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https://www.readbyqxmd.com/read/27911038/quantitating-the-cell-turning-images-into-numbers-with-imagej
#1
REVIEW
Ellen T Arena, Curtis T Rueden, Mark C Hiner, Shulei Wang, Ming Yuan, Kevin W Eliceiri
Modern biological research particularly in the fields of developmental and cell biology has been transformed by the rapid evolution of the light microscope. The light microscope, long a mainstay of the experimental biologist, is now used for a wide array of biological experimental scenarios and sample types. Much of the great developments in advanced biological imaging have been driven by the digital imaging revolution with powerful processors and algorithms. In particular, this combination of advanced imaging and computational analysis has resulted in the drive of the modern biologist to not only visually inspect dynamic phenomena, but to quantify the involved processes...
December 2, 2016: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/27910820/4d-bioprinting-the-next-generation-technology-for-biofabrication-enabled-by-stimuli-responsive-materials
#2
Yi-Chen Li, Yu Shrike Zhang, Ali Akpek, Su Ryon Shin, Ali Khademhosseini
Four-dimensional (4D) bioprinting, encompassing a wide range of disciplines including bioengineering, materials science, chemistry, and computer sciences, is emerging as the next-generation biofabrication technology. By utilizing stimuli-responsive materials and advanced three-dimensional (3D) bioprinting strategies, 4D bioprinting aims to create dynamic 3D patterned biological structures that can transform their shapes or behavior under various stimuli. In this review, we highlight the potential use of various stimuli-responsive materials for 4D printing and their extension into biofabrication...
December 2, 2016: Biofabrication
https://www.readbyqxmd.com/read/27909575/a-step-by-step-workflow-for-low-level-analysis-of-single-cell-rna-seq-data
#3
Aaron T L Lun, Davis J McCarthy, John C Marioni
Single-cell RNA sequencing (scRNA-seq) is widely used to profile the transcriptome of individual cells. This provides biological resolution that cannot be matched by bulk RNA sequencing, at the cost of increased technical noise and data complexity. The differences between scRNA-seq and bulk RNA-seq data mean that the analysis of the former cannot be performed by recycling bioinformatics pipelines for the latter. Rather, dedicated single-cell methods are required at various steps to exploit the cellular resolution while accounting for technical noise...
2016: F1000Research
https://www.readbyqxmd.com/read/27909348/rapid-cycloaddition-of-a-diazo-group-with-an-unstrained-dipolarophile
#4
Matthew R Aronoff, Brian Gold, Ronald T Raines
The cycloaddition of a diazoacetamide with ethyl 4,4,4-trifluorocrotonate proceeds with k = 0.1 M(-1)s(-1). This second-order rate constant rivals those of optimized strain-promoted azide- alkyne cycloadditions, even though the reaction does not release strain. The regioselectivity and a computational distortion/interaction analysis of the reaction energetics are consistent with the formation of an N-H…F-C hydrogen bond in the transition state and the electronic character of the trifluorocrotonate. Analogous reactions with an azidoacetamide dipole or with an acrylate or crotonate dipolarophile were much slower...
June 1, 2016: Tetrahedron Letters
https://www.readbyqxmd.com/read/27908307/evolution-of-imaging-findings-laboratory-and-functional-parameters-in-rheumatoid-arthritis-patients-after-one-year-of-treatment-with-anti-tnf-%C3%AE-agents
#5
Efstathios E Detorakis, Eleftherios Magkanas, Ismini Lasithiotaki, Prodromos Sidiropoulos, Dimitrios T Boumpas, Nicholas Gourtsoyiannis, Katerina Antoniou, Maria Raissaki
OBJECTIVES: To investigate the efficacy and safety of anti-TNF-α agent treatment compared to non-biologic DMARDs in rheumatoid arthritis patients. METHODS: 82 consecutive patients, 29 males, 53 females, aged 42-79, diagnosed with RA and suitable for anti-TNF-α treatment composed two study groups: 42 with pre-existing rheumatoid arthritis-related interstitial lung disease (RA-ILD) and 40 without RA-ILD. Respective control groups consisted of 44 patients with pre-existing RA-ILD and 44 patients without RA-ILD, treated with non-biologic DMARDs...
October 27, 2016: Clinical and Experimental Rheumatology
https://www.readbyqxmd.com/read/27906169/automated-identification-of-mouse-visual-areas-with-intrinsic-signal-imaging
#6
Ashley L Juavinett, Ian Nauhaus, Marina E Garrett, Jun Zhuang, Edward M Callaway
Intrinsic signal optical imaging (ISI) is a rapid and noninvasive method for observing brain activity in vivo over a large area of the cortex. Here we describe our protocol for mapping retinotopy to identify mouse visual cortical areas using ISI. First, surgery is performed to attach a head frame to the mouse skull (∼1 h). The next day, intrinsic activity across the visual cortex is recorded during the presentation of a full-field drifting bar in the horizontal and vertical directions (∼2 h). Horizontal and vertical retinotopic maps are generated by analyzing the response of each pixel during the period of the stimulus...
