Hasil untuk "q-bio.SC"

Ziyue Zheng, Loay J. Jabre, Matthew McIlvin et al.

Intracellular compartmentalization of proteins underpins their function and the metabolic processes they sustain. Various mass spectrometry-based proteomics methods (subcellular spatial proteomics) now allow high throughput subcellular protein localization. Yet, the curation, analysis and interpretation of these data remain challenging, particularly in non-model organisms where establishing reliable marker proteins is difficult, and in contexts where experimental replication and subcellular fractionation are constrained. Here, we develop FSPmix, a semi-supervised functional clustering method implemented as an open-source R package, which leverages partial annotations from a subset of marker proteins to predict protein subcellular localization from subcellular spatial proteomics data. This method explicitly assumes that protein signatures vary smoothly across subcellular fractions, enabling more robust inference under low signal-to-noise data regimes. We applied FSPmix to a subcellular proteomics dataset from a marine diatom, allowing us to assign probabilistic localizations to proteins and uncover potentially new protein functions. Altogether, this work lays the foundation for more robust statistical analysis and interpretation of subcellular proteomics datasets, particularly in understudied organisms.

S. J. Beck

Chuang Li, Yichen Wei, Chao Qin et al.

The strategic induction of cell death serves as a crucial immune defense mechanism for the eradication of pathogenic infections within host cells. Investigating the molecular mechanisms underlying immunogenic cell pathways has significantly enhanced our understanding of the host's immunity. This review provides a comprehensive overview of the immunogenic cell death mechanisms triggered by pathogen infections, focusing on the critical role of pattern recognition receptors. In response to infections, host cells dictate a variety of cell death pathways, including apoptosis, pyroptosis, necrosis, and lysosomal cell death, which are essential for amplifying immune responses and controlling pathogen dissemination. Key components of these mechanisms are host cellular receptors that recognize pathogen-associated ligands. These receptors activate downstream signaling cascades, leading to the expression of immunoregulatory genes and the production of antimicrobial cytokines and chemokines. Particularly, the inflammasome, a multi-protein complex, plays a pivotal role in these responses by processing pro-inflammatory cytokines and inducing pyroptotic cell death. Pathogens, in turn, have evolved strategies to manipulate these cell death pathways, either by inhibiting them to facilitate their replication or by triggering them to evade host defenses. This dynamic interplay between host immune mechanisms and pathogen strategies highlights the intricate co-evolution of microbial virulence and host immunity.

J. Bai, Y. Ban, J. Bian et al.

D. Raoult, H. Tissot-Dupont, C. Foucault et al.

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

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. Greenwald, Keith B. Hall

W. Cao, Ranjan Singh, I. Al-Naib et al.

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

Y. Akahane, T. Asano, B. Song et al.

A photonic nanocavity with a high Q factor of 100,000 and a modal volume V of 0.71 cubic wavelengths, is demonstrated. According to the cavity design rule that we discovered recently, we further improve a point-defect cavity in a two-dimensional (2D) photonic crystal (PC) slab, where the arrangement of six air holes near the cavity edges is fine-tuned. We demonstrate that the measured Q factor for the designed cavity increases by a factor of 20 relative to that for a cavity without displaced air holes, while the calculated modal volume remains almost constant.

P. N. Sadjang

Kristine H. Luce, J. Crowther, Michele Pole

J. Rhodes, B. Steinberg

K. Chung

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.

Eyal Bar-Shalom, Alexander Ovseevich, Michael Margaliot

We introduce and analyze two general dynamical models for unidirectional movement of particles along a circular chain and an open chain of sites. The models include a soft version of the simple exclusion principle, that is, as the density in a site increases the effective entry rate into this site decreases. This allows to model and study the evolution of "traffic jams" of particles along the chain. A unique feature of these two new models is that each site along the chain can have a different size. Although the models are nonlinear, they are amenable to rigorous asymptotic analysis. In particular, we show that the dynamics always converges to a steady-state, and that the steady-state densities along the chain and the steady-state output flow rate from the chain can be derived from the spectral properties of a suitable matrix, thus eliminating the need to numerically simulate the dynamics until convergence. This spectral representation also allows for powerful sensitivity analysis, i.e. understanding how a change in one of the parameters in the models affects the steady-state. We show that the site sizes and the transition rates from site to site play different roles in the dynamics, and that for the purpose of maximizing the steady-state output (or production) rate the site sizes are more important than the transition rates. We also show that the problem of finding parameter values that maximize the production rate is tractable. We believe that the models introduced here can be applied to study various natural and artificial processes including ribosome flow during mRNA translation, the movement of molecular motors along filaments of the cytoskeleton, pedestrian and vehicular traffic, evacuation dynamics, and more.