Search

Chest X-rays are the most commonly performed medical imaging exam, yet they are often misinterpreted by physicians. Here, we present an FDA-cleared, artificial intelligence (AI) system which uses a deep learning algorithm to assist physicians in the comprehensive detection and localization of abnormalities on chest X-rays. We trained and tested the AI system on a large dataset, assessed generalizability on publicly available data, and evaluated radiologist and non-radiologist physician accuracy when unaided and aided by the AI system. The AI system accurately detected chest X-ray abnormalities (AUC: 0.976, 95% bootstrap CI: 0.975, 0.976) and generalized to a publicly available dataset (AUC: 0.975, 95% bootstrap CI: 0.971, 0.978). Physicians showed significant improvements in detecting abnormalities on chest X-rays when aided by the AI system compared to when unaided (difference in AUC: 0.101, p < 0.001). Non-radiologist physicians detected abnormalities on chest X-ray exams as accurately as radiologists when aided by the AI system and were faster at evaluating chest X-rays when aided compared to unaided. Together, these results show that the AI system is accurate and reduces physician errors in chest X-ray evaluation, which highlights the potential of AI systems to improve access to fast, high-quality radiograph interpretation. [ABSTRACT FROM AUTHOR]

Background: Moyamoya is a progressive, non-atherosclerotic cerebral arteriopathy that may present in childhood and currently has no cure. Early diagnosis is critical to prevent a lifelong risk of neurological morbidity. Blood-oxygen-level-dependent (BOLD) MRI cerebrovascular reactivity (CVR) imaging provides a non-invasive, in vivo measure of autoregulatory capacity and cerebrovascular reserve. However, non-compliant or younger children require general anesthesia to achieve BOLD-CVR imaging. Objective: To determine the same-day repeatability of BOLD-CVR imaging under general anesthesia in children with moyamoya. Materials and methods: Twenty-eight examination pairs were included (mean patient age = 7.3 ± 4.0 years). Positive and negatively reacting voxels were averaged over signals and counted over brain tissue and vascular territory. The intraclass correlation coefficient (ICC), Wilcoxon signed-rank test, and Bland–Altman plots were used to assess the variability between the scans. Results: There was excellent-to-good (≥ 0.59) within-day repeatability in 18 out of 28 paired studies (64.3%). Wilcoxon signed-rank tests demonstrated no significant difference in the grey and white matter CVR estimates, between repeat scans (all p-values > 0.05). Bland–Altman plots of differences in mean magnitude of positive and negative and fractional positive and negative CVR estimates illustrated a reasonable degree of agreement between repeat scans and no systematic bias. Conclusion: BOLD-CVR imaging provides repeatable assessment of cerebrovascular reserve in children with moyamoya imaged under general anesthesia. [ABSTRACT FROM AUTHOR]

This paper introduces a novel graph-based filter method for automatic feature selection (abbreviated as GB-AFS) for multi-class classification tasks. The method determines the minimum combination of features required to sustain prediction performance while maintaining complementary discriminating abilities between different classes. It does not require any user-defined parameters such as the number of features to select. The minimum number of features is selected using our newly developed Mean Simplified Silhouette (abbreviated as MSS) index, designed to evaluate the clustering results for the feature selection task. To illustrate the effectiveness and generality of the method, we applied the GB-AFS method using various combinations of statistical measures and dimensionality reduction techniques. The experimental results demonstrate the superior performance of the proposed GB-AFS over other filter-based techniques and automatic feature selection approaches, and demonstrate that the GB-AFS method is independent of the statistical measure or the dimensionality reduction technique chosen by the user. Moreover, the proposed method maintained the accuracy achieved when utilizing all features while using only 7– 30 % of the original features. This resulted in an average time saving ranging from 15 % for the smallest dataset to 70 % for the largest. Our code is available at https://github.com/davidlevinwork/gbfs/. [ABSTRACT FROM AUTHOR]

Linear approximation methods suffer from Gibbs oscillations when approximating functions with jumps. Essentially non oscillatory subcell-resolution (ENO-SR) is a local technique avoiding oscillations and with a full order of accuracy, but a loss of regularity of the approximant appears. The goal of this paper is to introduce a new approach having both properties of full accuracy and regularity. In order to obtain it, we propose a three-stage algorithm: first, the data is smoothed by subtracting an appropriate non-smooth data sequence; then a chosen high order linear approximation operator is applied to the smoothed data and finally, an approximation with the proper jump or corner (jump in the first order derivative) discontinuity structure is reinstated by correcting the smooth approximation with the non-smooth element used in the first stage. This new procedure can be applied as subdivision scheme to design curves and surfaces both in point-value and in cell-average contexts. Using the proposed algorithm, we are able to construct approximations with high precision, with high piecewise regularity, and without smearing nor oscillations in the presence of discontinuities. These are desired properties in real applications as computer aided design or car design, among others. [ABSTRACT FROM AUTHOR]