January 2017: Nature Protocols
https://www.readbyqxmd.com/read/27905893/computational-prediction-of-multidisciplinary-team-decision-making-for-adjuvant-breast-cancer-drug-therapies-a-machine-learning-approach
#7
Frank P Y Lin, Adrian Pokorny, Christina Teng, Rachel Dear, Richard J Epstein
BACKGROUND: Multidisciplinary team (MDT) meetings are used to optimise expert decision-making about treatment options, but such expertise is not digitally transferable between centres. To help standardise medical decision-making, we developed a machine learning model designed to predict MDT decisions about adjuvant breast cancer treatments. METHODS: We analysed MDT decisions regarding adjuvant systemic therapy for 1065 breast cancer cases over eight years. Machine learning classifiers with and without bootstrap aggregation were correlated with MDT decisions (recommended, not recommended, or discussable) regarding adjuvant cytotoxic, endocrine and biologic/targeted therapies, then tested for predictability using stratified ten-fold cross-validations...
December 1, 2016: BMC Cancer
https://www.readbyqxmd.com/read/27904868/predictive-ability-of-18-f-fluorodeoxyglucose-positron-emission-tomography-computed-tomography-for-pathological-complete-response-and-prognosis-after-neoadjuvant-chemotherapy-in-triple-negative-breast-cancer-patients
#8
Sachiko Kiyoto, Yoshifumi Sugawara, Kohei Hosokawa, Rieko Nishimura, Natsumi Yamashita, Shozo Ohsumi, Teruhito Mochizuki
OBJECTIVES: The mortality of patients with locally advanced triple-negative breast cancer (TNBC) is high, and pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) is associated with improved prognosis. This retrospective study was designed and powered to investigate the ability of (18)F-fluorodeoxyglucose positron emission tomography/computed tomography ((18)F-FDG-PET/CT) to predict pathological response to NAC and prognosis after NAC. METHODS: The data of 32 consecutive women with clinical stage II or III TNBC from January 2006 to December 2013 in our institution who underwent FDG-PET/CT at baseline and after NAC were retrospectively analyzed...
2016: Asia Oceania Journal of Nuclear Medicine & Biology
https://www.readbyqxmd.com/read/27904481/3d-printed-nerve-guidance-channels-computer-aided-control-of-geometry-physical-cues-biological-supplements-and-gradients
#9
Blake N Johnson, Xiaofeng Jia
No abstract text is available yet for this article.
October 2016: Neural Regeneration Research
https://www.readbyqxmd.com/read/27903878/a-spiking-neural-model-of-adaptive-arm-control
#10
Travis DeWolf, Terrence C Stewart, Jean-Jacques Slotine, Chris Eliasmith
We present a spiking neuron model of the motor cortices and cerebellum of the motor control system. The model consists of anatomically organized spiking neurons encompassing premotor, primary motor, and cerebellar cortices. The model proposes novel neural computations within these areas to control a nonlinear three-link arm model that can adapt to unknown changes in arm dynamics and kinematic structure. We demonstrate the mathematical stability of both forms of adaptation, suggesting that this is a robust approach for common biological problems of changing body size (e...
November 30, 2016: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/27903820/agent-based-modelling-in-synthetic-biology
#11
REVIEW
Thomas E Gorochowski
Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903819/towards-designing-new-nano-scale-protein-architectures
#12
REVIEW
Jana Aupič, Fabio Lapenta, Žiga Strmšek, Roman Jerala
The complexity of designed bionano-scale architectures is rapidly increasing mainly due to the expanding field of DNA-origami technology and accurate protein design approaches. The major advantage offered by polypeptide nanostructures compared with most other polymers resides in their highly programmable complexity. Proteins allow in vivo formation of well-defined structures with a precise spatial arrangement of functional groups, providing extremely versatile nano-scale scaffolds. Extending beyond existing proteins that perform a wide range of functions in biological systems, it became possible in the last few decades to engineer and predict properties of completely novel protein folds, opening the field of protein nanostructure design...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27903590/anterior-cruciate-ligament-derived-stem-cells-transduced-with-bmp2-accelerate-graft-bone-integration-after-acl-reconstruction
#13
Yohei Kawakami, Koji Takayama, Tomoyuki Matsumoto, Ying Tang, Bing Wang, Yutaka Mifune, James H Cummins, Ryan J Warth, Ryosuke Kuroda, Masahiro Kurosaka, Freddie H Fu, Johnny Huard
BACKGROUND: Strong graft-bone integration is a prerequisite for successful graft remodeling after reconstruction of the anterior cruciate ligament (ACL) using soft tissue grafts. Novel strategies to accelerate soft tissue graft-bone integration are needed to reduce the need for bone-tendon-bone graft harvest, reduce patient convalescence, facilitate rehabilitation, and reduce total recovery time after ACL reconstruction. HYPOTHESIS: The application of ACL-derived stem cells with enhanced expression of bone morphogenetic protein 2 (BMP2) onto soft tissue grafts in the form of cell sheets will both accelerate and improve the quality of graft-bone integration after ACL reconstruction in a rat model...
