Complex Portal 2022: new curation frontiers.
Ontology highlight
ABSTRACT:
SUBMITTER: Meldal BHM
PROVIDER: S-EPMC8689886 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:A powerful early approach to evaluating the druggability of proteins involved determining the hit rate in NMR-based screening of a library of small compounds. Here, we show that a computational analog of this method, based on mapping proteins using small molecules as probes, can reliably reproduce druggability results from NMR-based screening and can provide a more meaningful assessment in cases where the two approaches disagree. We apply the method to a large set of proteins. The results show that, because the method is based on the biophysics of binding rather than on empirical parametrization, meaningful information can be gained about classes of proteins and classes of compounds beyond those resembling validated targets and conventionally druglike ligands. In particular, the method identifies targets that, while not druggable by druglike compounds, may become druggable using compound classes such as macrocycles or other large molecules beyond the rule-of-five limit.
| S-EPMC4762776 | biostudies-literature
Project description:The term 'biologging' refers to the use of miniaturized animal-attached tags for logging and/or relaying of data about an animal's movements, behaviour, physiology and/or environment. Biologging technology substantially extends our abilities to observe, and take measurements from, free-ranging, undisturbed subjects, providing much scope for advancing both basic and applied biological research. Here, we review highlights from the third international conference on biologging science, which was held in California, USA, from 1 to 5 September 2008. Over the last few years, considerable progress has been made with a range of recording technologies as well as with the management, visualization, integration and analysis of increasingly large and complex biologging datasets. Researchers use these techniques to study animal biology with an unprecedented level of detail and across the full range of ecological scales-from the split-second decision making of individuals to the long-term dynamics of populations, and even entire communities. We conclude our report by suggesting some directions for future research.
| S-EPMC2679933 | biostudies-literature
Project description:Esophageal cancer is the sixth most common cause of cancer related mortality worldwide. Advances in treatment have translated into steadily improving survival rates. Accurate preoperative staging of esophageal cancer is imperative in order to provide an accurate prognosis and direct patients to the most appropriate treatment. Current preoperative staging relies on imaging, most commonly endoscopic ultrasound (EUS), computed tomography (CT) and positron emission tomography (PET). A combination of these modalities should be used in preoperative staging, as each has advantages over another. Magnetic resonance imaging (MRI) has always shown promise in its ability to accurately stage esophageal cancer, though it has not been consistently adopted as a common tool for this purpose. Recent research has demonstrated that MRI can become an integral part of esophageal cancer clinical staging. Advances in MR technology that utilize radial sampling allow for shorter, free breathing techniques without degradation of image quality, resulting in improved capability for T and N staging of esophageal cancer. MRI enhanced with superparamagnetic iron oxide (SPIO) and ultrasmall SPIO (USPIO) nanoparticles has been shown to be useful for the detection of metastatic disease in lymph nodes. This article will review the current evidence in the role that imaging plays in staging esophageal cancer.
| S-EPMC8184422 | biostudies-literature
Project description:The Frontiers Media family has over 200 journals, which are each headed by usually one Field Chief Editor, and several thousand specialty sections, which are each headed by one or more Specialty Chief Editors. The year 2021 was the 10th anniversary of the founding of the Frontiers in Genetics journal and the Frontiers in Toxicogenomics specialty section of this journal. In 2021, we also announce one of the newest of the Frontiers journals-Frontiers in Toxicology which is part of the Frontiers Media family of journals but independent of Frontiers in Genetics. Dr. Ruden is the founding, and currently sole, Specialty Chief Editor of Frontiers in Toxicogenomics and one of 9 Specialty Chief Editors of Frontiers in Toxicology. As of 2021, Frontiers in Toxicogenomics has published over 138 articles and has over 370 Editors including 90 Associate Editors and 280 Review Editors. The Frontiers in Genetics impact factor was initially approximately 2.5 when it was first listed in PubMed in 2015 and has risen steadily to its current value of 4.8, which is typical for the majority of the over 200 Frontiers journals that have established impact factors. In this overview of the first decade of Frontiers in Toxicogenomics, we discuss the top 5 articles with the highest Scopus citations, which were all written in the first few years of the journal. The article with the highest number of citations, with 353 Scopus over 600 Google Scholar citations, and the highest average number of citations (67) that steadily increased from 10 citations in 2013 to 119 citations in 2021, was written in 2012 by Dr. Ruden's laboratory and titled, "Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift." The five most influential authors who published in the journal in the past 10 years based on Scopus citations of a particular paper are Dr. Ruden's laboratory, with 353 Scopus citations for the SnpSift paper mentioned above; Drs. Brock Christensen and Carmen J. Marsit, with 86 Scopus citations for their review, "Epigenomics in environmental health"; Dr. Michael Aschner and colleagues, with 61 Scopus citations for their paper "Genetic factors and manganese-induced neurotoxicity"; and Dr. Sandra C. dos Santos and colleagues, with 59 Scopus citations for their paper, "Yeast toxicogenomics: genome-wide responses to chemical stresses with impact in environmental health, pharmacology, and biotechnology." While the top 5 papers were published in the early years of the journal, we will also discuss a more recent article published in 2018 on a comparison of RNA-seq and microarray methods by Dr. Michael Liguori's laboratory, "Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies," that far exceeds the number of downloads and views of all the other articles published in the first 10 years of the journal and will likely be a top cited paper in the second decade highlights of this journal. Finally, we discuss where the Frontiers in Toxicogenomics specialty journal and the Frontiers in Toxicology journal will go to advance the field of toxicogenomics, and more generally, toxicology, in the future.
