Miracle-dz/UniFAR-FTUs huggingface dataset:
Applying PUB to the real world: rapid data assessment

Abstract. "Predictions in Ungauged Basins" are a challenging task – especially when it comes to meso-scale rural catchments. We present a rapid data assessment scheme based on a functional perspective on the landscape for a hydrological land use decision support model. A hierarchical merging of top down and bottom up approaches combines hydrology, soil physics, agronomy and meteorology in a common nomenclature. The study at hand is an example to bring PUB to real world application.
Optimum multiparameter analysis of mixing in the thermocline of the eastern Indian Ocean

A method of water mass analysis is developed which optimizes the use of all information contained in a hydrographic data set by solving an overdetermined linear set of mixing equations. It requires representation of water masses by a finite number of water types and observations from at least as many oceanographic parameters as water types. The procedure to establish the water types, find the correct weights for the parameters, and solve the mixing equations through minimization of the residuals is described in detail. The method is applied to a data set from the eastern Indian Ocean, where Indian Central Water and Australasian Mediterranean Water meet to produce a strong front in the thermocline. It is shown that although most of the water from the Indonesian archipelago is carried westward north of 11°S, contributions from the Australasian Mediterranean Water are found as far south as 25°S, particularly along the Australian shelf as a result of advection with the Leeuwin Current.
A MODEL FOR THE THERMODYNAMIC GROWTH OF SEA ICE IN NUMERICAL INVESTIGATIONS OF CLIMATE

Abstract A model is presented whereby the thickness and extent of sea ice may be predicted in climate simulations. A basic one-dimensional diffusion process is taken to act in the ice, with modifications due to penetration of solar radiation, melting of internal brine pockets, and accumulation of an insulating snow cover. This formulation is similar to that of a previous study by Maykut and Untersteiner, but the introduction of a streamlined numerical method makes the model more suitable for use at each grid point of a coupled atmosphere-ocean model. In spite of its simplicity, the ice model accurately reproduces the results of Maykut and Untersteiner for a wide variety of environmental conditions. In 25 paired experiments, annual average equilibrium thicknesses of ice agree within 24 cm for 75% of the cases; and the average absolute error for all cases is 22 cm. The new model has fewer computational requirements than one layer of ocean in the polar regions, and it can be further simplified if additional .
The Pleistocene geology and geomorphology of three gaps in the Midland Jurassic escarpment

Previous literature is reviewed and field and laboratory methods are discussed in relation to four areas. The type area of the Itchen drainage basin reveals the composite nature of ice movement within one glacial period. Shallow facies deposits of glacial Lake Harrison have been located and a spillway into the Cherwell, associated with a lake bench at 410 ft. O. D. , is considered to have been cut after most of the Older Drift had been deposited. Morphological features and gravel deposits along the Cherwell are described and a tentative link established between the sequence on the Itchen and Avon and that published for the Lower Cherwell-Upper Thames. In the Moreton gap, deposits are related to the history of Lake Harrison. Clays were laid down during the advance of the ice in an ‘extra-morainic’ lake, while a lake bench is related to a later ‘inter-morainic’ lake. Possible gaps in the Daventry-Kilsby-Rugby area are obscured by thick drift but glacial spillways may formerly have existed. The evidence suggests several possible overflows from Lake Harrison during the ice advance. The lake ceased to exist when the ice-front reached Moreton-in-the-Marsh but was re-established during the subsequent retreat. At least two levels of ponding and two points of overflow occurred at this time, before damming was suddenly ended and erosion of the present landscape commenced. The sequence of events in Lake Harrison is related to the rivers Cherwell, Evenlode, Stour and Itchen and correlated with those established for the Upper Thames, the Severn-Avon, and other areas.
Alzheimer's disease neuroimaging

