Miracle-dz/UniFAR-FTUs huggingface dataset:
Testing the use of microfossils to reconstruct great earthquakes at Cascadia

Coastal stratigraphy from the Pacific Northwest of the United States contains evidence of sudden subsidence during ruptures of the Cascadia subduction zone. Transfer functions (empirical relationships between assemblages and elevation) can convert microfossil data into coastal subsidence estimates. Coseismic deformation models use the subsidence values to constrain earthquake magnitudes. To test the response of foraminifera, the accuracy of the transfer function method, and the presence of a pre-seismic signal, we simulated a great earthquake near Coos Bay, Oregon, by transplanting a bed of modern high salt-marsh sediment into the tidal flat, an elevation change that mimics a coseismic subsidence of 0.64 m. The transplanted bed was quickly buried by mud; after 12 mo and 5 yr, we sampled it for foraminifera. Reconstruction of the simulated coseismic subsidence using our transfer function was 0.61 m, nearly identical to the actual elevation change. Our transplant experiment, and additional analyses spanning the A.D. 1700 earthquake contact at the nearby Coquille River 15 km to the south, show that sediment mixing may explain assemblage changes previously interpreted as evidence of pre-seismic land-level change in Cascadia and elsewhere.
Anti–Interleukin 10 Receptor Monoclonal Antibody Is an Adjuvant for T Helper Cell Type 1 Responses to Soluble Antigen Only in the Presence of Lipopolysaccharide

Soluble foreign antigen usually leads to a transient clonal expansion of antigen-specific T cells followed by the deletion and/or functional inactivation of the cells. As interleukin (IL)-10 is a key immunoregulatory cytokine, we questioned whether neutralization of IL-10 during priming with soluble antigen could prime for a subsequent T helper cell type 1 (Th1) effector recall response. By using an adoptive transfer model to track the fate of antigen-specific T cell receptor (TCR)-transgenic CD4+ T cells, we show that administration of soluble ovalbumin (OVA) protein, but not OVA323–339 peptide antigen, together with an anti–IL-10 receptor (R) mAb led to the enhancement of a Th1 response upon rechallenge. Lipopolysaccharide (LPS) present in the protein was necessary for priming for Th1 recall responses in the presence of anti–IL-10R mAb, as removal of LPS abrogated this effect. Moreover, addition of LPS to the peptide did not itself allow priming for recall Th1 effector responses unless endogenous levels of IL-10 were neutralized with an anti–IL-10R mAb. A significant increase in OVA-specific IgG1 and IgG2a isotypes was observed when the protein antigen was administered with anti–IL-10R mAb; however, this was not the case with peptide antigen administered together with anti–IL-10R and LPS. Our data, showing that LPS receptor signaling and neutralization of endogenous immunosuppressive cytokines is essential for Th1 priming, has important implications for the design of relevant vaccines for effective in vivo immunotherapy.
Apical Transport of Influenza A Virus Ribonucleoprotein Requires Rab11-positive Recycling Endosome

Influenza A virus RNA genome exists as eight-segmented ribonucleoprotein complexes containing viral RNA polymerase and nucleoprotein (vRNPs). Packaging of vRNPs and virus budding take place at the apical plasma membrane (APM). However, little is known about the molecular mechanisms of apical transport of newly synthesized vRNP. Transfection of fluorescent-labeled antibody and subsequent live cell imaging revealed that punctate vRNP signals moved along microtubules rapidly but intermittently in both directions, suggestive of vesicle trafficking. Using a series of Rab family protein, we demonstrated that progeny vRNP localized to recycling endosome (RE) in an active/GTP-bound Rab11-dependent manner. The vRNP interacted with Rab11 through viral RNA polymerase. The localization of vRNP to RE and subsequent accumulation to the APM were impaired by overexpression of Rab binding domains (RBD) of Rab11 family interacting proteins (Rab11-FIPs). Similarly, no APM accumulation was observed by overexpression of class II Rab11-FIP mutants lacking RBD. These results suggest that the progeny vRNP makes use of Rab11-dependent RE machinery for APM trafficking.
Monogenetic volcanoes of the terrestrial planets

