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Consolidation of Carbon Fiber (CF)/high‐performance thermoplastic composites is much less understood than the one of their thermoset counterparts. It is usually assumed that the consolidation quality is directly linked to the removal of voids within the sample during consolidation, leading to mechanical properties suitable for aerospace applications. A systematic study of the temporal evolution of CF/polyetherketoneketone (PEKK) samples' microstructure consolidated under low pressure in a rheometer is related to the increase in inter‐laminar shear strength. The results show that despite similar void contents well‐below 1 vol%, samples can present significant differences in ILSS values, from 80 to 95 MPa for cross‐ply samples, and from 98 to 112 MPa for unidirectional (UD) ones. A microstructural analysis shows that, for these materials, consolidation quality is rather related to a reorganization of the inter‐ply, a resin‐rich (~70 vol%) region of typical thickness 10 μm which is slowly repopulated in fibers during consolidation. Highlights: Microstructure of CF/PEKK composites is characterized over consolidation timeContrary to thermosets void content cannot be used to predict mechanical propertiesILSS increase over consolidation time is related to inter‐ply reorganizationInter‐ply microstructure and ILSS have a direct correlationThe repopulation in fibers of the resin‐rich inter‐ply is a slow process [ABSTRACT FROM AUTHOR]

A new handwritten twenty pages' manuscript of initiation to the Greek secret "friendly society" organization which was formed beginning of 19th century and essentially established the Greek independence against the Turks has been investigated. Historical accounts, spectroscopy analysis using Raman, X Ray Fluorescence and Near Infrared, for paper and ink characterization, as well as radiocarbon dating, and fractal of Minkowski Dimension algorithm of 5-lines and full-page handwritten text to identify number of scribers, and a novel preprocessing RGB color analysis of ink and paper identification have been applied. The investigation and results verify the dating of this manuscript to 1819, identify five types of iron gall inks, characterize the pulpwood and identify five different paper lots and four scribes from the ink content and handwritten styles of the compact five lines text and whole text pages. The results are mutually corroborated. [ABSTRACT FROM AUTHOR]

The feasibility of automated railway track segment characterisation, as part of a broader track condition based maintenance procedure, is explored via railway–vehicle–based random vibration signals and Statistical Time Series (STS) methods. In particular, three methods within a Multiple Model (MM) framework, which are founded on data-driven stochastic parametric models for the representation of the partial vehicle-rail dynamics, are employed. The random vibration signals are obtained from two sensors, which are mounted on the axlebox and the bogie frame, respectively, of an Athens Metro railway vehicle moving under three different speeds (60, 70 or 80 km/h). The performance assessment of the methods is based on two distinct track characterisation problems. The first corresponds to the characterisation of a specific track segment after 6 months of continuous use, while the second to the comparison between two nominally identical track segments which were installed with a 2 month time interval and are used by different numbers and types of trains. The results indicate deterioration of the track segment in the first characterisation problem and differences between the two nominally identical segments in the second. The superiority of the employed methods over a state-of-the-art method is also demonstrated via proper comparisons. [ABSTRACT FROM AUTHOR]

In this study we present halloysite clay mineral combined with TiO2, as promising new class of nanomaterials that can be used as an effective, cost-efficient, and environment-friendly procedure for the decomposition of tebuconazole, C16H22ClN3O, [(RS)-1-p-chlorophenyl-4,4-dimethyl-3-(1H-1,2,4- triazol-1-ylmethyl)-pentan-3-ol], TEB-fungicide, in water. For this purpose, halloysite–TiO2 nanoparticles are prepared using the sol-gel methodology combined with hydrothermal treatment of the samples in mild conditions. The halloysite–TiO2 nanocomposites are characterized by X-ray diffraction, scanning electron microscopy, transmission electron microscopy, and N2 sorption–desorption isotherms analysis by Brunauer–Emmett–Teller to determine specific surface area (SSA). The total pore volume of the halloysite 40%–TiO2 60% prepared nanocomposite and its SSA are 0.35 cm³/g and 188 m²/g, respectively. This nanocomposite showed a photocatalytic efficiency of 39.5% to TEB decomposition after 240 min under UV irradiation. The halloysite 30%–TiO2 70% nanocomposite has a total pore volume of 0.34 cm³/g and a SSA of 187 m²/g. This nanomaterial shows 40.0% photocatalytic efficiency for TEB destruction under UV exposure. The best photodegradation efficiency, 47.4% of TEB was achieved with the halloysite 10%–TiO2 90% nanomaterial, instead of 33.2% decomposition efficiency measured when commercial TiO2 (Degussa P25) was used. In this case, the halloysite 10%– TiO2 90% nanocomposite showed the highest SSA of 222 m²/g. The concentration of TEB did not show any significant change in all the samples after 150 min exposure under UV illumination. [ABSTRACT FROM AUTHOR]

The article focuses on the pulsating star, GSC 0476-1362 which is situated in the constellation of Aquilla and discusses its variabilty.

