Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagenesis in anoxic sediments from the California continental borderland and its influence on iron, sulfur, and magnetite behavior

Solid phase and pore water profiles of compounds containing iron and sulfur have been determined by wet chemical, magnetic, and X-ray diffraction techniques in three California continental borderland basins. The observed profiles have been fit by simple reaction-diffusion models in order to determine reaction rates and constrain budgets for iron and sulfur. More than 95% of the solid phase reduced sulfur is pyrite, and down core profiles are well fit by a model in which net sulfate reduction rates decrease exponentially with depth. Net sulfate reduction rates determined from models fit to solid phase reduced sulfur measurements and pore water sulfate profiles yield results that are consistent. Depth integrated sulfate reduction rates for modern sediments in San Pedro, Santa Catalina, and San Nicolas Basins are, 11.4, 6.3, and 6.3–8.8 (μmol cm-2yr-1), respectively. Measurements of solid phase iron species indicate that surficial sediments are enriched in easily-reducible ferric oxyhydroxides. The enrichment is maintained by a combination of oxidation of Fe2+ diffusing upward from underlying anoxic sediments, as well as input of fresh sediment enriched in ferric oxyhydroxides. The three primary sources for iron converted to pyrite and the sequence in which they are utilized are: ferric oxyhydroxides, magnetite and other crystalline oxides, and “exchangeable” iron in phyllosilicates. The majority (50–80%) of the iron converted to pyrite is from the silicates, and budgetary calculations indicate the amount of iron released from San Pedro basin silicates agrees within 35% with the amount of magnesium removed from pore water to solid phases. Fe2+ is enriched in near-surface pore waters because rates of dissolved iron production by oxyhydroxide reduction exceed rates of sulfate reduction and pyrite formation. At depth, pore waters are sulfidic because rates of sulfate reduction exceed rates of iron release from silicates. Sulfide produced at depth diffuses upward until it reaches sediments with available iron, causing a step-like increase in solid phase sulfur concentration. Over 90% of the magnetite present in surficial sediments is dissolved at depth due to reaction with H2S. A model is developed to predict the depth at which magnetite dissolution should occur, based on sulfate reduction rates and the flux of ferric oxyhydroxides. The results of this model predict the onset of dissolution at depths of 5–40 cm in different basins and agree well with the observed depths of magnetite dissolution.
Organic iron(III) speciation in surface transects across a frontal zone: the Chatham Rise, New Zealand

Iron (Fe) is a critical nutrient in marine systems and the organic complexation of Fe is a central factor of the marine biogeochemistry of Fe. In the present study, total dissolved Fe and its organic speciation were measured in filtered seawater samples ( 99.9%) by natural organic ligands, which were found to occur in excess of the dissolved Fe concentration at 1.29 ± 0.33 nm (equivalent to an excess over Fe of ~1.0 nm), and with a complex stability of log⁡ K ′ FeL,F e 3+ --> K′FeL,Fe3+ = 22.67 ± 0.22. The total ligand concentrations were consistently higher (~0.5 nm) in the ST and STC waters than in the SA waters. Our Fe data imply that the regional currents may be an important vehicle for transporting the elevated Fe across the front.
Assimilation of pCO2 data into a global coupled physical‐biogeochemical ocean model

[1] As part of the CARBOOCEAN project, measurements of the partial pressure of carbon dioxide (pCO2) in the ocean have been collected since 2001. Our aim was to use these data in a data assimilation context to improve the representation of pCO2 and its associated prognostic variables in biogeochemical models. Based upon a sequential framework a new method for the assimilation of pCO2 data was developed. This method had to account for oceanic pCO2 being a derived quantity with a functional dependence on temperature, salinity, dissolved inorganic carbon (DIC), and alkalinity. Our method calculates pCO2 increments using an analysis correction technique and then converts these into increments in model variables. Temperature and salinity are assumed to be error free, and so only DIC and alkalinity are updated. Furthermore, in DIC and alkalinity space increments are taken to be perpendicular to the local line of constant pCO2. Our method was tested by assimilating pCO2 data from 2006 into the NEMO-HadOCC biogeochemical model and then comparing the output from this model to a control with no pCO2 assimilation. While lack of data prevented the assimilation system from correcting a significant systematic error in the subpolar North Atlantic, results from this experiment showed that pCO2 assimilation, despite limited data, reduced RMS and mean errors and also brought the model closer to climatology in the subtropical North Atlantic.
Sequence analysis BRAT : bisulfite-treated reads analysis tool

