Miracle-dz/UniFAR-FTUs huggingface dataset:
THE NATURE AND TIMING OF THE MIDDLE DEVONIAN KAČÁK BIOEVENTS IN THE MARCELLUS SUBGROUP OF THE APPALACHIAN BASIN

ABSTRACT Intervals of faunal turnover in the fossil record are often preserved at unconformities, suggesting that their apparent abruptness is an artifact of geologic discontinuities. A detailed investigation of the Middle Devonian Kačák Bioevents of the Appalachian Basin focused on stratigraphically complete sections of eastern New York State to further elucidate the nature and timing of faunal turnover where not cloaked by an unconformity. The Lower Kačák Bioevent is fairly well constrained to the lower portion of the East Berne Member of the Mount Marion Formation. The Upper Kačák Bioevent is less well constrained to within the middle to upper East Berne Member, however. A thorough dissection of the East Berne Member has yielded the more precise timing of the initial Hamilton Fauna incursion, occurring at the level of the thin, fossiliferous, Dave Elliot Bed (DEB). The occurrence of the goniatite Tornoceras aff. mesopleuron below the DEB constrains the Hamilton incursion to the earliest Givetian age. The DEB fauna is composed of a single taxonomic holdover from the older Stony Hollow Fauna, while the entire rest of the DEB fauna carries over into the remaining Hamilton E-E (ecological–evolutionary) subunit. From the data at hand, this faunal incursion does not represent a gradual or step-wise incursion. When studied in the thickest, most conformable, stratigraphically complete sections preserved, this incursion occurs as an abrupt event. The pattern of faunal change preserved is a two-step extinction and turnover, with extinction occurring at the onset of dysoxic flooding (Lower Kačák Bioevent), followed by the rapid incursion of new fauna associated with sea-level fall (Upper Kačák Bioevent) in the area under consideration.
Daturametelins H, I, and J: Three New Withanolide Glycosides from Datura metel L.

Three new withanolide glycosides named daturametelins H–J (1–3), together with two known ones, daturataturin A (4) and 7,27‐dihydroxy‐1‐oxowitha‐2,5,24‐trienolide (5), were isolated from the MeOH extract of the aerial parts of Datura metel L. (Solanaceae). Their structures were determined mainly by spectroscopic techniques including 2D‐NMR (HMBC, HMQC, 1H,1H‐COSY, NOESY) and MS experiments. Compounds 1–5 were tested for their antiproliferative activity towards the human colorectal carcinoma (HCT‐116) cell line. The nonglycosidic compound 5 exhibited the highest activity of the tested withanolides, with an IC50 value of 3.2±0.2 μM (Table 3).
Textural immaturity of cumulates as an indicator of magma chamber processes: infiltration and crystal accumulation in the Rum Eastern Layered Intrusion

Textural maturity describes the extent to which rocks have approached textural equilibrium. For igneous rocks, this is a function of the time-integrated thermal history in the sub-solidus which, for cumulate rocks, generally translates to the cooling history via the rate of solidification of the accumulating crystal mush. The most straightforward way to quantify the textural maturity of orthocumulates (sensu lato) is to measure the angle subtended at the corners of interstitial grains. Texturally mature cumulates have angle populations with median values of c. 120°, whereas texturally immature cumulates have lower medians, inherited by the interstitial phase, which infills either an impingement texture in the accumulating mush or a texturally equilibrated pore topology. Textural observations of allivalites from the Rum Layered Suite demonstrate that stratigraphically localized excursions towards textural immaturity are the result of either transient, relatively rapid, solidification rates (perhaps a result of the arrival of cold crystal-laden bodies of fluid on the chamber floor) or late-stage infiltration of fully solidified cumulates by evolved liquids expelled upwards by compaction of underlying horizons. These two processes have distinct textural and compositional signatures.
Gully erosion prediction across a large region: Murray–Darling Basin, Australia

