related to the migration of SiO2 to colder region. However, the detailed mechanism has not been elucidated.

Visible-Light-Driven C-H Imidation of Arenes and Heteroarenes by a Phosphonium Ylide Organophotoredox Catalyst: Application to C-H Functionalization of Alkenes.

Phosphonium ylide catalysis through an oxidative quenching cycle has been developed for visible-light-driven C-H imidation of arenes and heteroarenes. The present protocol could be applied not only to trihalomethylative lactonization reactions involving trifluoromethyl, trichloromethyl, and tribromomethyl radicals but also to the first example of an organophotoredox-catalyzed imidative lactonization reaction involving a nitrogen-centered electrophilic radical species.

White epidermoid cyst transformation after stereotactic radiosurgery: illustrative case.

BACKGROUND: White epidermoid cysts (WECs) are a rare type of epidermoid cyst with atypical radiological features. The epidemiological aspects and mechanisms of their onset remain unknown. Herein, the authors report a unique case of WEC transformation from a typical epidermoid cyst after stereotactic radiosurgery (SRS), confirmed by radiological and pathological findings. OBSERVATIONS: The case involved a 78-year-old man with a history of 2 surgeries for a left cerebellopontine angle typical epidermoid cyst 23 years earlier and SRS using the CyberKnife for recurrent trigeminal neuralgia (TN) 14 years earlier. The tumor with high intensity on T1-weighted imaging, low intensity on T2-weighted imaging, without restriction on diffusion-weighted imaging had gradually enlarged after SRS. Therefore, a salvage surgery was performed via a left suboccipital craniotomy, and the intraoperative findings showed a cyst with a brown, viscous liquid component, consistent with those of WECs. Histopathologically, keratin calcification and hemorrhage were identified, leading to a diagnosis of WEC. The postoperative course was uneventful, and the TN resolved. No tumor recurrence was recorded at 2 years postoperatively. LESSONS: To the best of the authors' knowledge, this is the first world case of WEC transformation from a typical epidermoid cyst after SRS, confirmed by radiological and pathological findings. Radiation effects could have been involved in this transformation.

RNF213 p.Arg4810Lys Wild Type is Associated with De Novo Hemorrhage in Asymptomatic Hemispheres with Moyamoya Disease.

Clinical implications of RNF213 genetic variants, other than p.Arg4810Lys, in moyamoya disease (MMD), remain unclear. This study aimed to investigate the association of RNF213 variants with clinical phenotypes in MMD. This retrospective cohort study collected data regarding the clinical characteristics of 139 patients with MMD and evaluated the angioarchitectures of 253 hemispheres using digital subtraction angiography at diagnosis. All RNF213 exons were sequenced, and the associations of clinical characteristics and angiographical findings with p.Arg4810Lys, p.Ala4399Thr, and other rare variants (RVs) were examined. Among 139 patients, 100 (71.9%) had p.Arg4810Lys heterozygote (GA) and 39 (28.1%) had the wild type (GG). Fourteen RVs were identified and detetcted in 15/139 (10.8%) patients, and p.Ala4399Thr was detected in 17/139 (12.2%) patients. Hemispheres with GG and p.Ala4399Thr presented with significantly less ischemic events and more hemorrhagic events at diagnosis (p = 0.001 and p = 0.028, respectively). In asymptomatic hemispheres, those with GG were more susceptible to de novo hemorrhage than those with GA (adjusted hazard ratio [aHR] 5.36) with an increased risk when accompanied by p.Ala4399Thr or RVs (aHR 15.22 and 16.60, respectively). Within the choroidal anastomosis-positive hemispheres, GG exhibited a higher incidence of de novo hemorrhage than GA (p = 0.004). The GG of p. Arg4810Lys was a risk factor for de novo hemorrhage in asymptomatic MMD hemispheres. This risk increased with certain other variants and is observed in choroidal anastomosis-positive hemispheres. A comprehensive evaluation of RNF213 variants and angioarchitectures is essential for predicting the phenotype of asymptomatic hemispheres in MMD.

The E/e' ratio on echocardiography as an independent predictor of the improvement of left ventricular contraction in patients with heart failure with reduced ejection fraction.

