Miracle-dz/UniFAR-FTUs huggingface dataset:
A color guide to the petrography of sandstones, siltstones, shales and associated rocks

AAPG Memoir 109 is designed as a practical guide for students and professionals to learn the fundamentals of microscopic examination of sandstones, mudrocks, and associated rocks. With more than 1100 color illustrations, it covers the identification of grains, textures, and structures of clastic terrigenous rocks as well as their diagenetic alteration (compaction, cementation, dissolution, and replacement) and porosity reduction or enhancement. It also provides classification diagrams for formal description of those rocks and their porosity. Although the majority of the outcrop and subsurface examples come from the United States (35 states and Puerto Rico), there are representative photographs from 32 other countries, including many from the offshore areas. The foldout birefringence chart and an included DVD with Powerpoint files of all of the petrographic images provide additional aids for instructors and students.
DISSOCIATION OF CELLULAR IMMUNITY TO BRAIN PROTEIN AND DISEASE PRODUCTION

Fxperimental allergic encephalitis (EAE) ~ is a disease produced in animals by the injection, in complete Freund's adjuvant (CFA), of encephalitogenic protein (EP) derived from brain. The evidence is strong that the disease results from an immune response to the injected antigen and, until recently, it was believed that delayed sensitivity to the EP was directly related to the production of disease. It is possible to chemically modify the EP by treating it with 2-hydroxy-5-nitro-benzyl bromide (HNB) which blocks the single tryptophan residue and renders the molecule inactive in producing disease (1). The HNB-treated molecule is therefore termed nonencephalitogenic protein (NEP). The entire amino acid sequence of the EP derived from brain has recently been reported (2), and the major encephalitogenic determinant has been characterized and synthesized (3). It is a nonapeptide having the amino acid sequence Phe-Ser-Trp-AlaGlu-Gly-Gln-Lys. Additional studies showed that three amino acids were essential for the cncephalitogenic property of the peptides: Trp, Gin, and Lys, although the Lys could be replaced by another amino acid, Arg. The other amino acids in the sequence could be altered without destroying the encephalitogenic activity of the peptide (4). We have used these well-characterized antigens to further study cellular imnlunity in relationship to EAE. The present communication reports the results of experiments to determine cellular immune response to the EP, t he
LYMPHOID NEOPLASIA STAT3 mediates oncogenic addiction to TEL-AML1 in t(12;21) acute lymphoblastic leukemia

The t(12;21)(p13;q22) translocation is the most common chromosomal abnormality in pediatric leukemia. Although this rearrangement involves 2 well-characterized transcription factors, TEL and AML1, the molecular pathways affected by the result of the translocation remain largely unknown. Also in light of recent studies showing genetic and functional heterogeneities in cells responsible for cancer clone maintenance and propagation, targeting a single common deregulated pathway may be critical for the success of novel therapies. Here we describe a novel signaling pathway that is essential for oncogenic addiction in TEL-AML1 leukemia. Our data indicate a direct role for TEL-AML1, via increasing the activity of RAC1, in regulating the phosphorylation of signal transducer and activator of transcription 3 (STAT3), which results in transcriptional induction of MYC. We demonstrate that human leukemic cell lines carrying this translocation are highly sensitive to treatment with S3I-201, a specific STAT3 inhibitor, and, more interestingly, that primary human leukemic samples are also responsive to the drug in the same concentration range. Thus, STAT3inhibition representsa promising possibletherapeuticstrategy for the treatmentof TEL-AML1 leukemia. ( Blood . 2013;122(4):542-549)
An Inquiry into the Nature and Causes of the Wealth of Nations

