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Coherence vectors and correlation matrices are important functions frequently used in physics. The numerical calculation of these functions directly from their definitions, which involves Kronecker products and matrix multiplications, may seem to be a reasonable option. Notwithstanding, as we demonstrate in this article, some algebraic manipulations before programming can reduce considerably their computational complexity. Besides, we provide Fortran code to generate generalized Gell Mann matrices and to compute the optimized and unoptimized versions of the associated Bloch's vectors and correlation matrix, in the case of bipartite quantum systems. As a code test and application example, we consider the calculation of Hilbert-Schmidt quantum discords.

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Book Source: Digital Library of India Item 2015.214240 dc.contributor.author: Barrie, J.m dc.date.accessioned: 2015-07-09T18:39:29Z dc.date.available: 2015-07-09T18:39:29Z dc.date.digitalpublicationdate: 2003-03-14 dc.date.citation: 1923 dc.identifier.barcode: 1990010084288 dc.identifier.origpath: /data_copy/upload/0084/293 dc.identifier.copyno: 1 dc.identifier.uri: http://www.new.dli.ernet.in/handle/2015/214240 dc.description.scannerno: 4 dc.description.scanningcentre: IISc, Bangalore dc.description.main: 1 dc.description.tagged: 0 dc.description.totalpages: 431 dc.format.mimetype: application/pdf dc.language.iso: English dc.publisher.digitalrepublisher: Digital Library Of India dc.publisher: Charles Scribners Sons, Newyork dc.rights: In Public Domain dc.source.library: Carnegie Mellon University dc.title: Quantification

'QUANTIFICATION OF UNPAID WORK (4-May-2005)' from the Parliament Digital Library

Soil organic nitrogen has a complex origin, and is included in a large variety of specific or non specific materials, such as biochemical molecules, plant and animal residues, microbial bodies, and undetermined combinations proceeding from the chemical and biological synthesis of humic compounds. - The analysis and the identification of the nitrogen structures depend at first on the extraction methods, which are not generally very specific: acid hydrolysis, the most common method, shows a predominant contribution of aminoacids and of non-identified forms, called "unknown nitrogen". Osamines and non-hydrolysable nitrogen are generally less abundant. Alkaline extraction is less efficient than acid hydrolysis for the solubilization of nitrogen compounds. However, in many cases, the combined nitrogen forms seem to be more abundant in the humic extracts, than in the non extractable humin fraction, where proteins and amino-polysaccharides are concentmted. Chromatographic fractionation of humic acid hydrolysates allows to separate the simple fraction of peptidic and protein compounds, and the combined organic nitrogen, which is associated with aromatic polycondensates. - From a dynamic point of view, the complexity of the nitrogen organic structures affects its biodegradation: nitrogen of a simple amino-acid is more available for the microorganisms than nitrogen of the same amino-acid included in a protein or, all the more reason, in the wall structures of these microorganisms. However, in the active soils, nitrogen is also included in complex humic molecules synthetized by microorganisms. In that case, its conservation in soil is determined in a great part by the medium conditions, i.e. clay content, availability of organic substrates, etc. Nitrogen of the polyphenol-amino acid humic-like polycondensates seems to represent one of the most resistant forms of the combined nitrogen, and is probably similar to the resistant nitrogen forms of humic soils. - Measurements of the different forms of organic nitrogen must take into account the nature of the interactions between nitrogen compounds and soil mineral phases: the most available data are obtained trom the determination of the grain-size distribution of the associations. The less stable organic nitrogen fractions are preferentially associated to the finest mineral colloids, whereas the most organized and biological structures are included in coarser and more stable aggregates. The most resistant nitrogen seems to be present in the humic cementing agents of these aggregates. In short, the immobilization of nitrogen under organic form in soils is one of the main problems of the humification process. It is related, on the one hand, to the stabilization of biomoleculesand, on the other hand, to the neosynthesis of humic molecules. The determination of the forms of organic nitrogen not only leads to the evaluation of the mineralization potential of soil organic matter; in addition, it allows to understand the origin of the stabilization of organic nitrogen (for example structural, physico-chemical and biological stabilization), and to foresee, in a certain extent, the evolution of the organic matter added to the soil.

Website Validation Of A Digital PCR Method For Quantification Of DNA Copy Number Concentrations By Using A Certified Reference Material

This paper presents the application of recurrence plots (RPs)and recurrence quantification analysis (RQA) in model-based diagnostics of nonlinear systems. A detailed nonlinear mathematical model of a servo electro-hydraulic system has been used to demonstrate the procedure. Two faults have been considered associated with the servo valve including the increased friction between spool and sleeve and the degradation of the permanent magnet of the valve armature. The faults have been simulated in the system by the variation of the corresponding parameters in the model and the effect of these faults on the RPs and RQA parameters has been investigated.A regression-based artificial neural network has been finally developed and trained using the RQA parameters to estimate the original values of the faulty parameters and identify the severity of the faults in the system.

