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Background: Software for nuclear magnetic resonance (NMR) spectrometers offer general functionality of instrument control and data processing; these applications are often developed with non-scripting languages. NMR users need to flexibly integrate rapidly developing NMR applications with emerging technologies. Scripting systems offer open environments for NMR users to write custom programs. However, existing scripting systems have limited capabilities for both extending the functionality of NMR software's non-script main program and using advanced native script libraries to support specialized application domains (e.g., biomacromolecules and metabolomics). Therefore, it is essential to design a novel scripting system to address both of these needs. Result: Here, a novel NMR scripting system named SpinSPJ is proposed. It works as a plug-in in the Java based NMR spectrometer software SpinStudioJ. In the scripting system, both Java based NMR methods and original CPython based libraries are supported. A module has been developed as a bridge to integrate the runtime environments of Java and CPython. The module works as an extension in the CPython environment and interacts with Java via the Java Native Interface. Leveraging this bridge, Java based instrument control and data processing methods of SpinStudioJ can be called with the CPython style. Compared with traditional scripting systems, SpinSPJ better supports both extending the non-script main program and implementing advanced NMR applications with a rich variety of script libraries. NMR researchers can easily call functions of instrument control and data processing as well as developing complex functionality (such as multivariate statistical analysis, deep learning, etc.) with CPython native libraries. Conclusion: SpinSPJ offers a user-friendly environment to implement custom functionality leveraging its powerful basic NMR and rich CPython libraries. NMR applications with emerging technologies can be easily integrated. The scripting system is free of charge and can be downloaded by visiting http://www.spinstudioj.net/spinspj. [ABSTRACT FROM AUTHOR]

Flexibility and extensibility are important issues in the design of nuclear magnetic resonance (NMR) software, as these determine the ability to integrate a variety of continuously evolving data acquisition and processing methods. Here, SpinStudioJ is introduced. It is an NMR data acquisition and processing workbench with a plug‐in‐based architecture. The workbench is based on Eclipse Rich Client Platform, which provides a plug‐and‐play runtime mechanism and rich graphical user interface functionality. New data acquisition methods and processing algorithms can be easily integrated into the SpinStudioJ workbench by defining extension points, without the need to redistribute existing modules. The software is independent of operating systems, as it leverages the cross‐platform feature of the Java virtual machine. [ABSTRACT FROM AUTHOR]

Vitreous anteroposterior traction is an important factor that affects macular hole (MH) formation at the early stage, and vitreous tangential traction can lead to further hole expansion after hole formation. Recent studies have highlighted the significance of Müller cells for the pathogenesis of MH. Since the advent of MH treatment, success rates for MH closure have significantly improved, as has postoperative visual acuity. However, metamorphopsia, an initial and common symptom of MH, still exists. Metamorphopsia is significantly related to the deterioration of visual quality of life and can be used as an independent index to evaluate visual function before and after surgery. In MH patients, metamorphopsia has different manifestations representing different clinical implications. M-CHARTS, as a new means of inspection, can quantify the degrees of metamorphopsia, and with the development of optical coherence tomography (OCT), layer-by-layer scanning of the retinal structure has become possible. These methods enable detailed analysis of the connections between the degree of metamorphopsia and relevant OCT parameters. Preoperative OCT parameters can be used to evaluate the prognosis of the postoperative visual function of MH patients and are therefore of great significance in guiding the treatment of MH patients. [ABSTRACT FROM AUTHOR]

This article presents a new approach for system-level reliability management for multi/many core microprocessors. In the new approach, the electro-migration (EM) induced time to failure (TTF) at the system level is modeled as a resource, which is abstracted, from a recently proposed physics-based EM model, at the chip level. In this model, a single core can spend the TTF resources at different rates specified by the temperature and the related power consumption. As a result, the new resource-based EM model allows more flexible EM-reliability management for multi/many-core systems. As an application of the new model, we propose a novel task migration method to explicitly balance consumption of EM resources for all the cores. The new method aims at equalizing the probability of failure of each core, which will maximize the lifetime of the whole multi/many core system. To more efficiently regulate the lifetime of the multi/many core system, dynamic voltage and frequency scaling (by using different performance states (p-states), which can represent different operating voltages and frequencies) is further employed to compensate for the excessively consumed lifetime of all the cores when the chip is loaded with heavy tasks for a certain period of time. In this way, the TTF of all the cores could be compensated to meet the lifetime requirement, giving the multi/many core system more flexibility to handle heavy task assignment on demand. Experimental results on a 36-core processor platform show that the proposed task migration scheme could balance the lifetime consumption of all the cores, and maintain even-distributed TTF slacks across different cores, while the existing temperature-based task migration schemes lead to diverged TTF of cores. The results also show that the TTF consumption could be easily compensated for by switching to a low p-state, which could not be achieved if TTF consumption diverged across different cores. [ABSTRACT FROM AUTHOR]