It was the publication in 1776 of Adam Smith’s Inquiry into the Nature and Causes of the Wealth of Nations that marked the beginning of the ideological revolution explored in this article. Political economy had been much debated in the previous hundred years, but Smith’s formulation set the terms of discussion and over the next fifty years displaced a centuries-old rhetoric of economic values that had celebrated moderation, restraint, stewardship, and charity over greed, lust, and self-interest. During the American revolutionary era, when restless colonial elites began crafting explanations for their independence project, the publication of Smith’s treatise on political economy put into play a new framework for considering the wealth of nations. This new framework resonated as a scientific discourse alongside the equally important new “science of politics” made famous by the revolutionary Whigs. It resonated as well with the new sciences of nature that lately had been exposing immutable “laws” by which human beings now explained their physical world. In each realm—economy, politics, and the natural world—scientific reasoning promised to disable the tyranny of ancient prerogatives, superstitions, illegitimate customs, and fantastical explanations. These new scientific perspectives sometimes intersected directly and sometimes influenced each other only by induction.
The Daily Grind: Cash Needs, Labor Supply and Self-Control∗

Using detailed data on labor supply and daily shocks among 257 bicycle taxi drivers in Western Kenya, we show that labor supply responds to both unexpected and expected demands on income on the day money is needed, but does not adjust in days prior to expected needs. We find that the quitting hazard within a given work day increases discontinuously once earned income reaches the day’s cash need. We conjecture that workers set a personal rule of “earning enough for the day’s need” as an internal commitment device to provide effort. Since demands on income are empirically uncorrelated with the wage rate, this rule generates a negative wage elasticity. The inability to better arbitrage intertemporally has substantial welfare costs: greater variance in hours worked is associated with worse health, and we estimate a lower bound on lost
Polyphase formation and exhumation of high‐ to ultrahigh‐pressure rocks in continental subduction zone: Numerical modeling and application to the Sulu ultrahigh‐pressure terrane in eastern China

[1] High- to ultrahigh-pressure (HP-UHP) metamorphic rocks commonly form and exhume during the early continental collision, and many questions related to their origin still remain unresolved. We focus our study on explaining the poly metamorphic origins of many HP-UHP terranes composed of tectonic units having strongly variable ages, peak metamorphic conditions, and P-T paths. These features are especially well characterized for the Sulu UHP terrane in eastern China which we have chosen therefore as the reference case. We conducted 2-D thermomechanical numerical modeling of continental subduction associated with formation and exhumation of HP-UHP rocks. Our experiments suggest existence of several consequent episodes of (U)HP rocks exhumation related to the inherently cyclic origin of continental crust subduction-detachment-exhumation processes. Three major phases of these processes are identified in our reference model for the Sulu UHP terrane: (1) first and (2) second exhumation episodes of HP rocks originated in the subduction channel at lithospheric depths and (3) exhumation of UHP rocks originated at asthenospheric depths. Numerical models also suggest that subducted UHP rocks which are positively buoyant compared to the mantle may detach from the slab forming a flattened plume underplating the overriding lithosphere. This sublithospheric plume may exist for several million years being heated to 800–900°C by the surrounding hot mantle. At the later stage, upward extrusion of hot partially molten rocks from the plume may exhume high-temperature (HT) UHP complexes toward the surface.
Scale-Dependent Correspondence of Floristic and Edaphic Gradients across Salt Marsh Creeks

Biogeographers emphasize the presence of scale-dependence in vegetation–environment relationships. This research addresses the issue of scale-dependence, focusing on spatial correspondence of floristic and edaphic gradients across salt marsh creeks at Skallingen, Denmark. We employed a hierarchical approach, which compared vegetation and soil gradients at both fine and coarse scales. At the fine scale, we used ordination techniques to identify the gradient structure of vegetation and soil data acquired in 1-m2 plots along transects across creeks. For the coarse-scale comparison, we systematically aggregated the fine-scale information (i.e., gradient structure) into larger blocks, or topographic zones such as point bar, cutbank edge, and marsh interiors. We found poor correlations between vegetation and soil at the fine scale but an improved correspondence at the coarse scale. The poor correspondence was caused by differential spatial extents that the vegetation and soil factors exhibited responding to environmental variations. At the fine scale, modes of plant–plant interactions were the key determinant of species composition and varied significantly across tidal creeks. Soil properties responded less sensitively to topographic and hydrologic changes than vegetation did, however. As the scale of our analysis increased, the fine-scale floristic variation averaged out, and the overall compositional patterns were then governed by broader variations in environmental (edaphic) constraints. Our research accommodates the importance of both biological and environmental components by explicitly emphasizing their simultaneous significance, each perceived at different spatial scales. We conclude that the concept of scale-dependence might serve as an efficient conceptual framework in salt marsh biogeography.
Is the Martian crust also the Martian elastic lithosphere

