Perturbations and projections of Kalman–Bucy semigroups

© 2017 Elsevier B.V. We analyse various perturbations and projections of Kalman–Bucy semigroups and Riccati equations. For example, covariance inflation-type perturbations and localisation methods (projections) are common in the ensemble Kalman filtering literature. In the limit of these ensemble methods, the regularised sample covariance tends toward a solution of a perturbed/projected Riccati equation. With this motivation, results are given characterising the error between the nominal and regularised Riccati flows and Kalman–Bucy filtering distributions. New projection-type models are also discussed; e.g. Bose–Mesner projections. These regularisation models are also of interest on their own, and in, e.g., differential games, control of stochastic/jump processes, and robust control

The clinical application of electrical impedance technology in the detection of malignant neoplasms: a systematic review

Background: Electrical impedance technology has been well established for the last 20 years. Recently research has begun to emerge into its potential uses in the detection and diagnosis of pre-malignant and malignant conditions. The aim of this study was to systematically review the clinical application of electrical impedance technology in the detection of malignant neoplasms. Methods: A search of Embase Classic, Embase and Medline databases was conducted from 1980 to 22/02/2018 to identify studies reporting on the use of bioimpedance technology in the detection of pre-malignant and malignant conditions. The ability to distinguish between tissue types was defined as the primary endpoint, and other points of interest were also reported. Results: 731 articles were identified, of which 51 reported sufficient data for analysis. These studies covered 16 different cancer subtypes in a total of 7035 patients. As the studies took various formats, a qualitative analysis of each cancer subtype’s data was undertaken. All the studies were able to show differences in electrical impedance and/or related metrics between malignant and normal tissue. Conclusions: Electrical impedance technology provides a novel method for the detection of malignant tissue, with large studies of cervical, prostate, skin and breast cancers showing encouraging results. Whilst these studies provide promising insights into the potential of this technology as an adjunct in screening, diagnosis and intra-operative margin assessment, customised development as well as multi-centre clinical trials need to be conducted before it can be reliably employed in the clinical detection of malignant tissue

Multiplicative non‐gaussian model error estimation in data assimilation

Abstract: Model uncertainty quantification is an essential component of effective data assimilation. Model errors associated with sub‐grid scale processes are often represented through stochastic parameterizations of the unresolved process. Many existing Stochastic Parameterization schemes are only applicable when knowledge of the true sub‐grid scale process or full observations of the coarse scale process are available, which is typically not the case in real applications. We present a methodology for estimating the statistics of sub‐grid scale processes for the more realistic case that only partial observations of the coarse scale process are available. Model error realizations are estimated over a training period by minimizing their conditional sum of squared deviations given some informative covariates (e.g., state of the system), constrained by available observations and assuming that the observation errors are smaller than the model errors. From these realizations a conditional probability distribution of additive model errors given these covariates is obtained, allowing for complex non‐Gaussian error structures. Random draws from this density are then used in actual ensemble data assimilation experiments. We demonstrate the efficacy of the approach through numerical experiments with the multi‐scale Lorenz 96 system using both small and large time scale separations between slow (coarse scale) and fast (fine scale) variables. The resulting error estimates and forecasts obtained with this new method are superior to those from two existing methods

Detecting colorectal cancer using electrical impedance spectroscopy: an ex vivo feasibility study

Objective: Colorectal cancer is the fourth most common cancer worldwide, with a lifetime risk of around 20%. Current solutions do not allow clinicians to objectively assess tissue abnormality during endoscopy and perioperatively. A solution capable of objectively assessing samples in real time could greatly improve the treatment process. A solution that can be integrated in minimally invasive diagnostics and management strategies to provide real-time point-of-care information would be greatly transformative. Electrical impedance spectroscopy (EIS) may provide such a solution. In this paper, we present a feasibility study on using EIS in assessing colorectal tissue. Approach: We performed tetrapolar EIS using ZedScan on excised human colorectal tumour tissue and the matched normal colonic mucosa in 22 freshly resected specimens following elective surgery for colorectal cancer. Histopathological examination was used to confirm the final diagnosis. Statistical significance was assessed with Wilcoxon signed rank test. Main results: Tetrapolar EIS could discriminate cancer with statistically significant results when applying frequencies between 305 Hz – 625 kHz (p < 0.05). 300 Ω was set as the transfer impedance threshold to detect cancer. Thus, the area under the corresponding receiver operating characteristic curve for this threshold was 0.7105. Significance: This feasibility study demonstrates that impedance spectra changes in colorectal cancer tissue are detectable and may be statistically significant, suggesting that EIS has the potential to be the core technology in a novel non-invasive point of care test for detecting colorectal cancer. These results warrant further development and increasing the size of the study with a device specificity designed for colorectal cancer

