Signal processing for molecular and cellular biological physics:an emerging field

Recent advances in our ability to watch the molecular and cellular processes of life in action-such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer-raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied

A mild alkali treated jute fibre controlling the hydration behaviour of greener cement paste

To reduce the antagonistic effect of jute fibre on the setting and hydration of jute reinforced cement, modified jute fibre reinforcement would be a unique approach. The present investigation deals with the effectiveness of mild alkali treated (0.5%) jute fibre on the setting and hydration behaviour of cement. Setting time measurement, hydration test and analytical characterizations of the hardened samples (viz., FTIR, XRD, DSC, TGA and free lime estimation) were used to evaluate the effect of alkali treated jute fibre. From the hydration test, the time (t) required to reach maximum temperature for the hydration of control cement sample is estimated to be 860 min, whilst the time (t) is measured to be 1040 min for the hydration of a raw jute reinforced cement sample. However, the time (t) is estimated to be 1020 min for the hydration of an alkali treated jute reinforced cement sample. Additionally, from the analytical characterizations, it is determined that fibre-cement compatibility is increased and hydration delaying effect is minimized by using alkali treated jute fibre as fibre reinforcement. Based on the analyses, a model has been proposed to explain the setting and hydration behaviour of alkali treated jute fibre reinforced cement composite

A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon

The Exhibition as an Experiment: An Analogy and its Implications

The analogy of the exhibition as an experiment suggests innovative curatorial approaches that challenge institutional practices. This analogy has however a historical precedence in modernism when itbecame paradigmatic of the exhibitions at the Museum of ModernArt in New York in the 1940s, defining the curatorial approach of its founding director Alfred J Barr. This article considers this early useof the analogy of the exhibition as an experiment and further reflects on its redefinition at the turn of the 20th century by examining how both the notions of the exhibition and of the experiment havechanged over time. In particular, the article examines the different meanings and practices inferred by the concepts of the exhibition and the experiment in the first decades of the 20th century and in the present. It outlines how correspondences between cultural and scientific paradigms can be deployed to tease unacknowledged synergies between two modes of knowledge production (i.e. the art exhibition and the experiment) and address questions of presentness, authority and legitimacy that they imply

Barriers and progress in the treatment of low back pain

Low back pain is a common and costly condition and for most people is likely to be a recurrent problem throughout their lifetime. The management of patients with low back pain has been positively influenced by the rise in high quality clinical trials and systematic reviews in recent decades, and this body of evidence, synthesized in many clinical practice guidelines, has improved our knowledge about which treatments for low back pain are useful and which are not. For the largest group of patients, those with non-specific low back pain for whom a clear diagnosis cannot be given, the reality is that the treatments we have to offer tend to produce small effects, often only in the short term and none appear to effectively change long-term prognosis. This commentary summarizes the array of treatments currently available, notes the results of recent trials and guidelines and considers alternative approaches that may prove more valuable in achieving better patient outcomes in the future

A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci.

We conducted a multi-stage, genome-wide association study of bladder cancer with a primary scan of 591,637 SNPs in 3,532 affected individuals (cases) and 5,120 controls of European descent from five studies followed by a replication strategy, which included 8,382 cases and 48,275 controls from 16 studies. In a combined analysis, we identified three new regions associated with bladder cancer on chromosomes 22q13.1, 19q12 and 2q37.1: rs1014971, (P = 8 × 10⁻¹²) maps to a non-genic region of chromosome 22q13.1, rs8102137 (P = 2 × 10⁻¹¹) on 19q12 maps to CCNE1 and rs11892031 (P = 1 × 10⁻⁷) maps to the UGT1A cluster on 2q37.1. We confirmed four previously identified genome-wide associations on chromosomes 3q28, 4p16.3, 8q24.21 and 8q24.3, validated previous candidate associations for the GSTM1 deletion (P = 4 × 10⁻¹¹) and a tag SNP for NAT2 acetylation status (P = 4 × 10⁻¹¹), and found interactions with smoking in both regions. Our findings on common variants associated with bladder cancer risk should provide new insights into the mechanisms of carcinogenesis

Identification of genes required for soil survival in Burkholderia thailandensis by transposon-directed insertion site sequencing.