| S-EPMC9510767 | biostudies-literature
Project description:BackgroundThe Immune Epitope Database and Analysis Resource (IEDB) is dedicated to capturing, housing and analyzing complex immune epitope related data http://www.immuneepitope.org.DescriptionTo identify and extract relevant data from the scientific literature in an efficient and accurate manner, novel processes were developed for manual and semi-automated annotation.ConclusionFormalized curation strategies enable the processing of a large volume of context-dependent data, which are now available to the scientific community in an accessible and transparent format. The experiences described herein are applicable to other databases housing complex biological data and requiring a high level of curation expertise.
| S-EPMC1534061 | biostudies-literature
Project description:Schistosomes are digenean blood flukes of aves and mammals comprising 23 species. Some species are causative agents of human schistosomiasis, the second major neglected disease affecting over 230 million people worldwide. Modern technologies including the sequencing and characterization of nucleic acids and proteins have allowed large-scale analyses of parasites and hosts, opening new frontiers in biological research with potential biomedical and biotechnological applications. Nuclear genomes of the three most socioeconomically important species (S. haematobium, S. japonicum, and S. mansoni) have been sequenced and are under intense investigation. Mitochondrial genomes of six Schistosoma species have also been completely sequenced and analysed from an evolutionary perspective. Furthermore, DNA barcoding of mitochondrial sequences is used for biodiversity assessment of schistosomes. Despite the efforts in the characterization of Schistosoma genomes and transcriptomes, many questions regarding the biology and evolution of this important taxon remain unanswered. This paper aims to discuss some advances in the schistosome research with emphasis on genomics and transcriptomics. It also aims to discuss the main challenges of the current research and to point out some future directions in schistosome studies.
| S-EPMC3512318 | biostudies-literature
Project description:Articular cartilage injury is common after athletic injury and remains a difficult treatment conundrum both for the surgeon and athlete. Although recent treatments for damage to articular cartilage have been successful in alleviating symptoms, more durable and complete, long-term articular surface restoration remains the unattained goal. In this article, we look at both new ways to prevent damage to articular surfaces as well as new techniques to recreate biomechanically sound and biochemically true articular surfaces once an athlete injures this surface. This goal should include reproducing hyaline cartilage with a well-integrated and flexible subchondral base and the normal zonal variability in the articular matrix.A number of nonoperative interventions have shown early promise in mitigating cartilage symptoms and in preclinical studies have shown evidence of chondroprotection. These include the use of glucosamine, chondroitin, and other neutraceuticals, viscosupplementation with hyaluronic acid, platelet-rich plasma, and pulsed electromagnetic fields. Newer surgical techniques, some already in clinical study, and others on the horizon offer opportunities to improve the surgical restoration of the hyaline matrix often disrupted in athletic injury. These include new scaffolds, single-stage cell techniques, the use of mesenchymal stem cells, and gene therapy.Although many of these treatments are in the preclinical and early clinical study phase, they offer the promise of better options to mitigate the sequelae of athletically induced cartilage.
| S-EPMC4297164 | biostudies-other
Project description: Not available
| S-EPMC10768199 | biostudies-literature
Project description:Proton therapy offers dominant advantages over photon therapy due to the unique depth-dose characteristics of proton, which can cause a dramatic reduction in normal tissue doses both distal and proximal to the tumor target volume. In turn, this feature may allow dose escalation to the tumor target volume while sparing the tumor-neighboring susceptible organs at risk, which has the potential to reduce treatment toxicity and improve local control rate, quality of life and survival. Some dosimetric studies in various cancers have demonstrated the advantages over photon therapy in dose distributions. Further, it has been observed that proton therapy confers to substantial clinical advantage over photon therapy in head and neck, breast, hepatocellular, and non-small cell lung cancers. As such, proton therapy is regarded as the standard modality of radiotherapy in many pediatric cancers from the technical point of view. However, due to the limited clinical evidence, there have been concerns about the high cost of proton therapy from an economic point of view. Considering the treatment expenses for late radiation-induced toxicities, cost-effective analysis in many studies have shown that proton therapy is the most cost-effective option for brain, head and neck and selected breast cancers. Additional studies are warranted to better unveil the cost-effective values of proton therapy and to develop newer ways for better protection of normal tissues. This review aims at reviewing the recent studies on proton therapy to explore its benefits and cost-effectiveness in cancers. We strongly believe that proton therapy will be a common radiotherapy modality for most types of solid cancers in the future.
| S-EPMC6805548 | biostudies-literature
Project description:Sarcomas are a rare malignancy of mesenchymal tissues, comprizing a plethora of unique subtypes, with more than 60 types. The sheer heterogeneity of disease phenotype makes this a particularly difficult cancer to treat. Radiotherapy, chemotherapy and surgery have been employed for over three decades and, although effective in early disease (stages I-II), in later stages, where metastatic tumors are present, these treatments are less effective. Given the spectacular results obtained by cancer immunotherapy in a variety of solid cancers and leukemias, there is now a great interest in appliying this new realm of therapy for sarcomas. The widespread use of immunotherapy for sarcoma relies on immuno-profiling of subtypes, immunomonitoring for prognosis, preclinical studies and insight into the safety profile of these novel therapies. Herein, we discuss preclinical and clinical data highlighting how immunotherapy is being used in soft tissue sarcoma and bone sarcomas.
| S-EPMC7852926 | biostudies-literature