Granular energetic materials exhibit complex chaotic behavior due to the coexistence of a wide range of energy scales without scale separation. The main challenges involved in modeling the physical processes leading to initiation of explosive reactions are (i) the lack of a general model for heterogeneous granular media under compaction and (ii) the lack of a reliable multi-scale discrete-to-continuum framework for describing diffusion-advection-reaction processes in heterogeneous particulate media. This heterogeneity plays a major role in stress and heat localization, which is responsible for initiating reactions in energetic materials. In particular, hot-spots emerge as a consequence of visco-plastic pore collapse, intergranular friction, and granular compaction. We developed a number of computation tools for stochastic analysis of granular materials dynamics. These include a continuum-discrete model of heat dissipation/diffusion and a continuum-discrete model of compaction of a granular material with macro-pores. We have also proposed a class of randomly fluctuating macroscopic equations of motion for granular materials and powders.

AIVO Standard™ v3.0 introduces the Quantification Layer with the Prompt-Space Occupancy Score (PSOS™), a board-ready KPI that measures AI recommendation visibility across LLMs. This release adds governance and auditability features (confidence intervals, refusal classifications, provenance logging), enterprise and SME scoring modes, and board-level dashboards linking PSOS to ROI. Published on Zenodo with DOI: 10.5281/zenodo.17077554.

An apparatus, system, and method for non-destructible evaluation (NDE) of a material use thermography to rapidly detect and/or generally locate a feature such as, for example, damage or a defect in the material. The apparatus, system, and method also use ultrasound to specifically locate the feature in the material for quantification and/or evaluation either by an operator or by an external device suited for such purpose. Accordingly, the apparatus, system and method are particularly useful for NDE in applications such as the analysis of the structure of an aircraft, for example, in which the scale of the material to be analyzed is large, thus requiring the rapid NDE afforded by thermography, and in which quantification and/or evaluation of a feature must be performed with precision, thus requiring the relatively high-resolution NDE afforded by ultrasound.

Volume 2, which consists of appendices, includes the following: Sample locations; Well logs; Field data; Sampling and analysis instructions; Chain-of-custody forms; Analytical results; Dover AFB waste management summary tables; and Calculations.

Ongoing work seeks to apply the technology of resonance ionization mass spectrometry (RIMS) to problems related to nuclear forensics and, in particular, to the analysis and quantification of the debris from nuclear detonations. As part of this effort, modeling and simulation methods are being applied to analyze and predict the potential for ionization by laser excitation of isotopes of both uranium and plutonium. Early work focused on the ionization potential of isotopes of uranium, and the present effort has expanded and extended the previous work by identifying and integrating new data for plutonium isotopes. In addition to extending the effort to this important new element, the work described in this thesis implemented more accurate descriptions of the spatial distribution of the laser beams to improve the accuracy of model predictions compared with experimental results as well as an ability to readily incorporate new experimental data as they become available. The model is used to estimate ionization cross sections and to compare the relative excitation potential for two isotopes as a function of wavelength, irradiance, and bandwidth.

Philip Morris Records; publication

Philip Morris Records; publication

Philip Morris Records; publication

[211 leaves]

This article is from BMC Research Notes , volume 5 . Abstract Background: Downstream applications in metabolomics, as well as mathematical modelling, require data in a quantitative format, which may also necessitate the automated and simultaneous quantification of numerous metabolites. Although numerous applications have been previously developed for metabolomics data handling, automated calibration and calculation of the concentrations in terms of μmol have not been carried out. Moreover, most of the metabolomics applications are designed for GC-MS, and would not be suitable for LC-MS, since in LC, the deviation in the retention time is not linear, which is not taken into account in these applications. Moreover, only a few are web-based applications, which could improve stand-alone software in terms of compatibility, sharing capabilities and hardware requirements, even though a strong bandwidth is required. Furthermore, none of these incorporate asynchronous communication to allow real-time interaction with pre-processed results. Findings: Here, we present EasyLCMS (http://www.easylcms.es/), a new application for automated quantification which was validated using more than 1000 concentration comparisons in real samples with manual operation. The results showed that only 1% of the quantifications presented a relative error higher than 15%. Using clustering analysis, the metabolites with the highest relative error distributions were identified and studied to solve recurrent mistakes. Conclusions: EasyLCMS is a new web application designed to quantify numerous metabolites, simultaneously integrating LC distortions and asynchronous web technology to present a visual interface with dynamic interaction which allows checking and correction of LC-MS raw data pre-processing results. Moreover, quantified data obtained with EasyLCMS are fully compatible with numerous downstream applications, as well as for mathematical modelling in the systems biology field.

This article is from Sensors (Basel, Switzerland) , volume 13 . Abstract This paper comprehensively reviews the emerging topic of optoacoustic imaging from the image reconstruction and quantification perspective. Optoacoustic imaging combines highly attractive features, including rich contrast and high versatility in sensing diverse biological targets, excellent spatial resolution not compromised by light scattering, and relatively low cost of implementation. Yet, living objects present a complex target for optoacoustic imaging due to the presence of a highly heterogeneous tissue background in the form of strong spatial variations of scattering and absorption. Extracting quantified information on the actual distribution of tissue chromophores and other biomarkers constitutes therefore a challenging problem. Image quantification is further compromised by some frequently-used approximated inversion formulae. In this review, the currently available optoacoustic image reconstruction and quantification approaches are assessed, including back-projection and model-based inversion algorithms, sparse signal representation, wavelet-based approaches, methods for reduction of acoustic artifacts as well as multi-spectral methods for visualization of tissue bio-markers. Applicability of the different methodologies is further analyzed in the context of real-life performance in small animal and clinical in-vivo imaging scenarios.

