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Sarcopenia, a condition characterized by muscle weakness and mass loss, poses significant risks of accidents and complications. Traditional diagnostic methods often rely on physical function measurements like handgrip strength which can be challenging for affected patients, including those with stroke. To address these challenges, we propose a novel sarcopenia diagnosis model utilizing stimulated muscle contraction signals captured via wearable devices. Our approach achieved impressive results, with an accuracy of 93% and 100% in sarcopenia classification for male and female stroke patients, respectively. These findings underscore the significance of our method in diagnosing sarcopenia among stroke patients, offering a non-invasive and accessible solution., Competing Interests: Conflict of Interest: The authors have no potential conflicts of interest to disclose., (Copyright © 2024. Korean Society for Neurorehabilitation.)

Background and Purpose: Falls are not uncommon even in patients with early stages of Parkinson's disease (PD). The aims of this study were to determine the relationships between gait parameters and falls and identify crucial gait parameters for predicting future falls in patients with de novo PD., Methods: We prospectively recruited patients with de novo PD, and evaluated their baseline demographics, global cognitive function on the Montreal Cognitive Assessment test, and parkinsonian motor symptoms including their subtypes. Both forward gait (FG) and backward gait (BG) were measured using the GAITRite system. The history of falls in consecutive patients with de novo PD was examined along with 1 year of follow-up data., Results: Among the 76 patients with de novo PD finally included in the study, 16 (21.1%) were classified as fallers. Fallers had slower gait and shorter stride for FG and BG parameters than did non-fallers, while stride-time variability was greater in fallers but only for BG. Multivariable logistic regression analysis revealed that slow gait was an independent risk factor in BG., Conclusions: Among the patients with de novo PD, gait speed and stride length were more impaired for both FG and BG in fallers than in non-fallers. It was particularly notable that slow BG was significantly associated with future fall risk, indicating that BG speed is a potential biomarker for predicting future falls in patients with early-stage PD., Competing Interests: Kyum-Yil Kwon, a contributing editor of the Journal of Clinical Neurology, was not involved in the editorial evaluation or decision to publish this article. All remaining authors have declared no conflicts of interest., (Copyright © 2024 Korean Neurological Association.)

Introduction: Clarithromycin resistance is a crucial factor in the eradication of Helicobacter pylori. This study aimed to evaluate the performance of MmaxSure™ H. pylori & ClaR Assay (MmaxSure™) in the diagnosis and detection of clarithromycin resistance in H. pylori., Methods: Subjects who underwent esophagogastroduodenoscopy between April 2020 and October 2022 were enrolled. The diagnostic performances of MmaxSure™ and dual priming oligonucleotide (DPO)-based multiplex polymerase chain reaction (PCR) were compared with the rapid urease test and culture. Secondary gene sequencing analysis was performed in discordant cases of PCR tests., Results: A total of 156 gastric biopsy samples were analyzed. In H. pylori detection, MmaxSure™ showed a 95.9% sensitivity (95% CI: 90.6-98.6), a 42.7% specificity (95% CI: 26.3-60.7), and a kappa value of 0.457. For the detection of A2143G mutation samples, MmaxSure™ showed a 91.2% sensitivity (95% CI: 76.3-98.1), a 93.4% specificity (95% CI: 87.5-97.1), and a kappa value of 0.804. There were a total of 10 discordant cases compared to gene sequencing in A2143G mutation detection for MmaxSure™., Conclusion: In this study, MmaxSure™ showed comparable diagnostic performance to DPO-PCR in the detection of the H. pylori and A2143G mutation. Further research is needed to confirm the clinical effectiveness of the MmaxSure™ assay in H. pylori eradication., (© 2024 The Author(s). Published by S. Karger AG, Basel.)

Background: Identifying clarithromycin resistance is essential for eradicating Helicobacter pylori (HP). Therefore, we evaluated the performance of Allplex™ H.pylori & ClariR Assay (Allplex™) for diagnosing and detecting clarithromycin resistance in HP., Methods: Subjects who underwent esophagogastroduodenoscopy between April 2020 and August 2021 at Incheon St. Mary's hospital were enrolled in this study. The diagnostic performances of Allplex™ and dual priming oligonucleotide (DPO)-based multiplex polymerase chain reaction (PCR) were compared with sequencing as the gold standard., Results: A total of 142 gastric biopsy samples were analyzed. Gene sequencing revealed 124 HP infections, 42 A2143G mutations, 2 A2142G mutations, one dual mutation, and no A2142C mutation. DPO-PCR showed 96.0% sensitivity and 100.0% specificity for HP detection; the corresponding rates for Allplex™ were 99.2% and 100.0%. DPO-PCR showed 88.3% sensitivity and 82.0% specificity for A2143G mutation, and Allplex™ showed 97.6% and 96.0%. The Cohen's Kappa coefficient for overall test results was 0.56 for DPO-PCR and 0.95 for Allplex™., Conclusion: Allplex™ showed comparable diagnostic performance with direct gene sequencing and non-inferior diagnostic performance to DPO-PCR. Further research is required to confirm whether Allplex™ is an effective diagnostic tool for the eradication of HP., (© 2023. The Author(s).)

