Integrated seawater sampler and data acquisition system prototype : final report

This report documents the work performed by the Woods Hole Oceanographic Institution (WHOI) and the Battelle Memorial Institute from August 1988 to December 1992 in the NSF sponsored development of an Integrated Seawater Sampler and Data Acquisition Prototype. After a 6-month initial design study, a prototype underwater profiing unit was designed and constructed, containing the water acquisition subsystem, CTD and altimeter, control circuitry and batteries. A standard WHOI CTD was adapted for use in the underwater unit and was interfaced to the underwater controller which had a telemetry module connecting ít with a deck control unit. This enabled CTD data to be logged in normal fashion on shipboard while additional commands and diagnostics were sent over the telemetry link to command the underwater unit's water sampling process and receive diagnostic information on system performance. The water sampling subsystem consisted of 36 trays, each containing a plastic sample bag, the pump and control circuitry. The sample bags, initially sealed in a chemically clean environment, were opened by pumping the water out of the tray, thus forcing water into the bag by ambient pressure. The command system could select any bag, and control the water sampling procss from the surface with diagnostic information on system altitude, depth, orientation and cable tension displayed in real time for operator information. At sea tests confirmed the operation of the electrical and control system. Problems were encountered with the bags and seals which were partially solved by further post cruise efforts. However, the bag closing mechanism requires further development, and numerous small system improvements identified during the cruises need to be implemented to produce an operational water sampler. Finally, initial design tor a water sampler handling and storage unit and water extraction system were developed but not implemented. The detailed discussion of the prototype water sampler design, testing and evaluation, and new bag testing result are presented.Funding was provided by the National Science Foundation through Grant No. OCE8821977

Phase I of the Detecting and Evaluating Childhood Anxiety and Depression Effectively in Subspecialties (DECADES) Study: Development of an Integrated Mental Health Care Model for Pediatric Gastroenterology

Background: Children with gastrointestinal symptoms have a very high rate of anxiety and depression. Rapid identification of comorbid anxiety and depression is essential for effective treatment of a wide variety of functional gastrointestinal disorders. Objective: The objective of our study was to determine patient and parent attitudes toward depression, anxiety, and mental health screening during gastroenterology (GI) visits and to determine patient and parent preferences for communication of results and referral to mental health providers after a positive screen. Methods: We augmented standard qualitative group session methods with patient-centered design methods to assess patient and parent preferences. We used a variety of specific design methods in these sessions, including card sorting, projective methods, experience mapping, and constructive methods. Results: Overall, 11 families (11 patients and 14 parents) participated in 2 group sessions. Overall, patients and their parents found integrated mental health care to be acceptable in the subspecialty setting. Patients’ primary concerns were for the privacy and confidentiality of their screening results. Patients and their parents emphasized the importance of mental health services not interfering with the GI visit and collaboration between the GI physician, psychologist, and primary care provider. Conclusions: Patients and their families are open to integrated mental health care in the pediatric subspecialty clinic. The next phase of the DECADES study will translate patient and parent preferences into an integrated mental health care system and test its efficacy in the pediatric GI office. [J Participat Med 2018;10(3):e10655

Tumor innate immunity primed by specific interferon-stimulated endogenous retroviruses.

Mesenchymal tumor subpopulations secrete pro-tumorigenic cytokines and promote treatment resistance1-4. This phenomenon has been implicated in chemorefractory small cell lung cancer and resistance to targeted therapies5-8, but remains incompletely defined. Here, we identify a subclass of endogenous retroviruses (ERVs) that engages innate immune signaling in these cells. Stimulated 3 prime antisense retroviral coding sequences (SPARCS) are oriented inversely in 3' untranslated regions of specific genes enriched for regulation by STAT1 and EZH2. Derepression of these loci results in double-stranded RNA generation following IFN-γ exposure due to bi-directional transcription from the STAT1-activated gene promoter and the 5' long terminal repeat of the antisense ERV. Engagement of MAVS and STING activates downstream TBK1, IRF3, and STAT1 signaling, sustaining a positive feedback loop. SPARCS induction in human tumors is tightly associated with major histocompatibility complex class 1 expression, mesenchymal markers, and downregulation of chromatin modifying enzymes, including EZH2. Analysis of cell lines with high inducible SPARCS expression reveals strong association with an AXL/MET-positive mesenchymal cell state. While SPARCS-high tumors are immune infiltrated, they also exhibit multiple features of an immune-suppressed microenviroment. Together, these data unveil a subclass of ERVs whose derepression triggers pathologic innate immune signaling in cancer, with important implications for cancer immunotherapy

Kepler eclipsing binary stars. VII. the catalogue of eclipsing binaries found in the entire Kepler data set

