Miracle-dz/UniFAR-FTUs huggingface dataset:
Illite-Smectite Mixed-Layer Minerals in the Hydrothermal Alteration of Volcanic Rocks: I. One-Dimensional XRD Structure Analysis and Characterization of Component Layers

For a series of mixed-layer illite-smectite (I-S) minerals from a drillhole near the Kakkonda geothermal field, one-dimensional structure analysis by X-ray diffraction (XRD) was performed using Casaturated specimens in both air-dried and ethylene glycol-solvated states. The expandability characteristics of component layers were also examined by means of alkylammonium exchange and Li saturation. The K content in the illite layers was 1.5–1.7/O20(OH)4 in the I-S series from 3 to 85% of I-layer content (% I). The layer charge of the smectite layer varied slightly within the range of 0.3–0.5/O10(OH)2 by alkylammonium exchange experiments and the expandability was independent of the beidellite content within a range of 0–0.5 by the Li-saturation test. The degree of long-range ordering represented by Reichweite (R) parameters varied from R0 to R3 via R1 and R2 with increase in % I. The I-S samples contained <10% vermiculite as the third component and the vermiculite content tended to decrease with progressive illitization.In contrast to the smectitic R0 samples (<10% I), more illitic R0 (e.g. 35% I) and >R1 I-S samples showed complicated expandability with alkylammonium exchange. The XRD patterns of dodecylammonium-exchanged I-S samples can be interpreted by random interstratification of several types of sub-units such as layer-doublets, layer-triplets and layer-quartets present in the crystallites. This interpretation is consistent with the variation in the occurrence probabilities of layer-multiplets calculated from the junction probabilities and the proportions of layers. Because the interpretation indicates that I-S is a stack of various types of the sub-units, the smectite illitization can be described by a systematic change in the type and proportion of the sub-units constituting crystallites.
Vertical soil water movement in a tropical rainforest catchment in northeast queensland

In a tropical rainforest catchment, shallow piezometers respond almost instantaneously to rainfall, but the dominant ground water recharge mechanisms are not well understood. To improve understanding, the downward movement of soil water on a runoff plot was traced using tritiated water injected at 0·20 m below the surface which marks the lower boundary of active subsurface storm flow. The tritium pulse was translated slowly down the profile, apparently dominated by interstitial piston flow on the lines described by Zimmermann's theoretical model. This recharge mechanism accounted for about 35 per cent of rainfall or 50 per cent of throughfall. The pulse's advance may have also been delayed by the upward movement of soil water indicated by the distribution of hydraulic potential under different hydrological conditions. The result was an increase in soil water transit time particularly below 1·0 m. There was also evidence in the tracer profiles for rapid by-pass flow but the volumes concerned could not be quantified in this experiment.
Effects of immunosuppressive treatment on microsomal prostaglandin E synthase 1 and cyclooxygenases expression in muscle tissue of patients with polymyositis or dermatomyositis

Objectives: To investigate the expression of microsomal prostaglandin E (PGE) synthase 1 (mPGES-1) and cyclooxygenase (COX) in muscle biopsies from patients with polymyositis or dermatomyositis before and after conventional immunosuppressive treatment. Methods: mPGES-1 and COX expression was evaluated by immunohistochemistry in muscle tissue from healthy individuals and from patients with polymyositis or dermatomyositis before and after conventional immunosuppressive treatment. The number of inflammatory cell infiltrates, T lymphocytes and macrophages was estimated before and after treatment. To localise the mPGES-1 expression double immunofluorescence was performed with antibodies against mPGES-1, CD3, CD68, CD163 and a fibroblast marker. A functional index was used to assess muscle function. Results: In patients with myositis, mPGES-1, COX-2 and COX-1 expression was significantly higher compared to healthy individuals and associated with inflammatory cells. Double immunofluorescence demonstrated a predominant expression of mPGES-1 in macrophages. Conventional immunosuppressive treatment resulted in improved but still lower muscle function than normal. A decreased number of CD68-positive macrophages and reduced COX-2 expression in muscle tissue was also seen. By contrast, following the same treatment no significant changes were observed in muscle tissue regarding number of infiltrates, T lymphocytes, CD163-positive macrophages or mPGES-1 protein levels. Conclusions: Increased expression of mPGES-1, COX-1 and COX-2 at protein level was observed in muscle tissue from patients with myositis compared to healthy individuals. Conventional immunosuppressive treatment led to a significant downregulation of COX-2 in myositis muscle tissue. However, the expression of mPGES-1 and COX-1 remained unchanged indicating a role of these enzymes in the chronicity of these diseases.
Risk Assessment Analysis of Accelerated Gully Erosion in Ikpoba Okha Local Government Area of Edo State, Nigeria

