Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel subset of putative stem/progenitor CD34+Oct-4+ cells is the major target for SARS coronavirus in human lung

Identification of the nature of severe acute respiratory syndrome (SARS)-infected cells is crucial toward understanding the pathogenesis. Using multicolor colocalization techniques, we previously reported that SARS+ cells in the lung of fatally infected patients expressed the only known functional receptor, angiotensin-converting enzyme 2, and also a binding receptor, liver/lymph node–specific ICAM-3–grabbing non-integrin (CD209L). In this study, we show that SARS-infected cells also express the stem/progenitor cell markers CD34 and Oct-4, and do not express cytokeratin or surfactant. These putative lung stem/progenitor cells can also be identified in some non-SARS individuals and can be infected by SARS-coronavirus ex vivo. Infection of these cells may contribute to the loss of lung repair capacity that leads to respiratory failure as clinically observed.
On the Potential Causes of the Nonstationary Correlations between West African Precipitation and Atlantic Hurricane Activity

Abstract For years, various indices of seasonal West African precipitation have served as useful predictors of the overall tropical cyclone activity in the Atlantic Ocean. Since the mid-1990s, the correlation unexpectedly deteriorated. In the present study, statistical techniques are developed to describe the nonstationary nature of the correlations between annual measures of Atlantic tropical cyclone activity and three selected West African precipitation indices (namely, western Sahelian precipitation in June–September, central Sahelian precipitation in June–September, and Guinean coastal precipitation in the preceding year’s August–November period). The correlations between these parameters are found to vary over the period from 1921 to 2007 on a range of time scales. Additionally, considerable year-to-year variability in the strength of these correlations is documented by selecting subsamples of years with respect to various meteorological factors. Broadly, in years when the environment in the main dev.
Decadal Variability in the North Pacific: The Eastern North Pacific Mode*

Abstract Decadal variability in the North Pacific is studied in a series of coupled global ocean–atmosphere simulations using coupled modeling surgery—a set of modeling approaches that can be used to identify the origins and causes of a specific variability mode in the coupled climate system. Both modeling and observational studies suggest two distinctive internal modes in the North Pacific: the North Pacific mode (NPM) and the eastern North Pacific mode (ENPM). The ENPM originates from atmospheric stochastic forcing through spatial resonance. Both local ocean–atmosphere coupling and remote tropical teleconnective forcing can enhance the ENPM, but none of them is a necessary precondition. The influence of the tropical forcing in the midlatitudes is dominated by atmospheric teleconnection, while the oceanic teleconnection is negligible. The upper-ocean heat budget reveals that SST anomalies in the central North Pacific and the eastern North Pacific are generated by anomalous Ekman advection and surface hea.
Isotopic dilution methods to determine the gross transformation rates of nitrogen, phosphorus, and sulfur in soil: a review of the theory, methodologies, and limitations

The rates at which nutrients are released to, and removed from, the mineral nutrient pool are important in regulating the nutrient supply to plants. These nutrient transformation rates need to be taken into account when developing nutrient management strategies for economical and sustainable production. A method that is gaining popularity for determining the gross transformation rates of nutrients in the soil is the isotopic dilution technique. The technique involves labelling a soil mineral nutrient pool, e.g. NH4+, NO3−, PO43−, or SO42−, and monitoring the changes with time of the size of the labelled nutrient pool and the excess tracer abundance (atom%, if stable isotope tracer is used) or specific activity (if radioisotope is used) in the nutrient pool. Because of the complexity of the concepts and procedures involved, the method has sometimes been used incorrectly, and results misinterpreted. This paper discusses the isotopic dilution technique, including the theoretical background, the methodologies to determine the gross flux rates of nitrogen, phosphorus, and sulfur, and the limitations of the technique. The assumptions, conceptual models, experimental procedures, and compounding factors are discussed. Possible effects on the results by factors such as the uniformity of tracer distribution in the soil, changes in soil moisture content, substrate concentration, and aeration status, and duration of the experiment are also discussed. The influx and out-flux transformation rates derived from this technique are often contributed by several processes simultaneously, and thus cannot always be attributed to a particular nutrient transformation process. Despite the various constraints or possible compounding factors, the technique is a valuable tool that can provide important quantitative information on nutrient dynamics in the soil–plant system.
Photosystem II gene sequences of psbB and psbC clarify the phylogenetic position of Vanilla (Vanilloideae, Orchidaceae)