Gully erosion is a significant process for delivering sediment to streams, and can be the dominant erosion process in some regions. As with other forms of erosion, we need methods to predict the extent and patterns of gully erosion across large areas. Such methods also improve our understanding of the environmental controls on gully erosion. Here, patterns of gully density are predicted across the 1 × 106 km2 Murray–Darling Basin in Australia, using aerial photograph mapping of gullies across part of the Basin and a multivariate statistical model of a range of environmental factors. Across the Basin, at a 10-km grid resolution, gully density is predicted to vary from 0 to 1.2 km km–2, with 22% of the Basin having a gully density >0.1 km km–2 and 3% a density >0.5 km km–2. The model is reasonably successful at predicting the variations in mapped gully density compared with similar attempts to predict erosion processes at this scale. Hillslope gradient and mean annual rainfall are the most important single factors across the region. The predicted mean gully density across the Basin is 0.08 km km–2 and gullies contribute up to 27 × 106 t year–1 of sediment to the river network. This is more than the amount that has been estimated from the combined contribution of hillslope (14 × 106 t year–1) and riverbank (8.6 × 106 t year–1) erosion by other studies within the Basin.
Geochemical evolution of inactive pyritic tailings in the Elliot Lake uranium district

Geochemical data obtained between 1979 and 1983 from a network of piezometer nests and cores from three inactive uranium tailings impoundments in the Elliot Lake district indicate that oxidation of pyrite taking place in the shallow part of the zone above the water table is causing the chemistry of the pore water above and below the water table to change. A two-layer hydrochemical zonation has developed in which infiltration water from rain and snow has resulted in an upper zone of low-pH water with high concentrations of SO4, Fe, and heavy metals. This zone is gradually expanding downward at rates generally between 0.2 and 2 m/year, causing displacement of the original mill process water, which has neutral pH and low concentrations of heavy metals. High concentrations of Fe(III) at shallow depth in the zone above the water table indicate that ferric iron is an important oxidizer of pyrite in the presence of free oxygen.The pe of the groundwaters is controlled by the ferric–ferrous redox couple, and trend.
Effects of temperature abuse on survival of Vibrio vulnificus in oysters

Opaque and translucent morphotypes of a TnphoA-containing strain of Vibrio vulnificus were fed to oysters, which were subsequently stored at temperatures ranging from 0.5 to 22 degrees C for 10 days. Samples of oysters were homogenized and plated at intervals to determine the cell density of V. vulnificus and total aerobic population of bacteria present. At all temperatures, the numbers of V. vulnificus (both morphotypes) declined over the 10-day study period. The same observation was made with a lower inoculum of V. vulnificus. Identical experiments with shucked oysters showed a more rapid decrease in V. vulnificus. Identical experiments with shucked oysters showed a more rapid decrease in V. vulnificus to levels below limits of detection. Little change in the total bacterial counts was observed in shellstock oysters at any of the test temperatures, whereas incubation at the higher temperatures (17 and 22 degrees C) resulted in large increases in total counts in shucked oysters. These data suggest that temperature abuse of oysters may not be a factor in increasing the public health risk of V. vulnificus through raw oyster consumption. However, the data also suggest that even with proper storage, indigenous levels of V. vulnificus may remain sufficiently higher in shellstock oysters to produce infection in compromised hosts.
Weddell Sea Export Pathways from Surface Drifters

AbstractThe complex export pathways that connect the surface waters of the Weddell Sea with the Antarctic Circumpolar Current influence water mass modification, nutrient fluxes, and ecosystem dynamics. To study this exchange, 40 surface drifters, equipped with temperature sensors, were released into the northwestern Weddell Sea’s continental shelf and slope frontal system in late January 2012. Comparison of the drifter trajectories with a similar deployment in early February 2007 provides insight into the interannual variability of the surface circulation in this region. Observed differences in the 2007 and 2012 drifter trajectories are related to a variable surface circulation responding to changes in wind stress curl over the Weddell Gyre. Differences between northwestern Weddell Sea properties in 2007 and 2012 include 1) an enhanced cyclonic wind stress forcing over the Weddell Gyre in 2012; 2) an acceleration of the Antarctic Slope Current (ASC) and an offshore shift of the primary drifter export path.
Shoaling Internal Solitary Waves

