Miracle-dz/UniFAR-FTUs huggingface dataset:
Is the number of Antarctic icebergs really increasing

Icebergs released from the ice shelves and glaciers of Antarctica account for the majority of the continent's freshwater flux into the ocean. It is estimated that an average of nearly 2000 km3 [Jacobs et al., 1992] of ice are released from continental ice shelves and glaciers each year. Much of this ice is released in the form of very large icebergs, some of which are as large as 295 km×37 km. A recent article by Bindschadler and Rignot [2001] notes that the number of icebergs around Antarctica appears to be on the rise, potentially heralding a climate trend. Examination of the National Ice Center (NIC) Antarctic iceberg data base tends to support the observation of an increase in the number of icebergs. Further driving the concern is the size of recently calves icebergs such as the largest ever observed, B15 measuring 295 km×37 km, which calved from the Ross Ice Shelf in March 2000.
Recycling of protein subunits during DNA translocation and cleavage by Type I restriction-modification enzymes

The Type I restriction-modification enzymes comprise three protein subunits; HsdS and HsdM that form a methyltransferase (MTase) and HsdR that associates with the MTase and catalyses Adenosine-5′-triphosphate (ATP)-dependent DNA translocation and cleavage. Here, we examine whether the MTase and HsdR components can ‘turnover’ in vitro, i.e. whether they can catalyse translocation and cleavage events on one DNA molecule, dissociate and then re-bind a second DNA molecule. Translocation termination by both EcoKI and EcoR124I leads to HsdR dissociation from linear DNA but not from circular DNA. Following DNA cleavage, the HsdR subunits appear unable to dissociate even though the DNA is linear, suggesting a tight interaction with the cleaved product. The MTases of EcoKI and EcoAI can dissociate from DNA following either translocation or cleavage and can initiate reactions on new DNA molecules as long as free HsdR molecules are available. In contrast, the MTase of EcoR124I does not turnover and additional cleavage of circular DNA is not observed by inclusion of RecBCD, a helicase–nuclease that degrades the linear DNA product resulting from Type I cleavage. Roles for Type I restriction endonuclease subunit dynamics in restriction alleviation in the cell are discussed.
A tephrostratigraphic record for the last glacial–interglacial cycle from Lake Ohrid, Albania and Macedonia

Here we present a tephrostratigraphic record (core Co1202) recovered from the northeastern part of Lake Ohrid (Republics of Macedonia and Albania) reaching back to Marine Isotope Stage (MIS) 6. Overall ten horizons (OT0702‐1 to OT0702‐10) containing volcanic tephra have been recognised throughout the 14.94 m long sediment succession. Four tephra layers were visible at macroscopic inspection (OT0702‐4, OT0702‐6, OT0702‐8 and OT0702‐9), while the remaining six are cryptotephras (OT0702‐1, OT0702‐2, OT0702‐3, OT0702‐5, OT0702‐7 and OT0702‐10) identified from peaks in K, Zr and Sr intensities, magnetic susceptibility measurements, and washing and sieving of the sediments. Glass shards of tephra layers and cryptotephras were analysed with respect to their major element composition, and correlated to explosive eruptions of Italian volcanoes. The stratigraphy and the major element composition of tephra layers and cryptotephras allowed the correlation of OT0702‐1 to AD 472 or AD 512 eruptions of Somma‐Vesuvius, OT0702‐2 to the FL eruption of Mount Etna, OT0702‐3 to the Mercato from Somma‐Vesuvius, OT0702‐4 to SMP1‐e/Y‐3 eruption from the Campi Flegrei caldera, OT0702‐5 to the Codola eruption (Somma‐Vesuvius or Campi Flegrei), OT0702‐6 to the Campanian Ignimbrite/Y‐5 from the Campi Flegrei caldera, OT0702‐7 to the Green Tuff/Y‐6 eruption from Pantelleria Island, OT0702‐8 to the X‐5 eruption probably originating from the Campi Flegrei caldera, OT0702‐9 to the X‐6 eruption of generic Campanian origin, and OT0702‐10 to the P‐11 eruption from Pantelleria Island. The fairly well‐known ages of these tephra layers and parent eruptions provide new data on the dispersal and deposition of these tephras and, furthermore, allow the establishment of a chronological framework for core Co1202 for a first interpretation of major sedimentological changes. Copyright © 2009 John Wiley & Sons, Ltd.
Assimilating Doppler radar radial velocity and reflectivity observations in the weather research and forecasting model by a proper orthogonal-decomposition-based ensemble, three-dimensional variational assimilation method

