Miracle-dz/UniFAR-FTUs huggingface dataset:
Atmospheric carbon monoxide budget of the southern hemisphere: Implications of 13C/12C measurements

A large seasonal cycle has been observed in the 13C/12C isotopic ratio of CO in clean air in the extratropical southern hemisphere. This ratio is determined by the mixture of CO from isotopically distinct sources and is strongly influenced by the relative contributions of surface sources and the oxidation of CH4. We use a zonally averaged atmospheric model to relate atmospheric CO mixing ratios and 13C/12C isotopic ratios to the magnitude and distribution of CO sources and to explain the average seasonal cycles observed. The average 13C/12C ratio of CO emitted by surface sources in the southern hemisphere is larger than in the northern hemisphere and the southward flux of CO into the extratropical southern hemisphere is additionally enriched in 13C as a result of oxidation during transport. These effects partially offset the effect of highly depleted 13C/12C ratios in CO produced by CH4 oxidation. In the extratropical southern hemisphere, seasonal variation in the fraction of atmospheric CO derived from CH4 oxidation produces large changes in 13C/12 C which are partially offset by seasonal variations of surface sources. A good fit to observed average cycles can be obtained using surface source strengths consistent with previous estimates. However, the southern hemisphere data place strong constraints on the CH4 oxidation source and imply that either the CO yield per molecule of CH4 is about 0.7, compared with previous estimates of around 0.8, or that unidentified processes associated with CH4 oxidation cause 13C enrichment of about 4‰ in the CO produced.
The minimized dead‐end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles

One of the main challenges for protein redesign is the efficient evaluation of a combinatorial number of candidate structures. The modeling of protein flexibility, typically by using a rotamer library of commonly‐observed low‐energy side‐chain conformations, further increases the complexity of the redesign problem. A dominant algorithm for protein redesign is dead‐end elimination (DEE), which prunes the majority of candidate conformations by eliminating rigid rotamers that provably are not part of the global minimum energy conformation (GMEC). The identified GMEC consists of rigid rotamers (i.e., rotamers that have not been energy‐minimized) and is thus referred to as the rigid‐GMEC. As a postprocessing step, the conformations that survive DEE may be energy‐minimized. When energy minimization is performed after pruning with DEE, the combined protein design process becomes heuristic, and is no longer provably accurate: a conformation that is pruned using rigid‐rotamer energies may subsequently minimize to a lower energy than the rigid‐GMEC. That is, the rigid‐GMEC and the conformation with the lowest energy among all energy‐minimized conformations (the minimized‐GMEC) are likely to be different. While the traditional DEE algorithm succeeds in not pruning rotamers that are part of the rigid‐GMEC, it makes no guarantees regarding the identification of the minimized‐GMEC. In this paper we derive a novel, provable, and efficient DEE‐like algorithm, called minimized‐DEE (MinDEE), that guarantees that rotamers belonging to the minimized‐GMEC will not be pruned, while still pruning a combinatorial number of conformations. We show that MinDEE is useful not only in identifying the minimized‐GMEC, but also as a filter in an ensemble‐based scoring and search algorithm for protein redesign that exploits energy‐minimized conformations. We compare our results both to our previous computational predictions of protein designs and to biological activity assays of predicted protein mutants. Our provable and efficient minimized‐DEE algorithm is applicable in protein redesign, protein‐ligand binding prediction, and computer‐aided drug design. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008
Distribution of alteration zones in the upper oceanic crust