The problem of accelerated erosion has been on in Ikpoba-Okha Local Government Area (LGA) in particular and Nigeria at large for some decades now and all past attempts at solving the problem have proved ineffective and thus constituting risk to the people living around the gullies in the area. Therefore, this study aimed at determining sediment loss from the gully sites, the vulnerable areas and threat posed by impact of gullies in the study LGA. Oregbeni Housing Estate and Ede School gully erosion sites in the Ikpoba-Okha LGA were purposively selected for this study. Primary data were collected using GPS receiver.These include the geographic coordinates and elevation of the study gullies catchments which were integrated with the secondary data obtained from satellite image, topographic, geologic, road and lay out maps of the area using Arc GIS 9.3 software. The results of the satellite image classification analysis showed that accelerated gully erosion accounted for 2% (100466.57 m 2 ) of the total areal extent of the study LGA (5189010.57 m 2 ). Of this 2%, Queen Ede School gully accounted for 96957.13 m 2 . The total estimated sediment loss from Queen Ede School and Oregbeni Housing Estate gullies were 359,173.22 and 48,212.62 tonnes, respectively. These indicated severe land degradation in the study area.
A steeply dipping discontinuity in the lower mantle beneath Izu‐Bonin

We analyze the coda of teleseismic P waves to deterministically map seismic scatterers in a 1000 km on-a-side cube beneath the Izu-Bonin trench by migrating and stacking waveforms. This method was applied to several hundred short-period vertical-component western United States seismometer recordings of 17 deep-focus Izu-Bonin earthquakes. Except for isolated arrivals, the midmantle appears devoid of sharp discontinuities. S-to-P conversions at the 660-km discontinuity generated the largest signals; the 410-km discontinuity occasionally generated signals. Horizontal discontinuities poorly explain other signals; however, S-to-P conversions generated at a nearly north-south trending, steeply dipping discontinuity at 30°N, 145°E, and 1000 km beneath and parallel to the Izu-Bonin trench explain most additional signals. Observed coherent S-to-P conversions of 2-s period waves limit the width of a gradient zone to <7 km. Compressional and shear tomographic models [Grand et al., 1997; Widiyantoro, 1997] image a fast velocity structure at a similar depth and orientation extending southward from the middle of the Izu-Bonin trench to the Mariana trench. We interpret the sharp scattering surface as a subducted crust and the tomographically imaged structure as the cold thermal anomaly associated with an ancient slab. We observe neither the deep scatterer nor high-seismic wavespeeds north of 32°N. This feature is as much as 800 km east of recent deep earthquakes near 30°N and is at a latitude where the slab appears to extend horizontally on the 660-km discontinuity to the west of the seismicity. We suggest that this deep slab fragment was carried north 500–1000 km owing to oblique subduction. In this scenario, it would be associated with the near vertical subduction at the Mariana subduction zone.
Water Relations and CO2 Exchange of Tropical Bryophytes in a Lower Montane Rain Forest in Panama

: For 6 tropical bryophytes, measurements of the diel courses in water status and net CO2 exchange were made in a submontane tropical rain forest in Panama. In addition, the response of gas exchange to changes in photon flux density (PPFD) and thallus water content (WC) was studied under controlled conditions. Diel variation of WC was pronounced, and both low and high WC limited carbon gain considerably. Low PPFD, e.g. during rain storms, was less important in limiting CO2 exchange. More than half of the mean diurnal carbon gain of 2.9 mg C per g thallus carbon was lost during the night as respiration. Assuming that the average 24-h carbon gain was representative for the entire year, we estimated the net annual primary productivity of the mosses and liverworts to be 45% of the initial plant carbon content.
High‐resolution spectroscopy of the Io plasma torus during the Galileo mission

