Miracle-dz/UniFAR-FTUs huggingface dataset:
The Influence of Seasonal and Decadal Trends in Coastal Ocean Processes on the Population Biology of the krill species Euphausia pacifica: Results of a coupled ecosystem and individual based modeling study

Krill of the California Current play a crucial role in the transfer of primary production up to many commercially important higher trophic levels. Understanding the short time scale (weeks to seasonal) and long time scale (decadal) variability in abundance, condition, and spatial patterns that results from changes in ocean conditions is critical if we hope to manage the fishery of any higher trophic levels from more than a single species approach. I have coupled a suite of models in an attempt to understand the impacts of changing ocean conditions on this important prey item. The coastal ocean was simulated with a commonly used oceanographic model (Regional Ocean Modeling System) coupled with an ecosystem model (Nutrient, Phytoplankton, Zooplankton, Detritus). The coastal ocean was simulated from Newport, OR to Point Conception, CA over an 18-year period (1991 - 2008). These model results were used to force a 3-dimensional individual based model (IBM) that was parameterized to represent the krill species Euphausia pacifica . Biological processes of the IBM (growth, life-stage progression, mortality, reproduction, vertical migration) were compared to laboratory data and field data under varying food and temperature conditions to understand how well the model can reproduced known biological rates and processes. The model performs well at simulating growth, life stage progression, and reproduction, as these are the areas from which there is an abundance of data from which to parameterize the model. Results from simulations of larval and adult populations indicated the greatest amount growth in both larval and adult populations was over the six-month period from April through October. Mortality was greatest for larvae during the winter (when food resources are typically lowest), but mortality was greatest for adults during summer due to offshore transport of individuals to regions of warmer surface waters and reduced food concentration. Condition of individuals and mortality of individuals correlated positively with the more productive phase of the Pacific Decadal Oscillation and the North Pacific Decadal Oscillation, providing evidence the impact of ocean basin scale atmospheric conditions on krill. The impacts of atmospheric forcing on E. pacifica are important factors that control the distribution, abundance and productivity of this important prey item for many commercially important fisheries of the West Coast of the United States.
Systems Neuroscience

and neostriatal projection neurons develop intranuclear inclusions with a well-established timeline in which all neurons have the inclusions by 8 weeks of age. The animals show behavioral dysfunctions, and die at about 12–14 weeks of age. The relatively short lifespan and fast development of pathology makes these mice ideal for study of pathophysiology, as all of the projection neurons develop inclusions , and no notable neuronal death occurs. A number of in vitro studies have shown altered neurophysio-logical and neuroanatomical properties of neocortical and neostri-These studies show significant alterations in neocortical and neostri-atal electrophysiological properties including both intrinsic con-ductances and synaptic properties. Changes in the properties of neostriatal neurons include decreased resting membrane potential, increased input resistance, and pruning of dendritic branching and spine patterns. Physiological changes also include reductions in synaptic currents evoked by stimulation of neocortical white matter (Cepeda et al., 2003a). The changes in neuronal properties measured in vitro are crucial to understanding the effects of the neuropathology on cellular activity. However, in order to understand the changes in the corti-costriatal network properties caused by HD pathology, it is necessary to measure the activity of these neurons in the intact animal.
High Rayleigh number compressible convection in Venus' atmosphere: Penetration, entrainment, and turbulence

Numerical simulations of two-dimensional, nonlinear fully compressible convection at the subsolar point in the clouds of Venus are presented. One moderate Rayleigh number case (Raq = 6.8 × 106) and two high Rayleigh number (Raq = 1.1 × 109) cases are considered. Cloud-level convection is characterized by cold, narrow downwellings that deeply penetrate the underlying stable layer and that entrain warmer air from the overlying stable layer. The convection layer depth, as determined from the horizontally averaged static stability, spans 9 km (47–56 km altitude) and 14 km (46–60 km altitude) for the moderate Rayleigh number and high Rayleigh number simulations, respectively. In the high Rayleigh number cases, convective penetration extends over a scale height from the bottom of the convection layer down to 38 km altitude. Strong convective entrainment completely erodes the overlying stable layer in the high Raq cases and incorporates it into the convection layer. The timescale for entrainment of the overlying stable layer is roughly 1 day and may explain why cellular features are predominantly found near and downwind of the subsolar point. The high Rayleigh number simulations are convectively turbulent and exhibit a spectral energy cascade of k−3, where k is the horizontal wavenumber. Our results suggest that cellular features in the subsolar region are observed at the cloud tops because convection may extend to much higher altitudes there. Downward penetrative convection may also be responsible for turbulence observed in Venus' atmosphere at 45 km altitude.
Direct observational evidence linking atmospheric aerosol formation and cloud droplet activation

