On the Time Variation of Dust Extinction and Gas Absorption for Type Ia Supernovae Observed through a Nonuniform Interstellar Medium

For Type Ia supernovae (SNe Ia) observed through a nonuniform interstellar medium (ISM) in its host galaxy, we investigate whether the nonuniformity can cause observable time variations in dust extinction and in gas absorption due to the expansion of the SN photosphere with time. We show that, owing to the steep spectral index of the ISM density power spectrum, sizable density fluctuation amplitudes at the length scale of typical ISM structures () will translate to much smaller fluctuations on the scales of an SN photosphere. Therefore, the typical amplitude of time variation due to a nonuniform ISM, of absorption equivalent widths, and of extinction, would be small. As a result, we conclude that nonuniform ISM density should not impact cosmology measurements based on SNe Ia. We apply our predictions based on the ISM density power-law power spectrum to the observations of two highly reddened SNe Ia, SN 2012cu and SN 2014J

Supersymmetry on AdS3 and AdS4

We consider a supersymmetric extension of the algebra associated with three and four dimensional Anti de Sitter space. A representation of the supersymmetry operators in superspace is given. Supersymmetry invariant models are constructed for the superspace associated with AdS3.Comment: 14 pages, no figures. Final published version. Now includes a discussion of the relation of our approach to previous work on supersymmetry in AdS space

LRX Proteins play a crucial role in pollen grain and pollen tube cell wall development

Leucine-rich repeat extensins (LRXs) are chimeric proteins containing an N-terminal leucine-rich repeat (LRR) and a C-terminal extensin domain. LRXs are involved in cell wall formation in vegetative tissues and required for plant growth. However, the nature of their role in these cellular processes remains to be elucidated. Here, we used a combination of molecular techniques, light microscopy, and transmission electron microscopy to characterize mutants of pollen-expressed LRXs in Arabidopsis thaliana. Mutations in multiple pollen-expressed lrx genes causes severe defects in pollen germination and pollen tube (PT) growth, resulting in a reduced seed set. Physiological experiments demonstrate that manipulating Ca2+ availability partially suppresses the PT growth defects, suggesting that LRX proteins influence Ca2+-related processes. Furthermore, we show that LRX protein localizes to the cell wall, and its LRR-domain (which likely mediates protein-protein interactions) is associated with the plasma membrane. Mechanical analyses by cellular force microscopy and finite element method-based modelling revealed significant changes in the material properties of the cell wall and the fine-tuning of cellular biophysical parameters in the mutants compared to the wild type. The results indicate that LRX proteins might play a role in cell wall-plasma membrane communication, influencing cell wall formation and cellular mechanics

ESD Reviews: Model dependence in multi-model climate ensembles: weighting, sub-selection and out-of-sample testing

The rationale for using multi-model ensembles in climate change projections and impacts research is often based on the expectation that different models constitute independent estimates; therefore, a range of models allows a better characterisation of the uncertainties in the representation of the climate system than a single model. However, it is known that research groups share literature, ideas for representations of processes, parameterisations, evaluation data sets and even sections of model code. Thus, nominally different models might have similar biases because of similarities in the way they represent a subset of processes, or even be near-duplicates of others, weakening the assumption that they constitute independent estimates. If there are near-replicates of some models, then treating all models equally is likely to bias the inferences made using these ensembles. The challenge is to establish the degree to which this might be true for any given application. While this issue is recognised by many in the community, quantifying and accounting for model dependence in anything other than an ad-hoc way is challenging. Here we present a synthesis of the range of disparate attempts to define, quantify and address model dependence in multi-model climate ensembles in a common conceptual framework, and provide guidance on how users can test the efficacy of approaches that move beyond the equally weighted ensemble. In the upcoming Coupled Model Intercomparison Project phase 6 (CMIP6), several new models that are closely related to existing models are anticipated, as well as large ensembles from some models. We argue that quantitatively accounting for dependence in addition to model performance, and thoroughly testing the effectiveness of the approach used will be key to a sound interpretation of the CMIP ensembles in future scientific studies.</p

FGF2 overrides key pro-fibrotic features of bone marrow stromal cells isolated from Modic type 1 change patients

Extensive extracellular matrix production and increased cell-matrix adhesion by bone marrow stromal cells (BMSCs) are hallmarks of fibrotic alterations in the vertebral bone marrow known as Modic type 1 changes (MC1). MC1 are associated with non-specific chronic low-back pain. To identify treatment targets for MC1, in vitro studies using patient BMSCs are important to reveal pathological mechanisms. For the culture of BMSCs, fibroblast growth factor 2 (FGF2) is widely used. However, FGF2 has been shown to suppress matrix synthesis in various stromal cell populations. The aim of the present study was to investigate whether FGF2 affected the in vitro study of the fibrotic pathomechanisms of MC1-derived BMSCs. Transcriptomic changes and changes in cell-matrix adhesion of MC1-derived BMSCs were compared to intra-patient control BMSCs in response to FGF2. RNA sequencing and quantitative real-time polymerase chain reaction revealed that pro-fibrotic genes and pathways were not detectable in MC1-derived BMSCs when cultured in the presence of FGF2. In addition, significantly increased cell-matrix adhesion of MC1-derived BMSCs was abolished in the presence of FGF2. In conclusion, the data demonstrated that FGF2 overrides key pro-fibrotic features of MC1 BMSCs in vitro. Usage of FGF2-supplemented media in studies of fibrotic mechanisms should be critically evaluated as it could override normally dominant biological and biophysical cues

