Expression profiling of lymph nodes in tuberculosis patients reveal inflammatory milieu at site of infection

Extrapulmonary manifestations constitute 15 to 20% of tuberculosis cases, with lymph node tuberculosis (LNTB) as the most common form of infection. However, diagnosis and treatment advances are hindered by lack of understanding of LNTB biology. To identify host response, Mycobacterium tuberculosis infected lymph nodes from LNTB patients were studied by means of transcriptomics and quantitative proteomics analyses. The selected targets obtained by comparative analyses were validated by quantitative PCR and immunohistochemistry. This approach provided expression data for 8,728 transcripts and 102 proteins, differentially regulated in the infected human lymph node. Enhanced inflammation with upregulation of T-helper1-related genes, combined with marked dysregulation of matrix metalloproteinases, indicates tissue damage due to high immunoactivity at infected niche. This expression signature was accompanied by significant upregulation of an immunoregulatory gene, leukotriene A4 hydrolase, at both transcript and protein levels. Comparative transcriptional analyses revealed LNTB-specific perturbations. In contrast to pulmonary TB-associated increase in lipid metabolism, genes involved in fatty-acid metabolism were found to be downregulated in LNTB suggesting differential lipid metabolic signature. This study investigates the tissue molecular signature of LNTB patients for the first time and presents findings that indicate the possible mechanism of disease pathology through dysregulation of inflammatory and tissue-repair processes.

Proteomic profiling of forskolin-induced differentiated BeWo cells: an in-vitro model of cytotrophoblast differentiation

Placental trophoblastic differentiation is characterized by the fusion of monolayer cytotrophoblasts into syncytiotrophoblasts. During this process of differentiation, several morphological and biochemical changes are known to occur, and this model has been employed to investigate the changes that occur at the gene and protein level during differentiation. Using the sensitive technique of proteomics [two-dimensional gel electrophoresis (2DGE)], changes in protein profile were evaluated in the control and forskolin-induced differentiated cells of trophoblastic choriocarcinoma BeWo cell line. Several proteins were differentially expressed in control and differentiated cells. Four major proteins were up-regulated as assessed by silver staining, and were further characterized as c-h-ras p 21 (phosphorylated), retinoblastoma susceptibility protein I and integrase interactor protein 1. These proteins are known to play an important role in growth arrest of cells, and thus may play a role in initiating the process of differentiation.

Clinician perspective on molecular profiling of non-small-cell lung cancer

The article by Meric-Bernstam et al1 that was recently published in Journal of Clinical Oncology raises important questions about the clinical application of large-scale genomic testing. We congratulate the authors for this ambitious study, which successfully profiled 2,000 consecutive patients with advanced cancer. The next-generation sequencing (NGS) platform was used for 1,749 of 2,000 patients (87.5%). Of 789 patients with potentially actionable mutations, 83 (11%, or 4% of screened population) were enrolled in a genomically matched clinical study. As the editorial2 accompanying the article by Meric-Bernstam et al1 pointed out, the 4% figure, albeit disappointing, may be an underestimate because cancers such as lung adenocarcinoma and melanoma, for which ≥ 50% of patients have actionable mutations, were under-represented. ...

Profiling k-Iteration Paths : A Generalization of the Ball-Larus Profiling Algorithm

The Ball-Larus path-profiling algorithm is an efficient technique to collect acyclic path frequencies of a program. However, longer paths -those extending across loop iterations - describe the runtime behaviour of programs better. We generalize the Ball-Larus profiling algorithm for profiling k-iteration paths - paths that can span up to to k iterations of a loop. We show that it is possible to number suchk-iteration paths perfectly, thus allowing for an efficient profiling algorithm for such longer paths. We also describe a scheme for mixed-mode profiling: profiling different parts of a procedure with different path lengths. Experimental results show that k-iteration profiling is realistic.