In order to predict the current state and future development of the Earth's climate system, detailed knowledge on how atmospheric aerosol particles from various sources interact with clouds is needed. In this article we present, based on continuous aerosol measurements in a remote continental location, direct observational evidence that aerosol particles formed in the atmosphere from gaseous precursors eventually participate into cloud droplet activation. By combining the measurement data with theoretical calculations, we further demonstrate that the albedo of clouds may be significantly influenced by atmospheric aerosol formation, and that this process needs to be taken into account when estimating the indirect climatic effects of aerosols in the global atmosphere.
Stratification‐driven instabilities with bi‐kappa distribution functions in the Io plasma torus

[1] We extend our previous studies on plasma transport in the fast rotating magnetosphere of Jupiter. The present study uses a new kinetic Io plasma torus model in order to test the local stability criteria against stratification-driven low-frequency modes in this environment. Compared to the model used in our previous application, the new model introduces bi-kappa velocity distributions and plasma pressure anisotropies in order to reproduce most of the available observational data obtained in the torus. This generates radial profiles of plasma densities and temperatures that slightly differ from those used previously. Here we examine the implications of non bi-Maxwellian velocity distributions and of pressure anisotropies for the centrifugal interchange instability and for the resulting transport of plasma in the Io torus and further demonstrate how our theoretical findings can be applied to realistic environments.
(U‐Th)/He dating of terrestrial impact structures: The Manicouagan example

The accurate dating of meteorite impact structures on Earth has proven to be challenging. Melt sheets are amenable to high‐precision dating by the U‐Pb and 40Ar/39Ar methods, but many impact events do not produce them, or they are not preserved. In cases where high‐temperature shock metamorphism of the target materials has occurred without widespread melting, these isotopic chronometers may be partially reset and yield dates that are difficult to interpret unambiguously as the age of impact. However, the (U‐Th)/He chronometer is sensitive to thermal resetting and can provide a powerful new tool for dating impactites. We report (U‐Th)/He dates for accessory minerals from the Manicouagan impact structure in Quebec, Canada. Nine zircons from a melt sheet sample yield a weighted mean age of 213.2 ± 5.4 Ma (2SE), indistinguishable from the published 214 ± 1 Ma (2σ) U‐Pb zircon age for the impact. In contrast, five apatites from this sample yield dates between 205.9 ± 6.5 and 162.0 ± 5.3 Ma (2σ), indicating variable postimpact helium loss due to low‐temperature thermal disturbance. Preimpact titanite crystals from a shocked meta‐anorthosite sample yield two dates consistent with the impact age, at 212 ± 27 and 214 ± 13 Ma (2σ), and two younger dates of 189.6 ± 6.9 and 192.2 ± 9.8 Ma (2σ), suggestive of postimpact helium loss. These results indicate that (U‐Th)/He chronometry is a suitable method for dating impact events, although interpretation of the results requires recognition of possible 4He loss related to reheating subsequent to impact.
Geosynthetic Clay Liners Subjected to Differential Settlement

Geosynthetic clay liners (GCLs), which consist of a thin layer of bentonite attached to one or more geosynthetic materials, are receiving increased use as low-permeability barrier layers in waste-containment systems. Tests were performed in tanks to measure the hydraulic conductivity of GCLs that were subjected to differential settlement. In most cases the GCLs maintained a hydraulic conductivity of 1 × 10−7 cm/s or less when subjected to tensile strains of 1–>10%, depending on the material and test conditions. Overlapped GCL panels maintained their hydraulic integrity despite in-plane slippage of up to 25–100 mm. In general, the ability of GCLs to withstand differential settlement appears to be greater than that of compacted clay liners, but less than that of geomembranes. GCLs are a promising barrier material for situations in which differential settlement is expected, for example, in landfill final covers.
Analysis of surface settlement control with shield tunneling method

The surface settlement (SS) induced by shield tunneling method can be predicted using the modified Peck formula based on the modified gap parameters proposed in this work. The modified gap parameters considered shield tunneling parameters (STPs) can be expressed with the support pressure ratio of shield (), fill rate of grouting (β), and eccentricity ratio of shield (). Based on the actual cases of the Xi’an subway line 2 in China, the results of sensitivity and back analysis of STPs show that β has a minimal effect on SS,  has a significant influence on SS, and  has the maximum effect on SS. The maximum SS and surface curvature due to shield tunneling are be considered to control the permitted deformation according to the Chinese standards. Thus the control standards of STPs are obtained and suggested through the back analysis of damage classification by using the modified Peck formula.
Full‐wave reflection of lightning long‐wave radio pulses from the ionospheric D region: Comparison with midday observations of broadband lightning signals