OBJECTIVE: Clinical feature of heart failure with improved ejection fraction (HFimpEF) remains to be fully elucidated. The present study investigated the association of clinical and echocardiographic parameters with the subsequent improvement of left ventricular ejection fraction (LVEF) in heart failure with reduced ejection fraction (HFrEF). METHODS: From outpatients with a history of hospitalized for heart failure, 128 subjects diagnosed as HFrEF (LVEF <40%) on heart failure hospitalization were enrolled and longitudinally surveyed. During follow-up periods more than 1 year, 58 and 42 patients were identified as HFimpEF (improved LVEF to ≥40% and its increase of ≥10 points) and persistent HFrEF, respectively. RESULTS: There was no difference in age or sex between the two groups with HFimpEF and persistent HFrEF. The rate of ischemic heart disease was lower and that of tachyarrhythmia was higher in the HFimpEF group than in the persistent HFrEF group. At baseline (i.e., on heart failure hospitalization), LVEF did not differ between the two groups, but left ventricular systolic and diastolic diameters were already smaller and the ratio of early diastolic transmitral velocity to early diastolic tissue velocity (E/e') was lower in the HFimpEF group. A multiple logistic regression analysis revealed that lower baseline E/e' was a significant determinant of HFimpEF, independently of confounding factors such as ischemic heart disease, tachyarrhythmia, and baseline left ventricular dimension. CONCLUSION: Our findings indicate that the lower ratio of E/e' in the acute phase of heart failure onset is an independent predictor of the subsequent improvement of LVEF in HFrEF patients.

Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance.

Three domain fragments of a multi-domain protein, ER-60, were ligated in two short linker regions using asparaginyl endopeptidase not involving denaturation. To identify appropriate ligation sites, by selecting several potential ligation sites with fewer mutations around two short linker regions, their ligation efficiencies and the functions of the ligated ER-60s were examined experimentally. To evaluate the dependence of ligation efficiencies on the ligation sites computationally, steric hinderances around the sites for the ligation were calculated through molecular dynamics simulations. Utilizing the steric hindrance, a site-dependent ligation potential index was introduced as reproducing the experimental ligation efficiency. Referring to this index, the reconstruction of ER-60 was succeeded by the ligation of the three domains for the first time. In addition, the new ligation potential index well-worked for application to other domain ligations. Therefore, the index may serve as a more time-effective tool for multi-site ligations.

Genome-Wide Association Study of Intracranial Artery Stenosis Followed by Phenome-Wide Association Study.

The genetic background of intracranial artery stenosis (ICAS), a major cause of ischemic stroke, remains elusive. We performed the world's first genome-wide association study (GWAS) of ICAS using DNA samples from Japanese subjects, to identify the genetic factors associated with ICAS and their correlation with clinical features. We also conducted a phenome-wide association study (PheWAS) of the top variant identified via GWAS to determine its association with systemic disease. The GWAS involved 408 patients with ICAS and 349 healthy controls and utilized an Asian Screening Array of venous blood samples. The PheWAS was performed using genotypic and phenotypic data of the Biobank Japan Project, which contained information on 46 diseases and 60 quantitative trait data from > 150,000 Japanese individuals. The GWAS revealed that the East Asian-specific functional variant of RNF213, rs112735431 (c.14429G > A, p.Arg4810Lys), was associated with ICAS (odds ratio, 12.3; 95% CI 5.5 to 27.5; P = 7.8 × 10-10). Stratified analysis within ICAS cases demonstrated that clinical features of those with and without the risk allele were different. PheWAS indicated that high blood pressure and angina were significantly associated with RNF213 rs112735431. The first GWAS of ICAS, which stratifies subpopulations within the ICAS cases with distinct clinical features, revealed that RNF213 rs112735431 was the most significant variant associated with ICAS. Thus, RNF213 rs112735431 shows potential as an important clinical biomarker that characterizes pleiotropic risk in various vascular diseases, such as blood pressure and angina, thereby facilitating personalized medicine for systemic vascular diseases in East Asian populations.

Role of mixing thermodynamic properties on the Soret effect.

We demonstrate that the modified Kempers model, a recently developed theoretical model for the Soret effect in oxide melts, is applicable for predicting the composition dependence of the Soret coefficient in three binary molecular liquids with negative enthalpies of mixing. We compared the theoretical and experimental values for water/ethanol, water/methanol, water/ethylene glycol, water/acetone, and benzene/n-heptane mixtures. In water/ethanol, water/methanol, and water/ethylene glycol, which have negative enthalpies of mixing across the entire mole fraction range, the modified Kempers model successfully predicts the sign change of the Soret coefficient with high accuracy, whereas, in water/acetone and benzene/n-heptane, which have composition ranges with positive enthalpies of mixing, it cannot predict the sign change of the Soret coefficient. These results suggest that the model is applicable in composition ranges with negative enthalpies of mixing and provides a framework for predicting and understanding the Soret effect from the equilibrium thermodynamic properties of mixing, such as the partial molar volume, partial molar enthalpy of mixing, and chemical potential.