We present Doppler-resolved spectra of the Io plasma torus (IPT) acquired in September 1997 and October 1999. The spectra are used to demonstrate the decrease in T⊥(S+) with increasing radial distance beyond 6.0 RJ. In October 99, emissions of S III, O II, and S II were observed within a relatively short period allowing estimates of the mixing ratios of the three major species in the IPT immediately after the Galileo 124 encounter with Io. The results suggest that near the position of the ribbon feature, the three major species were nearly equally abundant. Comparison of the S II line ratio (which is electron density dependent) with the S II intensity suggests that the peak electron density in the ribbon may be just outside the position of the peak intensity of S II (the S II “ribbon”). Ion temperatures for S III were also derived. The data indicate that S III is not in thermal equilibrium with S II in the IPT (thereby supporting previous Galileo measurements). It has also been possible to study deviations from corotation in the IPT at high spatial resolution.
Effects of Chronic Exposure to an Environmentally Relevant Mixture of Brominated Flame Retardants on the Reproductive and Thyroid System in Adult Male Rats

Brominated flame retardants (BFRs) are incorporated into a wide variety of consumer products, are readily released into home and work environments, and are present in house dust. Studies using animal models have revealed that exposure to polybrominated diphenyl ethers (PBDEs) may impair adult male reproductive function and thyroid hormone physiology. Such studies have generally characterized the outcome of acute or chronic exposure to a single BFR technical mixture or congener but not the impact of environmentally relevant BFR mixtures. We tested whether exposure to the BFRs found in house dust would have an adverse impact on the adult male rat reproductive system and thyroid function. Adult male Sprague Dawley rats were exposed to a complex BFR mixture composed of three commercial brominated diphenyl ethers (52.1% DE-71, 0.4% DE-79, and 44.2% decaBDE-209) and hexabromocyclododecane (3.3%), formulated to mimic the relative congener levels in house dust. BFRs were delivered in the diet at target doses of 0, 0.02, 0.2, 2, or 20 mg/kg/day for 70 days. Compared with controls, males exposed to the highest dose of BFRs displayed a significant increase in the weights of the kidneys and liver, which was accompanied by induction of CYP1A and CYP2B P450 hepatic drug–metabolizing enzymes. BFR exposure did not affect reproductive organ weights, serum testosterone levels, testicular function, or sperm DNA integrity. The highest dose caused thyroid toxicity as indicated by decreased serum thyroxine (T4) and hypertrophy of the thyroid gland epithelium. At lower doses, the thickness of the thyroid gland epithelium was reduced, but no changes in hormone levels (T4 and thyroid-stimulating hormone) were observed. Thus, exposure to BFRs affected liver and thyroid physiology but not male reproductive parameters.
Species-Speciﬁc Variation in RELA Underlies Differences in NF- (cid:1) B Activity: a Potential Role in African Swine Fever Pathogenesis (cid:1)

African swine fever virus (ASFV) is a highly infectious disease of domestic pigs, with virulent isolates causing a rapidly fatal hemorrhagic fever. In contrast, the porcine species endogenous to Africa tolerate infection. The ability of the virus to persist in one host while killing another genetically related host implies that disease severity may be, in part, modulated by host genetic variation. To complement transcription proﬁling ap-proaches to identify the underlying genetic variation in the host response to ASFV, we have taken a candidate gene approach based on known signaling pathways that interact with the virus-encoded immunomodulatory protein A238L. We report the sequencing of these genes from different pig species and the identiﬁcation and initial in vitro characterization of polymorphic variation in RELA (p65; v-rel reticuloendotheliosis viral oncogene homolog A), the major component of the NF- (cid:1) B transcription factor. Warthog RELA and domestic pig RELA differ at three amino acids. Transient cell transfection assays indicate that this variation is reﬂected in reduced NF- (cid:1) B activity in vitro for warthog RELA but not for domestic pig RELA. Induction assays indicate that warthog RELA and domestic pig RELA are elevated essentially to the same extent. Finally, mutational studies indicate that the S531P site conveys the majority of the functional variation between warthog RELA and domestic pig RELA. We propose that the variation in RELA identiﬁed between the warthog and domestic pig has the potential to underlie the difference between tolerance and rapid death upon ASFV infection. Tris-glycine-SDS Tris-glycine mem-brane M2- peroxidase peroxidase (Sigma)-conjugated primary antibody antibody
The Uprooting of Trees: A Forest Process1

