Autoimmune diseases and male infertility: a systematic review

Κατά την διάρκεια των τελευταίων χρόνων νέες στοχευμένες θεραπείες έχουν αναπτυχθεί για την αντιμετώπιση των αυτοάνοσων νοσημάτων. Παρά ταύτα η γονιμότητα των ανδρών με αυτοάνοσα νοσήματα φαίνεται να επηρεάζεται είτε από την ίδια την νόσο είτε από την εκάστοτε αγωγή που χρησιμοποιείται. Η συγκεκριμένη εργασία συνοψίζοντας τριάντα εννέα άρθρα της παγκόσμιας βιβλιογραφίας τα οποία σχετίζονται την ανδρική υπογονιμότητα με δέκα αυτοάνοσα νοσήματα ( συστηματικός ερυθηματώδης λύκος, δερματομυοσίτιδα, κοιλιοκάκη, ουρική αρθρίτιδα, ρευματοειδής αρθρίτιδα, σαρκοείδωση, φλεγμονώδεις νόσοι του εντέρου, αγκυλοποιητική σπονδυλίτιδα,νόσος Behcet και ψωρίαση) επιχειρεί να αποκαλύψει την συνδεσή τους με την ανδρική υπογονιμότητα.During the last years new targeted regimen for several autoimmune diseases has been developed leading to an ameliorated quality of life for these patients. Nevertheless, their fertility potential seems to be impaired either by the activity of the autoimmune diseases or by the medical treatment used to suppress these conditions. A search of English-language articles from electronic databases was conducted for this paper. The results that were used referred to impaired fertility in male patients with systemic lupus erythematosus, Behcet’s disease, gout, dermatomyositis, celiac disease, rheumatoid arthritis, ankylosing spondylitis, inflammatory bowel disease, psoriasis and sarcoidosis. This systematic review intends to reveal how autoimmune diseases and their regimen affect male fertility

Vaginal cuff dehiscence after laparoscopic trachelectomy post hysterectomy: a case report and brief review of the literature

Vaginal cuff dehiscence (VCD) is a serious complication of total laparoscopic hysterectomy (TLH) or trachelectomy with high morbidity, as it can potentially lead to evisceration/bowel ischemia and sepsis. Authors present a case report of vaginal cuff dehiscence after laparoscopic trachelectomy. The patient reported post-coital onset of symptoms. She presented with acute abdomen and required urgent surgical intervention. In this case surgical management was dictated by the clinical manifestation. However, authors argue that conservative management is also an option for some of these patients and the decision regarding the management plan should be personalized according to the clinical presentation and the patient’s expectations. Emphasis should be given to avoid early onset of sexual activity during the immediate recovery period. Compared to women who underwent an abdominal or vaginal hysterectomy, those who had a laparoscopic procedure have less post-operative pain, shorter recovery period and often they are advised to return early to their normal habits and their work place.  It is expected that this group of patients feel well enough to resume sexual activity soon after their procedure. Therefore, our counselling is of paramount importance as it should be highlighted that sexual intercourse is possibly the most common triggering event for VCD which a serious complication with severe morbidity is. The resumption should, therefore, follow medical consultation and be individualized according to co-morbidities which could affect healing, intraoperative findings and evaluation of the whole recovery progress

Establishment of computational biology in Greece and Cyprus: Past, present, and future.

We review the establishment of computational biology in Greece and Cyprus from its inception to date and issue recommendations for future development. We compare output to other countries of similar geography, economy, and size—based on publication counts recorded in the literature—and predict future growth based on those counts as well as national priority areas. Our analysis may be pertinent to wider national or regional communities with challenges and opportunities emerging from the rapid expansion of the field and related industries. Our recommendations suggest a 2-fold growth margin for the 2 countries, as a realistic expectation for further expansion of the field and the development of a credible roadmap of national priorities, both in terms of research and infrastructure funding

Modernity and Contemporaneity

Modernity and Contemporaneity is the 3rd volume in the Hellenic-Serbian Philosophical Dialogue Series, a project that was initiated as an emphatic token of the will and commitment to establish permanent and fruitful collaboration between two strongly bonded Departments of Philosophy, this of the National and Kapodistrian University of Athens, and that of the University of Novi Sad respectively. This collaboration was founded from the very beginning upon friendship, mutual respect and strong engagement, as well us upon our firm resolution to establish a solid continuity in the editing project. The publication of this volume allows us to entertain feelings of contentment and confidence that this objective of the project has been accomplished.Publishe

BioTextQuest v2.0: An evolved tool for biomedical literature mining and concept discovery.

