MicroTCA implementation of synchronous Ethernet-Based DAQ systems for large scale experiments

Large LAr TPCs are among the most powerful detectors to address open problems in particle and astro-particle physics, such as CP violation in leptonic sector, neutrino properties and their astrophysical implications, proton decay search etc. The scale of such detector implies severe constraints on their readout and DAQ system. In this article we describe a data acquisition scheme for this new generation of large detectors. The main challenge is to propose a scalable and easy to use solution able to manage a large number of channels at the lowest cost. It is interesting to note that these constraints are very similar to those existing in Network Telecommunication Industry. We propose to study how emerging technologies like ATCA and $\mu$TCA could be used in neutrino experiments. We describe the design of an Advanced Mezzanine Board (AMC) including 32 ADC channels. This board receives 32 analogical channels at the front panel and sends the formatted data through the $\mu$TCA backplane using a Gigabit Ethernet link. The gigabit switch of the MCH is used to centralize and to send the data to the event building computer. The core of this card is a FPGA (ARIA-GX from ALTERA) including the whole system except the memories. A hardware accelerator has been implemented using a NIOS II $\mu$P and a Gigabit MAC IP. Obviously, in order to be able to reconstruct the tracks from the events a time synchronisation system is mandatory. We decided to implement the IEEE1588 standard also called Precision Timing Protocol, another emerging and promising technology in Telecommunication Industry. In this article we describe a Gigabit PTP implementation using the recovered clock of the gigabit link. By doing so the drift is directly cancelled and the PTP will be used only to evaluate and to correct the offset.Comment: Talk presented at the 2009 Real Time Conference, Beijing, May '09, submitted to the proceeding

A Search for New Physics with the BEACON Mission

The primary objective of the Beyond Einstein Advanced Coherent Optical Network (BEACON) mission is a search for new physics beyond general relativity by measuring the curvature of relativistic space-time around Earth. This curvature is characterized by the Eddington parameter \gamma -- the most fundamental relativistic gravity parameter and a direct measure for the presence of new physical interactions. BEACON will achieve an accuracy of 1 x 10^{-9} in measuring the parameter \gamma, thereby going a factor of 30,000 beyond the present best result involving the Cassini spacecraft. Secondary mission objectives include: (i) a direct measurement of the "frame-dragging" and geodetic precessions in the Earth's rotational gravitomagnetic field, to 0.05% and 0.03% accuracy correspondingly, (ii) first measurement of gravity's non-linear effects on light and corresponding 2nd order spatial metric's effects to 0.01% accuracy. BEACON will lead to robust advances in tests of fundamental physics -- this mission could discover a violation or extension of general relativity and/or reveal the presence of an additional long range interaction in physics. BEACON will provide crucial information to separate modern scalar-tensor theories of gravity from general relativity, probe possible ways for gravity quantization, and test modern theories of cosmological evolution.Comment: 8 pages, 2 figures, 2 table

Implementation of sub-nanosecond time-to-digital convertor in field-programmable gate array: applications to time-of-flight analysis in muon radiography

International audienceTime-of-flight (tof) techniques are standard techniques in high energy physics to determine particles propagation directions. Since particles velocities are generally close to c, the speed of light, and detectors typical dimensions at the meter level, the state-of-the-art tof techniques should reach sub-nanosecond timing resolution. Among the various techniques already available, the recently developed ring oscillator TDC ones, implemented in low cost FPGA, feature a very interesting figure of merit since a very good timing performance may be achieved with limited processing ressources. This issue is relevant for applications where unmanned sensors should have the lowest possible power consumption. Actually this article describes in details the application of this kind of tof technique to muon tomography of geological bodies. Muon tomography aims at measuring density variations and absolute densities through the detection of atmospheric muons flux's attenuation, due to the presence of matter. When the measured fluxes become very low, an identified source of noise comes from backwards propagating particles hitting the detector in a direction pointing to the geological body. The separation between through-going and backward-going particles, on the basis of the tof information is therefore a key parameter for the tomography analysis and subsequent previsions

Hemodynamic and anti-inflammatory effects of early esmolol use in hyperkinetic septic shock. a pilot study