Nucleotide sequences of the plastid genes psbB and psbC were obtained for 34 taxa to represent most genera currently classified within Vanilloideae (Orchidaceae). These genes code for two of the subunits that make up the Photosystem II protein P680, and have only rarely been used for reconstructing phylogenetic relationships among plants. We failed to amplify psbB from the achlorophyllous genera Cyrtosia and Lecanorchis, but were able to align full length copies of psbC sequences from two species of Cyrtosia with the other taxa. This was not the case for an anomalous psbC sequence obtained for Lecanorchis. Nucleotide variation within each of these genes is sufficient to resolve the major relationships among Vanilloideae, and the combined two‐gene tree is fully resolved at the genus level and highly supported. These gene trees demonstrate with a high degree of confidence (95% jackknife support) that a clade of mostly achlorophyllous tropical vines including Pseudovanilla and Erythrorchis are the sister group to Vanilla. The two New Caledonian endemic genera of Vanilloideae are sister to this pair, and Epistephium is sister to all remaining Vanillieae.
Consistency and the Lack Thereof in Pacific Decadal Oscillation Impacts on North American Winter Climate

AbstractImpacts of the Pacific decadal oscillation (PDO) on North American climate were initially assessed over one negative (~1943 to 1976) and one positive (1977 to ~1990) PDO regime. Release of the Twentieth Century Reanalysis and the recent occurrence of negative PDO years make it possible to study the stability of PDO teleconnections. This analysis identified consistency in broad-scale teleconnection patterns but also critical differences in the amplitude of circulation pattern, temperature, and precipitation anomalies between comparable phases of the PDO. Many of these discrepancies were apparent after controlling for long-term trends and the impact of ENSO and were associated with variability in Atlantic Ocean temperatures and in the northern annular mode. Results from this study suggest that not all of the climate variability attributed to the PDO derives solely from fluctuations in Pacific sea surface temperatures (SSTs), that the climatic impact of these SST anomalies varies over time, or that t.
Calibrating the Water-Hammer Response of a Field Pipe Network by Using a Mechanical Damping Model

Hydraulic transient field tests have been conducted in a water distribution network. Existing transient models are applied to model the measured responses, but poor matches are obtained apart from the estimation of the initial rise of pressure. Possible reasons for these discrepancies include the effects of demands, entrained air, unsteady friction, friction losses associated with small lateral pipes, and mechanical damping caused by the interaction of pipes and joints with surrounding soils (including the effects of vibration and different degrees of restraint). These effects are systematically investigated by inclusion of the previously mentioned phenomena in conceptual transient models and calibration to the measured field responses. A mechanical damping-based conceptual transient model is shown to be the only model that can be accurately calibrated to the measured field responses.
Relationships between magmatism, metamorphism and deformation in the Fraser Complex, Western Australia: constraints from new SHRIMP U–Pb zircon geochronology*

