Miracle-dz/UniFAR-FTUs huggingface dataset:
Multiple-point simulation integrating wells, three-dimensional seismic data, and geology

There are two significant challenges in building a reservoir model integrating all available information. One challenge is that wells and seismic data measure the reservoir at different scales of resolution. The other challenge lies in how to account for conceptual geological knowledge with resolution at multiple scales.In this paper, we present a case study of integrating well data, seismic data, and conceptual geologic models. The well and seismic data are of good quality, but conventional well-seismic data calibration indicates that the seismic data are unable to fully differentiate sand from shale. The reason for this poor well-seismic data calibration is that well log and seismic data measure the reservoir at different scales. Well logs are able to differentiate sand from shale, whereas seismic data are better at detecting larger scale depositional geometries.A new workflow is presented to deal with this problem. First, principal component analysis clustering is used to identify characteristic patterns of certain depositional facies, from which sandy and shaly channels are interpreted. Next, multiple-point geostatistical simulation is performed to build a depositional-facies model, which integrates both hard and soft data but also incorporates realistic depositional-facies geometries provided by our geological knowledge of this reservoir. Finally, different lithofacies (sand and shale) indicators and corresponding petrophysical properties are simulated honoring the limited well data.The results show that not only are the geological features better reproduced, but also is the uncertainty about the reservoir significantly reduced because of a better integration of corresponding three-dimensional seismic data.
Evaporative cooling of apple and pear orchards

Evaporative cooling (EC) is an orchard practice used to decrease fruit temperature during the hottest part of the day. Fruit sunburn occurs easily when temperatures and light intensity are high, and this decreases packouts. EC has also been used successfully to improve colour of blushed apple and pear cultivars. The response of different apple and pear cultivars to EC was studied during 2003/2004 at Welgevallen Experimental Farm, Stellenbosch. EC was activated during the day at temperatures above 30C to reduce sunburn and between 18h00 and 21h00 at temperatures above 22C to improve colour development. Three treatments were evaluated: Control without EC, early application starting from the second week in December 2003, and late application starting 2 4 weeks before harvest, 2004. Experiments were done on two apple cultivars (‘Royal Gala’ and ‘Cripps’ Pink’) and two pear cultivars (‘Forelle’ and ‘Rosemarie’). Generally, fruit under EC had more sunburn than control fruit, due to failure of the system on a hot day. Underlying physiological responses of trees and fruit to EC were also investigated, particularly the phenomenon of acclimation and the potential for colour development and heat stress. In both apple cultivars a significant increase in fruit skin anthocyanin concentration and a decrease in phenolic content was found as the season progressed. In both pear cultivars there was a significant decrease in both anthocyanin and phenolic content. No significant differences were found in anthocyanin content between treatments in either the apple or pear cultivars. In both apple cultivars a higher phenolic content was found in the peel of the EC treatments. A decrease of up to four percent in leaf and fruit surface temperature was found under EC. No significant difference in trunk circumference was found in any of the cultivars. The late EC treatment in ‘Cripps’ Pink’ had a significantly faster rate of budbreak than the control and early EC treatments. Significantly higher stomatal conductance and transpiration was observed in leaves under EC. Knowledge about the various effects evaporative cooling and the subsequent lowering of ambient temperatures has on fruit trees and fruit could contribute greatly to producers’ ability to grow high quality fruit.
Persistent unstable atmospheric boundary layer enhances sensible and latent heat loss in a tropical great lake: Lake Tanganyika

[1] Energy fluxes across the surface of lakes regulate heat storage and affect the water balance. Sensible and latent heat fluxes are affected by atmospheric stability, especially for large lakes. We examined the effect of atmospheric stability on the heat fluxes on seasonal time scales at Lake Tanganyika, East Africa, by estimating hourly sensible and latent heat fluxes and net radiation using thermistor chains and meteorological stations. The atmosphere was almost always unstable, in contrast to the atmosphere above North American Great Lakes which is unstable in winter and stable in summer. Persistent atmospheric instability resulted in a 13% and 18% increase in the annual mean heat loss by latent and sensible heat fluxes, respectively, relative to conditions of neutral stability. The persistent unstable atmosphere is caused by a higher water surface temperature compared with air temperature, which we argue is the case in general in (sub)tropical lakes. Low humidity further enhanced the frequency of unstable conditions and enhanced the exchange of heat and vapor from the lake to the atmosphere. The estimated heat fluxes were sensitive to the temporal scale of data inputs and to the local values of parameters such as air density. To our knowledge this is the first paper that demonstrates and quantifies the effect of atmospheric stability on latent and sensible heat fluxes from a lake on an annual basis, using data collected from the lake surface.
Signatures of the ULF geomagnetic activity in the surface air temperature in Antarctica