This article is from Sensors (Basel, Switzerland) , volume 13 . Abstract This paper comprehensively reviews the emerging topic of optoacoustic imaging from the image reconstruction and quantification perspective. Optoacoustic imaging combines highly attractive features, including rich contrast and high versatility in sensing diverse biological targets, excellent spatial resolution not compromised by light scattering, and relatively low cost of implementation. Yet, living objects present a complex target for optoacoustic imaging due to the presence of a highly heterogeneous tissue background in the form of strong spatial variations of scattering and absorption. Extracting quantified information on the actual distribution of tissue chromophores and other biomarkers constitutes therefore a challenging problem. Image quantification is further compromised by some frequently-used approximated inversion formulae. In this review, the currently available optoacoustic image reconstruction and quantification approaches are assessed, including back-projection and model-based inversion algorithms, sparse signal representation, wavelet-based approaches, methods for reduction of acoustic artifacts as well as multi-spectral methods for visualization of tissue bio-markers. Applicability of the different methodologies is further analyzed in the context of real-life performance in small animal and clinical in-vivo imaging scenarios.

This article is from BMC Neurology , volume 14 . Abstract Background: The extent to which MS patients with cognitive dysfunction can accurately self-report outcomes has been a crucial issue. The aim of this study was to quantify and compare the relevance of the quality of life (QoL) assessment between two populations with a high occurrence of cognitive dysfunction, specifically in individuals with multiple sclerosis (MS) and in individuals suffering from schizophrenia (SCZ). Methods: Design: A cross-sectional study was performed using the following inclusion criteria: MS and SCZ patients were diagnosed according to the McDonald criteria and DSM-IV criteria, respectively. Data on sociodemographic (age, gender, education level) and clinical (disease severity, disease duration) factors, QoL (disease-specific questionnaires, MusiQoL and SQoL) and cognitive performance (executive, memory, and attention functions) were collected. Non-impaired and impaired populations were defined according to the French norms. Psychometric properties were compared to those reported in reference populations, which were assessed in the respective validation studies. Suitability indices were provided used to quantitatively compare how the structures in the different populations matched with the initial structure of the questionnaires (reference populations). Results: One hundred and twenty-four MS patients and 113 SCZ patients were enrolled. Factor analysis was performed on the impaired populations and revealed that the questionnaire structure adequately matched the initial structure of the disease-specific QoL questionnaires. All of the suitability indices of construct and external validity in the non-impaired populations ranged from 70 to 100%. Conclusions: Our study suggested that cognitive dysfunction did not compromise the reliability or validity of the self-reported QoL questionnaires among subjects with cognitive dysfunction, such as MS and SCZ. Thus, this report may clarify the relevance of using self-reported QoL assessments in clinical practice.

We exhibit canonical middle-inverse Choice maps within categorical (Free-Variable) Theory of Primitive Recursion as well as in Theory of partial PR maps over the Theory of Primitive Recursion with predicate abstraction. Using these choice-maps, defined by mu-recursion, we address the Consistency problem for a minimal Quantified extension Q of latter two theories: We prove, that Q's exists-defined mu-operator coincides on PR predicates with that inherited from theory of partial PR maps. We strengthen Theory Q by axiomatically forcing the lexicographical order on its omega^omega to become a well-order: "finite descent". Resulting theory admits non-infinit PR-iterative descent schema (pi) which constitutes Cartesian PR Theory piR introduced in RCF2: Evaluation and Consistency. A suitable Cartesian subSystem of Q + wo(omega^omega) above, extension of piR "inside" Theory Q + wo(omega^omega), is shown to admit code self-evaluation: extension of formally partial code evaluation of piR into a "total" self-evaluation for the subSystem. Appropriate diagonal argument then shows inconsistency of this subsystem and (hence) of its extensions Q + wo(omega^omega) and ZF.

This article is from Journal of Cardiovascular Magnetic Resonance , volume 16 . Abstract None

This article is from Journal of Cardiovascular Magnetic Resonance , volume 16 . Abstract None

This article is from Journal of Cardiovascular Magnetic Resonance , volume 16 . Abstract None

