Calibrating Single-Ended Fiber-Optic Raman Spectra Distributed Temperature Sensing Data

Hydrologic research is a very demanding application of fiber-optic distributed temperature sensing (DTS) in terms of precision, accuracy and calibration. The physics behind the most frequently used DTS instruments are considered as they apply to four calibration methods for single-ended DTS installations. The new methods presented are more accurate than the instrument-calibrated data, achieving accuracies on the order of tenths of a degree root mean square error (RMSE) and mean bias. Effects of localized non-uniformities that violate the assumptions of single-ended calibration data are explored and quantified. Experimental design considerations such as selection of integration times or selection of the length of the reference sections are discussed, and the impacts of these considerations on calibrated temperatures are explored in two case studies

The Dual Impact of HIV-1 Infection and Aging on Naïve CD4+ T-Cells: Additive and Distinct Patterns of Impairment

HIV-1-infected adults over the age of 50 years progress to AIDS more rapidly than adults in their twenties or thirties. In addition, HIV-1-infected individuals receiving antiretroviral therapy (ART) present with clinical diseases, such as various cancers and liver disease, more commonly seen in older uninfected adults. These observations suggest that HIV-1 infection in older persons can have detrimental immunological effects that are not completely reversed by ART. As naïve T-cells are critically important in responses to neoantigens, we first analyzed two subsets (CD45RA+CD31+ and CD45RA+CD31-) within the naïve CD4+ T-cell compartment in young (20–32 years old) and older (39–58 years old), ART-naïve, HIV-1 seropositive individuals within 1–3 years of infection and in age-matched seronegative controls. HIV-1 infection in the young cohort was associated with lower absolute numbers of, and shorter telomere lengths within, both CD45RA+CD31+CD4+ and CD45RA+CD31-CD4+ T-cell subsets in comparison to age-matched seronegative controls, changes that resembled seronegative individuals who were decades older. Longitudinal analysis provided evidence of thymic emigration and reconstitution of CD45RA+CD31+CD4+ T-cells two years post-ART, but minimal reconstitution of the CD45RA+CD31-CD4+ subset, which could impair de novo immune responses. For both ART-naïve and ART-treated HIV-1-infected adults, a renewable pool of thymic emigrants is necessary to maintain CD4+ T-cell homeostasis. Overall, these results offer a partial explanation both for the faster disease progression of older adults and the observation that viral responders to ART present with clinical diseases associated with older adults

Calibrating Single-Ended Fiber-Optic Raman Spectra Distributed Temperature Sensing Data

Hydrologic research is a very demanding application of fiber-optic distributed temperature sensing (DTS) in terms of precision, accuracy and calibration. The physics behind the most frequently used DTS instruments are considered as they apply to four calibration methods for single-ended DTS installations. The new methods presented are more accurate than the instrument-calibrated data, achieving accuracies on the order of tenths of a degree root mean square error (RMSE) and mean bias. Effects of localized non-uniformities that violate the assumptions of single-ended calibration data are explored and quantified. Experimental design considerations such as selection of integration times or selection of the length of the reference sections are discussed, and the impacts of these considerations on calibrated temperatures are explored in two case studies.Keywords: temperature, distributed temperature sensing, hydrology, calibratio

Environmental temperature sensing using Raman spectra DTS fiber-optic methods

Raman spectra distributed temperature sensing (DTS) by fiber-optic cables has recently shown considerable promise for the measuring and monitoring of surface and near-surface hydrologic processes such as groundwater–surface water interaction, borehole circulation, snow hydrology, soil moisture studies, and land surface energy exchanges. DTS systems uniquely provide the opportunity to monitor water, air, and media temperatures in a variety of systems at much higher spatial and temporal frequencies than any previous measurement method. As these instruments were originally designed for fire and pipeline monitoring, their extension to the typical conditions encountered by hydrologists requires a working knowledge of the theory of operation, limitations, and system accuracies, as well as the practical aspects of designing either short- or long-term experiments in remote or challenging terrain. This work focuses on providing the hydrologic user with sufficient knowledge and specifications to allow sound decisions on the application and deployment of DTS systems.Keywords: Hydrology, Temperature, Fiber opti

Assessing the effectiveness of riparian restoration projects using Landsat and precipitation data from the cloud-computing application ClimateEngine.org

Riparian vegetation along streams provides a suite of ecosystem services in rangelands and thus is the target of restoration when degraded by over-grazing, erosion, incision, or other disturbances. Assessments of restoration effectiveness depend on defensible monitoring data, which can be both expensive and difficult to collect. We present a method and case study to evaluate the effectiveness of restoration of riparian vegetation using a web-based cloud-computing and visualization tool (ClimateEngine.org) to access and process remote sensing and climate data. Restoration efforts on an Eastern Oregon ranch were assessed by analyzing the riparian areas of four creeks that had in-stream restoration structures constructed between 2008 and 2011. Within each study area, we retrieved spatially and temporally aggregated values of summer (June, July, August) normalized difference vegetation index (NDVI) and total precipitation for each water year (October-September) from 1984 to 2017. We established a pre-restoration (1984-2007) linear regression between total water year precipitation and summer NDVI for each study area, and then compared the post-restoration (2012-2017) data to this pre-restoration relationship. In each study area, the post-restoration NDVI-precipitation relationship was statistically distinct from the pre-restoration relationship, suggesting a change in the fundamental relationship between precipitation and NDVI resulting from stream restoration. We infer that the in-stream structures, which raised the water table in the adjacent riparian areas, provided additional water to the streamside vegetation that was not available before restoration and reduced the dependence of riparian vegetation on precipitation. This approach provides a cost-effective, quantitative method for assessing the effects of stream restoration projects on riparian vegetation

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele

New insights into the genetic etiology of Alzheimer's disease and related dementias

Characterization of the genetic landscape of Alzheimer's disease (AD) and related dementias (ADD) provides a unique opportunity for a better understanding of the associated pathophysiological processes. We performed a two-stage genome-wide association study totaling 111,326 clinically diagnosed/'proxy' AD cases and 677,663 controls. We found 75 risk loci, of which 42 were new at the time of analysis. Pathway enrichment analyses confirmed the involvement of amyloid/tau pathways and highlighted microglia implication. Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. We also built a new genetic risk score associated with the risk of future AD/dementia or progression from mild cognitive impairment to AD/dementia. The improvement in prediction led to a 1.6- to 1.9-fold increase in AD risk from the lowest to the highest decile, in addition to effects of age and the APOE ε4 allele