Aging of the upper oceanic crust produces alteration zones that have distinct mineralogical and geochemical characteristics. Five zones are recognized in the Troodos ophiolite and in situ oceanic crust: (1) a sea-floor weathering zone (SWZ), (2) a low-temperature zone (LTZ), (3) a transition zone (TZ), (4) an upper dike zone (UDZ), and (5) a mineralized zone (MZ). The MZ may be overlain by the SWZ, LTZ, or TZ, but in the known examples it is always underlain by the UDZ. The development of the SWZ is dependent upon the duration of cold-seawater circulation, which is dependent upon seafloor topography and the rate and nature of sedimentation. The boundary between the low- and high-temperature zones is largely controlled by permeability contrasts. Lateral variation in the depth of this boundary indicates that the thermal gradient is not uniform within the crust. This, along with the evidence for disequilibrium assemblages, implies that regional metamorphic zones are not appropriate to describe the distribution of alteration effects.
Onset of North Atlantic Deep Water production coincident with inception of the Cenozoic global cooling trend

Here we show that the onset of deep water overflow from the Norwegian-Greenland Sea into the North Atlantic, interpreted to represent the onset of a modern-style North Atlantic Deep Water mass, commenced close to the early to middle Eocene boundary. This finding is based on the identification of a large, elongate contourite sediment drift, the “Judd Falls Drift,” in the Faeroe-Shetland Basin, through detailed mapping of high-resolution two-dimensional and three-dimensional seismic data. This sediment drift covers an area of ∼9000 km2 in one of the critical present-day deep water gateways into the North Atlantic Ocean. Interpretation of the body as a contourite drift is based on standard seismic-stratigraphic diagnostic criteria including tridirectional onlap, lensoid sediment geometry, upslope progradational configurations of stacked onlap units, and an erosional base cut in a deepwater setting. The internal reflection configuration indicates that the drift was deposited under a southwest-flowing current regime, which we propose represents the onset of North Atlantic Deep Water production, with continual deep water flow until at least the latest Eocene (ca. 35 million years ago [Ma]). Onset of drift deposition is dated by several key boreholes as occurring at ca. 50–49 Ma, across the early to middle Eocene boundary, and is coincident with independent geochemical evidence for major changes in the configuration of deep-sea circulation patterns, global biological production, and the onset of Cenozoic climatic cooling. These temporal concurrences suggest a strong link between the initiation of North Atlantic Deep Water production and Cenozoic global climate evolution.
Growth related zonations in authigenic and hydrothermal quartz characterized by SIMS-, EPMA-, SEM-CL- and SEM-CC-imaging

Abstract Authigenic quartz overgrowths and hydrothermal quartz crystals from locations in Oman and Switzerland have been investigated with SIMS, EPMA, SEM-CL and SEM-CC. All techniques reveal similar zonation patterns with SEM-CL having the best resolution followed by SEM-CC, EPMA and finally SIMS. The observed zonations reflect chemical and/or physical changes during growth in the precipitation environment or disequilibrium precipitation at the crystal surface (i.e. sectoral and intrasectoral zonation). Based on the total Al content, two types of authigenic quartz are distinguishable. When the Al concentration is <500 μg g-1, the predominant CL emission is at ~630 nm; in such quartzes, SEM-CL and SEM-CC are directly correlated, and signal intensities drop as a function of increasing Al concentration. In contrast, authigenic quartz with Al concentrations between 500 μg g-1 and 1000 μg g-1 has CL emission maxima at both ~630 nm and ~380-400 nm, at which point the panchromatic SEM-CL and SEM-CC intensities become decoupled.
Modal structure of chemical mass size distribution in the high Arctic aerosol

