Application of the ATLAS DAQ and Monitoring System for MDT and RPC Commissioning

The ATLAS DAQ and monitoring software are currently commonly used to test detectors during the commissioning phase. In this paper, their usage in MDT and RPC commissioning is described, both at the surface pre-commissioning and commissioning stations and in the ATLAS pit. Two main components are heavily used for detector tests. The ROD Crate DAQ software is based on the ATLAS Readout application. Based on the plug-in mechanism, it provides a complete environment to interface any kind of detector or trigger electronics to the ATLAS DAQ system. All the possible flavours of this application are used to test and run the MDT and RPC detectors at the pre-commissioning and commissioning sites. Ad-hoc plug-ins have been developed to implement data readout via VME, both with ROD prototypes and emulating final electronics to read out data with temporary solutions, and to provide trigger distribution and busy management in a multi-crate environment. Data driven event building functionality is also used to combine data from different detector technologies. Monitoring software provides a framework for on-line analysis during detector test. Monitoring applications have been developed for noise and cosmic tests and for pulse runs. The PERSINT event display has been interfaced to the monitoring system to provide an on-line event display for cosmic runs in the ATLAS pit

Cultural rights in the case-law of the International Court of Justice (ICJ)

One of the most remarkable developments of the new millennium has been the expansion of debates on culture at the highest levels of the international community’s decision-making processes. This development has necessarily had an impact on cultural rights empowerment, including enhancing their justiciability. Substantial progress has been made both at a regional and international level. Yet, not all thresholds have been reached. The International Court of Justice (‘ICJ’) has never explicitly addressed cultural rights in its case-law. Despite its ‘multicultural’ composition, it is only with great difficulty that the Court examines questions related to culture. However, a thorough examination of the jurisprudence of the ICJ reveals that opportunities to take cultural rights seriously have arisen more than once. Recent judgments of the Court reveal the emergence of a certain trend calling for a ‘culturally sensitive’ understanding of legal issues brought to the Hague. The present paper submits that this trend is beneficial not only for the protection of cultural rights, but also for the maintenance of human and cultural diversity, as well as for the survival and livelihood of indigenous peoples. In light of the urgent worldwide need for peace, addressing culture as a legal issue before the ICJ, in accordance with articles 36 and 60 of its statute, may be a fruitful pathway for the Court to follow in order to resolve international disputes

SAVI: a statistical algorithm for variant frequency identification

BACKGROUND: Many problems in biomedical research can be posed as a comparison between related samples (healthy vs. disease, subtypes of the same disease, longitudinal data representing the progression of a disease, etc). In the cases in which the distinction has a genetic or epigenetic basis, next-generation sequencing technologies have become a major tool for obtaining the difference between the samples. A commonly occurring application is the identification of somatic mutations occurring in tumor tissue samples driving a single cell to expand clonally. In this case, the progression of the disease can be traced through the trajectory of the frequency of the oncogenic alleles. Thus obtaining precise estimates of the frequency of abnormal alleles at various stages of the disease is paramount to understanding the processes driving it. Although the procedure is conceptually simple, technical difficulties arise due to inhomogeneous samples, existence of competing subclonal populations, and systematic and non-systematic errors introduced by the sequencing technologies. RESULTS: We present a method, Statistical Algorithm for Variant Frequency Identification (SAVI), to estimate the frequency of alleles in a set of samples. The method employs Bayesian analysis and uses an iterative procedure to derive empirical priors. The approach allows for the comparison of allele frequencies across several samples, e.g. normal/tumor pairs and more complex experimental designs comparing multiple samples in tumor progression, as well as analyzing sequencing data from RNA sequencing experiments. CONCLUSIONS: Analyzing sequencing data through estimating allele frequencies using empirical Bayes methods is a powerful complement to the ever-increasing throughput of the sequencing technologies

Dispersion-theoretical analysis of the nucleon electromagnetic form factors: Inclusion of time-like data

We update a recent dispersion--theoretical fit to the nucleon electromagnetic form factors by including the existing data in the time--like region. We show that while the time--like data for the proton can be described consistently with the existing world space--like data, this is not the case for the neutron. Another measurement of the process $e^+ e^- \to \bar n n$ is called for. We furthermore sharpen the previous estimate of the separation between the perturbative and the non--perturbative regime, which is characterized by a scale parameter $\Lambda^2 \simeq 10\,$GeV$^2$.Comment: 7 pp, LaTeX, uses epsf, 2 figures in separate file, four data points changed, slight changes in the fits, conclusions unchange

Morphometric brain changes during aging: Results from a Brazilian necropsy sample.