For many years the uprooting of trees has been recognized as a natural phenomenon. As such, it has usually been regarded as one of freakish occurrence noted for its direct and catastrophic results upon the trees immediately affected. Uprooting, it seems, has seldom been considered with enough perspective to reveal its basic relationship to the forest. A form of very detailed descriptive research was instigated in 1948 to document the developmental trends of the forest stands which had occurred on a 1-acre area. Uprooting was established conclusively as an important factor in the development of the area during the last 500 years. When uprooting is observed and interpreted on a limited area with the perspective afforded by 500 years, its role becomes that of a natural forest process, rather than a single event in the life history of a forest stand. As a process, it must be considered along with reproduction, growth, podsolization, and other generally recognized processes. Similarly, the series of actions and subsequent reactions associated with uprooting can be described quantitatively, qualitatively, and chronologically. More extensive research has indicated that uprooting is a general forest process in eastern North America. Its influences have many ramifications, and like most other natural processes, are highly variable. The soil is one of the components of the forest greatly affected by the process of uprooting.
Evolution of alluvial mudrock forced by early land plants

Mudrocks get a vegetative assist Mudrocks such as slate and shale are rarely found in stratigraphy older than about 500 million years. McMahon and Davies compiled a large database of mudrock occurrence over the past 3.5 billion years to help assess the origin of this ubiquitous rock type (see the Perspective by Fischer). Mudrocks appeared at the same time as did deep-rooted land plants. The interplay between plants and sedimentary rocks suggests that a change in erosion rate and the chemistry of sediments delivered to the oceans occurred around 500 million years ago. Science, this issue p. 1022; see also p. 994 Rooted land plants appear to help reduce erosion rate and promote mudrock lithification. Mudrocks are a primary archive of Earth’s history from the Archean eon to recent times, and their source-to-sink production and deposition play a central role in long-term ocean chemistry and climate regulation. Using original and published stratigraphic data from all 704 of Earth’s known alluvial formations from the Archean eon (3.5 billion years ago) to the Carboniferous period (0.3 billion years ago), we prove contentions of an upsurge in the proportion of mud retained on land coeval with vegetation evolution. We constrain the onset of the upsurge to the Ordovician-Silurian and show that alluvium deposited after land plant evolution contains a proportion of mudrock that is, on average, 1.4 orders of magnitude greater than the proportion contained in alluvium from the preceding 90% of Earth’s history. We attribute this shift to the ways in which vegetation revolutionized mud production and sediment flux from continental interiors.
Evolution of tropical and extratropical precipitation anomalies during the 1997–1999 ENSO cycle

The 1997–1999 El Niño–Southern Oscillation (ENSO) period was very powerful, but also well observed. Multiple satellite rainfall estimates combined with gauge observations allow for a quantitative analysis of precipitation anomalies in the tropics and elsewhere accompanying the 1997–1999 ENSO cycle. An examination of the evolution of the El Niño and accompanying precipitation anomalies revealed that a dry Maritime Continent (MC) preceded the formation of positive sea‐surface temperature (SST) anomalies in the eastern Pacific Ocean. Thirty‐ to sixty‐day oscillations in the winter of 1996–1997 may have contributed to this lag relationship. Furthermore, westerly wind burst events may have maintained the drought over the MC. The warming of the equatorial Pacific was then followed by an increase in convection. A rapid transition from El Niño to La Niña occurred in May 1998, but as early as October–November 1997, precipitation indices captured substantial changes in Pacific rainfall anomalies. The global precipitation patterns for this event were in good agreement with the strong consistent ENSO‐related precipitation signals identified in earlier studies. Differences included a shift in precipitation anomalies over Africa during the 1997–1998 El Niño and unusually wet conditions over northeast Australia during the later stages of the El Niño. Also, the typically wet region in the north tropical Pacific was mostly dry during the 1998–1999 La Niña. Reanalysis precipitation was compared with observations during this time period and substantial differences were noted. In particular, the model had a bias towards positive precipitation anomalies and the magnitudes of the anomalies in the equatorial Pacific were small compared with the observations. Also, the evolution of the precipitation field, including the drying of the MC and eastward progression of rainfall in the equatorial Pacific, was less pronounced for the model compared with the observations. Copyright © 2001 Royal Meteorological Society
The postcranial skeleton of the Middle Devonian lungfish Dipterus valenciennesi