Chemical mass size distributions of aerosol particles were measured in the remote marine boundary layer over the central Arctic Ocean as part of the Atmospheric Research Program on the Arctic Ocean Expedition 1996 (AOE-96). An inertial impaction method was used to classify aerosol particles into different size classes for subsequent chemical analysis. The particle chemical composition was determined by ion chromatography and by the particle-induced X-ray emission technique. Continuous particle size spectra were extracted from the raw data using a data inversion method. Clear and varying modal structures for aerosols consisting of primary sea-salt particles or of secondary particles related to dimethyl sulfide emissions were found. Concentration levels of all modes decreased rapidly when the distance from open sea increased. In the submicrometer size range the major ions found by ion chromatography were sulfate, methane sulfonate, and ammonium. They had most of the time a clear Aitken mode and one or two accumulation modes, with aerodynamic mass median diameters around 0.1 μm, 0.3 μm, and between 0.5-1.0 μm, respectively. The overall submicron size distributions of these three ions were quite similar, suggesting that they were internally mixed over most of this size range. The corresponding modal structure was consistent with the mass size distributions derived from the particle number size distributions measured with a differential mobility particle sizer. The Aitken to accumulation mode mass ratio for nss-sulfate and MSA was substantially higher during clear skies than during cloudy periods. Primary sea-salt particles formed a mode with an aerodynamic mass median diameter around 2 μm. In general, the resulting continuous mass size distributions displayed a clear modal structure consistent with our understanding of the two known major source mechanisms. One is the sea-salt aerosol emerging from seawater by bubble bursting. The other is related to dimethylsulfide (DMS) emissions from biogenic processes in seawater, followed by gas-to-particle conversion, formation of particulate sulfate and methane sulfonate (MSA) and neutralization by ammonia.
High‐resolution climate simulations with COSMO‐CLM over Italy: performance evaluation and climate projections for the 21st century

This study presents the results of dynamically downscaled climate simulations over Italy produced with the COSMO‐CLM model. Three simulations forced by ERA‐Interim Reanalysis were conducted respectively at a spatial resolution of 0.22°, 0.125° and 0.0715° over the period 1979–2011. The results were analysed in terms of 2‐m temperature and precipitation with the aim of assessing the model's ability to reproduce these important features of the Italian climate. The results were validated by comparing model output with different independent observational datasets. Values of temperature and precipitation show a general good agreement with observations, with a fair reduction of errors in all seasons as the resolution is increased. Two simulations at a spatial resolution of 0.0715°, driven by the global model CMCC‐CM, were performed over the period 1971–2100, employing the IPCC RCP4.5 and RCP8.5 scenarios. Climate projections show a significant warming expected in Italy at the end of the 21st century, along with a general reduction in precipitation, particularly evident in spring and summer.
ELEMENTOS INTERFERENTES NA QUALIDADE DA ÁGUA PARA IRRIGAÇÃO

For the development of agriculture in the world, water is a natural resource of greater relevance, since new technologies to increase productivity of agricultural areas are dependent on their availability. This importance is reflected in the high productivity of irrigated areas, where only 18% of the total agricultural areas account for approximately 40% of global agricultural production. The objective of this study was, by means of a literature review, evaluate and discuss some of the main types of water used and attributes that can affect the quality of water for irrigation. It was concluded that the use of lower quality water, such as wastewater or stillage, is an alternative to meet the high demand for water in relation to low supply. But for this, one must have a knowledge of the main attributes that pose interfere with the quality of water for irrigation, and
LLNL‐G3Dv3: Global P wave tomography model for improved regional and teleseismic travel time prediction

[ 1 ] We develop a global-scale P wave velocity model (LLNL-G3Dv3) designed to accurately predict seismic travel times at regional and teleseismic distances simultaneously. The model provides a new image of Earth ’ s interior, but the underlying practical purpose of the model is to provide enhanced seismic event location capabilities. The LLNL-G3Dv3 model is based on (cid:1) 2.8 million P and Pn arrivals that are re-processed using our global multiple-event locator called Bayesloc. We construct LLNL-G3Dv3 within a spherical tessellation based framework, allowing for explicit representation of undulating and discontinuous layers including the crust and transition zone layers. Using a multiscale inversion technique, regional trends as well as fine details are captured where the data allow. LLNL-G3Dv3 exhibits large-scale structures including cratons and superplumes as well numerous complex details in the upper mantle including within the transition zone. Particularly, the model reveals new details of a vast network of subducted slabs trapped within the transition beneath much of Eurasia, including beneath the Tibetan Plateau. We demonstrate the impact of Bayesloc multiple-event location on the resulting tomographic images through comparison with images produced without the benefit of multiple-event constraints (single-event locations). We find that the multiple-event locations allow for better reconciliation of the large set of direct P phases recorded at 0 – 97 (cid:3) distance and yield a smoother and more continuous image relative to the single-event locations. Travel times predicted from a 3-D model are also found to be strongly influenced by the initial locations of the input data, even when an iterative inversion/relocation technique is employed.
A micromorphological record of contemporary and relict pedogenic processes in soils of the Indo‐Gangetic Plains: implications for mineral weathering, provenance and climatic changes