Study of gas cavity size hysteresis in a packed bed using DEM

When a high velocity gas jet is introduced into a packed bed a cavity is formed. The size of the cavity shows hysteresis on increasing and decreasing gas flow rates. This hysteresis leads to different cavity sizes at same gas flow rate depending on the bed history. The size of cavity affects the gas flow profiles in the packed bed. In this study the cavity size hysteresis phenomenon has been modeled using discrete element method along with turbulent gas flow. A reasonable agreement has been found between computed and experimental results on cavity size ysteresis. The effect of various parameters, such as nozzle height from the bed bottom and packing height, on the cavity size hysteresis has been studied. It is found that inter-particle interaction forces along with gas drag and bed porosity play an important role in describing the cavity size hysteresis. The injection of gas flow allows the particles to go to an unconstrained state than they were previously in, and their ability to remain in that state, even under decreased gas drag force, leads to the phenomenon of cavity size hysteresis. (c) 2007 Elsevier Ltd. All rights reserved.

Analysis of gradually and spatially varied flow in sand-bed channels

Seepage through a sand bed affects the channel hydrodynamics, which in turn alters channel stability. Thus, the effect of seepage on its hydrodynamic parameters needs to be ascertained. The present work analyses spatially varied flow of a sand-bed channel subjected to seepage in the downward direction through a sand bed. Numerically calculated flow profiles affected by seepage have been verified using experimental observations. The present work also analyses the friction slope, velocity and bed shear stress variations along the channel for both seepage and no-seepage conditions. It was found that the downward seepage-induced channel flow has larger friction slope and bed shear stress than that of no-seepage.

Molecular characterization of sediment bacterial communities affected by fish farming

Fish farming introduces nutrients, microbes and a wide variety of chemicals such as heavy metals, antifoulants and antibiotics to the surrounding environment. Introduction of antibiotics has been linked with the increased incidence of antibiotic resistant pathogenic bacteria in the farm vicinities. In this thesis molecular methods such as quantitative PCR and DNA sequencing were applied to analyze bacterial communities in sediments from fish farms and pristine locations. Altogether four farms and four pristine sites were sampled in the Baltic Sea. Two farm and two pristine locations were sampled over a surveillance period of four years. Furthermore, a new methodology was developed as a part of the study that permits amplifying single microbial genomes and capturing them according to any genetic traits, including antibiotic resistance genes. The study revealed that several resistance genes for tetracycline were found at the sediment underneath the aquaculture farms. The copy number of these genes remained elevated even at a farm that had not used any antibiotics since year 2000, six years before this study started. Similarly, an increase in the amount of mercury resistance gene merA was observed at the aquaculture sediment. The persistence of the resistance genes in absence of any selection pressure from antibiotics or heavy metals suggests that the genes may be introduced to the sediment by the farming process. This is also supported by the diversity pattern of the merA gene between farm and pristine sediments. The bacterial community-level changes in response to fish farming were very complex and no single phylogenetic groups were found that would be typical to fish farm sediments. However, the community structures had some correlation with the exposure to fish farming. Our studies suggest that the established approaches to deal with antibiotic resistance at the aquaculture, such as antibiotic cycling, are fundamentally flawed because they cannot prevent the introduction of the resistance genes and resistant bacteria to the farm area by the farming process. Further studies are required to study the entire fish farming process to identify the sources of the resistance genes and the resistant bacteria. The results also suggest that in order to prevent major microbiological changes in the surrounding aquatic environment, the farms should not be founded in shallow water where currents do not transport sedimenting matter from the farms. Finally, the technique to amplify and select microbial genomes will potentially have a considerable impact in microbial ecology and genomics.

Modelling of void initiation and breaking phenomena in a packed bed

Void breaking and formation in a packed bed are important phenomena in stabilising and optimising the performance of reactors such as the blast furnace, spouted bed and catalytic regenerator. These phenomena have been studied using a mathematical model. The model is based on a previously published force balance approach to predict the cavity size. Limited numbers of experiments, at room temperature, have been carried out in order to compare the experimental results with theory. A good agreement has been found between the experimental and theoretical results. In addition, the predictions have been compared with published data, which give reasonable agreement. The role of various forces (friction, pressure and bed weight) on void initiation and breaking has been investigated. The effect of bed height, particle diameter and density, void fraction, as well as gas flow rate on void formation and breaking has also been studied.