SHRIMP U–Pb zircon isotopic data have been obtained for four samples collected from granitoids and paragneisses in the Fraser Complex, a large composite metagabbroic body cropping out in the Mesoproterozoic Albany‐Fraser Orogen of Western Australia. The data are combined with the results of field mapping and petrographic analysis to revise a model for the geological evolution of the Fraser Complex. Three main phases of deformation are recognised in the Fraser Complex (D1–3) associated with two metamorphic events (M1–2), which involve four distinguishable episodes of recrystallisation. The first metamorphic event recognised (M1a/D1) reached granulite facies and is characterised by peak T ≥800°C and P = 600–700 MPa. A syn‐M1a/D1 charnockite has a U–Pb SHRIMP zircon age of 1301 ± 6 Ma, which also provides an estimate for the age of intrusion of Fraser Complex gabbroic rocks. Disequilibrium textures comprising randomly oriented minerals (M1b), consistent with approximately isobaric cooling, formed in various .
A review of methods for estimating the contribution of glacial meltwater to total watershed discharge

Glaciers store water over a range of temporal scales with important implications for downstream human and natural systems. Assessment of the contribution of glacial meltwater runoff to total watershed discharge is an essential part of climate change risk assessment and sustainable water management in glacierized watersheds. Over the past decade, a range of techniques for quantifying the proportional contribution of glacial meltwater has been presented in the scientific literature. Here we examine five different methodological approaches: direct discharge measurement, glaciological approaches, hydrological balance equations, hydrochemical tracers, and hydrological modeling. After a brief summary of the role of glaciers in watershed hydrology, we evaluate each approach, with regard to their respective data requirements, assumptions, and associated uncertainties. Next, we discuss factors that researchers must consider in deciding upon a particular methodological approach, then conclude with a discussion of future research needs. We underscore the need for expanded meteorological, hydrological, and glaciological monitoring networks in glacierized watersheds worldwide, for more comprehensive assessment of uncertainty and for better integration of research with the specific needs of watershed stakeholders.
Age and Origin of Plutonic Intrusions in the Piedmont of the Southeastern Appalachians

Samples from 25 plutonic intrusions in the Piedmont, primarily of North and South Carolina, were analyzed to determine Rb-Sr whole-rock ages and initial Sr 87 /Sr 86 ratios. The 50-b.y. half-life for Rb 87 is used, and initial ratios are given relative to a Sr 87 /Sr 86 ratio of 0.7077 for the E and A SrCO 3 . The 14 whole-rock isochron ages occur in three groups: (1) 595 to 520 m.y. , (2) 415 to 385 m.y. , and (3) approximately 300 m.y. The initial Sr 87 /Sr 86 ratios for 14 granitic plutons range from 0.7023 to 0.7050; one granitic pluton has an initial ratio of 0.7062. Seven gabbrodiorite plutons have initial ratios of 0.7035 to 0.7042. The very low initial Sr 87 /Sr 86 ratios and their limited range indicate that the granitic magmas were derived from the lower crust; these magmas were not contaminated by or produced from older upper crustal rocks of sialic composition. The initial ratios suggest that the lower crust beneath the Piedmont 600 to 300 m.y. ago had a lower Rb/Sr ratio than did the lower crust beneath other continental areas during the same period of time. Whole-rock ages and petrographic studies indicate that the most recent significant metamorphic episode to affect the Piedmont occurred prior to 300 m.y. ago. The thermal peak of this last significant metamorphic event may have occurred between 380 to 420m.y. ago. The intensity and time of the metamorphic peak varied from place to place within the Piedmont. Many of the Piedmont mica ages probably have been affected by uplift and cooling of deep-seated rocks and thus have limited geologic significance.
Accumulation of permanent deformation during earthquake cycles on reverse faults

A two‐dimensional viscoelastic finite element model with a discrete stick‐slip thrust fault is used to investigate tectonic strain accumulation and release associated with repetitive earthquakes. Results show that although interseismic and coseismic motions are opposite in sign, they generally do not completely cancel each other over a seismic cycle, as normally presumed in elastic rebound theory. Complete elastic strain release adjacent to dip‐slip faults is inhibited by gravity, so that permanent deformation accumulates in the lithosphere with time. In the models, this permanent deformation is observed at the surface as large‐scale upwarping of a hanging wall anticline and depression of an adjacent footwall foreland basin. The results are supported by observation of similar features adjacent to reverse faults in active collisional mountain belts and along the coastal margin of some modern subduction zones.
Stone Age archaeological sites and environmental changes during the Holocene in the NW region of Russia

