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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]

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]

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]

Introduction: Retinitis pigmentosa (RP) caused by the photoreceptor cell degeneration is currently incurable and leads to partial or complete blindness eventually. 3,5-dimethoxy-4-hydroxy myricanol (DM) is a novel compound isolated from the leaves of Micromelum integerrimum, with proliferative activities on NIH3T3 cells. This study was to investigate whether DM could mitigate retinal degeneration of rd10 mice, a well-characterized mouse model of RP. Materials and method: Rd10 mice were treated with DM daily by intraperitoneal injection from postnatal day 12 (P12) to P26. Electroretinography (ERG) reflects the mass response of photoreceptor cells and was used to test the outer retinal function after DM treatment. Haematoxylin and Eosin staining was used to show the retinal morphology and evaluate the rod photoreceptor cell loss. TUNEL assay was used to detect the apoptosis-positive cells. Inflammatory factors were measured by ELISA to show the inflammatory response. Real-time PCR and western blot were applied to measure the gene and protein change to explore the underlying mechanisms. Results: Results showed that DM significantly improved the retinal function by increasing the ERG amplitude, preserving the retinal morphology, reducing photoreceptor cell apoptosis, decreasing inflammatory response, and inhibiting endoplasmic reticulum stress in rd10 mice. Conclusion: This is the first time when the protective effects of DM against photoreceptor cell degeneration of rd10 mice have been demonstrated, providing scientific rationale to develop DM as a potential agent to treat RP. [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]

In this brief, we propose an efficient parallel finite difference-based thermal simulation algorithm for 3-D-integrated circuits (ICs) using generalized minimum residual method (GMRES) solver on CPU-graphic processing unit (GPU) platforms. First, the new method starts from basic physics-based heat equations to model 3-D-ICs with intertier liquid cooling microchannels and directly solves the resulting partial differential equations. Second, we develop a new parallel GPU-GMRES solver to compute the resulting thermal systems on a CPU-GPU platform. We also explore different preconditioners (implicit and explicit) and study their performances on thermal circuits and other types of matrices. Experimental results show the proposed GPU-GMRES solver can deliver orders of magnitudes speedup over the parallel LU-based solver and up to $4\times$ speedup over CPU-GMRES for both dc and transient thermal analyzes on a number of thermal circuits and other published problems. [ABSTRACT FROM AUTHOR]

In this brief, a new distributed thermal management scheme using task migrations based on a new temperature metric called effective initial temperature is proposed to reduce the on-chip temperature variance and the occurrence of hot spots for many-core microprocessors. The new temperature metric derived from frequency domain moment matching technique incorporates both initial temperature and other transient effects to make optimized task migration decisions, which leads to more effective reduction of hot spots in the experiments on a 100-core microprocessor than the existing distributed thermal management methods. [ABSTRACT FROM PUBLISHER]

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]

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]

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]

Escherichia coli W, a sucrose-positive strain, was engineered for the homofermentative production of d-lactic acid through chromosomal deletion of the competing fermentative pathway genes ( adhE, frdABCD, pta, pflB, aldA) and the repressor gene ( cscR) of the sucrose operon, and metabolic evolution for improved anaerobic cell growth. The resulting strain, HBUT-D, efficiently fermented 100 g sucrose l into 85 g d-lactic acid l in 72-84 h in mineral salts medium with a volumetric productivity of ~1 g l h, a product yield of 85 % and d-lactic acid optical purity of 98.3 %, and with a minor by-product of 4 g acetate l. HBUT-D thus has great potential for production of d-lactic acid using an inexpensive substrate, such as sugar cane and/or beet molasses, which are primarily composed of sucrose. [ABSTRACT FROM AUTHOR]

A recessive genic male sterility (RGMS) line 20118 A was controlled by 2 recessive sterile genes (a and b) interacting with an inhibitor gene rf. Gene fr restored the fertility and was epistatic to a and b genes. The object of this study was to develop molecular markes linked to rf gene for marker - assisted selection of temporary maintainer line. By using a BC1 population from 20118A × M - 6029, 7 AFLP ( amplified fragment length polymorphisms) markers were obtained and male into a linkage map of rf gene. The genetic distances ranged from 3cM to 17cM. Among them, EA10MC03 marker was 3cM to rf gene. It was transferred into SCAR (sequence - characterized amplified region) marker using primer pair F3 and R3, which could identify the heterozygous individuals (Rfrf genotype) from homozygous one (RfRf genotype). The markers showed their ability in developing temporary maintainer line in the future. [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]

Core/periphery scientific communication is important for information transfer in terrorism literature. The mutual awareness between disciplinary journals contributors in the mainstream and those in the margins of the field enhances their social interaction. The usual case is that the mainstream of a discipline is visible through such indexes as the Web of Science (SCI) and the Journal Citation Report (JCR) the second of which assigns an impact factor to the most cited journals. In terrorism subject area, however, the reverse situation exists; only the peripheral journals in this field are indexed in JCR. From a scientific communication perspective, then, the core journals of terrorism writings are relatively invisible. This study attempts to identify the core and the periphery of journals dealing with terrorism, and suggests a way to bring them closer together. The assumption is that the quality and quantity of work in this field will increase as the distance between these two poles decreases. [ABSTRACT FROM AUTHOR]