Molecular Events in the Cell Types of the Olfactory Epithelium during Adult Neurogenesis

BACKGROUND: Adult neurogenesis, fundamental for cellular homeostasis in the mammalian olfactory epithelium, requires major shifts in gene expression to produce mature olfactory sensory neurons (OSNs) from multipotent progenitor cells. To understand these dynamic events requires identifying not only the genes involved but also the cell types that express each gene. Only then can the interrelationships of the encoded proteins reveal the sequences of molecular events that control the plasticity of the adult olfactory epithelium. RESULTS: Of 4,057 differentially abundant mRNAs at 5 days after lesion-induced OSN replacement in adult mice, 2,334 were decreased mRNAs expressed by mature OSNs. Of the 1,723 increased mRNAs, many were expressed by cell types other than OSNs and encoded proteins involved in cell proliferation and transcriptional regulation, consistent with increased basal cell proliferation. Others encoded fatty acid metabolism and lysosomal proteins expressed by infiltrating macrophages that help scavenge debris from the apoptosis of mature OSNs. The mRNAs of immature OSNs behaved dichotomously, increasing if they supported early events in OSN differentiation (axon initiation, vesicular trafficking, cytoskeletal organization and focal adhesions) but decreasing if they supported homeostatic processes that carry over into mature OSNs (energy production, axon maintenance and protein catabolism). The complexity of shifts in gene expression responsible for converting basal cells into neurons was evident in the increased abundance of 203 transcriptional regulators expressed by basal cells and immature OSNs. CONCLUSIONS: Many of the molecular changes evoked during adult neurogenesis can now be ascribed to specific cellular events in the OSN cell lineage, thereby defining new stages in the development of these neurons. Most notably, the patterns of gene expression in immature OSNs changed in a characteristic fashion as these neurons differentiated. Initial patterns were consistent with the transition into a neuronal morphology (neuritogenesis) and later patterns with neuronal homeostasis. Overall, gene expression patterns during adult olfactory neurogenesis showed substantial similarity to those of embryonic brain

Group descent algorithms for nonconvex penalized linear and logistic regression models with grouped predictors

Penalized regression is an attractive framework for variable selection problems. Often, variables possess a grouping structure, and the relevant selection problem is that of selecting groups, not individual variables. The group lasso has been proposed as a way of extending the ideas of the lasso to the problem of group selection. Nonconvex penalties such as SCAD and MCP have been proposed and shown to have several advantages over the lasso; these penalties may also be extended to the group selection problem, giving rise to group SCAD and group MCP methods. Here, we describe algorithms for fitting these models stably and efficiently. In addition, we present simulation results and real data examples comparing and contrasting the statistical properties of these methods

Thinking about Later Life: Insights from the Capability Approach

A major criticism of mainstream gerontological frameworks is the inability of such frameworks to appreciate and incorporate issues of diversity and difference in engaging with experiences of aging. Given the prevailing socially structured nature of inequalities, such differences matter greatly in shaping experiences, as well as social constructions, of aging. I argue that Amartya Sen’s capability approach (2009) potentially offers gerontological scholars a broad conceptual framework that places at its core consideration of human beings (their values) and centrality of human diversity. As well as identifying these key features of the capability approach, I discuss and demonstrate their relevance to thinking about old age and aging. I maintain that in the context of complex and emerging identities in later life that shape and are shaped by shifting people-place and people-people relationships, Sen’s capability approach offers significant possibilities for gerontological research

Molecular events in the cell types of the olfactory epithelium during adult neurogenesis

BACKGROUND: Adult neurogenesis, fundamental for cellular homeostasis in the mammalian olfactory epithelium, requires major shifts in gene expression to produce mature olfactory sensory neurons (OSNs) from multipotent progenitor cells. To understand these dynamic events requires identifying not only the genes involved but also the cell types that express each gene. Only then can the interrelationships of the encoded proteins reveal the sequences of molecular events that control the plasticity of the adult olfactory epithelium. RESULTS: Of 4,057 differentially abundant mRNAs at 5 days after lesion-induced OSN replacement in adult mice, 2,334 were decreased mRNAs expressed by mature OSNs. Of the 1,723 increased mRNAs, many were expressed by cell types other than OSNs and encoded proteins involved in cell proliferation and transcriptional regulation, consistent with increased basal cell proliferation. Others encoded fatty acid metabolism and lysosomal proteins expressed by infiltrating macrophages that help scavenge debris from the apoptosis of mature OSNs. The mRNAs of immature OSNs behaved dichotomously, increasing if they supported early events in OSN differentiation (axon initiation, vesicular trafficking, cytoskeletal organization and focal adhesions) but decreasing if they supported homeostatic processes that carry over into mature OSNs (energy production, axon maintenance and protein catabolism). The complexity of shifts in gene expression responsible for converting basal cells into neurons was evident in the increased abundance of 203 transcriptional regulators expressed by basal cells and immature OSNs. CONCLUSIONS: Many of the molecular changes evoked during adult neurogenesis can now be ascribed to specific cellular events in the OSN cell lineage, thereby defining new stages in the development of these neurons. Most notably, the patterns of gene expression in immature OSNs changed in a characteristic fashion as these neurons differentiated. Initial patterns were consistent with the transition into a neuronal morphology (neuritogenesis) and later patterns with neuronal homeostasis. Overall, gene expression patterns during adult olfactory neurogenesis showed substantial similarity to those of embryonic brain

