Plants are fascinating and complex organisms. A comprehensive understanding of the organization, function and evolution of plant genes is essential to disentangle important biological processes and ...to advance crop engineering and breeding strategies. The ultimate aim in deciphering complex biological processes is the discovery of causal genes and regulatory mechanisms controlling these processes. The recent surge of omics data has opened the door to a system-wide understanding of the flow of biological information underlying complex traits. However, dealing with the corresponding large data sets represents a challenging endeavor that calls for the development of powerful bioinformatics methods. A popular approach is the construction and analysis of gene networks. Such networks are often used for genome-wide representation of the complex functional organization of biological systems. Network based on similarity in gene expression are called (gene) co-expression networks. One of the major application of gene co-expression networks is the functional annotation of unknown genes. Constructing co-expression networks is generally straightforward. In contrast, the resulting network of connected genes can become very complex, which limits its biological interpretation. Several strategies can be employed to enhance the interpretation of the networks. A strategy in coherence with the biological question addressed needs to be established to infer reliable networks. Additional benefits can be gained from network-based strategies using prior knowledge and data integration to further enhance the elucidation of gene regulatory relationships. As a result, biological networks provide many more applications beyond the simple visualization of co-expressed genes. In this study we review the different approaches for co-expression network inference in plants. We analyse integrative genomics strategies used in recent studies that successfully identified candidate genes taking advantage of gene co-expression networks. Additionally, we discuss promising bioinformatics approaches that predict networks for specific purposes.
Electron transport in ZnO doped with 3at.% Sn, In, and Al processed using the sol–gel dip coating technique was investigated to obtain the correlation between the type of dopant and its effect on ...electrical and optical properties. A detailed analysis in terms of grain boundary transport was used to correlate the values of the figure of merit with the mean potential barrier height. We found that Al dopant leads to form the lowest mean barrier height among other dopants, which remarkably improves the figure of merit.
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•Electrical transport properties of undoped and In-doped CuO thin films are investigated.•Electrical transport is explained with Mott variable-range hopping conduction model.•The resistivity behavior ...is well figured out by fluctuations in the hopping distance and the density of states at the Fermi level.
Electrical transport properties of undoped and In-doped CuO thin films (1, 5 and 10at. %) are investigated by mean of resistivity in the temperature range of 115–300K. Electrical transport mechanism of films is explained on the basis of the variable-range hopping (VRH) conduction. Upon doping, appreciable changes are found in resistivity. Temperature dependent resistivity shows a complex correlation with increasing In concentration. This situation is well explained by fluctuations in the hopping distance and the density of states at the Fermi level.
Tool condition monitoring and machine tool diagnostics are performed using advanced sensors and computational intelligence to predict and avoid adverse conditions for cutting tools and machinery. ...Undesirable conditions during machining cause chatter, tool wear, and tool breakage, directly affecting the tool life and consequently the surface quality, dimensional accuracy of the machined parts, and tool costs. Tool condition monitoring is, therefore, extremely important for manufacturing efficiency and economics. Acoustic emission, vibration, power, and temperature sensors monitor the stability and efficiency of the machining process, collecting large amounts of data to detect tool wear, breakage, and chatter. Studies on monitoring the vibrations and acoustic emissions from machine tools have provided information and data regarding the detection of undesirable conditions. Herein, studies on tool condition monitoring are reviewed and classified. As Industry 4.0 penetrates all manufacturing sectors, the amount of manufacturing data generated has reached the level of big data, and classical artificial intelligence analyses are no longer adequate. Nevertheless, recent advances in deep learning methods have achieved revolutionary success in numerous industries. Deep multi-layer perceptron (DMLP), long-short-term memory (LSTM), convolutional neural network (CNN), and deep reinforcement learning (DRL) are among the most preferred methods of deep learning in recent years. As data size increases, these methods have shown promising performance improvement in prediction and learning, compared to classical artificial intelligence methods. This paper summarizes tool condition monitoring first, then presents the underlying theory of some of the most recent deep learning methods, and finally, attempts to identify new opportunities in tool condition monitoring, toward the realization of Industry 4.0.
RNA polymerase II mediates the transcription of all protein-coding genes in eukaryotic cells, a process that is fundamental to life. Genomic mutations altering this enzyme have not previously been ...linked to any pathology in humans, which is a testament to its indispensable role in cell biology. On the basis of a combination of next-generation genomic analyses of 775 meningiomas, we report that recurrent somatic p.Gln403Lys or p.Leu438_His439del mutations in POLR2A, which encodes the catalytic subunit of RNA polymerase II (ref. 1), hijack this essential enzyme and drive neoplasia. POLR2A mutant tumors show dysregulation of key meningeal identity genes, including WNT6 and ZIC1/ZIC4. In addition to mutations in POLR2A, NF2, SMARCB1, TRAF7, KLF4, AKT1, PIK3CA, and SMO, we also report somatic mutations in AKT3, PIK3R1, PRKAR1A, and SUFU in meningiomas. Our results identify a role for essential transcriptional machinery in driving tumorigenesis and define mutually exclusive meningioma subgroups with distinct clinical and pathological features.
In this paper we made a study on the effect of films thickness on the electrical conduction properties of nanostructured TiO
2 thin films deposited by d.c. reactive sputtering. The deposition was ...performed on heated (573
K) glass substrates, using water vapor as reactive gas. The electrical conductivity of the films was investigated in the temperature range 13–320
K. The temperature dependence of electrical conductivity between 80 and 320
K indicated that electrical conductivity in the films was controlled by potential barriers caused by depletion of carriers at grain boundaries in the material. Values of grain barrier heights and surface trap density at the grain boundaries were extracted from the high temperature data for the investigated samples. Both the grain barrier heights and surface trap density at the grain boundaries were found to depend significantly on film thickness into the deposition process. The low-temperature (
T
<
80
K) conductivity of the films was described in terms of variable-range hopping (VRH) conduction. Characteristic parameters describing the low-temperature conductivity, such as the hopping distance, hopping energy and density of states were determined, and their values as a function of film thickness were discussed in the light of variable-range hopping conduction model.