Blends of poly(lactic acid) (PLA) and poly(butylene adipate-co-terephthalate) (PBAT) are biodegradable polymers with opposite, yet complementary, physical and thermal properties. However, PLA and PBAT are immiscible and additives must be introduced to overcome their incompatibility and achieve their full potential as blended polymers. In this work, we describe the use of epoxidized canola oil (ECO) as a novel compatibilizer for PLA and PBAT. ECO was produced and characterized using Attenuated Total Reflectance Fourier-Transform Infrared spectroscopy (ATR-FTIR) and proton nuclear magnetic resonance (1H NMR). ATR-FTIR confirmed the epoxidation reaction, while 1H NMR was used to quantify the alkene-to-epoxy conversion rate. Polymer blends were prepared using a batch mixer and were characterized using ATR-FTIR, 1H NMR, scanning electron microscopy, differential scanning calorimetry, and mechanical analyses. The polymer blends containing ECO demonstrated a significant reduction in the PBAT dispersed phase size and thermal transitions of PLA (glass transition, cold crystallization, and melt temperatures), as well as a significant increase in elongation-at-break while maintaining the same tensile strength and Young's Modulus. [ABSTRACT FROM AUTHOR]

Idiopathic pulmonary fibrosis (IPF) is characterised by progressive fibrosing interstitial pneumonia with an associated irreversible decline in lung function and quality of life. IPF prevalence increases with age, appearing most frequently in patients aged > 50 years. Pulmonary vessel-like volume (PVV) has been found to be an independent predictor of mortality in IPF and other interstitial lung diseases, however its estimation can be impacted by artefacts associated with image segmentation methods and can be confounded by adjacent fibrosis. This study compares PVV in IPF patients (N = 21) with PVV from a healthy cohort aged > 50 years (N = 59). The analysis includes a connected graph-based approach that aims to minimise artefacts contributing to calculation of PVV. We show that despite a relatively low extent of fibrosis in the IPF cohort (20% of the lung volume), PVV is 2–3 times higher than in controls. This suggests that a standardised method to calculate PVV that accounts for tree connectivity could provide a promising tool to provide early diagnostic or prognostic information in IPF patients and other interstitial lung disease. [ABSTRACT FROM AUTHOR]

Given gridded cell-average data of a smooth multivariate function, we present a constructive explicit procedure for generating a high-order global approximation of the function. One contribution is the derivation of high-order approximations to point-values of the function directly from the cell-average data. The second contribution is the development of univariate B-spline-based high-order quasi-interpolation operators using cell-average data. Multivariate spline quasi-interpolation approximation operators are obtained by tensor product of the univariate operators. [ABSTRACT FROM AUTHOR]

In many applications, it is useful to use piecewise polynomials that satisfy certain regularity conditions at the joint points. Cubic spline functions emerge as good candidates having C2 regularity. On the other hand, if the data points present discontinuities, the classical spline approximations produce Gibbs oscillations. In a recent paper, we have introduced a new nonlinear spline approximation avoiding the presence of these oscillations. Unfortunately, this new reconstruction loses the C2 regularity. This paper introduces a new nonlinear spline that preserves the regularity at all the joint points except at the end points of an interval containing a discontinuity, and that avoids the Gibbs oscillations. [ABSTRACT FROM AUTHOR]

The paper deals with the problem of extrapolating data derived from sampling a C m function at scattered sites on a Lipschitz region Ω in R d to points outside of Ω in a computationally efficient way. While extrapolation problems go back to Whitney and many such problems have had successful theoretical resolutions, practical, computationally efficient implementations seem to be lacking. The goal here is to provide one way of obtaining such a method in a solid mathematical framework. The method utilized is a novel two-step moving least squares procedure (MLS) where the second step incorporates an error term obtained from the first MLS step. While the utility of the extrapolation degrades as a function of the distance to the boundary of Ω , the method gives rise to improved meshfree approximation error estimates when using the local Lagrange kernels related to certain radial basis functions. [ABSTRACT FROM AUTHOR]

Copyright of Canadian Journal of Anaesthesia / Journal Canadien d'Anesthésie is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

In this work, we present a new WENO B-spline-based quasi-interpolation algorithm. The novelty of this construction resides in the application of the WENO weights to the B-spline functions, that form a partition of unity, instead of the coefficients that multiply the B-spline functions of the spline. The result obtained conserves the smoothness of the original spline and presents adaption to discontinuities in the function. Another new idea that we introduce in this work is the use of different base weight functions from those proposed in classical WENO algorithms. Apart from introducing the construction of the new algorithms, we present theoretical results regarding the order of accuracy obtained at smooth zones and close to the discontinuity, as well as theoretical considerations about how to design the new weight functions. Through a tensor product strategy, we extend our results to several dimensions. In order to check the theoretical results obtained, we present an extensive battery of numerical experiments in one, two, and three dimensions that support our conclusions. [ABSTRACT FROM AUTHOR]