[1] Doppler radar observations with high spatial and temporal resolution can effectively improve the description of small-scale structures in the initial condition and enhance the mesoscale and microscale model skills of numerical weather prediction (NWP). In this paper, Doppler radar radial velocity and reflectivity are simultaneously assimilated into a weather research and forecasting (WRF) model by a proper orthogonal-decomposition-based ensemble, three-dimensional variational assimilation method (referred to as PODEn3DVar), which therefore forms the PODEn3DVar-based radar assimilation system (referred to as WRF-PODEn3DVar). The main advantages of WRF-PODEn3DVar over the standard WRF-3DVar are that (1) the PODEn3DVar provides flow-dependent covariances through the evolving ensemble of short-range forecasts, and (2) the PODEn3DVar analysis can be obtained directly without an iterative process, which significantly simplifies the assimilation. Results from real data assimilation experiments with the WRF model show that WRF-PODEn3DVar simulation yields better rainfall forecasting than radar retrieval, and radar retrieval is better than the standard WRF-3DVar assimilation, probably because of the flow-dependence character embedded in the WRF-PODEn3DVar.
Hydrogeological modeling of Northern Ireland drumlins in three dimensions

ii ACKNOWLEDGEMENTS . iv 1.0 Introduction . 1 1.1 Research Objectives . 2 2.0 Literature Review . 4 2.1 Irish Climate . 6 2.2 Bedrock Geology of Northern Ireland . 8 2.3 Characteristics of Glacial Till . 10 2.4 Hydrogeology of Northern Ireland Drumlins . 14 2.5 Hydrogeological Modeling . 16 3.0 Materials and Methods . 18 3.1 Study Sites . 18 3.1.1 Craigmore, Newry, County Down. 19 3.1. 2 Loughbrickland, County Down . 23 3.1. 3 Soil Testing . 27 3.1. 4 Laboratory Testing . 29 3.1. 5 Seismic Refraction Surveys . 31 3.2 Model Development . 33 3.2.1 Model Geometry . 34 3.2.2 Mesh Development . 35 3.2.3 Boundary Conditions . 36
Application of spaceborne scatterometer to study typhoon, tropical hydrologic balance, and El Niño

The high spatial resolution and global coverage of a spaceborne microwave scatterometer make it a powerful instrument to study phenomena ranging from typhoons to El Nino Southern Oscillations which have regional and short term economic and ecological impacts as well as effects on long term and global climate changes. In this report, the application of scatterometer data, by itself, to study the intensity and the evolution of a typhoon is demonstrated. The potential of combining wind vector and precipitable water derived from two spaceborne sensors to study the hydrologic balance in the tropics is discussed. The role of westerly wind bursts as a precursor of anomalous warming in the equatorial Pacific is investigated with coincident data from microwave scatterometer, altimeter, and radiometer.
Trends in extreme mean sea level pressure and their characteristics during the summer monsoon season over the Indian region

Using daily National Centers for Environmental Prediction/National Center for Atmospheric Research (NCEP/NCAR) (1948–2009) and European Centre for Medium-Range Weather Forecasts (ECMWF) ReAnalyses (ERA)-40 (1958–2001) reanalysis mean sea level pressure (MSLP) data, the frequencies in the extremes of low/high MSLP days were computed with the 10th and 90th percentiles during the summer monsoon season (June–September) over 11 zones of India, the Arabian Sea, the Bay of Bengal and all-India as a whole. We observed that the trends in the frequencies of high (low) MSLP days are increasing (decreasing), indicating a increase/decrease in anticyclonic/cyclonic activities, respectively, which affect the monsoon performance over the Indian region. The decreasing (increasing) tendency of the frequency of the low (high) MSLP days suggests a consistency between the extreme MSLP and its associated rainfall activities. The frequency of the high MSLP days over India is highly correlated negatively with the Indian summer monsoon rainfall (ISMR). The linear trends in the frequencies of the extreme low/high MSLP days for different zones and all-India are found to be highly significant (at the 0.1% level and above). After 1978, the trends in the series of low/high MSLP days are found to be more towards decreasing/increasing tendencies, respectively, whereas the frequencies of low MSLP days are much higher than those of high MSLP days during the late 1970s. The same characteristics were also evidenced from the analysis based on ECMWF ERA-40 data for the period 1958–2001. The possible causes of this may be El Niño events, greenhouse gases (GHGs), unprecedented surface warming and also tropospheric cooling trends during recent decades over the northern hemisphere as well as over the Indian region and major volcanic eruptions that occurred during the period 1978–2009.
Frequency Response Properties of Forced Climatic SST Anomaly Variability in the North Atlantic