Issues concerning the use of 19F nuclear magnetic resonance spectroscopy to study the molecular dynamics and microstructure of aqueous solutions of an associative polymer are presented.

Detailed geological mapping, structural investigation and amphibole chemistry analyses in southern Evia (Aegean Sea, Greece) allow us to place new constraints on the internal structural architecture and tectonic evolution of the Cycladic Blueschists. We show that the early deformation history was related to ESE directed thrusting resulting in the stacking of the Styra and Ochi nappes, which constitute the Cycladic Blueschist unit in Evia. These early thrust movements initiated just before and proceeded at peak conditions of the Eocene high-pressure metamorphism. Subsequent constrictional deformation gave rise to E-W trending upright folding accomplished at the early exhumation stage. The main ductile-stage exhumation occurred during a single deformation phase associated with the decompression of blueschist rocks from the stability field of crossite to that of actinolite. This phase was characterized by localization of ductile deformation into a series of major, tens of meters thick, ENE directed shear zones, which cut up-section in their transport direction and restack the early thrust and fold sequence, locally bringing the structurally lower Styra nappe over the higher Ochi nappe. It is suggested that these zones operated as thrusts rather than normal sense shear zones as has been previously argued and were possibly formed during the Oligocene ENE-ward extrusion of the blueschists. Brittle-ductile NE dipping normal faulting of post-early Miocene age was probably responsible for the final exhumation of rocks. [ABSTRACT FROM AUTHOR]

Pantellerian ware is a Late Roman cooking ware whose production centre was established on the island of Pantelleria by the pioneering research of Fulford and Peacock almost 20 years ago ( Peacock 1982 ; Fulford and Peacock 1984 ). Archaeological and archaeometric studies carried out by the authors of the present contribution during the past four years have aimed to fully characterize this ceramic class. Recurrent ceramic forms, their distribution over time and space, their petrographic characteristics and their chemical identity, as well as possible raw materials and their technological properties, were considered. The present paper is a comprehensive review of this archaeometric work and aims to establish a ‘reference group’. Using a representative number of samples of Pantellerian ware that were recently discovered in the island through archaeological field surveys or surface and submarine excavations, it was possible to characterize in detail the compositional variability of this ware in terms of chemistry and petrography. Furthermore, the physical properties of this ceramic type have been defined in order to better understand its performance characteristics, mainly in response to induced thermal stress. In the meantime, the experimental mixing and tempering of locally sampled raw materials have shed light on the ancient manufacturing process and have led to an approximation of the original paste. [ABSTRACT FROM AUTHOR]

Samples of Roman thin-walled ware from Segesta (northwestern Sicily), dating back to the early Imperial period, were studied by optical microscopy (OM) and Neutron Activation Analysis (NAA). Up to now, this class of Roman fine tableware has only occasionally been evaluated archaeometrically. Nevertheless, numerous production centres are believed to have been simultaneously active in the western Mediterranean area. Petrographic and chemical data seem to be in agreement with the archaeological hypothesis of local manufacture in Segesta for most of the analysed samples, through a comparison with kiln wasters and local raw materials. The effectiveness of thin-section petrography for determining the provenance of such a tiny tempered class of pottery and the integrated use of two different grouping procedures (petrography and chemistry) were also tested. [ABSTRACT FROM AUTHOR]

Summary Chronic necrotizing pulmonary aspergillosis is a rare infection encountered mainly in immunocompromised patients. We present the case of a young woman where the diagnosis of chronic necrotizing pulmonary aspergillosis was established after an open biopsy of the right lung. Liposomal amphotericin B was administered postoperatively for 10 days with moderate success. In a concise review we summarize the basic notions of chronic necrotizing pulmonary aspergillosis. [ABSTRACT FROM AUTHOR]

