Frequency of Gross Total Resection in Intra-axial Brain Tumors with Help of Neuronavigation

Introduction: Neuronavigation has become a ubiquitous tool in the surgical management of brain tumors. Neuronavigation is most useful as an adjunct to other brain-mapping techniques such as awake mapping and electrocorticography in the resection of lesions within eloquent motor and language areas. Neuronavigation is also commonly used in skull base tumors, especially for planning an operative trajectory in regions containing vital neurovascular structures and may be used for cerebrovascular surgery. The current study was planned to determine the frequency of gross total resection in intra-axial brain tumors with the help of neuronavigation.Material and Methods: This cross sectional study was carried out in the Department of Neurosurgery, Nishtar Medical College & Hospital, Multan, from September 2014 to March 2015. After approval from institutional ethical committee, seventy seven patients fulfilling the inclusion criteria were selected from the patient admitted in the Neurosurgical Department through the Out Patient Department and patients referred from other departments. After thorough counseling with the patient and his/her relatives, informed consent for procedure was taken.Results: Total 78 patients were included in the study. Out of these 78 (100%), 41 (52.6%) were male and 37 (47.4%) were female. As concern to the outcome variable (gross total resection), out of 78 (100%), in 61 (78.2%) patients gross total resection was present. On cross tabulation it was further clarified that in male patients’ gross total resection present in 32 patients and absent in 9 patients. Similarly in female patients gross total resection present in 29 patients and absent in 8 patients. P value was 0.747. Conclusion: Conclusion of our study is that neuronevigation is a usefull technique in for better gross total resection of intra axial brain tumor

Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri)

Background: In plants, basic leucine zipper transcription factors (TFs) play important roles in multiple biological processes such as anthesis, fruit growth & development and stress responses. However, systematic investigation and characterization of bZIP-TFs remain unclear in Chinese white pear. Chinese white pear is a fruit crop that has important nutritional and medicinal values. Results: In this study, 62 bZIP genes were comprehensively identified from Chinese Pear, and 54 genes were distributed among 17 chromosomes. Frequent whole-genome duplication (WGD) and dispersed duplication (DSD) were the major driving forces underlying the bZIP gene family in Chinese white pear. bZIP-TFs are classified into 13 subfamilies according to the phylogenetic tree. Subsequently, purifying selection plays an important role in the evolution process of PbbZIPs. Synteny analysis of bZIP genes revealed that 196 orthologous gene pairs were identified between Pyrus bretschneideri, Fragaria vesca, Prunus mume, and Prunus persica. Moreover, cis-elements that respond to various stresses and hormones were found on the promoter regions of PbbZIP, which were induced by stimuli. Gene structure (intron/exon) and different compositions of motifs revealed that functional divergence among subfamilies. Expression pattern of PbbZIP genes differential expressed under hormonal treatment abscisic acid, salicylic acid, and methyl jasmonate in pear fruits by real-time qRT-PCR. Conclusions: Collectively, a systematic analysis of gene structure, motif composition, subcellular localization, synteny analysis, and calculation of synonymous (Ks) and non-synonymous (Ka) was performed in Chinese white pear. Sixty-two bZIP-TFs in Chinese pear were identified, and their expression profiles were comprehensively analyzed under ABA, SA, and MeJa hormones, which respond to multiple abiotic stresses and fruit growth and development. PbbZIP gene occurred through Whole-genome duplication and dispersed duplication events. These results provide a basic framework for further elucidating the biological function characterizations under multiple developmental stages and abiotic stress responses.This work was performed at the school of Life Sciences, Anhui agricultural university, Hefei, China and was supported by National Natural Science Foundation of China (No. 31640068) and Natural Science Youth Foundation of Anhui Agricultural University (No. 2019zd01). These funding bodies had no role in the design of the study, collection, analysis, and interpretation of data or in writing the manuscript

Effect of animal manure, crop type, climate zone, and soil attributes on greenhouse gas emissions from agricultural soils A global meta-analysis

Agricultural lands, because of their large area and exhaustive management practices, have a substantial impact on the earth's carbon and nitrogen cycles, and agricultural activities consequence in discharges of greenhouse gases (GHGs). Globally, greenhouse gases (GHGs) emissions especially carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) from the agricultural sector are increasing due to anthropogenic activities. Although, the application of animal manure to the agricultural soil as an organic fertilizer not only improves soil health and agricultural production but also has a significant impact on GHGs emissions. But the extent of GHGs emissions in response to manure application under diverse environmental conditions is still uncertain. Here, a meta-analysis study was conducted using field data (48 peer-reviewed publications) published from 1989 to 2019. Meta-analysis results showed that poultry manure considerably increased CO2, CH4, and N2O emissions than pig and cattle manure. Furthermore, application of poultry manure also increased (¯(〖lnRR〗^ ) =0.141, 95% CI =0.526-0.356) GWP (global warming potential) of total soil GHGs emissions. While, the significant effects on CO2, CH4, and N2O emissions also occurred at manure rate > 320 kg N ha-1 and > 60% water filled pore space. The maximum concentrations of CO2, CH4, and N2O emissions were observed in neutral soils (¯(〖lnRR〗^ ) =3.375, 95% CI =3.323-3.428), alkaline soils (¯(〖lnRR〗^ ) =1.468, 95% CI =1.403-1.532), and acidic soils (¯(〖lnRR〗^ ) =2.355, 95% CI =2.390-2.400), respectively. Soil texture, climate zone and crop type were also found significant factors to increase GHGs emissions. Thus, this meta-analysis revealed a knowledge gap concerning the consequences of animal manure application and rate, climate zone, and physicochemical properties of soil on GHGs emissions from agricultural soils.Awais Shakoor would like to express his gratitude for the grant provided by the University of Lleida, Spain. The authors would like to appreciate the valuable comments from the editors and anonymous reviewers to improve the quality of this study