Abstract Frequency response properties of North Atlantic (5°–57°N) sea surface temperature anomaly (Tsa) variability with periods of several months to 20 years are characterized using the Comprehensive Ocean-Atmosphere Data Set (COADS). Significant direct forcing of Tsa variability by the anomalous wind field (primarily through the resulting anomalous surface turbulent heat flux) is observed in the westerly wind and trade wind belts. To characterize properties of the large-scale climatic Tsa response to this forcing over the entire frequency band resolved, it is necessary to consider the dual role of anomalous surface heat flux as both the dominant local forcing mechanism and the dominant damping mechanism, the latter through a negative linear feedback (Newtonian relaxation). At frequencies where wind forcing is important, good agreement exists between the frequency response function estimated from data and the same function theoretically predicted by a simple stochastic forcing model where the locally fo.
Hydrologic Factors Affecting Initial Willow Seedling Establishment along a Subalpine Stream, Colorado, U.S.A

Abstract Willows (Salix spp.) are important riparian plants along high elevation streams of western North America, but the hydrologic conditions needed for initial recruitment are not well defined. A replicated plot experiment was used to determine the effects of (1) elevation above the stream (high, middle, or low), (2) soil texture (sand or gravel), (3) watering to simulate additional rainfall, and (4) an upstream water diversion on soil water content and first-year willow seedling survival along a subalpine reach of the Colorado River. Soil water content varied with elevation (F = 163.8, p < 0.001) and soil texture (F = 387.3, p < 0.001), while the effect of the watering treatment was not statistically significant. Soil water content controlled first-year willow seedling survival (r2 = 0.257, p = 0.002), and no seedlings were found in plots with a mean soil water content of less than 15%. Sandy sites near the river elevation provide the optimal conditions for initial establishment of willows along this and other subalpine streams in the semiarid western United States. Potential establishment sites occur along abandoned channels and in drained beaver ponds, and creation of these sites depends on the occurrence of high flows. Therefore, as at lower elevation, cottonwood-dominated systems, maintenance of a flow regime that includes periodic high flows is essential for sustaining willow establishment along subalpine streams. The upstream diversion reduced the stream stage by up to 13 cm during the growing season, resulting in a similar decline in the water table level and a reduction of up to 15% in plot soil water content. Since seedling survival depends on the availability of soil water, water diversions may adversely affect willow establishment along subalpine streams.
The Pelican Thrust Zone: basal detachment between the Archean Sask Craton and Paleoproterozoic Flin Flon – Glennie Complex, western Trans-Hudson Orogen,

