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Directed Evolution

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https://www.readbyqxmd.com/read/28924302/robust-transport-over-networks
#1
Yongxin Chen, Tryphon Georgiou, Michele Pavon, Allen Tannenbaum
We consider transportation over a strongly connected, directed graph. The scheduling amounts to selecting transition probabilities for a discrete-time Markov evolution which is designed to be consistent with initial and final marginal constraints on mass transport. We address the situation where initially the mass is concentrated on certain nodes and needs to be transported in a certain time period to another set of nodes, possibly disjoint from the first. The random evolution is selected to be closest to a prior measure on paths in the relative entropy sense-such a construction is known as a Schrödinger bridge between the two given marginals...
September 2017: IEEE Transactions on Automatic Control
https://www.readbyqxmd.com/read/28923996/predicting-the-nature-of-supernova-progenitors
#2
REVIEW
Jose H Groh
Stars more massive than about 8 solar masses end their lives as a supernova (SN), an event of fundamental importance Universe-wide. The physical properties of massive stars before the SN event are very uncertain, both from theoretical and observational perspectives. In this article, I briefly review recent efforts to predict the nature of stars before death, in particular, by performing coupled stellar evolution and atmosphere modelling of single stars in the pre-SN stage. These models are able to predict the high-resolution spectrum and broadband photometry, which can then be directly compared with the observations of core-collapse SN progenitors...
October 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28923994/the-direct-identification-of-core-collapse-supernova-progenitors
#3
REVIEW
Schuyler D Van Dyk
To place core-collapse supernovae (SNe) in context with the evolution of massive stars, it is necessary to determine their stellar origins. I describe the direct identification of SN progenitors in existing pre-explosion images, particularly those obtained through serendipitous imaging of nearby galaxies by the Hubble Space Telescope I comment on specific cases representing the various core-collapse SN types. Establishing the astrometric coincidence of a SN with its putative progenitor is relatively straightforward...
October 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28923991/red-supergiants-as-supernova-progenitors
#4
REVIEW
Ben Davies
It is now well-established from pre-explosion imaging that red supergiants (RSGs) are the direct progenitors of Type-IIP supernovae. These images have been used to infer the physical properties of the exploding stars, yielding some surprising results. In particular, the differences between the observed and predicted mass spectrum has provided a challenge to our view of stellar evolutionary theory. However, turning what is typically a small number of pre-explosion photometric points into the physical quantities of stellar luminosity and mass requires a number of assumptions about the spectral appearance of RSGs, as well as their evolution in the last few years of life...
October 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28923156/functional-constructivism-in-search-of-formal-descriptors
#5
Irina Trofimova
The Functional Constructivism (FC) paradigm is an alternative to behaviorism and considers behavior as being generated every time anew, based on an individual's capacities, environmental resources and demands. Walter Freeman's work provided us with evidence supporting the FC principles. In this paper we make parallels between gradual construction processes leading to the formation of individual behavior and habits, and evolutionary processes leading to the establishment of biological systems. Referencing evolutionary theory, several formal descriptors of such processes are proposed...
October 2017: Nonlinear Dynamics, Psychology, and Life Sciences
https://www.readbyqxmd.com/read/28922601/substrate-dependence-of-the-freezing-dynamics-of-supercooled-water-films-a-high-speed-optical-microscope-study
#6
Elzbieta Pach, Laura Rodríguez, Albert Verdaguer
The freezing of supercooled water films on silicon-based surfaces was investigated using a high-speed camera coupled to an optical microscope. We were able to study in detail the two phases or stages in during water freezing; the first stage, faster, when dendritic grow occurs co-planar with the cold surface of the substrate and the second stage, slower, when the ice formed on the surface grows vertically until all the film is frozen. Several differentiated processes were identified during the freezing: two dimensional dendrite growing on the substrate interface, vertical dendrite growing, formation and evolution of ice domains, trapping of air bubbles in ice and freezing of the water film surface...
September 18, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28921660/rapid-whole-brain-gray-matter-imaging-using-single-slab-three-dimensional-dual-echo-fast-spin-echo-a-feasibility-study
#7
Hyunyeol Lee, Eung Yeop Kim, Chul-Ho Sohn, Jaeseok Park
PURPOSE: To achieve rapid, high resolution whole-brain gray matter (GM) imaging by developing a novel, single-slab three-dimensional dual-echo fast-spin-echo pulse sequence and GM-selective reconstruction. METHODS: Unlike conventional GM imaging that uses time-consuming double-inversion-recovery preparation, the proposed pulse sequence was designed to have two split portions along the echo train, in which the first half was dedicated to yield short inversion recovery (IR)-induced white matter suppression and variable-flip-angle-induced two-step GM signal evolution while the second half cerebrospinal fluid-only signals...