The variations of the Pc5 and Pc1‐2 ULF power and surface air temperature measured at Terra Nova Bay in Antarctica have been analyzed during the late declining phase of solar cycle 23 (2007–2008), in comparison with the simultaneous variations of the solar wind speed. The analysis focused on time scales of several days, which characterize the evolution of the solar wind stream structure. The temperature variations appear clearly during the local winters, while they are strongly reduced in the sunlit summers. During the local winters, the Pc5 and Pc1‐2 power and the temperature variations are significantly correlated, with the temperature delayed by a few days with respect to the ULF power. A time‐frequency analysis revealed common signals in the temperature and ULF power at periodicities related to the Sun's rotation period (~27, 13.5, and 9 days), which, in the same time intervals, characterize the solar wind speed and geomagnetic activity.
Methylation of Catechins and Procyanidins by Rat and Human Catechol- O -Methyltransferase: metabolite profiling and molecular modeling studies

Catechins and procyanidins are major polyphenols in plant-derived foods. Despite intensive studies in recent years, neither their biochemical nor their toxicological properties have been clarified sufficiently. This study aimed to compare the methylation of catechins and procyanidins by the enzyme catechol- O -methyltransferase in vitro . We conducted incubations with rat liver cytosol and human placental cytosol including S-adenosyl-L-methionine (SAM). The set of substrates comprised the catechins (-)-epicatechin (EC) and (+)-catechin (CAT), the procyanidin dimers B1, B2, B3, B4, B5 and B7 as well as procyanidin trimer C1. After extraction, metabolites were analyzed by means of LC-ESI-MS and LC-APCI-MS. EC and CAT were converted to two monomethylated metabolites each by human and rat COMT, with the 3'- O -methyl derivatives being consistently the main metabolites. Furthermore, the flavanyl units of procyanidins were methylated consecutively, leading to mono- and dimethylated dimeric metabolites as well as mono-, di- and trimethylated C1 metabolites. The methylation status of each flavanyl unit was determined by means of mass spectrometric quinone-methide fragmentation patterns. In addition, molecular modeling studies were performed with the aim to predict the preferred site of methylation and to verify the experimental data. In conclusion, our results indicate that the degree and position of methylation depends clearly on the three-dimensional structure of the entire substrate molecule. of monomethylated metabolites (m/z 591). After reaching a maximum after 10 to 40 min, the concentration of the monomethylated metabolites declined, accompanied by a continuous increase in the concentrations of dimethylated procyanidin metabolites (m/z 605).
Rates and Processes of Potassic Magma Evolution beneath Sangeang Api Volcano, East Sunda Arc, Indonesia

U-series isotopes can provide unique insights into the physical processes of magma evolution by constraining the time scales over which they operate. This, however, requires rock suites that provide a clear and complete record of the liquid line of descent. Sangeang Api volcano, in the east Sunda arc, provides such an opportunity because it erupts potassic lavas (SiO 2∼47-55%), which contain a spectrum of xenoliths interpreted to represent the cumulates complementary to the lavas. Combined, the cumulates and lavas span a large compositional range, which major and trace element modelling suggests reflects ∼70% polybaric crystallization that began at sub-Moho depths and continued into the upper crust. The parental magmas can be successfully modelled by ∼3% dynamic partial melting, in the presence of 0-4% residual garnet, of a mid-ocean ridge basalt (MORB) source enriched by ∼3% subducted Sunda sediment in addition to a contribution of fluid-mobile elements from the subducting slab. The effects of fluid addition and partial melting on U-Th disequilibria appear to be competing processes. A moderate range in Sr, Nd and Pb isotopes is interpreted to reflect a combination of source heterogeneity and <15% assimilation of Indian MORB crust. Neither interaction with metasomalized arc lithosphere nor the presence of enriched, plume-type mantle in the mantle wedge is required by our data. The cumulates and lavas have largely indistinguishable ( 230Th/ 232Th) over a wide range of U/Th ratios and thus any age differences are minimal relative to the half-life of 230Th. All whole rocks and minerals are characterized by 226Ra excesses and modelling of the 226Ra- 230Th-Ba data suggests that magmatic evolution beneath this arc volcano occurs on time scales of ∼2000 years. Combining this with simple numerical calculations we estimate that the Sangeang Api magma chamber is ∼6-10 km 3 in size, cooling rates are ∼0.05°C/yr and minimum crystal growth rates are (2-7) × 10 -13 cm/s. It is possible that a significant proportion of the crystal growth and differentiation occurred during isobaric decompression of magmas ascending through conduits. An implication is that the net magmatic flux across the Moho is of magmas that are already significantly evolved from primary magmas and this may be significantly for why average continental crust has an andesitic bulk composition even though the flux out of the mantle wedge is basaltic.
The values of VSP in interpretation

