Hasil untuk "q-bio.BM"

S. J. Beck

Jin-Can Liu, Li-Ya Tang, Xiao-Ying Sun et al.

Purpose The aim of this study was to explore whether electroacupuncture regulates phenotypic transformation of smooth muscle cells by inhibiting ferroptosis and inhibiting fibrosis, thereby improving bladder urination function after suprasacral spinal cord injury (SSCI). Methods The experiment was divided into sham, model, and electroacupuncture group. After 10 days of electroacupuncture intervention, urodynamic examination was performed, and bladder neck was taken for HE staining, tandem mass tag (TMT)-based quantitative proteomics analysis, Western blot(WB) detection, ferrous ion concentration detection and Masson staining. Conclusion Electroacupuncture may prevent the phenotype of bladder neck smooth muscle cells from transforming from contraction type to synthesis type by inhibiting ferroptosis, inhibit bladder neck fibrosis, improve bladder neck compliance, and thus improve bladder urination function after SSCI.

G. Andrews

Alex Morehead, Jeffrey Ruffolo, Aadyot Bhatnagar et al.

Generative models of macromolecules carry abundant and impactful implications for industrial and biomedical efforts in protein engineering. However, existing methods are currently limited to modeling protein structures or sequences, independently or jointly, without regard to the interactions that commonly occur between proteins and other macromolecules. In this work, we introduce MMDiff, a generative model that jointly designs sequences and structures of nucleic acid and protein complexes, independently or in complex, using joint SE(3)-discrete diffusion noise. Such a model has important implications for emerging areas of macromolecular design including structure-based transcription factor design and design of noncoding RNA sequences. We demonstrate the utility of MMDiff through a rigorous new design benchmark for macromolecular complex generation that we introduce in this work. Our results demonstrate that MMDiff is able to successfully generate micro-RNA and single-stranded DNA molecules while being modestly capable of joint modeling DNA and RNA molecules in interaction with multi-chain protein complexes. Source code: https://github.com/Profluent-Internships/MMDiff.

Steven B. Perfect, Kenneth W. Wiles

Yang Zhang, Gengmo Zhou, Zhewei Wei et al.

The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of molecules and the local interactions while ignoring the multi-level inter-molecular interactions between proteins and ligands, which often lead to sub-optimal performance. To solve this issue, we propose a novel global-local interaction (GLI) framework to predict protein-ligand binding affinity. In particular, our GLI framework considers the inter-molecular interactions between proteins and ligands, which involve not only the high-energy short-range interactions between closed atoms but also the low-energy long-range interactions between non-bonded atoms. For each pair of protein and ligand, our GLI embeds the long-range interactions globally and aggregates local short-range interactions, respectively. Such a joint global-local interaction modeling strategy helps to improve prediction accuracy, and the whole framework is compatible with various neural network-based modules. Experiments demonstrate that our GLI framework outperforms state-of-the-art methods with simple neural network architectures and moderate computational costs.

M. Gorodetsky, V. Ilchenko

A general model is presented for coupling of high-Q whispering-gallery modes in optical microsphere resonators with coupler devices that possess a discrete and continuous spectrum of propagating modes. By contrast to conventional high-Q optical cavities, in microspheres the independence of high intrinsic quality-factor and controllable parameters of coupling via an evanescent field offer a variety of regimes similar to those that are already available in rf devices. The theory is applied to data reported earlier on different types of couplers to microsphere resonators and is complemented by the experimental demonstration of enhanced coupling efficiency (∼80%) and variable loading regimes with Q>108 fused-silica microspheres.

R. Dearden, N. Friedman, Stuart J. Russell

Prabha Sankara Narayanan, Ashish Runthala

Enzyme is the major workhorse to carry out the diverse cellular functions. It catalyzes the biological reactions with a high specificity, with its topology playing a crucial role. For ecologically safe production of numerous bioproducts including drugs and chemicals, we have been striving to design the industrially useful enzyme molecules with highly improved catalytic capability. As the sequence space is enormous for an enzyme, its quick and effective exploration is quite improbable for the mutagenesis studies whose accuracy is greatly reliant on the prior information of the mutated sites and the extent of rigorous screening of the mutant libraries. Although directed evolution methods significantly aid the construction of a functionally improved molecule, their credibility depends on the successful excavation of the functionally similar sequence space in the available databases, encompassing billions of proteins. As deep learning methods aid us to extensively uncover the underlying network of all the key catalytic positions without any experimental data, their implementation has reliably increased the accuracy of directed evolution. The chapter comprehensively explains data mining and deep learning methods to further showcase their importance in enzyme engineering methods. The key biological and algorithmic limitations of these deep learning methodologies are lastly highlighted.