A Novel Auxiliary Agarolytic Pathway Expands Metabolic Versatility in the Agar-Degrading Marine Bacterium Colwellia echini A3(T)

Marine microorganisms encode a complex repertoire of carbohydrate-active enzymes (CAZymes) for the catabolism of algal cell wall polysaccharides. While the core enzyme cascade for degrading agar is conserved across agarolytic marine bacteria, gain of novel metabolic functions can lead to the evolutionary expansion of the gene repertoire. Here, we describe how two less-abundant GH96 a-agarases harbored in the agar-specific polysaccharide utilization locus (PUL) of Colwellia echini strain A3(T) facilitate the versatility of the agarolytic pathway. The cellular and molecular functions of the a-agarases examined by genomic, transcriptomic, and biochemical analyses revealed that alpha-agarases of C. echini A3(T) create a novel auxiliary pathway. alpha-Agarases convert even-numbered neoagarooligo-saccharides to odd-numbered agaro- and neoagarooligosaccharides, providing an alternative route for the depolymerization process in the agarolytic pathway. Comparative genomic analysis of agarolytic bacteria implied that the agarolytic gene repertoire in marine bacteria has been diversified during evolution, while the essential core agarolytic gene set has been conserved. The expansion of the agarolytic gene repertoire and novel hydrolytic functions, including the elucidated molecular functionality of alpha-agarase, promote metabolic versatility by channeling agar metabolism through different routes. IMPORTANCE Colwellia echini A3(T) is an example of how the gain of gene(s) can lead to the evolutionary expansion of agar-specific polysaccharide utilization loci (PUL). C. echini A3(T) encodes two a-agarases in addition to the core beta-agarolytic enzymes in its agarolytic PUL. Among the agar-degrading CAZymes identified so far, only a few alpha-agarases have been biochemically characterized. The molecular and biological functions of two alpha-agarases revealed that their unique hydrolytic pattern leads to the emergence of auxiliary agarolytic pathways. Through the combination of transcriptomic, genomic, and biochemical evidence, we elucidate the complete alpha-agarolytic pathway in C. echini A3(T). The addition of alpha-agarases to the agarolytic enzyme repertoire might allow marine agarolytic bacteria to increase competitive abilities through metabolic versatility

Removal of Acid Yellow 25 from Aqueous Solution by Chitin Prepared from Waste Snow Crab Legs

Acid Yellow 25 (AY25) is used in the textile industry for dyeing of natural and synthetic fibers, and is also used as a coloring agent in paints, inks, plastics, and leathers. Effluents from such industries are major sources of water pollution. Hence, it is important to find simple, efficient, and inexpensive ways to remove these dyes from wastewater. Here, we determined the suitability of chitin extracted from waste crab legs as an adsorbent for removing AY25 dye. The adsorption kinetics was modeled using pseudo-first order, pseudo-second order, and intraparticle diffusion equations to determine the rate controlling step. Results showed that the pseudo-second order adsorption mechanism is predominant, and the overall rate of the dye adsorption process is therefore controlled by an adsorption reaction. Adsorption isotherms were analyzed by utilizing the Langmuir, Freundlich, Dubinin-Radushkevich (D-R) and Temkin isotherm models at 23˚C, with data collected by using various initial dye concentrations with different chitin dosages. Our results show the highest correlation with the Langmuir model, consistent with the fact that chitin contains both a monolayer and homogeneous adsorption sites. Based on the D-R model, the adsorption of AY25 dye onto chitin is via chemisorption. Furthermore, we have concluded that the rate constants of both pseudo-second order adsorption and film diffusion are correlated to the initial dye concentrations and chitin dosages. In conclusion, chitin from waste crab legs is a very suitable adsorbent material that is capable of rapidly removing up to 95% of the initial concentration of AY25 dye at a pH of 2 and room temperature

Location and content of counselling and acceptance of postpartum IUD in Sri Lanka