Background: Several studies have shown that heart rate control with selective beta-1 blockers in septic shock is safe. In these trials, esmolol was administered 24 h after onset of septic shock in patients who remained tachycardic. While an earlier use of beta-blockers might be beneficial, such use remains challenging due to the difficulty in distinguishing between compensatory and non-compensatory tachycardia. Therefore, the Esmosepsis study was designed to study the effects of esmolol aimed at reducing the heart rate by 20% after the initial resuscitation process in hyperkinetic septic shock patients on (1) cardiac index and (2) systemic and regional hemodynamics as well as inflammatory patterns. Methods: Nine consecutive stabilized tachycardic hyperkinetic septic shock patients treated with norepinephrine for a minimum of 6 h were included. Esmolol was infused during 6 h in order to decrease the heart rate by 20%. The following data were recorded at hours H0 (before esmolol administration), H1–H6 (esmolol administration) and 1 h after esmolol cessation (H7): systolic arterial pressure, diastolic arterial pressure, mean arterial pressure, central venous pressure, heart rate, PICCO transpulmonary thermodilution, sublingual and musculo-cutaneous microcirculation, indocyanine green clearance and echocardiographic parameters, diuresis, lactate, and arterial and venous blood gases. Results: Esmolol was infused 9 (6.4–11.6) hours after norepinephrine introduction. Esmolol was ceased early in 3 out of 9 patients due to a marked increase in norepinephrine requirement associated with a picture of persistent cardiac failure at the lowest esmolol dose. For the global group, during esmolol infusion, norepinephrine infusion increased from 0.49 (0.34–0.83) to 0.78 (0.3–1.11) µg/min/kg. The use of esmolol was associated with a significant decrease in heart rate from 115 (110–125) to 100 (92–103) beats/min and a decrease in cardiac index from 4.2 (3.1–4.4) to 2.9 (2.5–3.7) l/min/m−2. Indexed stroke volume remained unchanged. Cardiac function index and global ejection fraction also markedly decreased. Using echocardiography, systolic, diastolic as well as left and right ventricular function parameters worsened. After esmolol cessation, all parameters returned to baseline values. Lactate and microcirculatory parameters did not change while the majority of pro-inflammatory proteins decreased in all patients. Conclusion: In the very early phase of septic shock, heart rate reduction using fast esmolol titration is associated with an increased risk of hypotension and decreased cardiac index despite maintained adequate tissue perfusion (NCT02068287)

The Scintillator Option For The Opera Target Tracker: Results On The Readout

Neutrino

Clinical Determinants and Prognostic Implications of Renin and Aldosterone in Patients with Symptomatic Heart Failure

Aims Activation of the renin-angiotensin-aldosterone system plays an important role in the pathophysiology of heart failure (HF) and has been associated with poor prognosis. There are limited data on the associations of renin and aldosterone levels with clinical profiles, treatment response, and study outcomes in patients with HF. Methods and results We analysed 2,039 patients with available baseline renin and aldosterone levels in BIOSTAT-CHF (a systems BIOlogy study to Tailored Treatment in Chronic Heart Failure). The primary outcome was the composite of all-cause mortality or HF hospitalization. We also investigated changes in renin and aldosterone levels after administration of mineralocorticoid receptor antagonists (MRAs) in a subset of the EPHESUS trial and in an acute HF cohort (PORTO). In BIOSTAT-CHF study, median renin and aldosterone levels were 85.3 (percentile(25-75) = 28-247) mu IU/mL and 9.4 (percentile(25-75) = 4.4-19.8) ng/dL, respectively. Prior HF admission, lower blood pressure, sodium, poorer renal function, and MRA treatment were associated with higher renin and aldosterone. Higher renin was associated with an increased rate of the primary outcome [highest vs. lowest renin tertile: adjusted-HR (95% CI) = 1.47 (1.16-1.86), P = 0.002], whereas higher aldosterone was not [highest vs. lowest aldosterone tertile: adjusted-HR (95% CI) = 1.16 (0.93-1.44), P = 0.19]. Renin and/or aldosterone did not improve the BIOSTAT-CHF prognostic models. The rise in aldosterone with the use of MRAs was observed in EPHESUS and PORTO studies. Conclusions Circulating levels of renin and aldosterone were associated with both the disease severity and use of MRAs. By reflecting both the disease and its treatments, the prognostic discrimination of these biomarkers was poor. Our data suggest that the "point" measurement of renin and aldosterone in HF is of limited clinical utility

Molecular and all solid DFT studies of the magnetic and chemical bonding properties within KM[Cr(CN)6_6] (M = V, Ni) complexes

A study at both the molecular and extended solid level in the framework DFT is carried out for KM[Cr(CN)$_6$] (M = V, Ni). From molecular calculations, the exchange parameters J are obtained, pointing to the expected magnetic ground states, i.e., antiferromagnetic for M = V with J = -296.5 cm$^{-1}$ and ferromagnetic for M = Ni with J = +40.5 cm$^{-1}$. From solid state computations the same ground states and J magnitudes are confirmed from energy differences. Furthermore an analysis of the site projected density of states and of the chemical bonding is developed in which the cyanide ion linkage is analyzed addressing some isomerism aspects.Comment: new results, 5 tables, 7 fig

