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Computational and Structural Biotechnology Journal

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https://www.readbyqxmd.com/read/28066534/chagas-disease-research-and-development-is-there-light-at-the-end-of-the-tunnel
#1
REVIEW
Eric Chatelain
Chagas disease, or American trypanosomiasis, is the result of infection by the parasite Trypanosoma cruzi. It is endemic in Latin America, and spreading around the globe due to human migration. Although it was first identified more than a century ago, only two old drugs are available for treatment and a lot of questions related to the disease progression, its pathologies, and not to mention the assessment of treatment efficacy, are subject to debate and remain to be answered. Indeed, the current status of evidence and data available does not allow any absolute statement related to treatment needs and outcome for Chagas patients to be made...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28066533/molecular-mechanism-of-binding-between-17%C3%AE-estradiol-and-dna
#2
Tamsyn A Hilder, Justin M Hodgkiss
Although 17β-estradiol (E2) is a natural molecule involved in the endocrine system, its widespread use in various applications has resulted in its accumulation in the environment and its classification as an endocrine-disrupting molecule. These molecules can interfere with the hormonal system, and have been linked to various adverse effects such as the proliferation of breast cancer. It has been proposed that E2 could contribute to breast cancer by the induction of DNA damage. Mass spectrometry has demonstrated that E2 can bind to DNA but the mechanism by which E2 interacts with DNA has yet to be elucidated...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28066532/matched-molecular-pair-analysis-in-short-algorithms-applications-and-limitations
#3
REVIEW
Christian Tyrchan, Emma Evertsson
Molecular matched pair (MMP) analysis has been used for more than 40 years within molecular design and is still an important tool to analyse potency data and other compound properties. The methods used to find matched pairs range from manual inspection, through supervised methods to unsupervised methods, which are able to find previously unknown molecular pairs. Recent publications demonstrate the value of automatic MMP analysis of publicly available bioactivity databases. The MMP concept has its limitations, but because of its easy to use and intuitive nature, it will remain one of the most important tools in the toolbox of many drug designers...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28018557/a-hybrid-computer-aided-diagnosis-system-for-prediction-of-breast-cancer-recurrence-hpbcr-using-optimized-ensemble-learning
#4
Mohammad R Mohebian, Hamid R Marateb, Marjan Mansourian, Miguel Angel Mañanas, Fariborz Mokarian
Cancer is a collection of diseases that involves growing abnormal cells with the potential to invade or spread to the body. Breast cancer is the second leading cause of cancer death among women. A method for 5-year breast cancer recurrence prediction is presented in this manuscript. Clinicopathologic characteristics of 579 breast cancer patients (recurrence prevalence of 19.3%) were analyzed and discriminative features were selected using statistical feature selection methods. They were further refined by Particle Swarm Optimization (PSO) as the inputs of the classification system with ensemble learning (Bagged Decision Tree: BDT)...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27994799/worsening-of-verbal-fluency-after-deep-brain-stimulation-in-parkinson-s-disease-a-focused-review
#5
REVIEW
Andreas Højlund, Mikkel V Petersen, Kousik Sarathy Sridharan, Karen Østergaard
Worsening of verbal fluency after treatment with deep brain stimulation in Parkinson's disease patients is one of the most often reported cognitive adverse effect. The underlying mechanisms of this decline are not well understood. The present focused review assesses the evidence for the reliability of the often-reported decline of verbal fluency, as well as the evidence for the suggested mechanisms including disease progression, reduced medication levels, electrode positions, and stimulation effect vs. surgical effects...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27994798/mining-textural-knowledge-in-biological-images-applications-methods-and-trends
#6
REVIEW
Santa Di Cataldo, Elisa Ficarra
Texture analysis is a major task in many areas of computer vision and pattern recognition, including biological imaging. Indeed, visual textures can be exploited to distinguish specific tissues or cells in a biological sample, to highlight chemical reactions between molecules, as well as to detect subcellular patterns that can be evidence of certain pathologies. This makes automated texture analysis fundamental in many applications of biomedicine, such as the accurate detection and grading of multiple types of cancer, the differential diagnosis of autoimmune diseases, or the study of physiological processes...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27980708/bioinformatics-strategies-for-taxonomy-independent-binning-and-visualization-of-sequences-in-shotgun-metagenomics
#7
REVIEW
Karel Sedlar, Kristyna Kupkova, Ivo Provaznik
