Additional insights into the adaptation of cotton plants under abiotic stresses by in silico analysis of conserved miRNAs in cotton expressed sequence tag database (dbEST)

Abiotic stress is the primary cause of crop losses worldwide. In addition to protein coding genes, microRNAs (miRNAs) have emerged as important players in plant stress responses. Though miRNAs are key in regulating many aspects of plant developmental plasticity under abiotic stresses, very few information are available in cotton. Hence, this study was conducted to identify the phylogenetically conserved miRNAs in cotton, using computational approaches. In this paper, we reported a set of miRNAs such as miR159, miR165, miR170, miR319, miR529, miR828, miR869, miR1030, miR1884, and miR2118 that are likely to be involved in abiotic stress response. Although, few of them have been described in literature for their specific role in fiber development, literature survey have shown that they may also be involved in abiotic stress response. Interestingly, miRNAs reported in this study were found to have several targets that are involved in abiotic stress resistance. Considering all together, it was concluded that these newly identified conserved microRNAs in cotton have great potential in future efforts to improve abiotic stress tolerance in cotton.Key words: miRNA, cotton, abiotic stress resistance, in silico analysis

Experimental Analysis of Surface Roughness and Tool Wear in Machining Process of Glass Fiber Reinforced Plastic Composites

The purpose of the present work is to analyze surface finish and tool wear on Glass fiber–reinforced plastic composites in turning operation faced out by the manufactures. In machining processes, maximum surface finish and less tool wear are important factors influencing the quality of the surface, tool life, and production output. Thus, the selection of tool and optimizing machining parameters are essential for perfect machining. Machining of GFRP material is difficult to carry out due to its anisotropic properties and non-homogeneous structure. The surface finish and tool wear with different parameters viz. speed, feed, depth of cut, fiber orientation and diameter of fiber should be taken very carefully during turning operation to optimize the desirable machining parameters for best quality as well as productivity

Scop3P : a comprehensive resource of human phosphosites within their full context

Protein phosphorylation is a key post-translational modification in many biological processes and is associated to human diseases such as cancer and metabolic disorders. The accurate identification, annotation, and functional analysis of phosphosites are therefore crucial to understand their various roles. Phosphosites are mainly analyzed through phosphoproteomics, which has led to increasing amounts of publicly available phosphoproteomics data. Several resources have been built around the resulting phosphosite information, but these are usually restricted to the protein sequence and basic site metadata. What is often missing from these resources, however, is context, including protein structure mapping, experimental provenance information, and biophysical predictions. We therefore developed Scop3P: a comprehensive database of human phosphosites within their full context. Scop3P integrates sequences (UniProtKB/Swiss-Prot), structures (PDB), and uniformly reprocessed phosphoproteomics data (PRIDE) to annotate all known human phosphosites. Furthermore, these sites are put into biophysical context by annotating each phosphoprotein with per-residue structural propensity, solvent accessibility, disordered probability, and early folding information. Scop3P, available at https://iomics.ugent.be/scop3p, presents a unique resource for visualization and analysis of phosphosites and for understanding of phosphosite structure–function relationships

Translabyrinthine resection of NF2 associated vestibular schwannoma with cochlear implant insertion

The authors present the case of a 24-year-old female with neurofibromatosis type 2. Growth of the left vestibular schwannoma and progressive hearing loss prompted the decision to proceed to translabyrinthine resection with cochlear nerve preservation and cochlear implant insertion. Complete resection with preservation of the facial and cochlear nerves was achieved. The patient had grade 1 facial function and was discharged on postoperative day 4 following suturing of a minor CSF leak. This case highlights the feasibility of cochlear nerve preservation and cochlear implant insertion in appropriately selected patients, offering a combination of effective tumor control and hearing rehabilitation. The video can be found here: https://stream.cadmore.media/r10.3171/2021.7.FOCVID2112