Thermal issue is the leading design constraint for 3-D stacked integrated circuits (ICs) and through silicon vias (TSVs) are used to effectively reduce the temperature of 3-D ICs. Normally, TSV is considered as a good thermal conductor in its vertical direction, and its vertical thermal resistance has been well modeled. However, lateral heat transfer of TSVs, which is also important, was largely ignored in the past. In this paper, we propose an accurate physics-based model for lateral thermal resistance of TSVs in terms of physical and material parameters, and study the conditions for model accuracy. For TSV arrays or farm, we show that the space or pitch between TSVs has a significant impact on TSV thermal behavior and should be properly considered in the TSV models. The proposed lateral thermal resistance model is fully compatible with the existing modeling approaches, and thus we could build a more accurate complete TSV thermal model. The new TSV thermal model can be easily integrated into a finite difference (FD) based thermal analysis framework to improve analysis efficiency. The accuracy of the model is validated against a commercial finite element tool—COMSOL. Experimental results show that the improved TSV thermal model (with proposed lateral thermal model) could greatly improve the accuracy of FD method in thermal simulation comparing with the existing method. [ABSTRACT FROM PUBLISHER]

Abstract: In this paper, we propose a new behavioral thermal modeling technique for high-performance microprocessors at package level. Firstly, the new approach applies the subspace identification method with the consideration of practical power maps with correlated power signals. We show that the input power signal needs to meet an independence requirement to ensure the model predictability and propose an iterative process to build the models with given error bounds. Secondly, we show that thermal systems fundamentally are nonlinear and then propose a piecewise linear (PWL) scheme to deal with nonlinear effects. The experimental results validated the proposed method on a realistic packaged integrated system modeled by the multi-domain/physics commercial tool, COMSOL. The new piecewise linear models can model thermal behaviors over wide temperature ranges or over different thermal boundary convective conditions due to different fan speeds. Further, the PWL modeling technique can lead to much smaller model order without accuracy loss, which translates to significant savings in both the simulation time and the time required to identify the reduced models compared to the simple modeling method by using the high order models. [Copyright &y& Elsevier]

Amyotrophic lateral sclerosis (ALS) is a fatal progressive neurodegenerative disorder. Current diagnosis time is about 12-months due to lack of objective methods. Previous brain white matter voxel based morphometry (VBM) studies in ALS reported inconsistent results. Fractal dimension (FD) has successfully been used to quantify brain WM shape complexity in various neurological disorders and aging, but not yet studied in ALS. Therefore, we investigated WM morphometric changes using FD analyses in ALS patients with different clinical phenotypes. We hypothesized that FD would better capture clinical features of the WM morphometry in different ALS phenotypes than VBM analysis. High resolution MRI T1-weighted images were acquired in controls (n = 11), and ALS patients (n = 89). ALS patients were assigned into four subgroups based on their clinical phenotypes.VBM analysis was carried out using SPM8. FD values were estimated for brain WM skeleton, surface and general structure in both controls and ALS patients using our previously published algorithm. No significant VBM WM changes were observed between controls and ALS patients and among the ALS subgroups. In contrast, significant (p<0.05) FD reductions in skeleton and general structure were observed between ALS with dementia and other ALS subgroups. No significant differences in any of the FD measures were observed between control and ALS patients. FD correlated significantly with revised ALS functional rating scale (ALSFRS-R) score a clinical measure of function. Results suggest that brain WM shape complexity is more sensitive to ALS disease process when compared to volumetric VBM analysis and FD changes are dependent on the ALS phenotype. Correlation between FD and clinical measures suggests that FD could potentially serve as a biomarker of ALS pathophysiology, especially after confirmation by longitudinal studies. [ABSTRACT FROM AUTHOR]

This study analyzes the usage data of a major engineering article database, IEEE Xplore, from 2005 to 2008, at Texas A&M University. Usage data collected from the IEEE Xplore statistics website demonstrated some interesting patterns of user behavior. Usage of the database increased steadily from 2005 to 2007, but dropped in 2008 due to the launch of the library's new website; off-campus usage was high in the first two years, but plunged in 2007 and 2008. Users from the Department of Electrical and Computer Engineering, and, to a lesser degree, from the Computer Science Department, were identified as major users of the database by IP statistics. The most heavily used journals and articles indicated that solid-state circuits, microwave, information theory, and power systems were probably among core research areas in electrical and computer engineering for the university. The impact of conference articles in this database increased continuously throughout these years. [ABSTRACT FROM AUTHOR]