[1] Correlations between topography, gravity, and areoid on Mars are used to constrain the crustal and lithospheric thicknesses on the planet. Assuming that the Hellas basin is in isostatic equilibrium with Airy compensation, point correlations between areoid anomalies and topography are used to obtain the mean crustal density and the crustal thickness. We find that the crustal thickness at the reference zero elevation is 90 ± 10 km. We also find that the mean crustal density is 2960 ± 50 kg m−3. We have also used several approaches to constrain the thickness of the elastic lithosphere. Using the spherical harmonic coefficients of the gravity potential and topography as a function of degrees, a relatively weak constraint on the globally averaged thickness of the elastic lithosphere is obtained. An improved constraint is obtained using wavelet transform analyses of great circle tracks of gravity and topography. The gravity-topography admittance as a function of wavelet wavelength constrains the globally averaged thickness of the elastic lithosphere to be in the range 90 ± 10 km. The observation that the mean thicknesses of the crust and elastic lithosphere are likely to be equal suggests that a rheologically tougher crust is the elastic lithosphere.
The 1999 Hector Mine Earthquake, Southern California: Vector Near-Field Displacements from ERS InSAR

Two components of fault slip are uniquely determined from two line-of-sight (LOS) radar interferograms by assuming that the fault-normal component of displacement is zero. We use this approach with ascending and descending interferograms from the ERS satellites to estimate surface slip along the Hector Mine earthquake rupture. The LOS displacement is determined by visually counting fringes to within 1 km of the outboard ruptures. These LOS estimates and uncertainties are then transformed into strike- and dip-slip estimates and uncertainties; the transformation is singular for a N–S oriented fault and optimal for an E–W oriented fault. In contrast to our previous strike-slip estimates, which were based only on a descending interferogram, we now find good agreement with the geological measurements, except at the ends of the rupture. The ascending interferogram reveals significant west-side-down dip-slip (∼1.0 m) which reduces the strike-slip estimates by 1 to 2 m, especially along the northern half of the rupture. A spike in the strike-slip displacement of 6 m is observed in central part of the rupture. This large offset is confirmed by subpixel cross correlation of features in the before and after amplitude images. In addition to strike slip and dip slip, we identify uplift and subsidence along the fault, related to the restraining and releasing bends in the fault trace, respectively. Our main conclusion is that at least two look directions are required for accurate estimates of surface slip even along a pure strike-slip fault. Models and results based only on a single look direction could have major errors. Our new estimates of strike slip and dip slip along the rupture provide a boundary condition for dislocation modeling. A simple model, which has uniform slip to a depth of 12 km, shows good agreement with the observed ascending and descending interferograms.
Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize[W]

Maize (Zea mays) has an exceptionally complex genome with a rich history in both epigenetics and evolution. We report genomic landscapes of representative epigenetic modifications and their relationships to mRNA and small RNA (smRNA) transcriptomes in maize shoots and roots. The epigenetic patterns differed dramatically between genes and transposable elements, and two repressive marks (H3K27me3 and DNA methylation) were usually mutually exclusive. We found an organ-specific distribution of canonical microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), indicative of their tissue-specific biogenesis. Furthermore, we observed that a decreasing level of mop1 led to a concomitant decrease of 24-nucleotide siRNAs relative to 21-nucleotide miRNAs in a tissue-specific manner. A group of 22-nucleotide siRNAs may originate from long-hairpin double-stranded RNAs and preferentially target gene-coding regions. Additionally, a class of miRNA-like smRNAs, whose putative precursors can form short hairpins, potentially targets genes in trans. In summary, our data provide a critical analysis of the maize epigenome and its relationships to mRNA and smRNA transcriptomes.
Redescription of Drepanopterus abonensis (Chelicerata: Eurypterida: Stylonurina) from the late Devonian of Portishead, UK