Even sophisticated seismic data processing does not usually result in an unambiguous geologic picture: we need to interpret seismic data because information of exploration interest (such as horizon depth, lithological type and saturant) is not readily available. So, given seismic data, their limitations, plus available well and subsurface control, the goal is to determine what lithologies and saturants are represented. This type of inference or inverse problem usually works at the limits of seismic resolution, thus ambiguities and nonuniqueness arise. Vertical seismic profiling (VSP) can provide a direct relationship between surface seismic data and well information. This relationship may help remove ambiguities in the interpretation and nonuniqueness in the inverse process. The VSP is also expected to give additional and complementary seismic values to be used in data processing (e.g., interval velocity, zero‐phase reflectivity).
Akap-lbc Anchors Protein Kinase a and Nucleates G␣ 12 -selective Rho-mediated Stress Fiber Formation*

Guanine nucleotide exchange factors of the Dbl family relay signals from membrane receptors to Rho family GTPases. We now demonstrate that a longer transcript of the Lbc gene encodes a chimeric molecule, which we have called AKAP-Lbc, that functions as an A-kinase-anchoring protein (AKAP) and a Rho-selective guanine nucleotide exchange factor. Expression of AKAP-Lbc in fibroblasts favors the formation of stress fibers in a Rho-dependent manner. Application of lysophosphatidic acid or selective expression of G␣ 12 enhances cellular AKAP-Lbc activation. Furthermore, biochemical studies indicate that AKAP-Lbc functions as an adaptor protein to selectively couple G␣ 12 to Rho. Thus, AKAP-Lbc anchors PKA and nucleates the assembly of a Rho-mediated signaling pathway. The transmission of information from the plasma membrane to the actin cytoskeleton is essential to control a variety of dynamic cellular processes including cell shape, motility, and adherence (1). Critical mediators of these events are the Rho family small molecular weight GTPases, Rho, Rac, and Cdc42, which regulate distinct actin remodeling events. Rho is primarily responsible for the assembly of actin stress fibers and focal adhesions, and Rac controls the formation of lamellipodia, while Cdc42 induces filopodial formation (1, 2). In addition to these effects, Rho has also been implicated in a variety of other critical cellular functions including gene transcription (3, 4) and progression through the cell cycle (5). Lysophosphatidic acid (LPA) and thrombin are the extracel-lular ligands that induce Rho signaling events (2). Binding of either ligand to distinct classes of cell surface receptors triggers a series of events that mobilize the pertussis toxin-insensitive heterotrimeric G protein subunits G␣ 12 and G␣ 13 (6, 7). The intracellular targets for either G␣ subunit are a growing family of guanine nucleotide exchange factors (GEFs) (8). These exchange factors dock with activated G␣ 12 and G␣ 13 and facilitate GTP loading of Rho. Individual cells express several Rho-GEFs, which activate distinct Rho signaling pathways (9). For example , p115 Rho-GEF interacts with G␣ 13 through a regulator of G protein signaling (RGS) domain located in the amino-terminal region of the exchange factor (10, 11). Likewise, a related module, the Lsc homology domain, governs docking of G␣ 13 to exchange factors such as PDZ Rho-GEF, KIAA0380, or GTRAP48 (12–14). A universal hallmark of exchange factors that activate GTP-ases of the Rho family is a conserved region of ϳ250 residues that contains a Dbl homology (DH) domain followed by a pleck-strin homology …
X-ray Structure of Bacteriorhodopsin at 2.5 Angstroms from Microcrystals Grown in Lipidic Cubic Phases