Effect of microstructural evolution on magnetic properties of Ni thin films

Copyright © Indian Academy of Sciences.The magnetic properties of Ni thin films, in the range 20–500 nm, at the crystalline-nanocrystalline interface are reported. The effect of thickness, substrate and substrate temperature has been studied. For the films deposited at ambient temperatures on borosilicate glass substrates, the crystallite size, coercive field and magnetization energy density first increase and achieve a maximum at a critical value of thickness and decrease thereafter. At a thickness of 50 nm, the films deposited at ambient temperature onto borosilicate glass, MgO and silicon do not exhibit long-range order but are magnetic as is evident from the non-zero coercive field and magnetization energy. Phase contrast microscopy revealed that the grain sizes increase from a value of 30–50 nm at ambient temperature to 120–150 nm at 503 K and remain approximately constant in this range up to 593 K. The existence of grain boundary walls of width 30–50 nm is demonstrated using phase contrast images. The grain boundary area also stagnates at higher substrate temperature. There is pronounced shape anisotropy as evidenced by the increased aspect ratio of the grains as a function of substrate temperature. Nickel thin films of 50 nm show the absence of long-range crystalline order at ambient temperature growth conditions and a preferred [111] orientation at higher substrate temperatures. Thin films are found to be thermally relaxed at elevated deposition temperature and having large compressive strain at ambient temperature. This transition from nanocrystalline to crystalline order causes a peak in the coercive field in the region of transition as a function of thickness and substrate temperature. The saturation magnetization on the other hand increases with increase in substrate temperature.University Grants Commission for Centre of Advanced Studies in Physic

Partitioning clustering algorithms for protein sequence data sets

<p>Abstract</p> <p>Background</p> <p>Genome-sequencing projects are currently producing an enormous amount of new sequences and cause the rapid increasing of protein sequence databases. The unsupervised classification of these data into functional groups or families, clustering, has become one of the principal research objectives in structural and functional genomics. Computer programs to automatically and accurately classify sequences into families become a necessity. A significant number of methods have addressed the clustering of protein sequences and most of them can be categorized in three major groups: hierarchical, graph-based and partitioning methods. Among the various sequence clustering methods in literature, hierarchical and graph-based approaches have been widely used. Although partitioning clustering techniques are extremely used in other fields, few applications have been found in the field of protein sequence clustering. It is not fully demonstrated if partitioning methods can be applied to protein sequence data and if these methods can be efficient compared to the published clustering methods.</p> <p>Methods</p> <p>We developed four partitioning clustering approaches using Smith-Waterman local-alignment algorithm to determine pair-wise similarities of sequences. Four different sets of protein sequences were used as evaluation data sets for the proposed methods.</p> <p>Results</p> <p>We show that these methods outperform several other published clustering methods in terms of correctly predicting a classifier and especially in terms of the correctness of the provided prediction. The software is available to academic users from the authors upon request.</p

Long non-coding RNAs: spatial amplifiers that control nuclear structure and gene expression

Over the past decade, it has become clear that mammalian genomes encode thousands of long non-coding RNAs (lncRNAs), many of which are now implicated in diverse biological processes. Recent work studying the molecular mechanisms of several key examples — including Xist, which orchestrates X chromosome inactivation — has provided new insights into how lncRNAs can control cellular functions by acting in the nucleus. Here we discuss emerging mechanistic insights into how lncRNAs can regulate gene expression by coordinating regulatory proteins, localizing to target loci and shaping three-dimensional (3D) nuclear organization. We explore these principles to highlight biological challenges in gene regulation, in which lncRNAs are well-suited to perform roles that cannot be carried out by DNA elements or protein regulators alone, such as acting as spatial amplifiers of regulatory signals in the nucleus

Allowable CO2 emissions based on regional and impact-related climate targets

This paper was accepted for publication in the journal Nature and the definitive published version is available at http://dx.doi.org/10.1038/nature16542© 2016 Macmillan Publishers Limited. All rights reserved. Global temperature targets, such as the widely accepted limit of an increase above pre-industrial temperatures of two degrees Celsius, may fail to communicate the urgency of reducing carbon dioxide (CO2) emissions. The translation of CO2 emissions into regional- and impact-related climate targets could be more powerful because such targets are more directly aligned with individual national interests. We illustrate this approach using regional changes in extreme temperatures and precipitation. These scale robustly with global temperature across scenarios, and thus with cumulative CO2 emissions. This is particularly relevant for changes in regional extreme temperatures on land, which are much greater than changes in the associated global mean