Biological hydrogen (H2) is a promising candidate for production of renewable hydrogen. Using entrapped cells rather than conventional suspended cell cultures for the production of H2 offers several advantages, such as improved production yields related to higher cell density, and enhanced resistance to substrate and end-product inhibition. In this study, H2 production by a novel isolate of Clostridium intestinale (strain URNW) was evaluated using cells entrapped within 2% calcium-alginate beads under strictly anaerobic conditions. Both immobilized cells and suspended cultures were studied in sequential batch-mode anaerobic fermentation over 192 h. The production of H2 in the headspace was examined for four different initial cellobiose concentrations (5, 10, 20, and 40 mM). Although a lag period for initiation of the fermentation process was observed for bacteria entrapped within hydrogel beads, the immobilized cells achieved both higher volumetric production rates (mmol H2/(L culture h)) and molar yields (mol H2/mol glucose equivalent) of H2 compared with suspended cultures. In the current study, the maximum cellobiose consumption rate of 0.40 mM/h, corresponding to 133.3 mg/(L h), was achieved after 72 h of fermentation by immobilized cells, generating a high hydrogen yield of 3.57 mol H2/mol cellobiose, whereas suspended cultures only yielded 1.77 mol H2/mol cellobiose. The results suggest that cells remain viable within the hydrogels and proliferated with a slow rate over the course of fermentation. The stable productivity of immobilized cells over 8 days with four changes of medium depicted that the immobilized cells of the isolated strain can successfully yield higher hydrogen and lower soluble metabolites than suspended cells suggesting a feasible process for future applications for bioH2 production. [ABSTRACT FROM AUTHOR]

Given function values on a uniform grid in a domain Ω in ℝ d , one is often interested in extending the values to a larger grid on a box B containing Ω. In particular, we are interested in "periodic extensions." For such extensions the discrete Fourier transform (DFT) of the resulting grid values on B is expected to provide good efficient approximation to the underlying function on Ω. This paper presents two different extension algorithms. The first method is a natural approach to this problem, aiming at achieving the fastest decay of the DFT coefficients of the extended data.The second is a fast algorithm which is appropriate for the univariate case and for limited cases of multivariate scenarios. It is shown that if a "good" periodic extension exists, the proposed method will find an extension with similar properties. [ABSTRACT FROM AUTHOR]

Background: The Value-Based Healthcare (VBH) concept is designed to improve individual healthcare outcomes without increasing expenditure, and is increasingly being used to determine resourcing of and reimbursement for medical services. Radiology is a major contributor to patient and societal healthcare at many levels. Despite this, some VBH models do not acknowledge radiology's central role; this may have future negative consequences for resource allocation. Methods, findings and interpretation: This multi-society paper, representing the views of Radiology Societies in Europe, the USA, Canada, Australia, and New Zealand, describes the place of radiology in VBH models and the healthcare value contributions of radiology. Potential steps to objectify and quantify the value contributed by radiology to healthcare are outlined. [ABSTRACT FROM AUTHOR]

Copyright of Canadian Journal of Anaesthesia / Journal Canadien d'Anesthésie is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

In order to avoid the curse of dimensionality, frequently encountered in big data analysis, there has been vast development in the field of linear and nonlinear dimension reduction techniques in recent years. These techniques (sometimes referred to as manifold learning) assume that the scattered input data is lying on a lower-dimensional manifold; thus the high dimensionality problem can be overcome by learning the lower dimensionality behavior. However, in real-life applications, data is often very noisy. In this work, we propose a method to approximate M a d-dimensional C m + 1 smooth submanifold of R n ( d ≪ n ) based upon noisy scattered data points (i.e., a data cloud). We assume that the data points are located "near" the lower-dimensional manifold and suggest a nonlinear moving least-squares projection on an approximating d-dimensional manifold. Under some mild assumptions, the resulting approximant is shown to be infinitely smooth and of high approximation order (i.e., O (h m + 1) , where h is the fill distance and m is the degree of the local polynomial approximation). The method presented here assumes no analytic knowledge of the approximated manifold and the approximation algorithm is linear in the large dimension n. Furthermore, the approximating manifold can serve as a framework to perform operations directly on the high-dimensional data in a computationally efficient manner. This way, the preparatory step of dimension reduction, which induces distortions to the data, can be avoided altogether. [ABSTRACT FROM AUTHOR]