This article is from Journal of Translational Medicine , volume 12 . Abstract Background: Experimental and human studies have demonstrated that innate immune mechanisms and consequent inflammatory reaction play a critical role in cardiac response to ischemic injury. Thus, the detection of immuno-inflammatory and cellular phenomena accompanying cardiac alterations during the early inflammatory phase of myocardial infarction (MI) may be an excellent diagnostic tool. Current knowledge of the chronology of the responses of myocardial tissue following the occurrence of ischemic insult, as well as the existence of numerous studies aiming to identify reliable markers in dating MI, induced us to investigate the myocardial specimens of MI fatal cases in order to better define the age of MI. Methods: We performed an immunohistochemical study and a Western blot analysis to evaluate detectable morphological changes in myocardial specimens of fatal MI cases and to quantify the effects of cardiac expression of inflammatory mediators (CD15, IL-1β, IL-6, TNF-α, IL-15, IL-8, MCP-1, ICAM-1, CD18, tryptase) and structural and functional cardiac proteins. Results: We observed a biphasic course of MCP-1: it was strongly expressed in the very early phase (0-4 hrs), to diminish in the early period (after 6-8 hrs). Again, our choice of IL-15 is explained by the synergism with neutrophilic granulocytes (CD15) and our study shows the potential for striking cytokine synergy in promoting fast, local neutrophil response in damaged tissues. A progressively stronger immunoreaction for the CD15 antibody was visible in the areas where the margination of circulating inflammatory cells was detectable, up to very strong expression in the oldest ones (>12 hours). Further, the induction of CD15, IL-15, MCP-1 expression levels was quantified by Western blot analysis. The results were as follows: IL-15/β-actin 0.80, CD15/β-actin 0.30, and MCP-1/β-actin 0.60, matching perfectly with the results of immunohistochemistry. Control hearts from traumatic death cases did not show any immunoreactivity to the pro-inflammatory markers, neither were there any reactions in Western blot analysis. Conclusions: Essential markers (i.e. IL-15, MCP-1) are suitable indicators of myocardial response to ischemic insult involving very early phase reaction (inflammatory response and cytokine release). In the very near future, proteomics may help clinicians and pathologists to better understand mechanisms relating to cardiac repair and remodeling and provide targets for future therapies.

This article is from Korean Journal of Ophthalmology : KJO , volume 28 . Abstract Purpose: To investigate the relationship between plasma TDRD7 mRNA and lens transparency, and to evaluate plasma TDRD7 mRNA as a potential marker for cataracts and its sub-type by quantitatively analyzing human peripheral blood. Methods: Plasma RNA was extracted from 40 patients with cataracts, and 30 normal controls of matched age and gender. Blood cholesterol and fasting glucose were measured, and the RNA extracted from the sample was synthesized into cDNA. After polymerase chain reaction, the results were compared after quantifying the TDRD7 mRNA using ABL1 mRNA for normalization. We analyzed the relative gene expression data via the ΔΔCt method. Results: The normalized 2-ΔΔCt of plasma TDRD7 mRNA based on ABL1 mRNA was 1.52 ± 0.63 in the case of the control group and 1.05 ± 0.34 in the case of the cataract patients, and the TDRD7 expression level of the cataract patients was lower than that of the control group (p = 0.048). The comparison of the genetic values of different types of cataracts demonstrated that the TDRD7 expression level of the cortical type and mixed type were lower than those of the nuclear type and posterior subcapsular opacity type (p = 0.017). Conclusions: Human cataracts and the TDRD7 gene loss-of-function mutations are strongly causally related, as the expression level of plasma TDRD7 mRNA in patients with cataracts was statistically significantly lower than in the normal control group.

This article is from Bioinformatics , volume 30 . Abstract Motivation: Several state-of-the-art methods for isoform identification and quantification are based on ℓ1-regularized regression, such as the Lasso. However, explicitly listing the—possibly exponentially—large set of candidate transcripts is intractable for genes with many exons. For this reason, existing approaches using the ℓ1-penalty are either restricted to genes with few exons or only run the regression algorithm on a small set of preselected isoforms.Results: We introduce a new technique called FlipFlop, which can efficiently tackle the sparse estimation problem on the full set of candidate isoforms by using network flow optimization. Our technique removes the need of a preselection step, leading to better isoform identification while keeping a low computational cost. Experiments with synthetic and real RNA-Seq data confirm that our approach is more accurate than alternative methods and one of the fastest available.Availability and implementation: Source code is freely available as an R package from the Bioconductor Web site (http://www.bioconductor.org/), and more information is available at http://cbio.ensmp.fr/flipflop.Contact:[email protected] information:Supplementary data are available at Bioinformatics online.

This article is from PLoS ONE , volume 9 . Abstract Human immunodeficiency virus type 1 (HIV-1) genetic diversity poses a challenge to reliable viral load monitoring. Discrepancies between different testing platforms have been observed, especially for non-clade-B virus. Therefore we compare, in antiretroviral therapy (ART)-naïve South African subjects predominantly infected with HIV-1 clade-C, three commercially available assays: the COBAS AmpliPrep/COBAS TaqMan HIV-1 Test version 2.0 by Roche (CAP/CTM v2.0), the BioMérieux NucliSens Version 2.0 Easy Q/Easy Mag (NucliSens v2.0) and the Roche COBAS Amplicor HIV-1 Monitor Test Version 1.5 (Amplicor v1.5). Strong linear correlation was observed and Bland-Altman analyses showed overall good agreement between the assays with mean viral load differences of 0.078 log cp/ml (NucliSens v2.0 – Amplicor v1.5), 0.260 log cp/ml (CAP/CTM v2.0 – Amplicor v1.5) and 0.164 log cp/ml (CAP/CTM v2.0 – NucliSens v2.0), indicating lower mean viral load results for the Amplicor v1.5 and higher mean readings for the CAP/CTM v2.0. Consistent with observations following previous comparisons of CAP/CTM v2.0 versus Amplicor v1.5, the CAP/CTM v2.0 assay detected low-level viremia (median 65 cp/ml) in more than one-third of those in whom viremia had been undetectable (