[1] The evolution and breaking of internal solitary waves in a shallow upper layer as they approach a constant bottom slope is examined through laboratory experiments. The waves are launched in a two-layer fluid through the standard lock-release method. In most experiments, the wave amplitude is significantly larger than the depth of the shallow upper layer so that they are not well described by Korteweg-de Vries theory. The dynamics of the shoaling waves are characterized by the Iribarren number, Ir, which measures the ratio of the topographic slope to the square root of the characteristic wave slope. This is used to classify breaking regimes as collapsing, plunging, surging, and nonbreaking for increasing values of Ir. For breaking waves, the maximum interface descent, Hi, is predicted to depend upon the topographic slope, s, and the incident wave’s amplitude and width, Asw and Lsw, respectively, as Hi ? ’ ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi 4sAswLsw p . This prediction is corroborated by our experiments. Likewise, we apply simple heuristics to estimate the speed of interface descent, and we characterize the speed and range of the consequent upslope flow of the lower layer after breaking has occurred.
Perturbation of the Activity of Replication Origin by Meiosis-specific Transcription*

We have determined the activity of all ARSs on the Saccharomyces cerevisiae chromosome VI as chromosomal replication origins in premeiotic S-phase by neutral/neutral two-dimensional gel electrophoresis. The comparison of origin activity of each origin in mitotic and premeiotic S-phase showed that one of the most efficient origins in mitotic S-phase, ARS605, was completely inhibited in premeiotic S-phase. ARS605 is located within the open reading frame of MSH4 gene that is transcribed specifically during an early stage of meiosis. Systematic analysis of relationships between MSH4 transcription and ARS605 origin activity revealed that transcription of MSH4 inhibited the ARS605 origin activity by removing origin recognition complex from ARS605. Deletion of UME6, a transcription factor responsible for repressing MSH4 during mitotic S-phase, resulted in inactivation of ARS605 in mitosis. Our finding is the first demonstration that the transcriptional regulation on the replication origin activity is related to changes in cell physiology. These results may provide insights into changes in replication origin activity in embryonic cell cycle during early developmental stages.
The p23 Protein of Citrus Tristeza Virus Controls Asymmetrical RNA Accumulation

ABSTRACT Citrus tristeza virus (CTV), a member of the Closteroviridae, has a 19.3-kb positive-stranded RNA genome that is organized into 12 open reading frames (ORFs) with the 10 3′ genes expressed via a nested set of nine or ten 3′-coterminal subgenomic mRNAs (sgRNAs). Relatively large amounts of negative-stranded RNAs complementary to both genomic and sgRNAs accumulate in infected cells. As is characteristic of RNA viruses, wild-type CTV produced more positive than negative strands, with the plus-to-minus ratios of genomic and sgRNAs estimated at 10 to 20:1 and 40 to 50:1, respectively. However, a mutant with all of the 3′ genes deleted replicated efficiently, but produced plus to minus strands at a markedly decreased ratio of 1 to 2:1. Deletion analysis of 3′-end genes revealed that the p23 ORF was involved in asymmetric RNA accumulation. A mutation which caused a frameshift after the fifth codon resulted in nearly symmetrical RNA accumulation, suggesting that the p23 protein, not a cis-acting element within the p23 ORF, controls asymmetric accumulation of CTV RNAs. Further in-frame deletion mutations in the p23 ORF suggested that amino acid residues 46 to 180, which contained RNA-binding and zinc finger domains, were indispensable for asymmetrical RNA accumulation, while the N-terminal 5 to 45 and C-terminal 181 to 209 amino acid residues were not absolutely required. Mutation of conserved cysteine residues to alanines in the zinc finger domain resulted in loss of activity of the p23 protein, suggesting involvement of the zinc finger in asymmetric RNA accumulation. The absence of p23 gene function was manifested by substantial increases in accumulation of negative-stranded RNAs and only modest decreases in positive-stranded RNAs. Moreover, the substantial decrease in the accumulation of negative-stranded coat protein (CP) sgRNA in the presence of the functional p23 gene resulted in a 12- to 15-fold increase in the expression of the CP gene. Apparently the excess negative-stranded sgRNA reduces the availability of the corresponding positive-stranded sgRNA as a messenger. Thus, the p23 protein controls asymmetric accumulation of CTV RNAs by downregulating negative-stranded RNA accumulation and indirectly increases expression of 3′ genes.
The Cross-Section of Foreign Currency Risk Premia and Consumption Growth Risk

