Solving the riddle of codon usage preferences: a test for translational selection

Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model

Growth of donor-derived dendritic cells from the bone marrow of murine liver auograft recipients in response to granulocyte/macrophage colony-stimulating factor

Allografts of the liver, which has a comparatively heavy leukocyte content compared with other vascularized organs, are accepted permanently across major histocompatibility complex barriers in many murine strain combinations without immunosuppressive therapy. It has been postulated that this inherent tolerogenicity of the liver may be a consequence of the migration and perpetuation within host lymphoid tissues of potentially tolerogenic donor-derived ("chimeric") leukocytes, in particular, the precursors of chimeric dendritic cells (DC). In this study, we have used granulocyte/macrophage colony-stimulating factor to induce the propagation of progenitors that give rise to DC (CD45+, CDllc+, 33D1+, nonlymphoid dendritic cell 145 +, major histocompatibility complex class II+, B7-1+) in li-tuid cultures of murine bone marrow cells. Using this technique, together with immunocytochemical and molecular methods, we show that, in addition to cells expressing female host (C3H) phenotype (H-2Kk+; I-E+; Y chromosome-), a minor population of male donor (B10)-derived cells (H-2Kb+; I-A+; Y chromosome+) can also be grown in 10-d DC cultures from the bone marrow of liver allograft recipients 14 d after transplant. Highly purified nonlymphoid dendritic cell 145+ DC sorted from these bone marrow-derived cell cultures were shown to comprise ~1-10% cells of donor origin (Y chromosome +) by polymerase chain reaction analysis. In addition, sorted DC stimulated naive, recipient strain T lymphocytes in primary mixed leukocyte cultures. Evidence was also obtained for the growth of donor-derived cells from the spleen but not the thymus. In contrast, donor ceils could not be propagated from the bone marrow or other lymphoid tissues of nonimmunosuppressed C3H mice rejecting cardiac allografrs from the same donor strain (B10). These findings provide a basis for the establishment and perpetuation of cell chimerism after organ transplantation. © 1995, Rockefeller University Press., All rights reserved

Inert gas clearance from tissue by co-currently and counter-currently arranged microvessels

To elucidate the clearance of dissolved inert gas from tissues, we have developed numerical models of gas transport in a cylindrical block of tissue supplied by one or two capillaries. With two capillaries, attention is given to the effects of co-current and counter-current flow on tissue gas clearance. Clearance by counter-current flow is compared with clearance by a single capillary or by two co-currently arranged capillaries. Effects of the blood velocity, solubility, and diffusivity of the gas in the tissue are investigated using parameters with physiological values. It is found that under the conditions investigated, almost identical clearances are achieved by a single capillary as by a co-current pair when the total flow per tissue volume in each unit is the same (i.e., flow velocity in the single capillary is twice that in each co-current vessel). For both co-current and counter-current arrangements, approximate linear relations exist between the tissue gas clearance rate and tissue blood perfusion rate. However, the counter-current arrangement of capillaries results in less-efficient clearance of the inert gas from tissues. Furthermore, this difference in efficiency increases at higher blood flow rates. At a given blood flow, the simple conduction-capacitance model, which has been used to estimate tissue blood perfusion rate from inert gas clearance, underestimates gas clearance rates predicted by the numerical models for single vessel or for two vessels with co-current flow. This difference is accounted for in discussion, which also considers the choice of parameters and possible effects of microvascular architecture on the interpretation of tissue inert gas clearance

Challenging Official Propaganda? Public Opinion Leaders on Sina Weibo.

This article examines the prominence of various user categories as opinion leaders, defined as initiators, agenda setters or disseminators, in 29 corruption cases exposed on SinaWeibo. It finds that ordinary citizens made up the largest category of initiators but that their power of opinion leadership was limited as they had to rely on media organizations to spread news about the cases. News organizations and online media were the main opinion leaders. Government and Party bodies initiated a fair number of cases and, despite not being strong agenda setters or disseminators, were able to dominate public opinion owing to the fact that news organizations and online media mainly published official announcements about the cases. Media organizations also played a secondary role as the voice of the people. While individuals from some other user categories were able to become prominent opinion leaders, news workers are likely to be the most promising user category to challenge official propaganda.Faculty Research Support Scheme of the Faculty of Arts and Social Sciences, the University of Sydney. University of Hong Kong Seed Funding Program for Basic Research and the General Research Fund, Research Grants Council, Hong Kong (Project Code: 17402314)