Recently, high-efficiency III-nitride photonic emitters (PEs) for next-generation displays have been studied. Although micro-light-emitting diodes (μ-LEDs), one of the III-nitride PEs, have attracted considerable attention because of their high efficiency and size flexibility, they have encountered technical limitations such as high defect rate, high processing cost, and low yield. To overcome these drawbacks of μ-LEDs, a lot of research on PEs using one-dimensional (1D) gallium nitride-related nanorods (GNRs) capable of horizontally self-positioning on the electrodes has been carried out. The degree of array of GNRs on the interdigitated electrodes (IDEs) is an important factor in the efficiency of the PEs using GNRs to obtain excellent single-pixel characteristics. Therefore, in this study, we demonstrate that the improved performance of self-arrayed GNRs was realized using the dielectrophoresis technique by changing the thickness of IDEs. In addition, the shape and size of vertically aligned GNRs were controlled by the wet process, and GNR-integrated PEs (GIPEs) were driven by perfectly horizontally self-arrayed GNRs on IDEs. The electroluminescence (EL) intensity of the GIPEs was measured at 4-20 V and showed a maximum intensity value at 15 V. Over the injection voltage at 20 V, the EL intensity decreased due to the high current density of GIPEs. The external quantum efficiency (EQE) property of the GIPEs showed a similar efficiency droop as that of conventional III-nitride PEs., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Background/aims: Recent epidemiologic studies have shown a continued increase in colorectal cancer incidence among younger adults. Little is known about the factors that contribute to the development of young-onset colorectal neoplasia (CRN)., Methods: A cross-sectional analysis was performed for individuals younger than 40 years who underwent colonoscopy in Seoul St. Mary's Hospital and its affiliated health screening center. High-risk CRN was defined as adenoma or sessile serrated lesion ≥ 10 mm, with three or more adenomas, villous histology, high grade dysplasia, or carcinoma., Results: Of these 13,621 included participants, 2,023 (14.9%) had one and more CRN. Young patients with CRN tended to be elderly, male, obese, smoker, having a habit of drinking, and having comorbidities such as hypertension, dyslipidemia, diabetes, and chronic kidney disease. In a multivariate analysis adjusted for age, sex, obesity, smoking status, and alcohol intake, old age (odds ratio [OR], 1.086; 95% confidence interval [CI], 1.054 to 1.119), male sex (OR, 1.748; 95% CI, 1.247 to 2.451), obesity (OR, 1.439; 95% CI, 1.133 to 1.828), and smoking (OR, 1.654; 95% CI, 1.287 to 2.127) were independent risk factors for overall CRN. Obesity and smoking as two modifiable factors increased the risk for high-risk CRN even more than for overall CRN (OR, 1.734; 95% CI, 1.168 to 2.575 and OR, 1.797; 95% CI, 1.172 to 2.753, respectively)., Conclusion: Obesity and smoking were modifiable risk factors for CRN in young adults. They increased the risk for highrisk CRN even more than for overall CRN. A colonoscopy might be beneficial for young individuals with these factors.

Objectives: This study aimed to compare susceptibility map-weighted imaging (SMwI) using various MRI machines (three vendors) with N-3-fluoropropyl-2-β-carbomethoxy-3-β-(4-iodophe nyl)nortropane ( 18 F-FP-CIT) PET in the diagnosis of neurodegenerative parkinsonism in a multi-centre setting., Methods: We prospectively recruited 257 subjects, including 157 patients with neurodegenerative parkinsonism, 54 patients with non-neurodegenerative parkinsonism, and 46 healthy subjects from 10 hospitals between November 2019 and October 2020. All participants underwent both SMwI and 18 F-FP-CIT PET. SMwI was interpreted by two independent reviewers for the presence or absence of abnormalities in nigrosome 1, and discrepancies were resolved by consensus. 18 F-FP-CIT PET was used as the reference standard. Inter-observer agreement was tested using Cohen's kappa coefficient. McNemar's test was used to test the agreement between the interpretations of SMwI and 18 F-FP-CIT PET per participant and substantia nigra (SN)., Results: The inter-observer agreement was 0.924 and 0.942 per SN and participant, respectively. The diagnostic sensitivity of SMwI was 97.9% and 99.4% per SN and participant, respectively; its specificity was 95.9% and 95.2%, respectively, and its accuracy was 97.1% and 97.7%, respectively. There was no significant difference between the results of SMwI and 18 F-FP-CIT PET (p > 0.05, for both SN and participant)., Conclusions: This study demonstrated that the high diagnostic performance of SMwI was maintained in a multi-centre setting with various MRI scanners, suggesting the generalisability of SMwI for determining nigrostriatal degeneration in patients with parkinsonism., Key Points: • Susceptibility map-weighted imaging helps clinicians to predict nigrostriatal degeneration. • The protocol for susceptibility map-weighted imaging can be standardised across MRI vendors. • Susceptibility map-weighted imaging showed diagnostic performance comparable to that of dopamine transporter PET in a multi-centre setting with various MRI scanners., (© 2021. The Author(s), under exclusive licence to European Society of Radiology.)

Near-eye display technology is a rapidly growing field owing to the recent emergence of augmented and mixed reality. Ultrafast response time, high resolution, high luminance, and a dynamic range for outdoor use are all important for non-pixelated, pupil-forming optics. The current mainstream technologies using liquid crystals and organic materials cannot satisfy all these conditions. Thus, finely patterned light-emissive solid-state devices with integrated circuits are often proposed to meet these requirements. In this study, we integrated several advanced technologies to design a prototype microscale light-emitting diode (LED) arrays using quantum dot (QD)-based color conversion. Wafer-scale epilayer transfer and the bond-before-pattern technique were used to directly integrate 5-µm-scale GaN LED arrays on a foreign silicon substrate. Notably, the lithography-level alignment with the bottom wafer opens up the possibility for ultrafast operation with circuit integration. Spectrally pure color conversion and solvent-free QD patterning were also achieved using an elastomeric topographical mask. Self-assembled monolayers were applied to selectively alter the surface wettability for a completely dry process. The final emissive-type LED array integrating QD, GaN, and silicon technology resulted in a 1270 PPI resolution that is far beyond the retinal limit., (© 2022. The Author(s).)