Abstract The axial skeleton and fin supports of the Middle Devonian lungfish Dipterus are described from a range of specimens from the Orcadian Basin of Scotland. The axial skeleton of the trunk region consists of intercentra, relatively short ribs, and neural arches bearing two rows of supraneural spines; posteriorly, the intercentra are replaced by haemal arches. The notochord seems to have been essentially unconstricted. There may have been two pairs of cranial ribs. In general terms the vertebral column resembles that of Neoceratodus but is more fully ossified. The only known paired fin support of Dipterus is an archipterygial structure resembling those of Neoceratodus, with at least seven mesomeres and jointed pre- and postaxial radials. The pectoral fin is rotated as in modern lungfishes. The median fin supports all consist of basal plates supporting radials. In the posterior dorsal fin support the posterior radials form a branched structure. The heterocercal tail is supported by segmental radials. A new body reconstruction is presented. The characters possessed by Dipterus offer support for a lungfish–porolepiform sistergroup relationship. All known lungfishes fit into a single cumulative series of postcranial morphologies. The evidence for a paedomorphic trend in lungfish phylogeny is interesting but inconclusive.
Episodic gravitational collapse and migration of the mountain chain during orogenic roll‐on in the Himalayas

An ∼W–E belt of maximum bulk horizontal shortening (the orogen core) moved North relative to the overlying crust to form the Himalayan Syntaxes due to roll‐on of this portion of the Indian plate. This displacement occurred below a lengthy succession of gently dipping decollements that formed episodically at a depth of ∼30 km along the orogen core due to numerous periods of gravitational collapse and spreading of the overlying ductile crust. Successively developed basal decollements were deformed when continued bulk horizontal shortening of the orogen core below reasserted dominance over the effects of gravitational collapse above causing refolding about steeply dipping axial planes. This resulted in northwards migration of the orogen core above depths of ∼30 km causing rocks metamorphosing at depths of ∼22 km on the north side of the orogen core to be moved to its south side with no change in depth as roll‐on progressed. Garnet porphyroblasts record this lengthy history of lateral migration across the orogen within their inclusion trails. The ∼6.4 kbar average pressures accompanying it were obtained from the Mn, Fe and Ca contents of successive garnet cores. Garnet grew at depths of ∼22 km until movement towards the surface initiated on successively developed decollements that accommodated the volume constraints of gravitational collapse and spreading on both sides of the orogen. The speed of extrusional displacement increased the further the rocks migrated from the orogen core developing mylonitic schists around the porphyroblasts. This truncated inclusion trails against all matrix foliations as the porphyroblasts were carried towards the surface. Indeed, these rocks were multiply deformed during at least four distinct periods of deformation after mylonitization began and prior to exposure above the Main Central Thrust (MCT). Three or more sub‐vertical and sub‐horizontal foliations were formed during each of the five changes in FIA trend (foliation inflection/intersection axes in porphyroblasts) preserved in these rocks. The inclusion trail asymmetries and P‐T of garnet core growth accompanying each FIA reveal that the first four changes in FIA trend, which define periods of tectonism about one direction of horizontal bulk shortening (relative plate motion), occurred on the north side of the orogen core. The fifth occurred on the south side of the orogen core and the switch in shear sense on gently dipping foliation planes that resulted from this shift to the south eventually led to the development of the MCT. When magnetic anomaly 22 that formed in the Southern Indian Ocean Ridge is taken into account, these five changes in FIA trend correlate markedly with changes in the motion of India relative to a constant Eurasia from 50 to c. 25 Ma. They reveal that Eurasia moved NNW during FIAs 1, 3 and 4 and SSE during FIA 5 when the shear sense on gently dipping foliations switched to top to the S. They suggest collision of India with Eurasia took place at 50 Ma, immediately prior to the development of FIA 1.