Abstract: Stylonurid eurypterids (Arthropoda: Chelicerata) include some of the largest known arthropods – bizarre sweep‐feeding hibbertopterids from the Carboniferous to end‐Permian. New material of Drepanopterus abonensis, a stylonurid from the Late Devonian (Famennian) of Portishead, south‐west England, offers key insights into this genus and its affinities. A redescription utilising the new material enables D. abonensis to be assigned as basal member of the Superfamily Hibbertopteroidea, the large‐sweep‐feeding forms, possessing a cleft metastoma and blades (modified blunt spines) on their anterior prosomal appendages. D. abonensis also shares characters such as a clavate telson and median ridge on the carapace with the proposed hibbertopteroid sister group the Kokomopteroidea. Hibbertopteroid eurypterids are the most long‐ranging stylonurids, surviving the decline and extinction of the other eurypterid families in the Late Devonian, their survival probably because of their sweep‐feeding mode of life, which was not in direct competition with their eurypterine relatives and other predators.
From Zero-offset to Common-offset with Diffractions

The simulation of a zero-offset section leads to a first interpretable time image and is still one of the key processing steps. While recent works have indicated that common-offset stacking leads to improved resolution and illumination in complex settings, the zero-offset approximations are reasonably accurate, when lateral heterogeneity is moderate. Due to the increased dimensionality of the problem, the common-offset stack is computationally expensive, though. We suggest a hybrid scheme in which the zero-offset operators are locally refined by their common-offset counterparts. We show that for diffractions, the necessary connection between the attributes is achieved by simple geometrical reasoning. Synthetic examples indicate that due to the symmetry of raypaths, the zero-offset diffraction attributes can directly be used to perform a common-offset stack, promising a high potential for improved prestack separation and inversion.
Prediction of liquid-liquid phase separation proteins using machine learning

The liquid-liquid phase separation (LLPS) of bio-molecules in cell underpins the formation of membraneless organelles, which are the condensates of protein, nucleic acid, or both, and play critical roles in cellular functions. The dysregulation of LLPS might be implicated in a number of diseases. Although the LLPS of biomolecules has been investigated intensively in recent years, the knowledge of the prevalence and distribution of phase separation proteins (PSPs) is still lag behind. Development of computational methods to predict PSPs is therefore of great importance for comprehensive understanding of the biological function of LLPS. Here, a sequence-based prediction tool using machine learning for LLPS proteins (PSPredictor) was developed. Our model can achieve a maximum 10-CV accuracy of 96.03%, and performs much better in identifying new PSPs than reported PSP prediction tools. As far as we know, this is the first attempt to make a direct and more general prediction on LLPS proteins only based on sequence information.
Cardiac Arrhythmogenic Remodeling in a Rat Model of Long-Term Intensive Exercise Training

Background— Recent clinical studies suggest that endurance sports may promote cardiac arrhythmias. The aim of this study was to use an animal model to evaluate whether sustained intensive exercise training induces potentially adverse myocardial remodeling and thus creates a potential substrate for arrhythmias. Methods and Results— Male Wistar rats were conditioned to run vigorously for 4, 8, and 16 weeks; time-matched sedentary rats served as controls. Serial echocardiograms and in vivo electrophysiological studies at 16 weeks were obtained in both groups. After euthanasia, ventricular collagen deposition was quantified by histological and biochemical studies, and messenger RNA and protein expression of transforming growth factor-&bgr;1, fibronectin-1, matrix metalloproteinase-2, tissue inhibitor of metalloproteinase-1, procollagen-I, and procollagen-III was evaluated in all 4 cardiac chambers. At 16 weeks, exercise rats developed eccentric hypertrophy and diastolic dysfunction, together with atrial dilation. In addition, collagen deposition in the right ventricle and messenger RNA and protein expression of fibrosis markers in both atria and right ventricle were significantly greater in exercise than in sedentary rats at 16 weeks. Ventricular tachycardia could be induced in 5 of 12 exercise rats (42%) and only 1 of 16 sedentary rats (6%; P=0.05). The fibrotic changes caused by 16 weeks of intensive exercise were reversed after an 8-week exercise cessation. Conclusions— In this animal model, we documented cardiac fibrosis after long-term intensive exercise training, together with changes in ventricular function and increased arrhythmia inducibility. If our findings are confirmed in humans, the results would support the notion that long-term vigorous endurance exercise training may in some cases promote adverse remodeling and produce a substrate for cardiac arrhythmias.
Effects of changes in environmental conditions on atmospheric mercury exchange: Comparative analysis from a rice paddy field during the two spring periods of 2001 and 2002