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

Unraveling the functional dark matter through global metagenomics

30 pages, 4 figures, 1 table, supplementary information https://doi.org/10.1038/s41586-023-06583-7.-- Data availability: All of the analysed datasets along with their corresponding sequences are available from the IMG system (http://img.jgi.doe.gov/). A list of the datasets used in this study is provided in Supplementary Data 8. All data from the protein clusters, including sequences, multiple alignments, HMM profiles, 3D structure models, and taxonomic and ecosystem annotation, are available through NMPFamsDB, publicly accessible at www.nmpfamsdb.org. The 3D models are also available at ModelArchive under accession code ma-nmpfamsdb.-- Code availability: Sequence analysis was performed using Tantan (https://gitlab.com/mcfrith/tantan), BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi), LAST (https://gitlab.com/mcfrith/last), HMMER (http://hmmer.org/) and HH-suite3 (https://github.com/soedinglab/hh-suite). Clustering was performed using HipMCL (https://bitbucket.org/azadcse/hipmcl/src/master/). Additional taxonomic annotation was performed using Whokaryote (https://github.com/LottePronk/whokaryote), EukRep (https://github.com/patrickwest/EukRep), DeepVirFinder (https://github.com/jessieren/DeepVirFinder) and MMseqs2 (https://github.com/soedinglab/MMseqs2). 3D modelling was performed using AlphaFold2 (https://github.com/deepmind/alphafold) and TrRosetta2 (https://github.com/RosettaCommons/trRosetta2). Structural alignments were performed using TMalign (https://zhanggroup.org/TM-align/) and MMalign (https://zhanggroup.org/MM-align/). All custom scripts used for the generation and analysis of the data are available at Zenodo (https://doi.org/10.5281/zenodo.8097349)Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matterWith the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

A new species of a snapping turtle (Pan-Chelydridae/Chelydropsis) from the Upper Miocene (MN9, early Vallesian) of Southwest Germany

Chelydropsis is a genus of the clade Pan-Chelydridae, which existed and was distributed in Eurasia from the Eocene to the end of the Pliocene. The Chelydropsis fossil record of North of the Alps is particularly rich throughout the Miocene. In this study, we describe a new Chelydropsis species from the Late Miocene (Vallesian, MN9) fossiliferous site of Höwenegg in southwestern Germany. The new species is based on a nearly complete Chelydropsis skeleton, which stands out among the best preserved and most complete specimens ever found until now. The new species, Chelydropsis heweneggensis sp. nov. is of particular importance. It differs from the coeval Chelydropsis murchisoni, which recent studies suggest is the only Chelydropsis species known to have existed in Europe from the Middle Miocene to the Pliocene. The species described herein thus adds to the diversity of the European Neogene Chelydropsis record.Fil: Pappa, Irena. University Of Patras (university Of Patras);Fil: Vlachos, Evangelos. Museo Paleontológico Egidio Feruglio; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Frey, Eberhard. Albert Ludwigs University of Freiburg; AlemaniaFil: Iliopoulos, George. University Of Patras (university Of Patras)

Efficient Algorithms for Handling Molecular Weighted Sequences

Abstract In this paper we introduce the Weighted Suffix Tree, an efficient data structure for computing string regularities in weighted sequences of molecular data. Molecular Weighted Sequences can model important biological processes such as the DNA Assembly Process or the DNA-Protein Binding Process. Thus pattern matching or identification of repeated patterns, in biological weighted sequences is a very important procedure in the translation of gene expression and regulation. We present time and space efficient algorithms for constructing the weighted suffix tree and some applications of the proposed data structure to problems taken from the Molecular Biology area such as pattern matching, repeats discovery, discovery of the longest common subsequence of two weighted sequences and computation of covers

OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis.

Extracting and processing information from documents is of great importance as lots of experimental results and findings are stored in local files. Therefore, extracting and analyzing biomedical terms from such files in an automated way is absolutely necessary. In this article, we present OnTheFly2.0, a web application for extracting biomedical entities from individual files such as plain texts, office documents, PDF files or images. OnTheFly2.0 can generate informative summaries in popup windows containing knowledge related to the identified terms along with links to various databases. It uses the EXTRACT tagging service to perform named entity recognition (NER) for genes/proteins, chemical compounds, organisms, tissues, environments, diseases, phenotypes and gene ontology terms. Multiple files can be analyzed, whereas identified terms such as proteins or genes can be explored through functional enrichment analysis or be associated with diseases and PubMed entries. Finally, protein-protein and protein-chemical networks can be generated with the use of STRING and STITCH services. To demonstrate its capacity for knowledge discovery, we interrogated published meta-analyses of clinical biomarkers of severe COVID-19 and uncovered inflammatory and senescence pathways that impact disease pathogenesis. OnTheFly2.0 currently supports 197 species and is available at http://bib.fleming.gr:3838/OnTheFly/ and http://onthefly.pavlopouloslab.info

IOS Press The Weighted Suffix Tree: An Efficient Data Structure for Handling Molecular Weighted Sequences and its Applications

Abstract. In this paper we introduce the Weighted Suffix Tree, an efficient data structure for computing string regularities in weighted sequences of molecular data. Molecular Weighted Sequences can model important biological processes such as the DNA Assembly Process or the DNA-Protein Binding Process. Thus pattern matching or identification of repeated patterns, in biological weighted sequences is a very important procedure in the translation of gene expression and regulation. We present time and space efficient algorithms for constructing the weighted suffix tree and some applications of the proposed data structure to problems taken from the Molecular Biology area such as pattern matching, repeats discovery, discovery of the longest common subsequence of two weighted sequences and computation of covers