[1] We are developing and testing a steep-incidence D region sounding method for inferring profile information, principally regarding electron density. The method uses lightning emissions (in the band 5-500 kHz) as the probe signal. The data are interpreted by comparison against a newly developed single-reflection model of the radio wave's encounter with the lower ionosphere. The ultimate application of the method will be to study transient, localized disturbances of the nocturnal D region, including those instigated by lightning itself. Prior to applying the method to study lightning-induced perturbations of the nighttime D region, we have performed a validation test against more stable and predictable daytime observations, where the profile of electron density is largely determined by direct solar X-ray illumination. This article reports on the validation test. Predictions from our recently developed full-wave ionospheric-reflection model are compared to statistical summaries of daytime lightning radiated waveforms, recorded by the Los Alamos Sferic Array. The comparison is used to retrieve best fit parameters for an exponential profile of electron density in the ionospheric D region. The optimum parameter values are compared to those found elsewhere using a narrowband beacon technique, which used totally different measurements, ranges, and modeling approaches from those of the work reported here.
Observational study of upper gastrointestinal tract bleeding events in patients taking duloxetine and nonsteroidal anti-inflammatory drugs: a case-control analysis

Purpose: To determine whether the concomitant use of duloxetine with prescription nonsteroidal anti-inflammatory drugs (NSAIDs) or aspirin was associated with an increased risk for upper gastrointestinal (UGI) bleeding compared with taking these analgesics alone. Methods: Truven Health Analytics MarketScan Research Databases were examined for hospital admissions of adult patients indexed from January 1, 2007–December 31, 2011. Cases were patients with UGI hemorrhage or peptic ulcer disease. Controls were randomly selected from the remaining admissions to match 10:1 with cases based on age, sex, and admission date. Prescription medication exposure groups of interest were: 1) no exposure to duloxetine, NSAIDs or aspirin; 2) duloxetine only; 3) NSAIDs or aspirin only; 4) duloxetine plus NSAIDs or aspirin. Logistic regression and relative excess risk due to interaction was utilized to estimate any increased risk of UGI bleeding for patients prescribed these medications across these groups. Results: There were 33,571 cases and 335,710 controls identified. Comparing exposure group 2 and group 4, the adjusted odds ratio was 1.03 (95% confidence interval [CI], 0.94, 1.12), and the adjusted relative excess risk due to interaction was 0.352 (95% CI: –0.18, 0.72) for risk of UGI bleeding, neither of which support an increased risk or an interaction between duloxetine and prescription NSAID or aspirin for these events. Conclusion: There was no evidence of an increased risk for UGI bleeding when duloxetine was taken with prescription NSAIDs or aspirin. In addition, there was no evidence of an interaction between duloxetine and prescription NSAIDs or aspirin for an increased risk of these events.
Targeting the endoplasmic reticulum-mitochondria interface sensitizes leukemia cells to cytostatics

Combination chemotherapy has proven to be a favorable strategy to treat acute leukemia. However, the introduction of novel compounds remains challenging and is hindered by a lack of understanding of their mechanistic interactions with established drugs. In the present study, we demonstrate a highly increased response of various acute leukemia cell lines, drug-resistant cells and patient-derived xenograft cells by combining the recently introduced protein disulfide isomerase inhibitor PS89 with cytostatics. In leukemic cells, a proteomics-based target fishing approach revealed that PS89 affects a whole network of endoplasmic reticulum homeostasis proteins. We elucidate that the strong induction of apoptosis in combination with cytostatics is orchestrated by the PS89 target B-cell receptor-associated protein 31, which transduces apoptosis signals at the endoplasmic reticulum -mitochondria interface. Activation of caspase-8 and cleavage of B-cell receptor-associated protein 31 stimulate a pro-apoptotic crosstalk including release of calcium from the endoplasmic reticulum and an increase in the levels of reactive oxygen species resulting in amplification of mitochondrial apoptosis. The findings of this study promote PS89 as a novel chemosensitizing agent for the treatment of acute leukemia and uncovers that targeting the endoplasmic reticulum - mitochondrial network of cell death is a promising approach in combination therapy.
Model experiments on the impact of Pacific sea surface temperature anomalies on blocking frequency