E. Kuramochi, M. Notomi, S. Mitsugi et al.

M. Borselli, T. Johnson, O. Painter

Using a combination of resist reflow to form a highly circular etch mask pattern and a low-damage plasma dry etch, high-quality-factor silicon optical microdisk resonators are fabricated out of silicon-on-insulator (SOI) wafers. Quality factors as high as Q = 5x10(6) are measured in these microresonators, corresponding to a propagation loss coefficient as small as alpha ~ 0.1 dB/cm. The different optical loss mechanisms are identified through a study of the total optical loss, mode coupling, and thermally-induced optical bistability as a function of microdisk radius (5-30 microm). These measurements indicate that optical loss in these high-Q microresonators is limited not by surface roughness, but rather by surface state absorption and bulk free-carrier absorption.

M. Valkama, M. Renfors, V. Koivunen

A. Klassen, S. Cano, A. Scott et al.

A. Greenwald, Keith B. Hall

F. Bannon, J.R. Clark, C. Nguyen

A. Sirunyan, A. Tumasyan, W. Adam et al.

A bstractA search is presented for a heavy resonance decaying into either a pair of Z bosons or a Z boson and a W boson (ZZ or WZ), with a Z boson decaying into a pair of neutrinos and the other boson decaying hadronically into two collimated quarks that are reconstructed as a highly energetic large-cone jet. The search is performed using the data collected with the CMS detector at the CERN LHC during 2016 in proton-proton collisions at a center-of-mass energy of 13 TeV, corresponding to a total integrated luminosity of 35.9 fb−1. No excess is observed in data with regard to background expectations. Results are interpreted in scenarios of physics beyond the standard model. Limits at 95% confidence level on production cross sections are set at 0.9 fb (63 fb) for spin-1 W′ bosons, included in the heavy vector triplet model, with mass 4.0 TeV (1.0 TeV), and at 0.5 fb (40 fb) for spin-2 bulk gravitons with mass 4.0 TeV (1.0 TeV). Lower limits are set on the masses of W′ bosons in the context of two versions of the heavy vector triplet model of 3.1TeV and 3.4 TeV, respectively.

P. N. Sadjang

F. Dolan, H. Osborn, Institiúid Ard-Léinn Bhailé et al.

Abstract The results of Romelsberger for an N = 1 superconformal index counting protected operators, satisfying a BPS condition and which cannot be combined to form long multiplets, are analysed further. The index is expressible in terms of single particle superconformal characters for N = 1 scalar and vector multiplets. For SQCD, involving SU ( N c ) gauge groups and appropriate numbers of flavours N f , the formula used to construct the index may be proved to give identical results for theories linked by Seiberg duality using recently proved theorems for q -series elliptic hypergeometric integrals. The discussion is also extended to Kutasov–Schwimmer dual theories in the large N c , N f limit and to dual theories with Sp ( N ) and SO ( N ) gauge groups. For the former, a transformation identity for elliptic hypergeometric integrals directly verifies that the index is the same for the electric and magnetic theory. For SO ( N ) theories the corresponding result may also be obtained from the same basic identity. An expansion of the index to several orders is also obtained in a form where the detailed protected operator content may be read off. Relevant mathematical results are reviewed.

M. Georgiev, A. Afonso, H. Neubauer et al.

Q fever is a disease of humans, caused by Coxiella burnetii, and a large range of animals can be infected. This paper presents a review of the epidemiology of Q fever in humans and farm animals between 1982 and 2010, using case studies from four European countries (Bulgaria, France, Germany and the Netherlands). The Netherlands had a large outbreak between 2007 and 2010, and the other countries a history of Q fever and Q fever research. Within all four countries, the serological prevalence of C. burnetii infection and reported incidence of Q fever varies broadly in both farm animals and humans. Proximity to farm animals and contact with infected animals or their birth products have been identified as the most important risk factors for human disease. Intrinsic farm factors, such as production systems and management, influence the number of outbreaks in an area. A number of disease control options have been used in these four countries, including measures to increase diagnostic accuracy and general awareness, and actions to reduce spillover (of infection from farm animals to humans) and human exposure. This study highlights gaps in knowledge, and future research needs.

P. N. Sadjang

In this paper, the $(p,q)$-derivative and the $(p,q)$-integration are investigated. Two suitable polynomials bases for the $(p,q)$-derivative are provided and various properties of these bases are given. As application, two $(p,q)$-Taylor formulas for polynomials are given, the fundamental theorem of $(p,q)$-calculus is included and the formula of $(p,q)$-integration by part is proved.