Clinical Significance of Sleep Desaturation in Hypoxemic Chronic Obstructive Pulmonary Disease: Studies in 130 Patients

We studied 130 patients with hypoxemic chronic obstructive lung disease to determine if nocturnal desaturation aggravates hypoxia-induced complications. All had tests of neuropsychological and physiological function known to be affected by chronic hypoxia. Of the 130 patients, 25 had complete polysomnography and 105 had their sleep judged visually and arterial oxygen saturation recorded continuously. Severe and mild desaturation groups were defined relative to the mean for both mean and maximal sleep desaturation, and the severity of waking complications were compared. No significant differences were noted between patients with mild and severe mean desaturation or maximal desaturation for hematocrit, neuropsychological tests, maximal exercise tolerance, or measures of quality of life. Waking pulmonary artery pressure did not differ significantly between patients with mild and severe mean desaturation or maximal desaturation, except in 20 patients with the most severe mean desaturation during sleep. We conclude that nocturnal desaturation does not aggravate hypoxia-induced complications in most patients who are chronically hypoxemic from chronic obstructive pulmonary disease

Phylogenetic analysis of human Chlamydia pneumoniae strains reveals a distinct Australian indigenous clade that predates European exploration of the continent

© 2015 Roulis et al. Background: The obligate intracellular bacterium Chlamydia pneumoniae is a common respiratory pathogen, which has been found in a range of hosts including humans, marsupials and amphibians. Whole genome comparisons of human C. pneumoniae have previously highlighted a highly conserved nucleotide sequence, with minor but key polymorphisms and additional coding capacity when human and animal strains are compared. Results: In this study, we sequenced three Australian human C. pneumoniae strains, two of which were isolated from patients in remote indigenous communities, and compared them to all available C. pneumoniae genomes. Our study demonstrated a phylogenetically distinct human C. pneumoniae clade containing the two indigenous Australian strains, with estimates that the most recent common ancestor of these strains predates the arrival of European settlers to Australia. We describe several polymorphisms characteristic to these strains, some of which are similar in sequence to animal C. pneumoniae strains, as well as evidence to suggest that several recombination events have shaped these distinct strains. Conclusions: Our study reveals a greater sequence diversity amongst both human and animal C. pneumoniae strains, and suggests that a wider range of strains may be circulating in the human population than current sampling indicates

Dynamic Bayesian belief network to model the development of walking and cycling schemes

This paper aims to describe a model which represents the formulation of decision-making processes (over a number of years) affecting the step-changes of walking and cycling (WaC) schemes. These processes can be seen as being driven by a number of causal factors, many of which are associated with the attitudes of a variety of factors, in terms of both determining whether any scheme will be implemented and, if it is implemented, the extent to which it is used. The outputs of the model are pathways as to how the future might unfold (in terms of a number of future time steps) with respect to specific pedestrian and cyclist schemes. The transitions of the decision making processes are formulated using a qualitative simulation method, which describes the step-changes of the WaC scheme development. In this article a Bayesian belief network (BBN) theory is extended to model the influence between and within factors in the dynamic decision making process

Lithium-ion battery degradation: how to model it

Predicting lithium-ion battery degradation is worth billions to the global automotive, aviation and energy storage industries, to improve performance and safety and reduce warranty liabilities. However, very few published models of battery degradation explicitly consider the interactions between more than two degradation mechanisms, and none do so within a single electrode. In this paper, the first published attempt to directly couple more than two degradation mechanisms in the negative electrode is reported. The results are used to map different pathways through the complicated path dependent and non-linear degradation space. Four degradation mechanisms are coupled in PyBaMM, an open source modelling environment uniquely developed to allow new physics to be implemented and explored quickly and easily. Crucially it is possible to see 'inside' the model and observe the consequences of the different patterns of degradation, such as loss of lithium inventory and loss of active material. For the same cell, five different pathways that can result in end-of-life have already been found, depending on how the cell is used. Such information would enable a product designer to either extend life or predict life based upon the usage pattern. However, parameterization of the degradation models remains as a major challenge, and requires the attention of the international battery community