Objective: The aim of this study was to assess the effects of dancing (using the Feldenkrais method) on motor and non-motor symptoms, quality of life (QoL), and objective parameters of gait at the time of intervention and at the end of the 1-year study period., Methods: This was a single-arm study in which 12 subjects with Parkinson's disease (PD) received dance intervention during a 6-month period. Objective motor scales, gait analysis, and questionnaires on non-motor symptoms were evaluated at baseline and at 3, 6, and 12 months., Results: Dance intervention decreased motor scale (Unified Parkinson's Disease Rating Scale and Tinetti scale) scores and improved gait disturbance (gait velocity and step length) without increasing levodopa equivalent dose. Furthermore, dancing decreased non-motor scale (Non-Motor Symptoms Scale and Montgomery-Asberg Depression Rating Scale) scores and improved QoL., Conclusion: Our findings suggest that dance intervention can be a complementary management method for PD patients.

Objective: The Four Square Step Test (FSST) is a tool that assesses dynamic balance during obstacle step-over. To date, few studies have used the FSST to measure balance in patients with Parkinson's disease (PD). This study aimed to verify that patients with PD, even at the de novo early stage, take more time to perform the FSST and identify which factors, cognitive status or cardinal motor symptoms, are related most to FSST scores., Methods: Thirty-five newly diagnosed drug-naïve patients with PD and 17 controls completed the FSST. The Unified Parkinson's Disease Rating Scale (UPDRS), Hoehn and Yahr (H&Y) stage, spatiotemporal gait parameters, and neuropsychological test battery were also assessed in the PD group., Results: Mean FSST performance time was 8.20 ± 1.61 seconds in patients with PD, which was significantly more than the control group (7.13 ± 1.10 seconds, p = 0.018). UPDRS part III total score and H&Y stage were not significantly associated with FSST, but among the UPDRS subscores, only the postural instability/gait disturbance subscore showed a significant association. Regarding the association between FSST and cognition, the Trail Making Test-B and the Color Word Stroop Test showed strongly inverse correlations with FSST (rho = -0.598 and -0.590, respectively). With respect to gait parameters, double support time was significantly associated with FSST score (rho = 0.342, p = 0.044); however, other parameters, including velocity and step length, were not associated with the FSST., Conclusion: The FSST can be used in the clinic to assess dynamic balance with cognitive demands even in the early stages of PD.

Milk fat globule-EGF factor 8 (MFG-E8) is an anti-inflammatory glycoprotein that mediates a wide spectrum of pathophysiological processes. MFG-E8 has been studied as a key regulator of cancer cell invasion, migration, and proliferation in different tissues and organs. However, potential roles of MFG-E8 in the growth and progression of liver cancer have not been investigated to date. Here, we analyzed 33 human hepatocellular carcinoma (HCC) samples and found that levels of MFG-E8 expression were significantly higher in HCC cells than in normal liver tissues. In addition, our in vitro gain-of-function study in three different HCC cell lines revealed that overexpression of MFG-E8 promoted the proliferation and migration of HCC cells, as determined by RT-qPCR, MTT assays, and wound healing analyses. Conversely, an MFG-E8 loss-of function study showed that proliferation capacity was significantly reduced by MFG-E8 knockdown in HCC cells. Additionally, MFG-E8 activity-neutralizing antibodies profoundly inhibited both migration and proliferation of HCC cells, attenuating their tumorigenic properties. These reductions in migration and proliferation were rescued by treatment of HCC cells with recombinant MFG-E8 protein. Furthermore, an in vivo HCC xenograft study showed that the number of proliferating HCC cells and tumor volume/weight were all significantly increased by MFG-E8 overexpression, compared to control mice. These results clearly show that MFG-E8 plays an important role in HCC progression and may provide a basis for future mechanistic studies and new strategies for the treatment of liver cancer., Competing Interests: The authors declare no conflict of interest.

In this study, HIV-1 Rev response element (RRE) RNA was detected via an Au-coated vertical silicon nanowire electrode array (VSNEA). The VSNEA was fabricated by combining bottom-up and top-down approaches and then immobilized by artificial peptides for the recognition of HIV-1 RRE. Differential pulse voltammetry (DPV) analysis was used to measure the electrochemical response of the peptide-immobilized VSNEA to the concentration and types of HIV-1 RRE RNA. DPV peaks showed linearity to the concentration of RNA with a detection limit down to 1.513 fM. It also showed the clear different peaks to the mutated HIV-1 RRE RNA. The high sensitivity and selectivity of VSNEA for the detection of HIV-1 RRE RNA may be attributed to the high surface-to-volume ratio and total overlap diffusion mode of ions of the one-dimensional nanowire electrodes.

