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https://www.readbyqxmd.com/read/28212080/improving-registration-robustness-for-image-guided-liver-surgery-in-a-novel-human-to-phantom-data-framework
#1
Jarrod Collins, Jared Weis, Jon Heiselman, Logan Clements, Amber Simpson, Willam Jarnagin, Michael Miga
In open image-guided liver surgery (IGLS), a sparse representation of the intraoperative organ surface can be acquired to drive image-to-physical registration. We hypothesize that uncharacterized error induced by variation in the collection patterns of organ surface data limits the accuracy and robustness of IGLS registration. Clinical validation of such registration methods is challenged due to the difficulty in obtaining data representative of the true state of organ deformation. We propose a novel human-to-phantom validation framework that transforms surface collection patterns from in vivo IGLS procedures (n=13) onto a well-characterized hepatic deformation phantom for the purpose of validating surface-driven, volumetric nonrigid registration methods...
February 13, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28212039/in-vitro-stepwise-reconstitution-of-amino-acid-derived-vinyl-isocyanide-biosynthesis-detection-of-an-elusive-intermediate
#2
Wei-Chen Chang, Dev Sanyal, Jhih-Liang Huang, Kuljira Ittiamornkul, Qin Zhu, Xinyu Liu
In vitro reconstitution of a newly discovered isonitrile synthase (AmbI1 and AmbI2) and the detection of an elusive intermediate (S)-3-(1H-indol-3-yl)-2-isocyanopropanoic acid 1 in indolyl vinyl isocyanide biogenesis are reported. The characterization of iron/2-oxoglutarate (Fe/2OG) dependent desaturases IsnB and AmbI3 sheds light on the possible mechanism underlying stereoselective alkene installation to complete the biosynthesis of (E)- and (Z)-3-(2-isocyanovinyl)-1H-indole 2 and 5. Establishment of a tractable isonitrile synthase system (AmbI1 and AmbI2) paves the way to elucidate the enigmatic enzyme mechanism for isocyanide formation...
February 17, 2017: Organic Letters
https://www.readbyqxmd.com/read/28208429/exact-results-for-power-spectrum-and-susceptibility-of-a-leaky-integrate-and-fire-neuron-with-two-state-noise
#3
Felix Droste, Benjamin Lindner
The response properties of excitable systems driven by colored noise are of great interest, but are usually mathematically only accessible via approximations. For this reason, dichotomous noise, a rare example of a colored noise leading often to analytically tractable problems, has been extensively used in the study of stochastic systems. Here, we calculate exact expressions for the power spectrum and the susceptibility of a leaky integrate-and-fire neuron driven by asymmetric dichotomous noise. While our results are in excellent agreement with simulations, they also highlight a limitation of using dichotomous noise as a simple model for more complex fluctuations: Both power spectrum and susceptibility exhibit an undamped periodic structure, the origin of which we discuss in detail...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28207381/personalized-models-of-human-atrial-electrophysiology-derived-from-endocardial-electrograms
#4
Cesare Corrado, John Whitaker, Henry Chubb, Steven Williams, Matthew Wright, Jaswinder Gill, Mark O'Neill, Steven Niederer
OBJECTIVE: Computational models represent a novel framework for understanding the mechanisms behind atrial fibrillation (AF) and offer a pathway for personalizing and optimizing treatment. The characterization of local electrophysiological properties across the atria during procedures remains a challenge. The aim of this work is to characterize the regional properties of the human atrium from multi-electrode catheter measurements. METHODS: We propose a novel method that characterizes regional electrophysiology properties by fitting parameters of an ionic model to conduction velocity and effective refractory period restitution curves obtained by a s1 s2 pacing protocol applied through a multi-electrode catheter...
May 30, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28202679/from-molecular-chaperones-to-membrane-motors-through-the-lens-of-a-mass-spectrometrist
#5
REVIEW
Carol V Robinson
Twenty-five years ago, we obtained our first mass spectra of molecular chaperones in complex with protein ligands and entered a new field of gas-phase structural biology. It is perhaps now time to pause and reflect, and to ask how many of our initial structure predictions and models derived from mass spectrometry (MS) datasets were correct. With recent advances in structure determination, many of the most challenging complexes that we studied over the years have become tractable by other structural biology approaches enabling such comparisons to be made...
February 8, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28202661/targeting-pak1
#6
REVIEW
Galina Semenova, Jonathan Chernoff
p21-Activated kinase 1 (PAK1) has attracted much attention as a potential therapeutic target due to its central role in many oncogenic signaling pathways, its frequent dysregulation in cancers and neurological disorders, and its tractability as a target for small-molecule inhibition. To date, several PAK1-targeting compounds have been developed as preclinical agents, including one that has been evaluated in a clinical trial. A series of ATP-competitive inhibitors, allosteric inhibitors and peptide inhibitors with distinct biochemical and pharmacokinetic properties represent useful laboratory tools for studies on the role of PAK1 in biology and in disease contexts, and could lead to promising therapeutic agents...