Purpose of review The aim of this study was to discuss the contribution of neuroimaging studies to our understanding of Alzheimer's disease. We now have the capability of measuring both tau and beta-amyloid (A&bgr;) proteins in the brain, which together with more traditional neuroimaging modalities, has led the field to focus on using neuroimaging to better characterize disease mechanisms underlying Alzheimer's disease. Recent findings Studies have utilized tau and A&bgr; PET, as well as [18F]fluorodeoxyglucose PET, and structural and functional MRI, to investigate the following topics: phenotypic variability in Alzheimer's disease , including how neuroimaging findings are related to clinical phenotype and age; multimodality analyses to investigate the relationships between different neuroimaging modalities and what that teaches us about disease mechanisms; disease staging by assessing neuroimaging changes in the very earliest phases of the disease in cognitively normal individuals and individuals carrying an autosomal dominant Alzheimer's disease mutation; and influence of other comorbidities and proteins to the disease process. Summary The findings shed light on the role of tau and A&bgr;, as well as age and other comorbidities, in the neurodegenerative process in Alzheimer's disease. This knowledge will be crucial in the development of better disease biomarkers and targeted therapeutic approaches.
Osmium abundance and isotope variations in mafic Mexican volcanic rocks: Evidence for crustal contamination and constraints on the geochemical behavior of osmium during partial melting and fractional crystallization

Primitive lavas and scoriae from the western Mexican Volcanic Belt (MVB) and the Mexican Basin and Range Province (MBRP) display a large range in Os concentrations and Os isotopes, with [Os] ranging from ∼10 to 320 ppt and 187Os/188Os ranging from ∼0.128 to 0.207. Os concentrations and Os isotopes are correlated with abundances of MgO and Ni and with other indices of fractional crystallization, indicating that Os behaved as a compatible element during fractional crystallization. The high oxygen fugacity of subduction‐related calc‐alkaline and lamprophyric magmas from the western MVB precludes significant sulfide fractionation. Therefore Os must be compatible in at least one phase other than sulfide (e.g., olivine and/or Cr‐spinel). The similarity of Os abundance trends in arc and nonarc suites suggests that Os concentrations are controlled primarily by equilibrium partitioning between melt with residual sulfide and silicate or oxide phases, and that DOs (sulfide/melt) is less than ∼2 × 105. Three chemically distinct Mexican volcanic suites, calc‐alkaline basalts and lamprophyres from the western MVB and intraplate‐type alkalic basalts from the MBRP, all display similar ranges in Os isotopes. Assimilation/fractional crystallization modeling suggests that the observed isotopic variations can be generated by minor (<12%) assimilation of Triassic age mafic lower crust. The least radiogenic samples still possess Os isotopes that are elevated relative to normal mantle peridotite. This difference may reflect variable input of radiogenic slab‐derived fluids or melts into the source region of the Mexican magmas, with the slab signature strongest in the lamprophyres and calc‐alkaline basalts and weakest in the intraplate‐type alkalic basalts. Correlations between Os isotopes and Os concentrations in other arc suites and mid‐ocean ridge basalts are unlikely to reflect mixing of distinct mantle components but instead reflect pervasive crustal (or seawater) contamination of magmas with low Os abundances.
Use of Antarctica for validating reflected solar radiation measured by satellite sensors

[1] A technique is presented for validating Sun-normalized radiances measured by polar orbiting sensors over Antarctica in the wavelength range 330–800 nm using model calculations for top of the atmosphere reflectances. An important input to these calculations is a model for the reflective properties of the snow surface, especially its directional nature. Details of this model are presented. Evaluations of the radiance calculations using OMI/Aura, MODIS/Aqua, and MISR/Terra data suggest that the surface representation is the largest source of uncertainty, representing ±1% in radiance at solar zenith angles less than 70°. Radiometric evaluations for limited wavelengths of MODIS, TOMS/Earth Probe, and OMI indicate that the first two are accurate to within the ±2% uncertainties in the technique. The OMI reflectances are lower than predictions by 2.5% to 8%, the smallest difference being near the nadir view and the largest at far off-nadir view angles. A time series of Antarctic 360 nm radiances measured by OMI from launch until 2007 is consistent with no change in sensor response in excess of 1%.
Sex-specific and lineage-specific alternative splicing in primates Material Supplemental