Aims: The dysregulation of TGF‐β signaling is a crucial pathophysiological process in tumorigenesis and progression. LncRNAs have diverse biological functions and are significant participants in the regulation of tumor signaling pathways. However, the clinical value of lncRNAs related to TGF‐β signaling in glioma is currently unclear. Methods: Data on glioma's RNA‐seq transcriptome, somatic mutation, DNA methylation data, and clinicopathological information were derived from the CGGA and TCGA databases. A prognostic lncRNA signature was constructed by Cox and LASSO regression analyses. TIMER2.0 database was utilized to deduce immune infiltration characteristics. "ELMER v.2" was used to reconstruct TF‐methylation‐gene regulatory network. Immunotherapy and chemotherapy response predictions were implemented by the TIDE algorithm and GDSC database, respectively. In vitro and in vivo experiments were conducted to verify the results and clarify the regulatory mechanism of lncRNA. Results: In glioma, a TGF‐β signaling‐related 15‐lncRNA signature was constructed, including AC010173.1, HOXA‐AS2, AC074286.1, AL592424.1, DRAIC, HOXC13‐AS, AC007938.1, AC010729.1, AC013472.3, AC093895.1, AC131097.4, AL606970.4, HOXC‐AS1, AGAP2‐AS1, and AC002456.1. This signature proved to be a reliable prognostic tool, with high risk indicating an unfavorable prognosis and being linked to malignant clinicopathological and genomic mutation traits. Risk levels were associated with different immune infiltration landscapes, where high risk was indicative of high levels of macrophage infiltration. In addition, high risk also suggested better immunotherapy and chemotherapy response. cg05987823 was an important methylation site in glioma progression, and AP‐1 transcription factor family participated in the regulation of signature lncRNA expression. AGAP2‐AS1 knockdown in in vitro and in vivo experiments inhibited the proliferation, migration, and invasion of glioma cells, as well as the growth of glioma, by downregulating the expression levels of NF‐κB and ERK 1/2 in the TGF‐β signaling pathway. Conclusions: A prognostic lncRNA signature of TGF‐β signaling was established in glioma, which can be used for prognostic judgment, immune infiltration status inference, and immunotherapy response prediction. AGAP2‐AS1 plays an important role in glioma progression. [ABSTRACT FROM AUTHOR]

Artefacts in high‐resolution multidimensional nuclear magnetic resonance (NMR) spectra, known as t1 noise, can significantly downgrade the spectral quality and remain a significant noise source, limiting the sensitivity of most two‐dimensional NMR experiments. In addition to highly sensitive hardware and experimental designs, data post‐processing is a relatively simple and cost‐effective method for suppressing t1 noise. In this study, histograms and quantiles were used to obtain a robust estimation of noise level. We constructed a weighted matrix to suppress the t1 noise. The weighted matrix was calculated from the logistic functions, which were adaptively computed from the spectrum. The proposed method is robust and effective in both simulations and actual experiments. Further, it can maintain the quantitative relationship of the spectrogram and is suitable for various complex peak types. [ABSTRACT FROM AUTHOR]

The influence of lecithin from egg yolk (LE) on calcium carbonate (CaCO3) biomineralization was investigated. In the present study, spherical CaCO3 particles were synthesized via coprecipitation in the presence of LE. LE multilamellar liposomes were first tuned by sonication to provide better control over the nucleation of CaCO3. Subsequently, monodisperse microspheres ~2 μm in size were generated by controlling the aggregation and growth of CaCO3 under appropriate concentrations of LE. In contrast to unstable vaterite, the microspheres generated in aqueous solution remained stable for at least 10 days without transforming into calcite, due to the strong interaction between the LE and calcium ions. The microspheres as drug carriers of doxorubicin (DOX) were assessed and were observed to have a good encapsulation efficiency, sustained drug release without a burst release and notable pH sensitivity. In addition, in vivo tumor inhibition examination demonstrated that DOX‑loaded CaCO3 microspheres formulation had more superior efficacy to significantly restrain tumor growth. These novel LE/CaCO3 hybrids may provide novel options for various biomedical applications. [ABSTRACT FROM AUTHOR]

