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https://www.readbyqxmd.com/read/29775783/ocimum-basilicum-mirnome-revisited-a-cross-kingdom-approach
#1
Maulikkumar Patel, Shanaya Patel, Naman Mangukia, Saumya Patel, Archana Mankad, Himanshu Pandya, Rakesh Rawal
O. basilicum is medicinally important herb having inevitable role in human health. However, the mechanism of action is largely unknown. Present study aims to understand the mechanism of regulation of key human target genes that could plausibly modulated by O. basilicum miRNAs in cross kingdom manner using computational and system biology approach. O. basilicum miRNA sequences were retrieved and their corresponding human target genes were identified using psRNA target and interaction analysis of hub nodes. Six O...
May 15, 2018: Genomics
https://www.readbyqxmd.com/read/29762023/reinforced-adversarial-neural-computer-for-de-novo-molecular-design
#2
Evgeny Putin, Arip Asadulaev, Yan Ivanenkov, Vladimir Aladinskiy, Benjamin Sánchez-Lengeling, Alán Aspuru-Guzik, Alex Zhavoronkov
In silico modeling is a crucial milestone in modern drug design & development. Although computer-aided approaches in this field are well-studied, the application of deep learning methods in this research area is at the beginning. In this work, we present an original deep neural network (DNN) architecture named RANC (Reinforced Adversarial Neural Computer) for the de novo design of novel small-molecule organic structures based on generative adversarial network (GAN) paradigm and reinforcement learning (RL)...
May 15, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29744615/systems-biology-systems-medicine-systems-pharmacology-the-what-and-the-why
#3
Angélique Stéphanou, Eric Fanchon, Pasquale F Innominato, Annabelle Ballesta
Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Although defining systems biology might be difficult, on the other hand its purpose is clear: systems biology, with its emerging subfields systems medicine and systems pharmacology, clearly aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop...
May 9, 2018: Acta Biotheoretica
https://www.readbyqxmd.com/read/29739980/systematic-analysis-of-demeter-like-dna-glycosylase-genes-shows-lineage-specific-smi-mir7972-involved-in-smdml1-regulation-in-salvia-miltiorrhiza
#4
Jiang Li, Caili Li, Shanfa Lu
DEMETER-like DNA glycosylases (DMLs) initiate the base excision repair-dependent DNA demethylation to regulate a wide range of biological processes in plants. Six putative SmDML genes, termed SmDML1-SmDML6, were identified from the genome of S. miltiorrhiza, an emerging model plant for Traditional Chinese Medicine (TCM) studies. Integrated analysis of gene structures, sequence features, conserved domains and motifs, phylogenetic analysis and differential expression showed the conservation and divergence of SmDMLs...
May 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29736721/a-quantitative-systems-pharmacology-approach-to-infer-pathways-involved-in-complex-disease-phenotypes
#5
Mark E Schurdak, Fen Pei, Timothy R Lezon, Diane Carlisle, Robert Friedlander, D Lansing Taylor, Andrew M Stern
Designing effective therapeutic strategies for complex diseases such as cancer and neurodegeneration that involve tissue context-specific interactions among multiple gene products presents a major challenge for precision medicine. Safe and selective pharmacological modulation of individual molecular entities associated with a disease often fails to provide efficacy in the clinic. Thus, development of optimized therapeutic strategies for individual patients with complex diseases requires a more comprehensive, systems-level understanding of disease progression...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29735690/precise-detection-of-de-novo-single-nucleotide-variants-in-human-genomes
#6
Laura Gómez-Romero, Kim Palacios-Flores, José Reyes, Delfino García, Margareta Boege, Guillermo Dávila, Margarita Flores, Michael C Schatz, Rafael Palacios
The precise determination of de novo genetic variants has enormous implications across different fields of biology and medicine, particularly personalized medicine. Currently, de novo variations are identified by mapping sample reads from a parent-offspring trio to a reference genome, allowing for a certain degree of differences. While widely used, this approach often introduces false-positive (FP) results due to misaligned reads and mischaracterized sequencing errors. In a previous study, we developed an alternative approach to accurately identify single nucleotide variants (SNVs) using only perfect matches...
May 7, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29731951/advanced-computational-methods-in-bio-mechanics
#7
REVIEW
Waleed M S Al Qahtani, Mohamed I El-Anwar
A novel partnership between surgeons and machines, made possible by advances in computing and engineering technology, could overcome many of the limitations of traditional surgery. By extending surgeons' ability to plan and carry out surgical interventions more accurately and with fewer traumas, computer-integrated surgery (CIS) systems could help to improve clinical outcomes and the efficiency of healthcare delivery. CIS systems could have a similar impact on surgery to that long since realised in computer-integrated manufacturing...
April 15, 2018: Open Access Macedonian Journal of Medical Sciences
https://www.readbyqxmd.com/read/29723612/ignoring-the-modeling-approaches-towards-the-shadowy-paths-in-nanomedicine
#8
REVIEW
Parichehr Hassanzadeh, Fatemeh Atyabi, Rassoul Dinarvand
Limited efficiency of the conventional therapeutic options against a variety of diseases has provoked nanotech-based research efforts to develop advanced materials and devices for targeted delivery of theranostics which may provide imminent breakthroughs in medicine. However, nonspecific distribution or inappropriate tissue penetration of nanoparticles, complexity of drug delivery process, insufficient drug accumulation, loss of targeting ability, occurrence of the unexpected phenomena, safety concerns, and data reliability have remained challenging...