A new Pseudomonas putida strain (AQ8) was isolated from a decommissioned oil refinery's soil in Italy and characterized for its ability to degrade BTEX. The draft genome of the new strain was sequenced and annotated for genes that encode enzymes putatively involved in BTEX degradation and quorum sensing. The strain was transformed with a plasmid expressing lactonase, which cleaves the autoinducer quorum sensing signal molecule, the acyl-homoserine lactone, to obtain a quorum sensing minus strain. P. putida AQ8 depleted the 40% on average of all the components of the initial BTEX concentration in 36 h. The quorum sensing minus strain, in the same time interval, depleted only the 10% of the initial BTEX concentration. The role of quorum sensing in regulating the expression of the annotated benzene/toluene dioxygenase gene (benzA) and biphenyl/toluene/benzene dioxygenase (bphA) genes, which are involved in BTEX degradation, was studied by quantitative RT-real-time quantitative (q)PCR analysis. The qPCR data showed decreased levels of expression of the benzA and bphA genes in the quorum sensing minus strain. Our results showed, for the first time, quorum sensing modulation of the level of transcription of dioxygenase genes in the upper BTEX oxidation pathway. [ABSTRACT FROM AUTHOR]

Purpose: Nabilone is a synthetic cannabinoid with properties that make it an appealing candidate as a postoperative nausea and vomiting (PONV) prophylactic adjunct. Nabilone has proven clinical utility in chemotherapy-related nausea and vomiting but has not been adequately tested for PONV. The purpose of this study was to evaluate the effectiveness of a single dose of nabilone for the prevention of PONV.Methods: This was a pragmatic single-centre randomized-controlled trial comparing oral nabilone vs placebo for the prevention of PONV. Eligible patients scheduled for elective surgery under general anesthesia who had a preoperative risk of PONV greater than 60% received either nabilone 0.5 mg or placebo orally prior to surgery. As part of the pragmatic design, the study medication was given in addition to any other combination of antiemetic prophylaxis. The primary outcome was the incidence of PONV. Secondary outcomes included the effect on pain, speed of recovery, and drug side effects.Results: Of the 340 patients randomized, 172 received nabilone and 168 received placebo. There was no difference in the incidence of PONV, which occurred in 20.9% in the nabilone group and 21.4% in the placebo group (relative risk, 0.98; 95% confidence interval, 0.89 to 1.11; P = 0.99). There were also no differences in pain scores, opioid consumption, or reported drug side effects.Conclusion: Oral nabilone 0.5 mg given as a single dose prior to surgery is ineffective in reducing PONV. This trial was registered at ClinicalTrials.gov, identifier: NCT02115529. [ABSTRACT FROM AUTHOR]

Stress-activated MAP kinases (SAPKs) respond to a wide variety of stressors. In most cases, the pathways through which specific stress signals are transmitted to the SAPKs are not known. Our recent findings have begun to address two important and related questions. First, do various stresses activate a SAPK through common pathways initiated at the cell surface, or through alternative, intracellular inputs? Second, how does an activated SAPK mount a specific response appropriate to the particular stress experienced? Our work has uncovered the mechanisms by which two stresses, arsenite treatment and DNA damage, stimulate the yeast SAPKs Hog1 and Mpk1, respectively. We found that these stresses activate the SAPKs through intracellular inputs that modulate their basal phosphorylation, rather than by activation of the protein kinase cascades known to stimulate them. Both stresses act through targeting, in different ways, the tyrosine-specific or dual-specificity protein phosphatases that normally maintain the SAPKs in a low-activity state. Previous work has demonstrated that basal signal flux through SAPK pathways is important for the sensitivity and dynamic response to external signals. Our work reveals that basal activity of SAPKs is additionally important to allow SAPK activation by intracellular inputs that modulate that activity. Additionally, because different stressors may activate SAPKs by modulation of basal signal through inputs at distinct nodes along the canonical activation pathway, stress-specific SAPK outputs may be controlled, in part, by the specific intracellular mechanisms of their activation. Thus, understanding the intracellular pathways through which various stressors activate SAPKs is likely to provide insight into how they elicit physiologically coherent responses to the specific stress experienced. [ABSTRACT FROM AUTHOR]

A metabolic, genomic and proteomic assessment of Fervidobacterium pennivorans strains was undertaken to clarify the metabolic and genetic capabilities of this Thermotogales species. The type strain Ven5 originally isolated from a hot mud spa in Italy, and a newly isolated strain (DYC) from a hot spring at Ngatamariki, New Zealand, were compared for metabolic and genomic differences. The fermentation profiles of both strains on cellobiose generated similar major end products (acetate, alanine, glutamate, H2, and CO2). The vast majority of end products produced were redox neutral, and carbon balances were in the range of 95-115%. Each strain showed distinct fermentation profiles on sugar substrates. The genome of strain DYC was sequenced and shown to have high sequence similarity and synteny with F. pennivorans Ven5 genome, suggesting they are the same species. The unique genome regions in Ven5, corresponded to genes involved in the Entner-Doudoroff pathway confirming our observation of DYC’s inability to utilize gluconate. Genome analysis was able to elucidate pathways involved in production of the observed end-products with the exception of alanine and glutamate synthesis which were resolved with less clarity due to poor sequence identity and missing critical enzymes within the pathway, respectively. [ABSTRACT FROM AUTHOR]