Summary: We present a new, accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. Our tool, BRAT, supports single and paired-end reads and handles input files containing reads and mates of different lengths. BRAT is faster, maps more unique paired-end reads and has higher accuracy than existing programs. The software package includes tools to end-trim low-quality bases of the reads and to report nucleotide counts for mapped reads on the reference genome. Availability: The source code is freely available for download at http://compbio.cs.ucr.edu/brat/ and is distributed as Open Source software under the GPLv3.0. Contact: elenah@cs.ucr.edu
Lagrangian reconstruction of ozone column and profile at the Arctic Lidar Observatory for Middle Atmosphere Research (ALOMAR) throughout the winter and spring of 1997–1998

We present a Lagrangian model-based technique to reconstruct ozone profile and column in support of the interpretation of ozone lidar observations made at the Arctic Lidar Observatory for Middle Atmosphere Research (ALOMAR). High-resolution ozone profiles as well as column ozone are reconstructed locally at ALOMAR, several times a day, regularly throughout the winter and spring of 1997/1998. The approach consists of calculating a large number of back trajectories to determine the origin of air parcels above ALOMAR and of using satellite observations to determine their ozone content. The blend of satellite observations with limited spatial and temporal coverage, and global gridded meteorological data is akin to a simplified form of data assimilation. The usefulness of the approach is demonstrated by a systematic comparison between reconstructed and observed ozone profiles and column and, in particular, their day-to-day variability. Abrupt changes in reconstructed and observed profile shape are caused by polar vortex displacements, deep intrusions of midlatitude air, or vortex edge filamentation. Prominent laminae are seen in the spring, as the vortex breaks down. Short-lived, large-amplitude total ozone peaks are seen in the model and observations, most prominently in February and March, when they are in excess of 100 Dobson units. They are shown to result from a combination of a lowering of isentropes in the lowermost stratosphere and of advection of ozone-rich air from the base of the polar vortex.
Changes of Snow Cover, Temperature, and Radiative Heat Balance over the Northern Hemisphere

Abstract Contemporary large-scale changes in satellite-derived snow cover were examined over the Northern Hemisphere extratropical land (NEL) areas. These areas encompass 55% of the land in the Northern Hemisphere. Snow cover (S) transient regions, the “centers of action” relative to interannual variations of snow cover, were identified for the years 1972–1992. During these years a global retreat in snow cover extent (SE) occurred in the second half of the hydrologic year (April–September). Mean annual SE has decreased by 10% (2.3 × 106 km2). Negative trends account for one-third to one-half of the interannual continental variance of SE. The historical influence of S on the planetary albedo and outgoing longwave radiation (OLR) is investigated. The mean annual response of the S feedback on the radiative balance (RB) is negative and suggests a large-scale heat redistribution. During autumn and early winter (up to January), however, the feedback of S on the planetary RB may he positive. Only by February doe.
Tracing Soil Particle Movement with Fe‐59

Rates and patterns of actual soil particle movement were established by measuring changes in radiation intensity with time on an eroding sandstone soil. Applying 300 mu c of fe (50) in a 5-foot line along the contour gave a better measure of soil erosion pattern than 100 mu c applied to a point. More than 70 percent of the isotope applied moved 3 or more inches downslope from the line of application. Apparently iron (50) forms mainly stable precipitates or reacts with existing ferric compounds on clay and silt particles because it is not found in the soil solution or on the soil base-exchange capacity. Only 20 percent of the Fe (50) was removed by 72-hour treatment with 30 percent H2O2. Over 90 percent of the Fe (50) was retained in the surface 1 cm of soil. /Author/
Interim Report: 100-NR-2 Apatite Treatability Test: Low Concentration Calcium Citrate-Phosphate Solution Injection for In Situ Strontium-90 Immobilization

Following an evaluation of potential Sr-90 treatment technologies and their applicability under 100-NR-2 hydrogeologic conditions, U.S. Department of Energy, Fluor Hanford, Inc., Pacific Northwest National Laboratory, and the Washington Department of Ecology agreed that the long-term strategy for groundwater remediation at 100-N Area will include apatite sequestration as the primary treatment, followed by a secondary treatment if necessary (most likely phytoremediation). Since then, the agencies have worked together to agree on which apatite sequestration technology has the greatest chance of reducing Sr-90 flux to the river at a reasonable cost. In July 2005, aqueous injection, (i.e., the introduction of apatite-forming chemicals into the subsurface) was endorsed as the interim remedy and selected for field testing. Studies are in progress to assess the efficacy of in situ apatite formation by aqueous solution injection to address both the vadose zone and the shallow aquifer along the 300 ft of shoreline where Sr-90 concentrations are highest. This report describes the field testing of the shallow aquifer treatment.
An autologistic regression model for increasing the accuracy of burned surface mapping using Landsat Thematic Mapper data

An autologistic regression model, which takes into account neighbouring associations, was developed and applied for burned land mapping using Landsat-5 Thematic Mapper data. The integration of the autocovariate component (estimated using a moving window of 3 @ 3 pixels) into the ordinary logistic regression model increased significantly the overall accuracy from 88.18% to 92.44%. In contrast, the accuracy derived with application of post-classification majority filters, which follow the same principles, were not significantly different to that derived with ordinary logistic regression.
The Cuillin layered igneous complex—evidence for multiple intrusion and former presence of a picritic liquid