Measurements of voltage changes in response to charge separation within membrane proteins can offer fundamental information on spectroscopically "invisible" steps. For example, results from studies of voltage changes associated with electron and proton transfer in cytochrome c oxidase could, in principle, be used to discriminate between different theoretical models describing the molecular mechanism of proton pumping. Earlier analyses of data from these measurements have been based on macroscopic considerations that may not allow for exploring the actual molecular mechanisms. Here, we have used a coarse-grained model describing the relation between observed voltage changes and specific charge-transfer reactions, which includes an explicit description of the membrane, the electrolytes, and the electrodes. The results from these calculations offer mechanistic insights at the molecular level. Our main conclusion is that previously assumed mechanistic evidence that was based on electrogenic measurements is not unique. However, the ability of our calculations to obtain reliable voltage changes means that we have a tool that can be used to describe a wide range of electrogenic charge transfers in channels and transporters, by combining voltage measurements with other experiments and simulations to analyze new mechanistic proposals.

Nonequilibrium pulling simulations have been a useful approach for investigating a variety of physical and biological problems. The major target in the simulations is to reconstruct reliable potentials of mean force (PMFs) or unperturbed free-energy profiles for quantitatively addressing both equilibrium mechanistic properties and contributions from nonequilibrium processes. While several current nonequilibrium methods were shown to be accurate in computing free-energy profiles in systems with relatively simple dynamics, they have proved to be unsuitable in more complicated systems. To extend the applicability of nonequilibrium sampling, we demonstrate a novel method that combines Minh-Adib's bidirectional estimator with nonlinear WHAM equations to reconstruct and assess PMFs from relatively fast pulling trajectories. We test the method in a one-dimensional model system and in a system of an antibiotic gramicidin-A (gA) channel, which is considered a significant challenge for nonequilibrium sampling. We identify key parameters for efficiently performing pulling simulations to improve and ensure the convergence and accuracy of estimated PMFs. We show that a few pulling trajectories of a relatively fast pulling speed v = 10 Å/ns can return a fair estimate of the PMF of a single potassium ion in gA.

The voltage sensitivity of membrane proteins is reflected in the response of the voltage sensing domains (VSDs) to the changes in membrane potential. This response is implicated in the displacement of positively charged residues, associated with the conformational changes of VSDs. The displaced charges generate nonlinear (i.e., voltage-dependent) capacitance current called the gating current (and its corresponding gating charge), which is a key experimental quantity that characterizes voltage activation in VSMP. However, the relevant theoretical/computational approaches, aimed to correlate the structural information on VSMP to electrophysiological measurements, have been rather limited, posing a broad challenge in computer simulations of VSMP. Concomitant with the development of our coarse-graining (CG) model of voltage coupling, we apply our theoretical framework for the treatments of voltage effects in membrane proteins to modeling the VSMP activation, taking the VSDs (Ci-VSD) derived from the Ciona intestinalis voltage sensitive phosphatase (Ci-VSP) as a model system. Our CG model reproduces the observed gating charge of Ci-VSD activation in several different perspectives. In particular, a new closed-form expression of the gating charge is evaluated in both nonequilibrium and equilibrium ways, while considering the fluctuation-dissipation relation that connects a nonequilibrium measurement of the gating charge to an equilibrium measurement of charge fluctuations (i.e., the voltage-independent linear component of membrane capacitance). In turn, the expression uncovers a novel link that connects an equilibrium measurement of the voltage-independent linear capacitance to a nonequilibrium measurement of the voltage-dependent nonlinear capacitance (whose integral over voltage is equal to the gating charge). In addition, our CG model yields capacitor-like voltage dependent free energy parabolas, resulting in the free energy difference and the free energy barrier for the Ci-VSD activation at "zero" (depolarization) membrane potential. Significantly, the resultant voltage dependent energetics enables a direct evaluation of capacitance-voltage relationship (C-V curve) as well as charge-voltage relationship (Q-V curve) that is in a good agreement with the observed measurement of Ci-VSD voltage activation. Importantly, an extension of our kinetic/thermodynamic model of voltage dependent activation in VSMP allows for novel derivations of voltage-dependent rate constants, whose parameters are expressed by the intrinsic properties of VSMP. These novel closed-form expressions offer a physicochemical foundation for the semiempirical Eyring-type voltage dependent rate equations that have been the cornerstone for the phenomenological (kinetic) descriptions of gating and membrane currents in the mechanistic study of ion channels and transporters. Our extended theoretical framework developed in the present study has potential implications on the roles played by gating charge fluctuations for the spike generations in nerve cells within the framework of the Hodgkin-Huxley-type model.

Obtaining a quantitative description of the membrane proteins stability is crucial for understanding many biological processes. However the advance in this direction has remained a major challenge for both experimental studies and molecular modeling. One of the possible directions is the use of coarse-grained models but such models must be carefully calibrated and validated. Here we use a recent progress in benchmark studies on the energetics of amino acid residue and peptide membrane insertion and membrane protein stability in refining our previously developed coarse-grained model (Vicatos et al., Proteins 2014;82:1168). Our refined model parameters were fitted and/or tested to reproduce water/membrane partitioning energetics of amino acid side chains and a couple of model peptides. This new model provides a reasonable agreement with experiment for absolute folding free energies of several β-barrel membrane proteins as well as effects of point mutations on a relative stability for one of those proteins, OmpLA. The consideration and ranking of different rotameric states for a mutated residue was found to be essential to achieve satisfactory agreement with the reference data., (© 2015 Wiley Periodicals, Inc.)