April 30, 2018: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/29717714/multi-position-data-collection-and-dynamic-beam-sizing-recent-improvements-to-the-automatic-data-collection-algorithms-on-massif-1
#9
Olof Svensson, Maciej Gilski, Didier Nurizzo, Matthew W Bowler
Macromolecular crystallography is now a mature and widely used technique that is essential in the understanding of biology and medicine. Increases in computing power combined with robotics have not only enabled large numbers of samples to be screened and characterized but have also enabled better decisions to be taken on data collection itself. This led to the development of MASSIF-1 at the ESRF, the first beamline in the world to run fully automatically while making intelligent decisions taking user requirements into account...
May 1, 2018: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/29706894/high-performance-agent-based-modeling-applied-to-vocal-fold-inflammation-and-repair
#10
Nuttiiya Seekhao, Caroline Shung, Joseph JaJa, Luc Mongeau, Nicole Y K Li-Jessen
Fast and accurate computational biology models offer the prospect of accelerating the development of personalized medicine. A tool capable of estimating treatment success can help prevent unnecessary and costly treatments and potential harmful side effects. A novel high-performance Agent-Based Model (ABM) was adopted to simulate and visualize multi-scale complex biological processes arising in vocal fold inflammation and repair. The computational scheme was designed to organize the 3D ABM sub-tasks to fully utilize the resources available on current heterogeneous platforms consisting of multi-core CPUs and many-core GPUs...
2018: Frontiers in Physiology
https://www.readbyqxmd.com/read/29704408/inter-subject-differences-in-circadian-coordination-captured-in-real-time-in-healthy-and-cancerous-individual-persons-during-their-daily-routine-using-a-mobile-internet-platform
#11
Sandra Komarzynski, Qi Huang, Pasquale F Innominato, Monique Maurice, Alexandre Arbaud, Jacques Beau, Mohamed Bouchahda, Ayhan Ulusakarya, Nicolas Beaumatin, Gabriele Breda, Bärbel Finkenstädt, Francis Levi
BACKGROUND: Experimental and epidemiologic studies have shown that circadian clocks disruption can play an important role in the development of cancer and metabolic diseases. The cellular clocks outside the brain are effectively coordinated by the body temperature rhythm. We hypothesized that concurrent measurements of body temperature and rest-activity rhythms would assess circadian clocks coordination in individual patients, thus enabling the integration of biological rhythms into precision medicine...
January 5, 2018: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/29702523/the-crosstalk-between-hematopoietic-stem-cells-and-their-niches
#12
Charles Durand, Pierre Charbord, Thierry Jaffredo
PURPOSE OF REVIEW: Hematopoietic stem cells (HSCs) reside in specific microenvironments also called niches that regulate HSC functions. Understanding the molecular and cellular mechanisms involved in the crosstalk between HSCs and niche cells is a major issue in stem cell biology and regenerative medicine. The purpose of this review is to discuss recent advances in this field with particular emphasis on the transcriptional landscape of HSC niche cells and the roles of extracellular vesicles (EVs) in the dialog between HSCs and their microenvironments...
April 26, 2018: Current Opinion in Hematology
https://www.readbyqxmd.com/read/29700076/computer-aided-biochemical-programming-of-synthetic-microreactors-as-diagnostic-devices
#13
Alexis Courbet, Patrick Amar, François Fages, Eric Renard, Franck Molina
Biological systems have evolved efficient sensing and decision-making mechanisms to maximize fitness in changing molecular environments. Synthetic biologists have exploited these capabilities to engineer control on information and energy processing in living cells. While engineered organisms pose important technological and ethical challenges, de novo assembly of non-living biomolecular devices could offer promising avenues toward various real-world applications. However, assembling biochemical parts into functional information processing systems has remained challenging due to extensive multidimensional parameter spaces that must be sampled comprehensively in order to identify robust, specification compliant molecular implementations...
April 26, 2018: Molecular Systems Biology
https://www.readbyqxmd.com/read/29698774/biofilm-inhibition-mechanism-from-extract-of-hymenocallis-littoralis-leaves
#14
Naiem H Nadaf, Rishikesh S Parulekar, Rahul S Patil, Trupti K Gade, Anjum A Momin, Shailesh R Waghmare, Maruti J Dhanavade, Akalpita U Arvindekar, Kailas D Sonawane
ETHNOPHARMACOLOGICAL RELEVANCE: Hymenocallis littoralis (Jacq.) Salisb. has been referred as beach spider lily and commonly known for its rich phytochemical diversity. Phytochemicals such as alkaloids, volatile constituents, phenols, flavonoids, flavonols extracted from different parts of these plants like bulbs, flowers, leaf, stem and root had been used in folk medicines from ancient times because of their excellent antimicrobial and antioxidant properties. The leaf and bulb extract of H...
