The high speed buffer board : a SAIL EIA-485 communications accelerator card for the vector measuring current meter

A High Speed Buffer Board (HSBB) has been developed for the Vector Measuring Current Meter (VMCM) to implement the transmission of data at 9600 baud over an EIA-485 link. The HSBB significantly extends the VMCM communication functionality, which was previously limited to 300 baud transmission via 20 mA current loop or FSK telemetry. The increased speed allows rapid sampling of a large number of current meters on a common cable and the EIA-485 circuitry, which was designed for low power operation, provides a useful multipoint communication method for data transmission over long cable lengths. SAIL protocol (IEEE 997) was utilized to coordinate data transfer by the instruments on a common link. An MC68HC11 microcontroller resides in the VMCM, buffering data it receives at 300 baud from the VMCM UART. In response to a jumper selectable SAIL address, the MC68HC11 offloads the data at 9600 baud via EIA-485 to the SAIL controller. Synchronous data collection from many instruments is ensured by the SAIL synoptic set command and an embedded resynchronization/reset command. The low power consumption allows deployments of six months or more with a standard VMCM battery stack.Funding was provided by the Office of Naval Research under Contract No. N00014-84-C-0134 and Grant No. N00014-90-J-1495

A data processing module for acoustic doppler current meters

This report describes the development of a Data Processing Module (DPM) designed for use with an RD Instruments Acoustic Doppler Current Meter (ADCM). The DPM is a self-powered unit in its own pressure case and its use requires no modification to the current meter. The motivation for this work was the desire for real-time monitoring and data transmission from an ADCM deployed at a remote site. The DPM serves as an interface between the ADCM and a satellite telemetry package consisting of a controller, an Argos Platform Transmit Terminal, and an antenna. The DPM accepts the data stream from the ADCM, processes the data and sends out the processed data upon request from the telemetry controller. The output of the ADCM is processed by eliminating unnecessary data combining quality control information into a small number of summary parameters, and averaging the remaining data in depth and time. For the implementation described here, eight data records of 719 bytes each, output from the ADCM at 15 minute intervals, were processed and averged over 2 hr intervals to produce a 34 byte output array.Funding was provided by the Office of Naval Research under Contract No. N00014-89-J-1288

Instrumentation for open ocean aquaculture monitoring

The Woods Hole Oceanographic Institution is assisting the University of New Hampshire by instrumenting a fish cage and mooring as part of their Open Ocean Aquaculture demonstration program in the Gulf of Maine. To understand these systems, the wave and current forcing and the response of the mooring and fish cage needs to be measured. A UNH mooring with an ADCP measured the current forcing. Tension in the mooring lines was measured by load cells deployed with the mooring during servicing in August 2000. Load cells were placed in each anchor line, and, in the NE corner, also in the two grid lines and the riser line to the fish cage. Low power recording systems were deployed on the load cell mounting bars by divers on 22 October 2000, recorded good data through January 2001, when they were turned around and redeployed. Three single load cell recorders were recovered in July 2001 and recorded though 23 June when their data storage filled. The four load cell system was recovered in March after a large winter storm, and had failed in early March. The wave forcing was measured with a wave rider buoy with a 3-axis accelerometer measuring its motion. The acceleration was integrated twice to obtain wave displacement. The system mooring contained a compliant elastic. The wave rider was deployed on 4 January 2001 and recovered on 17 March 2001 after a major Northeast storm. It recorded data throughout its deployment. The motion of the moored fish cage was measured by a motion package constructed around a 6-axis Motion-Pak and a PC-104 data system. The motion package was deployed on the fish cage from Jan into March 2001 and recorded motions thoughout without difficuly. It observed a major storm in early March where the counter weight was lost from the fish cage, and its increase in motion thereafter.Fudning was provided by National Oceanic and Atmospheric Adminstration for the Open Ocean Aquaculture Project under Contract No. NA86RG0016 to the University of New Hampshire and under Subcontracts 00-394 and 01-442 to the Woods Hole Oceanographic Institution

Measurement of H₂O₂ within living drosophila during aging using a ratiometric mass spectrometry probe targeted to the mitochondrial matrix

Hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) is central to mitochondrial oxidative damage and redox signaling, but its roles are poorly understood due to the difficulty of measuring mitochondrial H<sub>2</sub>O<sub>2</sub> in vivo. Here we report a ratiometric mass spectrometry probe approach to assess mitochondrial matrix H<sub>2</sub>O<sub>2</sub> levels in vivo. The probe, MitoB, comprises a triphenylphosphonium (TPP) cation driving its accumulation within mitochondria, conjugated to an arylboronic acid that reacts with H<sub>2</sub>O<sub>2</sub> to form a phenol, MitoP. Quantifying the MitoP/MitoB ratio by liquid chromatography-tandem mass spectrometry enabled measurement of a weighted average of mitochondrial H<sub>2</sub>O<sub>2</sub> that predominantly reports on thoracic muscle mitochondria within living flies. There was an increase in mitochondrial H<sub>2</sub>O<sub>2</sub> with age in flies, which was not coordinately altered by interventions that modulated life span. Our findings provide approaches to investigate mitochondrial ROS in vivo and suggest that while an increase in overall mitochondrial H<sub>2</sub>O<sub>2</sub> correlates with aging, it may not be causative

Charges in Gauge Theories

In this article we investigate charged particles in gauge theories. After reviewing the physical and theoretical problems, a method to construct charged particles is presented. Explicit solutions are found in the Abelian theory and a physical interpretation is given. These solutions and our interpretation of these variables as the true degrees of freedom for charged particles, are then tested in the perturbative domain and are demonstrated to yield infra-red finite, on-shell Green's functions at all orders of perturbation theory. The extension to collinear divergences is studied and it is shown that this method applies to the case of massless charged particles. The application of these constructions to the charged sectors of the standard model is reviewed and we conclude with a discussion of the successes achieved so far in this programme and a list of open questions.Comment: 47 pages, LaTeX, 14 figures, uses feynmp, necessary Metapost files included. Review to appear in Pramana, Journal of Physics. Minor LaTeX change to make page numbers visible on "Letter" paper forma

Coherence properties of focused X-ray beams at high-brilliance synchrotron sources

An analytical approach describing properties of focused partially coherent X-ray beams is presented. The method is based on the results of statistical optics and gives both the beam size and transverse coherence length at any distance behind an optical element. In particular, here Gaussian Schell-model beams and thin optical elements are considered. Limiting cases of incoherent and fully coherent illumination of the focusing element are discussed. The effect of the beam-defining aperture, typically used in combination with focusing elements at synchrotron sources to improve transverse coherence, is also analyzed in detail. As an example, the coherence properties in the focal region of compound refractive lenses at the PETRA III synchrotron source are analyzed

Circulating adrenomedullin estimates survival and reversibility of organ failure in sepsis: the prospective observational multinational Adrenomedullin and Outcome in Sepsis and Septic Shock-1 (AdrenOSS-1) study

Background: Adrenomedullin (ADM) regulates vascular tone and endothelial permeability during sepsis. Levels of circulating biologically active ADM (bio-ADM) show an inverse relationship with blood pressure and a direct relationship with vasopressor requirement. In the present prospective observational multinational Adrenomedullin and Outcome in Sepsis and Septic Shock 1 (, AdrenOSS-1) study, we assessed relationships between circulating bio-ADM during the initial intensive care unit (ICU) stay and short-term outcome in order to eventually design a biomarker-guided randomized controlled trial. Methods: AdrenOSS-1 was a prospective observational multinational study. The primary outcome was 28-day mortality. Secondary outcomes included organ failure as defined by Sequential Organ Failure Assessment (SOFA) score, organ support with focus on vasopressor/inotropic use, and need for renal replacement therapy. AdrenOSS-1 included 583 patients admitted to the ICU with sepsis or septic shock. Results: Circulating bio-ADM levels were measured upon admission and at day 2. Median bio-ADM concentration upon admission was 80.5 pg/ml [IQR 41.5-148.1 pg/ml]. Initial SOFA score was 7 [IQR 5-10], and 28-day mortality was 22%. We found marked associations between bio-ADM upon admission and 28-day mortality (unadjusted standardized HR 2.3 [CI 1.9-2.9]; adjusted HR 1.6 [CI 1.1-2.5]) and between bio-ADM levels and SOFA score (p < 0.0001). Need of vasopressor/inotrope, renal replacement therapy, and positive fluid balance were more prevalent in patients with a bio-ADM > 70 pg/ml upon admission than in those with bio-ADM ≤ 70 pg/ml. In patients with bio-ADM > 70 pg/ml upon admission, decrease in bio-ADM below 70 pg/ml at day 2 was associated with recovery of organ function at day 7 and better 28-day outcome (9.5% mortality). By contrast, persistently elevated bio-ADM at day 2 was associated with prolonged organ dysfunction and high 28-day mortality (38.1% mortality, HR 4.9, 95% CI 2.5-9.8). Conclusions: AdrenOSS-1 shows that early levels and rapid changes in bio-ADM estimate short-term outcome in sepsis and septic shock. These data are the backbone of the design of the biomarker-guided AdrenOSS-2 trial. Trial registration: ClinicalTrials.gov, NCT02393781. Registered on March 19, 2015