Biohybrid robots: recent progress, challenges, and perspectives.

The past ten years have seen the rapid expansion of the field of biohybrid robotics. By combining engineered, synthetic components with living biological materials, new robotics solutions have been developed that harness the adaptability of living muscles, the sensitivity of living sensory cells, and even the computational abilities of living neurons. Biohybrid robotics has taken the popular and scientific media by storm with advances in the field, moving biohybrid robotics out of science fiction and into real science and engineering. So how did we get here, and where should the field of biohybrid robotics go next? In this perspective, we first provide the historical context of crucial subareas of biohybrid robotics by reviewing the past 10+ years of advances in microorganism-bots and sperm-bots, cyborgs, and tissue-based robots. We then present critical challenges facing the field and provide our perspectives on the vital future steps toward creating autonomous living machines.

WNK1/HSN2 mediates neurite outgrowth and differentiation via a OSR1/GSK3ß-LHX8 pathway.

With no lysine kinase 1 (WNK1) phosphorylates and activates STE20/SPS1-related proline-alanine-rich protein kinase (SPAK) and oxidative stress responsive kinase 1 (OSR1) to regulate ion homeostasis in the kidney. Mutations in WNK1 result in dysregulation of the WNK1-SPAK/OSR1 pathway and cause pseudohypoaldosteronism type II (PHAII), a form of hypertension. WNK1 is also involved in the autosomal recessive neuropathy, hereditary sensory and autonomic neuropathy type II (HSANII). Mutations in a neural-specific splice variant of WNK1 (HSN2) cause HSANII. However, the mechanisms underlying HSN2 regulation in neurons and effects of HSN2 mutants remain unclear. Here, we found that HSN2 regulated neurite outgrowth through OSR1 activation and glycogen synthase kinase 3ß (GSK3ß). Moreover, HSN2-OSR1 and HSN2-GSK3ß signalling induced expression of LIM homeobox 8 (Lhx8), which is a key regulator of cholinergic neural function. The HSN2-OSR1/GSK3ß-LHX8 pathway is therefore important for neurite outgrowth. Consistently, HSN2 mutants reported in HSANII patients suppressed SPAK and OSR1 activation and LHX8 induction. Interestingly, HSN2 mutants also suppressed neurite outgrowth by preventing interaction of between wild-type HSN2 and GSK3ß. These results indicate that HSN2 mutants cause dysregulation of neurite outgrowth via GSK3ß in the HSN2 and/or WNK1 pathways.

Composition-dependent sign inversion of the Soret coefficient of SiO2 in binary borosilicate melts.

Using a laser-induced local-heating experiment combined with temperature analysis, we observed the composition-dependent sign inversion of the Soret coefficient of SiO2 in binary silicate melts, which was successfully explained by a modified Kempers model used for describing the Soret effect in oxide melts. In particular, the diffusion of SiO2 to the cold side under a temperature gradient, which is an anomaly in silicate melts, was observed in the SiO2-poor compositions. The theoretical model indicates that the thermodynamic mixing properties of oxides, partial molar enthalpy of mixing, and partial molar volume are the dominant factors for determining the migration direction of the SiO2 component under a temperature gradient.

Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations.

Solving structural ensembles of flexible biomolecules is a challenging research area. Here, we propose a method to obtain possible structural ensembles of a biomolecule based on small-angle X-ray scattering (SAXS) and molecular dynamics simulations. Our idea is to clip a time series that matches a SAXS profile from a simulation trajectory. To examine its practicability, we applied our idea to a multi-domain protein ER-60 and successfully extracted time series longer than 1 micro second from trajectories of coarse-grained molecular dynamics simulations. In the extracted time series, the domain conformation was distributed continuously and smoothly in a conformational space. Preferred domain conformations were also observed. Diversity among scattering curves calculated from each ER-60 structure was interpreted to reflect an open-close motion of the protein. Although our approach did not provide a unique solution for the structural ensemble of the biomolecule, each extracted time series can be an element of the real behavior of ER-60. Considering its low computational cost, our approach will play a key role to identify biomolecular dynamics by integrating SAXS, simulations, and other experiments.