Synopsis Much of the western Cuillin is formed by part of a funnel-shaped intrusion comprising layered ultrabasic rocks which range upwards from dunite to peridotite to allivalite (feldspar-olivine cumulate). The funnel-shaped intrusion has a marginal border group on which allivalites are banked. Recent mapping indicates that a peridotite mass previously regarded as a sill, is part of this layered sequence, and that inner, ultrabasic cumulates to the E are merely a downthrown portion of the same funnel-shaped mass. The eastern rocks were cut by a later pyroxene-rich magma from which feldspar-olivine-pyroxene cumulates were formed. In the lower dunite-peridotite-allivalite series (Unit 1), cumulus olivine and feldspar range from Fo90–86 and An91–85, respectively. In the upper unit (Unit 2) of feldspar-olivine-pyroxene cumulates cryptic variation is more complex; feldspar cores are An84–83, and olivines range from Fo77–67. The high level of the Cuillin complex suggests that there was insufficient room for a layered basic intrusion some 10,000 metres thick. Evidence is presented for successive pulses of ultrabasic magma, indicating that the complex as a whole comprises intrusions of tholeiitic affinity ranging broadly with time from ultrabasic to gabbroic, rather than a tectonically disrupted single, layered basic intrusion.
A Framework For Temporal Geographic Information

This paper defines the critical components of cartographic time and compares temporal and spatial topologies. Because time is topologically similar to space, spatial data structuring principles can be adapted to temporal data. We present three conceptualizations of temporal geographic information and select one as the most promising basis for a temporal geographic information system. This conceptualization creates a spatial composite of all geometric information (at all times), where each object has an attribute history distinct from that of its neighbors.
Simulations of the positioning accuracy of integrated vehicular navigation systems

The positioning performance of vehicular navigation systems based on a differential Global Position System (DGPS), dead-reckoning (DR), map matching (MM) and Kalman filter technologies are simulated. The vehicular navigation system using a 10-state extended Kalman filter to combine DGPS and DR can improve positioning accuracy. When DGPS signal obscuring occurs in the urban environment, DR with a map matching process can supplementally provide an accurate position for the vehicle. The simulation results of the paper can be used as a reference for the design, implementation and field tests of vehicular navigation systems.
Subtropical mode waters in the South Atlantic Ocean

This systematic study of the subtropical mode waters in the South Atlantic is based on hydrological data (the basin-wide South Atlantic Ventilation Experiment, Oceanus, and Ajax sections, and the World Ocean Circulation Experiment (WOCE) sections in the Brazil-Malvinas Confluence region), the WOCE expendable bathythermograph data set, and the atmospheric forcing produced by the National Centers for Environmental Prediction reanalysis. The main ventilation window of the subtropical gyre lies in the southwest and corresponds to the southern part of the recirculation region and to the overshoot of the Brazil Current (BC). Some ventilation occurs along the southern branch of the gyre through deep mixed layers in harsh winters and in the east through the rings shed by the Agulhas Current. However, the ventilation from the eastern border concerns a small volume of water with highly variable characteristics. Three main types of subtropical mode water are observed: the lightest around the 26.2 density surface and the second and third around the 26.5 and 26.7 density surfaces, respectively. The 26.2 subtropical mode water (STMW1) corresponds to potential temperatures between 16° and 18°C and salinities between 35.9 and 36.2. The STMW1 thickness does not exceed 150 m. The volume of the 26.5 mode water (STMW2) is larger. It is produced through the formation of deep mixed layers (reaching 300 m or more) in the active ventilation window over the BC overshoot. Its potential temperature ranges between 14° and 16°C, and its salinity ranges between 35.5 and 35.9. Its thickness can be above 300 m. The last component observed around the 26.7 density surface (STMW3) has a potential temperature between 12° and 14°C and a salinity of about 35.2 to 35.5. It is formed on the eastern flank of the BC overshoot and, during harsh winters, in the center of the southern branch of the gyre. Within the main ventilation window the STMWs exhibit quite a significant variability in characteristics and volume. There is a large interannual variability in the atmospheric forcing over the BC recirculation and BC extension, and the observed variations of the subtropical mode waters are qualitatively correlated to the atmospheric forcing variations.
The effects of malicious nodes on performance of mobile ad hoc networks

