Anaphe - OO Libraries and Tools for Data Analysis

The Anaphe project is an ongoing effort to provide an Object Oriented software environment for data analysis in HENP experiments. A range of commercial and public domain libraries is used to cover basic functionalities; on top of these libraries a set of HENP-specific C++ class libraries for histogram management, fitting, plotting and ntuple-like data analysis has been developed. In order to comply with the user requirements for a command-line driven tool, we have chosen to use a scripting language (Python) as the front-end for a data analysis tool. The loose coupling provided by the consequent use of (AIDA compliant) Abstract Interfaces for each component in combination with the use of shared libraries for their implementation provides an easy integration of existing libraries into modern scripting languages thus allowing for rapid application development. This integration is simplified even further using a specialised toolkit (SWIG) to create "shadow classes" for the Python language, which map the definitions of the Abstract Interfaces almost at a one-to-one level. This paper will give an overview of the architecture and design choices and will present the current status and future developments of the project

Using olive mill wastewate to improve performance in producing electricity from domestic wastewater by using single-chamber microbial fuel cell

Improving electricity generation from wastewater (DW) by using olive mill wastewater (OMW) was evaluated using single-chamber microbial fuel cells (MFC). Doing so single-chambers air cathode MFCs with platinum anode were fed with domestic wastewater (DW) alone and mixed with OMW at the ratio of 14:1 (w/w). MFCs fed with DW + OMW gave 0.38 V at 1 kO, while power density from polarization curve was of 124.6mW m 2. The process allowed a total reduction of TCOD and BOD5 of 60% and 69%, respectively, recovering the 29% of the coulombic efficiency. The maximum voltage obtained from MFC fed with DW + OMW was 2.9 times higher than that of cell fed with DW. DNA-fingerprinting showed high bacterial diversity for both experiments and the presence on anodes of exoelectrogenic bacteria, such as Geobacter spp. Electrodes selected peculiar consortia and, in particular, anodes of both experiments showed a similar specialization of microbial communities independently by feeding used

Translation and cross-cultural adaptation into italian of the self-administered FLARE-RA questionnaire for rheumatoid arthritis

The aim was to provide a translation into Italian with cross-cultural adaptation of the French FLARE-Rheumatoid Arthritis (RA) questionnaire, and to test its acceptability, feasibility, reliability and construct validity in a single-centre cohort study. The French version of the FLARE-RA questionnaire was cross-culturally adapted and translated into Italian following an established forward\u2013backward translation procedure, with independent translations and backtranslations. To validate the Italian version we tested the internal validity with Cronbach\u2019s alpha, test-retest reliability with the intraclass correlation coefficient, agreement between assessments with Bland-Altman plots and construct validity with Spearman\u2019s correlation coefficients. The questionnaire was tested on 283 consecutive RA outpatients (mean age 56.1\ub1}13.9 years, 226/283 females, median disease duration 12.6 years ranging from 0.2 to 70.6). For the global score (11 items) the Cronbach\u2019s alpha coefficient was 0.94. The intraclass correlation coefficient was 0.87 (95% CI, 0.76-0.96). The correlation of FLARE-RA global score was 0.59 (95% CI, 0.50-0.66) with the Disease Activity Score on 28 joints, 0.63 (95% CI, 0.55-0.71) with the Simplified Disease Activity Index, 0.77 (95% CI, 0.71-0.83) with the RA Impact of Disease and 0.67 (95% CI, 0.59-0.73) with the Health Assessment Questionnaire. The Italian version of the FLARE-RA is feasible, brief and easy to administer. The translated and cross-cultural adapted showed accordingly to be valid and reliable. This questionnaire has some practical advantages, such as clarity, comprehensiveness, simplicity, and a minimum filling time. The development of cross-cultural adapted questionnaires in different languages is of pivotal importance to obtain standardized and comparable data across countries

Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-specific library probes

Chromosome aberrations in two glioma cell lines were analyzed using biotinylated DNA library probes that specifically decorate chromosomes 1, 4, 7, 18 and 22 from pter to qter. Numerical changes, deletions and rearrangements of these chromosomes were radily visualized in metaphase spreads, as well as in early prophase and interphase nuclei. Complete chromosomes, deleted chromosomes and segments of translocated chromosomes were rapidly delineated in very complex karyotypes. Simultaneous hybridizations with additional subregional probes were used to further define aberrant chromosomes. Digital image analysis was used to quantitate the total complement of specific chromosomal DNAs in individual metaphase and interphase cells of each cell line. In spite of the fact that both glioma lines have been passaged in vitro for many years, an under-representation of chromosome 22 and an over-representation of chromosome 7 (specifically 7p) were observed. These observations agree with previous studies on gliomas. In addition, sequences of chromosome 4 were also found to be under-represented, especially in TC 593. These analyses indicate the power of these methods for pinpointing chromosome segments that are altered in specific types of tumors

Change in expression of the actin gene family during early sea urchin development

Expression of the actin gene family was studied during early sea urchin development using in vitro translation and nucleic acid hybridization techniques. Poly(A)+ RNA from four-cell and gastrula-stage S. purpuratus embryos was translated in vitro and the translation products were monitored for the presence of actin. In addition, poly(A)+ and total RNA were prepared from various stages of development, electrophoresed on agarose gels, transferred to diazobenzyloxymethyl paper, and then hybridized with a cloned actin cDNA probe. Results of these experiments indicate that there is a sharp increase in the level of RNA coding for actin during early development, and that there are two forms of actin specific RNA exhibiting different patterns of control.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24301/1/0000567.pd

