Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of assimilating ERS‐1 fast delivery wave data into the North Atlantic WAM model

The launch of the European ERS satellites has provided a new source of wave information that is particularly suitable for use in improving wave forecasts in the open ocean. We have implemented and tested a simple system for assimilating corrections to model wave fields produced by the WAM model, where the corrections are derived from inverted synthetic aperture radar (SAR) image spectra from ERS-1. Corrections are applied to significant wave height, mean period and direction for wave modes that are detectable in both the model and the SAR data. The system has been tested in a storm situation and in moderate conditions using buoy data and altimeter data, as well as SAR observations for verification. Overall, it is demonstrated that the net effect of assimilating SAR data is beneficial but very small. The small impact is due at least partly to relatively small spatial and temporal coverage of the SAR wave mode data. Locally larger impacts were found in the storm situation in individual cases where SAR observations were collocated with independent buoy observations.
Impact of Routine Management Procedures on the Welfare of Suckling Piglets

Piglets often undergo several painful treatments during the initial days of their lives. In this review, we investigate the acute (i.e., immediate), short-, and long-term implications of piglet processing on behavioral, physiological, clinical, and performance parameters, and how welfare impairments depend on performance instead of sham procedure, alternative techniques, or the age of the piglets. Welfare indicators that have been used to determine the least distressing procedures and knowledge gaps with regard to the procedures are identified and discussed. Tail docking and especially piglet castration have been the most researched topics, whereas marking for identification has been rarely addressed. Few or no studies have investigated the effects of teeth resection and tail docking on piglets of different age groups. Additionally, results are often found to be inconsistent, highlighting the need for additional research to determine the optimal age for processing. Studies comparing different processing techniques have produced contradictory results, but ear notching, teeth clipping, hot cautery tail docking, and tearing during castration have been determined to result in increased pain. Generally, a shorter procedure duration can reduce stress, with operator training having a distinct impact on piglet welfare during processing. As such, these topics should be further investigated.
Grading Distress of Different Animal Models for Gastrointestinal Diseases Based on Plasma Corticosterone Kinetics

Simple Summary Animal welfare is an important aspect of biomedical research. Many regulations have been implemented to combine high quality of research with minimal harm to laboratory animals. These guidelines also demand a prospective severity assessment of each animal model. A comparison of distress between animal models could allow realistic harm and benefit analysis and an appropriate use of refinement methods. However, studies comparing distress between different animal models are still rare. One good parameter for analyzing distress is the concentration of the stress hormone corticosterone in the blood. Therefore, we compared the corticosterone kinetics of distinct gastrointestinal animal models. The aim of this study was to evaluate which parameter the highest corticosterone concentration or the duration of increased stress hormone level could be used to quantify distress. We observed a significant increase of corticosterone 30 min after stress induction in all animal models. However, the corticosterone kinetics differed between the distinct interventions. Both the absolute value and the duration of increased corticosterone level correlated directly with an assessed distress score. We conclude that both variables of corticosterone kinetics are valid parameters to compare distress between animal models. Abstract Comparative studies for evaluating distress in established animal models are still rare. However, this issue is becoming more important as a consequence of worldwide appreciation of animal welfare. One good parameter for evaluating distress is the quantification of corticosterone. We hypothesized that not just the absolute value but also the duration of increased corticosterone concentration in the blood is an important aspect for evaluating animal distress. Therefore, we analyzed plasma corticosterone concentrations 30, 60, 120, and 240 min after induction of pancreatitis by cerulein, liver damage by carbon tetrachloride, liver damage by bile duct ligation, and after orthotopic injection of pancreatic cancer cells. We also evaluated corticosterone kinetics after injection of distinct carrier substances. Compared to phosphate buffered saline, dimethyl sulfoxide leads to dose-dependent higher and longer-lasting circulating corticosterone concentrations. In all disease models, we observed significantly increased corticosterone concentration 30 min after stress induction. However, the corticosterone kinetics differed among the animal models. Both the absolute value of corticosterone concentration and the duration correlated positively with the quantification of animal distress by a score sheet. This suggests that both variables of corticosterone kinetics might provide a solid basis for comparing and grading distress of different animal models.
Bifurcation of the Kuroshio Extension at the Shatsky Rise