February 8, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28191038/physiological-and-molecular-characterizations-of-the-interactions-in-two-cellulose-to-methane-cocultures
#7
Hongyuan Lu, Siu-Kin Ng, Yangyang Jia, Mingwei Cai, Patrick K H Lee
BACKGROUND: The interspecies interactions in a biomethanation community play a vital role in substrate degradation and methane (CH4) formation. However, the physiological and molecular mechanisms of interaction among the microbial members of this community remain poorly understood due to the lack of an experimentally tractable model system. In this study, we successfully established two coculture models combining the cellulose-degrading bacterium Clostridium cellulovorans 743B with Methanosarcina barkeri Fusaro or Methanosarcina mazei Gö1 for the direct conversion of cellulose to CH4...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28188220/cannabinoids-activate-monoaminergic-signaling-to-modulate-key-c-elegans-behaviors
#8
Mitchell Oakes, Wen Jing Law, Tobias Clark, Bruce Bamber, Richard Komuniecki
Cannabis or marijuana, a popular recreational drug, alters sensory perception and exerts a range of potential medicinal benefits. The present study demonstrates that the endogenous cannabinoid receptor agonists, 2-arachidonoylglycerol (2-AG) and anandamide (AEA) activate a canonical cannabinoid receptor in C. elegans and also modulate monoaminergic signaling at multiple levels. 2-AG or AEA inhibit nociception and feeding through a pathway requiring the cannabinoid-like receptor, NPR-19. 2-AG or AEA activate NPR-19 directly and cannabinoid-dependent inhibition can be rescued in npr-19 null animals by the expression of a human cannabinoid receptor, CB1, highlighting the orthology of the receptors...
February 10, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28187811/determinants-of-prognosis-in-neurocatastrophes
#9
K Sharma, R D Stevens
A neurocatastrophe or severe brain injury (SBI) is a central nervous system insult associated with a high likelihood of death or severe disability. While many etiologic processes may lead to SBI, the most common and best-studied clinical paradigms are traumatic brain injury and anoxic-ischemic encephalopathy following cardiac arrest. Clinical phenotypes following SBI include acute and chronic disorders of consciousness as well as a range of cognitive and behavioral impairments. A fundamental task for medical teams working in the acute phase is to estimate SBI recovery probabilities with the highest degree of accuracy possible...
2017: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/28186879/fluid-dynamic-models-for-bhattacharyya-based-discriminant-analysis
#10
Yung-Kyun Noh, Jihun Hamm, Frank Park, Byoung-Tak Zhang, Daniel D Lee
Classical discriminant analysis attempts to discover a low-dimensional subspace where class label information is maximally preserved under projection. Canonical methods for estimating the subspace optimize an information-theoretic criterion that measures the separation between the class-conditional distributions. Unfortunately, direct optimization of the information-theoretic criteria is generally non-convex and intractable in high-dimensional spaces. In this work, we propose a novel, tractable algorithm for discriminant analysis that considers the class-conditional densities as interacting fluids in the high-dimensional embedding space...
February 8, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28186671/modeling-neurodevelopmental-and-psychiatric-diseases-with-human-ipscs
#11
REVIEW
Zhexing Wen
Neurodevelopmental and psychiatric disorders, including autism spectrum disorder and schizophrenia, are complex and heterogeneous disorders that affect a large portion of the world's population. While the causes are still poorly understood, currently available treatments are limited; the development of rational therapeutics based on an understanding of the etiology and pathogenesis of the disease is imperative. The breakthrough technology of deriving induced pluripotent stem cells (iPSCs), reprogrammed from somatic cells of healthy subjects or patients, offers an unprecedented opportunity to recapitulate both normal and pathological development of human tissue, thereby opening up a new avenue for disease modeling and drug development in a more genetically tractable and disease-relevant system...
February 10, 2017: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/28186211/controlling-the-network-type-in-self-assembled-dipeptide-hydrogels
#12
Catherine Colquhoun, Emily R Draper, Ralf Schweins, Marco Marcello, Devkee Vadukul, Louise C Serpell, Dave J Adams
We show that the same low molecular weight gelator can form gels using three different methods. Gels were formed from a high pH solution either by adding a salt or by adding an acid; gels were also formed by adding water to a solution of the gelator in an organic solvent. The mechanical properties for the gels formed by the different methods are different from one another. We link this to the network type that is formed, as well as the fibrous structures that are formed. The salt-triggered gels show a significant number of fibres that tend to align...
February 10, 2017: Soft Matter
https://www.readbyqxmd.com/read/28183973/solving-the-quantum-many-body-problem-with-artificial-neural-networks
#13
Giuseppe Carleo, Matthias Troyer
The challenge posed by the many-body problem in quantum physics originates from the difficulty of describing the nontrivial correlations encoded in the exponential complexity of the many-body wave function. Here we demonstrate that systematic machine learning of the wave function can reduce this complexity to a tractable computational form for some notable cases of physical interest. We introduce a variational representation of quantum states based on artificial neural networks with a variable number of hidden neurons...
