This article describes the motivation, origin and evolution of the student symposia series organised by the ISCB Student Council. The meeting series started thirteen years ago in Madrid and has ...spread to four continents. The article concludes with the highlights of the most recent edition of annual Student Council Symposium held in conjunction with the 25th Conference on Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology, in Prague, in July 2017.
The Student Council of the International Society for Computational Biology (ISCB-SC) is a student-focused organization for researchers from all early career levels of training (undergraduates, ...masters, PhDs and postdocs) that organizes bioinformatics and computational biology activities across the globe. Among its activities, the ISCB-SC organizes several symposia in different continents, many times, with the help of the Regional Student Groups (RSGs) that are based on each region. In this editorial we highlight various key moments and learned lessons from the 14th Student Council Symposium (SCS, Chicago, USA), the 5th European Student Council Symposium (ESCS, Athens, Greece) and the 3rd Latin American Student Council Symposium (LA-SCS, Viña del Mar, Chile).
Abstract Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimer's disease. The Alzheimer's disease DREAM Challenge was ...designed as a computational crowdsourced project to benchmark the current state-of-the-art in predicting cognitive outcomes in Alzheimer's disease based on high dimensional, publicly available genetic and structural imaging data. This meta-analysis failed to identify a meaningful predictor developed from either data modality, suggesting that alternate approaches should be considered for prediction of cognitive performance.
Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues ...to grow. Over the past decade, high-throughput technologies such as the Affymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article's supplementary tables. Several value-added databases have employed additional manual efforts to overcome this limitation. However, none of these databases explicate annotations that distinguish human and animal models in neurodegeneration context. Therefore, adopting a more specific disease focus, in combination with dedicated disease ontologies, will better empower the selection of comparable studies with refined annotations to address the research question at hand. In this article, we describe the detailed development of NeuroTransDB, a manually curated database containing metadata annotations for neurodegenerative studies. The database contains more than 20 dimensions of metadata annotations within 31 mouse, 5 rat and 45 human studies, defined in collaboration with domain disease experts. We elucidate the step-by-step guidelines used to critically prioritize studies from public archives and their metadata curation and discuss the key challenges encountered. Curated metadata for Alzheimer's disease gene expression studies are available for download. Database URL: www.scai.fraunhofer.de/NeuroTransDB.html.
Hyperoxia-induced acute lung injury (HALI) is a key contributor to the pathogenesis of bronchopulmonary dysplasia (BPD) in neonates, for which no specific preventive or therapeutic agent is ...available. Here we show that lung micro-RNA (miR)-34a levels are significantly increased in lungs of neonatal mice exposed to hyperoxia. Deletion or inhibition of miR-34a improves the pulmonary phenotype and BPD-associated pulmonary arterial hypertension (PAH) in BPD mouse models, which, conversely, is worsened by miR-34a overexpression. Administration of angiopoietin-1, which is one of the downstream targets of miR34a, is able to ameliorate the BPD pulmonary and PAH phenotypes. Using three independent cohorts of human samples, we show that miR-34a expression is increased in type 2 alveolar epithelial cells in neonates with respiratory distress syndrome and BPD. Our data suggest that pharmacologic miR-34a inhibition may be a therapeutic option to prevent or ameliorate HALI/BPD in neonates.
Introduction: The isthmus is a communication between two or more root canals that contains pulp tissue. Its unpredictable location, variable prevalence, and anatomic complexity often result in ...challenging debridement. The knowledge of these factors may prove beneficial for successful endodontic treatment. The primary aim of this systematic review was to assess the prevalence and morphology of root canal isthmus (RCI) in human permanent teeth using micro-computed tomography (micro-CT) studies. The secondary aim was to assess the influence of demographic factors such as age, gender, and geographic region on the prevalence and morphology of the isthmus. Materials and Methods: An electronic search was conducted until January 2020. Studies published in the English language using micro-CT for the evaluation of isthmus prevalence and morphology were included. Sixteen articles met the inclusion criteria and were subjected to qualitative synthesis. Results: The prevalence of isthmus in the mesiobuccal root of maxillary first molars ranged from 8.9% to 70.8%, with maximum prevalence in the middle third of the root (49.50%–73%). The mesial root of mandibular molars had a prevalence ranging from 80.6% to 100% on full root analysis and 85%–88.89% in the apical third. Conclusion: The prevalence of RCI was higher in the mesiobuccal roots of maxillary molars and the mesial roots of mandibular molars, extending in the corono-apical direction with a complex and variable morphology. The influence of demographic factors on the prevalence of RCI could not be established clearly.
Aim The aim of this systematic review and network meta-analysis was to identify the best irrigant activation technique (IAT) for the removal of accumulated hard tissue debris (AHTD) from the mesial ...root of mandibular molars evaluated using micro-CT studies.Methods The research question was based on the PICO format. Four electronic databases - PubMed, Scopus, Embase and Web of Science - were searched for articles up to June 2020. Selected articles were assessed for bias using the Joanna Briggs Institute Critical appraisal tool. The network meta-analysis using a fixed-effects model and SUCRA ranking were performed. The quality of the evidence was assessed using the CINeMA framework.Results Eleven studies were included for qualitative synthesis while seven were included for quantitative synthesis. The risk of bias of all included articles was low. The results based on SUCRA values revealed the IAT shock wave-enhanced emission photoacoustic streaming (100%) resulted in the greatest reduction of the volume of AHTD from mesial roots of mandibular molars. Ranking of the other IATs was as follows: photon-induced photoacoustic streaming (87%), laser-activated irrigation (79.3%), XP EndoFinisher (71.2%), ultrasonically activated irrigation (59.6%), apical negative pressure (42.3%), EasyClean (37.4%), EDDY (26.2%), EndoActivator (24.2%), self-adjusting file (11.6%) and needle irrigation (11.3%).Conclusion None of the IATs rendered the root canals completely free of AHTD. The laser-activated irrigation groups fared better than all other interventions in reducing AHTD from the mesial roots of mandibular molars. The confidence rating ranged from low to high for indirect evidence and moderate to high for mixed evidence. Results must be interpreted with caution due to the laboratory nature of the included studies.
Dental implant is a device made of alloplastic (foreign) material implanted into the jaw bone beneath the mucosal layer to support a fixed or removable dental prosthesis. Dental implants are gaining ...immense popularity and wide acceptance because they not only replace lost teeth but also provide permanent restorations that do not interfere with oral function or speech or compromise the self-esteem of a patient. Appropriate treatment planning for replacement of lost teeth is required and imaging plays a pivotal role to ensure a satisfactory outcome. The development of pre-surgical imaging techniques and surgical templates helps the dentist place the implants with relative ease. This article focuses on various types of imaging modalities that have a pivotal role in implant therapy.
Dental implant is a device made of alloplastic (foreign) material implanted into the jaw bone beneath the mucosal layer to support a fixed or removable dental prosthesis. Dental implants are gaining ...immense popularity and wide acceptance because they not only replace lost teeth but also provide permanent restorations that do not interfere with oral function or speech or compromise the self-esteem of a patient. Appropriate treatment planning for replacement of lost teeth is required and imaging plays a pivotal role to ensure a satisfactory outcome. The development of pre-surgical imaging techniques and surgical templates helps the dentist place the implants with relative ease. This article focuses on various types of imaging modalities that have a pivotal role in implant therapy.
PDF