A 1/16° six-layer Pacific Ocean model north of 20°S is used to investigate the bifurcation of the Kuroshio Extension at the main Shatsky Rise and the pathway of the northern branch from the bifurcation to the subarctic front. Upper ocean-topographic coupling via a mixed barotropic-baroclinic instability is essential to this bifurcation and to the formation and mean pathway of the northern branch as are several aspects of the Shatsky Rise complex of topography and the latitude of the Kuroshio Extension in relation to the topography. The flow instabilities transfer energy to the abyssal layer where it is constrained by geostrophic contours of the bottom topography. The topographically constrained abyssal currents in turn steer upper ocean currents, which do not directly impinge on the bottom topography. This includes steering of mean pathways. Obtaining sufficient coupling requires very fine resolution of mesoscale variability and sufficient eastward penetration of the Kuroshio as an unstable inertial jet. Resolution of 1/8° for each variable was not sufficient in this case. The latitudinal extent of the main Shatsky Rise (31°N–36°N) and the shape of the downward slope on the north side are crucial to the bifurcation at the main Shatsky Rise, with both branches passing north of the peak. The well-defined, relatively steep and straight eastern edge of the Shatsky Rise topographic complex (30°N–42°N) and the southwestward abyssal flow along it play a critical role in forming the rest of the Kuroshio northern branch which flows in the opposite direction. A deep pass between the main Shatsky Rise and the rest of the ridge to the northeast helps to link the northern fork of the bifurcation at the main rise to the rest of the northern branch. Two 1/16° “identical twin” interannual simulations forced by daily winds 1981–1995 show that the variability in this region is mostly nondeterministic on all timescales that could be examined (up to 7 years in these 15-year simulations). A comparison of climatologically forced and interannual simulations over the region 150°E–180°E, 29°N–47°N showed greatly enhanced abyssal and upper ocean eddy kinetic energy and much stronger mean abyssal currents east of the Emperor Seamount Chain (about 170°E) in the interannual simulations but little difference west of 170°E. This greatly enhanced the upper ocean-topographic coupling in the interannual simulations east of 170°E. This coupling affected the latitudinal positioning of the eastward branches of the Kuroshio Extension and tended to reduce latitudinal movement compared to the climatologically forced simulation, including a particularly noticeable impact from the Hess Rise. Especially in the interannual simulations, effects of almost all topographic features in the region could be seen in the mean upper ocean currents (more so than in instantaneous currents), including meanders and bifurcations of major and minor currents, closed circulations, and impacts from depressions and rises of large and small amplitudes.
Examination of the relationship between outgoing infrared window and total longwave fluxes using satellite data

Abstract The relationship between narrowband and broadband thermal radiances is explored to determine the accuracy of outgoing longwave radiation derived from narrowband data. Infrared window (10.2–12.2 μm) data from the Geostationary Operational Environmental Satellite (GOES) are correlates with longwave (5.0–50.0 μm) data from the Earth Radiation Budget Experiment (ERBE)- A simple quadratic fit between the narrowband and longwave fluxes results in standard errors of 4.4%–5.3% for data that are matched closely in time and space. The use of matched regional flux data with temporal differences up to 59 minutes yields standard errors of 4.1%–5.4%. About 30% of the error may be attributed to limb darkening and spatial and temporal differences in the matched fluxes. The relationship shows a statistically significant dependence on the relative humidity of the atmosphere above the radiating surface. Although this dependency accounts for only about 1% of the standard error, it reduces the monthly mean regional e.
Modeling the Residential Infiltration of Outdoor PM2.5 in the Multi-Ethnic Study of Atherosclerosis and Air Pollution (MESA Air)

