Effective description of the short-time dynamics in open quantum systems

We address the dynamics of a bosonic system coupled to either a bosonic or a magnetic environment, and derive a set of sufficient conditions that allow one to describe the dynamics in terms of the effective interaction with a classical fluctuating field. We find that for short interaction times the dynamics of the open system is described by a Gaussian noise map for several different interaction models and independently on the temperature of the environment. In order to go beyond a qualitative understanding of the origin and physical meaning of the above short-time constraint, we take a general viewpoint and, based on an algebraic approach, suggest that any quantum environment can be described by classical fields whenever global symmetries lead to the definition of environmental operators that remain well defined when increasing the size, i.e. the number of dynamical variables, of the environment. In the case of the bosonic environment this statement is exactly demonstrated via a constructive procedure that explicitly shows why a large number of environmental dynamical variables and, necessarily, global symmetries, entail the set of conditions derived in the first part of the work.Comment: 9 pages, close to published versio

AMDA: an R package for the automated microarray data analysis

BACKGROUND: Microarrays are routinely used to assess mRNA transcript levels on a genome-wide scale. Large amount of microarray datasets are now available in several databases, and new experiments are constantly being performed. In spite of this fact, few and limited tools exist for quickly and easily analyzing the results. Microarray analysis can be challenging for researchers without the necessary training and it can be time-consuming for service providers with many users. RESULTS: To address these problems we have developed an automated microarray data analysis (AMDA) software, which provides scientists with an easy and integrated system for the analysis of Affymetrix microarray experiments. AMDA is free and it is available as an R package. It is based on the Bioconductor project that provides a number of powerful bioinformatics and microarray analysis tools. This automated pipeline integrates different functions available in the R and Bioconductor projects with newly developed functions. AMDA covers all of the steps, performing a full data analysis, including image analysis, quality controls, normalization, selection of differentially expressed genes, clustering, correspondence analysis and functional evaluation. Finally a LaTEX document is dynamically generated depending on the performed analysis steps. The generated report contains comments and analysis results as well as the references to several files for a deeper investigation. CONCLUSION: AMDA is freely available as an R package under the GPL license. The package as well as an example analysis report can be downloaded in the Services/Bioinformatics section of the Genopoli

Influence of pre-reproductive maternal enrichment on coping response to stress and expression of c-Fos and glucocorticoid receptors in adolescent offspring

Environmental enrichment (EE) is an experimental setting broadly used for investigating the effects of complex social, cognitive, and sensorimotor stimulations on brain structure and function. Recent studies point out that parental EE experience, even occurring in the pre-reproductive phase, affects neural development and behavioral trajectories of the offspring. In the present study we investigated the influences of pre-reproductive EE of female rats on maternal behavior and adolescent male offspring's coping response to an inescapable stressful situation after chronic social isolation. For this purpose female Wistar rats were housed from weaning to breeding age in enriched or standard environments. Subsequently, all females were mated and housed in standard conditions until offspring weaning. On the first post partum day (ppd 1), mother-pup interactions in undisturbed conditions were recorded. Further, after weaning the male pups were reared for 2 weeks under social isolation or in standard conditions, and then submitted or not to a single-session Forced Swim Test (FST). Offspring's neuronal activation and plastic changes were identified by immunohistochemistry for c-Fos and glucocorticoid receptors (GRs), and assessed by using stereological analysis. The biochemical correlates were measured in the hippocampus, amygdala and cingulate cortex, structures involved in hypothalamic-pituitary-adrenocortical axis regulation. Enriched dams exhibited increased Crouching levels in comparison to standard reared dams. In the offspring of both kinds of dams, social isolation reduced body weight, decreased Immobility, and increased Swimming during FST. Moreover, isolated offspring of enriched dams exhibited higher levels of Climbing in comparison to controls. Interestingly, in the amygdala of both isolated and control offspring of enriched dams we found a lower number of c-Fos immunopositive cells in response to FST and a higher number of GRs in comparison to the offspring of standard dams. These results highlight the profound influence of a stressful condition, such as the social isolation, on the brain of adolescent rats, and underline intergenerational effects of maternal experiences in regulating the offspring response to stress

Interaction does count: A cross-fostering study on transgenerational effects of pre-reproductive maternal enrichment

