WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes

The structural and conformational organization of chromosomes is crucial for gene expression regulation in eukaryotes and prokaryotes as well. Up to date, gene expression data generated using either microarray or RNA-sequencing are available for many bacterial genomes. However, differential gene expression is usually investigated with methods considering each gene independently, thus not taking into account the physical localization of genes along a bacterial chromosome. Here, we present WoPPER, a web tool integrating gene expression and genomic annotations to identify differentially expressed chromosomal regions in bacteria. RNA-sequencing or microarray-based gene expression data are provided as input, along with gene annotations. The user can select genomic annotations from an internal database including 2780 bacterial strains, or provide custom genomic annotations. The analysis produces as output the lists of positionally related genes showing a coordinated trend of differential expression. Graphical representations, including a circular plot of the analyzed chromosome, allow intuitive browsing of the results. The analysis procedure is based on our previously published R-package PREDA. The release of this tool is timely and relevant for the scientific community, as WoPPER will fill an existing gap in prokaryotic gene expression data analysis and visualization tools. WoPPER is open to all users and can be reached at the following URL: https://WoPPER.ba.itb.cnr.it

Results from CHIPIX-FE0, a Small Scale Prototype of a New Generation Pixel Readout ASIC in 65nm CMOS for HL-LHC

CHIPIX65-FE0 is a readout ASIC in CMOS 65nm designed by the CHIPIX65 project for a pixel detector at the HL-LHC, consisting of a matrix of 64x64 pixels of dimension 50x50 μm2. It is fully functional, can work at low thresholds down to 250e− and satisfies all the specifications. Results confirm low-noise, fast performance of both the synchronous and asynchronous front-end in a complex digital chip. CHIPIX65-FE0 has been irradiated up to 600 Mrad and is only marginally affected on analog performance. Further irradiation to 1 Grad will be performed. Bump bonding to silicon sensors is now on going and detailed measurements will be presented. The HL-LHC accelerator will constitute a new frontier for particle physics after year 2024. One major experimental challenge resides in the inner tracking detectors, measuring particle position: here the dimension of the sensitive area (pixel) has to be scaled down with respect to LHC detectors. This paper describes the results obtained by CHIPIX65-FE0, a readout ASIC in CMOS 65nm designed by the CHIPIX65 project as small-scale demonstrator for a pixel detector at the HL-LHC. It consists of a matrix of 64x64 pixels of dimension 50x50 um2 pixels and contains several pieces that are included in RD53A, a large scale ASIC designed by the RD53 Collaboration: two out of three front-ends (a synchronous and an asynchronous architecture); several building blocks; a (4x4) pixel region digital architecture with central local buffer storage, complying with a 3 GHz/cm2 hit rate and a 1 MHz trigger rate maintaining a very high efficiency (above 99%). The chip is 100% functional, either running in triggered or trigger-less mode. All building-blocks (DAC, ADC, Band Gap, SER, sLVS-TX/RX) and very front ends are working as expected. Analog performance shows a remarkably low ENC of 90e-, a fast-rise time below 25ns and low-power consumption (about 4μA/pixel) in both synchronous and asynchronous front-ends; a very linear behavior of CSA and discriminator. No significant cross talk from digital electronics has been measured, achieving a low threshold of 250e-. Signal digitization is obtained with a 5b-Time over Threshold technique and is shown to be fairly linear, working well either at 80 MHz or with higher frequencies of 300 MHz obtained with a tunable local oscillator. Irradiation results up to 600 Mrad at low temperature (-20°C) show that the chip is still fully functional and analog performance is only marginally degraded. Further irradiation will be performed up to 1 Grad either at low or room temperature, to further understand the level of radiation hardness of CHIPIX65-FE0. We are now in the process of bump bonding CHIPIX65-FE0 to 3D and possibly planar silicon sensors during spring. Detailed results will be presented in the conference paper

First Measurements of a Prototype of a New Generation Pixel Readout ASIC in 65 nm CMOS for Extreme Rate HEP Detectors at HL-LHC

A first prototype of a readout ASIC in CMOS 65nm for a pixel detector at High Luminosity LHC is described. The pixel cell area is 50x50 um2 and the matrix consists of 64x64 pixels. The chip was designed to guarantee high efficiency at extreme data rates for very low signals and with low power consumption. Two different analogue front-end designs, one synchronous and one asynchronous, were implemented, both occupying an area of 35x35 um2. ENC value is below 100e- for an input capacitance of 50 fF and in-time threshold below 1000e-. Leakage current compensation up to 50 nA with power consumption below 5 uW. A ToT technique is used to perform charge digitization with 5-bit precision using either a 40 MHz clock or a local Fast Oscillator up to 800 MHz. Internal 10-bit DAC's are used for biasing, while monitoring is provided by a 12-bit ADC. A novel digital architecture has been developed to ensure above 99.5% hit efficiency at pixel hit rates up to 3 GHz/cm2, trigger rates up to 1 MHz and trigger latency of 12.5 us. The total power consumption per pixel is below 5uW. Analogue dead-time is below 1%. Data are sent via a serializer connected to a CMOS-to-SLVS transmitter working at 320 MHz. All IP-blocks and front-ends used are silicon-proven and tested after exposure to ionizing radiation levels of 500-800 Mrad. The chip was designed as part of the Italian INFN CHIPIX65 project and in close synergy with the international CERN RD53 and was submitted in July 2016 for production. Early test results for both front-ends regarding minimum threshold, auto-zeroing and low-noise performance are high encouraging and will be presented in this paper