Background: Epidemiologic studies of fine particulate matter [aerodynamic diameter ≤ 2.5 μm (PM2.5)] typically use outdoor concentrations as exposure surrogates. Failure to account for variation in residential infiltration efficiencies (Finf) will affect epidemiologic study results. Objective: We aimed to develop models to predict Finf for > 6,000 homes in the Multi-Ethnic Study of Atherosclerosis and Air Pollution (MESA Air), a prospective cohort study of PM2.5 exposure, subclinical cardiovascular disease, and clinical outcomes. Methods: We collected 526 two-week, paired indoor–outdoor PM2.5 filter samples from a subset of study homes. PM2.5 elemental composition was measured by X-ray fluorescence, and Finf was estimated as the indoor/outdoor sulfur ratio. We regressed Finf on meteorologic variables and questionnaire-based predictors in season-specific models. Models were evaluated using the R2 and root mean square error (RMSE) from a 10-fold cross-validation. Results: The mean ± SD Finf across all communities and seasons was 0.62 ± 0.21, and community-specific means ranged from 0.47 ± 0.15 in Winston-Salem, North Carolina, to 0.82 ± 0.14 in New York, New York. Finf was generally greater during the warm (> 18°C) season. Central air conditioning (AC) use, frequency of AC use, and window opening frequency were the most important predictors during the warm season; outdoor temperature and forced-air heat were the best cold-season predictors. The models predicted 60% of the variance in 2-week Finf, with an RMSE of 0.13. Conclusions: We developed intuitive models that can predict Finf using easily obtained variables. Using these models, MESA Air will be the first large epidemiologic study to incorporate variation in residential Finf into an exposure assessment.
Increases in middle atmospheric water vapor as observed by the Halogen Occultation Experiment and the ground-based Water Vapor Millimeter-Wave Spectrometer from 1991 to 1997

Water vapor measurements made by the Halogen Occultation Experiment (HALOE) from 1991 to 1997 are compared with ground-based observations by the Water Vapor Millimeter-wave Spectrometers (WVMS) taken from 1992 to 1997 at Table Mountain, California (34.4°N, 242.3°E), and at Lauder, New Zealand (45.0°S, 169.7°E). The HALOE measurements show that an upward trend in middle atmospheric water vapor is present at all latitudes. The average trend in the HALOE water vapor retrievals at all latitudes in the 40–60 km range is 0.129 ppmv/yr, while the average trend observed by the WVMS instruments in this altitude range is 0.148 ppmv/yr. This trend is occurring below the altitude where changes in Lyman α associated with solar cycle variations should produce a significant increase in water vapor during this period, and is much larger than the ∼0.02 ppmv/yr trend in water vapor associated with increases in methane entering the stratosphere. In addition to the water vapor increase, HALOE measurements show that there is a temporal decrease in methane at altitudes between 40 and 70 km. This indicates an increase in the conversion of the available methane to water vapor, thus contributing to the observed increase in water vapor. The increase in water vapor observed by both instruments is larger than that which would be expected from the sum of all of the above effects. We therefore conclude that there has been a significant increase in the amount of water vapor entering the middle atmosphere. A temperature increase of ∼0.1 K/yr in regions of stratosphere-troposphere exchange could increase the saturation mixing ratio of water vapor by an amount consistent with the observed increase.
Place field repetition and spatial learning in a multicompartment environment