MobiDB: Intrinsically disordered proteins in 2021

The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in MobiDB version 4, regarding the database format, with novel types of annotations and an improved update process. The new website includes a re-designed user interface, a more effective search engine and advanced API for programmatic access. The new database schema gives more flexibility for the users, as well as simplifying the maintenance and updates. In addition, the new entry page provides more visualisation tools including customizable feature viewer and graphs of the residue contact maps. MobiDB v4 annotates the binding modes of disordered proteins, whether they undergo disorder-to-order transitions or remain disordered in the bound state. In addition, disordered regions undergoing liquid-liquid phase separation or post-translational modifications are defined. The integrated information is presented in a simplified interface, which enables faster searches and allows large customized datasets to be downloaded in TSV, Fasta or JSON formats. An alternative advanced interface allows users to drill deeper into features of interest. A new statistics page provides information at database and proteome levels. The new MobiDB version presents state-of-the-art knowledge on disordered proteins and improves data accessibility for both computational and experimental users.Fil: Piovesan, Damiano. Università di Padova; ItaliaFil: Necci, Marco. Università di Padova; ItaliaFil: Escobedo, Nahuel Abel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Monzon, Alexander Miguel. Università di Padova; ItaliaFil: Viczián, András. Università di Padova; ItaliaFil: Mičetić, Ivan. Università di Padova; ItaliaFil: Quaglia, Federica. Università di Padova; ItaliaFil: Paladin, Lisanna. Università di Padova; ItaliaFil: Ramasamy, Pathmanaban. Vrije Unviversiteit Brussel; Bélgica. University of Ghent; Bélgica. Interuniversity Institute of Bioinformatics in Brussels; BélgicaFil: Dosztányi, Zsuzsanna. Eötvös Loránd University; HungríaFil: Vranken, Wim F.. Vrije Unviversiteit Brussel; Bélgica. Interuniversity Institute of Bioinformatics in Brussels; BélgicaFil: Davey, Norman E.. The Institute Of Cancer Research; Reino UnidoFil: Parisi, Gustavo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Quilmes. Departamento de Ciencia y Tecnología; ArgentinaFil: Fuxreiter, Monika. Università di Padova; ItaliaFil: Tosatto, Silvio C. E.. Università di Padova; Itali

Computer-aided prediction of short-term tumor growth in sporadic vestibular schwannomas using both structural and dynamic-contrast enhanced MR imaging

Introduction:Recent studies have demonstrated that microvascular parameters derived from dynamic-contrast enhanced (DCE) MR imaging significantly correlate with tumor growth in vestibularschwannomas (VS). Other studies provide evidence that the use of artificial intelligence (AI)on structural MR data provides similar predictive value for tumor growth.Methods: This prospective study investigates the combination of structural and DCE imaging data for AI to predict short-term tumor growth in VS. A total of 110 newly diagnosed unilateral sporadic VS patients underwent both T2-weighted and DCE MR imaging. Established pipelines were used to estimate the values of DCE-derived parameters Ktrans, ve, and vp. Subsequently, tumors were delineated and only voxel values within the delineation were considered for the AI model development. Radiomic features were extracted from both the structural images and DCE-derived parameter maps. A classifier was trained on the radiomic features to predict tumor growth.Results: Growth was observed in 69 (63%) of the 110 patients during follow-up. A support vector machine (SVM) model was trained on Ktrans and ve radiomic features using five-fold-crossvalidation. This model resulted in an accuracy of 82.5%, sensitivity of 81.2%, specificity of 82.9%, and area-under-the-curve of 0.85. The predictive value of structural MR imaging features is currently under investigation, as well as the use of more complex AI models. It is hypothesized that the addition of structural features and increase in model complexity will improve the model's predictive power. Conclusion: Preliminary results have shown that DCE-derived parameter values exhibit a high predictive value for tumor growth prediction in sporadic VS. Other radiomic features and model types will be analyzed in order to investigate whether they improve the current AI model. These results will be presented during the conference.<br/

Computer-aided prediction of short-term tumor growth in sporadic vestibular schwannomas using both structural and dynamic-contrast enhanced MR imaging

Introduction:Recent studies have demonstrated that microvascular parameters derived from dynamic-contrast enhanced (DCE) MR imaging significantly correlate with tumor growth in vestibularschwannomas (VS). Other studies provide evidence that the use of artificial intelligence (AI)on structural MR data provides similar predictive value for tumor growth.Methods: This prospective study investigates the combination of structural and DCE imaging data for AI to predict short-term tumor growth in VS. A total of 110 newly diagnosed unilateral sporadic VS patients underwent both T2-weighted and DCE MR imaging. Established pipelines were used to estimate the values of DCE-derived parameters Ktrans, ve, and vp. Subsequently, tumors were delineated and only voxel values within the delineation were considered for the AI model development. Radiomic features were extracted from both the structural images and DCE-derived parameter maps. A classifier was trained on the radiomic features to predict tumor growth.Results: Growth was observed in 69 (63%) of the 110 patients during follow-up. A support vector machine (SVM) model was trained on Ktrans and ve radiomic features using five-fold-crossvalidation. This model resulted in an accuracy of 82.5%, sensitivity of 81.2%, specificity of 82.9%, and area-under-the-curve of 0.85. The predictive value of structural MR imaging features is currently under investigation, as well as the use of more complex AI models. It is hypothesized that the addition of structural features and increase in model complexity will improve the model's predictive power. Conclusion: Preliminary results have shown that DCE-derived parameter values exhibit a high predictive value for tumor growth prediction in sporadic VS. Other radiomic features and model types will be analyzed in order to investigate whether they improve the current AI model. These results will be presented during the conference.<br/

Generating operative workflows for vestibular schwannoma resection: a two-stage Delphi consensus in collaboration with British Skull Base Society. Part 1: the retrosigmoid approach

