Miracle-dz/UniFAR-FTUs huggingface dataset:
Hantaviruses: Genome Structure, Expression and Evolution Background

Introduction The isolation by Ho Wang Lee and collaborators of the virus causing Korean haemorrhagic fever, now called Hantaan virus (HTN), from the lungs of striped field mice (Apodemus agrarius) in 1976 (Lee & Lee, 1976) launched a new era in the study of haemorrhagic fever with renal syndrome (HFRS) throughout the world. This was soon followed by the discovery of the causative agent of the European form of HFRS, nephropathia epidemica, now known as Puumala virus (PUU) (Brummer-Korvenkontio et al., 1980), and of the urban rat virus, Seoul virus (SEO) (Lee et aI., 1980). The identification in 1993 of Sin Nombre virus (SN) as the causative agent of hantavirus-associated pulmonary syndrome (HPS) (Nichol et al., 1993 a) led to intensive search for further hantaviruses and as a result today a total of as many as 16 well-established sero/genotypes may be listed. It was largely the pioneering molecular virology studies by that gave hantaviruses the status of a separate genus, Hantavirus, in the family Bunyaviridae (Murphy et al., 1995). Hantaviruses, HTN being the prototype, are today recognized to have their own distinguishing features, both ecologically and in molecular properties. In contrast to viruses in other Bunyaviridae genera, hantaviruses are not transmitted by arthropods. The reservoir hosts of hantaviruses are specific rodents/insectivores; on occasion they infect humans but do not spread from human-to-human. These features make it of special interest to study the genetic evolution of hantaviruses. Hantaviruses are serologically related to one another but their proteins do not exhibit extensive sequence similarities or antigenic relationships to proteins of viruses representing other genera. On the one hand, hantaviruses give rise to severe clinical manifestations, HFRS and HPS. On the other hand, they cause no detectable cytopathology in cell cultures and produce persistent non-pathogenic infections in rodents. In this review, we summarize the current knowledge on genetic structure, protein expression and evolution of hantaviruses.
Regional streamflow trend detection with consideration of both temporal and spatial correlation

It is known that serial correlation within time series at sites and cross‐correlation among sites in a specific region will influence the ability of statistical tests to assess the field significance of trends over the region. However, serial and/or cross‐correlation has been ignored in field trend‐analyses. This study attempts to develop a methodology that takes into account both serial and cross‐correlation in the assessment of the field significance of trends. The regional average Mann–Kendall (RAMK) statistic is used to represent the regional properties of trends at a regional scale. The null distribution of the RAMK statistic is derived on the basis that the joint probability distribution of m independent normal variables is also normally distributed. The variance of the RAMK statistic is then modified by serial and cross‐correlation. The applicability of the method was demonstrated by applying it to assess the field significance of trends in annual mean, annual maximum, and annual minimum daily streamflow from 1967 to 1996 in ten major homogeneous climate regions of Canada. The results indicate that the method developed provides more accurate assessment of the field significance of trends than that without consideration of serial and cross‐correlation.
Variability of high latitude amplification of anthropogenic warming

Climate models have long predicted that the high latitude response of near‐surface air temperatures should be greater than at lower latitudes as a result of snow/ice feedbacks. Here we show that a regression analysis of observed global surface temperatures and anthropogenic and natural forcings could misleadingly suggest that climate models fail to capture the observed zonal mean pattern of response to anthropogenic forcings. A better approach to detecting changes and to determine consistency of climate models and observations is to use multiple features of the response pattern derived from physically‐based climate models, as has been done in optimal detection studies. We show that multi‐variable fingerprints can more easily detect anthropogenic changes thereby offering the potential to more robustly quantify anthropogenic influence on aspects of the climate system such as the cryosphere and the hydrological cycle.
Ground-water hydrology of the Willamette basin, Oregon