The two-dimensional (2D) growth of cubic-structured (silicon) Si nanosheets (SiNSs) was investigated. Freestanding, single-crystalline SiNSs with a thickness of 5-20 nm were grown on various Si substrates under an atmospheric chemical vapor deposition process. Systematic investigation indicated that a diffusion-limited aggregation (DLA) environment that leads to dendritic growth in <110> directions at the initial stage is essential for 2D growth. The kinetic aspects under DLA environments that ascribe to the dendritic and 2D growth were discussed. Under the more dilute conditions made by addition of Ar to the flow of H2, the SiNSs grew epitaxially on the substrates with periodic arrangement at a specific angle depending on the orientation of the substrate. It reveals that SiNSs always grew two dimensionally with exposing (111) surfaces. That is thermodynamically favorable.

A general theoretical framework is developed to account for the effects of an external potential on the energetics of membrane proteins. The framework is based on the free energy relation between two (forward/backward) probability densities, which was recently generalized to non-equilibrium processes, culminating in the work-fluctuation theorem. Starting from the probability densities of the conformational states along the "voltage coupling" reaction coordinate, we investigate several interconnected free energy relations between these two conformational states, considering voltage activation of ion channels. The free energy difference between the two conformational states at zero (depolarization) membrane potential (i.e., known as the chemical component of free energy change in ion channels) is shown to be equivalent to the free energy difference between the two "equilibrium" (resting and activated) conformational states along the one-dimensional voltage couplin reaction coordinate. Furthermore, the requirement that the application of linear response approximation to the free energy functionals of voltage coupling should satisfy the general free energy relations, yields a novel closed-form expression for the gating charge in terms of other basic properties of ion channels. This connection is familiar in statistical mechanics, known as the equilibrium fluctuation-response relation. The theory is illustrated by considering the coupling of a unit charge to the external voltage in the two sites near the surface of membrane, representing the activated and resting states. This is done using a coarse-graining (CG) model of membrane proteins, which includes the membrane, the electrolytes and the electrodes. The CG model yields Marcus-type voltage dependent free energy parabolas for the response of the electrostatic environment (electrolytes etc.) to the transition from the initial to the final configuratinal states, leading to equilibrium free energy difference and free energy barrier that follow the trend of the equilibrium fluctuation relation and the Marcus theory of electron transfer. These energetics also allow for a direct estimation of the voltage dependence of channel activation (Q-V curve), offering a quantitative rationale for a correlation between the voltage dependence parabolas and the Q-V curve, upon site-directed mutagenesis or drug binding. Taken together, by introducing the voltage coupling as the energy gap reaction coordinate, our framework brings new perspectives to the thermodynamic models of voltage activation in voltage-sensitive membrane proteins, offering an a framework for a better understating of the structure-function correlations of voltage gating in ion channels as well as electrogenic phenomena in ion pumps and transporters. Significantly, this formulation also provides a powerful bridge between the CG model of voltage coupling and the conventional macroscopic treatments., (Copyright © 2015 Elsevier B.V. All rights reserved.)

The behavior of mammalian cells on vertical nanowire (NW) arrays, including cell spreading and the dynamic distribution of focal adhesions and cytoskeletal proteins, has been intensively studied to extend the implications for cellular manipulations in vitro. Prompted by the result that cells on silicon (Si) NWs showed morphological changes and reduced migration rates, we have explored the transition of mesenchymal stem cells into a neuronal lineage by using SiNWs with varying lengths. When human mesenchymal stem cells (hMSCs) were cultured on the longest SiNWs for 3 days, most of the cells exhibited elongated shapes with neurite-like extensions and dot-like focal adhesions that were prominently observed along with actin filaments. Under these circumstances, the cell motility analyzed by live cell imaging was found to decrease due to the presence of SiNWs. In addition, the slowed growth rate, as well as the reduced population of S phase cells, suggested that the cell cycle was likely arrested in response to the differentiation process. Furthermore, we measured the mRNA levels of several lineage-specific markers to confirm that the SiNWs actually induced neuron-like differentiation of the hMSCs while hampering their osteogenic differentiation. Taken together, our results implied that SiNWs were capable of inducing active reorganization of cellular behaviors, collectively guiding the fate of hMSCs into the neural lineage even in the absence of any inducing reagent.

Electrical stimulation through direct electrical activation has been widely used to recover the function of neurons, primarily through the extracellular application of thin film electrodes. However, studies using extracellular methods show limited ability to reveal correlations between the cells and the electrical stimulation due to interference from external sources such as membrane capacitance and culture medium. Here, we demonstrate long-term intracellular electrical stimulation of undamaged pheochromocytoma (PC-12) cells by utilizing a vertical nanowire electrode array (VNEA). The VNEA was prepared by synthesizing silicon nanowires on a Si substrate through a vapor-liquid-solid (VLS) mechanism and then fabricating them into electrodes with semiconductor nanodevice processing. PC-12 cells were cultured on the VNEA for 4 days with intracellular electrical stimulation and then a 2-day stabilization period. Periodic scanning via two-photon microscopy confirmed that the electrodes pierced the cells without inducing damage. Electrical stimulation through the VNEA enhances cellular differentiation and neurite outgrowth by about 50% relative to extracellular stimulation under the same conditions. VNEA-mediated stimulation also revealed that cellular differentiation and growth in the cultures were dependent on the potential used to stimulate them. Intracellular stimulation using nanowires could pave the way for controlled cellular differentiation and outgrowth studies in living cells.