Abstract Background Genes of conserved order in bacterial genomes tend to evolve slower than genes whose order is not conserved. In addition, genes with a GC content lower than the GC content of the resident genome are known to be selectively silenced by the histone-like nucleoid structuring protein (H-NS) in Salmonella. Results In this study, we use a comparative genomics approach to demonstrate that in Salmonella, genes whose order is not conserved (or genes without homologs) in closely related bacteria possess a significantly lower average GC content in comparison to genes that preserve their relative position in the genome. Moreover, these genes are more frequently targeted by H-NS than genes that have conserved their genomic neighborhood. We also observed that duplicated genes that do not preserve their genomic neighborhood are, on average, under less selective pressure. Conclusions We establish a strong association between gene order, GC content and gene silencing in a model bacterial species. This analysis suggests that genes that are not under strong selective pressure (evolve faster than others) in Salmonella tend to accumulate more AT-rich mutations and are eventually silenced by H-NS. Our findings may establish new approaches for a better understanding of bacterial genome evolution and function, using information from functional and comparative genomics.

In the majority of downstream analysis pipelines for single-cell RNA sequencing (scRNA-seq), techniques like dimensionality reduction and feature selection are employed to address the problem of high-dimensional nature of the data. These approaches involve mapping the data onto a lower-dimensional space, eliminating less informative genes, and pinpointing the most pertinent features. This process ultimately leads to a reduction in the number of dimensions used for downstream analysis, which in turn speeds up the computation of large-scale scRNA-seq data. Most approaches are directed to isolate from biological background the genes characterizing different cells and or the condition under study by establishing lists of differentially expressed or coexpressed genes. Herein, we present scRNA-Explorer an open-source online tool for simplified and rapid scRNA-seq analysis designed with the end user in mind. scRNA-Explorer utilizes: (i) Filtering out uninformative cells in an interactive manner via a web interface, (ii) Gene correlation analysis coupled with an extra step of evaluating the biological importance of these correlations, and (iii) Gene enrichment analysis of correlated genes in order to find gene implication in specific functions. We developed a pipeline to address the above problem. The scRNA-Explorer pipeline allows users to interrogate in an interactive manner scRNA-sequencing data sets to explore via gene expression correlations possible function(s) of a gene of interest. scRNA-Explorer can be accessed at https://bioinformatics.med.uoc.gr/shinyapps/app/scrnaexplorer., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

The process of navigating through the landscape of biomedical literature and performing searches or combining them with bioinformatics analyses can be daunting, considering the exponential growth of scientific corpora and the plethora of tools designed to mine PubMed(®) and related repositories. Herein, we present BioTextQuest v2.0, a tool for biomedical literature mining. BioTextQuest v2.0 is an open-source online web portal for document clustering based on sets of selected biomedical terms, offering efficient management of information derived from PubMed abstracts. Employing established machine learning algorithms, the tool facilitates document clustering while allowing users to customize the analysis by selecting terms of interest. BioTextQuest v2.0 streamlines the process of uncovering valuable insights from biomedical research articles, serving as an agent that connects the identification of key terms like genes/proteins, diseases, chemicals, Gene Ontology (GO) terms, functions, and others through named entity recognition, and their application in biological research. Instead of manually sifting through articles, researchers can enter their PubMed-like query and receive extracted information in two user-friendly formats, tables and word clouds, simplifying the comprehension of key findings. The latest update of BioTextQuest leverages the EXTRACT named entity recognition tagger, enhancing its ability to pinpoint various biological entities within text. BioTextQuest v2.0 acts as a research assistant, significantly reducing the time and effort required for researchers to identify and present relevant information from the biomedical literature., Competing Interests: The authors declare no conflict of interest., (© 2024 Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.)

