Miracle-dz/UniFAR-FTUs huggingface dataset:
The application of sediment capping agents on phosphorus speciation and mobility in a sub-tropical dunal lake

Experimental sediment cores from Lake Ainsworth, Australia, were exposed to an induced 46-day, anoxic/oxic cycle in the laboratory, mimicking the seasonal thermal stratification cycle commonly observed in the lake’s waters every summer. Under oxic conditions the supply of phosphorus (P) and iron (Fe) to the overlying water was slow, however, induced anoxia led to an enhanced release of P and Fe from the sediments to the water column. An inverse relationship between total P, Fe and redox potential suggests that Lake Ainsworth sediments are redox sensitive. Phosphorus speciation analysis of Lake Ainsworth sediments revealed the presence of a large pool of organic P, reactive Fe-bound P, and CaCO3-bound P, the latter fraction decreasing during anoxic conditions. Two sediment-capping agents, a lanthanum modified bentonite clay and Bauxsol (a waste product from the aluminium smelting industry) were assessed for their ability to reduce the levels of P released from Lake Ainsworth sediments during the 46-day, anoxic/oxic cycle. The bentonite clay was highly effective at reducing plant available P in anoxic/oxic conditions, but levels of dissolved Fe were enhanced with its use. Although the use of Bauxsol to remove plant available P is not recommended in anoxic waters, its use in suspension in oxic waters warrants further study.
Interannual variability of Ulva prolifera blooms in the Yellow Sea

A massive Ulva prolifera bloom occurred in the Yellow Sea in 2008. Since then, green tide events have occurred every year and two other massive bloom events occurred in 2009 and 2013. In this article, we investigate the spatial and temporal patterns of U. prolifera green tides in the Yellow Sea during 2007–2013 using satellite images from operational MODIS instruments on board the Terra and Aqua satellites. Satellite sea surface temperature (SST) data and sea surface wind products were analysed to study their impacts on the occurrence and evolution of the floating macroalgae. Results show that the U. prolifera blooms were most likely caused by the rapid expansion of coastal Porphyra aquaculture in Jiangsu province, China. The SST was not a controlling factor influencing the size of the algal bloom or determining the blooming time. Surface wind played a significant role on the movement and distribution of the floating macroalgae, which causes an interannual variability in the spatial and temporal patterns of the U. prolifera blooms. The weak connection between the increase in Porphyra aquaculture and the size of the bloom implies that there must have been a nutrient supplier (or suppliers) for the extensive growth of the macroalgae in 2008, 2009, and 2013. The tide-induced upwelling between the Subei Bank and the western-central Yellow Sea seems to be a nutrient source.
Mineralogical correlation of surficial sediment from area drainages with selected sedimentary interbeds at the Idaho National Engineering Laboratory, Idaho

Ongoing research by the US Geological Survey at the INEL involves investigation of the migration of radioactive elements contained in low-level radioactive waste, hydrologic and geologic factors affecting waste movement, and geochemical factors that influence the chemical composition of the waste. Identification of the mineralogy of the Snake River Plain is needed to aid in the study of the hydrology and geochemistry of subsurface waste disposal. The US Geological Surveys project office at the Idaho National Engineering Laboratory, in cooperation with the US Department of Energy, used mineralogical data to correlate surficial sediment samples from the Big Lost River, Little Lost River, and Birch Greek drainages with selected sedimentary interbed core samples taken from test holes at the RWMC (Radioactive Waste Management Complex), TRA (Test Reactors Area), ICPP (Idaho Chemical Processing Plant), and TAN (Test Area North). Correlating the mineralogy of a particular present-day drainage area with a particular sedimentary interbed provides information on historical source of sediment for interbeds in and near the INEL. Mineralogical data indicate that surficial sediment samples from the Big Lost River drainage contained a larger amount of feldspar and pyroxene and a smaller amount of calcite and dolomite than samples from the Little Lost River and Birch Creek drainages. Mineralogical data from sedimentary interbeds at the RWMC, TRA, and ICPP correlate with surficial sediment of the present-day big Lost River drainage. Mineralogical data from a sedimentary interbed at TAN correlate with surficial sediment of the present-day Birch Creek drainage. 13 refs., 5 figs., 3 tabs.
MANIFOLDNET: A DEEP NEURAL NETWORK FOR MANIFOLD-VALUED DATA