Micromorphology has important application in earth surface process and landform studies particularly in alluvial settings such as the Indo‐Gangetic Plains (IGP) with different geomorphic surfaces to identify climatic changes and neotectonic events and their influence on pedogenesis. The soils of the IGP extending from arid upland in the west to per humid deltaic plains in the east developed on five geomorphic surfaces namely QIG1 to QIG5 originating during the last 13.5 ka. Four soil‐geomorphic systems across the entire IGP are identified as: (i) the western Yamuna Plains/Uplands, (ii) the Yamuna‐Ganga Interfluve, (iii) the Ganga‐Ghaghara Interfluve, and (iv) the Deltaic Plains.
A coupled model of the global cycles of carbonyl sulfide and CO2: A possible new window on the carbon cycle

Carbonyl sulfide (COS) is an atmospheric trace gas that participates in some key reactions of the carbon cycle and thus holds great promise for studies of carbon cycle processes. Global monitoring networks and atmospheric sampling programs provide concurrent data on COS and CO2 concentrations in the free troposphere and atmospheric boundary layer over vegetated areas. Here we present a modeling framework for interpreting these data and illustrate what COS measurements might tell us about carbon cycle processes. We implemented mechanistic and empirical descriptions of leaf and soil COS uptake into a global carbon cycle model (SiB 3) to obtain new estimates of the COS land flux. We then introduced these revised boundary conditions to an atmospheric transport model (Parameterized Chemical Transport Model) to simulate the variations in the concentration of COS and CO2 in the global atmosphere. To balance the threefold increase in the global vegetation sink relative to the previous baseline estimate, we propose a new ocean COS source. Using a simple inversion approach, we optimized the latitudinal distribution of this ocean source and found that it is concentrated in the tropics. The new model is capable of reproducing the seasonal variation in atmospheric concentration at most background atmospheric sites. The model also reproduces the observed large vertical gradients in COS between the boundary layer and free troposphere. Using a simulation experiment, we demonstrate that comparing drawdown of CO2 with COS could provide additional constraints on differential responses of photosynthesis and respiration to environmental forcing. The separation of these two distinct processes is essential to understand the carbon cycle components for improved prediction of future responses of the terrestrial biosphere to changing environmental conditions.
Liaison Psychiatry

Konziliární psychiatrie se zabývá diagnostikou a léčbou duševních onemocnění u somaticky nemocných pacientů. Duševní stav zapříčiněný psychiatrickým nebo somatickým onemocněním je v řadě případů obtížné zhodnotit nejen pro psychiatry, ale i pro somatické lékaře, kteří mohou bagatelizovat nebo opominout příznaky duševního onemocnění. Nedostatečná léčba duševních onemocnění u somaticky nemocných pacientů zvyšuje morbiditu a mortalitu pacientů.
Spatial variability in the flood vulnerability of urban areas in the headwater basins of Slovakia