Valence-bond charge-transfer solvation model for nonlinear optical properties of organic molecules in polar solvents

A simple model is developed for predicting solvation effects on the nonlinear optical properties of charge transfer organic materials such as 1,1 dicyano,6-(di-butyl amine) hexatriene. This model is based on the valence-bond charge-transfer (VB-CT) framework, using a continuum description of the solvent. The resulting VB-CT solvation model leads to analytic formulas for the absorption frequency (Eg), the polarizability (α), the hyperpolarizabilities (β,γ,δ), and the bond length alternation with only one solvent dependent parameter (ε, the dielectric constant of the solution). The theory involves just four solvent-independent parameters, V0, t, SF, and Q which are related to the band gap, bandwidth, geometry, and dipole moment of the CT molecule [plus a length (R DA) and force constant (k) derivable from standard force fields]. The results are in good agreement with experiment. © 1994 American Institute of Physics.published_or_final_versio

The valence-bond charge-transfer-exciton model for predicting nonlinear optical properties (hyperpolarizabililies and saturation length) of polymeric materials

A simple theory is developed and applied to the polarizability (α), second hyperpolarizability (γ), and the saturation lengths for nine polymeric materials. The theory is based on a valence bond view of the ground and excited states and considers the excited states as charge transfer excitons. It involves just two parameters which can be extracted from simple molecular orbital calculations and/or from experimental values of band gap and bandwidth. For the one system (oligothiophenes) with experimental data on saturation length, the predicted behavior of α and γ with polymer length is in good agreement with experiment. © 1994 American Institute of Physics.published_or_final_versio

The valence-bond charge-transfer-exciton model for predicting nonlinear optical properties (hyperpolarizabililies and saturation length) of polymeric materials

A simple theory is developed and applied to the polarizability (α), second hyperpolarizability (γ), and the saturation lengths for nine polymeric materials. The theory is based on a valence bond view of the ground and excited states and considers the excited states as charge transfer excitons. It involves just two parameters which can be extracted from simple molecular orbital calculations and/or from experimental values of band gap and bandwidth. For the one system (oligothiophenes) with experimental data on saturation length, the predicted behavior of α and γ with polymer length is in good agreement with experiment. © 1994 American Institute of Physics.published_or_final_versio

An Incremental Unified Framework for Small Defect Inspection

Artificial Intelligence (AI)-driven defect inspection is pivotal in industrial manufacturing. Yet, many methods, tailored to specific pipelines, grapple with diverse product portfolios and evolving processes. Addressing this, we present the Incremental Unified Framework (IUF), which can reduce the feature conflict problem when continuously integrating new objects in the pipeline, making it advantageous in object-incremental learning scenarios. Employing a state-of-the-art transformer, we introduce Object-Aware Self-Attention (OASA) to delineate distinct semantic boundaries. Semantic Compression Loss (SCL) is integrated to optimize non-primary semantic space, enhancing network adaptability for novel objects. Additionally, we prioritize retaining the features of established objects during weight updates. Demonstrating prowess in both image and pixel-level defect inspection, our approach achieves state-of-the-art performance, proving indispensable for dynamic and scalable industrial inspections. Our code will be released at \url{https://github.com/jqtangust/IUF}

Exploring 4D Quantum Hall Physics with a 2D Topological Charge Pump

The discovery of topological states of matter has profoundly augmented our understanding of phase transitions in physical systems. Instead of local order parameters, topological phases are described by global topological invariants and are therefore robust against perturbations. A prominent example thereof is the two-dimensional integer quantum Hall effect. It is characterized by the first Chern number which manifests in the quantized Hall response induced by an external electric field. Generalizing the quantum Hall effect to four-dimensional systems leads to the appearance of a novel non-linear Hall response that is quantized as well, but described by a 4D topological invariant - the second Chern number. Here, we report on the first observation of a bulk response with intrinsic 4D topology and the measurement of the associated second Chern number. By implementing a 2D topological charge pump with ultracold bosonic atoms in an angled optical superlattice, we realize a dynamical version of the 4D integer quantum Hall effect. Using a small atom cloud as a local probe, we fully characterize the non-linear response of the system by in-situ imaging and site-resolved band mapping. Our findings pave the way to experimentally probe higher-dimensional quantum Hall systems, where new topological phases with exotic excitations are predicted