Monogenetic volcanic activity has produced cinder cones and small shield volcanoes on the earth, moon, and Mars. Extraterrestrial cinder cones have median volumes only 25% as large as average terrestrial cinder cones, implying that their magma chambers are smaller and shallower (1 km depth vs 3 km). Ejection velocities for lunar and Martian cinder cones range from 20 to 70 m/sec, only 1/3 to 1/10 as high as for equal volume terrestrial eruptions. These low velocities imply low volatile contents for both Martian and lunar magmas.
Evapotranspiration of mixed shrub communities in phreatophytic zones of the Great Basin region of Nevada (USA)

In this study, evapotranspiration (ET) was estimated for three valleys (White River, Spring Valley and Snake Valley) in the Great Basin region of Nevada (USA) during a 3‐year period. ET estimates were based on an energy balance approach using the eddy covariance (EC) method and were scaled to the basin level by developing empirical relationships between ET and remotely sensed spectral data (Landsat). Annual EC–ET values for the three basins and previously published values attained for the same valleys during the same time period were correlated to average normalized difference vegetation index (NDVI) values for the growing period. Resulting empirical relationships accounted for 97% (p < 0·001) of the variation in the EC–ET estimate for the 10 May–5 September growing period, and 93% (p < 0·001) of the variation in the EC–ET estimates based on measured or projected yearly ET totals.
Transcriptional Regulation of CREB (Cyclic AMP Response Element‐Binding Protein) Expression in CATH.a Cells

Abstract: We have recently demonstrated that mRNA expression of cyclic AMP (cAMP) response element‐binding protein (CREB) is down‐regulated in CATH.a cells (a neural‐derived cell line) by activation of the cAMP pathway. We now demonstrate that this down‐regulation can be accounted for by a decrease in the rate of CREB gene transcription. It was found that cycloheximide, a protein synthesis inhibitor, prevented the forskolin‐induced decrease in CREB mRNA levels in CATH.a cells. Nuclear run‐on assays demonstrated that forskolin decreased the rate of CREB transcription by close to 50%. Moreover, forskolin decreased chloramphenicol acetyltransferase (CAT) activity in CATH.a cells transiently transfected with a construct containing 1,240 bp of CREB promoter fused to a CAT reporter plasmid. Possible mechanisms by which activation of the cAMP pathway leads to a decrease in CREB gene transcription are discussed.
EFFECT OF PACLOBUTRAZOL ON WHEAT SEEDLINGS UNDER LOW TEMPERATURE STRESS

Wheat (Triticum aestivum L., cv. Beloslava) seeds were imbibed for 24 h in a water solutions containing 0, 25 and 50 mg.l–1 of paclobutrazol. The seedlings were grown as a substrate culture under controlled climatic conditions. Seven-day-old plants were exposed to low temperature stress by placing them in a cold room at a temperature of 2±1oC for 10 days – the first phase of hardening, -4±1oC for 3 days – the second phase of hardening and freezing, -10±1oC for 1 day – the third phase of hardening and freezing. After exposure to stress, the seedlings were returned to a climatic chamber with controlled climatic conditions. Under stress conditions the growth rates of the PBZ-treated seedlings measured by height, fresh and dry weights were greater than the control. Low temperature stress (LTS) induced lipid peroxidation and increased peroxidase activity. It was also found that LTS decreased the chlorophyll and carotenoid levels. A decrease in fluorescence ratio (Fv/Fm) indicated lower photosynthetic efficiency. These deteriorative symptoms in the control seedlings were ameliorated by the PBZ treatment. Based on the results of triazoles studies, we presume that the stress protection caused by PBZ probably contributes to some extent to the enhanced activity of the free-radical scavenging systems.
The ACTN3 R577X Polymorphism across Three Groups of Elite Male European Athletes

