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Biological machines

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https://www.readbyqxmd.com/read/28545393/quantgenius-implementation-of-a-decision-support-system-for-qpcr-based-gene-quantification
#1
Špela Baebler, Miha Svalina, Marko Petek, Katja Stare, Ana Rotter, Maruša Pompe-Novak, Kristina Gruden
BACKGROUND: Quantitative molecular biology remains a challenge for researchers due to inconsistent approaches for control of errors in the final results. Due to several factors that can influence the final result, quantitative analysis and interpretation of qPCR data are still not trivial. Together with the development of high-throughput qPCR platforms, there is a need for a tool allowing for robust, reliable and fast nucleic acid quantification. RESULTS: We have developed "quantGenius" ( http://quantgenius...
May 25, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28544880/systems-wide-studies-uncover-commander-a-multiprotein-complex-essential-to-human-development
#2
REVIEW
Anna L Mallam, Edward M Marcotte
Recent mass spectrometry maps of the human interactome independently support the existence of a large multiprotein complex, dubbed "Commander." Broadly conserved across animals and ubiquitously expressed in nearly every human cell type examined thus far, Commander likely plays a fundamental cellular function, akin to other ubiquitous machines involved in expression, proteostasis, and trafficking. Experiments on individual subunits support roles in endosomal protein sorting, including the trafficking of Notch proteins, copper transporters, and lipoprotein receptors...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28541897/capacitive-micro-machined-ultrasound-transducers-for-interstitial-high-intensity-ultrasound-therapies
#3
W Apoutou N'Djin, Bjoern Gerold, Jeremy Vion, Michael Canney, An Nguyen-Dinh, Alexandre Carpentier, Jean-Yves Chapelon
Capacitive Micro-machined Ultrasound Transducers (CMUTs) exhibit several potential advantages over conventional piezo technologies for use in therapeutic ultrasound devices, including: ease of miniaturization and integration with electronics, broad bandwidth (>several MHz), and compatibility with magnetic resonance imaging (MRI). In this work, the electro-acoustic performance of CMUTs designed for interstitial high intensity contact ultrasound (HICU) applications was evaluated and the feasibility of generating ultrasound-induced heating and thermal destruction of biological tissues was studied...
May 24, 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/28541651/channel-crack-designed-gold-pu-sponge-for-highly-elastic-piezoresistive-sensor-with-excellent-detectability
#4
Yun-Hui Wu, Hai-Zhou Liu, Song Chen, Xuchu Dong, Ping-Ping Wang, Shuqi Liu, Yong Lin, Yong Wei, Lan Liu
It is a great challenge to fabricate piezoresistive sensors that possess high elasticity, large-area compliance and excellent detectability to satisfy both extremely tiny and large human activities monitoring. Herein, a novel and facile strategy is reported to manufacture highly elastic channel crack-based gold@PU sponge piezoresistive material. The elastic 3D conductive network is successfully prepared by gold ion sputtering, and channel cracks are skillfully designed on the 3D sponge skeletons. Such novel structure makes these fabricated sensors are capable of monitoring both tiny and large human motions, which originate from the nano-crack joint sensing mechanism and physical contact of conductive interconnected network...
May 25, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28540688/machine-learning-techniques-in-exploring-microrna-gene-discovery-targets-and-functions
#5
Sumi Singh, Ryan G Benton, Anurag Singh, Anshuman Singh
In recent years, the role of miRNAs in post-transcriptional gene regulation has provided new insights into the understanding of several types of cancers and neurological disorders. Although miRNA research has gathered great momentum since its discovery, traditional biological methods for finding miRNA genes and targets continue to remain a huge challenge due to the laborious tasks and extensive time involved. Fortunately, advances in computational methods have yielded considerable improvements in miRNA studies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28539121/network-mirroring-for-drug-repositioning
#6
Sunghong Park, Dong-Gi Lee, Hyunjung Shin
BACKGROUND: Although drug discoveries can provide meaningful insights and significant enhancements in pharmaceutical field, the longevity and cost that it takes can be extensive where the success rate is low. In order to circumvent the problem, there has been increased interest in 'Drug Repositioning' where one searches for already approved drugs that have high potential of efficacy when applied to other diseases. To increase the success rate for drug repositioning, one considers stepwise screening and experiments based on biological reactions...