Objective: An operative workflow systematically compartmentalises operations into hierarchal components of phases, steps, instrument, technique errors and event errors. Operative workflow provides a foundation for education, training, and understanding of surgical variation. In Part 1 we present a codified operative workflow for the retrosigmoid approach to vestibular schwannoma resection. / Methods: A mixed-method consensus process of literature review, small group Delphi consensus, followed by a national Delphi consensus was performed in collaboration with British Skull Base Society (BSBS). Each Delphi round was repeated until data saturation and over 90% consensus was reached. / Results: Eighteen consultant skull base surgeons (10 neurosurgeons; 8 ENT) with median 17.9 years of experience (IQR 17.5 years) of independent practice participated. There was a 100% response rate across both Delphi rounds. The operative workflow for the retrosigmoid approach contained 3 phases and 40 unique steps: Phase 1: approach and exposure; Phase 2: tumour debulking and excision; Phase 3: closure. For the retrosigmoid approach, technique and event error for each operative step was also described. / Conclusions: We present Part 1 of a national, multi-centre, consensus-derived codified operative workflow for the retrosigmoid and approach to vestibular schwannomas that encompasses phases, steps, instruments, technique errors, and event errors. The codified retrosigmoid approach presented in this manuscript can serve as foundational research for future work, such as operative workflow analysis or neurosurgical simulation and education

Generating Operative Workflows for Vestibular Schwannoma Resection: A Two-Stage Delphi's Consensus in Collaboration with the British Skull Base Society. Part 2: The Translabyrinthine Approach

Objective An operative workflow systematically compartmentalizes operations into hierarchal components of phases, steps, instrument, technique errors, and event errors. Operative workflow provides a foundation for education, training, and understanding of surgical variation. In this Part 2, we present a codified operative workflow for the translabyrinthine approach to vestibular schwannoma resection. Methods A mixed-method consensus process of literature review, small-group Delphi's consensus, followed by a national Delphi's consensus was performed in collaboration with British Skull Base Society (BSBS). Each Delphi's round was repeated until data saturation and over 90% consensus was reached. Results Seventeen consultant skull base surgeons (nine neurosurgeons and eight ENT [ear, nose, and throat]) with median of 13.9 years of experience (interquartile range: 18.1 years) of independent practice participated. There was a 100% response rate across both the Delphi rounds. The translabyrinthine approach had the following five phases and 57 unique steps: Phase 1, approach and exposure; Phase 2, mastoidectomy; Phase 3, internal auditory canal and dural opening; Phase 4, tumor debulking and excision; and Phase 5, closure. Conclusion We present Part 2 of a national, multicenter, consensus-derived, codified operative workflow for the translabyrinthine approach to vestibular schwannomas. The five phases contain the operative, steps, instruments, technique errors, and event errors. The codified translabyrinthine approach presented in this manuscript can serve as foundational research for future work, such as the application of artificial intelligence to vestibular schwannoma resection and comparative surgical research

The LEGATOS technique: A new tissue‐validated dynamic contrast‐enhanced MRI method for whole‐brain, high‐spatial resolution parametric mapping

From Wiley via Jisc Publications RouterHistory: received 2020-06-30, rev-recd 2021-04-23, accepted 2021-04-24, pub-electronic 2021-05-15Article version: VoRPublication status: PublishedFunder: Dowager Countess Eleanor Peel Trust; Id: http://dx.doi.org/10.13039/501100000832Funder: Cancer Research UK; Id: http://dx.doi.org/10.13039/501100000289; Grant(s): C8742/A18097Purpose: A DCE‐MRI technique that can provide both high spatiotemporal resolution and whole‐brain coverage for quantitative microvascular analysis is highly desirable but currently challenging to achieve. In this study, we sought to develop and validate a novel dual‐temporal resolution (DTR) DCE‐MRI‐based methodology for deriving accurate, whole‐brain high‐spatial resolution microvascular parameters. Methods: Dual injection DTR DCE‐MRI was performed and composite high‐temporal and high‐spatial resolution tissue gadolinium‐based‐contrast agent (GBCA) concentration curves were constructed. The high‐temporal but low‐spatial resolution first‐pass GBCA concentration curves were then reconstructed pixel‐by‐pixel to higher spatial resolution using a process we call LEGATOS. The accuracy of kinetic parameters (Ktrans, vp, and ve) derived using LEGATOS was evaluated through simulations and in vivo studies in 17 patients with vestibular schwannoma (VS) and 13 patients with glioblastoma (GBM). Tissue from 15 tumors (VS) was examined with markers for microvessels (CD31) and cell density (hematoxylin and eosin [H&E]). Results: LEGATOS derived parameter maps offered superior spatial resolution and improved parameter accuracy compared to the use of high‐temporal resolution data alone, provided superior discrimination of plasma volume and vascular leakage effects compared to other high‐spatial resolution approaches, and correlated with tissue markers of vascularity (P ≤ 0.003) and cell density (P ≤ 0.006). Conclusion: The LEGATOS method can be used to generate accurate, high‐spatial resolution microvascular parameter estimates from DCE‐MRI