This article is from Oncology Letters , volume 8 . Abstract Circulating cell-free microRNAs (miRNAs) are potential biomarkers of cancer. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is widely used in miRNA expression studies. The aim of this study was to identify suitable reference genes for RT-qPCR analyses of miRNA expression levels in pleural effusion. The expression levels of candidate reference miRNAs were investigated in 10 benign pleural effusion (BPE) and 10 lung adenocarcinoma-associated malignant pleural effusion (LA-MPE) samples using miRNA microarrays. The expression levels of candidate reference miRNAs, together with those of U6 small nuclear RNA (snRNA), RNU6B, RNU44 and RNU48 small RNAs, in 46 BPE and 45 LA-MPE samples were validated by RT-qPCR, and were analyzed using the NormFinder and BestKeeper algorithms. The impact of different normalization approaches on the detection of differential expression levels of miR-198 in BPE and LA-MPE samples was also assessed. As determined by the miRNA microarray data, five candidate reference miRNAs were identified. Following RT-qPCR validation, U6 snRNA, miR-192, miR-20a, miR-221, miR-222 and miR-16 were evaluated using the NormFinder and BestKeeper software programs. U6 snRNA and miR-192 were identified as single reference genes and the combination of these genes was preferred for the relative quantification of miRNA expression levels in pleural effusion. Normalization of miR-98 expression levels to those of U6 snRNA, miR-192 or a combination of these genes enabled the detection of a significant difference between BPE and LA-MPE samples. Therefore, U6 snRNA and miR-192 are recommended as reference genes for the relative quantification of miRNA expression levels in pleural effusion.

This article is from PLoS ONE , volume 9 . Abstract Cell-associated (CA) HIV-1 RNA is considered a potential marker for assessment of viral reservoir dynamics and antiretroviral therapy (ART) response in HIV-infected patients. Recent studies employed sensitive seminested real-time quantitative (q)PCR to quantify CA HIV-1 RNA. Digital PCR has been recently described as an alternative PCR-based technique for absolute quantification with higher accuracy compared to qPCR. Here, a comparison was made between the droplet digital PCR (ddPCR) and the seminested qPCR for quantification of unspliced (us) and multiply spliced (ms) CA HIV-1 RNA. Synthetic RNA standards and CA HIV-1 RNA from infected patients on and off ART (N = 34) were quantified with both methods. Correlations were observed between the methods both for serially diluted synthetic standards (usRNA: R2 = 0.97, msRNA: R2 = 0.92) and patient-derived samples (usRNA: R2 = 0.51, msRNA: R2 = 0.87). Seminested qPCR showed better quantitative linearity, accuracy and sensitivity in the quantification of synthetic standards than ddPCR, especially in the lower quantification ranges. Both methods demonstrated equally high detection rate of usRNA in patient samples on and off ART (91%), whereas ddPCR detected msRNA in larger proportion of samples from ART-treated patients (p = 0.13). We observed an average agreement between the methods for usRNA quantification in patient samples, albeit with a large standard deviation (bias = 0.05±0.75 log10). However, a bias of 0.94±0.36 log10 was observed for msRNA. No-template controls were consistently negative in the seminested qPCR, but yielded a positive ddPCR signal for some wells. Therefore, the false positive signals may have affected the detection power of ddPCR in this study. Digital PCR is promising for HIV nucleic acid quantification, but the false positive signals need further attention. Quantitative assays for CA HIV RNA have the potential to improve monitoring of patients on ART and to be used in clinical studies aimed at HIV eradication, but should be cross-validated by multiple laboratories prior to wider use.

This article is from PLoS ONE , volume 9 . Abstract Extracellular microRNAs (miRNAs) are under investigation as minimally-invasive biomarkers for a wide range of disease conditions. We have recently shown in a mouse model of the progressive muscle-wasting condition Duchenne muscular dystrophy (DMD) that a set of highly elevated serum miRNAs reflects the regenerative status of muscle. These miRNAs are promising biomarkers for monitoring DMD disease progression and the response to experimental therapies. The gold standard miRNA detection methodology is Reverse Transcriptase-quantitative Polymerase Chain Reaction (RT-qPCR), which typically exhibits high sensitivity and wide dynamic range. Accurate determination of miRNA levels is affected by RT-qPCR normalization method and therefore selection of the optimal strategy is of critical importance. Serum miRNA abundance was measured by RT-qPCR array in 14 week old mice, and by individual RT-qPCR assays in a time course experiment spanning 48 weeks. Here we utilize these two datasets to assess the validity of three miRNA normalization strategies (a) normalization to the average of all Cq values from array experiments, (b) normalization to a stably expressed endogenous reference miRNA, and (c) normalization to an external spike-in synthetic oligonucleotide. Normalization approaches based on endogenous control miRNAs result in an under-estimation of miRNA levels by a factor of ∼2. An increase in total RNA and total miRNA was observed in dystrophic serum which may account for this systematic bias. We conclude that the optimal strategy for this model system is to normalize to a synthetic spike-in control oligonucleotide.

