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computers in biology and medicine

Xiang-Tian Yu, Tao Zeng
The diversity and huge omics data take biology and biomedicine research and application into a big data era, just like that popular in human society a decade ago. They are opening a new challenge from horizontal data ensemble (e.g., the similar types of data collected from different labs or companies) to vertical data ensemble (e.g., the different types of data collected for a group of person with match information), which requires the integrative analysis in biology and biomedicine and also asks for emergent development of data integration to address the great changes from previous population-guided to newly individual-guided investigations...
2018: Methods in Molecular Biology
Caroline C Swift, Meryle J Eklund, Jacqueline M Kraveka, Adina L Alazraki
Neuroblastoma is an embryonic tumor of the peripheral sympathetic nervous system. It is the most common extracranial solid tumor of childhood and accounts for up to 15% of all pediatric cancer fatalities. The manifestation of neuroblastoma is variable depending on the location of the tumor and on the presence or absence of paraneoplastic syndromes. The prognosis of neuroblastoma is also highly variable, ranging from spontaneous regression to widespread metastatic disease that is unresponsive to treatment. The age of the patient, stage of disease, histopathologic results, and multiple biologic factors contribute to the presurgical and pretreatment risk stratification of a patient with neuroblastoma...
March 2018: Radiographics: a Review Publication of the Radiological Society of North America, Inc
Mark Gainey, Montserrat Carles, Michael Mix, Philipp T Meyer, Michael Bock, Anca-Ligia Grosu, Dimos Baltas
Recently, there has been an increase in the imaging modalities available for radiotherapy planning and radiotherapy prognostic outcome: dual energy computed tomography (CT; DECT), dynamic contrast enhanced CT, dynamic contrast enhanced magnetic resonance imaging (MRI), diffusion-weighted MRI, positron emission tomography-CT, dynamic contrast enhanced ultrasound, magnetic resonance spectroscopy and positron emission tomography-MR. These techniques enable more precise gross tumor volume definition than CT alone and moreover allow subvolumes within the gross tumor volume to be defined which may be given a boost dose or an individual voxelized dose prescription may be derived...
March 9, 2018: Future Oncology
Saeideh Jalali, Amir Zarrinhaghighi, Saman Sadraei, Younes Ghasemi, Amirhossein Sakhteman, Pouya Faridi
Background The plant Nardostachys jatamansi from Valerianaceae family is a well known antidepressant plant and has historically been used in traditional medicine. As N. jatamansi contains many different compounds, to identify its mechanisms of action, we need a network-based study. Network-based studies are becoming an increasingly important tool in understanding the mechanisms of actions of drugs. Systems pharmacology (SP) and bioinformatics are two emerging tools that use computation to develop an understanding of drug actions in molecular and cellular levels...
March 5, 2018: Current Drug Metabolism
Juan I Castrillo, Simone Lista, Harald Hampel, Craig W Ritchie
Alzheimer's disease (AD) is a complex multifactorial disease, involving a combination of genomic, interactome, and environmental factors, with essential participation of (a) intrinsic genomic susceptibility and (b) a constant dynamic interplay between impaired pathways and central homeostatic networks of nerve cells. The proper investigation of the complexity of AD requires new holistic systems-level approaches, at both the experimental and computational level. Systems biology methods offer the potential to unveil new fundamental insights, basic mechanisms, and networks and their interplay...
2018: Methods in Molecular Biology
Antonio Benedetto, Pietro Ballone
Empirical evidence and conceptual elaboration reveal and rationalise the remarkable affinity of organic ionic liquids for biomembranes. Cations of the so-called room-temperature ionic liquids (RTILs), in particular, are readily absorbed into the lipid fraction of biomembranes, causing a variety of observable biological effects, including generic cytotoxicity, broad anti-bacterial potential, and anti-cancer activity. Chemical-physics analysis of model systems made of phospholipid bilayers, RTIL ions and water confirm and partly explain this evidence, quantifying the mild destabilising effect of RTILs on structural, dynamical and thermodynamic properties of lipids in biomembranes...
March 6, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Gokhan Zengin, Devina Lobine, Adriano Mollica, Marcello Locatelli, Simone Carradori, Mohamad Fawzi Mahomoodally
The ethyl acetate, methanolic, and water extracts of Fibigia eriocarpa were assessed for a panoply of bioactivities. Total phenolic and flavonoid content were quantified as well as individual phenolic compounds by HPLC-DAD. The in-vitro antioxidant and enzyme (acetylcholinesterase (AChE), butyrylcholinesterase (BChE), tyrosinase, α-amylase, and α-glucosidase) inhibitory potential of the extracts were evaluated. In silico molecular docking was used to investigate possible interaction between dominant compounds and selected enzymes...