The Vaginal Microbiome: Disease, Genetics and the Environment

The vagina is an interactive interface between the host and the environment. Its surface is covered by a protective epithelium colonized by bacteria and other microorganisms. The ectocervix is nonsterile, whereas the endocervix and the upper genital tract are assumed to be sterile in healthy women. Therefore, the cervix serves a pivotal role as a gatekeeper to protect the upper genital tract from microbial invasion and subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease, and other gynecologic and reproductive disorders. Homeostasis of the microbiome in the vagina and ectocervix plays a paramount role in reproductive health. Depending on its composition, the microbiome may protect the vagina from infectious or non-infectious diseases, or it may enhance its susceptibility to them. Because of the nature of this organ, and the fact that it is continuously colonized by bacteria from birth to death, it is virtually certain that this rich environment evolved in concert with its microbial flora. Specific interactions dictated by the genetics of both the host and microbes are likely responsible for maintaining both the environment and the microbiome. However, the genetic basis of these interactions in both the host and the bacterial colonizers is currently unknown. _Lactobacillus_ species are associated with vaginal health, but the role of these species in the maintenance of health is not yet well defined. Similarly, other species, including those representing minor components of the overall flora, undoubtedly influence the ability of potential pathogens to thrive and cause disease. Gross alterations in the vaginal microbiome are frequently observed in women with bacterial vaginosis, but the exact etiology of this disorder is still unknown. There are also implications for vaginal flora in non-infectious conditions such as pregnancy, pre-term labor and birth, and possibly fertility and other aspects of women’s health. Conversely, the role of environmental factors in the maintenance of a healthy vaginal microbiome is largely unknown. To explore these issues, we have proposed to address the following questions:

*1.	Do the genes of the host contribute to the composition of the vaginal microbiome?* We hypothesize that genes of both host and bacteria have important impacts on the vaginal microbiome. We are addressing this question by examining the vaginal microbiomes of mono- and dizygotic twin pairs selected from the over 170,000 twin pairs in the Mid-Atlantic Twin Registry (MATR). Subsequent studies, beyond the scope of the current project, may investigate which host genes impact the microbial flora and how they do so.
*2.	What changes in the microbiome are associated with common non-infectious pathological states of the host?* We hypothesize that altered physiological (e.g., pregnancy) and pathologic (e.g., immune suppression) conditions, or environmental exposures (e.g., antibiotics) predictably alter the vaginal microbiome. Conversely, certain vaginal microbiome characteristics are thought to contribute to a woman’s risk for outcomes such as preterm delivery. We are addressing this question by recruiting study participants from the ~40,000 annual clinical visits to women’s clinics of the VCU Health System.
*3.	What changes in the vaginal microbiome are associated with relevant infectious diseases and conditions?* We hypothesize that susceptibility to infectious disease (e.g. HPV, _Chlamydia_ infection, vaginitis, vaginosis, etc.) is impacted by the vaginal microbiome. In turn, these infectious conditions clearly can affect the ability of other bacteria to colonize and cause pathology. Again, we are exploring these issues by recruiting participants from visitors to women’s clinics in the VCU Health System.

Three kinds of sequence data are generated in this project: i) rDNA sequences from vaginal microbes; ii) whole metagenome shotgun sequences from vaginal samples; and iii) whole genome shotgun sequences of bacterial clones selected from vaginal samples. The study includes samples from three vaginal sites: mid-vaginal, cervical, and introital. The data sets also include buccal and perianal samples from all twin participants. Samples from these additional sites are used to test the hypothesis of a per continuum spread of bacteria in relation to vaginal health. An extended set of clinical metadata associated with these sequences are deposited with dbGAP. We have currently collected over 4,400 samples from ~100 twins and over 450 clinical participants. We have analyzed and deposited data for 480 rDNA samples, eight whole metagenome shotgun samples, and over 50 complete bacterial genomes. These data are available to accredited investigators according to NIH and Human Microbiome Project (HMP) guidelines. The bacterial clones are deposited in the Biodefense and Emerging Infections Research Resources Repository ("http://www.beiresources.org/":http://www.beiresources.org/). 

In addition to the extensive sequence data obtained in this study, we are collecting metadata associated with each of the study participants. Thus, participants are asked to complete an extensive health history questionnaire at the time samples are collected. Selected clinical data associated with the visit are also obtained, and relevant information is collected from the medical records when available. This data is maintained securely in a HIPAA-compliant data system as required by VCU’s Institutional Review Board (IRB). The preponderance of these data (i.e., that judged appropriate by NIH staff and VCU’s IRB are deposited at dbGAP ("http://www.ncbi.nlm.nih.gov/gap":http://www.ncbi.nlm.nih.gov/gap). Selected fields of this data have been identified by NIH staff as ‘too sensitive’ and are not available in dbGAP. Individuals requiring access to these data fields are asked to contact the PI of this project or NIH Program Staff. 
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