It was however found that the soil-air exchange patterns of Hg during the two study periods, although investigated in similar seasonal cycles, contrast to a large extent. Upward emission prevailed in both the frequency and magnitude during the 1st study period, but dry deposition was seen more dominantly in terms of frequency during the 2nd study period. In light of the fact that the occurrence patterns of Asian Dust events differed greatly between the two study periods, the possible role of long-range transport of airborne pollutants (LRTAP) as sources of Hg into the study area has also been examined using information on air mass movement patterns. Because observed differences in Hg flux patterns generally reflect changes in environmental conditions across study periods, the bi-directional exchange patterns of Hg during the two field campaigns were explained in relation to highly diverse environmental conditions that persisted in each study period. INDEX TERMS: 6235 Planetology: Solar System Objects: Mercury; 0312 Atmospheric Composition and Structure: Air/sea constituent fluxes (3339, 4504); 7534 Solar Physics, Astrophysics, and Astronomy: Radio emissions; 0342 Atmospheric Composition and Structure: Middle atmosphere—energy deposition; KEYWORDS: regional background, soil-air exchange, emission, dry deposition, mercury Citation: Kim, K. -H. , M. -Y. Kim, J. Kim, and G. Lee, Effects of changes in environmental conditions on atmospheric mercury exchange: Comparative analysis from a rice paddy field during the two spring periods of 2001 and 2002, J. Geophys. Res., 108(D19), 4607, doi:10.1029/2003JD003375, 2003.
Zooplankton grazing dynamics: top‐down control of phytoplankton and its relationship to an estuarine habitat

Top‐down control of algal blooms was investigated in the Swan–Canning Estuary, to determine whether the resident zooplankton community was able to substantially reduce phytoplankton biomass through grazing, or whether high phytoplankton biomass effectively inhibited grazing. In situ grazing by zooplankton at two depths in the water column was measured over a diel period on six occasions and examined in relation to the biotic and abiotic habitat conditions.
Acoustic Doppler current profiler measurements of the velocity field of an ebb tidal jet

A broadband acoustic Doppler current profiler was used to measure the velocity field of the ebb tidal jet formed at the entrance to the Otago Harbour, South Island, New Zealand. Four separate surveys were conducted where various sets of transects were run continuously over a 13 hour period, producing time series of velocity profiles with 1 hour sampling over a grid with an across-jet resolution of 20 m and an along-jet resolution of 150 m. The velocity field of the ebb tidal jet is phase locked to the tidal response of the harbor, making it possible to combine the data from separate tidal cycle surveys to produce synoptic maps of the depth-averaged velocity field. The spatial structure of the ebb tidal jet at the time of peak flow exhibits many features of a classical plane jet. There is a strong asymmetry between the ebb and flood flow structures; the ebb flow extends beyond 2 km from the entrance, while the flood flow is limited to within 600 m of the coast. The flow along the jet axis becomes pulse-like in time with distance from the entrance. The pulse that develops propagates way from the entrance at a speed slower than the advective speed of the ebb jet. The formation of a propagating eddy observed along the eastern side of the jet suggests that this momentum pulse may be associated with the pair of separation eddies generated by the accelerating ebb tidal flow.