Background: The immediate postpartum IUD (PPIUD) is a long-acting, reversible method of contraception that can be used safely and effectively following a birth. To appropriately facilitate the immediate postpartum insertion of IUDs, women must be informed of the method’s availability and must be counselled on its benefits and risks prior to entering the delivery room. We examine the relationship between the location and quality of antenatal counselling and women’s acceptance of immediate postpartum IUD (PPIUD) in four hospitals in Sri Lanka. Methods: Data were collected between January 2015 and May 2015. Modified Poisson regressions with robust standard errors are used to assess the relationships between place of counselling, indicators of counselling quality, and PPIUD uptake following delivery. Results: We find that women who were counselled in hospital antenatal clinics and admission wards were much more likely to have a PPIUD inserted than women who were counselled in field clinics or during home visits. Hospital-based counselling had higher quality indicators for providing information on PPIUD, and women were more likely to receive PPIUD information leaflets in hospital locations than in lower-tiered clinics or during home visits. Women who were counselled at hospital locations also reported a higher level of satisfaction with the counselling that they received. Receipt of hospital-based counselling was also linked to higher PPIUD uptake, in spite of the fact that women were more likely to be given information about the risks and alternatives to PPIUD in hospitals. The information about the risks of and alternatives to PPIUD, whether provided in hospital or in non-hospital settings, tended to lower the likelihood of acceptance to have a PPIUD insertion. Counselling in hospital admission wards was focused on women who had not been counselled at field clinics. Conclusions: The study findings call for efforts that improve the training of midwives who provide PPIUD counselling at field clinics and during the home visits. We also recommend that routine PPIUD counselling be conducted in hospitals, even if women have already been counselled elsewhere

The clinical application of electrical impedance technology in the detection of malignant neoplasms: a systematic review

Background: Electrical impedance technology has been well established for the last 20 years. Recently research has begun to emerge into its potential uses in the detection and diagnosis of pre-malignant and malignant conditions. The aim of this study was to systematically review the clinical application of electrical impedance technology in the detection of malignant neoplasms. Methods: A search of Embase Classic, Embase and Medline databases was conducted from 1980 to 22/02/2018 to identify studies reporting on the use of bioimpedance technology in the detection of pre-malignant and malignant conditions. The ability to distinguish between tissue types was defined as the primary endpoint, and other points of interest were also reported. Results: 731 articles were identified, of which 51 reported sufficient data for analysis. These studies covered 16 different cancer subtypes in a total of 7035 patients. As the studies took various formats, a qualitative analysis of each cancer subtype’s data was undertaken. All the studies were able to show differences in electrical impedance and/or related metrics between malignant and normal tissue. Conclusions: Electrical impedance technology provides a novel method for the detection of malignant tissue, with large studies of cervical, prostate, skin and breast cancers showing encouraging results. Whilst these studies provide promising insights into the potential of this technology as an adjunct in screening, diagnosis and intra-operative margin assessment, customised development as well as multi-centre clinical trials need to be conducted before it can be reliably employed in the clinical detection of malignant tissue

Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity.

Genome rearrangements, a hallmark of cancer, can result in gene fusions with oncogenic properties. Using DNA paired-end-tag (DNA-PET) whole-genome sequencing, we analyzed 15 gastric cancers (GCs) from Southeast Asians. Rearrangements were enriched in open chromatin and shaped by chromatin structure. We identified seven rearrangement hot spots and 136 gene fusions. In three out of 100 GC cases, we found recurrent fusions between CLDN18, a tight junction gene, and ARHGAP26, a gene encoding a RHOA inhibitor. Epithelial cell lines expressing CLDN18-ARHGAP26 displayed a dramatic loss of epithelial phenotype and long protrusions indicative of epithelial-mesenchymal transition (EMT). Fusion-positive cell lines showed impaired barrier properties, reduced cell-cell and cell-extracellular matrix adhesion, retarded wound healing, and inhibition of RHOA. Gain of invasion was seen in cancer cell lines expressing the fusion. Thus, CLDN18-ARHGAP26 mediates epithelial disintegration, possibly leading to stomach H(+) leakage, and the fusion might contribute to invasiveness once a cell is transformed. Cell Rep 2015 Jul 14; 12(2):272-285

Time Varying Parameter Models for Catchments with Land Use Change: the Importance of Model Structure

Rapid population and economic growth in South-East-Asia has been accompanied by extensive land use change with consequent impacts on catchment hydrology. Modelling methodologies capable of handling changing land use conditions are therefore becoming ever more important, and are receiving increasing attention from hydrologists. A recently developed Data Assimilation based framework that allows model parameters to vary through time in response to signals of change in observations is considered for a medium sized catchment (2880 km²) in Northern Vietnam experiencing substantial but gradual land cover change. We investigate the efficacy of the method as well as the importance of the chosen model structure in ensuring the success of time varying parameter methods. The framework was utilized with two conceptual models (HBV and HyMOD) that gave good quality streamflow predictions during pre-change conditions. Although both time varying parameter models gave improved streamflow predictions under changed conditions compared to the time invariant parameter model, persistent biases for low flows were apparent in the HyMOD case. It was found that HyMOD was not suited to representing the modified baseflow conditions, resulting in extreme and unrealistic time varying parameter estimates. This work shows that the chosen model can be critical for ensuring the time varying parameter framework successfully models streamflow under changed land cover conditions. It also serves as an effective tool for separating the influence of climatic and land use change in retrospective studies where the lack of a paired control catchment precludes such an assessment