17. LSS was generated as described (16). Extracts rep-licated 75 to 100% of the input template (5 ng/␮l). Cycloheximide (0.1 mg/ml) was added to LSS before replication was assayed. 18. Demembranated sperm nuclei were prepared as described (4) and used at a final DNA concentration of 5 ng/␮l. Plasmid template ssM13 DNA was added to a 10 ng/␮l final concentration. DNA replication was measured by trichloroacetic acid precipitation of ra-diolabeled fragments (4, 10) and presented as a percent replication of the input template (5 ng/␮l). Alternatively , samples were ethanol precipitated, run on agarose gels, and autoradiographed. 19. Antibodies were covalently cross-linked to protein A (pA)—Sepharose (Seph) or pA-affiprep beads as described [E. Harlow and D. Lane, Antibodies: A Laboratory Manual (Cold Spring Harbor Laboratory , Cold Spring Harbor, NY, 1988)]. Immunodeple-tion was performed by mixing 1 volume LSS to 1.2 volumes antibody-coupled pA-Seph beads for 2 hours at 0°C with resuspension every 10 min. 20. LSS, Superdex column fraction, or eluted affiprep material were analyzed by SDS-PAGE, transferred to nitrocellulose, incubated with affinity-purified anti-hCDC34 immunoglobulin (Ig), and analyzed by enhanced chemiluminescence (Amersham). 21. Replication foci were analyzed by stated methods (10, 12). 22. Five volumes of LSS were incubated with one volume of coupled pA-affiprep beads for 3 hours at 4°C. Beads were washed with 15 volumes each of XB– [extract buffer: 100 mM KCl, 0.1 mM CaCl 2 , 1 mM MgCl 2 , and 10 mM Hepes (pH 7.7)] (one time), XB– with 500 mM KCl (three times), and 0. 5ϫ XB– (two times) (23). Immunodepleted LSS was added to the beads and assayed for replication. Alternatively , the washed beads were treated with 100 mM glycine (pH 2.5), and the eluate was neutralized with 1 M tris (pH 8). Samples were concentrated and analyzed by SDS-PAGE and silver stained or analyzed by immunoblotting. 23. S100 was generated by dilution of LSS with nine volumes 20 mM tris (pH 7.7), 100 mM KCl, 1 mM MgCl 2 , and 1 mM dithiothreitol followed by centrif-ugation for 1 hour at 100,000g. S100 was concentrated to its original volume and loaded onto a HiLoad 16/60 Superdex 200 column (Pharmacia). Fractions were concentrated to one-tenth their volume and incubated with anti-hCDC34 affiprep beads for 2.5 hours at 0°C with resuspension every 10 min. Beads were washed with XB– supplemented with KCl to 500 mM (XB– with 500 mM KCl), added to …
Imaging cell wall architecture in single Zinnia elegans tracheary elements

The chemical and structural organization of the plant cell wall was examined in Zinnia elegans tracheary elements (TEs), which specialize by developing prominent secondary wall thickenings underlying the primary wall during xylogenesis in vitro. Three imaging platforms were used in conjunction with chemical extraction of wall components to investigate the composition and structure of single Zinnia TEs. Using fluorescence microscopy with a green fluorescent protein-tagged Clostridium thermocellum family 3 carbohydrate-binding module specific for crystalline cellulose, we found that cellulose accessibility and binding in TEs increased significantly following an acidified chlorite treatment. Examination of chemical composition by synchrotron radiation-based Fourier-transform infrared spectromicroscopy indicated a loss of lignin and a modest loss of other polysaccharides in treated TEs. Atomic force microscopy was used to extensively characterize the topography of cell wall surfaces in TEs, revealing an outer granular matrix covering the underlying meshwork of cellulose fibrils. The internal organization of TEs was determined using secondary wall fragments generated by sonication. Atomic force microscopy revealed that the resulting rings, spirals, and reticulate structures were composed of fibrils arranged in parallel. Based on these combined results, we generated an architectural model of Zinnia TEs composed of three layers: an outermost granular layer, a middle primary wall composed of a meshwork of cellulose fibrils, and inner secondary wall thickenings containing parallel cellulose fibrils. In addition to insights in plant biology, studies using Zinnia TEs could prove especially productive in assessing cell wall responses to enzymatic and microbial degradation, thus aiding current efforts in lignocellulosic biofuel production.
Continuous intravenous epoprostenol for pulmonary hypertension due to the scleroderma spectrum of disease. A randomized, controlled trial.