March 5, 2018: Fundamental & Clinical Pharmacology
Kun-Hsing Yu, Tsung-Lu Lee, Chi-Shiang Wang, Yu-Ju Chen, Christopher Ré, Samuel C Kou, Jung-Hsien Chiang, Isaac S Kohane, Michael Snyder
There are more than 3.7 million published articles on the biological functions or disease implications of proteins, constituting an important resource of proteomics knowledge. However, it is difficult to summarize the millions of proteomics findings in the literature manually and quantify their relevance to the biology and diseases of interest. In this study, we developed a fully-automated bioinformatics framework to identify and prioritize proteins associated with any biological entity. We used the 22 targeted areas of the Biology/Disease-driven (B/D)-Human Proteome Project (HPP) as examples, prioritized the relevant proteins through their Protein Universal Reference Publication-Originated Search Engine (PURPOSE) scores, validated the relevance of the score by comparing the protein prioritization results with a curated database, computed the scores of proteins across the topics of B/D-HPP, and characterized the top proteins in the common model organisms...
March 5, 2018: Journal of Proteome Research
Rolf Apweiler, Tim Beissbarth, Michael R Berthold, Nils Blüthgen, Yvonne Burmeister, Olaf Dammann, Andreas Deutsch, Friedrich Feuerhake, Andre Franke, Jan Hasenauer, Steve Hoffmann, Thomas Höfer, Peter Lm Jansen, Lars Kaderali, Ursula Klingmüller, Ina Koch, Oliver Kohlbacher, Lars Kuepfer, Frank Lammert, Dieter Maier, Nico Pfeifer, Nicole Radde, Markus Rehm, Ingo Roeder, Julio Saez-Rodriguez, Ulrich Sax, Bernd Schmeck, Andreas Schuppert, Bernd Seilheimer, Fabian J Theis, Julio Vera, Olaf Wolkenhauer
New technologies to generate, store and retrieve medical and research data are inducing a rapid change in clinical and translational research and health care. Systems medicine is the interdisciplinary approach wherein physicians and clinical investigators team up with experts from biology, biostatistics, informatics, mathematics and computational modeling to develop methods to use new and stored data to the benefit of the patient. We here provide a critical assessment of the opportunities and challenges arising out of systems approaches in medicine and from this provide a definition of what systems medicine entails...
March 2, 2018: Experimental & Molecular Medicine
Steven M Bishop, Ari Ercole
OBJECTIVES: The reliable detection of peaks and troughs in physiological signals is essential to many investigative techniques in medicine and computational biology. Analysis of the intracranial pressure (ICP) waveform is a particular challenge due to multi-scale features, a changing morphology over time and signal-to-noise limitations. Here we present an efficient peak and trough detection algorithm that extends the scalogram approach of Scholkmann et al., and results in greatly improved algorithm runtime performance...
2018: Acta Neurochirurgica. Supplement
Erwan Poivet, Narmin Tahirova, Zita Peterlin, Lu Xu, Dong-Jing Zou, Terry Acree, Stuart Firestein
Crucial for any hypothesis about odor coding is the classification and prediction of sensory qualities in chemical compounds. The relationship between perceptual quality and molecular structure has occupied olfactory scientists throughout the 20th century, but details of the mechanism remain elusive. Odor molecules are typically organic compounds of low molecular weight that may be aliphatic or aromatic, may be saturated or unsaturated, and may have diverse functional polar groups. However, many molecules conforming to these characteristics are odorless...
February 2018: Science Advances
Liang Cui, Haitao Lu, Yie Hou Lee
In the past decade, advances in liquid chromatography-mass spectrometry (LC-MS) have revolutionized untargeted metabolomics analyses. By mining metabolomes more deeply, researchers are now primed to uncover key metabolites and their associations with diseases. The employment of untargeted metabolomics has led to new biomarker discoveries and a better mechanistic understanding of diseases with applications in precision medicine. However, many major pertinent challenges remain. First, compound identification has been poor, and left an overwhelming number of unidentified peaks...
February 27, 2018: Mass Spectrometry Reviews
Eugene P Rhee
Advances in technology and computing now permit the high-throughput analysis of multiple domains of biological information, including the genome, transcriptome, proteome, and metabolome. These omics approaches, particularly comprehensive analysis of the genome, have catalyzed major discoveries in science and medicine, including in nephrology. However, they also generate large complex data sets that can be difficult to synthesize from a clinical perspective. This article seeks to provide an overview that makes omics technologies relevant to the practicing nephrologist, framing these tools as an extension of how we approach patient care in the clinic...