Fusarium oxysporum (Fo) is an important species complex of soil-borne pathogenic fungi that cause vascular wilt diseases of agricultural crops and some opportunistic diseases of humans. The fungicide phenamacril has been extensively reported to have antifungal activity against Fusarium graminearum and Fusarium fujikuroi. In this study, we found that the amino acid substitutions (V151A and S418T) in Type I myosin FoMyo5 cause natural low resistance to phenamacril in the plant pathogenic Fo isolates. Therefore, we compared the transcriptomes of two phenamacril-resistant Fo isolates FoII5, Fo1st and one phenamacril-sensitive isolate Fo3_a after 1 μg/mL phenamacril treatment. Among the 2728 differentially expressed genes (DEGs), 14 DEGs involved in oxidation–reduction processes and MFS transporters, were significantly up-regulated in phenamacril-resistant isolates. On the other hand, 14 DEGs involved in ATP-dependent RNA helicase and ribosomal biogenesis related proteins, showed significantly down-regulated expression in both phenamacril-resistant and -sensitive isolates. These results indicated that phenamacril not only seriously affected the cytoskeletal protein binding and ATPase activity of sensitive isolate, but also suppressed ribosome biogenesis in all the isolates. Hence, this study helps us better understand resistance regulation mechanism and fungicidal activity of phenamacril and provide reference for the development of new fungicides to control Fo. [ABSTRACT FROM AUTHOR]

Abstract: Highly ordered TiO2 nanotube array with inner diameter of 120nm was formed by anodizing titanium foils and was further modified for enzyme immobilization and biosensing. AuNPs sized in 8–12nm were uniformly electrodeposited on TiO2 nanotube arrays by pulsed method. Glucose oxidase (GOD) was covalently immobilized on the surface of gold nanoparticles (AuNPs) modified TiO2 nanotube array electrode for the first time. Results demonstrate that the modified TiO2 nanotube array electrode exhibits good electrocatalytic performance and high sensitivity without any electron mediator. The covalently fabricated glucose biosensor shows higher immobilized ratio of GOD, good reproducibility and stability. These indicate AuNPs modified TiO2 nanotube array is an attractive material for using in the fabrication of biosensors because of its excellent biocompatibility, high specific surface area, unique nanostructure, and effective immobilization of biomolecules. This facile modification approach could be extended to prepare various TiO2 nanotube array based biosensors. [ABSTRACT FROM AUTHOR]

A large class of rock-like materials are composed of a plastic solid matrix in which various inclusions and pores are embedded. This paper is devoted to determine macroscopic inelastic responses of such materials by a nonlinear homogenization procedure. The plastic behavior of solid matrix is described by a plastic model based on the pressure-dependent Drucker-Prager criterion. The plastic strain field of solid matrix is divided into a volumetric part and a shear part. Unlike most mean-field methods previously developed, the strain field in the solid matrix is non-uniform and this non-uniform field is taken into account by using an incremental variational model. The whole loading history is divided into a limit number of increment. For the sake of simplicity, the behavior of solid matrix is first assumed to be elastic-perfectly plastic at each loading increment. With the help of a time derivative approximation, the local incremental potential of the solid matrix is deduced. By considering the effect of inclusions and pores, the effective incremental potential of the heterogeneous composite is determined and estimated with the help of a linear comparison material. The macroscopic stress of the composite is finally estimated from the effective incremental potential. The accuracy of the proposed model is assessed by a series of comparisons with reference results obtained from direct finite element simulations respectively for inclusion-reinforced and porous materials. Finally, by assuming that the general form of incremental variational model remains valid when the solid matrix exhibits an isotropic plastic hardening, the proposed model is extended by updating the value of frictional coefficient of solid matrix and keeping it as a constant at each loading increment. The proposed model in this case is also well validated by comparisons with finite element reference results. Moreover, as examples of application, the model is used to simulate laboratory tests performed on a cement mortar and a typical porous sandstone. • A micromechanical model is developed using incremental variational principle. • Non-uniform local strain fields are taken into account. • Pressure dependency and volumetric strain of plastic matrix are considered. • The efficiency of the model is verified through comparisons with FEM reference solutions. • The proposed model well predicts main features of experimental data for two typical rocks. [ABSTRACT FROM AUTHOR]