The present study aimed to establish the morphometric brain changes during aging in a necropsy series from Brazil and determine whether sexual dimorphisms interfere in these changes. Methods:A cross-sectional study was conducted at the São Paulo Autopsy Service in Brazil where, after informed consent, data was gathered from next of kin interview with reference to clinical status prior to death. Brain weight, volume and density measurements were taken and then adjusted for head circumference. Descriptive statistics and tests of hypothesis and correlations were applied, considering a p-value of 0.05. Results:414 subjects, mostly men (60.4%), with a mean age of 67.1 years, were included. The mean brain weight of the sample was 1219.2g±140.9and mean volume was 1217mL±152.3. The mean brain density of the sample was 1.0g/mL±0.09. Values differed between males and females in terms of weight and volume. Brain weight decreased during aging by about 45g per decade (r= -0.300; p<0.01) and volume by about 43mL (r= -0.278; p<0.00). Mean density of the sample was 1.0 g/mL in both genders. Conclusions:Brain weight and volume (with or without corrections) decreased during aging, and these reductions were more pronounced in women. Density remained unchanged for both genders. Further studies are needed to investigate factors associated to these reductions

Increased DNA Copy Number Variation Mosaicism in Elderly Human Brain.

Aging is a complex process strongly determined by genetics. Previous reports have shown that the genome of neuronal cells displays somatic genomic mosaicism including DNA copy number variations (CNVs). CNVs represent a significant source of genetic variation in the human genome and have been implicated in several disorders and complex traits, representing a potential mechanism that contributes to neuronal diversity and the etiology of several neurological diseases and provides new insights into the normal, complex functions of the brain. Nonetheless, the features of somatic CNV mosaicism in nondiseased elderly brains have not been investigated. In the present study, we demonstrate a highly significant increase in the number of CNVs in nondiseased elderly brains compared to the blood. In two neural tissues isolated from paired postmortem samples (same individuals), we found a significant increase in the frequency of deletions in both brain areas, namely, the frontal cortex and cerebellum. Also, deletions were found to be significantly larger when present only in the cerebellum. The sizes of the variants described here were in the 150-760 kb range, and importantly, nearly all of them were present in the Database of Genomic Variants (common variants). Nearly all evidence of genome structural variation in human brains comes from studies detecting changes in single cells which were interpreted as derived from independent, isolated mutational events. The observations based on array-CGH analysis indicate the existence of an extensive clonal mosaicism of CNVs within and between the human brains revealing a different type of variation that had not been previously characterized

Post-Mortem diagnosis of dementia by informant interview.

The diagnosis of normal cognition or dementia in the Brazilian Brain Bank of the Aging Brain Study Group (BBBABSG) has relied on postmortem interview with an informant. Objectives:To ascertain the sensitivity and specificity of postmortem diagnosis based on informant interview compared against the diagnosis established at a memory clinic. Methods:A prospective study was conducted at the BBBABSG and at the Reference Center for Cognitive Disorders (RCCD), a specialized memory clinic of the Hospital das Clínicas, University of São Paulo Medical School. Control subjects and cognitively impaired subjects were referred from the Hospital das Clínicas to the RCCD where subjects and their informants were assessed. The same informant was then interviewed at the BBBABSG. Specialists' panel consensus, in each group, determined the final diagnosis of the case, blind to other center's diagnosis. Data was compared for frequency of diagnostic equivalence. For this study, the diagnosis established at the RCCD was accepted as the gold standard. Sensitivity and specificity were computed. Results:Ninety individuals were included, 45 with dementia and 45 without dementia (26 cognitively normal and 19 cognitively impaired but non-demented). The informant interview at the BBBABSG had a sensitivity of 86.6% and specificity of 84.4% for the diagnosis of dementia, and a sensitivity of 65.3% and specificity of 93.7% for the diagnosis of normal cognition. Conclusions:The informant interview used at the BBBABSG has a high specificity and sensitivity for the diagnosis of dementia as well as a high specificity for the diagnosis of normal cognition

An Oncogenic Role for Alternative NF-κB Signaling in DLBCL Revealed upon Deregulated BCL6 Expression

SummaryDiffuse large B cell lymphoma (DLBCL) is a complex disease comprising diverse subtypes and genetic profiles. Possibly because of the prevalence of genetic alterations activating canonical NF-κB activity, a role for oncogenic lesions that activate the alternative NF-κB pathway in DLBCL has remained elusive. Here, we show that deletion/mutation of TRAF3, a negative regulator of the alternative NF-κB pathway, occurs in ∼15% of DLBCLs and that it often coexists with BCL6 translocation, which prevents terminal B cell differentiation. Accordingly, in a mouse model constitutive activation of the alternative NF-κB pathway cooperates with BCL6 deregulation in DLBCL development. This work demonstrates a key oncogenic role for the alternative NF-κB pathway in DLBCL development