Analysis of a thick plate with a circular hole resting on a smooth rigid bed and subjected to axisymmetric normal load

A solution for the stresses and displacements in an radially infinite thick plate having a circular hole, one face of which resting on a smooth rigid bed and the other face subjected to axisymmetric normal loading is given. The solution is obtained in terms of Fourier-Bessel series and integral for the Love's stress function. Numerical results are presented for one particular ratio of thickness of plate to the hole radius and loading. It is also shown that the Poisson's ratio has a predominant effect on certain stresses and displacements. The solution would be useful in the stress analysis of bolted joints.Eine Lösung für die Spannungen und Verschiebungen in einer radial, unendlich ausgedehnten, dicken Platte mit einem kreisförmigen Loch, wobei eine Seite auf einer ebenen, starren Unterlage aufliegt, die andere Seite durch eine achsensymmetrische Vertikallast belastet ist, wird angegeben. Die Lösung wird in Form von Fourier-Bessel-Reihen und Integralen der Loveschen Spannungsfunktion angegeben. Numerische Ergebnisse werden für ein bestimmtes Verhältnis der Plattendicke zum Lochradius sowie zur Belastung angegeben. Es wird auch gezeigt, daß das Poisssonsche Verhältnis einen besonderen Einfluß auf bestimmte Spannungen und Verschiebungen hat. Die Lösung ist anwendbar für die Spannungsermittlung von Bolzenverbindungen.

Genome-wide expression profiling identifies deregulated miRNAs in malignant astrocytoma

Malignant astrocytoma includes anaplastic astrocytoma (grade III) and glioblastoma (grade IV). Among them, glioblastoma is the most common primary brain tumor with dismal responses to all therapeutic modalities. We performed a large-scale, genome-wide microRNA (miRNA) (n=756) expression profiling of 26 glioblastoma, 13 anaplastic astrocytoma and 7 normal brain samples with an aim to find deregulated miRNA in malignant astrocytoma. We identified several differentially regulated miRNAs between these groups, which could differentiate glioma grades and normal brain as recognized by PCA. More importantly, we identified a most discriminatory 23-miRNA expression signature, by using PAM, which precisely distinguished glioblastoma from anaplastic astrocytoma with an accuracy of 95%. The differential expression pattern of nine miRNAs was further validated by real-time RT-PCR on an independent set of malignant astrocytomas (n-72) and normal samples (n=7). Inhibition of two glioblastoma-upregulated miRNAs (miR-21 and miR-23a) and exogenous overexpression of two glioblastoma-downregulated miRNAs (miR-218 and miR-219-5p) resulted in reduced soft agar colony formation but showed varying effects on cell proliferation and chemosensitivity. Thus we have identified the miRNA expression signature for malignant astrocytoma, in particular glioblastoma, and showed the miRNA involvement and their importance in astrocytoma development. Modern Pathology (2010) 23, 1404-1417; doi:10.1038/modpathol.2010.135; published online 13 August 2010

Incipient motion design of sand bed channels affected by bed suction

Seepage through sand bed channels in a downward direction (suction) reduces the stability of particles and initiates the sand movement. Incipient motion of sand bed channel with seepage cannot be designed by using the conventional approach. Metamodeling techniques, which employ a non-linear pattern analysis between input and output parameters and solely based on the experimental observations, can be used to model such phenomena. Traditional approach to find non-dimensional parameters has not been used in the present work. Parameters, which can influence the incipient motion with seepage, have been identified and non-dimensionalized in the present work. Non-dimensional stream power concept has been used to describe the process. By using these non-dimensional parameters; present work describes a radial basis function (RBF) metamodel for prediction of incipient motion condition affected by seepage. The coefficient of determination, R-2 of the model is 0.99. Thus, it can be said that model predicts the phenomena very well. With the help of the metamodel, design curves have been presented for designing the sand bed channel when it is affected by seepage. (C) 2010 Elsevier B.V. All rights reserved.

Sediment Volume Tests for Expansive Soil Identification and Classification

Equilibrium sediment volume tests are conducted on field soils to classify them based on their degree of expansivity and/or to predict the liquid limit of soils. The present technical paper examines different equilibrium sediment volume tests, critically evaluating each of them. It discusses the settling behavior of fine-grained soils during the soil sediment formation to evolve a rationale for conducting the latest version of equilibrium sediment volume test. Probable limitations of equilibrium sediment volume test and the possible solution to overcome the same have also been indicated.