This study aimed to investigate the biocontrol ability of Bacillus licheniformis HG03 against Rhizopus stolonifer causing agent of peach fruit rot and explore its mechanism. The biocontrol strain B. licheniformis HG03 was applied on inhibition of the pathogen Rhizopus stolonifer , which is expected to improve the preservation of peach fruit. The results revealed that the peach treated with B. licheniformis HG03 were significantly more resistant to postharvest soft rot when stored at 20 °C and high humidity. Comparison to the control, treatment with HG03 improved the activity of related enzymes and balanced the metabolism of reactive oxygen species. Such treatment reduced the accumulation of lipid peroxidation products and enhanced free radical scavenging ability of peaches. Furthermore, the transcriptome analysis revealed that the HG03 treatment activated MAPK signaling pathway, induced the expression of antioxidant activity-related genes and different WRKY transcription factors in plant pathogen interaction metabolic pathway. Hence, the results revealed that HG03 treatment is an effective biological control method to improve peach fruit disease resistance and prolong the storage time of peaches. • Bacillus licheniformis HG03 delayed soft rot development when applied to peaches stored at 20 °C at high humidity. • Presence of B. licheniformis HG03 led to the elevated activity of plant enzymes associated with disease resistance. • HG03 improved the free-radical-scavenging ability and disease resistance of fruit. • B. licheniformis HG03 upregulated a number of plant genes known to enhance resistance to pathogens. [ABSTRACT FROM AUTHOR]

Most existing gradient shimming methods for NMR spectrometers estimate field maps that resolve B 0 inhomogeneity spatially from dual gradient-echo (GRE) images acquired at different echo times. However, the distortions induced by B 0 inhomogeneity that always exists in the GRE images can result in estimated field maps that are distorted in both geometry and intensity, leading to inaccurate shimming. This work proposes a new gradient shimming method based on undistorted field map of B 0 inhomogeneity obtained by a more accurate field map estimation technique. Compared to the traditional field map estimation method, this new method exploits both the positive and negative polarities of the frequency encoded gradients to eliminate the distortions caused by B 0 inhomogeneity in the field map. Next, the corresponding automatic post-data procedure is introduced to obtain undistorted B 0 field map based on knowledge of the invariant characteristics of the B 0 inhomogeneity and the variant polarity of the encoded gradient. The experimental results on both simulated and real gradient shimming tests demonstrate the high performance of this new method. [ABSTRACT FROM AUTHOR]

Highlights: [•] Up-regulation of miR-34a inhibits cell viability. [•] Suppression of miR-34a enhances cell viability. [•] NOX2 is a target of miR-34a in A172 cells. [•] MiR-34a serves as a tumor suppressor in human glioma. [Copyright &y& Elsevier]

Highlights: [•] Inhibition of SOCE reduced H2O2-induced oxidative stress. [•] Inhibition of SOCE attenuated overload of Ca2+ after oxidative stress. [•] Inhibition of SOCE inhibited mitochondrial apoptosis after oxidative stress. [Copyright &y& Elsevier]

Salvianolic acid B (SalB), the main water-soluble bioactive compounds isolated from the traditional Chinese medical herb Danshen, has been shown to exert anti-cancer effect in several cancer cell lines. The aim of our study was to investigate the potential anti-cancer effect of SalB in human glioma U87 cells. We found that treatment with SalB significantly decreased cell viability of U87 cells in a dose- and time-dependent manner. SalB also enhanced the intracellular ROS generation and induced apoptotic cell death in U87 cells. Western blot analysis suggested that SalB increased the phosphorylation of p38 MAPK and p53 in a dose-dependent manner. Moreover, blocking p38 activation by specific inhibitor SB203580 or p38 specific siRNA partly reversed the anti-proliferative and pro-apoptotic effects, and ROS production induced by SalB treatment. The anti-tumor activity of SalB in vivo was also demonstrated in U87 xenograft glioma model. All of these findings extended the anti-cancer effect of SalB in human glioma cell lines, and suggested that these inhibitory effects of SalB on U87 glioma cell growth might be associated with p38 activation mediated ROS generation. Thus, SalB might be concerned as an effective and safe natural anticancer agent for glioma prevention and treatment. [ABSTRACT FROM AUTHOR]

Highlights: [•] A new phase correction method which is suitable for complex spectra is proposed. [•] A new strategy combining ‘coarse tuning’ with ‘fine tuning’ is introduced. [•] ‘Coarse tuning’ is to minimize the height difference of tail ends of the peaks. [•] The phase parameters are further optimized by a custom negative penalty function. [Copyright &y& Elsevier]

Abstract: A new automatic baseline correction method for Nuclear Magnetic Resonance (NMR) spectra is presented. It is based on an improved baseline recognition method and a new iterative baseline modeling method. The presented baseline recognition method takes advantages of three baseline recognition algorithms in order to recognize all signals in spectra. While in the iterative baseline modeling method, besides the well-recognized baseline points in signal-free regions, the ‘quasi-baseline points’ in the signal-crowded regions are also identified and then utilized to improve robustness by preventing the negative regions. The experimental results on both simulated data and real metabolomics spectra with over-crowded peaks show the efficiency of this automatic method. [Copyright &y& Elsevier]