Material Supplemental http://genome.cshlp. org/content/suppl/2009/12/16/gr.099226. 109.DC1. html P<P Published online December 15, 2009 in advance of the print journal. Open Access Freely available online through the Genome Research Open Access option. service Email alerting click here top right corner of the article or Receive free email alerts when new articles cite this article sign up in the box at the
CIANOBACTÉRIAS EM ESTEIRAS MICROBIANAS COLOFORMES DA LAGOA PITANGUINHA, RIO DE JANEIRO, BRASIL

CYANOBACTERIA IN COLOFORM MICROBIAL MATS FROM THE PITANGUINHA LAGOON, RIO DE JANEIRO STATE, BRAZIL. This study aims the identification of the cyanobacteria that constitutes the coloform microbial mats find in the bottom of the Pitanguinha Lagoon, Massambaba shoal, in the municipality of Araruama, Rio de Janeiro state (coordinates 22 o
Involvement of Bruton’s Tyrosine Kinase in Fc (cid:101) RI-dependent Mast Cell Degranulation and Cytokine Production

Summary We investigated the role of Bruton’s tyrosine kinase (Btk) in Fc (cid:101) RI-dependent activation of mouse mast cells, using xid and btk null mutant mice. Unlike B cell development, mast cell development is apparently normal in these btk mutant mice. However, mast cells derived from these mice exhibited significant abnormalities in Fc (cid:101) primed monoclonal mildly diminished early-phase and blunted late-phase anaphylactic reactions in response to antigen challenge in this mast cells derived from the bone marrow cells of xid or null mild impairments in degranulation, profound defects in the production of several cytokines, upon Fc (cid:101) RI cross-linking. Moreover, the transcriptional activities of these cytokine genes were severely reduced in Fc (cid:101) RI-stimulated btk mutant mast cells. The specificity of these effects of btk mutations was confirmed by the improvement in the ability of btk mutant mast cells to degranulate and to secrete cytokines after the retroviral transfer of wild-type btk cDNA, but not of vector or kinase-dead btk cDNA. Retroviral transfer of Emt ( (cid:53) Itk/Tsk), Btk’s closest relative, also partially improved the ability of btk mutant mast cells to secrete mediators. Taken together, these results demonstrate an important role for Btk in the full expression of Fc (cid:101) RI signal transduction in mast cells.
Variations in NO y composition at Idaho Hill, Colorado

Measurements of NO y and the principal constituent NO y species (NO, NO 2 , PAN, HNO 3 , PPN, NO 3 -) were taken during the fall of 1993 at a high-elevation site in the Colorado mountains west of Boulder. The meteorology provided two principal flow regimes: strong westerly flow, bringing drier and cleaner air over the Continental Divide from the west where emission sources are sparse, and weaker easterly upslope flow which brought moist and more polluted air from the Denver-Boulder urban corridor and perhaps from smaller more local sources such as the mountain town of Nederland. The upslope flow data generally indicate a balance between measured NO y and the separately measured NO y species with NO x , PAN, and HNO 3 accounting for over 90%. Under these conditions, NO x was the dominant fraction of NO y , and occasionally fresh emissions were indicated as shown by NO x /NO y close to unity. For downslope flow there was generally a shortfall in the NO y balance where measured NO y was higher than the constituent species by about 20%, on average. Known potential interferences in the measurements do not appear to account for the NO y deficit. Missing NO y correlated directly with NO x /NO y , O 3 , and aerosols and inversely with temperature. These relationships suggest the presence of one or more NO y species that were not measured by the individual techniques.
Digitizing vanishing heritage in the MENA region: Case of Qatar

Traditional buildings in Qatar and the Gulf countries, in general, are parts and components of a series of Islamic building styles, which, indubitably have adopted some of the construction and architectural styles left by preceding civilizations. Compared to other areas of the Islamic world, there appears to be very little and scarce research about the traditional architecture of Qatar. It can be argued that Qatar's architecture is not representative of the whole of the Gulf, but it is believed that it provides a reasonable place to look at if for no other reason than that it might be later compared with the architecture of other areas of the MENA region. It is also important to document what is still there - and what can be remembered - as there is now a tremendous threat of disappearance of what is left from the Qatari traditional architecture. Rostron notes this in his work on Qatar changes and development; "Although the transformations accomplished in Qatar since 1995 are quite revolutionary in essenc.
Seasonal Distributions, and Risk Assessment of Polychlorinated Biphenyls (PCBs) in the Surficial Sediments from the Turag River, Dhaka, Bangladesh