November 30, 2016: American Journal of Sports Medicine
https://www.readbyqxmd.com/read/27902924/simple-mechanisms-of-early-life-simulation-model-on-the-origin-of-semi-cells
#14
Adrian Klein, Martin Bock, Wolfgang Alt
The development of first cellular structures played an important role in the early evolution of life. Early evolution of life probably took place on a molecular level in a reactive environment. The iron-sulfur theory postulates the formation of cell-like structures on catalytic surfaces. Experiments show that H2S together with FeS and other metallic centers drive auto-catalytic surface reactions, in which organic molecules such as pyruvic and amino acids occur. It is questionable which mechanisms are needed to form cell-like structures under these conditions...
November 27, 2016: Bio Systems
https://www.readbyqxmd.com/read/27902692/correction-multi-level-modeling-of-light-induced-stomatal-opening-offers-new-insights-into-its-regulation-by-drought
#15
(no author information available yet)
[This corrects the article DOI: 10.1371/journal.pcbi.1003930.].
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27901606/protein-folding-prediction-in-a-cubic-lattice-in-hydrophobic-polar-model
#16
Nicola Yanev, Metodi Traykov, Peter Milanov, Borislav Yurukov
The tertiary structure of the proteins determines their functions. Therefore, the predicting of protein's tertiary structure, based on the primary amino acid sequence from long time, is the most important and challenging subject in biochemistry, molecular biology, and biophysics. One of the most popular protein structure prediction methods, called Hydrophobic-Polar (HP) model, is based on the observation that in polar environment hydrophobic amino acids are in the core of the molecule-in contact between them and more polar amino acids are in contact with the polar environment...
November 30, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/27901061/inter-individual-variability-and-modeling-of-electrical-activity-a-possible-new-approach-to-explore-cardiac-safety
#17
Jean-Yves Le Guennec, Jérôme Thireau, Aude Ouillé, Julien Roussel, Jérôme Roy, Serge Richard, Sylvain Richard, Eric Martel, Pascal Champéroux
Safety pharmacology aims to predict rare side effects of new drugs. We explored whether rare pro-arrhythmic effects could be linked to the variability of the effects of these drugs on ion currents and whether taking into consideration this variability in computational models could help to better detect and predict cardiac side effects. For this purpose, we evaluated how intra- and inter-individual variability influences the effect of hERG inhibition on both the action potential duration and the occurrence of arrhythmias...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900742/-precision-nursing-individual-based-knowledge-translation
#18
Li-Chi Chiang, Mei-Ling Yeh, Sui-Lung Su
U.S. President Obama announced a new era of precision medicine in the Precision Medicine Initiative (PMI). This initiative aims to accelerate the progress of personalized medicine in light of individual requirements for prevention and treatment in order to improve the state of individual and public health. The recent and dramatic development of large-scale biologic databases (such as the human genome sequence), powerful methods for characterizing patients (such as genomics, microbiome, diverse biomarkers, and even pharmacogenomics), and computational tools for analyzing big data are maximizing the potential benefits of precision medicine...
December 2016: Hu Li za Zhi the Journal of Nursing
https://www.readbyqxmd.com/read/27900575/glycosaminoglycanomics-where-we-are
#19
Sylvie Ricard-Blum, Frédérique Lisacek
Glycosaminoglycans regulate numerous physiopathological processes such as development, angiogenesis, innate immunity, cancer and neurodegenerative diseases. Cell surface GAGs are involved in cell-cell and cell-matrix interactions, cell adhesion and signaling, and host-pathogen interactions. GAGs contribute to the assembly of the extracellular matrix and heparan sulfate chains are able to sequester growth factors in the ECM. Their biological activities are regulated by their interactions with proteins. The structural heterogeneity of GAGs, mostly due to chemical modifications occurring during and after their synthesis, makes the development of analytical techniques for their profiling in cells, tissues, and biological fluids, and of computational tools for mining GAG-protein interaction data very challenging...
November 30, 2016: Glycoconjugate Journal
https://www.readbyqxmd.com/read/27900235/technical-challenges-in-mass-spectrometry-based-metabolomics
#20
Fumio Matsuda
Metabolomics is a strategy for analysis, and quantification of the complete collection of metabolites present in biological samples. Metabolomics is an emerging area of scientific research because there are many application areas including clinical, agricultural, and medical researches for the biomarker discovery and the metabolic system analysis by employing widely targeted analysis of a few hundred preselected metabolites from 10-100 biological samples. Further improvement in technologies of mass spectrometry in terms of experimental design for larger scale analysis, computational methods for tandem mass spectrometry-based elucidation of metabolites, and specific instrumentation for advanced bioanalysis will enable more comprehensive metabolome analysis for exploring the hidden secrets of metabolism...
2016: Mass Spectrometry
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