Ontology-driven hypothesis generation to explain anomalous patient responses to treatment

Within the medical domain there are clear expectations as to how a patient should respond to treatments administered. When these responses are not observed it can be challenging for clinicians to understand the anomalous responses. The work reported here describes a tool which can detect anomalous patient responses to treatment and further suggest hypotheses to explain the anomaly. In order to develop this tool, we have undertaken a study to determine how Intensive Care Unit (ICU) clinicians identify anomalous patient responses; we then asked further clinicians to provide potential explanations for such anomalies. The high level reasoning deployed by the clinicians has been captured and generalised to form the procedural component of the ontology-driven tool. An evaluation has shown that the tool successfully reproduced the clinician’s hypotheses in the majority of cases. Finally, the paper concludes by describing planned extensions to this work.     

Cardiovascular phenotype characterization in mice by high resolution magnetic resonance imaging

9. Conclusion Due to its high temporal and spatial resolution, magnetic resonance imaging meets the requirements for accurate and robust in vivo visualization of the murine cardiovascular system. As an intrinsically three-dimensional imaging technique, it allows for quantification of LV volumes without relying on geometric models. Therefore, MRI is uniquely suited for the investigation of morphologic and functional changes in models of heart failure. The potential application of MRI in the mouse comprises visualization of cardiovascular anatomy and pathology in newborn and adult mice, detection of LV geometric and functional changes both acutely and chronically, visualization of cardiac microstructures such as cardiac valves and coronary arteries, and characterization and quantification of arteriosclerotic plaques in major murine arteries. Furthermore, MR spectroscopy applied to the mouse heart can give important information on in vivo myocardial metabolism. Thus, we feel confident that high resolution MRI may substantially contribute to the understanding of the basic mechanisms of a variety of cardiovascular diseases.     

Oscillation and convergence behaviours exhibited in an ‘unstable’ second‐order digital filter with saturation‐type non‐linearity

This letter explains the oscillatory behaviours exhibited in a second‐order digital filter with saturation‐type non‐linearity via the Hopf bifurcation theorem. It is shown that depending on the bifurcation parameter, the state variables may converge to zero even when the eigenvalues of the system matrix are outside the unit circle. Copyright © 2004 John Wiley & Sons, Ltd. abstract     

Ultra‐Performance Liquid Chromatography‐Mass Spectrometry Analysis of Free and Esterified Oxygenated Derivatives from Docosahexaenoic Acid in Rat Brain

Docosahexaenoic acid (DHA), a prominent long‐chain fatty acid of the omega‐3 family, is present at high amount in brain tissues, especially in membrane phospholipids. This polyunsaturated fatty acid is the precursor of various oxygenated lipid mediators involved in diverse physiological and pathophysiological processes. Characterization of DHA‐oxygenated metabolites is therefore crucial for better understanding the biological roles of DHA. In this study, we identified and measured, by ultrahigh‐performance liquid chromatography coupled with tandem mass spectrometry, a number of oxygenated products derived from DHA in exsanguinated and nonexsanguinated brains. These metabolites were found both in free form and esterified in phospholipids. Interestingly, both (R)‐ and (S)‐monohydroxylated fatty acid stereoisomers were observed free and esterified in phospholipids. Monohydroxylated metabolites were the main derivatives; however, measurable amounts of dihydroxylated products such as protectin DX were detected. Moreover, exsanguination allowed discriminating brain oxygenated metabolites from those generated in blood. These results obtained in healthy rats allowed an overview on the brain oxygenated metabolism of DHA, which deserves further research in pathophysiological conditions, especially in neurodegenerative diseases.     