11 Polychlorinated biphenyls (PCBs) assessment in sediments of Turag River, Dhaka, Bangladesh 12 has been conducted for the first time. This River provides critical ecological services to agriculture, 13 industry, and transportation. However, the Turag River is one of the most industrially polluted 14 rivers surrounding Dhaka in Bangladesh. In this study, six PCB congeners namely PCB 10, PCB 15 28, PCB 52, PCB 138, PCB 153, and PCB 180, were analyzed in surface sediments by GC-ECD 16 at 9 sampling sites. Pre-monsoon and post-monsoon season sampling were collected in this study. The total concentrations of PCBs varied from 344.49 to 0.22 ng/g dw and 10.6 to 1.68 ng/g dw in 18 pre-monsoon and post-monsoon, respectively. The paramount contributor congener to the total 19 PCBs was PCB 180 and was found at all sites. The ecological risk assessment indicated a high 20 potential risk in pre-monsoon ( � = 277.32) and low potential risk in post-monsoon ( = 25.69). Sediment quality guideline quotients (SQGQs) showed that PCBs in pre-monsoon would cause no 22 or moderate biological effects on organisms at most sampling sites except in surface sediments of site S5 (high biological effects), while no adverse ecotoxicological effect was observed in post- 24 monsoon. Considering both probable effect level (PEL) and threshold effect level (TEL), the new 25 sediment quality guideline quotient (NSQGQ) showed that in post-monsoon PCBs contamination 26 would cause moderate biological effects, while in pre-monsoon the findings remained consistent 27 with the findings of SQGQ. This study gave a quick look at the PCB contamination scenario in the 28 Turag River sediments and also allowed for a comparison between the investigated River and other 29 rivers worldwide. 30 31
Ultra-sensitive mutation detection and genome-wide DNA copy number reconstruction by error corrected circulating tumour DNA sequencing

Minimally invasive circulating free DNA (cfDNA) analysis can portray cancer genome landscapes but highly sensitive and specific genetic approaches are necessary to accurately detect mutations with often low variant frequencies. We developed a targeted cfDNA sequencing technology using novel off-the-shelf molecular barcodes for error correction, in combination with custom solution hybrid capture enrichment. Modelling based on cfDNA yields from 58 patients shows that our assay, which requires 25ng of cfDNA input, should be applicable to >95% of patients with metastatic colorectal cancer. Sequencing of a 163.3 kb target region including 32 genes detected 100% of single nucleotide variants with 0.15% variant frequency in cfDNA spike-in experiments. Molecular barcode error correction reduced false positive mutation calls by 98.6%. In a series of 28 patients with metastatic colorectal cancers, 80 out of 91 (88%) mutations previously detected by tumour tissue sequencing were called in the cfDNA. Call rates were similar for single nucleotide variants and small insertions/deletions. Mutations only called in cfDNA but not detectable in matched tumour tissue included, among others, a subclonal resistance driver mutation to anti-EGFR antibodies in the KRAS gene, multiple activating PIK3CA mutations in each of two patients (indicative of parallel evolution), and TP53 mutations originating from clonal haematopoiesis. Furthermore, we demonstrate that cfDNA off-target read analysis allows the reconstruction of genome wide copy number aberration profiles from 71% of these 28 cases. This error-corrected ultra-deep cfDNA sequencing assay with a target region that can be readily customized enables broad insights into cancer genomes and evolution.
Fuzzy contrast enhancement for images in the compressed domain

Our objective is to investigate image processing directly in the compressed domain, without full decompression. Compressed domain image processing algorithms provide a powerful computational alternative to classical (pixel level) based implementations. The field is just emerging and the algorithms reported in the literature are mostly based on linear arithmetic operations between pixels. In this paper, the problem of implementing a non- linear operator, using compressed domain processing is addressed. A new algorithm for digital image enhancement, using fuzzy theory, adapted to the frequency content of each coefficient block in the DCT (Discrete Cosine Transform) encoded JPEG image is developed and proposed.
Asian Jet Waveguide and a Downstream Extension of the North Atlantic Oscillation