February 10, 2017: Science
https://www.readbyqxmd.com/read/28178876/designing-fecal-microbiota-transplant-trials-that-account-for-differences-in-donor-stool-efficacy
#14
Scott W Olesen, Thomas Gurry, Eric J Alm
Fecal microbiota transplantation is a highly effective intervention for patients suffering from recurrent Clostridium difficile, a common hospital-acquired infection. Fecal microbiota transplantation's success as a therapy for C. difficile has inspired interest in performing clinical trials that experiment with fecal microbiota transplantation as a therapy for other conditions like inflammatory bowel disease, obesity, diabetes, and Parkinson's disease. Results from clinical trials that use fecal microbiota transplantation to treat inflammatory bowel disease suggest that, for at least one condition beyond C...
January 1, 2017: Statistical Methods in Medical Research
https://www.readbyqxmd.com/read/28174307/a-bioengineered-three-dimensional-cell-culture-platform-integrated-with-microfluidics-to-address-antimicrobial-resistance-in-tuberculosis
#15
Magdalena K Bielecka, Liku B Tezera, Robert Zmijan, Francis Drobniewski, Xunli Zhang, Suwan Jayasinghe, Paul Elkington
: Antimicrobial resistance presents one of the most significant threats to human health, with the emergence of totally drug-resistant organisms. We have combined bioengineering, genetically modified bacteria, longitudinal readouts, and fluidics to develop a transformative platform to address the drug development bottleneck, utilizing Mycobacterium tuberculosis as the model organism. We generated microspheres incorporating virulent reporter bacilli, primary human cells, and an extracellular matrix by using bioelectrospray methodology...
February 7, 2017: MBio
https://www.readbyqxmd.com/read/28171746/macrophage-functions-in-tissue-patterning-and-disease-new-insights-from-the-fly
#16
REVIEW
Will Wood, Paul Martin
Macrophages are multifunctional innate immune cells that seed all tissues within the body and play disparate roles throughout development and in adult tissues, both in health and disease. Their complex developmental origins and many of their functions are being deciphered in mammalian tissues, but opportunities for live imaging and the genetic tractability of Drosophila are offering complementary insights into how these fascinating cells integrate a multitude of guidance cues to fulfill their many tasks and migrate to distant sites to either direct developmental patterning or raise an inflammatory response...
February 6, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28167577/a-statistical-state-dynamics-approach-to-wall-turbulence
#17
REVIEW
B F Farrell, D F Gayme, P J Ioannou
This paper reviews results obtained using statistical state dynamics (SSD) that demonstrate the benefits of adopting this perspective for understanding turbulence in wall-bounded shear flows. The SSD approach used in this work employs a second-order closure that retains only the interaction between the streamwise mean flow and the streamwise mean perturbation covariance. This closure restricts nonlinearity in the SSD to that explicitly retained in the streamwise constant mean flow together with nonlinear interactions between the mean flow and the perturbation covariance...
March 13, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28163917/mitochondrial-mutations-and-metabolic-adaptation-in-pancreatic-cancer
#18
Rae-Anne Hardie, Ellen van Dam, Mark Cowley, Ting-Li Han, Seher Balaban, Marina Pajic, Mark Pinese, Mary Iconomou, Robert F Shearer, Jessie McKenna, David Miller, Nicola Waddell, John V Pearson, Sean M Grimmond, Leonid Sazanov, Andrew V Biankin, Silas Villas-Boas, Andrew J Hoy, Nigel Turner, Darren N Saunders
BACKGROUND: Pancreatic cancer has a five-year survival rate of ~8%, with characteristic molecular heterogeneity and restricted treatment options. Targeting metabolism has emerged as a potentially effective therapeutic strategy for cancers such as pancreatic cancer, which are driven by genetic alterations that are not tractable drug targets. Although somatic mitochondrial genome (mtDNA) mutations have been observed in various tumors types, understanding of metabolic genotype-phenotype relationships is limited...
2017: Cancer & Metabolism
https://www.readbyqxmd.com/read/28163785/efficient-estimation-of-the-maximum-metabolic-productivity-of-batch-systems
#19
Peter C St John, Michael F Crowley, Yannick J Bomble
BACKGROUND: Production of chemicals from engineered organisms in a batch culture involves an inherent trade-off between productivity, yield, and titer. Existing strategies for strain design typically focus on designing mutations that achieve the highest yield possible while maintaining growth viability. While these methods are computationally tractable, an optimum productivity could be achieved by a dynamic strategy in which the intracellular division of resources is permitted to change with time...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28163161/zebrafish-models-of-autism-spectrum-disorder
#20
REVIEW
Daria A Meshalkina, Marina N Kizlyk, Elana V Kysil, Adam D Collier, David J Echevarria, Murilo S Abreu, Leonardo J G Barcellos, Cai Song, Jason E Warnick, Evan J Kyzar, Allan V Kalueff
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder characterized by motor, social and cognitive deficits that develop early during childhood. The pathogenesis of ASD is not well characterized and involves a multifaceted interaction between genetic, neurobiological and environmental factors. Animal (experimental) models possess evolutionarily conserved behaviors and molecular pathways that are highly relevant for studying ASD. The zebrafish (Danio rerio) is a relatively new animal model with promise for understanding the pathogenesis of complex brain disorders and discovering novel treatments...
February 3, 2017: Experimental Neurology
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