The Willamette Basin is a topographic and structural trough that lies between the Coast Range and the Cascade Range (fig. 1). The basin lowland is divided into five sedi-mentary subbasins that are separated by local uplands of the Columbia River Basalt Group lavas. Stream drainages between the basins are restricted by narrow water gaps that cut into the Columbia River Basalt Group or older, low-permeability bed-rock. Variations in the depositional histories of each subbasin have created hydrogeologic conditions that are distinct but broadly related by common features of the geologic history of the entire basin (Woodward and others, 1998). A general geologic history of the basin is presented below to provide a setting for understanding the main geologic controls on the groundwater hydrology of the basin. Detailed geologic histories can be found in The Coast Range is composed of uplifted Tertiary marine sedimentary rocks and related marine volcanic and intrusive rocks. The Cascade Range is an accumulation of volcanic lavas and debris erupted from continental volcanoes. Tertiary marine strata and older Cascade volcanic rocks interfinger at depth beneath the Willamette Valley to form the bedrock foundation of the lowland. During the initial formation of the Cascade Range, around 35–40 million years ago, the ancestral Pacific shoreline was located near the present foothills of the range at the eastern margin of the Willamette lowland (Orr and others, 1992). As the Cascade Range grew by the accumulation of volcanic debris, east-west compressive forces began to uplift the area currently occupied by the Coast Range and depress the area that is now the Willamette lowland. As this process continued, the valley gradually became isolated from the sea and began to accumulate sediments deposited by rivers draining the Cascade Range and the rising Coast Range. Around 16 to 14 million years ago, numerous large-volume lava flows of the Columbia River Basalt Group erupted from vents east of the Cascade Range, entered the northern valley through a gap in the Cascade Range, and flooded low-lying areas as far south as Salem (Beeson and others, 1989a). During and after the emplacement of the Columbia River basalt lavas, the Coast Range continued to rise and the Columbia River basalt lavas and underlying bedrock were distorted by
Pb–Zn occurrences and their Pb-isotopic signatures bearing on metallogeny and mineral exploration—Paleozoic sedimentary rocks, northern Appalachians, Quebec

Galena Pb-isotope ratios of epithermal vein and disseminated sulfide occurrences in the Taconian Orogen and Siluro-Devonian basin cluster around 17.90–18.05 for 206Pb/204Pb and 37.70–38.00 for 208Pb/204Pb. The major source of Pb in most, if not all, occurrences is a fairly common continental crust, a characteristic found in published analyses of Grenville feldspar Pb. A southwest to northeast increase in galena 206Pb/204Pb ratios is ascribed to the supply of several types of detritus from Grenville basement during the Cambro-Ordovician: coarse-grained, K-feldspar-bearing in the southwest, grading into fine-grained phyllitic, and relatively more highly radiogenic in the northeast.Emplacement (i) of Pb–Zn–barite veins and disseminations, commonly of homogeneous crustal Pb-isotopic signature, was late Taconian; (ii) of Pb–Zn–quartz veins, of less homogeneous signature, was post-Taconian; and (iii) of Pb–Zn–carbonate veins, relatively highly radiogenic and commonly homogeneous, was late or post-Acadian. Signa.
The Influence of the Mineral Content of Clays on their Stabilization by Cement

Stabilization of clay soils can be brought about by mixing with cement. This results in the formation of gelatinous products within the interstices of the soil which crystallize as the hardening process develops. The strength of the stabilized soil is developed as the cement hydrates. The various clay minerals in a clay soil influence the ease with which it can be stabilized with cement. Kaolinite appears to have little effect on the hydration of cement and hardening proceeds normally. Well organized illite may be regarded as inert as far as cement stabilization is concerned. By contrast clay minerals with an expansive lattice, notably montmorillonite, have a profound influence on the hardening of cement. Clay soils with an appreciable content of such minerals will, however, respond to cement stabilization if pre-treated with lime. Certain components found in clays, particularly organic matter and sulphates, retard or prevent proper hydration and therefore prove deleterious to soil-cement mixtures.
Incorporation of a permafrost model into a large‐scale ecosystem model: Evaluation of temporal and spatial scaling issues in simulating soil thermal dynamics