May 18, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28537738/a-peptoid-square-helix-via-synergistic-control-of-backbone-dihedral-angles
#7
Benjamin Craig Gorske, Emily M Mumford, Charles G Gerrity, Imelda Ko
The continued expansion of the fields of macromolecular chemistry and nanoscience has motivated the development of new secondary structures that can serve as architectural elements of innovative materials, molecular machines, biological probes, and even commercial medicines. Synthetic foldamers are particularly attractive systems for developing such elements because they are specifically designed to facilitate synthetic manipulation and functional diversity. However, relatively few predictive design principles exist that permit both rational and modular control of foldamer secondary structure, while maintaining the capacity for facile diversification of displayed functionality...
May 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28534781/reviving-the-two-state-markov-chain-approach
#8
Andrzej Mizera, Jun Pang, Qixia Yuan
Probabilistic Boolean networks (PBNs) is a well-established computational framework for modelling biological systems. The steady-state dynamics of PBNs is of crucial importance in the study of such systems. However, for large PBNs, which often arise in systems biology, obtaining the steady-state distribution poses a significant challenge. In this paper, we revive the two-state Markov chain approach to solve this problem. This paper contributes in three aspects. First, we identify a problem of generating biased results with the approach and we propose a few heuristics to avoid such a pitfall...
May 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28533015/in%C3%A2-vitro-comparison-of-the-load-bearing-capacity-of-ceramic-and-metal-ceramic-resin-bonded-fixed-dental-prostheses-in-the-posterior-region
#9
Wolfgang Bömicke, Moritz Waldecker, Johannes Krisam, Peter Rammelsberg, Stefan Rues
STATEMENT OF PROBLEM: The clinical use of ceramic resin-bonded fixed dental prostheses (RBFDPs) in the posterior region is desirable for esthetic and biological reasons but has been associated with many technical problems, including fractures or chipping of the veneer. Although these problems may be overcome by using monolithic zirconia, information is lacking about the load-bearing capacity of resin-bonded monolithic zirconia restorations for replacing a molar. PURPOSE: The purpose of this in vitro study was to compare the load-bearing capacity (Fu), the load at initial damage (F1d), and the failure pattern of posterior RBFDPs fabricated from monolithic zirconia (MZr), veneered zirconia (VZr), and veneered cobalt-chromium (VCo)...
May 20, 2017: Journal of Prosthetic Dentistry
https://www.readbyqxmd.com/read/28532336/changing-techniques-in-crop-plant-classification-molecularization-at-the-national-institute-of-agricultural-botany-during-the-1980s
#10
Matthew Holmes
Modern methods of analysing biological materials, including protein and DNA sequencing, are increasingly the objects of historical study. Yet twentieth-century taxonomic techniques have been overlooked in one of their most important contexts: agricultural botany. This paper addresses this omission by harnessing unexamined archival material from the National Institute of Agricultural Botany (NIAB), a British plant science organization. During the 1980s the NIAB carried out three overlapping research programmes in crop identification and analysis: electrophoresis, near infrared spectroscopy (NIRS) and machine vision systems...
April 2017: Annals of Science
https://www.readbyqxmd.com/read/28531339/limtox-a-web-tool-for-applied-text-mining-of-adverse-event-and-toxicity-associations-of-compounds-drugs-and-genes
#11
Andres Cañada, Salvador Capella-Gutierrez, Obdulia Rabal, Julen Oyarzabal, Alfonso Valencia, Martin Krallinger
A considerable effort has been devoted to retrieve systematically information for genes and proteins as well as relationships between them. Despite the importance of chemical compounds and drugs as a central bio-entity in pharmacological and biological research, only a limited number of freely available chemical text-mining/search engine technologies are currently accessible. Here we present LimTox (Literature Mining for Toxicology), a web-based online biomedical search tool with special focus on adverse hepatobiliary reactions...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28528643/a-new-method-for-cryo-sectioning-cell-monolayers-using-a-correlative-workflow
#12
Androniki Kolovou, Martin Schorb, Abul Tarafder, Carsten Sachse, Yannick Schwab, Rachel Santarella-Mellwig
Cryo-electron microscopy (cryo-EM) techniques have made a huge advancement recently, providing close to atomic resolution of the structure of protein complexes. Interestingly, this imaging technique can be performed in cells, giving access to the molecular machines in their natural context, therefore bridging structural and cell biology. However, in situ structural electron microscopy faces one major challenge, which is the ability to focus on specific subcellular regions to capture the objects of interest...