The primary Kepler Mission provided nearly continuous monitoring of ~200,000 objects with unprecedented photometric precision. We present the final catalog of eclipsing binary systems within the 105 deg2 Kepler field of view. This release incorporates the full extent of the data from the primary mission (Q0-Q17 Data Release). As a result, new systems have been added, additional false positives have been removed, ephemerides and principal parameters have been recomputed, classifications have been revised to rely on analytical models, and eclipse timing variations have been computed for each system. We identify several classes of systems including those that exhibit tertiary eclipse events, systems that show clear evidence of additional bodies, heartbeat systems, systems with changing eclipse depths, and systems exhibiting only one eclipse event over the duration of the mission. We have updated the period and galactic latitude distribution diagrams and included a catalog completeness evaluation. The total number of identified eclipsing and ellipsoidal binary systems in the Kepler field of view has increased to 2878, 1.3% of all observed Kepler targets

Inter-laboratory reproducibility of fast gas chromatography–electron impact–time of flight mass spectrometry (GC–EI–TOF/MS) based plant metabolomics

The application of gas chromatography–mass spectrometry (GC–MS) to the ‘global’ analysis of metabolites in complex samples (i.e. metabolomics) has now become routine. The generation of these data-rich profiles demands new strategies in data mining and standardisation of experimental and reporting aspects across laboratories. As part of the META-PHOR project’s (METAbolomics for Plants Health and OutReach: http://www.meta-phor.eu/) priorities towards robust technology development, a GC–MS ring experiment based upon three complex matrices (melon, broccoli and rice) was launched. All sample preparation, data processing, multivariate analyses and comparisons of major metabolite features followed standardised protocols, identical models of GC (Agilent 6890N) and TOF/MS (Leco Pegasus III) were also employed. In addition comprehensive GC×GC–TOF/MS was compared with 1 dimensional GC–TOF/MS. Comparisons of the paired data from the various laboratories were made with a single data processing and analysis method providing an unbiased assessment of analytical method variants and inter-laboratory reproducibility. A range of processing and statistical methods were also assessed with a single exemplary dataset revealing near equal performance between them. Further investigations of long-term reproducibility are required, though the future generation of global and valid metabolomics databases offers much promise

Concentrated oat β-glucan, a fermentable fiber, lowers serum cholesterol in hypercholesterolemic adults in a randomized controlled trial

BACKGROUND: Soluble fibers lower serum lipids, but are difficult to incorporate into products acceptable to consumers. We investigated the physiological effects of a concentrated oat β-glucan on cardiovascular disease (CVD) endpoints in human subjects. We also compared the fermentability of concentrated oat β-glucan with inulin and guar gum in a model intestinal fermentation system. METHODS: Seventy-five hypercholesterolemic men and women were randomly assigned to one of two treatments: 6 grams/day concentrated oat β-glucan or 6 grams/day dextrose (control). Fasting blood samples were collected at baseline, week 3, and week 6 and analyzed for total cholesterol, HDL cholesterol, LDL cholesterol, triglycerides, glucose, insulin, homocysteine and C-reactive protein (CRP). To estimate colonic fermentability, 0.5 g concentrated oat β-glucan was incubated in a batch model intestinal fermentation system, using human fecal inoculum to provide representative microflora. Fecal donors were not involved with the β-glucan feeding trial. Inulin and guar gum were also incubated in separate serum bottles for comparison. RESULTS: Oat β-glucan produced significant reduction from baseline in total cholesterol (-0.3 ± 0.1 mmol/L) and LDL cholesterol (-0.3 ± 0.1 mmol/L), and the reduction in LDL cholesterol were significantly greater than in the control group (p = 0.03). Concentrated oat β-glucan was a fermentable fiber and produced total SCFA and acetate concentrations similar to inulin and guar gum. Concentrated oat β-glucan produced the highest concentrations of butyrate at 4, 8, and 12 hours. CONCLUSION: Six grams concentrated oat β-glucan per day for six weeks significantly reduced total and LDL cholesterol in subjects with elevated cholesterol, and the LDL cholesterol reduction was greater than the change in the control group. Based on a model intestinal fermentation, this oat β-glucan was fermentable, producing higher amounts of butyrate than other fibers. Thus, a practical dose of β-glucan can significantly lower serum lipids in a high-risk population and may improve colon health

Atmospheric CO2 sequestration in iron and steel slag: Consett, Co. Durham, UK

Carbonate formation in waste from the steel industry could constitute a non-trivial proportion of global requirements to remove carbon dioxide from the atmosphere at potentially low cost. To constrain this potential, we examined atmospheric carbon dioxide sequestration in a >20 million tonne legacy slag deposit in northern England, UK. Carbonates formed from the drainage water of the heap had stable carbon and oxygen isotope values between -12 and -25 ‰ and -5 and -18 ‰ for δ13C and δ18O respectively, suggesting atmospheric carbon dioxide sequestration in high pH solutions. From the analyses of solution saturation states, we estimate that between 280 and 2,900 tCO2 have precipitated from the drainage waters. However, by combining a thirty-seven-year dataset of the drainage water chemistry with geospatial analysis, we estimate that <1 % of the maximum carbon capture potential of the deposit may have been realised. This implies that uncontrolled deposition of slag is insufficient to maximise carbon sequestration, and there may be considerable quantities of unreacted legacy deposits available for atmospheric carbon sequestration

Basin-scale transport of hydrothermal dissolved metals across the South Pacific Ocean

Hydrothermal venting along mid-ocean ridges exerts an important control on the chemical composition of sea water by serving as a major source or sink for a number of trace elements in the ocean(1-3). Of these, iron has received considerable attention because of its role as an essential and often limiting nutrient for primary production in regions of the ocean that are of critical importance for the global carbon cycle(4). It has been thought that most of the dissolved iron discharged by hydrothermal vents is lost from solution close to ridge-axis sources(2,5) and is thus of limited importance for ocean biogeochemistry(6). This long-standing view is challenged by recent studies which suggest that stabilization of hydrothermal dissolved iron may facilitate its longrange oceanic transport(7-10). Such transport has been subsequently inferred from spatially limited oceanographic observations(11-13). Here we report data from the US GEOTRACES Eastern Pacific Zonal Transect (EPZT) that demonstrate lateral transport of hydrothermal dissolved iron, manganese, and aluminium from the southern East Pacific Rise (SEPR) several thousand kilometres westward across the South Pacific Ocean. Dissolved iron exhibits nearly conservative (that is, no loss from solution during transport and mixing) behaviour in this hydrothermal plume, implying a greater longevity in the deep ocean than previously assumed(6,14). Based on our observations, we estimate a global hydrothermal dissolved iron input of three to four gigamoles per year to the ocean interior, which is more than fourfold higher than previous estimates(7,11,14). Complementary simulations with a global-scale ocean biogeochemical model suggest that the observed transport of hydrothermal dissolved iron requires some means of physicochemical stabilization and indicate that hydrothermally derived iron sustains a large fraction of Southern Ocean export productio

Set Pseudophasors to Stun for Flow Cytometry

Study of signal transduction in live cells benefits from the ability to visualize and quantify light emitted by fluorescent proteins (XFPs) fused to different signaling proteins. However, because cell signaling proteins are often present in small numbers, and because the XFPs themselves are poor fluorophores, the amount of emitted light, and the observable signal in these studies, is often small. An XFP's fluorescence lifetime contains additional information about the immediate environment of the fluorophore that can augment the information from its weak light signal. Here, we constructed and expressed in Saccharomyces cerevisiae variants of Teal Fluorescent Protein (TFP) and Citrine that were isospectral but had shorter fluorescence lifetimes, ∼ 1.5 ns vs ∼ 3 ns. We modified microscopic and flow cytometric instruments to measure fluorescence lifetimes in live cells. We developed digital hardware and a measure of lifetime called a "pseudophasor" that we could compute quickly enough to permit sorting by lifetime in flow. We used these abilities to sort mixtures of cells expressing TFP and the short-lifetime TFP variant into subpopulations that were respectively 97% and 94% pure. This work demonstrates the feasibility of using information about fluorescence lifetime to help quantify cell signaling in living cells at the high throughput provided by flow cytometry. Moreover, it demonstrates the feasibility of isolating and recovering subpopulations of cells with different XFP lifetimes for subsequent experimentation

A low-eccentricity migration pathway for a 13-h-period Earth analogue in a four-planet system

It is commonly accepted that exoplanets with orbital periods shorter than one day, also known as ultra-short-period (USP) planets, formed further out within their natal protoplanetary disks before migrating to their current-day orbits via dynamical interactions. One of the most accepted theories suggests a violent scenario involving high-eccentricity migration followed by tidal circularization. Here we present the discovery of a four-planet system orbiting the bright (V = 10.5) K6 dwarf star TOI-500. The innermost planet is a transiting, Earth-sized USP planet with an orbital period of ~13 hours, a mass of 1.42 \ub1 0.18 M⊕, a radius of 1.166−0.058+0.061R⊕ and a mean density of 4.89−0.88+1.03gcm−3. Via Doppler spectroscopy, we discovered that the system hosts 3 outer planets on nearly circular orbits with periods of 6.6, 26.2 and 61.3 days and minimum masses of 5.03 \ub1 0.41 M⊕, 33.12 \ub1 0.88 M⊕ and 15.05−1.11+1.12M⊕, respectively. The presence of both a USP planet and a low-mass object on a 6.6-day orbit indicates that the architecture of this system can be explained via a scenario in which the planets started on low-eccentricity orbits then moved inwards through a quasi-static secular migration. Our numerical simulations show that this migration channel can bring TOI-500 b to its current location in 2 Gyr, starting from an initial orbit of 0.02 au. TOI-500 is the first four-planet system known to host a USP Earth analogue whose current architecture can be explained via a non-violent migration scenario