Pre-reproductive environmental enrichment of female rats influences sensorimotor development and spatial behavior of the offspring, possibly through the changed maternal nurturing. Nevertheless, maternal care could be not the solely responsible for changing offspring developmental trajectories. To disentangle the specific contribution to the transgenerational inheritance of pre- and post-natal factors, a cross-fostering study was performed. Female rats were reared in an enriched environment from weaning to sexual maturity, while control female rats were reared under standard conditions. Following mating with standard-reared males, all females were housed individually. Immediately after delivery, in- or cross-fostering manipulations were performed so that any foster dams received pups born to another dam of the same (in-fostering) or the opposite (cross-fostering) pre-reproductive rearing condition. In lactating dams maternal care and nesting activities were assessed, while in their male pups spatial abilities were assessed through Morris Water Maze (MWM) test at post-natal day 45. Moreover, the expression of Brain-Derived-Neurotrophic-Factor (BDNF) was evaluated in the hippocampus and frontal cortex of dams and pups at weaning. Pre-reproductive maternal environmental enrichment, followed by adoption procedures, loosened its potential in modifying maternal care and offspring developmental trajectories, as indicated by the lack of differences between in-fostered groups of dams and pups. In addition, enriched dams rearing standard pups showed the least complex maternal repertoire (the highest sniffing duration and the lowest nest quality), and their pups showed a reduced spatial learning in the MWM. Nevertheless, pre-reproductive maternal enrichment kept influencing neurotrophic pattern, with enriched dams expressing increased frontal BDNF levels (regardless of the kind of fostered pups), and their offspring expressing increased hippocampal BDNF levels. The present findings enlighten the crucial importance of the early mother-pups interactions in influencing maternal care and offspring phenotype, with the enriched dam-standard pups couple resulting in the most maladaptive encounter. Our study thus sustains that the bidirectional interactions between mother and pups are able to deeply shape offspring phenoty

Gene Expression Profiles Identify Inflammatory Signatures in Dendritic Cells

Dendritic cells (DCs) constitute a heterogeneous group of antigen-presenting leukocytes important in activation of both innate and adaptive immunity. We studied the gene expression patterns of DCs incubated with reagents inducing their activation or inhibition. Total RNA was isolated from DCs and gene expression profiling was performed with oligonucleotide microarrays. Using a supervised learning algorithm based on Random Forest, we generated a molecular signature of inflammation from a training set of 77 samples. We then validated this molecular signature in a testing set of 38 samples. Supervised analysis identified a set of 44 genes that distinguished very accurately between inflammatory and non inflammatory samples. The diagnostic performance of the signature genes was assessed against an independent set of samples, by qRT-PCR. Our findings suggest that the gene expression signature of DCs can provide a molecular classification for use in the selection of anti-inflammatory or adjuvant molecules with specific effects on DC activity

Classification of dendritic cell phenotypes from gene expression data

<p>Abstract</p> <p>Background</p> <p>The selection of relevant genes for sample classification is a common task in many gene expression studies. Although a number of tools have been developed to identify optimal gene expression signatures, they often generate gene lists that are too long to be exploited clinically. Consequently, researchers in the field try to identify the smallest set of genes that provide good sample classification. We investigated the genome-wide expression of the inflammatory phenotype in dendritic cells. Dendritic cells are a complex group of cells that play a critical role in vertebrate immunity. Therefore, the prediction of the inflammatory phenotype in these cells may help with the selection of immune-modulating compounds.</p> <p>Results</p> <p>A data mining protocol was applied to microarray data for murine cell lines treated with various inflammatory stimuli. The learning and validation data sets consisted of 155 and 49 samples, respectively. The data mining protocol reduced the number of probe sets from 5,802 to 10, then from 10 to 6 and finally from 6 to 3. The performances of a set of supervised classification models were compared. The best accuracy, when using the six following genes --Il12b, Cd40, Socs3, Irgm1, Plin2 and Lgals3bp-- was obtained by Tree Augmented Naïve Bayes and Nearest Neighbour (91.8%). Using the smallest set of three genes --Il12b, Cd40 and Socs3-- the performance remained satisfactory and the best accuracy was with Support Vector Machine (95.9%). These data mining models, using data for the genes Il12b, Cd40 and Socs3, were validated with a human data set consisting of 27 samples. Support Vector Machines (71.4%) and Nearest Neighbour (92.6%) gave the worst performances, but the remaining models correctly classified all the 27 samples.</p> <p>Conclusions</p> <p>The genes selected by the data mining protocol proposed were shown to be informative for discriminating between inflammatory and steady-state phenotypes in dendritic cells. The robustness of the data mining protocol was confirmed by the accuracy for a human data set, when using only the following three genes: Il12b, Cd40 and Socs3. In summary, we analysed the longitudinal pattern of expression in dendritic cells stimulated with activating agents with the aim of identifying signatures that would predict or explain the dentritic cell response to an inflammatory agent.</p