Polarized Thermal Conductivity of Two-Dimensional Dusty Plasmas

The computation of thermalt properties of dusty plasmas is substantial task in the area of science and technology. The thermal conductivity (λ) has been computed by applying polarization effect through molecular dynamics (MD) simulations of two dimensional (2D) strongly coupled complex dusty plasmas (SCCDPs). The effects of polarization on thermal conductivity have been measured for a wide range of Coulomb coupling (Γ) and Debye screening (κ) parameters using homogeneous non-equilibrium molecular dynamics (HNEMD) method for suitable system sizes. The HNEMD simulation method is employed at constant external force field strength (F*) and varying polarization effects. The algorithm provides precise results with rapid convergence and minute dimension effects. The outcomes have been compared with earlier available simulation results of molecular dynamics, theoretical predictions and experimental results of complex dusty plasma liquids. The calculations show that the kinetic energy of SCCDPS depends upon the system temperature (≡ 1/Г) and it is independent of higher screening parameter. Furthermore, it has shown that the presented HNEMD method has more reliable results than those obtained through earlier known numerical methods

Zinc Finger-Homeodomain Transcriptional Factors (ZHDs) in Upland Cotton (Gossypium hirsutum): Genome-Wide Identification and Expression Analysis in Fiber Development

Zinc finger-homeodomain (ZHD) genes encode a family of plant-specific transcription factors that not only participate in the regulation of plant growth and development but also play an important role in the response to abiotic stress. The ZHD gene family has been studied in several model plants, including Solanum lycopersicum, Zea mays, Oryza sativa, and Arabidopsis thaliana. However, a comprehensive study of the genes of the ZHD family and their roles in fiber development and pigmentation in upland cotton has not been completed. To address this gap, we selected a brown fiber cultivar for our study; brown color in cotton is one of the most desired colors in the textile industry. The natural colored fibers require less processing and little dying, thereby eliminating dye costs and chemical residues. Using bioinformatics approaches, we identified 37 GhZHD genes from Gossypium hirsutum and then divided these genes into seven groups based on their phylogeny. The GhZHD genes were mostly conserved in each subfamily with minor variations in motif distribution and gene structure. These genes were largely distributed on 19 of the 26 upland cotton chromosomes. Among the Gossypium genomes, the paralogs and orthologs of the GhZHD genes were identified and further characterized. Furthermore, among the paralogs, we observed that the ZHD family duplications in Gossypium genomes (G. hirsutum, G. arboreum, and G. raimondii) were probably derived from segmental duplication or genome-wide duplication (GWD) events. Through a combination of qRT-PCR and proanthocyanidins (PA) accumulation analyses in brown cotton fibers, we concluded that the candidate genes involved in early fiber development and fiber pigment synthesis include the following: GhZHD29, GhZHD35, GhZHD30, GhZHD31, GhZHD11, GhZHD27, GhZHD18, GhZHD15, GhZHD16, GhZHD22, GhZHD6, GhZHD33, GhZHD13, GhZHD5, and GhZHD23. This study delivers insights into the evolution of the GhZHD genes in brown cotton, serves as a valuable resource for further studies, and identifies the conditions necessary for improving the quality of brown cotton fiber

In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing

High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies

Large Scale Simulations for Dust Acoustic Waves in Weakly Coupled Dusty Plasmas

Dust acoustic wave of three-dimensional (3D) dusty plasmas (DPs) has been computed using equilibrium molecular dynamics (EMD) simulations for plasma parameters of Coulomb coupling strength (Γ) and Debye screening (κ). New simulations of wave properties such as longitudinal current correlation (LCC) CL(k, t) function have been investigated for 3D weakly DPs (WCDPs), for the first time. EMD results, CL (k, t) have been simulated for four normalized wave numbers (k = 0, 1, 2, and 3). Our simulations illustrate that the frequency and amplitude of oscillation vary with increasing of Γ and κ. Moreover, present simulations of CL (k, t) illustrate that the varying behavior has been observed for changing (Γ, κ) and system sizes (N). Current investigation illustrates that amplitude of wave oscillation increases with a decrease in Γ and N. However, there are slightly change in the value of CL (k, t) and its fluctuation increases with an increasing k. The obtained outcomes have found to be more acceptable than those that of previous numerical, theoretical, and experimental data. EMD simulation has been performed with an increasing sequence for WCDPs and it serves to benchmark improved approach for future energy generation applications