We grew silicon nanowires (SiNWs) by a vapor-liquid-solid (VLS) mechanism using metal catalysts of gold (Au), titanium (Ti), manganese (Mn), and iron (Fe) under a high flow rate of hydrogen (H2). This combination of catalyst types and high gas flow rate revealed the potential for growing various SiNWs, including kinked SiNWs (with Au), ultra-thin SiNWs having diameters about 5 nm (with Ti), rough-surfaced SiNWs (with Mn), and ribbon-shaped SiNWs tens of microns in width (with Fe). The high flow rate of gas affects the VLS mechanism differently for each combination; for example, it induces an unstable solid-liquid interfaces (with Au), active etching of the catalyst (with Ti), sidewall deposition by a vapor-solid (VS) mechanism, and an asymmetric precipitation of Si in the catalyst (with Fe). Our combinatorial approach may provide a new path for the structural modulation of SiNWs via the VLS mechanism., Pacs: 80; 81; 82.

Measurements of voltage changes in response to charge separation within membrane proteins can offer fundamental information on mechanisms of charge transport and displacement processes. A recent example is provided by studies of cytochrome c oxidase. However, the interpretation of the observed voltage changes in terms of the number of charge equivalents and transfer distances is far from being trivial or unique. Using continuum approaches to describe the voltage generation may involve significant uncertainties and reliable microscopic simulations are not yet available. Here, we attempt to solve this problem by using a coarse-grained model of membrane proteins, which includes an explicit description of the membrane, the electrolytes, and the electrodes. The model evaluates the gating charges and the electrode potentials (c.f. measured voltage) upon charge transfer within the protein. The accuracy of the model is evaluated by a comparison of measured voltage changes associated with electron and proton transfer in bacterial photosynthetic reaction centers to those calculated using our coarse-grained model. The calculations reproduce the experimental observations and thus indicate that the method is of general use. Interestingly, it is found that charge-separation processes with different spatial directions (but the same distance perpendicular to the membrane) can give similar observed voltage changes, which indicates that caution should be exercised when using simplified interpretation of the relationship between charge displacement and voltage changes.

Since the discovery of graphene, growth of two-dimensional (2D) nanomaterials has greatly attracted attention. However, spontaneous growth of atomic two-dimensional (2D) materials is limitedly permitted for several layered-structure crystals, such as graphene, MoS2, and h-BN, and otherwise it is notoriously difficult. Here we report the gas-phase 2D growth of silicon (Si), that is cubic in symmetry, via dendritic growth and an interdendritic filling mechanism and to form Si nanosheets (SiNSs) of 1 to 13 nm in thickness. Thin SiNSs show strong thickness-dependent photoluminescence in visible range including red, green, and blue (RGB) emissions with the associated band gap energies ranging from 1.6 to 3.2 eV; these emission energies were greater than those from Si quantum dots (SiQDs) of the similar sizes. We also demonstrated that electrically driven white, as well as blue, emission in a conventional organic light-emitting diode (OLED) geometry with the SiNS assembly as the active emitting layers. Tunable light emissions in visible range in our observations suggest practical implications for novel 2D Si nanophotonics.

Quantitative structure-based modeling of voltage activation of ion channels is very challenging. For example, it is very hard to reach converging results, by microscopic simulations while macroscopic treatments involve major uncertainties regarding key features. The current work overcomes some of the above challenges by using our recently developed coarse-grained (CG) model in simulating the activation of the Kv1.2 channel. The CG model has allowed us to explore problems that cannot be fully addressed at present by microscopic simulations, while providing insights on some features that are not usually considered in continuum models, including the distribution of the electrolytes between the membrane and the electrodes during the activation process and thus the physical nature of the gating current. Here, we demonstrate that the CG model yields realistic gating charges and free energy landscapes that allow us to simulate the fluctuating gating current in the activation processes. Our ability to simulate the time dependence of the fast gating current allows us to reproduce the observed trend and provides a clear description of its relationship to the landscape involved in the activation process.

The single living cell action potential was measured in an intracellular mode by using a vertical nanoelectrode. For intracellular interfacing, Si nanowires were vertically grown in a controlled manner, and optimum conditions, such as diameter, length, and nanowire density, were determined by culturing cells on the nanowires. Vertical nanowire probes were then fabricated with a complimentary metal-oxide-semiconductor (CMOS) process including sequential deposition of the passivation and electrode layers on the nanowires, and a subsequent partial etching process. The fabricated nanowire probes had an approximately 60-nm diameter and were intracellular. These probes interfaced with a GH3 cell and measured the spontaneous action potential. It successfully measured the action potential, which rapidly reached a steady state with average peak amplitude of approximately 10 mV, duration of approximately 140 ms, and period of 0.9 Hz.

Au-coated vertical silicon nanowire electrode array (VSNEA) was fabricated using a combination of bottom-up and top-down approaches by chemical vapor deposition and complementary metal-oxide-semiconductor process for biomolecule sensing. To verify the feasibility for the detection of biomolecules, Au-coated VSNEA was functionalized using peptides having a fluorescent probe. Cyclic voltammograms of the peptide-functionalized Au-coated VSNEA show a steady-state electrochemical current behavior. Because of the critically small dimension and vertically aligned nature of VSNEA, the current density of Au-coated VSNEA was dramatically higher than that of Au film electrodes. Au-coated VSNEA further showed a large current difference with and without peptides that was nine times more than that of Au film electrodes. These results indicate that Au-coated VSENA is highly effective device to detect peptides compared to conventional thin-film electrodes. Au-coated VSNEA can also be used as a divergent biosensor platform in many applications.