General model of a foam bed reactor

A general model of a foam bed reactor has been developed which rigorously accounts for the extent of gas absorption with chemical reaction occurring in both the storage and foam sections. Its applicability extends to a wide spectrum of reaction velocities. The possibilities of the predominance of the bulk-liquid reaction in the storage section or the absorption with reaction in the foam section can be handled as merely special cases of the general analysis. The importance of foam for carrying out a particular gas-liquid reaction is characterised by a criterion in terms of the fractional rate of reaction in the foam section. Trends of variations in the concentrations of dissolved free A, solute B, and gas-phase A with time of operation of the reactor are presented. The nature of the variation in the fractional rate of reaction in the foam section with time, at different reaction velocities, and the effect of the liquid flow rate (across the storage section) on the transience are also illustrated. Finally, the predictions of the general model have been validated using the available experimental data on the oxidation of sodium sulphide in a foam bed reactor. The agreement between the experimental and the present theoretical information is fairly good, apart from being more insightful than all the previous models of this reactor.

Molecular profiling of indoor microbial communities in moisture damaged and non-damaged buildings

Epidemiological studies have shown an elevation in the incidence of asthma, allergic symptoms and respiratory infections among people living or working in buildings with moisture and mould problems. Microbial growth is suspected to have a key role, since the severity of microbial contamination and symptoms show a positive correlation, while the removal of contaminated materials relieves the symptoms. However, the cause-and-effect relationship has not been well established and knowledge of the causative agents is incomplete. The present consensus of indoor microbes relies on culture-based methods. Microbial cultivation and identification is known to provide qualitatively and quantitatively biased results, which is suspected to be one of the reasons behind the often inconsistent findings between objectively measured microbiological attributes and health. In the present study the indoor microbial communities were assessed using culture-independent, DNA based methods. Fungal and bacterial diversity was determined by amplifying and sequencing the nucITS- and16S-gene regions, correspondingly. In addition, the cell equivalent numbers of 69 mould species or groups were determined by quantitative PCR (qPCR). The results from molecular analyses were compared with results obtained using traditional plate cultivation for fungi. Using DNA-based tools, the indoor microbial diversity was found to be consistently higher and taxonomically wider than viable diversity. The dominant sequence types of fungi, and also of bacteria were mainly affiliated with well-known microbial species. However, in each building they were accompanied by various rare, uncultivable and unknown species. In both moisture-damaged and undamaged buildings the dominant fungal sequence phylotypes were affiliated with the classes Dothideomycetes (mould-like filamentous ascomycetes); Agaricomycetes (mushroom- and polypore-like filamentous basidiomycetes); Urediniomycetes (rust-like basidiomycetes); Tremellomycetes and the family Malasseziales (both yeast-like basidiomycetes). The most probable source for the majority of fungal types was the outdoor environment. In contrast, the dominant bacterial phylotypes in both damaged and undamaged buildings were affiliated with human-associated members within the phyla Actinobacteria and Firmicutes. Indications of elevated fungal diversity within potentially moisture-damage-associated fungal groups were recorded in two of the damaged buildings, while one of the buildings was characterized by an abundance of members of the Penicillium chrysogenum and P. commune species complexes. However, due to the small sample number and strong normal variation firm conclusions concerning the effect of moisture damage on the species diversity could not be made. The fungal communities in dust samples showed seasonal variation, which reflected the seasonal fluctuation of outdoor fungi. Seasonal variation of bacterial communities was less clear but to some extent attributable to the outdoor sources as well. The comparison of methods showed that clone library sequencing was a feasible method for describing the total microbial diversity, indicated a moderate quantitative correlation between sequencing and qPCR results and confirmed that culture based methods give both a qualitative and quantitative underestimate of microbial diversity in the indoor environment. However, certain important indoor fungi such as Penicillium spp. were clearly underrepresented in the sequence material, probably due to their physiological and genetic properties. Species specific qPCR was a more efficient and sensitive method for detecting and quantitating individual species than sequencing, but in order to exploit the full advantage of the method in building investigations more information is needed about the microbial species growing on damaged materials. In the present study, a new method was also developed for enhanced screening of the marker gene clone libraries. The suitability of the screening method to different kinds of microbial environments including biowaste compost material and indoor settled dusts was evaluated. The usability was found to be restricted to environments that support the growth and subsequent dominance of a small number microbial species, such as compost material.