Recent studies have shown that place cells in the hippocampus possess firing fields that repeat in physically similar, parallel environments. These results imply that it should be difficult for animals to distinguish parallel environments at a behavioral level. To test this, we trained rats on a novel odor‐location task in an environment with four parallel compartments which had previously been shown to yield place field repetition. A second group of animals was trained on the same task, but with the compartments arranged in different directions, an arrangement we hypothesised would yield less place field repetition. Learning of the odor‐location task in the parallel compartments was significantly impaired relative to learning in the radially arranged compartments. Fewer animals acquired the full discrimination in the parallel compartments compared to those trained in the radial compartments, and the former also required many more sessions to reach criterion compared to the latter. To confirm that the arrangement of compartments yielded differences in place cell repetition, in a separate group of animals we recorded from CA1 place cells in both environments. We found that CA1 place cells exhibited repeated fields across four parallel local compartments, but did not do so when the same compartments were arranged radially. To confirm that the differences in place field repetition across the parallel and radial compartments depended on their angular arrangement, and not incidental differences in access to an extra‐maze visual landmark, we repeated the recordings in a second set of rats in the absence of the orientation landmark. We found, once again, that place fields showed repetition in parallel compartments, and did not do so in radially arranged compartments. Thus place field repetition, or lack thereof, in these compartments was not dependent on extra‐maze cues. Together, these results imply that place field repetition constrains spatial learning. © 2016 The Authors Hippocampus Published by Wiley Periodicals, Inc.
Uncertainties in observationally based estimates of temperature change in the free atmosphere

Uncertainties are quantified in atmospheric temperature changes derived from satellites, radiosondes, and the reanalyses of the National Center for Environmental Prediction and European Centre for Medium-Range Weather Forecasts (NCEP and ERA). To facilitate intercomparison, we compute from the reanalyses and radiosonde data deep layer temperatures equivalent to those estimated from the satellite-based Microwave Sounding Unit (MSU). Equivalent MSU temperatures generated using global mean weighting functions and a radiative transfer code give similar results. NCEP's pre-1979 global mean lower stratospheric temperature anomalies diverge markedly from radiosonde data. A smaller offset occurs in the midtroposphere. These differences are attributed to a likely warm bias in the tropical lower stratosphere in the temperature retrievals used by NCEP from November 1978 onward, and changes in the error characteristics of the assimilation model's simulation of the lower stratosphere. In the lower troposphere, ERA and NCEP show different global mean trends due to differences in assimilation strategy, input observational data, quality control procedures, and model physics. Over 1979–1993, ERA warms by 0.106°C/decade, while NCEP cools by 0.028°C/decade. Applying the HadRT1.1 (radiosonde) data availability mask to NCEP improves the agreement between these data sets. Neglecting coverage differences can yield misleading results in MSU-radiosonde trend comparisons. Substantial trend uncertainties also arise from coverage differences between various radiosonde data sets. Version c of the MSU lower tropospheric temperature retrieval fails to adjust explicitly for orbital decay. If this were applied without any additional adjustments, it would resolve an important discrepancy: in MSUc the lower troposphere has cooled in relation to the midtroposphere, while the reverse is the case for both reanalyses and for the radiosonde data examined here.
Association between BMI, Blood Pressure, and Age: Study among Tangkhul Naga Tribal Males of Northeast India

Purpose. To find the prevalence of overweight/obesity and hypertension, and to study the association between BMI, blood pressure, and age. Methods. Cross-sectional study was carried out among 257 Tangkhul Naga males of Northeast India, age ranging from 20–70 years. The subjects were divided into five different age groups to study age trend. Results. Mean systolic, and diastolic BP was higher among subjects with elevated BMI and among older subjects. Minimum BP was found among underweight and maximum among obese. BP was found lowest among the youngest age group and higher among the elderly subjects. BMI was also found to be associated with age independently. Although the magnitude of correlation differed, there was significant positive correlation among BMI, age, systolic and diastolic BP. Odd ratios showed overweight/obese subjects to be more likely to have hypertension than those with normal BMI. Changing socioeconomic environment intensifies the prevalence of overweight/obesity and hypertension among the Tangkhul Nagas.
Comment on “Widespread tropical atmospheric drying from 1979 to 1995” by Schroeder and McGuirk

Schroeder and McGuirk [1998, hereafter SM] recently presented an analysis of a satellite-based precipitable water (W) dataset and concluded that a widespread drying of the tropical atmosphere occurred between two periods, 1979-87 and 1989-95. SM's conclusion isat odds with other published work on this topic. We note that the trends from other studies of radiosonde data that are consistent with their results are
Assessment of DNA methylation differences between carriers of APOE ε4 and APOE ε2