This article is from BMC Microbiology , volume 14 . Abstract Background: Burkholderia pseudomallei (Bp), a Gram-negative, motile, facultative intracellular bacterium is the causative agent of melioidosis in humans and animals. The Bp genome encodes a repertoire of virulence factors, including the cluster 3 type III secretion system (T3SS-3), the cluster 1 type VI secretion system (T6SS-1), and the intracellular motility protein BimA, that enable the pathogen to invade both phagocytic and non-phagocytic cells. A unique hallmark of Bp infection both in vitro and in vivo is its ability to induce cell-to-cell fusion of macrophages to form multinucleated giant cells (MNGCs), which to date are semi-quantitatively reported following visual inspection. Results: In this study we report the development of an automated high-content image acquisition and analysis assay to quantitate the Bp induced MNGC phenotype. Validation of the assay was performed using T6SS-1 (∆hcp1) and T3SS-3 (∆bsaZ) mutants of Bp that have been previously reported to exhibit defects in their ability to induce MNGCs. Finally, screening of a focused small molecule library identified several Histone Deacetylase (HDAC) inhibitors that inhibited Bp-induced MNGC formation of macrophages. Conclusions: We have successfully developed an automated HCI assay to quantitate MNGCs induced by Bp in macrophages. This assay was then used to characterize the phenotype of the Bp mutants for their ability to induce MNGC formation and identify small molecules that interfere with this process. Successful application of chemical genetics and functional reverse genetics siRNA approaches in the MNGC assay will help gain a better understanding of the molecular targets and cellular mechanisms responsible for the MNGC phenotype induced by Bp, by other bacteria such as Mycobacterium tuberculosis, or by exogenously added cytokines.

This article is from F1000Research , volume 3 . Abstract Analysis of ascitic fluid should help to identify and characterize malignant cells in gastrointestinal cancer. However, despite a high specificity, the sensitivity of traditional ascitic fluid cytology remains insufficient, at around 60%. Since 2004 the CellSearch ® technology has shown its advantages in the detection of circulating tumor cells (CTCs) in peripheral blood, which can perform an accurate diagnosis and molecular analysis at the same time. To our knowledge, no previous study has explored the potential utility of this technology for the detection and quantification of tumor cells in ascitic fluid samples. Herein we report a case of metastatic esophageal adenocarcinoma in a 70-year-old man presenting with dysphagia and a large amount of fluid in the peritoneal cavity. Analysis of a peripheral blood sample and ascites sample with the CellSearch ® technology both revealed the presence of putative tumor cells that were positive for epithelial cell adhesion molecule (EpCAM) and cytokeratin (CK) expression. This study confirmed the hematogenous dissemination of esophageal cancer by the detection of circulating tumor cells in the peripheral blood, and is the first to demonstrate that tumor cells can be identified in ascitic fluid by using CellSearch ® technology.

The retinal vascular morphological caliber changes reveal the signs of systemic health disorder and life threat diseases such as cardio and cerebral diseases. The quantitative vascular parameters like narrowed arteries, widened venules, reduced artery-vein ratio (AVR) have been associated with aforesaid disorders and diseases. Hence the quantitative biomarker AVR is important parameter in diagnosing variety of diseases. The accurate quantification of AVR be possible if and only if accurate classification of arteries and vein is done. In this paper, we proposed a deep learning based robust vessel segmentation and classification algorithm based on spatial U-Net and the accuracy of the algorithm is 97.8%. In the quantification process, this algorithm is applied on region of interest (RoI) of a fundus image and measured the AVR values using central retinal artery equivalent (CRAE) and central retinal vein equivalent (CRVE). The experimentation is carried on the digital retinal images for vessel extraction (DRIVE) dataset. The outcome of this work is the AVR observed to be >0.4 in normal retinal case and AVR value <0.4 for unhealthy case. 

The retinal vascular morphological caliber changes reveal the signs of systemic health disorder and life threat diseases such as cardio and cerebral diseases. The quantitative vascular parameters like narrowed arteries, widened venules, reduced artery-vein ratio (AVR) have been associated with aforesaid disorders and diseases. Hence the quantitative biomarker AVR is important parameter in diagnosing variety of diseases. The accurate quantification of AVR be possible if and only if accurate classification of arteries and vein is done. In this paper, we proposed a deep learning based robust vessel segmentation and classification algorithm based on spatial U-Net and the accuracy of the algorithm is 97.8%. In the quantification process, this algorithm is applied on region of interest (RoI) of a fundus image and measured the AVR values using central retinal artery equivalent (CRAE) and central retinal vein equivalent (CRVE). The experimentation is carried on the digital retinal images for vessel extraction (DRIVE) dataset. The outcome of this work is the AVR observed to be >0.4 in normal retinal case and AVR value <0.4 for unhealthy case. 