Economical production of medium-chain length polyhydroxyalkanoates (mcl-PHA) is dependent on efficient cultivation processes. This work describes growth and mcl-PHA synthesis characteristics of Pseudomonas putida LS46 when grown on medium-chain length fatty acids (octanoic acid) and lower-cost long-chain fatty acids (LCFAs, derived from hydrolyzed canola oil) in microaerophilic environments. Growth on octanoic acid ceased when the oxygen uptake rate was limited by the oxygen transfer rate, and mcl-PHA accumulated to 61.9% of the cell dry mass. From LCFAs, production of non-PHA cell mass continued at a rate of 0.36 g L−1 h−1 under oxygen-limited conditions, while mcl-PHA accumulated simultaneously to 31% of the cell dry mass. The titer of non-PHA cell mass from LCFAs at 14 h post-inoculation was double that obtained from octanoic acid in bioreactors operated with identical feeding and aeration conditions. While the productivity for octanoic acid was higher by 14 h, prolonged cultivation on LCFAs achieved similar productivity but with twice the PHA titer. Simultaneous co-feeding of each substrate demonstrated the continued cell growth under microaerophilic conditions characteristic of LCFAs, and the resulting polymer was dominant in C8 monomers. Furthermore, co-feeding resulted in improved PHA titer and volumetric productivity compared to either substrate individually. These results suggest that LCFAs improve growth of P. putida in oxygen-limited environments and could reduce production costs since more non-PHA cell mass, the cellular factories required to produce mcl-PHA and the most oxygen-intensive cellular process, can be produced for a given oxygen transfer rate. [ABSTRACT FROM AUTHOR]

In this work, we present a method that will allow us to remove outliers from a data set. Given the measurements of a function f = g + e on a set of sample points X⊂ℝd, where g∈CM+1(ℝd) is the function of interest and e is the deviation from the function g. We will say that a sample point x ∈ X is an outlier if the difference e(x) = f(x) − g(x) is large. We show that by analyzing the approximation errors on our sample set X, we may predict which of the sample points are outliers. Furthermore, we can identify outliers of very small deviations, as well as ones with large deviations. [ABSTRACT FROM AUTHOR]

This study characterizes a cryptic (pro)phage-related sequence within the Caldibacillus debilis GB1 genome, designated CBP1.CBP1 is a Siphoviridae-like genome highly related to GBVS1 from Geobacillus sp. 6k51. The CBP1genome is a 37,315 bp region containing 69 putative ORFs with a GC content of 42% flanked on both sides by host DNA integrated into the main bacterial chromosome (contig 16). Bioinformatic analyses identified cassettes of genes within the CBP1 genome that were similar in function, yet distinct in sequence, from genes previously identified in GBVS1. All of CBP1 genes had less than 60% amino acid sequence identity with GBVS1by tBLASTx, with the exception of the TMP repeat gene. CBP1 possessed all the necessary genes to undergo a temperate/lytic phage life cycle, including excision, replication, structural genes, DNA packaging, and cell lyses. Proteomic analysis of CBP1 revealed the expression of 5 proteins. One of the expressed proteins was a transcriptional regulator protein homologous to the bacteriophage λ repressor protein (cI) expressed in high amounts from the CBP1 region, consistent with a lysogenic phage in a repressed state. The CBP1 protein expression profile during host growth provides unique insight into thermophilic Siphoviridae-like phages in the repressed state within their host cells. [ABSTRACT FROM AUTHOR]

We analyze the mixing behavior of the biased exclusion process on a path of length n as the bias $$\beta _n$$ tends to 0 as $$n \rightarrow \infty $$ . We show that the sequence of chains has a pre-cutoff, and interpolates between the unbiased exclusion and the process with constant bias. As the bias increases, the mixing time undergoes two phase transitions: one when $$\beta _n$$ is of order 1 / n, and the other when $$\beta _n$$ is order $$\log n/n$$ . [ABSTRACT FROM AUTHOR]