Speciation of tin ions in oxide glass containing iron oxide through solvent extraction and inductively coupled plasma atomic emission spectrometry after the decomposition utilizing ascorbic acid.

Determining the concentrations of different Sn ions in glass containing iron oxide by wet chemical analysis is a challenge because a redox reaction occurs between Sn2+ and Fe3+. A chemical analysis method for determining the concentrations of Sn2+ and Sn4+ in soda lime glass containing iron oxide was proposed. A mixture of ascorbic acid, hydrochloric acid, and hydrofluoric acid was used to decompose the sample in a vessel with nitrogen flow. Ascorbic acid functioned as a reductant for Fe3+. Subsequently, the Sn2+ were separated as a diethyldithiocarbamate complex. Furthermore, inductively coupled plasma atomic emission spectroscopy was used to determine the concentrations of Sn4+ and total Sn, from which the concentration of Sn2+ can be calculated. The results were validated by comparing ratios of Sn2+ to total Sn to results obtained using Mössbauer spectroscopy. The results were in agreement, thereby validating the use of the proposed approach.

Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach.

In the cyanobacterial circadian clock system, KaiA, KaiB and KaiC periodically assemble into a large complex. Here we determined the overall structure of their fully assembled complex by integrating experimental and computational approaches. Small-angle X-ray and inverse contrast matching small-angle neutron scatterings coupled with size-exclusion chromatography provided constraints to highlight the spatial arrangements of the N-terminal domains of KaiA, which were not resolved in the previous structural analyses. Computationally built 20 million structural models of the complex were screened out utilizing the constrains and then subjected to molecular dynamics simulations to examine their stabilities. The final model suggests that, despite large fluctuation of the KaiA N-terminal domains, their preferential positionings mask the hydrophobic surface of the KaiA C-terminal domains, hindering additional KaiA-KaiC interactions. Thus, our integrative approach provides a useful tool to resolve large complex structures harboring dynamically fluctuating domains.

Enhanced O-GlcNAc modification induced by the RAS/MAPK/CDK1 pathway is required for SOX2 protein expression and generation of cancer stem cells.

Cancer stem cells (CSCs) have tumour initiation, self-renewal, and long-term tumour repopulation properties, and it is postulated that differentiated somatic cells can be reprogrammed to CSCs by oncogenic signals. We previously showed that oncogenic HRASV12 conferred tumour initiation capacity in tumour suppressor p53-deficient (p53-/-) primary mouse embryonic fibroblasts (MEFs) through transcription factor NF-κB-mediated enhancement of glucose uptake; however, the underlying mechanisms of RAS oncogene-induced CSC reprogramming have not been elucidated. Here, we found that the expression of the reprogramming factor SOX2 was induced by HRASV12 in p53-/- MEFs. Moreover, gene knockout studies revealed that SOX2 is an essential factor for the generation of CSCs by HRASV12 in mouse and human fibroblasts. We demonstrated that HRASV12-induced cyclin-dependent kinase 1 (CDK1) activity and subsequent enhancement of protein O-GlcNAcylation were required for SOX2 induction and CSC generation in these fibroblasts and cancer cell lines containing RAS mutations. Moreover, the CDK inhibitor dinaciclib and O-GlcNAcylation inhibitor OSMI1 reduced the number of CSCs derived from these cells. Taken together, our results reveal a signalling pathway and mechanism for CSC generation by oncogenic RAS and suggest the possibility that this signalling pathway is a therapeutic target for CSCs.

An ultrafast piezoelectric Z-scanner with a resonance frequency above 1.1 MHz for high-speed atomic force microscopy.

The Z-scanner is the major component limiting the speed performance of all current high-speed atomic force microscopy systems. Here, we present an ultrafast piezoelectric Z-scanner with a resonance frequency above 1.1 MHz, achieving a record response time of ∼0.14 µs, approximately twice as fast as conventional piezoelectric-based Z-scanners. In the mechanical design, a small piezo-stack is supported at its bottom four vertices on a cone-like hollow, allowing the resonance frequency of the Z-scanner to remain as high as that of the piezo in free vibration. Its maximum displacement, ∼190 nm at 50 V, is large enough for imaging bio-molecules. For imaging bio-molecules in a buffer solution, the upper half of the Z-scanner is wrapped in a thin film resistant to water and chemicals, providing an excellent waterproof and mechanical durability without lowering the resonance frequency. We demonstrate that this Z-scanner can observe actin filaments, fragile biological polymers, for more than five times longer than the conventional Z-scanner at a tip velocity of 800 µm/s.