2017: Methods in Cell Biology
https://www.readbyqxmd.com/read/28526268/structural-and-functional-aspects-of-the-nonribosomal-peptide-synthetase-condensation-domain-superfamily-discovery-dissection-and-diversity
#13
REVIEW
Kristjan Bloudoff, T Martin Schmeing
Nonribosomal peptide synthetases (NRPSs) are incredible macromolecular machines that produce a wide range of biologically- and therapeutically-relevant molecules. During synthesis, peptide elongation is performed by the condensation (C) domain, as it catalyzes amide bond formation between the nascent peptide and the amino acid it adds to the chain. Since their discovery more than two decades ago, C domains have been subject to extensive biochemical, bioinformatic, mutagenic, and structural analyses. They are composed of two lobes each with homology to chloramphenicol acetyltransferase, have two binding sites for their two peptidyl carrier protein-bound ligands, and have an active site with conserved motif HHxxxDG located between the two lobes...
May 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28525568/scenery-a-web-application-for-causal-network-reconstruction-from-cytometry-data
#14
Georgios Papoutsoglou, Giorgos Athineou, Vincenzo Lagani, Iordanis Xanthopoulos, Angelika Schmidt, Szabolcs Éliás, Jesper Tegnér, Ioannis Tsamardinos
Flow and mass cytometry technologies can probe proteins as biological markers in thousands of individual cells simultaneously, providing unprecedented opportunities for reconstructing networks of protein interactions through machine learning algorithms. The network reconstruction (NR) problem has been well-studied by the machine learning community. However, the potentials of available methods remain largely unknown to the cytometry community, mainly due to their intrinsic complexity and the lack of comprehensive, powerful and easy-to-use NR software implementations specific for cytometry data...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28524769/machine-learning-for-epigenetics-and-future-medical-applications
#15
Lawrence B Holder, M Muksitul Haque, Michael K Skinner
Understanding epigenetic processes holds immense promise for medical applications. Advances in Machine Learning (ML) are critical to realize this promise. Previous studies used epigenetic data sets associated with the germline transmission of epigenetic transgenerational inheritance of disease and novel ML approaches to predict genome-wide locations of critical epimutations. A combination of Active Learning (ACL) and Imbalanced Class Learning (ICL) was used to address past problems with ML to develop a more efficient feature selection process and address the imbalance problem in all genomic data sets...
May 19, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/28523272/structural-elements-regulating-aaa-protein-quality-control-machines
#16
REVIEW
Chiung-Wen Chang, Sukyeong Lee, Francis T F Tsai
Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/28521503/meeting-report-for-synthetic-biology-for-natural-products-2017-the-interface-of-meta-genomics-machine-learning-and-natural-product-discovery
#17
Michael J Smanski, David Mead, Claes Gustafsson, Michael G Thomas
No abstract text is available yet for this article.
May 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28520764/rib-biomechanical-properties-exhibit-diagnostic-potential-for-accurate-ageing-in-forensic-investigations
#18
Andrea Bonicelli, Bledar Xhemali, Elena F Kranioti, Peter Zioupos
Age estimation remains one of the most challenging tasks in forensic practice when establishing a biological profile of unknown skeletonised remains. Morphological methods based on developmental markers of bones can provide accurate age estimates at a young age, but become highly unreliable for ages over 35 when all developmental markers disappear. This study explores the changes in the biomechanical properties of bone tissue and matrix, which continue to change with age even after skeletal maturity, and their potential value for age estimation...
2017: PloS One
https://www.readbyqxmd.com/read/28520598/imaging-plus-x-multimodal-models-of-neurodegenerative-disease
#19
Neil P Oxtoby, Daniel C Alexander
PURPOSE OF REVIEW: This article argues that the time is approaching for data-driven disease modelling to take centre stage in the study and management of neurodegenerative disease. The snowstorm of data now available to the clinician defies qualitative evaluation; the heterogeneity of data types complicates integration through traditional statistical methods; and the large datasets becoming available remain far from the big-data sizes necessary for fully data-driven machine-learning approaches...
May 16, 2017: Current Opinion in Neurology
https://www.readbyqxmd.com/read/28514769/identification-of-long-non-coding-rnas-biomarkers-associated-with-progression-of-endometrial-carcinoma-and-patient-outcomes
#20
Yanan Sun, Xiaoyan Zou, Jun He, Yuqin Mao
Endometrial carcinoma is a complex disease characterized by both genetic, epigenetic and environmental factors. Increasing evidence has suggested that long non-coding RNAs (lncRNAs) play important roles in the development and progression of cancers. In this study, we performed a comparison analysis for lncRNA expression between patients with early-stage (stage I/II) and those with advanced-stage (stage III/IV) derived from The Cancer Genome Atlas (TCGA) project and identified 17 differentially expressed lncRNAs using student t-test...
April 30, 2017: Oncotarget
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