Abstract Anomalous atmospheric fields associated with the North Atlantic Oscillation (NAO) are analyzed on interannual and intraseasonal time scales in order to examine the extent to which the NAO is a regional phenomenon. Analyses on the interannual time scale reveal that the NAO signal is relatively confined to the Euro–Atlantic sector in December while it extends toward East Asia and the North Pacific in February. The difference is most clearly seen in the meridional wind anomaly, which shows a wave train along the Asian jet, collocated with an anomalous vorticity source near the jet entrance. Diagnoses using a linear barotropic model indicate that this wave train is interpreted as quasi-stationary Rossby waves trapped on the Asian jet waveguide, and effectively excited by the anomalous upper-level convergence over the Mediterranean Sea. It is found that, when the NAO accompanies the Mediterranean convergence (MC) anomaly, most frequently seen in February, the NAO indeed has a much wider horizontal str.
Upper tropospheric drying and the “transition to break” in the Indian summer monsoon during 1999

METEOSAT pixel measurements reveal a striking new observation that rapid southward propagating deep clouds, on diurnal scale, are embedded in the northward migrating cloud structures from near equator upto 20N during active phases of 1999 summer monsoon. For the first time, we show that, “while the deep convection is on” during the active phase, an abrupt atmospheric drying occurs three days before the commencement of break in layers between 600 and 200 hPa over Continental Tropical Convergence Zone (CTCZ) with drastic reduction in Upper Tropospheric relative Humidity to ∼30%. East‐West circulation cells induce subsidence over CTCZ and hence upper tropospheric drying. Continued drying and simultaneous weakening of low level convergence by ∼50% causes the transition to break. Subsidence associated with intense convection near foot hills of Himalayas weakens low level convergence. A rapid shift occurs in divergence field during transition with convergence replacing intense divergence at upper levels over CTCZ.
Determinants of on-farm diversification: The case of farmers in Catalonia

En las ultimas decadas, el sector agricola y ganadero en Espana ha experimentado una disminucion de su contribucion al PIB y al empleo. Dado que la industria alimentaria y el mantenimiento de los recursos naturales en las zonas rurales dependen de las explotaciones agricolas y ganaderas,, es relevante analizar la diversificacion de las explotaciones agricolas como estrategia para aumentar sy rentabilidad y evitar su abandono. Este trabajo analiza los factores que explican la participacion en actividades de diversificacion en las explotaciones agricolas en Cataluna. Un modelo teorico explica las decisioens de asignacion del tiempo de los agricultores. El analisis empirico se realiza con una muestra de 3.435 explotaciones de la Encuesta sobre la Estructura de las Explotaciones Agricolas del 2007. Los resultados de un modelo logit evidencian que la ubicacion en zonas desfavorecidas y un bajo peso del sector primario en el PIB favorecen la diversificacion agricola. Las explotaciones que son propiedad de personas juridicas, la extension de la tierra cultivable y el margen bruto tambien afectan positivamente a la diversificacion. Las explotaciones dedicadas tanto a la agricultura extensiva como a la intensiva diversifican. Por ultumo, la formacion y edad del responsable de la explotacion influyen positiva y negativamente, respectivamente, en la diversificacion. In recent decades, the agriculture and livestock sector in Spain has experienced a decline in its contribution to GDP and employment. Since the food industry and the maintenance of natural resources in rural areas largely depend on agriculture and livestock farms, analising on-farm diversification as a strategy to increase profitability and to try to avoid their abandonment is a relevant issue. This paper explores the factors affecting participation by farmers in Catalonia in on-farm diversification activities. A theoretical model explains farmers' time allocation decisions. The analysis of the 2007 Farm Structural Survey with a sample size of 3,435 farms using a logit model reveals that location in disadvantage areas and a low weight of the primary sector in GDP encourage on-farm diversification. Holdings owned by legal persons, arable land size and gross margin also exhibit a positive impact on diversification. Holdings engaged in both extensive and intensive farming also carry out on-farm diversification. Finally, agricultural training and age of the farm manager positively and negatively influence diversification, respectively.