Synthesis of poly-[3-hydroxybutyrate] (PHB) by Cupriavidus necator H16 in batch cultures was evaluated using three biodiesel-derived by-products as the sole carbon sources: waste glycerol (REG-80, refined to 80 % purity with negligible free fatty acids); glycerol bottom (REG-GB, with up to 65 % glycerol and 35 % free fatty acids), and free fatty acids (REG-FFA, with up to 75 % FFA and no glycerol). All the three substrates supported growth and PHB production by C. necator, with polymer accumulation ranging from 9 to 84 % cell dry weight (cdw), depending on the carbon source. To help understand these differences, proteomic analysis indicated that although C. necator H16 was able to accumulate PHB during growth on all three biodiesel by-products, no changes in the levels of PHB synthesis enzymes were observed. However, significant changes in the levels of expression were observed for two Phasin proteins involved with PHB accumulation, and for a number of gene products in the fatty acid β-oxidation pathway, the Glyoxylate Shunt, and the hydrogen (H) synthesis pathways in C. necator cells cultured with different substrates. The glycerol transport protein (GlpF) was induced in REG-GB and REG-80 glycerol cultures only. Cupriavidus necator cells cultured with REG-GB and REG-FFA showed up-regulation of β-oxidation and Glyoxylate Shunt pathways proteins at 24 h pi, but H synthesis pathways enzymes were significantly down-regulated, compared with cells cultured with waste glycerol. Our data confirmed earlier observations of constitutive expression of PHB synthesis proteins, but further suggested that C. necator H16 cells growing on biodiesel-derived glycerol were under oxidative stress. [ABSTRACT FROM AUTHOR]

The influence of the shift parameter β upon the convergence of the u-transformation may be crucial. It is shown, through a specific example, that a clever choice of β can improve the convergence acceleration rate of the u-transformation, while a wrong choice may even imply divergence of the method. A constructive approach for choosing an optimal shift parameter β is presented, based upon the exactness class (model) of the u-transformation. The parameter β which defines the best fitted model to a specific sequence is chosen for the acceleration of that sequence. [ABSTRACT FROM AUTHOR]

Given function values at scattered points in $${\mathbb {R}}^d$$ , possibly with noise, one of the ways of generating approximation to the function is by the method of moving least-squares (MLS). The method consists of computing local polynomials which approximate the data in a locally weighted least-squares sense. The resulting approximation is smooth, and is well approximating if the underlying function is smooth. Yet, as any least-squares based method it is quite sensitive to outliers in the data. It is well known that least- $$\ell _1$$ approximations are not sensitive to outliers. However, due to the nature of the $$\ell _1$$ norm, using it in the framework of a 'moving' approximation will not give a smooth, or even a continuous approximation. This paper suggests an error measure which is between the $$\ell _1$$ and the $$\ell _2$$ norms, with the advantages of both. Namely, yielding smooth approximations which are not too sensitive to outliers. A fast iterative method for computing the approximation is demonstrated and analyzed. It is shown that for a scattered data taken from a smooth function, with few outliers, the new approximation gives an $$O(h)$$ approximation error to the function. [ABSTRACT FROM AUTHOR]

Biodiesel production-derived waste glycerol (WG) was previously investigated as potential carbon source for medium chain length polyhydroxyalkanoate (mcl-PHA) production by Pseudomonas putida LS46. In this study, we evaluated the effect of impurities in the WG on P. putida LS46 physiology during exponential growth and corresponding changes in transcription and protein expression profiles compared with cells grown on pure, reagent grade glycerol. High concentration of metal ions, such as Na, and numbers of heavy metals ion, such as copper, ion, zinc, were detected in biodiesel-derived WG. Omics analysis from the corresponding cultures suggested altered expression of genes involved in transport and metabolism of ammonia and heavy metal ions. Expression of three groups of heavy metal homeostasis genes was significantly changed (mostly upregulated) in WG cultures and included the following: copper-responded cluster 1 and 2 genes, primarily containing cusABC; two copies of copAB and heavy metal translocating P-type ATPase; Fur-regulated, TonB-dependent siderophore receptor; and several cobalt/zinc/cadmium transporters. Expression of these genes suggests regulation of intracellular concentrations of heavy metals during growth on biodiesel-derived glycerol. Finally, a number of genes involved in adapting to, or metabolizing free fatty acids and other nonheavy metal contaminants, such as Na, were also upregulated in P. putida LS46 grown on biodiesel-derived glycerol. [ABSTRACT FROM AUTHOR]

