Elephant Seals and Temperature Data: Calibrations and Limitations.

NASA Astrophysics Data System (ADS)

Simmons, S. E.; Tremblay, Y.; Costa, D. P.

2006-12-01

In recent years with technological advances, instruments deployed on diving marine animals have been used to sample the environment in addition to their behavior. Of all oceanographic variables one of the most valuable and easiest to record is temperature. Here we report on a series of lab calibration and field validation experiments that consider the accuracy of temperature measurements from animal borne ocean samplers. Additionally we consider whether sampling frequency or animal behavior affects the quality of the temperature data collected by marine animals. Rapid response, external temperature sensors on eight Wildlife Computers MK9 time-depth recorders (TDRs) were calibrated using water baths at the Naval Postgraduate School (Monterey, CA). These water baths are calibrated using a platinum thermistor to 0.001° C. Instruments from different production batches were calibrated before and after deployments on adult female northern elephant seals, to examine tag performance over time and under `normal' usage. Tag performance in the field was validated by comparisons with temperature data from a Seabird CTD. In April/May of 2004, casts to 200m were performed over the Monterey Canyon using a CTD array carrying MK9s. These casts were performed before and after the release of a juvenile elephant seal from the boat. The seal was also carrying an MK9 TDR, allowing the assessment of any animal effect on temperature profiles. Sampling frequency during these field validations was set at one second intervals and the data from TDRs on both the CTD and the seals was sub-sampled at four, eight, 30 and 300 (5 min) seconds. The sub-sampled data was used to determine thermocline depth, a thermocline depth zone and temperature gradients and assess whether sampling frequency or animal behavior affects the quality of temperature data. Preliminary analyses indicate that temperature sensors deployed on elephant seals can provide water column temperature data of high quality and precision.

Physical oceanographic data from the OTEC Punta Tuna, Puerto Rico Site, September 1979-June 1980

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frye, D.; Davison, A.; Leavitt, K.

1981-01-01

The first results of an oceanographic measurement program being conducted off the southeast corner of Puerto Rico are presented. The study site is a proposed OTEC site and is located about 20 km off Punta Tuna. The objectives of the measurement program are to document the physical oceanography of the site as related to the engineering and environmental factors involved in OTEC design and operation. Oceanographic measurements include: (1) a subsurface mooring instrumented with five current, temperature, and pressure recorders; and (2) quarterly hydrographic cruises to measure salinity, temperature, and depth profiles on a grid of 33 stations in themore » vicinity of the mooring site. The first cruise, conducted between 16 and 21 June 1980, included the initial mooring deployment and a CTD (conductivity, temperature, and depth) and XBT (expendable bathythermograph) survey. The CTD/XBT measurements are presented. Also included are results of in situ current, temperature, and pressure measurements made during two previous programs. In September 1979, Coastal Marine Research (CMR) deployed a mooring at approximately the same site as the present mooring. Results from three of these instruments are included. The Naval Underwater Systems Center deployed a mooring at this site in February 1979 and partial results from one instrument on this mooring are also presented. (WHK)« less

Hydrographic observations by instrumented marine mammals in the Sea of Okhotsk

NASA Astrophysics Data System (ADS)

Nakanowatari, Takuya; Ohshima, Kay I.; Mensah, Vigan; Mitani, Yoko; Hattori, Kaoru; Kobayashi, Mari; Roquet, Fabien; Sakurai, Yasunori; Mitsudera, Humio; Wakatsuchi, Masaaki

2017-09-01

The Sea of Okhotsk is a challenging environment for obtaining in situ data and satellite observation in winter due to sea ice cover. In this study, we evaluated the validity of hydrographic observations by marine mammals (e.g., seals and sea lions) equipped with oceanographic conductivity-temperature-depth (CTD) sensors. During 4-yr operations from 2011 to 2014, we obtained total of 997 temperature-salinity profiles in and around the Soya Strait, Iony Island, and Urup Strait. The hydrographic data were mainly obtained from May to August and the maximum profile depth in shelf regions almost reaches to the seafloor, while valuable hydrographic data under sea ice cover were also obtained. In strong thermoclines, the seal-derived data sometimes showed positive biases in salinity with spike-like signal. For these salinity biases, we applied a new thermal mass inertia correction scheme, effectively reducing spurious salinity biases in the seasonal thermocline. In the Soya Strait and the adjacent region, the detailed structure of the Soya Warm Current including the cold-water belt was well identified. Dense water up to 27.0σθ, which can be a potential source of Okhotsk Sea Intermediate Water, has flowed from the Soya Strait into the Sea of Okhotsk in mid-winter (February). In summer, around the Iony Island and Urup Strait, remarkable cold and saline waters are localized in the surface layers. These regions are also characterized by weak stratification, suggesting the occurrence of tidally induced vertical mixing. Thus, CTD-tag observations have a great potential in monitoring data-sparse regions in the Sea of Okhotsk.

Characterizing turbulent overturns in CTD-data

NASA Astrophysics Data System (ADS)

van Haren, Hans; Gostiaux, Louis

2014-06-01

We are concerned with the shape of overturns due to irreversible effects of turbulent mixing through internal wave breaking in the ocean. Vertical (z) overturn displacements (d) are computed from ship-borne SeaBird-911 CTD-data using the well-established method of reordering unstable portions in vertical density profiles. When displayed as a function of z, the displacements d(z) reveal a characteristic zigzag shape. Here, we primarily investigate the particular slope (z/d) of this zigzag signature after assigning the displacements to the end-point depths. Using model-overturns we show that this slope equals ½ for a solid-body-rotation, while a more sophisticated Rankine-vortex overturn-model, here employed in the vertical, has slopes slightly >½ in the interior and >1 along the sides. In the case of a near-homogeneous layer, displacement-points fill a parallelogram with side-edges having a slope of 1. The models are used to interpret overturn shapes in NE-Atlantic-Ocean-data from moderately deep, turbulent waters above Rockall Bank (off Ireland) and from deep, weakly stratified waters above Mount Josephine (off Portugal). These are compared with salinity-compensated intrusion data in Mediterranean-outflow-waters in the Canary Basin. Dynamically, most overturns are found to resemble the half-turn Rankine-vortex model and very few a, small-only, solid-body-rotation. Additionally, the usefulness and uselessness of upcast-CTD-data are discussed for overturn characterization.

Measurement of antinuclear antibodies and their fine specificities: time for a change in strategy?

PubMed

Otten, Henny G; Brummelhuis, Walter J; Fritsch-Stork, Ruth; Leavis, Helen L; Wisse, Bram W; van Laar, Jacob M; Derksen, Ronald H W M

2017-01-01

The current strategy for antinuclear antibody (ANA) analysis involves screening for presence with a subsequent detailed analysis of their specificity. The aim of this study is to compare the clinical and financial efficacy of this strategy between different commercial tests in a large cohort of unselected patients. In all consecutive 1030 patients associations were defined between results from different ANA test systems and the pre-test probability for connective tissue disease (CTDs). Test systems were used for screening (ANA-IIF vs. CTD screen) and definition of their fine specificity (profile 3 line blot vs. CTD single analytes). Positive ANA-IIF and/or CTD screen results were found in 304 sera. Further analysis for ANA-specificity by profile 3 line blot and CTD single analytes showed 86 discrepant results of which more than a third are clinically relevant, with the CTD single analyte assay performing better than the line blot in supporting or confirming the presence of a CTD. Autoantigens present in one test but absent in the other were of minor practical use. The ANA screening and identification strategies currently employed are not cost-effective as 83% of tests were performed in order to find specific autoantibodies in patients without the fitting clinical signs or symptoms. This causes many unexpected positive results and subsequent confusion with regard to interpretation. We advocate that some autoantigens should be excluded from the line blot and CTD assays and propose the use of a cost-effective and selective ANA specificity testing purely based on clinical guidance.

--No Title--

Science.gov Websites

Properties (CTD/profile data) Trawl Survey Data (including oceanographic profiles) Shiptrack Surface Properties (hull-mounted sensor data) Temperature & Salinity Anomalies (by region) Drifter Tracks eMOLT

Mechanisms Controlling Hypoxia Data Atlas: High-resolution hydrographic and chemical observations from 2003-2014

NASA Astrophysics Data System (ADS)

Zimmerle, H.; DiMarco, S. F.

2016-02-01

The Mechanisms Controlling Hypoxia (MCH) project consisted of 31 cruises from 2003-2014 with an objective to investigate the physical and biogeochemical processes that control the hypoxic zone on the Texas-Louisiana shelf in the northern Gulf of Mexico. The known seasonal low oxygen conditions in this region are the result of river-derived nutrients, freshwater input, and wind. The MCH Data Atlas showcases in situ data and subsequent products produced during the duration of the project, focusing on oceanographic observations from 2010-2014. The Atlas features 230 high-resolution vertical sections from nine cruises using the Acrobat undulating towed vehicle that contained a CTD along with sensors measuring oxygen, fluorescence, and turbidity. Vertical profiles along the 20-meter isobaths section feature temperature, salinity, chlorophyll, and dissolved oxygen from the Acrobat towfish and CTD rosette as well as separate selected profiles from the CTD. Surface planview maps show the horizontal distribution of temperature, salinity, chlorophyll, beam transmission, and CDOM observed by the shipboard flow-through system. Bottom planview maps present the horizontal distribution of dissolved oxygen as well as temperature and salinity from the CTD rosette and Acrobat towfish along the shelf's seafloor. Informational basemaps display the GPS cruise track as well as individual CTD stations for each cruise. The shelf concentrations of CTD rosette bottle nutrients, including nitrate, nitrite, phosphate, ammonia, and silicate are displayed in select plots. Shipboard ADCP current velocity fields are also represented. MCH datasets and additional products are featured as an electronic version to compliment the published atlas. The MCH Data Atlas provides a showcase for the spatial and temporal variability of the environmental parameters associated with the annual hypoxic event and will be a useful tool in the continued monitoring and assessment of Gulf coastal hypoxia.

Laparoscopic Antireflux Surgery in Patients with Connective Tissue Diseases.

PubMed

Menezes, Mariano A; Herbella, Fernando A M; Patti, Marco G

2016-04-01

Different connective tissue diseases (CTDs), such as dermatomyositis, mixed CTD, rheumatoid arthritis, polymyositis, lupus, and Behçet's, may affect the esophagus, impairing its motor function. The muscular atrophy and fibrosis caused by the autoimmune vasculitis and neuronal dysfunction affect the esophageal body and the lower esophageal sphincter, leading to a clinical presentation of dysphagia and gastroesophageal reflux disease (GERD). The belief that the impaired esophageal motility may negatively affect surgical outcome has led to the common recommendation of avoiding laparoscopic antireflux surgery (LARS) for fear of creating or worsening dysphagia. This review focuses on the evaluation of the outcome of LARS in patients with CTD. Specifically, this review shows that the literature on LARS and CTDs is scarce and most studies have a small number of patients and a short follow-up. Furthermore, a subanalysis of the outcome based on the type of CTD or the manometric profile is still elusive. In the setting of these limitations, it appears that results are good and comparable to those of patients with GERD and without a CTD. Morbidity and mortality are insignificant even considering the systemic manifestations of the CTD. LARS should not be denied to patients with CTD and GERD.

Chlorophyll-a thin layers in the Magellan fjord system: The role of the water column stratification

NASA Astrophysics Data System (ADS)

Ríos, Francisco; Kilian, Rolf; Mutschke, Erika

2016-08-01

Fjord systems represent hotspots of primary productivity and organic carbon burial. However, the factors which control the primary production in mid-latitude fjords are poorly understood. In this context, results from the first fine-scale measurements of bio-oceanographic features in the water column of fjords associated with the Strait of Magellan are presented. A submersible fluorescence probe (FP) was used to measure the Chlorophyll-a (Chl-a) concentration in situ, along with conductivity, temperature, hydrostatic pressure (depth) and dissolved oxygen (CTD-O2) of the water column. The Austral spring results of 14 FP-CTD-O2 profiles were used to define the vertical and horizontal patches of the fluorescent pigment distribution and their spatial relations with respect to the observed hydrographic features. Three zones with distinct water structures were defined. In all zones, the 'brown' spectral group (diatoms and dinoflagellates) predominated accounting for >80 wt% of the phytoplankton community. Thin layers with high Chl-a concentration were detected in 50% of the profiles. These layers harbored a substantial amount (30-65 wt%) of the phytoplankton biomass. Stratification was positively correlated to the occurrence of Chl-a thin layers. In stable and highly stratified water columns the integrated Chl-a concentration was higher and frequently located within thin layers whereas well mixed water columns displayed lower values and more homogeneous vertical distribution of Chl-a. These results indicate that mixing/stability processes are important factors accounting to the vertical distribution of Chl-a in Magellan fjords.

Uncertainties in Climatological Seawater Density Calculations

NASA Astrophysics Data System (ADS)

Dai, Hao; Zhang, Xining

2018-03-01

In most applications, with seawater conductivity, temperature, and pressure data measured in situ by various observation instruments e.g., Conductivity-Temperature-Depth instruments (CTD), the density which has strong ties to ocean dynamics and so on is computed according to equations of state for seawater. This paper, based on density computational formulae in the Thermodynamic Equation of Seawater 2010 (TEOS-10), follows the Guide of the expression of Uncertainty in Measurement (GUM) and assesses the main sources of uncertainties. By virtue of climatological decades-average temperature/Practical Salinity/pressure data sets in the global ocean provided by the National Oceanic and Atmospheric Administration (NOAA), correlation coefficients between uncertainty sources are determined and the combined standard uncertainties uc>(ρ>) in seawater density calculations are evaluated. For grid points in the world ocean with 0.25° resolution, the standard deviations of uc>(ρ>) in vertical profiles cover the magnitude order of 10-4 kg m-3. The uc>(ρ>) means in vertical profiles of the Baltic Sea are about 0.028kg m-3 due to the larger scatter of Absolute Salinity anomaly. The distribution of the uc>(ρ>) means in vertical profiles of the world ocean except for the Baltic Sea, which covers the range of >(0.004,0.01>) kg m-3, is related to the correlation coefficient r>(SA,p>) between Absolute Salinity SA and pressure p. The results in the paper are based on sensors' measuring uncertainties of high accuracy CTD. Larger uncertainties in density calculations may arise if connected with lower sensors' specifications. This work may provide valuable uncertainty information required for reliability considerations of ocean circulation and global climate models.

Glider Observations of Internal Tide Packets on the Australian Northwest Shelf

NASA Astrophysics Data System (ADS)

Book, J. W.; Steinberg, C. R.; Brinkman, R. M.; Jones, N. L.; Lowe, R.; Ivey, G. N.; Pattiaratchi, C. B.; Rice, A. E.

2016-02-01

The rapid profiling capabilities (less than 10 minutes per profile in 100 m of water excluding surfacing times) of autonomous gliders were utilized to study the structure of non-linear internal tide packets on the Australian Northwest Shelf. A total of five gliders were deployed on the shelf from 11 February - 21 April 2012 with more than 2900 glider CTD profiles collected during the final three weeks of this time period when the internal tide activity was intense. In general the internal tide packets showed high degrees of non-linearity, for example in one case a glider observed a 62 m rise of the 28° isotherm over 2.25 hours in a shelf location of 90 meters water depth. In addition to the glider measurements, moored strings of CTD sensors were used to measure the internal tide packets at fixed positions and the results show that the wave packets vary significantly with respect to their structure and arrival times from one tidal period to the next. This fact complicates interpretation of the glider data as wave packet spatial evolution is non-stationary and cannot be simply recovered from repeat glider visits to the same location. Furthermore, the packets were found to move at speeds near or greater (e.g., 0.55 m/s) than the speed that the gliders were moving. Despite these challenges, the gliders offer the only resource that can measure the spatial structure of the wave packets beyond the scope of our limited mooring positions. Therefore, we have implemented methods such as time-augmented empirical orthogonal functions to combine these glider measurements with the fixed mooring measurements in order to better understand the spatial and temporal patterns of the wave packet evolution over the slope and shelf of this region.

On the freshwater budget in the eastern tropical Atlantic during the development of the cold tongue

NASA Astrophysics Data System (ADS)

Schlundt, Michael; Krahmann, Gerd; Brandt, Peter; Karstensen, Johannes

2013-04-01

The most striking sea surface temperature (SST) phenomenon in the tropical Atlantic is the seasonal appearance of the Atlantic Cold Tongue (ACT). Onset, duration, spatial extent and strength of cooling are subject to significant interannual variability. The ACT onset is also associated with remarkable changes in upper ocean salinity. To examine the different contributions to these changes we here focus on and present a mixed layer freshwater budget in the eastern tropical Atlantic. Our investigation is based on an exceptionally large set of observations during the onset of the ACT in late boreal spring/ early boreal summer 2011: more than 5400 CTD-profiles acquired by seven gliders running simultaneously to two research cruises, 180 ship based CTD-profiles, time series data from the PIRATA buoy array as well as measurements from the Argo float program are used to derive mixed layer depth, lateral and vertical salinity gradients. To derive turbulent mixing and inferred diapycnal salt flux, microstructure observations are taken into account. Furthermore satellite measurements of sea surface salinity (SSS) by the SMOS mission and of SST by the TMI radiometer as well as atmospheric reanalysis data and the OSCAR project products are implemented. Freshwater budget terms were calculated for different sub-regions. These sub-regions are chosen using pre-defined thresholds in SSS, SST or mixed layer depth. Overall the freshwater budget is dominated by the net surface freshwater flux and horizontal advection by strong zonal currents. Other terms, like entrainment and diapycnal mixing are found to be regionally important. In particular, the observed increase in salinity in the near-equatorial region during ACT onset is found to be the result of the northward migration of the ITCZ associated with reduced net surface freshwater flux at the equator as well as mixing of salty subsurface waters into the surface mixed layer.

Revisiting the co-existence of Attention-Deficit/Hyperactivity Disorder and Chronic Tic Disorder in childhood-The case of colour discrimination, sustained attention and interference control.

PubMed

Uebel-von Sandersleben, Henrik; Albrecht, Björn; Rothenberger, Aribert; Fillmer-Heise, Anke; Roessner, Veit; Sergeant, Joseph; Tannock, Rosemary; Banaschewski, Tobias

2017-01-01

Attention Deficit / Hyperactivity Disorder (ADHD) and Chronic Tic Disorder (CTD) are two common and frequently co-existing disorders, probably following an additive model. But this is not yet clear for the basic sensory function of colour processing sensitive to dopaminergic functioning in the retina and higher cognitive functions like attention and interference control. The latter two reflect important aspects for psychoeducation and behavioural treatment approaches. Colour discrimination using the Farnsworth-Munsell 100-hue Test, sustained attention during the Frankfurt Attention Inventory (FAIR), and interference liability during Colour- and Counting-Stroop-Tests were assessed to further clarify the cognitive profile of the co-existence of ADHD and CTD. Altogether 69 children were classified into four groups: ADHD (N = 14), CTD (N = 20), ADHD+CTD (N = 20) and healthy Controls (N = 15) and compared in cognitive functioning in a 2×2-factorial statistical model. Difficulties with colour discrimination were associated with both ADHD and CTD factors following an additive model, but in ADHD these difficulties tended to be more pronounced on the blue-yellow axis. Attention problems were characteristic for ADHD but not CTD. Interference load was significant in both Colour- and Counting-Stroop-Tests and unrelated to colour discrimination. Compared to Controls, interference load in the Colour-Stroop was higher in pure ADHD and in pure CTD, but not in ADHD+CTD, following a sub-additive model. In contrast, interference load in the Counting-Stroop did not reveal ADHD or CTD effects. The co-existence of ADHD and CTD is characterized by additive as well as sub-additive performance impairments, suggesting that their co-existence may show simple additive characteristics of both disorders or a more complex interaction, depending on demand. The equivocal findings on interference control may indicate limited validity of the Stroop-Paradigm for clinical assessments.

Revisiting the co-existence of Attention-Deficit/Hyperactivity Disorder and Chronic Tic Disorder in childhood—The case of colour discrimination, sustained attention and interference control

PubMed Central

Rothenberger, Aribert; Fillmer-Heise, Anke; Roessner, Veit; Sergeant, Joseph; Tannock, Rosemary; Banaschewski, Tobias

2017-01-01

Objective Attention Deficit / Hyperactivity Disorder (ADHD) and Chronic Tic Disorder (CTD) are two common and frequently co-existing disorders, probably following an additive model. But this is not yet clear for the basic sensory function of colour processing sensitive to dopaminergic functioning in the retina and higher cognitive functions like attention and interference control. The latter two reflect important aspects for psychoeducation and behavioural treatment approaches. Methods Colour discrimination using the Farnsworth-Munsell 100-hue Test, sustained attention during the Frankfurt Attention Inventory (FAIR), and interference liability during Colour- and Counting-Stroop-Tests were assessed to further clarify the cognitive profile of the co-existence of ADHD and CTD. Altogether 69 children were classified into four groups: ADHD (N = 14), CTD (N = 20), ADHD+CTD (N = 20) and healthy Controls (N = 15) and compared in cognitive functioning in a 2×2-factorial statistical model. Results Difficulties with colour discrimination were associated with both ADHD and CTD factors following an additive model, but in ADHD these difficulties tended to be more pronounced on the blue-yellow axis. Attention problems were characteristic for ADHD but not CTD. Interference load was significant in both Colour- and Counting-Stroop-Tests and unrelated to colour discrimination. Compared to Controls, interference load in the Colour-Stroop was higher in pure ADHD and in pure CTD, but not in ADHD+CTD, following a sub-additive model. In contrast, interference load in the Counting-Stroop did not reveal ADHD or CTD effects. Conclusion The co-existence of ADHD and CTD is characterized by additive as well as sub-additive performance impairments, suggesting that their co-existence may show simple additive characteristics of both disorders or a more complex interaction, depending on demand. The equivocal findings on interference control may indicate limited validity of the Stroop-Paradigm for clinical assessments. PMID:28594866

First oceanographic observations on the Wandel Sea shelf in Northeast Greenland: Tracing the Arctic Ocean outflow through the western Fram Strait

NASA Astrophysics Data System (ADS)

Dmitrenko, Igor A.; Kirillov, Sergei A.; Rudels, Bert; Babb, David G.; Pedersen, Leif T.; Rysgaard, Soeren; Kristoffersen, Yngve; Barber, David G.

2016-04-01

The first-ever conductivity-temperature-depth (CTD) observations on the Wandel Sea shelf in North Eastern Greenland were collected from the land-fast ice in April-May 2015 as a part of the Arctic Science Partnership collaboration during the first research campaign at the Villum Research Station. They were complemented by (i) the ice-tethered profiler (ITP) and Acoustic Dopler Current Profiler (ADCP) mooring observations in ~300 m of the tidewater glacier outlet from the Flade Isblink Ice Cap and (ii) CTDs taken in June-July 2015 along the Wandel Sea continental slope during the Norwegian FRAM 2014-15 sea ice drift. The CTD profiles deeper than 100 m are used to reveal the origin of water masses and determine the extent to which these water masses have interacted with ambient water from the continental slope. The subsurface water layer from ~20-70 m depth is comprised of freshened water (30-32 psu) that is likely associated with the Pacific Water outflow from the Arctic Ocean through the western Fram Strait. The underlying halocline layer centered at ~80 m (~33 psu) separates the Pacific Water layer from a deeper (<140 m) layer of modified Polar Water that has interacted with the warm Atlantic Water outflow through Fram Strait. The Atlantic Water layer with temperature above 0°C is recorded below 140 m. Over the outer shelf, the halocline layer shows numerous cold density-compensated intrusions indicating lateral interaction with an ambient Polar Water mass across the continental slope. Mooring data shows an enhanced shelf-slope interaction responding the storm event in 23-24 April 2015 with northerly winds exceeding 10 m/s. The on-shelf transport of a cold and turbid water from the upper continental slope results in enhanced interleaving within the depth range of the halocline layer (~70-100 m). Our observations of Pacific Water in the Wandel Sea subsurface layer are set in the context of upstream observations in the Beaufort Sea for 2002-2011 and downstream observations from the Northeast Water Polynya (1992-1993), and clearly show the modification of Pacific Water during its advection across the Arctic Ocean from the Bering Strait to Fram Strait. Moreover, the Wandel Sea shelf and continental slope water shows a different water mass structure indicating the different origin and pathways of the on-shore and off-shore branches of the Arctic Ocean outflow through the Western Fram Strait.

Intense mesoscale variability in the Sardinia Sea

NASA Astrophysics Data System (ADS)

Russo, Aniello; Borrione, Ines; Falchetti, Silvia; Knoll, Michaela; Fiekas, Heinz-Volker; Heywood, Karen; Oddo, Paolo; Onken, Reiner

2015-04-01

From the 6 to 25 June 2014, the REP14-MED sea trial was conducted by CMRE, supported by 20 partners from six different nations. The at-sea activities were carried out onboard the research vessels Alliance (NATO) and Planet (German Ministry of Defense), comprising a marine area of about 110 x 110 km2 to the west of the Sardinian coast. More than 300 CTD casts typically spaced at 10 km were collected; both ships continuously recorded vertical profiles of currents by means of their ADCPs, and a ScanFish® and a CTD chain were towed for almost three days by Alliance and Planet, respectively, following parallel routes. Twelve gliders from different manufacturers (Slocum, SeaGliderTM and SeaExplorer) were continuously sampling the study area following zonal tracks spaced at 10 km. In addition, six moorings, 17 surface drifters and one ARVOR float were deployed. From a first analysis of the observations, several mesoscale features were identified in the survey area, in particular: (i) a warm-core anticyclonic eddy in the southern part of the domain, about 50 km in diameter and with the strongest signal at about 50-m depth (ii) another warm-core anticyclonic eddy of comparable dimensions in the central part of the domain, but extending to greater depth than the former one, and (iii) a small (less than 15 km in diameter) cold-core cyclonic eddy of Winter Intermediate Water in the depth range between 170 m and 370 m. All three eddies showed intensified currents, up to 50 cm s-1. The huge high-resolution observational data set and the variety of observation techniques enabled the mesoscale features and their variability to be tracked for almost three weeks. In order to obtain a deeper understanding of the mesoscale dynamic behaviour and their interactions, assimilation studies with an ocean circulation model are underway.

Hydraulic Control and Mixing in Chesapeake Bay

NASA Astrophysics Data System (ADS)

Ott, M. W.

2006-05-01

Properly modeling the exchange rate at the mouths of estuarine bays is critical to understanding the effects of freshwater and pollutants on the hydrographic and biological conditions within these bays. There is evidence that hydraulic control occurs at certain locations in the deeper channels of Chesapeake Bay and may be a mechanism in limiting the exchange rate. In addition, the vertical and horizontal mixing associated with the resulting hydraulic jumps has implications both for the hydrographic conditions and circulation, as well as for primary productivity within Chesapeake Bay. Shipboard acoustic Doppler current profiler (ADCP) data, as well as conductivity-temperature-depth (CTD) profiles were collected during the spring of 2005 at various locations within Chesapeake Bay to better understand the occurrence and strength of hydraulic controls in relation to the phases of the fortnightly and semi-diurnal tidal cycles as well as to topography. Mixing is shown to occur alternatively over both hollows and bumps, depending on the tidal phase, and the strength and effects if this mixing is compared.

Testing of SIR (a transformable robotic submarine) in Lake Tahoe for future deployment at West Antarctic Ice Sheet grounding lines of Siple Coast

NASA Astrophysics Data System (ADS)

Powell, R. D.; Scherer, R. P.; Griffiths, I.; Taylor, L.; Winans, J.; Mankoff, K. D.

2011-12-01

A remotely operated vehicle (ROV) has been custom-designed and built by DOER Marine to meet scientific requirements for exploring subglacial water cavities. This sub-ice rover (SIR) will explore and quantitatively document the grounding zone areas of the Ross Ice Shelf cavity using a 3km-long umbilical tether by deployment through an 800m-long ice borehole in a torpedo shape, which is also its default mode if operational failure occurs. Once in the ocean cavity it transforms via a diamond-shaped geometry into a rectangular form when all of its instruments come alive in its flight mode. Instrumentation includes 4 cameras (one forward-looking HD), a vertical scanning sonar (long-range imaging for spatial orientation and navigation), Doppler current meter (determine water current velocities), multi-beam sonar (image and swath map bottom topography), sub-bottom profiler (profile sub-sea-floor sediment for geological history), CTD (determine salinity, temperature and depth), DO meter (determine dissolved oxygen content in water), transmissometer (determine suspended particulate concentrations in water), laser particle-size analyzer (determine sizes of particles in water), triple laser-beams (determine size and volume of objects), thermistor probe (measure in situ temperatures of ice and sediment), shear vane probe (determine in situ strength of sediment), manipulator arm (deploy instrumentation packages, collect samples), shallow ice corer (collect ice samples and glacial debris), water sampler (determine sea water/freshwater composition, calibrate real-time sensors, sample microbes), shallow sediment corer (sample sea floor, in-ice and subglacial sediment for stratigraphy, facies, particle size, composition, structure, fabric, microbes). A sophisticated array of data handling, storing and displaying will allow real-time observations and environmental assessments to be made. This robotic submarine and other instruments will be tested in Lake Tahoe in September, 2011 and results will be presented on its trials and geological and biological findings down to the deepest depths of the lake. Other instruments include a 5m-ling percussion corer for sampling deeper sediments, an ice-tethered profiler with CTD and ACDP, and in situ oceanographic mooring designed to fit down a narrow (30cm-diameter) ice borehole that include interchangeable packages of ACDPs, CTDs, transmissometers, laser particle-size analyzer, DO meter, automated multi-port water sampler, water column nutrient analyzer, sediment porewater chemistry analyzer, down-looking color camera (see figure), and altimeter.

Dissolved and Particulate 230Th - 232Th systematics in the Central Equatorial Pacific Ocean

NASA Astrophysics Data System (ADS)

Lopez, G. I.; Marcantonio, F.

2013-12-01

To complement our work in the eastern Equatorial Pacific, we have measured total and dissolved 230Th and 232Th in the central Equatorial Pacific at two sites, one at 8°N and the other at the equator (ML1208-03CTD; 00° 13.166' S, 155° 57.668' W and ML1208-12CTD; 8° 19.989' N, 159° 18.000' W). The two seawater casts were collected in May 2012 during an NSF-funded "Line Islands" cruise to test for the extent of advection or diffusion of dissolved 230Th from the oligotrophic North Pacific gyre (low particle flux) to the more productive equatorial region (high particle flux). Our thorium results are similar to previous data published for the western and central North Pacific Ocean. Dissolved 230Th concentrations range from 1.1 fg/kg at 100 m to 30.8 fg/kg at 4400 m, while dissolved 232Th concentrations span from 8.1 pg/kg at 900 m to 19.7 pg/kg at 4400 m. The pattern of the dissolved 230Th profile at 8°N is essentially linear from the surface to 2000 m. From 2000 m to 3000 m, the dissolved 230Th concentrations are constant, and then from 3000 m to the bottom, the profile is linear again. At the same site, the particulate fraction of the total seawater 230Th increases exponentially from about 0% at the surface to 38% at 4400 m. From 0 to 3000 m at 8°N, dissolved 232Th concentrations display a relatively constant pattern (variability of about 20%). From 3000 m to 4400 m, dissolved 232Th contents are more variable, but generally increase toward greater depths. The proportion of 232Th in the particulate fraction of the total seawater sample increases exponentially with depth to a value of 58% in the bottommost sample. We will present additional data from the equator and assess the particulate dynamics that control the distribution of thorium isotopes in central equatorial Pacific seawater.

Observations of The Dense Storfjord Plume Using A Ctd-mounted Adp

NASA Astrophysics Data System (ADS)

Fer, I.; Skogseth, R.; Haugan, P. M.

Observations were made of the outflow of the dense bottom water plume from Stor- fjord (110 km long and 190 m deep at maximum depth) in the Svalbard Archipelago, using a CTD mounted ADP at densely spaced hydrographic stations during May 28 - June 2, 2001. Due to heavy ice inside the fjord, measurements were made from about 70 km downstream of a 115 m deep sill (7645 N) and onward. The dense bottom water generated by strong winter cooling, enhanced ice formation, and the consequent brine rejection drains into and fills the depressions of the fjord and cascades following the bathymetry. Data acquired by ADP allow for examination of the velocity structure associated with the plume as close as 1 m to the bottom with 1 m resolution in the vertical. The plume water was observed to have salinities within 34.9 - 35.1 psu with temperatures close to the freezing point temperature. The plume has a thickness of 51 +/- 20 m, and a density difference of 0.14 +/- 0.03 kg m-3 from the ambient wa- ters. The velocity profiles yield the most well-defined two-layered structure near the sloping sides with a mean plume speed of 0.15 +/- 0.04 m s-1, relative to the ambient waters. Mean overall Richardson number, estimated using these profiles, are within the range of 2 to 4. The plume is less distinct with respect to the velocity profile when it reaches the plane, Storfjordrenna, after cascading about 50 m in vertical. The width of the plume increases from about 8 km to 25 km along its path of 105 km leading to an entrainment rate of 5x10-4, when the plume thickness and speed are assumed constant. The values compare well with those obtained from moorings in the same region in the past, as well as those obtained from laboratory experiments of turbulent gravity currents flowing down a slope.

Multi-Scale 4DVAR Assimilation of Glider Teams on the North Carolina Shelf

NASA Astrophysics Data System (ADS)

Osborne, J. J. V.; Carrier, M.; Book, J. W.; Barron, C. N.; Rice, A. E.; Rowley, C. D.; Smedstad, L.; Souopgui, I.; Teague, W. J.

2017-12-01

We demonstrate a method to assimilate glider profile data from multiple gliders in close proximity ( 10 km or less). Gliders were deployed in a field experiment from 17 May until 4 June 2017, north of Cape Hatteras and inshore of the Gulf Stream. Gliders were divided into two teams, generally two or three gliders per team. One team was tasked with station keeping and the other with moving and sampling regions of high variability in temperature and salinity. Glider data are assimilated into the Relocatable Navy Coastal Ocean Model (RELO NCOM) with four dimensional variational assimilation (NCOM-4DVAR). RELO NCOM is used by the US Navy to predict the ocean. RELO NCOM is a baroclinic, Boussinesq, free-surface, and hydrostatic ocean model with a flexible sigma-z vertical coordinate. Two domains are used, one focused north and one focused south of Cape Hatteras. The domains overlap near the gliders, thus providing two forecasts near the gliders. Both domains have 1 km horizontal resolution. Data are assimilated in a newly-developed multi-scale data-processing and assimilating approach using NCOM-4DVAR. This enables NCOM-4DVAR to use many more observations than standard NCOM-4DVAR, improving the analysis and forecast. Assimilation experiments use station-keeping glider data, moving glider data, or all glider data. Sea surface temperature (SST) data and satellite altimeter (SSH) data are also assimilated. An additional experiment omits glider data but still assimilates SST and SSH data. Conductivity, temperature, and depth (CTD) profiles from the R/V Savannah are used for validation, including data from an underway CTD (UCTD). Data from glider teams have the potential to significantly improve model forecasts. Missions using teams of gliders can be planned to maximize data assimilation for optimal impact on model predictions.

Characterization of double diffusive convection step and heat budget in the deep Arctic Ocean

NASA Astrophysics Data System (ADS)

Zhou, S.; Lu, Y.

2013-12-01

In this paper, we explore the hydrographic structure and heat budget in deep Canada Basin using data measured with McLane-Moored-Profilers (MMPs), bottom-pressure-recorders (BPRs), and conductivity-temperature-depth (CTD) profilers. From the bottom upward, a homogenous bottom layer and its overlaying double diffusive convection (DDC) steps are well identified at Mooring A (75oN, 150oW). We find that the deep water is in weak diapycnal mixing because the effective diffusivity of the bottom layer is ~1.8×10-5 m 2s-1 while that of the other steps is ~10-6 m 2s-1. The vertical heat flux through DDC steps is evaluated with different methods. We find that the heat flux (0.1-11 mWm-2) is much smaller than geothermal heating (~50 mWm-2), which suggests that the stack of DDC steps acts as a thermal barrier in the deep basin. Moreover, the temporal distributions of temperature and salinity differences across the interface are exponential, while those of heat flux and effective diffusivity are found to be approximately log-normal. Both are the result of strong intermittency. Between 2003 and 2011, temperature fluctuation close to the sea floor distributed asymmetrically and skewed towards positive values, which provides direct indication that geothermal heating is transferred into ocean. Both BPR and CTD data suggest that geothermal heating, not the warming of upper ocean, is the dominant mechanism responsible for the warming of deep water. As the DDC steps prevent the vertical heat transfer, geothermal heating will be unlikely to have significant effect on the middle and upper oceans.

Characterization of double diffusive convection steps and heat budget in the deep Arctic Ocean

NASA Astrophysics Data System (ADS)

Zhou, Sheng-Qi; Lu, Yuan-Zheng

2013-12-01

In this paper, we explore the hydrographic structure and heat budget in the deep Canada Basin by using data measured with McLane-Moored-Profilers (MMP), bottom pressure recorders (BPR), and conductivity-temperature-depth (CTD) profilers. Upward from the bottom, a homogeneous bottom layer and its overlaying double diffusive convection (DDC) steps are well identified at Mooring A (75°N,150°W). We find that the deep water is in weak diapycnal mixing because the effective diffusivity of the bottom layer is ˜1.8 × 10-5 m2s-1, while that of the other steps is ˜10-6 m2s-1. The vertical heat flux through the DDC steps is evaluated by using different methods. We find that the heat flux (0.1-11 mWm -2) is much smaller than geothermal heating (˜50 mWm -2). This suggests that the stack of DDC steps acts as a thermal barrier in the deep basin. Moreover, the temporal distributions of temperature and salinity differences across the interface are exponential, whereas those of heat flux and effective diffusivity are found to be approximately lognormal. Both are the result of strong intermittency. Between 2003 and 2011, temperature fluctuations close to the sea floor were distributed asymmetrically and skewed toward positive values, which provide a direct observation that geothermal heating was transferred into the ocean. Both BPR and CTD data suggest that geothermal heating and not the warming of the upper ocean is the dominant mechanism responsible for the warming of deep water. As the DDC steps prevent vertical heat transfer, geothermal heating is unlikely to have a significant effect on the middle and upper Arctic Ocean.

Tidal and residual circulation in a semi-arid bay: Coquimbo Bay, Chile

NASA Astrophysics Data System (ADS)

Valle-Levinson, Arnoldo; Moraga, Julio; Olivares, Jorge; Blanco, José Luis

2000-11-01

Velocity profiles and time-series data were combined with conductivity-temperature-depth (CTD) casts to describe the general circulation at tidal and subtidal scales in a bay of semi-arid climate, Coquimbo Bay (˜30°S), Chile. This was the first study that used a towed acoustic Doppler current profiler (ADCP) in coastal Chilean waters and is one of the very few in semi-arid bays. The ADCP was towed for two semi-diurnal tidal cycles in early austral autumn, between March 23 and 24, 1997 along a triangular trajectory that covered most of the bay. Additional data consisted of moored current meters and CTD casts. The observations indicated the presence of a surface layer, above the pycnocline, that showed predominantly diurnal variability forced by the breeze regime and by tides. The tidal circulation in the surface layer featured amplitudes of 10 cm/s within an anticyclonic gyre that occupied most of the bay. The subtidal circulation in the surface was characterized by a pair of counter-rotating gyres. The northernmost three-fourths of the bay showed an anticyclonic gyre, and the observations over the southern fourth implied a cyclonic gyre. The subtidal anticyclonic gyre had a counterpart rotating in opposite direction within a lower layer, underneath the pycnocline. The lower layer showed semidiurnal variability in addition to diurnal variability and was insulated by the pycnocline from heat and momentum fluxes through the air-water interface. Circulations that resemble estuarine and anti-estuarine patterns were found associated with the subtidal gyres. A horizontal divergence related to a 10 cm/s near-surface outflow around Point Tortuga, to the south of the bay entrance, allowed the development of upward motion off the Point, as evidenced by the tilt of the isopycnals at the entrance to the bay.

Seasonal cycle of the mixed layer depth, of the seasonal thermocline and of the upper-ocean heat rate in the Mediterranean Sea: an observational approach

NASA Astrophysics Data System (ADS)

Houpert, Loïc; Testor, Pierre; Durrieu de Madron, Xavier; Somot, Samuel; D'Ortenzio, Fabrizio; Estournel, Claude; Lavigne, Héloïse

2014-05-01

We present a relatively high resolution Mediterranean climatology (0.5°x0.5°x12 months) of the seasonal thermocline based on a comprehensive collection of temperature profiles of the last 44 years (1969-2012). The database includes more than 190,000 profiles, merging CTD, XBT, profiling floats, and gliders observations. This data set is first used to describe the seasonal cycle of the mixed layer depth and of the seasonal thermocline and on the whole Mediterranean on a monthly climatological basis. Our analysis discriminates several regions with coherent behaviors, in particular the deep water formation sites, characterized by significant differences in the winter mixing intensity. Heat Storage Rate (HSR) is calculated as the time rate of change of the heat content due to variations in the temperature integrated from the surface down to the base of the seasonal thermocline. Heat Entrainment Rate (HER) is calculated as the time rate of change of the heat content due to the deepening of thermocline base. We propose a new independent estimate of the seasonal cycle of the Net surface Heat Flux, calculated on average over the Mediterranean Sea for the 1979-2011 period, based only on in-situ observations. We used our new climatologies of HSR and of HER, combined to existing climatology of the horizontal heat flux at Gibraltar Strait. Although there is a good agreement between our estimation of NHF, from observations, with modeled NHF, some differences may be noticed during specific periods. A part of these differences may be explained by the high temporal and spatial variability of the Mixed Layer Depth and of the seasonal thermocline, responsible for very localized heat transfer in the ocean.

Emory University: High-Throughput Protein-Protein Interaction Analysis for Hippo Pathway Profiling | Office of Cancer Genomics

Cancer.gov

The CTD2 Center at Emory University used high-throughput protein-protein interaction (PPI) mapping for Hippo signaling pathway profiling to rapidly unveil promising PPIs as potential therapeutic targets and advance functional understanding of signaling circuitry in cells. Read the abstract.

Mesoscale variability observed in the Northern Adriatic in autumn 2016

NASA Astrophysics Data System (ADS)

Pasaric, Zoran; Iva, Medjugorac; Nastjenka, Supic; Tamara, Djakovac; Mirko, Orlic

2017-04-01

Quasi-synoptic measurements of hydrographic properties were performed in the Northern Adriatic along the transect extending from Rovinj to the Po River mouth in an approximately east-west direction. The depth along the transect slowly varies between 30 and 40 m. Three one-day cruises were conducted, the first on 12 Nov, the second on 18 Nov, and the third on 25 Nov 2016. During the first and the third cruise the sampling was done with a CTD probe lowered from the surface to the bottom, at eleven stations placed nearly equidistantly along the transect. Average distance between the stations was 6 km. The second cruise was conducted with a towed yo-yo profiler equipped with the CTD probe and continuously undulating between the surface and some 4 m above the bottom. With roughly three undulations per kilometer, horizontal resolution along the transect was about 200 m. The data suggest that three processes occurred during the cruises: 1) surface cooling and related vertical mixing, 2) intrusion of high-salinity waters into the western part of the transect, and 3) propagation of a mesoscale formation in a westward direction. The existence and propagation of the mesoscale feature is supported by a simple analytical model of topographic Rossby waves. By assuming that the bottom varies linearly in the direction perpendicular to the transect, the propagation speed of O(1 km/day) is obtained - in agreement with the observations.

Path homogeneity along a horizontal line-of-sight path during the FESTER experiment: first results

NASA Astrophysics Data System (ADS)

Gunter, W. H.; Maritz, B.; Koago, M.; Wainman, C. K.; Gardener, M. E.; February, F.; van Eijk, A. M. J.

2016-10-01

The First European South African Experiment (FESTER) was conducted over about a 10 month period at the Institute of Maritime Technology (IMT) in False Bay, South Africa. One of the important goals was the establishment of the air-sea temperature difference (ASTD) homogeneity along the main propagation link atmospheric path since it is a basic assumption for most of the atmospheric turbulence models (caused by refractive index variations). The ASTD was measured from a small scientific work boat (called Sea Lab) moving along a straight in- and outbound track along the main propagation link path. The air temperature on-board was measured using standard weather sensors, while the sea surface temperature was measured using a long wavelength infrared radiometer, which was compared to the bulk sea temperature half a meter below the sea surface. This was obtained by an under water temperature sensor mounted on a `surfboard' that was towed alongside Sea Lab. Vertical water temperature profiles were also measured along the main propagation path in order to determine the depth of the surface mixed layer and thermocline using a Conductivity Temperature Depth profiler (CTD). First results investigated the ASTD variation along the horizontal line-of-sight path used by the principal electro-optic transmission link monitoring equipment (i.e. scintillometer and multi-spectral radiometer-transmissometer system).

pCO2 Observations from a Vertical Profiler on the upper continental slope off Vancouver Island: Physical controls on biogeochemical processes.

NASA Astrophysics Data System (ADS)

Mihaly, S. F.

2016-02-01

We analyse two six month sets of data collected from a vertical profiler on Ocean Networks Canada's NEPTUNE observatory over the summer and early fall of 2012 and 2014. The profiler is in 400 m of water on the upper slope of the continental shelf. The site is away from direct influence of canyons, but is in a region of strong internal tide generation. Both seasonally varying semidiurnal internal tidal currents and diurnal shelf waves are observed. The near surface mean flow is weak and seasonally alternates between the California and Alaskan Currents. Mid-depth waters are influenced by the poleward flowing Californian undercurrent and the deep waters by seasonally varying wind-driven Ekman transport. The profiling package consists of a CTD, an oxygen optode, a pCO2 sensor, Chlorophyll fluorometer/turbidity, CDOM and is co-located with an upward-looking bottom-mounted 75kHz ADCP that measures currents to 30 m below sea surface. With these first deep-sea profiled time series measurements of pCO2, we endeavor to model how the local physical dynamics exert control over the variability of water properties over the slope and shelf and what the variability of the non-conservative tracers of pCO2 and O2 can tell us about the biogeochemistry of the region.

Mixed layer warming-deepening in the Mediterranean Sea and its effect on the marine environment

NASA Astrophysics Data System (ADS)

Rivetti, Irene; Boero, Ferdinando; Fraschetti, Simonetta; Zambianchi, Enrico; Lionello, Piero

2015-04-01

This work aims at investigating the evolution of the ocean mixed layer in the Mediterranean Sea and linking it to the occurrence of mass mortalities of benthic invertebrates. The temporal evolution of selected parameters describing the mixed layer and the seasonal thermocline is provided for the whole Mediterranean Sea for spring, summer and autumn and for the period 1945-2011. For this analysis all temperature profiles collected in the basin with bottles, Mechanical Bathy-Thermographs (MBT), eXpendable Bathy-Thermographs (XBT), and Conductivity-Temperature-Depth (CTD) have been used (166,990). These data have been extracted from three public sources: the MEDAR-MEDATLAS, the World Ocean Database 2013 and the MFS-VOS program. Five different methods for estimating the mixed layer depth are compared using temperature profiles collected at the DYFAMED station in the Ligurian Sea and one method, the so-called three-segment method, has been selected for a systematic analysis of the evolution of the uppermost part of the whole Mediterranean Sea. This method approximates the upper water column with three segments representing mixed layer, thermocline and deep layer and has shown to be the most suitable method for capturing the mixed layer depth for most shapes of temperature profiles. Mass mortalities events of benthic invertebrates have been identified by an extensive search of all data bases in ISI Web of Knowledge considering studies published from 1945 to 2011. Studies reporting the geographical coordinates, the timing of the events, the species involved and the depth at which signs of stress occurred have been considered. Results show a general increase of thickness and temperature of the mixed layer, deepening and cooling of the thermocline base in summer and autumn. Possible impacts of these changes are mass mortalities events of benthic invertebrates that have been documented since 1983 mainly in summer and autumn. It is also shown that most mass mortalities occurred in months with anomalously high mixed layer depth temperature leading to the conclusion that warming of upper Mediterranean Sea has allowed interannual temperature variability to reach environmental conditions beyond the thermal tolerance of some species.

Water Quality and Plankton in the United States Nearshore Waters of Lake Huron

EPA Science Inventory

We conducted an intensive survey for the US nearshore of Lake Huron along a continuous segment (523 km) from Port Huron Michigan to Detour Passage. A depth contour of 20 m was towed with a CTD, fluorometer, transmissometer, and laser optical plankton counter (LOPC). The continu...

Using Sediment Profile Imagery (SPI) to Quantify ...

EPA Pesticide Factsheets

We present the results of monthly sediment and water quality surveys to evaluate the impact of intermittent, seasonal hypoxia on benthic habitat condition. This study was conducted in the Pensacola Bay (Florida) estuary across nine sites extending from the mouth of the Escambia River down-estuary to the outlet into the Gulf of Mexico. The sites span the full salinity gradient and cover a range of sediment types and dissolved oxygen statuses. Monthly sediment profile imagery (SPI) was captured from each site in conjunction with water column conductivity-temperature-depth (CTD) profiles and sediment grabs to evaluate sediment characteristics and macrobenthic community composition. The results of this study will be used to evaluate the use of SPI to determine effects of water quality on the health of benthic communities in Gulf Coast estuaries. Whereas recent water quality management efforts in Florida (e.g., numeric nutrient criteria, marine dissolved oxygen standard) assumed linkages between dissolved oxygen and aquatic life use attainment based on laboratory tests, SPI methods can potentially provide an assessment of these relationships in realistic field settings. The work presented here is in support of better indicators and endpoints and will help improve quantitative relationships between nutrient pollution and ecosystem condition. The audience that would be interested in this presentation includes scientists and managers from across the southeastern U

High prevalence of eosinophilic esophagitis in patients with inherited connective tissue disorders

PubMed Central

Abonia, J. Pablo; Wen, Ting; Stucke, Emily M.; Grotjan, Tommie; Griffith, Molly S.; Kemme, Katherine A.; Collins, Margaret H.; Putnam, Philip E.; Franciosi, James P.; von Tiehl, Karl F.; Tinkle, Brad T.; Marsolo, Keith A.; Martin, Lisa J.; Ware, Stephanie M.; Rothenberg, Marc E.

2013-01-01

Background Eosinophilic esophagitis (EoE) is an emerging chronic inflammatory disease mediated by immune hypersensitization to multiple foods and strongly associated with atopy and esophageal remodeling. Objective We provide clinical and molecular evidence indicating a high prevalence of EoE in patients with inherited connective tissue disorders (CTDs). Methods We examined the rate of EoE among patients with CTDs and subsequently analyzed esophageal mRNA transcript profiles in patients with EoE with or without CTD features. Results We report a cohort of 42 patients with EoE with a CTD-like syndrome, representing 0.8% of patients with CTDs and 1.3% of patients with EoE within our hospital-wide electronic medical record database and our EoE research registry, respectively. An 8-fold risk of EoE in patients with CTDs (relative risk, 8.1; 95% confidence limit, 5.1-12.9; χ21 = 112.0; P < 10−3) was present compared with the general population. Esophageal transcript profiling identified a distinct subset of genes, including COL8A2, in patients with EoE and CTDs. Conclusion There is a remarkable association of EoE with CTDs and evidence for a differential expression of genes involved in connective tissue repair in this cohort. Thus, we propose stratification of patients with EoE and CTDs into a subset referred to as EoE-CTD. PMID:23608731

Seasonal Ice Zone Reconnaissance Surveys Coordination

DTIC Science & Technology

2014-09-30

profiler (AXCP) ocean velocity shear (Morison), UpTempO buoy measurements of sea surface temperature (SST), sea level atmospheric pressure ( SLP ), and...and prediction…. Steele UpTempO buoy drops for SLP , SST, SSS, & surface velocity Visible and Thermal Images of the SIZ from the Coast Guard...Expendable CTD, AXCP= Air Expendable Current Profiler, SLP = Sea Level atmospheric Pressure, SST= Seas Surface Temperature, A/C= aircraft, SIC=Sea Ice

XBT Fall-rate study in the Southern Ocean

NASA Astrophysics Data System (ADS)

Ribeiro, N.; Mata, M. M.; Azevedo, J. L.

2016-02-01

Several studies have observed a more prominent warming of the Southern Ocean when compared to other ocean regions of the world in response to global climate change. However, the vast majority of available temperature data for that region is composed by eXpendable BathyTermographers profiles (XBTs). These probes are not equipped with a pressure sensor and thus do not measure depth directly. Depth is inferred by a fall-rate equation offered by the manufacturer that does not seem to adequately represent the extremely cold and high viscosity conditions of the region. Probes fall slower than expected and thus lead to an overestimation in heat content for those areas. In this study, a set of 850 collocated XBT (DB/T7 type) and CTD stations obtained from World Ocean Database (2013) and separated by a maximum distance of 12.5 nm and 10 hours is used. Those pairs are used to identify and quantify the depth errors in the XBT's temperature profiles, proposing a regional equation correction able to represent the peculiarities of the region. Hanawa et al. (1995) and Cheng et al. (2014) correction methods were applied to the dataset, with the latter producing better results. For the pairs in Drake Passage (151), South of Africa (244) and South of Tasmania (455), we found the ideal A coefficients to change by -0.88%, -1.4% and -2.2% from the original values, respectively. When a temperature profile is more homogeneous, there is no significant change if different values of B are used, which was proven to be true since they were .0021 for Drake Passage and .0020 for the other chokings. The ideal fall-rate equation for the Southern Ocean was determined using all pairs, being defined as instead of the proposed by the manufacturer. Overall, the results further support the hypothesis of a regional dependence of the XBT fall-rate on water temperature, and suggest the need of developing a bias correction scheme specific for the polar regions.

Field Results for an Arctic AUV Designed for Characterizing Circulation and Ice Thickness

NASA Astrophysics Data System (ADS)

Bellingham, J. G.; Kirkwood, W. J.; Tervalon, N.; Cokelet, E.; Thomas, H.; Sibenac, M.; Gashler, D.; McEwen, R.; Henthorn, R.; Shane, F.; Osborn, D. J.; Johnson, K.; Overland, J.; Stein, P.; Bahlavouni, A.; Anderson, D.

2002-12-01

An Autonomous Underwater Vehicle designed for operation at high latitudes and under ice completed its first Arctic field tests from the USCGC Healy in fall of 2001. The ALTEX AUV has been under development since 1998, and is being created to provide: unprecedented endurance, ability to navigate at high latitudes, a depth rating of 1500 to 4500 meters depending on payload, and the capability to relay data through the ice to satellites via data buoys. The AUV's initial applications are focused on tracking the warm Atlantic Layer inflow - the primary source of seawater to the Arctic Ocean. Consequently the primary payloads are twin pumped CTD systems. Oxygen and nitrate sensors provide the ability to use NO as a tracer. An ice profiling sonar allows the AUV to estimate the ice thickness in real-time and is designed to generate high quality post-processed ice draft data comparable to that collected through the SCICEX program. The experiments in October aboard the USCGC Healy generated numerous water column and under-ice data sets. Traditional ship-based CTD operations were used to provide a comparison data set for AUV water column measurements. The post-processed ice draft results show reasonable ice profiles and have the potential, when combined with other science data collected, to shed some additional light on upper water column processes in ice-covered regions. Cruise results include: operating the AUV from the USCGC Healy in the ice pack, demonstrating inertial navigation system performance, obtaining oceanographic sections with the AUV, obtaining ice draft measurements with an AUV born sonar, and testing the data-buoy system. This work is supported by the National Science Foundation under grant NSF-OPP 9910290. The Packard Foundation and the Office of Naval Research have also provided support. The project was initiated under the National Ocean Partnership Program under contract N00014-98-1-0814.

The Miniaturized Autonomous Moored Profiler

DTIC Science & Technology

2004-07-20

power sleep mode. All collected data is stored on a flashcard memory module for later retrieval or remote transmission. With the optical telemetry...board flashcard for later retrieval or remote transmission. Although the descent operation ultimately depends upon the cable-pay, the CTD remains on

Seasonal cycle of oceanic mixed layer and upper-ocean heat fluxes in the Mediterranean Sea from in-situ observations.

NASA Astrophysics Data System (ADS)

Houpert, Loïc; Testor, Pierre; Durrieu de Madron, Xavier; Estournel, Claude; D'Ortenzio, Fabrizio

2013-04-01

Heat fluxes across the ocean-atmosphere interface play a crucial role in the upper turbulent mixing. The depth reached by this turbulent mixing is indicated by an homogenization of seawater properties in the surface layer, and is defined as the Mixed Layer Depth (MLD). The thickness of the mixed layer determines also the heat content of the layer that directly interacts with the atmosphere. The seasonal variability of these air-sea fluxes is crucial in the calculation of heat budget. An improvement in the estimate of these fluxes is needed for a better understanding of the Mediterranean ocean circulation and climate, in particular in Regional Climate Models. There are few estimations of surface heat fluxes based on oceanic observations in the Mediterranean, and none of them are based on mixed layer observations. So, we proposed here new estimations of these upper-ocean heat fluxes based on mixed layer. We present high resolution Mediterranean climatology (0.5°) of the mean MLD based on a comprehensive collection of temperature profiles of last 43 years (1969-2012). The database includes more than 150,000 profiles, merging CTD, XBT, ARGO Profiling floats, and gliders observations. This dataset is first used to describe the seasonal cycle of the mixed layer depth on the whole Mediterranean on a monthly climatological basis. Our analysis discriminates several regions with coherent behaviors, in particular the deep water formation sites, characterized by significant differences in the winter mixing intensity. Heat storage rates (HSR) were calculated as the time rate of change of the heat content integrated from the surface down to a specific depth that is defined as the MLD plus an integration constant. Monthly climatology of net heat flux (NHF) from ERA-Interim reanalysis was balanced by the 1°x1° resolution heat storage rate climatology. Local heat budget balance and seasonal variability in the horizontal heat flux are then discussed by taking into account uncertainties, due to errors in monthly value estimation and to intra-annual and inter-annual variability.

Blooms and subsurface phytoplankton layers on the Scotian Shelf: Insights from profiling gliders

NASA Astrophysics Data System (ADS)

Ross, Tetjana; Craig, Susanne E.; Comeau, Adam; Davis, Richard; Dever, Mathieu; Beck, Matthew

2017-08-01

Understanding how phytoplankton respond to their physical environment is key to predicting how bloom dynamics might change under future climate change scenarios. Phytoplankton are at the base of most marine food webs and play an important role in drawing CO2 out of the atmosphere. Using nearly 5 years of simultaneous CTD, irradiance, chlorophyll a fluorescence and optical backscattering observations obtained from Slocum glider missions, we observed the subsurface phytoplankton populations across the Scotian Shelf, near Halifax (Nova Scotia, Canada) along with their physical environment. Bloom conditions were observed in each of the 5 springs, with the average chlorophyll in the upper 60 m of water generally exceeding 3 mg m- 3. These blooms occurred when the upper water column stratification was at its lowest, in apparent contradiction of the critical depth hypothesis. A subsurface chlorophyll layer was observed each summer at about 30 m depth, which was below the base of the mixed layer. This subsurface layer lasted 3-4 months and contained, on average, 1/4 of the integrated water column chlorophyll found during the spring bloom. This suggests that a significant portion of the primary productivity over the Scotian Shelf occurs at depths that cannot be observed by satellites-highlighting the importance of including subsurface observations in the monitoring of future changes to primary productivity in the ocean.

Maintenance of Coastal Surface Blooms by Surface Temperature Stratification and Wind Drift

PubMed Central

Ruiz-de la Torre, Mary Carmen; Maske, Helmut; Ochoa, José; Almeda-Jauregui, César O.

2013-01-01

Algae blooms are an increasingly recurrent phenomenon of potentially socio-economic impact in coastal waters globally and in the coastal upwelling region off northern Baja California, Mexico. In coastal upwelling areas the diurnal wind pattern is directed towards the coast during the day. We regularly found positive Near Surface Temperature Stratification (NSTS), the resulting density stratification is expected to reduce the frictional coupling of the surface layer from deeper waters and allow for its more efficient wind transport. We propose that the net transport of the top layer of approximately 2.7 kilometers per day towards the coast helps maintain surface blooms of slow growing dinoflagellate such as Lingulodinium polyedrum. We measured: near surface stratification with a free-rising CTD profiler, trajectories of drifter buoys with attached thermographs, wind speed and direction, velocity profiles via an Acoustic Doppler Current Profiler, Chlorophyll and cell concentration from water samples and vertical migration using sediment traps. The ADCP and drifter data agree and show noticeable current shear within the first meters of the surface where temperature stratification and high cell densities of L. polyedrum were found during the day. Drifters with 1m depth drogue moved towards the shore, whereas drifters at 3 and 5 m depth showed trajectories parallel or away from shore. A small part of the surface population migrated down to the sea floor during night thus reducing horizontal dispersion. The persistent transport of the surface bloom population towards shore should help maintain the bloom in favorable environmental conditions with high nutrients, but also increasing the potential socioeconomic impact of the blooms. The coast wise transport is not limited to blooms but includes all dissolved and particulate constituents in surface waters. PMID:23593127

Maintenance of coastal surface blooms by surface temperature stratification and wind drift.

PubMed

Ruiz-de la Torre, Mary Carmen; Maske, Helmut; Ochoa, José; Almeda-Jauregui, César O

2013-01-01

Algae blooms are an increasingly recurrent phenomenon of potentially socio-economic impact in coastal waters globally and in the coastal upwelling region off northern Baja California, Mexico. In coastal upwelling areas the diurnal wind pattern is directed towards the coast during the day. We regularly found positive Near Surface Temperature Stratification (NSTS), the resulting density stratification is expected to reduce the frictional coupling of the surface layer from deeper waters and allow for its more efficient wind transport. We propose that the net transport of the top layer of approximately 2.7 kilometers per day towards the coast helps maintain surface blooms of slow growing dinoflagellate such as Lingulodinium polyedrum. We measured: near surface stratification with a free-rising CTD profiler, trajectories of drifter buoys with attached thermographs, wind speed and direction, velocity profiles via an Acoustic Doppler Current Profiler, Chlorophyll and cell concentration from water samples and vertical migration using sediment traps. The ADCP and drifter data agree and show noticeable current shear within the first meters of the surface where temperature stratification and high cell densities of L. polyedrum were found during the day. Drifters with 1m depth drogue moved towards the shore, whereas drifters at 3 and 5 m depth showed trajectories parallel or away from shore. A small part of the surface population migrated down to the sea floor during night thus reducing horizontal dispersion. The persistent transport of the surface bloom population towards shore should help maintain the bloom in favorable environmental conditions with high nutrients, but also increasing the potential socioeconomic impact of the blooms. The coast wise transport is not limited to blooms but includes all dissolved and particulate constituents in surface waters.

4-D Current Experiment Using AUV and HF-Radar

DTIC Science & Technology

1998-01-01

the NICOP project at FAU. RESULTS Measurements of bathymetry, current and CTD measurements were acquired in shallow water on 5 and 11 Dec 97 in a lawn ... mower pattern (An et al., 1998). These surveys were conducted over about a 3 h period at a constant water depth of 7 m in the vicinity of an ADCP. On

Application of acoustic-Doppler current profiler and expendable bathythermograph measurements to the study of the velocity structure and transport of the Gulf Stream

NASA Technical Reports Server (NTRS)

Joyce, T. M.; Dunworth, J. A.; Schubert, D. M.; Stalcup, M. C.; Barbour, R. L.

1988-01-01

The degree to which Acoustic-Doppler Current Profiler (ADCP) and expendable bathythermograph (XBT) data can provide quantitative measurements of the velocity structure and transport of the Gulf Stream is addressed. An algorithm is used to generate salinity from temperature and depth using an historical Temperature/Salinity relation for the NW Atlantic. Results have been simulated using CTD data and comparing real and pseudo salinity files. Errors are typically less than 2 dynamic cm for the upper 800 m out of a total signal of 80 cm (across the Gulf Stream). When combined with ADCP data for a near-surface reference velocity, transport errors in isopycnal layers are less than about 1 Sv (10 to the 6th power cu m/s), as is the difference in total transport for the upper 800 m between real and pseudo data. The method is capable of measuring the real variability of the Gulf Stream, and when combined with altimeter data, can provide estimates of the geoid slope with oceanic errors of a few parts in 10 to the 8th power over horizontal scales of 500 km.

Synoptic eddy-resolving Ocean Surveys over the Slope of the Chukchi Sea 2016 and 2017

NASA Astrophysics Data System (ADS)

Muenchow, A.; Elmer, C.; Badiey, M.; Eickmeier, J.; Ryan, P. A.

2017-12-01

Mild weather and warm waters kept the outer continental shelf of the Chukchi Sea ice-free in 2016 when we conducted ocean surveys as part of the Canada Basin Acoustic Propagation Experiment (CANAPE). We used standard CTD and ADCP profiling systems aboard R/V Sikuliaq to describe ocean density and velocity fields at 3 km scales across and 6 km scales along the slope. Our survey covers 800 km2between the 100-m and 400-m isobaths and resolves the internal Rossby radius of deformation which represents the dominant spatial (or eddy) scale for a density-stratified ocean. Our early November 2016 data revealed Bering Sea Summer Waters with temperatures exceeding 1.0 C at 80-m depth near the 200-m isobath. Three-dimensional distribution of this water and associated density gradients suggests a current to the east. The flow is likely unstable, we speculate, because it spawns eddy-like features that we will describe. We will test this hypothesis with ocean current shear estimated from vessel-mounted ADCP profiles. A similar survey is planned for October 2017, when USCGC Healy will re-visit the area to recover ocean moorings deployed prior to the 2016 surveys.

A snapshot of internal waves and hydrodynamic instabilities in the southern Bay of Bengal

NASA Astrophysics Data System (ADS)

Lozovatsky, Iossif; Wijesekera, Hemantha; Jarosz, Ewa; Lilover, Madis-Jaak; Pirro, Annunziata; Silver, Zachariah; Centurioni, Luca; Fernando, H. J. S.

2016-08-01

Measurements conducted in the southern Bay of Bengal (BoB) as a part of the ASIRI-EBoB Program portray the characteristics of high-frequency internal waves in the upper pycnocline as well as the velocity structure with episodic events of shear instability. A 20 h time series of CTD, ADCP, and acoustic backscatter profiles down to 150 m as well as temporal CTD measurements in the pycnocline at z = 54 m were taken to the east of Sri Lanka. Internal waves of periods ˜10-40 min were recorded at all depths below a shallow (˜20-30 m) surface mixed layer in the background of an 8 m amplitude internal tide. The absolute values of vertical displacements associated with high-frequency waves followed the Nakagami distribution with a median value of 2.1 m and a 95% quintile 6.5 m. The internal wave amplitudes are normally distributed. The tails of the distribution deviate from normality due to episodic high-amplitude displacements. The sporadic appearance of internal waves with amplitudes exceeding ˜5 m usually coincided with patches of low Richardson numbers, pointing to local shear instability as a possible mechanism of internal-wave-induced turbulence. The probability of shear instability in the summer BoB pycnocline based on an exponential distribution of the inverse Richardson number, however, appears to be relatively low, not exceeding 4% for Ri < 0.25 and about 10% for Ri < 0.36 (K-H billows). The probability of the generation of asymmetric breaking internal waves and Holmboe instabilities is above ˜25%.

Arctic Ocean outflow and glacier-ocean interactions modify water over the Wandel Sea shelf (northeastern Greenland)

NASA Astrophysics Data System (ADS)

Dmitrenko, Igor A.; Kirillov, Sergey A.; Rudels, Bert; Babb, David G.; Toudal Pedersen, Leif; Rysgaard, Søren; Kristoffersen, Yngve; Barber, David G.

2017-12-01

The first-ever conductivity-temperature-depth (CTD) observations on the Wandel Sea shelf in northeastern Greenland were collected in April-May 2015. They were complemented by CTDs taken along the continental slope during the Norwegian FRAM 2014-2015 drift. The CTD profiles are used to reveal the origin of water masses and interactions with ambient water from the continental slope and the tidewater glacier outlet. The subsurface water is associated with the Pacific water outflow from the Arctic Ocean. The underlying halocline separates the Pacific water from a deeper layer of polar water that has interacted with the warm Atlantic water outflow through the Fram Strait, recorded below 140 m. Over the outer shelf, the halocline shows numerous cold density-compensated intrusions indicating lateral interaction with an ambient polar water mass across the continental slope. At the front of the tidewater glacier outlet, colder and turbid water intrusions were observed at the base of the halocline. On the temperature-salinity plots these stations indicate a mixing line that is different from the ambient water and seems to be conditioned by the ocean-glacier interaction. Our observations of Pacific water are set within the context of upstream observations in the Beaufort Sea and downstream observations from the Northeast Water Polynya, and clearly show the modification of Pacific water during its advection across the Arctic Ocean. Moreover, ambient water over the Wandel Sea slope shows different thermohaline structures indicating the different origin and pathways of the on-shore and off-shore branches of the Arctic Ocean outflow through the western Fram Strait.

Storm-induced water dynamics and thermohaline structure at the tidewater Flade Isblink Glacier outlet to the Wandel Sea (NE Greenland)

NASA Astrophysics Data System (ADS)

Kirillov, Sergei; Dmitrenko, Igor; Rysgaard, Søren; Babb, David; Toudal Pedersen, Leif; Ehn, Jens; Bendtsen, Jørgen; Barber, David

2017-11-01

In April 2015, an ice-tethered conductivity-temperature-depth (CTD) profiler and a down-looking acoustic Doppler current profiler (ADCP) were deployed from the landfast ice near the tidewater glacier terminus of the Flade Isblink Glacier in the Wandel Sea, NE Greenland. The 3-week time series showed that water dynamics and the thermohaline structure were modified considerably during a storm event on 22-24 April, when northerly winds exceeded 15 m s-1. The storm initiated downwelling-like water dynamics characterized by on-shore water transport in the surface (0-40 m) layer and compensating offshore flow at intermediate depths. After the storm, currents reversed in both layers, and the relaxation phase of downwelling lasted ˜ 4 days. Although current velocities did not exceed 5 cm s-1, the enhanced circulation during the storm caused cold turbid intrusions at 75-95 m depth, which are likely attributable to subglacial water from the Flade Isblink Ice Cap. It was also found that the semidiurnal periodicities in the temperature and salinity time series were associated with the lunar semidiurnal tidal flow. The vertical structure of tidal currents corresponded to the first baroclinic mode of the internal tide with a velocity minimum at ˜ 40 m. The tidal ellipses rotate in opposite directions above and below this depth and cause a divergence of tidal flow, which was observed to induce semidiurnal internal waves of about 3 m height at the front of the glacier terminus. Our findings provide evidence that shelf-basin interaction and tidal forcing can potentially modify coastal Wandel Sea waters even though they are isolated from the atmosphere by landfast sea ice almost year-round. The northerly storms over the continental slope cause an enhanced circulation facilitating a release of cold and turbid subglacial water to the shelf. The tidal flow may contribute to the removal of such water from the glacial terminus.

Upper ocean mixing processes and their impact on the mixed layer heat balance during the onset of the Atlantic Cold Tongue.

NASA Astrophysics Data System (ADS)

Dengler, M.; Brandt, P.; McPhaden, M. J.; Thomsen, S.; Krahmann, G.; Fischer, T.; Freitag, P.; Hummels, R.

2012-04-01

An extensive measurement program within the Atlantic Cold Tongue (ACT) region was carried out during the ACT onset in boreal summer 2011. During two consecutive cruises shipboard microstructure profiles, conductivity-temperature-depth-O2 (CTD-O2) profiles and shipboard velocity profiles were collected between mid-May and mid-July. The shipboard measurements were complemented by a Glider swarm experiment during which 5400 CTD-O2 profiles were collected along specified transects within the ACT region. One of those Gliders was equipped with a MicroRider turbulence package and collected a 5-week microstructure time series of about hourly-resolution in the center of the cold tongue on the equator at 10°W. The MicroRider/Glider package was circling a PIRATA mooring from which additionally high-resolution acoustic Doppler current profiles are available for this time period to allow analysis of the background conditions. In this contribution we use a subset from the above data to detail mixing processes in the upper stratified ocean and describe the background conditions favoring enhanced mixing. From end of May to mid-July, sea surface temperature decreased from 26°C to below 22°C at 10°W. During the whole period of autonomous microstructure observations, strong bursts of turbulence were observed extending from the mixed layer into the upper thermocline. These bursts lasted for 3-5 hours and were found to penetrate to about 30m below the base of the mixed layer. They were observed to occur predominately during night-time while during day-time they were less frequent. Dissipation rates of turbulent kinetic energy (ɛ) during these bursts were above 3x10-6Wkg-1 in the upper stratified water column and turbulent eddy diffusivities (Kρ) often reached 1x10-3m2s-1. The data set suggests that strength and frequency of occurrence of the turbulent bursts is modulated by the presents of Tropical Instability Waves which additionally enhance background shear at the equator. The presents of internal waves having frequencies close to the buoyancy frequency during enhanced mixing events will be discussed. From the first 6 days of microstructure data, a diapycnal heat flux divergence from the mixed layer into the upper stratified ocean of 80Wm-2 was inferred. Other contributions to the mixed layer heat balance will be examined to evaluate their relevance during ACT onset.

Hydrothermal venting on the flanks of Heard and McDonald islands, southern Indian Ocean

NASA Astrophysics Data System (ADS)

Lupton, J. E.; Arculus, R. J.; Coffin, M.; Bradney, A.; Baumberger, T.; Wilkinson, C.

2017-12-01

Heard Island and the nearby McDonald Islands are two sites of active volcanism associated with the so-called Kerguelen mantle plume or hot spot. In fact, it has been proposed that the Kerguelen hot spot is currently located beneath Heard Island. During its maiden maximum endurance voyage (IN2016_V01), the recently commissioned Australian R/V Investigator conducted a detailed bathymetric and water column survey of the waters around Heard Island and the McDonald Islands as well as other sites on the Kerguelen Plateau. Some 50 hydrographic profiles were completed using the CTD/rosette system equipped with trace metal sampling and a nephelometer for suspended particle concentrations. In addition to the hydrographic profiles, 244 bubble plumes were detected in the vicinity of the Heard and McDonald Islands using the ship's multibeam system. It is thought that the bubble plumes observed on sea knolls and other seafloor surrounding the McDonald Islands are likely hydrothermal in origin, while plumes northeast of Heard Island may be biogenic methane from cold seeps. At 29 of the hydrographic stations water samples for helium isotope measurements were drawn from the CTD rosette and hermetically sealed into copper tubing for subsequent shorebased mass spectrometer and gas chromatograph analysis. In this paper we report results for 3He/4He ratios and CO2 and CH4 concentrations in water samples collected with the CTD/rosette, and discuss how these results are correlated with suspended particle concentrations and temperature anomalies.

Evidence for the existence of Persian Gulf Water and Red Sea Water in the Bay of Bengal

NASA Astrophysics Data System (ADS)

Jain, Vineet; Shankar, D.; Vinayachandran, P. N.; Kankonkar, A.; Chatterjee, Abhisek; Amol, P.; Almeida, A. M.; Michael, G. S.; Mukherjee, A.; Chatterjee, Meenakshi; Fernandes, R.; Luis, R.; Kamble, Amol; Hegde, A. K.; Chatterjee, Siddhartha; Das, Umasankar; Neema, C. P.

2017-05-01

The high-salinity water masses that originate in the North Indian Ocean are Arabian Sea High-Salinity Water (ASHSW), Persian Gulf Water (PGW), and Red Sea Water (RSW). Among them, only ASHSW has been shown to exist in the Bay of Bengal. We use CTD data from recent cruises to show that PGW and RSW also exist in the bay. The presence of RSW is marked by a deviation of the salinity vertical profile from a fitted curve at depths ranging from 500 to 1000 m; this deviation, though small (of the order of 0.005 psu and therefore comparable to the CTD accuracy of 0.003 psu), is an order of magnitude larger than the 0.0003 psu fluctuations associated with the background turbulence or instrument noise in this depth regime, allowing us to infer the existence of RSW throughout the bay. PGW is marked by the presence of a salinity maximum at 200-450 m; in the southwestern bay, PGW can be distinguished from the salinity maximum due to ASHSW because of the intervening Arabian Sea Salinity Minimum. This salinity minimum and the maximum associated with ASHSW disappear east and north of the south-central bay (85°E, 8°N) owing to mixing between the fresher surface waters that are native to the bay (Bay of Bengal Water or BBW) with the high-salinity ASHSW. Hence, ASHSW is not seen as a distinct water mass in the northern and eastern bay and the maximum salinity over most of the bay is associated with PGW. The surface water over most of the bay is therefore a mixture of ASHSW and the low-salinity BBW. As a corollary, we can also infer that the weak oxygen peak seen within the oxygen-minimum zone in the bay at a depth of 250-400 m is associated with PGW. The hydrographic data also show that these three high-salinity water masses are advected into the bay by the Summer Monsoon Current, which is seen to be a deep current extending to 1000 m. These deep currents extend into the northern bay as well, providing a mechanism for spreading ASHSW, PGW, and RSW throughout the bay.

Seasonal, Oceanographic and Atmospheric Drivers of Diving Behaviour in a Temperate Seal Species Living in the High Arctic

PubMed Central

Blanchet, Marie-Anne; Lydersen, Christian; Ims, Rolf A.; Kovacs, Kit M.

2015-01-01

The harbour seal (Phoca vitulina) population in Svalbard marks the northernmost limit of the species’ range. This small population experiences environmental extremes in sea and air temperatures, sea ice cover and also in light regime for this normally temperate species. This study deployed Conductivity Temperature Depth Satellite Relay Data Loggers (CTD-SRDLs) on 30 adult and juvenile harbour seals in 2009 and 2010 to study their foraging behaviour across multiple seasons. A total of 189,104 dives and 16,640 CTD casts (mean depth 72 m ± 59) were recorded. Individuals dove to a mean depth of 41 m ± 24 with a maximum dive depth range of 24 – 403 m. Dives lasted on average 204 sec ± 120 with maximum durations ranging between 240 – 2,220 sec. Average daily depth and duration of dives, number of dives, time spent diving and dive time/surface time were influenced by date, while sex, age, sea-ice concentration and their interactions were not particularly influential. Dives were deeper (~150 m), longer (~480 sec), less numerous (~250 dives/day) and more pelagic during the winter/early spring compared to the fall and animals spent proportionally less time at the bottom of their dives during the winter. Influxes of warm saline water, corresponding to Atlantic Water characteristics, were observed intermittently at depths ~100 m during both winters in this study. The seasonal changes in diving behaviour were linked to average weekly wind stresses from the north or north-east, which induced upwelling events onto the shelf through offshore Ekman transport. During these events the shelf became flooded with AW from the West Spitsbergen Current, which presumably brought Atlantic fish species close to shore and within the seals’ foraging depth-range. Predicted increased in the influx of AW in this region are likely going to favour the growth and geographic expansion of this harbour seal population in the future. PMID:26196289

Autonomous Research Vessels for Adaptive Upper-Ocean Process Studies

DTIC Science & Technology

2014-09-30

system with the goal  of extending  its mission robustness,  adaptabilit and science capabilities beyond that  of the   Arduino -­‐ based ones... measure the interplay between these finescale dynamics and turbulence, which ultimately drives  the  irreversible  heat/freshwater  transports...profiling in Greenland  Fjords. acquiring CTD cast (and ADCP profiles) within m of a Greenland iceberg.APPROACH: Our first ARV (ARV Rob) was based on

Mean hydrography on the continental shelf from 26 repeat glider deployments along Southeastern Australia

NASA Astrophysics Data System (ADS)

Schaeffer, Amandine; Roughan, Moninya; Austin, Tim; Everett, Jason D.; Griffin, David; Hollings, Ben; King, Edward; Mantovanelli, Alessandra; Milburn, Stuart; Pasquer, Benedicte; Pattiaratchi, Charitha; Robertson, Robin; Stanley, Dennis; Suthers, Iain; White, Dana

2016-08-01

Since 2008, 26 glider missions have been undertaken along the continental shelf of southeastern Australia. Typically these missions have spanned the continental shelf on the inshore edge of the East Australian Current from 29.5-33.5°S. This comprehensive dataset of over 33,600 CTD profiles from the surface to within 10 m of the bottom in water depths ranging 25-200 m provides new and unprecedented high resolution observations of the properties of the continental shelf waters adjacent to a western boundary current, straddling the region where it separates from the coast. The region is both physically and biologically significant, and is also in a hotspot of ocean warming. We present gridded mean fields for temperature, salinity and density, but also dissolved oxygen and chlorophyll-a fluorescence indicative of phytoplankton biomass. This data will be invaluable for understanding shelf stratification, circulation, biophysical and bio-geochemical interactions, as well as for the validation of high-resolution ocean models or serving as teaching material.

Analysis of the spatio-temporal variability of seawater quality in the southeastern Arabian Gulf.

PubMed

Mezhoud, Nahla; Temimi, Marouane; Zhao, Jun; Al Shehhi, Maryam Rashed; Ghedira, Hosni

2016-05-15

In this study, seawater quality measurements, including salinity, sea surface temperature (SST), chlorophyll-a (Chl-a), Secchi disk depth (SDD), pH, and dissolved oxygen (DO), were made from June 2013 to November 2014 at 52 stations in the southeastern Arabian Gulf. Significant variability was noticed for all collected parameters. Salinity showed a decreasing trend, and Chl-a, DO, pH, and SDD demonstrated increasing trends from shallow onshore stations to deep offshore ones, which could be attributed to variations of ocean circulation and meteorological conditions from onshore to offshore waters, and the likely effects of desalination plants along the coast. Salinity and temperature were high in summer and low in winter while Chl-a, SDD, pH, and DO indicated an opposite trend. The CTD profiles showed vertically well-mixed structures. Qualitative analysis of phytoplankton showed a high diversity of species without anomalous species found except in Ras Al Khaimah stations where diatoms were the dominating ones. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mean hydrography on the continental shelf from 26 repeat glider deployments along Southeastern Australia.

PubMed

Schaeffer, Amandine; Roughan, Moninya; Austin, Tim; Everett, Jason D; Griffin, David; Hollings, Ben; King, Edward; Mantovanelli, Alessandra; Milburn, Stuart; Pasquer, Benedicte; Pattiaratchi, Charitha; Robertson, Robin; Stanley, Dennis; Suthers, Iain; White, Dana

2016-08-30

Since 2008, 26 glider missions have been undertaken along the continental shelf of southeastern Australia. Typically these missions have spanned the continental shelf on the inshore edge of the East Australian Current from 29.5-33.5°S. This comprehensive dataset of over 33,600 CTD profiles from the surface to within 10 m of the bottom in water depths ranging 25-200 m provides new and unprecedented high resolution observations of the properties of the continental shelf waters adjacent to a western boundary current, straddling the region where it separates from the coast. The region is both physically and biologically significant, and is also in a hotspot of ocean warming. We present gridded mean fields for temperature, salinity and density, but also dissolved oxygen and chlorophyll-a fluorescence indicative of phytoplankton biomass. This data will be invaluable for understanding shelf stratification, circulation, biophysical and bio-geochemical interactions, as well as for the validation of high-resolution ocean models or serving as teaching material.

A Simple Parameterization of Mixing of Passive Scalars in Turbulent Flows

NASA Astrophysics Data System (ADS)

Nithianantham, Ajithshanthar; Venayagamoorthy, Karan

2015-11-01

A practical model for quantifying the turbulent diascalar diffusivity is proposed as Ks = 1 . 1γ'LTk 1 / 2 , where LT is defined as the Thorpe length scale, k is the turbulent kinetic energy and γ' is one-half of the mechanical to scalar time scale ratio, which was shown by previous researchers to be approximately 0 . 7 . The novelty of the proposed model lies in the use of LT, which is a widely used length scale in stably stratified flows (almost exclusively used in oceanography), for quantifying turbulent mixing in unstratified flows. LT can be readily obtained in the field using a Conductivity, Temperature and Depth (CTD) profiler. The turbulent kinetic energy is mostly contained in the large scales of the flow field and hence can be measured in the field or modeled in numerical simulations. Comparisons using DNS data show remarkably good agreement between the predicted and exact diffusivities. Office of Naval Research and National Science Foundation.

An analysis of the clinical features of lung cancer in patients with connective tissue diseases.

PubMed

Saijo, Atsuro; Hanibuchi, Masaki; Goto, Hisatsugu; Toyoda, Yuko; Tezuka, Toshifumi; Nishioka, Yasuhiko

2017-03-01

Patients with connective tissue diseases (CTDs) are at increased risk for lung cancer (LC); interstitial lung disease (ILD) is a common form of organ dysfunction in cases of CTD. However, the influence of ILD on the treatment and prognosis in LC patients with CTD is unclear. Between January 2010 and December 2014, 27 patients among all patients with CTD at our institution were diagnosed with primary LC. We retrospectively analyzed the clinical features, treatment modalities, and outcomes of these patients, and evaluated the potential prognostic factors. Forty-four LC patients without CTD were also analyzed as a control cohort. LC patients with CTD had a significantly higher incidence of ILD as a complication compared with those without CTD (52% and 14%, respectively). CTD-associated ILD (CTD-ILD) at diagnosis was associated with significantly worse survival in LC patients with CTD. Multivariate analysis demonstrated that the complication of CTD-ILD was an independent poor prognostic factor in LC patients with CTD. The incidence of acute exacerbation (AE) of CTD-ILD was 21% among LC patients with CTD, and all of these patients died despite intensive treatment including high-dose corticosteroids. The restrictions in curative therapy for LC due to the presence of ILD and AE of CTD-ILD were thought to be the major reasons for the poor outcome. LC patients with CTD had a high prevalence of ILD, and the presence of CTD-ILD was significantly associated with poor prognosis. Copyright © 2017 The Japanese Respiratory Society. Published by Elsevier B.V. All rights reserved.

Systematic heat flow measurements across the Wagner Basin, northern Gulf of California

NASA Astrophysics Data System (ADS)

Neumann, Florian; Negrete-Aranda, Raquel; Harris, Robert N.; Contreras, Juan; Sclater, John G.; González-Fernández, Antonio

2017-12-01

A primary control on the geodynamics of rifting is the thermal regime. To better understand the geodynamics of rifting in the northern Gulf of California we systematically measured heat-flow across the Wagner Basin, a tectonically active basin that lies near the southern terminus of the Cerro Prieto fault. The heat flow profile is 40 km long, has a nominal measurement spacing of ∼1 km, and is collocated with a seismic reflection profile. Heat flow measurements were made with a 6.5-m violin-bow probe. Although heat flow data were collected in shallow water, where there are significant temporal variations in bottom water temperature, we use CTD data collected over many years to correct our measurements to yield accurate values of heat flow. After correction for bottom water temperature, the mean and standard deviation of heat flow across the western, central, and eastern parts of the basin are 220 ± 60, 99 ± 14, 889 ± 419 mW m-2, respectively. Corrections for sedimentation would increase measured heat flow across the central part of basin by 40 to 60%. We interpret the relatively high heat flow and large variability on the western and eastern flanks in terms of upward fluid flow at depth below the seafloor, whereas the lower and more consistent values across the central part of the basin are suggestive of conductive heat transfer. Moreover, heat flow across the central basin is consistent with gabbroic underplating at a depth of 15 km and suggests that continental rupture here has not gone to completion.

Ocean Color Patterns Help to Predict Depth of Optical Layers in Coastal Marine Waters

DTIC Science & Technology

2012-02-09

Space Center, NASA, MS 39529, USA 3Institut des Sciences de la Mer, Universite du Quebec a Rimouski, Canada, *E-mail: martin_montes@uqar. qc. ca...depth was derived from CTD variables (i.e., temperature and conductivity without pressure correction) and using the standard UNESCO polynomial equation... la y *,es^ S Si es ti m at ed nt er re y B a n an d up ), th e up pe r te d in w h i 5112 ^ "a :*J ? tf?^ •a Mis a a •S M ^ « a fo

A Quantitative Approach to Determine Analogous Areas Using Environmental Parameters

DTIC Science & Technology

2008-03-01

degrees Celsius COADS Comprehensive Ocean - Atmosphere Data Set CONUS Continental United States CTD Conductivity/Temperature/Depth probe...consolidation of a marine database. Out of this effort came the Comprehensive Ocean - Atmosphere Data Set (COADS). The original 17 data sets were...National Oceanic and Atmospheric Administration (NOAA) has compiled a database of total sediment thickness of the global oceans and seas. These data are

Fission yeast RNA triphosphatase reads an Spt5 CTD code

DOE PAGES

Doamekpor, Selom K.; Schwer, Beate; Sanchez, Ana M.; ...

2014-11-20

mRNA capping enzymes are directed to nascent RNA polymerase II (Pol2) transcripts via interactions with the carboxy-terminal domains (CTDs) of Pol2 and transcription elongation factor Spt5. Fission yeast RNA triphosphatase binds to the Spt5 CTD, comprising a tandem repeat of nonapeptide motif TPAWNSGSK. Here we report the crystal structure of a Pct1·Spt5-CTD complex, which revealed two CTD docking sites on the Pct1 homodimer that engage TPAWN segments of the motif. Each Spt5 CTD interface, composed of elements from both subunits of the homodimer, is dominated by van der Waals contacts from Pct1 to the tryptophan of the CTD. The boundmore » CTD adopts a distinctive conformation in which the peptide backbone makes a tight U-turn so that the proline stacks over the tryptophan. We show that Pct1 binding to Spt5 CTD is antagonized by threonine phosphorylation. Our results fortify an emerging concept of an “Spt5 CTD code” in which (i) the Spt5 CTD is structurally plastic and can adopt different conformations that are templated by particular cellular Spt5 CTD receptor proteins; and (ii) threonine phosphorylation of the Spt5 CTD repeat inscribes a binary on–off switch that is read by diverse CTD receptors, each in its own distinctive manner.« less

Fission yeast RNA triphosphatase reads an Spt5 CTD code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doamekpor, Selom K.; Schwer, Beate; Sanchez, Ana M.

mRNA capping enzymes are directed to nascent RNA polymerase II (Pol2) transcripts via interactions with the carboxy-terminal domains (CTDs) of Pol2 and transcription elongation factor Spt5. Fission yeast RNA triphosphatase binds to the Spt5 CTD, comprising a tandem repeat of nonapeptide motif TPAWNSGSK. Here we report the crystal structure of a Pct1·Spt5-CTD complex, which revealed two CTD docking sites on the Pct1 homodimer that engage TPAWN segments of the motif. Each Spt5 CTD interface, composed of elements from both subunits of the homodimer, is dominated by van der Waals contacts from Pct1 to the tryptophan of the CTD. The boundmore » CTD adopts a distinctive conformation in which the peptide backbone makes a tight U-turn so that the proline stacks over the tryptophan. We show that Pct1 binding to Spt5 CTD is antagonized by threonine phosphorylation. Our results fortify an emerging concept of an “Spt5 CTD code” in which (i) the Spt5 CTD is structurally plastic and can adopt different conformations that are templated by particular cellular Spt5 CTD receptor proteins; and (ii) threonine phosphorylation of the Spt5 CTD repeat inscribes a binary on–off switch that is read by diverse CTD receptors, each in its own distinctive manner.« less

Variation of subsurface chlorophyll maximum layer from the vertical profiler and in-situ observation in the eastern coastal region of Korea (the East/Japan Sea)

NASA Astrophysics Data System (ADS)

Son, Y. T.; Chang, K. I.; Nam, S.; Kang, D. J.

2016-02-01

Coastal monitoring buoy (called it as ESROB) has been continually operated to monitor meteorological (wind, air temperature, air pressure, PAR) and oceanic properties (temperature, salinity, current, chlorophyll fluorescence, DO, turbidity) using equipment such as CTD, fluorometer and WQM (Water Quality Monitor) in the eastern coastal region of Korea (the East/Japan Sea) since April 2011. The ESROB produced temporal evolution of physical and biogeochemical parameters of the water column with high resolution of 10 min interval. In order to understand horizontal influence of physical and biogeochemical parameters on variation of subsurface chlorophyll maximum layer (SCM), interdisciplinary in-situ surveys with small R/V in the study area for about week were conducted in June/October 2014 and in May 2015. A wirewalker, a wave-driven vertically profiling platform (Rainville and Pinkel 2001), was also deployed at two points (about 30 m and 80 m water depth) along cross-shore direction with the ESROB for about one or two weeks with in-situ survey durations. The wirewalker was equipped with CTD, turbidity and chlorophyll a fluorometer profiler, which was completed approximately every 3 10 minute depending on sea surface state. The SCM was observed in almost every deployment nearest coast, except for June in 2014, with variation of semi- and diurnal time periods. Temporal evolution of the wirewalker showed that disappearance and reoccurrence of the SCM within the water column in October 2014, which was associated with vertical mixing induced by strong wind stress. Low salinity plume in the surface layer and shoaling of bottom cold water were concurrently observed after homogeneous water column, affecting another condition to the vertical distribution of chlorophyll a in this coastal region. Moreover in-situ observation with densely points and temporal interval for 1 day revealed that distribution with high concentration of chlorophyll a on isopycnal was association with the horizontal local circulation that has influence on stability (vertical stratification and shear) of the water column. Optical and biogeochemical parameter analyzed from the water samples, affecting on the variation of chlorophyll a concentration within the water column, will be also discussed in the presentation of Ocean Science Meeting.

Chemical Fluxes from a Recently Erupted Submarine Volcano on the Mariana Arc

NASA Astrophysics Data System (ADS)

Buck, N. J.; Resing, J. A.; Lupton, J. E.; Larson, B. I.; Walker, S. L.; Baker, E. T.

2016-12-01

While hydrothermal circulation is paramount to the geochemical budget for a wide array of elements, relatively few flux estimates exist in the literature. To date most studies have concentrated on constraining global and vent-field scale inputs originating from ocean spreading ridges. The goal of this study is to directly measure the chemical flux from an active submarine volcano injecting hydrothermal fluids into the surface ocean. Ahyi Seamount, a submarine intraoceanic arc volcano located in the Northern Mariana Islands, has a summit depth <100 m and erupted in May 2014. In November 2014 a hydrothermal plume originating from Ahyi was sampled aboard the R/V Roger Revelle during the Submarine Ring of Fire 2014 Ironman Expedition. Shipboard hull mounted Acoustic Doppler Current Profile data was collected to provide current vector measurements to be used in combination with continuous and discrete CTD data. Towed CTD sections were conducted perpendicular to the current direction - a sampling strategy that optimizes chemical flux estimate calculations by reducing complexities introduced by temporal variability in the speed and direction of plume dispersion. The Ahyi plume had a significant optical backscatter signal accompanied by evidence of reduced chemical species and a lowered pH. It was sampled for He isotopes, CH4, H2, H2S, total CO2, nutrients, TSM and total and dissolved Fe and Mn. Laboratory analyses found enriched concentrations of H2, 3He, CO2 and Fe, consistent with a recent eruption. Preliminary flux calculations estimate a Fe input of 16 mmol s-1. This indicates shallow submarine arc volcanoes are capable of supplying appreciable quantities of Fe into the surface ocean. Further laboratory analyses and calculations to characterize and constrain the fluxes of other chemical constituents are underway.

The evolution of water property in the Mackenzie Bay polynya during Antarctic winter

NASA Astrophysics Data System (ADS)

Xu, Zhixin; Gao, Guoping; Xu, Jianping; Shi, Maochong

2017-10-01

Temperature and salinity profile data, collected by southern elephant seals equipped with autonomous CTD-Satellite Relay Data Loggers (CTD-SRDLs) during the Antarctic wintertime in 2011 and 2012, were used to study the evolution of water property and the resultant formation of the high density water in the Mackenzie Bay polynya (MBP) in front of the Amery Ice Shelf (AIS). In late March the upper 100-200 m layer is characterized by strong halocline and inversion thermocline. The mixed layer keeps deepening up to 250 m by mid-April with potential temperature remaining nearly the surface freezing point and sea surface salinity increasing from 34.00 to 34.21. From then on until mid-May, the whole water column stays isothermally at about -1.90℃ while the surface salinity increases by a further 0.23. Hereafter the temperature increases while salinity decreases along with the increasing depth both by 0.1 order of magnitude vertically. The upper ocean heat content ranging from 120.5 to 2.9 MJ m-2, heat flux with the values of 9.8-287.0 W m-2 loss and the sea ice growth rates of 4.3-11.7 cm d-1 were estimated by using simple 1-D heat and salt budget methods. The MBP exists throughout the whole Antarctic winter (March to October) due to the air-sea-ice interaction, with an average size of about 5.0×103 km2. It can be speculated that the decrease of the salinity of the upper ocean may occur after October each year. The recurring sea-ice production and the associated brine rejection process increase the salinity of the water column in the MBP progressively, resulting in, eventually, the formation of a large body of high density water.

Hydrography of the Gulf of Maine and Massachusetts Bay, data report for R/V OCEANUS cruise 181, 5-15 February 1987

USGS Publications Warehouse

Moody, John A.; Butman, Bradford; Shoukimas, Polly; Donoghue, Terence G.

1990-01-01

During Cruise 181, a total of 95 hydrographic profiles were obtained by means of a conductivity-temperature-depth (CTD) profiler. Stations are numbered sequentially and station information is tabulated in table 1. The stations were arranged in ten transects (figure 1). Section 1 was across the Great South Channel and section 7 was across the Northeast Channel--the two main oceanic entrances and exits of the Gulf of Maine. Section 2 was along a saddle (Rodgers Pass) separating Wilkinson Basin from Georges Basin. Sections 3,5, and 10 were across different regions of Wilkinson Basin and all intersected at the longterm mooring site W1 in the center of Wilkinson Basin; section 8 was a dog-leg section through the southern portion of Jordan Basin; and sections 6 (east-west) and 9 (north-south) were within Georges Basin. A severe winter storm (see table 2 and 3) occurred between February 9 and 10 and work was stopped while the OCEANUS rode out the storm in Cape Cod Bay and repaired storm damage. Section 4 across Massachusetts Bay and section 5 across Wilkinson Basin, were repeated twice, once before the storm (sections 4a and 5a) and once after the storm (sections 4b and 5b).

Cyclophosphamide, thalidomide, and dexamethasone (CTD) as initial therapy for patients with multiple myeloma unsuitable for autologous transplantation

PubMed Central

Davies, Faith E.; Gregory, Walter M.; Russell, Nigel H.; Bell, Sue E.; Szubert, Alexander J.; Coy, Nuria Navarro; Cook, Gordon; Feyler, Sylvia; Byrne, Jenny L.; Roddie, Huw; Rudin, Claudius; Drayson, Mark T.; Owen, Roger G.; Ross, Fiona M.; Jackson, Graham H.; Child, J. Anthony

2011-01-01

As part of the randomized MRC Myeloma IX trial, we compared an attenuated regimen of cyclophosphamide, thalidomide, and dexamethasone (CTDa; n = 426) with melphalan and prednisolone (MP; n = 423) in patients with newly diagnosed multiple myeloma ineligible for autologous stem-cell transplantation. The primary endpoints were overall response rate, progression-free survival, and overall survival (OS). The overall response rate was significantly higher with CTDa than MP (63.8% vs 32.6%; P < .0001), primarily because of increases in the rate of complete responses (13.1% vs 2.4%) and very good partial responses (16.9% vs 1.7%). Progression-free survival and OS were similar between groups. In this population, OS correlated with the depth of response (P < .0001) and favorable interphase fluorescence in situ hybridization profile (P < .001). CTDa was associated with higher rates of thromboembolic events, constipation, infection, and neuropathy than MP. In elderly patients with newly diagnosed multiple myeloma (median age, 73 years), CTDa produced higher response rates than MP but was not associated with improved survival outcomes. We highlight the importance of cytogenetic profiling at diagnosis and effective management of adverse events. This trial was registered at International Standard Randomized Controlled Trials Number as #68454111. PMID:21652683

Ocean mixing in deep-sea trenches: New insights from the Challenger Deep, Mariana Trench

NASA Astrophysics Data System (ADS)

van Haren, Hans; Berndt, Christian; Klaucke, Ingo

2017-11-01

Reliable very deep shipborne SBE 911plus Conductivity Temperature Depth (CTD) data to within 60 m from the bottom and Kongsberg EM122 0.5° × 1° multibeam echosounder data are collected in the Challenger Deep, Mariana Trench. A new position and depth are given for the deepest point in the world's ocean. The data provide insight into the interplay between topography and internal waves in the ocean that lead to mixing of the lowermost water masses on Earth. Below 5000 m, the vertical density stratification is weak, with a minimum buoyancy frequency N = 1.0 ± 0.6 cpd, cycles per day, between 6500 and 8500 m. In that depth range, the average turbulence is coarsely estimated from Thorpe-overturning scales, with limited statistics to be ten times higher than the mean values of dissipation rate εT = 3 ± 2 × 10-11 m2 s-3 and eddy diffusivity KzT = 2 ± 1.5 × 10-4 m2 s-1 estimated for the depth range between 10,300 and 10,850 m, where N = 2.5 ± 0.6 cpd. Inertial and meridionally directed tidal inertio-gravity waves can propagate between the differently stratified layers. These waves are suggested to be responsible for the observed turbulence. The turbulence values are similar to those recently estimated from CTD and moored observations in the Puerto Rico Trench. Yet, in contrast to the Puerto Rico Trench, seafloor morphology in the Mariana Trench shows up to 500 m-high fault scarps on the incoming tectonic plate and a very narrow trench, suggesting that seafloor topography does not play a crucial role for mixing.

Controlling effects of mesoscale eddies on thermohaline structure and in situ chlorophyll distribution in the western North Pacific

NASA Astrophysics Data System (ADS)

Gao, Wei; Wang, Zhenyan; Zhang, Kainan

2017-11-01

Based on the conductivity, temperature and depth (CTD) data collected at 93 hydrographic stations during a marine cruise and on contemporary satellite altimeter observations, a series of eddies have been observed passing over the stratified upper water of the Parece Vela Basin. The results from hydrographic measurements and in situ chlorophyll fluorescence measurements have revealed that these eddies exerted significant controlling effects on the thermohaline structure and chlorophyll distribution, especially on the prevalent subsurface chlorophyll maximum layer (SCML). Based on these observations and particulate beam attenuation coefficient (cp) data, the in situ phytoplankton bloom around the pycnocline can be largely attributable to the formation of a well-developed SCML in the studied system. The uplift of the cold subsurface water within the cyclone, shoaling the pycnocline to a shallower layer, resulted in a low-temperature anomaly and different salinity anomalies at different depths. This uplift in the cyclone further caused the SCML to appear at a shallower depth with a higher in situ chlorophyll concentration than that in the normal domain. Conversely, the sinking of the warm surface water to the subsurface layer within the anticyclone depressed the pycnocline to a deeper layer and generated a high-temperature anomaly and opposite salinity anomalies compared with the cyclone. The sinking of the pycnocline within the anticyclone considerably influenced the characteristics of the SCML, which had a deeper depth and a lower in situ chlorophyll concentration than that of the normal sea. This study contributes rare quasi-synchronous CTD observations capturing mesoscale eddies and provides valuable descriptions of the variations in the SCML under the influence of mesoscale eddies based on in situ optical measurements from the seldom-discussed western North Pacific.

Hydrodynamic variability of the Cretan Sea derived from Argo float profiles and multi-parametric buoy measurements during 2010-2012

NASA Astrophysics Data System (ADS)

Kassis, Dimitris; Korres, Gerasimos; Petihakis, George; Perivoliotis, Leonidas

2015-12-01

In this work, we examine the complex hydrology of the Cretan Sea, an important area which affects the dynamics of the Eastern Mediterranean basin. We use T/S profile data derived from the first Argo float deployed in the area during June 2010 within the framework of the Greek Argo program. Temperature and salinity profiles were measured over a 2-year period, analyzed, and combined with time series data recorded from the POSEIDON E1-M3A multi-parametric instrumentation platform operating in the area since 2007. The acquired datasets have been enriched with available CTD profiles taken on the mooring site during cruise maintenance surveys. The combined research activities resulted in a large dataset of physical properties allowing extended geographical coverage and an in-depth analysis of the Cretan Sea dynamics during this 2-year period. Data analysis shows significant variability of water masses of different origin at subsurface and deep layers. This confirms previous findings describing the area as transitional with water masses of different origin meeting and interacting. Furthermore, additional features of the area are described combining information from satellite altimetry. In this study, new circulation systems are identified at intermediate and subsurface layers affecting both the dynamic behavior of the basin's upper thermocline and the intermediate/deep water mass tempo-spatial variability. We further investigate the physical properties of the water column and suggest an updated mesoscale circulation picture based on the dynamics of the variable hydrological regimes of the Cretan Sea basin.

Seasonal Ice Zone Reconnaissance Surveys Coordination

DTIC Science & Technology

2016-03-30

sea surface temperature (SST), sea level atmospheric pressure ( SLP ), and velocity (Steele), and dropsonde measurements of atmospheric properties...aircraft), cloud top/base heights UpTempO buoys for understanding and prediction…. Steele UpTempO buoy drops for SLP , SST, SSS, & surface velocity...reflectance, skin temperature, visible imagery AXCTD= Air Expendable CTD, AXCP= Air Expendable Current Profiler, SLP = Sea Level atmospheric

A Superhelical Spiral in the Escherichia coli DNA Gyrase A C-terminal Domain Imparts Unidirectional Supercoiling Bias

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruthenburg,A.; Graybosch, D.; Huetsch, J.

DNA gyrase is unique among type II topoisomerases in that its DNA supercoiling activity is unidirectional. The C-terminal domain of the gyrase A subunit (GyrA-CTD) is required for this supercoiling bias. We report here the x-ray structure of the Escherichia coli GyrA-CTD (Protein Data Bank code 1ZI0). The E. coli GyrA-CTD adopts a circular-shaped {beta}-pinwheel fold first seen in the Borrelia burgdorferi GyrA-CTD. However, whereas the B. burgdorferi GyrA-CTD is flat, the E. coli GyrA-CTD is spiral. DNA relaxation assays reveal that the E. coli GyrA-CTD wraps DNA inducing substantial (+) superhelicity, while the B. burgdorferi GyrA-CTD introduces a moremore » modest (+) superhelicity. The observation of a superhelical spiral in the present structure and that of the Bacillus stearothermophilus ParC-CTD structure suggests unexpected similarities in substrate selectivity between gyrase and Topo IV enzymes. We propose a model wherein the right-handed ((+) solenoidal) wrapping of DNA around the E. coli GyrA-CTD enforces unidirectional (-) DNA supercoiling.« less

Structural dynamics of native and V260E mutant C-terminal domain of HIV-1 integrase

NASA Astrophysics Data System (ADS)

Sangeetha, Balasubramanian; Muthukumaran, Rajagopalan; Amutha, Ramaswamy

2015-04-01

The C-terminal domain (CTD) of HIV-1 integrase is a five stranded β-barrel resembling an SH3 fold. Mutational studies on isolated CTD and full-length IN have reported V260E mutant as either homo-dimerization defective or affecting the stability and folding of CTD. In this study, molecular dynamics simulation techniques were used to unveil the effect of V260E mutation on isolated CTD monomer and dimer. Both monomeric and dimeric forms of wild type and V260E mutant are highly stable during the simulated period. However, the stabilizing π-stacking interaction between Trp243 and Trp243' at the dimer interface is highly disturbed in CTD-V260E (>6 Å apart). The loss in entropy for dimerization is -30 and -25 kcal/mol for CTD-wt and CTD-V260E respectively signifying a weak hydrophobic interaction and its perturbation in CTD-V260E. The mutant Glu260 exhibits strong attraction/repulsion with all the basic/acidic residues of CTD. In addition to this, the dynamics of CTD-wild type and V260E monomers at 498 K was analyzed to elucidate the effect of V260E mutation on CTD folding. Increase in SASA and reduction in the number of contacts in CTD-V260E during simulation highlights the instability caused by the mutation. In general, V260E mutation affects both multimerization and protein folding with a pronounced effect on protein folding rather than multimerization. This study emphasizes the importance of the hydrophobic nature and SH3 fold of CTD in proper functioning of HIV integrase and perturbing this nature would be a rational approach toward designing more selective and potent allosteric anti-HIV inhibitors.

Absolute geostrophic currents over the SR02 section south of Africa in December 2009

NASA Astrophysics Data System (ADS)

Tarakanov, Roman

2017-04-01

The structure of the absolute geostrophic currents is investigated on the basis of CTD-, SADCP- and LADCP-data over the hydrographic section occupied south of Africa from the Good Hope Cape to 57° S along the Prime Meridian, and on the basis of satellite data on absolute dynamic topography (ADT) produced by Ssalto/Duacs and distributed by Aviso, with a support from Cnes (http://www.aviso.altimetry.fr/duacs/). Thus the section crossed the subtropical zone (at the junction of the subtropical gyres of the Indian and Atlantic oceans), the Antarctic Circumpolar Current (ACC) and terminated at the northern periphery of the Weddell Gyre. A total of 87 stations were occupied here with CTD-, and LADCP-profiling in the entire water column. The distance between stations was 20 nautical miles. Absolute geostrophic currents were calculated between each pair of CTD-stations with barotropic correction based on two methods: by SADCP data and by ADT at these stations. The subtropical part of the section crossed a large segment of the Agulhas meander, already separated from the current and disintegrating into individual eddies. In addition, smaller formed cyclones and anticyclones of the Agulhas Current were also observed in this zone. These structural elements of the upper layer of the ocean currents do not penetrate deeper than 1000-1500 m. Oppositely directed barotropic currents with velocities up to 30 cm/s were observed below these depths extending to the ocean bottom. Such large velocities agree well with the data of the bottom tracking of Lowered ADCP. Only these data were the reliable results of LADCP measurements because of the high transparency of the deep waters of the subtropical zone. The total transport of absolute geostrophic currents in the section is estimated as 144 and 179 Sv to the east, based on the SADCP and ADT barotropic correction, respectively. A transport of 4 (2) Sv to the east was observed on the northern periphery of the Weddell Gyre, 187 (182) Sv to the east was in the ACC zone (up to Subtropical front), 47 (5) Sv to the west was in the subtropical zone. The total transport of abyssal barotropic currents in the subtropical zone was 18 to the west (7 to the east).

Thickness distributions and evolution of growth mechanisms of NH4-illite from the fossil hydrothermal system of Harghita Bai, Eastern Carpathians, Romania

USGS Publications Warehouse

Bobos, Iuliu; Eberl, Dennis D.

2013-01-01

The crystal growth of NH4-illite (NH4-I) from the hydrothermal system of Harghita Bãi (Eastern Carpathians) was deduced from the shapes of crystal thickness distributions (CTDs). The 4-illite-smectite (I-S) interstratified structures (R1, R2, and R3-type ordering) with a variable smectite-layer content. The NH4-I-S (40–5% S) structures were identified underground in a hydrothermal breccia structure, whereas the K-I/NH4-I mixtures were found at the deepest level sampled (−110 m). The percentage of smectite interlayers generally decreases with increasing depth in the deposit. This decrease in smectite content is related to the increase in degree of fracturing in the breccia structure and corresponds to a general increase in mean illite crystal thickness. In order to determine the thickness distributions of NH4-I crystals (fundamental illite particles) which make up the NH4-I-S interstratified structures and the NH4,-I/K-I mixtures, 27 samples were saturated with Li+ and aqueous solutions of PVP-10 to remove swelling and then were analyzed by X-ray diffraction. The profiles for the mean crystallite thickness (Tmean) and crystallite thickness distribution (CTD) of NH4-I crystallites were determined by the Bertaut-Warren-Averbach method using the MudMaster computer code. The Tmean of NH4-I from NH4-I-S samples ranges from 3.4 to 7.8 nm. The Tmean measured for the NH4-I/K-I mixture phase ranges from 7.8 nm to 11.7 nm (NH4-I) and from 12.1 to 24.7 nm (K-I).The CTD shapes of NH4-I fundamental particles are asymptotic and lognormal, whereas illites from NH4-I/K-I mixtures have bimodal shapes related to the presence of two lognormal-like CTDs corresponding to NH4-I and K-I.The crystal-growth mechanism for NH4-I samples was simulated using the Galoper code. Reaction pathways for NH4-I crystal nucleation and growth could be determined for each sample by plotting their CTD parameters on an α–β2 diagram constructed using Galoper. This analysis shows that NH4-I crystals underwent simultaneous nucleation and growth, followed by surface-controlled growth without simultaneous nucleation.

Connective Tissue Disease-associated Interstitial Lung Diseases (CTD-ILD) - Report from OMERACT CTD-ILD Working Group.

PubMed

Khanna, Dinesh; Mittoo, Shikha; Aggarwal, Rohit; Proudman, Susanna M; Dalbeth, Nicola; Matteson, Eric L; Brown, Kevin; Flaherty, Kevin; Wells, Athol U; Seibold, James R; Strand, Vibeke

2015-11-01

Interstitial lung disease (ILD) is common in connective tissue disease (CTD) and is the leading cause of mortality. Investigators have used certain outcome measures in randomized controlled trials (RCT) in CTD-ILD, but the lack of a systematically developed, CTD-specific index that captures all measures relevant and meaningful to patients with CTD-ILD has left a large and conspicuous gap in CTD-ILD research. The CTD-ILD working group, under the aegis of the Outcome Measures in Rheumatology (OMERACT) initiative, has completed a consensus group exercise to reach harmony on core domains and items for inclusion in RCT in CTD-ILD. During the OMERACT 12 meeting, consensus was sought on domains and core items for inclusion in RCT. In addition, consensus was pursued on a definition of response in RCT. Consensus was defined as ≥ 75% agreement among the participants. OMERACT 12 participants endorsed the domains with minimal modifications. Clinically meaningful progression for CTD-ILD was proposed as ≥ 10% relative decline in forced vital capacity (FVC) or ≥ 5% to < 10% relative decline in FVC and ≥ 15% relative decline in DLCO. There is consensus on domains for inclusion in RCT in CTD-ILD and on a definition of clinically meaningful progression. Data-driven approaches to validate these results in different cohorts and RCT are needed.

Coastal water monitoring using a vertical profiler

NASA Astrophysics Data System (ADS)

Kim, Dong Guk; Seo, Seongbong; Park, Young-Gyu; Min, Hong Sik

2017-04-01

Using a profiler system, the Aqualog, composed of a moored wire and a carrier in which a CTD was installed, we have been monitoring coastal water in Korea since August 2016. With this monitoring system, we were able to observe rapid warming of surface water that resulted in large damage to fish farms. The profiles showed that the warming was associated with low salinity water due to the fresh water discharge from the Yangtze River. We also observed change in water properties due to a typhoon. Along the Korean coast there are many aquafarms, which are becoming more vulnerable to environmental change. With the data from the profiler we would be able to help the aquafarms to sustain.

Sustaining observations in the polar oceans

PubMed Central

Abrahamsen, E. P.

2014-01-01

Polar oceans present a unique set of challenges to sustained observations. Sea ice cover restricts navigation for ships and autonomous measurement platforms alike, and icebergs present a hazard to instruments deployed in the upper ocean and in shelf seas. However, the important role of the poles in the global ocean circulation provides ample justification for sustained observations in these regions, both to monitor the rapid changes taking place, and to better understand climate processes in these traditionally poorly sampled areas. In the past, the vast majority of polar measurements took place in the summer. In recent years, novel techniques such as miniature CTD (conductivity–temperature–depth) tags carried by seals have provided an explosion in year-round measurements in areas largely inaccessible to ships, and, as ice avoidance is added to autonomous profiling floats and gliders, these promise to provide further enhancements to observing systems. In addition, remote sensing provides vital information about changes taking place in sea ice cover at both poles. To make these observations sustainable into the future, improved international coordination and collaboration is necessary to gain optimum utilization of observing networks. PMID:25157189

Estimation of Geotropic Currents in the Bay of Bengal using In-situ Observations.

NASA Astrophysics Data System (ADS)

T, V. R.

2014-12-01

Geostraphic Currents (GCs) can be estimated from temperature and salinity observations. In this study an attempt has been made to compute GC using temperature and salinity observations from Expendable Bathy Thermograph (XBT) and CTD over Bay of Bengal (BoB). Although in recent time we have Argo observations but it is for a limited period and coarse temporal resolutions. In BoB Bengal, where not enough simultaneous hydrographic temperature and salinity data are available with reasonable spatial resolution (~one degree spatial resolution) and for a longer period. To overcome the limitations of GC computed from XBT profiles, temperature-salinity relationships were used from simultaneous temperature and salinity observations. We have demonstrated that GCs can be computed with an accuracy of less than 8.5 cm/s (root mean square error) at the surface with respect to temperature from XBT and salinity from climatological record. This error reduces with increasing depth. Finally, we demonstrated the application of this approach to study the temporal variation of the GCs during 1992 to 2012 along an XBT transect.

Mean hydrography on the continental shelf from 26 repeat glider deployments along Southeastern Australia

PubMed Central

Schaeffer, Amandine; Roughan, Moninya; Austin, Tim; Everett, Jason D.; Griffin, David; Hollings, Ben; King, Edward; Mantovanelli, Alessandra; Milburn, Stuart; Pasquer, Benedicte; Pattiaratchi, Charitha; Robertson, Robin; Stanley, Dennis; Suthers, Iain; White, Dana

2016-01-01

Since 2008, 26 glider missions have been undertaken along the continental shelf of southeastern Australia. Typically these missions have spanned the continental shelf on the inshore edge of the East Australian Current from 29.5–33.5°S. This comprehensive dataset of over 33,600 CTD profiles from the surface to within 10 m of the bottom in water depths ranging 25–200 m provides new and unprecedented high resolution observations of the properties of the continental shelf waters adjacent to a western boundary current, straddling the region where it separates from the coast. The region is both physically and biologically significant, and is also in a hotspot of ocean warming. We present gridded mean fields for temperature, salinity and density, but also dissolved oxygen and chlorophyll-a fluorescence indicative of phytoplankton biomass. This data will be invaluable for understanding shelf stratification, circulation, biophysical and bio-geochemical interactions, as well as for the validation of high-resolution ocean models or serving as teaching material. PMID:27575831

Western Arctic Shelf-Basin Interactions Experiment: Processing and Calibration of Moored Profiler Data from the Beaufort Shelf Edge Mooring Array

DTIC Science & Technology

2006-12-01

EM-CTD and ACM data (MMP only) were extracted from a PC flashcard on the MP controller and converted to ASCII file format. The MP reports engineering...downloaded from the flashcards of the MP instruments and unpacked, we used the processing system developed by John Toole at the Woods Hole Oceanographic

Use of multiple sensor technologies for quality control of in situ biogeochemical measurements: A SeaCycler case study

NASA Astrophysics Data System (ADS)

Atamanchuk, Dariia; Koelling, Jannes; Lai, Jeremy; Send, Uwe; Wallace, Douglas

2017-04-01

Over the last two decades observing capacity for the global ocean has increased dramatically. Emerging sensor technologies for dissolved gases, nutrients and bio-optical properties in seawater are allowing extension of in situ observations beyond the traditionally measured salinity, temperature and pressure (CTD). However the effort to extend observations using autonomous instruments and platforms carries the risk of losing the level of data quality achievable through conventional water sampling techniques. We will present results from a case study with the SeaCycler profiling winch focusing on quality control of the in-situ measurements. A total of 13 sensors were deployed from May 2016 to early 2017 on SeaCycler's profiling sensor float, including CTD, dissolved oxygen (O2, 3 sensors), carbon dioxide (pCO2, 2 sensors), nutrients, velocity sensors, fluorometer, transmissometer, single channel PAR sensor, and others. We will highlight how multiple measurement technologies (e.g. for O2 and CO2) complement each other and result in a high quality data product. We will also present an initial assessment of the bio-optical data, their implications for seasonal phytoplankton dynamics and comparisons to climatologies and ocean-color data products obtained from the MODIS satellite.

Simultaneous application of multiple platforms (Glider, Scanfish, profiling mooring, CTD) to improve detection and quantification of temporal ocean dynamics

NASA Astrophysics Data System (ADS)

Meyer, D.; Prien, R. D.; Lips, U.; Naumann, M.; Liblik, T.; Schulz-Bull, D. E.

2016-02-01

Ocean dynamics are difficult to observe given the broad spectrum of temporal and spatial scales. Robotic technology can be used to address this issue, and help to investigate the variability of physical and biogeochemical processes. This work focuses on ocean robots and in particular on glider technology which seems to be one of the most promising oceanographic tools for future marine research. In this context, we present the results of an observational program conducted in the Baltic Sea combining a profiling mooring (GODESS - Gotland Deep Environmental Sampling Station) and glider technology (Slocum). The temporal variability is captured by the mooring, while the spatial variability is obtained from the glider sampling the surrounding area. Furthermore, classical CTD-measurements and an underwater vehicle (Scanfish) are used simultaneously by two different research vessels to validate and complement the observing network. The main aim of the study is to identify possible synergies between the different platforms and to get a better understanding of maximizing the information content of the data collected by this network. The value and the quality of the data of each individual platform is analyzed and their contribution to the performance of the network itself evaluated.

Anticancer effects of cantharidin in A431 human skin cancer (Epidermoid carcinoma) cells in vitro and in vivo.

PubMed

Li, Chi-Chuan; Yu, Fu-Shun; Fan, Ming-Jen; Chen, Ya-Yin; Lien, Jin-Cherng; Chou, Yu-Cheng; Lu, Hsu-Feng; Tang, Nou-Ying; Peng, Shu-Fen; Huang, Wen-Wen; Chung, Jing-Gung

2017-03-01

Cantharidin (CTD), a potential anticancer agent of Traditional Chinese Medicine has cytotxic effects in different human cancer cell lines. The cytotoxic effects of CTD on A431 human skin cancer (epidermoid carcinoma) cells in vitro and in A431 cell xenograft mouse model were examined. In vitro, A431 human skin cell were treated with CTD for 24 and 48 h. Cell phase distribution, ROS production, Ca 2+ release, Caspase activity and the level of apoptosis associated proteins were measured. In vivo, A431 cell xenograft mouse model were examined. CTD-induced cell morphological changes and decreased percentage of viable A431 cells via G0/G1 phase arrest and induced apoptosis. CTD-induced G0/G1 phase arrest through the reduction of protein levels of cyclin E, CDK6, and cyclin D in A431 cells. CTD-induced cell apoptosis of A431 cells also was confirm by DNA gel electrophoresis showed CTD-induced DNA fragmentation. CTD reduced the mitochondrial membrane potential and stimulated release of cytochrome c, AIF and Endo G in A431 cells. Flow cytometry demonstrated that CTD increased activity of caspase-8, -9 and -3. However, when cells were pretreated with specific caspase inhibitors activity was reduced and cell viability increased. CTD increased protein levels of death receptors such as DR4, DR5, TRAIL and levels of the active form of caspase-8, -9 and -3 in A431 cells. AIF and Endo G proteins levels were also enhanced by CTD. In vivo studies showed that CTD significantly inhibited A431 cell xenograft tumors in mice. Taken together, these in vitro and in vivo results provide insight into the mechanisms of CTD on cell growth and tumor production. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 723-738, 2017. © 2016 Wiley Periodicals, Inc.

Dissipation in the Baltic proper during winter stratification

NASA Astrophysics Data System (ADS)

Lass, Hans Ulrich; Prandke, Hartmut; Liljebladh, Bengt

2003-06-01

Profiles of dissipation rates and stratification between 10 and 120 m depth were measured with a loosely tethered profiler over a 9-day winter period in the Gotland Basin of the Baltic Sea. Supplementary measurements of current profiles were made with moored ADCPs. Temporal and spatial patterns of the stratification were observed by means of towed CTD. Shallow freshwater lenses in the surface mixed layer, mesoscale eddies, inertial oscillations, and inertial waves as part of the internal wave spectrum provided the marine physical environment for the small-scale turbulence. Two well-separated turbulence regimes were detected. The turbulence in the surface mixed layer was well correlated with the wind. The majority of the energy flux from the wind to the turbulent kinetic energy was dissipated within the surface mixed layer. A minor part of this flux was consumed by changes of the potential energy of the fresh water lenses. The penetration depth Hpen of the wind-driven turbulence into the weakly stratified surface mixed layer depended on the local wind speed (W10) as Hpen = cW103/2 Active erosion of the Baltic halocline by wind-driven turbulence is expected for wind speeds greater than 14 m/s. The turbulence in the strongly stratified interior of the water column was quite independent of the meteorological forcing at the sea surface. The integrated production of turbulent kinetic energy exceeded the energy loss of inertial oscillations in the surface layer suggesting additional energy sources which might have been provided by inertial wave radiation during geostrophic adjustment of coastal jets and mesoscale eddies. The averaged dissipation rate profile in the stratified part of the water column, best fitted by ɛ ∝ EN, was different from the scaling of the dissipation in the thermocline of the ocean [, 1986]. The diapycnical mixing coefficient (Kv) was best fit by Kv = a0/N according to [1987] with a0 ≈ 0.87 × 10-7 m2/s2. The diapycnal diffusivity estimated from the dissipation rate was lower than those estimated by the bulk method.

Molecular Dissection of the Homotrimeric Sliding Clamp of T4 Phage: Two Domains of a Subunit Display Asymmetric Characteristics.

PubMed

Singh, Manika Indrajit; Jain, Vikas

2016-01-26

Sliding clamp proteins are circular dimers or trimers that encircle DNA and serve as processivity factors during DNA replication. Their presence in all the three domains of life and in bacteriophages clearly indicates their high level of significance. T4 gp45, besides functioning as the DNA polymerase processivity factor, also moonlights as the late promoter transcription determinant. Here we report a detailed biophysical analysis of gp45. The chemical denaturation of gp45 probed by circular dichroism spectroscopy, tryptophan fluorescence anisotropy, and blue-native polyacrylamide gel electrophoresis suggests that the protein follows a three-state denaturation profile and displays an intermediate molten globule-like state. The three-state transition was found to be the result of the sequential unfolding of the two domains, the N-terminal domain (NTD) and the C-terminal domain (CTD), of gp45. The experiments involving Trp fluorescence quenching by acrylamide demonstrate that the CTD undergoes substantial changes in conformation during formation of the intermediate state. Further biophysical dissection of the individual domain reveals contrasting properties of the two domains. The NTD unfolds at low urea concentrations and is also susceptible to protease cleavage, whereas the CTD resists urea-mediated denaturation and is not amenable to protease digestion even at higher urea concentrations. These experiments allow us to conclude that the two domains of gp45 differ in their dynamics. While the CTD shows stability and rigidity, we find that the NTD is unstable and flexible. We believe that the asymmetric characteristics of the two domains and the interface they form hold significance in gp45 structure and function.

C-terminal domain of SMYD3 serves as a unique HSP90-regulated motif in oncogenesis

PubMed Central

Harriss, June; Das, Chhaya; Zhu, Li; Edwards, Melissa; Shaaban, Salam; Tucker, Haley

2015-01-01

The SMYD3 histone methyl transferase (HMTase) and the nuclear chaperone, HSP90, have been independently implicated as proto-oncogenes in several human malignancies. We show that a degenerate tetratricopeptide repeat (TPR)-like domain encoded in the SMYD3 C-terminal domain (CTD) mediates physical interaction with HSP90. We further demonstrate that the CTD of SMYD3 is essential for its basal HMTase activity and that the TPR-like structure is required for HSP90-enhanced enzyme activity. Loss of SMYD3-HSP90 interaction leads to SMYD3 mislocalization within the nucleus, thereby losing its chromatin association. This results in reduction of SMYD3-mediated cell proliferation and, potentially, impairment of SMYD3′s oncogenic activity. These results suggest a novel approach for blocking HSP90-driven malignancy in SMYD3-overexpressing cells with a reduced toxicity profile over current HSP90 inhibitors. PMID:25738358

78 FR 9098 - Self-Regulatory Organizations; Miami International Securities Exchange LLC; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-07

... executed contract for the MIAX Clearing Trade Drop (``CTD''), a messaging interface that will provide real... proposes to establish a new Port Fee for the MIAX CTD. CTD provides Exchange Members, their clearing firms... are routed to a CTD connection containing certain information. The information includes, among other...

77 FR 35691 - Update to Electronic Common Technical Document Module 1

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-14

... Electronic Common Technical Document (eCTD) Module 1, which is used for electronic submission of... they are received with a limit of 350. SUPPLEMENTARY INFORMATION: The eCTD is an International... Research (CBER) have been receiving submissions in the eCTD format since 2003, and the eCTD has been the...

Role of Autoantibodies in the Diagnosis of Connective-Tissue Disease ILD (CTD-ILD) and Interstitial Pneumonia with Autoimmune Features (IPAF)

PubMed Central

Jee, Adelle S.; Adelstein, Stephen; Bleasel, Jane; Keir, Gregory J.; Nguyen, MaiAnh; Sahhar, Joanne; Youssef, Peter; Corte, Tamera J.

2017-01-01

The diagnosis of interstitial lung disease (ILD) requires meticulous evaluation for an underlying connective tissue disease (CTD), with major implications for prognosis and management. CTD associated ILD (CTD-ILD) occurs most commonly in the context of an established CTD, but can be the first and/or only manifestation of an occult CTD or occur in patients who have features suggestive of an autoimmune process, but not meeting diagnostic criteria for a defined CTD—recently defined as “interstitial pneumonia with autoimmune features” (IPAF). The detection of specific autoantibodies serves a critical role in the diagnosis of CTD-ILD, but there remains a lack of data to guide clinical practice including which autoantibodies should be tested on initial assessment and when or in whom serial testing should be performed. The implications of detecting autoantibodies in patients with IPAF on disease behaviour and management remain unknown. The evaluation of CTD-ILD is challenging due to the heterogeneity of presentations and types of CTD and ILD that may be encountered, and thus it is imperative that immunologic tests are interpreted in conjunction with a detailed rheumatologic history and examination and multidisciplinary collaboration between respiratory physicians, rheumatologists, immunologists, radiologists and pathologists. PMID:28471413

Nitrogen-assisted Three-phase Equilibrium in Hydrate Systems Composed of Water, Methane, Carbon Dioxide, and Nitrogen

NASA Astrophysics Data System (ADS)

Darnell, K.; Flemings, P. B.; DiCarlo, D. A.

2016-12-01

In June 2016, seawater samples at sediment-seawater interface and sediment samples were collected by the he Jiaolong, China's manned submersible, at four sampling sites located in the Yap Trench. Seawater samples from different depths of the trench were also collected by CTD. Chemical parameters, including pH, alkanility, concentrations of dissolved inorganic carbon, dissolved and total organic carbon, methane, dimethylsulfoniopropionate, nutrients, carbohydrates, and amino acids were analyzed in the seawater samples. Concentrations of total organic carbon, six constant elements and nine trace elements were determined in the sediment samples. All the vertical profiles of the chemical parameters in the seawater have unique characteristics. Our resluts also showed that the carbonate compensation depth (CCD) was between 4500 m and 5000 m in the trench. The hadal sediment at 6500 m depth under the CCD line was siliceous ooze favored for the burial of orgaic carbon, attributed to accumulation of surface sediment by gravity flow. The abyssal sediment at the 4500 m depth was calcareous ooze. Various microfossils, such as discoasters and diatoms, were identified in different sediment layers of the sediment samples.Based on the ratios of Fe/Al and Ti/Al, and the correlation between different elements, the sediment in the Yap Trench were derived from biogenic, terrestrial, volcanic and autogenic sources. The ratios of Ni/Co and V/Cr showed that the deposition environment of the trench should be oxidative, arributed to inflow of the Antractic bottom oxygen-rich seawater.The high concentraiont of Ca in the sediment from the station 371-Yap-S02 below 4 cm depth indicated that there was no large-scale volcanic eruption in the research area and the volcanic materials in the sediment might orginated from the Mariana Volcanic Arc, and the Carolyn Ridge has been slowly sinking on the east side of the trench due to plate subduction. This study is the first systematic study of chemical characteristics in the seawater and sediment of the Yap Trench.

Chemical Characteristics of Seawater and Sediment in the Yap Trench

NASA Astrophysics Data System (ADS)

Ding, H.; Sun, C.; Yang, G.

2017-12-01

In June 2016, seawater samples at sediment-seawater interface and sediment samples were collected by the he Jiaolong, China's manned submersible, at four sampling sites located in the Yap Trench. Seawater samples from different depths of the trench were also collected by CTD. Chemical parameters, including pH, alkanility, concentrations of dissolved inorganic carbon, dissolved and total organic carbon, methane, dimethylsulfoniopropionate, nutrients, carbohydrates, and amino acids were analyzed in the seawater samples. Concentrations of total organic carbon, six constant elements and nine trace elements were determined in the sediment samples. All the vertical profiles of the chemical parameters in the seawater have unique characteristics. Our resluts also showed that the carbonate compensation depth (CCD) was between 4500 m and 5000 m in the trench. The hadal sediment at 6500 m depth under the CCD line was siliceous ooze favored for the burial of orgaic carbon, attributed to accumulation of surface sediment by gravity flow. The abyssal sediment at the 4500 m depth was calcareous ooze. Various microfossils, such as discoasters and diatoms, were identified in different sediment layers of the sediment samples.Based on the ratios of Fe/Al and Ti/Al, and the correlation between different elements, the sediment in the Yap Trench were derived from biogenic, terrestrial, volcanic and autogenic sources. The ratios of Ni/Co and V/Cr showed that the deposition environment of the trench should be oxidative, arributed to inflow of the Antractic bottom oxygen-rich seawater.The high concentraiont of Ca in the sediment from the station 371-Yap-S02 below 4 cm depth indicated that there was no large-scale volcanic eruption in the research area and the volcanic materials in the sediment might orginated from the Mariana Volcanic Arc, and the Carolyn Ridge has been slowly sinking on the east side of the trench due to plate subduction. This study is the first systematic study of chemical characteristics in the seawater and sediment of the Yap Trench.

Deletion of the COOH-Terminal Domain of CXC Chemokine Receptor 4 Leads to the Down-regulation of Cell-to-Cell Contact, Enhanced Motility and Proliferation in Breast Carcinoma Cells

PubMed Central

Ueda, Yukiko; Neel, Nicole F.; Schutyser, Evemie; Raman, Dayanidhi; Richmond, Ann

2009-01-01

The CXC chemokine receptor 4 (CXCR4) contributes to the metastasis of human breast cancer cells. The CXCR4 COOH-terminal domain (CTD) seems to play a major role in regulating receptor desensitization and down-regulation. We expressed either wild-type CXCR4 (CXCR4-WT) or CTD-truncated CXCR4 (CXCR4-ΔCTD) in MCF-7 human mammary carcinoma cells to determine whether the CTD is involved in CXCR4-modulated proliferation of mammary carcinoma cells. CXCR4-WT-transduced MCF-7 cells (MCF-7/CXCR4-WT cells) do not differ from vector-transduced MCF-7 control cells in morphology or growth rate. However, CXCR4-ΔCTD-transduced MCF-7 cells (MCF-7/CXCR4-ΔCTD cells) exhibit a higher growth rate and altered morphology, potentially indicating an epithelial-to-mesenchymal transition. Furthermore, extracellular signal-regulated kinase (ERK) activation and cell motility are increased in these cells. Ligand induces receptor association with β-arrestin for both CXCR4-WT and CXCR4-ΔCTD in these MCF-7 cells. Overexpressed CXCR4-WT localizes predominantly to the cell surface in unstimulated cells, whereas a significant portion of overexpressed CXCR4-ΔCTD resides intracellularly in recycling endosomes. Analysis with human oligomicroarray, Western blot, and immunohistochemistry showed that E-cadherin and Zonula occludens are down-regulated in MCF-7/CXCR4-ΔCTD cells. The array analysis also indicates that mesenchymal marker proteins and certain growth factor receptors are up-regulated in MCF-7/CXCR4-ΔCTD cells. These observations suggest that (a) the overexpression of CXCR4-ΔCTD leads to a gain-of-function of CXCR4-mediated signaling and (b) the CTD of CXCR4-WT may perform a feedback repressor function in this signaling pathway. These data will contribute to our understanding of how CXCR4-ΔCTD may promote progression of breast tumors to metastatic lesions. PMID:16740704

Long-Term Observations of Nitrogen and Phosphorus Export in Paired-Agricultural Watersheds under Controlled and Conventional Tile Drainage.

PubMed

Sunohara, M D; Gottschall, N; Wilkes, G; Craiovan, E; Topp, E; Que, Z; Seidou, O; Frey, S K; Lapen, D R

2015-09-01

Controlled tile drainage (CTD) regulates water and nutrient export from tile drainage systems. Observations of the effects of CTD imposed en masse at watershed scales are needed to determine the effect on downstream receptors. A paired-watershed approach was used to evaluate the effect of field-to-field CTD at the watershed scale on fluxes and flow-weighted mean concentrations (FWMCs) of N and P during multiple growing seasons. One watershed (467-ha catchment area) was under CTD management (treatment [CTD] watershed); the other (250-ha catchment area) had freely draining or uncontrolled tile drainage (UCTD) (reference [UCTD] watershed). The paired agricultural watersheds are located in eastern Ontario, Canada. Analysis of covariance and paired tests were used to assess daily fluxes and FWMCs during a calibration period when CTD intervention on the treatment watershed was minimal (2005-2006, when only 4-10% of the tile-drained area was under CTD) and a treatment period when the treatment (CTD) watershed had prolific CTD intervention (2007-2011 when 82% of tile drained fields were controlled, occupying >70% of catchment area). Significant linear regression slope changes assessed using ANCOVA ( ≤ 0.1) for daily fluxes from upstream and downstream monitoring sites pooled by calibration and treatment period were -0.06 and -0.20 (stream water) (negative values represent flux declines in CTD watershed), -0.59 and -0.77 (NH-N), -0.14 and -0.15 (NO-N), -1.77 and -2.10 (dissolved reactive P), and -0.28 and 0.45 (total P). Total P results for one site comparison contrasted with other findings likely due to unknown in-stream processes affecting total P loading, not efficacy of CTD. The FWMC results were mixed and inconclusive but suggest physical abatement by CTD is the means by which nutrient fluxes are predominantly reduced at these scales. Overall, our study results indicate that CTD is an effective practice for reducing watershed scale fluxes of stream water, N, and P during the growing season. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Hydrographic Conditions in the Gulf of Carpentaria During Australian Monsoon Experiment

NASA Astrophysics Data System (ADS)

Inoue, M.; Steinberg, C.; Wolanski, E.; Ridd, P.

2002-12-01

Gulf of Carpentaria located in the northern Australia, is a shallow wide basin with the deepest bottom depths of approximately 60 m. It is connected to Arafura Sea to the north and west, and to the Torres Strait to the east. Hydrographic surveys of the Gulf of Carpentaria were carried out in January and March, 1987 as part of Australian Monsoon Experiment. During the January survey, Tropical Cyclone (TC) Irma was formed in the Gulf of Carpentaria. An east-west CTD section at 13o52'S was occupied twice, one prior to and during, and the other after the formation of TC Irma. In addition, two post-Irma east-west sections were occupied at 12o40'S and 11o30'S. The pre-cyclone section indicates a well-defined stratified two-layer system, while the post-cyclone sections show deepening of the surface warm layer due to significant mixing by TC Irma. Overall, significant cooling of near surface warm water on the order of more than 1oC was observed. Significant heat loss estimated for the water column has presumably contributed toward the development of TC Irma. In February 1987, TC Jason was formed in the gulf. During the March survey, two east-west CTD sections were occupied at 11o30'S and 13o52'S. The March survey reveals notable warming of the bottom water. Detailed discussion of the CTD data from the two cruises will be presented.

Altimeter and Oceanographic in Situ Measurements in the Area of the Greenland-Iceland-Norwegian Sea, 1987-1988

DTIC Science & Technology

1992-06-01

of CTD data; J. Boyd for collecting AXBT data; Steve Piacsek from SACLANTCEN for GDEM data and help in arrangement of Planet Cruise; P. Minnett from...FCTE ft OCT -992 00 "Orgsnrdl oontot4ns color platgs: All DTIC reproduot- Ions Will be In blaok and white* Pavel Pistek Ocean Sensing and Prediction...temperature-depth and thermistor chain data collected by the West German ship WFS Planet , airborne expendable bathythermograph data deployed by P-3

Mercury in the Black Sea - results of the 2013 GEOTRACES MEDBlack cruise

NASA Astrophysics Data System (ADS)

Heimbürger, L. E.; Sonke, J.; Rijkenberg, M. J. A.; Gerringa, L. J.; De Baar, H. J. W.

2014-12-01

Inorganic mercury (Hg), whether of natural or anthropogenic origin, can be converted into the neurotoxin methylmercury (MeHg). Today we believe this conversion occurs during the bacterial remineralization of sinking organic matter in the oceanic water column. The Black Sea with its high organic matter inputs and anoxic deep waters is an excellent study site to investigate in more detail the processes yielding MeHg. To date only one vertical profile of Hg species near the Western shelf and one vertical profile in the Western Gyre are published (Lamborg et al. 2008). We will present new results of the 2013 Dutch-led GEOTRACES MEDBlack cruise in the Black Sea. Research vessel "Pelagia" occupied 12 full depth stations along an east-west transect from 13 to 25 July 2013. High resolution vertical profiles were sampled using a titanium ultraclean CTD frame (de Baar et al., 2008) equipped with 24 x 24L PVDF samplers. Samples were filtered (0.2µm, Sartobran 300), drawn into pre-cleaned 250mL Savillex PFA bottles and acidified to 0.4% (v:v) with double-distilled HCl. Dissolved MeHg, as the sum of monomethylHg and dimethylHg, was analyzed via isotope dilution gas chromatography sector field inductively coupled mass spectrometry. Total dissolved Hg was determined following the US EPA 1631 method. We will present high resolution vertical Hg species profiles, including one ultra-high resolution profile (1 sample every 5m-depth) to understand the dynamics along the chemocline (Luther et al., 1991). We will also present the results of the GEOTRACES international intercalibration exercise for dissolved MeHg and dissolved total Hg in surface seawater that we organized during the same cruise. References De Baar HJW, Timmermans KR, Laan P, De Porto HH, Ober S, Blom JJ, Bakker MC, Schilling J, Sarthou G, Smit MG, Klunder M. Titan: A new facility for ultraclean sampling of trace elements and isotopes in the deep oceans in the international Geotraces program. Mar. Chem. 2008, 111(1-2): 4-21. Lamborg CH, Yiğiterhan O, Fitzgerald WF, Balcom PH, Hammerschmidt CR, Murray J.Vertical distribution of mercury species at two sites in the Western Black Sea. Mar.Chem. 2008, 111(1-2): 77-89. Luther III GW, Church TM, Powell D. Sulfur speciation and sulfide oxidation in the water column of the Black Sea. DSR I 1991, 38:1121-1137.

Association of serum KL-6 levels with interstitial lung disease in patients with connective tissue disease: a cross-sectional study.

PubMed

Oguz, Ekin Oktay; Kucuksahin, Orhan; Turgay, Murat; Yildizgoren, Mustafa Turgut; Ates, Askin; Demir, Nalan; Kumbasar, Ozlem Ozdemir; Kinikli, Gulay; Duzgun, Nursen

2016-03-01

It was aimed to evaluate KL-6 glycoprotein levels to determine if it may be a diagnostic marker for the connective tissue diseases (CTDs) predicting CTD-related interstitial lung diseases (ILDs) (CTD-ILD) development and to examine if there was a difference between patients and healthy controls. The study included 113 patients with CTD (45 CTD without lung involvement, 68 CTD-ILD) and 45 healthy control subjects. KL-6 glycoprotein levels were analyzed with ELISA in patients and the control group. The relationship between KL-6 glycoprotein levels and CTD-ILD was assessed. In the comparison of all the groups in the study, significantly higher levels of KL-6 were determined in the CTD-ILD group than in either the CTD without pulmonary involvement group or the healthy control group (p < 0.008 and p < 0.001, respectively). There was no statistically significant difference between the KL-6 levels in the healthy control group and the CTD without pulmonary involvement group (p = 0.289). The KL-6 levels did not differ significantly according to the connective tissue diseases in the diagnostic groups (systemic lupus erythematosus, Sjögren's syndrome, rheumatoid arthritis, mixed connective tissue disease, scleroderma, polymyositis/ dermatomyositis). In the healthy control group, there was a statistically significant difference between KL-6 levels in smokers and non-smokers. Smokers had significantly higher serum KL-6 levels compared with non-smokers (p < 0.05). There was no statistically significant difference between smoking status (pack-year) and serum KL-6 levels. There was no statistically significant correlation between serum KL-6 levels and time since diagnosis of CTD and CTD-ILD. The level of KL-6 as a predictive factor could be used to identify the clinical development of ILD before it is detected on imaging modality. Further prospective clinical studies are needed to define whether levels of KL-6 might have prognostic value or might predict progressive ILD.

[Impaired endometrial receptivity in primary infertility in women with undifferentiated connective tissue dysplasia and hereditary thrombophilia].

PubMed

Zanozin, A S; Demura, T A; Kolosovsky, D Yu; Faizullina, N M; Kogan, E A

The concurrence of undifferentiated connective tissue dysplasia (uCTD) and hereditary thrombophilia (HT) often accompanies female infertility, in the pathogenesis of which impaired endometrial receptivity plays an important role. to investigate endometrial morphological and immunophenotypic features in patients with primary infertility in the presence of uCTD and HT. The pipelle endometrial biopsy specimens taken in the implantation window were examined in 81 patients, including 13 women with a clinical diagnosis of uCTD, 40 with HT, 19 with uCTD concurrent with HT, and in a control group of 9 heathy surrogate mothers. Morphological, immunohistochemical, and morphometric examinations were done to study the paraffin-embedded endometrial biopsy sections stained with hematoxylin and eosin, pikrofuksin by van Gieson, and with toluidine blue. Immunohistochemical tests were carried out using primary antibodies against ER, PgR, LIF, PAI-1, VEGF, Collagen I, Collagen III, fibronectin, laminin, MMP-2, and MMP-9. The uCTD, HT, and uCTD + HT groups were found to have signs of decreased endometrial receptivity as dramatically lower counts of mature pinopodes, slower endometrial maturation, reduced expression of the receptivity marker LIF, and deviations of the stromal progesterone-estrogen index from the normal value. Sclerotic foci with type III collagen accumulation were detected in the endometrial stroma. uCTD and HT and especially their concurrence are commonly a concomitant disease and risk factors for infertility in women due to impaired endometrial receptivity. In uCTD, connective tissue remodeling processes are substantially retarded, which ultimately leads to increased processes of endometrial stromal sclerosis, reduced endometrial receptivity, and infertility. The most pronounced morphological and immunophenotypical changes have been ascertained to develop in the uCTD + NT group. The findings may be used to predict and devise new infertility treatments in patients with uCTD + NT.

Pichicuco 7: Gulf of California CTD Data Report: U.S. Research Vessel, R/V New Horizon,

DTIC Science & Technology

1985-03-01

de Investigaciones Scientificas y de Educacion Superior de Ensenada, Ensenada, B.C.. Mexico. %i- Table of Contents Abstract...hydrographic characteristics, especially as they might apply to water mass formation processes in the northern Gulf. This report presents individual profiles...investigadores del Cen- Investigaci6n Cientiica y Educaci6n Superior de tro de Investigacidn Cientifica y Educacion Ensenada and Scripps Institution of

Suppression Analysis Reveals a Functional Difference between the Serines in Positions Two and Five in the Consensus Sequence of the C-Terminal Domain of Yeast RNA Polymerase II

PubMed Central

Yuryev, A.; Corden, J. L.

1996-01-01

The largest subunit of RNA polymerase II contains a repetitive C-terminal domain (CTD) consisting of tandem repeats of the consensus sequence Tyr(1)Ser(2)Pro(3)Thr(4) Ser(5)Pro(6) Ser(7). Substitution of nonphosphorylatable amino acids at positions two or five of the Saccharomyces cerevisiae CTD is lethal. We developed a selection ssytem for isolating suppressors of this lethal phenotype and cloned a gene, SCA1 (suppressor of CTD alanine), which complements recessive suppressors of lethal multiple-substitution mutations. A partial deletion of SCA1 (sca1Δ::hisG) suppresses alanine or glutamate substitutions at position two of the consensus CTD sequence, and a lethal CTD truncation mutation, but SCA1 deletion does not suppress alanine or glutamate substitutions at position five. SCA1 is identical to SRB9, a suppressor of a cold-sensitive CTD truncation mutation. Strains carrying dominant SRB mutations have the same suppression properties as a sca1Δ::hisG strain. These results reveal a functional difference between positions two and five of the consensus CTD heptapeptide repeat. The ability of SCA1 and SRB mutant alleles to suppress CTD truncation mutations suggest that substitutions at position two, but not at position five, cause a defect in RNA polymerase II function similar to that introduced by CTD truncation. PMID:8725217

Crystal structures of Lymnaea stagnalis AChBP in complex with neonicotinoid insecticides imidacloprid and clothianidin

PubMed Central

Ihara, Makoto; Okajima, Toshihide; Yamashita, Atsuko; Oda, Takuma; Hirata, Koichi; Nishiwaki, Hisashi; Morimoto, Takako; Akamatsu, Miki; Ashikawa, Yuji; Kuroda, Shun’ichi; Mega, Ryosuke; Kuramitsu, Seiki; Sattelle, David B.

2008-01-01

Neonicotinoid insecticides, which act on nicotinic acetylcholine receptors (nAChRs) in a variety of ways, have extremely low mammalian toxicity, yet the molecular basis of such actions is poorly understood. To elucidate the molecular basis for nAChR–neonicotinoid interactions, a surrogate protein, acetylcholine binding protein from Lymnaea stagnalis (Ls-AChBP) was crystallized in complex with neonicotinoid insecticides imidacloprid (IMI) or clothianidin (CTD). The crystal structures suggested that the guanidine moiety of IMI and CTD stacks with Tyr185, while the nitro group of IMI but not of CTD makes a hydrogen bond with Gln55. IMI showed higher binding affinity for Ls-AChBP than that of CTD, consistent with weaker CH–π interactions in the Ls-AChBP–CTD complex than in the Ls-AChBP–IMI complex and the lack of the nitro group-Gln55 hydrogen bond in CTD. Yet, the NH at position 1 of CTD makes a hydrogen bond with the backbone carbonyl of Trp143, offering an explanation for the diverse actions of neonicotinoids on nAChRs. PMID:18338186

The RNA polymerase II CTD coordinates transcription and RNA processing

PubMed Central

Hsin, Jing-Ping; Manley, James L.

2012-01-01

The C-terminal domain (CTD) of the RNA polymerase II largest subunit consists of multiple heptad repeats (consensus Tyr1–Ser2–Pro3–Thr4–Ser5–Pro6–Ser7), varying in number from 26 in yeast to 52 in vertebrates. The CTD functions to help couple transcription and processing of the nascent RNA and also plays roles in transcription elongation and termination. The CTD is subject to extensive post-translational modification, most notably phosphorylation, during the transcription cycle, which modulates its activities in the above processes. Therefore, understanding the nature of CTD modifications, including how they function and how they are regulated, is essential to understanding the mechanisms that control gene expression. While the significance of phosphorylation of Ser2 and Ser5 residues has been studied and appreciated for some time, several additional modifications have more recently been added to the CTD repertoire, and insight into their function has begun to emerge. Here, we review findings regarding modification and function of the CTD, highlighting the important role this unique domain plays in coordinating gene activity. PMID:23028141

Correlation Between Geological Stuctures and Gas Hydrate amount Offshore the South Shetland Island — Preliminary Results

NASA Astrophysics Data System (ADS)

Loreto, M. F.; Tinivella, U.; Accaino, F.; Giustiniani, M.

2010-05-01

Sediments of the accretionary prism, present along the continental margin of the Peninsula Antarctica SW of Elephant Island, are filled by gas hydrates as evidenced by a strong BSR. A multidisciplinary geophysical dataset, represented by seismic data, multibeam, chirp profiles, CTD and core samples, was acquired during three oceanographic cruises. The estimation of gas hydrate and free gas concentrations is based on the P-wave velocity analysis. In order to extract a detailed and reliable velocity field, we have developed and optimized a procedure that includes the pre-stack depth migration to determine, iteratively and with a layer stripping approach method, the velocity field and the depth-migrated seismic section. The final velocity field is then translated in terms of gas hydrate and free gas amounts by using theoretical approaches. Several seismic sections have been processed in the investigated area. The final 2D velocity sections have been translated in gas-phase concentration sections, considering the gas distribution within sediments both uniformly and patchly distributed. The free gas layer is locally present and, consequently, the base of the free gas reflector was identified only in some lines or part of them. The hydrate layer shows important lateral variations of hydrate concentration in correspondence of geological features, such as faults and folds. The intense fluid migration along faults and different fluid accumulation in correspondence of geological structures can control the gas hydrate concentration and modify the geothermal field in the surrounding area.

The Cancer Target Discovery and Development Network Dashboard Allows Users to Search for Interesting Data and Results | Office of Cancer Genomics

Cancer.gov

The CTD2 Dashboard hosts analyzed data and other evidence generated by the CTD2 Network. It is a web interface for the research community to browse and search CTD2 Network data related to genes, proteins, and compounds from individual CTD2 Centers, or explore observations across multiple Centers.

Critical Thinking Disposition of Nurse Practitioners in Taiwan.

PubMed

Hsu, Hsiu-Ying; Chang, Shu-Chen; Chang, Ai-Ling; Chen, Shiah-Lian

2017-09-01

Critical thinking disposition (CTD) is crucial for nurse practitioners who face complex patient care scenarios. This study explored the CTD of nurse practitioners and related factors. The study was a cross-sectional descriptive design. A purposive sample was recruited from a medical center and its hospital branches in central Taiwan. A structured questionnaire was used to collect data from 210 nurse practitioners. The participants obtained the highest average score on systematicity and analyticity. CTD had a significant positive correlation with fundamental knowledge readiness, professional knowledge readiness, and confidence in making clinical decisions. Professional knowledge readiness, education level, and on-the-job training predicted the score of the participants on overall CTD. On-the-job training and education level may influence the CTD of nurse practitioners. Providing formal or on-the-job continuing education training to nurse practitioners may help enhance their CTD. J Contin Educ Nurs. 2017;48(9):425-430. Copyright 2017, SLACK Incorporated.

Stirring by deep cyclones and the evolution of Denmark strait overflow water observed at line W

NASA Astrophysics Data System (ADS)

Andres, M.; Toole, J. M.; Torres, D. J.; Smethie, W. M.; Joyce, T. M.; Curry, R. G.

2016-03-01

Shipboard velocity and water property data from 18 transects across the North Atlantic Deep Western Boundary Current (DWBC) near 40 °N are examined to study the evolution of the Denmark Strait Overflow Water (DSOW) component of the DWBC and mixing between DSOW and the interior. The examined transects along Line W - which stretches from the continental shelf south of New England to Bermuda - were made between 1994 and 2014. The shipboard data comprise measurements at regular stations of velocity from lowered acoustic Doppler current profilers, CTD profiles and trace gas chlorofluorocarbon (CFC) concentrations from bottle samples at discrete depths. Comparison of the Line W velocity sections with concurrent sea surface height maps from satellite altimetry indicates that large cyclones in the deep ocean accompany intermittent quasi-stationary meander troughs in the Gulf Stream path at Line W. A composite of 5 velocity sections along Line W suggests that a typical cyclone reaches swirl speeds of greater than 30 cm s-1 at 3400-m depth and has a radius (distance between the center and the maximum velocity) of 75 km. Tracer data suggest that these cyclones affect not only the deep velocity structure along Line W, but also provide a mechanism for water exchange between the DWBC's DSOW and the interior. Vigorous exchange is corroborated by a mismatch in the CFC-11:CFC-12 and CFC-113:CFC-12 ratio ages calculated for DSOW at Line W. During the most recent 5-year period (2010-2014), a decrease in DSOW density has been driven by warming (increasing by almost 0.1 °C) as salinity has increased only slightly (by 0.003, which is close to the 0.002 uncertainty of the measurements). The abyssal ocean offshore of the DWBC and Gulf Stream and deeper than 3000-m depth has freshened at a rate of 6×10-4 yr-1 since at least 2003. Density here remains nearly unchanged over this period, due to temperature compensation, though a linear cooling trend in the abyssal ocean (to compensate the freshening) is not statistically significant.

From SYNOP to AMOC: Stirring by deep cyclones and the evolution of Denmark Strait Overflow Water observed at Line W

NASA Astrophysics Data System (ADS)

Andres, M.; Toole, J. M.; Torres, D. J.; Smethie, W. M., Jr.; Joyce, T. M.; Curry, R. G.

2016-02-01

Shipboard velocity and property data from 18 transects across the North Atlantic Deep Western Boundary Current (DWBC) near 40˚N are analyzed to study the evolution of the Denmark Strait Overflow Water (DSOW) component of the DWBC and its mixing with the interior. The transects were made between 1994 and 2014 and lie along Line W, which reaches from the continental shelf south of New England to Bermuda. Measurements comprise velocity from lowered acoustic Doppler current profilers (LADCPs), CTD profiles, and trace gas chlorofluorocarbon (CFC) concentrations from bottle samples at discrete depths at 26 regular stations or a subset of these stations. In each transect, DSOW exhibits a distinct CFC concentration maximum in the abyssal ocean (> 3000 m depth) along the sloped western boundary. Sea surface height (SSH) maps from satellite altimetry indicate that quasi-stationary meander troughs of the Gulf Stream path in the upper ocean were present at Line W during 5 of the 18 sections. For these 5 sections, the LADCP velocity sections suggest the upper ocean trough is accompanied by a large cyclone in the deep ocean in the DSOW density layer. The occurrence of deep cyclones in conjunction with Gulf Stream troughs as inferred from the LADCP sections along Line W is consistent with previous observations (from 1988 to 1990) in the region from a moored array in the Synoptic Ocean Prediction (SYNOP) experiment. The SYNOP array suggested deep cyclones are present here about 35% of the time. The composite velocity section produced from the 5 Line W transects sampling through a Gulf Stream trough suggests that a typical cyclone reaches swirl speeds of greater than 30 cm/s at 3400 m depth and has a radius (distance between the center and the maximum velocity) of 75 km. The tracer data suggest that these cyclones affect not only the deep velocity structure along Line W, but also provide a mechanism for water exchange between the DWBC and the interior.

Lung cancer in connective tissue disease-associated interstitial lung disease: clinical features and impact on outcomes.

PubMed

Watanabe, Satoshi; Saeki, Keigo; Waseda, Yuko; Murata, Akari; Takato, Hazuki; Ichikawa, Yukari; Yasui, Masahide; Kimura, Hideharu; Hamaguchi, Yasuhito; Matsushita, Takashi; Yamada, Kazunori; Kawano, Mitsuhiro; Furuichi, Kengo; Wada, Takashi; Kasahara, Kazuo

2018-02-01

Lung cancer (LC) adversely impacts survival in patients with idiopathic pulmonary fibrosis. However, little is known about LC in patients with connective tissue disease-associated interstitial lung disease (CTD-ILD). The aim of this study was to evaluate the prevalence of and risk factors for LC in CTD-ILD, and the clinical characteristics and survival of CTD-ILD patients with LC. We conducted a single-center, retrospective review of patients with CTD-ILD from 2003 to 2016. Patients with pathologically diagnosed LC were identified. The prevalence, risk factors, and clinical features of LC and the impact of LC on CTD-ILD patient outcomes were observed. Of 266 patients with CTD-ILD, 24 (9.0%) had LC. CTD-ILD with LC was more likely in patients who were older, male, and smokers; had rheumatoid arthritis, a usual interstitial pneumonia pattern, emphysema on chest computed tomography scan, and lower diffusing capacity of the lung carbon monoxide (DLco)% predicted; and were not receiving immunosuppressive therapy. Multivariate analysis indicated that the presence of emphysema [odds ratio (OR), 8.473; 95% confidence interval (CI), 2.241-32.033] and nonuse of immunosuppressive therapy (OR, 8.111; 95% CI, 2.457-26.775) were independent risk factors for LC. CTD-ILD patients with LC had significantly worse survival than patients without LC (10-year survival rate: 28.5% vs. 81.8%, P<0.001). LC is associated with the presence of emphysema and nonuse of immunosuppressive therapy, and contributes to increased mortality in patients with CTD-ILD.

Role of the RNA polymerase α subunits in CII-dependent activation of the bacteriophage λ pE promoter: identification of important residues and positioning of the α C-terminal domains

PubMed Central

Kedzierska, Barbara; Lee, David J.; Węgrzyn, Grzegorz; Busby, Stephen J. W.; Thomas, Mark S.

2004-01-01

The bacteriophage λ CII protein stimulates the activity of three phage promoters, pE, pI and paQ, upon binding to a site overlapping the –35 element at each promoter. Here we used preparations of RNA polymerase carrying a DNA cleavage reagent attached to specific residues in the C-terminal domain of the RNA polymerase α subunit (αCTD) to demonstrate that one αCTD binds near position –41 at pE, whilst the other αCTD binds further upstream. The αCTD bound near position –41 is oriented such that its 261 determinant is in close proximity to σ70. The location of αCTD in CII-dependent complexes at the pE promoter is very similar to that found at many activator-independent promoters, and represents an alternative configuration for αCTD at promoters where activators bind sites overlapping the –35 region. We also used an in vivo alanine scan analysis to show that the DNA-binding determinant of αCTD is involved in stimulation of the pE promoter by CII, and this was confirmed by in vitro transcription assays. We also show that whereas the K271E substitution in αCTD results in a drastic decrease in CII-dependent activation of pE, the pI and paQ promoters are less sensitive to this substitution, suggesting that the role of αCTD at the three lysogenic promoters may be different. PMID:14762211

CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network

PubMed Central

Aksoy, Bülent Arman; Dančík, Vlado; Smith, Kenneth; Mazerik, Jessica N.; Ji, Zhou; Gross, Benjamin; Nikolova, Olga; Jaber, Nadia; Califano, Andrea; Schreiber, Stuart L.; Gerhard, Daniela S.; Hermida, Leandro C.; Jagu, Subhashini

2017-01-01

Abstract The Cancer Target Discovery and Development (CTD2) Network aims to use functional genomics to accelerate the translation of high-throughput and high-content genomic and small-molecule data towards use in precision oncology. As part of this goal, and to share its conclusions with the research community, the Network developed the ‘CTD2 Dashboard’ [https://ctd2-dashboard.nci.nih.gov/], which compiles CTD2 Network-generated conclusions, termed ‘observations’, associated with experimental entities, collected by its member groups (‘Centers’). Any researcher interested in learning about a given gene, protein, or compound (a ‘subject’) studied by the Network can come to the CTD2 Dashboard to quickly and easily find, review, and understand Network-generated experimental results. In particular, the Dashboard allows visitors to connect experiments about the same target, biomarker, etc., carried out by multiple Centers in the Network. The Dashboard’s unique knowledge representation allows information to be compiled around a subject, so as to become greater than the sum of the individual contributions. The CTD2 Network has broadly defined levels of validation for evidence (‘Tiers’) pertaining to a particular finding, and the CTD2 Dashboard uses these Tiers to indicate the extent to which results have been validated. Researchers can use the Network’s insights and tools to develop a new hypothesis or confirm existing hypotheses, in turn advancing the findings towards clinical applications. Database URL: https://ctd2-dashboard.nci.nih.gov/ PMID:29220450

Sustaining observations in the polar oceans.

PubMed

Abrahamsen, E P

2014-09-28

Polar oceans present a unique set of challenges to sustained observations. Sea ice cover restricts navigation for ships and autonomous measurement platforms alike, and icebergs present a hazard to instruments deployed in the upper ocean and in shelf seas. However, the important role of the poles in the global ocean circulation provides ample justification for sustained observations in these regions, both to monitor the rapid changes taking place, and to better understand climate processes in these traditionally poorly sampled areas. In the past, the vast majority of polar measurements took place in the summer. In recent years, novel techniques such as miniature CTD (conductivity-temperature-depth) tags carried by seals have provided an explosion in year-round measurements in areas largely inaccessible to ships, and, as ice avoidance is added to autonomous profiling floats and gliders, these promise to provide further enhancements to observing systems. In addition, remote sensing provides vital information about changes taking place in sea ice cover at both poles. To make these observations sustainable into the future, improved international coordination and collaboration is necessary to gain optimum utilization of observing networks. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Pneumocystis jirovecii pneumonia in mycophenolate mofetil-treated patients with connective tissue disease: analysis of 17 cases.

PubMed

Zhang, Yongfeng; Zheng, Yi

2014-12-01

The association of Pneumocystis jirovecii pneumonia (PJP) with connective tissue disease (CTD) and mycophenolate mofetil's (MMF) potent activity against PJP have been separately reported. Until now, there have been no papers describing the occurrence of PJP following MMF treatment in CTD patients. The objective of this study was to describe the clinical features, risk factors, outcomes of PJP in patients with CTD and investigates the effects of MMF on the occurrence of PJP in China. In this retrospective cohort study, we performed a chart review, analyzing clinical features, treatment, and outcomes of PJP in patients with CTD in a single hospital. A total of 17 cases met the inclusion criteria of having PJP and a CTD diagnosis: systemic lupus erythematosus; polymyositis; dermatomyositis; rheumatoid arthritis; Wegener's granulomatosis; and microscopic polyangiitis. Sixteen patients were treated with glucocorticoids (GCs) plus immunosuppressive drugs. Only one patient had GCs without immunosuppressive drugs. Ten subjects (62.5 %) received MMF (1-1.5 g/day), and all ten had lymphopenia. The mortality rates of MMF and non-MMF patients were 50 and 14 %, respectively. This study is the first report of PJP following MMF plus GC treatment in patients with CTD. CTD itself may be a risk factor for PJP. When CTD patients receiving MMF therapy have low lymphocyte counts and/or CD4 lymphocyte counts <250/µL, we should be care of occurrence of PJP.

Transport of the Norwegian Atlantic current as determined from satellite altimetry

NASA Technical Reports Server (NTRS)

Pistek, Pavel; Johnson, Donald R.

1992-01-01

Relatively warm and salty North Atlantic surface waters flow through the Faeroe-Shetland Channel into the higher latitudes of the Nordic Seas, preserving an ice-free winter environment for much of the exterior coast of northern Europe. This flow was monitored along the Norwegian coast using Geosat altimetry on two ascending arcs during the Exact Repeat Mission in 1987-1989. Concurrent undertrack CTD surveys were used to fix a reference surface for the altimeter-derived SSH anomalies, in effect creating time series of alongtrack surface dynamic height topographies. Climatologic CTD casts were then used, with empirical orthogonal function (EOF) analysis, to derive relationships between historical surface dynamic heights and vertical temperature and salinity profiles. Applying these EOF relationships to the altimeter signals, mean transports of volume, heat, and salt were calculated at approximately 2.9 Sverdrups, 8.1 x 10 exp 11 KCal/s and 1.0 x 10 exp 8 Kg/s, respectively. Maximum transports occurred in February/March and minimum in July/August.

Documentation of Software for the Neil Brown Instrument Systems/NORDA Velocity/CTD Profiler.

DTIC Science & Technology

1982-07-01

maximum pressure of sensor M - cast start time (dec. days) * (12- 13 - cast end time (141 - magnetic variation shp’s speed (kt) 19 -ship’s heading...100 C I 265 10? C CHECK THAT THE TIPOE FIELDS APE EACH IN RA4 6E 1084 C 0T .. -- 105 49. VAR (153 .CE,24*.00 Ilo -___-TO_999- 106 IF 4VARfib6).G(E.6r

Quantum chemical calculations and molecular docking studies of 5-(4-chlorobenzylidene)thiazolidine-2,4-dione(CTD) and its mannich product 5-(4-chlorobenzylidene)-3-(morpholinomethyl)thiazolidine-2,4-dione (CMTD)

NASA Astrophysics Data System (ADS)

Fatma, Shaheen; Bishnoi, Abha; Verma, Anil Kumar; Singh, Vineeta; Srivastava, Krishna

2018-04-01

This work presents the synthesis of 5-(4-chlorobenzylidene)thiazolidine-2,4-dione (CTD) by Claisen condensation of thiazolidine-2,4-dione and mannich product of CTD, 5-(4-chlorobenzylidene)-3-(morpholinomethyl)thiazolidine-2,4-dione (CMTD). The static first hyperpolarizability values for thiazolidine-2,4-dione derivatives have been calculated as 10.28 × 10-30 esu for CTD and 19.42 × 10-30 esu for CMTD. The gradual increase in hyperpolarizability values of synthesized thiazolidine-2,4-dione derivatives from CTD to CMTD is due to the blockage of sbnd NH group on CTD by mannich reaction. The structures of these compounds have been derived by spectroscopic(IR, UV, Mass, 1H and 13C NMR) analysis as well as with the help of theoretical studies. The high values of first static hyperpolarizability indicate that the synthesized derivatives are suitable as non-linear optical (NLO) material. CTD with MIC value of 12.5 μg/mL can be developed as an alternative drug for the treatment of enteric fever. Calculated frontier orbital gap values suggest that the CMTD is a soft molecule with high chemical reactivity and is more polarizable as compared to the CTD. Molecular electrostatic potential is calculated for the optimized geometry of the molecules to estimate their chemical reactivity. The inhibitor CTD forms a stable complex with 3-dehydroquinase enzyme of Salmonella typhi. It is evident from the ligand receptor interactions and a binding affinity value of -5.88 kcal/mol and an inhibition constant of 49.22 μM. This is further confirmed by the experimental biological data. The molecular docking studies are supportive of the antibacterial activity of CTD exhibiting high inhibition constant and binding energy.

Ergonomics: CTD management evaluation tool.

PubMed

Ostendorf, J S; Rogers, B; Bertsche, P K

2000-01-01

Cumulative trauma disorder (CTD) occurrences peaked in number in 1994 and although decreasing in 1995, still accounted for 62% of all illness cases reported. A CTD Management Evaluation Tool was developed to assist Occupational Safety and Health Compliance Officers (CSHOs) in program evaluation and documentation of the occupational health management component and the need for an ergonomics program. Occupational and environmental health nurses may use the tool not only to reduce and prevent CTD occurrences, but also as a benchmark for program evaluation.

The distal C-terminal region of the KcsA potassium channel is a pH-dependent tetramerization domain.

PubMed

Kamnesky, Guy; Shaked, Hadassa; Chill, Jordan H

2012-05-04

The intracellular C-terminal domain (CTD) of KcsA, a bacterial homotetrameric potassium channel, is a 40-residue-long segment that natively adopts a helical bundle conformation with 4-fold symmetry. A hallmark of KcsA behavior is pH-induced conformational change, which leads to the opening of the channel at acidic pH. Previous studies have reached conflicting conclusions as to the role of the CTD in this transition. Here, we investigate the involvement of this domain in pH-mediated channel opening by NMR using a soluble peptide corresponding to residues 128-160 of the CTD (CTD34). At neutral pH, CTD34 exhibits concentration-dependent spectral changes consistent with oligomer formation. We prove this slowly tumbling species to be a tetramer with a dissociation constant of (2.0±0.5)×10(-)(11) M(3) by NMR and sedimentation equilibrium experiments. Whereas monomeric CTD34 is only mildly helical, secondary chemical shifts prove that the tetrameric species adopts a tight native-like helical bundle conformation. The tetrameric species undergoes pH-dependent dissociation, and CTD34 is fully monomeric below pH 5.0. The structural basis for this phenomenon is the destabilization of the tetrameric CTD34 by protonation of residue H145 in the monomeric form of the peptide. We conclude that (i) the CTD34 peptide is independently capable of forming a tetrameric helical bundle, and (ii) this structurally significant conformational shift is modulated by the effects of solution pH on residue H145. Therefore, the involvement of this domain in the pH gating of the channel is strongly suggested. Copyright © 2012 Elsevier Ltd. All rights reserved.

Predictive value of nailfold capillaroscopy in patients with Raynaud's phenomenon.

PubMed

Meli, Madeleine; Gitzelmann, Gabriela; Koppensteiner, Renate; Amann-Vesti, Beatrice R

2006-03-01

The objective of this study was to evaluate the long-term follow-up of patients with Raynaud's phenomenon (RP) and pathological nailfold capillaroscopy (NC) in order to analyse the predictive value of specific features of capillaroscopy for the development of a connective tissue disease (CTD). From 1992 to 2002, NC alone or combined with fluorescence videomicroscopy with sodium fluorescein (NaF) was performed in 1024 consecutive patients because of RP. We analysed the follow-up and pathological features of NC in all patients who had neither clinical nor serological signs of a CTD at the time of NC. Of 308 patients with neither serological findings nor clinical signs of CTD but with RP and pathological features in NC suspicious for CTD, follow-up data were available for 133 patients. An additional NaF test had been performed in 51 (38.4%) patients. After a mean follow-up of 6.5 years (range: 1-15 years), 109 patients had developed a CTD and 24 patients did not show any clinical signs or serological markers for a CTD after a mean follow-up of 8.5 years (range: 2-15 years). There were no differences in age, duration of RP or of follow-up in patients who developed a CTD compared to patients who did not. Significantly more giant capillaries (p=0.0001), avascular fields (p=0.02) and irregular architecture (p=0.0001) had been observed in patients who had developed a CTD during the follow-up of 6.5 years. The presence of giant capillaries, avascular fields and irregular architecture of nailfold capillaries is predictive for the development of a CTD in patients with RP.

Ambrisentan response in connective tissue disease-associated pulmonary arterial hypertension (CTD-PAH) - A subgroup analysis of the ARIES-E clinical trial.

PubMed

Fischer, Aryeh; Denton, Christopher P; Matucci-Cerinic, Marco; Gillies, Hunter; Blair, Christiana; Tislow, James; Nathan, Steven D

2016-08-01

Pulmonary arterial hypertension (PAH) is a condition which may lead to right ventricular failure and early mortality and is an important complication in patients with connective tissue disease (CTD). Previously, the endothelin A selective receptor antagonist, ambrisentan, demonstrated efficacy and safety in treating patients with PAH due to WHO Group I etiologies. These analyses describe the 3-year efficacy and safety of ambrisentan in patients specifically with CTD associated PAH (CTD-PAH). Patients with CTD-PAH participating in the ARIES-1 and -2 clinical trials and their long-term extension were evaluated. Efficacy evaluations including 6-min walk distance (6MWD), clinical worsening, and survival were collected at routine study visits. Additional analyses of 6MWD categorical (30 m) breakpoints were conducted to determine any relationship between 6MWD and a prognostic threshold for survival. 124 patients with CTD-PAH were evaluated. 62.6%, 57.3%, and 58.2% of CTD-PAH patients treated with ambrisentan exhibited increases in 6MWD at 1-, 2-, and 3- years respectively. At 3 years, 64% of patients were free from clinical worsening and 76% of patients were still alive (Kaplan-Meier estimates). Identified factors holding prognostic relevance for survival include: baseline functional class, CTD-PAH subgroup, patient sex, improvement in 6MWD ≥30 m over the first 12 weeks of treatment, the most recent 6MWD, and a 6MWD absolute threshold of 222 m. These first analyses of the 3-year treatment of CTD-PAH patients with ambrisentan revealed fewer clinical worsening events and improved survival compared to historical controls. Key exercise parameters were also identified which appear important in guiding treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Acquisition of Oceanographic Measurements from Baleen Whales and Acquisition of Oceanographic Measurements from Baleen Whales: Field Deployments of Tags Developed Under Grant ONR (N00014-13-1-0854)

DTIC Science & Technology

2015-09-30

Jonas Teilmann Department of Bioscience Aarhus University Fredriksborgvej 399 DK-4000 Roskilde Denmark phone: +45 21424291 fax: +45 87 16 87 51...Mammal Research Unit (SMRU, www.smru.st-andrews.ac.uk), University of St. Andrews, Scotland. WORK COMPLETED The project developed a prototype CTD...temperature and depth components from that work along with the tag controller/transmitter etc, are all still valid. • The risk for building a new tag fall

Interpreting & Biomechanics. PEPNet Tipsheet

ERIC Educational Resources Information Center

PEPNet-Northeast, 2001

2001-01-01

Cumulative trauma disorder (CTD) refers to a collection of disorders associated with nerves, muscles, tendons, bones, and the neurovascular (nerves and related blood vessels) system. CTD symptoms may involve the neck, back, shoulders, arms, wrists, or hands. Interpreters with CTD may experience a variety of symptoms including: pain, joint…

Korean Nursing Students' Acquisition of Evidence-Based Practice and Critical Thinking Skills.

PubMed

Kim, Sang Suk; Kim, Eun Joo; Lim, Ji Young; Kim, Geun Myun; Baek, Hee Chong

2018-01-01

Evidence-based practice (EBP) is essential for enhancing nurses' quality of care. We identified Korean nursing students' practices, attitudes, and knowledge concerning EBP, as well as their critical thinking disposition (CTD). The EBP Questionnaire (EBPQ) was administered to a convenience sample of 266 nursing students recruited from four nursing schools in Seoul and its metropolitan area. Average EBPQ and CTD total scores were 4.69 ± 0.64 and 3.56 ± 0.32, respectively. Students who were ages ⩾23 years, male, and satisfied with their major demonstrated higher EBPQ and CTD scores. EBPQ scores were significantly correlated with CTD scores (r = .459, p < .01), and CTD was an explanatory factor of EBP (adjusted R 2 = 0.200). It is necessary to develop comprehensive teaching strategies to help nursing students improve their CTD and information utilization skills, as well as integrate EBP in undergraduate programs to enhance nurses' EBP abilities. [J Nurs Educ. 2018;57(1):21-27.]. Copyright 2018, SLACK Incorporated.

Sustained-release microsphere formulation containing an agrochemical by polyurethane polymerization during an agitation granulation process.

PubMed

Terada, Takatoshi; Tagami, Manabu; Ohtsubo, Toshiro; Iwao, Yasunori; Noguchi, Shuji; Itai, Shigeru

2016-07-25

In this report, a new solventless microencapsulation method by synthesizing polyurethane (PU) from polyol and isocyanate during an agglomeration process in a high-speed mixing apparatus was developed. Clothianidin (CTD), which is a neonicotinoid insecticide and highly effective against a wide variety of insect pests, was used as the model compound. The microencapsulated samples covered with PU (CTD microspheres) had a median diameter of <75μm and sustained-release properties. The CTD microspheres were analyzed by synchrotron X-ray computed tomography measurements. Multiple cores of CTD and other solid excipient were dispersed in PU. Although voids appeared in the CTD microspheres after CTD release, the spherical shape of the microspheres remained stable and no change in its framework was observed. The experimental release data were highly consistent with the Baker-Lonsdale model derived from drug release of spherical monolithic dispersions and consistent with the computed tomography measurements. Copyright © 2016 Elsevier B.V. All rights reserved.

Comprehensive nitrogen budgets for controlled tile drainage fields in eastern ontario, Canada.

PubMed

Sunohara, M D; Craiovan, E; Topp, E; Gottschall, N; Drury, C F; Lapen, D R

2014-03-01

Excessive N loading from subsurface tile drainage has been linked to water quality degradation. Controlled tile drainage (CTD) has the potential to reduce N losses via tile drainage and boost crop yields. While CTD can reduce N loss from tile drainage, it may increase losses through other pathways. A multiple-year field-scale accounting of major N inputs and outputs during the cropping season was conducted on freely drained and controlled tile drained agricultural fields under corn ( L.)-soybean [ (L.) Merr.] production systems in eastern Ontario, Canada. Greater predicted gaseous N emissions for corn and soybean and greater observed lateral seepage N losses were observed for corn and soybean fields under CTD relative to free-draining fields. However, observed N losses from tile were significantly lower for CTD fields, in relation to freely drained fields. Changes in residual soil N were essentially equivalent between drainage treatments, while mass balance residual terms were systematically negative (slightly more so for CTD). Increases in plant N uptake associated with CTD were observed, probably resulting in higher grain yields for corn and soybean. This study illustrates the benefits of CTD in decreasing subsurface tile drainage N losses and boosting crop yields, while demonstrating the potential for CTD to increase N losses via other pathways related to gaseous emissions and groundwater seepage. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Evaluation of an automated connective tissue disease screening assay in Korean patients with systemic rheumatic diseases

PubMed Central

Jeong, Seri; Yang, Heeyoung; Hwang, Hyunyong

2017-01-01

This study aimed to evaluate the diagnostic utilities of the automated connective tissues disease screening assay, CTD screen, in patients with systemic rheumatic diseases. A total of 1093 serum samples were assayed using CTD screen and indirect immunofluorescent (IIF) methods. Among them, 162 were diagnosed with systemic rheumatic disease, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and mixed connective tissue disease (MCT). The remaining 931 with non-systemic rheumatic disease were assigned to the control group. The median ratios of CTD screen tests were significantly higher in the systemic rheumatic disease group than in the control group. The positive likelihood ratios of the CTD screen were higher than those of IIF in patients with total rheumatic diseases (4.1 vs. 1.6), including SLE (24.3 vs. 10.7). The areas under the receiver operating characteristic curves (ROC-AUCs) of the CTD screen for discriminating total rheumatic diseases, RA, SLE, and MCT from controls were 0.68, 0.56, 0.92 and 0.80, respectively. The ROC-AUCs of the combinations with IIF were significantly higher in patients with total rheumatic diseases (0.72) and MCT (0.85) than in those of the CTD screen alone. Multivariate analysis indicated that both the CTD screen and IIF were independent variables for predicting systemic rheumatic disease. CTD screen alone and in combination with IIF were a valuable diagnostic tool for predicting systemic rheumatic diseases, particularly for SLE. PMID:28273146

Evaluation of an automated connective tissue disease screening assay in Korean patients with systemic rheumatic diseases.

PubMed

Jeong, Seri; Yang, Heeyoung; Hwang, Hyunyong

2017-01-01

This study aimed to evaluate the diagnostic utilities of the automated connective tissues disease screening assay, CTD screen, in patients with systemic rheumatic diseases. A total of 1093 serum samples were assayed using CTD screen and indirect immunofluorescent (IIF) methods. Among them, 162 were diagnosed with systemic rheumatic disease, including rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and mixed connective tissue disease (MCT). The remaining 931 with non-systemic rheumatic disease were assigned to the control group. The median ratios of CTD screen tests were significantly higher in the systemic rheumatic disease group than in the control group. The positive likelihood ratios of the CTD screen were higher than those of IIF in patients with total rheumatic diseases (4.1 vs. 1.6), including SLE (24.3 vs. 10.7). The areas under the receiver operating characteristic curves (ROC-AUCs) of the CTD screen for discriminating total rheumatic diseases, RA, SLE, and MCT from controls were 0.68, 0.56, 0.92 and 0.80, respectively. The ROC-AUCs of the combinations with IIF were significantly higher in patients with total rheumatic diseases (0.72) and MCT (0.85) than in those of the CTD screen alone. Multivariate analysis indicated that both the CTD screen and IIF were independent variables for predicting systemic rheumatic disease. CTD screen alone and in combination with IIF were a valuable diagnostic tool for predicting systemic rheumatic diseases, particularly for SLE.

Catching the Dream Annual Report, 2002.

ERIC Educational Resources Information Center

Chavers, Dean, Ed.

2002-01-01

In 2002, Catching the Dream (CTD) provided college scholarships to 208 American Indian students as well as grants to improve education in schools that serve Native students. This annual report describes CTD's programs and activities in 2002. Contents include short descriptions of CTD's scholarship, fellowship, and internship programs; describe…

Fine-scale hydrodynamics influence the spatio-temporal distribution of harbour porpoises at a coastal hotspot

NASA Astrophysics Data System (ADS)

Jones, A. R.; Hosegood, P.; Wynn, R. B.; De Boer, M. N.; Butler-Cowdry, S.; Embling, C. B.

2014-11-01

The coastal Runnelstone Reef, off southwest Cornwall (UK), is characterised by complex topography and strong tidal flows and is a known high-density site for harbour porpoise (Phocoena phocoena); a European protected species. Using a multidisciplinary dataset including: porpoise sightings from a multi-year land-based survey, Acoustic Doppler Current Profiling (ADCP), vertical profiling of water properties and high-resolution bathymetry; we investigate how interactions between tidal flow and topography drive the fine-scale porpoise spatio-temporal distribution at the site. Porpoise sightings were distributed non-uniformly within the survey area with highest sighting density recorded in areas with steep slopes and moderate depths. Greater numbers of sightings were recorded during strong westward (ebbing) tidal flows compared to strong eastward (flooding) flows and slack water periods. ADCP and Conductivity Temperature Depth (CTD) data identified fine-scale hydrodynamic features, associated with cross-reef tidal flows in the sections of the survey area with the highest recorded densities of porpoises. We observed layered, vertically sheared flows that were susceptible to the generation of turbulence by shear instability. Additionally, the intense, oscillatory near surface currents led to hydraulically controlled flow that transitioned from subcritical to supercritical conditions; indicating that highly turbulent and energetic hydraulic jumps were generated along the eastern and western slopes of the reef. The depression and release of isopycnals in the lee of the reef during cross-reef flows revealed that the flow released lee waves during upslope currents at specific phases of the tidal cycle when the highest sighting rates were recorded. The results of this unique, fine-scale field study provide new insights into specific hydrodynamic features, produced through tidal forcing, that may be important for creating predictable foraging opportunities for porpoises at a local scale. Information on the functional mechanisms linking porpoise distribution to static and dynamic physical habitat variables is extremely valuable to the monitoring and management of the species within the context of European conservation policies and marine renewable energy infrastructure development.

Measuring and modeling the effects of drainage water management on soil greenhouse gas fluxes from corn and soybean fields.

PubMed

Nangia, V; Sunohara, M D; Topp, E; Gregorich, E G; Drury, C F; Gottschall, N; Lapen, D R

2013-11-15

Controlled tile drainage can boost crop yields and improve water quality, but it also has the potential to increase GHG emissions. This study compared in-situ chamber-based measures of soil CH4, N2O, and CO2 fluxes for silt loam soil under corn and soybean cropping with conventional tile drainage (UTD) and controlled tile drainage (CTD). A semi-empirical model (NEMIS-NOE) was also used to predict soil N2O fluxes from soils using observed soil data. Observed N2O and CH4 fluxes between UTD and CTD fields during the farming season were not significantly different at 0.05 level. Soils were primarily a sink for CH4 but in some cases a source (sources were associated exclusively with CTD). The average N2O fluxes measured ranged between 0.003 and 0.028 kg N ha(-1) day(-1). There were some significantly higher (p ≤ 0.05) CO2 fluxes associated with CTD relative to UTD during some years of study. Correlation analyses indicated that the shallower the water table, the greater the CO2 fluxes. Higher corn plant C for CTD tended to offset estimated higher CTD CO2 C losses via soil respiration by ∼100-300 kg C ha(-1). There were good fits between observed and predicted (NEMIS-NOE) N2O fluxes for corn (R(2) = 0.70) and soybean (R(2) = 0.53). Predicted N2O fluxes were higher for CTD for approximately 70% of the paired-field study periods suggesting that soil physical factors, such as water-filled pore space, imposed by CTD have potentially strong impacts on net N fluxes. Model predictions of daily cumulative N2O fluxes for the agronomically-active study period for corn-CTD and corn-UTD, as a percentage of total N fertilizer applied, were 3.1% and 2.6%, respectively. For predicted N2O fluxes on basis of yield units, indices were 0.0005 and 0.0004 (kg N kg(-1) crop grain yield) for CTD and UTD corn fields, respectively, and 0.0011 and 0.0005 for CTD and UTD soybean fields, respectively. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Short-term hydrophysical and biological variability over the northeastern Black Sea continental slope as inferred from multiparametric tethered profiler surveys

NASA Astrophysics Data System (ADS)

Ostrovskii, Alexander; Zatsepin, Andrey

2011-06-01

This presentation introduces a new ocean autonomous profiler for multiparametric surveys at fixed geographical locations. The profiler moves down and up along a mooring line, which is taut vertically between a subsurface flotation and an anchor. This observational platform carries such modern oceanographic equipment as the Nortek Aquadopp-3D current meter and the Teledyne RDI Citadel CTD-ES probe. The profiler was successfully tested in the northeastern Black Sea during 2007-2009. By using the profiler, new data on the layered organization of the marine environment in the waters over the upper part of the continental slope were obtained. The temporal variability of the fine-scale structure of the acoustic backscatter at 2 MHz was interpreted along with biooptical and chemical data. The patchy patterns of the acoustic backscatter were associated with physical and biological processes such as the advection, propagation of submesoscale eddy, thermocline displacement, and diel migration of zooplankton. Further applications of the multidisciplinary moored profiler technology are discussed.

Structural conversion of the transformer protein RfaH: new insights derived from protein structure prediction and molecular dynamics simulations.

PubMed

Balasco, Nicole; Barone, Daniela; Vitagliano, Luigi

2015-01-01

Recent structural investigations have shown that the C-terminal domain (CTD) of the transcription factor RfaH undergoes unique structural modifications that have a profound impact into its functional properties. These modifications cause a complete change in RfaH(CTD) topology that converts from an α-hairpin to a β-barrel fold. To gain insights into the determinants of this major structural conversion, we here performed computational studies (protein structure prediction and molecular dynamics simulations) on RfaH(CTD). Although these analyses, in line with literature data, suggest that the isolated RfaH(CTD) has a strong preference for the β-barrel fold, they also highlight that a specific region of the protein is endowed with a chameleon conformational behavior. In particular, the Leu-rich region (residues 141-145) has a good propensity to adopt both α-helical and β-structured states. Intriguingly, in the RfaH homolog NusG, whose CTD uniquely adopts the β-barrel fold, the corresponding region is rich in residues as Val or Ile that present a strong preference for the β-structure. On this basis, we suggest that the presence of this Leu-rich element in RfaH(CTD) may be responsible for the peculiar structural behavior of the domain. The analysis of the sequences of RfaH family (PfamA code PF02357) unraveled that other members potentially share the structural properties of RfaH(CTD). These observations suggest that the unusual conformational behavior of RfaH(CTD) may be rare but not unique.

Interpretacion y Biomecanica. Hoja de consejos de PEPNet (Interpreting and Biomechanics. PEPNet Tipsheet)

ERIC Educational Resources Information Center

DeGroote, Bill; Morrison, Carolyn

2010-01-01

This publication, written in Spanish, describes cumulative trauma disorder (CTD), which refers to a collection of disorders associated with nerves, muscles, tendons, bones, and the neurovascular (nerves and related blood vessels) system. CTD symptoms may involve the neck, back, shoulders, arms, wrists, or hands. Interpreters with CTD may…

78 FR 51192 - Secure Supply Chain Pilot Program

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-20

... (PDF) and using the Electronic Common Technical Document (eCTD) format and the Electronic Submissions.... The PDF file name should contain ``3676'' as part of the file name, and the eCTD leaf title should.... For further information regarding eCTD, please refer to the Web site at http://www.fda.gov/Drugs...

78 FR 34393 - Electronic Submission of Tobacco Product Applications and Other Information; Public Workshop...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-07

... manufacturers experienced with electronic Common Technical Document (eCTD); vendors of software used to support... electronic submission workshop will include discussion on eCTD, which is an International Conference on Harmonization (ICH) specification developed by ICH and its member parties. The eCTD provides an organizational...

Molecular dynamics study of the phosphorylation effect on the conformational states of the C-terminal domain of RNA polymerase II.

PubMed

Yonezawa, Yasushige

2014-05-01

The carboxyl-terminal domain (CTD) of RNA polymerase II in eukaryotes regulates mRNA processing processes by recruiting various regulation factors. A main function of the CTD relies on the heptad consensus sequence (YSPTSPS). The CTD dynamically changes its conformational state to recognize and bind different regulation factors. The dynamical conformation changes are caused by modifications, mainly phosphorylation and dephosphorylation, to the serine residues. In this study, we investigate the conformational states of the unit consensus CTD peptide with various phosphorylation patterns of the serine residues by extended ensemble simulations. The results show that the CTD without phosphorylation has a flexible disordered structure distributed between twisted and extended states, but phosphorylation tends to reduce the conformational space. It was found that phosphorylation induces a β-turn around the phosphorylated serine residue and the cis conformation of the proline residue significantly inhibits the β-turn formation. The β-turn should contribute to specific CTD binding of the different regulation factors by changing the conformation propensity combined with induced fit.

Cytoplasmic tail domain of glycoprotein B is essential for HHV-6 infection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mahmoud, Nora F.; Faculty of Pharmacy, Suez Canal University, Ismailia; Jasirwan, Chyntia

2016-03-15

Human herpesvirus 6 (HHV-6) glycoprotein B (gB) is an abundantly expressed viral glycoprotein required for viral entry and cell fusion, and is highly conserved among herpesviruses. The present study examined the function of HHV-6 gB cytoplasmic tail domain (CTD). A gB CTD deletion mutant was constructed which, in contrast to its revertant, could not be reconstituted. Moreover, deletion of gB cytoplasmic tail impaired the intracellular transport of gB protein to the trans-Golgi network (TGN). Taken together, these results suggest that gB CTD is critical for HHV-6 propagation and important for intracellular transportation. - Highlights: • Glycoprotein B (gB) is highlymore » conserved among herpesviruses. • HHV-6 gB is also abundantly expressed in virions. • In the present study, we showed the function of HHV-6 gB cytoplasmic tail domain (CTD). • We found that deletion of gB CTD impairs the intracellular transport of gB protein to the trans-Golgi network (TGN), and CTD of gB is critical for HHV-6 propagation.« less

Monitoring hypoxia: approaches to addressing a complex phenomenon in the Black Sea

NASA Astrophysics Data System (ADS)

Friedrich, Jana; Janssen, Felix; He, Yunchang; Holtappels, Moritz; Konovalov, Sergey; Prien, Ralf; Rehder, Gregor; Stanev, Emil

2014-05-01

In this contribution we present an overview of results and share experiences from monitoring and assessing various hypoxia phenomena in the Black Sea. The focus is on approaches and technologies for monitoring of, e.g., mesoscale seasonal patterns in water column oxygenation, multi-decadal trends in oxycline boundary shifts, fast oxygen fluctuations at the pelagic redoxcline and the sediment-water interface, and seasonal changes in bottom-water oxygen. The various temporal scales (from hours to decades) and spatial patterns (from local to basin-scale) in water column oxygenation were addressed using state-of-the-art technologies, e.g., a free-falling pump CTD, a profiling instrumentation platform, ARGO floats equipped with oxygen optodes, static moorings equipped with oxygen optodes, and long-term monitoring programs based on standard CTD casts. Examples from four study sites in the Black Sea and one in the Baltic Sea are presented. Oxygen sensor equipped ARGO type profiling floats proved to be powerful tools to resolve seasonal changes in water column oxygenation and emphasize the importance of mesoscale processes for oxygen distribution in the Black Sea basin. Existing multi-decadal time-series monitoring data based on standard CTD measurements revealed the imprint of climate change and eutrophication on long-term oxygen distributions in the central Black Sea and hence, highlight the importance of maintaining long-term commitments to oxygen monitoring programs. Monitoring data from the last 90 years reflect the rising of the upper boundary of the suboxic zone in the 1970s and 1980s due to eutrophication, and again in the 1990s and 2000s due to NAO forcing, while eutrophication relaxed. Such long time series data allow separating out the effects that climatic forcing and eutrophication exert on oxygen depletion i.e., in the Black Sea. A free-falling pump-CTD provided high-resolution profiles of oxygen and reduced compounds in the Bosporus outflow to the Black Sea, and proved highly suitable to resolve oxygen intrusions into highly stratified systems and hence, to identify and localize processes in complex redoxclines. We also present an example of novel technology applied in the Baltic Sea, which would be highly suitable for the Black Sea. The time series recordings of the profiling instrumentation platform GODESS in the Gotland Basin allowed a thorough characterization of oscillating redoxclines as temporally dynamic, three-dimensional systems. Stand-alone static moorings equipped with optical oxygen sensors, current meters, and turbidity sensors allowed to resolve fast oxygen fluctuations at the sediment-water interface due to, e.g., internal waves and Ekman pumping on the Crimean shelf and identified the formation of seasonal (summer) hypoxia as an highly dynamic process on the north-western Black Sea shelf. This comprehensive study within the EU-FP7 project HYPOX ("In situ monitoring of oxygen depletion in hypoxic ecosystems of coastal and open seas, and land-locked water bodies", www.hypox.net) was able to address many aspects of hypoxia, e.g., in the Black Sea, and revealed the vital need for dedicated oxygen monitoring programs to adequately address the risk of hypoxia formation and ecosystem response. The challenge in any kind of monitoring is to choose the appropriate approach and technology that is suited to resolve the temporal and spatial scales on which the phenomenon occurs.

The clinical impact of Anti-DFS70 antibodies in undifferentiated connective tissue disease: case reports and a review of the literature.

PubMed

Infantino, M; Meacci, F; Grossi, V; Manfredi, M; Li Gobbi, F; Sarzi-Puttini, P; Atzeni, F; Benucci, M

2017-02-01

Anti-nuclear antibody (ANA) positivity suggests CTD but can also lead to a diagnosis of UCTD when a patient does not fulfill the CTD diagnostic criteria. An anti-dense fine speckled (DFS) immunofluorescence (IIF) pattern can be observed when using an ANA test on HEp-2 cells and is due to the presence of antibodies to the nuclear DFS70 antigen that has rarely found in CTD. Serological testing for anti-DFS70 antibodies could therefore play a very interesting negative predictive role in stratifying patients on the basis of the evolution of UCTD to CTD. We described two patients ANA and anti-DFS70 positive in which the use of new method allowing the immunoadsorption of anti-DFS70 antibodies has permitted to exclude the incorrect diagnosis of CTD.

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II.

PubMed

Lu, Huasong; Yu, Dan; Hansen, Anders S; Ganguly, Sourav; Liu, Rongdiao; Heckert, Alec; Darzacq, Xavier; Zhou, Qiang

2018-06-01

Hyperphosphorylation of the C-terminal domain (CTD) of the RPB1 subunit of human RNA polymerase (Pol) II is essential for transcriptional elongation and mRNA processing 1-3 . The CTD contains 52 heptapeptide repeats of the consensus sequence YSPTSPS. The highly repetitive nature and abundant possible phosphorylation sites of the CTD exert special constraints on the kinases that catalyse its hyperphosphorylation. Positive transcription elongation factor b (P-TEFb)-which consists of CDK9 and cyclin T1-is known to hyperphosphorylate the CTD and negative elongation factors to stimulate Pol II elongation 1,4,5 . The sequence determinant on P-TEFb that facilitates this action is currently unknown. Here we identify a histidine-rich domain in cyclin T1 that promotes the hyperphosphorylation of the CTD and stimulation of transcription by CDK9. The histidine-rich domain markedly enhances the binding of P-TEFb to the CTD and functional engagement with target genes in cells. In addition to cyclin T1, at least one other kinase-DYRK1A 6 -also uses a histidine-rich domain to target and hyperphosphorylate the CTD. As a low-complexity domain, the histidine-rich domain also promotes the formation of phase-separated liquid droplets in vitro, and the localization of P-TEFb to nuclear speckles that display dynamic liquid properties and are sensitive to the disruption of weak hydrophobic interactions. The CTD-which in isolation does not phase separate, despite being a low-complexity domain-is trapped within the cyclin T1 droplets, and this process is enhanced upon pre-phosphorylation by CDK7 of transcription initiation factor TFIIH 1-3 . By using multivalent interactions to create a phase-separated functional compartment, the histidine-rich domain in kinases targets the CTD into this environment to ensure hyperphosphorylation and efficient elongation of Pol II.

The key DNA-binding residues in the C-terminal domain of Mycobacterium tuberculosis DNA gyrase A subunit (GyrA)

PubMed Central

Huang, You-Yi; Deng, Jiao-Yu; Gu, Jing; Zhang, Zhi-Ping; Maxwell, Anthony; Bi, Li-Jun; Chen, Yuan-Yuan; Zhou, Ya-Feng; Yu, Zi-Niu; Zhang, Xian-En

2006-01-01

As only the type II topoisomerase is capable of introducing negative supercoiling, DNA gyrase is involved in crucial cellular processes. Although the other domains of DNA gyrase are better understood, the mechanism of DNA binding by the C-terminal domain of the DNA gyrase A subunit (GyrA-CTD) is less clear. Here, we investigated the DNA-binding sites in the GyrA-CTD of Mycobacterium tuberculosis gyrase through site-directed mutagenesis. The results show that Y577, R691 and R745 are among the key DNA-binding residues in M.tuberculosis GyrA-CTD, and that the third blade of the GyrA-CTD is the main DNA-binding region in M.tuberculosis DNA gyrase. The substitutions of Y577A, D669A, R691A, R745A and G729W led to the loss of supercoiling and relaxation activities, although they had a little effect on the drug-dependent DNA cleavage and decatenation activities, and had no effect on the ATPase activity. Taken together, these results showed that the GyrA-CTD is essential to DNA gyrase of M.tuberculosis, and promote the idea that the M.tuberculosis GyrA-CTD is a new potential target for drug design. It is the first time that the DNA-binding sites in GyrA-CTD have been identified. PMID:17038336

Overexpression of YB1 C-terminal domain inhibits proliferation, angiogenesis and tumorigenicity in a SK-BR-3 breast cancer xenograft mouse model.

PubMed

Shi, Jian-Hong; Cui, Nai-Peng; Wang, Shuo; Zhao, Ming-Zhi; Wang, Bing; Wang, Ya-Nan; Chen, Bao-Ping

2016-01-01

Y-box-binding protein 1 (YB1) is a multifunctional transcription factor with vital roles in proliferation, differentiation and apoptosis. In this study, we have examined the role of its C-terminal domain (YB1 CTD) in proliferation, angiogenesis and tumorigenicity in breast cancer. Breast cancer cell line SK-BR-3 was infected with GFP-tagged YB1 CTD adenovirus expression vector. An 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) proliferation assay showed that YB1 CTD decreased SK-BR-3 cell proliferation, and down-regulated cyclin B1 and up-regulated p21 levels in SK-BR-3 cells. YB1 CTD overexpression changed the cytoskeletal organization and slightly inhibited the migration of SK-BR-3 cells. YB1 CTD also inhibited secreted VEGF expression in SK-BR-3 cells, which decreased SK-BR-3-induced EA.hy926 endothelial cell angiogenesis in vitro. YB1 CTD overexpression attenuated the ability of SK-BR-3 cells to form tumours in nude mice, and decreased in vivo VEGF levels and angiogenesis in the xenografts in SK-BR-3 tumour-bearing mice. Taken together, our findings demonstrate the vital role of YB1 CTD overexpression in inhibiting proliferation, angiogenesis and tumorigenicity of breast cancer cell line SK-BR-3.

Intact Arabidopsis RPB1 functions in stem cell niches maintenance and cell cycling control.

PubMed

Zhang, Qian-Qian; Li, Ying; Fu, Zhao-Ying; Liu, Xun-Biao; Yuan, Kai; Fang, Ying; Liu, Yan; Li, Gang; Zhang, Xian-Sheng; Chong, Kang; Ge, Lei

2018-05-12

Plant meristem activity depends on accurate execution of transcriptional networks required for establishing optimum functioning of stem cell niches. An Arabidopsis mutant card1-1 (constitutive auxin response with DR5:GFP) that encodes a truncated RPB1 (RNA Polymerase II's largest subunit) with shortened C-terminal domain (CTD) was identified. Phosphorylation of the CTD repeats of RPB1 is coupled to transcription in eukaryotes. Here we uncover that the truncated CTD of RPB1 disturbed cell cycling and enlarged the size of shoot and root meristem. The defects in patterning of root stem cell niche in card1-1 indicates that intact CTD of RPB1 is necessary for fine-tuning the specific expression of genes responsible for cell-fate determination. The gene-edited plants with different CTD length of RPB1, created by CRISPR-CAS9 technology, confirmed that both the full length and the DK-rich tail of RPB1's CTD play roles in the accurate transcription of CYCB1;1 encoding a cell-cycle marker protein in root meristem and hence participate in maintaining root meristem size. Our experiment proves that the intact RPB1 CTD is necessary for stem cell niche maintenance, which is mediated by transcriptional regulation of cell cycling genes. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

Heat-shock inactivation of the TFIIH-associated kinase and change in the phosphorylation sites on the C-terminal domain of RNA polymerase II.

PubMed

Dubois, M F; Vincent, M; Vigneron, M; Adamczewski, J; Egly, J M; Bensaude, O

1997-02-15

The C-terminal domain (CTD) of the RNA polymerase II largest subunit (RPB1) plays a central role in transcription. The CTD is unphosphorylated when the polymerase assembles into a preinitiation complex of transcription and becomes heavily phosphorylated during promoter clearance and entry into elongation of transcription. A kinase associated to the general transcription factor TFIIH, in the preinitiation complex, phosphorylates the CTD. The TFIIH-associated CTD kinase activity was found to decrease in extracts from heat-shocked HeLa cells compared to unstressed cells. This loss of activity correlated with a decreased solubility of the TFIIH factor. The TFIIH-kinase impairment during heat-shock was accompanied by the disappearance of a particular phosphoepitope (CC-3) on the RPB1 subunit. The CC-3 epitope was localized on the C-terminal end of the CTD and generated in vitro when the RPB1 subunit was phosphorylated by the TFIIH-associated kinase but not by another CTD kinase such as MAP kinase. In apparent discrepancy, the overall RPB1 subunit phosphorylation increased during heat-shock. The decreased activity in vivo of the TFIIH kinase might be compensated by a stress-activated CTD kinase such as MAP kinase. These results also suggest that heat-shock gene transcription may have a weak requirement for TFIIH kinase activity.

Heat-shock inactivation of the TFIIH-associated kinase and change in the phosphorylation sites on the C-terminal domain of RNA polymerase II.

PubMed Central

Dubois, M F; Vincent, M; Vigneron, M; Adamczewski, J; Egly, J M; Bensaude, O

1997-01-01

The C-terminal domain (CTD) of the RNA polymerase II largest subunit (RPB1) plays a central role in transcription. The CTD is unphosphorylated when the polymerase assembles into a preinitiation complex of transcription and becomes heavily phosphorylated during promoter clearance and entry into elongation of transcription. A kinase associated to the general transcription factor TFIIH, in the preinitiation complex, phosphorylates the CTD. The TFIIH-associated CTD kinase activity was found to decrease in extracts from heat-shocked HeLa cells compared to unstressed cells. This loss of activity correlated with a decreased solubility of the TFIIH factor. The TFIIH-kinase impairment during heat-shock was accompanied by the disappearance of a particular phosphoepitope (CC-3) on the RPB1 subunit. The CC-3 epitope was localized on the C-terminal end of the CTD and generated in vitro when the RPB1 subunit was phosphorylated by the TFIIH-associated kinase but not by another CTD kinase such as MAP kinase. In apparent discrepancy, the overall RPB1 subunit phosphorylation increased during heat-shock. The decreased activity in vivo of the TFIIH kinase might be compensated by a stress-activated CTD kinase such as MAP kinase. These results also suggest that heat-shock gene transcription may have a weak requirement for TFIIH kinase activity. PMID:9016617

Using seismic reflection data to reveal high-resolution structure and pathway of the upper Western Boundary Undercurrent core at Eirik Drift

NASA Astrophysics Data System (ADS)

Müller-Michaelis, Antje; Uenzelmann-Neben, Gabriele

2015-12-01

The method of seismic oceanography was applied to identify fine structure and pathways of the Western Boundary Undercurrent (WBUC) at Eirik Drift, 200 km south of Greenland. Three high-velocity cores of the WBUC were distinguished: a deep core in depths >2600 m which carries Denmark Strait Overflow Water, an upper core in depths between ~1900 and 3000 m transporting Iceland-Scotland Overflow Water, and a split-off of this upper core, which crosses the main crest of Eirik Drift at depths between ~1900 and 2400 m. For the upper WBUC core a detailed analysis of the structure was conducted. The WBUC core has as a domed structure, which changes in style, width and height above seafloor along the lines of the changing topography. We proved not only the influence of the topography on pathway and structure of the WBUC core but also that this information cannot be gained by measuring the overflow waters with discrete CTD stations.

A vertical wall in the Whittard Canyon with a novel community assemblage

NASA Astrophysics Data System (ADS)

Johnson, Mark; White, Martin; Wilson, Annette; Wuerzberg, Laura; Schwabe, Enrico; Folch, Helka; Allcock, Louise

2013-04-01

We describe a hitherto unreported community from a vertical wall in the Whittard Canyon system on the Atlantic Margin. The wall extended vertically for about 100 m from approximately 750 m depth. We explored the wall with an ROV and discovered an assemblage cominated by large limid bivalves Acesta excavata and deep-water oysters Neopycnodonte zibrowii at very high densities, particularly at overhangs. The assemblage also contained deep-water corals (including solitary corals). It had high numbers of flytrap anemones and had many mobile species associated with it including crustaceans such as Paramola cuvieri and Bathynectes longispina, echinoderms and fishes. We took CTD transects in the area of the wall and beam attenuation indicated nepheloid layers present in the water column. The greatest densities of suspended material at the ROV dive site were at the depth of the wall. We hypothesise that internal waves concentrate suspended sediment at the foot of the vertical wall. This may provide the resources to support the high density of large filter feeders at these depths.

Visible and Thermal Imaging of Sea Ice and Open Water from Coast Guard Arctic Domain Awareness Flights

DTIC Science & Technology

2014-09-30

dropsondes, micro- aircraft), cloud top/base heights Arctic Ocean Surface Temperature project Steele Buoy drops for SLP , SST, SSS, & surface velocity...Colón & Vancas (NIC) Drop buoys for SLP , temperature and surface velocity Waves & Fetch in the MIZ Thompson SWIFTS buoys measuring wave energy...Expendable CTD, AXCP= Air Expendable Current Profiler, SLP = Sea Level atmospheric Pressure, SST= Seas Surface Temperature, A/C= aircraft, FSD= Floe Size Distribution, SIC=Sea Ice Concentration

Rsp5 WW domains interact directly with the carboxyl-terminal domain of RNA polymerase II.

PubMed

Chang, A; Cheang, S; Espanel, X; Sudol, M

2000-07-07

RSP5 is an essential gene in Saccharomyces cerevisiae and was recently shown to form a physical and functional complex with RNA polymerase II (RNA pol II). The amino-terminal half of Rsp5 consists of four domains: a C2 domain, which binds membrane phospholipids; and three WW domains, which are protein interaction modules that bind proline-rich ligands. The carboxyl-terminal half of Rsp5 contains a HECT (homologous to E6-AP carboxyl terminus) domain that catalytically ligates ubiquitin to proteins and functionally classifies Rsp5 as an E3 ubiquitin-protein ligase. The C2 and WW domains are presumed to act as membrane localization and substrate recognition modules, respectively. We report that the second (and possibly third) Rsp5 WW domain mediates binding to the carboxyl-terminal domain (CTD) of the RNA pol II large subunit. The CTD comprises a heptamer (YSPTSPS) repeated 26 times and a PXY core that is critical for interaction with a specific group of WW domains. An analysis of synthetic peptides revealed a minimal CTD sequence that is sufficient to bind to the second Rsp5 WW domain (Rsp5 WW2) in vitro and in yeast two-hybrid assays. Furthermore, we found that specific "imperfect" CTD repeats can form a complex with Rsp5 WW2. In addition, we have shown that phosphorylation of this minimal CTD sequence on serine, threonine and tyrosine residues acts as a negative regulator of the Rsp5 WW2-CTD interaction. In view of the recent data pertaining to phosphorylation-driven interactions between the RNA pol II CTD and the WW domain of Ess1/Pin1, we suggest that CTD dephosphorylation may be a prerequisite for targeted RNA pol II degradation.

Evidence-based diuretics: focus on chlorthalidone and indapamide.

PubMed

DiNicolantonio, James J; Bhutani, Jaikrit; Lavie, Carl J; O'Keefe, James H

2015-03-01

Thiazide and thiazide-like diuretics are cornerstone treatments for hypertension. However, unlike chlorthalidone (CTD) and indapamide (IDP), hydrochlorothiazide (HCTZ) lacks evidence for reducing morbidity and mortality as monotherapy compared with placebo or control. Despite this fact, HCTZ is prescribed much more frequently than CTD or IDP. We believe that all hypertension guidelines should follow the National Institute for Health and Excellence (NICE) and make IDP and CTD first choice 'thiazide-like diuretics.' This article will focus on the available evidence pertaining to HCTZ versus CTD and IDP. We will review the pharmacological differences between these three diuretics, as well as the clinical trial data and important side effects.

Histopathology of lung disease in the connective tissue diseases.

PubMed

Vivero, Marina; Padera, Robert F

2015-05-01

The pathologic correlates of interstitial lung disease (ILD) secondary to connective tissue disease (CTD) comprise a diverse group of histologic patterns. Lung biopsies in patients with CTD-associated ILD tend to demonstrate simultaneous involvement of multiple anatomic compartments of the lung. Certain histologic patterns tend to predominate in each defined CTD, and it is possible in many cases to confirm connective tissue-associated lung disease and guide patient management using surgical lung biopsy. This article will cover the pulmonary pathologies seen in rheumatoid arthritis, systemic sclerosis, myositis, systemic lupus erythematosus, Sjögren syndrome, and mixed CTD. Copyright © 2015 Elsevier Inc. All rights reserved.

cis-Proline-mediated Ser(P)[superscript 5] Dephosphorylation by the RNA Polymerase II C-terminal Domain Phosphatase Ssu72

DOE Office of Scientific and Technical Information (OSTI.GOV)

Werner-Allen, Jon W.; Lee, Chul-Jin; Liu, Pengda

2012-05-16

RNA polymerase II coordinates co-transcriptional events by recruiting distinct sets of nuclear factors to specific stages of transcription via changes of phosphorylation patterns along its C-terminal domain (CTD). Although it has become increasingly clear that proline isomerization also helps regulate CTD-associated processes, the molecular basis of its role is unknown. Here, we report the structure of the Ser(P){sup 5} CTD phosphatase Ssu72 in complex with substrate, revealing a remarkable CTD conformation with the Ser(P){sup 5}-Pro{sup 6} motif in the cis configuration. We show that the cis-Ser(P){sup 5}-Pro{sup 6} isomer is the minor population in solution and that Ess1-catalyzed cis-trans-proline isomerizationmore » facilitates rapid dephosphorylation by Ssu72, providing an explanation for recently discovered in vivo connections between these enzymes and a revised model for CTD-mediated small nuclear RNA termination. This work presents the first structural evidence of a cis-proline-specific enzyme and an unexpected mechanism of isomer-based regulation of phosphorylation, with broad implications for CTD biology« less

Clinical Correlates and Mediators of Self-Concept in Youth with Chronic Tic Disorders.

PubMed

Hanks, Camille E; McGuire, Joseph F; Lewin, Adam B; Storch, Eric A; Murphy, Tanya K

2016-02-01

This study investigated the clinical correlates and mediators of self-concept in youth with Chronic Tic Disorders (CTD). Ninety-seven youth aged 6-17 (M = 11.1 ± 2.89; 79.4 % male) with CTD were administered the Yale Global Tic Severity Scale, the Piers-Harris Children's Self-Concept Scale-Second Edition, and self-report and clinician-administered measures assessing behavioral and psychological difficulties and comorbid conditions. Youth with CTD had a slightly below average level of self-concept, with 20 % (n = 19) exhibiting low self-concept. Youth with CTD-only had greater self-concept relative to youth with CTD and obsessive-compulsive disorder (OCD) (p = 0.04) or CTD, OCD, and attention deficit hyperactivity disorder (ADHD) combined (p = 0.009). Medium-to-large-sized associations were observed between youth's self-concept and clinical characteristics (e.g., severity of ADHD, OCD and depressive symptoms). Youth's self-concept partially mediated the relationship between tic severity and depressive symptom severity, and the interaction between tic impairment and youth's reliance on avoidant coping strategies moderated youth's self-concept. Implications, limitations, and recommendations for future interventions are discussed.

Clinical Correlates and Mediators of Self-Concept in Youth with Chronic Tic Disorders

PubMed Central

Hanks, Camille E.; McGuire, Joseph F.; Lewin, Adam B.; Storch, Eric A.

2015-01-01

This study investigated the clinical correlates and mediators of self-concept in youth with Chronic Tic Disorders (CTD). Ninety-seven youth aged 6–17 (M = 11.1 ± 2.89; 79.4 % male) with CTD were administered the Yale Global Tic Severity Scale, the Piers-Harris Children’s Self-Concept Scale—Second Edition, and self-report and clinician-administered measures assessing behavioral and psychological difficulties and comorbid conditions. Youth with CTD had a slightly below average level of self-concept, with 20 % (n = 19) exhibiting low self-concept. Youth with CTD-only had greater self-concept relative to youth with CTD and obsessive–compulsive disorder (OCD) (p = 0.04) or CTD, OCD, and attention deficit hyperactivity disorder (ADHD) combined (p = 0.009). Medium-to-large-sized associations were observed between youth’s self-concept and clinical characteristics (e.g., severity of ADHD, OCD and depressive symptoms). Youth’s self-concept partially mediated the relationship between tic severity and depressive symptom severity, and the interaction between tic impairment and youth’s reliance on avoidant coping strategies moderated youth’s self-concept. Implications, limitations, and recommendations for future interventions are discussed. PMID:25791488

Chromatin Condensing Functions of the Linker Histone C-terminal Domain are mediated by Specific Amino Acid Composition and Intrinsic Protein Disorder†

PubMed Central

Lu, Xu; Hamkalo, Barbara; Parseghian, Missag H.; Hansen, Jeffrey C.

2009-01-01

Linker histones bind to the nucleosomes and linker DNA of chromatin fibers, causing changes in linker DNA structure and stabilization of higher order folded and oligomeric chromatin structures. Linker histones affect chromatin structure acting primarily through their ~100 residue C-terminal domain (CTD). We have previously shown that the ability of the linker histone H1° to alter chromatin structure was localized to two discontinuous 24-/25-residue CTD regions (Lu, X., and Hansen, J. C. (2004) J Biol Chem 279, 8701–8707). To determine the biochemical basis for these results, we have characterized chromatin model systems assembled with endogenous mouse somatic H1 isoforms, or recombinant H1° CTD mutants in which the primary sequence has been scrambled, the amino acid composition mutated, or the location of various CTD regions swapped. Our results indicate that specific amino acid composition plays a fundamental role in molecular recognition and function by the H1 CTD. Additionally, these experiments support a new molecular model for CTD function, and provide a biochemical basis for the redundancy observed in H1 isoform knockout experiments in vivo. PMID:19072710

Studies on the wintertime current structure and T-S fine-structure in the Taiwan Strait

NASA Astrophysics Data System (ADS)

Hu, Jianyu; Fu, Zilang; Wu, Lianxing

1990-12-01

A cruise through the western sea area of the Taiwan Strait was carried out by the R/V Dong Fang Hong in December, 1987. Eight anchored and 10 not anchored stations were set up. Over 25 time-series current observations were made at each station and CTD (Conductivity-temperature-depth) measurements were made at 5 anchored and 10 not anchored stations. Based on the measured data. fine-structures and step-like vertical structures of temperature and salinity were analysed and a tentative wintertime current structure in the Taiwan Strait was described.

Relationship between cognitive and non-cognitive symptoms of delirium.

PubMed

Rajlakshmi, Aarya Krishnan; Mattoo, Surendra Kumar; Grover, Sandeep

2013-04-01

To study relationship between the cognitive and the non-cognitive symptoms of delirium. Eighty-four patients referred to psychiatry liaison services and met DSM-IVTR criteria of delirium were assessed using the Delirium Rating Scale Revised-1998 (DRSR-98) and Cognitive Test for Delirium (CTD). The mean DRS-R-98 severity score was 17.19 and DRS-R-98 total score was 23.36. The mean total score on CTD was 11.75. The mean scores on CTD were highest for comprehension (3.47) and lowest for vigilance (1.71). Poor attention was associated with significantly higher motor retardation and higher DRS-R-98 severity scores minus the attention scores. There were no significant differences between those with and without poor attention. Higher attention deficits were associated with higher dysfunction on all other domains of cognition on CTD. There was significant correlation between cognitive functions as assessed on CTD and total DRS-R-98 score, DRS-R-98 severity score and DRS-R-98 severity score without the attention item score. However, few correlations emerged between CTD domains and CTD total scores with cognitive symptom total score of DRS-R-98 (items 9-13) and non-cognitive symptom total score of DRS-R-98 (items 1-8). Our study suggests that in delirium, cognitive deficits are quite prevalent and correlate with overall severity of delirium. Attention deficit is a core symptom of delirium. Copyright © 2012 Elsevier B.V. All rights reserved.

Top-Down Charge Transfer Dissociation (CTD) of Gas-Phase Insulin: Evidence of a One-Step, Two-Electron Oxidation Mechanism

NASA Astrophysics Data System (ADS)

Li, Pengfei; Kreft, Iris; Jackson, Glen P.

2018-02-01

Top-down analyses of protonated insulin cations of charge states of 4+, 5+, or 6+ were performed by exposing the isolated precursor ions to a beam of helium cations with kinetic energy of more than 6 keV, in a technique termed charge transfer dissociation (CTD). The 100 ms charge transfer reaction resulted in approximately 20% conversion efficiency to other intact charge exchange products (CTnoD), and a range of low abundance fragment ions. To increase backbone and sulfide cleavages, and to provide better structural information than straightforward MS2 CTD, the CTnoD oxidized products were isolated and subjected to collisional activation at the MS3 level. The MS3 CTD/CID reaction effectively broke the disulfide linkages, separated the two chains, and yielded more structurally informative fragment ions within the inter-chain cyclic region. CTD also provided doubly oxidized intact product ions at the MS2 level, and resonance ejection of the singly oxidized product ion revealed that the doubly oxidized product originates directly from the isolated precursor ion and not from consecutive CTD reactions of a singly oxidized intermediate. MS4 experiments were employed to help identify potential radical cations and diradical cations, but the results were negative or inconclusive. Nonetheless, the two-electron oxidation process is a demonstration of the very large potential energy (>20 eV) available through CTD, and is a notable capability for a 3D ion trap platform.

Better care provided to patients with tuberculosis at county designated TB hospitals (CTD) compared to non-CTDs in rural China.

PubMed

Yuan, Li; Zhang, Hui; Zhou, Changming; Jiang, Weili; Zhao, Qi; Biao, Xu

2017-01-13

The primary unit of tuberculosis (TB) medical care in China is the county TB dispensary or county designated hospital (CTD), where patients can receive free diagnosis and treatment. However, a substantial number of patients seek their anti-TB treatment from general health facilities (Non-CTDs). This study aimed to investigate the first anti-TB treatment experience and choice of health facilities of retreated TB patients and their determinants. A cross-sectional study was conducted in Jiangsu, Shandong and Sichuan provinces. All registered re-treated TB patients were investigated using a structured questionnaire covering information on demographics, socio-economic characteristics, and previous anti-TB treatment experiences. Totally, 75.3% of 544 patients visited CTD directly for initial treatment. Patients who were female (OR:1.71, 95% CI: 1.01-2.87), over 40 years of age (OR:2.80, 95% CI: 1.24-6.33), from Jiangsu (OR:3.07, 95% CI: 1.57-6.01) and Sichuan (OR:4.47, 95% CI: 2.29-8.73) and those diagnosed before 2005 (OR:6.87, 95% CI: 4.24-11.13) had a significant higher risk receiving their initial treatment at a non-CTD. Patients were more likely to have standardized diagnosis and treatment regimens in CTD (89.8%) than in non-CTDs (65.9%). Patients treated in non-CTDs versus in CTD had a lower possibility to complete their treatment course during first TB episode (χ 2  = 3.926, P = 0.048), but there was no significant difference in the cure rate between different facilities (CTD 60.8%, Non-CTDs 59.1%). Patients in non-CTDs incurred higher costs (1,360 CNY) than those treated in CTD (920CNY). CTD play a key role in the National Tuberculosis Control Program. Patients should be guided to seek health care in county designated hospital, where they are more likely to receive appropriate examinations, treatment regimens and rigorous supervision, and to bear a lighter economic burden.

Large Kelvin-Helmholtz Billow Trains Observed in the Kuroshio above a Seamount

NASA Astrophysics Data System (ADS)

Chang, M. H.; Jheng, S. Y.; Lien, R. C.

2016-02-01

Trains of large Kelvin-Helmholtz (KH) billows were observed within the Kuroshio core, off southeastern Taiwan, at 230-m depth above a seamount in shipboard echo sounder, ADCP, and LADCP/CTD profiling, and moored ADCP measurements. The large KH billow trains were present in a strong shear band along 0.55 ms-1 isotach within the Kuroshio core as a result of the Kuroshio current interacting with the rapid changing topography. Each individual billow, resembling a cats' eye, had a horizontal length scale of 200 m and a vertical amplitude scale of 100 m, and a propagation timescale of 7 minutes, near local buoyancy period. Overturns were frequently observed in both the billow core and the upper eyelid. The shear instability criterion (Ri < 0.25) was reached in the billow core. The dissipation rate of turbulent kinetic energy in the core and in the eyelid is comparable at an average value of O(10-4) WKg-1 and a maximum value of O(10-3) WKg-1. The KH billows derive energy from the Kuroshio kinetic energy. The corresponding turbulence mixing allows the water mass exchange between the Kuroshio and the surrounding water. These small-scale processes play an important role in the energy and water mass budgets within the Kuroshio.

Helicopter- and ship-based measurements of mesoscale ocean color and thermal features in the marginal ice zone

NASA Astrophysics Data System (ADS)

Tanis, Fred J.; Manley, Thomas O.; Mitchell, Brian G.

1990-09-01

Eddies along the Polar Front/Marginal Ice Zone (MIZ) in Fram Strait are thought to make important contributions to nutrient flux and stimulation of primary productivity. During the Coordinated Eastern Arctic Regional Experiment (CEAREX) helicopter-based measurements of upwelling radiance were made in four visible spectral bands and in the thermal IR across mesoscale features associated with the MIZ. These structures were mapped by flying a grid pattern over the ocean surface to define eddy boundaries. Subsequently, the area was also sampled vertically with CTD and spectral radiometer profilers. Data obtained from a single structure were integrated to construct a three dimensional picture of physical and optical properties. Volume modeling of temperature, salinity, and density fields obtained from CTD survey define the subsurface eddy structure and are in good agreement with infrared derived characteristics. Maximum temperature in the core was found to be four degrees higher than the surrounding water. Volume modeling further indicates that a subsurface layer of Arctic Intermediate Water is intrinsically associated with the surface expression of the eddy. The ratio of upwelling radiances, L(44l)/L(565), was found to be correlated to surface chlorophyll, particulate absorption coefficient, and in water determinations of L using the optical profiling system. The remote sensing reflectance ratio along with the IR sea surface temperature were found to be useful to detect the surface expression of the eddy and to indicate near surface biological and physical processes.

Improved statistical method for temperature and salinity quality control

NASA Astrophysics Data System (ADS)

Gourrion, Jérôme; Szekely, Tanguy

2017-04-01

Climate research and Ocean monitoring benefit from the continuous development of global in-situ hydrographic networks in the last decades. Apart from the increasing volume of observations available on a large range of temporal and spatial scales, a critical aspect concerns the ability to constantly improve the quality of the datasets. In the context of the Coriolis Dataset for ReAnalysis (CORA) version 4.2, a new quality control method based on a local comparison to historical extreme values ever observed is developed, implemented and validated. Temperature, salinity and potential density validity intervals are directly estimated from minimum and maximum values from an historical reference dataset, rather than from traditional mean and standard deviation estimates. Such an approach avoids strong statistical assumptions on the data distributions such as unimodality, absence of skewness and spatially homogeneous kurtosis. As a new feature, it also allows addressing simultaneously the two main objectives of an automatic quality control strategy, i.e. maximizing the number of good detections while minimizing the number of false alarms. The reference dataset is presently built from the fusion of 1) all ARGO profiles up to late 2015, 2) 3 historical CTD datasets and 3) the Sea Mammals CTD profiles from the MEOP database. All datasets are extensively and manually quality controlled. In this communication, the latest method validation results are also presented. The method has already been implemented in the latest version of the delayed-time CMEMS in-situ dataset and will be deployed soon in the equivalent near-real time products.

Improved Statistical Method For Hydrographic Climatic Records Quality Control

NASA Astrophysics Data System (ADS)

Gourrion, J.; Szekely, T.

2016-02-01

Climate research benefits from the continuous development of global in-situ hydrographic networks in the last decades. Apart from the increasing volume of observations available on a large range of temporal and spatial scales, a critical aspect concerns the ability to constantly improve the quality of the datasets. In the context of the Coriolis Dataset for ReAnalysis (CORA) version 4.2, a new quality control method based on a local comparison to historical extreme values ever observed is developed, implemented and validated. Temperature, salinity and potential density validity intervals are directly estimated from minimum and maximum values from an historical reference dataset, rather than from traditional mean and standard deviation estimates. Such an approach avoids strong statistical assumptions on the data distributions such as unimodality, absence of skewness and spatially homogeneous kurtosis. As a new feature, it also allows addressing simultaneously the two main objectives of a quality control strategy, i.e. maximizing the number of good detections while minimizing the number of false alarms. The reference dataset is presently built from the fusion of 1) all ARGO profiles up to early 2014, 2) 3 historical CTD datasets and 3) the Sea Mammals CTD profiles from the MEOP database. All datasets are extensively and manually quality controlled. In this communication, the latest method validation results are also presented. The method has been implemented in the latest version of the CORA dataset and will benefit to the next version of the Copernicus CMEMS dataset.

Conductivity Cell Thermal Inertia Correction Revisited

NASA Astrophysics Data System (ADS)

Eriksen, C. C.

2012-12-01

Salinity measurements made with a CTD (conductivity-temperature-depth instrument) rely on accurate estimation of water temperature within their conductivity cell. Lueck (1990) developed a theoretical framework for heat transfer between the cell body and water passing through it. Based on this model, Lueck and Picklo (1990) introduced the practice of correcting for cell thermal inertia by filtering a temperature time series using two parameters, an amplitude α and a decay time constant τ, a practice now widely used. Typically these two parameters are chosen for a given cell configuration and internal flushing speed by a statistical method applied to a particular data set. Here, thermal inertia correction theory has been extended to apply to flow speeds spanning well over an order of magnitude, both within and outside a conductivity cell, to provide predictions of α and τ from cell geometry and composition. The extended model enables thermal inertia correction for the variable flows encountered by conductivity cells on autonomous gliders and floats, as well as tethered platforms. The length scale formed as the product of cell encounter speed of isotherms, α, and τ can be used to gauge the size of the temperature correction for a given thermal stratification. For cells flushed by dynamic pressure variation induced by platform motion, this length varies by less than a factor of 2 over more than a decade of speed variation. The magnitude of correction for free-flow flushed sensors is comparable to that of pumped cells, but at an order of magnitude in energy savings. Flow conditions around a cell's exterior are found to be of comparable importance to thermal inertia response as flushing speed. Simplification of cell thermal response to a single normal mode is most valid at slow speed. Error in thermal inertia estimation arises from both neglect of higher modes and numerical discretization of the correction scheme, both of which can be easily quantified. Consideration of thermal inertia correction enables assessment of various CTD sampling schemes. Spot sampling by pumping a cell intermittently provides particular challenges, and may lead to biases in inferred salinity that are comparable to climate signals reported from profiling float arrays.

Instrument developments for chemical and physical characterization, mapping and sampling of extreme environments (Antarctic sub ice environment)

NASA Astrophysics Data System (ADS)

Vogel, S. W.; Powell, R. D.; Griffith, I.; Lawson, T.; Schiraga, S.; Ludlam, G.; Oen, J.

2009-12-01

A number of instrumentation is currently under development designed to enable the study of subglacial environments in Antarctica through narrow kilometer long boreholes. Instrumentation includes: - slim line Sub-Ice ROV (SIR), - Geochemical Instrumentation Package for Sub Ice Environments (GIPSIE) to study geochemical fluxes in water and across the sediment water interface (CO2, CH4, dO, NH4, NO3, Si, PO4, pH, redox, T, H2, HS, O2, N2O, CTD, particle size, turbidity, color camera, current meter and automated water sampler) with real-time telemetry for targeted sampling, - long term energy-balance mooring system, - active source slide hammer sediment corer, and - integration of a current sensor into the ITP profiler. The instrumentation design is modular and suitable for remote operated as well as autonomous long-term deployment. Of interest to the broader science community is the development of the GIPSIE and efforts to document the effect of sample recovery from depth on the sample chemistry. The GIPSIE is a geochemical instrumentation package with life stream telemetry, allowing for user controlled targeted sampling of water column and the water sediment interphase for chemical and biological work based on actual measurements and not a preprogrammed automated system. The porewater profiler (pH, redox, T, H2, HS, O2, N2O) can penetrate the upper 50 cm of sediment and penetration is documented with real time video. Associated with GIPSIE is an on-site lab set-up, utilizing a set of identical sensors. Comparison between the insitu measurements and measurements taken onsite directly after samples are recovered from depth permits assessing the effect of sample recovery on water and sediment core chemistry. Sample recovery related changes are mainly caused by changes in the pressure temperature field and exposure of samples to atmospheric conditions. Exposure of anaerobic samples to oxygen is here a specific concern. Recovery from depth effects in generally pH, solubility of gases and nutrients and can initiate complex chemical reaction, the product of which is later measured in the lab. Further information on the instrument developments can be found at http://jove.geol.niu.edu/faculty/svogel/Technology/Technology-index.html

[Morphological features of the myometrium in connective tissue dysplasia in women with uterine inertia].

PubMed

Konovalov, P V; Mitrofanova, L B; Gorshkov, A N; Ovsyannikov, F A

2015-01-01

to reveal the morphological features of the lower uterine segment myometrium in connective tissue dysplasia (CTD) in women with uterine inertia. Histological, immunohistochemical (with antibodies against collagen types I and III, matrix metalloproteinases 1 and 9 (MMR-1, MMP-9), tissue inhibitor of metalloproteinase 1 (TIMP-1), fibronectin; fibulin-5, connexin-43), electron microscopic, and electron immunocytochemical studies with morphometry of myometrial fragments from 15 parturient women with CTD and uterine inertia (a study group) and those from 10 women without CTD (a control group). The myometrium in CTD exhibited the decreased expression of connextin-43, fibulin-5, TIMP-1, collagens types I and III with collagen type III predominance and the unchanged levels of fibronectin and MMP-1 and MMP-9. Electron microscopy and immunocytochemistry showed fewer intercellular contacts and the dramatically lower expression of connexin-43 than in the control. A set of found myometrial changes in women with uterine inertia is a manifestation of CTD.

Workplace discrimination and cumulative trauma disorders: the national EEOC ADA research project.

PubMed

Armstrong, Amy J; McMahon, Brian T; West, Steven L; Lewis, Allen

2005-01-01

Employment discrimination of persons with cumulative trauma disorders (CTDs) was explored using the Integrated Mission System dataset of the US Equal Employment Opportunity Commission. Demographic characteristics and merit resolutions of the Charging Parties (persons with CTD) were compared to individuals experiencing other physical, sensory and neurological impairments. Factors compared also included industry designation, geographic region, and size of Respondents against which allegations were filed. Persons with CTD had proportionately greater allegations among large Respondents (greater than 500 workers) engaged in manufacturing, utilities, transportation, finance insurance and real estate. The types of discrimination Issues that were proportionately greater in the CTD group included layoff, failure to reinstate, and failure to provide reasonable accommodation. The CTD group was significantly less likely than the comparison group to be involved in discrimination Issues such as assignment to less desirable duty, shift or work location; demotion; termination, or failure to hire or provide training. Persons with CTD had higher proportions of merit Resolutions where allegations were voluntarily withdrawn by the Charging Party with benefits.

Reconciling healthcare professional and patient perspectives in the development of disease activity and response criteria in connective tissue disease-related interstitial lung diseases.

PubMed

Saketkoo, Lesley Ann; Mittoo, Shikha; Frankel, Sid; LeSage, Daphne; Sarver, Catherine; Phillips, Kristine; Strand, Vibeke; Matteson, Eric L

2014-04-01

Interstitial lung diseases (ILD), including those related to connective tissue disease (CTD), and idiopathic pulmonary fibrosis (IPF) carry high morbidity and mortality. Great efforts are under way to develop and investigate meaningful treatments in the context of clinical trials. However, efforts have been challenged by a lack of validated outcome measures and by inconsistent use of measures in clinical trials. Lack of consensus has fragmented effective use of strategies in CTD-ILD and IPF, with a history of resultant difficulties in obtaining agency approval of treatment interventions. Until recently, the patient perspective to determine domains and outcome measures in CTD-ILD and IPF had never been applied. Efforts described here demonstrate unequivocally the value and influence of patient involvement on core set development. Regarding CTD-ILD, this is the first OMERACT working group to directly address a manifestation/comorbidity of a rheumatic disease (ILD) as well as a disease not considered rheumatic (IPF). The OMERACT 11 proceedings of the CTD-ILD Working Group describe the forward and lateral process to include both the medical and patient perspectives in the urgently needed identification of a core set of preliminary domains and outcome measures in CTD-ILD and IPF.

Analysis of the MRPL3, DNAJC13 and OFCC1 variants in Chinese Han patients with TS-CTD.

PubMed

Guo, Yi; Deng, Xiong; Zhang, Jie; Su, Linyan; Xu, Hongbo; Luo, Ziqiang; Deng, Hao

2012-05-23

Tourette syndrome/chronic tic phenotype (TS-CTD) is a neurological disorder manifested particularly by motor and vocal tics and associated with a variety of behavioral abnormalities. Recently, the mitochondrial ribosomal protein L3 gene (MRPL3) S75N, the DnaJ (Hsp40) homolog subfamily C member 13 gene (DNAJC13) A2057S, the orofacial cleft 1 candidate 1 gene (OFCC1) R129G and c.-5A>G variants are reported to be associated with Tourette syndrome/chronic tic phenotype (TS-CTD) in patients of European ancestry. To evaluate whether these variants are associated with TS-CTD in Chinese Han patients, we screened 132 Chinese Han patients from Mainland China. None of the 132 samples from patients with TS-CTD showed the MRPL3 S75N, DNAJC13 A2057S, OFCC1 R129G and c.-5A>G variants, and these variants probably are a rare cause of TS-CTD in a Chinese Han ethnic group. Genetic heterogeneity of TS should be considered and tests designed to detect these variants in Chinese Han ethnic group probably will not have a diagnostic utility in clinical practice. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Detecting deep sea hydrothermal vents with a split-beam echosounder

NASA Astrophysics Data System (ADS)

Gray, L. M.; Jerram, K.

2016-12-01

In May 2016, the NOAA Office of Exploration and Research exploration vessel, Okeanos Explorer, conducted a remotely operated vehicle (ROV) dive on a series of active `black smoker' hydrothermal vents at 3,300 m depth in the western Pacific Ocean near the Mariana Trench. The ROV system traversed 800 m along the seafloor and detected three distinct vent sites. The vent chimneys ranged in heights from 5 m to 30 m above the seafloor and vent fluid temperatures were measured as high as 337 °C. Immediately following the ROV dive, the Okeanos Explorer mapped the vent field with an 18 kHz split-beam echosounder traditionally used for fishery research and a 30 kHz multibeam echosounder with midwater capability. Six passes were made over the field, transiting at 4-5 knots on various headings. There was a clear and repeatable signal in the split-beam echogram from the venting but less obvious indication in the multibeam data. `Black smokers' have traditionally been detected using repeat conductivity-temperature-depth (CTD) `tow-yo' casts. Our field observations suggest an alternative, and potentially more efficient, method of detecting hydrothermal vent plumes within the beamwidth of the split-beam echosounder to inform ROV dive plans. Methods previously applied for locating marine gas seeps on the seafloor with split-beam echosounders can be applied to estimate the hydrothermal vent positions in this dataset and compared to the recorded ROV positions at each site. Additionally, assuming relatively stable venting and ambient conditions, the ROV position and CTD data recorded from the vehicles can be used to better understand the observed midwater acoustic backscatter signatures of the hydrothermal vent plumes.

Fine-scale thermohaline ocean structure retrieved with 2-D prestack full-waveform inversion of multichannel seismic data: Application to the Gulf of Cadiz (SW Iberia)

NASA Astrophysics Data System (ADS)

Dagnino, D.; Sallarès, V.; Biescas, B.; Ranero, C. R.

2016-08-01

This work demonstrates the feasibility of 2-D time-domain, adjoint-state acoustic full-waveform inversion (FWI) to retrieve high-resolution models of ocean physical parameters such as sound speed, temperature and salinity. The proposed method is first described and then applied to prestack multichannel seismic (MCS) data acquired in the Gulf of Cadiz (SW Iberia) in 2007 in the framework of the Geophysical Oceanography project. The inversion strategy flow includes specifically designed data preconditioning for acoustic noise reduction, followed by the inversion of sound speed in the shotgather domain. We show that the final sound speed model has a horizontal resolution of ˜ 70 m, which is two orders of magnitude better than that of the initial model constructed with coincident eXpendable Bathy Thermograph (XBT) data, and close to the theoretical resolution of O(λ). Temperature (T) and salinity (S) are retrieved with the same lateral resolution as sound speed by combining the inverted sound speed model with the thermodynamic equation of seawater and a local, depth-dependent T-S relation derived from regional conductivity-temperature-depth (CTD) measurements of the National Oceanic and Atmospheric Administration (NOAA) database. The comparison of the inverted T and S models with XBT and CTD casts deployed simultaneously to the MCS acquisition shows that the thermohaline contrasts are resolved with an accuracy of 0.18oC for temperature and 0.08 PSU for salinity. The combination of oceanographic and MCS data into a common, pseudo-automatic inversion scheme allows to quantitatively resolve submeso-scale features that ought to be incorporated into larger-scale ocean models of oceans structure and circulation.

Relationship between Ocean Bottom Pressure Variations and Baroclinic Eddy off Kushiro-Tokachi

NASA Astrophysics Data System (ADS)

Hasegawa, T.; Nagano, A.; Matsumoto, H.; Ariyoshi, K.

2016-02-01

The scope of this study is to reveal relationships between ocean bottom pressure (BP) variations related to ocean plate changes, and oceanic climate changes. We analyzed BP data at stations PG1 (41.7040N-144.4375E) and PG2 (42.2365N-144.8454E) obtained from the Long-Term Deep Sea Floor Observatory off Kushiro-Tokachi in the Kuril Trench, gridded daily sea surface height (SSH) data provided by AVISO, and conductivity-temperature-depth (CTD) data at a repeated observation line off Akkeshi (A-line) from 2004 to 2013. In addition, we used Nino-3 index, which is the major index for El Nino/Southern Oscillation (ENSO) and is given by the CPC/NOAA. It is suggested that SSH at PG1 and PG2 similarly vary affected by the Oyashio, the western boundary current of the North Pacific subarctic gyre, and El Nino events in 2006 and 2007 via atmospheric telconnections. BP time series at PG1 and PG2 are almost in phase in most of the analysis period, but from the early 2006 to the end of 2007, are quit discrepant in amplitude; at that occasion, BP at PG1 is much higher than that at PG2. Expecting a peculiar hydrographic feature at the occasion, CTD data along the A-line in January 2007 are analyzed. A lenticular eddy was found to exist in a layer between 1500 and 3000 dbar and to deepen substantially isopycnals of approximately 27.7 sigma-theta around a depth of 2000 dbar. Probably due to the baroclinic eddy feature, BP is kept low at PG2, while high at PG1. The subthermocline water occupying the deep eddy are considered not to be originated in the North Pacific but to be derived from the Southern Ocean.

Self-esteem in adults with Tourette syndrome and chronic tic disorders: The roles of tic severity, treatment, and comorbidity.

PubMed

Weingarden, Hilary; Scahill, Lawrence; Hoeppner, Susanne; Peterson, Alan L; Woods, Douglas W; Walkup, John T; Piacentini, John; Wilhelm, Sabine

2018-07-01

Tourette syndrome (TS) and chronic tic disorders (CTD) are stigmatizing disorders that may significantly impact self-esteem. Alternatively, comorbid psychiatric illnesses may affect self-esteem more than tics themselves. Extant research on self-esteem in TS/CTD is limited, has inconsistently examined the effect of comorbidities on self-esteem, and yields mixed findings. This study aimed to clarify the roles of tics versus comorbid diagnoses on self-esteem in a large, carefully diagnosed sample of adults with TS/CTD (N = 122) receiving 10 weeks of Comprehensive Behavioral Intervention for Tics (CBIT) or Psychoeducation and Supportive Therapy (PST). Baseline self-esteem did not differ between adults with TS/CTD only and normative means, whereas self-esteem was significantly lower among adults with TS/CTD with a comorbid psychiatric illness. In a multiple regression testing the baseline association between tic severity, presence of comorbid psychiatric illness, and depression severity with self-esteem, comorbidity and depression severity were significantly associated with self-esteem, whereas tic severity was not. Finally, using a generalized linear model, we tested the effects of treatment assignment, comorbidity, and their interaction on changes in self-esteem across treatment, controlling for baseline depression severity. Results showed that for those with a comorbid illness, self-esteem improved significantly more with CBIT than with PST. Comorbid illnesses appear to affect self-esteem more so than tics among adults with TS/CTD. Therapeutic attention should be paid to treating comorbid diagnoses alongside tics when treating TS/CTD. Copyright © 2018 Elsevier Inc. All rights reserved.

Initial combination therapy with ambrisentan and tadalafil in connective tissue disease-associated pulmonary arterial hypertension (CTD-PAH): subgroup analysis from the AMBITION trial

PubMed Central

Coghlan, John Gerry; Galiè, Nazzareno; Barberà, Joan Albert; Frost, Adaani E; Ghofrani, Hossein-Ardeschir; Hoeper, Marius M; Kuwana, Masataka; McLaughlin, Vallerie V; Peacock, Andrew J; Simonneau, Gérald; Vachiéry, Jean-Luc; Blair, Christiana; Gillies, Hunter; Miller, Karen L; Harris, Julia H N; Langley, Jonathan; Rubin, Lewis J

2017-01-01

Background Patients with connective tissue disease-associated pulmonary arterial hypertension (CTD-PAH), in particular systemic sclerosis (SSc), had an attenuated response compared with idiopathic PAH in most trials. Thus, there is uncertainty regarding the benefit of PAH-targeted therapy in some forms of CTD-PAH. Objective To explore the safety and efficacy of initial combination therapy with ambrisentan and tadalafil versus ambrisentan or tadalafil monotherapy in patients with CTD-PAH and SSc-PAH enrolled in the AMBITION trial. Methods This was a post hoc analysis of patients with CTD-PAH and SSc-PAH from AMBITION, an event-driven, double-blind trial in patients with WHO functional class II/III PAH. Treatment-naive patients were randomised 2:1:1 to once-daily initial combination therapy with ambrisentan plus tadalafil or monotherapy with ambrisentan or tadalafil, respectively. The primary endpoint was time to the first clinical failure event (first occurrence of death, hospitalisation for worsening PAH, disease progression or unsatisfactory long-term clinical response). Results In the primary analysis set (N=500), 187 patients had CTD-PAH, of whom 118 had SSc-PAH. Initial combination therapy reduced the risk of clinical failure versus pooled monotherapy in each subgroup: CTD-PAH (HR 0.43 (95% CI 0.24 to 0.77)) and SSc-PAH (0.44 (0.22 to 0.89)). The most common AE was peripheral oedema, which was reported more frequently with initial combination therapy than monotherapy in the two PAH subgroups. The relative frequency of adverse events between those on combination therapy versus monotherapy was similar across subgroups. Conclusions This post hoc subgroup analysis provides evidence that CTD-PAH and SSc-PAH patients benefit from initial ambrisentan and tadalafil combination therapy. Trial registration number NCT01178073, post results. PMID:28039187

Initial combination therapy with ambrisentan and tadalafil in connective tissue disease-associated pulmonary arterial hypertension (CTD-PAH): subgroup analysis from the AMBITION trial.

PubMed

Coghlan, John Gerry; Galiè, Nazzareno; Barberà, Joan Albert; Frost, Adaani E; Ghofrani, Hossein-Ardeschir; Hoeper, Marius M; Kuwana, Masataka; McLaughlin, Vallerie V; Peacock, Andrew J; Simonneau, Gérald; Vachiéry, Jean-Luc; Blair, Christiana; Gillies, Hunter; Miller, Karen L; Harris, Julia H N; Langley, Jonathan; Rubin, Lewis J

2017-07-01

Patients with connective tissue disease-associated pulmonary arterial hypertension (CTD-PAH), in particular systemic sclerosis (SSc), had an attenuated response compared with idiopathic PAH in most trials. Thus, there is uncertainty regarding the benefit of PAH-targeted therapy in some forms of CTD-PAH. To explore the safety and efficacy of initial combination therapy with ambrisentan and tadalafil versus ambrisentan or tadalafil monotherapy in patients with CTD-PAH and SSc-PAH enrolled in the AMBITION trial. This was a post hoc analysis of patients with CTD-PAH and SSc-PAH from AMBITION, an event-driven, double-blind trial in patients with WHO functional class II/III PAH. Treatment-naive patients were randomised 2:1:1 to once-daily initial combination therapy with ambrisentan plus tadalafil or monotherapy with ambrisentan or tadalafil, respectively. The primary endpoint was time to the first clinical failure event (first occurrence of death, hospitalisation for worsening PAH, disease progression or unsatisfactory long-term clinical response). In the primary analysis set (N=500), 187 patients had CTD-PAH, of whom 118 had SSc-PAH. Initial combination therapy reduced the risk of clinical failure versus pooled monotherapy in each subgroup: CTD-PAH (HR 0.43 (95% CI 0.24 to 0.77)) and SSc-PAH (0.44 (0.22 to 0.89)). The most common AE was peripheral oedema, which was reported more frequently with initial combination therapy than monotherapy in the two PAH subgroups. The relative frequency of adverse events between those on combination therapy versus monotherapy was similar across subgroups. This post hoc subgroup analysis provides evidence that CTD-PAH and SSc-PAH patients benefit from initial ambrisentan and tadalafil combination therapy. NCT01178073, post results. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Spatial and temporal variability of phytoplankton chlorophyll and carbon in the equatorial Pacific, 2005 to 2008: Observations from ships and satellites.

NASA Astrophysics Data System (ADS)

Craig, J. D.; Strutton, P. G.; Evans, W.

2008-12-01

A database of chlorophyll fluorescence, particulate backscatter and beam attenuation was constructed from 17 cruises spanning the equatorial Pacific between August 2005 and February 2008. These optical measurements serve at least two important purposes. First, they can be used to document changes in phytoplankton abundance and physiology in a globally significant ecosystem. Second, they represent an important validation database for satellite observations that form the core of emerging primary productivity models. The data consist of CTD profiles from the surface to 1000m at least every degree of latitude between 8N and 8S, from near the Galapagos to beyond the date line. The optical data were calibrated with in situ samples of chlorophyll and particulate organic carbon (POC) from 4 of the 17 cruises. Chlorophyll concentration was derived from a multiple linear regression of chlorophyll fluorescence, time of day and depth, to account for photoinhibition of the fluorescence signal near the surface during the day. POC was derived from both particulate backscatter and beam attenuation. The optical data were then used to produce maps and latitude-depth sections of chlorophyll and POC for cruises where no in situ samples exist. In the eastern and central equatorial Pacific, phytoplankton chlorophyll to carbon ratios decreased by 30 to 50 percent during the weak El Nino conditions of 2006-2007. This change was due mostly to a decrease in chlorophyll, while POC remained relatively constant. In the western Pacific, the decrease in chl:C was absent, but an increase occurred in early 2008 when the system recovered from El Nino. Changes in chl:C, mostly indicative of photoadaptation, were also observed with depth and latitude as upwelled waters from the equator move poleward. Satellite-based maps of chlorophyll, phytoplankton C and chl:C were also produced and compared with the in situ optical measurements, with mostly good agreement.

Operation and Hydrodynamic Evaluations of a Controlled-Depth Towed Depressor Designed to House a Conductivity, Temperature, Depth (CTD) Instrument System

DTIC Science & Technology

1981-03-01

ljIi 0 10 20 30 40 50 60 70 80 LENGTH (W) Figure 2 - Predicted Tension in Remote Sensor Cable at 10 Knots as a Function of Cable Length for Two Remote...10.0 -8.0 -10 4.11 0.68 40 5.0 -8.0 -15 0.66 0.44 41 8.0 -8.0 -15 1.57 0.41 42 10.0 -8.0 -15 2.63 0.44 43 5.0 -8.0 -20 0.48 0.32 44 8.0 -8.0 -20 0.89...HH fIH 1 IH r-4 H r- rIH rIH 4 i HHH.-4H H -4 rIH HHHHH r Cfr- 40 00 0 0q - zI - ri-4- oi 0 -A- \\.o. m M- r-. A- - rA- r-c r(0 P4 r

Cumulative trauma disorders among apparel manufacturing employees in the southeastern United States.

PubMed

Dignan, M; Hayes, D; Main, H; Parker, K

1996-11-01

Factors associated with cumulative trauma disorders (CTDs) of the upper extremities were studied retrospectively, using data from three apparel manufacturing plants in the southeastern United States. Reported CTDs among the employees at risk during fiscal years 1991 and 1992 were analyzed focusing on individual and plant variables. Results showed that CTD rates increased from 1991 to 1992 and fluctuated in a cyclical pattern each year, peaking during January, March, and August. Employee age and duration of employment were associated with CTD rates. Employees aged 45 to 49 had higher CTD rates than those in any other age groups. Employees with 1 to 3 years' experience had higher CTD rates than employees with more years of service.

The IAOOS arctic network project, status and prospect

NASA Astrophysics Data System (ADS)

Pelon, J.; Provost, C.; Sennechael, N.; Calzas, M.; Blouzon, F.; Gascard, J. C.

2015-12-01

It is quite clear that for studying Arctic climate changes, and better understand interacting processes it is essential to follow an integrated approach for observing and modeling the whole Arctic system encompassing the atmosphere, the ocean and sea-ice at once. Due to the difficulties in retrieving key parameters, satellite observations alone are not the right answer. The project we are developing, is an attempt to tackle this challenge by providing and maintaining a new integrated observing network of instrumented buoys over the Arctic Ocean in order to collect simultaneously and in real time information related to the state of the upper Ocean, the lower Atmosphere and the Arctic sea-ice/snow. It is planned to operate several autonomous platforms in a network in the Arctic Ocean for a period of at least 5 years. Each platform is equipped to vertically sense and profile key variables in the ocean, sea-ice and atmosphere using - CTD (conductivity, temperature, depth) vertical profilers sensors collecting ocean temperature and salinity down to 800m depth, - Temperature and heat conductivity in snow and ice from ice-mass-balance systems - Cloud and aerosol lidar profiling of the lower atmosphere - Diffuse and direct solar flux using wide angle radiometer - Meteorological standard parameters at the surface Platforms allow measurements to be transmitted in near real time via Iridium satellites. As they will be drifting, it is planned to replace part of them every year. Major tests were performed deploying progressively fully equipped IAOOS platform at the North Pole in April 2012, 2013 and 2014. These platforms drifted from the North Pole in April to Fram Strait (September, October) providing spring summer and fall field data. Important fieldwork for IAOOS was also taking place within the Norwegian ice camp on board R/V Lance organized by the Norsk Polar Institute from January to June 2015, as part of the Norwegian young ICE (N-ICE 2015) cruise project. These intensive tests were very timely. The first IAOOS array deployment will start in August 2015 from R/V Araon during the Korean cruise organized by the KOPRI in the Canadian Basin and from R/V Polarstern during the German cruise TRANSARC II organized by the Alfred Wegener Institute in the Eurasian Basin. First results obtained in the frame of IAOOS will be presented and discussed.

Numerical analysis of internal solitary wave generation around a Island in Kuroshio Current using MITgcm.

NASA Astrophysics Data System (ADS)

Kodaira, Tsubasa; Waseda, Takuji

2013-04-01

We have conducted ADCP and CTD measurements from 31/8/2010 to 2/9/2010 at the Miyake Island, located approximately 180 km south of Tokyo. The Kuroshio Current approached the island in this period, and the PALSAR image showed parabolic bright line upstream of the island. This bright line may be a surface signature of large amplitude internal solitary wave. Although our measurements did not explicitly show evidence of the internal solitary wave, critical condition might have been satisfied because of the Kuroshio Current and strong seasonal thermocline. To discover the generation mechanism of the large amplitude internal solitary wave at the Miyake Island, we have conducted non-hydrostatic numerical simulation with the MITgcm. A simple box domain, with open boundaries at all sides, is used. The island is simplified to circular cylinder or Gaussian Bell whose radius is 3km at ocean surface level. The size of the domain is 40kmx40kmx500m for circular cylinder cases and 80kmx80kmx500m for Gaussian bell cases. By looking at our CTD data, we have chosen for initial and boundary conditions a tanh function for vertical temperature profile. Salinity was kept constant for simplicity. Vertical density profile is also described by tanh function because we adopt linear type of equation of state. Vertical velocity profile is constant or linearly changed with depth; the vertical mean speed corresponds to the linear phase speed of the first baroclinic mode obtained by solving the eigen-value problem. With these configurations, we have conducted two series of simulations: shear flow through cylinder and uniform flow going through Gaussian Bell topography. Internal solitary waves were generated in front of the cylinder for the first series of simulations with shear flow. The generated internal waves almost purely consisted of 1st baroclinic component. Their intensities were linearly related with upstream vertical shear strength. As the internal solitary wave became larger, its width became wider compared to the KdV solution described by Grimshaw (2002). This is predicted because higher order analytical solution for 2-layer fluids, i.e. the eKdV solution, gives broader solitary wave shape than that of the KdV solution because of the cubic nonlinear term. When we look at the surface velocity distribution, a parabolic shape corresponding to internal solitary wave is clearly seen. According to the fully nonlinear theoretical model for internal wave between two fluids having background linear shear flow profiles (Choi and Camassa1999), the shape of internal wave is influenced by the velocity shear as well. However, we could not clarify the effect of vertical shear because there is no fully nonlinear analytical solution for large amplitude internal wave in continuously stratified fluid. Second series of simulations with uniform flow going through Gaussian Bell topography show that internal solitary wave shows up from sides of the topography. This generation is similar to the one developed in lee side of sill topography by tidal flow. With broader bell topography, generated internal waves become larger. This makes sense because forcing region is wider. A horizontal shape of the internal solitary wave is not parabolic but the two bending line forms from the sides of the island. However, no solitary wave in front of the island develops. Our results imply that vertical shear profile is needed for the formation of the depression type internal solitary, and explains the parabolic bright line observed in the SAR image

Interstitial Lung Disease in India. Results of a Prospective Registry.

PubMed

Singh, Sheetu; Collins, Bridget F; Sharma, Bharat B; Joshi, Jyotsna M; Talwar, Deepak; Katiyar, Sandeep; Singh, Nishtha; Ho, Lawrence; Samaria, Jai Kumar; Bhattacharya, Parthasarathi; Gupta, Rakesh; Chaudhari, Sudhir; Singh, Tejraj; Moond, Vijay; Pipavath, Sudhakar; Ahuja, Jitesh; Chetambath, Ravindran; Ghoshal, Aloke G; Jain, Nirmal K; Devi, H J Gayathri; Kant, Surya; Koul, Parvaiz; Dhar, Raja; Swarnakar, Rajesh; Sharma, Surendra K; Roy, Dhrubajyoti J; Sarmah, Kripesh R; Jankharia, Bhavin; Schmidt, Rodney; Katiyar, Santosh K; Jindal, Arpita; Mangal, Daya K; Singh, Virendra; Raghu, Ganesh

2017-03-15

Interstitial lung disease (ILD) is a heterogeneous group of acute and chronic inflammatory and fibrotic lung diseases. Existing ILD registries have had variable findings. Little is known about the clinical profile of ILDs in India. To characterize new-onset ILDs in India by creating a prospective ILD using multidisciplinary discussion (MDD) to validate diagnoses. Adult patients of Indian origin living in India with new-onset ILD (27 centers, 19 Indian cities, March 2012-June 2015) without malignancy or infection were included. All had connective tissue disease (CTD) serologies, spirometry, and high-resolution computed tomography chest. ILD pattern was defined by high-resolution computed tomography images. Three groups independently made diagnoses after review of clinical data including that from prompted case report forms: local site investigators, ILD experts at the National Data Coordinating Center (NDCC; Jaipur, India) with MDD, and experienced ILD experts at the Center for ILD (CILD; Seattle, WA) with MDD. Cohen's κ was used to assess reliability of interobserver agreement. A total of 1,084 patients were recruited. Final diagnosis: hypersensitivity pneumonitis in 47.3% (n = 513; exposure, 48.1% air coolers), CTD-ILD in 13.9%, and idiopathic pulmonary fibrosis in 13.7%. Cohen's κ: 0.351 site investigator/CILD, 0.519 site investigator/NDCC, and 0.618 NDCC/CILD. Hypersensitivity pneumonitis was the most common new-onset ILD in India, followed by CTD-ILD and idiopathic pulmonary fibrosis; diagnoses varied between site investigators and CILD experts, emphasizing the value of MDD in ILD diagnosis. Prompted case report forms including environmental exposures in prospective registries will likely provide further insight into the etiology and management of ILD worldwide.

Evolution of CO2 in lakes Monoun and Nyos, Cameroon, before and during controlled degassing

USGS Publications Warehouse

Kusakabe, M.; Ohba, T.; Issa,; Yoshida, Y.; Satake, H.; Ohizumi, T.; Evans, William C.; Tanyileke, G.; Kling, G.W.

2008-01-01

Evolution of CO2 in Lakes Monoun and Nyos (Cameroon) before and during controlled degassing is described using results of regular monitoring obtained during the last 21 years. The CO2(aq) profiles soon after the limnic eruptions were estimated for Lakes Monoun and Nyos using the CTD data obtained in October and November 1986, respectively. Based on the CO2(aq) profiles through time, the CO2 Content and its change over time were calculated for both lakes. The CO2 accumulation rate calculated from the pre-degassing data, was constant after the limnic eruption at Lake Nyos (1986-2001), whereas the rate appeared initially high (1986-1996) but later slowed down (1996-2003) at Lake Monoun. The CO2 concentration at 58 m depth in Lake Monoun in January 2003 was very close to saturation due to the CO2 accumulation. This situation is suggestive of a mechanism for the limnic eruption, because it may take place spontaneously without receiving an external trigger. The CO2 content of the lakes decreased significantly after controlled degassing started in March 2001 at Lake Nyos and in February 2003 at Lake Monoun. The current content is lower than the content estimated soon after the limnic eruption at both lakes. At Monoun the degassing rate increased greatly after February 2006 due to an increase of the number of degassing pipes and deepening of the pipe intake depth. The current CO2 content is ???40% of the maximum content attained just before the degassing started. At current degassing rates the lower chemocline will subside to the degassing pipe intake depth of 93 m in about one year. After this depth is reached, the gas removal rate will progressively decline because water of lower CO2(aq) concentration will be tapped by the pipes. To keep the CO2 content of Lake Monoun as small as possible, it is recommended to set up a new, simple device that sends deep water to the surface since natural recharge of CO2 will continue. Controlled degassing at Lake Nyos since 2001 has also reduced the CO2 content. It is currently slightly below the level estimated after the limnic eruption in 1986. However, the current CO2 content still amounts to 80% of the maximum level of 14.8 giga moles observed in January 2001. The depth of the lower chemocline may reach the pipe intake depth of 203 m within a few years. After this situation is reached the degassing rate with the current system will progressively decline, and it would take decades to remove the majority of dissolved gases even if the degassing system keeps working continuously. Additional degassing pipes must be installed to speed up gas removal from Lake Nyos in order to make the area safer for local populations. Copyright ?? 2008 by The Geochemical Society of Japan.

Suicide in Tourette's and Chronic Tic Disorders.

PubMed

Fernández de la Cruz, Lorena; Rydell, Mina; Runeson, Bo; Brander, Gustaf; Rück, Christian; D'Onofrio, Brian M; Larsson, Henrik; Lichtenstein, Paul; Mataix-Cols, David

2017-07-15

Persons with neuropsychiatric disorders are at increased risk of suicide, but there is little data concerning Tourette's and chronic tic disorders (TD/CTD). We aimed to quantify the risk of suicidal behavior in a large nationwide cohort of patients with TD/CTD, establish the contribution of psychiatric comorbidity to this risk, and identify predictors of suicide. Using a validated algorithm, we identified 7736 TD/CTD cases in the Swedish National Patient Register during a 44-year period (1969-2013). Using a matched case-cohort design, patients were compared with general population control subjects (1:10 ratio). Risk of suicidal behavior was estimated using conditional logistic regressions. Predictors of suicidal behavior in the TD/CTD cohort were studied using Cox regression models. In unadjusted models, TD/CTD patients, compared with control subjects, had an increased risk of both dying by suicide (odds ratio: 4.39; 95% confidence interval [CI]: 2.89-6.67) and attempting suicide (odds ratio: 3.86; 95% CI: 3.50-4.26). After adjusting for psychiatric comorbidities, the risk was reduced but remained substantial. Persistence of tics beyond young adulthood and a previous suicide attempt were the strongest predictors of death by suicide in TD/CTD patients (hazard ratio: 11.39; 95% CI: 3.71-35.02, and hazard ratio: 5.65; 95% CI: 2.21-14.42, respectively). TD/CTD are associated with substantial risk of suicide. Suicidal behavior should be monitored in these patients, particularly in those with persistent tics, history of suicide attempts, and psychiatric comorbidities. Preventive and intervention strategies aimed to reduce the suicidal risk in this group are warranted. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Lysines in the RNA Polymerase II C-Terminal Domain Contribute to TAF15 Fibril Recruitment.

PubMed

Janke, Abigail M; Seo, Da Hee; Rahmanian, Vahid; Conicella, Alexander E; Mathews, Kaylee L; Burke, Kathleen A; Mittal, Jeetain; Fawzi, Nicolas L

2018-05-01

Many cancer-causing chromosomal translocations result in transactivating protein products encoding FET family (FUS, EWSR1, TAF15) low-complexity (LC) domains fused to a DNA binding domain from one of several transcription factors. Recent work demonstrates that higher-order assemblies of FET LC domains bind the carboxy-terminal domain of the large subunit of RNA polymerase II (RNA pol II CTD), suggesting FET oncoproteins may mediate aberrant transcriptional activation by recruiting RNA polymerase II to promoters of target genes. Here we use nuclear magnetic resonance (NMR) spectroscopy and hydrogel fluorescence microscopy localization and fluorescence recovery after photobleaching to visualize atomic details of a model of this process, interactions of RNA pol II CTD with high-molecular weight TAF15 LC assemblies. We report NMR resonance assignments of the intact degenerate repeat half of human RNA pol II CTD alone and verify its predominant intrinsic disorder by molecular simulation. By measuring NMR spin relaxation and dark-state exchange saturation transfer, we characterize the interaction of RNA pol II CTD with amyloid-like hydrogel fibrils of TAF15 and hnRNP A2 LC domains and observe that heptads far from the acidic C-terminal tail of RNA pol II CTD bind TAF15 fibrils most avidly. Mutation of CTD lysines in heptad position 7 to consensus serines reduced the overall level of TAF15 fibril binding, suggesting that electrostatic interactions contribute to complex formation. Conversely, mutations of position 7 asparagine residues and truncation of the acidic tail had little effect. Thus, weak, multivalent interactions between TAF15 fibrils and heptads throughout RNA pol II CTD collectively mediate complex formation.

LONG-TERM EFFECTS OF CHLORTHALIDONE VS HYDROCHLOROTHIAZIDE ON ELECTROCARDIOGRAPHIC LEFT VENTRICULAR HYPERTROPHY IN THE MULTIPLE RISK FACTOR INTERVENTION TRIAL

PubMed Central

Ernst, Michael E.; Neaton, James D.; Grimm, Richard H.; Collins, Gary; Thomas, William; Soliman, Elsayed Z.; Prineas, Ronald J.

2011-01-01

Chlorthalidone (CTD) reduces 24-hour blood pressure more effectively than hydrochlorothiazide (HCTZ), but whether this influences electrocardiographic left ventricular hypertrophy (LVH) is uncertain. One source of comparative data is the Multiple Risk Factor Intervention Trial (MRFIT), which randomly assigned 8,012 hypertensive men to special intervention (SI) or usual care (UC). SI participants could use CTD or HCTZ initially; previous analyses have grouped clinics by their main diuretic used (C-clinics: CTD; H-clinics: HCTZ). After 48 months, SI participants receiving HCTZ were recommended to switch to CTD, in part, because higher mortality was observed for SI compared to UC participants in H-clinics, while the opposite was found in C-clinics. In this analysis, we examined change in continuous measures of electrocardiographic LVH using both an ecologic analysis by previously-reported C- or H-clinic groupings, and an individual participant analysis where use of CTD or HCTZ by SI participants was considered and updated annually. Through 48 months, differences between SI and UC in LVH were larger for C-clinics compared to H-clinics (Sokolow-Lyon: −93.9 vs −54.9 μV, P=0.049; Cornell voltage: −68.1 vs −35.9 μV, P=0.019; Cornell voltage product: −4.6 vs −2.2 μV/ms, P=0.071; left ventricular mass: −4.4 vs −2.8 gm, P=0.002). At the individual participant level, Sokolow-Lyon and left ventricular mass were significantly lower for SI men receiving CTD compared to HCTZ through 48 months and 84 months of follow-up. Our findings on LVH support the idea that greater blood pressure reduction with CTD than HCTZ may have led to differences in mortality observed in MRFIT. PMID:22025372

Comparison of cyclophosphamide-thalidomide-dexamethasone to bortezomib-cyclophosphamide-dexamethasone as induction therapy for multiple myeloma patients in Brazil.

PubMed

Vigolo, Suelen; Zuckermann, Joice; Bittencourt, Rosane Isabel; Silla, Lúcia; Pilger, Diogo André

2017-09-01

Chemotherapy followed by autologous hematopoietic stem cell transplantation (HSCT) remains the standard treatment for multiple myeloma (MM). Thalidomide or bortezomib may be combined with cyclophosphamide and dexamethasone, in what are known as the CTD and VCD protocols, respectively. The objective of this study was to evaluate the clinical characteristics and response rates obtained with CTD and VCD, observing whether the inclusion of bortezomib to treat MM patients in Brazil increases therapeutic efficiency. Forty-three MM patients treated with induction protocols CTD and VCD between January 2010 and March 2015 were included. The parameters analyzed were staging, frequency of comorbidities prior to treatment, response rates obtained at each induction cycle, progression-free survival, and overall survival of patients. Very good partial response and complete response obtained with the VCD protocol were superior, compared with the CTD treatment. The presence of comorbidities was similar in the two groups, except kidney failure, which prevailed in the VCD group. Also, 78.3% and 48.3% of patients treated with the VCD and CTD protocols underwent autologous HSCT, respectively. In patients given the VCD protocol, 45.5% had complete response before autologous HSCT. Among those given CTD, this number was only 7.1% (p=0.023). Disease progression after autologous HSCT did not differ between the two groups. VCD afforded better responses than the CTD protocol, and improved patient condition before autologous HSCT. However, more studies are necessary including more patients and addressing various clinical conditions, besides the analysis of cost-effectiveness of these treatments. Copyright © 2017 King Faisal Specialist Hospital & Research Centre. Published by Elsevier B.V. All rights reserved.

Cdc15 Phosphorylates the C-terminal Domain of RNA Polymerase II for Transcription during Mitosis.

PubMed

Singh, Amit Kumar; Rastogi, Shivangi; Shukla, Harish; Asalam, Mohd; Rath, Srikanta Kumar; Akhtar, Md Sohail

2017-03-31

In eukaryotes, the basal transcription in interphase is orchestrated through the regulation by kinases (Kin28, Bur1, and Ctk1) and phosphatases (Ssu72, Rtr1, and Fcp1), which act through the post-translational modification of the C-terminal domain (CTD) of the largest subunit of RNA polymerase II. The CTD comprises the repeated Tyr-Ser-Pro-Thr-Ser-Pro-Ser motif with potential epigenetic modification sites. Despite the observation of transcription and periodic expression of genes during mitosis with entailing CTD phosphorylation and dephosphorylation, the associated CTD specific kinase(s) and its role in transcription remains unknown. Here we have identified Cdc15 as a potential kinase phosphorylating Ser-2 and Ser-5 of CTD for transcription during mitosis in the budding yeast. The phosphorylation of CTD by Cdc15 is independent of any prior Ser phosphorylation(s). The inactivation of Cdc15 causes reduction of global CTD phosphorylation during mitosis and affects the expression of genes whose transcript levels peak during mitosis. Cdc15 also influences the complete transcription of clb2 gene and phosphorylates Ser-5 at the promoter and Ser-2 toward the 3' end of the gene. The observation that Cdc15 could phosphorylate Ser-5, as well as Ser-2, during transcription in mitosis is in contrast to the phosphorylation marks put by the kinases in interphase (G 1 , S, and G 2 ), where Cdck7/Kin28 phosphorylates Ser-5 at promoter and Bur1/Ctk1 phosphorylates Ser-2 at the 3' end of the genes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Tadalafil in idiopathic or heritable pulmonary arterial hypertension (PAH) compared to PAH associated with connective tissue disease.

PubMed

Galiè, Nazzareno; Denton, Christopher P; Dardi, Fabio; Manes, Alessandra; Mazzanti, Gaia; Li, Baohui; Varanese, Lucio; Esler, Anne; Harmon, Cathi; Palazzini, Massimiliano

2017-05-15

The primary objective of this post hoc analysis was to evaluate clinical outcomes of tadalafil in patients with pulmonary arterial hypertension (PAH) associated with connective tissue disease (CTD-PAH) compared with patients with idiopathic/heritable PAH (I/H-PAH) for primary and key secondary efficacy endpoints, and safety. This analysis included adult patients with CTD-PAH or I/H-PAH who participated in the PHIRST and PHIRST-2 studies. Patients were randomized 1:1:1:1:1 to tadalafil (2.5, 10, 20, or 40mg) or placebo in the PHIRST study and the majority of these patients were subsequently assigned 40mg in PHIRST-2. Patients taking 20mg in PHIRST without demonstrating clinical worsening continued on 20mg in PHIRST-2. Outcomes analyzed included 6MWD, WHO-FC, and incidence and time to first occurrence of clinical worsening. Safety was assessed through evaluation of adverse events (AEs), clinical laboratory data, electrocardiograms, and physical examinations. Increased 6MWD in PHIRST was maintained in both CTD-PAH and I/H-PAH subgroups for 52weeks. Patients with CTD-PAH tended to be older, were more likely female, had lower exercise capacity, were more likely to have clinical worsening, and experienced AEs more frequently than patients with I/H-PAH. The effect of tadalafil treatment in patients enrolled in both PHIRST studies was detectable for both I/H-PAH and CTD-PAH subgroups. In general, subgroup differences were modest. Patients with CTD-PAH may perform less well than patients with I/H-PAH in safety and efficacy measures in all treatment groups, which is similar to other studies demonstrating a worse prognosis for patients with CTD-PAH. Copyright © 2017. Published by Elsevier B.V.

Long-Term Monitoring of Waterborne Pathogens and Microbial Source Tracking Markers in Paired Agricultural Watersheds under Controlled and Conventional Tile Drainage Management

PubMed Central

Wilkes, Graham; Brassard, Julie; Edge, Thomas A.; Gannon, Victor; Gottschall, Natalie; Jokinen, Cassandra C.; Jones, Tineke H.; Khan, Izhar U. H.; Marti, Romain; Sunohara, Mark D.; Topp, Edward

2014-01-01

Surface waters from paired agricultural watersheds under controlled tile drainage (CTD) and uncontrolled tile drainage (UCTD) were monitored over 7 years in order to determine if there was an effect of CTD (imposed during the growing season) on occurrences and loadings of bacterial and viral pathogens, coliphages, and microbial source tracking markers. There were significantly lower occurrences of human, ruminant, and livestock (ruminant plus pig) Bacteroidales markers in the CTD watershed in relation to the UCTD watershed. As for pathogens, there were significantly lower occurrences of Salmonella spp. and Arcobacter spp. in the CTD watershed. There were no instances where there were significantly higher quantitative loadings of any microbial target in the CTD watershed, except for F-specific DNA (F-DNA) and F-RNA coliphages, perhaps as a result of fecal inputs from a hobby farm independent of the drainage practice treatments. There was lower loading of the ruminant marker in the CTD watershed in relation to the UCTD system, and results were significant at the level P = 0.06. The odds of Salmonella spp. occurring increased when a ruminant marker was present relative to when the ruminant marker was absent, yet for Arcobacter spp., the odds of this pathogen occurring significantly decreased when a ruminant marker was present relative to when the ruminant marker was absent (but increased when a wildlife marker was present relative to when the wildlife marker was absent). Interestingly, the odds of norovirus GII (associated with human and swine) occurring in water increased significantly when a ruminant marker was present relative to when a ruminant marker was absent. Overall, this study suggests that fecal pollution from tile-drained fields to stream could be reduced by CTD utilization. PMID:24727274

Carbon and oxygen isotopic disequilibrium during calcification of Globigerina bulloides in the Southern ocean

NASA Astrophysics Data System (ADS)

K, P.; Ghosh, P.; N, A.

2015-12-01

Oxygen and carbon isotopes in planktonic foraminifera Globigerina bulloides recovered from the water column of 0-1000 m depth across the meridional transect i.e. 10°N to 53°S of Indian ocean were compared with the available data from the core-top samples across the same transect. We also recorded in situ temperatures of the water column based on probe (CTD) profiles. The δ18O and δ13C values measured in the core top samples matches with the tow results. The equilibrium δ18O of calcite calculated from known temperature and δ18O of water column allowed us to compare the observed δ18O of formaminieral shell with the expected equilibrium values. Our comparison of carbonate composition in the samples between 10°N till 40°S showed excellent match with the expected equilibrium δ18O values established from the water collected at depth range of ~75-200m, however beyond 40°S the disequilibrium was pronounced with heavier δ18O (enriched by ~1.5‰) recorded in the carbonate as compared with the expected equilibrium δ18O values established from water. This observation was further verified with δ13C measurement of shell carbonates comparing with the equilibrium δ13C of calcite calculated with known temperature and δ13C of dissolved inorganic carbon in the water column. The δ13C of the shell carbonate was found heavier as compared to the expected equilibrium δ13C. Both δ18O and δ13C showed simultaneous enrichment signature in the region beyond 40°S suggesting role of processes such as leaching along with dissolution of shell carbonate in a relatively acidic condition.

Sofosbuvir as treatment against dengue?

PubMed

Gan, Chye Sheng; Lim, See Khai; Chee, Chin Fei; Yusof, Rohana; Heh, Choon Han

2018-02-01

Dengvaxia ® (CTD-TDV), the only licensed tetravalent dengue vaccine by Sanofi Pasteur, was made available since 2015. However, administration of CTD-TDV, in general, has not received the prequalification recommendation from the World Health Organization. Having a universal antidengue agent for treatment will therefore beneficial. Accordingly, the development of nucleoside inhibitors specific to dengue viral polymerase that perturb dengue infection has been studied by many. Alternatively, we have used a marketed anti-HCV prodrug sofosbuvir to study its in silico and in vitro effects against dengue. As a result, the active metabolite of sofosbuvir (GS-461203) was predicted to bind to the catalytic motif (Gly-Asp-Asp) of dengue viral polymerase with binding affinity of -6.9 kcal/mol. Furthermore, sofosbuvir demonstrated excellent in vitro viral inhibition with an EC 90 of 0.4 μm. In addition, this study demonstrated the requirement of specific liver enzymes to activate the prodrug into GS-461203 to exert its antidengue potential. All in all, sofosbuvir should be subjected to in-depth studies to provide information of its efficacy toward dengue and its lead potential as DENV polymerase inhibitor in human subjects. In conclusion, we have expended the potential of the clinically available drug sofosbuvir as treatment for dengue. © 2017 John Wiley & Sons A/S.

Salinity Processes in the Upper Ocean Regional Study (SPURS)

NASA Image and Video Library

2012-09-04

CTD instruments used to measure Conductivity, Temperature, and Depth, are seen onboard the Woods Hole Oceanographic Institution's research vessel Knorr on Tuesday, Sept. 4, 2012, in Woods Hole, Mass. The CTDs will be deployed in the Atlantic Ocean as part of the Salinity Processes in the Upper Ocean Regional Study (SPURS) which is set to sail on Sept. 6. The NASA-sponsored expedition will sail to the North Atlantic's saltiest spot to get a detailed, 3-D picture of how salt content fluctuates in the ocean's upper layers and how these variations are related to shifts in rainfall patterns around the planet. Photo Credit: (NASA/Bill Ingalls)

Specific threonine-4 phosphorylation and function of RNA polymerase II CTD during M phase progression

PubMed Central

Hintermair, Corinna; Voß, Kirsten; Forné, Ignasi; Heidemann, Martin; Flatley, Andrew; Kremmer, Elisabeth; Imhof, Axel; Eick, Dirk

2016-01-01

Dynamic phosphorylation of Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 heptad-repeats in the C-terminal domain (CTD) of the large subunit coordinates progression of RNA polymerase (Pol) II through the transcription cycle. Here, we describe an M phase-specific form of Pol II phosphorylated at Thr4, but not at Tyr1, Ser2, Ser5, and Ser7 residues. Thr4 phosphorylated Pol II binds to centrosomes and midbody and interacts with the Thr4-specific Polo-like kinase 1. Binding of Pol II to centrosomes does not require the CTD but may involve subunits of the non-canonical R2TP-Prefoldin-like complex, which bind to and co-localize with Pol II at centrosomes. CTD Thr4 mutants, but not Ser2 and Ser5 mutants, display severe mitosis and cytokinesis defects characterized by multipolar spindles and polyploid cells. We conclude that proper M phase progression of cells requires binding of Pol II to centrosomes to facilitate regulation of mitosis and cytokinesis in a CTD Thr4-P dependent manner. PMID:27264542

Specific threonine-4 phosphorylation and function of RNA polymerase II CTD during M phase progression.

PubMed

Hintermair, Corinna; Voß, Kirsten; Forné, Ignasi; Heidemann, Martin; Flatley, Andrew; Kremmer, Elisabeth; Imhof, Axel; Eick, Dirk

2016-06-06

Dynamic phosphorylation of Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 heptad-repeats in the C-terminal domain (CTD) of the large subunit coordinates progression of RNA polymerase (Pol) II through the transcription cycle. Here, we describe an M phase-specific form of Pol II phosphorylated at Thr4, but not at Tyr1, Ser2, Ser5, and Ser7 residues. Thr4 phosphorylated Pol II binds to centrosomes and midbody and interacts with the Thr4-specific Polo-like kinase 1. Binding of Pol II to centrosomes does not require the CTD but may involve subunits of the non-canonical R2TP-Prefoldin-like complex, which bind to and co-localize with Pol II at centrosomes. CTD Thr4 mutants, but not Ser2 and Ser5 mutants, display severe mitosis and cytokinesis defects characterized by multipolar spindles and polyploid cells. We conclude that proper M phase progression of cells requires binding of Pol II to centrosomes to facilitate regulation of mitosis and cytokinesis in a CTD Thr4-P dependent manner.

Complex structure of the fission yeast SREBP-SCAP binding domains reveals an oligomeric organization.

PubMed

Gong, Xin; Qian, Hongwu; Shao, Wei; Li, Jingxian; Wu, Jianping; Liu, Jun-Jie; Li, Wenqi; Wang, Hong-Wei; Espenshade, Peter; Yan, Nieng

2016-11-01

Sterol regulatory element-binding protein (SREBP) transcription factors are master regulators of cellular lipid homeostasis in mammals and oxygen-responsive regulators of hypoxic adaptation in fungi. SREBP C-terminus binds to the WD40 domain of SREBP cleavage-activating protein (SCAP), which confers sterol regulation by controlling the ER-to-Golgi transport of the SREBP-SCAP complex and access to the activating proteases in the Golgi. Here, we biochemically and structurally show that the carboxyl terminal domains (CTD) of Sre1 and Scp1, the fission yeast SREBP and SCAP, form a functional 4:4 oligomer and Sre1-CTD forms a dimer of dimers. The crystal structure of Sre1-CTD at 3.5 Å and cryo-EM structure of the complex at 5.4 Å together with in vitro biochemical evidence elucidate three distinct regions in Sre1-CTD required for Scp1 binding, Sre1-CTD dimerization and tetrameric formation. Finally, these structurally identified domains are validated in a cellular context, demonstrating that the proper 4:4 oligomeric complex formation is required for Sre1 activation.

The C-terminal domain of connexin43 modulates cartilage structure via chondrocyte phenotypic changes

PubMed Central

Gago-Fuentes, Raquel; Bechberger, John F.; Varela-Eirin, Marta; Varela-Vazquez, Adrian; Acea, Benigno; Fonseca, Eduardo

2016-01-01

Chondrocytes in cartilage and bone cells population express connexin43 (Cx43) and gap junction intercellular communication (GJIC) is essential to synchronize cells for coordinated electrical, mechanical, metabolic and chemical communication in both tissues. Reduced Cx43 connectivity decreases chondrocyte differentiation and defective Cx43 causes skeletal defects. The carboxy terminal domain (CTD) of Cx43 is located in the cytoplasmic side and is key for protein functions. Here we demonstrated that chondrocytes from the CTD-deficient mice, K258stop/Cx43KO and K258stop/K258stop, have reduced GJIC, increased rates of proliferation and reduced expression of collagen type II and proteoglycans. We observed that CTD-truncated mice were significantly smaller in size. Together these results demonstrated that the deletion of the CTD negatively impacts cartilage structure and normal chondrocyte phenotype. These findings suggest that the proteolytic cleavage of the CTD under pathological conditions, such as under the activation of metalloproteinases during tissue injury or inflammation, may account for the deleterious effects of Cx43 in cartilage and bone disorders such as osteoarthritis. PMID:27682878

Interoceptive Accuracy in Youth with Tic Disorders: Exploring Links with Premonitory Urge, Anxiety and Quality of Life.

PubMed

Pile, Victoria; Lau, Jennifer Y F; Topor, Marta; Hedderly, Tammy; Robinson, Sally

2018-05-18

Aberrant interoceptive accuracy could contribute to the co-occurrence of anxiety and premonitory urge in chronic tic disorders (CTD). If it can be manipulated through intervention, it would offer a transdiagnostic treatment target for tics and anxiety. Interoceptive accuracy was first assessed consistent with previous protocols and then re-assessed following an instruction attempting to experimentally enhance awareness. The CTD group demonstrated lower interoceptive accuracy than controls but, importantly, this group difference was no longer significant following instruction. In the CTD group, better interoceptive accuracy was associated with higher anxiety and lower quality of life, but not with premonitory urge. Aberrant interoceptive accuracy may represent an underlying trait in CTD that can be manipulated, and relates to anxiety and quality of life.

Glaucophane chloritoid-bearing assemblages from NE Oman: petrologic significance and a petrogenetic grid for high P metapelites

NASA Astrophysics Data System (ADS)

El-Shazly, A. K.; Liou, J. G.

1991-04-01

Pelitic layers and lenses interbedded with blueschists and eclogites in Saih Hatat, NE Oman contain chloritoid- and sodic amphibole-bearing mineral assemblages that are useful for reconstructing the P-T history of the area. Textural and mineral chemical relations suggest that coexisting glaucophane (Gln) and chloritoid (Ctd) formed at the expense of chlorite (Chl)+paragonite (Pg) and later broke down to garnet (Gt)+Pg during prograde metamorphism according to the reaction: Gln+Ctd+Qz=Gt+Pg+H2O. During retrogression, Gln and Chl first formed at the expense of Gt and Pg, followed by the breakdown of Ctd and Gt to Chl. The final stages of retrogression are marked by the breakdown of Gln to an aggregate of Chl+albite (Ab). A projection from quartz (Qz), H2O and phengite (Ph) on the (Al2O3+Fe2O3)-(FeO+MgO)-Na2O plane in the system NFMASH is best suited for the representation of the phase relations in high P metapelites. Petrogenetic grids for the model systems NMASH and NFASH were calculated using program GEO-CALC (Berman et al. 1987) and its database (Berman 1988) after the retrieval of S{i/o}and ΔH{f/o}for Gln and Ctd by mathematical programming and calculating all possible reactions among Gln, Ctd, Chl, jadeite (Jd), Ab, Gt, Pg, talc (Tc), pyrophyllite (Prl) and kyanite (Ky). The calculated petrogenetic grid for the system NFASH shows that Fe-Ctd and ferroglaucophane coexist at P>6.5 kbar and T<525°C, whereas the assemblage: Ct-Gln-Pg is stable between 435 and 630°C and P>6 kbar. This grid is consistent with the P-T estimates for high P metapelites from Oman, New Caledonia, Seward Peninsula, Ile de Groix, Sifnos and Peloponnese, where Gln+Ctd bearing units are interbedded with cofacial mafic blueschists and eclogites. The grid also explains the observed textural relations in the metapelites of Oman, and is consistent with the “clockwise” P-T path proposed for this area, but differs from the grids of Guiraud et al. (1990) in showing a larger stability field for Gln+Ctd that overlaps with the stability fields of Jd+Qz as well as Ab. The petrogenetic grid calculated for the system NMASH shows that Mg-Ctd+Gln-bearing assemblages require unusually low geothermal gradients to form in metapelites. It also shows that Mg-rich Ctd+Tc coexist at high pressures over a wider P-T range than predicted by Guiraud et al. (1990). This grid can therefore be applied to high P metamorphic assemblages from the eastern and western Alps.

Correlation-based perfusion mapping using time-resolved MR angiography: A feasibility study for patients with suspicions of steno-occlusive craniocervical arteries.

PubMed

Nam, Yoonho; Jang, Jinhee; Park, Sonya Youngju; Choi, Hyun Seok; Jung, So-Lyung; Ahn, Kook-Jin; Kim, Bum-Soo

2018-05-22

To explore the feasibility of using correlation-based time-delay (CTD) maps produced from time-resolved MR angiography (TRMRA) to diagnose perfusion abnormalities in patients suspected to have steno-occlusive lesions in the craniocervical arteries. Twenty-seven patients who were suspected to have steno-occlusive lesions in the craniocervical arteries underwent both TRMRA and brain single-photon emission computed tomography (SPECT). TRMRA was performed on the supra-aortic area after intravenous injection of a 0.03 mmol/kg gadolinium-based contrast agent. Time-to-peak (TTP) maps and CTD maps of the brain were automatically generated from TRMRA data, and their quality was assessed. Detection of perfusion abnormalities was compared between CTD maps and the time-series maximal intensity projection (MIP) images from TRMRA and TTP maps. Correlation coefficients between quantitative changes in SPECT and parametric maps for the abnormal perfusion areas were calculated. The CTD maps were of significantly superior quality than TTP maps (p < 0.01). For perfusion abnormality detection, CTD maps (kappa 0.84, 95% confidence interval [CI] 0.67-1.00) showed better agreement with SPECT than TTP maps (0.66, 0.46-0.85). For perfusion deficit detection, CTD maps showed higher accuracy (85.2%, 95% CI 66.3-95.8) than MIP images (66.7%, 46-83.5), with marginal significance (p = 0.07). In abnormal perfusion areas, correlation coefficients between SPECT and CTD (r = 0.74, 95% CI 0.34-0.91) were higher than those between SPECT and TTP (r = 0.66, 0.20-0.88). CTD maps generated from TRMRA were of high quality and offered good diagnostic performance for detecting perfusion abnormalities associated with steno-occlusive arterial lesions in the craniocervical area. • Generation of perfusion parametric maps from time-resolved MR angiography is clinically useful. • Correlation-based delay maps can be used to detect perfusion abnormalities associated with steno-occlusive craniocervical arteries. • Estimation of correlation-based delay is robust for low signal-to-noise 4D MR data.

A randomized titrate-to-target study comparing fixed-dose combinations of azilsartan medoxomil and chlorthalidone with olmesartan and hydrochlorothiazide in stage-2 systolic hypertension.

PubMed

Cushman, William C; Bakris, George L; White, William B; Weber, Michael A; Sica, Domenic; Roberts, Andrew; Lloyd, Eric; Kupfer, Stuart

2018-04-01

Azilsartan medoxomil (AZL-M), an angiotensin II receptor blocker, has been developed in fixed-dose combinations (FDCs) with chlorthalidone (CTD). We compared FDCs of AZL-M/CTD 20/12.5 mg once daily titrated to 40/25 mg if needed or AZL-M/CTD 40/12.5 mg once daily titrated to 80/25 mg if needed with an olmesartan medoxomil (OLM)-hydrochlorothiazide (HCTZ) 20/12.5 mg FDC once daily titrated to 40/25 mg if needed in a randomized, double-blind, 8-week study of 1085 participants with clinic SBP 160-190 mmHg and DBP 119 mmHg or less. Titration to higher doses occurred at week 4 if BP was at least 140/90 mmHg (≥130/80 mmHg if diabetes or chronic kidney disease). The primary endpoint was change from baseline in clinic SBP; 24-h ambulatory BP monitoring was also measured. Greater reductions in clinic SBP from a baseline of 165 mmHg were observed (P < 0.001) in both AZL-M/CTD arms (-37.6 and -38.2 mmHg) versus OLM/HCTZ (-31.5 mmHg), despite greater dose titration in the OLM/HCTZ group. At 8 weeks, both AZL-M/CTD FDCs reduced 24-h SBP more than OLM/HCTZ (-26.4 and -27.9 versus -20.7 mmHg; both P < 0.001), and higher proportions in both AZL-M/CTD groups achieved target BP compared with the OLM/HCTZ group (69.4 and 68.9 versus 54.7%, both P < 0.001). Adverse events leading to drug discontinuation occurred in 6.2, 9.5, and 3.1% with the AZL-M/CTD lower and higher doses, and OLM/HCTZ, respectively. This large, titration-to-target BP study demonstrated AZL-M/CTD FDCs to have superior antihypertensive efficacy compared with the maximum approved dose of OLM/HCTZ.

A randomized titrate-to-target study comparing fixed-dose combinations of azilsartan medoxomil and chlorthalidone with olmesartan and hydrochlorothiazide in stage-2 systolic hypertension

PubMed Central

Cushman, William C.; Bakris, George L.; White, William B.; Weber, Michael A.; Sica, Domenic; Roberts, Andrew; Lloyd, Eric; Kupfer, Stuart

2018-01-01

Background: Azilsartan medoxomil (AZL-M), an angiotensin II receptor blocker, has been developed in fixed-dose combinations (FDCs) with chlorthalidone (CTD). Objective/methods: We compared FDCs of AZL-M/CTD 20/12.5 mg once daily titrated to 40/25 mg if needed or AZL-M/CTD 40/12.5 mg once daily titrated to 80/25 mg if needed with an olmesartan medoxomil (OLM)-hydrochlorothiazide (HCTZ) 20/12.5 mg FDC once daily titrated to 40/25 mg if needed in a randomized, double-blind, 8-week study of 1085 participants with clinic SBP 160–190 mmHg and DBP 119 mmHg or less. Titration to higher doses occurred at week 4 if BP was at least 140/90 mmHg (≥130/80 mmHg if diabetes or chronic kidney disease). The primary endpoint was change from baseline in clinic SBP; 24-h ambulatory BP monitoring was also measured. Results: Greater reductions in clinic SBP from a baseline of 165 mmHg were observed (P < 0.001) in both AZL-M/CTD arms (−37.6 and −38.2 mmHg) versus OLM/HCTZ (−31.5 mmHg), despite greater dose titration in the OLM/HCTZ group. At 8 weeks, both AZL-M/CTD FDCs reduced 24-h SBP more than OLM/HCTZ (−26.4 and −27.9 versus −20.7 mmHg; both P < 0.001), and higher proportions in both AZL-M/CTD groups achieved target BP compared with the OLM/HCTZ group (69.4 and 68.9 versus 54.7%, both P < 0.001). Adverse events leading to drug discontinuation occurred in 6.2, 9.5, and 3.1% with the AZL-M/CTD lower and higher doses, and OLM/HCTZ, respectively. Conclusion: This large, titration-to-target BP study demonstrated AZL-M/CTD FDCs to have superior antihypertensive efficacy compared with the maximum approved dose of OLM/HCTZ. PMID:29334491

Structure of Atg7 Alone and its Atg8-Bound Forms

NASA Astrophysics Data System (ADS)

Noda, Nobuo

Atg7 is a noncanonical E1 enzyme that activates Atg8 and transfers it to Atg3 (E2 enzyme), thus playing an essential role in conjugating Atg8 with phosphatidylethanolamine and thus in autophagy. Atg7 protomer is comprised of two globular domains, the N-terminal domain (NTD) and the C-terminal domain (CTD), and forms a homodimer through CTD. Atg7-Atg8 complex structures and biochemical analyses revealed that Atg8 is initially recognized by the C-terminal tail of CTD and is then transferred to the adenylation domain in CTD, where Atg8 Gly116 is adenylated and thioester-linked to the catalytic cysteine of Atg7. Atg8 is then transferred to Atg3 bound to the NTD of the opposite protomer within an Atg7 dimer via a trans mechanism.

Creatine Transporter Deficiency: Screening of Males with Neurodevelopmental Disorders and Neurocognitive Characterization of a Case.

PubMed

Thurm, Audrey; Himelstein, Daniel; DʼSouza, Precilla; Rennert, Owen; Jiang, Susanqi; Olatunji, Damilola; Longo, Nicola; Pasquali, Marzia; Swedo, Susan; Salomons, Gajja S; Carrillo, Nuria

2016-05-01

Creatine transporter deficiency (CTD) is an X-linked, neurometabolic disorder associated with intellectual disability that is characterized by brain creatine (Cr) deficiency and caused by mutations in SLC6A8, the Cr transporter 1 protein gene. CTD is identified by elevated urine creatine/creatinine (Cr/Crn) ratio or reduced Cr peak on brain magnetic resonance spectroscopy; the diagnosis is confirmed by decreased Cr uptake in cultured fibroblasts, and/or identification of a mutation in the SLC6A8 gene. Prevalence studies suggest this disorder may be underdiagnosed. We sought to identify cases from a well-characterized cohort of children diagnosed with neurodevelopmental disorders. Urine screening for CTD was performed on a cohort of 46 males with autism spectrum disorder (ASD) and 9 males with a history of non-ASD developmental delay (DD) classified with intellectual disability. We identified 1 patient with CTD in the cohort based on abnormal urine Cr/Crn, and confirmed the diagnosis by the identification of a novel frameshift mutation in the SLC6A8 gene. This patient presented without ASD but with intellectual disability, and was characterized by a nonspecific phenotype of early language delay and DD that persisted into moderate-to-severe intellectual disability, consistent with previous descriptions of CTD. Identification of patients with CTD is possible by measuring urine Cr and Crn levels and the current case adds to the growing literature of neurocognitive deficits associated with the disorder that affect cognition, language and behavior in childhood.

The effects of gender discrimination on refugee torture survivors: a cross-cultural traumatology perspective.

PubMed

Kira, Ibrahim A; Smith, Iris; Lewandowski, Linda; Templin, Thomas

2010-09-01

Trauma developmental theory identifies gender discrimination (GD) as a type of persistent, ongoing trauma that has the potential for serious, negative effects on mental health. This study was conducted to examine the potential role of GD in the development of cumulative trauma disorders (CTD) and symptoms of posttraumatic stress disorder (PTSD) as well as the role of GD in mediating the effects of other traumas on these disorders. The sample included 160 female torture survivors from more than 30 countries. Measures of PTSD, CTD, and types of trauma exposure were acquired as part of a larger study on refugee torture survivors. Structural equation modeling was used to test several plausible models for the direct and indirect effects of GD on PTSD and CTD, within the context of other trauma exposure. Results suggest that GD mediates the effects of identity traumas on CTD and PTSD. GD also had direct effects on CTD, including relationships with dissociation, suicidality, and deficits in executive function. GD did not appear to directly influence the development of PTSD. The implications of these results for assessment and treatment of women's trauma-related disorders as well as strategies for their prevention are discussed.

Structure of the Z Ring-associated Protein, ZapD, Bound to the C-terminal Domain of the Tubulin-like Protein, FtsZ, Suggests Mechanism of Z Ring Stabilization through FtsZ Cross-linking.

PubMed

Schumacher, Maria A; Huang, Kuo-Hsiang; Zeng, Wenjie; Janakiraman, Anuradha

2017-03-03

Cell division in most bacteria is mediated by the tubulin-like FtsZ protein, which polymerizes in a GTP-dependent manner to form the cytokinetic Z ring. A diverse repertoire of FtsZ-binding proteins affects FtsZ localization and polymerization to ensure correct Z ring formation. Many of these proteins bind the C-terminal domain (CTD) of FtsZ, which serves as a hub for FtsZ regulation. FtsZ ring-associated proteins, ZapA-D (Zaps), are important FtsZ regulatory proteins that stabilize FtsZ assembly and enhance Z ring formation by increasing lateral assembly of FtsZ protofilaments, which then form the Z ring. There are no structures of a Zap protein bound to FtsZ; therefore, how these proteins affect FtsZ polymerization has been unclear. Recent data showed ZapD binds specifically to the FtsZ CTD. Thus, to obtain insight into the ZapD-CTD interaction and how it may mediate FtsZ protofilament assembly, we determined the Escherichia coli ZapD-FtsZ CTD structure to 2.67 Å resolution. The structure shows that the CTD docks within a hydrophobic cleft in the ZapD helical domain and adopts an unusual structure composed of two turns of helix separated by a proline kink. FtsZ CTD residue Phe-377 inserts into the ZapD pocket, anchoring the CTD in place and permitting hydrophobic contacts between FtsZ residues Ile-374, Pro-375, and Leu-378 with ZapD residues Leu-74, Trp-77, Leu-91, and Leu-174. The structural findings were supported by mutagenesis coupled with biochemical and in vivo studies. The combined data suggest that ZapD acts as a molecular cross-linking reagent between FtsZ protofilaments to enhance FtsZ assembly. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

The HIP1 initiator element plays a role in determining the in vitro requirement of the dihydrofolate reductase gene promoter for the C-terminal domain of RNA polymerase II.

PubMed

Buermeyer, A B; Thompson, N E; Strasheim, L A; Burgess, R R; Farnham, P J

1992-05-01

We examined the ability of purified RNA polymerase (RNAP) II lacking the carboxy-terminal heptapeptide repeat domain (CTD), called RNAP IIB, to transcribe a variety of promoters in HeLa extracts in which endogenous RNAP II activity was inhibited with anti-CTD monoclonal antibodies. Not all promoters were efficiently transcribed by RNAP IIB, and transcription did not correlate with the in vitro strength of the promoter or with the presence of a consensus TATA box. This was best illustrated by the GC-rich, non-TATA box promoters of the bidirectional dihydrofolate reductase (DHFR)-REP-encoding locus. Whereas the REP promoter was transcribed by RNAP IIB, the DHFR promoter remained inactive after addition of RNAP IIB to the antibody-inhibited reactions. However, both promoters were efficiently transcribed when purified RNAP with an intact CTD was added. We analyzed a series of promoter deletions to identify which cis elements determine the requirement for the CTD of RNAP II. All of the promoter deletions of both DHFR and REP retained the characteristics of their respective full-length promoters, suggesting that the information necessary to specify the requirement for the CTD is contained within approximately 65 bp near the initiation site. Furthermore, a synthetic minimal promoter of DHFR, consisting of a single binding site for Sp1 and a binding site for the HIP1 initiator cloned into a bacterial vector sequence, required RNAP II with an intact CTD for activity in vitro. Since the synthetic minimal promoter of DHFR and the smallest REP promoter deletion are both activated by Sp1, the differential response in this assay does not result from upstream activators. However, the sequences around the start sites of DHFR and REP are not similar and our data suggest that they bind different proteins. Therefore, we propose that specific initiator elements are important for determination of the requirement of some promoters for the CTD.

Long-term monitoring of waterborne pathogens and microbial source tracking markers in paired agricultural watersheds under controlled and conventional tile drainage management.

PubMed

Wilkes, Graham; Brassard, Julie; Edge, Thomas A; Gannon, Victor; Gottschall, Natalie; Jokinen, Cassandra C; Jones, Tineke H; Khan, Izhar U H; Marti, Romain; Sunohara, Mark D; Topp, Edward; Lapen, David R

2014-06-01

Surface waters from paired agricultural watersheds under controlled tile drainage (CTD) and uncontrolled tile drainage (UCTD) were monitored over 7 years in order to determine if there was an effect of CTD (imposed during the growing season) on occurrences and loadings of bacterial and viral pathogens, coliphages, and microbial source tracking markers. There were significantly lower occurrences of human, ruminant, and livestock (ruminant plus pig) Bacteroidales markers in the CTD watershed in relation to the UCTD watershed. As for pathogens, there were significantly lower occurrences of Salmonella spp. and Arcobacter spp. in the CTD watershed. There were no instances where there were significantly higher quantitative loadings of any microbial target in the CTD watershed, except for F-specific DNA (F-DNA) and F-RNA coliphages, perhaps as a result of fecal inputs from a hobby farm independent of the drainage practice treatments. There was lower loading of the ruminant marker in the CTD watershed in relation to the UCTD system, and results were significant at the level P = 0.06. The odds of Salmonella spp. occurring increased when a ruminant marker was present relative to when the ruminant marker was absent, yet for Arcobacter spp., the odds of this pathogen occurring significantly decreased when a ruminant marker was present relative to when the ruminant marker was absent (but increased when a wildlife marker was present relative to when the wildlife marker was absent). Interestingly, the odds of norovirus GII (associated with human and swine) occurring in water increased significantly when a ruminant marker was present relative to when a ruminant marker was absent. Overall, this study suggests that fecal pollution from tile-drained fields to stream could be reduced by CTD utilization. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

The influence of tributary flow density differences on the hydrodynamic behavior of a confluent meander bend and implications for flow mixing

NASA Astrophysics Data System (ADS)

Herrero, Horacio S.; Díaz Lozada, José M.; García, Carlos M.; Szupiany, Ricardo N.; Best, Jim; Pagot, Mariana

2018-03-01

The goal of this study is to evaluate the influence of tributary flow density differences on hydrodynamics and mixing at a confluent meander bend. A detailed field characterization is performed using an Acoustic Doppler Current Profiler (ADCP) for quantification of the 3D flow field, flow discharge and bathymetry, as well as CTD measurements (conductivity, temperature, depth) to characterize the patterns of mixing. Satellite images of the confluence taken at complementary times to the field surveys were analyzed to evaluate the confluence hydrodynamics at different flow conditions. The results illustrate the differences in hydrodynamics and mixing length in relation to confluences with equal density tributaries. At low-density differences, and higher discharge ratio (Qr) between the two rivers, the flow is similar to equi-density confluent meander bends. In contrast, at high-density differences (low Qr), the tributary flow is confined to near the confluence but the density difference causes the flow to move across channel. In this case, the density difference causes the lateral spread of the tributary flow to be greater than at a greater Qr when the density difference is less. These results illustrate the potential importance of density differences between tributaries in determining the rate and spatial extent of mixing and sediment dispersal at confluent meander bends.

Direct evidence of warm water access to the Totten Glacier sub-ice shelf cavity

NASA Astrophysics Data System (ADS)

Orsi, A. H.; Rintoul, S. R.; Silvano, A.; van Wijk, E.; Pena-Molino, B.; Rosenberg, M. A.

2015-12-01

The Totten Glacier holds enough ice to raise global sea level by 3.5 m, is thinning according to (some) satellite data, and is grounded well below sea level on a retrograde bed and hence is potentially unstable. Basal melt driven by ocean heat flux has been linked to ice shelf thinning elsewhere in Antarctica, but no oceanographic measurements had been made near the Totten. In January 2015 the RSV Aurora Australis was the first ship to reach the Totten calving front. Observations from ship-board CTD, moorings and profiling floats provide direct confirmation that warm water reaches the ice shelf cavity. Warm water is present near the sea floor at every station deeper than 300 m depth, with maximum temperatures at mid-shelf >0.5°C. Mooring data confirm that the warm water is present year-round. A deep (>1100 m) channel at the calving front allows warm water (-0.4°C, >2°C above the local freezing point) to access the ice shelf cavity. The contrast between the oceanographic conditions near the Totten and near the Mertz Glacier is stark, although they are separated by only 30 degrees of longitude. East Antarctic ice shelves have often been assumed to behave in a similar manner and to be invulnerable to ocean change; these measurements suggest these assumptions need to be reconsidered.

Variability of stratification according to operation of the tidal power plant in Lake Sihwa, South Korea.

NASA Astrophysics Data System (ADS)

Woo, S. B.; Song, J. I.; Jang, T. H.; Park, C. J.; Kwon, H. K.

2017-12-01

Artificial forcing according to operation of the tidal power plant (TPP) affects the physical environmental changes near the power plant. Strong turbulence by generation is expected to change the stratification structure of the Lake Sihwa inside. In order to examine the stratification changes by the power plant operation, ship bottom mounted observation were performed for 13 hours using an acoustic Doppler current profiler (ADCP) and Conductivity-Temperature-Depth (CTD) in Lake Sihwa at near TPP. The strong stratification in Sihwa Lake is maintained before TPP operation. The absence of external forces and freshwater inflow from the land forms the stratification in the Lake. Strong winds in a stratification statement lead to two-layer circulation. After wind event, multi-layer velocity structure is formed which lasted for approximately 4 h. After TPP operation, the jet flow was observed in entire water column at the beginning of the power generation. Vortex is formed by strong jet flow and maintained throughout during power generation period. Strong turbulence flow is generated by the turbine blades, enhancing vertical mixing. External forces, which dominantly affect Lake Sihwa, have changed from the wind to the turbulent flow. The stratification was extinguished by strong turbulent flow and becomes fully-mixed state. Changes in stratification structure are expected to affect material transport and ecological environment change continuously.

Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data.

PubMed

Hettne, Kristina M; Boorsma, André; van Dartel, Dorien A M; Goeman, Jelle J; de Jong, Esther; Piersma, Aldert H; Stierum, Rob H; Kleinjans, Jos C; Kors, Jan A

2013-01-29

Availability of chemical response-specific lists of genes (gene sets) for pharmacological and/or toxic effect prediction for compounds is limited. We hypothesize that more gene sets can be created by next-generation text mining (next-gen TM), and that these can be used with gene set analysis (GSA) methods for chemical treatment identification, for pharmacological mechanism elucidation, and for comparing compound toxicity profiles. We created 30,211 chemical response-specific gene sets for human and mouse by next-gen TM, and derived 1,189 (human) and 588 (mouse) gene sets from the Comparative Toxicogenomics Database (CTD). We tested for significant differential expression (SDE) (false discovery rate -corrected p-values < 0.05) of the next-gen TM-derived gene sets and the CTD-derived gene sets in gene expression (GE) data sets of five chemicals (from experimental models). We tested for SDE of gene sets for six fibrates in a peroxisome proliferator-activated receptor alpha (PPARA) knock-out GE dataset and compared to results from the Connectivity Map. We tested for SDE of 319 next-gen TM-derived gene sets for environmental toxicants in three GE data sets of triazoles, and tested for SDE of 442 gene sets associated with embryonic structures. We compared the gene sets to triazole effects seen in the Whole Embryo Culture (WEC), and used principal component analysis (PCA) to discriminate triazoles from other chemicals. Next-gen TM-derived gene sets matching the chemical treatment were significantly altered in three GE data sets, and the corresponding CTD-derived gene sets were significantly altered in five GE data sets. Six next-gen TM-derived and four CTD-derived fibrate gene sets were significantly altered in the PPARA knock-out GE dataset. None of the fibrate signatures in cMap scored significant against the PPARA GE signature. 33 environmental toxicant gene sets were significantly altered in the triazole GE data sets. 21 of these toxicants had a similar toxicity pattern as the triazoles. We confirmed embryotoxic effects, and discriminated triazoles from other chemicals. Gene set analysis with next-gen TM-derived chemical response-specific gene sets is a scalable method for identifying similarities in gene responses to other chemicals, from which one may infer potential mode of action and/or toxic effect.

Next-generation text-mining mediated generation of chemical response-specific gene sets for interpretation of gene expression data

PubMed Central

2013-01-01

Background Availability of chemical response-specific lists of genes (gene sets) for pharmacological and/or toxic effect prediction for compounds is limited. We hypothesize that more gene sets can be created by next-generation text mining (next-gen TM), and that these can be used with gene set analysis (GSA) methods for chemical treatment identification, for pharmacological mechanism elucidation, and for comparing compound toxicity profiles. Methods We created 30,211 chemical response-specific gene sets for human and mouse by next-gen TM, and derived 1,189 (human) and 588 (mouse) gene sets from the Comparative Toxicogenomics Database (CTD). We tested for significant differential expression (SDE) (false discovery rate -corrected p-values < 0.05) of the next-gen TM-derived gene sets and the CTD-derived gene sets in gene expression (GE) data sets of five chemicals (from experimental models). We tested for SDE of gene sets for six fibrates in a peroxisome proliferator-activated receptor alpha (PPARA) knock-out GE dataset and compared to results from the Connectivity Map. We tested for SDE of 319 next-gen TM-derived gene sets for environmental toxicants in three GE data sets of triazoles, and tested for SDE of 442 gene sets associated with embryonic structures. We compared the gene sets to triazole effects seen in the Whole Embryo Culture (WEC), and used principal component analysis (PCA) to discriminate triazoles from other chemicals. Results Next-gen TM-derived gene sets matching the chemical treatment were significantly altered in three GE data sets, and the corresponding CTD-derived gene sets were significantly altered in five GE data sets. Six next-gen TM-derived and four CTD-derived fibrate gene sets were significantly altered in the PPARA knock-out GE dataset. None of the fibrate signatures in cMap scored significant against the PPARA GE signature. 33 environmental toxicant gene sets were significantly altered in the triazole GE data sets. 21 of these toxicants had a similar toxicity pattern as the triazoles. We confirmed embryotoxic effects, and discriminated triazoles from other chemicals. Conclusions Gene set analysis with next-gen TM-derived chemical response-specific gene sets is a scalable method for identifying similarities in gene responses to other chemicals, from which one may infer potential mode of action and/or toxic effect. PMID:23356878

The CTD Teacher Opinion Poll.

ERIC Educational Resources Information Center

Arato, Agnes

1985-01-01

Within the framework of Hungary's Curriculum Theory Department (CTD-80) national assessment, 2,391 teachers from 70 general schools were surveyed. The questionnaire included teachers' characteristics, reaction to the new curriculum, and teaching practices. The results are described. (GDC)

Mediating role of critical thinking disposition in the relationship between perceived barriers to research use and evidence-based practice.

PubMed

Kim, Sun-Ae; Song, Youngshin; Sim, Hee-Sook; Ahn, Eun-Kyong; Kim, Jung-Hee

2015-01-01

Despite the importance of critical thinking in clinical and educational settings, little is known about its role in evidence-based practice (EBP). This study examined whether critical thinking disposition (CTD) mediates the relationship between perceived barriers to research use and EBP in clinical nurses (N=409). A path diagram using structural equation modeling was used to estimate the direct and indirect effects of perceived barriers to research use on EBP, controlling for CTD as a mediator. CTD partially mediated the relationship between perceived barriers to research use and EBP. Furthermore, the hypothesized mediation model demonstrated an appropriate fit to the data. Individual and organizational efforts are needed to help nurses further improve their critical thinking skills. CTD is important as research barriers to engage effectively in EBP. Without the skills to evaluate evidence carefully, research utilization may be compromised.

A conserved Mediator–CDK8 kinase module association regulates Mediator–RNA polymerase II interaction

PubMed Central

Tsai, Kuang-Lei; Sato, Shigeo; Tomomori-Sato, Chieri; Conaway, Ronald C.; Conaway, Joan W.; Asturias, Francisco J.

2013-01-01

The CDK8 kinase module (CKM) is a conserved, dissociable Mediator subcomplex whose component subunits were genetically linked to the RNA polymerase II (RNAPII) carboxy-terminal domain (CTD) and individually recognized as transcriptional repressors before Mediator was identified as a preeminent complex in eukaryotic transcription regulation. We used macromolecular electron microscopy and biochemistry to investigate the subunit organization, structure, and Mediator interaction of the Saccharomyces cerevisiae CKM. We found that interaction of the CKM with Mediator’s Middle module interferes with CTD-dependent RNAPII binding to a previously unknown Middle module CTD-binding site targeted early on in a multi-step holoenzyme formation process. Taken together, our results reveal the basis for CKM repression, clarify the origin of the connection between CKM subunits and the CTD, and suggest that a combination of competitive interactions and conformational changes that facilitate holoenzyme formation underlie the Mediator mechanism. PMID:23563140

Phosphorylation-regulated Binding of RNA Polymerase II to Fibrous Polymers of Low Complexity Domains

PubMed Central

Xiang, Siheng; Wu, Leeju; Theodoropoulos, Pano; Mirzaei, Hamid; Han, Tina; Xie, Shanhai; Corden, Jeffry L.; McKnight, Steven L.

2014-01-01

SUMMARY The low complexity (LC) domains of the products of the fused in sarcoma (FUS), Ewings sarcoma (EWS) and TAF15 genes are translocated onto a variety of different DNA-binding domains and thereby assist in driving the formation of cancerous cells. In the context of the translocated fusion proteins, these LC sequences function as transcriptional activation domains. Here we show that polymeric fibers formed from these LC domains directly bind the C-terminal domain (CTD) of RNA polymerase II in a manner reversible by phosphorylation of the iterated, heptad repeats of the CTD. Mutational analysis indicates that the degree of binding between the CTD and the LC domain polymers correlates with the strength of transcriptional activation. These studies offer a simple means of conceptualizing how RNA polymerase II is recruited to active genes in its unphosphorylated state, and released for elongation following phosphorylation of the CTD. PMID:24267890

Turbulence observations in the Gulf of Trieste under moderate wind forcing and different water column stratification

NASA Astrophysics Data System (ADS)

Marcello Falcieri, Francesco; Kantha, Lakshmi; Benetazzo, Alvise; Bergamasco, Andrea; Bonaldo, Davide; Barbariol, Francesco; Malačič, Vlado; Sclavo, Mauro; Carniel, Sandro

2016-03-01

The oceanographic campaign CARPET2014 (Characterizing Adriatic Region Preconditionig EvenTs), (30 January-4 February 2014) collected the very first turbulence data in the Gulf of Trieste (northern Adriatic Sea) under moderate wind (average wind speed 10 m s-1) and heat flux (net negative heat flux ranging from 150 to 400 W m-2). Observations consisted of 38 CTD (Conductivity, Temperature, Depth) casts and 478 microstructure profiles (grouped into 145 ensembles) with three sets of yoyo casts, each lasting for about 12 consecutive hours. Averaging closely repeated casts, such as the ensembles, can lead to a smearing effect when in the presence of a vertical density structure with strong interfaces that can move up or down between subsequent casts under the influence of tides and internal waves. In order to minimize the smearing effect of such displacements on mean quantities, we developed an algorithm to realign successive microstructure profiles to produce sharper and more meaningful mean profiles of measured turbulence parameters. During the campaign, the water column in the gulf evolved from well-mixed to stratified conditions due to Adriatic waters intruding at the bottom along the gulf's south-eastern coast. We show that during the warm and relatively dry winter, the water column in the Gulf of Trieste, even under moderate wind forcing, was not completely mixed due to the influence of bottom waters intruding from the open sea. Inside the gulf, two types of water intrusions were found during yoyo casts: one coming from the northern coast of the Adriatic Sea (i.e. cooler, fresher and more turbid) and one coming from the open sea in front of the Po Delta (i.e. warmer, saltier and less turbid). The two intrusions had different impacts on turbulence kinetic energy dissipation rate profiles. The former, with high turbidity, acted as a barrier to wind-driven turbulence, while the latter, with low sediment concentrations and a smaller vertical density gradient, was not able to suppress downward penetration of turbulence from the surface.

Prenatal and early postnatal NOAEL-dose clothianidin exposure leads to a reduction of germ cells in juvenile male mice

PubMed Central

YANAI, Shogo; HIRANO, Tetsushi; OMOTEHARA, Takuya; TAKADA, Tadashi; YONEDA, Naoki; KUBOTA, Naoto; YAMAMOTO, Anzu; MANTANI, Youhei; YOKOYAMA, Toshifumi; KITAGAWA, Hiroshi; HOSHI, Nobuhiko

2017-01-01

Neonicotinoids are pesticides used worldwide. They bind to insect nicotinic acetylcholine receptors (nAChRs) with high affinity. We previously reported that clothianidin (CTD), one of the latest neonicotinoids, reduced antioxidant expression and induced germ cell death in the adult testis of vertebrates. Here, we investigated the male reproductive toxicity of prenatal and early postnatal exposure to CTD, because it is likely that developmental exposure more severely affects the testis compared to adults due to the absence of the blood-testis barrier. Pregnant C57BL/6 mice were given water gel blended with CTD (0, 10 or 50 mg/kg/day; no-observed-adverse-effect-level [NOAEL for mice]: 47.2 mg/kg/day) between gestational day 1 and 14 days post-partum. We then examined the testes of male offspring at postnatal day 14. The testis weights and the numbers of germ cells per seminiferous tubule were decreased in the CTD-50 group, and abnormal tubules containing no germ cells appeared. Nevertheless, the apoptotic cell number and proliferative activity were not significantly different between the control and CTD-exposed groups. There were no significant differences in the androgen-related parameters, such as the Leydig cell volume per testis, the Sertoli cell number and the tubule diameter. The present study is the first demonstration that in utero and lactational exposures to CTD at around the NOAEL for mice reduce the germ cell number, but our findings suggest that these exposures do not affect steroidogenesis in Leydig cells during prenatal or early postnatal life. PMID:28579575

A Thermodynamic Model for Genome Packaging in Hepatitis B Virus.

PubMed

Kim, Jehoon; Wu, Jianzhong

2015-10-20

Understanding the fundamentals of genome packaging in viral capsids is important for finding effective antiviral strategies and for utilizing benign viral particles for gene therapy. While the structure of encapsidated genomic materials has been routinely characterized with experimental techniques such as cryo-electron microscopy and x-ray diffraction, much less is known about the molecular driving forces underlying genome assembly in an intracellular environment and its in vivo interactions with the capsid proteins. Here we study the thermodynamic basis of the pregenomic RNA encapsidation in human Hepatitis B virus in vivo using a coarse-grained molecular model that captures the essential components of nonspecific intermolecular interactions. The thermodynamic model is used to examine how the electrostatic interaction between the packaged RNA and the highly charged C-terminal domains (CTD) of capsid proteins regulate the nucleocapsid formation. The theoretical model predicts optimal RNA content in Hepatitis B virus nucleocapsids with different CTD lengths in good agreement with mutagenesis measurements, confirming the predominant role of electrostatic interactions and molecular excluded-volume effects in genome packaging. We find that the amount of encapsidated RNA is not linearly correlated with the net charge of CTD tails as suggested by earlier theoretical studies. Our thermodynamic analysis of the nucleocapsid structure and stability indicates that ∼10% of the CTD residues are free from complexation with RNA, resulting in partially exposed CTD tails. The thermodynamic model also predicts the free energy of complex formation between macromolecules, which corroborates experimental results for the impact of CTD truncation on the nucleocapsid stability. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Pulmonary MR imaging with ultra-short TEs: utility for disease severity assessment of connective tissue disease patients.

PubMed

Ohno, Yoshiharu; Nishio, Mizuho; Koyama, Hisanobu; Takenaka, Daisuke; Takahashi, Masaya; Yoshikawa, Takeshi; Matsumoto, Sumiaki; Obara, Makoto; van Cauteren, Marc; Sugimura, Kazuro

2013-08-01

To evaluate the utility of pulmonary magnetic resonance (MR) imaging with ultra-short echo times (UTEs) at a 3.0 T MR system for pulmonary functional loss and disease severity assessments of connective tissue disease (CTD) patients with interstitial lung disease (ILD). This prospective study was approved by the institutional review board, and written informed consent was obtained from 18 CTD patients (eight men and ten women) and eight normal subjects with suspected chest disease (three men and five women). All subjects underwent thin-section MDCT, pulmonary MR imaging with UTEs, pulmonary function test and serum KL-6. Regional T2 maps were generated from each MR data set, and mean T2 values were determined from ROI measurements. From each thin-section MDCT data set, CT-based disease severity was evaluated with a visual scoring system. Mean T2 values for normal and CTD subjects were statistically compared by using Student's t-test. To assess capability for pulmonary functional loss and disease severity assessments, mean T2 values were statistically correlated with pulmonary functional parameters, serum KL-6 and CT-based disease severity. Mean T2 values for normal and CTD subjects were significantly different (p=0.0019) and showed significant correlations with %VC, %DLCO, serum KL-6 and CT-based disease severity of CTD patients (p<0.05). Pulmonary MR imaging with UTEs is useful for pulmonary functional loss and disease severity assessments of CTD patients with ILD. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Salinity Processes in the Upper Ocean Regional Study (SPURS)

NASA Image and Video Library

2012-09-04

Sean Whelan, a Marine Technician for the Woods Hole Oceanographic Institution, prepares CTD instruments used to measure Conductivity, Temperature, and Depth, onboard the Institute's research vessel Knorr on Tuesday, Sept. 4, 2012, in Woods Hole, Mass. The CTDs will be deployed in the Atlantic Ocean as part of the Salinity Processes in the Upper Ocean Regional Study (SPURS) which is set to sail on Sept. 6. The NASA-sponsored expedition will sail to the North Atlantic's saltiest spot to get a detailed, 3-D picture of how salt content fluctuates in the ocean's upper layers and how these variations are related to shifts in rainfall patterns around the planet. Photo Credit: (NASA/Bill Ingalls)

Pinatubo Lake Chemistry and Degassing 1991-2010

NASA Astrophysics Data System (ADS)

Schwandner, F. M.; Newhall, C. G.; Christenson, B. W.; Apfelbeck, C. A.; Arpa, M. C. B.; Vaquilar, R.; Bariso, E.

2016-12-01

We review the history of degassing, bathymetry and water chemistry of the crater lake of Mt. Pinatubo (Philippines) using data obtained during 1991-2001, and 2010. In late 1992, the initial small lake had a significant acid-sulfate component from a volcanic degassing through a hydrothermal system and the lake, and anhydrite dissolution. Subsequently, this component was "drowned" by rainfall (2-4 m/y), meteoric groundwater draining from the crater walls into the lake, and a few neutral chloride crater wall springs. Conductivity-Temperature-Depth (CTD) measurements in August 2000 found a strong inverted thermal gradient below 20m depth, reaching over 70°C at 50-60 m depth. By January 2001 the lake had homogenized and was much cooler (27°C at all depths), and it was again well-mixed and still cool when re-surveyed in June 2001 and November 2010. By 2010, the lake was well mixed, at neutral pH, with no significant vertical or horizontal structure. Bubbling of a predominantly carbon dioxide (CO2) gas phase persists throughout the lake's history, some from 1991-92 magma and some from degassing of the long-standing (pre-1991) hydrothermal system fed from a deeper magmatic or mantle source. Crater wall fumaroles emit boiling-point hydrothermal gases dominated by water, air, and CO2.

Cruise Summary of WHP P6, A10, I3 and I4 Revisits in 2003

NASA Astrophysics Data System (ADS)

Kawano, T.; Uchida, H.; Schneider, W.; Kumamoto, Y.; Nishina, A.; Aoyama, M.; Murata, A.; Sasaki, K.; Yoshikawa, Y.; Watanabe, S.; Fukasawa, M.

2004-12-01

Japan Agency for Marin-Earth Science and Technology (JAMSTEC) conducted a research cruise to round in the southern hemisphere by R/V Mirai. In this presentation, we introduce an outline of the cruise and data quality obtained during the cruise. The cruise started on Aug. 3, 2003 in Brisbane, Australia and sailed eastward until it reached Fremantle, Australia on Feb. 19, 2004. It contained six legs and legs 1, 2, 4 and 5 were revisits of WOCE Hydrographic Program (WHP) sections P6W, P6E, A10 and I3/I4, respectively. The sections consisted of about 500 hydrographic stations in total. On each station, CTD profiles and up to 36 water samples by 12L Niskin-X bottles were taken from the surface to within 10 m of the bottom. Water samples were analyzed at every station for salinity, dissolved oxygen (DO), and nutrients and at alternate stations for concentration of freons, dissolved inorganic carbon (CT), total alkalinity (AT), pH, and so on. Approximately 17,000 samples were obtained for salinity. The standard seawater was measured repeatedly to estimate the uncertainty caused by the setting and stability of the salinometer. The standard deviation of 699 repeated runs of standard seawater was 0.0002 in salinity. Replicate samples, which are a pair of samples drawn from the same Niskin bottle to different sample bottles, were taken to evaluate the overall uncertainty. The standard deviation of absolute differences of 2,769 replicates was also 0.0002 in salinity. For DO, about 13,400 samples were obtained. The analysis was made by a photometric titration technique. The reproducibility estimated from the absolute standard deviation of 1,625 replicates was about 0.09 umol/kg. CTD temperature was calibrated against a deep ocean standards thermometer (SBE35) which was attached to the CTD using a polynomial expression Tcal = T - (a +b*P + c*t), where Tcal is calibrated temperature, T is CTD temperature, P is CTD pressure and t is time. Calibration coefficients, a, b and c, were determined for each station by minimizing the sum of absolute deviation from SBE35 temperature below 2,000dbar. CTD salinity and DO were fitted to values obtained by sampled water analysis using similar polynomials. These corrections yielded deviations of about 0.0002 K in temperature, 0.0003 in salinity and 0.6 umol/kg in DO. Nutrients analyses were accomplished on 16,000 samples using the reference material of nutrients in seawater (RMNS). To establish the traceability and to get higher quality data, 500 bottles of RMNS from the same lot and 150 sets of RMNSs were used. The precisions of phosphate, nitrate and silicate measurements were 0.18 %, 0.17 % and 0.16 % in terms of median of those at 493 stations, respectively. The nutrients concentrations could be expressed with uncertainties explicitly because of the repeated runs of RMNSs. All the analyses for the CO{2}-system parameters in water columns were finished onboard. Analytical precisions of CT, AT and pH were estimated to be \\sim1.0 umol/kg, \\sim2.0 umol/kg, and \\sim7*10-4 pH unit, respectively. Approximately 6,300 samples were obtained for CFC-11 and CFC-12. The concentrations were determined with an electron capture detector - gas chromatograph (ECD-GC) attached the purge and trapping system. The reproducibility estimated from the absolute standard deviation of 365 replicates was less than 1% with respect to the surface concentrations.

77 FR 69634 - International Conference on Harmonisation; Guidance on Q11 Development and Manufacture of Drug...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-20

... Document (CTD). The guidance is intended to harmonize the scientific and technical principles relating to... sections of the CTD. A summary of changes includes the following: (1) Revisions to the introduction and...

Creatine Transporter Deficiency in Two Brothers with Autism Spectrum Disorder.

PubMed

Aydin, Halil Ibrahim

2018-01-15

Creatine transporter deficiency (CTD) is a treatable, X-linked, inborn error of metabolism. Two brothers with autism spectrum disorder were diagnosed with CTD at the ages of 17 and 12 years. Both were found to have a previously reported hemizygous p.408delF (c.1216_1218delTTC) deletion mutation. Both patients were given creatine monohydrate, L-arginine, L-glycine and S-adenosylmethionine, which partially improved the behavioral problems. Serum creatinine levels, creatine peak at brain MR spectroscopy or creatine/creatinine ratio in urine should be evaluated to identify CTD in children with autistic behavior and language disorders.

Addison's disease secondary to connective tissue diseases: a report of six cases.

PubMed

Zhang, Zhuo-li; Wang, Yu; Zhou, Wei; Hao, Yan-jie

2009-04-01

Addison's disease is an autoimmune process. However, Addison's disease associated with connective tissue diseases (CTD) is only occasionally reported. Here, we report six cases of Addison's disease secondary to a variety of CTD, which include systemic lupus erythematosus, Takayasu arteritis, systemic sclerosis, ankylosing spondylitis (AS) and antiphospholipid antibody syndrome. The association of Addison's disease with Takayasu arteritis and AS is reported for the first time. We also found high prevalence of hypothyroidism as concomitant autoimmune disorder. Our case series highlight the autoimmune features of Addison's disease. Therefore, we suggest considering adrenal dysfunction in patients with CTD.

Cor triatriatum dexter, atrial septal defects, and pulmonary stenosis-a rare association.

PubMed

Simsek, Ziya; Koza, Yavuzer; Tas, Hakan

2014-04-01

Cor triatriatum dexter (CTD) is an extremely rare congenital anomaly in which the right atrium is divided into 2 chambers by a membrane. The estimated incidence of cor triatriatum has been reported as 0.1% of congenital cardiac malformations. The septation of the right atrium in the setting of CTD is the result of failed resorption of the right valve of the sinus venosus. This results in anterolateral and posteromedial portions of the divided right atrium. CTD can be diagnosed at any age, especially if it is incidentally discovered. © 2014, Wiley Periodicals, Inc.

Phenol degradation by TiO2 photocatalysts combined with different pulsed discharge systems.

PubMed

Zhang, Yi; Lu, Jiani; Wang, Xiaoping; Xin, Qing; Cong, Yanqing; Wang, Qi; Li, Chunjuan

2013-11-01

Films of TiO2 nanotubes distributed over the inner surface of a discharge reactor cylinder (CTD) or adhered to a stainless steel electrode surface (PTD) in a discharge reactor were compared with a single-discharge (SD) system to investigate their efficiencies in phenol degradation. Morphology studies indicated that the TiO2 film was destroyed in the PTD system, but that there was no change in the CTD system after discharge. X-ray diffraction results revealed that the anatase phase of the original sample was preserved in the CTD system, but that an anatase-to-rutile phase transformation occurred in the PTD system after discharge. The highest efficiencies of phenol degradation and total organic carbon (TOC) mineralization were observed in the CTD system, and there was no decrease in phenol degradation efficiency upon reuse of a TiO2 film, indicating high catalysis activity and stability of the TiO2 photocatalysts in the combined treatment. TiO2 photocatalysts favored the formation of hydrogen peroxide and disfavored the formation of ozone. A greater degree of oxidation of intermediates and higher energy efficiency in phenol oxidation were observed with the TiO2-plasma systems, especially in the CTD system, compared to those with the SD system. Copyright © 2013 Elsevier Inc. All rights reserved.

Bowhead whales feed on plankton concentrated by estuarine and tidal currents in Academy Bay, Sea of Okhotsk

NASA Astrophysics Data System (ADS)

Rogachev, Konstantin A.; Carmack, Eddy C.; Foreman, Michael G. G.

2008-08-01

Academy Bay in the Sea of Okhotsk is an important summertime feeding ground for pelagic-feeding Bowhead whales ( Balaena mysticetus) in the western subarctic North Pacific. The present work combines satellite observations with physical (CTD, currents, tides) and biological (zooplankton sampling) measurements. Data obtained aboard the RV Lugovoe in August-September 2003 and July-August 2004 show dense populations of zooplankton (such as copepods Calanus glacialis, Pseudocalanus sp., pteropods Limacina helicina, and chaetognaths Sagitta sp.) that are concentrated by physical mechanisms within this critically important ecosystem. We show that near-bottom, cold water intrusions from the northern Sea of Okhotsk associated with the estuarine circulation advect arctic herbivorous calanoids ( Calanus glacialis) and mollusks Limacina helicina into the region. Satellite and in situ observations that include conductivity-temperature-depth (CTD) data and measurements of tidal currents are used to study the nature of the estuarine circulation. Results show an anticyclonic circulation, associated with the effect of earth's rotation. An analytical model shows horizontally convergent flows in the lower layer toward the western coast of the bay that push water upward along the steep slope. This together with zooplankton vertical migration leads to aggregation. Thus the combination of the residual eddy formation and swimming behavior act to concentrate zooplankton near the cape and to provide the necessary densities of planktonic food supply for Bowhead whales.

X-ray Photoelectron Spectroscopy of High-κ Dielectrics

NASA Astrophysics Data System (ADS)

Mathew, A.; Demirkan, K.; Wang, C.-G.; Wilk, G. D.; Watson, D. G.; Opila, R. L.

2005-09-01

Photoelectron spectroscopy is a powerful technique for the analysis of gate dielectrics because it can determine the elemental composition, the chemical states, and the compositional depth profiles non-destructively. The sampling depth, determined by the escape depth of the photoelectrons, is comparable to the thickness of current gate oxides. A maximum entropy algorithm was used to convert photoelectron collection angle dependence of the spectra to compositional depth profiles. A nitrided hafnium silicate film is used to demonstrate the utility of the technique. The algorithm balances deviations from a simple assumed depth profile against a calculated depth profile that best fits the angular dependence of the photoelectron spectra. A flow chart of the program is included in this paper. The development of the profile is also shown as the program is iterated. Limitations of the technique include the electron escape depths and elemental sensitivity factors used to calculate the profile. The technique is also limited to profiles that extend to the depth of approximately twice the escape depth. These limitations restrict conclusions to comparison among a family of similar samples. Absolute conclusions about depths and concentrations must be used cautiously. Current work to improve the algorithm is also described.

Quantitative evaluation of sputtering induced surface roughness and its influence on AES depth profiles of polycrystalline Ni/Cu multilayer thin films

NASA Astrophysics Data System (ADS)

Yan, X. L.; Coetsee, E.; Wang, J. Y.; Swart, H. C.; Terblans, J. J.

2017-07-01

The polycrystalline Ni/Cu multilayer thin films consisting of 8 alternating layers of Ni and Cu were deposited on a SiO2 substrate by means of electron beam evaporation in a high vacuum. Concentration-depth profiles of the as-deposited multilayered Ni/Cu thin films were determined with Auger electron spectroscopy (AES) in combination with Ar+ ion sputtering, under various bombardment conditions with the samples been stationary as well as rotating in some cases. The Mixing-Roughness-Information depth (MRI) model used for the fittings of the concentration-depth profiles accounts for the interface broadening of the experimental depth profiling. The interface broadening incorporates the effects of atomic mixing, surface roughness and information depth of the Auger electrons. The roughness values extracted from the MRI model fitting of the depth profiling data agrees well with those measured by atomic force microscopy (AFM). The ion sputtering induced surface roughness during the depth profiling was accordingly quantitatively evaluated from the fitted MRI parameters with sample rotation and stationary conditions. The depth resolutions of the AES depth profiles were derived directly from the values determined by the fitting parameters in the MRI model.

Analysis of turbulent mixing in Dewakang Sill, Southern Makassar Strait

NASA Astrophysics Data System (ADS)

Risko; Atmadipoera, A. S.; Jaya, I.; Sudjono, E. H.

2017-01-01

Dewakang Sill is located in southern Makassar Strait, conveying major path of Indonesian Throughflow (ITF), as a confluence region of different water masses, such as salty Pacific water and fresh Java Sea water. Its depth is about 680 m which blocks the ITF flow below this depth into Flores Sea. This research aimed to estimate turbulent mixing in the Dewakang Sill by applying Thorpe analysis using 24 hours “yoyo” CTD data sets, acquired from MAJAFLOX Cruise in August 2015. The results showed that stratification of water masses is dominated by Pacific water origin. Those are North Pacific Subtropical thermocline and Intermediate water masses. Mean dissipation of turbulent kinetic energy (ɛ) and turbulent vertical diffusivity (Kρ ) value in the Dewakang Sill are of O(1.08 × 10-6)Wkg-1, and O(2.84 × 10-4) m2s-1 respectively. High correlation between epsilon and internal waves oscillation suggested that internal tidal waves activities are the major forcing for turbulent mixing in the study area.

Pore-Water Chemistry and Hydrology in a Spring-Fed River: Implications for Hyporheic Control of Nutrient Cycling and Speleogenesis

NASA Astrophysics Data System (ADS)

Kurz, M. J.; Martin, J. B.; Cohen, M. J.

2010-12-01

Hyporheic exchange is important for nutrient cycling in rivers, but little is known about the magnitude of this process in karst systems or its influence on speleogenesis and the formation of river channels. We use four pore-water depth profiles to assess nutrient and carbonate processing in the hyporheic zone (HZ) of the Ichetucknee River (north-central, Florida). Co-located pairs of stilling wells equipped with conductivity, temperature, depth (CTD) sensors are used to continuously monitor the hydraulic gradients within the HZ to determine flow directions and temporal variability of groundwater exchange. The Ichetucknee River is sourced from six major and numerous small springs which discharge from the karstic Floridan Aquifer. Downstream and diel variations in nitrate concentrations, specific conductivity and calcite saturation state reflect in-stream processing, but hyporheic exchange should also influence the overall dynamics of nutrient and carbonate fluxes in the river. Our depth profiles and stilling wells are located at four sites in a cross-channel transect and extend through unconsolidated sediment to the solid carbonate of the Floridan Aquifer 35-156 cm below the river bed. Decreasing DOC, pH, and DO concentrations and increased DIC are indicative of organic carbon remineralization in the shallow sediments. Increasing alkalinity, Ca concentrations, specific conductivity and decreasing calcite saturation state indicate carbonate dissolution being driven by the decreasing pH. Decreasing nitrate concentrations indicate denitrification and increasing phosphate concentration could be a result of carbonate dissolution or OC remineralization. Most of these changes appear to occur in the upper 60cm of sediment, below which many concentrations return to values observed in the groundwater, suggesting water discharges from the Floridan Aquifer at the base of the sediment. Hydraulic head is higher in the pore waters than the river indicating groundwater then discharges to the river. Initial modeling of the system indicates that flow through the channel sediment moves horizontally and discharges into the river through the incised channel rather than upwards through the most reactive hyporheic sediments. While differences in chemical composition between the pore water and river water suggest the chemically altered pore water could affect chemical composition of the river it remains unclear the relative fractions of ground water and chemically altered pore water that flow into the river. Future work will attempt to quantify the magnitude of these exchanges over a range of hydrologic conditions.

The CTD-80 Survey Introduction.

ERIC Educational Resources Information Center

Kadar-Fulop, Judit; Bathory, Zoltan

1985-01-01

Hungary's national institute of education carried out the Curriculum Theory Department (CTD-80) national asessment in 1980. Reading, mathematics, and practical science achievement were measured, as well as teacher attitudes. Particular emphasis was placed on eighth-grade students; fourth graders were tested in reading. (GDC)

The CTD Science Practical Survey.

ERIC Educational Resources Information Center

Bathory, Zoltan

1985-01-01

As part of Hungary's Curriculum Theory Department (CTD-80) assessment, 1,543 14-year-olds were tested in the performance of science experiments in physics and chemistry. Skills included observing, measuring, hypothesizing, and drawing conclusions. Results are presented, and implications for curriculum are suggested. (GDC)

Coastal ocean forecasting with an unstructured grid model in the southern Adriatic and northern Ionian seas

NASA Astrophysics Data System (ADS)

Federico, Ivan; Pinardi, Nadia; Coppini, Giovanni; Oddo, Paolo; Lecci, Rita; Mossa, Michele

2017-01-01

SANIFS (Southern Adriatic Northern Ionian coastal Forecasting System) is a coastal-ocean operational system based on the unstructured grid finite-element three-dimensional hydrodynamic SHYFEM model, providing short-term forecasts. The operational chain is based on a downscaling approach starting from the large-scale system for the entire Mediterranean Basin (MFS, Mediterranean Forecasting System), which provides initial and boundary condition fields to the nested system. The model is configured to provide hydrodynamics and active tracer forecasts both in open ocean and coastal waters of southeastern Italy using a variable horizontal resolution from the open sea (3-4 km) to coastal areas (50-500 m). Given that the coastal fields are driven by a combination of both local (also known as coastal) and deep-ocean forcings propagating along the shelf, the performance of SANIFS was verified both in forecast and simulation mode, first (i) on the large and shelf-coastal scales by comparing with a large-scale survey CTD (conductivity-temperature-depth) in the Gulf of Taranto and then (ii) on the coastal-harbour scale (Mar Grande of Taranto) by comparison with CTD, ADCP (acoustic doppler current profiler) and tide gauge data. Sensitivity tests were performed on initialization conditions (mainly focused on spin-up procedures) and on surface boundary conditions by assessing the reliability of two alternative datasets at different horizontal resolution (12.5 and 6.5 km). The SANIFS forecasts at a lead time of 1 day were compared with the MFS forecasts, highlighting that SANIFS is able to retain the large-scale dynamics of MFS. The large-scale dynamics of MFS are correctly propagated to the shelf-coastal scale, improving the forecast accuracy (+17 % for temperature and +6 % for salinity compared to MFS). Moreover, the added value of SANIFS was assessed on the coastal-harbour scale, which is not covered by the coarse resolution of MFS, where the fields forecasted by SANIFS reproduced the observations well (temperature RMSE equal to 0.11 °C). Furthermore, SANIFS simulations were compared with hourly time series of temperature, sea level and velocity measured on the coastal-harbour scale, showing a good agreement. Simulations in the Gulf of Taranto described a circulation mainly characterized by an anticyclonic gyre with the presence of cyclonic vortexes in shelf-coastal areas. A surface water inflow from the open sea to Mar Grande characterizes the coastal-harbour scale.

Pulmonary Function and Survival in Idiopathic vs Secondary Usual Interstitial Pneumonia

PubMed Central

Strand, Matthew J.; Sprunger, David; Cosgrove, Gregory P.; Fernandez-Perez, Evans R.; Frankel, Stephen K.; Huie, Tristan J.; Olson, Amy L.; Solomon, Joshua; Brown, Kevin K.

2014-01-01

BACKGROUND: The usual interstitial pneumonia (UIP) pattern of lung injury may occur in the setting of connective tissue disease (CTD), but it is most commonly found in the absence of a known cause, in the clinical context of idiopathic pulmonary fibrosis (IPF). Our objective was to observe and compare longitudinal changes in pulmonary function and survival between patients with biopsy-proven UIP found in the clinical context of either CTD or IPF. METHODS: We used longitudinal data analytic models to compare groups (IPF [n = 321] and CTD-UIP [n = 56]) on % predicted FVC (FVC %) or % predicted diffusing capacity of the lung for carbon monoxide (Dlco %), and we used both unadjusted and multivariable techniques to compare survival between these groups. RESULTS: There were no significant differences between groups in longitudinal changes in FVC % or Dlco % up to diagnosis, or from diagnosis to 10 years beyond (over which time, the mean decrease in FVC % per year [95% CI] was 4.1 [3.4, 4.9] for IPF and 3.5 [1.8, 5.1] for CTD-UIP, P = .49 for difference; and the mean decrease in Dlco % per year was 4.7 [4.0, 5.3] for IPF and 4.3 [3.0, 5.6] for CTD-UIP, P = .60 for difference). Despite the lack of differences in pulmonary function, subjects with IPF had worse survival in unadjusted (log-rank P = .003) and certain multivariable analyses. CONCLUSIONS: Despite no significant differences in changes in pulmonary function over time, patients with CTD-UIP (at least those with certain classifiable CTDs) live longer than patients with IPF—an observation that we suspect is due to an increased rate of mortal acute exacerbations in patients with IPF. PMID:24700149

Phosphatase Rtr1 Regulates Global Levels of Serine 5 RNA Polymerase II C-Terminal Domain Phosphorylation and Cotranscriptional Histone Methylation.

PubMed

Hunter, Gerald O; Fox, Melanie J; Smith-Kinnaman, Whitney R; Gogol, Madelaine; Fleharty, Brian; Mosley, Amber L

2016-09-01

In eukaryotes, the C-terminal domain (CTD) of Rpb1 contains a heptapeptide repeat sequence of (Y1S2P3T4S5P6S7)n that undergoes reversible phosphorylation through the opposing action of kinases and phosphatases. Rtr1 is a conserved protein that colocalizes with RNA polymerase II (RNAPII) and has been shown to be important for the transition from elongation to termination during transcription by removing RNAPII CTD serine 5 phosphorylation (Ser5-P) at a selection of target genes. In this study, we show that Rtr1 is a global regulator of the CTD code with deletion of RTR1 causing genome-wide changes in Ser5-P CTD phosphorylation and cotranscriptional histone H3 lysine 36 trimethylation (H3K36me3). Using chromatin immunoprecipitation and high-resolution microarrays, we show that RTR1 deletion results in global changes in RNAPII Ser5-P levels on genes with different lengths and transcription rates consistent with its role as a CTD phosphatase. Although Ser5-P levels increase, the overall occupancy of RNAPII either decreases or stays the same in the absence of RTR1 Additionally, the loss of Rtr1 in vivo leads to increases in H3K36me3 levels genome-wide, while total histone H3 levels remain relatively constant within coding regions. Overall, these findings suggest that Rtr1 regulates H3K36me3 levels through changes in the number of binding sites for the histone methyltransferase Set2, thereby influencing both the CTD and histone codes. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Reduced specificity of autobiographical memories in young people with tic disorders.

PubMed

Pile, Victoria; Robinson, Sally; Roberts, Elystan; Topor, Marta; Hedderly, Tammy; Lau, Jennifer Y F

2018-05-01

Depression is common in Tourette syndrome and Chronic Tic Disorders (TS/CTD) and contributes to significant impairment. The specificity of autobiographical memories is implicated in an individual's sense of self and their daily functioning but also in the onset and development of depression in the general population. Here, we examined whether memory specificity is reduced in young people with TS/CTD, relative to control participants, and whether memory specificity is associated with depression. Thirty young people with TS/CTD (14 females; age: x̅ = 11.31; SD = 1.66; 87% White British) and twenty-six (12 females; age: x̅ = 11.23; SD = 2.43; 77% White British) control participants completed the study. Participants completed the Autobiographical Memory Task, which asks participants to respond with a specific memory to cue words, and a questionnaire measure of depressive symptoms. There was no significant difference between the two groups in terms of age, gender, ethnicity, IQ and depressive symptomatology. Young people with TS/CTD had less specific autobiographical memories than their peers (p < 0.001, r = 0.49). Across both groups, increased memory specificity for positive cue words was associated with reduced depressive symptomatology (p < 0.001, R 2  = 0.51). Our findings indicate that autobiographical memory in young people with TS is characterised by a lack of specificity and, as with neurotypical peers, reduced memory specificity for positive words is associated with depressive symptoms. Autobiographical memory specificity could be an important factor in understanding mood symptoms that characterise young people with TS/CTD and may be an important cognitive target to reduce the development of depression in young people with TS/CTD. Copyright © 2018 Elsevier Inc. All rights reserved.

The 13-kD FK506 Binding Protein, FKBP13, Interacts with a Novel Homologue of the Erythrocyte Membrane Cytoskeletal Protein 4.1

PubMed Central

Walensky, Loren D.; Gascard, Philippe; Field, Michael E.; Blackshaw, Seth; Conboy, John G.; Mohandas, Narla; Snyder, Solomon H.

1998-01-01

We have identified a novel generally expressed homologue of the erythrocyte membrane cytoskeletal protein 4.1, named 4.1G, based on the interaction of its COOH-terminal domain (CTD) with the immunophilin FKBP13. The 129-amino acid peptide, designated 4.1G–CTD, is the first known physiologic binding target of FKBP13. FKBP13 is a 13-kD protein originally identified by its high affinity binding to the immunosuppressant drugs FK506 and rapamycin (Jin, Y., M.W. Albers, W.S. Lane, B.E. Bierer, and S.J. Burakoff. 1991. Proc. Natl. Acad. Sci. USA. 88:6677– 6681); it is a membrane-associated protein thought to function as an ER chaperone (Bush, K.T., B.A. Henrickson, and S.K. Nigam. 1994. Biochem. J. [Tokyo]. 303:705–708). We report the specific association of FKBP13 with 4.1G–CTD based on yeast two-hybrid, in vitro binding and coimmunoprecipitation experiments. The histidyl-proline moiety of 4.1G–CTD is required for FKBP13 binding, as indicated by yeast experiments with truncated and mutated 4.1G–CTD constructs. In situ hybridization studies reveal cellular colocalizations for FKBP13 and 4.1G–CTD throughout the body during development, supporting a physiologic role for the interaction. Interestingly, FKBP13 cofractionates with the red blood cell homologue of 4.1 (4.1R) in ghosts, inside-out vesicles, and Triton shell preparations. The identification of FKBP13 in erythrocytes, which lack ER, suggests that FKBP13 may additionally function as a component of membrane cytoskeletal scaffolds. PMID:9531554

The Characteristics of Marine Environment around the Ieodo in Aug. 2016

NASA Astrophysics Data System (ADS)

Choi, E.; KIM, S. H.; KIM, E.; KIM, B. N.; CHOI, B. K.

2017-12-01

The sea area around Ieodo is analyzed from the CTD data and the S-ADCP data observed in 23 Aug. 2016. Ieodo, an underwater reef, is located 149 km southwest of Marado in Republic of Korea. It has 4 peaks and is about 4.6 meter below sea level. It stretches about 600m north to south and 750m east to west from its top. It has the same geographical characteristics as the seamount. In the sea area around Ieodo, the northward flow appeared during the ebb tide, the southward flow appeared during the flood tide. The strong stratification formed in summer seems to change the depth depending on the sea water current. The thermocline depth becomes deeper at the north of the Ieodo when the northward current flows and the upwelling flow occurs. And the thermocline depth becomes shallower at the south when the southward current flows and the downwelling flow occurs. In this way, the upwelling and downwelling seems to be according to the tide's direction. Acknowledgements This research was a part of the projects entitled "Construction of Ocean Research Stations and their application Studies, Phase 2", funded by the Ministry of Oceans and Fisheries, Korea.

Hydrothermal plumes in the Gulf of Aden, as characterized by light transmission, Mn, Fe, CH4 and δ13C-CH4 anomalies

NASA Astrophysics Data System (ADS)

Gamo, Toshitaka; Okamura, Kei; Hatanaka, Hiroshi; Hasumoto, Hiroshi; Komatsu, Daisuke; Chinen, Masakazu; Mori, Mutsumi; Tanaka, Junya; Hirota, Akinari; Tsunogai, Urumu; Tamaki, Kensaku

2015-11-01

We conducted water column surveys to search for hydrothermal plumes over the spreading axes in the Gulf of Aden between 45°35‧E and 52°42‧E. We measured light transmission and chemical tracers Mn, Fe, CH4 and δ13C of CH4 in seawater taken using a CTD-Carrousel multi-sampling system at 12 locations including a control station in the Arabian Sea. We recognized three types of hydrothermal plumes at depths of 650 to 900 m (shallow plumes), 1000 to 1200 m (intermediate plumes), and >1500 m (deep plumes). The shallow plumes were apparently originated from newly discovered twin seamounts (12°03-06‧N and 45°35-41‧E) at the westernmost survey area, where two-dimensional distributions of light transmission and Mn were mapped by tow-yo observations of the CTD-sampling system with an in situ auto-analyzer GAMOS. The maximum concentrations of Mn, Fe, and CH4 of 46 nM, 251 nM, and 15 nM, respectively, were observed for collected seawater within the shallow plumes. The intermediate plumes were characterized by anomalies of light transmission, Mn, Fe, and δ13C of CH4, but by little CH4 anomalies, suggesting that CH4 had been consumed down to the background level during the aging of the plumes. Anomalies of δ3He already reported by the World Ocean Circulation Experiment (WOCE) program exhibited a hydrothermal plume-like peak at 2000 m depth in the Gulf of Aden, which seems to coincide with the deep plumes observed in this study. The endmember δ13C-CH4 values for the shallow and the deep plumes were estimated to be in a range between -10‰ and -15‰, demonstrating that the sources of CH4 are not biogenic but magmatic as similarly observed at sediment-starved mid-oceanic ridges.

C-MORE Science Kits: Putting Technology in the Hands of K-12 Teachers and Students

NASA Astrophysics Data System (ADS)

Achilles, K.; Weersing, K.; Daniels, C.; Puniwai, N.; Matsuzaki, J.; Bruno, B. C.

2008-12-01

The Center for Microbial Oceanography: Research and Education (C-MORE) is a NSF Science and Technology Center based at the University of Hawaii. The C-MORE education and outreach program offers a variety of resources and professional development opportunities for science educators, including online resources, participation in oceanography research cruises, teacher-training workshops, mini-grants to incorporate microbial oceanography-related content and activities into their classroom and, most recently, C- MORE science kits. C-MORE science kits provide hands-on classroom, field, and laboratory activities related to microbial oceanography for K-12 students. Each kit comes with complete materials and instructions, and is available free of charge to Hawaii's public school teachers. Several kits are available nationwide. C-MORE science kits cover a range of topics and technologies and are targeted at various grade levels. Here is a sampling of some available kits: 1) Marine Murder Mystery: The Case of the Missing Zooxanthellae. Students learn about the effect of climate change and other environmental threats on coral reef destruction through a murder-mystery experience. Participants also learn how to use DNA to identify a suspect. Grades levels: 3-8. 2) Statistical sampling. Students learn basic statistics through an exercise in random sampling, with applications to microbial oceanography. The laptops provided with this kit enable students to enter, analyze, and graph their data using EXCEL. Grades levels: 6-12. 3) Chlorophyll Lab. A research-quality fluorometer is used to measure the chlorophyll content in marine and freshwater systems. This enables students to compare biomass concentrations in samples collected from various locations. Grades levels: 9-12. 4) Conductivity-Temperature-Depth (CTD). Students predict how certain variables (e.g., temperature, pressure, chlorophyll, oxygen) vary with depth. A CTD, attached to a laptop computer, is deployed into deep water off a dock or a ship to collect real-time data and test their hypotheses. Grades levels: 9-12.

An Analysis of Effects of Background Variables on Student Achievement Based on the CTD Survey Data.

ERIC Educational Resources Information Center

Tolgyesi, Miklos

1985-01-01

Factors contributing to achievement were investigated as part of Hungary's Curriculum Theory Department (CTD-80) national assessment. Parent's education and occupation and student's sex predicted achievement results. School characteristics did not predict achievement or attitudes. (Author/GDC)

Methane Distribution In Plumes Of The South Mariana Back-arc Spreading Center

NASA Astrophysics Data System (ADS)

Toki, T.; Hirota, A.; Tsunogai, U.; Gamo, T.; Nakamura, K.; Noguchi, T.; Taira, N.; Oomori, T.; Ishibashi, J.; Utsumi, M.

2004-12-01

In the South Mariana Back-arc Spreading Center, two methane plumes were observed in water column based on analysis of methane in seawater samples collected during the R/V Thompson expeditions in 2003 around water depth of 2,700 m over the Fryer site on the ridge-axis seamount (12\\deg57.22N, 143\\deg37.16E, depth: 2,850 m). The estimated end-member isotopic compositions of methane in the two plumes are \\delta13C_{CH4} = -5‰ PDB and -50‰ PDB. These values indicated that the two plumes were originated from the different sources. During YK03-09 cruise using the submersible Shinkai 6500 from October to November in 2003, detailed seafloor observation discovered sulfide chimneys emitting black and clear hydrothermal fluid on the off-axis seamount at Pika site (12°55.15N, 143°36.96E, depth: 2,773 m). The result of analysis of isotopic composition of methane in the hydrothermal fluids recovered from the off-axis hydrothermal vents using WHATS (Water and Hydrothermal Atsuryoku Tight Sampler) was averaged value of -4‰ PDB (standard deviation = 1‰ PDB, n = 3). Hydrothermal fluids from the Fryer site were also sampled and were measured: average value = -6.7‰ PDB, standard deviation = 0.3‰ PDB, n = 3. During the R/V Thompson expeditions in March 2004 using ROV ROPOS, 11 ROPOS dives and CTD-RMS plume surveys were conducted, and newly discovered a huge hydrothermal structure with active fluid venting at Achaean site on the ridge skirt (12°56.37N, 143°37.92E, depth: 2,990 m). The δ ^{13}C_{CH4} value of the fluid sample from the site using ROCS (Rotary Clean Seawater sampler) was -14.7‰ PDB. Analysis of isotopic composition of methane in the plume samples collected using the CTD-hydrocast at water depth of 2,500 m over the Archaean site showed -45‰ PDB. Source of methane (δ ^{13}C_{CH4} = -50‰ PDB), however, in the two plumes of the South Mariana Back-arc Spreading Center has been missing. The δ ^{13}C of methane cannot be considered in sediment-starved seafloor hydrothermal fluids as the results from an abiogenic reaction in magma. Alternative explanation would be the secondary stimulated plume of methane that is formed in invertebrate guts of zooplankton swarmed about microbes in the plume, as proposed about a subsurface CH_{4} maximum in the upper oceanic water column. The secondary methane plume may be associated with methane plume without a corresponding enrichment in ^{3}He, observed in the Mariana Trough Back-arc basin at 14° N.

Idiopathic Interstitial Pneumonia Associated With Autoantibodies: A Large Case Series Followed Over 1 Year.

PubMed

Collins, Bridget F; Spiekerman, Charles F; Shaw, Megan A; Ho, Lawrence A; Hayes, Jennifer; Spada, Carolyn A; Stamato, Caroline M; Raghu, Ganesh

2017-07-01

Some patients with autoimmune characteristics and idiopathic interstitial pneumonia, particularly usual interstitial pneumonia (UIP), do not fit neatly into the category of connective tissue disease-associated interstitial lung disease (CTD-ILD), idiopathic pulmonary fibrosis (IPF), or recently proposed yet to be validated criteria for interstitial pneumonia with autoimmune features (IPAF). Outcomes of these patients are unknown. This was a retrospective single-center study. Analyses of variance compared differences in mean change in FVC and diffusion capacity (Dlco) over 1 year among 124 well-defined patients (20 patients with positive autoantibodies with or without symptoms of connective tissue disease [AI-ILD], 15 patients with IPAF, 36 patients with CTD-ILD, and 53 patients with IPF with negative CTD serologies [Lone-IPF]). Of the patients, 75% with AI-ILD, 33% with IPAF, and 33% with CTD-ILD had UIP. Initial FVC and Dlco were similarly moderately reduced across groups. Mean change in FVC over 12 months was as follows: -60 mL (IPAF), -110 mL (AI-ILD), -10 mL (CTD-ILD), and -90 mL (Lone-IPF) (P = .52). Mean change in Dlco was as follows: 2.39 mL/mm Hg/min (IPAF), -1.15 mL/mm Hg/min (AI-ILD), -0.27 mL/mm Hg/min (CTD-ILD), and -1.05 mL/mm Hg/min (Lone-IPF) (P < .001). By pattern of disease, the mean change in FVC was as follows: -140 mL (UIP), 10 mL (nonspecific interstitial pneumonia), and 12 mL (unclassifiable/other) (P = .001). No clinically significant differences in pulmonary function to distinguish between patients with AI-ILD, IPAF, CTD-ILD, and Lone-IPF were observed after 1 year. Longer periods of follow-up are needed to understand the outcomes of these patients. It is not yet clear whether AI-ILD is a distinct phenotype or a variant of the newly proposed entity IPAF. Copyright © 2017 American College of Chest Physicians. Published by Elsevier Inc. All rights reserved.

Expression of human PQBP-1 in Drosophila impairs long-term memory and induces abnormal courtship.

PubMed

Yoshimura, Natsue; Horiuchi, Daisuke; Shibata, Masao; Saitoe, Minoru; Qi, Mei-Ling; Okazawa, Hitoshi

2006-04-17

Frame shift mutations of the polyglutamine binding protein-1 (PQBP1) gene lead to total or partial truncation of the C-terminal domain (CTD) and cause mental retardation in human patients. Interestingly, normal Drosophila homologue of PQBP-1 lacks CTD. As a model to analyze the molecular network of PQBP-1 affecting intelligence, we generated transgenic flies expressing human PQBP-1 with CTD. Pavlovian olfactory conditioning revealed that the transgenic flies showed disturbance of long-term memory. In addition, they showed abnormal courtship that male flies follow male flies. Abnormal functions of PQBP-1 or its binding partner might be linked to these symptoms.

Trawling-induced daily sediment resuspension in the flank of a Mediterranean submarine canyon

NASA Astrophysics Data System (ADS)

Martín, Jacobo; Puig, Pere; Palanques, Albert; Ribó, Marta

2014-06-01

Commercial bottom trawling is one of the anthropogenic activities causing the biggest impact on the seafloor due to its recurrence and global distribution. In particular, trawling has been proposed as a major driver of sediment dynamics at depths below the reach of storm waves, but the issue is at present poorly documented with direct observations. This paper analyses changes in water turbidity in a tributary valley of the La Fonera (=Palamós) submarine canyon, whose flanks are routinely exploited by a local trawling fleet down to depths of 800 m. A string of turbidimeters was deployed at 980 m water depth inside the tributary for two consecutive years, 2010-2011. The second year, an ADCP profiled the currents 80 m above the seafloor. The results illustrate that near-bottom water turbidity at the study site is heavily dominated, both in its magnitude and temporal patterns, by trawling-induced sediment resuspension at the fishing ground. Resuspended sediments are channelised along the tributary in the form of sediment gravity flows, being recorded only during working days and working hours of the trawling fleet. These sediment gravity flows generate turbid plumes that extend to at least 100 m above the bottom, reaching suspended sediment concentrations up to 236 mg l-1 close to the seafloor (5 m above bottom). A few hours after the end of daily trawling activities, water turbidity progressively decreases but resuspended particles remain in suspension for several hours, developing bottom and intermediate nepheloid layers that reach background levels ˜2 mg l-1 before trawling activities resume. The presence of these nepheloid layers was recorded in a CTD+turbidimeter transect conducted across the fishing ground a few hours after the end of a working day. These results highlight that deep bottom trawling can effectively replace natural processes as the main driving force of sediment resuspension on continental slope regions and generate increased near-bottom water turbidity that propagates from fishing grounds to wider and deeper areas via sediment gravity flows and nepheloid layer development.

The CTD Reading Study.

ERIC Educational Resources Information Center

Kadar-Fulop, Judit

1985-01-01

Reading ability of fourth- and eighth-grade Hungarians was assessed as part of the national CTD-80 (Curriculum Theory Department) survey. The texts used in the reading tests are analyzed, as are the reading tasks involved. Resulting achievement test results are presented and described in terms of the text characteristics. (GDC)

The outer-membrane export signal of Porphyromonas gingivalis type IX secretion system (T9SS) is a conserved C-terminal β-sandwich domain

PubMed Central

de Diego, Iñaki; Ksiazek, Miroslaw; Mizgalska, Danuta; Koneru, Lahari; Golik, Przemyslaw; Szmigielski, Borys; Nowak, Magdalena; Nowakowska, Zuzanna; Potempa, Barbara; Houston, John A.; Enghild, Jan J.; Thøgersen, Ida B.; Gao, Jinlong; Kwan, Ann H.; Trewhella, Jill; Dubin, Grzegorz; Gomis-Rüth, F. Xavier; Nguyen, Ky-Anh; Potempa, Jan

2016-01-01

In the recently characterized Type IX Secretion System (T9SS), the conserved C-terminal domain (CTD) in secreted proteins functions as an outer membrane translocation signal for export of virulence factors to the cell surface in the Gram-negative Bacteroidetes phylum. In the periodontal pathogen Porphyromonas gingivalis, the CTD is cleaved off by PorU sortase in a sequence-independent manner, and anionic lipopolysaccharide (A-LPS) is attached to many translocated proteins, thus anchoring them to the bacterial surface. Here, we solved the atomic structure of the CTD of gingipain B (RgpB) from P. gingivalis, alone and together with a preceding immunoglobulin-superfamily domain (IgSF). The CTD was found to possess a typical Ig-like fold encompassing seven antiparallel β-strands organized in two β-sheets, packed into a β-sandwich structure that can spontaneously dimerise through C-terminal strand swapping. Small angle X-ray scattering (SAXS) revealed no fixed orientation of the CTD with respect to the IgSF. By introducing insertion or substitution of residues within the inter-domain linker in the native protein, we were able to show that despite the region being unstructured, it nevertheless is resistant to general proteolysis. These data suggest structural motifs located in the two adjacent Ig-like domains dictate the processing of CTDs by the T9SS secretion pathway. PMID:27005013

Clinical Features of Idiopathic Interstitial Pneumonia with Systemic Sclerosis-Related Autoantibody in Comparison with Interstitial Pneumonia with Systemic Sclerosis

PubMed Central

Yamakawa, Hideaki; Hagiwara, Eri; Kitamura, Hideya; Yamanaka, Yumie; Ikeda, Satoshi; Sekine, Akimasa; Baba, Tomohisa; Iso, Shinichiro; Okudela, Koji; Iwasawa, Tae; Takemura, Tamiko; Kuwano, Kazuyoshi; Ogura, Takashi

2016-01-01

Background Patients with idiopathic interstitial pneumonias sometimes have a few features of connective tissue disease (CTD) and yet do not fulfil the diagnostic criteria for any specific CTD. Objective This study was conducted to elucidate the characteristics, prognosis, and disease behavior in patients with interstitial lung disease (ILD) associated with systemic sclerosis (SSc)-related autoantibodies. Methods We retrospectively analyzed medical records of 72 ILD patients: 40 patients with SSc (SSc-ILD) and 32 patients with SSc-related autoantibody-positive ILD but not with CTD (ScAb-ILD), indicating lung-dominant CTD with SSc-related autoantibody. Results Patients with SSc-ILD were predominantly females and non-smokers, and most had nonspecific interstitial pneumonia confirmed by high-resolution computed tomography (HRCT) and pathological analysis. However, about half of the patients with ScAb-ILD were male and current or ex-smokers. On HRCT analysis, honeycombing was more predominant in patients with ScAb-ILD than with SSc-ILD. Pathological analysis showed the severity of vascular intimal or medial thickening in the SSc-ILD patients to be significantly higher than that in the ScAb-ILD patients. Survival curves showed that the patients with ScAb-ILD had a significantly poorer outcome than those with SSc-ILD. Conclusion Data from this study suggest that lung-dominant CTD with SSc-related autoantibody is a different disease entity from SSc-ILD. PMID:27564852

Protein-Protein Interaction Reagents | Office of Cancer Genomics

Cancer.gov

The CTD2 Center at Emory University has a library of genes used to study protein-protein interactions in mammalian cells. These genes are cloned in different mammalian expression vectors. A list of available cancer-associated genes can be accessed below. Emory_CTD^2_PPI_Reagents.xlsx Contact: Haian Fu

Use of Constant Time Delay and Attentional Responses with Adolescents.

ERIC Educational Resources Information Center

Wolery, Mark; And Others

1991-01-01

This study examined effectiveness of a constant time delay (CTD) procedure in teaching social studies and health facts to five adolescents with learning or behavioral disorders. Students were given praise with and without additional information. Results indicated CTD procedures were reliable and effective, and students acquired nontargeted as well…

The Development of an Instrument to Measure Creative Teaching Abilities.

ERIC Educational Resources Information Center

Riley, John F.

The development of an instrument to measure creative teaching abilities, the Creative Teaching Dilemma (CTD), involved three phases. The instrument was constructed and refined, and scoring procedures were outlined. The activities comprising the CTD included defining the teaching dilemma, gathering additional facts, identifying and stating the…

Physical Chemical and in-situ CTD (Conductivity/Temperature/Depth) Data from the Ajax Expedition in the South Atlantic Ocean.

DTIC Science & Technology

1985-12-15

SALINITY SIGMA SIGMA S1; KA OVA DYN M T OXYGEN 000 I10 P04 Nn lA? 02 09 A EG C ’Er, C TAETA 2 4 MIL PCI UP/IL U MIL UIL 04/L . 15L 2,641 .641 03.923...epart ment i if the Nays t S TOI KA Priest fi 1ce N,,’.,l OLcin Sysrenis Center Prof C’ G 11 Rititf N) 0 ?% R /( %R San Iliego. C A 921 i2 I nisersity if...Dr. Adriana Huyer Cambridge, MA 02139 U.S. Dept. of Commerce, NOAA School of Oceanography Geophysical Fluid Dynamics Lab Oregon State University Dr

Depth profile measurement with lenslet images of the plenoptic camera

NASA Astrophysics Data System (ADS)

Yang, Peng; Wang, Zhaomin; Zhang, Wei; Zhao, Hongying; Qu, Weijuan; Zhao, Haimeng; Asundi, Anand; Yan, Lei

2018-03-01

An approach for carrying out depth profile measurement of an object with the plenoptic camera is proposed. A single plenoptic image consists of multiple lenslet images. To begin with, these images are processed directly with a refocusing technique to obtain the depth map, which does not need to align and decode the plenoptic image. Then, a linear depth calibration is applied based on the optical structure of the plenoptic camera for depth profile reconstruction. One significant improvement of the proposed method concerns the resolution of the depth map. Unlike the traditional method, our resolution is not limited by the number of microlenses inside the camera, and the depth map can be globally optimized. We validated the method with experiments on depth map reconstruction, depth calibration, and depth profile measurement, with the results indicating that the proposed approach is both efficient and accurate.

Pavilion Lake, British Columbia, Canada - An investigation of potentially unique freshwater microbialites, and their application to Mars exploration.

NASA Astrophysics Data System (ADS)

Lim, D. S.; Laval, B.; Slater, G.; Andersen, D.; Airo, A.; Mullins, G.; Schulze-Makuch, D.; Cady, S.; McKay, C.

2005-12-01

Pavilion Lake, B. C., Canada has become the first target site of an on-going NASA effort to investigate the Mars analogue potential of terrestrial lacustrine carbonates. A combination of hypothesis and exploration driven research activities are underway to study the unusual freshwater microbialite structures found in this lake. These structures are of interest in terms of models of Precambrian reefs and may also be relevant to carbonate formation in ancient lakes on Mars. Laval et al. (2000) provides an overview of the morphological characteristics of the microbialites, and explores the physical limnology of Pavilion Lake. Several key hypotheses and questions related to the role of biology in the formation of the microbialites, and the effect of varying light levels on the microbialite morphologies have since resulted from Laval et al., but to date remain unanswered. In August 2004, the Pavilion Lake Research Project (PLRP) was established to commence a new round of investigations into Pavilion Lake, to test hypotheses concerning the factors controlling carbonate formation, and to collect further exploration data related to understanding the lake's limnology and development. Laval et al. classified the differing microbialite structures into four depth categories: shallow to intermediate (5-10m), intermediate (~20m), intermediate to deep (20-30m), and deep facies (30-35m). There is a variation of the morphology and mechanical strength of the structures with depth, which may reflect a change in the relative role of biotic and non-biotic precipitation with lowering light levels. Recent field investigations (August 2005) revealed carbonate structures at depths beyond what was reported in Laval et al. (2000). These new structures appear at 46-55m, and are morphologically distinct from the previously described microbialites. Here we present our current research activities at Pavilion Lake, along with recent data collection results. Excursions to the lake have included the use of SCUBA to sample collect and to install a variety of sensors including a thermistor chain and a Licor light meter. Seepage meters have also been placed in strategic regions of the lake to collect incoming lake groundwater for future chemical limnological analyses and hydrological mapping of the area. In addition, conventional Conductivity/Temperature/Depth (CTD) profiles and water sampling has been conducted during a winter and summer period, and will be presented here. Microbialite samples recovered from each of the discernible morphological depth transects have been investigated for relative variations in d13C isotopic signatures, and the results will presented here.

First scientific dives of the Nereid Under Ice hybrid ROV in the Arctic Ocean.

NASA Astrophysics Data System (ADS)

German, C. R.; Boetius, A.; Whitcomb, L. L.; Jakuba, M.; Bailey, J.; Judge, C.; McFarland, C.; Suman, S.; Elliott, S.; Katlein, C.; Arndt, S.; Bowen, A.; Yoerger, D.; Kinsey, J. C.; Mayer, L.; Nicolaus, M.; Laney, S.; Singh, H.; Maksym, T. L.

2014-12-01

The first scientific dives of the new Nereid Under Ice (NUI) hybrid ROV were conducted in the Arctic Ocean in July 2014 on RV Polarstern cruise PS86, a German-US collaboration. NUI is the latest in a family of vehicles derived from the Nereus prototype, using a single optical fiber to provide real-time telemetry to and from a battery-powered vehicle allowing much greater lateral maneuverability relative to its support ship than a conventional ROV. During PS86, dives conducted in the Arctic Ocean (typical water depths ~4000m) were completed in >80% ice cover beneath multi-year ice that was typically 2-4m thick (increasing to depths of up to 20m beneath ridges). Dives extended up to 800m away from the ship and, over dive durations of approximately 5 hours each, covered survey tracklines of up to 3.7km at depths varying from "landing" on the underside of the sea-ice to maximum depths of 45m to conduct upward looking multibeam sonar mapping. Ultimately, the vehicle will be capable of both AUV and ROV mode operations at ranges of 10-20km away from the support ship and at up to 2000m water depth (including seafloor as well as under ice operations). During the current cruise, the following major science suites were utilized to prove a range of scientific capabilities of the vehicle in ice-covered oceans: multibeam mapping of rugged topography beneath multi-year sea-ice; video- and digital still photography of the under side of the ice, biota associated with the ice-water interface (algal material) and abundant fauna in the immediately underlying water column (ctenophores, larvaceans, copepods were all notable for their abundance in our study site over the Gakkel Ridge near 83N, 6W). Other scientific activities included: vertical profiles combining CTD data with a suite of biosensors to investigate the structure of primary productivity and biogeochemical cycling in minimally distrubed areas of the sunlit under-ice water column, revealing high stratification associated with meltwater formation; lateral surveys of radiance and irradiance (together with co-registered measurements on top of the same ice-floe on our last dive) to investigate light availability and variability as a function of ice-cover. We will present examples of each of these data sets, together with an outline of suggested future activities that NUI could pursue.

The Comparative Toxicogenomics Database (CTD): A Resource for Comparative Toxicological Studies

PubMed Central

CJ, Mattingly; MC, Rosenstein; GT, Colby; JN, Forrest; JL, Boyer

2006-01-01

The etiology of most chronic diseases involves interactions between environmental factors and genes that modulate important biological processes (Olden and Wilson, 2000). We are developing the publicly available Comparative Toxicogenomics Database (CTD) to promote understanding about the effects of environmental chemicals on human health. CTD identifies interactions between chemicals and genes and facilitates cross-species comparative studies of these genes. The use of diverse animal models and cross-species comparative sequence studies has been critical for understanding basic physiological mechanisms and gene and protein functions. Similarly, these approaches will be valuable for exploring the molecular mechanisms of action of environmental chemicals and the genetic basis of differential susceptibility. PMID:16902965

Interpreting Repeated Temperature-Depth Profiles for Groundwater Flow

NASA Astrophysics Data System (ADS)

Bense, Victor F.; Kurylyk, Barret L.; van Daal, Jonathan; van der Ploeg, Martine J.; Carey, Sean K.

2017-10-01

Temperature can be used to trace groundwater flows due to thermal disturbances of subsurface advection. Prior hydrogeological studies that have used temperature-depth profiles to estimate vertical groundwater fluxes have either ignored the influence of climate change by employing steady-state analytical solutions or applied transient techniques to study temperature-depth profiles recorded at only a single point in time. Transient analyses of a single profile are predicated on the accurate determination of an unknown profile at some time in the past to form the initial condition. In this study, we use both analytical solutions and a numerical model to demonstrate that boreholes with temperature-depth profiles recorded at multiple times can be analyzed to either overcome the uncertainty associated with estimating unknown initial conditions or to form an additional check for the profile fitting. We further illustrate that the common approach of assuming a linear initial temperature-depth profile can result in significant errors for groundwater flux estimates. Profiles obtained from a borehole in the Veluwe area, Netherlands in both 1978 and 2016 are analyzed for an illustrative example. Since many temperature-depth profiles were collected in the late 1970s and 1980s, these previously profiled boreholes represent a significant and underexploited opportunity to obtain repeat measurements that can be used for similar analyses at other sites around the world.

Construct Validity Examination of Critical Thinking Dispositions for Undergraduate Students in University Putra Malaysia

ERIC Educational Resources Information Center

Ghadi, Ibrahim; Alwi, Nor Hayati; Bakar, Kamariah Abu; Talib, Othman

2012-01-01

This research aims to evaluate the psychology properties of the construct validity for the Critical Thinking Disposition (CTD) instrument. The CTD instrument consists of 39 Likert-type items measuring seven dispositions, namely analyticity, open-mind, truth-seeking, systematicity, self-confidence inquisitiveness and maturity. The study involves…

Scholarships and School Improvement: Annual Report of Catching the Dream.

ERIC Educational Resources Information Center

Chavers, Dean, Ed.

2001-01-01

This issue of "The Native Scholar" is comprised entirely of the annual report of Catching the Dream (CTD), an organization that awards scholarships to Native American students and grants for improving Native American schools. CTD scholarship programs are described, as are scholarships in general and how to find them. Fourteen scholarship websites…

Using the Constructivist Tridimensional Design Model for Online Continuing Education for Health Care Clinical Faculty

ERIC Educational Resources Information Center

Seo, Kay Kyeong-Ju; Engelhard, Chalee

2014-01-01

This article presents a new paradigm for continuing education of Clinical Instructors (CIs): the Constructivist Tridimensional (CTD) model for the design of an online curriculum. Based on problem-based learning, self-regulated learning, and adult learning theory, the CTD model was designed to facilitate interactive, collaborative, and authentic…

Observational and Incidental Learning by Children with Autism during Small Group Instruction

ERIC Educational Resources Information Center

Ledford, Jennifer R.; Gast, David L.; Luscre, Deanna; Ayres, Kevin M.

2008-01-01

This study evaluated the acquisition of incidental and observational information presented to 6 children with autism in a small group instructional arrangement using a constant time delay (CTD) procedure. A multiple probe design across behaviors, replicated across 6 participants, was used to evaluate the effectiveness of the CTD procedure and to…

[WMSDs in supermarket cashiers].

PubMed

Di Pede, Cinzia; Manuli, Gianluca; Dini, Fulvia; Pinelli, Marco; Turini, Lucia; Mariani, Maurizio; Taddeo, Domenico

2011-01-01

High prevalence of Cumulative Trauma Disorders (CTD) of shoulder and wristle among supermarket cashiers have been reported by several studies. To evaluate CTD prevalence in a group of supermarket cashiers in Pisa area is the aim of this study. Standardized Questionnaire and clinical examination have been performed in 128 female supermarket cashiers. In subjects having Symptoms and Signs, Elettroneurography and Echography have been performed. 54 subjects had Paresthesias and performed elettroneurography: 44 (34,4%) had Median nerve impairment at the wrist and among them 37 cases were bilateral; 15 had Ulnar nerve impairment (11,7%), among them 8 were bilateral. Moreover we have performed the echographies in all the 25 subjects with a positive medical examination of the shoulder and they all (19,5% del totale) showed a rotator cuff tendinosis. 25 subjects with CTD (44,6%) showed a comorbidity. An index called BiCo considering both bilaterality and comorbility has been calculated. The percentage of CTD is much more elevated than in general population and many workers present comorbility and bilaterality: a strategy for primary prevention improving ergonomy and information is needed.

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information

PubMed Central

Wilbur, W. John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical–gene interactions, chemical–disease relationships and gene–disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein–protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team. PMID:23160415

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.

PubMed

Kim, Sun; Kim, Won; Wei, Chih-Hsuan; Lu, Zhiyong; Wilbur, W John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical-gene interactions, chemical-disease relationships and gene-disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein-protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team.

The ESASSI-08 cruise in the South Scotia Ridge region: preliminary analysis of hydrodynamic and biogeochemical data

NASA Astrophysics Data System (ADS)

Gomis, D.; Flexas, M. M.; Palmer, M.; Jordà, G.; Orsi, A. H.; Yvon-Lewis, S. A.

2009-04-01

The ESASSI-08 oceanographic cruise carried out in January 2008 was the major milestone of ESASSI, the Spanish component of SASSI (a core project of the International Polar Year devoted to study the shelf-slope exchanges in different locations of Antarctica). The sampling strategy of the cruise consisted of 11 full-depth CTD/ADCP sections across the northern and southern slope of the South Scotia Ridge (SSR), between Elephant and Orkney Islands. The sections extend from shelf waters to open sea and the profiles were gathered at an unprecedented spatial resolution over the slope (about 2 nm). Water samples for chemical and biological analysis were also collected at each station; the analyzed parameters include trace gases (CFCs), oxygen isotopes, carbon-related parameters, and nutrients. In this presentation we show the overall distribution of the main variables across the different sections. Namely, we present: a water mass analysis (in terms of potential temperature, salinity and neutral density), estimates of velocities and fluxes across different transects and distributions of biogeochemical parameters. The ultimate aims of the ESASSI project are: 1) to elucidate the fate of the ASF when it enters the SSR from the Weddell Sea; 2) to estimate the shelf-slope exchanges for different parameters; and 3) to quantify the importance of the ventilation associated with intermediate waters flowing over the SSR with respect to the ventilation associated with bottom waters that are blocked by the SSR and flow around the Orkney Plateau.

Structural and sequencing analysis of local target DNA recognition by MLV integrase.

PubMed

Aiyer, Sriram; Rossi, Paolo; Malani, Nirav; Schneider, William M; Chandar, Ashwin; Bushman, Frederic D; Montelione, Gaetano T; Roth, Monica J

2015-06-23

Target-site selection by retroviral integrase (IN) proteins profoundly affects viral pathogenesis. We describe the solution nuclear magnetic resonance structure of the Moloney murine leukemia virus IN (M-MLV) C-terminal domain (CTD) and a structural homology model of the catalytic core domain (CCD). In solution, the isolated MLV IN CTD adopts an SH3 domain fold flanked by a C-terminal unstructured tail. We generated a concordant MLV IN CCD structural model using SWISS-MODEL, MMM-tree and I-TASSER. Using the X-ray crystal structure of the prototype foamy virus IN target capture complex together with our MLV domain structures, residues within the CCD α2 helical region and the CTD β1-β2 loop were predicted to bind target DNA. The role of these residues was analyzed in vivo through point mutants and motif interchanges. Viable viruses with substitutions at the IN CCD α2 helical region and the CTD β1-β2 loop were tested for effects on integration target site selection. Next-generation sequencing and analysis of integration target sequences indicate that the CCD α2 helical region, in particular P187, interacts with the sequences distal to the scissile bonds whereas the CTD β1-β2 loop binds to residues proximal to it. These findings validate our structural model and disclose IN-DNA interactions relevant to target site selection. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Assessment of Cumulative Trauma Disorder (CTD) Risk for 3 Different Tasks Constructing and Repairing Multi-Layer Insulation (MLI) Blankets, Preparing the Dough for a Pizza, and Operating the Becton-Dickinson FACSAria Flow Cytometer

NASA Technical Reports Server (NTRS)

Gentzler, Marc; Kline, Martin; Palmer, Andrew; Terrone, Mark

2007-01-01

The Cumulative Trauma Disorder (CTD) risks for three different tasks using McCauley-Bell and Badiru's (1993) formula based on task, personal, and organizational factors were examined. For the Multi-Layer Insulation (MLI) blanket task, the results showed that the task, personal, and organizational risks were at about the same level. The personal risk factors for this task were evaluated using a hypothetical female employee age 52. For the pizza dough task, it was shown that the organizational risk was particularly high, with task related factors also at quite dangerous levels. On the other hand, there was a very low level of personal risk factors, based on a female age 17. The flow cytometer task was assessed with three different participants, a11 of whom had quite disparate levels of personal risk, which slightly affected the overall CTD risk. This reveals how individual difference variables certainly need to be considered. The task and organizational risks for this task were rated at about the same moderate level. The overall CTD risk averaged across the three participants was .335, indicating some risk. Compruing across the tasks revealed that the pizza dough task created the greatest overall CTD risk by far (.568), with the MLI (.325) and flow cytometer task (.335) having some risk associated with them. Future research should look into different tasks for more of a comparison

Bedside talc pleurodesis for malignant pleural effusion: factors affecting success.

PubMed

Aydogmus, Umit; Ozdemir, Servet; Cansever, Levent; Sonmezoglu, Yasar; Kocaturk, Celalettin Ibrahim; Bedirhan, Mehmet Ali

2009-03-01

To determine the factors affecting the success of bedside talc slurry (TS) used for symptomatic treatment of patients with malignant pleural effusion (MPE). Data of 113 effusions in 103 MPE patients treated between 1999 and 2007 were retrospectively evaluated for the study. The study group involved 73 patients whose follow-up information was available out of 81 patients treated by TS. Causes of MPE were lung cancer in 22 patients (30.1%) and breast carcinoma in 21 patients (28.8%). The success rate of TS was significantly higher if the time period between radiological diagnosis of effusion and administration of TS was less than 30 days (P= .02), or spontaneous expansion was attained after chest tube drainage (CTD) (P= .01). Success rate was higher for patients with daily drainage of less than 200 ml before TS than patients with more than 200 ml of daily drainage (P= .01). Dose of talc, either 4 g or above (P= .34), primary cause of MPE (P= .53), time to termination of CTD (P= .57), amount of drainage when CTD was terminated (P= .23), and time period between CTD and administration of TS (P= .20) did not show a statistically significant effect on the success of TS. In the treatment of malignant pleural effusion, patients with daily drainage of less than 200 ml before TS developed less recurrence than patients with daily drainage of more than 200 ml. Longer time period between the diagnosis of MPE and onset of CTD increased recurrence.

Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database.

PubMed

Davis, Allan Peter; Wiegers, Thomas C; King, Benjamin L; Wiegers, Jolene; Grondin, Cynthia J; Sciaky, Daniela; Johnson, Robin J; Mattingly, Carolyn J

2016-01-01

Strategies for discovering common molecular events among disparate diseases hold promise for improving understanding of disease etiology and expanding treatment options. One technique is to leverage curated datasets found in the public domain. The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) manually curates chemical-gene, chemical-disease, and gene-disease interactions from the scientific literature. The use of official gene symbols in CTD interactions enables this information to be combined with the Gene Ontology (GO) file from NCBI Gene. By integrating these GO-gene annotations with CTD's gene-disease dataset, we produce 753,000 inferences between 15,700 GO terms and 4,200 diseases, providing opportunities to explore presumptive molecular underpinnings of diseases and identify biological similarities. Through a variety of applications, we demonstrate the utility of this novel resource. As a proof-of-concept, we first analyze known repositioned drugs (e.g., raloxifene and sildenafil) and see that their target diseases have a greater degree of similarity when comparing GO terms vs. genes. Next, a computational analysis predicts seemingly non-intuitive diseases (e.g., stomach ulcers and atherosclerosis) as being similar to bipolar disorder, and these are validated in the literature as reported co-diseases. Additionally, we leverage other CTD content to develop testable hypotheses about thalidomide-gene networks to treat seemingly disparate diseases. Finally, we illustrate how CTD tools can rank a series of drugs as potential candidates for repositioning against B-cell chronic lymphocytic leukemia and predict cisplatin and the small molecule inhibitor JQ1 as lead compounds. The CTD dataset is freely available for users to navigate pathologies within the context of extensive biological processes, molecular functions, and cellular components conferred by GO. This inference set should aid researchers, bioinformaticists, and pharmaceutical drug makers in finding commonalities in disease mechanisms, which in turn could help identify new therapeutics, new indications for existing pharmaceuticals, potential disease comorbidities, and alerts for side effects.

Evolution of RNA-Protein Interactions: Non-Specific Binding Led to RNA Splicing Activity of Fungal Mitochondrial Tyrosyl-tRNA Synthetases

PubMed Central

Lamech, Lilian T.; Mallam, Anna L.; Lambowitz, Alan M.

2014-01-01

The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (mtTyrRS; CYT-18 protein) evolved a new function as a group I intron splicing factor by acquiring the ability to bind group I intron RNAs and stabilize their catalytically active RNA structure. Previous studies showed: (i) CYT-18 binds group I introns by using both its N-terminal catalytic domain and flexibly attached C-terminal anticodon-binding domain (CTD); and (ii) the catalytic domain binds group I introns specifically via multiple structural adaptations that occurred during or after the divergence of Peziomycotina and Saccharomycotina. However, the function of the CTD and how it contributed to the evolution of splicing activity have been unclear. Here, small angle X-ray scattering analysis of CYT-18 shows that both CTDs of the homodimeric protein extend outward from the catalytic domain, but move inward to bind opposite ends of a group I intron RNA. Biochemical assays show that the isolated CTD of CYT-18 binds RNAs non-specifically, possibly contributing to its interaction with the structurally different ends of the intron RNA. Finally, we find that the yeast mtTyrRS, which diverged from Pezizomycotina fungal mtTyrRSs prior to the evolution of splicing activity, binds group I intron and other RNAs non-specifically via its CTD, but lacks further adaptations needed for group I intron splicing. Our results suggest a scenario of constructive neutral (i.e., pre-adaptive) evolution in which an initial non-specific interaction between the CTD of an ancestral fungal mtTyrRS and a self-splicing group I intron was “fixed” by an intron RNA mutation that resulted in protein-dependent splicing. Once fixed, this interaction could be elaborated by further adaptive mutations in both the catalytic domain and CTD that enabled specific binding of group I introns. Our results highlight a role for non-specific RNA binding in the evolution of RNA-binding proteins. PMID:25536042

Evolution of RNA-protein interactions: non-specific binding led to RNA splicing activity of fungal mitochondrial tyrosyl-tRNA synthetases.

PubMed

Lamech, Lilian T; Mallam, Anna L; Lambowitz, Alan M

2014-12-01

The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (mtTyrRS; CYT-18 protein) evolved a new function as a group I intron splicing factor by acquiring the ability to bind group I intron RNAs and stabilize their catalytically active RNA structure. Previous studies showed: (i) CYT-18 binds group I introns by using both its N-terminal catalytic domain and flexibly attached C-terminal anticodon-binding domain (CTD); and (ii) the catalytic domain binds group I introns specifically via multiple structural adaptations that occurred during or after the divergence of Peziomycotina and Saccharomycotina. However, the function of the CTD and how it contributed to the evolution of splicing activity have been unclear. Here, small angle X-ray scattering analysis of CYT-18 shows that both CTDs of the homodimeric protein extend outward from the catalytic domain, but move inward to bind opposite ends of a group I intron RNA. Biochemical assays show that the isolated CTD of CYT-18 binds RNAs non-specifically, possibly contributing to its interaction with the structurally different ends of the intron RNA. Finally, we find that the yeast mtTyrRS, which diverged from Pezizomycotina fungal mtTyrRSs prior to the evolution of splicing activity, binds group I intron and other RNAs non-specifically via its CTD, but lacks further adaptations needed for group I intron splicing. Our results suggest a scenario of constructive neutral (i.e., pre-adaptive) evolution in which an initial non-specific interaction between the CTD of an ancestral fungal mtTyrRS and a self-splicing group I intron was "fixed" by an intron RNA mutation that resulted in protein-dependent splicing. Once fixed, this interaction could be elaborated by further adaptive mutations in both the catalytic domain and CTD that enabled specific binding of group I introns. Our results highlight a role for non-specific RNA binding in the evolution of RNA-binding proteins.

Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database

PubMed Central

Davis, Allan Peter; Johnson, Robin J.; Lennon-Hopkins, Kelley; Sciaky, Daniela; Rosenstein, Michael C.; Wiegers, Thomas C.; Mattingly, Carolyn J.

2012-01-01

The Comparative Toxicogenomics Database (CTD) is a public resource that promotes understanding about the effects of environmental chemicals on human health. CTD biocurators read the scientific literature and manually curate a triad of chemical–gene, chemical–disease and gene–disease interactions. Typically, articles for CTD are selected using a chemical-centric approach by querying PubMed to retrieve a corpus containing the chemical of interest. Although this technique ensures adequate coverage of knowledge about the chemical (i.e. data completeness), it does not necessarily reflect the most current state of all toxicological research in the community at large (i.e. data currency). Keeping databases current with the most recent scientific results, as well as providing a rich historical background from legacy articles, is a challenging process. To address this issue of data currency, CTD designed and tested a journal-centric approach of curation to complement our chemical-centric method. We first identified priority journals based on defined criteria. Next, over 7 weeks, three biocurators reviewed 2425 articles from three consecutive years (2009–2011) of three targeted journals. From this corpus, 1252 articles contained relevant data for CTD and 52 752 interactions were manually curated. Here, we describe our journal selection process, two methods of document delivery for the biocurators and the analysis of the resulting curation metrics, including data currency, and both intra-journal and inter-journal comparisons of research topics. Based on our results, we expect that curation by select journals can (i) be easily incorporated into the curation pipeline to complement our chemical-centric approach; (ii) build content more evenly for chemicals, genes and diseases in CTD (rather than biasing data by chemicals-of-interest); (iii) reflect developing areas in environmental health and (iv) improve overall data currency for chemicals, genes and diseases. Database URL: http://ctdbase.org/ PMID:23221299

Heat-shock-specific phosphorylation and transcriptional activity of RNA polymerase II.

PubMed

Egyházi, E; Ossoinak, A; Lee, J M; Greenleaf, A L; Mäkelä, T P; Pigon, A

1998-07-10

The carboxyl-terminal domain (CTD) of the largest RNA polymerase II (pol II) subunit is a target for extensive phosphorylation in vivo. Using in vitro kinase assays it was found that several different protein kinases can phosphorylate the CTD including the transcription factor IIH-associated CDK-activating CDK7 kinase (R. Roy, J. P. Adamczewski, T. Seroz, W. Vermeulen, J. P. Tassan, L. Schaeffer, E. A. Nigg, J. H. Hoeijmakers, and J. M. Egly, 1994, Cell 79, 1093-1101). Here we report the colocalization of CDK7 and the phosphorylated form of CTD (phosphoCTD) to actively transcribing genes in intact salivary gland cells of Chironomus tentans. Following a heat-shock treatment, both CDK7 and pol II staining disappear from non-heat-shock genes concomitantly with the abolishment of transcriptional activity of these genes. In contrast, the actively transcribing heat-shock genes, manifested as chromosomal puff 5C on chromosome IV (IV-5C), stain intensely for phosphoCTD, but are devoid of CDK7. Furthermore, the staining of puff IV-5C with anti-PCTD antibodies was not detectably influenced by the TFIIH kinase and transcription inhibitor 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole (DRB). Following heat-shock treatment, the transcription of non-heat-shock genes was completely eliminated, while newly formed heat-shock gene transcripts emerged in a DRB-resistant manner. Thus, heat shock in these cells induces a rapid clearance of CDK7 from the non-heat-shock genes, indicating a lack of involvement of CDK7 in the induction and function of the heat-induced genes. The results taken together suggest the existence of heat-shock-specific CTD phosphorylation in living cells. This phosphorylation is resistant to DRB treatment, suggesting that not only phosphorylation but also transcription of heat-shock genes is DRB resistant and that CDK7 in heat shock cells is not associated with TFIIH.

Interactive effects of dietary adaptation period length and titration diet type on apparent ileal phosphorus digestibility and phosphorus retention in growing broilers.

PubMed

Perryman, K R; Cattley, R C; Masey O'Neill, H V; Bedford, M R; Dozier, W A

2016-10-01

Two experiments were conducted to examine the effects of different corn titration diets and dietary adaptation period length (DAPL) on intestinal histology, apparent ileal P digestibility (AIPD), and apparent P retention (APR) in Ross × Ross 708 male broilers from 20 to 24 d of age. It was hypothesized that purified ingredients in nutrient-deficient titration diets may affect P availability with varying DAPL. In experiment 1, 1,152 broilers were utilized in a 3 × 3 factorial treatment structure with 3 diets (control, 25% corn titration diet [25CTD], or 75% corn titration diet [75CTD]) and 3 DAPL (0, 24, or 72 h). Experiment 2 was conducted with 576 broilers as a 4 × 3 factorial arrangement with 4 diets (control, 25CTD, 75CTD, or nitrogen-free diet [NFD]) and 3 DAPL (24, 48, or 72 h). All diets contained purified ingredients except for the control diet, which had the same formulation as the common starter and served as a control for DAPL. The NFD diet was fed as a highly purified protein-free diet. Broilers were fed a common diet until 19 d of age and then transferred to experimental diets at 20 d of age. In experiment 1, diet type did not affect (P > 0.05) intestinal histology. However, diet type and DAPL each influenced (P.≤.0.001) diet AIPD. Higher (P.≤.0.001) AIPD was measured for the control diet compared with the 75CDT, and the 25CTD had the lowest AIPD. Following a 24 h DAPL, AIPD was higher (P.≤.0.001) than after a DAPL of 0 or 72 h. In experiment 2, diet type × DAPL interactions (P.≤.0.001) were observed for APR of the control diet, 75CTD, and NFD, but not the 25CTD. Because APR of the control diet was affected by varying DAPL, factors other than differences in diet type may have been responsible for inconsistencies in the measure of P availability. Furthermore, no clear evidence was observed that broilers were able to adapt to P-deficient diets by increasing APR or AIPD. In conclusion, a standard DAPL should be established as a means to reduce variability associated with measuring of feedstuff P availability. © 2016 Poultry Science Association Inc.

Rituximab versus cyclophosphamide for the treatment of connective tissue disease-associated interstitial lung disease (RECITAL): study protocol for a randomised controlled trial.

PubMed

Saunders, Peter; Tsipouri, Vicky; Keir, Gregory J; Ashby, Deborah; Flather, Marcus D; Parfrey, Helen; Babalis, Daphne; Renzoni, Elisabetta A; Denton, Christopher P; Wells, Athol U; Maher, Toby M

2017-06-15

Interstitial lung disease (ILD) frequently complicates systemic autoimmune disorders resulting in considerable morbidity and mortality. The connective tissue diseases (CTDs) most frequently resulting in ILD include: systemic sclerosis, idiopathic inflammatory myositis (including dermatomyositis, polymyositis and anti-synthetase syndrome) and mixed connective tissue disease. Despite the development, over the last two decades, of a range of biological therapies which have resulted in significant improvements in the treatment of the systemic manifestations of CTD, the management of CTD-associated ILD has changed little. At present there are no approved therapies for CTD-ILD. Following trials in scleroderma-ILD, cyclophosphamide is the accepted standard of care for individuals with severe or progressive CTD-related ILD. Observational studies have suggested that the anti-CD20 monoclonal antibody, rituximab, is an effective rescue therapy in the treatment of refractory CTD-ILD. However, before now, there have been no randomised controlled trials assessing the efficacy of rituximab in this treatment population. RECITAL is a UK, multicentre, prospective, randomised, double-blind, double-dummy, controlled trial funded by the Efficacy and Mechanism Evaluation Programme of the Medical Research Council and National Institute for Health Research. The trial will compare rituximab 1 g given intravenously, twice at an interval of 2 weeks, with intravenously administered cyclophosphamide given monthly at a dose of 600 mg/m 2 body surface area in individuals with ILD due to systemic sclerosis, idiopathic inflammatory myositis (including anti-synthetase syndrome) or mixed connective tissue disease. A total of 116 individuals will be randomised 1:1 to each of the two treatment arms, with stratification based on underlying CTD, and will be followed for a total of 48 weeks from first dose. The primary endpoint for the study will be change in forced vital capacity (FVC) at 24 weeks. Key secondary endpoints include: safety, change in FVC at 48 weeks as well as survival, change in oxygen requirements, total 48-week corticosteroid exposure and utilisation of health care resources. This is the first randomised control trial to study the efficacy of rituximab as first-line treatment in CTD-associated ILD. The results generated should provide important information on the treatment of a life-threatening complication affecting a rare group of CTDs. ClinicalTrials.gov, NCT01862926. Registered on 22 May 2013.

On the cyclonic eddy generation in Panay Strait, Philippines

NASA Astrophysics Data System (ADS)

Flament, P. J.; Repollo, C. L. A.; Flores-vidal, X.; Villanoy, C.

2016-12-01

High Frequency Doppler Radar (HFDR), shallow pressure gauges and Acoustic Doppler Current Profiler (ADCP) time-series observations during the Philippine Straits Dynamics Experiment (PhilEx) were analyzed to describe the mesoscale currents in Panay Strait, Philippines. Low frequency surface currents inferred from three HFDR (July 2008 { July 2009), revealed a clear seasonal signal in concurrent with the reversal of the Asian monsoon. The mesoscale cyclonic eddy west of Panay Island is generated during the winter northeast (NE) monsoon. This causes changes in the strength, depth and width of the intra-seasonal Panay coastal jet as its eastern limb. Winds from QuikSCAT satellite and from a nearby airport indicate that these flow structures correlate with the strength and direction of the prevailing local wind. An intensive survey of the cyclonic eddy in February 8-9, 2009, obtaining a 24-hour successive cross-shore Conductivity-Temperature- Depth (CTD) sections in conjunction with shipboard ADCP measurements showed a well- developed cyclonic eddy characterized by near-surface velocities reaching 50 cm/s. This observation coincides with the intensification of the wind in between Mindoro and Panay islands generating a positive wind stress curl in the lee of Panay, which in turn induces divergent surface currents. Water column response from the mean transects showed a pronounced signal of upwelling, indicated by the doming of isotherms and isopycnals. A pressure gradient then was sets up, resulting in the spin-up of a cyclonic eddy in geostrophic balance. Evaluation of the surface vorticity balance equation suggests that the wind stress curl via Ekman pumping mechanism provides the necessary input in the formation and evolution of the cyclonic eddy. In particular, the cumulative effect of the wind stress curl plays a key role on the generation of the eddy. The Beta-effect on the other hand may led to propagation of the eddy westward.

Remote sensing observations of phytoplankton increases triggered by successive typhoons

NASA Astrophysics Data System (ADS)

Huang, Lei; Zhao, Hui; Pan, Jiayi; Devlin, Adam

2017-12-01

Phytoplankton blooms in the Western North Pacific, triggered by two successive typhoons with different intensities and translation speeds under different pre-existing oceanic conditions, were observed and analyzed using remotely sensed chlorophyll-a (Chl-a), sea surface temperature (SST), and sea surface height anomaly (SSHA) data, as well as typhoon parameters and CTD (conductivity, temperature, and depth) profiles. Typhoon Sinlaku, with relatively weaker intensity and slower translation speed, induced a stronger phytoplankton bloom than Jangmi with stronger intensity and faster translation speed (Chl-a>0.18 mg·m‒3 versus Chl-a<0.15 mg·m‒3) east of Taiwan Island. Translation speed may be one of the important mechanisms that affect phytoplankton blooms in the study area. Pre-existing cyclonic circulations provided a relatively unstable thermodynamic structure for Sinlaku, and therefore cold water with rich nutrients could be brought up easily. The mixed-layer deepening caused by Typhoon Sinlaku, which occurred first, could have triggered an unfavorable condition for the phytoplankton bloom induced by Typhoon Jangmi which followed afterwards. The sea surface temperature cooling by Jangmi was suppressed due to the presence of the thick upper-ocean mixed-layer, which prevented the deeper cold water from being entrained into the upper-ocean mixed layer, leading to a weaker phytoplankton augment. The present study suggests that both wind (including typhoon translation speed and intensity) and pre-existing conditions (e.g., mixed-layer depths, eddies, and nutrients) play important roles in the strong phytoplankton bloom, and are responsible for the stronger phytoplankton bloom after Sinlaku's passage than that after Jangmi's passage. A new typhoon-influencing parameter is introduced that combines the effects of the typhoon forcing (including the typhoon intensity and translation speed) and the oceanic pre-condition. This parameter shows that the forcing effect of Sinlaku was stronger than that of Jangmi.

Requirement for the E1 Helicase C-Terminal Domain in Papillomavirus DNA Replication In Vivo.

PubMed

Bergvall, Monika; Gagnon, David; Titolo, Steve; Lehoux, Michaël; D'Abramo, Claudia M; Melendy, Thomas; Archambault, Jacques

2016-01-06

The papillomavirus (PV) E1 helicase contains a conserved C-terminal domain (CTD), located next to its ATP-binding site, whose function in vivo is still poorly understood. The CTD is comprised of an alpha helix followed by an acidic region (AR) and a C-terminal extension termed the C-tail. Recent biochemical studies on bovine papillomavirus 1 (BPV1) E1 showed that the AR and C-tail regulate the oligomerization of the protein into a double hexamer at the origin. In this study, we assessed the importance of the CTD of human papillomavirus 11 (HPV11) E1 in vivo, using a cell-based DNA replication assay. Our results indicate that combined deletion of the AR and C-tail drastically reduces DNA replication, by 85%, and that further truncation into the alpha-helical region compromises the structural integrity of the E1 helicase domain and its interaction with E2. Surprisingly, removal of the C-tail alone or mutation of highly conserved residues within the domain still allows significant levels of DNA replication (55%). This is in contrast to the absolute requirement for the C-tail reported for BPV1 E1 in vitro and confirmed here in vivo. Characterization of chimeric proteins in which the AR and C-tail from HPV11 E1 were replaced by those of BPV1 indicated that while the function of the AR is transferable, that of the C-tail is not. Collectively, these findings define the contribution of the three CTD subdomains to the DNA replication activity of E1 in vivo and suggest that the function of the C-tail has evolved in a PV type-specific manner. While much is known about hexameric DNA helicases from superfamily 3, the papillomavirus E1 helicase contains a unique C-terminal domain (CTD) adjacent to its ATP-binding site. We show here that this CTD is important for the DNA replication activity of HPV11 E1 in vivo and that it can be divided into three functional subdomains that roughly correspond to the three conserved regions of the CTD: an alpha helix, needed for the structural integrity of the helicase domain, followed by an acidic region (AR) and a C-terminal tail (C-tail) that have been shown to regulate the oligomerization of BPV1 E1 in vitro. Characterization of E1 chimeras revealed that, while the function of the AR could be transferred from BPV1 E1 to HPV11 E1, that of the C-tail could not. These results suggest that the E1 CTD performs multiple functions in DNA replication, some of them in a virus type-specific manner. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Requirement for the E1 Helicase C-Terminal Domain in Papillomavirus DNA Replication In Vivo

PubMed Central

Bergvall, Monika; Gagnon, David; Titolo, Steve; Lehoux, Michaël; D'Abramo, Claudia M.

2016-01-01

ABSTRACT The papillomavirus (PV) E1 helicase contains a conserved C-terminal domain (CTD), located next to its ATP-binding site, whose function in vivo is still poorly understood. The CTD is comprised of an alpha helix followed by an acidic region (AR) and a C-terminal extension termed the C-tail. Recent biochemical studies on bovine papillomavirus 1 (BPV1) E1 showed that the AR and C-tail regulate the oligomerization of the protein into a double hexamer at the origin. In this study, we assessed the importance of the CTD of human papillomavirus 11 (HPV11) E1 in vivo, using a cell-based DNA replication assay. Our results indicate that combined deletion of the AR and C-tail drastically reduces DNA replication, by 85%, and that further truncation into the alpha-helical region compromises the structural integrity of the E1 helicase domain and its interaction with E2. Surprisingly, removal of the C-tail alone or mutation of highly conserved residues within the domain still allows significant levels of DNA replication (55%). This is in contrast to the absolute requirement for the C-tail reported for BPV1 E1 in vitro and confirmed here in vivo. Characterization of chimeric proteins in which the AR and C-tail from HPV11 E1 were replaced by those of BPV1 indicated that while the function of the AR is transferable, that of the C-tail is not. Collectively, these findings define the contribution of the three CTD subdomains to the DNA replication activity of E1 in vivo and suggest that the function of the C-tail has evolved in a PV type-specific manner. IMPORTANCE While much is known about hexameric DNA helicases from superfamily 3, the papillomavirus E1 helicase contains a unique C-terminal domain (CTD) adjacent to its ATP-binding site. We show here that this CTD is important for the DNA replication activity of HPV11 E1 in vivo and that it can be divided into three functional subdomains that roughly correspond to the three conserved regions of the CTD: an alpha helix, needed for the structural integrity of the helicase domain, followed by an acidic region (AR) and a C-terminal tail (C-tail) that have been shown to regulate the oligomerization of BPV1 E1 in vitro. Characterization of E1 chimeras revealed that, while the function of the AR could be transferred from BPV1 E1 to HPV11 E1, that of the C-tail could not. These results suggest that the E1 CTD performs multiple functions in DNA replication, some of them in a virus type-specific manner. PMID:26739052

Depth profiling analysis of solar wind helium collected in diamond-like carbon film from Genesis

DOE PAGES

Bajo, Ken-ichi; Olinger, Chad T.; Jurewicz, Amy J.G.; ...

2015-01-01

The distribution of solar-wind ions in Genesis mission collectors, as determined by depth profiling analysis, constrains the physics of ion solid interactions involving the solar wind. Thus, they provide an experimental basis for revealing ancient solar activities represented by solar-wind implants in natural samples. We measured the first depth profile of ⁴He in a collector; the shallow implantation (peaking at <20 nm) required us to use sputtered neutral mass spectrometry with post-photoionization by a strong field. The solar wind He fluence calculated using depth profiling is ~8.5 x 10¹⁴ cm⁻². The shape of the solar wind ⁴He depth profile ismore » consistent with TRIM simulations using the observed ⁴He velocity distribution during the Genesis mission. It is therefore likely that all solar-wind elements heavier than H are completely intact in this Genesis collector and, consequently, the solar particle energy distributions for each element can be calculated from their depth profiles. Ancient solar activities and space weathering of solar system objects could be quantitatively reproduced by solar particle implantation profiles.« less

Constant Time Delay: One Way to Provide Positive Behavioral Support for Students with Emotional and Behavioral Disorders

ERIC Educational Resources Information Center

Stevens, Kay B.; Lingo, Amy S.

2005-01-01

Teachers of students with emotional and behavioral disorders (EBD) understand conceptually, emotionally, and legally the importance of using research-based procedures as well as positive behavioral supports. One way to provide positive behavioral support for students with EBD is constant time delay (CTD). CTD is an instructional delivery procedure…

Beyond Critical Thinking Skills: Investigating the Relationship between Critical Thinking Skills and Dispositions through Different Online Instructional Strategies

ERIC Educational Resources Information Center

Yang, Ya-Ting C.; Chou, Heng-An

2008-01-01

The purpose of this study was to investigate (1) the relationship between critical thinking skills (CTS) and critical thinking dispositions (CTD), and (2) the effectiveness of different levels of instructional strategy (asynchronous online discussions (AODs), CTS instruction via AODs, and CTS instruction with CTD cultivation via AODs) in improving…

Caregivers as Teachers: Using Constant Time Delay To Teach Adults How To Use Constant Time Delay.

ERIC Educational Resources Information Center

Wall, Maureen E.; Gast, David L.

1997-01-01

A study involving four caregivers evaluated the effectiveness of a systematic instructional procedure known as constant time delay (CTD) in teaching caregivers how to use CTD to teach their adolescent or adult children, siblings, or clients with disabilities, response chain skills. Results found the procedure to be effective. (CR)

A new non-pharmacological vacuum therapy for female sexual dysfunction.

PubMed

Billups, K L; Berman, L; Berman, J; Metz, M E; Glennon, M E; Goldstein, I

2001-01-01

Although Female Sexual Dysfunction (FSD) affects 40% of American women, there is no FDA-approved pharmaceutical therapy. The EROS-CTD (Clitoral Therapy Device, UroMetrics, Inc., St. Paul, MN) treatment is the first FDA cleared-to-market therapy for FSD. Clitoral engorgement is believed to play an important role in female sexual arousal and overall sexual satisfaction. The EROS-CTD is a small, battery-powered device designed to enhance clitoral engorgement, increase blood flow to the clitoris, and ultimately improve arousal in women with FSD. The objective of this study was to assess the effectiveness of the EROS-CTD on sexual arousal (genital sensation, vaginal lubrication, ability to reach orgasm, and sexual satisfaction) in normal volunteers and women with FSD.

Hybrid Organic/Inorganic Materials Depth Profiling Using Low Energy Cesium Ions

NASA Astrophysics Data System (ADS)

Noël, Céline; Houssiau, Laurent

2016-05-01

The structures developed in organic electronics, such as organic light emitting diodes (OLEDs) or organic photovoltaics (OPVs) devices always involve hybrid interfaces, joining metal or oxide layers with organic layers. No satisfactory method to probe these hybrid interfaces physical chemistry currently exists. One promising way to analyze such interfaces is to use in situ ion beam etching, but this requires ion beams able to depth profile both inorganic and organic layers. Mono- or diatomic ion beams commonly used to depth profile inorganic materials usually perform badly on organics, while cluster ion beams perform excellently on organics but yield poor results when organics and inorganics are mixed. Conversely, low energy Cs+ beams (<500 eV) allow organic and inorganic materials depth profiling with comparable erosion rates. This paper shows a successful depth profiling of a model hybrid system made of metallic (Au, Cr) and organic (tyrosine) layers, sputtered with 500 eV Cs+ ions. Tyrosine layers capped with metallic overlayers are depth profiled easily, with high intensities for the characteristic molecular ions and other specific fragments. Metallic Au or Cr atoms are recoiled into the organic layer where they cause some damage near the hybrid interface as well as changes in the erosion rate. However, these recoil implanted metallic atoms do not appear to severely degrade the depth profile overall quality. This first successful hybrid depth profiling report opens new possibilities for the study of OLEDs, organic solar cells, or other hybrid devices.

Structural characterization of molecular complexes formed by trimethoprim and cimitidine with 2,3,5,6-tetrachloro-1,4-benzoquinone

NASA Astrophysics Data System (ADS)

Balraj, C.; Ganesh, K.; Elango, K. P.

2011-07-01

Spectroscopic and spectrofluorimetric techniques have been employed to investigate the structure of the charge transfer (CT) complexes of Trimethoprim (TMP) and Cimitidine (CTD) drugs with 2,3,5,6-tetrachloro-1,4-benzoquinone ( p-chloranil, p-CHL). The stoichiometry of the complexes was found to be 1:2 for TMP- p-CHL system and 1:1 for CTD- p-CHL system. The thermodynamic results indicated that the formation of molecular complex between the donors and the acceptor is spontaneous and endothermic. The results of electronic spectral studies indicated that the formation constant for CTD- p-CHL system is found to be higher than that for TMP- p-CHL system. The observation is well supported by the results of fluorescence quenching studies and the association constants calculated for CTD- p-CHL system is 36.2 × 10 3 mol L -1 and that for TMP- p-CHL system is 2.6 × 10 3 mol L -1. The kinetic results, in both the cases, indicated that the interaction is first order each with respect to the concentration of the donor and the acceptor. The physico-chemical parameters viz. oscillator strength, dipole moment, ionization potential and dissociation energy of the complexes were also determined and discussed. Structural characterization of the complexes were done using FT-IR and 1H NMR spectral techniques and the results indicated that, in TMP, the free NH 2 group while in CTD the pyrazole N sbnd H moiety involves in complexation with the acceptor, p-CHL.

LRET Determination of Molecular Distances during pH Gating of the Mammalian Inward Rectifier Kir1.1b.

PubMed

Nanazashvili, Mikheil; Sánchez-Rodríguez, Jorge E; Fosque, Ben; Bezanilla, Francisco; Sackin, Henry

2018-01-09

Gating of the mammalian inward rectifier Kir1.1 at the helix bundle crossing (HBC) by intracellular pH is believed to be mediated by conformational changes in the C-terminal domain (CTD). However, the exact motion of the CTD during Kir gating remains controversial. Crystal structures and single-molecule fluorescence resonance energy transfer of KirBac channels have implied a rigid body rotation and/or a contraction of the CTD as possible triggers for opening of the HBC gate. In our study, we used lanthanide-based resonance energy transfer on single-Cys dimeric constructs of the mammalian renal inward rectifier, Kir1.1b, incorporated into anionic liposomes plus PIP 2 , to determine unambiguous, state-dependent distances between paired Cys residues on diagonally opposite subunits. Functionality and pH dependence of our proteoliposome channels were verified in separate electrophysiological experiments. The lanthanide-based resonance energy transfer distances measured in closed (pH 6) and open (pH 8) conditions indicated neither expansion nor contraction of the CTD during gating, whereas the HBC gate widened by 8.8 ± 4 Å, from 6.3 ± 2 to 15.1 ± 6 Å, during opening. These results are consistent with a Kir gating model in which rigid body rotation of the large CTD around the permeation axis is correlated with opening of the HBC hydrophobic gate, allowing permeation of a 7 Å hydrated K ion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Zooglider - an Autonomous Vehicle for Optical and Acoustic Sensing of Marine Zooplankton

NASA Astrophysics Data System (ADS)

Ohman, M. D.; Davis, R. E.; Sherman, J. T.; Grindley, K.; Whitmore, B. M.

2016-02-01

We will present results from early sea trials of the Zooglider, an autonomous zooplankton glider designed and built by the Instrument Development Group at Scripps. The Zooglider is built upon a modified Spray glider and includes a low power camera with telecentric lens and a custom dual frequency sonar (200/1000 kHz). The imaging system quantifies zooplankton as they flow through a sampling tunnel within a well-defined sampling volume. The maximum operating depth is 500 m. Other sensors include a pumped CTD and Chl-a fluorometer. The Zooglider permits in situ measurements of mesozooplankton distributions and three dimensional orientation in relation to other biotic and physical properties of the ocean water column. Zooglider development is supported by the Gordon and Betty Moore Foundation.

Optical Constituents at the Mouth of the Columbia River: Variability and Signature in Remotely Sensed Reflectance

DTIC Science & Technology

2013-09-30

constructed at BIO, carried the new Machine Vision Floc Camera (MVFC), a Sequoia Scientific LISST 100x Type B, an RBR CTD, and two pressure-actuated...WetStar CDOM fluorometer, a Sequoia Scientific flow control switch, and a SeaBird 37 CTD. The flow-control switch allows the ac- 9 to collect 0.2-um

Using the Technology of Critical Thinking Development (CTD) as a Means of Forming Competencies of Students Majoring in "Life Safety"

ERIC Educational Resources Information Center

Kayumova, Leysan R.; Morozova, Marina A.

2016-01-01

The relevance of the research problem is caused by the need to use various teaching methods and techniques in training students majoring in pedagogical specialties while implementing the competency approach in education. Information about the technology of critical thinking development (CTD) in future teachers training is limited, and the…

The Effectiveness of a Constant Time Delay Procedure on Teaching Lifetime Sport Skills to Adolescents with Severe to Profound Intellectual Disabilities.

ERIC Educational Resources Information Center

Zhang, Jiabei; And Others

1995-01-01

A constant time delay (CTD) procedure was used to teach four adolescents with severe/profound intellectual disabilities to perform bowling, throwing, and putting. Results indicated that the adolescents could be effectively taught gross motor lifetime sport skills with the CTD procedure and that verbal description plus physical assistance could be…

Review of Recent Research Using Constant Time Delay to Teach Chained Tasks to Persons with Developmental Disabilities

ERIC Educational Resources Information Center

Dogoe, Maud; Banda, Devender R.

2009-01-01

We reviewed twelve studies that used the constant time delay (CTD) procedure to teach chained tasks to individuals with developmental disabilities from years 1996-2006. Variables analyzed include types of tasks that have been taught with the procedure, how effective CTD has been in teaching participants, and whether researchers have investigated…

A Review of the Accomplishments of the CTD² Network | Office of Cancer Genomics

Cancer.gov

The Office of Cancer Genomics (OCG) Cancer Target Discovery and Development or CTD2 initiative was established by the National Cancer Institute (NCI) to accelerate the “translation” of high-throughput, high-content genomic data to the bedside through functional genomics. The CTD2 initiative is a collaborative network of 13 different research teams, or Centers.

The Discovery of Deep Oil Plumes at the Deepwater Horizon Oil Spill Site (Invited)

NASA Astrophysics Data System (ADS)

Diercks, A. R.; Asper, V. L.; Highsmith, R. C.; Woolsey, M.; Lohrenz, S. E.; McLetchie, K.; Gossett, A.; Lowe, M., III; Joung, D.; McKay, L.

2010-12-01

In May 2010, the National Institute for Undersea Science and Technology (NIUST), a partnership of the University of Mississippi, the University of Southern Mississippi and NOAA, had a 17-day research cruise aboard the UNOLS vessel R/V Pelican scheduled. Two weeks before departure, the Deepwater Horizon oil platform burned and sank, resulting in an uncontrolled oil spill at a depth of ~1500 m at Mississippi Canyon Block 252. The initial mission plan to do AUV surveys of wrecks and hydrate outcrops in the northern Gulf of Mexico, some of them very close to the site of the accident, was abandoned in favor of responding to the still uncontrolled oil spill. The primary goals of the redefined cruise were to acquire baseline and early impact data for seafloor sediments and subsurface distribution of oil and gas hydrates as close as possible in time and space to the origin of the oil spill. Investigating an oil spill nearly a mile deep in the ocean presents special benthic sampling and subsurface oil detection challenges. NIUST’s AUV’s were unloaded from the ship and a large main winch installed to allow operation of a full ocean depth box corer for collecting sediment samples in water depths up to 2000 m. During the first five-day leg of the cruise, a total of 28 box cores were collected. The Pelican returned to port (Cocodrie, LA) to drop off sediment and water samples for immediate analyses, and to take on more sampling gear and supplies for the second leg of the cruise, including an Acrobat, a CDOM fluorometer, a Video Ray ROV, and a CO2 sensor in addition to the already installed CTD Rosette with O2 sensor and beam transmissometer. During Leg 2, CTD stations were plotted to cover the area surrounding the wreck site and at various water depths to map the subsurface water column structure and chemistry as baseline values for future investigations and especially to look for submerged oil and/or gas hydrates. Early in the water column sampling, a subsurface feature was discovered at 1200 to 1400 m depth. This layer was detected by three independent sensors, CDOM (colored dissolved organic matter) fluorometer, beam transmissometer, and dissolved oxygen sensor. All three instruments responded in unison with greater fluorescence and beam attenuation and decreased O2 concentration. These signals were first observed at a station 5 miles from the accident site. Second and third station measurements at 2.5 miles, and at 1.25 miles from the spill site, showed the same signal but with significantly greater magnitude. Following this discovery, the sampling plan for the remaining days of the cruise was changed to map the newly discovered feature. This paper will discuss our data acquired during this cruise aboard the RV Pelican and its original discovery of the deep oil plumes from the Deepwater Horizon well.

FT-IR Study Reveals Intrinsically Disordered Nature of Heat Shock Protein 90

NASA Astrophysics Data System (ADS)

Xie, Aihua; Neto, David; Balch, Maurie; Hendriks, Johnny; Causey, Oliver; Deng, Junpeng; Matts, Robert

Heat shock protein 90 (Hsp90) is a highly conserved chaperone protein that enables the proper folding of a large number of structurally diverse proteins (a.k.a., clients) in the crowded cytosolic environment and plays a key role in regulating the heat shock response. A long standing open question is how Hsp90 accommodates the structural diversity of a large cohort of client proteins? We report ATR FTIR study on structural properties of Hsp90 C-terminal domain (CTD) and their temperature dependences. Effects of temperature on Hsp90 structure are dissected into the C-terminal domain (CTD) and the N-terminal/middle domain (NTMD). One of our major findings reveals that within a narrow temperature window across the physiological temperatures (35 to 45 C), Hsp90CTD exhibits significant increases in protein aggregation and increases in unordered structures. Despite the intrinsically disordered nature of Hsp90CTD, it retains a protected hydrophobic core at 40 C. Implications of these results will be discussed in the light of the structural dynamics and client diversity of Hsp90. AX is grateful for Grant supports from OCAST HR10-078 and NSF MRI DBI1338097.

Activation and modulation of human α4β2 nicotinic acetylcholine receptors by the neonicotinoids clothianidin and imidacloprid

PubMed Central

Li, Ping; Ann, Jason; Akk, Gustav

2013-01-01

Neonicotinoids are synthetic, nicotine-derived insecticides used for agricultural and household pest control. While highly effective at activating insect nicotinic receptors, many neonicotinoids are also capable of directly activating and/or modulating the activation of vertebrate nicotinic receptors. In this study, we have investigated the actions of the neonicotinoids clothianidin (CTD) and imidacloprid (IMI) on human neuronal α4β2 nicotinic acetylcholine receptors. The data demonstrate that the compounds are weak agonists of the human receptors with relative peak currents of 1–4 % of the response to 1 mM acetylcholine (ACh). Coapplication of IMI strongly inhibited currents elicited by ACh. From Schild plot analysis, we estimate that the affinity of IMI to the human α4β2 receptor is 18 µM. The application of low concentrations of CTD potentiated responses to low concentrations of ACh, suggesting that receptors occupied by one ACh and one CTD molecule have a higher gating efficacy than receptors with one ACh bound. Interestingly, subunit stoichiometry affected inhibition by CTD, with (α4)2(β2)3 receptors significantly more strongly inhibited than the (α4)3(β2)2 receptors. PMID:21538459

Interstitial lung disease in systemic autoimmune rheumatic diseases: a comprehensive review.

PubMed

Atzeni, Fabiola; Gerardi, Maria Chiara; Barilaro, Giuseppe; Masala, Ignazio Francesco; Benucci, Maurizio; Sarzi-Puttini, Piercarlo

2018-01-01

Interstitial lung diseases (ILDs) are among the most serious complications associated with systemic rheumatic diseases, and lead to significant morbidity and mortality; they may also be the first manifestation of connective tissue diseases (CTDs). The aim of this narrative review is to summarise the data concerning the pathogenesis of CTD/ILD and its distinguishing features in different rheumatic diseseas. Areas covered: The pathogenesis, clinical aspects and treatment of ILD associated with rheumatic systemic diseases and CTDs were reviewed by searching the PubMed, Medline, and Cochrane Library databases for papers published between 1995 and February 2017 using combinations of words or terms. Articles not written in English were excluded. Expert commentary: The management of CTD-ILD is challenging because of the lack of robust data regarding the treatments used, the heterogeneity of the diseases themselves, and the scarcity of well-defined outcome measures. Treatment decisions are often made clinically on the basis of functional, radiographic progression, and exacerbating factors such as age and the burden of comorbidities. Given the complexities of diagnosis and the paucity of treatment trials, the management of CTD patients with ILD requires multidisciplinary collaboration between rheumatologists and pulmonologists in CTD-ILD clinics.

Analysis of costs to dispense prescriptions in independently owned, closed-door long-term care pharmacies.

PubMed

Carroll, Norman V; Rupp, Michael T; Holdford, David A

2014-03-01

The need for accurate calculation of long-term care (LTC) pharmacies' costs to dispense (CTD) has become more important as payers have moved toward reimbursement models based on pharmacies' actual acquisition cost for drug products and the Centers for Medicare Medicaid Services (CMS) has implemented requirements that LTC pharmacies must dispense prescriptions for certain branded drugs in 14-day-or-less quantities. To (a) calculate the average cost that the typical independently owned, closed-door LTC pharmacy currently incurs to dispense and deliver a prescription to the resident of a client LTC facility and (b) estimate how CMS-mandated changes to a 14-day-or-less dispensing cycle would affect the typical LTC pharmacy's average CTD. The data requirements and measurement model were developed by academic researchers in consultation with an industry advisory committee of independent LTC pharmacy owners. A survey instrument was constructed to collect financial and operating data required to calculate the CTD. Surveys were distributed via 3 dissemination channels to approximately 1,000 independently owned, closed-door LTC pharmacies. The National Community Pharmacists Association mailed surveys to their LTC members; 3 major national wholesalers distributed surveys to their LTC customers through their newsletters; and 3 LTC group purchasing organizations distributed the surveys to their members through emails, newsletters, mailings, and/or regional meetings. Each pharmacy's CTD was calculated by dividing total LTC dispensing-related 
costs by the total number of prescriptions dispensed. Dispensing-related costs included costs incurred to physically dispense and deliver prescriptions (e.g., dispensing pharmacists' and technicians' salaries and costs of medication containers) and costs incurred to support the dispensing function (e.g., salaries of delivery and medical records personnel). A model based on dispensing-related fixed, variable, and semivariable costs was developed to examine the impact of shorter dispensing cycles on LTC pharmacies' CTD. A prescription volume increase of 19% was assumed based on converting only solid oral branded drugs to short-cycle dispensing. A diverse sample of 64 closed-door LTC pharmacies returned usable surveys. Sales from dispensing to LTC facilities accounted for more than 98% of total sales. Respondents indicated that they currently dispensed 23% of total doses in 14-day-or-less cycles and 76% in 28-31 day cycles. Most pharmacies used automated medication packaging technology, heat and cold package sealers, bar code systems, sterile compounding hoods, LTC printers or labelers, and electronic prescribing. The median CTD was $13.54 with an interquartile range (25th to 75th percentiles) of $10.51 to $17.66. More than half of dispensing-related costs were from personnel expense, of which pharmacists and managers accounted for more than 40%. The results of the fixed and variable cost modeling suggested that converting solid oral brand-name drugs from 30-day to 14-day dispensing cycles would lower the median per prescription CTD to between $11.63 and $12.54, depending on the assumptions made about the effects of semivariable costs. However, this decrease in per prescription dispensing cost is dwarfed by an increase in total dispensing cost incurred by pharmacies that results from doubling the monthly volume of short-cycle prescriptions that must be dispensed. The result is that the typical LTC pharmacy in our sample incurred a CTD of $13.54 if the medication is dispensed in a 30-day cycle or $23.26 if the medication is dispensed in two 14-day cycles (at a cost of $11.63 for each cycle dispensed). Our results indicated a median CTD of $13.54 for the typical independently owned, closed-door LTC pharmacy. Moving to a shorter cycle would reduce pharmacies' average per-prescription CTD but would increase the number of prescriptions dispensed per month. Our results indicated that transitioning solid oral branded products to 14-day cycles would reduce the median CTD to a minimum of $11.63 but would increase total dispensing costs because each sold oral branded prescription would require twice the number of monthly dispensing events.

The Changing Microbial Community Along the Orca Basin Pycnocline

NASA Astrophysics Data System (ADS)

Hyde, A.; Nigro, L. M.; Montoya, J. P.; Joye, S. B.; Teske, A.

2016-02-01

Orca Basin in the Gulf of Mexico is the largest seafloor brine basin in the world, with a brine depth up to 220 m and an areal extent of 123 km2. Within the chemocline and pycnocline of Orca Basin, salinity, temperature, oxygen concentration, porewater chemistry, and microbial community composition change within approx. 100 meters, from fully oxic and marine saline deepwater conditions at 2150 m to anoxic hypersaline brine at 2250 m depth. Previous surveys of Orca Basin have detected distinct peaks of metal-cycling bacteria, and of archaeal lipids in the Orca Basin chemocline. The steep pycnocline slows down the sinking speed and therefore concentrates organic matter and microbial populations from the water column; it also allows in-situ growth of microbial populations that can take advantage of coexisting electron donors and acceptors. To survey the microbial community structure and stratification in Orca Basin, we performed a high-throughput bacterial 16S rRNA gene sequencing of filter samples from the Orca Basin deep water, chemocline and brine, collected in April 2014 on RV Atlantis. Widely spaced 50 m sample intervals from 1800 to 2350 m depth were complemented with fine-scale sampling every ten meters between 2150 and 2250 m depth, centered on the pycno- and chemocline as evident from CTD data, and with additional samples taken at 2125, 2275, and 2375 m depth. While we expect abundant and diverse chemosynthetic interface bacteria and halophiles, we are also exploring the possibility that the Orca Basin pycnocline preserves and amplifies microbial hydrocarbon signatures in the Gulf of Mexico, as in a long-term particle trap.

Long non-coding RNA-CTD-2108O9.1 represses breast cancer metastasis by influencing leukemia inhibitory factor receptor.

PubMed

Wang, Mozhi; Wang, Mengshen; Wang, Zhenning; Yu, Xueting; Song, Yongxi; Wang, Chong; Xu, Yujie; Wei, Fengheng; Zhao, Yi; Xu, Yingying

2018-06-01

Breast cancer (BC) is an aggressive malignant disease in women worldwide with a high tendency to metastasize. However, important biomarkers for BC metastasis remain largely undefined. In the present study, we identified that long non-coding RNA-CTD-2108O9.1 is downregulated in BC tissues and cells and acts as a metastatic inhibitor of BC. Mechanistic investigation determined that lncRNA-CTD-2108O9.1 represses metastasis by targeting leukemia inhibitory factor receptor (LIFR), which is designated as a metastasis suppressor in BC. Our study characterizes a significant tumor suppressor active in BC metastasis repression through the known metastasis inhibitor LIFR. © 2018 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

The C-terminal domain of Nrf1 negatively regulates the full-length CNC-bZIP factor and its shorter isoform LCR-F1/Nrf1β; both are also inhibited by the small dominant-negative Nrf1γ/δ isoforms that down-regulate ARE-battery gene expression.

PubMed

Zhang, Yiguo; Qiu, Lu; Li, Shaojun; Xiang, Yuancai; Chen, Jiayu; Ren, Yonggang

2014-01-01

The C-terminal domain (CTD, aa 686-741) of nuclear factor-erythroid 2 p45-related factor 1 (Nrf1) shares 53% amino acid sequence identity with the equivalent Neh3 domain of Nrf2, a homologous transcription factor. The Neh3 positively regulates Nrf2, but whether the Neh3-like (Neh3L) CTD of Nrf1 has a similar role in regulating Nrf1-target gene expression is unknown. Herein, we report that CTD negatively regulates the full-length Nrf1 (i.e. 120-kDa glycoprotein and 95-kDa deglycoprotein) and its shorter isoform LCR-F1/Nrf1β (55-kDa). Attachment of its CTD-adjoining 112-aa to the C-terminus of Nrf2 yields the chimaeric Nrf2-C112Nrf1 factor with a markedly decreased activity. Live-cell imaging of GFP-CTD reveals that the extra-nuclear portion of the fusion protein is allowed to associate with the endoplasmic reticulum (ER) membrane through the amphipathic Neh3L region of Nrf1 and its basic c-tail. Thus removal of either the entire CTD or the essential Neh3L portion within CTD from Nrf1, LCR-F1/Nrf1β and Nrf2-C112Nrf1, results in an increase in their transcriptional ability to regulate antioxidant response element (ARE)-driven reporter genes. Further examinations unravel that two smaller isoforms, 36-kDa Nrf1γ and 25-kDa Nrf1δ, act as dominant-negative inhibitors to compete against Nrf1, LCR-F1/Nrf1β and Nrf2. Relative to Nrf1, LCR-F1/Nrf1β is a weak activator, that is positively regulated by its Asn/Ser/Thr-rich (NST) domain and acidic domain 2 (AD2). Like AD1 of Nrf1, both AD2 and NST domain of LCR-F1/Nrf1β fused within two different chimaeric contexts to yield Gal4D:Nrf1β607 and Nrf1β:C270Nrf2, positively regulate their transactivation activity of cognate Gal4- and Nrf2-target reporter genes. More importantly, differential expression of endogenous ARE-battery genes is attributable to up-regulation by Nrf1 and LCR-F1/Nrf1β and down-regulation by Nrf1γ and Nrf1δ.

Initial Psychometric Properties of a Brief Parent-Report Instrument for Assessing Tic Severity in Children with Chronic Tic Disorders

ERIC Educational Resources Information Center

Chang, Susanna; Himle, Michael B.; Tucker, Benjamin T. P.; Woods, Douglas W.; Piacentini, John

2009-01-01

This article describes the development and initial psychometric properties of the Parent Tic Questionnaire (PTQ)--a new measure assessing the number, frequency, and intensity of motor and vocal tics in children and adolescents with Chronic Tic Disorder (CTD). Parents of 40 children with a CTD completed the PTQ as part of a larger assessment…

The Effects of Embedded Skill Instruction on the Acquisition of Target and Nontarget Skills in Preschoolers with Developmental Delays.

ERIC Educational Resources Information Center

Daugherty, Stefanie; Grisham-Brown, Jennifer; Hemmeter, Mary Louise

2001-01-01

In the current study, a constant time delay (CTD) procedure was embedded in classroom activities and routines to teach counting to three preschool children with speech and language delays. CTD was effective in teaching numbers to all three children. One child out of two also was able to acquire non-target information. (Contains references.) (CR)

The risk of cancer in patients with connective tissue diseases but without dermatomyositis or polymyositis: A multicenter cohort study conducted over 15 years in China.

PubMed

Xu, Wei; Guo, Huan; Liu, Zhi; Chen, Chen; Lei, Cong-Cong

2016-09-01

To investigate the relative risk of cancer in Chinese patients with connective tissue diseases (CTD) associated with and without dermatomyositis or polymyositis. A retrospective, multicenter cohort study investigated 32,380 CTD patients (2334 diagnosed with dermatomyositis or polymyositis) without a history of malignancies treated from January 1, 1997, to December 31, 2011. Standardized incidence ratios (SIR) of cancers determined the incidence of malignancies during follow-up. The data was compared with the cancer morbidity of the general population from the Chinese Cancer Registry Annual Report of National Central Cancer Registry. A total of 113 patients (348.98 per 100,000) developed cancer during follow-up, 75 (249.62 per 100,000) were patients with CTD without dermatomyositis or polymyositis. The risk of cancer among patients with CTD was increased (SIR=1.45, 95% confidence interval [CI] 1.22-1.71), and this risk increased with age (<40 years: SIR=1.00 [95%CI 0.45-2.21]; 41-60 years: SIR=1.53 [95%CI 1.17-2.00]; and >60 years SIR=2.34 (95%CI 0.93-2.77]) and the time of follow-up (<1year: SIR=1.22 [95%CI 0.88-1.70]; 1-5 years: SIR=1.14 [95%CI 0.79-1.65]; and 6-10 years SIR=1.70 [95%CI 1.34-2.85]), but was similar between genders (male SIR=1.60 [95%CI 1.10-2.31] and female SIR=1.25 [95%CI 1.01-1.55]). The cancer risk among CTD patients without dermatomyositis or polymyositis was not affected (SIR=0.93, 95%CI 0.75-1.16), regardless of gender, age, or follow-up. The cancer risk for patients with CTD without dermatomyositis or polymyositis was not increased or decreased, but it was increased when patients with dermatomyositis or polymyositis were included. Copyright © 2016 European Federation of Immunological Societies. Published by Elsevier B.V. All rights reserved.

Web services-based text-mining demonstrates broad impacts for interoperability and process simplification.

PubMed

Wiegers, Thomas C; Davis, Allan Peter; Mattingly, Carolyn J

2014-01-01

The Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation tasks collectively represent a community-wide effort to evaluate a variety of text-mining and information extraction systems applied to the biological domain. The BioCreative IV Workshop included five independent subject areas, including Track 3, which focused on named-entity recognition (NER) for the Comparative Toxicogenomics Database (CTD; http://ctdbase.org). Previously, CTD had organized document ranking and NER-related tasks for the BioCreative Workshop 2012; a key finding of that effort was that interoperability and integration complexity were major impediments to the direct application of the systems to CTD's text-mining pipeline. This underscored a prevailing problem with software integration efforts. Major interoperability-related issues included lack of process modularity, operating system incompatibility, tool configuration complexity and lack of standardization of high-level inter-process communications. One approach to potentially mitigate interoperability and general integration issues is the use of Web services to abstract implementation details; rather than integrating NER tools directly, HTTP-based calls from CTD's asynchronous, batch-oriented text-mining pipeline could be made to remote NER Web services for recognition of specific biological terms using BioC (an emerging family of XML formats) for inter-process communications. To test this concept, participating groups developed Representational State Transfer /BioC-compliant Web services tailored to CTD's NER requirements. Participants were provided with a comprehensive set of training materials. CTD evaluated results obtained from the remote Web service-based URLs against a test data set of 510 manually curated scientific articles. Twelve groups participated in the challenge. Recall, precision, balanced F-scores and response times were calculated. Top balanced F-scores for gene, chemical and disease NER were 61, 74 and 51%, respectively. Response times ranged from fractions-of-a-second to over a minute per article. We present a description of the challenge and summary of results, demonstrating how curation groups can effectively use interoperable NER technologies to simplify text-mining pipeline implementation. Database URL: http://ctdbase.org/ © The Author(s) 2014. Published by Oxford University Press.

Web services-based text-mining demonstrates broad impacts for interoperability and process simplification

PubMed Central

Wiegers, Thomas C.; Davis, Allan Peter; Mattingly, Carolyn J.

2014-01-01

The Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation tasks collectively represent a community-wide effort to evaluate a variety of text-mining and information extraction systems applied to the biological domain. The BioCreative IV Workshop included five independent subject areas, including Track 3, which focused on named-entity recognition (NER) for the Comparative Toxicogenomics Database (CTD; http://ctdbase.org). Previously, CTD had organized document ranking and NER-related tasks for the BioCreative Workshop 2012; a key finding of that effort was that interoperability and integration complexity were major impediments to the direct application of the systems to CTD's text-mining pipeline. This underscored a prevailing problem with software integration efforts. Major interoperability-related issues included lack of process modularity, operating system incompatibility, tool configuration complexity and lack of standardization of high-level inter-process communications. One approach to potentially mitigate interoperability and general integration issues is the use of Web services to abstract implementation details; rather than integrating NER tools directly, HTTP-based calls from CTD's asynchronous, batch-oriented text-mining pipeline could be made to remote NER Web services for recognition of specific biological terms using BioC (an emerging family of XML formats) for inter-process communications. To test this concept, participating groups developed Representational State Transfer /BioC-compliant Web services tailored to CTD's NER requirements. Participants were provided with a comprehensive set of training materials. CTD evaluated results obtained from the remote Web service-based URLs against a test data set of 510 manually curated scientific articles. Twelve groups participated in the challenge. Recall, precision, balanced F-scores and response times were calculated. Top balanced F-scores for gene, chemical and disease NER were 61, 74 and 51%, respectively. Response times ranged from fractions-of-a-second to over a minute per article. We present a description of the challenge and summary of results, demonstrating how curation groups can effectively use interoperable NER technologies to simplify text-mining pipeline implementation. Database URL: http://ctdbase.org/ PMID:24919658

Particulate organic matter fluxes and hydrodynamics at the Tisler cold-water coral reef

NASA Astrophysics Data System (ADS)

Wagner, Hannes; Purser, Autun; Thomsen, Laurenz; Jesus, Carlos César; Lundälv, Tomas

2011-03-01

Cold-water coral reefs occur in many regions of the world's oceans. Fundamental questions regarding their functioning remain unanswered. These include the biogeochemical influence of reefs on their environment ("reef effects") and the influence of hydrodynamic processes on reef nutrition. In a succession of field campaigns in 2007 and 2008, these questions were addressed at the Tisler cold-water coral reef, which is centered on a sill peak in the Norwegian Skagerrak. A variety of methodological approaches were used. These consisted of the collection of CTD and chlorophyll profiles, current measurements, sampling of particulate organic matter (POM) in the benthic boundary layer (BBL) across the reef with subsequent chemical analyses, and the chemical analysis of freshly released Lophelia pertusa mucus. CTD and chlorophyll profiles indicated that downstream of the sill crest, downwelling delivered warmer, fresher and chlorophyll richer water masses down to the BBL. Both sides of the reef received downwelling nutrition delivery, as flow direction over the reef reversed periodically. Several chemical composition indicators revealed that suspended POM was significantly fresher on the downstream side of the reef than on the upstream side. L. pertusa mucus from the Tisler Reef was labile in composition, as indicated by a low C/N ratio and a high amino acid degradation index (DI) value. Particulate organic carbon (POC) content in the BBL was significantly depleted across the reef. Lateral depositional fluxes were calculated to be 18-1485 mg POC m -2 d -1, with a mean of 459 mg POC m -2 d -1. We propose that the combination of fresh, downwelling POM with mucus released from the reef was the cause of the greater lability of the downstream POM. Our data on POC depletion across the reef suggest that cold-water coral reefs could play an important role in carbon cycling along continental margins.

Deep inflow into the Mozambique Basin

NASA Astrophysics Data System (ADS)

Read, J. F.; Pollard, R. T.

1999-02-01

More than 200 conductivity-temperature-depth (CTD) stations were worked around the Southwest Indian Ridge and Del Caño Rise as part of the World Ocean Circulation Experiment. A selection of these data provides information about the inflow of bottom water into the Mozambique Basin. The basin is closed below 3000 m, yet the inflow is significantly large, of order 1 Sv (1 Sv = 106 m3 s-1). Estimates of the basin-scale upwelling at 4000 m suggest that the vertical velocity is also large, 10 × 10-5 cm s-1 or more, an order of magnitude greater than global ocean estimates. Examination of the characteristics of the bottom water in the Mozambique and Agulhas Basins and the Prince Edward Fracture Zone shows that bottom water enters the Mozambique Basin from the Agulhas Basin and also directly from the Enderby Basin. Most of the transport enters the Mozambique Basin via the Agulhas Basin, where two regions of northward flow below 4000 m are found. The major flow, on the eastern flank of the Mozambique Ridge, is through and above the deep, extending (5900 m) trench that connects the Agulhas and Mozambique Basins. The second, weaker flow enters the Transkei Basin along the deep eastern flank of the Agulhas Plateau, then turning east into the Mozambique Basin. The only source of bottom water to the Agulhas Basin is the Enderby Basin, but a more direct route between the Enderby and Mozambique Basins exists via the Prince Edward fracture, which extends deeper than 4000 m throughout its length and links the two basins directly across the Southwest Indian Ridge. Full depth CTD stations trace the changing characteristics of the deep and bottom water in the fracture, and moored current meter data show the strength and persistence of the throughflow. Strong mixing with the overlying deep water elevates the salt content of the bottom water by comparison with the other water in the Mozambique Basin. Thus two distinct bottom waters of the Mozambique Basin originate in the same place (the Enderby Basin), and their different characteristics are solely a function of the routes they have taken and the processes encountered along the different pathways.

Collaborating with the local community of Kullorsuaq, Greenland to obtain high-quality hydrographic measurements near Alison Glacier

NASA Astrophysics Data System (ADS)

Porter, D. F.; Turrin, M.; Tinto, K. J.; Giulivi, C. F.; Cochran, J. R.; Bell, R. E.

2014-12-01

Warming ocean waters around Greenland have been implicated, along with warmer air temperatures, in the rapid increase of melt of the tidewater glaciers that drain the ice sheet. Most available regional oceanographic measurements have been collected during the summer seasons and are concentrated near the largest and most accessible glaciers. In order to gain a more comprehensive picture of the changing environment around the entirety of Greenland, more fjords, especially in the north, must be sampled. In July 2014, we travelled to Kullorsuaq in Northwest Greenland in order to foster a partnership with the local community to obtain new hydrographic data from CTD casts near Alison Glacier (74.6N, 57W). The terminus of this glacier abruptly retreated 10 km between 2000 and 2006. Although adequate observations from that time period are unavailable, our recently collected temperature and salinity data suggests that the deep water near Alison is similar to the waters further south, where near-synchronous ocean warming and glacial acceleration has been documented. Over the course of two sampling days, a hand-operated winch from a small boat was used to make standard CTD casts in front of Alison Glacier. We find evidence of glacial and mélange melt and the signature of both Polar and Atlantic Water masses at depth. Along-fjord casts illustrate how the ocean waters are modified as they circulate in and out of the fjord and the interaction of this water with the melting glacial front. At 500m depths, ocean temperatures are about 3°C above the in-situ freezing point of seawater, suggesting a possible influence of warm ocean waters on the mass loss of Alison Glacier. Using NASA Operation IceBridge and satellite altimetry data, we relate our new hydrographic data to the observed recent changes in Alison Glacier. An additional important result is that this short field campaign uncovered the possibility of working with local Greenlandic communities to aid scientists in both environmental monitoring and scientific discovery. Plans are underway to collaborate with the same and other communities in Greenland to take additional oceanographic measurements throughout the year.

Insights Into Ice-Ocean Interactions on Earth and Europa

NASA Astrophysics Data System (ADS)

Lawrence, J.; Schmidt, B. E.; Winslow, L.; Doran, P. T.; Kim, S.; Walker, C. C.; Buffo, J.; Skidmore, M. L.; Soderlund, K. M.; Blankenship, D. D.; Bramall, N. E.; Johnson, A.; Rack, F. R.; Stone, W.; Kimball, P.; Clark, E.

2016-12-01

Europa and Earth appear to be drastically different worlds, yet below their icy crusts the two likely share similar oceanic conditions including temperatures, pressures (relatively), and salinity. Earth's ice shelves provide an important analog for the physiochemical, and potentially microbial, characteristics of icy worlds. NASA's ASTEP program funded Sub-Ice Marine and PLanetary-analog Ecosystems (SIMPLE) to help address the fundamental processes occurring at ice ocean interfaces, the extent and limitations of life in sub-ice environments, and how environmental properties and biological communities interact. The relationships between currents, temperature, and salinity with physical processes such as melt, freeze, and marine ice accretion at the basal surfaces of ice shelves influence habitability yet are poorly understood even on Earth. Resultant processes such as the inclusion of ocean-derived material in ice shelves and the transport of biotics from the interface towards the surface via ablation, convection, and diapirism also have important astrobiological implications for Europa.Here, we present results from CTD and imaging data gathered at multiple locations beneath the McMurdo Ice Shelf (MIS) to highlight how the ice and ocean interact in a Europan analog environment. Over the course of three years, the SIMPLE team observed heterogeneity in the water column and basal ice beneath the MIS. During the recent 2015 field season we deployed ARTEMIS, an AUV capable of characterizing the interface over multiple kilometer missions, and conducted daily CTD casts to 480 m (bottom depth 529 m) in November adjacent to the terminus of the MIS to capture temporal variation in the water column. These casts show the presence of transient water masses related to the tidal period, each containing a single or double temperature minimum (down to -1.97 °C from -1.93 °C) between 60 to 150 m depth. Further comparisons between years and sampling locations demonstrate the homogeneity of the subshelf environment even on the scale of tens of kilometers. The technologies supported by SIMPLE are also supporting the ice penetrating radar on the upcoming Europa Flagship mission, and will hopefully inform future ocean world exploration.

Primary hydrothermal input above nonbuoyant plume level in the water column.

NASA Astrophysics Data System (ADS)

Nakamura, K.

2008-12-01

Accumulating in-situ Eh measurements of seawater by CTD hydrothermal plume chasing above ridges in various oceans suggest that some ill-diluted reduced water can be eventually observed above nonbuoyant plume level, which indicate locations of buoyant rising plume penetration through spread nonbuoyant plume. Such location can even be intentionally detectable by successive three to four orthogonal CTD tow-yo operations. See an example in the South Atlantic (http://www.divediscover.whoi.edu/expedition12/daily/080109.html). Large/rapid voltage drops recorded by in- situ Eh (ORP) electrodes on moving platform like CTD (non-equilibrated measurement) occur when electrodes pass from oxygen-controlled to sulfide-controlled redox condition. Assuming a common chemical compositions of 350 deg C hydrothermal fluid source, the calculated redox potential of mixture of hydrothermal fluid and ambient seawater shows a sharp discontinuity around the dilution factor of 130 (aquatic chemistry textbooks of Morel(1983) p.345, (1993) p.460). In popular turbulent plume models based on Morton, Taylor and Turner (1956, point source and homogeneous dilution by ambient seawater entrainment along by an amount proportional to the vertical velocity in the plume), the dilution factors at the level of zero rising momentum are calculated as 5500 to 10,000 (ex., McDuff, 1995). Evidence of redox anomalies above nonbuoyant plume level contradicts momentum overshoot by popular turbulent plume models and prefers a plume cap overshoot in starting plume (Turner, 1973) or heterogeneous dilution. Turner's starting plume were thought to be generated by on and off of buoyant fluid input. The plume cap is assumed to have vortex structure like thermal and resistant to dilution. In the ridge environment with ocean tide it is likely generated spatially and temporary by semidiurnal to diurnal bottom current direction change. Some recent AUV profiles cross-cutting rising buoyant plume will be also presented to discuss on internal structure of rising plume. The primary hydrothermal input above nonbuoyant plume level is important for vertical chemical and biological transport in the water column as well as exploration strategy to locate vents on the seafloor.

Direct band gap measurement of Cu(In,Ga)(Se,S){sub 2} thin films using high-resolution reflection electron energy loss spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heo, Sung; College of Information and Communication Engineering, Sungkyunkwan University, Cheoncheon-dong 300, Jangan-gu, Suwon 440-746; Lee, Hyung-Ik

2015-06-29

To investigate the band gap profile of Cu(In{sub 1−x},Ga{sub x})(Se{sub 1−y}S{sub y}){sub 2} of various compositions, we measured the band gap profile directly as a function of in-depth using high-resolution reflection energy loss spectroscopy (HR-REELS), which was compared with the band gap profile calculated based on the auger depth profile. The band gap profile is a double-graded band gap as a function of in-depth. The calculated band gap obtained from the auger depth profile seems to be larger than that by HR-REELS. Calculated band gaps are to measure the average band gap of the spatially different varying compositions with respectmore » to considering its void fraction. But, the results obtained using HR-REELS are to be affected by the low band gap (i.e., out of void) rather than large one (i.e., near void). Our findings suggest an analytical method to directly determine the band gap profile as function of in-depth.« less

Azathioprine response in patients with fibrotic connective tissue disease-associated interstitial lung disease.

PubMed

Oldham, Justin M; Lee, Cathryn; Valenzi, Eleanor; Witt, Leah J; Adegunsoye, Ayodeji; Hsu, Scully; Chen, Lena; Montner, Steven; Chung, Jonathan H; Noth, Imre; Vij, Rekha; Strek, Mary E

2016-12-01

Azathioprine is a commonly prescribed therapy for connective tissue disease-associated interstitial lung disease (CTD-ILD). Combination therapy that included azathioprine was recently shown to increase the risk of death and hospitalization in patients with idiopathic pulmonary fibrosis. Whether azathioprine increases the risk of adverse outcomes in patients with fibrotic CTD-ILD, including those with CTD-associated usual interstitial pneumonia (UIP), remains unknown. A retrospective cohort analysis was performed to determine the combined incidence rate of death, transplant and respiratory hospitalization associated with azathioprine exposure. A fibrotic CTD-ILD cohort treated with mycophenolate mofetil served as a comparator group. Incidence rates were compared with an incidence rate ratio (IRR) generated by negative binomial regression. Longitudinal pulmonary function response was then assessed using mixed effects linear regression models. Fifty-four patients were treated with azathioprine and forty-three with mycophenolate. Medication discontinuation due to non-respiratory side effects occurred in 27% and 5% of the azathioprine and mycophenolate cohorts, respectively. The combined incidence rate of adverse outcomes was 0.015 and 0.013 for azathioprine and mycophenolate, respectively (IRR 1.23; 95% CI 0.49-3.12; p = 0.66). Similar incidence rates were observed among those with CTD-UIP (IRR 0.83; 95% CI 0.21-3.31; p = 0.79). Both groups demonstrated pulmonary function stability over time, with the azathioprine group demonstrating a marginal improvement. A significant minority of patients could not tolerate azathioprine due to non-respiratory side effects. Of those who did tolerate azathioprine, a similar incidence of adverse outcomes was observed as those treated with mycophenolate. Both therapies were associated with stability in pulmonary function. Copyright © 2016 Elsevier Ltd. All rights reserved.

A CTD-Pfizer collaboration: manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions.

PubMed

Davis, Allan Peter; Wiegers, Thomas C; Roberts, Phoebe M; King, Benjamin L; Lay, Jean M; Lennon-Hopkins, Kelley; Sciaky, Daniela; Johnson, Robin; Keating, Heather; Greene, Nigel; Hernandez, Robert; McConnell, Kevin J; Enayetallah, Ahmed E; Mattingly, Carolyn J

2013-01-01

Improving the prediction of chemical toxicity is a goal common to both environmental health research and pharmaceutical drug development. To improve safety detection assays, it is critical to have a reference set of molecules with well-defined toxicity annotations for training and validation purposes. Here, we describe a collaboration between safety researchers at Pfizer and the research team at the Comparative Toxicogenomics Database (CTD) to text mine and manually review a collection of 88,629 articles relating over 1,200 pharmaceutical drugs to their potential involvement in cardiovascular, neurological, renal and hepatic toxicity. In 1 year, CTD biocurators curated 254,173 toxicogenomic interactions (152,173 chemical-disease, 58,572 chemical-gene, 5,345 gene-disease and 38,083 phenotype interactions). All chemical-gene-disease interactions are fully integrated with public CTD, and phenotype interactions can be downloaded. We describe Pfizer's text-mining process to collate the articles, and CTD's curation strategy, performance metrics, enhanced data content and new module to curate phenotype information. As well, we show how data integration can connect phenotypes to diseases. This curation can be leveraged for information about toxic endpoints important to drug safety and help develop testable hypotheses for drug-disease events. The availability of these detailed, contextualized, high-quality annotations curated from seven decades' worth of the scientific literature should help facilitate new mechanistic screening assays for pharmaceutical compound survival. This unique partnership demonstrates the importance of resource sharing and collaboration between public and private entities and underscores the complementary needs of the environmental health science and pharmaceutical communities. Database URL: http://ctdbase.org/

Text Mining Effectively Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database

PubMed Central

Johnson, Robin J.; Lay, Jean M.; Lennon-Hopkins, Kelley; Saraceni-Richards, Cynthia; Sciaky, Daniela; Murphy, Cynthia Grondin; Mattingly, Carolyn J.

2013-01-01

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a public resource that curates interactions between environmental chemicals and gene products, and their relationships to diseases, as a means of understanding the effects of environmental chemicals on human health. CTD provides a triad of core information in the form of chemical-gene, chemical-disease, and gene-disease interactions that are manually curated from scientific articles. To increase the efficiency, productivity, and data coverage of manual curation, we have leveraged text mining to help rank and prioritize the triaged literature. Here, we describe our text-mining process that computes and assigns each article a document relevancy score (DRS), wherein a high DRS suggests that an article is more likely to be relevant for curation at CTD. We evaluated our process by first text mining a corpus of 14,904 articles triaged for seven heavy metals (cadmium, cobalt, copper, lead, manganese, mercury, and nickel). Based upon initial analysis, a representative subset corpus of 3,583 articles was then selected from the 14,094 articles and sent to five CTD biocurators for review. The resulting curation of these 3,583 articles was analyzed for a variety of parameters, including article relevancy, novel data content, interaction yield rate, mean average precision, and biological and toxicological interpretability. We show that for all measured parameters, the DRS is an effective indicator for scoring and improving the ranking of literature for the curation of chemical-gene-disease information at CTD. Here, we demonstrate how fully incorporating text mining-based DRS scoring into our curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency. PMID:23613709

Cryo-electron microscopy structures of the SARS-CoV spike glycoprotein reveal a prerequisite conformational state for receptor binding.

PubMed

Gui, Miao; Song, Wenfei; Zhou, Haixia; Xu, Jingwei; Chen, Silian; Xiang, Ye; Wang, Xinquan

2017-01-01

The global outbreak of SARS in 2002-2003 was caused by the infection of a new human coronavirus SARS-CoV. The infection of SARS-CoV is mediated mainly through the viral surface glycoproteins, which consist of S1 and S2 subunits and form trimer spikes on the envelope of the virions. Here we report the ectodomain structures of the SARS-CoV surface spike trimer in different conformational states determined by single-particle cryo-electron microscopy. The conformation 1 determined at 4.3 Å resolution is three-fold symmetric and has all the three receptor-binding C-terminal domain 1 (CTD1s) of the S1 subunits in "down" positions. The binding of the "down" CTD1s to the SARS-CoV receptor ACE2 is not possible due to steric clashes, suggesting that the conformation 1 represents a receptor-binding inactive state. Conformations 2-4 determined at 7.3, 5.7 and 6.8 Å resolutions are all asymmetric, in which one RBD rotates away from the "down" position by different angles to an "up" position. The "up" CTD1 exposes the receptor-binding site for ACE2 engagement, suggesting that the conformations 2-4 represent a receptor-binding active state. This conformational change is also required for the binding of SARS-CoV neutralizing antibodies targeting the CTD1. This phenomenon could be extended to other betacoronaviruses utilizing CTD1 of the S1 subunit for receptor binding, which provides new insights into the intermediate states of coronavirus pre-fusion spike trimer during infection.

Carboxyl-terminal Domain of Transient Receptor Potential Vanilloid 1 Contains Distinct Segments Differentially Involved in Capsaicin- and Heat-induced Desensitization*

PubMed Central

Joseph, John; Wang, Sen; Lee, Jongseok; Ro, Jin Y.; Chung, Man-Kyo

2013-01-01

Multiple Ca2+-dependent processes are involved in capsaicin-induced desensitization of transient receptor potential vanilloid 1 (TRPV1), but desensitization of TRPV1 by heat occurs even in the absence of extracellular Ca2+, although the mechanisms are unknown. In this study, we tested the hypothesis that capsaicin and heat desensitize TRPV1 through distinct mechanisms involving distinct structural segments of TRPV1. In HEK293 cells that heterologously express TRPV1, we found that heat-induced desensitization was not affected by the inclusion of intracellular ATP or alanine mutation of Lys155, both of which attenuate capsaicin-induced desensitization, suggesting that heat-induced desensitization occurs through mechanisms distinct from capsaicin-induced desensitization. To determine protein domains involved in heat-induced desensitization, we generated chimeric proteins between TRPV1 and TRPV3, a heat-gated channel lacking heat-induced desensitization. We found that TRPV1 with the carboxyl-terminal domain (CTD) of TRPV3 retained heat activation but was impaired in heat-induced desensitization. Further experiments using chimeric or deletion mutants within TRPV1 CTD indicated that the distal half of CTD regulates the activation and desensitization of TRPV1 in modality-specific manners. Within the distal CTD, we identified two segments that distinctly regulated capsaicin- and heat-induced desensitization. The results suggest that the activation and desensitization of TRPV1 by capsaicin and heat can be modulated differentially and disproportionally through different regions of TRPV1 CTD. Identifying the domains involved in thermal regulation of TRPV1 may facilitate the development of novel anti-hyperalgesic approaches aimed at attenuating activation and enhancing desensitization of TRPV1 by thermal stimuli. PMID:24174527

Forecast of drifter trajectories using a Rapid Environmental Assessment based on CTD observations

NASA Astrophysics Data System (ADS)

Sorgente, R.; Tedesco, C.; Pessini, F.; De Dominicis, M.; Gerin, R.; Olita, A.; Fazioli, L.; Di Maio, A.; Ribotti, A.

2016-11-01

A high resolution submesoscale resolving ocean model was implemented in a limited area north of Island of Elba where a maritime exercise, named Serious Game 1 (SG1), took place on May 2014 in the framework of the project MEDESS-4MS (Mediterranean Decision Support System for Marine Safety). During the exercise, CTD data have been collected responding to the necessity of a Rapid Environmental Assessment, i.e. to a rapid evaluation of the marine conditions able to provide sensible information for initialisation of modelling tools, in the scenario of possible maritime accidents. The aim of this paper is to evaluate the impact of such mesoscale-resolving CTD observations on short-term forecasts of the surface currents, within the framework of possible oil-spill related emergencies. For this reason, modelling outputs were compared with Lagrangian observations at sea: the high resolution modelled currents, together with the ones of the coarser sub-regional model WMED, are used to force the MEDSLIK-II oil-spill model to simulate drifter trajectories. Both ocean models have been assessed by comparing the prognostic scalar and vector fields as an independent CTD data set and with real drifter trajectories acquired during SG1. The diagnosed and prognosed circulation reveals that the area was characterised by water masses of Atlantic origin influenced by small mesoscale cyclonic and anti-cyclonic eddies, which govern the spatial and temporal evolution of the drifter trajectories and of the water masses distribution. The assimilation of CTD data into the initial conditions of the high resolution model highly improves the accuracy of the short-term forecast in terms of location and structure of the thermocline and positively influence the ability of the model in reproducing the observed paths of the surface drifters.

The role of nailfold capillaroscopy in interstitial lung diseases - can it differentiate idiopathic cases from collagen tissue disease associated interstitial lung diseases?

PubMed

Çakmakçı Karadoğan, Dilek; Balkarlı, Ayşe; Önal, Özgür; Altınışık, Göksel; Çobankara, Veli

2015-01-01

Nailfold capillaroscopy (NFC) is a non-invasive diagnostic test that is mostly used for early diagnosis of collagen tissue diseases (CTDs). We aimed to evaluate whether NFC findings could be a clue for discriminating idiopathic interstitial lung diseases (ILD) from CTD associated ILDs (CTD-ILD). Additionally it was aimed to determine whether NFC could be helpful in discriminating usual interstitial pneumonia (UIP) pattern from non-specific interstitial pneumonia (NSIP) pattern. We grouped patients into three main groups: 15 CTD-ILD, 18 idiopathic ILD, and 17 patients in the control group. The CTD-ILD group was split into two subgroups: 8 patients with Sjögren's syndrome (SJS)-associated ILD and 7 with rheumatoid arthritis (RA)-associated ILD. The idiopathic-ILD group consisted of 10 idiopathic NSIP and 8 IPF patients. The control group consisted of 10 SJS and 7 RA patients without lung disease. None of the patients were on acute exacerbation at the time of examination, and none had Reynaud's phenomenon. Mean capillary density was significantly reduced only in the CTD-ILD group as compared to the control group (p= 0.006). In subgroup analysis, it was determined that RA-ILD, IPF, and SJS-ILD subgroups had more severe capillaroscopic abnormalities. Mean capillary density in patients with the UIP pattern was reduced compared to patients with the NSIP pattern and those in the control group; p values were 0.008 and < 0.001, respectively. This study is to be the first describing and comparing the nailfold capillaroscopic findings of patients with NSIP and UIP patterns. NFC findings can be helpful in discriminating UIP patterns from NSIP patterns. But to show its role in differentiating idiopathic disease, more studies with more patients are needed.

Compositional depth profiles of the type 316 stainless steel undergone the corrosion in liquid lithium using laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Li, Ying; Ke, Chuan; Liu, Xiang; Gou, Fujun; Duan, Xuru; Zhao, Yong

2017-12-01

Liquid metal lithium cause severe corrosion on the surface of metal structure material that used in the blanket and first wall of fusion device. Fast and accurate compositional depth profile measurement for the boundary layer of the corroded specimen will reveal the clues for the understanding and evaluation of the liquid lithium corrosion process as well as the involved corrosion mechanism. In this work, the feasibility of laser-induced breakdown spectroscopy for the compositional depth profile analysis of type 316 stainless steel which was corroded by liquid lithium in certain conditions was demonstrated. High sensitivity of LIBS was revealed especially for the corrosion medium Li in addition to the matrix elements of Fe, Cr, Ni and Mn by the spectral analysis of the plasma emission. Compositional depth profile analysis for the concerned elements which related to corrosion was carried out on the surface of the corroded specimen. Based on the verified local thermodynamic equilibrium shot-by-shot along the depth profile, the matrix effect was evaluated as negligible by the extracted physical parameter of the plasmas generated by each laser pulse in the longitudinal depth profile. In addition, the emission line intensity ratios were introduced to further reduce the impact on the emission line intensity variations arise from the strong inhomogeneities on the corroded surface. Compositional depth profiles for the matrix elements of Fe, Cr, Ni, Mn and the corrosion medium Li were constructed with their measured relative emission line intensities. The distribution and correlations of the concerned elements in depth profile may indicate the clues to the complicated process of composition diffusion and mass transfer. The results obtained demonstrate the potentiality of LIBS as an effective technique to perform spectrochemical measurement in the research fields of liquid metal lithium corrosion.

Nitric oxide assisted C60 secondary ion mass spectrometry for molecular depth profiling of polyelectrolyte multilayers.

PubMed

Zappalà, G; Motta, V; Tuccitto, N; Vitale, S; Torrisi, A; Licciardello, A

2015-12-15

Secondary ion mass spectrometry (SIMS) with polyatomic primary ions provides a successful tool for molecular depth profiling of polymer systems, relevant in many technological applications. Widespread C60 sources, however, cause in some polymers extensive damage with loss of molecular information along depth. We study a method, based on the use of a radical scavenger, for inhibiting ion-beam-induced reactions causing sample damage. Layered polystyrene sulfonate and polyacrylic acid based polyelectrolyte films, behaving differently towards C60 beam-induced damage, were selected and prepared as model systems. They were depth profiled by means of time-of-flight (TOF)-SIMS in dual beam mode, using fullerene ions for sputtering. Nitric oxide was introduced into the analysis chamber as a radical scavenger. The effect of sample cooling combined with NO-dosing on the quality of depth profiles was explored. NO-dosing during C60-SIMS depth profiling of >1 micrometer-thick multilayered polyelectrolytes allows detection, along depth, of characteristic fragments from systems otherwise damaged by C60 bombardment, and increases sputtering yield by more than one order of magnitude. By contrast, NO has little influence on those layers that are well profiled with C60 alone. Such leveling effect, more pronounced at low temperature, leads to a dramatic improvement of profile quality, with a clear definition of interfaces. NO-dosing provides a tool for extending the applicability, in SIMS depth profiling, of the widely spread fullerene ion sources. In view of the acceptable erosion rates on inorganics, obtainable with C60, the method could be of relevance also in connection with the 3D-imaging of hybrid polymer/inorganic systems. Copyright © 2015 John Wiley & Sons, Ltd.

Laser microprobe and resonant laser ablation for depth profile measurements of hydrogen isotope atoms contained in graphite.

PubMed

Yorozu, M; Yanagida, T; Nakajyo, T; Okada, Y; Endo, A

2001-04-20

We measured the depth profile of hydrogen atoms in graphite by laser microprobing combined with resonant laser ablation. Deuterium-implanted graphite was employed for the measurements. The sample was ablated by a tunable laser with a wavelength corresponding to the resonant wavelength of 1S-2S of deuterium with two-photon excitation. The ablated deuterium was ionized by a 2 + 1 resonant ionization process. The ions were analyzed by a time-of-flight mass spectrometer. The deuterium ions were detected clearly with the resonant ablation. The detection limit was estimated to be less than 10(16) atoms/cm(3) in our experiments. We determined the depth profile by considering the etching profile and the etching rate. The depth profile agreed well with Monte Carlo simulations to within a precision of 23 mum for the center position and 4-mum precision for distributions for three different implantation depths.

Numerical modeling of thermal regime in inland water bodies with field measurement data

NASA Astrophysics Data System (ADS)

Gladskikh, D.; Sergeev, D.; Baydakov, G.; Soustova, I.; Troitskaya, Yu.

2018-01-01

Modification of the program complex LAKE, which is intended to compute the thermal regimes of inland water bodies, and the results of its validation in accordance with the parameters of lake part of Gorky water reservoir are reviewed in the research. The modification caused changing the procedure of input temperature profile assignment and parameterization of surface stress on air-water boundary in accordance with the consideration of wind influence on mixing process. Also the innovation consists in combined methods of gathering meteorological parameters from files of global meteorological reanalysis and data of hydrometeorological station. Temperature profiles carried out with CTD-probe during expeditions in the period 2014-2017 were used for validation of the model. The comparison between the real data and the numerical results and its assessment based on time and temperature dependences in control points, correspondence of the forms of the profiles and standard deviation for all performed realizations are provided. It is demonstrated that the model reproduces the results of field measurement data for all observed conditions and seasons. The numerical results for the regimes with strong mixing are in the best quantitative and qualitative agreement with the real profiles. The accuracy of the forecast for the ones with strong stratification near the surface is lower but all specificities of the forms are correctly reproduced.

Acquisition of an Underway CTD System for the Flow Encountering Abrupt Topography DRI

DTIC Science & Technology

2015-09-30

Acquisition of an Underway CTD System for the Flow Encountering Abrupt Topography DRI T. M. Shaun Johnston Scripps Institution of Oceanography...westward flow in the North Equatorial Current (NEC) encounters tall, steep, submarine topography and islands. During the Flow Encountering Abrupt... Topography (FLEAT) DRI, investigators will determine: • Whether appreciable energy/momentum is lost from the large-scale NEC flow to smaller scales and

The Effect of a Constant Time Delay Procedure on Teaching an Adult with Severe Mental Retardation a Recreation Bowling Skill

ERIC Educational Resources Information Center

Zhang, Jiabei; Cote, Bridget; Chen, Shihui; Liu, John

2004-01-01

The purpose of this study was to examine the effect of a constant time delay (CTD) procedure on teaching a recreational bowling skill to a 39-year-old male with severe mental retardation. The CTD procedure used 5 seconds as delay interval, task direction as target stimulus, physical assistance as controlling prompt, and oral praise as reinforcer.…

Comparison of Constant Time Delay and Simultaneous Prompting Procedures: Teaching Functional Sight Words to Students with Intellectual Disabilities and Autism Spectrum Disorder

ERIC Educational Resources Information Center

Swain, Rasheeda; Lane, Justin D.; Gast, David L.

2015-01-01

Constant time delay (CTD) and simultaneous prompting (SP) are effective response prompting procedures for teaching students with moderate to severe disabilities. The purpose of this study was to compare the efficiency of CTD and SP when teaching functional sight words to four students, 8-11 years of age, with moderate intellectual disability (ID)…

Degradation of submandibular gland AQP5 by parasympathetic denervation of chorda tympani and its recovery by cevimeline, an M3 muscarinic receptor agonist.

PubMed

Li, Xuefei; Azlina, Ahmad; Karabasil, Mileva Ratko; Purwanti, Nunuk; Hasegawa, Takahiro; Yao, Chenjuan; Akamatsu, Tetsuya; Hosoi, Kazuo

2008-07-01

By chorda tympani denervation (CTD, parasympathectomy), the aquaporin 5 (AQP5), but not AQP1, protein level in the rat submandibular gland (SMG) was significantly decreased, dropping to 37% of that of the contralateral gland at 4 wk. The protein levels of AQP5 and AQP1 were not significantly affected by denervation of the cervical sympathetic trunk (sympathectomy). Administration of cevimeline hydrochloride, an M3 muscarinic receptor agonist (10 mg/kg for 7 days po), but not pilocarpine (0.3 mg/kg for 7 days po), recovered the AQP5 protein level reduced by CTD and increased the AQP1 protein level above the control one. The mRNA level of AQP5 was scarcely affected by CTD and cevimeline hydrochloride administration. Administration of chloroquine (50 mg/kg for 7 days po), a denaturant of lysosomes, increased the AQP5 protein level reduced by CTD. An extract obtained from the submandibular lysosomal fraction degraded the AQP5 protein in the total membrane fraction in vitro. These results suggest the possible regulation of the AQP5 protein level in the SMG by the parasympathetic nerves/M3 muscarinic receptor agonist and imply the involvement of lysosomal enzymes, but not a transcriptional mechanism, in this regulation.

Gene-Environment Interplay in Twin Models

PubMed Central

Hatemi, Peter K.

2013-01-01

In this article, we respond to Shultziner’s critique that argues that identical twins are more alike not because of genetic similarity, but because they select into more similar environments and respond to stimuli in comparable ways, and that these effects bias twin model estimates to such an extent that they are invalid. The essay further argues that the theory and methods that undergird twin models, as well as the empirical studies which rely upon them, are unaware of these potential biases. We correct this and other misunderstandings in the essay and find that gene-environment (GE) interplay is a well-articulated concept in behavior genetics and political science, operationalized as gene-environment correlation and gene-environment interaction. Both are incorporated into interpretations of the classical twin design (CTD) and estimated in numerous empirical studies through extensions of the CTD. We then conduct simulations to quantify the influence of GE interplay on estimates from the CTD. Due to the criticism’s mischaracterization of the CTD and GE interplay, combined with the absence of any empirical evidence to counter what is presented in the extant literature and this article, we conclude that the critique does not enhance our understanding of the processes that drive political traits, genetic or otherwise. PMID:24808718

Tubular Crystals and Helical Arrays: Structural Determination of HIV-1 Capsid Assemblies Using Iterative Helical Real-Space Reconstruction

PubMed Central

Zhang, Peijun; Meng, Xin; Zhao, Gongpu

2013-01-01

Helical structures are important in many different life forms and are well-suited for structural studies by cryo-EM. A unique feature of helical objects is that a single projection image contains all the views needed to perform a three-dimensional (3D) crystallographic reconstruction. Here, we use HIV-1 capsid assemblies to illustrate the detailed approaches to obtain 3D density maps from helical objects. Mature HIV-1 particles contain a conical- or tubular-shaped capsid that encloses the viral RNA genome and performs essential functions in the virus life cycle. The capsid is composed of capsid protein (CA) oligomers which are helically arranged on the surface. The N-terminal domain (NTD) of CA is connected to its C-terminal domain (CTD) through a flexible hinge. Structural analysis of two- and three-dimensional crystals provided molecular models of the capsid protein (CA) and its oligomer forms. We determined the 3D density map of helically assembled HIV-1 CA hexamers at 16 Å resolution using an iterative helical real-space reconstruction method. Docking of atomic models of CA-NTD and CA-CTD dimer into the electron density map indicated that the CTD dimer interface is retained in the assembled CA. Furthermore, molecular docking revealed an additional, novel CTD trimer interface. PMID:23132072

Dynamic Vertical Profiles of Peat Porewater Chemistry in a Northern Peatland

DOE Office of Scientific and Technical Information (OSTI.GOV)

Griffiths, Natalie A.; Sebestyen, Stephen D.

We measured pH, cations, nutrients, and total organic carbon (TOC) over 3 years to examine weekly to monthly variability in porewater chemistry depth profiles (0–3.0 m) in an ombrotrophic bog in Minnesota, USA. We also compared temporal variation at one location to spatial variation in depth profiles at 16 locations across the bog. Most solutes exhibited large gradients with depth. pH increased by two units and calcium concentrations increased over 20 fold with depth, and may reflect peatland development from minerotrophic to ombrotrophic conditions. Ammonium concentrations increased almost 20 fold and TOC concentrations decreased by half with depth, and thesemore » patterns likely reflect mineralization of peat or decomposition of TOC. There was also considerable temporal variation in the porewater chemistry depth profiles. Ammonium, soluble reactive phosphorus, and potassium showed greater temporal variation in near-surface porewater, while pH, calcium, and TOC varied more at depth. This variation demonstrates that deep peat porewater chemistry is not static. Lastly, temporal variation in solute chemistry depth profiles was greater than spatial variation in several instances, especially in shallow porewaters. In conclusion, characterizing both temporal and spatial variability is necessary to ensure representative sampling in peatlands, especially when calculating solute pools and fluxes and parameterizing process-based models.« less

Dynamic Vertical Profiles of Peat Porewater Chemistry in a Northern Peatland

DOE PAGES

Griffiths, Natalie A.; Sebestyen, Stephen D.

2016-10-14

We measured pH, cations, nutrients, and total organic carbon (TOC) over 3 years to examine weekly to monthly variability in porewater chemistry depth profiles (0–3.0 m) in an ombrotrophic bog in Minnesota, USA. We also compared temporal variation at one location to spatial variation in depth profiles at 16 locations across the bog. Most solutes exhibited large gradients with depth. pH increased by two units and calcium concentrations increased over 20 fold with depth, and may reflect peatland development from minerotrophic to ombrotrophic conditions. Ammonium concentrations increased almost 20 fold and TOC concentrations decreased by half with depth, and thesemore » patterns likely reflect mineralization of peat or decomposition of TOC. There was also considerable temporal variation in the porewater chemistry depth profiles. Ammonium, soluble reactive phosphorus, and potassium showed greater temporal variation in near-surface porewater, while pH, calcium, and TOC varied more at depth. This variation demonstrates that deep peat porewater chemistry is not static. Lastly, temporal variation in solute chemistry depth profiles was greater than spatial variation in several instances, especially in shallow porewaters. In conclusion, characterizing both temporal and spatial variability is necessary to ensure representative sampling in peatlands, especially when calculating solute pools and fluxes and parameterizing process-based models.« less

The impact of glacier meltwater on the underwater noise field in a glacial bay

NASA Astrophysics Data System (ADS)

Glowacki, Oskar; Moskalik, Mateusz; Deane, Grant B.

2016-12-01

Ambient noise oceanography is proving to be an efficient and effective tool for the study of ice-ocean interactions in the bays of marine-terminating glaciers. However, obtaining quantitative estimates of ice melting or calving processes from ambient noise requires an understanding of how sound propagation through the bay attenuates and filters the noise spectrum. Measurements of the vertical structure in sound speed in the vicinity of the Hans Glacier in Hornsund Fjord, Spitsbergen, made with O(130) CTD casts between May and November 2015, reveal high-gradient, upward-refracting sound speed profiles created by cold, fresh meltwater during summer months. Simultaneous recordings of underwater ambient noise made at depths of 1, 10, and 20 m in combination with propagation model calculations using the model Bellhop illustrate the dominant role these surface ducts play in shaping the underwater soundscape. The surface ducts lead to a higher intensity and greater variability of acoustic energy in the near-surface layer covered by glacially modified waters relative to deeper waters, indicating deeper zones as most appropriate for interseasonal acoustic monitoring of the glacial melt. Surface waveguides in Hornsund are relatively shallow and trap sound above O(1 kHz). Deeper waveguides observed elsewhere will also trap low-frequency sounds, such as those generated by calving events for example. Finally, the ambient noise field in Hornsund is shown to be strongly dependent on the distribution of ice throughout the bay, stressing the importance of performing complementary environmental measurements when interpreting the results of acoustic surveys.

Disruption of a cyclonic eddy circulation by wind stress in Prince William Sound, Alaska

NASA Astrophysics Data System (ADS)

Halverson, Mark J.; Carter Ohlmann, J.; Johnson, Mark A.; Scott Pegau, W.

2013-07-01

Oceanographic observations made during the Sound Predictions 2009 field experiment in Prince William Sound, Alaska, have documented rapid changes in the upper water column (0-40m) circulation. An assortment of drifting buoys, sampling four different depths, and HF radar surface current mapping, revealed three modes of circulation: anticyclonic, open cyclonic, and closed cyclonic. Each mode was observed at least once within an 18-day window, and the transition between them took as little as a day. Time-resolved hydrographic measurements show that the mass field was variable, but generally arranged such that the surface geostrophic flow should be in a closed-core cyclonic eddy configuration. Observations show that the mass field was likely influenced by relatively low salinity water flowing into Prince William Sound from the shelf, and from local freshwater input. We quantitatively examine why a closed-core circulation was not always observed by focusing on the transition between the closed and open cyclonic flow patterns. The western region of the central sound is a key area for this transition. Here, the high-frequency radar revealed that the closed circulation was established when the net flow shifted direction from northward to southward. A detailed comparison of the meridional geostrophic and wind-driven flows, using measured winds and hydrographic data from CTD profiles and two autonomous vehicles, shows that the geostrophic flow was mostly southward while the wind-driven flow was mostly northward. A net southward flow can be caused by a decrease in the northward wind-driven flow or an increase in the southward geostrophic flow.

Isopycnal diffusivity in the tropical North Atlantic oxygen minimum zone

NASA Astrophysics Data System (ADS)

Köllner, Manuela; Visbeck, Martin; Tanhua, Toste; Fischer, Tim

2017-04-01

Isopycnal diffusivity plays an important role in the ventilation of the Eastern Tropical North Atlantic (ETNA) Oxygen Minimum Zone (OMZ). Lateral tracer transport is described by isopycnal diffusivity and mean advection of the tracer (e.g. oxygen), together they account for up to 70% of the oxygen supply for the OMZ. One of the big challenges is to separate diffusivity from advection. Isopycnal diffusivity was estimated to be Ky=(500 ± 200) m2 s-1 and Kx=(1200 ± 600) m2 s-1 by Banyte et. al (2013) from a Tracer Release Experiment (TRE). Hahn et al. (2014) estimated a meridional eddy diffusivity of 1350 m2 s-1 at 100 m depth decaying to less than 300 m2 s-1 below 800 m depth from repeated ship sections of CTD and ADCP data in addition with hydrographic mooring data. Uncertainties of the estimated diffusivities were still large, thus the Oxygen Supply Tracer Release Experiment (OSTRE) was set up to estimate isopycnal diffusivity in the OMZ using a newly developed sampling strategy of a control volume. The tracer was released in 2012 in the core of the OMZ at approximately 410 m depth and mapped after 6, 15 and 29 months in a regular grid. In addition to the calculation of tracer column integrals from vertical tracer profiles a new sampling method was invented and tested during two of the mapping cruises. The mean eddy diffusivity during OSTRE was found to be about (300 ± 130) m2 s-1. Additionally, the tracer has been advected further to the east and west by zonal jets. We compare different analysis methods to estimate isopycnal diffusivity from tracer spreading and show the advantage of the control volume surveys and control box approach. From the control box approach we are estimating the strength of the zonal jets within the OMZ core integrated over the TRE time period. References: Banyte, D., Visbeck, M., Tanhua, T., Fischer, T., Krahmann, G.,Karstensen, J., 2013. Lateral Diffusivity from Tracer Release Experiments in the Tropical North Atlantic Thermocline. Journal of Geophysical Research 118. Hahn, J., Brandt, P., Greatbatch, R., Krahmann, G., Körtzinger, A., 2014. Oxygen variance and meridional oxygen supply in the Tropical North East Atlantic oxygen minimum zone. Climate Dynamics 43, 2999-3024.

Upper Water Structure and Mixed Layer Depth in Sub-Tropical Waters: The Seats Station in the Northern South China Sea

NASA Astrophysics Data System (ADS)

Wong, G. T. F.; Tai, J. H.

2014-12-01

702 CTD profiles were collected in the subtropical northern South China Sea at and in the vicinity of the SouthEast Asian Time-series Study (SEATS) station (18.2oN, 115.8oE) between 17.5 and 18.5oN and 115.3 and 116.3oE in 64 cruises in 1997 to 2013. The hydrographic structure of the upper water above the permanent thermocline may be classified into 4 principal types: (a) classic type (an almost isopycnic upper water); (b) stepwise type (with one or more small but significant step-increases in σθ in the upper water); (c) graded type (an approximately constant depth gradient in a monotonic increase in σθ in the upper water); and (d) mixed type (a combination of the stepwise and graded types). The 4 types of upper water were found in 75, 14, 5, and 6% of the cruises, respectively. Ten schemes were applied to these data to determine the mixed layer depth (MLD): 4 fixed temperature difference (FTD) methods (0.2, 0.5, 0.8 and 1.0oC decrease from 10 m); 1 fixed density difference (FDD) method (0.125 σθ increase from 10 m); 1 fixed temperature gradient (FTG) method (at 0.05oC/m); 3 fixed density gradient (FDG) methods (at 0.01, 0.05 and 0.1 σθ/m); and the maximum density gradient (MDG) method. MLD could not be clearly depicted in the 3 minor types of upper water. In the classical type, while similar MLD-s were found in a large majority of the cruises among all 10 methods, substantial discrepancies among methods could be found. The most consistent results, generally within ±5 m, were found among the FDG method at 0.05, 0.1 σθ/m and FTD method at 0.8 and 1.0oC. The MDG method gave consistently deeper MLD by ~8 m. If that difference was taken into account, the results were generally consistent with those from the other 4 methods. The remaining 5 methods could all yield MLD-s shallower than the first 4 methods by >10 m as they failed to capture the bottom of the mixed layer as indicated by visual inspection.

Influence of hydrography of Central Mexican Pacific in the spatial variation of inorganic nutrients during 2010

NASA Astrophysics Data System (ADS)

Olivos-Ortiz, A.; Gaviño-Rodríguez, J. H.; Quijano-Scheggia, S.; Pelayo-Martinez, G.; Torres-Orozco, E.; Calva-Chavez, M.

2014-12-01

The Mexican Central Pacific (MCP) is considered an oligotrophic area that holds important populations of different species with ecological and economic importance like marine mammals, billfish and tunas. Hydrographic mechanisms are responsible to interplay with the biogeochemical cycles of nutrients to support primary productivity for these food webs. It is argued that seasonal upwelling of bottom waters rich in nutrients generates distributed in patches of high-productivity, which are also linked to topographic continental forcing. The goal of this study is determine the presence of water masses, depth of the mixed layer, temperature, salinity, patterns of geostrophic currents and their influence on the spatiotemporal variability of inorganic nutrients. For that pupose, three oceanographic cruises were conducted in January, May-June, and October of 2010 off the coast of the MCP. Each campaign consisted of 15 stations in five perpendicular transects with stations at 2, 50 and 100 nm offshore. At each station samples were taken to determine the concentration of NO3-+ NO2-, NH4+, PO43- and SiO2 at 0, 10, 25, 50, 75, 100, 150 and 200 m depth. CTD casts were made up to 500m to obtain profiles of salinity, temperature, water masses, and identify geostrophic currents (direction and intensity). Identified water masses were: Pacific Tropical Surface Water (PTSW), Pacific Equatorial Surface Water (PESW), Equatorial Pacific Water (EPW), California Current Water (CCW), Subtropical Subsurface Water (STSsW), and Pacific Intermediate Water (PIT); these water masses were present in all three seasons being more clear the presence of CCW during autumn and PTSW in winter. The interaction between coastal topography, geostrophic circulation, and the depth of the mixed layer (55m oceanic part in January and 10m coastal area in October) were the factors that determined the location of areas of high concentration of nutrients. The distribution of nutrients was heterogeneous, characterized by mesoscale structures beyond the continental shelf or coastal upwelling events; no significant difference between concentrations at different seasons of the year with the following ranges: 1.2-8.9 uM NO3-+ NO2-, NH4+ 0.8-12.4 mM, 0.1-5.0 mM PO43-, and 3.2-14.5 mM SiO2.

Intermittent large amplitude internal waves observed in Port Susan, Puget Sound

NASA Astrophysics Data System (ADS)

Harris, J. C.; Decker, L.

2017-07-01

A previously unreported internal tidal bore, which evolves into solitary internal wave packets, was observed in Port Susan, Puget Sound, and the timing, speed, and amplitude of the waves were measured by CTD and visual observation. Acoustic Doppler current profiler (ADCP) measurements were attempted, but unsuccessful. The waves appear to be generated with the ebb flow along the tidal flats of the Stillaguamish River, and the speed and width of the resulting waves can be predicted from second-order KdV theory. Their eventual dissipation may contribute significantly to surface mixing locally, particularly in comparison with the local dissipation due to the tides. Visually the waves appear in fair weather as a strong foam front, which is less visible the farther they propagate.

Spatial distribution of microbial biomass, activity, community structure, and the biodegradation of linear alkylbenzene sulfonate (LAS) and linear alcohol ethoxylate (LAE) in the subsurface.

PubMed

Federle, T W; Ventullo, R M; White, D C

1990-12-01

The vertical distribution of microbial biomass, activity, community structure and the mineralization of xenobiotic chemicals was examined in two soil profiles in northern Wisconsin. One profile was impacted by infiltrating wastewater from a laundromat, while the other served as a control. An unconfined aquifer was present 14 meters below the surface at both sites. Biomass and community structure were determined by acridine orange direct counts and measuring concentrations of phospholipid-derived fatty acids (PLFA). Microbial activity was estimated by measuring fluorescein diacetate (FDA) hydrolysis, thymidine incorporation into DNA, and mixed amino acid (MAA) mineralization. Mineralization kinetics of linear alkylbenzene sulfonate (LAS) and linear alcohol ethoxylate (LAE) were determined at each depth. Except for MAA mineralization rates, measures of microbial biomass and activity exhibited similar patterns with depth. PLFA concentration and rates of FDA hydrolysis and thymidine incorporation decreased 10-100 fold below 3 m and then exhibited little variation with depth. Fungal fatty acid markers were found at all depths and represented from 1 to 15% of the total PLFAs. The relative proportion of tuberculostearic acid (TBS), an actinomycete marker, declined with depth and was not detected in the saturated zone. The profile impacted by wastewater exhibited higher levels of PLFA but a lower proportion of TBS than the control profile. This profile also exhibited faster rates of FDA hydrolysis and amino acid mineralization at most depths. LAS was mineralized in the upper 2 m of the vadose zone and in the saturated zone of both profiles. Little or no LAS biodegradation occurred at depths between 2 and 14 m. LAE was mineralized at all depths in both profiles, and the mineralization rate exhibited a similar pattern with depth as biomass and activity measurements. In general, biomass and biodegradative activities were much lower in groundwater than in soil samples obtained from the same depth.

Combination of ORP and pH sensors in tow-yo studies to map redox and acid-base anomalies in seawater due to hydrothermal activity in shallow areas

NASA Astrophysics Data System (ADS)

Santana-Casiano, J. M.; González-Dávila, M.; Fraile-Nuez, E.; Santana-González, C.; Baker, E. T.; Resing, J. A.; Walker, S. L.

2016-12-01

The detection of activity from low-temperature hydrothermal vents, where the increase in temperature is not evident, requires the utilization of alternative sensors that respond to emissions of certain chemical species. The character of both reduced and acid fluids in the volcanic emissions in the El Hierro submarine volcano allowed us to detect anomalies related with changes in the chemical potential and the proton concentration using ORP and pH sensors, respectively. Tow-yos with these sensors provided the approximate locations of the emissions plotting δ(ORP)/δt and ΔpH versus the latitude or longitude. The ORP sensor responds very quickly to the presence of reduced chemicals in the water column. The magnitude of this change is examined by the time derivative of ORP, δ(ORP)/δt. For pH changes, ΔpH, the mean pH for each depth at a reference station in an area not affected by the vent emission is subtracted from each point measured near the volcanic edifice. The submarine volcano of El Hierro, in its degasification stage, provided an excellent opportunity to apply CTD-pH-ORP tow-yo methodology and to study the effect of CO2 emission on the seawater carbonate system, the global carbon flux, and local ocean acidification. Detailed surveys of the volcanic edifice were carried out during VULCANO 0314 and VULCANA0615 cruises using several CTD-pH-ORP tow-yo studies, localizing the redox and acidic changes, which were used to obtain surface maps of anomalies. CTD-pH-ORP yo-yo studies were also conducted that included discrete sampling for carbonate system parameters and total dissolved Fe(II), TDFe(II). The inputs of CO2 along multiple sections combined with measurements of oceanic currents produced an estimated volcanic CO2 flux = 6.0 105 ± 1.1 105 kg d-1and increases the acidity above the volcano by 20%. From the yo-yo studies important anomalies in both pHT and TDFe(II) were observed. The increased TDFe(II) concentrations and the low associated pHT values may be acting as an important fertilization event in the seawater around the volcano at the Island of El Hierro providing optimal conditions for the regeneration of the area.

Neutron Depth Profiling: Overview and Description of NIST Facilities

PubMed Central

Downing, R. G.; Lamaze, G. P.; Langland, J. K.; Hwang, S. T.

1993-01-01

The Cold Neutron Depth Profiling (CNDP) instrument at the NIST Cold Neutron Research Facility (CNRF) is now operational. The neutron beam originates from a 16 L D2O ice cold source and passes through a filter of 135 mm of single crystal sapphire. The neutron energy spectrum may be described by a 65 K Maxwellian distribution. The sample chamber configuration allows for remote controlled scanning of 150 × 150 mm sample areas including the varying of both sample and detector angle. The improved sensitivity over the current thermal depth profiling instrument has permitted the first nondestructive measurements of 17O profiles. This paper describes the CNDP instrument, illustrates the neutron depth profiling (NDP) technique with examples, and gives a separate bibliography of NDP publications. PMID:28053461

Randomized interpolative decomposition of separated representations

NASA Astrophysics Data System (ADS)

Biagioni, David J.; Beylkin, Daniel; Beylkin, Gregory

2015-01-01

We introduce an algorithm to compute tensor interpolative decomposition (dubbed CTD-ID) for the reduction of the separation rank of Canonical Tensor Decompositions (CTDs). Tensor ID selects, for a user-defined accuracy ɛ, a near optimal subset of terms of a CTD to represent the remaining terms via a linear combination of the selected terms. CTD-ID can be used as an alternative to or in combination with the Alternating Least Squares (ALS) algorithm. We present examples of its use within a convergent iteration to compute inverse operators in high dimensions. We also briefly discuss the spectral norm as a computational alternative to the Frobenius norm in estimating approximation errors of tensor ID. We reduce the problem of finding tensor IDs to that of constructing interpolative decompositions of certain matrices. These matrices are generated via randomized projection of the terms of the given tensor. We provide cost estimates and several examples of the new approach to the reduction of separation rank.

Akt phosphorylation regulates the tumour-suppressor merlin through ubiquitination and degradation.

PubMed

Tang, Xiaoling; Jang, Sung-Wuk; Wang, Xuerong; Liu, Zhixue; Bahr, Scott M; Sun, Shi-Yong; Brat, Daniel; Gutmann, David H; Ye, Keqiang

2007-10-01

The neurofibromatosis-2 (NF2) tumour-suppressor gene encodes an intracellular membrane-associated protein, called merlin, whose growth-suppressive function is dependent on its ability to form interactions through its intramolecular amino-terminal domain (NTD) and carboxy-terminal domain (CTD). Merlin phosphorylation plays a critical part in dictating merlin NTD/CTD interactions as well as in controlling binding to its effector proteins. Merlin is partially regulated by phosphorylation of Ser 518, such that hyperphosphorylated merlin is inactive and fails to form productive intramolecular and intermolecular interactions. Here, we show that the protein kinase Akt directly binds to and phosphorylates merlin on residues Thr 230 and Ser 315, which abolishes merlin NTD/CTD interactions and binding to merlin's effector protein PIKE-L and other binding partners. Furthermore, Akt-mediated phosphorylation leads to merlin degradation by ubiquitination. These studies demonstrate that Akt-mediated merlin phosphorylation regulates the function of merlin in the absence of an inactivating mutation.

The C-Terminal Domain of Nrf1 Negatively Regulates the Full-Length CNC-bZIP Factor and Its Shorter Isoform LCR-F1/Nrf1β; Both Are Also Inhibited by the Small Dominant-Negative Nrf1γ/δ Isoforms that Down-Regulate ARE-Battery Gene Expression

PubMed Central

Zhang, Yiguo; Qiu, Lu; Li, Shaojun; Xiang, Yuancai; Chen, Jiayu; Ren, Yonggang

2014-01-01

The C-terminal domain (CTD, aa 686–741) of nuclear factor-erythroid 2 p45-related factor 1 (Nrf1) shares 53% amino acid sequence identity with the equivalent Neh3 domain of Nrf2, a homologous transcription factor. The Neh3 positively regulates Nrf2, but whether the Neh3-like (Neh3L) CTD of Nrf1 has a similar role in regulating Nrf1-target gene expression is unknown. Herein, we report that CTD negatively regulates the full-length Nrf1 (i.e. 120-kDa glycoprotein and 95-kDa deglycoprotein) and its shorter isoform LCR-F1/Nrf1β (55-kDa). Attachment of its CTD-adjoining 112-aa to the C-terminus of Nrf2 yields the chimaeric Nrf2-C112Nrf1 factor with a markedly decreased activity. Live-cell imaging of GFP-CTD reveals that the extra-nuclear portion of the fusion protein is allowed to associate with the endoplasmic reticulum (ER) membrane through the amphipathic Neh3L region of Nrf1 and its basic c-tail. Thus removal of either the entire CTD or the essential Neh3L portion within CTD from Nrf1, LCR-F1/Nrf1β and Nrf2-C112Nrf1, results in an increase in their transcriptional ability to regulate antioxidant response element (ARE)-driven reporter genes. Further examinations unravel that two smaller isoforms, 36-kDa Nrf1γ and 25-kDa Nrf1δ, act as dominant-negative inhibitors to compete against Nrf1, LCR-F1/Nrf1β and Nrf2. Relative to Nrf1, LCR-F1/Nrf1β is a weak activator, that is positively regulated by its Asn/Ser/Thr-rich (NST) domain and acidic domain 2 (AD2). Like AD1 of Nrf1, both AD2 and NST domain of LCR-F1/Nrf1β fused within two different chimaeric contexts to yield Gal4D:Nrf1β607 and Nrf1β:C270Nrf2, positively regulate their transactivation activity of cognate Gal4- and Nrf2-target reporter genes. More importantly, differential expression of endogenous ARE-battery genes is attributable to up-regulation by Nrf1 and LCR-F1/Nrf1β and down-regulation by Nrf1γ and Nrf1δ. PMID:25290918

Under-Ice Operations with AUVS in High Latitudes

NASA Astrophysics Data System (ADS)

Ferguson, J.; Kaminski, C. D.

2012-12-01

In 2010 and 2011, ISE Explorer Autonomous Underwater Vehicles (AUV), built for Natural Resources Canada (NRCan), were deployed to Canada's high Arctic. The mission was to undertake under-ice bathymetric surveys supporting Canada's submission under the United Nations Convention on the Law of the Sea (UNCLOS). During these deployments several under-ice records were broken and several new technologies were demonstrated. The NRCan AUV is a 5000 meter depth rated vehicle, with several innovative additions to make it suitable for arctic survey work. Most notable are a depth rated variable ballast system, a 1300 Hz long-range homing system, and under-ice charging and data transfer capabilities. The Explorer's range was extended to approximately 450 km by adding a hull section to accommodate extra batteries. The scientific payload onboard included a Seabird SBE49 Conductivity-Temperature-Depth (CTD) sensor, Knudsen singlebeam echosounder, and a Kongsberg Simrad EM2000 multibeam echosounder. In 2010, operations were conducted from an ice camp near Borden Island (78°14'N, 112°39'W) operating through an ice hole. Following several test missions, the AUV spent 10 days surveying under ice before being successfully recovered. In total, close to 1100 km of under-ice survey was undertaken at depths to 3160 meters. A further set of operations was carried out in August and September 2011 from the Canadian Icebreaker CCGS Louis St. Laurent operating with the American Icebreaker USCGS Healy. Here the operations were much further north to latitudes of 88°30' N and to depths of 3500 meters. In this paper, the 2010 ice camp and the 2011 icebreaker missions are described, with an outline of technology developments that were undertaken, the preparations that were necessary for the success of the missions and finally, the outcome of the missions themselves.

Depth resolution and preferential sputtering in depth profiling of sharp interfaces

NASA Astrophysics Data System (ADS)

Hofmann, S.; Han, Y. S.; Wang, J. Y.

2017-07-01

The influence of preferential sputtering on depth resolution of sputter depth profiles is studied for different sputtering rates of the two components at an A/B interface. Surface concentration and intensity depth profiles on both the sputtering time scale (as measured) and the depth scale are obtained by calculations with an extended Mixing-Roughness-Information depth (MRI)-model. The results show a clear difference for the two extreme cases (a) preponderant roughness and (b) preponderant atomic mixing. In case (a), the interface width on the time scale (Δt(16-84%)) increases with preferential sputtering if the faster sputtering component is on top of the slower sputtering component, but the true resolution on the depth scale (Δz(16-84%)) stays constant. In case (b), the interface width on the time scale stays constant but the true resolution on the depth scale varies with preferential sputtering. For similar order of magnitude of the atomic mixing and the roughness parameters, a transition state between the two extremes is obtained. While the normalized intensity profile of SIMS represents that of the surface concentration, an additional broadening effect is encountered in XPS or AES by the influence of the mean electron escape depth which may even cause an additional matrix effect at the interface.

Profilometric characterization of DOEs with continuous microrelief

NASA Astrophysics Data System (ADS)

Korolkov, V. P.; Ostapenko, S. V.; Shimansky, R. V.

2008-09-01

Methodology of local characterization of continuous-relief diffractive optical elements has been discussed. The local profile depth can be evaluated using "approximated depth" defined without taking a profile near diffractive zone boundaries into account. Several methods to estimate the approximated depth have been offered.

Comparison of Air Fluorescence and Ionization Measurements of E.M. Shower Depth Profiles: Test of a UHECR Detector Technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belz, J.; Cao, Z.; Huentemeyer, P.

Measurements are reported on the fluorescence of air as a function of depth in electromagnetic showers initiated by bunches of 28.5 GeV electrons. The light yield is compared with the expected and observed depth profiles of ionization in the showers. It validates the use of atmospheric fluorescence profiles in measuring ultra high energy cosmic rays.

Effects of Hydrothermal Scavenging of 230Th in the Eastern Equatorial Pacific Translated to the Deep Waters of the Central Equatorial Pacific

NASA Astrophysics Data System (ADS)

Lopez, G. I.; Marcantonio, F.

2014-12-01

Although we were not involved in the 2013 US GEOTRACES zonal transect in the eastern tropical south Pacific, our results in the central tropical Pacific are complementary in that they shed light on the extensive hydrothermal plume emanating from the East Pacific Rise (EPR). Specifically, we have analyzed dissolved 230Th concentrations at high-resolution within the water column at two locations (ML1208-12CTD; 8° 19.989' N, 159° 18.000' W, and ML1208-03CTD; 00° 13.166' S, 155° 57.668' W) sampled as part of a cruise to the Line Islands. The pattern of the dissolved 230Th concentration profile at 8°N is essentially linear from the surface to 2000 m and generally follows a reversible scavenging model. However, from 2000 m to 3000 m, the dissolved 230Th concentrations are constant, before linearly increasing again from 3000 m to the bottom. At this site dissolved 230Th concentrations range from 1.06 fg/kg at 100 m to 55.15 fg/kg at 4600 m. At the equator, dissolved 230Th concentrations are slightly lower, and range from undetectable at 25 m to 19.07 fg/kg at 3038 m. A nearly indistinguishable pattern in dissolved 230Th concentrations occurs in the profile at the equator compared to that from 8°N. The deep-water deviation from linearity between 2 and 3 km in the 230Th profiles (lower concentrations than expected) at both sites coincides well with the interval of the water column which has the highest concentrations of 3He. This 3He-rich signal has been traced to hydrothermal plumes from the EPR, thousands of km away (Lupton et al., 1998). We hypothesize that the lower concentrations of 230Th in deep waters of the central equatorial Pacific are a result of: 1) scavenging of water-column 230Th by Fe-Mn particulates contained within the EPR hydrothermal plume, and 2) lateral export of these 230Th-deficient deep waters approximately 7000 km westward. We will discuss the implications that the transport of this signature across vast distances has on water residence and transport times. Reference: Lupton, J. (1998) J. Geophys. Res. 103, 15,853-15,868.

Profiling defect depth in composite materials using thermal imaging NDE

NASA Astrophysics Data System (ADS)

Obeidat, Omar; Yu, Qiuye; Han, Xiaoyan

2018-04-01

Sonic Infrared (IR) NDE, is a relatively new NDE technology; it has been demonstrated as a reliable and sensitive method to detect defects. SIR uses ultrasonic excitation with IR imaging to detect defects and flaws in the structures being inspected. An IR camera captures infrared radiation from the target for a period of time covering the ultrasound pulse. This period of time may be much longer than the pulse depending on the defect depth and the thermal properties of the materials. With the increasing deployment of composites in modern aerospace and automobile structures, fast, wide-area and reliable NDE methods are necessary. Impact damage is one of the major concerns in modern composites. Damage can occur at a certain depth without any visual indication on the surface. Defect depth information can influence maintenance decisions. Depth profiling relies on the time delays in the captured image sequence. We'll present our work on the defect depth profiling by using the temporal information of IR images. An analytical model is introduced to describe heat diffusion from subsurface defects in composite materials. Depth profiling using peak time is introduced as well.

Molecular determinants of tetramerization in the KcsA cytoplasmic domain.

PubMed

Kamnesky, Guy; Hirschhorn, Orel; Shaked, Hadassa; Chen, Jingfei; Yao, Lishan; Chill, Jordan H

2014-10-01

The cytoplasmic C-terminal domain (CTD) of KcsA, a bacterial homotetrameric potassium channel, is an amphiphilic domain that forms a helical bundle with four-fold symmetry mediated by hydrophobic and electrostatic interactions. Previously we have established that a CTD-derived 34-residue peptide associates into a tetramer in a pH-dependent manner (Kamnesky et al., JMB 2012;418:237-247). Here we further investigate the molecular determinants of tetramer formation in the CTD by characterizing the kinetics of monomer-tetramer equilibrium for 10 alanine mutants using NMR, sedimentation equilibrium (SE) and molecular dynamics simulation. NMR and SE concur in finding single-residue contributions to tetramer stability to be in the 0.5 to 3.5 kcal/mol range. Hydrophobic interactions between residues lining the tetramer core generally contributed more to formation of tetramer than electrostatic interactions between residues R147, D149 and E152. In particular, alanine replacement of residue R147, a key contributor to inter-subunit salt bridges, resulted in only a minor effect on tetramer dissociation. Mutations outside of the inter-subunit interface also influenced tetramer stability by affecting the tetramerization on-rate, possibly by changing the inherent helical propensity of the peptide. These findings are interpreted in the context of established paradigms of protein-protein interactions and protein folding, and lay the groundwork for further studies of the CTD in full-length KcsA channels. © 2014 The Protein Society.

Molecular determinants of tetramerization in the KcsA cytoplasmic domain

PubMed Central

Kamnesky, Guy; Hirschhorn, Orel; Shaked, Hadassa; Chen, Jingfei; Yao, Lishan; Chill, Jordan H

2014-01-01

The cytoplasmic C-terminal domain (CTD) of KcsA, a bacterial homotetrameric potassium channel, is an amphiphilic domain that forms a helical bundle with four-fold symmetry mediated by hydrophobic and electrostatic interactions. Previously we have established that a CTD-derived 34-residue peptide associates into a tetramer in a pH-dependent manner (Kamnesky et al., JMB 2012;418:237-247). Here we further investigate the molecular determinants of tetramer formation in the CTD by characterizing the kinetics of monomer-tetramer equilibrium for 10 alanine mutants using NMR, sedimentation equilibrium (SE) and molecular dynamics simulation. NMR and SE concur in finding single-residue contributions to tetramer stability to be in the 0.5 to 3.5 kcal/mol range. Hydrophobic interactions between residues lining the tetramer core generally contributed more to formation of tetramer than electrostatic interactions between residues R147, D149 and E152. In particular, alanine replacement of residue R147, a key contributor to inter-subunit salt bridges, resulted in only a minor effect on tetramer dissociation. Mutations outside of the inter-subunit interface also influenced tetramer stability by affecting the tetramerization on-rate, possibly by changing the inherent helical propensity of the peptide. These findings are interpreted in the context of established paradigms of protein-protein interactions and protein folding, and lay the groundwork for further studies of the CTD in full-length KcsA channels. PMID:25042120

The WD40 domain of ATG16L1 is required for its non-canonical role in lipidation of LC3 at single membranes.

PubMed

Fletcher, Katherine; Ulferts, Rachel; Jacquin, Elise; Veith, Talitha; Gammoh, Noor; Arasteh, Julia M; Mayer, Ulrike; Carding, Simon R; Wileman, Thomas; Beale, Rupert; Florey, Oliver

2018-02-15

A hallmark of macroautophagy is the covalent lipidation of LC3 and insertion into the double-membrane phagophore, which is driven by the ATG16L1/ATG5-ATG12 complex. In contrast, non-canonical autophagy is a pathway through which LC3 is lipidated and inserted into single membranes, particularly endolysosomal vacuoles during cell engulfment events such as LC3-associated phagocytosis. Factors controlling the targeting of ATG16L1 to phagophores are dispensable for non-canonical autophagy, for which the mechanism of ATG16L1 recruitment is unknown. Here we show that the WD repeat-containing C-terminal domain (WD40 CTD) of ATG16L1 is essential for LC3 recruitment to endolysosomal membranes during non-canonical autophagy, but dispensable for canonical autophagy. Using this strategy to inhibit non-canonical autophagy specifically, we show a reduction of MHC class II antigen presentation in dendritic cells from mice lacking the WD40 CTD Further, we demonstrate activation of non-canonical autophagy dependent on the WD40 CTD during influenza A virus infection. This suggests dependence on WD40 CTD distinguishes between macroautophagy and non-canonical use of autophagy machinery. © 2018 The Authors. Published under the terms of the CC BY 4.0 license.

NOAEL-dose of a neonicotinoid pesticide, clothianidin, acutely induce anxiety-related behavior with human-audible vocalizations in male mice in a novel environment.

PubMed

Hirano, Tetsushi; Yanai, Shogo; Takada, Tadashi; Yoneda, Naoki; Omotehara, Takuya; Kubota, Naoto; Minami, Kiichi; Yamamoto, Anzu; Mantani, Youhei; Yokoyama, Toshifumi; Kitagawa, Hiroshi; Hoshi, Nobuhiko

2018-01-05

Neonicotinoids are novel systemic pesticides acting as agonists on the nicotinic acetylcholine receptors (nAChRs) of insects. Experimental studies have revealed that neonicotinoids pose potential risks for the nervous systems of non-target species, but the brain regions responsible for their behavioral effects remain incompletely understood. This study aimed to assess the neurobehavioral effects of clothianidin (CTD), a later neonicotinoid developed in 2001 and widely used worldwide, and to explore the target regions of neonicotinoids in the mammalian brain. A single-administration of 5 or 50mg/kg CTD to male C57BL/6N mice at or below the no-observed-adverse-effect level (NOAEL) induced an acute increase in anxiety during the elevated plus-maze test. In addition, mice in the CTD-administered group spontaneously emitted human-audible vocalizations (4-16kHz), which are behavioral signs of aversive emotions, and showed increased numbers of c-fos immunoreactive cells in the paraventricular thalamic nucleus and dentate gyrus of the hippocampus. In conclusion, mice exposed to NOAEL-dose CTD would be rendered vulnerable to a novel environment via the activation of thalamic and hippocampal regions related to stress responses. These findings should provide critical insight into the neurobehavioral effects of neonicotinoids on mammals. Copyright © 2017 Elsevier B.V. All rights reserved.

The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database

PubMed Central

Davis, Allan Peter; Wiegers, Thomas C.; Murphy, Cynthia G.; Mattingly, Carolyn J.

2011-01-01

The Comparative Toxicogenomics Database (CTD) is a public resource that promotes understanding about the effects of environmental chemicals on human health. CTD biocurators read the scientific literature and convert free-text information into a structured format using official nomenclature, integrating third party controlled vocabularies for chemicals, genes, diseases and organisms, and a novel controlled vocabulary for molecular interactions. Manual curation produces a robust, richly annotated dataset of highly accurate and detailed information. Currently, CTD describes over 349 000 molecular interactions between 6800 chemicals, 20 900 genes (for 330 organisms) and 4300 diseases that have been manually curated from over 25 400 peer-reviewed articles. This manually curated data are further integrated with other third party data (e.g. Gene Ontology, KEGG and Reactome annotations) to generate a wealth of toxicogenomic relationships. Here, we describe our approach to manual curation that uses a powerful and efficient paradigm involving mnemonic codes. This strategy allows biocurators to quickly capture detailed information from articles by generating simple statements using codes to represent the relationships between data types. The paradigm is versatile, expandable, and able to accommodate new data challenges that arise. We have incorporated this strategy into a web-based curation tool to further increase efficiency and productivity, implement quality control in real-time and accommodate biocurators working remotely. Database URL: http://ctd.mdibl.org PMID:21933848

Spacing requirements for interactions between the C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase and the cAMP receptor protein.

PubMed Central

Lloyd, G S; Busby, S J; Savery, N J

1998-01-01

During transcription initiation at bacterial promoters, the C-terminal domain of the RNA polymerase alpha subunit (alphaCTD) can interact with DNA-sequence elements (known as UP elements) and with activator proteins. We have constructed a series of semi-synthetic promoters carrying both an UP element and a consensus DNA-binding site for the Escherichia coli cAMP receptor protein (CRP; a factor that activates transcription by making direct contacts with alphaCTD). At these promoters, the UP element was located at a variety of distances upstream of the CRP-binding site, which was fixed at position -41.5 bp upstream of the transcript start. At some positions, the UP element caused enhanced promoter activity whereas, at other positions, it had very little effect. In no case was the CRP-dependence of the promoter relieved. DNase I and hydroxyl-radical footprinting were used to study ternary RNA polymerase-CRP-promoter complexes formed at two of the most active of these promoters, and co-operativity between the binding of CRP and purified alpha subunits was studied. The footprints show that alphaCTD binds to the UP element as it is displaced upstream but that this displacement does not prevent alphaCTD from being contacted by CRP. Models to account for this are discussed. PMID:9461538

Magnetic Nonuniformity and Thermal Hysteresis of Magnetism in a Manganite Thin Film [Depth profiling of magnetization and coupling of strain with magnetization in (La 0.4Pr 0.6) 0.67Ca 0.33MnO 3 films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Surendra; Fitzsimmons, M. R.; Lookman, T.

We measured the chemical and magnetic depth profiles of a single crystalline film grown on a NdGaO 3 substrate using x-ray reflectometry, electron microscopy, electron energy-loss spectroscopy and polarized neutron reflectometry. Our data indicate that the film exhibits coexistence of different magnetic phases as a function of depth. The magnetic depth profile is correlated with a variation of chemical composition with depth. The thermal hysteresis of ferromagnetic order in the film suggests a first order ferromagnetic transition at low temperatures

Patterns in bacterial and archaeal community structure and diversity in western Beaufort Sea sediments and waters

NASA Astrophysics Data System (ADS)

Hamdan, L. J.; Sikaroodi, M.; Coffin, R. B.; Gillevet, P. M.

2010-12-01

A culture-independent phylogenetic study of microbial communities in water samples and sediment cores recovered from the Beaufort Sea slope east of Point Barrow, Alaska was conducted. The goal of the work was to describe community composition in sediment and water samples and determine the influence of local environmental conditions on microbial populations. Archaeal and bacterial community composition was studied using length heterogeneity-polymerase chain reaction (LH-PCR) and multitag pyrosequencing (MTPS). Sediment samples were obtained from three piston cores on the slope (~1000m depth) arrayed along an east-west transect and one core from a depth of approximately 2000m. Discrete water samples were obtained using a CTD-rosette from three locations adjacent to piston core sites. Water sample were selected at three discrete depths within a vertically stratified (density) water column. The microbial community in near surface waters was distinct from the community observed in deeper stratified layers of the water column. Multidimensional scaling analysis (MDS) revealed that water samples from mid and deep stratified layers bore high similarity to communities in cores collected in close proximity. Overall, the highest diversity (bacteria and archaea) was observed in a core which had elevated methane concentration relative to other locations. Geochemical (e.g., bulk organic and inorganic carbon pools, nutrients, metabolites) and physical data (e.g. depth, water content) were used to reveal the abiotic factors structuring microbial communities. The analysis indicates that sediment water content (porosity) and inorganic carbon concentration are the most significant structuring elements on Beaufort shelf sedimentary microbial communities.

Maine Geological Survey Borehole Temperature Profiles

DOE Data Explorer

Marvinney, Robert

2013-11-06

This dataset includes temperature profiles from 30 boreholes throughout Maine that were selected for their depth, location, and lithologies encountered. Depths range from about 300 feet to 2,200 feet. Most of the boreholes selected for measurement were completed in granite because this lithology can be assumed to be nearly homogeneous over the depth of the borehole. Boreholes were also selected to address gaps in existing geothermal datasets. Temperature profiles were collected in October and November, 2012.

Nondestructive strain depth profiling with high energy X-ray diffraction: System capabilities and limitations

NASA Astrophysics Data System (ADS)

Zhang, Zhan; Wendt, Scott; Cosentino, Nicholas; Bond, Leonard J.

2018-04-01

Limited by photon energy, and penetration capability, traditional X-ray diffraction (XRD) strain measurements are only capable of achieving a few microns depth due to the use of copper (Cu Kα1) or molybdenum (Mo Kα1) characteristic radiation. For deeper strain depth profiling, destructive methods are commonly necessary to access layers of interest by removing material. To investigate deeper depth profiles nondestructively, a laboratory bench-top high-energy X-ray diffraction (HEXRD) system was previously developed. This HEXRD method uses an industrial 320 kVp X-Ray tube and the Kα1 characteristic peak of tungsten, to produces a higher intensity X-ray beam which enables depth profiling measurement of lattice strain. An aluminum sample was investigated with deformation/load provided using a bending rig. It was shown that the HEXRD method is capable of strain depth profiling to 2.5 mm. The method was validated using an aluminum sample where both the HEXRD method and the traditional X-ray diffraction method gave data compared with that obtained using destructive etching layer removal, performed by a commercial provider. The results demonstrate comparable accuracy up to 0.8 mm depth. Nevertheless, higher attenuation capabilities in heavier metals limit the applications in other materials. Simulations predict that HEXRD works for steel and nickel in material up to 200 µm, but experiment results indicate that the HEXRD strain profile is not practical for steel and nickel material, and the measured diffraction signals are undetectable when compared to the noise.

Upper mantle electrical conductivity for seven subcontinental regions of the Earth

USGS Publications Warehouse

Campbell, W.H.; Schiffmacher, E.R.

1988-01-01

Spherical harmonic analysis coefficients of the external and internal parts of the quiet-day geomagnetic field variations (Sq) separated for the 7 continental regions of the observatories have been used to determine conductivity profiles to depths of about 600 km by the Schmucker equivalent substitute conductor method. The profiles give evidence of increases in conductivity between about 150 and 350 km depth, then a general increase in conductivity thereafter. For South America we found a high conductivity at shallow depths. The European profile showed a highly conducting layer near 125 km. At the greater depths, Europe, Australia and South America had the lowest values of conductivity. North America and east Asia had intermediate values whereas the African and central Asian profiles both showed the conductivities rising rapidly beyond 450 km depth. The regional differences indicate that there may be considerable lateral heterogeneity of electrical conductivity in the Earth's upper mantle. -Authors

Hardness depth profile of lattice strained cemented carbide modified by high-energy boron ion implantation

NASA Astrophysics Data System (ADS)

Yoshida, Y.; Matsumura, A.; Higeta, K.; Inoue, T.; Shimizu, S.; Motonami, Y.; Sato, M.; Sadahiro, T.; Fujii, K.

1991-07-01

The hardness depth profiles of cemented carbides which were implanted with high-energy B + ions have been estimated using a dynamic microhardness tester. The B + implantations into (16% Co)-cemented WC alloys were carried out under conditions where the implantation energies were 1-3 MeV and the fluences 1 × 10 17-1 × 10 18ions/cm 2. The profiles show that the implanted layer becomes harder as fluences are chosen at higher values and there is a peak at a certain depth which depends on the implantation energy. In X-ray diffraction (XRD) studies of the implanted surface the broadened refraction peaks of only WC and Co are detected and the increments of lattice strain and of residual stress in the near-surface region are observed. It is supposed that the hardening effect should be induced by an increase in residual stress produced by lattice strain. The hardness depth profile in successive implantation of ions with different energies agrees with the compounded profile of each one of the implantations. It is concluded that the hardness depth profile can be controlled under adequate conditions of implantation.

Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database

PubMed Central

Davis, Allan Peter; Wiegers, Thomas C.; King, Benjamin L.; Wiegers, Jolene; Grondin, Cynthia J.; Sciaky, Daniela; Johnson, Robin J.; Mattingly, Carolyn J.

2016-01-01

Strategies for discovering common molecular events among disparate diseases hold promise for improving understanding of disease etiology and expanding treatment options. One technique is to leverage curated datasets found in the public domain. The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) manually curates chemical-gene, chemical-disease, and gene-disease interactions from the scientific literature. The use of official gene symbols in CTD interactions enables this information to be combined with the Gene Ontology (GO) file from NCBI Gene. By integrating these GO-gene annotations with CTD’s gene-disease dataset, we produce 753,000 inferences between 15,700 GO terms and 4,200 diseases, providing opportunities to explore presumptive molecular underpinnings of diseases and identify biological similarities. Through a variety of applications, we demonstrate the utility of this novel resource. As a proof-of-concept, we first analyze known repositioned drugs (e.g., raloxifene and sildenafil) and see that their target diseases have a greater degree of similarity when comparing GO terms vs. genes. Next, a computational analysis predicts seemingly non-intuitive diseases (e.g., stomach ulcers and atherosclerosis) as being similar to bipolar disorder, and these are validated in the literature as reported co-diseases. Additionally, we leverage other CTD content to develop testable hypotheses about thalidomide-gene networks to treat seemingly disparate diseases. Finally, we illustrate how CTD tools can rank a series of drugs as potential candidates for repositioning against B-cell chronic lymphocytic leukemia and predict cisplatin and the small molecule inhibitor JQ1 as lead compounds. The CTD dataset is freely available for users to navigate pathologies within the context of extensive biological processes, molecular functions, and cellular components conferred by GO. This inference set should aid researchers, bioinformaticists, and pharmaceutical drug makers in finding commonalities in disease mechanisms, which in turn could help identify new therapeutics, new indications for existing pharmaceuticals, potential disease comorbidities, and alerts for side effects. PMID:27171405

The Binding of Plasmodium falciparum Adhesins and Erythrocyte Invasion Proteins to Aldolase Is Enhanced by Phosphorylation.

PubMed

Diaz, Suraya A; Martin, Stephen R; Howell, Steven A; Grainger, Munira; Moon, Robert W; Green, Judith L; Holder, Anthony A

2016-01-01

Aldolase has been implicated as a protein coupling the actomyosin motor and cell surface adhesins involved in motility and host cell invasion in the human malaria parasite Plasmodium falciparum. It binds to the cytoplasmic domain (CTD) of type 1 membrane proteins of the thrombospondin-related anonymous protein (TRAP) family. Other type 1 membrane proteins located in the apical organelles of merozoites, the form of the parasite that invades red blood cells, including apical membrane antigen 1 (AMA1) and members of the erythrocyte binding ligand (EBL) and reticulocyte binding homologue (RH) protein families have been implicated in host cell binding and invasion. Using a direct binding method we confirm that TRAP and merozoite TRAP (MTRAP) bind aldolase and show that the interaction is mediated by more than just the C-terminal six amino acid residues identified previously. Single amino acid substitutions in the MTRAP CTD abolished binding to aldolase. The CTDs of AMA1 and members of the EBL and RH protein families also bound to aldolase. MTRAP competed with AMA1 and RH4 for binding to aldolase, indicating overlapping binding sites. MTRAP CTD was phosphorylated in vitro by both calcium dependent kinase 1 (CDPK1) and protein kinase A, and this modification increased the affinity of binding to aldolase by ten-fold. Phosphorylation of the CTD of members of the EBL and RH protein families also increased their affinity for aldolase in some cases. To examine whether or not MTRAP expressed in asexual blood stage parasites is phosphorylated, it was tagged with GFP, purified and analysed, however no phosphorylation was detected. We propose that CTD binding to aldolase may be dynamically modulated by phosphorylation, and there may be competition for aldolase binding between different CTDs. The use and efficiency of alternate invasion pathways may be determined by the affinity of adhesins and cell invasion proteins for aldolase, in addition to their host ligand specificity.

ToF-SIMS Depth Profiling Of Insulating Samples, Interlaced Mode Or Non-interlaced Mode?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Zhaoying; Jin, Ke; Zhang, Yanwen

2014-11-01

Dual beam depth profiling strategy has been widely adopted in ToF-SIMS depth profiling, in which two basic operation modes, interlaced mode and non-interlaced mode, are commonly used. Generally, interlaced mode is recommended for conductive or semi-conductive samples, whereas non-interlaced mode is recommended for insulating samples, where charge compensation can be an issue. Recent publications, however, show that the interlaced mode can be used effectively for glass depth profiling, despite the fact that glass is an insulator. In this study, we provide a simple guide for choosing between interlaced mode and non-interlaced mode for insulator depth profiling. Two representative cases aremore » presented: (1) depth profiling of a leached glass sample, and (2) depth profiling of a single crystal MgO sample. In brief, the interlaced mode should be attempted first, because (1) it may provide reasonable-quality data, and (2) it is time-saving for most cases, and (3) it introduces low H/C/O background. If data quality is the top priority and measurement time is flexible, non-interlaced mode is recommended because interlaced mode may suffer from low signal intensity and poor mass resolution. A big challenge is tracking trace H/C/O in a highly insulating sample (e.g., MgO), because non-interlaced mode may introduce strong H/C/O background but interlaced mode may suffer from low signal intensity. Meanwhile, a C or Au coating is found to be very effective to improve the signal intensity. Surprisingly, the best analyzing location is not on the C or Au coating, but at the edge (outside) of the coating.« less

Comparison of seasonal variability of Aquarius sea surface salinity time series with in situ observations in the Karimata Strait, Indonesia

NASA Astrophysics Data System (ADS)

Susanto, R. D.; Setiawan, A.; Zheng, Q.; Sulistyo, B.; Adi, T. R.; Agustiadi, T.; Trenggono, M.; Triyono, T.; Kuswardani, A.

2016-12-01

The seasonal variability of a full lifetime of Aquarius sea surface salinity time series from August 25, 2011 to June 7, 2015 is compared to salinity time series obtained from in situ observations in the Karimata Strait. The Karimata Strait plays dual roles in water exchange between the Pacific and the Indian Ocean. The salinity in the Karimata Strait is strongly affected by seasonal monsoon winds. During the boreal winter monsoon, northwesterly winds draws low salinity water from the South China Sea into the Java Sea and at the same time, the Java Sea receives an influx of the Indian Ocean water via the Sunda Strait. The Java Sea water will reduce the main Indonesian throughflow in the Makassar Strait. Conditions are reversed during the summer monsoon. Low salinity water from the South China Sea also controls the vertical structure of water properties in the upper layer of the Makassar Strait and the Lombok Strait. As a part of the South China Sea and Indonesian Seas Transport/Exchange (SITE) program, trawl resistance bottom mounted CTD was deployed in the Karimata Strait in mid-2010 to mid-2016 at water depth of 40 m. CTD casts during the mooring recoveries and deployments are used to compare the bottom salinity data. This in situ salinity time series is compared with various Aquarius NASA salinity products (the level 2, level 3 ascending and descending tracks and the seven-days rolling averaged) to check the consistency, correlation and statistical analysis. The preliminary results show that the seasonal variability of Aquarius salinity time series has larger amplitude variability compared to that of in situ data.

Target-depth estimation in active sonar: Cramer-Rao bounds for a bilinear sound-speed profile.

PubMed

Mours, Alexis; Ioana, Cornel; Mars, Jérôme I; Josso, Nicolas F; Doisy, Yves

2016-09-01

This paper develops a localization method to estimate the depth of a target in the context of active sonar, at long ranges. The target depth is tactical information for both strategy and classification purposes. The Cramer-Rao lower bounds for the target position as range and depth are derived for a bilinear profile. The influence of sonar parameters on the standard deviations of the target range and depth are studied. A localization method based on ray back-propagation with a probabilistic approach is then investigated. Monte-Carlo simulations applied to a summer Mediterranean sound-speed profile are performed to evaluate the efficiency of the estimator. This method is finally validated on data in an experimental tank.

Depth elemental characterization of 1D self-aligned TiO2 nanotubes using calibrated radio frequency glow discharge optical emission spectroscopy (GDOES)

NASA Astrophysics Data System (ADS)

Mohajernia, Shiva; Mazare, Anca; Hwang, Imgon; Gaiaschi, Sofia; Chapon, Patrick; Hildebrand, Helga; Schmuki, Patrik

2018-06-01

In this work we study the depth composition of anodic TiO2 nanotube layers. We use elemental depth profiling with Glow Discharge Optical Emission Spectroscopy and calibrate the results of this technique with X-ray photoelectron spectroscopy (XPS) and energy dispersive spectroscopy (EDS). We establish optimized sputtering conditions for nanotubular structures using the pulsed RF mode, which causes minimized structural damage during the depth profiling of the nanotubular structures. This allows to obtain calibrated sputter rates that account for the nanotubular "porous" morphology. Most importantly, sputter-artifact free compositional profiles of these high aspect ratio 3D structures are obtained, as well as, in combination with SEM, elegant depth sectional imaging.

Carbon Dioxide, Hydrographic, and Chemical Data Obtained During the R/V Thomas G. Thompson Cruise in the Pacific Ocean

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sabine, C.L.; Key, R.M.; Hall, M.

1999-08-01

This data documentation discusses the procedures and methods used to measure total carbon dioxide (TCO2), total alkalinity (TALK), and radiocarbon (delta 14C), at hydrographic stations, as well as the underway partial pressure of CO2 (pCO2) during the R/V Thomas G. Thompson oceanographic cruise in the Pacific Ocean (Section P10). Conducted as part of the World Ocean Circulation Experiment (WOCE), the cruise began in Suva, Fiji, on October 5, 1993, and ended in Yokohama, Japan, on November 10, 1993. Measurements made along WOCE Section P10 included pressure, temperature, salinity [measured by conductivity temperature, and depth sensor (CTD)], bottle salinity, bottle oxygen,more » phosphate, nitrate, silicate, chlorofluorocarbons (CFC-11, CFC-12), TCO2, TALK, delta 14C, and underway pCO2.« less

Kin28 regulates the transient association of Mediator with core promoters

PubMed Central

Jeronimo, Célia; Robert, François

2014-01-01

Mediator is an essential, broadly utilized eukaryotic transcriptional co-activator. How and what it communicates from activators to RNA polymerase II (RNAPII) remains an open question. Here we performed genome-wide location profiling of Saccharomyces cerevisiae Mediator subunits. Mediator is not found at core promoters but rather occupies the upstream activating sequence (UAS), upstream of the pre-initiation complex. In the absence of Kin28 (CDK7) kinase activity, or in cells where the RNAPII C-terminal domain (CTD) is mutated to replace Ser5 with alanines, however, Mediator accumulates at core promoters together with RNAPII. We propose that Mediator is quickly released from promoters upon Ser5 phosphorylation by Kin28 (CDK7), which also allows for RNAPII to escape from the promoter. PMID:24704787

Evaluating the NOAA Coastal and Marine Ecological Classification Standard in estuarine systems: A Columbia River Estuary case study

NASA Astrophysics Data System (ADS)

Keefer, Matthew L.; Peery, Christopher A.; Wright, Nancy; Daigle, William R.; Caudill, Christopher C.; Clabough, Tami S.; Griffith, David W.; Zacharias, Mark A.

2008-06-01

A common first step in conservation planning and resource management is to identify and classify habitat types, and this has led to a proliferation of habitat classification systems. Ideally, classifications should be scientifically and conceptually rigorous, with broad applicability across spatial and temporal scales. Successful systems will also be flexible and adaptable, with a framework and supporting lexicon accessible to users from a variety of disciplines and locations. A new, continental-scale classification system for coastal and marine habitats—the Coastal and Marine Ecological Classification Standard (CMECS)—is currently being developed for North America by NatureServe and the National Oceanic and Atmospheric Administration (NOAA). CMECS is a nested, hierarchical framework that applies a uniform set of rules and terminology across multiple habitat scales using a combination of oceanographic (e.g. salinity, temperature), physiographic (e.g. depth, substratum), and biological (e.g. community type) criteria. Estuaries are arguably the most difficult marine environments to classify due to large spatio-temporal variability resulting in rapidly shifting benthic and water column conditions. We simultaneously collected data at eleven subtidal sites in the Columbia River Estuary (CRE) in fall 2004 to evaluate whether the estuarine component of CMECS could adequately classify habitats across several scales for representative sites within the estuary spanning a range of conditions. Using outputs from an acoustic Doppler current profiler (ADCP), CTD (conductivity, temperature, depth) sensor, and PONAR (benthic dredge) we concluded that the CMECS hierarchy provided a spatially explicit framework in which to integrate multiple parameters to define macro-habitats at the 100 m 2 to >1000 m 2 scales, or across several tiers of the CMECS system. The classification's strengths lie in its nested, hierarchical structure and in the development of a standardized, yet flexible classification lexicon. The application of the CMECS to other estuaries in North America should therefore identify similar habitat types at similar scales as we identified in the CRE. We also suggest that the CMECS could be improved by refining classification thresholds to better reflect ecological processes, by direct integration of temporal variability, and by more explicitly linking physical and biological processes with habitat patterns.

Depth Profilometry via Multiplexed Optical High-Coherence Interferometry

PubMed Central

Kazemzadeh, Farnoud; Wong, Alexander; Behr, Bradford B.; Hajian, Arsen R.

2015-01-01

Depth Profilometry involves the measurement of the depth profile of objects, and has significant potential for various industrial applications that benefit from non-destructive sub-surface profiling such as defect detection, corrosion assessment, and dental assessment to name a few. In this study, we investigate the feasibility of depth profilometry using an Multiplexed Optical High-coherence Interferometry MOHI instrument. The MOHI instrument utilizes the spatial coherence of a laser and the interferometric properties of light to probe the reflectivity as a function of depth of a sample. The axial and lateral resolutions, as well as imaging depth, are decoupled in the MOHI instrument. The MOHI instrument is capable of multiplexing interferometric measurements into 480 one-dimensional interferograms at a location on the sample and is built with axial and lateral resolutions of 40 μm at a maximum imaging depth of 700 μm. Preliminary results, where a piece of sand-blasted aluminum, an NBK7 glass piece, and an optical phantom were successfully probed using the MOHI instrument to produce depth profiles, demonstrate the feasibility of such an instrument for performing depth profilometry. PMID:25803289

Depth profilometry via multiplexed optical high-coherence interferometry.

PubMed

Kazemzadeh, Farnoud; Wong, Alexander; Behr, Bradford B; Hajian, Arsen R

2015-01-01

Depth Profilometry involves the measurement of the depth profile of objects, and has significant potential for various industrial applications that benefit from non-destructive sub-surface profiling such as defect detection, corrosion assessment, and dental assessment to name a few. In this study, we investigate the feasibility of depth profilometry using an Multiplexed Optical High-coherence Interferometry MOHI instrument. The MOHI instrument utilizes the spatial coherence of a laser and the interferometric properties of light to probe the reflectivity as a function of depth of a sample. The axial and lateral resolutions, as well as imaging depth, are decoupled in the MOHI instrument. The MOHI instrument is capable of multiplexing interferometric measurements into 480 one-dimensional interferograms at a location on the sample and is built with axial and lateral resolutions of 40 μm at a maximum imaging depth of 700 μm. Preliminary results, where a piece of sand-blasted aluminum, an NBK7 glass piece, and an optical phantom were successfully probed using the MOHI instrument to produce depth profiles, demonstrate the feasibility of such an instrument for performing depth profilometry.

High Spectral Resolution Lidar Data

DOE Data Explorer

Eloranta, Ed

2004-12-01

The HSRL provided calibrated vertical profiles of optical depth, backscatter cross section and depoloarization at a wavelength of 532 nm. Profiles were acquired at 2.5 second intervals with 7.5 meter resolution. Profiles extended from an altitude of 100 m to 30 km in clear air. The lidar penetrated to a maximum optical depth of ~ 4 under cloudy conditions. Our data contributed directly to the aims of the M-PACE experiment, providing calibrated optical depth and optical backscatter measurements which were not available from any other instrument.

Spectral analysis of aeromagnetic profiles for depth estimation principles, software, and practical application

USGS Publications Warehouse

Sadek, H.S.; Rashad, S.M.; Blank, H.R.

1984-01-01

If proper account is taken of the constraints of the method, it is capable of providing depth estimates to within an accuracy of about 10 percent under suitable circumstances. The estimates are unaffected by source magnetization and are relatively insensitive to assumptions as to source shape or distribution. The validity of the method is demonstrated by analyses of synthetic profiles and profiles recorded over Harrat Rahat, Saudi Arabia, and Diyur, Egypt, where source depths have been proved by drilling.

Unfolding of a Temperature-Sensitive Domain Controls Voltage-Gated Channel Activation.

PubMed

Arrigoni, Cristina; Rohaim, Ahmed; Shaya, David; Findeisen, Felix; Stein, Richard A; Nurva, Shailika Reddy; Mishra, Smriti; Mchaourab, Hassane S; Minor, Daniel L

2016-02-25

Voltage-gated ion channels (VGICs) are outfitted with diverse cytoplasmic domains that impact function. To examine how such elements may affect VGIC behavior, we addressed how the bacterial voltage-gated sodium channel (BacNa(V)) C-terminal cytoplasmic domain (CTD) affects function. Our studies show that the BacNa(V) CTD exerts a profound influence on gating through a temperature-dependent unfolding transition in a discrete cytoplasmic domain, the neck domain, proximal to the pore. Structural and functional studies establish that the BacNa(V) CTD comprises a bi-partite four-helix bundle that bears an unusual hydrophilic core whose integrity is central to the unfolding mechanism and that couples directly to the channel activation gate. Together, our findings define a general principle for how the widespread four-helix bundle cytoplasmic domain architecture can control VGIC responses, uncover a mechanism underlying the diverse BacNa(V) voltage dependencies, and demonstrate that a discrete domain can encode the temperature-dependent response of a channel. Copyright © 2016 Elsevier Inc. All rights reserved.

Unfolding of a temperature-sensitive domain controls voltage-gated channel activation

PubMed Central

Arrigoni, Cristina; Rohaim, Ahmed; Shaya, David; Findeisen, Felix; Stein, Richard A.; Nurva, Shailika Reddy; Mishra, Smriti; Mchaourab, Hassane S.; Minor, Daniel L.

2016-01-01

Voltage-gated ion channels (VGICs) are outfitted with diverse cytoplasmic domains that impact function. To examine how such elements may affect VGIC behavior, we addressed how the bacterial voltage-gated sodium channel (BacNaV) C-terminal cytoplasmic domain (CTD) affects function. Our studies show that the BacNaV CTD exerts a profound influence on gating through a temperature-dependent unfolding transition in a discrete cytoplasmic domain, the neck domain, proximal to the pore. Structural and functional studies establish that the BacNaV CTD comprises a bi-partite four-helix bundle that bears an unusual hydrophilic core whose integrity is central to the unfolding mechanism and that couples directly to the channel activation gate. Together, our findings define a general principle for how the widespread four-helix bundle cytoplasmic domain architecture can control VGIC responses, uncover a mechanism underlying the diverse BacNaV voltage dependencies, and demonstrate that a discrete domain can encode the temperature dependent response of a channel. PMID:26919429

Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli

PubMed Central

Singh, S.; Folkers, G.E.; Bonvin, A.M.J.J.; Boelens, R.; Wechselberger, R.; Niztayev, A.; Kaptein, R.

2002-01-01

The C-terminal domain of the UvrC protein (UvrC CTD) is essential for 5′ incision in the prokaryotic nucleotide excision repair process. We have determined the three-dimensional structure of the UvrC CTD using heteronuclear NMR techniques. The structure shows two helix–hairpin–helix (HhH) motifs connected by a small connector helix. The UvrC CTD is shown to mediate structure-specific DNA binding. The domain binds to a single-stranded–double-stranded junction DNA, with a strong specificity towards looped duplex DNA that contains at least six unpaired bases per loop (‘bubble DNA’). Using chemical shift perturbation experiments, the DNA-binding surface is mapped to the first hairpin region encompassing the conserved glycine–valine–glycine residues followed by lysine–arginine–arginine, a positively charged surface patch and the second hairpin region consisting of glycine–isoleucine–serine. A model for the protein– DNA complex is proposed that accounts for this specificity. PMID:12426397

Structural analyses of Ca2+/CaM interaction with NaV channel C-termini reveal mechanisms of calcium-dependent regulation

PubMed Central

Wang, Chaojian; Chung, Ben C.; Yan, Haidun; Wang, Hong-Gang; Lee, Seok-Yong; Pitt, Geoffrey S.

2014-01-01

Ca2+ regulates voltage-gated Na+ (NaV) channels and perturbed Ca2+ regulation of NaV function is associated with epilepsy syndromes, autism, and cardiac arrhythmias. Understanding the disease mechanisms, however, has been hindered by a lack of structural information and competing models for how Ca2+ affects NaV channel function. Here, we report the crystal structures of two ternary complexes of a human NaV cytosolic C-terminal domain (CTD), a fibroblast growth factor homologous factor, and Ca2+/calmodulin (Ca2+/CaM). These structures rule out direct binding of Ca2+ to the NaV CTD, and uncover new contacts between CaM and the NaV CTD. Probing these new contacts with biochemical and functional experiments allows us to propose a mechanism by which Ca2+ could regulate NaV channels. Further, our model provides hints towards understanding the molecular basis of the neurologic disorders and cardiac arrhythmias caused by NaV channel mutations. PMID:25232683

Charge Transfer Dissociation of Complex Oligosaccharides: Comparison with Collision-Induced Dissociation and Extreme Ultraviolet Dissociative Photoionization

NASA Astrophysics Data System (ADS)

Ropartz, David; Li, Pengfei; Fanuel, Mathieu; Giuliani, Alexandre; Rogniaux, Hélène; Jackson, Glen P.

2016-10-01

The structural characterization of oligosaccharides still challenges the field of analytical chemistry. Tandem mass spectrometry offers many advantages toward this aim, although the generic fragmentation method (low-energy collision-induced dissociation) shows clear limitations and is often insufficient to retrieve some essential structural information on these molecules. In this work, we present the first application of helium charge transfer dissociation (He-CTD) to characterize the structure of complex oligosaccharides. We compare this method with low-energy collision-induced dissociation and extreme-ultraviolet dissociative photoionization (XUV-DPI), which was shown previously to ensure the successful characterization of complex glycans. Similarly to what could be obtained by XUV-DPI, He-CTD provides a complete description of the investigated structures by producing many informative cross-ring fragments and no ambiguous fragmentation. Unlike XUV-DPI, which is performed at a synchrotron source, He-CTD has the undeniable advantage of being implementable in a conventional benchtop ion trap in a conventional laboratory setting.

Crystal structure of an HIV assembly and maturation switch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagner, Jonathan M.; Zadrozny, Kaneil K.; Chrustowicz, Jakub

Virus assembly and maturation proceed through the programmed operation of molecular switches, which trigger both local and global structural rearrangements to produce infectious particles. HIV-1 contains an assembly and maturation switch that spans the C-terminal domain (CTD) of the capsid (CA) region and the first spacer peptide (SP1) of the precursor structural protein, Gag. The crystal structure of the CTD-SP1 Gag fragment is a goblet-shaped hexamer in which the cup comprises the CTD and an ensuing type II β-turn, and the stem comprises a 6-helix bundle. The β-turn is critical for immature virus assembly and the 6-helix bundle regulates proteolysismore » during maturation. This bipartite character explains why the SP1 spacer is a critical element of HIV-1 Gag but is not a universal property of retroviruses. Our results also indicate that HIV-1 maturation inhibitors suppress unfolding of the CA-SP1 junction and thereby delay access of the viral protease to its substrate.« less

Sirt1 carboxyl-domain is an ATP-repressible domain that is transferrable to other proteins

PubMed Central

Kang, Hyeog; Oka, Shinichi; Lee, Duck-Yeon; Park, Junhong; Aponte, Angel M.; Jung, Young-Sang; Bitterman, Jacob; Zhai, Peiyong; He, Yi; Kooshapur, Hamed; Ghirlando, Rodolfo; Tjandra, Nico; Lee, Sean B.; Kim, Myung K.; Sadoshima, Junichi; Chung, Jay H.

2017-01-01

Sirt1 is an NAD+-dependent protein deacetylase that regulates many physiological functions, including stress resistance, adipogenesis, cell senescence and energy production. Sirt1 can be activated by energy deprivation, but the mechanism is poorly understood. Here, we report that Sirt1 is negatively regulated by ATP, which binds to the C-terminal domain (CTD) of Sirt1. ATP suppresses Sirt1 activity by impairing the CTD's ability to bind to the deacetylase domain as well as its ability to function as the substrate recruitment site. ATP, but not NAD+, causes a conformational shift to a less compact structure. Mutations that prevent ATP binding increase Sirt1's ability to promote stress resistance and inhibit adipogenesis under high-ATP conditions. Interestingly, the CTD can be attached to other proteins, thereby converting them into energy-regulated proteins. These discoveries provide insight into how extreme energy deprivation can impact Sirt1 activity and underscore the complex nature of Sirt1 structure and regulation. PMID:28504272

Evaluation of Variable-Depth Liner Configurations for Increased Broadband Noise Reduction

NASA Technical Reports Server (NTRS)

Jones, M. G.; Watson, W. R.; Nark, D. M.; Howerton, B. M.

2015-01-01

This paper explores the effects of variable-depth geometry on the amount of noise reduction that can be achieved with acoustic liners. Results for two variable-depth liners tested in the NASA Langley Grazing Flow Impedance Tube demonstrate significant broadband noise reduction. An impedance prediction model is combined with two propagation codes to predict corresponding sound pressure level profiles over the length of the Grazing Flow Impedance Tube. The comparison of measured and predicted sound pressure level profiles is sufficiently favorable to support use of these tools for investigation of a number of proposed variable-depth liner configurations. Predicted sound pressure level profiles for these proposed configurations reveal a number of interesting features. Liner orientation clearly affects the sound pressure level profile over the length of the liner, but the effect on the total attenuation is less pronounced. The axial extent of attenuation at an individual frequency continues well beyond the location where the liner depth is optimally tuned to the quarter-wavelength of that frequency. The sound pressure level profile is significantly affected by the way in which variable-depth segments are distributed over the length of the liner. Given the broadband noise reduction capability for these liner configurations, further development of impedance prediction models and propagation codes specifically tuned for this application is warranted.

Transient response of the Northwestern Iberian upwelling regime.

PubMed

Ferreira Cordeiro, Nuno Gonçalo; Dubert, Jesus; Nolasco, Rita; Desmond Barton, Eric

2018-01-01

The hydrography and dynamics of NW Iberian margin were explored for July 2009, based on a set of in situ and remote sensing observations. Zonal sections of standard CTD casts, towed CTD (SeaSoar), Acoustic Doppler Current Profilers (ADCP) and Lagrangian surveys were made to characterize cycles of upwelling and relaxation in this region. Two periods of northerly winds, bounded by relaxation periods, were responsible for the formation of an upwelling front extending to the shelf edge. An equatorward flow was quickly set up on the shelf responding to the northerly wind pulses. South of Cape Silleiro, the development and subsequent relaxation of an upwelling event was intensively surveyed in the shelf, following a Lagrangian drifter transported by the upwelling jet. This region is part of an upwelling center extending from Cape Silleiro to Porto, where the surface temperature was colder than the neighboring regions, under upwelling favorable winds. As these winds relaxed, persistent poleward flow developed, originating south of the upwelling center and consisting in an inner-shelf tongue of warm waters. During an event of strong southerly wind, the poleward flow was observed to extend to the whole continental shelf. Although the cruise was executed during summertime, the presence of river-plumes was observed over the shelf. The interaction of the plumes with the circulation on the shelf was also described in terms of coastal convergence and offshore advection. The sampling of the offshore and slope regions showed the presence of the Iberian poleward current offshore and a persistent equatorward flow over the upper slope.

MDCT quantification is the dominant parameter in decision–making regarding chest tube drainage for stable patients with traumatic pneumothorax

PubMed Central

Cai, Wenli; Lee, June-Goo; Fikry, Karim; Yoshida, Hiroyuki; Novelline, Robert; de Moya, Marc

2013-01-01

It is commonly believed that the size of a pneumothorax is an important determinant of treatment decision, in particular regarding whether chest tube drainage (CTD) is required. However, the volumetric quantification of pneumothoraces has not routinely been performed in clinics. In this paper, we introduced an automated computer-aided volumetry (CAV) scheme for quantification of volume of pneumothoraces in chest multi-detect CT (MDCT) images. Moreover, we investigated the impact of accurate volume of pneumothoraces in the improvement of the performance in decision-making regarding CTD in the management of traumatic pneumothoraces. For this purpose, an occurrence frequency map was calculated for quantitative analysis of the importance of each clinical parameter in the decision-making regarding CTD by a computer simulation of decision-making using a genetic algorithm (GA) and a support vector machine (SVM). A total of 14 clinical parameters, including volume of pneumothorax calculated by our CAV scheme, was collected as parameters available for decision-making. The results showed that volume was the dominant parameter in decision-making regarding CTD, with an occurrence frequency value of 1.00. The results also indicated that the inclusion of volume provided the best performance that was statistically significant compared to the other tests in which volume was excluded from the clinical parameters. This study provides the scientific evidence for the application of CAV scheme in MDCT volumetric quantification of pneumothoraces in the management of clinically stable chest trauma patients with traumatic pneumothorax. PMID:22560899

Mindfulness-based stress reduction for Tourette Syndrome and Chronic Tic Disorder: a pilot study.

PubMed

Reese, Hannah E; Vallejo, Zayda; Rasmussen, Jessica; Crowe, Katherine; Rosenfield, Elizabeth; Wilhelm, Sabine

2015-03-01

In this pilot study we sought to develop and test a modified form of mindfulness-based stress reduction (MBSR-tics) for the treatment of Tourette Syndrome (TS) and Chronic Tic Disorder (CTD). Our specific aims were: 1) To determine the feasibility and acceptability of an 8-week trial of MBSR-tics in individuals 16 and older with TS or CTD and 2) To determine the efficacy of an 8-week trial of MBSR-tics in individuals 16 and older with TS or CTD. Eighteen individuals age 16-67 completed an uncontrolled open trial of MBSR-tics. The intervention consisted of 8 weekly 2-hour classes and one 4hour retreat in the fifth or sixth week of the program. Symptomatic assessments were performed at baseline, post-treatment, and one-month follow-up. MBSR-tics proved to be a feasible and acceptable intervention. It resulted in significant improvement in tic severity and tic-related impairment. 58.8% of subjects were deemed treatment responders. Therapeutic gains were maintained at 1-month follow-up. Improvements in tic severity were correlated with increases in self-reported levels of mindfulness. This small open pilot study provides preliminary support for the feasibility, acceptability, and efficacy of MBSR-tics for individuals 16 or older with TS or CTD. A larger randomized controlled trial with blind assessment is necessary to confirm these initial, promising findings. Trial Registration Partners Clinical Trials Registry Number 2011P000606 (clinicaltrials.partners.org). Copyright © 2014 Elsevier Inc. All rights reserved.

Caenorhabditis elegans fibroblast growth factor receptor signaling can occur independently of the multi-substrate adaptor FRS2.

PubMed

Lo, Te-Wen; Bennett, Daniel C; Goodman, S Jay; Stern, Michael J

2010-06-01

The components of receptor tyrosine kinase signaling complexes help to define the specificity of the effects of their activation. The Caenorhabditis elegans fibroblast growth factor receptor (FGFR), EGL-15, regulates a number of processes, including sex myoblast (SM) migration guidance and fluid homeostasis, both of which require a Grb2/Sos/Ras cassette of signaling components. Here we show that SEM-5/Grb2 can bind directly to EGL-15 to mediate SM chemoattraction. A yeast two-hybrid screen identified SEM-5 as able to interact with the carboxy-terminal domain (CTD) of EGL-15, a domain that is specifically required for SM chemoattraction. This interaction requires the SEM-5 SH2-binding motifs present in the CTD (Y(1009) and Y(1087)), and these sites are required for the CTD role of EGL-15 in SM chemoattraction. SEM-5, but not the SEM-5 binding sites located in the CTD, is required for the fluid homeostasis function of EGL-15, indicating that SEM-5 can link to EGL-15 through an alternative mechanism. The multi-substrate adaptor protein FRS2 serves to link vertebrate FGFRs to Grb2. In C. elegans, an FRS2-like gene, rog-1, functions upstream of a Ras/MAPK pathway for oocyte maturation but is not required for EGL-15 function. Thus, unlike the vertebrate FGFRs, which require the multi-substrate adaptor FRS2 to recruit Grb2, EGL-15 can recruit SEM-5/Grb2 directly.

The combined effect of clothianidin and environmental stress on the behavioral and reproductive function in male mice

PubMed Central

HIRANO, Tetsushi; YANAI, Shogo; OMOTEHARA, Takuya; HASHIMOTO, Rie; UMEMURA, Yuria; KUBOTA, Naoto; MINAMI, Kiichi; NAGAHARA, Daichi; MATSUO, Eiko; AIHARA, Yoshiko; SHINOHARA, Ryota; FURUYASHIKI, Tomoyuki; MANTANI, Youhei; YOKOYAMA, Toshifumi; KITAGAWA, Hiroshi; HOSHI, Nobuhiko

2015-01-01

Neonicotinoids, some of the most widely used pesticides in the world, act as agonists to the nicotinic acetylcholine receptors (nAChRs) of insects, resulting in death from abnormal excitability. Neonicotinoids unexpectedly became a major topic as a compelling cause of honeybee colony collapse disorder, which is damaging crop production that requires pollination worldwide. Mammal nAChRs appear to have a certain affinity for neonicotinoids with lower levels than those of insects; there is thus rising concern about unpredictable adverse effects of neonicotinoids on vertebrates. We hypothesized that the effects of neonicotinoids would be enhanced under a chronic stressed condition, which is known to alter the expression of targets of neonicotinoids, i.e., neuronal nAChRs. We performed immunohistochemical and behavioral analyses in male mice actively administered a neonicotinoid, clothianidin (CTD; 0, 10, 50 and 250 mg/kg/day), for 4 weeks under an unpredictable chronic stress procedure. Vacuolated seminiferous epithelia and a decrease in the immunoreactivity of the antioxidant enzyme glutathione peroxidase 4 were observed in the testes of the CTD+stress mice. In an open field test, although the locomotor activities were not affected, the anxiety-like behaviors of the mice were elevated by both CTD and stress. The present study demonstrates that the behavioral and reproductive effects of CTD become more serious in combination with environmental stress, which may reflect our actual situation of multiple exposure. PMID:25960033

Structural and functional probing of PorZ, an essential bacterial surface component of the type-IX secretion system of human oral-microbiomic Porphyromonas gingivalis.

PubMed Central

Lasica, Anna M.; Goulas, Theodoros; Mizgalska, Danuta; Zhou, Xiaoyan; de Diego, Iñaki; Ksiazek, Mirosław; Madej, Mariusz; Guo, Yonghua; Guevara, Tibisay; Nowak, Magdalena; Potempa, Barbara; Goel, Apoorv; Sztukowska, Maryta; Prabhakar, Apurva T.; Bzowska, Monika; Widziolek, Magdalena; Thøgersen, Ida B.; Enghild, Jan J.; Simonian, Mary; Kulczyk, Arkadiusz W.; Nguyen, Ky-Anh; Potempa, Jan; Gomis-Rüth, F. Xavier

2016-01-01

Porphyromonas gingivalis is a member of the human oral microbiome abundant in dysbiosis and implicated in the pathogenesis of periodontal (gum) disease. It employs a newly described type-IX secretion system (T9SS) for secretion of virulence factors. Cargo proteins destined for secretion through T9SS carry a recognition signal in the conserved C-terminal domain (CTD), which is removed by sortase PorU during translocation. Here, we identified a novel component of T9SS, PorZ, which is essential for surface exposure of PorU and posttranslational modification of T9SS cargo proteins. These include maturation of enzyme precursors, CTD removal and attachment of anionic lipopolysaccharide for anchorage in the outer membrane. The crystal structure of PorZ revealed two β-propeller domains and a C-terminal β-sandwich domain, which conforms to the canonical CTD architecture. We further documented that PorZ is itself transported to the cell surface via T9SS as a full-length protein with its CTD intact, independently of the presence or activity of PorU. Taken together, our results shed light on the architecture and possible function of a novel component of the T9SS. Knowledge of how T9SS operates will contribute to our understanding of protein secretion as part of host-microbiome interactions by dysbiotic members of the human oral cavity. PMID:27883039

Efficacy and toxicity of the combination chemotherapy of thalidomide, alkylating agent, and steroid for relapsed/refractory myeloma patients: a report from the Korean Multiple Myeloma Working Party (KMMWP) retrospective study.

PubMed

Kwon, Jihyun; Min, Chang-Ki; Kim, Kihyun; Han, Jae-Joon; Moon, Joon Ho; Kang, Hye Jin; Eom, Hyeon-Seok; Kim, Min Kyoung; Kim, Hyo Jung; Yoon, Dok Hyun; Lee, Jeong-Ok; Lee, Won Sik; Lee, Jae Hoon; Lee, Je-Jung; Choi, Yoon-Seok; Kim, Sung Hyun; Yoon, Sung-Soo

2017-01-01

We analyzed the treatment responses, toxicities, and survival outcomes of patients with relapsed or refractory multiple myeloma who received daily thalidomide, cyclophosphamide, and dexamethasone (CTD) or daily thalidomide, melphalan, and prednisolone (MTP) at 17 medical centers in Korea. Three-hundred and seventy-six patients were enrolled. The combined chemotherapy of thalidomide, corticosteroid, and an alkylating agent (TAS) was second-line chemotherapy in 142 (37.8%) patients, and third-line chemotherapy in 135 (35.9%) patients. The response rate overall was 69.4%. Patients who were not treated with bortezomib and lenalidomide before TAS showed a higher response rate compared to those who were exposed to these agents. The estimated median progression-free survival and overall survival times were 10.4 months and 28.0 months, respectively. The adverse events during TAS were generally tolerable, but 39 (10.4%) patients experienced severe infectious complications. There were no differences in terms of efficacy between CTD and MTP, but infectious complications were more common in CTD group. TAS is an effective treatment regimen which induces a high response rate in relapsed or refractory multiple myeloma patients. Due to the high incidence of grade 3 or 4 infection, proper management of infection is necessary during the TAS treatment, especially the CTD. © 2016 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Quantitative detection of caffeine in human skin by confocal Raman spectroscopy--A systematic in vitro validation study.

PubMed

Franzen, Lutz; Anderski, Juliane; Windbergs, Maike

2015-09-01

For rational development and evaluation of dermal drug delivery, the knowledge of rate and extent of substance penetration into the human skin is essential. However, current analytical procedures are destructive, labor intense and lack a defined spatial resolution. In this context, confocal Raman microscopy bares the potential to overcome current limitations in drug depth profiling. Confocal Raman microscopy already proved its suitability for the acquisition of qualitative penetration profiles, but a comprehensive investigation regarding its suitability for quantitative measurements inside the human skin is still missing. In this work, we present a systematic validation study to deploy confocal Raman microscopy for quantitative drug depth profiling in human skin. After we validated our Raman microscopic setup, we successfully established an experimental procedure that allows correlating the Raman signal of a model drug with its controlled concentration in human skin. To overcome current drawbacks in drug depth profiling, we evaluated different modes of peak correlation for quantitative Raman measurements and offer a suitable operating procedure for quantitative drug depth profiling in human skin. In conclusion, we successfully demonstrate the potential of confocal Raman microscopy for quantitative drug depth profiling in human skin as valuable alternative to destructive state-of-the-art techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

Direct depth distribution measurement of deuterium in bulk tungsten exposed to high-flux plasma

DOE PAGES

Taylor, Chase N.; Shimada, M.

2017-05-08

Understanding tritium retention and permeation in plasma-facing components is critical for fusion safety and fuel cycle control. Glow discharge optical emission spectroscopy (GD-OES) is shown to be an effective tool to reveal the depth profile of deuterium in tungsten. Results confirm the detection of deuterium. Furthermore, a ~46 µm depth profile revealed that the deuterium content decreased precipitously in the first 7 µm, and detectable amounts were observed to depths in excess of 20 µm. The large probing depth of GD-OES (up to 100s of µm) enables studies not previously accessible to the more conventional techniques for investigating deuterium retention.more » Of particular applicability is the use of GD-OES to measure the depth profile for experiments where high diffusion is expected: deuterium retention in neutron irradiated materials, and ultra-high deuterium fluences in burning plasma environment.« less

Direct depth distribution measurement of deuterium in bulk tungsten exposed to high-flux plasma

NASA Astrophysics Data System (ADS)

Taylor, C. N.; Shimada, M.

2017-05-01

Understanding tritium retention and permeation in plasma-facing components is critical for fusion safety and fuel cycle control. Glow discharge optical emission spectroscopy (GD-OES) is shown to be an effective tool to reveal the depth profile of deuterium in tungsten. Results confirm the detection of deuterium. A ˜46 μm depth profile revealed that the deuterium content decreased precipitously in the first 7 μm, and detectable amounts were observed to depths in excess of 20 μm. The large probing depth of GD-OES (up to 100s of μm) enables studies not previously accessible to the more conventional techniques for investigating deuterium retention. Of particular applicability is the use of GD-OES to measure the depth profile for experiments where high deuterium concentration in the bulk material is expected: deuterium retention in neutron irradiated materials, and ultra-high deuterium fluences in burning plasma environment.

Depth profiling of ion-induced damage in D9 alloy using X-ray diffraction

NASA Astrophysics Data System (ADS)

Dey, S.; Gayathri, N.; Mukherjee, P.

2018-04-01

The ion-induced depthwise damage profile in 35 MeV α-irradiated D9 alloy samples with doses of 5 × 1015 He2+/cm2, 6.4 × 1016 He2+/cm2 and 2 × 1017 He2+/cm2 has been assessed using X-ray diffraction technique. The microstructural characterisation has been done along the depth from beyond the stopping region (peak damage region) to the homogeneous damage region (surface) as simulated from SRIM. The parameters such as domain size and microstrain have been evaluated using two different X-ray diffraction line profile analysis techniques. The results indicate that at low dose the damage profile shows a prominent variation as a function of depth but, with increasing dose, it becomes more homogeneous along the depth. This suggests that enhanced defect diffusion and their annihilation in pre-existing and newly formed sinks play a significant role in deciding the final microstructure of the irradiated sample as a function of depth.

Quantitative operando visualization of the energy band depth profile in solar cells.

PubMed

Chen, Qi; Mao, Lin; Li, Yaowen; Kong, Tao; Wu, Na; Ma, Changqi; Bai, Sai; Jin, Yizheng; Wu, Dan; Lu, Wei; Wang, Bing; Chen, Liwei

2015-07-13

The energy band alignment in solar cell devices is critically important because it largely governs elementary photovoltaic processes, such as the generation, separation, transport, recombination and collection of charge carriers. Despite the expenditure of considerable effort, the measurement of energy band depth profiles across multiple layers has been extremely challenging, especially for operando devices. Here we present direct visualization of the surface potential depth profile over the cross-sections of operando organic photovoltaic devices using scanning Kelvin probe microscopy. The convolution effect due to finite tip size and cantilever beam crosstalk has previously prohibited quantitative interpretation of scanning Kelvin probe microscopy-measured surface potential depth profiles. We develop a bias voltage-compensation method to address this critical problem and obtain quantitatively accurate measurements of the open-circuit voltage, built-in potential and electrode potential difference.

Quantitative operando visualization of the energy band depth profile in solar cells

PubMed Central

Chen, Qi; Mao, Lin; Li, Yaowen; Kong, Tao; Wu, Na; Ma, Changqi; Bai, Sai; Jin, Yizheng; Wu, Dan; Lu, Wei; Wang, Bing; Chen, Liwei

2015-01-01

The energy band alignment in solar cell devices is critically important because it largely governs elementary photovoltaic processes, such as the generation, separation, transport, recombination and collection of charge carriers. Despite the expenditure of considerable effort, the measurement of energy band depth profiles across multiple layers has been extremely challenging, especially for operando devices. Here we present direct visualization of the surface potential depth profile over the cross-sections of operando organic photovoltaic devices using scanning Kelvin probe microscopy. The convolution effect due to finite tip size and cantilever beam crosstalk has previously prohibited quantitative interpretation of scanning Kelvin probe microscopy-measured surface potential depth profiles. We develop a bias voltage-compensation method to address this critical problem and obtain quantitatively accurate measurements of the open-circuit voltage, built-in potential and electrode potential difference. PMID:26166580

Investigating turbulent mixing rates and the internal wave field in the Southern Ocean: microstructure and finestructure data from DIMES

NASA Astrophysics Data System (ADS)

Sheen, K.; Naveira-Garabato, A. C.; Brearley, J. A.

2012-04-01

The principal objective of the Diapycnal and Isopycnal Mixing Experiment in the Southern Ocean (DIMES) is to investigate the role of turbulent mixing in mediating the vertical and horizontal transport of water masses, which shape the overturning circulation. Here, microstructure and finestructure data, collected as part of this multi-component experiment, are presented. Direct observations of turbulent energy dissipation rates show that mid-depth diapycnal diffusivities increase progressively from O(10-5 m2s-1) in the Pacific sector of the Antarctic Circumpolar Current (ACC) to O(10-4 m2s-1) in the Scotia Sea. Analysis of coincident LADCP and CTD data demonstrates that enhanced turbulent dissipation rates are associated with a more energetic, less inertial internal wave field and increased upward energy propagation. Breaking lee waves, a process enhanced by stronger flow and rougher topography found in the eastern sections, is likely to be a key mechanism in determining the distribution of turbulent mixing in the ACC. Spatially varying discrepancies between the microstructure and finestructure mixing observations indicate regions where wave-wave interaction models break down and internal waves interact with the mean flow. An episodic enhancement of current velocities at 2000 m depth is observed in the northwest Scotia Sea in both LADCP and mooring data. Finestructure analysis indicates that this mid-depth jet has a profound impact of the internal wave field, causing both internal wave reflection and critical layer dissipation.

ORP and pH measurements to detect redox and acid-base anomalies from hydrothermal activity

NASA Astrophysics Data System (ADS)

Santana-Casiano, J. M.; González-Dávila, M.; Fraile-Nuez, E.

2017-12-01

The Tagoro submarine volcano is located 1.8 km south of the Island of El Hierro at 350 m depth and rises up to 88 m below sea level. It was erupting melting material for five months, from October 2011 to March 2012, changing drastically the physical-chemical properties of the water column in the area. After this eruption, the system evolved to a hydrothermal system. The character of both reduced and acid of the hydrothermal emissions in the Tagoro submarine volcano allowed us to detect anomalies related with changes in the chemical potential and the proton concentration using ORP and pH sensors, respectively. Tow-yos using a CTD-rosette with these two sensors provided the locations of the emissions plotting δ(ORP)/δt and ΔpH versus the latitude or longitude. The ORP sensor responds very quickly to the presence of reduced chemicals in the water column. Changes in potential are proportional to the amount of reduced chemical species present in the water. The magnitude of these changes are examined by the time derivative of ORP, δ(ORP)/δt. To detect changes in the pH, the mean pH for each depth at a reference station in an area not affected by the vent emission is subtracted from each point measured near the volcanic edifice, defining in this way ΔpH. Detailed surveys of the volcanic edifice were carried out between 2014 and 2016 using several CTD-pH-ORP tow-yo studies, localizing the ORP and pH changes, which were used to obtain surface maps of anomalies. Moreover, meridional tow-yos were used to calculate the amount of volcanic CO2 added to the water column. The inputs of CO2 along multiple sections combined with measurements of oceanic currents produced an estimated volcanic CO2 flux = 6.0 105 ± 1.1 105 kg d-1 which increases the acidity above the volcano by 20%. Sites like the Tagoro submarine volcano, in its degasification stage, provide an excellent opportunity to study the carbonate system in a high CO2 world, the volcanic contribution to the global volcanic carbon flux, and the potential environmental impact of these emissions on the surrounding ocean and the ecosystem.

Temporal variability of neustonic ichthyoplankton assemblages of the eastern Pacific warm pool: Can community structure be linked to climate variability?

NASA Astrophysics Data System (ADS)

Ignacio Vilchis, L.; Ballance, Lisa T.; Watson, William

2009-01-01

Considerable evidence exists, showing an accelerated warming trend on earth during the past 40-50 years, attributed mainly to anthropogenic factors. Much of this excess heat is stored in the world's oceans, likely resulting in increased environmental variability felt by marine ecosystems. The long-term effects of this phenomenon on oceanic tropical ecosystems are largely unknown, and our understanding of its effects could be facilitated by long-term studies of how species compositions change with time. Ichthyoplankton, in particular, can integrate physical, environmental and ecological factors making them excellent model taxa to address this question. While on eight (1987-1990, 1992 and 1998-2000) NOAA Fisheries cruises to the eastern Pacific warm pool, we characterized the thermal and phytoplankton pigment structure of the water column, as well as the neustonic ichthyoplankton community using CTD casts and Manta (surface) net tows. Over the 13-year period, 852 CTD and Manta tow stations were completed. We divided the study area into three regions based on regional oceanography, thermocline depth and productivity, as well as a longitudinal gradient in species composition among stations. We then analyzed temporal trends of ichthyoplankton species composition within each region by pooling stations by region and year and making pairwise comparisons of community similarity between all combinations of the eight cruises within each region. We also identified environment-specific species assemblages and station groupings using hierarchical clustering and non-metric multi-dimensional scaling (MDS). Our analyses revealed a longitudinal gradient in community structure and temporal stability of ichthyoplankton species composition. Over the 13 years ichthyoplankton assemblages in the two westernmost regions varied less than in the eastern region. MDS and cluster analyses identified five ichthyoplankton assemblages that corresponded to oceanographic habitats and a gradient in community composition. We hypothesize that the changes in thermocline depth during the El Niños of 1987-1988, 1997-1998 and the extended period of warmth during 1990-1994 altered productivity sufficiently to cause a shift in the abundances of foundation species of the upwelling systems of the eastern Pacific warm pool. Our study suggests that ichthyoplankton assemblages in oligotrophic waters are more resilient to changes in the thermocline than assemblages in upwelling regions; or that oligotrophic regions simply have less physical variation compared to upwelling regions.

Genetic Algorithm for Opto-thermal Skin Hydration Depth Profiling Measurements

NASA Astrophysics Data System (ADS)

Cui, Y.; Xiao, Perry; Imhof, R. E.

2013-09-01

Stratum corneum is the outermost skin layer, and the water content in stratum corneum plays a key role in skin cosmetic properties as well as skin barrier functions. However, to measure the water content, especially the water concentration depth profile, within stratum corneum is very difficult. Opto-thermal emission radiometry, or OTTER, is a promising technique that can be used for such measurements. In this paper, a study on stratum corneum hydration depth profiling by using a genetic algorithm (GA) is presented. The pros and cons of a GA compared against other inverse algorithms such as neural networks, maximum entropy, conjugate gradient, and singular value decomposition will be discussed first. Then, it will be shown how to use existing knowledge to optimize a GA for analyzing the opto-thermal signals. Finally, these latest GA results on hydration depth profiling of stratum corneum under different conditions, as well as on the penetration profiles of externally applied solvents, will be shown.

He, U, and Th Depth Profiling of Apatite and Zircon Using Laser Ablation Noble Gas Mass Spectrometry and SIMS

NASA Astrophysics Data System (ADS)

Monteleone, B. D.; van Soest, M. C.; Hodges, K. V.; Hervig, R.; Boyce, J. W.

2008-12-01

Conventional (U-Th)/He thermochronology utilizes single or multiple grain analyses of U- and Th-bearing minerals such as apatite and zircon and does not allow for assessment of spatial variation in concentration of He, U, or Th within individual crystals. As such, age calculation and interpretation require assumptions regarding 4He loss through alpha ejection, diffusive redistribution of 4He, and U and Th distribution as an initial condition for these processes. Although models have been developed to predict 4He diffusion parameters, correct for the effect of alpha ejection on calculated cooling ages, and account for the effect of U and Th zonation within apatite and zircon, measurements of 4He, U, and Th distribution have not been combined within a single crystal. We apply ArF excimer laser ablation, combined with noble gas mass spectrometry, to obtain depth profiles within apatite and zircon crystals in order to assess variations in 4He concentration with depth. Our initial results from pre-cut, pre-heated slabs of Durango apatite, each subjected to different T-t schedules, suggest a general agreement of 4He profiles with those predicted by theoretical diffusion models (Farley, 2000). Depth profiles through unpolished grains give reproducible alpha ejection profiles in Durango apatite that deviate from alpha ejection profiles predicted for ideal, homogenous crystals. SIMS depth profiling utilizes an O2 primary beam capable of sputtering tens of microns and measuring sub-micron resolution variation in [U], [Th], and [Sm]. Preliminary results suggest that sufficient [U] and [Th] zonation is present in Durango apatite to influence the form of the 4He alpha ejection profile. Future work will assess the influence of measured [U] and [Th] zonation on previously measured 4He depth profiles. Farley, K.A., 2000. Helium diffusion from apatite; general behavior as illustrated by Durango fluorapatite. J. Geophys. Res., B Solid Earth Planets 105 (2), 2903-2914.

Interpretation of TOF SIMS depth profiles from ultrashallow high-k dielectric stacks assisted by hybrid collisional computer simulation

NASA Astrophysics Data System (ADS)

Ignatova, V. A.; Möller, W.; Conard, T.; Vandervorst, W.; Gijbels, R.

2005-06-01

The TRIDYN collisional computer simulation has been modified to account for emission of ionic species and molecules during sputter depth profiling, by introducing a power law dependence of the ion yield as a function of the oxygen surface concentration and by modelling the sputtering of monoxide molecules. The results are compared to experimental data obtained with dual beam TOF SIMS depth profiling of ZrO2/SiO2/Si high-k dielectric stacks with thicknesses of the SiO2 interlayer of 0.5, 1, and 1.5 nm. Reasonable agreement between the experiment and the computer simulation is obtained for most of the experimental features, demonstrating the effects of ion-induced atomic relocation, i.e., atomic mixing and recoil implantation, and preferential sputtering. The depth scale of the obtained profiles is significantly distorted by recoil implantation and the depth-dependent ionization factor. A pronounced double-peak structure in the experimental profiles related to Zr is not explained by the computer simulation, and is attributed to ion-induced bond breaking and diffusion, followed by a decoration of the interfaces by either mobile Zr or O.

Unique sail-like structure of cor triatriatum dexter in three-dimensional echocardiogram.

PubMed

Low, Ting Ting; Uy, Celia Catherine C; Wong, Raymond Ching Chiew

2014-08-01

Cor triatriatum dexter (CTD) is an extremely rare congenital condition arising from the persistence of the right valve of the sinus venosus. It divides the right atrium (RA) into 2 separate chambers. We report a case of a 50-year-old man who had an incidental finding of CTD on transesophageal echocardiogram. An incomplete membrane of the RA was seen, and three-dimensional echocardiogram delineated the structure clearly as a triangular sail-like structure with multiple orifices and a fenestration. © 2013, Wiley Periodicals, Inc.

Collaborative Research to Advance Precision Medicine in the Post-Genomic World | Office of Cancer Genomics

Cancer.gov

My name is Subhashini Jagu, and I am the Scientific Program Manager for the Cancer Target Discovery and Development (CTD2) Network at the Office of Cancer Genomics (OCG). In my new role, I help CTD2 work toward its mission, which is to develop new scientific approaches to accelerate the translation of genomic discoveries into new treatments. Collaborative efforts that bring together a variety of expertise and infrastructure are needed to understand and successfully treat cancer, a highly complex disease.

Entitymetrics: Measuring the Impact of Entities

PubMed Central

Ding, Ying; Song, Min; Han, Jia; Yu, Qi; Yan, Erjia; Lin, Lili; Chambers, Tamy

2013-01-01

This paper proposes entitymetrics to measure the impact of knowledge units. Entitymetrics highlight the importance of entities embedded in scientific literature for further knowledge discovery. In this paper, we use Metformin, a drug for diabetes, as an example to form an entity-entity citation network based on literature related to Metformin. We then calculate the network features and compare the centrality ranks of biological entities with results from Comparative Toxicogenomics Database (CTD). The comparison demonstrates the usefulness of entitymetrics to detect most of the outstanding interactions manually curated in CTD. PMID:24009660

Collection of Arctic Ocean Data from US Navy Submarines on the New SCICEX Program

NASA Astrophysics Data System (ADS)

Smethie, W. M.; Sambrotto, R.; Boyd, T.; Richter-Menge, J.; Corbett, J.

2011-12-01

The SCICEX submarine Arctic science program originated in the 1990s when six dedicated science cruises were conducted in the Arctic Ocean aboard US Navy Sturgeon class submarines. After the cold war era Sturgeon class submarines were retired, several Science Accommodation cruises, for which a few days for scientific measurements were added to planned submarine transits through the Arctic Ocean, were carried out when opportunities arose. Renewed interest in conducting further Science Accommodation cruises on a regular basis to better document and understand how the Arctic Ocean responds to climate change resulted in publication of a scientific plan in 2010 (http://www.arctic.gov/publications/scicex_plan.pdf). In the spring of 2011 testing of data collection and water sampling methods aboard newer Virginia and Seawolf class submarines on transit from a Navy ice camp in the Beaufort Sea, was conducted in order to develop protocols and evaluate techniques. Ice draft measurements were also taken in the vicinity of the ice camp and near the North Pole to evaluate new data collection systems. This evaluation will include a comparison of the ice draft data with a comprehensive set of in situ ice thickness measurements taken near the ice camp. Under-ice submarine-launched eXpendable Condutivity Temperature Depth (XCTD) probes were deployed from the USS Connecticut (SSN-22), a Seawolf class submarine, and the resulting profiles compared to CTD casts from the APLIS ice station and historical profiles. Water samples were collected through the hull for measurements of tritium, helium isotopes, oxygen isotopes, chlorofluorocarbons, sulfur hexafluoride, nutrients, dissolved organic carbon, bacterioplankton, phytoplankton and particulates levels. These samples were returned to Lamont-Doherty Earth Observatory and were in the process of being measured at the time this abstract was written. Measurements completed at this time indicate good samples can be collected for CFC-12, nutrients and biological and inorganic particulates. Measurements of the other samples will be completed and reported on at the meeting. Early results indicate that both of the submarine types evaluated are capable of reliably collecting important information on water temperature, salinity, tracers, chemistry, and biology and ice draft.

Soil coring at multiple field environments can directly quantify variation in deep root traits to select wheat genotypes for breeding.

PubMed

Wasson, A P; Rebetzke, G J; Kirkegaard, J A; Christopher, J; Richards, R A; Watt, M

2014-11-01

We aim to incorporate deep root traits into future wheat varieties to increase access to stored soil water during grain development, which is twice as valuable for yield as water captured at younger stages. Most root phenotyping efforts have been indirect studies in the laboratory, at young plant stages, or using indirect shoot measures. Here, soil coring to 2 m depth was used across three field environments to directly phenotype deep root traits on grain development (depth, descent rate, density, length, and distribution). Shoot phenotypes at coring included canopy temperature depression, chlorophyll reflectance, and green leaf scoring, with developmental stage, biomass, and yield. Current varieties, and genotypes with breeding histories and plant architectures expected to promote deep roots, were used to maximize identification of variation due to genetics. Variation was observed for deep root traits (e.g. 111.4-178.5cm (60%) for depth; 0.09-0.22cm/°C day (144%) for descent rate) using soil coring in the field environments. There was significant variation for root traits between sites, and variation in the relative performance of genotypes between sites. However, genotypes were identified that performed consistently well or poorly at both sites. Furthermore, high-performing genotypes were statistically superior in root traits than low-performing genotypes or commercial varieties. There was a weak but significant negative correlation between green leaf score (-0.5), CTD (0.45), and rooting depth and a positive correlation for chlorophyll reflectance (0.32). Shoot phenotypes did not predict other root traits. This study suggests that field coring can directly identify variation in deep root traits to speed up selection of genotypes for breeding programmes. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

A perspective on two chemometrics tools: PCA and MCR, and introduction of a new one: Pattern recognition entropy (PRE), as applied to XPS and ToF-SIMS depth profiles of organic and inorganic materials

NASA Astrophysics Data System (ADS)

Chatterjee, Shiladitya; Singh, Bhupinder; Diwan, Anubhav; Lee, Zheng Rong; Engelhard, Mark H.; Terry, Jeff; Tolley, H. Dennis; Gallagher, Neal B.; Linford, Matthew R.

2018-03-01

X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) are much used analytical techniques that provide information about the outermost atomic and molecular layers of materials. In this work, we discuss the application of multivariate spectral techniques, including principal component analysis (PCA) and multivariate curve resolution (MCR), to the analysis of XPS and ToF-SIMS depth profiles. Multivariate analyses often provide insight into data sets that is not easily obtained in a univariate fashion. Pattern recognition entropy (PRE), which has its roots in Shannon's information theory, is also introduced. This approach is not the same as the mutual information/entropy approaches sometimes used in data processing. A discussion of the theory of each technique is presented. PCA, MCR, and PRE are applied to four different data sets obtained from: a ToF-SIMS depth profile through ca. 100 nm of plasma polymerized C3F6 on Si, a ToF-SIMS depth profile through ca. 100 nm of plasma polymerized PNIPAM (poly (N-isopropylacrylamide)) on Si, an XPS depth profile through a film of SiO2 on Si, and an XPS depth profile through a film of Ta2O5 on Ta. PCA, MCR, and PRE reveal the presence of interfaces in the films, and often indicate that the first few scans in the depth profiles are different from those that follow. PRE and backward difference PRE provide this information in a straightforward fashion. Rises in the PRE signals at interfaces suggest greater complexity to the corresponding spectra. Results from PCA, especially for the higher principal components, were sometimes difficult to understand. MCR analyses were generally more interpretable.

Meteoric 10Be in soil profiles - A global meta-analysis

USGS Publications Warehouse

Graly, Joseph A.; Bierman, Paul R.; Reusser, Lucas J.; Pavich, Milan J.

2010-01-01

In order to assess current understanding of meteoric 10Be dynamics and distribution in terrestrial soils, we assembled a database of all published meteoric 10Be soil depth profiles, including 104 profiles from 27 studies in globally diverse locations, collectively containing 679 individual measurements. This allows for the systematic comparison of meteoric 10Be concentration to other soil characteristics and the comparison of profile depth distributions between geologic settings. Percent clay, 9Be, and dithionite-citrate extracted Al positively correlate to meteoric 10Be in more than half of the soils where they were measured, but the lack of significant correlation in other soils suggests that no one soil factor controls meteoric 10Be distribution with depth. Dithionite-citrate extracted Fe and cation exchange capacity are only weakly correlated to meteoric 10Be. Percent organic carbon and pH are not significantly related to meteoric 10Be concentration when all data are complied.The compilation shows that meteoric 10Be concentration is seldom uniform with depth in a soil profile. In young or rapidly eroding soils, maximum meteoric 10Be concentrations are typically found in the uppermost 20 cm. In older, more slowly eroding soils, the highest meteoric 10Be concentrations are found at depth, usually between 50 and 200 cm. We find that the highest measured meteoric 10Be concentration in a soil profile is an important metric, as both the value and the depth of the maximum meteoric 10Be concentration correlate with the total measured meteoric 10Be inventory of the soil profile.In order to refine the use of meteoric 10Be as an estimator of soil erosion rate, we compare near-surface meteoric 10Be concentrations to total meteoric 10Be soil inventories. These trends are used to calibrate models of meteoric 10Be loss by soil erosion. Erosion rates calculated using this method vary based on the assumed depth and timing of erosional events and on the reference data selected.

Breadth and Depth of Vocabulary Knowledge and Their Effects on L2 Vocabulary Profiles

ERIC Educational Resources Information Center

Bardakçi, Mehmet

2016-01-01

Breadth and depth of vocabulary knowledge have been studied from many different perspectives, but the related literature lacks serious studies dealing with their effects on vocabulary profiles of EFL learners. In this paper, with an aim to fill this gap, the relative effects of breadth and depth of vocabulary knowledge on L2 vocabulary profiles…

Estimating the Soil Temperature Profile from a Single Depth Observation: A Simple Empirical Heatflow Solution

NASA Technical Reports Server (NTRS)

Holmes, Thomas; Owe, Manfred; deJeu, Richard

2007-01-01

Two data sets of experimental field observations with a range of meteorological conditions are used to investigate the possibility of modeling near-surface soil temperature profiles in a bare soil. It is shown that commonly used heat flow methods that assume a constant ground heat flux can not be used to model the extreme variations in temperature that occur near the surface. This paper proposes a simple approach for modeling the surface soil temperature profiles from a single depth observation. This approach consists of two parts: 1) modeling an instantaneous ground flux profile based on net radiation and the ground heat flux at 5cm depth; 2) using this ground heat flux profile to extrapolate a single temperature observation to a continuous near surface temperature profile. The new model is validated with an independent data set from a different soil and under a range of meteorological conditions.

XPS investigation of depth profiling induced chemistry

NASA Astrophysics Data System (ADS)

Pratt, Quinn; Skinner, Charles; Koel, Bruce; Chen, Zhu

2017-10-01

Surface analysis is an important tool for understanding plasma-material interactions. Depth profiles are typically generated by etching with a monatomic argon ion beam, however this can induce unintended chemical changes in the sample. Tantalum pentoxide, a sputtering standard, and PEDOT:PSS, a polymer that was used to mimic the response of amorphous carbon-hydrogen co-deposits, were studied. We compare depth profiles generated with monatomic and gas cluster argon ion beams (GCIB) using X-ray photoelectron spectroscopy (XPS) to quantify chemical changes. In both samples, monatomic ion bombardment led to beam-induced chemical changes. Tantalum pentoxide exhibited preferential sputtering of oxygen and the polymer experienced significant bond modification. Depth profiling with clusters is shown to mitigate these effects. We present sputtering rates for Ta2O5 and PEDOT:PSS as a function of incident energy and flux. Support was provided through DOE Contract Number DE-AC02-09CH11466.

Influence of surface topography on depth profiles obtained with secondary-ion mass spectrometry

NASA Astrophysics Data System (ADS)

Walker, A. J.; Borchert, M. T.; Vriezema, C. J.; Zalm, P. C.

1990-11-01

Lithographically generated well-defined surface topography of submicron dimensions has been etched into silicon (100) previously implanted with 25 keV 11B to a fluence of 2×1014 atoms/cm2. The thus-obtained samples were depth profiled via secondary-ion mass spectrometry (SIMS). The boron concentration distributions measured were contrasted against those found on undisturbed flat parts of the target. From this intercomparison the otherwise trivial observation that surface topography causes profile distortion becomes suddenly alarming as an apparent improvement of depth resolution occurs. Scanning electron microscope images enable identification of the origin of this remarkable phenomenon. The present results imply that (i) the hitherto commonly accepted assumption in the interpretation of SIMS depth profiles that perceived gradients are never steeper than actual ones is subject to revision; (ii) it may prove very difficult, if not impossible, to construct SIMS equipment for reliable on-chip analysis of submicron details.

An optical fiber expendable seawater temperature/depth profile sensor

NASA Astrophysics Data System (ADS)

Zhao, Qiang; Chen, Shizhe; Zhang, Keke; Yan, Xingkui; Yang, Xianglong; Bai, Xuejiao; Liu, Shixuan

2017-10-01

Marine expendable temperature/depth profiler (XBT) is a disposable measuring instrument which can obtain temperature/depth profile data quickly in large area waters and mainly used for marine surveys, scientific research, military application. The temperature measuring device is a thermistor in the conventional XBT probe (CXBT)and the depth data is only a calculated value by speed and time depth calculation formula which is not an accurate measurement result. Firstly, an optical fiber expendable temperature/depth sensor based on the FBG-LPG cascaded structure is proposed to solve the problems of the CXBT, namely the use of LPG and FBG were used to detect the water temperature and depth, respectively. Secondly, the fiber end reflective mirror is used to simplify optical cascade structure and optimize the system performance. Finally, the optical path is designed and optimized using the reflective optical fiber end mirror. The experimental results show that the sensitivity of temperature and depth sensing based on FBG-LPG cascade structure is about 0.0030C and 0.1%F.S. respectively, which can meet the requirements of the sea water temperature/depth observation. The reflectivity of reflection mirror is in the range from 48.8% to 72.5%, the resonant peak of FBG and LPG are reasonable and the whole spectrum are suitable for demodulation. Through research on the optical fiber XBT (FXBT), the direct measurement of deep-sea temperature/depth profile data can be obtained simultaneously, quickly and accurately. The FXBT is a new all-optical seawater temperature/depth sensor, which has important academic value and broad application prospect and is expected to replace the CXBT in the future.

Domain Interaction Studies of Herpes Simplex Virus 1 Tegument Protein UL16 Reveal Its Interaction with Mitochondria

PubMed Central

Chadha, Pooja; Sarfo, Akua; Zhang, Dan; Abraham, Thomas; Carmichael, Jillian

2016-01-01

ABSTRACT The UL16 tegument protein of herpes simplex virus 1 (HSV-1) is conserved among all herpesviruses and plays many roles during replication. This protein has an N-terminal domain (NTD) that has been shown to bind to several viral proteins, including UL11, VP22, and glycoprotein E, and these interactions are negatively regulated by a C-terminal domain (CTD). Thus, in pairwise transfections, UL16 binding is enabled only when the CTD is absent or altered. Based on these results, we hypothesized that direct interactions occur between the NTD and the CTD. Here we report that the separated and coexpressed functional domains of UL16 are mutually responsive to each other in transfected cells and form complexes that are stable enough to be captured in coimmunoprecipitation assays. Moreover, we found that the CTD can associate with itself. To our surprise, the CTD was also found to contain a novel and intrinsic ability to localize to specific spots on mitochondria in transfected cells. Subsequent analyses of HSV-infected cells by immunogold electron microscopy and live-cell confocal imaging revealed a population of UL16 that does not merely accumulate on mitochondria but in fact makes dynamic contacts with these organelles in a time-dependent manner. These findings suggest that the domain interactions of UL16 serve to regulate not just the interaction of this tegument protein with its viral binding partners but also its interactions with mitochondria. The purpose of this novel interaction remains to be determined. IMPORTANCE The HSV-1-encoded tegument protein UL16 is involved in multiple events of the virus replication cycle, ranging from virus assembly to cell-cell spread of the virus, and hence it can serve as an important drug target. Unfortunately, a lack of both structural and functional information limits our understanding of this protein. The discovery of domain interactions within UL16 and the novel ability of UL16 to interact with mitochondria in HSV-infected cells lays a foundational framework for future investigations aimed at deciphering the structure and function of not just UL16 of HSV-1 but also its homologs in other herpesviruses. PMID:27847362

Evaluation of computer-based computer tomography stratification against outcome models in connective tissue disease-related interstitial lung disease: a patient outcome study.

PubMed

Jacob, Joseph; Bartholmai, Brian J; Rajagopalan, Srinivasan; Brun, Anne Laure; Egashira, Ryoko; Karwoski, Ronald; Kokosi, Maria; Wells, Athol U; Hansell, David M

2016-11-23

To evaluate computer-based computer tomography (CT) analysis (CALIPER) against visual CT scoring and pulmonary function tests (PFTs) when predicting mortality in patients with connective tissue disease-related interstitial lung disease (CTD-ILD). To identify outcome differences between distinct CTD-ILD groups derived following automated stratification of CALIPER variables. A total of 203 consecutive patients with assorted CTD-ILDs had CT parenchymal patterns evaluated by CALIPER and visual CT scoring: honeycombing, reticular pattern, ground glass opacities, pulmonary vessel volume, emphysema, and traction bronchiectasis. CT scores were evaluated against pulmonary function tests: forced vital capacity, diffusing capacity for carbon monoxide, carbon monoxide transfer coefficient, and composite physiologic index for mortality analysis. Automated stratification of CALIPER-CT variables was evaluated in place of and alongside forced vital capacity and diffusing capacity for carbon monoxide in the ILD gender, age physiology (ILD-GAP) model using receiver operating characteristic curve analysis. Cox regression analyses identified four independent predictors of mortality: patient age (P < 0.0001), smoking history (P = 0.0003), carbon monoxide transfer coefficient (P = 0.003), and pulmonary vessel volume (P < 0.0001). Automated stratification of CALIPER variables identified three morphologically distinct groups which were stronger predictors of mortality than all CT and functional indices. The Stratified-CT model substituted automated stratified groups for functional indices in the ILD-GAP model and maintained model strength (area under curve (AUC) = 0.74, P < 0.0001), ILD-GAP (AUC = 0.72, P < 0.0001). Combining automated stratified groups with the ILD-GAP model (stratified CT-GAP model) strengthened predictions of 1- and 2-year mortality: ILD-GAP (AUC = 0.87 and 0.86, respectively); stratified CT-GAP (AUC = 0.89 and 0.88, respectively). CALIPER-derived pulmonary vessel volume is an independent predictor of mortality across all CTD-ILD patients. Furthermore, automated stratification of CALIPER CT variables represents a novel method of prognostication at least as robust as PFTs in CTD-ILD patients.

The hydrothermal exploration system on the 'Qianlong2' AUV

NASA Astrophysics Data System (ADS)

Tao, W.; Tao, C.; Jinhui, Z.; Cai, L.; Guoyin, Z.

2016-12-01

ABSTRACT: Qianlong2, is a fully Autonomous Underwater Vehicle (AUV) designed for submarine resources research, especially for polymetallic sulphides, and the survey depths of is up to 4500 m. Qianlong2 had successfully explored hydrothermal vent field on the Southwest Indian Ridge (SWIR), and collected conductance, temperature and depth (CTD), turbidity, and Oxidation-Reduction Potential (ORP) data. It also had mapped precise topography by high resolution side scan sonar (HRBSSS) during every dive; and obtained photographs of sulfide deposits during some dives. Here, we detailedly described the implementation of investigation, data administration, and fast mapping of hydrothermal exploration system by Qianlong2. Giving a description of how to remove the platform magnetic interference by using magnetic data during Qianlong2 spin. Based on comprehensive hydrochemical anomalies, we get a rapid method for finding the localization of hydrothermal vents. Taking one dive as an example, we systemically showed the process about how to analyse hydrothermal survey data and acquire the location results of hydrothermal vents. Considering that this method is effective and can be used in other deep-submergence assets such as human occupied vehicles (HOVs) and remotely operated vehicles (ROVs) during further studies. Finally, we discussed how to promote and optimize the installation and application of those sensors and how to improve Qianlong2's autonomy of investigation.

Depth-Related Changes in Community Structure of Culturable Mineral Weathering Bacteria and in Weathering Patterns Caused by Them along Two Contrasting Soil Profiles

PubMed Central

Huang, Jing; Xi, Jun; Huang, Zhi; Wang, Qi; Zhang, Zhen-Dong

2014-01-01

Bacteria play important roles in mineral weathering and soil formation. However, few reports of mineral weathering bacteria inhabiting subsurfaces of soil profiles have been published, raising the question of whether the subsurface weathering bacteria are fundamentally distinct from those in surface communities. To address this question, we isolated and characterized mineral weathering bacteria from two contrasting soil profiles with respect to their role in the weathering pattern evolution, their place in the community structure, and their depth-related changes in these two soil profiles. The effectiveness and pattern of bacterial mineral weathering were different in the two profiles and among the horizons within the respective profiles. The abundance of highly effective mineral weathering bacteria in the Changshu profile was significantly greater in the deepest horizon than in the upper horizons, whereas in the Yanting profile it was significantly greater in the upper horizons than in the deeper horizons. Most of the mineral weathering bacteria from the upper horizons of the Changshu profile and from the deeper horizons of the Yanting profile significantly acidified the culture media in the mineral weathering process. The proportion of siderophore-producing bacteria in the Changshu profile was similar in all horizons except in the Bg2 horizon, whereas the proportion of siderophore-producing bacteria in the Yanting profile was higher in the upper horizons than in the deeper horizons. Both profiles existed in different highly depth-specific culturable mineral weathering community structures. The depth-related changes in culturable weathering communities were primarily attributable to minor bacterial groups rather than to a change in the major population structure. PMID:24077700

MDCT quantification is the dominant parameter in decision-making regarding chest tube drainage for stable patients with traumatic pneumothorax.

PubMed

Cai, Wenli; Lee, June-Goo; Fikry, Karim; Yoshida, Hiroyuki; Novelline, Robert; de Moya, Marc

2012-07-01

It is commonly believed that the size of a pneumothorax is an important determinant of treatment decision, in particular regarding whether chest tube drainage (CTD) is required. However, the volumetric quantification of pneumothoraces has not routinely been performed in clinics. In this paper, we introduced an automated computer-aided volumetry (CAV) scheme for quantification of volume of pneumothoraces in chest multi-detect CT (MDCT) images. Moreover, we investigated the impact of accurate volume of pneumothoraces in the improvement of the performance in decision-making regarding CTD in the management of traumatic pneumothoraces. For this purpose, an occurrence frequency map was calculated for quantitative analysis of the importance of each clinical parameter in the decision-making regarding CTD by a computer simulation of decision-making using a genetic algorithm (GA) and a support vector machine (SVM). A total of 14 clinical parameters, including volume of pneumothorax calculated by our CAV scheme, was collected as parameters available for decision-making. The results showed that volume was the dominant parameter in decision-making regarding CTD, with an occurrence frequency value of 1.00. The results also indicated that the inclusion of volume provided the best performance that was statistically significant compared to the other tests in which volume was excluded from the clinical parameters. This study provides the scientific evidence for the application of CAV scheme in MDCT volumetric quantification of pneumothoraces in the management of clinically stable chest trauma patients with traumatic pneumothorax. Copyright © 2012 Elsevier Ltd. All rights reserved.

The disordered C-terminal domain of human DNA glycosylase NEIL1 contributes to its stability via intramolecular interactions.

PubMed

Hegde, Muralidhar L; Tsutakawa, Susan E; Hegde, Pavana M; Holthauzen, Luis Marcelo F; Li, Jing; Oezguen, Numan; Hilser, Vincent J; Tainer, John A; Mitra, Sankar

2013-07-10

NEIL1 [Nei (endonuclease VIII)-like protein 1], one of the five mammalian DNA glycosylases that excise oxidized DNA base lesions in the human genome to initiate base excision repair, contains an intrinsically disordered C-terminal domain (CTD; ~100 residues), not conserved in its Escherichia coli prototype Nei. Although dispensable for NEIL1's lesion excision and AP lyase activities, this segment is required for efficient in vivo enzymatic activity and may provide an interaction interface for many of NEIL1's interactions with other base excision repair proteins. Here, we show that the CTD interacts with the folded domain in native NEIL1 containing 389 residues. The CTD is poised for local folding in an ordered structure that is induced in the purified fragment by osmolytes. Furthermore, deletion of the disordered tail lacking both Tyr and Trp residues causes a red shift in NEIL1's intrinsic Trp-specific fluorescence, indicating a more solvent-exposed environment for the Trp residues in the truncated protein, which also exhibits reduced stability compared to the native enzyme. These observations are consistent with stabilization of the native NEIL1 structure via intramolecular, mostly electrostatic, interactions that were disrupted by mutating a positively charged (Lys-rich) cluster of residues (amino acids 355-360) near the C-terminus. Small-angle X-ray scattering (SAXS) analysis confirms the flexibility and dynamic nature of NEIL1's CTD, a feature that may be critical to providing specificity for NEIL1's multiple, functional interactions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Ebselen, a Small-Molecule Capsid Inhibitor of HIV-1 Replication.

PubMed

Thenin-Houssier, Suzie; de Vera, Ian Mitchelle S; Pedro-Rosa, Laura; Brady, Angela; Richard, Audrey; Konnick, Briana; Opp, Silvana; Buffone, Cindy; Fuhrmann, Jakob; Kota, Smitha; Billack, Blase; Pietka-Ottlik, Magdalena; Tellinghuisen, Timothy; Choe, Hyeryun; Spicer, Timothy; Scampavia, Louis; Diaz-Griffero, Felipe; Kojetin, Douglas J; Valente, Susana T

2016-04-01

The human immunodeficiency virus type 1 (HIV-1) capsid plays crucial roles in HIV-1 replication and thus represents an excellent drug target. We developed a high-throughput screening method based on a time-resolved fluorescence resonance energy transfer (HTS-TR-FRET) assay, using the C-terminal domain (CTD) of HIV-1 capsid to identify inhibitors of capsid dimerization. This assay was used to screen a library of pharmacologically active compounds, composed of 1,280in vivo-active drugs, and identified ebselen [2-phenyl-1,2-benzisoselenazol-3(2H)-one], an organoselenium compound, as an inhibitor of HIV-1 capsid CTD dimerization. Nuclear magnetic resonance (NMR) spectroscopic analysis confirmed the direct interaction of ebselen with the HIV-1 capsid CTD and dimer dissociation when ebselen is in 2-fold molar excess. Electrospray ionization mass spectrometry revealed that ebselen covalently binds the HIV-1 capsid CTD, likely via a selenylsulfide linkage with Cys198 and Cys218. This compound presents anti-HIV activity in single and multiple rounds of infection in permissive cell lines as well as in primary peripheral blood mononuclear cells. Ebselen inhibits early viral postentry events of the HIV-1 life cycle by impairing the incoming capsid uncoating process. This compound also blocks infection of other retroviruses, such as Moloney murine leukemia virus and simian immunodeficiency virus, but displays no inhibitory activity against hepatitis C and influenza viruses. This study reports the use of TR-FRET screening to successfully identify a novel capsid inhibitor, ebselen, validating HIV-1 capsid as a promising target for drug development. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Occlusion pressure analysis role in partitioning of pulmonary vascular resistance in CTEPH.

PubMed

Toshner, Mark; Suntharalingam, Jay; Fesler, Pierre; Soon, Elaine; Sheares, Karen K; Jenkins, David; White, Paul; Morrell, Nicholas W; Naeije, Robert; Pepke-Zaba, Joanna

2012-09-01

Flow-directed pulmonary artery occlusion is posited to enable partitioning of vascular resistance into small and large vessels. As such it may have a role in assessment for pulmonary endarterectomy. To test if the occlusion technique distinguished small from large vessel disease we studied 59 subjects with chronic thromboembolic pulmonary hypertension (CTEPH), idiopathic pulmonary arterial hypertension (IPAH), and connective tissue disease (CTD)-associated PAH. At right heart catheterisation, occlusion pressures were recorded. With fitting of the pressure decay curve, pulmonary vascular resistance was partitioned into downstream (small vessels) and upstream (large vessels, Rup). 47 patients completed the study; 14 operable CTEPH, 15 inoperable CTEPH, 13 idiopathic or CTD-PAH and five post-operative CTEPH. There was a significant difference in mean Rup in the proximal operable CTEPH group 87.3 (95% CI 84.1-90.5); inoperable CTEPH mean 75.8 (95% CI 66.76-84.73), p=0.048; and IPAH/CTD, mean 77.1 (95% CI 71.86-82.33), p=0.003. Receiver operating characteristic curves to distinguish operable from inoperable CTEPH demonstrated an area under the curve of 0.75, p=0.0001. A cut-off of 79.3 gave 100% sensitivity (95% CI 73.5-100%) but 57.1% specificity (95% CI 28.9-82.3%). In a subgroup analysis of multiple lobar sampling there was demonstrable heterogeneity. Rup is significantly increased in operable proximal CTEPH compared with non-operable distal CTEPH and IPAH/CTD-PAH. Rup variability in patients with CTEPH and PAH is suggestive of pathophysiological heterogeneity.

Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape

PubMed Central

Ramírez-Sarmiento, César A.; Noel, Jeffrey K.; Valenzuela, Sandro L.; Artsimovitch, Irina

2015-01-01

RfaH is a virulence factor from Escherichia coli whose C-terminal domain (CTD) undergoes a dramatic α-to-β conformational transformation. The CTD in its α-helical fold is stabilized by interactions with the N-terminal domain (NTD), masking an RNA polymerase binding site until a specific recruitment site is encountered. Domain dissociation is triggered upon binding to DNA, allowing the NTD to interact with RNA polymerase to facilitate transcription while the CTD refolds into the β-barrel conformation that interacts with the ribosome to activate translation. However, structural details of this transformation process in the context of the full protein remain to be elucidated. Here, we explore the mechanism of the α-to-β conformational transition of RfaH in the full-length protein using a dual-basin structure-based model. Our simulations capture several features described experimentally, such as the requirement of disruption of interdomain contacts to trigger the α-to-β transformation, confirms the roles of previously indicated residues E48 and R138, and suggests a new important role for F130, in the stability of the interdomain interaction. These native basins are connected through an intermediate state that builds up upon binding to the NTD and shares features from both folds, in agreement with previous in silico studies of the isolated CTD. We also examine the effect of RNA polymerase binding on the stabilization of the β fold. Our study shows that native-biased models are appropriate for interrogating the detailed mechanisms of structural rearrangements during the dramatic transformation process of RfaH. PMID:26230837

On the Subsurface Chlorophyll Maximum layer in the Black Sea Romanian shelf waters

NASA Astrophysics Data System (ADS)

Vasiliu, Dan; Gomoiu, Marian-Traian; Secrieru, Dan; Caraus, Ioan; Balan, Sorin

2013-04-01

By analyzing data recorded in 38 sampling stations (bottom depths between 16 and 200 m) covering the entire Romanian shelf, from the Danube's mouths to the southern part of the coast, the authors study Subsurface Chlorophyll Maximum (SCM) from May 2009 to April 2011. Chlorophyll a (Chla), seawater temperature, salinity, sigma T, dissolved oxygen, ph, beam attenuation, were measured over the water column depth with the CTD probe and averaged over 1-db intervals (about 1 m depth). Nutrients and phytoplankton qualitative and quantitative parameters were recorded from different depths according to water masses stratification (inscribed in the research protocol of the cruise). In late winter/early spring, due to strong mixing processes of water masses, SCM was not observed in the Black Sea shelf waters. In spring (May), the Danube's increased discharges, characteristic to that period, strongly affected the vertical distribution of Chla, particularly in the area of the Danube's direct influence, where Chla reached maximum in the surface layer (19.76 - 30.39 µg.l-1). In the deeper sampling stations, a relatively weak SCM (Chla within 0.77 - 1.21 µg.l-1) was observed, mainly at the lower limit of the euphotic zone (between 30 and 40 m depths). Here, the position and magnitude of SCM seemed to be controlled mainly by the light conditions; the seasonal thermocline was not well contoured yet. In the warm season, once the stratification becomes stronger, the magnitude of SCM increased (Chla varies between 1.45 - 2.12 µg.l-1). The SCM was well pronounced below the upper boundary of thermocline, at depths between 20 and 25 m, where the dissolved oxygen concentrations have also reached the highest values (>10 mg.l-1 O2), thus suggesting strong photosynthetic processes, where both nutrient and light conditions are favorable. A particular situation was found in July 2010, when abnormally high discharges from the Danube led to a well pronounced SCM (3.23 - 6.87 µg.l-1 Chla) above thermocline (within 8 - 12 m depths) in the shallow waters, the nutrients being not limitative factors. Keywords Chlorophyll a, Subsurface Chlorophyll Maximum layer, the Black Sea, the Danube

Upper Ocean Profiles Measurements with ASIP

NASA Astrophysics Data System (ADS)

Ward, B.; Callaghan, A. H.; Fristedt, T.; Vialard, J.; Cuypers, Y.; Weller, R. A.; Grosch, C. E.

2009-04-01

This presentation describes results from the Air-Sea Interaction Profiler (ASIP), an autonomous profiling instrument for upper ocean measurements. The measurements from ASIP are well suited to enhancing research on air-sea interfacial and near surface processes. Autonomous profiling is accomplished with a thruster, which submerges ASIP to a programmed depth. Once this depth is reached the positively buoyant instrument will ascend to the surface acquiring data. ASIP can profile from a maximum depth of 100 m to the surface, allowing both mixed layer and near-surface measurements to be conducted. The sensor payload on ASIP include microstructure sensors (two shear probes and a thermistor); a slow response accurate thermometer; a pair of conductivity sensors; pressure for a record of depth; PAR for measurements of light absorption in the water column. Other non-environmental sensors are acceleration, rate, and heading for determination of vehicle motion. Power is provided with rechargable lithium-ion batteries, supplying 1000 Whr, allowing approximately 300 profiles. ASIP also contains an iridium/GPS system, which allows realtime reporting of its position. ASIP was deployed extensively during the Cirene Indian Ocean campaign and our results focus on the data from the temperature, salinity, light, and shear sensors.

Geophysical techniques for reconnaissance investigations of soils and surficial deposits in mountainous terrain

USGS Publications Warehouse

Olson, C.G.; Doolittle, J.A.

1985-01-01

Two techniques were assessed for their capabilities in reconnaissance studies of soil characteristics: depth to the water table and depth to bedrock beneath surficial deposits in mountainous terrain. Ground-penetrating radar had the best near-surface resolution in the upper 2 m of the profile and provided continuous interpretable imagery of soil profiles and bedrock surfaces. Where thick colluvium blankets side slopes, the GPR could not consistently define the bedrock interface. In areas with clayey or shaley sediments, the GPR is also more limited in defining depth and is less reliable. Seismic refraction proved useful in determining the elevation of the water table and depth to bedrock, regardless of thickness of overlying material, but could not distinguish soil-profile characteristics.-from Authors

The effects of wavelength on photodegradation depth profiles in Japanese cedar (Cryptomeria japonica D. Don) earlywood

Treesearch

Yutaka Kataoka; Makoto Kiguchi; R. Sam Williams; Philip D. Evans

2006-01-01

FT-IR microscopy was used to depth profile the photodegradation of Japanese cedar earlywood exposed to monochromatic light in the UV and visible ranges (band pass: 20nm). Parallel experiments assessed the transmission of the light through thin sections of Japanese cedar. The depth of photodegradation increased with wavelength up to and including the violet region of...

TFIIH and P-TEFb Coordinate Transcription with Capping Enzyme Recruitment at Specific Genes in Fission Yeast

PubMed Central

Viladevall, Laia; St. Amour, Courtney V.; Rosebrock, Adam; Schneider, Susanne; Zhang, Chao; Allen, Jasmina J.; Shokat, Kevan M.; Schwer, Beate; Leatherwood, Janet K.; Fisher, Robert P.

2009-01-01

Summary Cyclin-dependent kinases (CDKs) are subunits of transcription factor (TF) IIH and positive transcription elongation factor b (P-TEFb). To define their functions, we mutated the TFIIH-associated kinase Mcs6 and P-TEFb homologs Cdk9 and Lsk1 of fission yeast, making them sensitive to bulky purine analogs. Selective inhibition of Mcs6 or Cdk9 blocks cell division, alters RNA polymerase (Pol) II carboxyl-terminal domain (CTD) phosphorylation and represses specific, overlapping subsets of transcripts. At a common target gene, both CDKs must be active for normal Pol II occupancy, and Spt5—a CDK substrate and regulator of elongation—accumulates disproportionately to Pol II when either kinase is inhibited. In contrast, Mcs6 activity is sufficient, and necessary, to recruit the Cdk9/Pcm1 (mRNA cap methyltransferase) complex. In vitro, phosphorylation of the CTD by Mcs6 stimulates subsequent phosphorylation by Cdk9. We propose that TFIIH primes the CTD and promotes recruitment of P-TEFb/Pcm1, serving to couple elongation and capping of select pre-mRNAs. PMID:19328067

Allosteric control of transcription in GntR family of transcription regulators: A structural overview.

PubMed

Jain, Deepti

2015-07-01

The GntR family of transcription regulators constitutes one of the most abundant family of transcription factors. These modulators are involved in a variety of mechanisms controlling various metabolic processes. GntR family members are typically two domain proteins with a smaller N-terminus domain (NTD) with conserved architecture of winged-helix-turn-helix (wHTH) for DNA binding and a larger C-terminus domain (CTD) or the effector binding domain which is also involved in oligomerization. Interestingly, the CTD shows structural heterogeneity depending upon the type of effector molecule that it binds and displays structural homology to various classes of proteins. Binding of the effector molecule to the CTD brings about a conformational change in the transcription factor such that its affinity for its cognate DNA sequence is altered. This review summarizes the structural information available on the members of GntR family and discusses the common features of the DNA binding and operator recognition within the family. The variation in the allosteric mechanism employed by the members of this family is also discussed. © 2015 International Union of Biochemistry and Molecular Biology.

The Comparative Toxicogenomics Database: update 2017.

PubMed

Davis, Allan Peter; Grondin, Cynthia J; Johnson, Robin J; Sciaky, Daniela; King, Benjamin L; McMorran, Roy; Wiegers, Jolene; Wiegers, Thomas C; Mattingly, Carolyn J

2017-01-04

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between chemicals and gene products, and their relationships to diseases. Core CTD content (chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature) are integrated with each other as well as with select external datasets to generate expanded networks and predict novel associations. Today, core CTD includes more than 30.5 million toxicogenomic connections relating chemicals/drugs, genes/proteins, diseases, taxa, Gene Ontology (GO) annotations, pathways, and gene interaction modules. In this update, we report a 33% increase in our core data content since 2015, describe our new exposure module (that harmonizes exposure science information with core toxicogenomic data) and introduce a novel dataset of GO-disease inferences (that identify common molecular underpinnings for seemingly unrelated pathologies). These advancements centralize and contextualize real-world chemical exposures with molecular pathways to help scientists generate testable hypotheses in an effort to understand the etiology and mechanisms underlying environmentally influenced diseases. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Structural and functional insights into 5'-ppp RNA pattern recognition by the innate immune receptor RIG-I.

PubMed

Wang, Yanli; Ludwig, Janos; Schuberth, Christine; Goldeck, Marion; Schlee, Martin; Li, Haitao; Juranek, Stefan; Sheng, Gang; Micura, Ronald; Tuschl, Thomas; Hartmann, Gunther; Patel, Dinshaw J

2010-07-01

RIG-I is a cytosolic helicase that senses 5'-ppp RNA contained in negative-strand RNA viruses and triggers innate antiviral immune responses. Calorimetric binding studies established that the RIG-I C-terminal regulatory domain (CTD) binds to blunt-end double-stranded 5'-ppp RNA a factor of 17 more tightly than to its single-stranded counterpart. Here we report on the crystal structure of RIG-I CTD bound to both blunt ends of a self-complementary 5'-ppp dsRNA 12-mer, with interactions involving 5'-pp clearly visible in the complex. The structure, supported by mutation studies, defines how a lysine-rich basic cleft within the RIG-I CTD sequesters the observable 5'-pp of the bound RNA, with a stacked phenylalanine capping the terminal base pair. Key intermolecular interactions observed in the crystalline state are retained in the complex of 5'-ppp dsRNA 24-mer and full-length RIG-I under in vivo conditions, as evaluated from the impact of binding pocket RIG-I mutations and 2'-OCH(3) RNA modifications on the interferon response.

Crystal Structure of the Ternary Complex of a NaV C-Terminal Domain, a Fibroblast Growth Factor Homologous Factor, and Calmodulin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Chaojian; Chung, Ben C.; Yan, Haidun

2012-11-13

Voltage-gated Na{sup +} (Na{sub V}) channels initiate neuronal action potentials. Na{sub V} channels are composed of a transmembrane domain responsible for voltage-dependent Na{sup +} conduction and a cytosolic C-terminal domain (CTD) that regulates channel function through interactions with many auxiliary proteins, including fibroblast growth factor homologous factors (FHFs) and calmodulin (CaM). Most ion channel structural studies have focused on mechanisms of permeation and voltage-dependent gating but less is known about how intracellular domains modulate channel function. Here we report the crystal structure of the ternary complex of a human NaV CTD, an FHF, and Ca{sup 2+}-free CaM at 2.2 {angstrom}.more » Combined with functional experiments based on structural insights, we present a platform for understanding the roles of these auxiliary proteins in NaV channel regulation and the molecular basis of mutations that lead to neuronal and cardiac diseases. Furthermore, we identify a critical interaction that contributes to the specificity of individual NaV CTD isoforms for distinctive FHFs.« less

Lithium diffusion in polyether ether ketone and polyimide stimulated by in situ electron irradiation and studied by the neutron depth profiling method

NASA Astrophysics Data System (ADS)

Vacik, J.; Hnatowicz, V.; Attar, F. M. D.; Mathakari, N. L.; Dahiwale, S. S.; Dhole, S. D.; Bhoraskar, V. N.

2014-10-01

Diffusion of lithium from a LiCl aqueous solution into polyether ether ketone (PEEK) and polyimide (PI) assisted by in situ irradiation with 6.5 MeV electrons was studied by the neutron depth profiling method. The number of the Li atoms was found to be roughly proportional to the diffusion time. Regardless of the diffusion time, the measured depth profiles in PEEK exhibit a nearly exponential form, indicating achievement of a steady-state phase of a diffusion-reaction process specified in the text. The form of the profiles in PI is more complex and it depends strongly on the diffusion time. For the longer diffusion time, the profile consists of near-surface bell-shaped part due to Fickian-like diffusion and deeper exponential part.

Abundant Hydrothermal Venting in the Southern Ocean Near 62°S/159°E on the Australian-Antarctic Ridge

NASA Astrophysics Data System (ADS)

Baker, E. T.; Hahm, D.; Rhee, T. S.; Park, S. H.; Lupton, J. E.; Walker, S. L.; Choi, H.

2014-12-01

Circum-Antarctic Ridges (CARs) comprise almost one-third of the global Mid-Ocean Ridge, yet remain terra incognita for hydrothermal activity and chemosynthetic ecosystems. The InterRidge Vents Database lists only 3 confirmed (visualized) and 35 inferred (plume evidence) active sites along the ~21,000 km of CARs. Here, we report on a multi-year effort to locate and characterize hydrothermal activity on two 1st-order segments of the Australian-Antarctic Ridge that are perhaps more isolated from other known vent fields than any other vent site on the Mid-Ocean Ridge. KR1 is a 300-km-long segment near 62°S/159°E, and KR2 a 90-km-long segment near 60°S/152.5°E. We used profiles collected by Miniature Autonomous Plume Recorders (MAPRs) on rock corers in March and December of 2011 to survey each segment, and an intensive CTD survey in Jan/Feb 2013 to pinpoint sites and sample plumes on KR1. Optical and oxidation-reduction potential (ORP, aka Eh) anomalies indicate multiple active sites on both segments. Seven profiles on KR2 found 3 sites, each separated by ~25 km. Forty profiles on KR1 identified 13 sites, some within a few km of each other. The densest site concentration on KR1 occurred along a relatively inflated, 90-km-long section near the segment center. CTD tows covered 20 km of the eastern, most inflated portion of this area, finding two 6-km-long zones centered near 158.6°E and 158.8°E with multiple plume anomalies. Three ORP anomalies within 50 m of the seafloor indicate precise venting locations. We call this area the Mujin "Misty Harbor" vent field. Vent frequency sharply decreases away from Mujin. 3He/heat ratios determined from 20 plume samples in the Mujin field were mostly <0.015 fM/J, indicative of chronic venting, but 3 samples, 0.021-0.034 fM/J, are ratios typical of a recent eruption. The spatial density of hydrothermal activity along KR1 and KR2 is similar to other intermediate-rate spreading ridges. We calculate the plume incidence (ph) along KR1 and KR2 as the mean of the fraction of MAPR casts detecting a plume in each 2nd-order segment. For all 6 segments, ph=0.37±0.25, consistent with the prediction of 0.33 from the global trend of ph for a spreading rate of 68 mm/yr.

Calibration procedures and first data set of Southern Ocean chlorophyll a profiles collected by elephant seal equipped with a newly developed CTD-fluorescence tags

NASA Astrophysics Data System (ADS)

Guinet, C.; Xing, X.; Walker, E.; Monestiez, P.; Marchand, S.; Picard, B.; Jaud, T.; Authier, M.; `Cotté, C.; Dragon, A. C.; Diamond, E.; Antoine, D.; Lovell, P.; Blain, S.; D'Ortenzio, F.; Claustre, H.

2012-08-01

In-situ observation of the marine environment has traditionally relied on ship-based platforms. The obvious consequence is that physical and biogeochemical properties have been dramatically undersampled, especially in the remote Southern Ocean (SO). The difficulty in obtaining in situ data represents the major limitations to our understanding, and interpretation of the coupling between physical forcing and the biogeochemical response. Southern elephant seals (Mirounga leonina) equipped with a new generation of oceanographic sensors can measure ocean structure in regions and seasons rarely observed with traditional oceanographic platforms. Over the last few years, seals have allowed for a considerable increase in temperature and salinity profiles from the SO. However we were still lacking information on the spatio-temporal variation of phytoplankton concentration. This information is critical to assess how the biological productivity of the SO, with direct consequences on the amount of CO2 "fixed" by the biological pump, will respond to global warming. In this research program, we use an innovative sampling fluorescence approach to quantify phytoplankton concentration at sea. For the first time, a low energy consumption fluorometer was added to Argos CTD-SRDL tags, and these novel instruments were deployed on 27 southern elephant seals between 25 December 2007 and the 4 February 2011. As many as 3388 fluorescence profiles associated with temperature and salinity measurements were thereby collected from a vast sector of the Southern Indian Ocean. This paper address the calibration issue of the fluorometer before being deployed on elephant seals and present the first results obtained for the Indian Sector of the Southern Ocean. This in situ system is implemented in synergy with satellite ocean colour radiometry. Satellite-derived data is limited to the surface layer and is restricted over the SO by extensive cloud cover. However, with the addition of these new tags, we're able to assess the 3 dimension distribution of phytoplankton concentration by foraging southern elephant seals. This approach reveals that for the Indian sector of the SO, the surface chlorophyll a (chl a) concentrations provided by MODIS were underestimated by a factor of the order of 2-3 compared to in situ measurements. The scientific outcomes of this program include an improved understanding of both the present state and variability in ocean biology, and the accompanying biogeochemistry, as well as the delivery of real-time and open-access data to scientists (doi:10.7491/MEMO.1x).

Calibration procedures and first dataset of Southern Ocean chlorophyll a profiles collected by elephant seals equipped with a newly developed CTD-fluorescence tags

NASA Astrophysics Data System (ADS)

Guinet, C.; Xing, X.; Walker, E.; Monestiez, P.; Marchand, S.; Picard, B.; Jaud, T.; Authier, M.; Cotté, C.; Dragon, A. C.; Diamond, E.; Antoine, D.; Lovell, P.; Blain, S.; D'Ortenzio, F.; Claustre, H.

2013-02-01

In situ observation of the marine environment has traditionally relied on ship-based platforms. The obvious consequence is that physical and biogeochemical properties have been dramatically undersampled, especially in the remote Southern Ocean (SO). The difficulty in obtaining in situ data represents the major limitations to our understanding, and interpretation of the coupling between physical forcing and the biogeochemical response. Southern elephant seals (Mirounga leonina) equipped with a new generation of oceanographic sensors can measure ocean structure in regions and seasons rarely observed with traditional oceanographic platforms. Over the last few years, seals have allowed for a considerable increase in temperature and salinity profiles from the SO, but we were still lacking information on the spatiotemporal variation of phytoplankton concentration. This information is critical to assess how the biological productivity of the SO, with direct consequences on the amount of CO2 "fixed'' by the biological pump, will respond to global warming. In this research programme, we use an innovative sampling fluorescence approach to quantify phytoplankton concentration at sea. For the first time, a low energy consumption fluorometer was added to Argos CTD-SRDL tags, and these novel instruments were deployed on 27 southern elephant seals between 25 December 2007 and the 4 February 2011. As many as 3388 fluorescence profiles associated with temperature and salinity measurements were thereby collected from a vast sector of the Southern Indian Ocean. This paper addresses the calibration issue of the fluorometer before being deployed on elephant seals and presents the first results obtained for the Indian sector of the Southern Ocean. This in situ system is implemented in synergy with satellite ocean colour radiometry. Satellite-derived data is limited to the surface layer and is restricted over the SO by extensive cloud cover. However, with the addition of these new tags, we are able to assess the 3-dimension distribution of phytoplankton concentration by foraging southern elephant seals. This approach reveals that for the Indian sector of the SO, the surface chlorophyll a (chl a) concentrations provided by MODIS were underestimated by a factor 2 compared to chl a concentrations estimated from HPLC corrected in situ fluorescence measurements. The scientific outcomes of this programme include an improved understanding of both the present state and variability in ocean biology, and the accompanying biogeochemistry, as well as the delivery of real-time and open-access data to scientists (doi:10.7491/MEMO.1).

Towards nanometric resolution in multilayer depth profiling: a comparative study of RBS, SIMS, XPS and GDOES.

PubMed

Escobar Galindo, Ramón; Gago, Raul; Duday, David; Palacio, Carlos

2010-04-01

An increasing amount of effort is currently being directed towards the development of new functionalized nanostructured materials (i.e., multilayers and nanocomposites). Using an appropriate combination of composition and microstructure, it is possible to optimize and tailor the final properties of the material to its final application. The analytical characterization of these new complex nanostructures requires high-resolution analytical techniques that are able to provide information about surface and depth composition at the nanometric level. In this work, we comparatively review the state of the art in four different depth-profiling characterization techniques: Rutherford backscattering spectroscopy (RBS), secondary ion mass spectrometry (SIMS), X-ray photoelectron spectroscopy (XPS) and glow discharge optical emission spectroscopy (GDOES). In addition, we predict future trends in these techniques regarding improvements in their depth resolutions. Subnanometric resolution can now be achieved in RBS using magnetic spectrometry systems. In SIMS, the use of rotating sample holders and oxygen flooding during analysis as well as the optimization of floating low-energy ion guns to lower the impact energy of the primary ions improves the depth resolution of the technique. Angle-resolved XPS provides a very powerful and nondestructive technique for obtaining depth profiling and chemical information within the range of a few monolayers. Finally, the application of mathematical tools (deconvolution algorithms and a depth-profiling model), pulsed sources and surface plasma cleaning procedures is expected to greatly improve GDOES depth resolution.

High-resolution depth profiling using a range-gated CMOS SPAD quanta image sensor.

PubMed

Ren, Ximing; Connolly, Peter W R; Halimi, Abderrahim; Altmann, Yoann; McLaughlin, Stephen; Gyongy, Istvan; Henderson, Robert K; Buller, Gerald S

2018-03-05

A CMOS single-photon avalanche diode (SPAD) quanta image sensor is used to reconstruct depth and intensity profiles when operating in a range-gated mode used in conjunction with pulsed laser illumination. By designing the CMOS SPAD array to acquire photons within a pre-determined temporal gate, the need for timing circuitry was avoided and it was therefore possible to have an enhanced fill factor (61% in this case) and a frame rate (100,000 frames per second) that is more difficult to achieve in a SPAD array which uses time-correlated single-photon counting. When coupled with appropriate image reconstruction algorithms, millimeter resolution depth profiles were achieved by iterating through a sequence of temporal delay steps in synchronization with laser illumination pulses. For photon data with high signal-to-noise ratios, depth images with millimeter scale depth uncertainty can be estimated using a standard cross-correlation approach. To enhance the estimation of depth and intensity images in the sparse photon regime, we used a bespoke clustering-based image restoration strategy, taking into account the binomial statistics of the photon data and non-local spatial correlations within the scene. For sparse photon data with total exposure times of 75 ms or less, the bespoke algorithm can reconstruct depth images with millimeter scale depth uncertainty at a stand-off distance of approximately 2 meters. We demonstrate a new approach to single-photon depth and intensity profiling using different target scenes, taking full advantage of the high fill-factor, high frame rate and large array format of this range-gated CMOS SPAD array.

Auger analysis of a fiber/matrix interface in a ceramic matrix composite

NASA Technical Reports Server (NTRS)

Honecy, Frank S.; Pepper, Stephen V.

1988-01-01

Auger electron spectroscopy (AES) depth profiling was used to characterize the fiber/matrix interface of an SiC fiber, reaction bonded Si3N4 matrix composite. Depth profiles of the as received double coated fiber revealed concentration oscillations which disappeared after annealing the fiber in the environment used to fabricate the composite. After the composite was fractured, the Auger depth profiles showed that failure occurred in neither the Beta-SiC fiber body nor in the Si3N4 matrix but, concurrently, at the fiber coating/matrix interface and within the fiber coating itself.

Boron depth profiles and residual damage following rapid thermal annealing of low-temperature BSi molecular ion implantation in silicon

NASA Astrophysics Data System (ADS)

Liang, J. H.; Wang, S. C.

2007-08-01

The influence of substrate temperature on both the implantation and post-annealing characteristics of molecular-ion-implanted 5 × 1014 cm-2 77 keV BSi in silicon was investigated in terms of boron depth profiles and damage microstructures. The substrate temperatures under investigation consisted of room temperature (RT) and liquid nitrogen temperature (LT). Post-annealing treatments were performed using rapid thermal annealing (RTA) at 1050 °C for 25 s. Boron depth profiles and damage microstructures in both the as-implanted and as-annealed specimens were determined using secondary ion mass spectrometry (SIMS) and transmission electron microscopy (TEM), respectively. The as-implanted results revealed that, compared to the RT specimen, the LT specimen yields a shallower boron depth profile with a reduced tail into the bulk. An amorphous layer containing a smooth amorphous-to-crystalline (a/c) interface is evident in the LT specimen while just the opposite is true in the as-implanted RT one. The as-annealed results illustrated that the extension of the boron depth profile into the bulk via transient-enhanced diffusion (TED) in the LT specimen is less than it is in the RT one. Only residual defects are visible in the LT specimen while two clear bands of dislocation loops appear in the RT one.

Vertical observation of molecular hydrogen and carbon monoxide: Implication for non-photochemical H2 production at ocean surface and subsurface

NASA Astrophysics Data System (ADS)

Kawagucci, S.; Narita, T.; Obata, H.; Ogawa, H.; Gamo, T.

2009-12-01

Biological nitrogen fixation is a key metabolism controlling marine N-cycling and also known as a main H2 source. Recently, it was proposed that a monitoring of surface H2 concentration could be used quickly to figure out the spatial extent of biological nitrogen fixation activity without onboard incubation required for currently used methods for detecting the activity. However, H2 behavior in ocean water was still unresolved. This study carried out vertical observation of H2 and CO concentrations in south of Japan, western North Pacific. Because carbon monoxide, CO, in seawater has no relation with nitrogen fixation metabolism and is produced dominantly by the photochemical reaction, which is an altanative H2 source, simultaneous observation and comparison of H2 and CO concentration is helpful to investigate H2 behavior in ocean water. Reductive gases in seawater were observed during the R/V Tansei-maru KT-08-14 cruise by using a wired CTD-CMS (CTD-carousel multiple sampling) system to conduct vertical sampling (at most 200 m depth) and by using a plastic bucket for sampling surface seawater. The sample in the Niskin-X bottle was directed to the bottom of a 120 mL brown-colored glass vial allowed to overflow by 2 volumes before the tube was slowly withdrawn. After the addition of 0.5 mL HgCl2-saturated solution for poisoning, the PTFE-lined butyl-gum septum was used to cap the vials. Molecular hydrogen (H2) and carbon monoxide (CO) were analyzed at an onboard laboratory within 6 hours after subsampling. 20 mL of sample water was substituted by 20 mL of H2- and CO-free air using a gas-tight syringe; then the vial was put on an automatic shaker and shaken upside down for 6 minutes to achieve a complete equilibrium between the dissolved and head space gases in the vial. The equilibrated headspace was taken by another gas-tight syringe and then injected into a gas chromatograph equipped with a trace reduced gas detector. Vertical distribution of dissolved H2 and CO concentration were observed. Apparently different vertical distributions between H2 and CO concentration were revealed at all the observed stations. At a station where N-nutrient was depleted through surface mixed layer, H2 was supersaturated at the surface while CO concentration was constant through the depths. In contrast, at another station where some amount of terrestrial humic matter was introduced into the surface, H2 concentration was constantly undersaturated through the depth while vertical distribution of CO concentration showed the highest at the surface and exponentially decreased to deep. These facts suggest that H2 production involved with nitrogen fixation played an important role for H2 behavior in ocean water while photochemical H2 production would be a minor process. In addition to the surface, H2 supersaturation accoumpanied with little CO concentration rise were observed at depths just below the mixed layer in pycnocline with Chlorophyll maximum.

Complete A-V block: incidental or a part of cor triatriatum dexter.

PubMed

Guler, Y; Akgun, T; Toprak, C; Guler, A; Esen, A M

2014-05-01

Cor triatriatum dexter (CTD) is an extremely rare cardiac anomaly in which the right atrium is divided into two distinct chambers by a membrane. The persistence of the right valve of sinus venosus results in a complete septation of the right atrium. This anomaly is frequently associated with other right-sided cardiac abnormalities. Its clinical manifestation and the need for intervention are determined by the number and the size of the fenestrations on the membrane, associated cardiac anomalies and arrhythmias. We describe a case of CTD in a patient with complete atrioventricular (A-V) block.

Determination of rare earth elements concentration at different depth profile of Precambrian pegmatites using instrumental neutron activation analysis.

PubMed

Sadiq Aliyu, Abubakar; Musa, Yahaya; Liman, M S; Abba, Habu T; Chaanda, Mohammed S; Ngene, Nnamani C; Garba, N N

2018-01-01

The Keffi area hosts abundant pegmatite bodies as a result of the surrounding granitic intrusions. Keffi is part of areas that are geologically classified as North Central Basement Complex. Data on the mineralogy and mineralogical zonation of the Keffi pegmatite are scanty. Hence the need to understand the geology and mineralogical zonation of Keffi pegmatites especially at different depth profiles is relevant as a study of the elemental composition of the pegmatite is essential for the estimation of its economic viability. Here, the relative standardization method of instrumental neutron activation analysis (INAA) has been used to investigate the vertical deviations of the elemental concentrations of rare earth elements (REEs) at different depth profile of Keffi pegmatite. This study adopted the following metrics in investigating the vertical variations of REEs concentrations. Namely, the total contents of rare earth elements (∑REE); ratio of light to heavy rare earth elements (LREE/HREE), which defines the enrichment or depletion of REEs; europium anomaly (Eu/Sm); La/Lu ratio relative to chondritic meteorites. The study showed no significant variations in the total content of rare elements between the vertical depth profiles (100-250m). However, higher total concentrations of REEs (~ 92.65ppm) were recorded at the upper depth of the pegmatite and the europium anomaly was consistently negative at all the depth profiles suggesting that the Keffi pegmatite is enriched with light REEs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dynamic vertical profiles of peat porewater chemistry in a northern peatland

Treesearch

Natalie A. Griffiths; Stephen D. Sebestyen

2016-01-01

We measured pH, cations, nutrients, and total organic carbon (TOC) over 3 years to examine weekly to monthly variability in porewater chemistry depth profiles (0–3.0 m) in an ombrotrophic bog in Minnesota, USA. We also compared temporal variation at one location to spatial variation in depth profiles at 16 locations across the bog. Most solutes exhibited large...

Ovule identity mediated by pre-mRNA processing in Arabidopsis

PubMed Central

Rodríguez-Cazorla, Encarnación; Candela, Héctor; Bailey-Steinitz, Lindsay J.; Yanofsky, Martin F.; Martínez-Laborda, Antonio

2018-01-01

Ovules are fundamental for plant reproduction and crop yield as they are the precursors of seeds. Therefore, ovule specification is a critical developmental program. In Arabidopsis thaliana, ovule identity is redundantly conferred by the homeotic D-class genes SHATTERPROOF1 (SHP1), SHP2 and SEEDSTICK (STK), phylogenetically related to the MADS-domain regulatory gene AGAMOUS (AG), essential in floral organ specification. Previous studies have shown that the HUA-PEP activity, comprised of a suite of RNA-binding protein (RBP) encoding genes, regulates AG pre-mRNA processing and thus flower patterning and organ identity. Here, we report that the HUA-PEP activity additionally governs ovule morphogenesis. Accordingly, in severe hua-pep backgrounds ovules transform into flower organ-like structures. These homeotic transformations are most likely due to the dramatic reduction in SHP1, SHP2 and STK activity. Our molecular and genome-wide profiling strategies revealed the accumulation of prematurely terminated transcripts of D-class genes in hua-pep mutants and reduced amounts of their respective functional messengers, which points to pre-mRNA processing misregulation as the origin of the ovule developmental defects in such backgrounds. RNA processing and transcription are coordinated by the RNA polymerase II (RNAPII) carboxyl-terminal domain (CTD). Our results show that HUA-PEP activity members can interact with the CTD regulator C-TERMINAL DOMAIN PHOSPHATASE-LIKE1 (CPL1), supporting a co-transcriptional mode of action for the HUA-PEP activity. Our findings expand the portfolio of reproductive developmental programs in which HUA-PEP activity participates, and further substantiates the importance of RNA regulatory mechanisms (pre-mRNA co-transcriptional regulation) for correct gene expression during plant morphogenesis. PMID:29329291

Depth profiles of oxygen precipitates in nitride-coated silicon wafers subjected to rapid thermal annealing

NASA Astrophysics Data System (ADS)

Voronkov, V. V.; Falster, R.; Kim, TaeHyeong; Park, SoonSung; Torack, T.

2013-07-01

Silicon wafers, coated with a silicon nitride layer and subjected to high temperature Rapid Thermal Annealing (RTA) in Ar, show—upon a subsequent two-step precipitation anneal cycle (such as 800 °C + 1000 °C)—peculiar depth profiles of oxygen precipitate densities. Some profiles are sharply peaked near the wafer surface, sometimes with a zero bulk density. Other profiles are uniform in depth. The maximum density is always the same. These profiles are well reproduced by simulations assuming that precipitation starts from a uniformly distributed small oxide plates originated from RTA step and composed of oxygen atoms and vacancies ("VO2 plates"). During the first step of the precipitation anneal, an oxide layer propagates around this core plate by a process of oxygen attachment, meaning that an oxygen-only ring-shaped plate emerges around the original plate. These rings, depending on their size, then either dissolve or grow during the second part of the anneal leading to a rich variety of density profiles.

High-sensitivity aeromagnetic survey of the US Atlantic continental margin.

USGS Publications Warehouse

Behrendt, John C.; Klitgord, Kim D.

1980-01-01

The US Geological Survey contracted a high-sensitivity, digital aeromagnetic survey that was flown over the US Atlantic continental margin over a period of 15 months between 1974 and 1976. The 185 000 km of profile data have a relative accuracy approaching a few tenths of a nanotesla, which allowed compilation into maps at a scale of 1:250 000, with a contour interval of 2 nT. Automatic data processing using the Werner method allowed calculations of apparent depth to sources of the magnetic anomalies on all of the profiles, assuming a dike or interface as a source. Comparison of the computed depths to magnetic basement with multichannel seismic profiles across the survey area helped to reduce ambiguities in magnetic depth estimates and enabled interpolation of basement structures between seismic profiles. The resulting map showing depth to basement of the Atlantic continental margin is compatible with available multichannel seismic data, and we consider it a reasonable representation of the base of the sedimentary column. -Authors

Perfect Composition Depth Profiling of Ionic Liquid Surfaces Using High-resolution RBS/ERDA.

PubMed

Nakajima, Kaoru; Zolboo, Enkhbayar; Ohashi, Tomohiro; Lísal, Martin; Kimura, Kenji

2016-01-01

In order to reveal the surface structures of large molecular ionic liquids (ILs), the near-surface elemental depth distributions of 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C n C 1 Im][Tf 2 N], n = 2, 6, 10) were studied using high-resolution Rutherford backscattering spectroscopy (HRBS) in combination with high-resolution elastic recoil detection analysis (HR-ERDA). The elemental depth profiles of all constituent elements, including hydrogen, were derived from HR-ERDA/HRBS measurements, so that the profiles would reproduce both HR-ERDA and HRBS spectra simultaneously. The derived elemental depth profiles agree with state-of-the-art molecular dynamics simulations, indicating the feasibility of this method. A controversy concerning the preferential orientation of [C 2 C 1 Im] at the surface has been resolved by this new combination analysis; namely, the [C 2 C 1 Im] cation has a preferential orientation with the ethyl chain pointing towards the vacuum in the topmost molecular layer.

Objective fitting of hemoglobin dynamics in traumatic bruises based on temperature depth profiling

NASA Astrophysics Data System (ADS)

Vidovič, Luka; Milanič, Matija; Majaron, Boris

2014-02-01

Pulsed photothermal radiometry (PPTR) allows noninvasive measurement of laser-induced temperature depth profiles. The obtained profiles provide information on depth distribution of absorbing chromophores, such as melanin and hemoglobin. We apply this technique to objectively characterize mass diffusion and decomposition rate of extravasated hemoglobin during the bruise healing process. In present study, we introduce objective fitting of PPTR data obtained over the course of the bruise healing process. By applying Monte Carlo simulation of laser energy deposition and simulation of the corresponding PPTR signal, quantitative analysis of underlying bruise healing processes is possible. Introduction of objective fitting enables an objective comparison between the simulated and experimental PPTR signals. In this manner, we avoid reconstruction of laser-induced depth profiles and thus inherent loss of information in the process. This approach enables us to determine the value of hemoglobin mass diffusivity, which is controversial in existing literature. Such information will be a valuable addition to existing bruise age determination techniques.

Depth profiling of high energy nitrogen ions implanted in the <1 0 0>, <1 1 0> and randomly oriented silicon crystals

NASA Astrophysics Data System (ADS)

Erić, M.; Petrović, S.; Kokkoris, M.; Lagoyannis, A.; Paneta, V.; Harissopulos, S.; Telečki, I.

2012-03-01

This work reports on the experimentally obtained depth profiles of 4 MeV 14N2+ ions implanted in the <1 0 0>, <1 1 0> and randomly oriented silicon crystals. The ion fluence was 1017 particles/cm2. The nitrogen depth profiling has been performed using the Nuclear Reaction Analysis (NRA) method, via the study of 14N(d,α0)12C and 14N(d,α1)12C nuclear reactions, and with the implementation of SRIM 2010 and SIMNRA computer simulation codes. For the randomly oriented silicon crystal, change of the density of silicon matrix and the nitrogen "bubble" formation have been proposed as the explanation for the difference between the experimental and simulated nitrogen depth profiles. During the implantation, the RBS/C spectra were measured on the nitrogen implanted and on the virgin crystal spots. These spectra provide information on the amorphization of the silicon crystals induced by the ion implantation.

LINKING Lyα AND LOW-IONIZATION TRANSITIONS AT LOW OPTICAL DEPTH

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jaskot, A. E.; Oey, M. S.

2014-08-20

We suggest that low optical depth in the Lyman continuum (LyC) may relate the Lyα emission, C II and Si II absorption, and C II* and Si II* emission seen in high-redshift galaxies. We base this analysis on Hubble Space Telescope Cosmic Origins Spectrograph spectra of four Green Pea (GP) galaxies, which may be analogs of z > 2 Lyα emitters (LAEs). In the two GPs with the strongest Lyα emission, the Lyα line profiles show reduced signs of resonant scattering. Instead, the Lyα profiles resemble the Hα line profiles of evolved star ejecta, suggesting that the Lyα emission originatesmore » from a low column density and similar outflow geometry. The weak C II absorption and presence of non-resonant C II* emission in these GPs support this interpretation and imply a low LyC optical depth along the line of sight. In two additional GPs, weak Lyα emission and strong C II absorption suggest a higher optical depth. These two GPs differ in their Lyα profile shapes and C II* emission strengths, however, indicating different inclinations of the outflows to our line of sight. With these four GPs as examples, we explain the observed trends linking Lyα, C II, and C II* in stacked LAE spectra, in the context of optical depth and geometric effects. Specifically, in some galaxies with strong Lyα emission, a low LyC optical depth may allow Lyα to escape with reduced scattering. Furthermore, C II absorption, C II* emission, and Lyα profile shape can reveal the optical depth, constrain the orientation of neutral outflows in LAEs, and identify candidate LyC emitters.« less

Domain activities of PapC usher reveal the mechanism of action of an Escherichia coli molecular machine.

PubMed

Volkan, Ender; Ford, Bradley A; Pinkner, Jerome S; Dodson, Karen W; Henderson, Nadine S; Thanassi, David G; Waksman, Gabriel; Hultgren, Scott J

2012-06-12

P pili are prototypical chaperone-usher pathway-assembled pili used by Gram-negative bacteria to adhere to host tissues. The PapC usher contains five functional domains: a transmembrane β-barrel, a β-sandwich Plug, an N-terminal (periplasmic) domain (NTD), and two C-terminal (periplasmic) domains, CTD1 and CTD2. Here, we delineated usher domain interactions between themselves and with chaperone-subunit complexes and showed that overexpression of individual usher domains inhibits pilus assembly. Prior work revealed that the Plug domain occludes the pore of the transmembrane domain of a solitary usher, but the chaperone-adhesin-bound usher has its Plug displaced from the pore, adjacent to the NTD. We demonstrate an interaction between the NTD and Plug domains that suggests a biophysical basis for usher gating. Furthermore, we found that the NTD exhibits high-affinity binding to the chaperone-adhesin (PapDG) complex and low-affinity binding to the major tip subunit PapE (PapDE). We also demonstrate that CTD2 binds with lower affinity to all tested chaperone-subunit complexes except for the chaperone-terminator subunit (PapDH) and has a catalytic role in dissociating the NTD-PapDG complex, suggesting an interplay between recruitment to the NTD and transfer to CTD2 during pilus initiation. The Plug domain and the NTD-Plug complex bound all of the chaperone-subunit complexes tested including PapDH, suggesting that the Plug actively recruits chaperone-subunit complexes to the usher and is the sole recruiter of PapDH. Overall, our studies reveal the cooperative, active roles played by periplasmic domains of the usher to initiate, grow, and terminate a prototypical chaperone-usher pathway pilus.

A Study of Future Communications Concepts and Technologies for the National Airspace System-Part III

NASA Technical Reports Server (NTRS)

Ponchak, Denise S.; Apaza, Rafael D.; Wichgersm Joel M.; Haynes, Brian; Roy, Aloke

2014-01-01

The National Aeronautics and Space Administration (NASA) Glenn Research Center (GRC) is investigating current and anticipated wireless communications concepts and technologies that the National Airspace System (NAS) may need in the next 50 years. NASA has awarded three NASA Research Announcements (NAR) studies with the objective to determine the most promising candidate technologies for air-to-air and air-to-ground data exchange and analyze their suitability in a post-NextGen NAS environment. This paper will present progress made in the studies and describe the communications challenges and opportunities that have been identified as part of the study. NASA's NextGen Concepts and Technology Development (CTD) Project integrates solutions for a safe, efficient and high-capacity airspace system through joint research efforts and partnerships with other government agencies. The CTD Project is one of two within NASA's Airspace Systems Program and is managed by the NASA Ames Research Center. Research within the CTD Project is in support the 2011 NASA Strategic Plan Sub-Goal 4.1: Develop innovative solutions and advanced technologies, through a balanced research portfolio, to improve current and future air transportation. The focus of CTD is on developing capabilities in traffic flow management, dynamic airspace configuration, separation assurance, super density operations and airport surface operations. Important to its research is the development of human/automation information requirements and decisionmaking guidelines for human-human and human-machine airportal decision-making. Airborne separation, oceanic intrail climb/descent and interval management applications depend on location and intent information of surrounding aircraft. ADS-B has been proposed to provide the information exchange, but other candidates such as satellite-based receivers, broadband or airborne internet, and cellular communications are possible candidate's.

Undifferentiated connective tissue disease and interstitial lung disease: Trying to define patterns.

PubMed

Alberti, María Laura; Paulin, Francisco; Toledo, Heidegger Mateos; Fernández, Martín Eduardo; Caro, Fabián Matías; Rojas-Serrano, Jorge; Mejía, Mayra Edith

To identify clinical or immunological features in patients with undifferentiated connective tissue disease (UCTD) associated interstitial lung disease (ILD), in order to group them and recognize different functional and high resolution computed tomography (HRCT) behavior. Retrospective cohort study. Patients meeting Kinder criteria for UCTD were included. We defined the following predictive variables: 'highly specific' connective tissue disease (CTD) manifestations (Raynaud's phenomenon, dry eyes or arthritis), high antinuclear antibody (ANA) titer (above 1: 320), and 'specific' ANA staining patterns (centromere, cytoplasmic and nucleolar patterns). We evaluated the following outcomes: change in the percentage of the predicted forced vital capacity (FVC%) during the follow-up period, and HRCT pattern. Sixty-six patients were included. Twenty-nine (43.94%) showed at least one 'highly specific' CTD manifestation, 16 (28.57%) had a 'specific' ANA staining pattern and 29 (43.94%) high ANA titer. Patients with 'highly specific' CTD manifestations were younger (mean [SD] 52 years [14.58] vs 62.08 years [9.46], P<.001), were more likely men (10.34% vs 48.65%, P<.001) and showed a smaller decline of the FVC% (median [interquartile range] 1% [-1 to 10] vs -6% [-16 to -4], P<.006). In the multivariate analysis, the presence of highly specific manifestations was associated with improvement in the FVC% (B coefficient of 13.25 [95% confidence interval, 2.41 to 24.09]). No association was observed in relation to the HRCT pattern. The presence of 'highly specific' CTD manifestations was associated with female sex, younger age and better functional behavior. These findings highlight the impact of the clinical features in the outcome of patients with UCTD ILD. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Reumatología y Colegio Mexicano de Reumatología. All rights reserved.

Structural basis of HIV-1 capsid recognition by PF74 and CPSF6

DOE PAGES

Bhattacharya, Akash; Alam, Steven L.; Fricke, Thomas; ...

2014-12-17

Upon infection of susceptible cells by HIV-1, the conical capsid formed by ~250 hexamers and 12 pentamers of the CA protein is delivered to the cytoplasm. In this study, the capsid shields the RNA genome and proteins required for reverse transcription. In addition, the surface of the capsid mediates numerous host–virus interactions, which either promote infection or enable viral restriction by innate immune responses. In the intact capsid, there is an intermolecular interface between the N-terminal domain (NTD) of one subunit and the C-terminal domain (CTD) of the adjacent subunit within the same hexameric ring. The NTD–CTD interface is criticalmore » for capsid assembly, both as an architectural element of the CA hexamer and pentamer and as a mechanistic element for generating lattice curvature. Here we report biochemical experiments showing that PF-3450074 (PF74), a drug that inhibits HIV-1 infection, as well as host proteins cleavage and polyadenylation specific factor 6 (CPSF6) and nucleoporin 153 kDa (NUP153), bind to the CA hexamer with at least 10-fold higher affinities compared with nonassembled CA or isolated CA domains. The crystal structure of PF74 in complex with the CA hexamer reveals that PF74 binds in a preformed pocket encompassing the NTD–CTD interface, suggesting that the principal inhibitory target of PF74 is the assembled capsid. Likewise, CPSF6 binds in the same pocket. Given that the NTD–CTD interface is a specific molecular signature of assembled hexamers in the capsid, binding of NUP153 at this site suggests that key features of capsid architecture remain intact upon delivery of the preintegration complex to the nucleus.« less

Wear-Induced Changes in FSW Tool Pin Profile: Effect of Process Parameters

NASA Astrophysics Data System (ADS)

Sahlot, Pankaj; Jha, Kaushal; Dey, G. K.; Arora, Amit

2018-06-01

Friction stir welding (FSW) of high melting point metallic (HMPM) materials has limited application due to tool wear and relatively short tool life. Tool wear changes the profile of the tool pin and adversely affects weld properties. A quantitative understanding of tool wear and tool pin profile is crucial to develop the process for joining of HMPM materials. Here we present a quantitative wear study of H13 steel tool pin profile for FSW of CuCrZr alloy. The tool pin profile is analyzed at multiple traverse distances for welding with various tool rotational and traverse speeds. The results indicate that measured wear depth is small near the pin root and significantly increases towards the tip. Near the pin tip, wear depth increases with increase in tool rotational speed. However, change in wear depth near the pin root is minimal. Wear depth also increases with decrease in tool traverse speeds. Tool pin wear from the bottom results in pin length reduction, which is greater for higher tool rotational speeds, and longer traverse distances. The pin profile changes due to wear and result in root defect for long traverse distance. This quantitative understanding of tool wear would be helpful to estimate tool wear, optimize process parameters, and tool pin shape during FSW of HMPM materials.

Characterization of near-stoichiometric Ti:LiNbO(3) strip waveguides with varied substrate refractive index in the guiding layer.

PubMed

Zhang, De-Long; Zhang, Pei; Zhou, Hao-Jiang; Pun, Edwin Yue-Bun

2008-10-01

We have demonstrated the possibility that near-stoichiometric Ti:LiNbO(3) strip waveguides are fabricated by carrying out vapor transport equilibration at 1060 degrees C for 12 h on a congruent LiNbO(3) substrate with photolithographically patterned 4-8 microm wide, 115 nm thick Ti strips. Optical characterizations show that these waveguides are single mode at 1.5 microm and show a waveguide loss of 1.3 dB/cm for TM mode and 1.1 dB/cm for TE mode. In the width/depth direction of the waveguide, the mode field follows the Gauss/Hermite-Gauss function. Secondary-ion-mass spectrometry (SIMS) was used to study Ti-concentration profiles in the depth direction and on the surface of the 6 microm wide waveguide. The result shows that the Ti profile follows a sum of two error functions along the width direction and a complementary error function in the depth direction. The surface Ti concentration, 1/e width and depth, and mean diffusivities along the width and depth directions of the guide are similar to 3.0 x 10(21) cm(-3), 3.8 microm, 2.6 microm, 0.30 and 0.14 microm(2)/h, respectively. Micro-Raman analysis was carried out on the waveguide endface to characterize the depth profile of Li composition in the guiding layer. The results show that the depth profile of Li composition also follows a complementary error function with a 1/e depth of 3.64 microm. The mean ([Li(Li)]+[Ti(Li)])/([Nb(Nb)]+[Ti(Nb)]) ratio in the waveguide layer is about 0.98. The inhomogeneous Li-composition profile results in a varied substrate index in the guiding layer. A two-dimensional refractive index profile model in the waveguide is proposed by taking into consideration the varied substrate index and assuming linearity between Ti-induced index change and Ti concentration. The net waveguide surface index increments at 1545 nm are 0.0114 and 0.0212 for ordinary and extraordinary rays, respectively. Based upon the constructed index model, the fundamental mode field profile was calculated using the beam propagation method, and the mode sizes and effective index versus the Ti-strip width were calculated for three lower TM and TE modes using the variational method. An agreement between theory and experiment is obtained.

Decomposition of ultrathin LiF cathode underlayer in organic-based devices evidenced by ToF-SIMS depth profiling

NASA Astrophysics Data System (ADS)

Pakhomov, Georgy L.; Drozdov, Mikhail N.; Travkin, Vlad V.; Bochkarev, Mikhail N.

2017-11-01

In this work we investigate the chemical composition of an archetypal thin-film organic device with the Ag/LiF cathode using the time-of-flight secondary ion mass spectrometry (ToF-SIMS) with depth profiling. The LiF cathode underlayer is partly decomposed because a significant amount of lithium is released into the bulk of the multilayer device. The released lithium diffuses all the way to the substrate, accumulating, as revealed by ToF-SIMS depth profiles, at the interfaces rather than uniformly doping the underlying layers. Particularly, the bottom anode becomes chemically modified.

Analyses of hydrogen in quartz and in sapphire using depth profiling by ERDA at atmospheric pressure: Comparison with resonant NRA and SIMS

NASA Astrophysics Data System (ADS)

Reiche, Ina; Castaing, Jacques; Calligaro, Thomas; Salomon, Joseph; Aucouturier, Marc; Reinholz, Uwe; Weise, Hans-Peter

2006-08-01

Hydrogen is present in anhydrous materials as a result of their synthesis and of their environment during conservation. IBA provides techniques to measure H concentration depth profiles allowing to identify various aspects of the materials including the history of objects such as gemstones used in cultural heritage. A newly established ERDA set-up, using an external microbeam of alpha particles, has been developed to study hydrated near-surface layers in quartz and sapphire by non-destructive H depth profiling in different atmospheres. The samples were also analysed using resonant NRA and SIMS.

GIS Well Temperature Data from the Roosevelt Hot Springs, Utah FORGE Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gwynn, Mark; Hill, Jay; Allis, Rick

This is a GIS point feature shapefile representing wells, and their temperatures, that are located in the general Utah FORGE area near Milford, Utah. There are also fields that represent interpolated temperature values at depths of 200 m, 1000 m, 2000 m, 3000 m, and 4000 m. in degrees Fahrenheit. The temperature values at specific depths as mentioned above were derived as follows. In cases where the well reached a given depth (200 m and 1, 2, 3, or 4 km), the temperature is the measured temperature. For the shallower wells (and at deeper depths in the wells reaching onemore » or more of the target depths), temperatures were extrapolated from the temperature-depth profiles that appeared to have stable (re-equilibrated after drilling) and linear profiles within the conductive regime (i.e. below the water table or other convective influences such as shallow hydrothermal outflow from the Roosevelt Hydrothermal System). Measured temperatures/gradients from deeper wells (when available and reasonably close to a given well) were used to help constrain the extrapolation to greater depths. Most of the field names in the attribute table are intuitive, however HF = heat flow, intercept = the temperature at the surface (x-axis of the temperature-depth plots) based on the linear segment of the plot that was used to extrapolate the temperature profiles to greater depths, and depth_m is the total well depth. This information is also present in the shapefile metadata.« less

Strong-field Photoionization of Sputtered Neutral Molecules for Molecular Depth Profiling

PubMed Central

Willingham, D; Brenes, D. A.; Wucher, A

2009-01-01

Molecular depth profiles of an organic thin film of guanine vapor deposited onto a Ag substrate are obtained using a 40 keV C60 cluster ion beam in conjunction with time-of-flight secondary ion mass spectrometric (ToF-SIMS) detection. Strong-field, femtosecond photoionization of intact guanine molecules is used to probe the neutral component of the profile for direct comparison with the secondary ion component. The ability to simultaneously acquire secondary ions and photoionized neutral molecules reveals new fundamental information about the factors that influence the properties of the depth profile. Results show that there is an increased ionization probability for protonated molecular ions within the first 10 nm due to the generation of free protons within the sample. Moreover, there is a 50% increase in fragment ion signal relative to steady state values 25 nm before reaching the guanine/Ag interface as a result of interfacial chemical damage accumulation. An altered layer thickness of 20 nm is observed as a consequence of ion beam induced chemical mixing. In general, we show that the neutral component of a molecular depth profile using the strong-field photoionization technique can be used to elucidate the effects of variations in ionization probability on the yield of molecular ions as well as to aid in obtaining accurate information about depth dependent chemical composition that cannot be extracted from TOF-SIMS data alone. PMID:20495665

The biological pump: Profiles of plankton production and consumption in the upper ocean

NASA Astrophysics Data System (ADS)

Longhurst, Alan R.; Glen Harrison, W.

The ‘biological pump’ mediates flux of carbon to the interior of the ocean by interctions between the components of the vertically-structured pelagic ecosystem of the photic zone. Chlorophyll profiles are not a simple indicator of autotrophic biomass or production, because of non-linearities in the physiology of cells and preferential vertical distribution of taxa. Profiles of numbers or biomass of heterotrophs do not correspond with profiles of consumption, because of depth-selection (taxa, seasons) for reasons unconnected with feeding. Depths of highest plant biomass, chlorophyll and growth rate coincide when these depths are shallow, but become progressively separated in profiles where they are deeper - so that highest growth rate lies progressively shallower than the chloropyll maximum. It is still uncertain how plant biomass is distributed in deep profiles. Depths of greatest heterotroph biomass (mesozooplankton) are usually close to depths of fastest plant growth rate, and thus lie shallower than the chlorophyll maximum in profiles where this itself is deep. This correlation is functional, and relates to the role of heterotrophs in excreting metabolic wastes (especially ammonia), which may fuel a significant component of integrated algal production, especially in the oligotrophic ocean. Some, but not all faecal material from mesozooplankton of the photic zone appears in vertical flux below the pycnocine, depending on the size of the source organisms, and the degree of vertical mixing above the pycnocline. Diel, but probably not seasonal, vertical migration is significant in the vertical flux of dissolved nitrogen. Regional generalisations of the vertical relations of the main components of the ‘biological pump’ now appear within reach, and an approach is suggested.

The Effect of Borehole Flow on Salinity Profiles From Deep Monitor Wells in Hawaii

NASA Astrophysics Data System (ADS)

Rotzoll, K.; Hunt, C. D.; El-Kadi, A. I.

2008-12-01

Ground-water resource management in Hawaii is based partly on salinity profiles from deep wells that are used to monitor the thickness of freshwater lenses and the transition zone between freshwater and saltwater. Vertical borehole flow in these wells may confound understanding of the actual salinity-depth profiles in the basaltic aquifers and lead to misinterpretations that hamper effective water-resource management. Causes and effects of borehole flow on salinity profiles are being evaluated at 40 deep monitor wells in Hawaii. Step- like changes in fluid electrical conductivity with respect to depth are indicative of borehole flow and are evident in almost all available salinity profiles. A regional trend in borehole flow direction, expected from basin-wide ground-water flow dynamics, is evident as major downward flow components in inland recharge areas and major upward flow components in discharge areas near the coast. The midpoint of the transition zone in one deep monitor well showed inconsequential depth displacements in response to barometric pressure and tidal fluctuations and to pumping from nearby wellfields. Commonly, the 1 mS/cm conductivity value is used to indicate the top of the transition zone. Contrary to the more stable midpoint, the depth of the 1 mS/cm conductivity value may be displaced by as much as 200 m in deep monitor wells near pumping wellfields. The displacement is complemented with an increase in conductivity at a particular depth in the upper part of the profile. The observed increase in conductivity is linear with increase in nearby pumpage. The largest deviations from expected aquifer-salinity profiles occur in deep monitor wells located in the area extending from east Pearl Harbor to Kalihi on Oahu, which coincides with the most heavily pumped part of the aquifer.

Migration of fallout radiocaesium in a grassland soil from 1986 to 2001. Part I: activity-depth profiles of (134)Cs and (137)Cs.

PubMed

Schimmack, W; Schultz, W

2006-09-15

The temporal changes of the vertical distribution of (134)Cs (deposited by the Chernobyl fallout in 1986) and (137)Cs (deposited by the Chernobyl and the global fallout) in the soil were investigated at an undisturbed Bavarian grassland site in Germany. At ten sampling dates between 1986 and 2001, the activity density of (134)Cs and (137)Cs was determined in various soil layers down to 80 cm depth. In 2001, the small-scale spatial variability of the radiocaesium activity was determined by sampling five plots within 10 m(2) (coefficient of variation about 20% for the upper soil layers). Between 1987 and 1990, substantial changes of the activity-depth profiles were observed. The percentage depth distributions of (134)Cs and (137)Cs were rather similar. The 50%-depth of the accumulated activity increased from 2.4 cm in 1988 to 5.3 cm in 2001 for (134)Cs and from 2.7 to 5.8 cm for (137)Cs. This indicates that at the study site the migration data of Chernobyl-derived (137)Cs can be estimated by those of total (137)Cs. In the second part of this study, the activity-depth profiles will be evaluated by the convection-dispersion model [Schimmack, W, Feria Márquez, F. Migration of fallout radiocaesium in a grassland soil from 1986 to 2001. Part II: Evaluation of the activity-depth profiles by transport models. Sci Total Environ 2006-this issue].

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

PubMed Central

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils. PMID:28611747

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers.

PubMed

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria , Chloroflexi , and Firmicutes increased whereas Cyanobacteria , β -proteobacteria , and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota , Thaumarchaeota , and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and identified as the key driver in shaping both bacterial and archaeal community structure, but did not directly affect microbial functional structure. The distinctive pattern of microbial taxonomic and functional composition along soil profiles implied functional redundancy within these paddy soils.

Technical note: GODESS - a profiling mooring in the Gotland Basin

NASA Astrophysics Data System (ADS)

Prien, Ralf D.; Schulz-Bull, Detlef E.

2016-07-01

This note describes a profiling mooring with an interdisciplinary suite of sensors taking profiles between 180 and 30 m depth. It consists of an underwater winch, moored below 180 m depth, and a profiling instrumentation platform. In its described setup it can take about 200 profiles at pre-programmed times or intervals with one set of batteries. This allows for studies over an extended period of time (e.g. two daily profiles over a time of 3 months). The Gotland Deep Environmental Sampling Station (GODESS) in the Eastern Gotland Basin of the Baltic Sea is aimed at investigations of redoxcline dynamics. The described system can be readily adapted to other research foci by changing the profiling instrumentation platform and its payload.

Hydrothermal Plume Activity at Teahitia Seamount: Re-Awakening of the Society Islands Hot-Spot?

NASA Astrophysics Data System (ADS)

German, C. R.; Xu, G.; Yeo, I. A.; Walker, S. L.; Moffett, J.; Cutter, G. A.; Devey, C. W.; Hyvernaud, O.; Reymond, D.; Resing, J. A.

2016-12-01

We report results from a combined mapping and CTD-rosette investigation of the summit of Teahitia Seamount, Society Islands hot-spot, that indicates that high temperature venting may have been present by late 2013 at a site that only hosted low-temperature vents ( 30°C) when previously visited by submersible, 25 years earlier. In 2013, a non-buoyant hydrothermal plume containing high concentrations (>100nmol/L) of both dissolved and total dissolvable Fe was observed at an apparent rise-height of 110-140m above a seafloor source at 1500-1530m water depth, implying a heat-flux for the underlying venting of 13-35MW. From a comparison to the past evolution of venting at Loihi seamount (Hawaii), coupled with an examination of recent seismicity detected by the Polynesian Seismic Network, we hypothesize that venting at Teahitia may have undergone perturbation only recently and that this, in turn, may be linked to a re-awakening of the Society Islands hotspot.

Selectivity of silica species in ocean observed from seasonal and local changes

NASA Astrophysics Data System (ADS)

Tanaka, Miho; Takahashi, Kazuya; Nemoto, Masao; Horimoto, Naho

2013-03-01

Silicic acids, derived from SiO2 (silica), have several chemical forms in solution. Silica is a nutrient for diatoms, which are phytoplankton in oceans. Silica species can be used as a tracer to examine the behavior of silica in nature. The speciation for silica by FAB-MS (fast atom bombardment mass spectrometry) has been carried out for seawater samples from Tokyo Bay and Sagami Bay to investigate the seasonal and locational changes of the depth profiles of silica species. The species, [Si(OH)2O2Na+]-, [Si2(OH)5O2]- ([dimer]-), [Si2(OH)4O3Na+]-, [Si(OH)7O5-] ([cyclic tetramer]-), [Si4(OH)6O6Na+]-, [Si(OH)9O]- ([linear tetramer]-) and [Si4(OH)8O5Na+]- were mainly identified by FAB-MS. The seasonal and locational changes and the reproducibility of depth profiles of silica species were determined from October 2001 to July 2002. The depth profile of the ratio of linear tetramer to cyclic tetramer reflects the activity of diatoms, implying that the linear tetramer is the preferred "food" for diatoms. In particular, the depth profile for the ratio of linear tetramer to cyclic tetramer exhibits a critical changes that depend on the season. Furthermore, the depth profiles for the samples from Sagami Bay (open ocean) indicate that seawater is easily exchanged by ocean currents (the Japan Current). Thus, silica speciation by FAB-MS can give us a new tracer indicating the characteristics of the seawater budget, which change with depth, season and ocean locality.

IET. Control and equipment building (TAN620) sections. Depth and profile ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

IET. Control and equipment building (TAN-620) sections. Depth and profile of earthen shield tunnels. Ralph M. Parsons 902-4-ANP-620-A-321. Date: February 1954. INEEL index code no. 035-0620-00-693-106906 - Idaho National Engineering Laboratory, Test Area North, Scoville, Butte County, ID

Lidar Ratios for Dust Aerosols Derived From Retrievals of CALIPSO Visible Extinction Profiles Constrained by Optical Depths from MODIS-Aqua and CALIPSO/CloudSat Ocean Surface Reflectance Measurements

NASA Technical Reports Server (NTRS)

Young, Stuart A.; Josset, Damien B.; Vaughan, Mark A.

2010-01-01

CALIPSO's (Cloud Aerosol Lidar Infrared Pathfinder Satellite Observations) analysis algorithms generally require the use of tabulated values of the lidar ratio in order to retrieve aerosol extinction and optical depth from measured profiles of attenuated backscatter. However, for any given time or location, the lidar ratio for a given aerosol type can differ from the tabulated value. To gain some insight as to the extent of the variability, we here calculate the lidar ratio for dust aerosols using aerosol optical depth constraints from two sources. Daytime measurements are constrained using Level 2, Collection 5, 550-nm aerosol optical depth measurements made over the ocean by the MODIS (Moderate Resolution Imaging Spectroradiometer) on board the Aqua satellite, which flies in formation with CALIPSO. We also retrieve lidar ratios from night-time profiles constrained by aerosol column optical depths obtained by analysis of CALIPSO and CloudSat backscatter signals from the ocean surface.

Distribution and depth profiles of polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans, and polychlorinated biphenyls in sediment collected from offshore waters of Central Vietnam.

PubMed

Tri, Tran Manh; Anh, Hoang Quoc; Tham, Trinh Thi; Van Quy, Tran; Long, Nguyen Quang; Nhung, Dao Thi; Nakamura, Masafumi; Nishida, Masayo; Maeda, Yasuaki; Van Boi, Luu; Minh, Tu Binh

2016-05-15

Concentrations of PCBs and OCPs were measured in 35 surface sediment samples collected from offshore waters of Central Vietnam. The mean concentrations of PCBs, HCHs, and DDTs in surface sediments were 86.5, 37.0, and 44.5pgg(-1), respectively. Additionally, nine PCDDs, eleven PCDFs, and twelve dl-PCBs were also examined in 19 sediment core samples collected from five locations. Concentration of PCDDs, PCDFs, and dl-PCBs ranged from 200 to 460, 0.39 to 2.9, and 1.6 to 22pgg(-1), respectively. OCDD was detected at the highest concentration, ranged from 100 to 300pgg(-1). Generally, the concentrations of PCDD/Fs at shallower depths were higher, meanwhile the depth profiles of dl-PCBs in sediment cores were different than the depth profiles of PCDD/Fs. The results suggest that the pollution of PCBs might be from many different sources leading to the variation between depths. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quality DOTS management and empowering tuberculosis patients.

PubMed

Chugh, Satish

2009-03-01

Central Tuberculosis Division (CTD) has covered whole of India under DOTS. IMA is a proud partner of RNTCP which is managed by CTD. International Standards for Tuberculosis Care is expected from all healthcare providers. The basic principles of care is same worldwide. IMA GFATM RNTCP PPM is completing 2 years of its inception. Sensitisation programme and district training programmes has yielded DOTS/DMC centres in the target states. IMA is having 100% commitment for containing tuberculosis in India. There are International Standards for quality management in tuberculosis control, some of the Standards are elaborated in this write-up. In the Indian context, DOTS needs some innovations that is discussed in this article.

Threonine-4 of mammalian RNA polymerase II CTD is targeted by Polo-like kinase 3 and required for transcriptional elongation

PubMed Central

Hintermair, Corinna; Heidemann, Martin; Koch, Frederic; Descostes, Nicolas; Gut, Marta; Gut, Ivo; Fenouil, Romain; Ferrier, Pierre; Flatley, Andrew; Kremmer, Elisabeth; Chapman, Rob D; Andrau, Jean-Christophe; Eick, Dirk

2012-01-01

Eukaryotic RNA polymerase II (Pol II) has evolved an array of heptad repeats with the consensus sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 at the carboxy-terminal domain (CTD) of the large subunit (Rpb1). Differential phosphorylation of Ser2, Ser5, and Ser7 in the 5′ and 3′ regions of genes coordinates the binding of transcription and RNA processing factors to the initiating and elongating polymerase complexes. Here, we report phosphorylation of Thr4 by Polo-like kinase 3 in mammalian cells. ChIPseq analyses indicate an increase of Thr4-P levels in the 3′ region of genes occurring subsequently to an increase of Ser2-P levels. A Thr4/Ala mutant of Pol II displays a lethal phenotype. This mutant reveals a global defect in RNA elongation, while initiation is largely unaffected. Since Thr4 replacement mutants are viable in yeast we conclude that this amino acid has evolved an essential function(s) in the CTD of Pol II for gene transcription in mammalian cells. PMID:22549466

COMPUTING THERAPY FOR PRECISION MEDICINE: COLLABORATIVE FILTERING INTEGRATES AND PREDICTS MULTI-ENTITY INTERACTIONS.

PubMed

Regenbogen, Sam; Wilkins, Angela D; Lichtarge, Olivier

2016-01-01

Biomedicine produces copious information it cannot fully exploit. Specifically, there is considerable need to integrate knowledge from disparate studies to discover connections across domains. Here, we used a Collaborative Filtering approach, inspired by online recommendation algorithms, in which non-negative matrix factorization (NMF) predicts interactions among chemicals, genes, and diseases only from pairwise information about their interactions. Our approach, applied to matrices derived from the Comparative Toxicogenomics Database, successfully recovered Chemical-Disease, Chemical-Gene, and Disease-Gene networks in 10-fold cross-validation experiments. Additionally, we could predict each of these interaction matrices from the other two. Integrating all three CTD interaction matrices with NMF led to good predictions of STRING, an independent, external network of protein-protein interactions. Finally, this approach could integrate the CTD and STRING interaction data to improve Chemical-Gene cross-validation performance significantly, and, in a time-stamped study, it predicted information added to CTD after a given date, using only data prior to that date. We conclude that collaborative filtering can integrate information across multiple types of biological entities, and that as a first step towards precision medicine it can compute drug repurposing hypotheses.

COMPUTING THERAPY FOR PRECISION MEDICINE: COLLABORATIVE FILTERING INTEGRATES AND PREDICTS MULTI-ENTITY INTERACTIONS

PubMed Central

REGENBOGEN, SAM; WILKINS, ANGELA D.; LICHTARGE, OLIVIER

2015-01-01

Biomedicine produces copious information it cannot fully exploit. Specifically, there is considerable need to integrate knowledge from disparate studies to discover connections across domains. Here, we used a Collaborative Filtering approach, inspired by online recommendation algorithms, in which non-negative matrix factorization (NMF) predicts interactions among chemicals, genes, and diseases only from pairwise information about their interactions. Our approach, applied to matrices derived from the Comparative Toxicogenomics Database, successfully recovered Chemical-Disease, Chemical-Gene, and Disease-Gene networks in 10-fold cross-validation experiments. Additionally, we could predict each of these interaction matrices from the other two. Integrating all three CTD interaction matrices with NMF led to good predictions of STRING, an independent, external network of protein-protein interactions. Finally, this approach could integrate the CTD and STRING interaction data to improve Chemical-Gene cross-validation performance significantly, and, in a time-stamped study, it predicted information added to CTD after a given date, using only data prior to that date. We conclude that collaborative filtering can integrate information across multiple types of biological entities, and that as a first step towards precision medicine it can compute drug repurposing hypotheses. PMID:26776170

Disease-Homologous Mutation in the Cation Diffusion Facilitator Protein MamM Causes Single-Domain Structural Loss and Signifies Its Importance

PubMed Central

Barber-Zucker, Shiran; Uebe, René; Davidov, Geula; Navon, Yotam; Sherf, Dror; Chill, Jordan H.; Kass, Itamar; Bitton, Ronit; Schüler, Dirk; Zarivach, Raz

2016-01-01

Cation diffusion facilitators (CDF) are highly conserved, metal ion efflux transporters that maintain divalent transition metal cation homeostasis. Most CDF proteins contain two domains, the cation transporting transmembrane domain and the regulatory cytoplasmic C-terminal domain (CTD). MamM is a magnetosome-associated CDF protein essential for the biomineralization of magnetic iron-oxide particles in magnetotactic bacteria. To investigate the structure-function relationship of CDF cytoplasmic domains, we characterized a MamM M250P mutation that is synonymous with the disease-related mutation L349P of the human CDF protein ZnT-10. Our results show that the M250P exchange in MamM causes severe structural changes in its CTD resulting in abnormal reduced function. Our in vivo, in vitro and in silico studies indicate that the CTD fold is critical for CDF proteins’ proper function and support the previously suggested role of the CDF cytoplasmic domain as a CDF regulatory element. Based on our results, we also suggest a mechanism for the effects of the ZnT-10 L349P mutation in human. PMID:27550551

A multi-sensor land mine detection system: hardware and architectural outline of the Australian RRAMNS CTD system

NASA Astrophysics Data System (ADS)

Abeynayake, Canicious; Chant, Ian; Kempinger, Siegfried; Rye, Alan

2005-06-01

The Rapid Route Area and Mine Neutralisation System (RRAMNS) Capability Technology Demonstrator (CTD) is a countermine detection project undertaken by DSTO and supported by the Australian Defence Force (ADF). The limited time and budget for this CTD resulted in some difficult strategic decisions with regard to hardware selection and system architecture. Although the delivered system has certain limitations arising from its experimental status, many lessons have been learned which illustrate a pragmatic path for future development. RRAMNS a similar sensor suite to other systems, in that three complementary sensors are included. These are Ground Probing Radar, Metal Detector Array, and multi-band electro-optic sensors. However, RRAMNS uses a unique imaging system and a network based real-time control and sensor fusion architecture. The relatively simple integration of each of these components could be the basis for a robust and cost-effective operational system. The RRAMNS imaging system consists of three cameras which cover the visible spectrum, the mid-wave and long-wave infrared region. This subsystem can be used separately as a scouting sensor. This paper describes the system at its mid-2004 status, when full integration of all detection components was achieved.