p53FamTaG: a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data

<p>Abstract</p> <p>Background</p> <p>The p53 gene family consists of the three genes p53, p63 and p73, which have polyhedral non-overlapping functions in pivotal cellular processes such as DNA synthesis and repair, growth arrest, apoptosis, genome stability, angiogenesis, development and differentiation. These genes encode sequence-specific nuclear transcription factors that recognise the same responsive element (RE) in their target genes. Their inactivation or aberrant expression may determine tumour progression or developmental disease. The discovery of several protein isoforms with antagonistic roles, which are produced by the expression of different promoters and alternative splicing, widened the complexity of the scenario of the transcriptional network of the p53 family members. Therefore, the identification of the genes transactivated by p53 family members is crucial to understand the specific role for each gene in cell cycle regulation. We have combined a genome-wide computational search of p53 family REs and microarray analysis to identify new direct target genes. The huge amount of biological data produced has generated a critical need for bioinformatic tools able to manage and integrate such data and facilitate their retrieval and analysis.</p> <p>Description</p> <p>We have developed the p53FamTaG database (p53 FAMily TArget Genes), a modular relational database, which contains p53 family direct target genes selected in the human genome searching for the presence of the REs and the expression profile of these target genes obtained by microarray experiments. p53FamTaG database also contains annotations of publicly available databases and links to other experimental data.</p> <p>The genome-wide computational search of the REs was performed using PatSearch, a pattern-matching program implemented in the DNAfan tool. These data were integrated with the microarray results we produced from the overexpression of different isoforms of p53, p63 and p73 stably transfected in isogenic cell lines, allowing the comparative study of the transcriptional activity of all the proteins in the same cellular background.</p> <p>p53FamTaG database is available free at <url>http://www2.ba.itb.cnr.it/p53FamTaG/</url></p> <p>Conclusion</p> <p>p53FamTaG represents a unique integrated resource of human direct p53 family target genes that is extensively annotated and provides the users with an efficient query/retrieval system which displays the results of our microarray experiments and allows the export of RE sequences. The database was developed for supporting and integrating high-throughput <it>in silico</it> and experimental analyses and represents an important reference source of knowledge for research groups involved in the field of oncogenesis, apoptosis and cell cycle regulation.</p

Direct Femtosecond Laser Fabrication of Superhydrophobic Aluminum Alloy Surfaces with Anti-icing Properties

Ice formation is a serious issue in many fields, from energy to aerospace, compromising the devices&rsquo; efficiency and security. Superhydrophobicity has been demonstrated to be correlated to the anti-icing properties of surfaces. However, fabricating surfaces with robust water repellence properties also at subzero temperature is still a great challenge. In this work, femtosecond laser (fs-laser) texturing is exploited to produce superhydrophobic surfaces with anti-icing properties on Al2024, an aluminum alloy of great interest in cold environments, in particular for aircraft production. Our textured substrates present self-cleaning properties and robust water repellency at subzero temperatures. Moreover, outstanding anti-icing properties are achieved on the textured surfaces at &minus;20 &deg;C, with water droplets bouncing off the surface before freezing

BASIC32: A New ASIC for Silicon Photomultiplier Detectors

Silicon Photomultipliers (SiPM) have shown to be excellent substitutes for more traditional and bulky Photomultiplier Tubes (PMT) in many photon detection applications, thanks essentially to their high quantum efficiency, lowbias voltage and immunity to magnetic fields.However, they pose some challenging design constraints on the design of the electronic front-end (FE) due to their intrinsic high gain and speed. In particular, when changing from low to high light levels of exposition, they produce output signals whose amplitude may span over about three order of magnitude with rise times of less than 1 ns. This is of particular concern when developing integrated multichannel electronics in deep submicron technology. We report here on the realization of a 32-channel ASIC in CMOS technology, based on an innovative current-mode architecture. Besides presenting the experimental results of the ASIC characterization, some perspective indications are given concerning the work currently in progress

Irradiation of VFAT3: A 128-channel charge-sensitive front-end device for the CMS GEM phase-2 upgrade

VFAT3 is a 128-channel charge-sensitive front-end ASIC explicitly designed for the CMS GEM phase-2 upgrades. LHC is undergoing major upgrades for HL-LHC, where the particle rate is expected to increase up to 5 times with respect to the nominal LHC luminosity of 1034 cm−2 s−1. It is, therefore, necessary to monitor the evolution of the VFAT3 response due to aging in the radiation environment by total ionizing dose (TID) test. The device operation could also be interrupted by a single high-energy particle. Thus, the estimation of the single event upset (SEU) cross-section is essential as well. We summarize irradiation test results that validate the suitability of VFAT3 for CMS GEM upgrade.SCOPUS: cp.jinfo:eu-repo/semantics/publishe