The ACTN3 R577X polymorphism (rs1815739) is a strong candidate to influence elite athletic performance. Yet, controversy exists in the literature owing to between-studies differences in the ethnic background and sample size of the cohorts, the latter being usually low, which makes comparisons difficult. In this case:control genetic study we determined the association between elite athletic status and the ACTN3 R577X polymorphism within three cohorts of European Caucasian men, i.e. Spanish, Polish and Russian [633 cases (278 elite endurance and 355 power athletes), and 808 non-athletic controls]. The odds ratio (OR) of a power athlete harbouring the XX versus the RR genotype compared with sedentary controls was 0.54 [95% confidence interval (CI): 0.34–0.48; P = 0.006]. We also observed that the OR of an endurance athlete having the XX versus the RR genotype compared with power athletes was 1.88 (95%CI: 1.07–3.31; P = 0.028). In endurance athletes, the OR of a “world-class” competitor having the XX genotype versus the RR+RX genotype was 3.74 (95%CI: 1.08–12.94; P = 0.038) compared with those of a lower (“national”) competition level. No association (P>0.1) was noted between the ACTN3 R577X polymorphism and competition level (world-class versus national-level) in power athletes. Our data provide comprehensive support for the influence of the ACTN3 R577X polymorphism on elite athletic performance.
Coulumb Fluid, Painlevé Transcendents, and the Information Theory of MIMO Systems

In this paper, we compute two important information-theoretic quantities which arise in the application of multiple-input multiple-output (MIMO) antenna wireless communication systems: the distribution of the mutual information of multiantenna Gaussian channels, and the Gallager random coding upper bound on the error probability achievable by finite-length channel codes. We show that the mathematical problem underpinning both quantities is the computation of certain Hankel determinants generated by deformed versions of classical weight functions. For single-user MIMO systems, it is a deformed Laguerre weight; for multiuser MIMO systems, it is a deformed Jacobi weight. We apply two different methods to characterize each of these Hankel determinants. First, we employ the ladder operators of the corresponding monic rthogonal polynomials to give an exact characterization of the Hankel determinants in terms of Painlevé differential equations. This turns out to be a Painlevé V for the single-user MIMO scenario and a Painlevé VI for the multiuser scenario. We then introduce Coulomb fluid linear statistics methods to derive closed-form approximations for the MIMO mutual information distribution and the error probability which, although formally valid for large matrix dimensions, are shown to give accurate results even when the matrix dimensions are small. Focusing on the single-user mutual information distribution, we then employ the exact Painlevé V representation with the help of the Coulomb fluid linear statistics approximation to yield deeper insights into the scaling behavior in terms of the number of antennas and signal-to-noise ratio (SNR). Among other things, these results allow us to study the asymptotic Gaussianity of the distribution as the number of antennas increase, and to investigate when and why such approximations break down as the SNR increases. Based on the Painlevé, we also derive recursive formulas for explicitly computing in closed form any desired number of correction terms to the asymptotic mean and variance, as well as closed-form asymptotic expressions for any desired number of higher order cumulants. Using these cumulants, we propose new closed-form approximations to the mutual information distribution which are shown to be very accurate, not only in the bulk but also in the tail region of interest for the outage probability.
The Effect of Estrogens, River Water, and Treated Wastewater on Vitellogenin Induction of Japanese Medaka 1

Abstract: The objective of this study is to evaluate the effect of estrogens on fish endocrine disruption in river water and treated wastewater. Endogenous estrogen estrone (E1), 17β‐estradiol (E2), river water, and treated wastewater were used for exposure tests on male Japanese medaka. Vitellogenin induction in male medaka was regarded as the endpoint of endocrine disruption. The effective concentrations of E1 and E2 on vitellogenin induction in medaka were evaluated by breeding medaka for 14 days in tanks with various concentrations of E1 or E2. Vitellogenin induction increased with elapse of time during exposure, with higher estrogen concentrations causing greater vitellogenin induction. According to the test results, the lowest observed effect concentrations (LOECs) of E1 and E2 were estimated to be 31.6 and 5.0 ng/l, respectively; and the E2 equivalent (EEQ) LOEC value of E1 was 5.2 ng‐E2/l, derived by multiplying the relative potency of E1 by that of E2 as estimated in this study. In continuous exposure tests using river water or treated wastewater, the estrogenic activity, an index of total estrogenic potential measured by yeast screen assay and expressed as EEQ, varied widely during the exposure tests, and significant vitellogenin induction was observed after several days of high levels of estrogenic activity in water. Vitellogenin concentration tended to significantly increase if EEQ exceeded the level of 5 ng‐E2/l. The threshold value was substantially the same as the results for E1 and E2 exposure tests of medaka. Consequently, EEQ over 5 ng‐E2/l was revealed to have the potential to cause endocrine disruption of male medaka. As estrogenic activity exceeding 5 ng‐E2/l was observed in some rivers in Japan, total estrogenic potential needs to be further decreased at wastewater treatment plants to prevent fish endocrine disruption.
The length of the glaciers in the world: a straightforward method for the automated calculation of glacier center lines