Objectives: Multicenter studies reporting outcomes following tracheostomy in children with congenital heart disease are limited, particularly in patients with single ventricle physiology. We aimed to describe clinical characteristics and outcomes in a multicenter cohort of patients with single ventricle physiology who underwent tracheostomy before Fontan operation., Design: Multicenter retrospective cohort study., Setting: Twenty-one tertiary care pediatric institutions participating in the Collaborative Research from the Pediatric Cardiac Intensive Care Society., Patients: We reviewed 99 children with single ventricle physiology who underwent tracheostomy before the Fontan operation at 21 institutions participating in Collaborative Research from the Pediatric Cardiac Intensive Care Society between January 2010 and December 2020, with follow-up through December 31, 2021., Interventions: None., Measurements and Main Results: Death occurred in 51 of 99 patients (52%). Cox proportional hazard analysis was performed to determine factors associated with death after tracheostomy. Results are presented as hazard ratio (HR) with 95% CIs. Nonrespiratory indication(s) for tracheostomy (HR, 2.21; 95% CI, 1.14-4.32) and number of weeks receiving mechanical ventilation before tracheostomy (HR, 1.06; 95% CI, 1.02-1.11) were independently associated with greater hazard of death. In contrast, diagnosis of tricuspid atresia or Ebstein's anomaly was associated with less hazard of death (HR, 0.16; 95% CI, 0.04-0.69). Favorable outcome, defined as survival to Fontan operation or decannulation while awaiting Fontan operation with viable cardiopulmonary physiology, occurred in 29 of 99 patients (29%). Median duration of mechanical ventilation before tracheostomy was shorter in patients who survived to favorable outcome (6.1 vs. 12.1 wk; p < 0.001), and only one of 16 patients with neurologic indications for tracheostomy and 0 of ten patients with cardiac indications for tracheostomy survived to favorable outcome., Conclusions: For children with single ventricle physiology who undergo tracheostomy, mortality risk is high and should be carefully considered when discussing tracheostomy as an option for these children. Favorable outcomes are possible, although thoughtful attention to patient selection and tracheostomy timing are likely necessary to achieve this goal., Competing Interests: Dr. Mastropietro received funding from Telan, Meltz, Wallace, and Eide Law Firm, and Bioporto. Dr. Werho received funding from University of California San Diego; his institution received funding from the American Heart Association; and he disclosed that he is a board member of the Pediatric Cardiac Intensive Care Society and the Pediatric Cardiac Critical Care Consortium. Dr. Yates received funding from Alexion Pharmaceuticals. The remaining authors have disclosed that they do not have any potential conflicts of interest., (Copyright © 2024 by the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies.)

Schizophrenia (SCZ) is a chronic, severe, and complex psychiatric disorder that affects all aspects of personal functioning. While SCZ has a very strong biological component, there are still no objective diagnostic tests. Lately, special attention has been given to epigenetic biomarkers in SCZ. In this study, we introduce a three-step, automated machine learning (AutoML)-based, data-driven, biomarker discovery pipeline approach, using genome-wide DNA methylation datasets and laboratory validation, to deliver a highly performing, blood-based epigenetic biosignature of diagnostic clinical value in SCZ. Publicly available blood methylomes from SCZ patients and healthy individuals were analyzed via AutoML, to identify SCZ-specific biomarkers. The methylation of the identified genes was then analyzed by targeted qMSP assays in blood gDNA of 30 first-episode drug-naïve SCZ patients and 30 healthy controls (CTRL). Finally, AutoML was used to produce an optimized disease-specific biosignature based on patient methylation data combined with demographics. AutoML identified a SCZ-specific set of novel gene methylation biomarkers including IGF2BP1, CENPI, and PSME4. Functional analysis investigated correlations with SCZ pathology. Methylation levels of IGF2BP1 and PSME4, but not CENPI were found to differ, IGF2BP1 being higher and PSME4 lower in the SCZ group as compared to the CTRL group. Additional AutoML classification analysis of our experimental patient data led to a five-feature biosignature including all three genes, as well as age and sex, that discriminated SCZ patients from healthy individuals [AUC 0.755 (0.636, 0.862) and average precision 0.758 (0.690, 0.825)]. In conclusion, this three-step pipeline enabled the discovery of three novel genes and an epigenetic biosignature bearing potential value as promising SCZ blood-based diagnostics., (© 2024. The Author(s).)