Self-Medication as Adaptive Plasticity: Increased Ingestion of Plant Toxins by Parasitized Caterpillars

Self-medication is a specific therapeutic behavioral change in response to disease or parasitism. The empirical literature on self-medication has so far focused entirely on identifying cases of self-medication in which particular behaviors are linked to therapeutic outcomes. In this study, we frame self-medication in the broader realm of adaptive plasticity, which provides several testable predictions for verifying self-medication and advancing its conceptual significance. First, self-medication behavior should improve the fitness of animals infected by parasites or pathogens. Second, self-medication behavior in the absence of infection should decrease fitness. Third, infection should induce self-medication behavior. The few rigorous studies of self-medication in non-human animals have not used this theoretical framework and thus have not tested fitness costs of self-medication in the absence of disease or parasitism. Here we use manipulative experiments to test these predictions with the foraging behavior of woolly bear caterpillars (Grammia incorrupta; Lepidoptera: Arctiidae) in response to their lethal endoparasites (tachinid flies). Our experiments show that the ingestion of plant toxins called pyrrolizidine alkaloids improves the survival of parasitized caterpillars by conferring resistance against tachinid flies. Consistent with theoretical prediction, excessive ingestion of these toxins reduces the survival of unparasitized caterpillars. Parasitized caterpillars are more likely than unparasitized caterpillars to specifically ingest large amounts of pyrrolizidine alkaloids. This case challenges the conventional view that self-medication behavior is restricted to animals with advanced cognitive abilities, such as primates, and empowers the science of self-medication by placing it in the domain of adaptive plasticity theory

A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships

<p>Abstract</p> <p>Background</p> <p>Substitution matrices are key parameters for the alignment of two protein sequences, and consequently for most comparative genomics studies. The composition of biological sequences can vary importantly between species and groups of species, and classical matrices such as those in the BLOSUM series fail to accurately estimate alignment scores and statistical significance with sequences sharing marked compositional biases.</p> <p>Results</p> <p>We present a general and simple methodology to build matrices that are especially fitted to the compositional bias of proteins. Our approach is inspired from the one used to build the BLOSUM matrices and is based on learning substitution and amino acid frequencies on real sequences with the corresponding compositional bias. We applied it to the large scale comparison of Mollicute AT-rich genomes. The new matrix, MOLLI60, was used to predict pairwise orthology relationships, as well as homolog families among 24 Mollicute genomes. We show that this new matrix enables to better discriminate between true and false orthologs and improves the clustering of homologous proteins, with respect to the use of the classical matrix BLOSUM62.</p> <p>Conclusions</p> <p>We show in this paper that well-fitted matrices can improve the predictions of orthologous and homologous relationships among proteins with a similar compositional bias. With the ever-increasing number of sequenced genomes, our approach could prove valuable in numerous comparative studies focusing on atypical genomes.</p

Anti-Bacterial Effects of Poly-N-Acetyl-Glucosamine Nanofibers in Cutaneous Wound Healing: Requirement for Akt1

Treatment of cutaneous wounds with poly-N-acetyl-glucosamine nanofibers (sNAG) results in increased kinetics of wound closure in diabetic animal models, which is due in part to increased expression of several cytokines, growth factors, and innate immune activation. Defensins are also important for wound healing and anti-microbial activities. Therefore, we tested whether sNAG nanofibers induce defensin expression resulting in bacterial clearance.The role of sNAG in defensin expression was examined using immunofluoresence microscopy, pharmacological inhibition, and shRNA knockdown in vitro. The ability of sNAG treatment to induce defensin expression and bacterial clearance in WT and AKT1-/- mice was carried out using immunofluoresent microscopy and tissue gram staining. Neutralization, using an antibody directed against β-defensin 3, was utilized to determine if the antimicrobial properties of sNAG are dependent on the induction of defensin expression.sNAG treatment causes increased expression of both α- and β-type defensins in endothelial cells and β-type defensins in keratinocytes. Pharmacological inhibition and shRNA knockdown implicates Akt1 in sNAG-dependent defensin expression in vitro, an activity also shown in an in vivo wound healing model. Importantly, sNAG treatment results in increased kinetics of wound closure in wild type animals. sNAG treatment decreases bacterial infection of cutaneous wounds infected with Staphylococcus aureus in wild type control animals but not in similarly treated Akt1 null animals. Furthermore, sNAG treatment of S. aureus infected wounds show an increased expression of β-defensin 3 which is required for sNAG-dependent bacterial clearance. Our findings suggest that Akt1 is involved in the regulation of defensin expression and the innate immune response important for bacterial clearance. Moreover, these findings support the use of sNAG nanofibers as a novel method for enhancing wound closure while simultaneously decreasing wound infection