Glacier length is an important measure of glacier geometry but global inventories are mostly lacking length data. Only recently semi-automated approaches to measure glacier length have been developed and applied regionally. Here we present a ﬁrst global assessment of glacier length using a fully automated method based on 5 glacier surface slope, distance to the glacier margins and a set of trade-o ﬀ functions. The method is developed for East Greenland, evaluated for the same area as well as for Alaska, and eventually applied to all ∼ 200000 glaciers around the globe. The evaluation highlights accurately calculated glacier length where DEM quality is good (East Greenland) and limited precision on low quality DEMs (parts of Alaska). Measured 10 length of very small glaciers is subject to a certain level of ambiguity. The global calculation shows that only about 1.5 % of all glaciers are longer than 10 km with Bering Glacier (Alaska/Canada) being the longest glacier in the world at a length of 196 km. Based on model output we derive global and regional area-length scaling laws. Dif-ferences among regional scaling parameters appear to be related to characteristics of 15 topography and glacier mass balance. The present study adds glacier length as a central parameter to global glacier inventories. Global and regional scaling laws might proof beneﬁcial in conceptual glacier models.
Variational Assimilation of XBT Data. Part 1

Abstract A variations method based on the adjoint equation technique is used to assimilate data in a relatively simple linear reduced gravity model of the tropical Pacific. Real XBT data are used by identifying the depth of the 16°C isotherm depth with the model layer depth. It is shown that the XBT data contain large scale information that corrects the model first guess. However, the model is not capable of fitting the data in the eastern Pacific for the whole assimilation period. Regions not seeded by the data are explicitly shown and the impact of data from different times on the initial state is also discussed.
Hypoxia-mediated alterations and their role in the HER-2/neuregulated CREB status and localization

The cAMP-responsive element-binding protein (CREB) is involved in the tumorigenicity of HER-2/neu-overexpressing murine and human tumor cells, but a link between the HER-2/neu-mediated CREB activation, its posttranslational modification and localization and changes in the cellular metabolism, due to an altered (tumor) microenvironment remains to be established. The present study demonstrated that shRNA-mediated silencing of CREB in HER-2/neu-transformed cells resulted in decreased tumor formation, which was associated with reduced angiogenesis, but increased necrotic and hypoxic areas in the tumor. Hypoxia induced pCREBSer133, but not pCREBSer121 expression in HER-2/neu-transformed cells. This was accompanied by upregulation of the hypoxia-inducible genes GLUT1 and VEGF, increased cell migration and matrix metalloproteinase-mediated invasion. Treatment of HER-2/neu+ cells with signal transduction inhibitors targeting in particular HER-2/neu was able to revert hypoxia-controlled CREB activation. In addition to changes in the phosphorylation, hypoxic response of HER-2/neu+ cells caused a transient ubiquitination and SUMOylation as well as a co-localization of nuclear CREB to the mitochondrial matrix. A mitochondrial localization of CREB was also demonstrated in hypoxic areas of HER-2/neu+ mammary carcinoma lesions. This was accompanied by an altered gene expression pattern, activity and metabolism of mitochondria leading to an increased respiratory rate, oxidative phosphorylation and mitochondrial membrane potential and consequently to an enhanced apoptosis and reduced cell viability. These data suggest that the HER-2/neu-mediated CREB activation caused by a hypoxic tumor microenvironment contributes to the neoplastic phenotype of HER-2/neu+ cells at various levels.
Significance of Visual Evoked Potentials in the Assessment of Visual Field Defects in Primary Open-Angle Glaucoma: A Review