Abstract The region of NW Russia connecting with the Baltic Sea presents a dynamic ecological system that was sensitive to environmental changes during the Holocene. Certain factors affected environmental changes in the region during the Holocene: deglaciation processes, that finally terminated about 9 cal ka BP; eustatic sea-level changes; and tectonic movements, which are basically considered in the region as isostatic uplift processes. Contextual remains of ancient human occupation sites can be the only evidence of surface stabilization in monotonous sediments, such as aquatic and subaquatic deposits. Prehistoric settlements also mark ancient shorelines. The latter is of great importance for studying the history of water oscillations and coastal-line displacements on the territory of NW Russia. The transgressive–regressive stages of the Baltic Sea (at c. 10.15 cal ka BP, the Ancylus transgression; at c. 7.6–7.0 cal ka BP, the Littorina transgression) have an impact on the positions of prehistorical sites. The complex investigations of the Stone Age archaeological settlements on the Karelian Isthmus and in the Dvina–Lovat’ basin, and their altitudes below sea level, allowed us to reconstruct palaeoenvironmental changes during the Holocene, the chronology of cultural–historical processes and the adaptation strategy of ancient people to environmental conditions in this territory.
Permafrost in a dynamic environment

B11E-01, F258. Cannone N, Dramis F, Guglielmin M. 2002. Relationships between permafrost and vegetation in different geographical environments: Antarctica and Alps. EOS Trans. AGU 83(47): Fall Meet. Suppl., Abstract B72D-
Heat Flux Estimates for the Western North Atlantic. Part II: The Upper-Ocean Heat Balance

Abstract The assimilation of temperature and altimetric velocity into a numerical model of the upper-ocean mixed layer in Part I allowed an analysis of the upper ocean heat budget for the western North Atlantic Ocean over the 2.5-year period of the Geosat Exact Repeat Mission (November 1986–April 1989). The balance of terms varied regionally: south of the Gulf Stream advection was relatively unimportant in the heat budget, and the ocean responded passively to changes in surface flux. Within the Gulf Stream and to the north of it, cooling of the upper ocean by advection was as large as 0.15°C/day for periods of several weeks. An analysis of the advection term showed that cooling by Ekman transport was opposed by warming from the geostrophic currents of the Gulf Stream, with cooling typically stronger by a factor of 2 because nonuniform Ekman transport disrupted the normal alignment between isotherms and sea surface height contours. There is a complex ocean-atmosphere coupling in this region: in addition to.
Comments on the electromagnetic "smoke ring" concept

The electromagnetic (EM) fields in a one‐dimensional (1-D) earth due to a dipole or loop transmitter have been studied by a number of authors, including Lewis and Lee (1978), Pridmore (1978), Nabighian (1979), and Hoversten and Morrison (1982). Nabighian (1979) aptly described the time‐domain‐induced current system in a homogeneous half‐space as resembling a “smoke ring” blown by the transmitter, which moves outwards and downwards and diminishes in amplitude with increasing time after the transmitter is turned off. In a homogeneous half‐space, the physical electric field maximum moves outward from the transmitter loop edge at an angle of approximately 30° with the surface. Hoversten and Morrison (1982) show how the direction of propagation of the time‐domain electric field maximum is affected by conductivity structure. In the case of a highly conductive overburden over a resistive basement, the electric field maximum travels essentially horizontally away from the transmitter, and is effectively trapped in.
Contribution of rice straw carbon to CH4 emission from rice paddies using 13C‐enriched rice straw