One of main steps in a study of microbial communities is resolving their composition, diversity and function. In the past, these issues were mostly addressed by the use of amplicon sequencing of a target gene because of reasonable price and easier computational postprocessing of the bioinformatic data. With the advancement of sequencing techniques, the main focus shifted to the whole metagenome shotgun sequencing, which allows much more detailed analysis of the metagenomic data, including reconstruction of novel microbial genomes and to gain knowledge about genetic potential and metabolic capacities of whole environments...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27942354/heart-failure-diagnosis-severity-estimation-and-prediction-of-adverse-events-through-machine-learning-techniques
#8
REVIEW
Evanthia E Tripoliti, Theofilos G Papadopoulos, Georgia S Karanasiou, Katerina K Naka, Dimitrios I Fotiadis
Heart failure is a serious condition with high prevalence (about 2% in the adult population in developed countries, and more than 8% in patients older than 75 years). About 3-5% of hospital admissions are linked with heart failure incidents. Heart failure is the first cause of admission by healthcare professionals in their clinical practice. The costs are very high, reaching up to 2% of the total health costs in the developed countries. Building an effective disease management strategy requires analysis of large amount of data, early detection of the disease, assessment of the severity and early prediction of adverse events...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27872688/functional-roles-for-exosomal-micrornas-in-the-tumour-microenvironment
#9
REVIEW
Emma Bell, Molly A Taylor
Extracellular microRNAs are released from cells both passively and actively. The presence of these microRNAs in the tumour microenvironment (TME) can significantly impact on the plasticity of cancer cells leading to the promotion of metastatic and angiogenic processes. These extracellular microRNAs can act not only on other cancer cells, but also cells present in the TME, such as immune cells, endothelial cells, fibroblasts, and others acting to subvert the host immune system and drive tumour progression. In this review we highlight the current understanding of both the mechanisms by which microRNAs are released from tumour cells and the downstream functional effects that extracellular microRNAs have on recipient cells...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27872687/determining-the-molecular-pathways-underlying-the-protective-effect-of-non-steroidal-anti-inflammatory-drugs-for-alzheimer-s-disease-a-bioinformatics-approach
#10
Alejo J Nevado-Holgado, Simon Lovestone
Alzheimer's disease (AD) represents a substantial unmet need, due to increasing prevalence in an ageing society and the absence of a disease modifying therapy. Epidemiological evidence shows a protective effect of non steroidal anti inflammatory (NSAID) drugs, and genome wide association studies (GWAS) show consistent linkage to inflammatory pathways; both observations suggesting anti-inflammatory compounds might be effective in AD therapy although clinical trials to date have not been positive. In this study, we use pathway enrichment and fuzzy logic to identify pathways (KEGG database) simultaneously affected in both AD and by NSAIDs (Sulindac, Piroxicam, Paracetamol, Naproxen, Nabumetone, Ketoprofen, Diclofenac and Aspirin)...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27924191/a-decade-of-biochemical-and-structural-studies-of-the-dna-repair-machinery-of-deinococcus-radiodurans-major-findings-functional-and-mechanistic-insight-and-challenges
#11
REVIEW
Joanna Timmins, Elin Moe
No abstract text is available yet for this article.
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27924190/network-analysis-of-human-post-mortem-microarrays-reveals-novel-genes-micrornas-and-mechanistic-scenarios-of-potential-importance-in-fighting-huntington-s-disease
#12
Sreedevi Chandrasekaran, Danail Bonchev
Huntington's disease is a progressive neurodegenerative disorder characterized by motor disturbances, cognitive decline, and neuropsychiatric symptoms. In this study, we utilized network-based analysis in an attempt to explore and understand the underlying molecular mechanism and to identify critical molecular players of this disease condition. Using human post-mortem microarrays from three brain regions (cerebellum, frontal cortex and caudate nucleus) we selected in a four-step procedure a seed set of highly modulated genes...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27904714/facilitating-the-commercialization-and-use-of-organ-platforms-generated-by-the-microphysiological-systems-tissue-chip-program-through-public-private-partnerships
#13
REVIEW
Christine A Livingston, Kristin M Fabre, Danilo A Tagle
Microphysiological systems (organs-on-chips, tissue chips) are devices designed to recapitulate human physiology that could be used to better understand drug responses not easily addressed using other in vivo systems or in vitro animal models. Although still in development, initial results seem promising as tissue chips exhibit in vivo systems-like functional responses. The National Center for Advancing Translation Science (NCATS) identifies this technology as a potential tool that could improve the process of getting safer, more effective treatments to patients, and has led to the Tissue Chip Program, which aims to develop, integrate and validate major organ systems for testing...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27872686/engineering-translation-in-mammalian-cell-factories-to-increase-protein-yield-the-unexpected-use-of-long-non-coding-sineup-rnas
#14
REVIEW
Silvia Zucchelli, Laura Patrucco, Francesca Persichetti, Stefano Gustincich, Diego Cotella