The Pelican Thrust Zone is a 3-7 km-wide recrystallized mylonite zone, along which Paleoproterozoic arc volcano-plutonic and derived sedimentary rocks of the Flin Flon - Glennie Complex were thrust over an Archean package (Jan Lake Complex) consisting of ca. 3.1 Ga calc-alkaline orthogneisses, pelitic migmatites, and a ca. 2.45 Ga tholeiitic charnockite-norite intrusive suite. A regional northeast-plunging stretching lineation and a variety of kinematic indicators imply southwesterly transport, matching that of other coeval shallower crustal-level structures observed throughout the northern Flin Flon Domain and southern flank of the Kisseynew Domain (e.g., Sturgeon-Weir and Annabel Lake shear zones). Subsequent east-side-up displacement on the Tabbernor Fault, together with domal fold interference, has exposed the Pelican Window and mantling mylonite zone, where it has been seismically profiled along Lithoprobe transects. Tectonic windows also expose Archean rocks in the Glennie Domain to the west, where similar southwest-verging, recrystallized mylonite zones have been documented. Together, these zones record collision and underplating of the Flin Flon - Glennie Complex by the Archean Sask Craton during prolonged protocontinent-continent collision over a minimum 1826-1805 Ma interval. Resume : La zone de chevauchement Pelican est une zone de mylonite recristallisee, d'une largeur de 3-7 km, le long de laquelle des roches volcano-plutoniques d'un arc datant du Paleoproterozoique et des roches sedimentaires derivees du complexe de Flin Flon - Glennie ont ete chevauchees par-dessus un ensemble archeen (le complexe de Jan Lake) qui est compose d'orthogneiss calco-alcalins et de migmatites pelitiques (âgees d'environ 3,1 Ga) ainsi que d'une suite intrusive charnockite-norite tholeiitique (âgee d'environ 2,45 Ga). Une lineation regionale d'etirement, a pendage nord-est et divers indicateurs cinematiques correspondent a un transport vers le sud-ouest, rejoignant celui d'autres structures contemporaines de niveaux crustaux moins profonds observees a travers tout le domaine de Flin Flon nord et le flanc sud du domaine Kisseynew (p. ex. les zones de cisaillement de Sturgeon-Weir et d'Annabel Lake). Un deplacement subsequent, le cote est vers le haut, le long de la faille de Tabbernor, avec une interference de plis de dome, a fait affleurer la fenetre Pelican et la zone mylonitique qui la recouvre; elle a ete determinee par des profils sismiques le long des transects Lithoprobe. Des fenetres tectoniques permettent aussi l'affleurement de roches archeennes du do- maine de Glennie, vers l'ouest, la ou ont ete documentees des zones semblables de mylonites recristallisees a pendage sud-ouest. Ensemble, ces zones enregistrent la collision et le sous-placage du complexe de Flin Flon - Glennie par le craton archeen Sask au cours d'une collision prolongee entre le protocontinent et le continent au cours d'un intervalle d'au moins 1826 a 1805 Ma.
Control of DNA minor groove width and Fis protein binding by the purine 2-amino group

The width of the DNA minor groove varies with sequence and can be a major determinant of DNA shape recognition by proteins. For example, the minor groove within the center of the Fis–DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto the protein surface. G/C base pairs within this segment, which is not contacted by the Fis protein, reduce binding affinities up to 2000-fold over A/T-rich sequences. We show here through multiple X-ray structures and binding properties of Fis–DNA complexes containing base analogs that the 2-amino group on guanine is the primary molecular determinant controlling minor groove widths. Molecular dynamics simulations of free-DNA targets with canonical and modified bases further demonstrate that sequence-dependent narrowing of minor groove widths is modulated almost entirely by the presence of purine 2-amino groups. We also provide evidence that protein-mediated phosphate neutralization facilitates minor groove compression and is particularly important for binding to non-optimally shaped DNA duplexes.
Site-specific labeling of an anti-MUC1 antibody: probing the effects of conjugation and linker chemistry on the internalization process

Antibody-drug conjugates (ADCs) have recently received enormous attention as an attractive approach for cancer therapy. Although ADC design has been believed to be important for the relative efficacy of ADCs, it remains unexplored how the structural characteristics of ADCs would impact the internalization process and intracellular trafficking of the molecules. Herein, we report our efforts in investigating the cellular endocytosis implications of the conjugation and linker chemistry in designing antibody-based agents. A series of anti-MUC1 single-chain variable fragment (scFv-SM3) conjugates were designed with unique structural characteristics ranging from conjugation methods, sites of attachment and linker chemistry. In vitro confocal imaging showed that both random lysine-conjugation and site-specific conjugation, including C-terminus modification or internal site conjugation, could afford antibody conjugates with similar binding affinity and cellular uptake to target-expressing cells. Time-course internalization studies demonstrated that SM3-conjugates with short polyethylene glycol linkers outcompeted those that lack any hydrophilic linkers for higher cellular uptake and faster internalization rate. The SM3-conjugates with the highest affinity and internalization rate were also tested in mouse xenograft models using MUC1-overexpressing tumor cells. Our results indicate that the linker and conjugation chemistry play an important role in the internalization process of antibody conjugates, and this in turn could impact the therapeutic effects of ADCs.
Estimation of Daily Winter Precipitation in the Snowy Mountains of Southeastern Australia