This study evaluated whether a model of permafrost dynamics with a 0.5-day resolution internal time step that is driven by monthly climate inputs is adequate for representing the soil thermal dynamics in a large-scale ecosystem model. An extant version of the Goodrich model was modified to develop a soil thermal model (STM) with the capability to operate with either 0.5-hour or 0.5-day internal time steps and to be driven with either daily or monthly input data. The choice of internal time step had little effect on the simulation of soil thermal dynamics of a black spruce site in Alaska. The use of monthly climate inputs to drive the model resulted in an error of less than 1°C in the upper organic soil layer and in an accurate simulation of seasonal active layer dynamics. Uncertainty analyses of the STM driven with monthly climate inputs identified that soil temperature estimates of the upper organic layer were most sensitive to variability in parameters that described snow thermal conductivity, moss thickness, and moss thermal conductivity. The STM was coupled to the Terrestrial Ecosystem Model (TEM), and the performance of the coupled model was verified for the simulation of soil temperatures in applications to a black spruce site in Canada and to white spruce, aspen, and tundra sites in Alaska. A 1°C error in the temperature of the upper organic soil layer had little influence on the carbon dynamics simulated for the black spruce site in Canada. Application of the model across the range of black spruce ecosystems in North America demonstrated that the STM-TEM has the capability to operate over temporal and spatial domains that consider substantial variation in surface climate given that spatial variability in key structural characteristics and physical properties of the soil thermal regime are described.
Biogeochemical simulation of nitrous oxide cycle based on the major nitrogen processes

[1] We modeled the biogeochemical nitrogen cycle with specific emphasis on N2O behavior to describe the global N2O cycle system quantitatively. Here all the major nitrogen cycle processes are included plus the processes directly related to N2O. The model includes 24 nitrogen reservoirs: 3 in the stratosphere (N2O, N2, and NOx), 4 in the troposphere (N2O, N2, NH3, and NOx), 7 on land (biospheric, N2O, NOx, PON, DON, NH4+, and NO3−), 6 in surface-ocean (biospheric, PON, DON, N2O, NH4+, and NO3−), 3 in the deep ocean (N2O, NH4+, NO3−), and sedimentary organic nitrogen. The exploration of the steady state flux combination, which produces the tropospheric N2O concentration profile consistent with observations, provided the most likely estimates of the N2O emissions from soils, rivers, and oceans, including contributions from nitrification and denitrification. Full incorporation of nitrogen species facilitated an analysis of the influences of various nitrogen cycle processes on tropospheric N2O concentration. Our sensitivity analyses revealed that the tropospheric N2O concentration was linked closely to other nitrogen species and was especially sensitive to terrestrial biological activities via nitrogen fixation, nitrogen assimilation, and ammonification. This result implies that the N2O budget in the troposphere can be constrained well by these terrestrial processes.
The Black Sea General Circulation and Climatic Temperature and Salinity Fields

Abstract : The Black Sea is a nearly enclosed ocean basin, exhibiting many features common with larger ocean basins. Lacking an open boundary and having a limited exchange with sources of fresh and salt water, this basin is an ideal laboratory for developing and evaluating numerical circulation models. The present report describes one numerical models of the Black Sea, developed by Bulgarian and Russian scientists. The new approach has the advantages of both diagnostic models (incorporation of experimental data) and prognostic models (producing hydrodynamical adjustment and filtered fields). Successive application of diagnostic and prognostic models is used. The temperature and salinity fields obtained from observations, and currents obtained from diagnostic models, are used as the initial approximation to the prognostic model. Judicious selection of an integration time prevents over-smoothing of the results while preserving the stability of the solution.
High‐accuracy photogrammetric technique for human spine measurement