INTRODUCTIONThe Apolipoprotein E (APOE) {varepsilon}4 allele is the strongest genetic risk factor for Alzheimers disease (AD), while the {varepsilon}2 allele confers protection. Previous studies report differential DNA methylation of APOE between {varepsilon}4 and {varepsilon}2 carriers but associations with epigenome-wide methylation are unknown.nnMETHODSThe EPIC array was used to identify methylation differences between AD-free APOE {varepsilon}4 (n=2469) and {varepsilon}2 (n=1108) carriers using epigenome-wide association analysis and differentially methylated region (DMR) approaches. Results were explored using pathway and meQTL analyses.nnRESULTSDifferentially methylated positions were identified in APOE, surrounding genes and genes outside of this locus (DHCR24, LDLR and ABCG1). DMRs were identified in SREBF2, LDLR and SQLE. Pathway and meQTL analyses implicated lipid-related processes; however, blood cholesterol levels could not fully account for the associations.nnDISCUSSIONAPOE {varepsilon}4 vs. {varepsilon}2 carrier status is associated with epigenome-wide methylation differences in cis and trans in genes involved in lipid homeostasis.
Expansile cribriform Gleason pattern 4 has histopathologic and molecular features of aggressiveness and greater risk of biochemical failure compared to glomerulation Gleason pattern 4

Molecular testing of prostate cancer biopsies with Gleason pattern 4 suggests the expansile cribriform pattern is more aggressive than the glomerulation pattern. These two extreme patterns have not been compared at prostatectomy. We hypothesized that at prostatectomy the expansile cribriform pattern would be associated with histopathologic and molecular features of aggressiveness and with greater risk of biochemical recurrence (BCR) than the glomerulation pattern.
The stratigraphy and palaeontology of the 'Keuper' Series of the central Midlands of England

A reappraisal of the stratigraphical status of the formations constituting the series traditionally termed 'Keuper' in central England is given, based on palaeontological and sedimentological evidence. The 'Keuper' Sandstone is a fluvial facies representing a sub-aerial deltaic environment and is of upper Scythian and Anisian age. At the base of the 'Keuper' Sandstone is a significant disconformity which is probably equivalent to the Hardegsen Disconformity of Germany. The 'Keuper' Waterstones are a marine or semi-marine facies of transgressive nature and represent the distal facies belt of the delta complex. The Waterstones facies is of lower Ladinian age in the central Midlands but is probably older in more northerly districts (Cheshire, Yorkshire, etc). The Keuper Marl is of Keuper age, representing at least the upper Ladinian and Carnian stages of the European Keuper, and is largely the deposit of a hypersaline epeiric sea. A correlation chart and a series of palaeographical maps, based on the new evidence provided in this paper, are presented.
Experience-Dependent, Rapid Structural Changes in Hippocampal Pyramidal Cell Spines

Morphological changes in dendritic spines may contribute to the fine tuning of neural network connectivity. The relationship between spine morphology and experience-dependent neuronal activity, however, is largely unknown. In the present study, we combined 2 histological analyses to examine this relationship: 1) Measurement of spines of neurons whose morphology was visualized in brain sections of mice expressing membrane-targeted green florescent protein (Thy1-mGFP mice) and 2) Categorization of CA1 neurons by immunohistochemical monitoring of Arc expression as a putative marker of recent neuronal activity. After mice were exposed to a novel, enriched environment for 60 min, neurons that expressed Arc had fewer small spines and more large spines than Arc-negative cells. These differences were not observed when the exploration time was shortened to 15 min. This net-balanced structural change is consistent with both synapse-specific enhancement and suppression. These results provide the first evidence of rapid morphological changes in spines that were preferential to a subset of neurons in association with an animal's experiences.