April 23, 2018: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/29688313/automatic-selection-of-verification-tools-for-efficient-analysis-of-biochemical-models
#15
Mehmet Emin Bakir, Savas Konur, Marian Gheorghe, Natalio Krasnogor, Mike Stannett
Motivation: Formal verification is a computational approach that checks system correctness (in relation to a desired functionality). It has been widely used in engineering applications to verify that systems work correctly. Model checking, an algorithmic approach to verification, looks at whether a system model satisfies its requirements specification. This approach has been applied to a large number of models in systems and synthetic biology as well as in systems medicine. Model checking is, however, computationally very expensive, and is not scalable to large models and systems...
April 24, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29667640/-the-efficiency-of-the-application-of-the-modern-computed-technologies-in-the-clinical-practice-and-the-prospects-for-the-further-use-of-the-biomechanical-3d-models-in-forensic-medicine
#16
I Yu Makarov, A V Svetlakov, A V Sotin, S V Shigeev, A A Gusarov, S A Smirenin, V V Emelin, V B Stragis, V A Fetisov
To-day, the computer-assisted 3D-technologies for the mathematical simulation of the engineering facilities are extensively used for the purpose of technical calculations in all branches of industry and building. The positive experience gained with the application of the 3D-models finds wide application in the joined investigations on the topical problems of the prosthetic and surgical treatment of bones, teeth, joints, cardiac valves, blood vessels, etc. The objective of the present study was the analysis of the positive experience with the involvement of the specialists in the design and practical application of 3D-models for the solution of problems facing the medical prosthetics and the management of various pathological conditions...
2018: Sudebno-meditsinskaia Ekspertiza
https://www.readbyqxmd.com/read/29664602/engineering-persistent-luminescence-nanoparticles-for-biological-applications-from-biosensing-bioimaging-to-theranostics
#17
Shao-Kai Sun, He-Fang Wang, Xiu-Ping Yan
Persistent luminescence nanoparticles (PLNPs) are unique optical materials emitting long-lasting luminescence after ceasing excitation. Such a unique optical feature allows luminescence detection without constant external illumination to avoid the interferences of autofluorescence and scattering light from biological fluids and tissues. Besides, near-infrared (NIR) PLNPs have advantages of deep penetration and the reactivation of the persistent luminescence (PL) by red or NIR light. These features make the application of NIR-emitting PLNPs in long-term bioimaging no longer limited by the lifetime of PL...
April 17, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29664161/affinity-driven-covalent-modulator-of-glyceraldehyde-3-phosphate-dehydrogenase-gapdh-cascade
#18
Jeffy Chern, Chun-Ping Lu, Zhanxiong Fang, Ching-Ming Chang, Kuo-Feng Hua, Yi-Ting Chen, Cheng Yang Ng, Yi-Lin Sophia Chen, Yulin Lam, Shih-Hsiung Wu
Traditional medicines provide a fertile ground to explore potent lead compounds; yet, their transformation into modern drugs is fraught with challenges in deciphering the target that is mechanistically valid for its biological activity. Herein we revealed Z-(+)-isochaihulactone 1 exhibited significant inhibition against MDR cancer cell lines and mice xenografts. By NMR spectroscopy, 1 was shown to resist to an off-targeting thiolate, thus giving 1 a target covalent inhibitor-like (TCI) property. By identifying the pharmacophore of 1 (α,β-unsaturated moiety), a 1-derived probe was designed and synthesized for TCI-oriented activity-based proteome profiling (TCI-ABPP)...
April 17, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29662297/graphics-processing-unit-enhanced-genetic-algorithms-for-solving-the-temporal-dynamics-of-gene-regulatory-networks
#19
REVIEW
Raúl García-Calvo, J L Guisado, Fernando Diaz-Del-Rio, Antonio Córdoba, Francisco Jiménez-Morales
Understanding the regulation of gene expression is one of the key problems in current biology. A promising method for that purpose is the determination of the temporal dynamics between known initial and ending network states, by using simple acting rules. The huge amount of rule combinations and the nonlinear inherent nature of the problem make genetic algorithms an excellent candidate for finding optimal solutions. As this is a computationally intensive problem that needs long runtimes in conventional architectures for realistic network sizes, it is fundamental to accelerate this task...
2018: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/29650893/-towards-development-of-innovative-cancer-therapies-trans-omics-approach
#20
Reika Kawabata-Iwakawa, Masahiko Nishiyama
Comprehensive genomic and transcriptome analyses using next-generation sequencing(NGS)analysis has lead a discovery of a variety of novel driver gene mutations and new therapeutic targets for cancer patients, and has remarkably improved outcome of the patients through the development novel molecular targeting drugs. Even so, in so-called intractable or refractory cancers, those "druggable"alterations common to the diseases are rarely found due to the high diversity of the tumor. Furthermore, most of molecular target therapy is known to acquire the resistance to the drug by means of multiple factors such as up-regulation of the partially inhibited pathway, mutation of the target, activation of alternative pathways, histological translocation, and oncogene de-addiction...
March 2018: Gan to Kagaku Ryoho. Cancer & Chemotherapy
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