Data comparing surgical systemic-to-pulmonary artery shunt and patent ductus arteriosus (PDA) stent as the initial palliation procedure for patients with pulmonary atresia with intact ventricular septum (PA-IVS) are limited. We sought to compare characteristics and outcomes in a multicenter cohort of patients with PA-IVS undergoing surgical shunts versus PDA stents. We retrospectively reviewed neonates with PA-IVS from 2009 to 2019 in 19 United States centers. Bivariate comparisons and multivariable logistic regression analysis were performed to determine the relationship between initial palliation strategy and outcomes including major adverse cardiovascular events (MACE): stroke, mechanical circulatory support, cardiac arrest, or death. 187 patients were included: 38 PDA stents and 149 surgical shunts. Baseline characteristics did not differ statistically between groups. Post-procedural MACE occurred in 4 patients (11%) with PDA stents versus 38 (26%) with surgical shunts, p = 0.079. Overall, the initial palliation strategy was not significantly associated with MACE (aOR:0.37; 95% CI,0.13-1.02). In patients with moderate-to-severe right ventricle hypoplasia, PDA stents were significantly associated with decreased odds of MACE (aOR:0.36; 95% CI,0.13-0.99). PDA stents were associated with lower vasoactive inotrope scores (median 0 versus 5, p < 0.001), greater likelihood to be extubated at the end of their procedure (37% versus 4%, p < 0.001), and shorter duration of mechanical ventilation (median 24 versus 96 h, p < 0.001). PDA stents were associated with significantly more unplanned reinterventions for hypoxemia compared to surgical shunts (42% vs. 20%, p = 0.009). In this multicenter study, neonates with PA-IVS who underwent PDA stenting received less vasoactive and ventilatory support postoperatively compared to those who had surgical shunts. Furthermore, patients with the most severe morphology had decreased odds of MACE., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The fields of Metagenomics and Metatranscriptomics involve the examination of complete nucleotide sequences, gene identification, and analysis of potential biological functions within diverse organisms or environmental samples. Despite the vast opportunities for discovery in metagenomics, the sheer volume and complexity of sequence data often present challenges in processing analysis and visualization. This article highlights the critical role of advanced visualization tools in enabling effective exploration, querying, and analysis of these complex datasets. Emphasizing the importance of accessibility, the article categorizes various visualizers based on their intended applications and highlights their utility in empowering bioinformaticians and non-bioinformaticians to interpret and derive insights from meta-omics data effectively., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Contemporary multicenter data regarding midterm outcomes for neonates with pulmonary atresia with intact ventricular septum are lacking. We sought to describe outcomes in a contemporary multicenter cohort, determine factors associated with end-states, and evaluate the effect of right ventricular coronary dependency and coronary atresia on transplant-free survival. Neonates treated during 2009-2019 in 19 United States centers were reviewed. Competing risks analysis was performed to determine cumulative risk of each end-state, and multivariable regression analyses were performed to identify factors associated with each end-state and transplant-free survival. We reviewed 295 patients. Median tricuspid valve Z-score was - 3.06 (25%, 75%: - 4.00, - 1.52). Final end-state was biventricular repair for 45 patients (15.2%), one-and-a half ventricle for 16 (5.4%), Fontan for 75 (25.4%), cardiac transplantation for 29 (9.8%), and death for 54 (18.3%). Seventy-six patients (25.7%) remained in mixed circulation. Cumulative risk estimate of death was 10.9%, 16.1%, 16.9%, and 18.8% at 1, 6 months, 1 year, and 5 years, respectively. Tricuspid valve Z-score was inversely, and coronary atresia positively associated with death or transplantation [odds ratio (OR) = 0.46, (95% confidence interval (CI) = 0.29-0.75, p < 0.001) and OR = 3.75 (95% CI 1.46-9.61, p = 0.011), respectively]. Right ventricular coronary dependency and left coronary atresia had a significant effect on transplant-free survival (log-rank p < 0.001). In a contemporary multicenter cohort of patients with PAIVS, consisting predominantly of patients with moderate-to-severe right ventricular hypoplasia, we observed favorable survival outcomes. Right ventricular coronary dependency and left, but not right, coronary atresia significantly worsens transplant-free survival., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Aim: To evaluate the alterations of the retinal microvasculature and foveal avascular zone in patients with Parkinson's disease (PD) using optical coherence tomography angiography (OCT-A)., Methods: A retrospective study of PD patients examined in the Ophthalmology Department of the General Hospital of Athens, "Georgios Gennimatas" from March 2021 to March 2022 was conducted. Totally 44 patients with PD were included and 18 healthy controls were examined, hence a total of 124 eyes were enrolled in the study. The foveal and parafoveal superficial and deep capillary plexus vascular density (fSCP-VD, fDCP-VD, pSCP-VD, pDCP-CD) and foveal avascular zone (FAZ) were quantified with OCTA. Optical coherence tomography (OCT) was used to measure macular thickness. Our statistical analysis was conducted by using a mixed effect linear regression model., Results: After adjustment for age and gender, the mean parafoveal superficial capillary plexus vascular density (pSCP-VD) and mean parafoveal deep capillary plexus vascular density (pDCP-VD) were significantly decreased in individuals with PD ( P <0.001 in both) by -2.35 (95%CI -3.3, -1.45) and -7.5 (95%CI -10.4, -4.6) respectively. fSCP-VD and fDCP-VD didn't approach statistical significance. The FAZ area and perimeter were significantly decreased ( P <0.001 in both) by -0.1 mm 2 (95%CI -0.13, -0.07) and -0.49 mm 2 (95%CI -0.66, -0.32) respectively. Circularity didn't approach statistical significance. Central retinal thickness (CRT) was significantly decreased in individuals with PD ( P <0.001) by -23.1 µm (95%CI -30.2, -16) and temporal retinal thickness (TRT) was decreased ( P =0.025) by -11 µm (95%CI -22, -1.5) while nasal retinal thickness (NRT) only approached statistical significance ( P =0.066)., Conclusion: The mean pSCP-VD, pDCP-VD, CRT and TRT are significantly decreased and FAZ is altered in individuals with PD. These findings can be potentially used as biomarkers for the diagnosis and evaluation of early PD., (International Journal of Ophthalmology Press.)