A novel strain of Pseudomonas putida LS46 was isolated from wastewater on the basis of its ability to synthesize medium chain-length polyhydroxyalkanoates (mcl-PHAs). P.putida LS46 was differentiated from other P.putida strains on the basis of cpn60 (UT). The complete genome of P.putida LS46 was sequenced and annotated. Its chromosome is 5,86,2556 bp in size with GC ratio of 61.69. It is encoding 5316 genes, including 7 rRNA genes and 76 tRNA genes. Nucleotide sequence data of the complete P. putida LS46 genome was compared with nine other P. putida strains (KT2440, F1, BIRD-1, S16, ND6, DOT-T1E, UW4, W619 and GB-1) identified either as biocontrol agents or as bioremediation agents and isolated from different geographical region and different environment. BLASTn analysis of whole genome sequences of the ten P. putida strains revealed nucleotide sequence identities of 86.54 to 97.52%. P.putida genome arrangement was LS46 highly similar to P.putida BIRD1 and P.putida ND6 but was markedly different than P.putida DOT-T1E, P.putida UW4 and P.putida W619. Fatty acid biosynthesis ( fab), fatty acid degradation ( fad) and PHA synthesis genes were highly conserved among biocontrol and bioremediation P.putida strains. Six genes in pha operon of P. putida LS46 showed >98% homology at gene and proteins level. It appears that polyhydroxyalkanoate (PHA) synthesis is an intrinsic property of P. putida and was not affected by its geographic origin. However, all strains, including P. putida LS46, were different from one another on the basis of house keeping genes, and presence of plasmid, prophages, insertion sequence elements and genomic islands. While P. putida LS46 was not selected for plant growth promotion or bioremediation capacity, its genome also encoded genes for root colonization, pyoverdine synthesis, oxidative stress (present in other soil isolates), degradation of aromatic compounds, heavy metal resistance and nicotinic acid degradation, manganese (Mn II) oxidation. Genes for toluene or naphthalene degradation found in the genomes of P. putida F1, DOT-T1E, and ND6 were absent in the P. putida LS46 genome. Heavy metal resistant genes encoded by the P. putida W619 genome were also not present in the P. putida LS46 genome. Despite the overall similarity among genome of P.putida strains isolated for different applications and from different geographical location a number of differences were observed in genome arrangement, occurrence of transposon, genomic islands and prophage. It appears that P.putida strains had a common ancestor and by acquiring some specific genes by horizontal gene transfer it differed from other related strains. [ABSTRACT FROM AUTHOR]

Higher initial glycerol loadings (620 mM) have a negative effect on growth and 1,3-propanediol (1,3-PDO) synthesis in Clostridium butyricum DSM 10702 relative to lower initial glycerol concentrations (170 mM). To help understand metabolic shifts associated with elevated glycerol, protein expression levels were quantified by LC/MS/MS analyses. Thirty one (31) proteins involved in conversion of glycerol to 1,3-PDO and other by-products were analyzed by multiple reaction monitoring (MRM). The analyses revealed that high glycerol concentrations reduced cell growth. The expression levels of most proteins in glycerol catabolism pathways were down-regulated, consistent with the slower growth rates observed. However, at high initial glycerol concentrations, some of the proteins involved in the butyrate synthesis pathways such as a putative ethanol dehydrogenase (CBY_3753) and a 3-hydroxybutyryl-CoA dehydrogenase (CBY_3045) were up-regulated in both exponential and stationary growth phases. Expression levels of proteins (CBY_0500, CBY_0501 and CBY_0502) involved in the reductive pathway of glycerol to 1,3-PDO were consistent with glycerol consumption and product concentrations observed during fermentation at both glycerol concentrations, and the molar yields of 1,3-PDO were similar in both cultures. This is the first report that correlates expression levels of glycerol catabolism enzymes with synthesis of 1,3-PDO in C. butyricum. The results revealed that significant differences in the expression of a small subset of proteins were observed between exponential and stationary growth phases at both low and high glycerol concentrations. [ABSTRACT FROM AUTHOR]

This paper presents a new method for the analysis of convergence and smoothness of univariate nonuniform subdivision schemes. The analysis involves ideas from the theory of asymptotically equivalent subdivision schemes and nonuniform Laurent polynomial representation together with a new perturbation result. Application of the new method is presented for the analysis of interpolatory subdivision schemes based upon extended Chebyshev systems and for a class of smoothly varying schemes. [ABSTRACT FROM AUTHOR]

Microfluidic systems can better control cellular microenvironments and therefore are increasingly used for cell migration research. However, most existing systems are impractical to use without specialized facilities and researchers. Toward removing this barrier, we developed a compact USB microscope-based Microfluidic Chemotaxis Analysis System (UMCAS). This system integrates microfluidic devices, live cell imaging, environmental control and data analysis to provide a solution for rapid microfluidic cell migration and chemotaxis experiments with real-time result reporting. This developed system was successfully validated by testing neutrophil chemotaxis. [ABSTRACT FROM AUTHOR]