It is generally recognized that the application of rice straw (RS) increases CH4 emission from rice paddies. To estimate the contribution of RS carbon to CH4 emission, a pot experiment was conducted using 13C-enriched RS. The percentage contributions of RS carbon to CH4 emission throughout the rice growth period were 10±1, 32±3, and 43±3% for the treatments with RS applied at the rates of 2, 4, and 6 g kg−1 soil, respectively. The increase in the rate of application of RS increased CH4 emission derived from both RS carbon and other carbon sources. The percentage contribution of RS carbon to CH4 emission was larger in the earlier period (maximum 96%) when the decomposition rate of RS was larger. After RS decomposition had slowed, CH4 emission derived from RS carbon decreased. However, the δ13C values of CH4 emitted from the pots with 13C-enriched RS applied at rates of 4 and 6 g kg−1 soil were significantly higher than those from the pots with natural RS until the harvesting stage. An increased atom-13C% of roots of rice plants growing in the pots with 6 g kg−1 of 13C-enriched RS at around the maximum tiller number stage and a decrease during the following 2 months suggested that rice plants assimilated RS carbon once and then released a portion of it. This supply of RS carbon from roots may be one of the sources of CH4 in the late period of rice growth.
Serviceorientierte Architekturen: Vom Konzept zum Einsatz in der Praxis

Serviceorientierte Architekturen (SOA) werden gegenwartig als Ansatz fur eine einfachere und flexiblere inner- und zwischenbetriebliche Integration heterogener Anwendungssysteme diskutiert. Dieser Beitrag entwickelt ein SOA-Architekturmodell und untersucht seine Auspragung in vier Praxisbeispielen. Er identifiziert aus den Fallstudien ausserdem typische Architekturtreiber, Einsatzziele, Nutzenpotenziale und Architekturmassnahmen einer SOA-Umsetzung in der Praxis.
Elchaxylon, a new corystosperm based on permineralized stems from the Late Triassic of Argentina

Artabe, A.E. & Zamuner, A.B. , March 2007. Elchaxylon, a new corystosperm based on permineralized stems from the Late Triassic of Argentina. Alcheringa 31, 85‐96. ISSN 0311-5518. Anatomically preserved stems of Late Triassic corystosperms from the Río Blanco Formation of Argentina are described and assigned to Elchaxylon zavattieriae gen. et sp. nov. The polyxylic gymnospermous axes have two discontinuous cambial rings, which develop centrifugal secondary xylem and centripetal secondary xylem around the mesarch primary xylem bundles. The centrifugal undivided pycnoxylic secondary xylem incorporates uniseriate rays, uni- to biseriate radial pitting either alternate or opposite, and one or two simple pits in each cross-field. Atypical secondary growth is restricted to localized development of centripetal secondary xylem (inverted xylem). Elchaxylon could represent a basal member of the rhexoxyloid lineage. This basal clade is characterized by limited centripetal secondary xylem, lack of perimedullar bundles, and modest development of centrifugal xylem. Analia E. Artabe [aeartabe@museo.fcnym. unlp.edu. ar] and Alba B. Zamuner [azamuer@museo.fcnym. unlp.edu. ar]. División Paleobotánica, Facultad de Ciencias Naturales y Museo, Universidad Nacional de La Plata, Paseo del Bosque SN, 1900 La Plata, Argentina and Consejo Nacional de Investigaciones Científicas y Técnicas; received 20.5. 2005, revised and accepted 14.9. 2005.
MIT Open Access

The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the A β 40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer’s disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements. The free energy landscape of a protein provides a direct representation of the probability of measuring particular values of specific parameters that describe its conformational properties. The knowledge of the free energy landscape of a protein offers therefore the possibility of rationalising important aspects of its behaviour, including its stability, mechanisms of folding and molecular recognition, and the possibility of misfolding and aggregation 1–7 . It is thus highly desirable to extend this type of description to intrinsically disordered proteins, which are characterized by the absence of a well-defined structure under native conditions and play key roles in a variety of biochemical processes, including in particular signaling and regulation 8–13 . By bringing together experiments and computer simulations it has been recently possible to make great