September 16, 2017: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
https://www.readbyqxmd.com/read/28921510/development-of-a-formaldehyde-biosensor-with-application-to-synthetic-methylotrophy
#8
Benjamin M Woolston, Timothy Roth, Ishwar Kohale, David Liu, Gregory Stephanopoulos
Formaldehyde is a prevalent environmental toxin and a key intermediate in single carbon metabolism. The ability to monitor formaldehyde concentration is therefore of interest for both environmental monitoring and for metabolic engineering of native and synthetic methylotrophs, but current methods suffer from low sensitivity, complex workflows, or require expensive analytical equipment. Here we develop a formaldehyde biosensor based on the FrmR repressor protein and cognate promoter of E. coli. Optimization of the native repressor binding site and regulatory architecture enabled detection at levels as low as 1 µM...
September 16, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28921508/selection-on-skewed-characters-and-the-paradox-of-stasis
#9
Suzanne Bonamour, Céline Teplitsky, Anne Charmantier, Pierre-André Crochet, Luis-Miguel Chevin
Observed phenotypic responses to selection in the wild often differ from predictions based on measurements of selection and genetic variance. An overlooked hypothesis to explain this paradox of stasis is that a skewed phenotypic distribution affects natural selection and evolution. We show through mathematical modelling that, when a trait selected for an optimum phenotype has a skewed distribution, directional selection is detected even at evolutionary equilibrium, where it causes no change in the mean phenotype...
September 18, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28921059/very-early-systemic-sclerosis-and-pre-systemic-sclerosis-definition-recognition-clinical-relevance-and-future-directions
#10
REVIEW
Silvia Bellando-Randone, Marco Matucci-Cerinic
PURPOSE OF REVIEW: The approach to systemic sclerosis (SSc) has changed over the years with an increasing focus on the very early diagnosis of the disease. The terminology identifying patients in the early phase of SSc has been significantly confusing in the last three decades. The purpose of this article is to analyze how the concept of "very early SSc" has evolved over the years, which is the role of an early diagnosis and how early treat patients. RECENT FINDINGS: Several attempts have been made over time, to create more sensitive and specific classification criteria to include the largest number of SSc patients, also in the earliest phase...
September 18, 2017: Current Rheumatology Reports
https://www.readbyqxmd.com/read/28920402/-preparation-and-transformation-optimization-for-supercompetent-b-subtilis-sck6-cells
#11
Xinzhi Li, Zhenghui Lu, Yuling Zhou, Shiyu Li, Guimin Zhang
Bacillus subtilis is Gram-positive aerobic bacterium and widely used as a heterologous protein expression host because of its safety and high protein secretion property. However, comparing to Escherichia coli, the low transformation efficiency limits the application of B. subtilis as a host cell for directed evolution of heterologous enzymes. Therefore, we optimized the competent cell preparation conditions for conventional plasmid, including the alteration of the medium, the concentration of inducer, the plasmid type, and other parameters...
April 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28919205/adaptive-evolution-leads-to-cross-species-incompatibility-in-the-pirna-transposon-silencing-machinery
#12
Swapnil S Parhad, Shikui Tu, Zhiping Weng, William E Theurkauf
Reproductive isolation defines species divergence and is linked to adaptive evolution of hybrid incompatibility genes. Hybrids between Drosophila melanogaster and Drosophila simulans are sterile, and phenocopy mutations in the PIWI interacting RNA (piRNA) pathway, which silences transposons and shows pervasive adaptive evolution, and Drosophila rhino and deadlock encode rapidly evolving components of a complex that binds to piRNA clusters. We show that Rhino and Deadlock interact and co-localize in simulans and melanogaster, but simulans Rhino does not bind melanogaster Deadlock, due to substitutions in the rapidly evolving Shadow domain...
September 9, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28918464/what-s-next-in-complex-networks-capturing-the-concept-of-attacking-play-in-invasive-team-sports
#13
REVIEW
João Ramos, Rui J Lopes, Duarte Araújo
The evolution of performance analysis within sports sciences is tied to technology development and practitioner demands. However, how individual and collective patterns self-organize and interact in invasive team sports remains elusive. Social network analysis has been recently proposed to resolve some aspects of this problem, and has proven successful in capturing collective features resulting from the interactions between team members as well as a powerful communication tool. Despite these advances, some fundamental team sports concepts such as an attacking play have not been properly captured by the more common applications of social network analysis to team sports performance...
September 16, 2017: Sports Medicine
https://www.readbyqxmd.com/read/28918073/a-directed-evolution-approach-to-select-for-novel-adeno-associated-virus-capsids-on-an-hiv-1-producer-t-cell-line
#14
Dawn P Wooley, Priyanka Sharma, John R Weinstein, Poornima Kotha Lakshmi Narayan, David V Schaffer, Katherine J D A Excoffon
A directed evolution approach was used to select for Adeno-associated virus (AAV) capsids that would exhibit more tropism toward an HIV-1 producer T cell line with the long-term goal of developing improved gene transfer vectors. A library of AAV variants was used to infect H9T cells previously infected or uninfected by HIV-1 followed by AAV amplification with wild-type adenovirus. Six rounds of biological selection were performed, including negative selection and diversification after round three. The H9T cells were successfully infected with all three wild-type viruses (AAV, adenovirus, and HIV-1)...