Identification and Comprehensive Genome-Wide Analysis of Glutathione S-Transferase Gene Family in Sweet Cherry (Prunus avium) and Their Expression Profiling Reveals a Likely Role in Anthocyanin Accumulation

Glutathione S-transferases (GSTs) in plants are multipurpose enzymes that are involved in growth and development and anthocyanins transportation. However, members of the GST gene family were not identified in sweet cherry (Prunus avium). To identify the GST genes in sweet cherry, a genome-wide analysis was conducted. In this study, we identified 67 GST genes in P. avium genome and nomenclature according to chromosomal distribution. Phylogenetic tree analysis revealed that PavGST genes were classified into seven chief subfamily: TCHQD, Theta, Phi, Zeta, Lambda, DHAR, and Tau. The majority of the PavGST genes had a relatively well-maintained exon–intron and motif arrangement within the same group, according to gene structure and motif analyses. Gene structure (introns-exons) and conserved motif analysis revealed that the majority of the PavGST genes showed a relatively well-maintained motif and exons–introns configuration within the same group. The chromosomal localization, GO enrichment annotation, subcellular localization, syntenic relationship, Ka/Ks analysis, and molecular characteristics were accomplished using various bioinformatics tools. Mode of gene duplication showed that dispersed duplication might play a key role in the expansion of PavGST gene family. Promoter regions of PavGST genes contain numerous cis-regulatory components, which are involved in multiple stress responses, such as abiotic stress and phytohormones responsive factors. Furthermore, the expression profile of sweet cherry PavGSTs showed significant results under LED treatment. Our findings provide the groundwork for future research into induced LED anthocyanin and antioxidants deposition in sweet cherries

Canopy Height Estimation at Landsat Resolution Using Convolutional Neural Networks

Forest structure estimation is very important in geological, ecological and environmental studies. It provides the basis for the carbon stock estimation and effective means of sequestration of carbon sources and sinks. Multiple parameters are used to estimate the forest structure like above ground biomass, leaf area index and diameter at breast height. Among all these parameters, vegetation height has unique standing. In addition to forest structure estimation it provides the insight into long term historical changes and the estimates of stand age of the forests as well. There are multiple techniques available to estimate the canopy height. Light detection and ranging (LiDAR) based methods, being the accurate and useful ones, are very expensive to obtain and have no global coverage. There is a need to establish a mechanism to estimate the canopy height using freely available satellite imagery like Landsat images. Multiple studies are available which contribute in this area. The majority use Landsat images with random forest models. Although random forest based models are widely used in remote sensing applications, they lack the ability to utilize the spatial association of neighboring pixels in modeling process. In this research work, we define Convolutional Neural Network based model and analyze that model for three test configurations. We replicate the random forest based setup of Grant et al., which is a similar state-of-the-art study, and compare our results and show that the convolutional neural networks (CNN) based models not only capture the spatial association of neighboring pixels but also outperform the state-of-the-art

Antioxidant profiling of indigenous oat cultivars with special reference to avenanthramides

International audienceOat (Avena sativa) of the South Asian region, particularly Pakistan, remains neglected fordecades. Oat is unique in terms of the presence of exceptional polyphenolic compoundsknown as avenanthramides (AVAs). AVAs have therapeutic effects and behave as antioxidative,anti-proliferative, and vasodilatory agents. The present work was designed to explore thenutritional and antioxidant aspects of oat, especially of their phenolic content, includingAVAs. Three cultivars of oat (S-2000, S-2011, and L-632) were examined for their proximatecomposition and mineral profile. Conventional solvents (acetone, ethanol, and methanol) andsupercritical carbon dioxide (SC-CO2) were used for polyphenol extraction. Extracts werespectrophotometrically analysed for their phytochemical profile and antioxidant activity. Vitalavenanthramides (AVA-A, AVA-B, and AVA-C) were quantified through HPLC/UV-Visdetector. The data reported highest total phenolic content (222.72 mg GAE/100 g) and totalflavonoid content (137.13 mg QE/100 g) in S-2011 with maximum antioxidant activity(1,1-diphenyl-2-picrylhydrazyl IC50 = 12.38 mg/ml and ferric reducing antioxidant power =39.98 μmol/g). This highest antioxidant potential was examined in supercritical extract whilemethanol evaluated the best among conventional solvents. Best extractions were furtheranalysed with HPLC for the quantification of AVAs. SC-CO2 extraction recorded maximumconcentrations of AVA-A (137.84 μg/g), AVA-B (105.10 μg/g), and AVA-C (119.86 μg/g) inS-2011 cultivar. In conclusion, oat is the rich source of antioxidants with the presence ofexceptional AVAs