An underground drip water monitoring network to characterize rainfall recharge of groundwater at different geologies, environments, and climates across Australia

Understanding when and why groundwater recharge occurs is of fundamental importance for the sustainable use of this essential freshwater resource for humans and ecosystems. However, accurately capturing this component of the water balance is widely acknowledged to be a major challenge. Direct physical measurements identifying when groundwater recharge is occurring are possible by utilizing a sensor network of hydrological loggers deployed in underground spaces located in the vadose zone. Through measurements of water percolating into these spaces from above, we can record the potential groundwater recharge process in action. By using automated sensors, it is possible to precisely determine when recharge occurs (which event, month, or season and for which climate condition). Combined with daily rainfall data, it is possible to quantify the “rainfall recharge threshold”, the amount of rainfall needed to generate groundwater recharge, and its temporal and spatial variability. Australia's National Groundwater Recharge Observing System (NGROS) provides the first dedicated sensor network for observing groundwater recharge at an event scale across a wide range of geologies, environments, and climate types representing a wide range of Australian hydroclimates. Utilizing tunnels, mines, caves, and other subsurface spaces located in the vadose zone, the sensors effectively record “deep drainage”, water that can move beyond the shallow subsurface and root zone to generate groundwater recharge. The NGROS has the temporal resolution to capture individual recharge events, with multiple sensors deployed at each site to constrain the heterogeneity of recharge between different flow paths, and to quantify (including uncertainty bounds) rainfall recharge thresholds. Established in 2022, the network is described here together with examples of data being generated.</p

A suggested classification for two groups of Campylobacter myoviruses

Most Campylobacter bacteriophages isolated to date have long contractile tails and belong to the family Myoviridae. Based on their morphology, genome size and endonuclease restriction profile, Campylobacter phages were originally divided into three groups. The recent genome sequencing of seven virulent campylophages reveal further details of the relationships between these phages at the genome organization level. This article details the morphological and genomic features among the campylophages, investigates their taxonomic position, and proposes the creation of two new genera, the “Cp220likevirus” and “Cp8unalikevirus” within a proposed subfamily, the “Eucampyvirinae”.AMK would like to thank Andre Villegas for developing "extractUpStreamDNA". The authors are thankful to Denis Arutyunov and Jessica Sacher for helpful discussions and help with phage preparations, and to Cheryl Nargang for her help with nucleotide sequencing and analysis of gp047 homolog from phage F336. The bacteriophage receptor-binding protein studies were funded by an Alberta Innovates Scholar Award (CMS) and a Natural Sciences and Engineering Research Council of Canada Strategic Grant (CMS). RL and AMK are chair and vice chair, respectively, of the prokaryotic virus subcommittee of the ICTV (International Committee for Taxonomy of Viruses)

A Cognitive Model of an Epistemic Community: Mapping the Dynamics of Shallow Lake Ecosystems

We used fuzzy cognitive mapping (FCM) to develop a generic shallow lake ecosystem model by augmenting the individual cognitive maps drawn by 8 scientists working in the area of shallow lake ecology. We calculated graph theoretical indices of the individual cognitive maps and the collective cognitive map produced by augmentation. The graph theoretical indices revealed internal cycles showing non-linear dynamics in the shallow lake ecosystem. The ecological processes were organized democratically without a top-down hierarchical structure. The steady state condition of the generic model was a characteristic turbid shallow lake ecosystem since there were no dynamic environmental changes that could cause shifts between a turbid and a clearwater state, and the generic model indicated that only a dynamic disturbance regime could maintain the clearwater state. The model developed herein captured the empirical behavior of shallow lakes, and contained the basic model of the Alternative Stable States Theory. In addition, our model expanded the basic model by quantifying the relative effects of connections and by extending it. In our expanded model we ran 4 simulations: harvesting submerged plants, nutrient reduction, fish removal without nutrient reduction, and biomanipulation. Only biomanipulation, which included fish removal and nutrient reduction, had the potential to shift the turbid state into clearwater state. The structure and relationships in the generic model as well as the outcomes of the management simulations were supported by actual field studies in shallow lake ecosystems. Thus, fuzzy cognitive mapping methodology enabled us to understand the complex structure of shallow lake ecosystems as a whole and obtain a valid generic model based on tacit knowledge of experts in the field.Comment: 24 pages, 5 Figure

Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants.

A locus on human chromosome 11q23 tagged by marker rs3802842 was associated with colorectal cancer (CRC) in a genome-wide association study; this finding has been replicated in case-control studies worldwide. In order to identify biologic factors at this locus that are related to the etiopathology of CRC, we used microarray-based target selection methods, coupled to next-generation sequencing, to study 103 kb at the 11q23 locus. We genotyped 369 putative variants from 1,030 patients with CRC (cases) and 1,061 individuals without CRC (controls) from the Ontario Familial Colorectal Cancer Registry. Two previously uncharacterized genes, COLCA1 and COLCA2, were found to be co-regulated genes that are transcribed from opposite strands. Expression levels of COLCA1 and COLCA2 transcripts correlate with rs3802842 genotypes. In colon tissues, COLCA1 co-localizes with crystalloid granules of eosinophils and granular organelles of mast cells, neutrophils, macrophages, dendritic cells and differentiated myeloid-derived cell lines. COLCA2 is present in the cytoplasm of normal epithelial, immune and other cell lineages, as well as tumor cells. Tissue microarray analysis demonstrates the association of rs3802842 with lymphocyte density in the lamina propria (p = 0.014) and levels of COLCA1 in the lamina propria (p = 0.00016) and COLCA2 (tumor cells, p = 0.0041 and lamina propria, p = 6 × 10(-5)). In conclusion, genetic, expression and immunohistochemical data implicate COLCA1 and COLCA2 in the pathogenesis of colon cancer. Histologic analyses indicate the involvement of immune pathways

Impaired Negative Selection of T Cells in Hodgkin's Disease Antigen CD30–Deficient Mice

AbstractCD30 is found on Reed–Sternberg cells of Hodgkin's disease and on a variety of non-Hodgkin's lymphoma cells and is up-regulated on cells after Epstein–Barr virus, human T cell leukemia virus, and HIV infections. We report here that the thymus in CD30-deficient mice contains elevated numbers of thymocytes. Activation-induced death of thymocytes after CD3 cross-linking is impaired both in vitro and in vivo. Breeding the CD30 mutation separately into αβTCR- or γδTCR-transgenic mice revealed a gross defect in negative but not positive selection. Thus, like TNF-receptors and Fas/Apo-1, the CD30 receptor is involved in cell death signaling. It is also an important coreceptor that participates in thymic deletion

Immunocluster provides a computational framework for the nonspecialist to profile high-dimensional cytometry data

High-dimensional cytometry is an innovative tool for immune monitoring in health and disease, and it has provided novel insight into the underlying biology as well as biomarkers for a variety of diseases. However, the analysis of large multiparametric datasets usually requires specialist computational knowledge. Here, we describe ImmunoCluster (https://github.com/ kordastilab/ImmunoCluster), an R package for immune profiling cellular heterogeneity in highdimensional liquid and imaging mass cytometry, and flow cytometry data, designed to facilitate computational analysis by a nonspecialist. The analysis framework implemented within ImmunoCluster is readily scalable to millions of cells and provides a variety of visualization and analytical approaches, as well as a rich array of plotting tools that can be tailored to users’ needs. The protocol consists of three core computational stages: (1) data import and quality control; (2) dimensionality reduction and unsupervised clustering; and (3) annotation and differential testing, all contained within an R-based open-source framework