Close range photogrammetry has been recognised as an essential tool for the capture of high‐accuracy spatial data for medical applications, in particular work involving dynamic human body parts such as limbs. Offline and online photogrammetric systems are readily available for a number of common applications. However, off‐the‐shelf systems are not always appropriate because of project site conditions. To achieve high measurement accuracy in a field environment, a modified field camera calibration technique was introduced. The technique is particularly important where each camera is limited to one captured image during calibration, as the camera and the calibration testfield are in fixed positions. In this paper a custom‐built imaging system designed for the study of the human spine in an outdoor environment is introduced. The discussion addresses: (1) imaging system design; (2) modified field calibration techniques; and (3) a case study on human spines. Two field camera calibration techniques were evaluated, both of which improved the accuracy of the prototype system, the use of a detachable target board offering the best results. This modified camera calibration procedure has improved the 3D measurement accuracy from 1·25 ± 0·3 mm to 0·43 ± 0·1 mm. The improvement is at a level achievable in the laboratory. The technique is considered to provide accurate and reliable anthropometric landmark measurement at low cost. This was evaluated in a clinical setting where diurnal changes in spine length and contour were measured in a cohort of 30 university students. The capability of the technique to measure sagittal and frontal angular changes provides a novel way of examining changes in spine shape.
On the Curvature of Oceanic Arcs

Oceanic arcs and deep-sea trenches are the surface expressions of oceanic plates subducting into the Earth's mantle. We use a new numerical technique for simulating the dynamical evolution of the lithosphere-mantle interaction in order to assess the causes of arc curvature. We group the possible causes into two classes, external feedback between the migrating lithosphere and the secondary induced mantle flow, and internal heterogeneities within the lithosphere, e.g., owing to differences in cooling ages of the plate at the trench. We statistically assess that almost all arcs on the Earth can be described by these hypotheses. The method is also directly applied to the Tonga and Aleutian arcs, bringing new insights on the origin of their shapes.
Impact of anthropogenic activities and natural inputs on oceanographic characteristics of water and geochemistry of surface sediments in different sites along the Egyptian Red Sea Coast

-1 ) in both Qola'an and Shalatein, also Abu Dabab and Qala'an areas shows high pH values (8.00 and 8.04) due to the presence of dense sea grass cover. The sediment types generally changes from sand to slightly gravelly sand or muddy sand, also the surface sediments are mainly medium sand, moderately to poorly sorted. Geochemically, the factor controlling the carbonate content of studies sediments includes material supply of biogenic and terrigenous components. Therefore, sediments of El-Hamrawein, Sharm el-Bahari, Abu Dabab and Shalatein areas are terrigenous sediments, while sediments of Qola'an area south Marsa Alam are highly carbonates. In general, organic matter (4.82%) is higher in the sediments relative to adjacent areas due to high contributions of terrestrial materials by wadis and anthropogenic factors.
Fitting concentration and load rating curves with generalized linear models

Generalized linear models may be used as a systematic and flexible alternative to existing practices in fitting sediment or solute concentration and load rating curves. Through widely available statistical software they offer a one‐step solution to the common and awkward problem that a bias correction is needed when estimating total loads. In particular, using a logarithmic link function has an advantage over logarithmic transformation of concentration or load, as generalized linear models return predictions directly on the original measured scale; there is thus no need for back‐transformation or subsequent correction factors. Example analyses are given for suspended sediment concentration for an upland stream in the Northern Pennines and for phosphorus load for the Illinois River. General criteria for choosing models and good practice in the use of figures of model merit and of residual plots are also discussed in detail. Copyright © 2007 John Wiley & Sons, Ltd.
Relict rock glaciers and protalus lobes in the British Isles: implications for Late Pleistocene mountain geomorphology and palaeoclimate

Many relict rock glaciers and protalus lobes have been described in mountainous areas of the British Isles. This paper reviews their distribution, chronology, supposed origin and development, and places the research within current investigations and knowledge. Rock glaciers and protalus lobes are located in a number of different topographic locations and settings. They developed at the base of steep cliffs following the catastrophic failure of rock faces, at the base of scree slopes following the gradual accumulation of rock debris and in association with glaciers. Protalus lobes probably developed in response to the permafrost creep of talus material while rock glaciers formed through the deformation and sliding of large bodies of buried ice. Rock glaciers probably developed, or were last active, during the Younger Dryas, although the possibility exists that some of these landforms are Dimlington Stadial in age. The development of protalus lobes during the Younger Dryas suggests that precipitation levels were low and permafrost was widespread during this time. The lack of rock glaciers (sensu stricto) in the British Isles compared with other mountain areas is believed to be a consequence of the rock type and relative scarcity of weathered debris for their formation rather than a lack of suitable sites or appropriate environmental conditions. Copyright © 2007 John Wiley & Sons, Ltd.
Comparing current and desired ecological conditions at a landscape scale in the Cumberland Plateau and Mountains, USA