Visual evoked potentials is an important visual electrophysiological tool which has been used for the evaluation of visual field defects in primary open-angle glaucoma and is an appropriate objective measure of optic nerve function. Significant correlations between the magnitude of the VEP parameters and MD of Humphrey static perimetry suggest that the impaired visual cortical responses observed in glaucoma patients can be revealed by both electrophysiological and psychophysical methods. In addition, the severity of global glaucomatous damage evidenced by reduction in MD could depend on the delay in neural conduction from retina to the visual cortex as revealed by the significant correlation between VEP latencies and MD which also supports the validity of the VEP testing in progression of glaucoma.
Artificial neural networks for diagnosis of hepatitis disease

Recently, neural networks have become a very important method in the field of medical diagnostics. The objective of this work is to diagnose hepatitis disease by using different neural network architectures. Standard feedforward networks and a hybrid network were investigated. Results obtained show that especially the hybrid network can be successfully used for diagnosing of hepatitis.
Consolidation of Multimodel Forecasts by Ridge Regression: Application to Pacific Sea Surface Temperature

Abstract The performance of ridge regression methods for consolidation of multiple seasonal ensemble prediction systems is analyzed. The methods are applied to predict SST in the tropical Pacific based on ensembles from the Development of a European Multimodel Ensemble System for Seasonal-to-Interannual Prediction (DEMETER) models, plus two of NCEP’s operational models. Strategies to increase the ratio of the effective sample size of the training data to the number of coefficients to be fitted are proposed and tested. These strategies include objective selection of a smaller subset of models, pooling of information from neighboring grid points, and consolidating all ensemble members rather than each model’s ensemble average. In all variations of the ridge regression consolidation methods tested, increased effective sample size produces more stable weights and more skillful predictions on independent data. While the scores may not increase significantly as the effective sampling size is increased, the bene.
MINERALOGY, MINERAL COMPOSITIONS AND FLUID EVOLUTION AT THE WENZEL HYDROTHERMAL DEPOSIT, SOUTHERN GERMANY: IMPLICATIONS FOR THE FORMATION OF KONGSBERG-TYPE SILVER DEPOSITS

The post-Variscan Wenzel vein-type deposit near Wolfach, in the Black Forest, Germany, the type locality of the Ag–Sb alloy dyscrasite, was investigated by ore microscopy, electron-microprobe analysis, stable isotope and fluid-inclusion analysis. Three stages of mineralization could be distinguished. Whereas the first stage is a typical sulfide mineralization including galena and tetrahedrite, the second and third stage show a sulfide-poor association of Ag–Sb alloys, as well as Fe, Co and Ni arsenides and sulfarsenides, in a calcite matrix. The main ore minerals of this stage are allargentum and dyscrasite. The microprobe data for the diarsenides show extensive, and partly hitherto undocumented, solid solution in Fe–Co–Ni space. Seven distinct generations of calcite were distinguished. The δ13C (V–PDB) and δ18O (V–SMOW) values of these generations show a positively correlated trend that evolves from −13.0 to −4.0‰ and from 12.3 to 23.6‰, respectively. Fluid-inclusion data of stage I show homogenization temperatures of 100–180°C at salinities of 17–26 wt. % NaCl eq. Fluid inclusions in stage-II calcite display similar, but more restricted values, 110–150°C and 25–28 wt. % NaCl eq., respectively. The stage-III fluid inclusions show similar temperatures of homogenization, but different salinities. Earlier calcite of this stage contains inclusions with salinities of 27–30 wt. % NaCl eq., whereas later calcite has lower salinities, 3–10 wt. % NaCl eq. The initial temperatures of ice melting of most fluid inclusions range between −45 and −60°C and are typical of an H2O–NaCl–CaCl2 fluid. On the basis of all available geochemical data and phase-equilibrium constraints, we favor a model in which basement-derived near-neutral-pH hydrothermal fluids remobilized older products of mineralization. Mixing of these fluids with more alkaline formation-waters from the Mesozoic cover rocks resulted in the precipitation of the silver alloys in an enrichment zone at P–T conditions of 120–150°C and approximately 200 bars. A significant shift in pH from near-neutral to alkaline can explain the abundant association of silver alloys with calcite gangue and the general absence of quartz in the enriched ore zone. This conceptual model can be applied to similar ore deposits worldwide, where rich silver ores are hosted by calcite-rich and quartz-poor assemblages of gangue minerals.