Abstract Sensitivity experiments with a perpetual January version of a low-resolution general circulation model are conducted to investigate the influence of Pacific sea surface temperature (SST) anomalies on blocking in the Northern Hemisphere. Six 1200-day integrations, each of which contains a different specified SST anomaly superimposed upon a fixed climatological SST distribution, are compared with a 1200-day control simulation to examine the impact of both equatorial Pacific and midlatitude North Pacific anomalous forcing. An ensemble of eight independent 90-day realizations is extracted from each simulation. Distributions of the ensemble-mean differences in the total number of blocking days from the control simulation are presented, along with estimates of the statistic significance of these differences. Pacific SST anomalies do not strongly affect the total number of days in which a block is present anywhere over the North Pacific basin, but they apparently can affect the preferred regions over th.
Effects of Sediment Deposition on Aboveground Net Primary Productivity, Vegetation Composition, Structure, and Fine Root Dynamics in Riparian Forests

The importance of riparian forests in water quality improvement through sediment trapping has been well documented. Quantification and identification of sources of sediment deposition has been the focus of many studies. However, how riparian systems respond to high rates of sediment deposition is still unknown. This study was conducted at Fort Benning, GA, where intensive military traffic on sandy roads has generated movement of large amounts of sediment into riparian forests associated with ephemeral streams. The objective of this study was to evaluate how excessive sediment deposition affects riparian forest function, composition and structure. Two paired plots were established in each of nine ephemeral streams, to encompass a wide range of sediment deposition. One treatment plot (upper plot) was established in the upper reaches of each ephemeral stream and another (lower plot) was located farther down, beyond visual evidence of sediment deposition. Comparisons between treatments and among disturbance categories were made in terms of aboveground net primary productivity, litterfall nutrient contents, leaf area index, and changes in vegetation composition and structure. These were assessed by documenting understory vegetation in terms of number
Cooperation of the ER-shaping proteins atlastin, lunapark, and reticulons to generate a tubular membrane network

In higher eukaryotes, the endoplasmic reticulum (ER) contains a network of membrane tubules, which transitions into sheets during mitosis. Network formation involves curvature-stabilizing proteins, including the reticulons (Rtns), as well as the membrane-fusing GTPase atlastin (ATL) and the lunapark protein (Lnp). Here, we have analyzed how these proteins cooperate. ATL is needed to not only form, but also maintain, the ER network. Maintenance requires a balance between ATL and Rtn, as too little ATL activity or too high Rtn4a concentrations cause ER fragmentation. Lnp only affects the abundance of three-way junctions and tubules. We suggest a model in which ATL-mediated fusion counteracts the instability of free tubule ends. ATL tethers and fuses tubules stabilized by the Rtns, and transiently sits in newly formed three-way junctions. Lnp subsequently moves into the junctional sheets and forms oligomers. Lnp is inactivated by mitotic phosphorylation, which contributes to the tubule-to-sheet conversion of the ER. DOI: http://dx.doi. org/10.7554/eLife.18605. 001
Frontal Non-Invasive Neurostimulation Modulates Antisaccade Preparation in Non-Human Primates

A combination of oculometric measurements, invasive electrophysiological recordings and microstimulation have proven instrumental to study the role of the Frontal Eye Field (FEF) in saccadic activity. We hereby gauged the ability of a non-invasive neurostimulation technology, Transcranial Magnetic Stimulation (TMS), to causally interfere with frontal activity in two macaque rhesus monkeys trained to perform a saccadic antisaccade task. We show that online single pulse TMS significantly modulated antisaccade latencies. Such effects proved dependent on TMS site (effects on FEF but not on an actively stimulated control site), TMS modality (present under active but not sham TMS on the FEF area), TMS intensity (intensities of at least 40% of the TMS machine maximal output required), TMS timing (more robust for pulses delivered at 150 ms than at 100 post target onset) and visual hemifield (relative latency decreases mainly for ipsilateral AS). Our results demonstrate the feasibility of using TMS to causally modulate antisaccade-associated computations in the non-human primate brain and support the use of this approach in monkeys to study brain function and its non-invasive neuromodulation for exploratory and therapeutic purposes.
Characteristics of composited AVHRR data and problems in their classification

Abstract Unsupervised classification procedures were applied to a temporal sequence of fifteen bi-weekly composited NDVI images produced from AVHRR LAC data. Individual examination of the input images appeared to show substantial contamination due to clouds which persist through the compositing period. These apparent cloud features dominated the results of the clustering procedures. The composites also include large numbers of far off-nadir pixels. This causes severe spatial smoothing and produces a blurred image appearance. Further combining the data to monthly composites largely eliminated the cloud cover problem, but did not necessarily reduce the frequency of large view zenith angles. Preprocessing of high temporal frequency; low spatial resolution data such as that provided by AVHRR and the planned EOS MODIS instrument must more effectively remove the effects of clouds, correct for anisotropic scattering from the atmosphere and bi-directional reflectance from the surface, and should be biased towards.