GaN has been utilized in optoelectronics for two decades. However, p-type doping still remains crucial for realization of high performance GaN optoelectronics. Though Mg has been used as a p-dopant, its efficiency is low due to the formation of Mg-H complexes and/or structural defects in the course of doping. As a potential alternative p-type dopant, Cu has been recognized as an acceptor impurity for GaN. Herein, we report the fabrication of Cu-doped GaN nanowires (Cu:GaN NWs) and their p-type characteristics. The NWs were grown vertically via a vapor-liquid-solid (VLS) mechanism using a Au/Ni catalyst. Electrical characterization using a nanowire-field effect transistor (NW-FET) showed that the NWs exhibited n-type characteristics. However, with further annealing, the NWs showed p-type characteristics. A homo-junction structure (consisting of annealed Cu:GaN NW/n-type GaN thin film) exhibited p-n junction characteristics. A hybrid organic light emitting diode (OLED) employing the annealed Cu:GaN NWs as a hole injection layer (HIL) also demonstrated current injected luminescence. These results suggest that Cu can be used as a p-type dopant for GaN NWs.

Understanding how living cells interact with nanostructures is integral to a better understanding of the fundamental principles of biology and the development of next-generation biomedical/bioenergy devices. Recent studies have demonstrated that mammalian cells can recognize nanoscale topographies and respond to these structures. From this perspective, there is a growing recognition that nanostructures, along with their specific physicochemical properties, can also be used to regulate the responses and motions of bacterial cells. Here, by utilizing a well-defined silicon nanowire array platform and single-cell imaging, we present direct evidence that Shewanella oneidensis MR-1 can recognize nanoscale structures and that their swimming patterns and initial attachment locations are strongly influenced by the presence of nanowires on a surface. Analyses of bacterial trajectories revealed that MR-1 cells exhibited a confined diffusion mode in the presence of nanowires and showed preferential attachment to the nanowires, whereas a superdiffusion mode was observed in the absence of nanowires. These results demonstrate that nanoscale topography can affect bacterial movement and attachment and play an important role during the early stages of biofilm formation.

Free energy perturbation, a method for computing the free energy difference between two states, is often combined with non-Boltzmann biased sampling techniques in order to accelerate the convergence of free energy calculations. Here we present a new extension of the Bennett acceptance ratio (BAR) method by combining it with umbrella sampling (US) along a reaction coordinate in configurational space. In this approach, which we call Bennett acceptance ratio with umbrella sampling (BAR-US), the conditional histogram of energy difference (a mapping of the 3N-dimensional configurational space via a reaction coordinate onto 1D energy difference space) is weighted for marginalization with the associated population density along a reaction coordinate computed by US. This procedure produces marginal histograms of energy difference, from forward and backward simulations, with higher overlap in energy difference space, rendering free energy difference estimations using BAR statistically more reliable. In addition to BAR-US, two histogram analysis methods, termed Bennett overlapping histograms with US (BOH-US) and Bennett-Hummer (linear) least square with US (BHLS-US), are employed as consistency and convergence checks for free energy difference estimation by BAR-US. The proposed methods (BAR-US, BOH-US, and BHLS-US) are applied to a 1-dimensional asymmetric model potential, as has been used previously to test free energy calculations from non-equilibrium processes. We then consider the more stringent test of a 1-dimensional strongly (but linearly) shifted harmonic oscillator, which exhibits no overlap between two states when sampled using unbiased Brownian dynamics. We find that the efficiency of the proposed methods is enhanced over the original Bennett's methods (BAR, BOH, and BHLS) through fast uniform sampling of energy difference space via US in configurational space. We apply the proposed methods to the calculation of the electrostatic contribution to the absolute solvation free energy (excess chemical potential) of water. We then address the controversial issue of ion selectivity in the K(+) ion channel, KcsA. We have calculated the relative binding affinity of K(+) over Na(+) within a binding site of the KcsA channel for which different, though adjacent, K(+) and Na(+) configurations exist, ideally suited to these US-enhanced methods. Our studies demonstrate that the significant improvements in free energy calculations obtained using the proposed methods can have serious consequences for elucidating biological mechanisms and for the interpretation of experimental data.

Heavily phosphorus-doped silicon nanowires (Si NWs) show intriguing transport phenomena at low temperature. As we decrease the temperature, the resistivity of the Si NWs initially decreases, like metals, and starts to increase logarithmically below a resistivity minimum temperature (T(min)), which is accompanied by (i) a zero-bias dip in the differential conductance and (ii) anisotropic negative magnetoresistance (MR), depending on the angle between the applied magnetic field and current flow. These results are associated with the impurity band conduction and electron scattering by the localized spins at phosphorus donor states. The analysis on the MR reveals that the localized spins are coupled antiferromagnetically at low temperature via the exchange interaction.

The mechanism by which K(+) channels select for K(+) over Na(+) ions has been debated for the better part of a century. The prevailing view is that K(+) channels contain highly conserved sites that selectively bind K(+) over Na(+) ions through optimal coordination. We demonstrate that a series of alternating sites within the KcsA channel selectivity filter exists, which are thermodynamically selective for either K(+) (cage made from two planes of oxygen atoms) or Na(+) ions (a single plane of four oxygen atoms). By combining Bennett free energy perturbation calculations with umbrella sampling, we show that when K(+) and Na(+) are both permitted to move into their preferred positions, the thermodynamic preference for K(+) over Na(+) is significantly reduced throughout the entire selectivity filter. We offer a rationale for experimental measures of thermodynamic preference for K(+) over Na(+) from Ba(2+) blocking data, by demonstrating that the presence of Ba(2+) ions exaggerates K(+) over Na(+) thermodynamic stability due to the different binding locations of these ions. These studies reveal that K(+) channel selectivity may not be associated with the thermodynamics of ions in crystallographic K(+) binding sites, but requires consideration of the kinetic barriers associated with the different multi-ion permeation mechanisms.