Aggregate consumption growth risk explains why low interest rate currencies do not appreciate as much as the interest rate differential and why high interest rate currencies do not depreciate as much as the interest rate differential. Domestic investors earn negative excess returns on low interest rate currency portfolios and positive excess returns on high interest rate currency portfolios. Because high interest rate currencies depreciate on average when domestic consumption growth is low and low interest rate currencies appreciate under the same conditions, low interest rate currencies provide domestic investors with a hedge against domestic aggregate consumption growth risk.
Inhibition of Different Lassa Virus Strains by Alpha and Gamma Interferons and Comparison with a Less Pathogenic Arenavirus

ABSTRACT The high pathogenicity of Lassa virus is assumed to involve resistance to the effects of interferon (IFN). We have analyzed the effects of alpha IFN (IFN-α), IFN-γ, and tumor necrosis factor alpha (TNF-α) on replication of Lassa virus compared to the related, but less pathogenic, lymphocytic choriomeningitis virus (LCMV). Three low-passage Lassa virus strains (AV, NL, and CSF), isolated from humans with mild to fulminant Lassa fever, were tested. Lassa virus replication was inhibited by IFN-α and IFN-γ, but not TNF-α, in Huh7 and Vero cells. The degree of IFN sensitivity of a Lassa virus isolate did not correlate with disease severity in human patients. Furthermore, cytokine effects observed for Lassa virus and LCMV (strains CH-5692, Armstrong, and WE) were similar. To address the mechanisms involved in the IFN effect, we used cell lines in which overexpression of IFN-stimulated proteins promyelocytic leukemia protein (PML) and Sp100 could be induced. Both proteins reside in PML bodies, a cellular target of the LCMV and Lassa virus Z proteins. Overexpression of PML or Sp100 did not affect replication of either virus. This, together with the previous finding that PML knockout facilitates LCMV replication in vitro and in vivo (M. Djavani, J. Rodas, I. S. Lukashevich, D. Horejsh, P. P. Pandolfi, K. L. Borden, and M. S. Salvato, J. Virol. 75:6204-6208, 2001; W. V. Bonilla, D. D. Pinschewer, P. Klenerman, V. Rousson, M. Gaboli, P. P. Pandolfi, R. M. Zinkernagel, M. S. Salvato, and H. Hengartner, J. Virol. 76:3810-3818, 2002), describes PML as a mediator within the antiviral pathway rather than as a direct effector protein. In conclusion, the high pathogenicity of Lassa virus compared to LCMV is probably not due to increased resistance to the effects of IFN-α or IFN-γ. Both cytokines inhibit replication which is relevant for the design of antiviral strategies against Lassa fever with the aim of enhancing the IFN response.
Identification of Novel Antigenic Proteins in a Complex Anaplasma marginale Outer Membrane Immunogen by Mass Spectrometry and Genomic Mapping

ABSTRACT Immunization with purified Anaplasma marginale outer membranes induces complete protection against infection that is associated with CD4+ T-lymphocyte-mediated gamma interferon secretion and immunoglobulin G2 (IgG2) antibody titers. However, knowledge of the composition of the outer membrane immunogen is limited. Recent sequencing and annotation of the A. marginale genome predicts at least 62 outer membrane proteins (OMP), enabling a proteomic and genomic approach for identification of novel OMP by use of IgG serum antibody from outer membrane vaccinates. Outer membrane proteins were separated by two-dimensional electrophoresis, and proteins recognized by total IgG and IgG2 in immune sera of outer membrane-vaccinated cattle were detected by immunoblotting. Immunoreactive protein spots were excised and subjected to liquid chromatography-tandem mass spectrometry. A database search of the A. marginale genome identified 24 antigenic proteins that were predicted to be outer membrane, inner membrane, or membrane-associated proteins. These included the previously characterized surface-exposed outer membrane proteins MSP2, operon associated gene 2 (OpAG2), MSP3, and MSP5 as well as recently identified appendage-associated proteins. Among the 21 newly described antigenic proteins, 14 are annotated in the A. marginale genome and include type IV secretion system proteins, elongation factor Tu, and members of the MSP2 superfamily. The identification of these novel antigenic proteins markedly expands current understanding of the composition of the protective immunogen and provides new candidates for vaccine development.
Eclogite-Facies Mineral Inclusions in Clinozoisite from Paleozoic Blueschist, Central Chugoku Mountains, Southwest Japan: Evidence of Regional Eclogite-Facies Metamorphism