Early Laser for Burn Scars (ELABS): protocol for a multi-centre randomised, controlled trial of both the effectiveness and cost-effectiveness of the treatment of hypertrophic burn scars with Pulsed Dye Laser and standard care compared to standard care alone [version 1; peer review: 2 approved]

This paper outlines the protocol for a study that is being carried out at multiple centres across the UK in the next three years. It is a Research for Patient Benefit (RfPB) study funded by the National Institute for Healthcare Research (NIHR). The aim is to assess the effectiveness of treating hypertrophic burns scars with pulsed dye laser (PDL) at an early stage of scar formation. The objective is to improve Quality of Life for the patient by improving both the appearance and quality of burn scarring, as well as reducing its psychological impact. This is a parallel-arm randomised, controlled trial to compare PDL and standard care against standard care alone. The difference is measured between baseline and six-month follow-up. Recruits are within three months of healing from a burn injury; with wounds showing a defined potential for hypertrophic scarring. A total of 120 patients are recruited in a multi-centre study; with randomisation in a 1:1 allocation to each arm. The treatment arm receives 3 PDL treatments at six-week intervals in addition to standard care, whereas the control arm receives standard care alone. The primary outcome is the patient-rated part of the Patient and Observer Scar Scale (POSAS). Psychological and psycho-social impact is evaluated using the CARe burn scale (UWE, Bristol) and Quality Adjusted Life Years (QALY) is determined using the Short-Form Health Survey (SF-12). The study evaluates both the cost-effectiveness through an economic analysis and the patient-reported experience of the treatment by phone interviews

Detection of rare functional variants using group ISIS

Genome-wide association studies have been firmly established in investigations of the associations between common genetic variants and complex traits or diseases. However, a large portion of complex traits and diseases cannot be explained well by common variants. Detecting rare functional variants becomes a trend and a necessity. Because rare variants have such a small minor allele frequency (e.g., <0.05), detecting functional rare variants is challenging. Group iterative sure independence screening (ISIS), a fast group selection tool, was developed to select important genes and the single-nucleotide polymorphisms within. The performance of the group ISIS and group penalization methods is compared for detecting important genes in the Genetic Analysis Workshop 17 data. The results suggest that the group ISIS is an efficient tool to discover genes and single-nucleotide polymorphisms associated to phenotypes

Some , And Possibly All, Scalar Inferences Are Not Delayed: Evidence For Immediate Pragmatic Enrichment

Scalar inferences are commonly generated when a speaker uses a weaker expression rather than a stronger alternative, e.g., John ate some of the apples implies that he did not eat them all. This article describes a visual-world study investigating how and when perceivers compute these inferences. Participants followed spoken instructions containing the scalar quantifier some directing them to interact with one of several referential targets (e.g., Click on the girl who has some of the balloons). Participants fixated on the target compatible with the implicated meaning of some and avoided a competitor compatible with the literal meaning prior to a disambiguating noun. Further, convergence on the target was as fast for some as for the non-scalar quantifiers none and all. These findings indicate that the scalar inference is computed immediately and is not delayed relative to the literal interpretation of some. It is argued that previous demonstrations that scalar inferences increase processing time are not necessarily due to delays in generating the inference itself, but rather arise because integrating the interpretation of the inference with relevant information in the context may require additional time. With sufficient contextual support, processing delays disappear

Intersections of Jane Jacobs’ conditions for diversity and low-carbon urban systems: a look at four global cities

Countless cities are rapidly developing across the globe, pressing the need for clear urban planning and design recommendations geared towards sustainability. This article examines the intersections of Jane Jacobs’ four conditions for diversity with low-carbon and low-energy use urban systems in four cities around the world: Lyon (France), Chicago (United-States), Kolkata (India), and Singapore (Singapore). After reviewing Jacobs’ four conditions for diversity, we introduce the four cities and describe their historical development context. We then present a framework to study the cities along three dimensions: population and density, infrastructure development/use, and climate and landscape. These cities differ in many respects and their analysis is instructive for many other cities around the globe. Jacobs’ conditions are present in all of them, manifested in different ways and to varying degrees. Overall we find that the adoption of Jacobs' conditions seems to align well with concepts of low-carbon urban systems, with their focus on walkability, transit-oriented design, and more efficient land use (i.e., smaller unit sizes). Transportation sector emissions seems to demonstrate a stronger influence from the presence of Jacobs' conditions, while the link was less pronounced in the building sector. Kolkata, a low-income, developing world city, seems to possess many of Jacobs' conditions, while exhibiting low per capita emissions - maintaining both of these during its economic expansion will take careful consideration. Greenhouse gas mitigation, however, is inherently an in situ problem and the first task must therefore be to gain local knowledge of an area before developing strategies to lower its carbon footprint

The spatial footprint of the knowledge economy: the role of intangible investment in shaping regional inequalities in Great Britain

Since the advent of the knowledge economy it has become evident that the territorial footprint of investment in intangible assets is largely asymmetrical. First, these types of assets tend to be distributed unevenly across space. Second, intangible assets are an important source of productivity growth and competitiveness. Although significant advances have been made in measuring intangible assets and accounting for their effects in economic outcomes, their exact nature remains vague. Within the National Accounts framework the majority of intangibles are, even now, still treated as intermediate expenditure. Consequently, intangibles are largely excluded from conventional measures of output and investment, making it difficult to account for their spatial effects. The present paper adjusts Gross Value Added (GVA) data for NUTS3 regions in Great Britain for intangibles. The adjusted series are then used to investigate trends in regional inequalities in GVA per employee in this country during the pre-recession period 1995-2007