AbstractWintertime precipitation in the Snowy Mountains provides water for agriculture, industry, and domestic use in inland southeastern Australia. Unlike most of Australia, much of this precipitation falls as snow, and it is recorded by a private network of heated tipping-bucket gauges. These observations are used in the present study to assess the accuracy of a poor man’s ensemble (PME) prediction of precipitation in the Snowy Mountains based on seven numerical weather prediction models. While the PME performs quite well, there is significant underestimation of precipitation intensity. It is shown that indicators of the synoptic environment can be used to improve the PME estimates of precipitation. Four synoptic regimes associated with different precipitation classes are identified from upper-air data. The reliability of the PME forecasts can be sharpened by considering the precipitation in each of the four synoptic classes. A linear regression, based on the synoptic classification and the PME estimate.
Specific cancer-associated mutations in the switch III region of Ras increase tumorigenicity by nanocluster augmentation

Hotspot mutations of Ras drive cell transformation and tumorigenesis. Less frequent mutations in Ras are poorly characterized for their oncogenic potential. Yet insight into their mechanism of action may point to novel opportunities to target Ras. Here, we show that several cancer-associated mutations in the switch III region moderately increase Ras activity in all isoforms. Mutants are biochemically inconspicuous, while their clustering into nanoscale signaling complexes on the plasma membrane, termed nanocluster, is augmented. Nanoclustering dictates downstream effector recruitment, MAPK-activity, and tumorigenic cell proliferation. Our results describe an unprecedented mechanism of signaling protein activation in cancer. DOI: http://dx.doi. org/10.7554/eLife.08905. 001
Wave Directions in a Narrow Bay

Abstract In slanting fetch conditions the direction of actively growing waves is strongly controlled by the fetch geometry. The effect was found to be pronounced in the long and narrow Gulf of Finland in the Baltic Sea, where it significantly modifies the directional wave climate. Three models with different assumptions on the directional coupling between the wave components were used to analyze the physics responsible for the directional behavior of the waves in the gulf. The directionally decoupled model produced the direction at the spectral peak correctly when the slanting fetch geometry was narrow but gave a weaker steering than observed when the fetch geometry was broader. The method of Donelan estimated well the direction at the spectral peak in well-defined slanting fetch conditions, but overestimated the longer fetch components during wave growth from a more complex shoreline. Neither the decoupled nor the Donelan model reproduced the observed shifting of direction with the frequency. The perform.
A survey of accessory mineral assemblages in peralkaline and more aluminous A-type granites of the southeast coastal area of China

Abstract An extensive belt of A-type granite exists along the southeast coast of China. The granites are divided into peralkaline and more aluminous subgroups which differ in mineral assemblages, mineral compositions and textures. In the peralkaline subgroup, primary magmatic Th-rich zircon is typically overgrown by Th-poor zircon containing thorite micro-inclusions. REE minerals in this subgroup are dominated by allanite-(Ce), chevkinite-(Ce), titanite and pyrochlore. Fe-Ti oxides are titanian magnetite and Mn-rich ilmenite. In contrast, in the more aluminous subgroup rocks, zircon is weakly zoned and exhibits very low Th but relatively high U contents. The REE minerals are dominated by Th-rich monazite-(Ce). Titanium-poor magnetite, pyrophanite and rutile are the major Fe-Ti oxides. These occurrences indicate that peralkaline magmas favour the formation of REE silicates, whereas magmas with higher alumina saturation stabilize REE phosphates. Peralkaline granites crystallized at temperatures 50−100°C greater than the more aluminous granites, but under lower oxidation conditions. These differences in formation conditions of the two A-type granite subgroups, deduced by accessory mineral characteristics, are inferred to be related to magma derivation at different crustal levels, with peralkaline magma deriving from a deeper crustal level with more mantle input.
Influence of regional scale information on the global circulation: A two‐way nesting climate simulation

The influence of regional scale information on the global circulation has been investigated through the development and application of the so‐called “two‐way nesting” technique. The two‐way nesting climate model system consists of a spectral atmospheric general circulation model and a grid point regional atmospheric model. Two simulations of 10 years each have been carried out with and without the feedback of the regional model to the global model. For the regional model domain the Maritime Continent covering the tropical area of the Indonesian islands has been selected as a key region influencing the global climate. The analysis of the global atmospheric temperature field shows a clear improvement through the regional model feedback; the systematic error with respect to re‐analysis data can be reduced even in regions far away from the regional model domain.