Responsiveness of the Oswestry Disability Index and the Roland Morris Disability Questionnaire in Italian subjects with sub-acute and chronic low back pain

Introduction An ability to assess longitudinal changes in health status is crucial for the outcome measures used in treatment efficacy trials. The aim of this study was to verify the responsiveness of the Italian versions of the Oswestry Disability Index (ODI) and the Roland Morris Disability Questionnaire (RMDQ) in subjects with subacute or chronic low back pain (LBP). Material and methods At the beginning and end of an 8 week rehabilitation programme, 179 patients completed a booklet containing the ODI, the RMDQ, a 0-10 numerical rating scale (NRS), and the 36-item Short-Form Health Survey (SF-36). A global perception of change scale was also completed at the end of the programme, and collapsed to produce a dichotomous outcome (i.e. improved vs. not improved). Responsiveness was assessed by means of distribution methods [minimum detectable change (MDC); effect size (ES); standardised response mean (SRM)] and anchorbased methods (ROC curves). Results The MDC for the ODI and RMDQ was, respectively, 13.67 and 4.87; the ESwas 0.53 and 0.68; and the SRM was 0.80 and 0.81. ROC analysis revealed an area under the curve of 0.71 for the ODI and 0.64 for the RMDQ, thus indicating discriminating capacity; the best cut-off point for the dichotomous outcome was 9.5 for the ODI (sensitivity 76% and specificity 63%) and 2.5 for the RMDQ (sensitivity 62% and specificity 55%). These estimates were comparable between the subacute and chronic subjects. Both the ODI and the RMDQ moderately correlated with the SF-36 and NRS (Spearman's and Pearson's correlation coefficients of>0.30). Conclusion The Italian ODI and RMDQ proved to be sensitive in detecting clinical changes after conservative treatment for subacute and chronic LBP.Our findings are consistentwith those published in the literature, thus allowing cross-cultural comparisons and stimulating cross-national studies. © 2011 Springer-Verlag

CONFRONTO DEI PARAMETRI GEOTECNICI E GEOFISICI PRE E POST BLAST TEST PRESSO IL SITO SPERIMENTALE DI MIRABELLO (FE)

L'articolo presenta alcuni risultati preliminari derivanti dal primo esperimento di liquefazione indotta tramite blast test realizzato in Italia, presso Mirabello (FE), comune fortemente colpito da fenomeni di liquefazione durante la sequenza sismica verificatasi in Emilia-Romagna nel 2012. In particolare diverse indagini in sito con tecniche invasive e non invasive sono state eseguite prima e dopo le detonazioni per confrontare la variazione dei parametri geotecnici e geofisici nel tempo

Exposure to an Enriched Environment Accelerates Recovery from Cerebellar Lesion

The exposure to enriched environments allows the maintenance of normal cognitive functioning even in the presence of brain pathology. Up until now, clinical and experimental studies have investigated environmental effects mainly on the symptoms linked to the presence of neuro-degenerative diseases, and no study has yet analyzed whether prolonged exposure to complex environments allows modifying the clinical expression and compensation of deficits of cerebellar origin. In animals previously exposed to complex stimulations, the effects of cerebellar lesions have been analyzed to verify whether a prolonged and intense exposure to complex stimulations affected the compensation of motor and cognitive functions following a cerebellar lesion. Hemicerebellectomized or intact animals housed in enriched or standard conditions were administered spatial tests. Postural asymmetries and motor behavior were also assessed. Exposure to the enriched environment almost completely compensated the effects of the hemicerebellectomy. In fact, the motor and cognitive performances of the enriched hemicerebellectomized animals were similar to those of the intact animals. The plastic changes induced by enhanced mental and physical activity seem to provide the development of compensatory responses against the disrupting motor and cognitive consequences of the cerebellar damage