In the new paradigm of flood defence, the control of flooding by technical means is supported by an emphasis on the reduction of vulnerability to flooding by economic, social and environmental means. The aim of the present work was to assess the vulnerability of basic urban units (BUUs) located in the headwater basins of Slovakia. Vulnerability was expressed in terms of proxy variables. Using a combination of these variables, specific indices were established. These indices represented the potential for susceptibility to damage, resistance to flooding and resilience after flooding of the social and economic systems in these BUUs. The assessment of vulnerability was based on an application of the multi‐atribute decision‐making approach. The overall vulnerability of a BUU was calculated via a summation of the specific vulnerability indices. Using visualisation in GIS, the BUUs were grouped into three classes, of low, medium and high vulnerability. Second, evaluation of BUUs from the point of view of expected negative consequences of flooding was done.
Microbiological risk assessment in feedingstuffs for food-producing animals 1 Scientific Opinion of the Panel on Biological Hazards

SUMMARY Following a request from the Health and Consumer Protection, Directorate General, European Commission, the Panel on Biological Hazards was asked to deliver a scientific opinion on Microbiological Risk Assessment in feedingstuffs for food-producing animals for both public health and animal health. In accordance with the terms of reference, this report does not consider hazards such as BSE/TSE agents, parasites and virus, or contamination by fungi and mycotoxins.
Atrazine persistence and toxicity in two irrigated soils of Australia

The persistence of atrazine in two contrasting irrigated soils from the Riverine Plain of south-eastern Australia was measured in the laboratory at three constant temperatures. Particularly at lower temperatures atrazine was more persistent, by an order of magnitude, than reported for soils overseas; but in two successive field experiments, encompassing both surface and incorporated applications of atrazine in the heavier soil, residues measured after about 7 months were within the range expected from the literature. The measured residues were 2-6 times smaller than predicted using a simulation model, probably reflecting volatilization and other losses which are not included in the model, but which are expected to be substantial at the extremely high soil surface temperatures observed in the field. Comparative measurements of aged residues in the heavy clay soil showed higher results from chemical analysis of acetonitrile-water soil extracts than by in situ glasshouse bioassay using oats and turnips, demonstrating that only one third of the extractable residue was available to crops. Comparison of soil-based and hydroponic assay using soybeans showed that this soil reduced the effective atrazine concentration in solution by at least 16-fold, but sensitive crops could still be damaged when grown in rotation after tolerant crops, or if irrigated with contaminated water.
Forcing of Tropical SST Anomalies by Wintertime AO-like Variability

Abstract A lagged maximum covariance analysis (MCA) is utilized to investigate large-scale patterns of covariability between sea surface temperature (SST) in the global tropics and 500-mb geopotential height (Z500) in the extratropics at monthly to interannual time scales distinct from the conventional El Nino–Southern Oscillation (ENSO) signal during the Northern Hemisphere (NH) winter. The first MCA mode indicates a strong impact of tropical SST anomalies associated with ENSO on the extratropical atmosphere. The second MCA mode corresponds with coupling between Arctic Oscillation (AO)-like atmospheric variations and tropical SST anomalies. An AO-like MCA mode appears to depict an atmosphere-to-ocean forcing, in which the tropical ocean responds to the higher extratropical AO-like atmospheric anomalies with an intraseasonal time lag. In winter, AO-like atmospheric variability is associated with the northern tropical Atlantic mode and the tropical Pacific ENSO Modoki mode through enhanced or weakened trad.
Reliance on Episodic vs. Procedural Systems in Decision-Making Depends on Individual Differences in Their Relative Neural Efficiency

Experiential decision-making can be explained as a result of either memory-based or reinforcement-based processes. Here, for the first time, we show that individual preferences between a memory-based and a reinforcement-based strategy, even when the two are functionally equivalent in terms of expected payoff, are adaptively shaped by individual differences in resting-state brain connectivity between the corresponding brain regions. Using computational cognitive models to identify which mechanism was most likely used by each participant, we found that individuals with comparatively stronger connectivity between memory regions prefer a memory-based strategy, while individuals with comparatively stronger connectivity between sensorimotor and habit-formation regions preferentially rely on a reinforcement-based strategy. These results suggest that human decision-making is adaptive and sensitive to the neural costs associated with different strategies.