While annotation of the genome sequence of Clostridium thermocellum has allowed predictions of pathways catabolizing cellobiose to end products, ambiguities have persisted with respect to the role of various proteins involved in electron transfer reactions. A combination of growth studies modulating carbon and electron flow and multiple reaction monitoring (MRM) mass spectrometry measurements of proteins involved in central metabolism and electron transfer was used to determine the key enzymes involved in channeling electrons toward fermentation end products. Specifically, peptides belonging to subunits of ferredoxin-dependent hydrogenase and NADH:ferredoxin oxidoreductase (NFOR) were low or below MRM detection limits when compared to most central metabolic proteins measured. The significant increase in H versus ethanol synthesis in response to either co-metabolism of pyruvate and cellobiose or hypophosphite mediated pyruvate:formate lyase inhibition, in conjunction with low levels of ferredoxin-dependent hydrogenase and NFOR, suggest that highly expressed putative bifurcating hydrogenases play a substantial role in reoxidizing both reduced ferredoxin and NADH simultaneously. However, product balances also suggest that some of the additional reduced ferredoxin generated through increased flux through pyruvate:ferredoxin oxidoreductase must be ultimately converted into NAD(P)H either directly via NADH-dependent reduced ferredoxin:NADP oxidoreductase (NfnAB) or indirectly via NADPH-dependent hydrogenase. While inhibition of hydrogenases with carbon monoxide decreased H production 6-fold and redirected flux from pyruvate:ferredoxin oxidoreductase to pyruvate:formate lyase, the decrease in CO was only 20 % of that of the decrease in H, further suggesting that an alternative redox system coupling ferredoxin and NAD(P)H is active in C. thermocellum in lieu of poorly expressed ferredoxin-dependent hydrogenase and NFOR. [ABSTRACT FROM AUTHOR]

Growth, end-product synthesis, enzyme activities, and transcription of select genes associated with the 'malate shunt,' pyruvate catabolism, H synthesis, and ethanol production were studied in the cellulolytic anaerobe, Clostridium thermocellum ATCC 27405, during open-batch fermentation of cellobiose to determine the effect of elevated N and H gas sparging on metabolism using a 14-L fermenter with a 7-L working volume. The metabolic shift from acetate, H, and CO to ethanol and formate in response to high H versus high N sparging (20 mL s) was accompanied by (a) a 2-fold increase in nicotinamide adenine dinucleotide (NADH)-dependent alcohol dehydrogenase (Adh) activity, (b) a 10-fold increase in adhE transcription, and (c) a 3-fold decrease in adhZ transcription. A similar, but less pronounced, metabolic shift was also observed when the rate of N sparging was decreased from 20 to 2 mL s, during which (a) NADH-dependent ADH and pyruvate: ferredoxin oxidoreductase (PFOR) activities increased by ∼1.5-fold, (b) adhY transcription increased 6-fold, and (c) transcription of selected pfor genes increased 2-fold. Here we demonstrate that transcription of genes involved in ethanol metabolism is tightly regulated in response to gas sparging. We discuss the potential impacts of dissolved H on electron carrier (NADH, NADPH, ferredoxin) oxidation and how these electron carriers can redirect carbon and electron flux and regulate adhE transcription. [ABSTRACT FROM AUTHOR]

In this paper, we study a family of lattice walks which are related to the Hadamard conjecture. There is a bijection between paths of these walks which originate and terminate at the origin and equivalence classes of partial Hadamard matrices. Therefore, the existence of partial Hadamard matrices can be proved by showing that there is positive probability of a random walk returning to the origin after a specified number of steps. Moreover, the number of these designs can be approximated by estimating the return probabilities. We use the inversion formula for the Fourier transform of the random walk to provide such estimates. We also include here an upper bound, derived by elementary methods, on the number of partial Hadamard matrices. [ABSTRACT FROM AUTHOR]

Green coordinates require to build an enclosing cage around a shape that is deformed by manipulating the cage. In this paper, we build upon the local differences of Green coordinates and propose a method to deform a shape locally without constructing a cage. Second, we derive linear formulas to directly interpolate points on the shape to desired locations using an umbrella shaped cell. Moreover, we set up an influence region to confine the deformation in a local area. Finally, we suggest a method to automatically construct an umbrella shaped cell and thus update it consecutively while the shape is deforming. Experiments have shown that the suggested approach delivers smooth local deformations and enables shape manipulations at an interactive rate. [ABSTRACT FROM AUTHOR]

We study the Glauber dynamics for the Ising model on the complete graph, also known as the Curie–Weiss Model. For β < 1, we prove that the dynamics exhibits a cut-off: the distance to stationarity drops from near 1 to near 0 in a window of order n centered at [2(1 − β)]−1 n log n. For β = 1, we prove that the mixing time is of order n3/2. For β > 1, we study metastability. In particular, we show that the Glauber dynamics restricted to states of non-negative magnetization has mixing time O( n log n). [ABSTRACT FROM AUTHOR]