We applied a landscape conservation approach that quantifies current and desired ecological conditions for 10680 km2 of diverse forests in the Cumberland Plateau and Mountains of Tennessee and Kentucky. In this case study, forest cover was classified using Landsat Enhanced Thematic Mapper (ETM) imagery and evaluated with forest inventory data. Landform forest associations were characterized by combining forest cover, physiographic descriptions of remnant and historical forests, and forest structure and composition from the inventory data. These landform forest associations estimate current forest conditions and, in comparison with a projection of potential natural forest conditions, indicated that upland deciduous forests in the Plateau have the greatest reduction in cover, particularly in small private ownerships. Although of similar species composition, upland deciduous forests in the Plateau also possessed younger stands with smaller trees than observed from potential old-growth conditions. These results provide scientific guidance for transitioning these forests toward desired ecological conditions through regional conservation initiatives.
Extraction and analysis of morphologic and hydrologic properties for Luvuvhu River Catchment in Limpopo province, South Africa

Physiographic and topographic changes in Luvuvhu River Catchment are negatively impacting on the catchment hydrology of the area. A study was carried out to extract and analyze the morphologic and hydrologic properties using GIS techniques. Digital Elevation Modeling hydro-processing procedures were used within an ArcGIS environment where Arc hydro tools were used to extract and show the spatial distribution of the properties. A hydrologically correct Digital Elevation Modeling (DEM) was generated and used to obtain primary and derived terrain elements. The results showed the automated delineation of sub-catchments and the spatial distribution of morphometric and hydrologic properties. The analysis showed how the physiographic changes were
Behavior of Vapam and Methylisothiocyanate in Soils1

An investigation was undertaken to study the behavior of the fungicide Vapam (sodium-N-methyldithiocarbamate) and its toxic degradation product MIT (methylisothiocyanate) in soils to obtain the necessary parameters for predicting the distribution of these compounds when applied in irrigation water. These parameters include absorption by the soil components, the degradation of Vapam to MIT and the subsequent breakdown of MIT to nontoxic substances, and the distribution of MIT between the liquid, gaseous, and adsorbed phases in the soil. Adsorption was determined by both batch and flow methods. The results indicated that degradation of both Vapam and MIT followed first-order kinetics. The breakdown of Vapam to MIT was rapid, half-life generally < 30 min at moisture contents below saturation, while MIT was found to persist for 2 weeks or more. The rapid breakdown of Vapam will result in a soil solution containing mainly MIT. MIT adsorption was relatively low (Kads = 0.41 and 0.57 ml/g for the soils higher in clay and organic matter content). The soils with the lower adsorption coefficients (Kads < 0.05) will give a practically uniform MIT distribution with depth when Vapam is applied at a constant concentration in the irrigation water. The behavior of Vapam in heavy textured soils needs further investigation.
Predicting spatio-temporal failure in large scale observational and micro scale experimental systems

Forecasting has become an essential part of modern thought, but the practical limitations still are manifold. We addressed future rates of change by comparing models that take into account time, and models that focus more on space. Cox regression confirmed that linear change can be safely assumed in the short-term. Spatially explicit Poisson regression, provided a ceiling value for the number of deforestation spots. With several observed and estimated rates, it was decided to forecast using the more robust assumptions. A Markov-chain cellular automaton thus projected 5-year deforestation in the Amazonian Arc of Deforestation, showing that even a stable rate of change would largely deplete the forest area. More generally, resolution and implementation of the existing models could explain many of the modelling difficulties still affecting forecasting.