Introduction: Even though shoulder dislocation is thought to be the most common dislocation treated in the Emergency Department, inferior ones, known as Luxatio Erecta, comprise only 0.5% of them. Taking into consideration the rareness of unilateral Luxatio Erecta, bilateral cases should be even fewer. The purpose of this paper is to identify the reported number of cases of Traumatic Bilateral Luxatio Erecta in the literature over the last 100 years and to summarize the mechanism of injury, the initial management, and the complications of these patients., Materials and Methods: We performed a systematic review of the literature regarding Traumatic Bilateral Luxatio Erecta. All articles published until 31st of December 2022 in PubMed and Google Scholar databases were searched using the terms "luxatio erecta", 'inferior dislocation", and "bilateral"., Results: Eighty-two articles were retrieved from PubMed and Google Scholar search. Forty-four of them were initially included in our review. Six additional articles meeting the inclusion criteria were found from cross-references., Conclusion: The presence of this injury is extremely rare with only 51 cases in the literature. The incidence of concomitant injuries and complications seems to be extremely high and neurological deficits were detected on 42.8% of patients with Bilateral Luxatio Erecta. To our knowledge, this is the first systematic review of the literature regarding Traumatic Bilateral Luxatio Erecta that includes articles not only in English, a fact that provides more reliability on the estimation of the real number of cases of this rare injury compared to any other review on this subject to date., (© 2023. The Author(s).)

Several selective macroautophagy receptor and adaptor proteins bind members of the Atg8 (autophagy related 8) family using short linear motifs (SLiMs), most often referred to as Atg8-family interacting motifs (AIMs) or LC3-interacting regions (LIRs). AIM/LIR motifs have been extensively studied during the last fifteen years, since they can uncover the underlying biological mechanisms and possible substrates for this key catabolic process of eukaryotic cells. Prompted by the fact that experimental information regarding LIR motifs can be found scattered across heterogeneous literature resources, we have developed LIRcentral (https://lircentral.eu), a freely available online repository for user-friendly access to comprehensive, high-quality information regarding LIR motifs from manually curated publications. Herein, we describe the development of LIRcentral and showcase currently available data and features, along with our plans for the expansion of this resource. Information incorporated in LIRcentral is useful for accomplishing a variety of research tasks, including: (i) guiding wet biology researchers for the characterization of novel instances of LIR motifs, (ii) giving bioinformaticians/computational biologists access to high-quality LIR motifs for building novel prediction methods for LIR motifs and LIR containing proteins (LIRCPs) and (iii) performing analyses to better understand the biological importance/features of functional LIR motifs. We welcome feedback on the LIRcentral content and functionality by all interested researchers and anticipate this work to spearhead a community effort for sustaining this resource which will further promote progress in studying LIR motifs/LIRCPs. Abbreviations : AIM, Atg8-family interacting motif; Atg8, autophagy related 8; GABARAP, GABA type A receptor-associated protein; LIR, LC3-interacting region; LIRCP, LIR-containing protein; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; PMID, PubMed identifier; PPI, protein-protein interaction; SLiM, short linear motif.

Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Vasileiou et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)