Transposon-directed insertion site sequencing was used to identify genes required by Burkholderia thailandensis to survive in plant/soil microcosms. A total of 1,153 genetic loci fulfilled the criteria as being likely to encode survival characteristics. Of these, 203 (17.6 %) were associated with uptake and transport systems; 463 loci (40.1 %) coded for enzymatic properties, 99 of these (21.4 %) had reduction/oxidation functions; 117 (10.1 %) were gene regulation or sensory loci; 61 (5.3 %) encoded structural proteins found in the cell envelope or with enzymatic activities related to it, distinct from these, 46 (4.0 %) were involved in chemotaxis and flagellum, or pilus synthesis; 39 (3.4 %) were transposase enzymes or were bacteriophage-derived; and 30 (2.6 %) were involved in the production of antibiotics or siderophores. Two hundred and twenty genes (19.1 %) encoded hypothetical proteins or those of unknown function. Given the importance of motility and pilus formation in microcosm persistence the nature of the colonization of the rhizosphere was examined by confocal microscopy. Wild type B. thailandensis expressing red fluorescent protein was inoculated into microcosms. Even though the roots had been washed, the bacteria were still present but they were motile with no attachment having taken place, perhaps being retained in a biofilm

Inheriting library cards to Babel and Alexandria: Contemporary metaphors for the digital library

Librarians have been consciously adopting metaphors to describe library concepts since the nineteenth century, helping us to structure our understanding of new technologies. We have drawn extensively on these figurative frameworks to explore issues surrounding the digital library, yet very little has been written to date which interrogates how these metaphors have developed over the years. Previous studies have explored library metaphors, using either textual analysis or ethnographic methods to investigate their usage. However, this is to our knowledge the first study to use bibliographic data, corpus analysis, qualitative sentiment weighting and close reading to study particular metaphors in detail. It draws on a corpus of over 450 articles to study the use of the metaphors of the Library of Alexandria and Babel, concluding that both have been extremely useful as framing metaphors for the digital library. However, their longstanding use has seen them become stretched as metaphors, meaning that the field’s figurative framework now fails to represent the changing technologies which underpin contemporary digital libraries

A randomized controlled pilot study of a brief web-based mindfulness training

Background: Mindfulness has been shown to be effective in treating various medical and mental problems. Especially its incorporation in cognitive-behavioural interventions has improved long-term outcomes of those treatments. It has also been shown, that brief mindfulness-based trainings are effective in reducing distress. There have been few web-based interventions incorporating mindfulness techniques in their manual and it remains unclear whether a brief web-based mindfulness intervention is feasible. Methods: Out of 50 adults (different distress levels; exclusion criteria: < 18 years, indication of psychotic or suicidal ideation in screening) who were recruited via e-mail and screened online, 49 were randomized into an immediate 2-weeks-treatment group (N = 28) or a waitlist-control group (N = 21), starting with a 2-week delay. Distress (BSI), perceived stress (PSQ), mindfulness (FMI), as well as mood and emotion regulation (PANAS/SEK-27) were measured at pre-, post- and 3-month follow-up (3MFU). Intention-to-treat analyses using MI for missing data and per-protocol analyses (≥ 50% attendance) were performed. Results: 26 participants of the treatment group completed post-measures. Most measures under ITT-analysis revealed no significant improvement for the treatment group, but trends with medium effect sizes for PSQ (d = 0.46) and PANASneg (d = 0.50) and a small, non-significant effect for FMI (d = 0.29). Per-protocol analyses for persons who participated over 50% of the time revealed significant treatment effects for PSQ (d = 0.72) and PANASneg (d = 0.77). Comparing higher distressed participants with lower distressed participants, highly distressed participants seemed to profit more of the training in terms of distress reduction (GSI, d = 0.85). Real change (RCI) occurred for PSQ in the treatment condition (OR = 9). Results also suggest that participants continued to benefit from the training at 3MFU. Conclusion: This study of a brief web-based mindfulness training indicates that mindfulness can be taught online and may improve distress, perceived stress and negative affect for regular users. Although there were no significant improvements, but trends, for most measures under ITT, feasibility of such a program was demonstrated and also that persons continued to use techniques of the training in daily life