Developing deep neural networks (DNNs) for manifold-valued data sets has gained much interest of late in the deep learning research community. Examples of manifold-valued data include data from omnidirectional cameras on automobiles, drones etc., diffusion magnetic resonance imaging, elastography and others. In this paper, we present a novel theoretical framework for DNNs to cope with manifold-valued data inputs. In doing this generalization, we draw parallels to the widely popular convolutional neural networks (CNNs). We call our network the ManifoldNet. As in vector spaces where convolutions are equivalent to computing the weighted mean of functions, an analogous definition for manifold-valued data can be constructed involving the computation of the weighted Fréchet Mean (wFM). To this end, we present a provably convergent recursive computation of the wFM of the given data, where the weights makeup the convolution mask, to be learned. Further, we prove that the proposed wFM layer achieves a contraction mapping and hence the ManifoldNet does not need the additional non-linear ReLU unit used in standard CNNs. Operations such as pooling in traditional CNN are no longer necessary in this setting since wFM is already a pooling type operation. Analogous to the equivariance of convolution in Euclidean space to translations, we prove that the wFM is equivariant to the action of the group of isometries admitted by the Riemannian manifold on which the data reside. This equivariance property facilitates weight sharing within the network. We present experiments, using the ManifoldNet framework, to achieve video classification and image reconstruction using an auto-encoder+decoder setting. Experimental results demonstrate the efficacy of ManifoldNet in the context of classification and reconstruction accuracy.
The interior structure of terrestrial planets : an application to Mars

The Earth's interior structure is well known from seismic experiments. From them we precisely know the size and state of the core and the density and rheological properties within the planet. This information, complemented with rock sample analysis, has been used to constrain the thermal state of the Earth and deduce the composition of the mantle and the core. By contrast, we know very little about the interior structure of other terrestrial planets. Our knowledge is limited to the bulk properties - such as the average densities and moment of inertia (except Venus) - and the fact that they all have at least a partially liquid core. Their composition and thermal state are only weakly constrained. With the aim of elucidating the interior structure, we construct detailed interior structure models applicable to terrestrial planets. We then show how knowledge of the model parameters can be inferred from the data provided by space missions, earth-bound measurements, and laboratory experiences from high pressure physics. As a case study, we infer the model parameters for two different data sets related to the planet Mars. The main aim of the first study is to constrain the state, size, and composition of the core by using existing geodesy data. In this study we do not infer the thermal state and mineralogy of the mantle but use results that have been obtained from independent studies relating to the thermal evolution and composition of Mars. The objective of the second study is to ascertain whether the mineralogy and the thermal state of the Martian mantle can be inferred by combining geodesy, seismic, and magnetic induction data. The first study shows that Mars has no solid inner core and that the liquid core contains a large fraction of sulfur. The absence of a solid inner is in agreement with the absence of a global magnetic field. We estimate the radius of the core to be 1616 +/-137 km and its sulfur concentration to be 12+/-6wt%. We also show that it is possible for Mars to have a thin layer of perovskite at the bottom of the mantle. The second study shows that the temperature of the mantle and its mineralogical composition can be determined with a high confidence. The robustness of our method is also tested by using incomplete and missing data sets.
Constant Rate of Loading Test on Ultra-Soft Soil

The conventional consolidation test on ultra-soft soil takes a long time to complete due to the viscous effect in the early stage of compression. Instead of conducting the test until the end-of-primary (EOP) consolidation at each loading step, the testing time can be shortened if the test is carried out at a constant rate of loading (CRL). In this study the CRL tests were carried out at various loading rates. The settlement and pore pressure behavior were studied, and a suitable rate of loading (1 kPa/800 s) was determined. The proposed rate of loading is slightly slower than the rate of loading for natural clay suggested by others. The transition point between viscous stage and soil stage can be determined from the measured peak pore pressure. The compression indices, the large strain coefficient of consolidation, and the coefficient of permeability can also be determined from the CRL test with the proposed equations. This paper discussed the experimental test on ultra-soft soil at a CRL.
Gyrothyris williamsi sp. nov. and inter-relationships of some taxa from waters around New Zealand and the southern oceans (Rhynchonelliformea: Terebratelloidea)