February 23, 2018: American Journal of Kidney Diseases: the Official Journal of the National Kidney Foundation
Marilo Olivares-Vicente, Enrique Barrajon-Catalan, Maria Herranz-Lopez, Antonio Segura-Carretero, Jorge Joven, Jose Antonio Encinar, Vicente Micol
Edible plants such as Hibiscus sabdariffa, Lippia citriodora, Rosmarinus officinalis and Olea europaea, are rich in bioactive compounds that represent most of the phenolic compounds families and have exhibited potential benefits in human health. These plants have been commonly used in folk medicine for their potential therapeutic properties in human chronic diseases. Recent evidence on these plants leads to postulate that polyphenols may account for such effects. Nevertheless, the compounds or metabolites that are responsible for reaching the molecular targets are still unknown...
February 19, 2018: Current Drug Metabolism
Joshua Chang, David Paydarfar
The ability to define the unique features of an input stimulus needed to control switch-like behavior in biological systems is an important problem in computational biology and medicine. We show in this study how highly complex and intractable optimization problems can be simplified by restricting the search to the signal's extrema as key feature points, and evolving the extrema features towards optimal solutions that closely match solutions derived from gradient-based methods. Our results suggest a model-independent approach for solving a class of optimization problems related to controlling switch-like state transitions...
February 21, 2018: Scientific Reports
Leonardo G Ferreira, Glaucius Oliva, Adriano D Andricopulo
Scientific and technological breakthroughs have compelled the current players in drug discovery to increasingly incorporate knowledge-based approaches. This evolving paradigm, which has its roots attached to the recent advances in medicinal chemistry, molecular and structural biology, has unprecedentedly demanded the development of up-to-date computational approaches, such as bio- and chemo-informatics. These tools have been pivotal to catalyzing the ever-increasing amount of data generated by the molecular sciences, and to converting the data into insightful guidelines for use in the research pipeline...
February 15, 2018: Anais da Academia Brasileira de Ciências
Guillaume Noell, Rosa Faner, Alvar Agustí
Human health and disease are emergent properties of a complex, nonlinear, dynamic multilevel biological system: the human body. Systems biology is a comprehensive research strategy that has the potential to understand these emergent properties holistically. It stems from advancements in medical diagnostics, "omics" data and bioinformatic computing power. It paves the way forward towards "P4 medicine" (predictive, preventive, personalised and participatory), which seeks to better intervene preventively to preserve health or therapeutically to cure diseases...
March 31, 2018: European Respiratory Review: An Official Journal of the European Respiratory Society
Fatemeh Ajalloueian, Greg Lemon, Jöns Hilborn, Ioannis S Chronakis, Magdalena Fossum
The urinary bladder is a complex organ with the primary functions of storing urine under low and stable pressure and micturition. Many clinical conditions can cause poor bladder compliance, reduced capacity, and incontinence, requiring bladder augmentation or use of regenerative techniques and scaffolds. To replicate an organ that is under frequent mechanical loading and unloading, special attention towards fulfilling its biomechanical requirements is necessary. Several biological and synthetic scaffolds are available, with various characteristics that qualify them for use in bladder regeneration in vitro and in vivo, including in the treatment of clinical conditions...
February 13, 2018: Nature Reviews. Urology
Qi Zhao, Di Xie, Hongsheng Liu, Fan Wang, Gui-Ying Yan, Xing Chen
In the biological field, the identification of the associations between microRNAs (miRNAs) and diseases has been paid increasing attention as an extremely meaningful study for the clinical medicine. However, it is expensive and time-consuming to confirm miRNA-disease associations by experimental methods. Therefore, in recent years, several effective computational models for predicting the potential miRNA-disease associations have been developed. In this paper, we proposed the Spy and Super Cluster strategy for MiRNA-Disease Association prediction (SSCMDA) based on known miRNA-disease associations, integrated disease similarity and integrated miRNA similarity...
January 5, 2018: Oncotarget
Robert D Barrows, Kristin M Blacklock, Paul R Rablen, Sagar D Khare, Spencer Knapp
Replacement of the sulfur atom in biologically active diaryl and heteroaryl thioethers (Ar-S-Ar', HAr-S-Ar, and HAr-S-HAr') with any of several one-atom or two-atom linkers can be expected to reduce the susceptibility of the analogue to metabolic oxidation, a well-documented problem for thioethers intended for medicinal chemistry applications. Ab initio calculations indicate how well various proposed thioether isosteric groups, including some new and unusual ones, may perform structurally and electronically in replacing the bridging sulfur atom...
February 1, 2018: Journal of Molecular Graphics & Modelling
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