This open access book brings together the latest developments from industry and research on automated driving and artificial intelligence. Environment perception for highly automated driving heavily employs deep neural networks, facing many challenges. How much data do we need for training and testing? How to use synthetic data to save labeling costs for training? How do we increase robustness and decrease memory usage? For inevitably poor conditions: How do we know that the network is uncertain about its decisions? Can we understand a bit more about what actually happens inside neural networks? This leads to a very practical problem particularly for DNNs employed in automated driving: What are useful validation techniques and how about safety? This book unites the views from both academia and industry, where computer vision and machine learning meet environment perception for highly automated driving. Naturally, aspects of data, robustness, uncertainty quantification, and, last but not least, safety are at the core of it. This book is unique: In its first part, an extended survey of all the relevant aspects is provided. The second part contains the detailed technical elaboration of the various questions mentioned above.

This article is from Virology Journal , volume 8 . Abstract Background: Begomovirus is a genus of phytopathogenic single-stranded DNA viruses, transmitted by the whitefly Bemisia tabaci. This genus includes emerging and economically significant viruses such as those associated with Tomato Yellow Leaf Curl Disease, for which diagnostic tools are needed to prevent dispersion and new introductions. Five real-time PCRs with an internal tomato reporter gene were developed for accurate detection and quantification of monopartite begomoviruses, including two strains of the Tomato yellow leaf curl virus (TYLCV; Mld and IL strains), the Tomato leaf curl Comoros virus-like viruses (ToLCKMV-like viruses) and the two molecules of the bipartite Potato yellow mosaic virus. These diagnostic tools have a unique standard quantification, comprising the targeted viral and internal report amplicons. These duplex real-time PCRs were applied to artificially inoculated plants to monitor and compare their viral development. Results: Real-time PCRs were optimized for accurate detection and quantification over a range of 2 × 109 to 2 × 103 copies of genomic viral DNA/μL for TYLCV-Mld, TYLCV-IL and PYMV-B and 2 × 108 to 2 × 103 copies of genomic viral DNA/μL for PYMV-A and ToLCKMV-like viruses. These real-time PCRs were applied to artificially inoculated plants and viral loads were compared at 10, 20 and 30 days post-inoculation. Different patterns of viral accumulation were observed between the bipartite and the monopartite begomoviruses. Interestingly, PYMV accumulated more viral DNA at each date for both genomic components compared to all the monopartite viruses. Also, PYMV reached its highest viral load at 10 dpi contrary to the other viruses (20 dpi). The accumulation kinetics of the two strains of emergent TYLCV differed from the ToLCKMV-like viruses in the higher quantities of viral DNA produced in the early phase of the infection and in the shorter time to reach this peak viral load. Conclusions: To detect and quantify a wide range of begomoviruses, five duplex real-time PCRs were developed in association with a novel strategy for the quantification standard. These assays should be of a great interest for breeding programs and epidemiological surveys to monitor viral populations.

This article is from BMC Musculoskeletal Disorders , volume 14 . Abstract Background: The study quantified the relative contributions of estrogen (E2) and total testosterone (TT) to variation in bone mineral density in men and women. Methods: This was a cross-sectional study which involved 200 men and 415 women aged 18 to 89 years. BMD at the lumbar spine (LS) and femoral neck (FN) was measured by DXA. Serum levels of E2 and TT were measured by electrochemiluminescence immunoassays. The association between E2, TT, and BMD was analyzed by the multiple linear regression model, adjusting for age and BMI. The contribution of each hormone to the variation in BMD was quantified by the bootstrap method. Results: In women, higher serum levels of E2, but not TT, were significantly associated with greater BMD at the FN (P = 0.001) and LS (P 

This article is from BMC Musculoskeletal Disorders , volume 14 . Abstract Background: The study quantified the relative contributions of estrogen (E2) and total testosterone (TT) to variation in bone mineral density in men and women. Methods: This was a cross-sectional study which involved 200 men and 415 women aged 18 to 89 years. BMD at the lumbar spine (LS) and femoral neck (FN) was measured by DXA. Serum levels of E2 and TT were measured by electrochemiluminescence immunoassays. The association between E2, TT, and BMD was analyzed by the multiple linear regression model, adjusting for age and BMI. The contribution of each hormone to the variation in BMD was quantified by the bootstrap method. Results: In women, higher serum levels of E2, but not TT, were significantly associated with greater BMD at the FN (P = 0.001) and LS (P 

This article is from BMC Musculoskeletal Disorders , volume 14 . Abstract Background: The study quantified the relative contributions of estrogen (E2) and total testosterone (TT) to variation in bone mineral density in men and women. Methods: This was a cross-sectional study which involved 200 men and 415 women aged 18 to 89 years. BMD at the lumbar spine (LS) and femoral neck (FN) was measured by DXA. Serum levels of E2 and TT were measured by electrochemiluminescence immunoassays. The association between E2, TT, and BMD was analyzed by the multiple linear regression model, adjusting for age and BMI. The contribution of each hormone to the variation in BMD was quantified by the bootstrap method. Results: In women, higher serum levels of E2, but not TT, were significantly associated with greater BMD at the FN (P = 0.001) and LS (P 