Identification and Optimization of Microbial Attractants for <Emphasis Type="Italic">Philornis downsi</Emphasis>, an Invasive Fly Parasitic on Galapagos Birds

We investigated the role of olfactory cues from actively fermenting yeast (Saccharomyces cerevisiae) in attraction of adult Philornis downsi and identified two synergistically attractive yeast volatiles. Larvae of this invasive fly parasitize the hatchlings of passerines and threaten the Galapagos avifauna. Gas chromatography coupled with electroantennographic detection (GC-EAD), coupled gas chromatography-mass spectrometry (GC-MS), and field trapping experiments were used to identify volatile compounds from a yeast-sugar solution. EAD responses were consistently elicited by 14 yeast volatiles. In a series of field trapping experiments, a mixture of the 14 EAD-active compounds was similarly attractive to P. downsi when compared to the yeast-sugar solution, and we found that acetic acid and ethanol were essential for attraction. A mixture of 0.03 % acetic acid and 3 % ethanol was as attractive as the 14-component blend, but was not as attractive as the yeast-sugar solution. Philornis downsi showed positive and negative dose-responses to acetic acid in the ranges of 0.01 ~ 0.3 % and 0.3 ~ 9 %, respectively. Further optimization showed that the mixture of 1 % acetic acid and 3 % ethanol was as attractive as the yeast-sugar solution. Both mixtures of acetic acid and ethanol were more selective than the yeast-sugar solution in terms of non-target moths and Polistes versicolor wasps captured. These results indicate that acetic acid and ethanol produced by yeasts are crucial for P. downsi attraction to fermented materials on which they feed as adults and can be used to manage this invasive fly in Galapagos.     

Translational Read-Through Therapy of RPGR Nonsense Mutations

X-chromosomal retinitis pigmentosa (RP) frequently is caused by mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene. We evaluated the potential of PTC124 (Ataluren, Translama^TM) treatment to promote ribosomal read-through of premature termination codons (PTC) in RPGR. Expression constructs in HEK293T cells showed that the efficacy of read-through reagents is higher for UGA than UAA PTCs. We identified the novel hemizygous nonsense mutation c.1154T > A, p.Leu385* ({"type":"entrez-nucleotide","attrs":{"text":"NM_000328.3","term_id":"1677500221"}}NM_000328.3) causing a UAA PTC in RPGR and generated patient-derived fibroblasts. Immunocytochemistry of serum-starved control fibroblasts showed the RPGR protein in a dot-like expression pattern along the primary cilium. In contrast, RPGR was no longer detectable at the primary cilium in patient-derived cells. Applying PTC124 restored RPGR at the cilium in approximately 8% of patient-derived cells. RT-PCR and Western blot assays verified the pathogenic mechanisms underlying the nonsense variant. Immunofluorescence stainings confirmed the successful PTC124 treatment. Our results showed for the first time that PTC124 induces read-through of PTCs in RPGR and restores the localization of the RPGR protein at the primary cilium in patient-derived cells. These results may provide a promising new treatment option for patients suffering from nonsense mutations in RPGR or other genetic diseases.     

Physical filtration efficiency analysis of a polyaniline hybrid composite filter with graphite oxide for particulate matter 2.5

Particulate matter (PM) 2.5 pollution is a prevalent environmental and public health issue that has raised serious global concerns. Because standard heating, ventilation, and air conditioning filters are incapable of filtering out PM 2.5 particles efficiently, different methods of PM 2.5 filtration, such as physical filtration and electrostatic filtration, are under investigation to develop a filter with a high filtration efficiency and a low pressure drop. According to various studies, pressure drop has a significant influence on the filtration efficiency. An equation for the theoretical trend was generated based on the composite data gathered from similar filtration studies and was used to evaluate the relationship between pressure drop and filtration efficiency. Here, the theoretical equation indicated that the filtration efficiency increased as the pressure drop on a filter increased until 0.01 psi where the efficiency remained near constant at approximately 99.9%. In this study, we introduce a graphite oxide (GO) and polyaniline (PANi) composite hybrid filter in order to create a low-pressure (1.2 psi) drop filter. By adding GO flakes to the PANi matrix, we not only produced a highly permeable filter while allowing continuous gas flow, but also achieved a remarkable and highly effective PM 2.5 filter with a filtration efficiency of 99.7 ± 0.08%.     