Silicon nanoribbons (Si NRs) with a thickness of about 30 nm and a width up to a few micrometers were synthesized. Systematic observations indicate that Si NRs evolve via the following sequences: the growth of basal nanowires assisted with a Pt catalyst by a vapor-liquid-solid (VLS) mechanism, followed by the formation of saw-like edges on the basal nanowires and the planar filling of those edges by a vapor-solid (VS) mechanism. Si NRs have twins along the longitudinal < 110 > growth of the basal nanowires that also extend in < 112 > direction to edge of NRs. These twins appear to drive the lateral growth by a reentrant twin mechanism. These twins also create a mirror-like crystallographic configuration in the anisotropic surface energy state and appear to further drive lateral saw-like edge growth in the < 112 > direction. These outcomes indicate that the Si NRs are grown by a combination of the two mechanisms of a Pt-catalyst-assisted VLS mechanism for longitudinal growth and a twin-assisted VS mechanism for lateral growth.

We synthesized free-standing Si nanosheets (NSs) with a thickness of about <2 nm using a chemical vapor deposition process and studied their optical properties. The Si NSs were formed by the formation of frameworks first along six different <110> directions normal to [111], its zone axis, and then by filling the spaces between the frameworks along the <112> directions under high flow rate of processing gas. The Si NSs showed blue emission at 435 nm, and absorbance and photoluminescence (PL) excitation measurements indicate that enhanced direct band transition attributes to the emission. Time-resolved PL measurement, which showed PL emission at 435 nm and a radiative lifetime of 1.346 ns, also indicates the enhanced direct band gap transition in these Si NSs. These outcomes indicate that dimensionality of Si nanostructures may affect the band gap transition and, in turn, the optical properties.

We report on bifurcate reactions on the surface of well-aligned Si(1-x)Ge(x) nanowires that enable fabrication of two different coaxial heterostructure nanowires. The Si(1-x)Ge(x) nanowires were grown in a chemical vapor transport process using SiCl(4) gas and Ge powder as a source. After the growth of nanowires, SiCl(4) flow was terminated while O(2) gas flow was introduced under vacuum. On the surface of nanowires was deposited Ge by the vapor from the Ge powder or oxidized into SiO(2) by the O(2) gas. The transition from deposition to oxidation occurred abruptly at 2 torr of O(2) pressure without any intermediate region and enables selectively fabricated Ge/Si(1-x)Ge(x) or SiO(2)/Si(1-x)Ge(x) coaxial heterostructure nanowires. The rate of deposition and oxidation was dominated by interfacial reaction and diffusion of oxygen through the oxide layer, respectively.

Potassium channels allow K(+) ions to diffuse through their pores while preventing smaller Na(+) ions from permeating. Discrimination between these similar, abundant ions enables these proteins to control electrical and chemical activity in all organisms. Selection occurs at the narrow selectivity filter containing structurally identified K(+) binding sites. Selectivity is thought to arise because smaller ions such as Na(+) do not bind to these K(+) sites in a thermodynamically favorable way. Using the model K(+) channel KcsA, we examined how intracellular Na(+) and Li(+) interact with the pore and the permeant ions using electrophysiology, molecular dynamics simulations and X-ray crystallography. Our results suggest that these small cations have a separate binding site within the K(+) selectivity filter. We propose that selective permeation from the intracellular side primarily results from a large energy barrier blocking filter entry for Na(+) and Li(+) in the presence of K(+), not from a difference of binding affinity between ions.

We present a new method for multiple sequence alignment (MSA), which we call MSACSA. The method is based on the direct application of a global optimization method called the conformational space annealing (CSA) to a consistency-based score function constructed from pairwise sequence alignments between constituting sequences. We applied MSACSA to two MSA databases, the 82 families from the BAliBASE reference set 1 and the 366 families from the HOMSTRAD set. In all 450 cases, we obtained well optimized alignments satisfying more pairwise constraints producing, in consequence, more accurate alignments on average compared with a recent alignment method SPEM. One of the advantages of MSACSA is that it provides not just the global minimum alignment but also many distinct low-lying suboptimal alignments for a given objective function. This is due to the fact that conformational space annealing can maintain conformational diversity while searching for the conformations with low energies. This characteristics can help us to alleviate the problem arising from using an inaccurate score function. The method was the key factor for our success in the recent blind protein structure prediction experiment.

A novel method for ab initio prediction of protein tertiary structures, PROFESY (PROFile Enumerating SYstem), is proposed. This method utilizes the secondary structure prediction information of a query sequence and the fragment assembly procedure based on global optimization. Fifteen-residue-long fragment libraries are constructed using the secondary structure prediction method PREDICT, and fragments in these libraries are assembled to generate full-length chains of a query protein. Tertiary structures of 50 to 100 conformations are obtained by minimizing an energy function for proteins, using the conformational space annealing method that enables one to sample diverse low-lying local minima of the energy. We apply PROFESY for benchmark tests to proteins with known structures to demonstrate its feasibility. In addition, we participated in CASP5 and applied PROFESY to four new-fold targets for blind prediction. The results are quite promising, despite the fact that PROFESY was in its early stages of development. In particular, PROFESY successfully provided us the best model-one structure for the target T0161., (Copyright 2004 Wiley-Liss, Inc.)