September 13, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28915920/current-situation-of-h9n2-subtype-avian-influenza-in-china
#15
REVIEW
Min Gu, Lijun Xu, Xiaoquan Wang, Xiufan Liu
In China, H9N2 subtype avian influenza outbreak is firstly reported in Guangdong province in 1992. Subsequently, the disease spreads into vast majority regions nationwide and has currently become endemic there. Over vicennial genetic evolution, the viral pathogenicity and transmissibility have showed an increasing trend as year goes by, posing serious threat to poultry industry. In addition, H9N2 has demonstrated significance to public health as it could not only directly infect mankind, but also donate partial or even whole cassette of internal genes to generate novel human-lethal reassortants like H5N1, H7N9, H10N8 and H5N6 viruses...
September 15, 2017: Veterinary Research
https://www.readbyqxmd.com/read/28915361/cultural-change-the-how-and-the-why
#16
Michael E W Varnum, Igor Grossmann
More than half a century of cross-cultural research has demonstrated group-level differences in psychological and behavioral phenomena, from values to attention to neural responses. However, cultures are not static, with several specific changes documented for cultural products, practices, and values. How and why do societies change? Here we juxtapose theory and insights from cultural evolution and social ecology. Evolutionary approaches enable an understanding of the how of cultural change, suggesting transmission mechanisms by which the contents of culture may change...
September 1, 2017: Perspectives on Psychological Science: a Journal of the Association for Psychological Science
https://www.readbyqxmd.com/read/28914897/dual-frequency-doppler-lidar-for-wind-detection-with-a-superconducting-nanowire-single-photon-detector
#17
Mingjia Shangguan, Haiyun Xia, Chong Wang, Jiawei Qiu, Shengfu Lin, Xiankang Dou, Qiang Zhang, Jian-Wei Pan
A dual-frequency direct detection Doppler lidar is demonstrated using a superconducting nanowire single-photon detector (SNSPD) at 1.5 μm. The so-called double-edge technique is implemented by using a dual-frequency laser pulse, rather than using a double-channel Fabry-Perot interferometer. Such a modification to the reported lidars enhances the frequency stability in the system level. Using the time-division multiplexing method, only one piece of SNSPD is used in the optical receiver, making the system simplified and robust...
September 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28914463/burrowing-with-a-kinetic-snout-in-a-snake-elapidae-aspidelaps-scutatus
#18
Alexandra Deufel
Of the few elongate, fossorial vertebrates that have been examined for their burrowing mechanics, all were found to use an akinetic, reinforced skull to push into the soil, powered mostly by trunk muscles. Reinforced skulls were considered essential for head-first burrowing. In contrast, I found that the skull of the fossorial shield-nosed cobra (Aspidelaps scutatus) is not reinforced and retains the kinetic potential typical of many non-fossorial snakes. Aspidelaps scutatus burrows using a greatly enlarged rostral scale that is attached to a kinetic snout that is independently mobile with respect to the rest of the skull...
September 15, 2017: Journal of Morphology
https://www.readbyqxmd.com/read/28914093/problematizing-men-s-suicide-mental-health-and-well-being
#19
Philippe Roy, Gilles Tremblay, Émilie Duplessis-Brochu
BACKGROUND: The Province of Quebec, Canada (PQ), witnessed a drastic rise in suicide among adult men between 1990 and 2000, followed by a continuous drop since then. At the end of the 1990s, men's suicide became recognized as a social issue, leading to implementation of gender-responsive strategies focusing on positive aspects of masculinity. Many of these strategies received positive assessments. AIMS: This article offers a critical overview of the evolution of social responses to men's suicide in PQ...
September 15, 2017: Crisis
https://www.readbyqxmd.com/read/28913932/hox-d-genes-and-the-fin-to-limb-transition-insights-from-fish-studies
#20
REVIEW
Ana Paço, Renata Freitas
Genes in the 5' extremity of the HoxD cluster encode DNA-binding transcription factors essential for development of the autopod and digits, regulating primarily gene expression and, consequently, morphogenesis and skeletal differentiation. Comparative studies focused on their expression and regulation have led to the idea that evolution of a bimodal regulation of the HoxD cluster, mainly due to the activation of cis-regulatory units in the centromeric side of the cluster, was a fundamental mechanism that potentiated the fin-to-limb transition in vertebrates...
September 14, 2017: Genesis: the Journal of Genetics and Development
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