Mammalian cells are an indispensable tool for the production of recombinant proteins in contexts where function depends on post-translational modifications. Among them, Chinese Hamster Ovary (CHO) cells are the primary factories for the production of therapeutic proteins, including monoclonal antibodies (MAbs). To improve expression and stability, several methodologies have been adopted, including methods based on media formulation, selective pressure and cell- or vector engineering. This review presents current approaches aimed at improving mammalian cell factories that are based on the enhancement of translation...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27830053/unbiased-mitoproteome-analyses-confirm-non-canonical-rna-expanded-codon-translations
#15
Hervé Seligmann
Proteomic MS/MS mass spectrometry detections are usually biased towards peptides cleaved by experimentally added digestion enzyme(s). Hence peptides resulting from spontaneous degradation and natural proteolysis usually remain undetected. Previous analyses of tryptic human proteome data (cleavage after K, R) detected non-canonical tryptic peptides translated according to tetra- and pentacodons (codons expanded by silent mono- and dinucleotides), and from transcripts systematically (a) deleting mono-, dinucleotides after trinucleotides (delRNAs), (b) exchanging nucleotides according to 23 bijective transformations...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27800126/cryo-electron-microscopy-analysis-of-structurally-heterogeneous-macromolecular-complexes
#16
REVIEW
Slavica Jonić
Cryo-electron microscopy (cryo-EM) has for a long time been a technique of choice for determining structure of large and flexible macromolecular complexes that were difficult to study by other experimental techniques such as X-ray crystallography or nuclear magnetic resonance. However, a fast development of instruments and software for cryo-EM in the last decade has allowed that a large range of complexes can be studied by cryo-EM, and that their structures can be obtained at near-atomic resolution, including the structures of small complexes (e...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27800125/a-review-on-automatic-analysis-techniques-for-color-fundus-photographs
#17
REVIEW
Renátó Besenczi, János Tóth, András Hajdu
In this paper, we give a review on automatic image processing tools to recognize diseases causing specific distortions in the human retina. After a brief summary of the biology of the retina, we give an overview of the types of lesions that may appear as biomarkers of both eye and non-eye diseases. We present several state-of-the-art procedures to extract the anatomic components and lesions in color fundus photographs and decision support methods to help clinical diagnosis. We list publicly available databases and appropriate measurement techniques to compare quantitatively the performance of these approaches...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27761201/the-promises-of-quantitative-systems-pharmacology-modelling-for-drug%C3%A2-development
#18
REVIEW
V R Knight-Schrijver, V Chelliah, L Cucurull-Sanchez, N Le Novère
Recent growth in annual new therapeutic entity (NTE) approvals by the U.S. Food and Drug Administration (FDA) suggests a positive trend in current research and development (R&D) output. Prior to this, the cost of each NTE was considered to be rising exponentially, with compound failure occurring mainly in clinical phases. Quantitative systems pharmacology (QSP) modelling, as an additional tool in the drug discovery arsenal, aims to further reduce NTE costs and improve drug development success. Through in silico mathematical modelling, QSP can simulate drug activity as perturbations in biological systems and thus understand the fundamental interactions which drive disease pathology, compound pharmacology and patient response...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27761200/catch-me-if-you-can-leukemia-escape-after-cd19-directed-t-cell-immunotherapies
#19
REVIEW
Marco Ruella, Marcela V Maus
Immunotherapy is the revolution in cancer treatment of this last decade. Among multiple approaches able to harness the power of the immune system against cancer, T cell based immunotherapies represent one of the most successful examples. In particular, biotechnological engineering of protein structures, like the T cell receptor or the immunoglobulins, allowed the generation of synthetic peptides like chimeric antigen receptors and bispecific antibodies that are able to redirect non-tumor specific T cells to recognize and kill leukemic cells...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27721960/zebrafish-small-molecule-screens-taking-the-phenotypic-plunge
#20
Charles H Williams, Charles C Hong
Target based chemical screens are a mainstay of modern drug discovery, but the effectiveness of this reductionist approach is being questioned in light of declines in pharmaceutical R & D efficiency. In recent years, phenotypic screens have gained increasing acceptance as a complementary/alternative approach to early drug discovery. We discuss the various model organisms used in phenotypic screens, with particular focus on zebrafish, which has emerged as a leading model of in vivo phenotypic screens. Additionally, we anticipate therapeutic opportunities, particularly in orphan disease space, in the context of rapid advances in human Mendelian genetics, electronic health record (EHR)-enabled genome-phenome associations, and genome editing...
2016: Computational and Structural Biotechnology Journal
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