This article is from BMC Musculoskeletal Disorders , volume 14 . Abstract Background: The study quantified the relative contributions of estrogen (E2) and total testosterone (TT) to variation in bone mineral density in men and women. Methods: This was a cross-sectional study which involved 200 men and 415 women aged 18 to 89 years. BMD at the lumbar spine (LS) and femoral neck (FN) was measured by DXA. Serum levels of E2 and TT were measured by electrochemiluminescence immunoassays. The association between E2, TT, and BMD was analyzed by the multiple linear regression model, adjusting for age and BMI. The contribution of each hormone to the variation in BMD was quantified by the bootstrap method. Results: In women, higher serum levels of E2, but not TT, were significantly associated with greater BMD at the FN (P = 0.001) and LS (P 

This article is from BMC Musculoskeletal Disorders , volume 14 . Abstract Background: The study quantified the relative contributions of estrogen (E2) and total testosterone (TT) to variation in bone mineral density in men and women. Methods: This was a cross-sectional study which involved 200 men and 415 women aged 18 to 89 years. BMD at the lumbar spine (LS) and femoral neck (FN) was measured by DXA. Serum levels of E2 and TT were measured by electrochemiluminescence immunoassays. The association between E2, TT, and BMD was analyzed by the multiple linear regression model, adjusting for age and BMI. The contribution of each hormone to the variation in BMD was quantified by the bootstrap method. Results: In women, higher serum levels of E2, but not TT, were significantly associated with greater BMD at the FN (P = 0.001) and LS (P 

This article is from BMC Musculoskeletal Disorders , volume 14 . Abstract Background: The study quantified the relative contributions of estrogen (E2) and total testosterone (TT) to variation in bone mineral density in men and women. Methods: This was a cross-sectional study which involved 200 men and 415 women aged 18 to 89 years. BMD at the lumbar spine (LS) and femoral neck (FN) was measured by DXA. Serum levels of E2 and TT were measured by electrochemiluminescence immunoassays. The association between E2, TT, and BMD was analyzed by the multiple linear regression model, adjusting for age and BMI. The contribution of each hormone to the variation in BMD was quantified by the bootstrap method. Results: In women, higher serum levels of E2, but not TT, were significantly associated with greater BMD at the FN (P = 0.001) and LS (P 

This article is from BMC Musculoskeletal Disorders , volume 14 . Abstract Background: The study quantified the relative contributions of estrogen (E2) and total testosterone (TT) to variation in bone mineral density in men and women. Methods: This was a cross-sectional study which involved 200 men and 415 women aged 18 to 89 years. BMD at the lumbar spine (LS) and femoral neck (FN) was measured by DXA. Serum levels of E2 and TT were measured by electrochemiluminescence immunoassays. The association between E2, TT, and BMD was analyzed by the multiple linear regression model, adjusting for age and BMI. The contribution of each hormone to the variation in BMD was quantified by the bootstrap method. Results: In women, higher serum levels of E2, but not TT, were significantly associated with greater BMD at the FN (P = 0.001) and LS (P 

This article is from BMC Musculoskeletal Disorders , volume 14 . Abstract Background: The study quantified the relative contributions of estrogen (E2) and total testosterone (TT) to variation in bone mineral density in men and women. Methods: This was a cross-sectional study which involved 200 men and 415 women aged 18 to 89 years. BMD at the lumbar spine (LS) and femoral neck (FN) was measured by DXA. Serum levels of E2 and TT were measured by electrochemiluminescence immunoassays. The association between E2, TT, and BMD was analyzed by the multiple linear regression model, adjusting for age and BMI. The contribution of each hormone to the variation in BMD was quantified by the bootstrap method. Results: In women, higher serum levels of E2, but not TT, were significantly associated with greater BMD at the FN (P = 0.001) and LS (P 

This paper attempts to answer a question: for a given traversal area, how to quantify the geometric impact of anchor placement on localization performance. We present a theoretical framework for quantifying the anchor placement impact. An experimental study, as well as the field test using a UWB ranging technology, is presented. These experimental results validate the theoretical analysis. As a byproduct, we propose a two-phase localization method (TPLM) and show that TPLM outperforms the least-square method in localization accuracy by a huge margin. TPLM performs much faster than the gradient descent method and slightly better than the gradient descent method in localization accuracy. Our field test suggests that TPLM is more robust against noise than the least-square and gradient descent methods.

This paper attempts to answer a question: for a given traversal area, how to quantify the geometric impact of anchor placement on localization performance. We present a theoretical framework for quantifying the anchor placement impact. An experimental study, as well as the field test using a UWB ranging technology, is presented. These experimental results validate the theoretical analysis. As a byproduct, we propose a two-phase localization method (TPLM) and show that TPLM outperforms the least-square method in localization accuracy by a huge margin. TPLM performs much faster than the gradient descent method and slightly better than the gradient descent method in localization accuracy. Our field test suggests that TPLM is more robust against noise than the least-square and gradient descent methods.