Autogenous regulation of Escherichia coli polynucleotide phosphorylase expression revisited

The Escherichia coli polynucleotide phosphorylase (PNPase, encoded by pnp), a phosphorolytic exoribonuclease, post-transcriptionally regulates its own expression at the level of mRNA stability and translation. Its primary transcript is very efficiently processed by RNase III, an endonuclease that makes a staggered double strand cleavage about in the middle of a long stem-loop in the 5'-untranslated region. The processed pnp mRNA is then rapidly degraded in a PNPase-dependent manner. Two non-mutually exclusive models have been proposed to explain PNPase autogenous regulation. The earlier one suggested that PNPase impedes translation of the RNase III processed pnp mRNA thus exposing the transcript to degradative pathways. More recently this has been replaced by the current model, which maintains that PNPase would simply degrade the promoter proximal small RNA generated by the RNase III endonucleolytic cleavage thus destroying the double stranded structure at the 5'-end that otherwise stabilizes the pnp mRNA. In our opinion, however, the first model was not completely ruled out. Moreover, the RNA decay pathway acting upon the pnp mRNA after disruption of the 5' double stranded structure remained to be determined. Here we provide additional support to the current model and show that the RNase III-processed pnp mRNA devoid of the double stranded structure at its 5'-end is not translatable and is degraded by RNase E in a PNPase-independent manner. Thus the role of PNPase in autoregulation is simply to remove, in concert with RNase III, the 5'-fragment of the cleaved structure that both allows translation and prevents the RNase E-mediated PNPase-independent degradation of the pnp transcript

Long-range attraction between particles in dusty plasma and partial surface tension of dusty phase boundary

Effective potential of a charged dusty particle moving in homogeneous plasma has a negative part that provides attraction between similarly charged dusty particles. A depth of this potential well is great enough to ensure both stability of crystal structure of dusty plasma and sizable value of surface tension of a boundary surface of dusty region. The latter depends on the orientation of the surface relative to the counter-ion flow, namely, it is maximal and positive for the surface normal to the flow and minimal and negative for the surface along the flow. For the most cases of dusty plasma in a gas discharge, a value of the first of them is more than sufficient to ensure stability of lenticular dusty phase void oriented across the counter-ion flow.Comment: LATEX, REVTEX4, 7 pages, 6 figure

Epstein-Barr Virus in Cutaneous T-Cell Lymphomas: Evaluation of the Viral Presence and Significance in Skin and Peripheral Blood

The importance of viral agents in the development of cutaneous T-cell lymphomas (CTCL) is still debated. For this purpose, we retrospectively evaluated the Epstein-Barr virus (EBV) presence in Sézary syndrome (SS), mycosis fungoides (MF), inflammatory dermatoses (ID), and healthy donors (HD) using different approaches: EBV-DNA was quantified in skin biopsies and peripheral blood using real-time PCR, EBV-encoded small RNA (EBER) transcripts were detected by in situ hybridization (ISH), and latent membrane protein1-2 antigens were detected by immunohistochemistry. Skin biopsies were EBV-DNA-positive in 8/30 (27%) SS, 7/71 (10%) MF, and 2/18 (11%) ID patients and in none of the 25 normal skin samples. Positive mRNA (EBER) signals, always confined to cerebriform T lymphocytes, were found in 5/30 SS patients (17%), whereas signals in all MF and ID patients were negative. The presence of EBV-DNA in skin and blood samples was associated with a significantly lower survival in MF/SS patients. In evaluating EBV serological status, most (>70%) SS, MF, and ID patients showed a serological reactivation demonstrated by the presence of anti-EA IgG. In conclusion, although the finding of EBV-DNA in CTCL does not prove its etiopathogenetic role and may be related instead to immunosuppression, our study demonstrates that it has prognostic relevance

General population job exposure matrix applied to a pooled study of prevalent carpal tunnel syndrome

A job exposure matrix may be useful for the study of biomechanical workplace risk factors when individual-level exposure data are unavailable. We used job title–based exposure data from a public data source to construct a job exposure matrix and test exposure-response relationships with prevalent carpal tunnel syndrome (CTS). Exposures of repetitive motion and force from the Occupational Information Network were assigned to 3,452 active workers from several industries, enrolled between 2001 and 2008 from 6 studies. Repetitive motion and force exposures were combined into high/high, high/low, and low/low exposure groupings in each of 4 multivariable logistic regression models, adjusted for personal factors. Although force measures alone were not independent predictors of CTS in these data, strong associations between combined physical exposures of force and repetition and CTS were observed in all models. Consistent with previous literature, this report shows that workers with high force/high repetition jobs had the highest prevalence of CTS (odds ratio = 2.14–2.95) followed by intermediate values (odds ratio = 1.09–2.27) in mixed exposed jobs relative to the lowest exposed workers. This study supports the use of a general population job exposure matrix to estimate workplace physical exposures in epidemiologic studies of musculoskeletal disorders when measures of individual exposures are unavailable