System Tests of the ATLAS Pixel Detector

The innermost part of the ATLAS (A Toroidal LHC ApparatuS) experiment at the LHC (Large Hadron Collider) will be a pixel detector, which is presently under construction. Once installed into the experimental area, access will be extremely limited. To ensure that the integrated detector assembly operates as expected, a fraction of the detector which includes the power supplies and monitoring system, the optical readout, and the pixel modules themselves, has been assembled and operated in a laboratory setting for what we refer to as system tests. Results from these tests are presented.Comment: 5 Pages, 9 Figures, to appear in Proceedings of the Eleventh Workshop on Electronics for LHC and Future Experiment

Distributed Electro-Mechanical Coupling Effects in a Dielectric Elastomer Membrane Array

Background Dielectric elastomer (DE) transducers permit to efectively develop large-deformation, energy-efcient, and compliant mechatronic devices. By arranging many DE elements in an array-like confguration, a soft actuator/sensor system capable of cooperative features can be obtained. When many DE elements are densely packed onto a common elastic membrane, spatial coupling efects introduce electro-mechanical interactions among neighbors, which strongly afect the system actuation and sensing performance. To efectively design cooperative DE systems, those coupling efects must be systematically characterized and understood frst. Objective As a frst step towards the development of complex cooperative DE systems, in this work we present a systematic characterization of the spatial electro-mechanical interactions in a 1-by-3 array of silicone DEs. More specifcally, we investigate how the force and capacitance characteristics of each DE in the array change when its neighbors are subject to diferent types of mechanical or electrical loads. Force and capacitance are chosen for this investigation, since those quantities are directly tied to the DE actuation and sensing behaviors, respectively. Methods An electro-mechanical characterization procedure is implemented through a novel experimental setup, which is specifcally developed for testing soft DE arrays. The setup allows to investigate how the force and capacitance characteristics of each DE are afected by static deformations and/or electrical voltages applied to its nearby elements. Diferent combinations of electro-mechanical loads and DE neighbors are considered in an extensive experimental campaign. Results The conducted investigation shows the existence of strong electro-mechanical coupling efects among the diferent array elements. The interaction intensity depends on multiple parameters, such as the distance between active DEs or the amount of deformation/voltage applied to the neighbors, and provides essential information for the design of array actuators. In some cases, such coupling efects may lead to changes in force up to 9% compared to the reference confguration. A further coupling is also observed in the DE capacitive response, and opens up the possibility of implementing advanced and/or distributed self-sensing strategies in future applications. Conclusion By means of the conducted experiments, we clearly show that the actuation and sensing characteristics of each DE in the array are strongly infuenced by the electro-mechanical loading state of its neighbors. The coupling efects may signifcantly afect the overall cooperative system performance, if not properly accounted for during the design. In future works, the obtained results will allow developing cooperative DE systems which are robust to, and possibly take advantage of, such spatial coupling efects

Longitudinal genome-wide methylation study of Roux-en-Y gastric bypass patients reveals novel CpG sites associated with essential hypertension

Background: Essential hypertension is a significant risk factor for cardiovascular diseases. Emerging research suggests a role of DNA methylation in blood pressure physiology. We aimed to investigate epigenetic associations of promoter related CpG sites to essential hypertension in a genome-wide methylation approach. Methods: The genome-wide methylation pattern in whole blood was measured in 11 obese patients before and six months after Roux-en-Y gastric bypass surgery using the Illumina 450 k beadchip. CpG sites located within 1500 bp of the transcriptional start site of adjacent genes were included in our study, resulting in 124 199 probes investigated in the subsequent analysis. Percent changes in methylation states and SBP measured before and six months after surgery were calculated. These parameters were correlated to each other using the Spearman's rank correlation method (Edgeworth series approximation). To further investigate the detected relationship between candidate CpG sites and systolic blood pressure levels, binary logistic regression analyses were performed in a larger and independent cohort of 539 individuals aged 19-101 years to elucidate a relationship between EH and the methylation state in candidate CpG sites. Results: We identified 24 promoter associated CpG sites that correlated with change in SBP after RYGB surgery (p < 10-16). Two of these CpG loci (cg00875989, cg09134341) were significantly hypomethylated in dependency of EH (p < 10-03). These results were independent of age, BMI, ethnicity and sex. Conclusions: The identification of these novel CpG sites may contribute to a further understanding of the epigenetic regulatory mechanisms underlying the development of essential hypertension

The solute transport and binding profile of a novel nucleobase cation symporter 2 from the honeybee pathogen Paenibacillus larvae

