697 research outputs found
Heteropolymer Sequence Design and Preferential Solvation of Hydrophilic Monomers: One More Application of Random Energy Model
In this paper, we study the role of surface of the globule and the role of
interactions with the solvent for designed sequence heteropolymers using random
energy model (REM). We investigate the ground state energy and surface monomer
composition distribution. By comparing the freezing transition in random and
designed sequence heteropolymers, we discuss the effects of design. Based on
our results, we are able to show under which conditions solvation effect
improves the quality of sequence design. Finally, we study sequence space
entropy and discuss the number of available sequences as a function of imposed
requirements for the design quality
RED-PSM: Regularization by Denoising of Partially Separable Models for Dynamic Imaging
Dynamic imaging addresses the recovery of a time-varying 2D or 3D object at
each time instant using its undersampled measurements. In particular, in the
case of dynamic tomography, only a single projection at a single view angle may
be available at a time, making the problem severely ill-posed. In this work, we
propose an approach, RED-PSM, which combines for the first time two powerful
techniques to address this challenging imaging problem. The first, are
partially separable models, which have been used to efficiently introduce a
low-rank prior for the spatio-temporal object. The second is the recent
Regularization by Denoising (RED), which provides a flexible framework to
exploit the impressive performance of state-of-the-art image denoising
algorithms, for various inverse problems. We propose a partially separable
objective with RED and a computationally efficient and scalable optimization
scheme with variable splitting and ADMM. Theoretical analysis proves the
convergence of our objective to a value corresponding to a stationary point
satisfying the first-order optimality conditions. Convergence is accelerated by
a particular projection-domain-based initialization. We demonstrate the
performance and computational improvements of our proposed RED-PSM with a
learned image denoiser by comparing it to a recent deep-prior-based method
known as TD-DIP. Although the main focus is on dynamic tomography, we also show
the performance advantages of RED-PSM in a cardiac dynamic MRI setting
Two-photon spin injection in semiconductors
A comparison is made between the degree of spin polarization of electrons
excited by one- and two-photon absorption of circularly polarized light in bulk
zincblende semiconductors. Time- and polarization-resolved experiments in
(001)-oriented GaAs reveal an initial degree of spin polarization of 49% for
both one- and two-photon spin injection at wavelengths of 775 and 1550 nm, in
agreement with theory. The macroscopic symmetry and microscopic theory for
two-photon spin injection are reviewed, and the latter is generalized to
account for spin-splitting of the bands. The degree of spin polarization of
one- and two-photon optical orientation need not be equal, as shown by
calculations of spectra for GaAs, InP, GaSb, InSb, and ZnSe using a 14x14 k.p
Hamiltonian including remote band effects. By including the higher conduction
bands in the calculation, cubic anisotropy and the role of allowed-allowed
transitions can be investigated. The allowed-allowed transitions do not
conserve angular momentum and can cause a high degree of spin polarization
close to the band edge; a value of 78% is calculated in GaSb, but by varying
the material parameters it could be as high as 100%. The selection rules for
spin injection from allowed-allowed transitions are presented, and interband
spin-orbit coupling is found to play an important role.Comment: 12 pages including 7 figure
Визначення кількості рослинних антиоксидантів для захисту гірких хмелевих речовин від окисної деструкції
Досліджено кінетику окиснення гірких речовин водного розчину екстракту хмелю у прискорених умовах з різною концентрацією антиоксидантів із рослинної сировини. Визначено ефективну концентрацію антиоксидантів із кори дубу, трави звіробою та трави м'яти.Kinetics of bitter matters in aquatic solution of hope extract in speed-up terms with different concentration of antioxidants from the digister are investigated. Certainly effective concentration of antioxidants from the bark oak, st-john's-wort herbares and mint herbares are determinated
Safe and complete contig assembly via omnitigs
Contig assembly is the first stage that most assemblers solve when
reconstructing a genome from a set of reads. Its output consists of contigs --
a set of strings that are promised to appear in any genome that could have
generated the reads. From the introduction of contigs 20 years ago, assemblers
have tried to obtain longer and longer contigs, but the following question was
never solved: given a genome graph (e.g. a de Bruijn, or a string graph),
what are all the strings that can be safely reported from as contigs? In
this paper we finally answer this question, and also give a polynomial time
algorithm to find them. Our experiments show that these strings, which we call
omnitigs, are 66% to 82% longer on average than the popular unitigs, and 29% of
dbSNP locations have more neighbors in omnitigs than in unitigs.Comment: Full version of the paper in the proceedings of RECOMB 201
Improving teaching: Enhancing ways of being university teachers
My aim in this paper is to theorize my teaching in a course for experienced university teachers, in a context of increased attention to such courses. My focus in the course is transforming and enhancing ways of being university teachers, through integrating knowing, acting and being. In other words, epistemology is not seen as an end in itself, but rather it is in the service of ontology. In the paper, I explore and illustrate how this focus on ontology is enacted in the course
A New Framework for Music Education Knowledge and Skill
This study investigates perceptions of secondary school band and orchestra teachers regarding the relative importance of knowledge and skill categories to professional success, using a framework modeled after Schulman (1986, 1987). Band and orchestra teachers in secondary schools (N = 214) complete an anonymous, online survey ranking the relative importance of various knowledge and skill categories. Participants rank pedagogical content knowledge, content knowledge, and general pedagogical knowledge highest. There are no significant differences in the rankings of the categories among various subgroups at the p < .05 level. Results confirm the applicability of Schulman's model to music education. This framework has implications for undergraduate, graduate, and continuing professional education. Analysis of categories' interaction provides insight into effective classroom instruction.Yeshttps://us.sagepub.com/en-us/nam/manuscript-submission-guideline
Tissue underlying the intestinal epithelium elicits proliferation of intestinal stem cells following cytotoxic damage
The goals of this study were to document the proliferative response of intestinal stem cells (ISCs) during regeneration after damage from doxorubicin (DXR) and to characterize the signals responsible for ISC activation. To this end, jejuni from DXR-treated mice were harvested for histology, assessment of ISC numbers and proliferation by flow cytometry, crypt culture, and RNA analyses. Histology showed that crypt depth and width were increased 4 days after DXR. At this time point, flow cytometry on tissue collected 1 hour after EdU administration revealed increased numbers of CD24loUEA− ISCs and increased percentage of ISCs cycling. In culture, crypts harvested from DXR-treated mice were equally proliferative as those of control mice. Addition of subepithelial intestinal tissue (SET) collected 4 days after DXR elicited increased budding (1.4 ± 0.3 vs. 5.1 ± 1.0 buds per enteroid). Microarray analysis of SET collected 4 days after DXR revealed 1,030 differentially expressed transcripts. Cross comparison of Gene Ontology terms considered relevant to ISC activation pointed to 10 candidate genes. Of these the epidermal growth factor (EGF) family member amphiregulin and the BMP antagonist chordin-like 2 were chosen for further study. In crypt culture, amphiregulin alone did not elicit significant budding, but amphiregulin in combination with BMP antagonism showed marked synergism (yielding 6.3 ± 0.5 buds per enteroid). These data suggest a critical role for underlying tissue in regulating ISC behavior after damage, and point to synergism between amphiregulin and chordin-like 2 as factors which may account for activation of ISCs in the regenerative phase
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