Elucidation of the Clustered Nano-Architecture of Radiation-Induced DNA Damage Sites and Surrounding Chromatin in Cancer Cells: A Single Molecule Localization Microscopy Approach

In cancer therapy, the application of (fractionated) harsh radiation treatment is state of the art for many types of tumors. However, ionizing radiation is a “double-edged sword”—it can kill the tumor but can also promote the selection of radioresistant tumor cell clones or even initiate carcinogenesis in the normal irradiated tissue. Individualized radiotherapy would reduce these risks and boost the treatment, but its development requires a deep understanding of DNA damage and repair processes and the corresponding control mechanisms. DNA double strand breaks (DSBs) and their repair play a critical role in the cellular response to radiation. In previous years, it has become apparent that, beyond genetic and epigenetic determinants, the structural aspects of damaged chromatin (i.e., not only of DSBs themselves but also of the whole damage-surrounding chromatin domains) form another layer of complex DSB regulation. In the present article, we summarize the application of super-resolution single molecule localization microscopy (SMLM) for investigations of these structural aspects with emphasis on the relationship between the nano-architecture of radiation-induced repair foci (IRIFs), represented here by γH2AX foci, and their chromatin environment. Using irradiated HeLa cell cultures as an example, we show repair-dependent rearrangements of damaged chromatin and analyze the architecture of γH2AX repair clusters according to topological similarities. Although HeLa cells are known to have highly aberrant genomes, the topological similarity of γH2AX was high, indicating a functional, presumptively genome type-independent relevance of structural aspects in DSB repair. Remarkably, nano-scaled chromatin rearrangements during repair depended both on the chromatin domain type and the treatment. Based on these results, we demonstrate how the nano-architecture and topology of IRIFs and chromatin can be determined, point to the methodological relevance of SMLM, and discuss the consequences of the observed phenomena for the DSB repair network regulation or, for instance, radiation treatment outcomes.     

Focal Ischemic Injury to the Early Neonatal Rat Brain Models Cognitive and Motor Deficits with Associated Histopathological Outcomes Relevant to Human Neonatal Brain Injury

Neonatal arterial ischemic stroke is one of the more severe birth complications. The injury can result in extensive neurological damage and is robustly associated with later diagnoses of cerebral palsy (CP). An important part of efforts to develop new therapies include the on-going refinement and understanding of animal models that capture relevant clinical features of neonatal brain injury leading to CP. The potent vasoconstrictor peptide, Endothelin-1 (ET-1), has previously been utilised in animal models to reduce local blood flow to levels that mimic ischemic stroke. Our previous work in this area has shown that it is an effective and technically simple approach for modelling ischemic injury at very early neonatal ages, resulting in stable deficits in motor function. Here, we aimed to extend this model to also examine the impact on cognitive function. We show that focal delivery of ET-1 to the cortex of Sprague Dawley rats on postnatal day 0 (P0) resulted in impaired learning in a touchscreen-based test of visual discrimination and correlated with important clinical features of CP including damage to large white matter structures.     

Utilization of different tall oils for improving the water resistance of cellulosic fibers

This study was conducted to assess the effect of the pulping by-products crude tall oil (CTO), distilled tall oil (DTO), and tall oil fatty acid (TOFA) on dynamic water vapor sorption behavior, interfiber strength, and thermal stability of cellulosic paper-sheets. The results were compared against those obtained in cellulose papers treated with the conventional petroleum-derived hydrophobic agent hydrowax and in untreated ones. The tall oil treatments caused strong reduction in equilibrium moisture content of the paper-sheets during adsorption and desorption runs. The same trend was noticed for the hydrowax-treated papers, however, it was less pronounced than the CTO-treated and DTO-treated samples in the relative humidity range of 75–95%. The sorption hysteresis was considerably decreased after the treatments. The ultimate dry-tensile strengths of the paper-sheets were significantly reduced by TOFA and hydrowax treatments, while CTO and DTO showed comparable strength as that of untreated control. The ultimate wet-strengths of the paper-sheets were improved after the treatments. The thermal stability of the specimens was improved by the tall oil treatments, and the hydrowax-treated samples illustrated lower degradation temperature than the untreated control. The results are promising for the use of tall oils as alternative hydrophobic agents of cellulosic fiber-based products, such as wood panels and paper packaging. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019 , 136, 47303.