An eclogite-facies assemblage garnet + omphacite + rutile + glaucophane + quartz occurs as inclusions in clinozoisite porphyroblasts in a high-grade blueschist block in the Paleozoic Osayama serpentinite mélange of the Chugoku Mountains, southwest Japan. Textual relations, and parageneses and compositions of minerals, indicate that the high-grade block experienced peak eclogite-facies metamorphism (M 1) and subsequent blueschist-facies overprinting (M 2). Moreover, low-P amphibolite-facies minerals (M 0) that may represent remnants of pre-subduction conditions are locally preserved in the protolith. Omphacite + adjacent garnet inclusion pairs in clinozoisite give a minimum P = 1.1-1.3 GPa at T = ~480-550°C. Many petrologic similarities between the Osayama eclogite and the Hida Mountains eclogite provide evidence for a regional eclogite-facies metamorphism in Paleozoic terranes of southwest Japan. Considering available petrotectonic information regarding eastern Asia, we suggest two alternative models: (1) Japanese Paleozoic eclogites may represent "Pacific-type" subduction prior to collision between the Sino-Korean and Yangtze blocks, which occurred on both western and eastern sides of the Qinling-Dabie-Sulu belt; or (2) Japanese Paleozoic eclogites may represent part of a Paleozoic "Pacific-type" subduction chain, which is continuous from the China-Russia border through Japan southward to North Korea.
Using Climate Predictions to Better Serve Society's Needs

Societies have always faced challenges and opportunities arising from variations in climate and have often flourished or collapsed, depending on their ability to adapt to such changes. In light of these challenges, there is a growing and urgent need to improve society's resilience to climate-related hazards and better manage the risks and opportunities from climate variability and climate change. This situation was recognized by governments, scientists, and decision makers at the World Climate Conference-3 in 2009, subsequently leading to the creation of the Global Framework for Climate Services (GFCS) under the leadership of several United Nations agencies.
Sex differences in the prevalence of human birth defects: a population-based study.

BACKGROUND Sex differences in the prevalence of several human birth defects have often been reported in the literature, but the extent of sex differences for most birth defects is unknown. To determine the full extent of sex differences in birth defects in a population, we examined population-based data from the Metropolitan Atlanta Congenital Defects Program (MACDP). METHODS MACDP records were analyzed for 1968 through 1995. We determined the sex-specific prevalence of all major birth defects, using the total number of live births by sex during these years as the denominator. For each specific defect, we calculated a relative risk with regard to sex on the basis of the ratio of prevalence among males to prevalence among females. Male-female relative risks were also determined for total major birth defects and for several broad categories of defects. RESULTS The overall prevalence of major defects at birth was 3.9% among males and 2.8% among females. All but two of the major categories of birth defects (nervous system defects and endocrine system defects) had a higher prevalence among males. Defects of the sex organs were eight and one-half times more prevalent among males and accounted for about half of the increased risk of birth defects among males relative to females. Urinary tract defects were 62% more prevalent among males, and gastrointestinal tract defects were 55% more prevalent among males. Among specific defect types, twofold or greater differences in prevalence by sex were common. CONCLUSIONS Our data indicate that sex differences in the prevalence of specific human birth defects are common, and male infants are at greater risk for birth defects than female infants. Several mechanisms have been proposed to account for these differences.
From rotating needles to stability of waves; emerging connections between combinatorics, analysis and PDE

We survey the interconnections between geometric combinatorics (such as the Kakeya problem), arithmetic combinatorics (such as the classical problem of determining which sets contain arithmetic progressions), oscillatory integrals (such as the Bochner-Riesz, restriction, and local smoothing problems), and the local and global well-posedness theory for non-linear dispersive and wave equations.