Wireless ad hoc networking offers convenient infrastructureless communication over the shared wireless channel. However, the nature of ad hoc networks makes them vulnerable to security attacks. Unlike their wired counterpart, infrastructureless ad hoc networks do not have a clear line of defense, their topology is dynamically changing, and every mobile node can receive messages from its neighbors and can be contacted by all other nodes in its neighborhood. This poses a great danger to network security if some nodes behave in a malicious manner. The immediate concern about the security in this type of networks is how to protect the network and the individual mobile nodes against malicious act of rogue nodes from within the network. This paper is concerned with security aspects of wireless ad hoc networks. We shall present results of simulation experiments on ad hoc network's performance in the presence of malicious nodes. We shall investigate two types of attacks and the consequences will be simulated and quantified in terms of loss of packets and other factors. The results show that network performance, in terms of successful packet delivery ratios, significantly deteriorates when malicious nodes act according to the defined misbehaving characteristics.
AVA analysis and geological dip estimation via two-way wave-equation based extended images

In this paper, we present an efficient way to compute extended images for all subsurface offsets without explicitly calculating the source and receiver wavefields for all the sources. Because the extended images contain all possible subsurface offsets, we compute the angle-domain image gathers by selecting the subsurface offset that is aligned with the local dip. We also propose a method to compute the local dip information directly from common-image-point gathers. To assess the quality of the angle-domain common-image-points gathers we compute the angle-dependent reflectivity coefficients and compare them with theoretical reflectivity coefficients yielded by the (linearized) Zoeppritz equations for a few synthetic models.
The Stability of Thermohaline Circulation in a Two-Box Model

Abstract In Stommel’s simple two-box model, which has provided an insight on the thermohaline circulation and climate instability mechanisms, a linear mass transport was used. However, a scaling law based on geostrophy and advective–diffusive heat balance suggests a nonlinear mass transport relation for the oceans. By including this nonlinear mass transport relation to Stommel’s box model, it is possible to study the effects of the thermocline, which was not considered before, on the stability of the thermohaline circulation while keeping the simplicity of Stommel’s box model. The results were compared with those obtained with the traditional model using a linear mass transport relation. The thermal mode circulation of the nonlinear model is significantly more stable than that of the linear model, suggesting the thermohaline catastrophe is less likely to occur in the present North Atlantic if the thermocline is considered. In the nonlinear model, the circulation removes density anomalies rapidly so that s.
Climate Modelers Struggle to Understand Global Warming

In the sweltering summer of 1988 the public heard claims that global warming from the greenhouse effect had definitely begun. In the chilly winter of 1989/90 they are hearing skeptics question whether it will ever arrive. Just as temperatures fluctuate about an average value, the mean opinion on global warming falls somewhere between these extremes.
A flower algorithm for autonomous star identification in space surveillance

The recent increase of space threats yields the idea of using the existing star trackers to perform surveillance of space objects from space. In the missions, due to the observer attitude dynamics, smearing affects the observed stars on the image in space surveillance. Besides, the reflecting flying space objects or debris as spurious stars affects the attitude determination. These are devastating for most star identification algorithms in star trackers. To resolve the problems, this paper defines a star pattern, called Flower code, which is composed of angular distances and circular angles as the characteristics of the pivot star. The angular distances are used for initial lookup table match. Moreover, the circular angles are used for the cyclic dynamic match between the sensor pattern and the pattern candidates from the initial match. The focus of the results is the evaluation of the influence of the reflecting flying spacecraft or debris as spurious stars and the attitude dynamics of the observer spacecraft, on the performance of the algorithms. A number of experiments are carried out on simulated images. The results demonstrated that the proposed method is efficient and robust.
Empirical age spectra for the lower tropical stratosphere from in situ observations of CO2: Implications for stratospheric transport

Empirical age spectra for the lower tropical stratosphere (from the tropopause to ∼19.5 km) have been derived from in situ measurements of CO 2 , using information provided by the vertical propagation of the tropospheric seasonal cycle and long-term positive trend. Our method provides accurate and unambiguous mean ages for this region which are difficult to obtain by simple analysis of lag times from tracer measurements. We find that the air is 30-40% younger in northern spring than in autumn. For example, at 460 K the mean age (relative to the tropical tropopause) was 0.4 years in March and 0.6 years in September. The phase lag times and attenuation of CO 2 seasonal extrema in the stratosphere are shown to depend on seasonal variations in transport rates and on the presence of harmonics in the CO 2 boundary condition with frequencies higher than 2π/yr. Profiles of stratospheric water vapor, generated from the derived age spectra with a stratospheric boundary condition based on observed tropical tropopause temperatures, are consistent with in situ observations of H 2 O. Comparison of the predicted water vapor seasonal cycle with satellite observations suggests that satellite-borne instruments underestimate the amplitude near the tropical tropopause. We relate the empirical age spectra to the analytic solution for the 1-D advection-diffusion tracer continuity equation to obtain seasonally resolved estimates of the ascent rate and the vertical diffusion coefficient. The derived age spectra provide a unique observation-based diagnostic for evaluating the simulation of tracer transport in models.