BACKGROUND Pulmonary hypertension is a progressive and often fatal complication of the scleroderma spectrum of disease for which no treatment has been proven effective in a randomized trial. OBJECTIVE To determine the effect of epoprostenol on pulmonary hypertension secondary to the scleroderma spectrum of disease. DESIGN Randomized, open-label, controlled trial. SETTING 17 pulmonary hypertension referral centers. PATIENTS 111 patients with moderate to severe pulmonary hypertension. INTERVENTION Epoprostenol plus conventional therapy or conventional therapy alone. MEASUREMENTS The primary outcome measure was exercise capacity. Other measures were cardiopulmonary hemodynamics, signs and symptoms of pulmonary hypertension and scleroderma, and survival. RESULTS Exercise capacity improved with epoprostenol (median distance walked in 6 minutes, 316 m at 12 weeks compared with 270 m at baseline) but decreased with conventional therapy (192 m at 12 weeks compared with 240 m at baseline). The difference between treatment groups in the median distance walked at week 12 was 108 m (95% CI, 55.2 m to 180.0 m) (P < 0.001). Hemodynamics improved at 12 weeks with epoprostenol. The changes in mean pulmonary artery pressure for the epoprostenol and conventional therapy groups were -5.0 and 0.9 mm Hg, respectively (difference, -6.0 mm Hg [CI, -9.0 to -3.0 mm Hg), and the mean changes in pulmonary vascular resistance were -4.6 and 0.9 mm Hg/L per minute, respectively (difference, -5.5 mm Hg/L per minute [CI, -7.3 to -3.7 mm Hg/L per minute). Twenty-one patients treated with epoprostenol and no patients receiving conventional therapy showed improved New York Heart Association functional class. Borg Dyspnea Scores and Dyspnea-Fatigue Ratings improved in the epoprostenol group. Trends toward greater improvement in severity of the Raynaud phenomenon and fewer new digital ulcers were seen in the epoprostenol group. Four patients in the epoprostenol group and five in the conventional therapy group died (P value not significant). Side effects of epoprostenol therapy included jaw pain, nausea, and anorexia. Adverse events related to the epoprostenol delivery system included sepsis, cellulitis, hemorrhage, and pneumothorax (4% incidence for each condition). CONCLUSIONS Continuous epoprostenol therapy improves exercise capacity and cardiopulmonary hemodynamics in patients with pulmonary hypertension due to the scleroderma spectrum of disease.
Phytoplankton and photosynthetic light response in the Coastal Transition Zone off northern California in June 1987

In June 1987 the geostrophic flow in the coastal transition zone off northern California (between 50 and 150 km off the coast from Point Reyes to just north of Cape Mendocino) was dominated by a well-defined, southward-meandering current. Three vertical sections are presented that show the hydrographic structure of the current down to 100 m and its relationship to the distribution of phytoplankton biomass. The sections show that the geostrophic adjustment brought cold, saline, deep water up to the surface on the low steric height, or cold side of the flow, and that this upwelled water supported a relatively large diatom biomass (chlorophyll-a concentrations between 1 and 10 mg m−3). We present particle size spectra and photomicrographs of the phytoplankton that show that the diatom biomass was dominated by chain-forming species (e.g., Skeletonema costatum, Chaetoceros spp., Thalassiosira spp., and Rhizosolenia alata, but also a single-celled Actinocyclus sp.). Photosynthetic light response measurements reveal that these diatom communities were capable of high photosynthetic rates (Pmax between 5 and 25 mg C mg Chla−1 h−1). Although most of the diatoms were located in cold, slow-moving water on the low side of the current, some were being carried downstream. High chlorophyll concentrations were observed at depths > 75 m in and along the cold edge of the flow in all of our sections; we show evidence that in two out of three cases this was the result of water mass subduction.