Meningiomas are mostly benign brain tumours, with a potential for becoming atypical or malignant. On the basis of comprehensive genomic, transcriptomic and epigenomic analyses, we compared benign ...meningiomas to atypical ones. Here, we show that the majority of primary (de novo) atypical meningiomas display loss of NF2, which co-occurs either with genomic instability or recurrent SMARCB1 mutations. These tumours harbour increased H3K27me3 signal and a hypermethylated phenotype, mainly occupying the polycomb repressive complex 2 (PRC2) binding sites in human embryonic stem cells, thereby phenocopying a more primitive cellular state. Consistent with this observation, atypical meningiomas exhibit upregulation of EZH2, the catalytic subunit of the PRC2 complex, as well as the E2F2 and FOXM1 transcriptional networks. Importantly, these primary atypical meningiomas do not harbour TERT promoter mutations, which have been reported in atypical tumours that progressed from benign ones. Our results establish the genomic landscape of primary atypical meningiomas and potential therapeutic targets.
A large fraction of plant genomes is composed of transposable elements (TE), which provide a potential source of novel genes through "domestication"-the process whereby the proteins encoded by TE ...diverge in sequence, lose their ability to catalyse transposition and instead acquire novel functions for their hosts. In Arabidopsis, ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) arose by domestication of the nuclease component of Harbinger class TE and acquired a new function as a component of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a histone H3K27me3 methyltransferase involved in regulation of host genes and in some cases TE. It was not clear how ALP1 associated with PRC2, nor what the functional consequence was. Here, we identify ALP2 genetically as a suppressor of Polycomb-group (PcG) mutant phenotypes and show that it arose from the second, DNA binding component of Harbinger transposases. Molecular analysis of PcG compromised backgrounds reveals that ALP genes oppose silencing and H3K27me3 deposition at key PcG target genes. Proteomic analysis reveals that ALP1 and ALP2 are components of a variant PRC2 complex that contains the four core components but lacks plant-specific accessory components such as the H3K27me3 reader LIKE HETEROCHROMATION PROTEIN 1 (LHP1). We show that the N-terminus of ALP2 interacts directly with ALP1, whereas the C-terminus of ALP2 interacts with MULTICOPY SUPPRESSOR OF IRA1 (MSI1), a core component of PRC2. Proteomic analysis reveals that in alp2 mutant backgrounds ALP1 protein no longer associates with PRC2, consistent with a role for ALP2 in recruitment of ALP1. We suggest that the propensity of Harbinger TE to insert in gene-rich regions of the genome, together with the modular two component nature of their transposases, has predisposed them for domestication and incorporation into chromatin modifying complexes.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Background: The effects of commonly used antimicrobial and anticariogenic agents on the adhesion of pit and fissure sealants were investigated in this study. Aims: The aim of this study is to ...evaluate the effects of erbium, chromium: yttrium-scandium-gallium-garnet (Er, Cr:YSGG) laser disinfection, casein phosphopeptides-amorphous calcium phosphate (CPP-ACP) containing paste and sodium hypochlorite application before the placement of a resin-based pit and fissure sealant on the shear bond strength of primary tooth enamel. Materials and Methods: The shear bond strength test evaluated the bond strength of sealants on the buccal enamel surfaces of primary molar teeth. The study groups were pit and fissure sealant without any preapplication, pre application of disinfection with Er, Cr:YSGG laser, disinfection with Er, Cr:YSGG laser and CPP-ACP containing paste, sodium hypochlorite, sodium hypochlorite and CPP-ACP containing paste and CPP-ACP containing paste. The pit and fissure sealants were placed using 4 mm diameter, 2 mm height cylindrical plastic tubes. Shear force was applied to each sample. The surfaces of the broken samples were detected under stereomicroscope and were grouped as adhesive, cohesive, and mixed. The results of the study were evaluated using the SPSS 16.0 package program for statistical analysis Results: The groups where sodium hypochlorite and sodium hypochlorite with CPP-ACP were applied showed the lowest bond strength (p < 0.05). It was observed that most of the failures in these groups were adhesive-type failures. No significant difference was observed between the shear bond strengths of the other groups (p < 0.05). Conclusions: Er, Cr: YSGG laser and CPP-ACP containing paste are alternative methods for pre-application of fissure sealants.
Intracranial aneurysm (IA) rupture leads to subarachnoid hemorrhage, a sudden-onset disease that often causes death or severe disability. Although genome-wide association studies have identified ...common genetic variants that increase IA risk moderately, the contribution of variants with large effect remains poorly defined. Using whole-exome sequencing, we identified significant enrichment of rare, deleterious mutations in PPIL4, encoding peptidyl-prolyl cis-trans isomerase-like 4, in both familial and index IA cases. Ppil4 depletion in vertebrate models causes intracerebral hemorrhage, defects in cerebrovascular morphology and impaired Wnt signaling. Wild-type, but not IA-mutant, PPIL4 potentiates Wnt signaling by binding JMJD6, a known angiogenesis regulator and Wnt activator. These findings identify a novel PPIL4-dependent Wnt signaling mechanism involved in brain-specific angiogenesis and maintenance of cerebrovascular integrity and implicate PPIL4 gene mutations in the pathogenesis of IA.
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