Here, we report that a novel nucleobase cation symporter 2 encoded in the genome of the honeybee bacterial pathogen Paenibacillus larvae reveals high levels of amino acid sequence similarity to the Escherichia coli and Bacillus subtilis uric acid and xanthine transporters. This transporter is named P. larvae uric acid permease-like protein (PlUacP). Even though PlUacP displays overall amino acid sequence similarities, has common secondary structures, and shares functional motifs and functionally important amino acids with E. coli xanthine and uric acid transporters, these commonalities are insufficient to assign transport function to PlUacP. The solute transport and binding profile of PlUacP was determined by radiolabeled uptake experiments via heterologous expression in nucleobase transporter-deficient Saccharomyces cerevisiae strains. PlUacP transports the purines adenine and guanine and the pyrimidine uracil. Hypoxanthine, xanthine, and cytosine are not transported by PlUacP, but, along with uric acid, bind in a competitive manner. PlUacP has strong affinity for adenine Km 7.04 ± 0.18 μm, and as with other bacterial and plant NCS2 proteins, PlUacP function is inhibited by the proton disruptor carbonyl cyanide m-chlorophenylhydrazone. The solute transport and binding profile identifies PlUacP as a novel nucleobase transporter

Roux-En Y Gastric Bypass Surgery Induces Genome-Wide Promoter-Specific Changes in DNA Methylation in Whole Blood of Obese Patients

Context DNA methylation has been proposed to play a critical role in many cellular and biological processes. Objective To examine the influence of Roux-en-Y gastric bypass (RYGB) surgery on genome-wide promoter-specific DNA methylation in obese patients. Promoters are involved in the initiation and regulation of gene transcription. Methods Promoter-specific DNA methylation in whole blood was measured in 11 obese patients (presurgery BMI >35 kg/m2, 4 females), both before and 6 months after RYGB surgery, as well as once only in a control group of 16 normal-weight men. In addition, body weight and fasting plasma glucose were measured after an overnight fast. Results The mean genome-wide distance between promoter-specific DNA methylation of obese patients at six months after RYGB surgery and controls was shorter, as compared to that at baseline (p<0.001). Moreover, postsurgically, the DNA methylation of 51 promoters was significantly different from corresponding values that had been measured at baseline (28 upregulated and 23 downregulated, P<0.05 for all promoters, Bonferroni corrected). Among these promoters, an enrichment for genes involved in metabolic processes was found (n = 36, P<0.05). In addition, the mean DNA methylation of these 51 promoters was more similar after surgery to that of controls, than it had been at baseline (P<0.0001). When controlling for the RYGB surgery-induced drop in weight (-24% of respective baseline value) and fasting plasma glucose concentration (-16% of respective baseline value), the DNA methylation of only one out of 51 promoters (~2%) remained significantly different between the pre-and postsurgery time points. Conclusions Epigenetic modifications are proposed to play an important role in the development of and predisposition to metabolic diseases, including type II diabetes and obesity. Thus, our findings may form the basis for further investigations to unravel the molecular effects of gastric bypass surgery. Clinical Trial ClinicalTrials.gov NCT0173074

Ultralong Copper Phthalocyanine Nanowires with New Crystal Structure and Broad Optical Absorption

The development of molecular nanostructures plays a major role in emerging organic electronic applications, as it leads to improved performance and is compatible with our increasing need for miniaturisation. In particular, nanowires have been obtained from solution or vapour phase and have displayed high conductivity, or large interfacial areas in solar cells. In all cases however, the crystal structure remains as in films or bulk, and the exploitation of wires requires extensive post-growth manipulation as their orientations are random. Here we report copper phthalocyanine (CuPc) nanowires with diameters of 10-100 nm, high directionality and unprecedented aspect ratios. We demonstrate that they adopt a new crystal phase, designated eta-CuPc, where the molecules stack along the long axis. The resulting high electronic overlap along the centimetre length stacks achieved in our wires mediates antiferromagnetic couplings and broadens the optical absorption spectrum. The ability to fabricate ultralong, flexible metal phthalocyanine nanowires opens new possibilities for applications of these simple molecules

Large phenotype jumps in biomolecular evolution

By defining the phenotype of a biopolymer by its active three-dimensional shape, and its genotype by its primary sequence, we propose a model that predicts and characterizes the statistical distribution of a population of biopolymers with a specific phenotype, that originated from a given genotypic sequence by a single mutational event. Depending on the ratio g0 that characterizes the spread of potential energies of the mutated population with respect to temperature, three different statistical regimes have been identified. We suggest that biopolymers found in nature are in a critical regime with g0 in the range 1-6, corresponding to a broad, but not too broad, phenotypic distribution resembling a truncated Levy flight. Thus the biopolymer phenotype can be considerably modified in just a few mutations. The proposed model is in good agreement with the experimental distribution of activities determined for a population of single mutants of a group I ribozyme.Comment: to appear in Phys. Rev. E; 7 pages, 6 figures; longer discussion in VII, new fig.

Interoperability and FAIRness through a novel combination of Web technologies

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general- or special-purpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs