Gastroesophageal reflux and pulmonary fibrosis in scleroderma: a study using pH-impedance monitoring

RATIONALE: Interstitial lung disease (ILD) in patients with systemic sclerosis (SSc) is associated with increased morbidity and mortality. Gastroesophageal reflux (GER) is considered a contributing factor in the pathogenesis of ILD. OBJECTIVES: To characterize GER (acid and nonacid) in patients with SSc with and without ILD. METHODS: Patients with SSc underwent pulmonary high-resolution computer tomography (HRCT) scan and 24-hour impedance-pH monitoring off-proton pump inhibitor therapy. The presence of pulmonary fibrosis was assessed using validated HRCT-scores. Reflux monitoring parameters included number of acid and nonacid reflux episodes, proximal migration of the refluxate, and distal esophageal acid exposure. Unless otherwise specified, data are presented as median (25th-75th percentile). MEASUREMENTS AND MAIN RESULTS: Forty consecutive patients with SSc (35 female; mean age, 53 yr; range, 24-71; 15 patients with diffuse and 25 with limited SSc) were investigated; 18 (45%) patients with SSc had pulmonary fibrosis (HRCT score >or= 7). Patients with SSc with ILD had higher (P < 0.01) esophageal acid exposure (10.3 [7.5-15] vs. 5.2 [1.5-11]), higher (P < 0.01) number of acid (41 [31-58] vs. 19 [10-23]) and nonacid (25 [20-35] vs. 17 [11-19]) reflux episodes, and higher (P < 0.01) number of reflux episodes reaching the proximal esophagus (42.5 [31-54] vs. 15 [8-22]) compared with patients with SSc with normal HRCT scores. Pulmonary fibrosis scores (HRCT score) correlated well with the number of reflux episodes in the distal (r(2) = 0.637) and proximal (r(2) = 0.644) esophagus. CONCLUSIONS: Patients with SSc with ILD have more severe reflux (i.e., more reflux episodes and more reflux reaching the proximal esophagus). Whether or not the development of ILD in patients with SSc can be prevented by reflux-reducing treatments needs to be investigated.

Expression, purification, and projection structure by single particle electron microscopy of functional human TRPM4 heterologously expressed in Xenopus laevis oocytes

Despite efforts implicating the cationic channel transient receptor potential melastatin member 4 (TRPM4) to cardiac, nervous, and immunological pathologies, little is known about its structure and function. In this study, we optimized the requirements for purification and extraction of functional human TRPM4 protein and investigated its supra-molecular assembly. We selected the Xenopus laevis oocyte expression system because it lacks endogenous TRPM4 expression, it is known to overexpress functional human membrane channels, can be used for structure-function analysis within the same system, and is easily scaled to improve yield and develop moderate throughput capabilities through the use of robotics. Negative-stain electron microscopy (EM) revealed various sized low-resolution particles. Single particle analysis identified the majority of the projections represented the monomeric form with additional oligomeric structures potentially characterized as tetramers. Two-electrode voltage clamp electrophysiology demonstrated that human TRPM4 is functionally expressed at the oocyte plasma membrane. This study opens the door for medium-throughput screening and structure-function determination of this important therapeutically relevant target.

Expression, purification, and structural insights for the human uric acid transporter, GLUT9, using the Xenopus laevis oocytes system.

The urate transporter, GLUT9, is responsible for the basolateral transport of urate in the proximal tubule of human kidneys and in the placenta, playing a central role in uric acid homeostasis. GLUT9 shares the least homology with other members of the glucose transporter family, especially with the glucose transporting members GLUT1-4 and is the only member of the GLUT family to transport urate. The recently published high-resolution structure of XylE, a bacterial D-xylose transporting homologue, yields new insights into the structural foundation of this GLUT family of proteins. While this represents a huge milestone, it is unclear if human GLUT9 can benefit from this advancement through subsequent structural based targeting and mutagenesis. Little progress has been made toward understanding the mechanism of GLUT9 since its discovery in 2000. Before work can begin on resolving the mechanisms of urate transport we must determine methods to express, purify and analyze hGLUT9 using a model system adept in expressing human membrane proteins. Here, we describe the surface expression, purification and isolation of monomeric protein, and functional analysis of recombinant hGLUT9 using the Xenopus laevis oocyte system. In addition, we generated a new homology-based high-resolution model of hGLUT9 from the XylE crystal structure and utilized our purified protein to generate a low-resolution single particle reconstruction. Interestingly, we demonstrate that the functional protein extracted from the Xenopus system fits well with the homology-based model allowing us to generate the predicted urate-binding pocket and pave a path for subsequent mutagenesis and structure-function studies.

Anamorphic pixels for multi-channel superresolution

Superresolution from plenoptic cameras or camera arrays is usually treated similarly to superresolution from video streams. However, the transformation between the low-resolution views can be determined precisely from camera geometry and parallax. Furthermore, as each low-resolution image originates from a unique physical camera, its sampling properties can also be unique. We exploit this option with a custom design of either the optics or the sensor pixels. This design makes sure that the sampling matrix of the complete system is always well-formed, enabling robust and high-resolution image reconstruction. We show that simply changing the pixel aspect ratio from square to anamorphic is sufficient to achieve that goal, as long as each camera has a unique aspect ratio. We support this claim with theoretical analysis and image reconstruction of real images. We derive the optimal aspect ratios for sets of 2 or 4 cameras. Finally, we verify our solution with a camera system using an anamorphic lens.

Placental Uric Acid Transport System: Glucose Transporter 9 (SLC2A9)

Placental Uric Acid Transport System: Glucose Transporter 9 (SLC2A9). INTRODUCTION: Pre-eclampsia, a pregnancy-specific disease, contributes substantially to perinatal morbidity and mortality of both the mother and her child. Pre-eclampsia is often associated with high maternal urate serum levels, which in turn has been shown to play a role in the pathogenesis of this disease. The aim of this study was to investigate the glucose transporter GLUT9-mediated placental uric acid transport system. METHODS: In this study western blot, immunofluorescence techniques as well as a transepithelial transport (Transwell) model were used to assess GLUT9 protein expression and, respectively, uric acid transport activity. Electrophysiological techniques and transmission electron microscopy (TEM) were used to characterize the properties and the structure of GLUT9. RESULTS: Uric acid is transported across a BeWo choriocarcinoma cell monolayer with 530 pmol/min. We could successfully overexpress and for the first time purify the GLUT9b isoform using the Xenopus laevis oocytes expression system. Chloride seems to modulate the urate transport system. TEM revealed that GLUT9b isoform is present as monomer and dimmer in the Xenopus laevis overexpression model. A class average of all the particles allowed us to develop a first model of human GLUT9b structure, which was derived from the published crystal structure of the bacterial homologue of GLUT1-4. CONCLUSIONS: In vitro the “materno-fetal” transport of uric acid is slow indicating that in vivo the fetus might be protected from short-term fluctuations of maternal urate serum levels. The low-resolution structure obtained from TEM validates the proposed homology model regarding the structure of human GLUT9b. In ongoing studies this model is used to perform virtual screening to identify novel modulators of the urate transport system enabling the development of novel therapies in pregnancy complications.

Fusion of fundus images and MRI data of the human eye

Purpose Ophthalmologists are confronted with a set of different image modalities to diagnose eye tumors e.g., fundus photography, CT and MRI. However, these images are often complementary and represent pathologies differently. Some aspects of tumors can only be seen in a particular modality. A fusion of modalities would improve the contextual information for diagnosis. The presented work attempts to register color fundus photography with MRI volumes. This would complement the low resolution 3D information in the MRI with high resolution 2D fundus images. Methods MRI volumes were acquired from 12 infants under the age of 5 with unilateral retinoblastoma. The contrast-enhanced T1-FLAIR sequence was performed with an isotropic resolution of less than 0.5mm. Fundus images were acquired with a RetCam camera. For healthy eyes, two landmarks were used: the optic disk and the fovea. The eyes were detected and extracted from the MRI volume using a 3D adaption of the Fast Radial Symmetry Transform (FRST). The cropped volume was automatically segmented using the Split Bregman algorithm. The optic nerve was enhanced by a Frangi vessel filter. By intersection the nerve with the retina the optic disk was found. The fovea position was estimated by constraining the position with the angle between the optic and the visual axis as well as the distance from the optic disk. The optical axis was detected automatically by fitting a parable on to the lens surface. On the fundus, the optic disk and the fovea were detected by using the method of Budai et al. Finally, the image was projected on to the segmented surface using the lens position as the camera center. In tumor affected eyes, the manually segmented tumors were used instead of the optic disk and macula for the registration. Results In all of the 12 MRI volumes that were tested the 24 eyes were found correctly, including healthy and pathological cases. In healthy eyes the optic nerve head was found in all of the tested eyes with an error of 1.08 +/- 0.37mm. A successful registration can be seen in figure 1. Conclusions The presented method is a step toward automatic fusion of modalities in ophthalmology. The combination enhances the MRI volume with higher resolution from the color fundus on the retina. Tumor treatment planning is improved by avoiding critical structures and disease progression monitoring is made easier.

Sodium-Dependent Phosphate Transporters in Osteoclast Differentiation and Function

Osteoclasts are multinucleated bone degrading cells. Phosphate is an important constituent of mineralized bone and released in significant quantities during bone resorption. Molecular contributors to phosphate transport during the resorptive activity of osteoclasts have been controversially discussed. This study aimed at deciphering the role of sodium-dependent phosphate transporters during osteoclast differentiation and bone resorption. Our studies reveal RANKL-induced differential expression of sodium-dependent phosphate transport protein IIa (NaPi-IIa) transcript and protein during osteoclast development, but no expression of the closely related NaPi-IIb and NaPi-IIc SLC34 family isoforms. In vitro studies employing NaPi-IIa-deficient osteoclast precursors and mature osteoclasts reveal that NaPi-IIa is dispensable for bone resorption and osteoclast differentiation. These results are supported by the analysis of structural bone parameters by high-resolution microcomputed tomography that yielded no differences between adult NaPi-IIa WT and KO mice. By contrast, both type III sodium-dependent phosphate transporters Pit-1 and Pit-2 were abundantly expressed throughout osteoclast differentiation, indicating that they are the relevant sodium-dependent phosphate transporters in osteoclasts and osteoclast precursors. We conclude that phosphate transporters of the SLC34 family have no role in osteoclast differentiation and function and propose that Pit-dependent phosphate transport could be pivotal for bone resorption and should be addressed in further studies.

Facial Nerve Image Enhancement from CBCT using Supervised Learning Technique

Facial nerve segmentation plays an important role in surgical planning of cochlear implantation. Clinically available CBCT images are used for surgical planning. However, its relatively low resolution renders the identification of the facial nerve difficult. In this work, we present a supervised learning approach to enhance facial nerve image information from CBCT. A supervised learning approach based on multi-output random forest was employed to learn the mapping between CBCT and micro-CT images. Evaluation was performed qualitatively and quantitatively by using the predicted image as input for a previously published dedicated facial nerve segmentation, and cochlear implantation surgical planning software, OtoPlan. Results show the potential of the proposed approach to improve facial nerve image quality as imaged by CBCT and to leverage its segmentation using OtoPlan.

Full correction for spatially distributed speed-of-sound in echo ultrasound based on measuring aberration delays via transmit beam steering

Aberrations of the acoustic wave front, caused by spatial variations of the speed-of-sound, are a main limiting factor to the diagnostic power of medical ultrasound imaging. If not accounted for, aberrations result in low resolution and increased side lobe level, over all reducing contrast in deep tissue imaging. Various techniques have been proposed for quantifying aberrations by analysing the arrival time of coherent echoes from so-called guide stars or beacons. In situations where a guide star is missing, aperture-based techniques may give ambiguous results. Moreover, they are conceptually focused on aberrators that can be approximated as a phase screen in front of the probe. We propose a novel technique, where the effect of aberration is detected in the reconstructed image as opposed to the aperture data. The varying local echo phase when changing the transmit beam steering angle directly reflects the varying arrival time of the transmit wave front. This allows sensing the angle-dependent aberration delay in a spatially resolved way, and thus aberration correction for a spatially distributed volume aberrator. In phantoms containing a cylindrical aberrator, we achieved location-independent diffraction-limited resolution as well as accurate display of echo location based on reconstructing the speed-of-sound spatially resolved. First successful volunteer results confirm the clinical potential of the proposed technique.

Sulfur Isotopic Ratios at 67P/Churyumov-Gerasimenko and Characterization of ROSINA-DFMS FM & FS

Comets are thought to be the most pristine bodies present in the Solar System. In consequence of spending the majority of their existence beyond 30 AU, their composition can give insights on the physical and chemical conditions during their formation. Since August 2014 the European Space Agency spacecraft Rosetta accompanies the Jupiter family comet 67P/Churyumov-Gerasimenko on its way to perihelion and beyond. In this study the isotope fractionation of 34S are reported in H2S, OCS, SO2, S2, and CS2 at 67P. In addition for the first time the isotope fractionation for 33S is presented for cometary volatiles. The ratio 32S/33S is given for H2S, SO2 and a tentative value is given for CS2. With a mean value of -50 ± 22‰ and -306 ± 31‰ for δ34S and δ33S respectively, H2S shows a significant depletion in both 34S and 33S. For SO2 the depletion is less distinct with δ34S and δ33S being -67 ± 40‰ and -130 ± 53‰, respectively. The strongest depletion is present for CS2 with -114 ± 21‰and -276 ± 55‰, respectively. For OCS and S2 only δ34S could be determined which is -252 ± 77‰ and -357 ± 145‰, respectively. A comparison with sulfur isotopic ratios measured in SiC grains revealed that both SiC grains and the five volatile species have similar sulfur isotopic ratios. However, it is beyond the scope of this work to investigate the possibility of a link between SiC grains and cometary ices. Nevertheless, mass-dependent or mass-independent fractionation due to photo dissociation can be ruled out as sole cause of the seen depletion of 33S and 34S. Furthermore, an upper limit of (9.64 ± 0.19)·10.4 for D/H in HDS has been determined. This value is about a factor two higher than D/H in H2O for the same comet reported by (Altwegg et al., 2015). Besides the investigation concerning isotopic ratios of sulfur bearing species in this work the calibration and characterization of ROSINA/DFMS has been continued. Here it is reported about the deviation of the mass scale for MCP/LEDA low resolution spectra and the calibration measurements performed in the laboratory. Furthermore the outcome of the attempt to describe the sensitivity of DFMS with an empirical function will be discussed. The last part of the characterization of DFMS is dedicated to determine the so-called individual pixel gain for the laboratory and the flight model. Moreover, correlation between the depletion’s manifestation of the MCP with respect to the applied voltages has been investigated for both models. It has been found that further measurements are needed to understand the manifestation of depletion at the laboratory model. For the model on board of Rosetta it could be shown that most of the present feature are due to the usage of the MCP and suggestions have been made in order to answer the remaining question considering the depletion of the MCP.

Sedimentological, physical, bulk geochemical, elemental and rock magnetic properties of the Middle to Late Pleistocene Rodderberg (Eifel/Germany)

The sediment record from Rodderberg potentially provides a climate and environmental record spanning at least the last ca 130 ka. Results from a low resolution pilot study reveal characteristic fluctuations that can be related to global climate variability as reflected in marine isotope stages and document the potential of this site for continuous and high-resolution investigations of the Middle to Late Pleistocene. Here we document the tentative lithology drilled, and show how the elemental composition can be interpreted with regard to lake level fluctuations, related redox conditions, but also to grain-size distribution and changes in lacustrine productivity. Finally, based on major lithological changes, a preliminary depth/age model is suggested that allows reassessing published luminescence ages from the same site.

Lacustrine sediments from two setions in northern Greece

We investigated two lignite quarries in northern Greece for orbital and suborbital climate variability. Sections Lava and Vegora are located at the southern and northern boundaries of the Ptolemais Basin, a northwest southeast elongated intramontane basin that contains Upper Miocene to Lower Pliocene lacustrine sediments. Sediments show cyclic alterations of marl-rich (light), and coal-rich or clay-rich (dark) strata on a decimeter to meter scale. First, we established low-resolution ground-truth stratigraphy based on paleomagnetics and biostratigraphy. Accordingly, the lower 67 m and 65 m that were investigated in both sections Vegora and Lava, respectively, belong to the Upper Miocene and cover a time period of 6.85 to 6.57 and 6.46 to 5.98 Ma at sedimentation rates of roughly 14 and 22 cm/ka. In order to obtain a robust and high-resolution chronology, we then tuned carbonate minima (low L* values; high magnetic susceptibility values) to insolation minima. Besides the known dominance of orbital precession and eccentricity, we detected a robust hemi-precessional cycle in most parameters, most likely indicative for monsoonal influence on climate. Moreover, the insolation-forced time series indicate a number of millennial-scale frequencies that are statistically significant with dominant periods of 1.5-8 kyr. Evolutionary spectral analysis indicates that millennial-scale climate variability documented for the Ptolemais Basin resembles the one that is preserved in ice-core records of Greenland. Most cycles show durations of several tens of thousands of years before they diminish or cease. This is surprising because the generally argued cause for Late Quaternary millennial-scale variability is associated with the presence of large ice sheets, which cannot be the case for the Upper Miocene. Possible explanations maybe a direct response to solar forcing, an influence on the formation of North Atlantic Deep Water through the outflow of high-salinity water, or an atmospheric link to the North Atlantic Oscillation.

Organic matter C and N composition and N. pachyderma stable isotope ratios of ODP Hole 188-1166A sediments

We report the results of downhole stable isotopic (d13Corg [organic carbon] and d15N) and elemental measurements (total organic carbon [TOC], total nitrogen [TN], and carbon/nitrogen [C/N]) of sedimentary organic matter (SOM) along with stable isotopic measurements (d18O and d13C) of left-coiling Neogloboquadrina pachyderma planktonic foraminifers from Ocean Drilling Program Site 1166. TOC and TN measurements indicate a large change from organic-rich preglacial sediments with primary organic matter to organic-poor early glacial and glacial sediments, with mainly recycled organic matter. Results of the stable isotopic measurements of SOM show a range of values that are typical of both marine and terrestrial organic matter, probably reflecting a mixture of the two. However, C/N values are mostly high (>15), suggesting greater input and/or preservation of terrestrial organic matter. Foraminifers are only present in glacial/glaciomarine sediments of latest Pliocene to Pleistocene age at Site 1166 (lithostratigraphic Unit I). The majority of this unit has d13Corg and TOC values that are similar to those of glacial sediments recovered at Site 1167 (lithostratigraphic Unit II) on the slope and may have the same source(s). Although the low resolution of the N. pachyderma (s.) d18O and d13C data set precludes any specific paleoclimatic interpretation, downcore variations in foraminifer d18O and d13C values of 0.5 per mil to 1 per mil amplitude may indicate glacial-interglacial changes in ice volume/temperature in the Prydz Bay region.

Global raster maps indicating the habitat suitability for 7 suborders of cold water octocorals (Octocorallia found deeper than 50m)

This dataset consists of global raster maps indicating the habitat suitability for 7 suborders of cold water octocorals (Octocorallia found deeper than 50m). Maps present a relative habitat suitability index ranging from 0 (unsuitable) to 100 (highly suitable). Two maps are provided for each suborder (Alcyoniina, Calcaxonia, Holaxonia, Scleraxonia, Sessiliflorae, Stolonifera, and Subselliflorae). A publicly accessable low resolution map (grid size 10x10 arc-minutes) and a restricted access high resolution map (grid size 30x30 arc-seconds). Maps are geotiff format incorporating LZW compression to reduce file size. Please contact the corresponding author (Chris Yesson) for access to the high resolution data.

Dive depth frequency of 23 adult male southern elephant seals (Mirounga leonina) from Marion Island and King George Island

Access to different environments may lead to inter-population behavioural changes within a species that allow populations to exploit their immediate environments. Elephant seals from Marion Island (MI) and King George Island (KGI) (Isla 25 de Mayo) forage in different oceanic environments and evidently employ different foraging strategies. This study elucidates some of the factors influencing the diving behaviour of male southern elephant seals from these populations tracked between 1999 and 2002. Mixed-effects models were used to determine the influence of bathymetry, population of origin, body length (as a proxy for size) and individual variation on the diving behaviour of adult male elephant seals from the two populations. Males from KGI and MI showed differences in all dive parameters. MI males dived deeper and longer (median: 652.0 m and 34.00 min) than KGI males (median: 359.1 m and 25.50 min). KGI males appeared to forage both benthically and pelagically while MI males in this study rarely reached depths close to the seafloor and appeared to forage pelagically. Model outputs indicate that males from the two populations showed substantial differences in their dive depths, even when foraging in areas of similar water depth. Whereas dive depths were not significantly influenced by the size of the animals, size played a significant role in dive durations, though this was also influenced by the population that elephant seals originated from. This study provides some support for inter-population differences in dive behaviour of male southern elephant seals.