ABSTRACT This paper describes a terebratelloid articulate brachiopod, Gyrothyris williamsi sp. nov., based on 95 specimens from seamounts on the Lord Howe Rise, Coral Sea, SW Pacific Ocean. The new species is attributed to Gyrothyris on the basis of (a) morphological and growth trajectory similarities; (b) phylogenetic analyses of an alignment of DNA sequence (∼2900-sites) obtained from nuclear-encoded small- and large-subunit ribosomal RNA genes (SSU and LSU); and (c) the presence of a distinctive, two-part deletion in the LSU gene. It is distinguished morphologically from Gyrothyris mawsoni and its subspecies by both internal and external morphology and by its isolated geographical distribution, which extends the patchy, known range of this genus to an area some 2000 km north of its previous northern limit around New Zealand. Phylogenetic analyses of the rDNAs and of mitochondrial cox1 gene sequences (663 sites) confirm previous indications that the New Zealand endemic terebratelloid genera form a clade (Neothyris (Calloria, Gyrothyris, Terebratella), but the position of Terebratella with respect to Calloria and Gyrothyris remains weakly established. These sequences disagree inexplicably about the closeness of the relationship between Neothyris parva and N. lenticularis. Analyses of the first sequences from Calloria variegata, a species restricted to the Hauraki Gulf, New Zealand, are consistent with the possibility that it originated locally, and recently, from C. inconspicua. Magellania venosa from S. America/Falklands joins with Antarctic Magellania fragilis and M. joubini to form an rDNA clade that excludes Terebratalia as the putative sister-group of the New Zealand terebratelloid clade. The cox1 (but not the rDNA) sequences of the New Zealand clade pass a test for clock-like rates of evolution, and maximum likelihood pairwise distances suggest that if genetic isolation between the ancestor of Antarctic Magellania and the last common ancestor of the New Zealand terebratelloid clade was initiated by separation of the Antarctic and New Zealand plates ∼90 Mya, isolation from M. venosa was initiated earlier, perhaps ∼145 Mya. However, in the simple phylogenetic reconstruction presented here from cox1 sequences, S. American and Antarctic Magellania spp. do not yield a well-supported clade, perhaps because of differences in base composition.
Evaluation of high-resolution sea ice models on the basis of statistical and scaling properties of Arctic sea ice drift and deformation

Sea ice drift and deformation from models are evaluated on the basis of statistical and scaling properties. These properties are derived from two observation data sets: the RADARSAT Geophysical Processor System (RGPS) and buoy trajectories from the International Arctic Buoy Program (IABP). Two simulations obtained with the Louvain-la-Neuve Ice Model (LIM) coupled to a high-resolution ocean model and a simulation obtained with the Los Alamos Sea Ice Model (CICE) were analyzed. Model ice drift compares well with observations in terms of large-scale velocity field and distributions of velocity fluctuations although a significant bias on the mean ice speed is noted. On the other hand, the statistical properties of ice deformation are not well simulated by the models: (1) The distributions of strain rates are incorrect: RGPS distributions of strain rates are power law tailed, i.e., exhibit "wild randomness," whereas models distributions remain in the Gaussian attraction basin, i.e., exhibit "mild randomness. " (2) The models are unable to reproduce the spatial and temporal correlations of the deformation fields: In the observations, ice deformation follows spatial and temporal scaling laws that express the heterogeneity and the intermittency of deformation. These relations do not appear in simulated ice deformation. Mean deformation in models is almost scale independent. The statistical properties of ice deformation are a signature of the ice mechanical behavior. The present work therefore suggests that the mechanical framework currently used by models is inappropriate. A different modeling framework based on elastic interactions could improve the representation of the statistical and scaling properties of ice deformation.
Interannual variability of summer sea ice thickness in the Siberian and central Arctic under different atmospheric circulation regimes

Extensive drill hole and electromagnetic induction measurements of sea ice thickness in the Siberian and central Arctic Seas in the summers of 1993, 1995, and 1996 reveal significant interannual variability. In the Laptev Sea, minimum and maximum modal first-year ice thicknesses amounted to 1.25 and 1.85 m in 1995 and 1996, respectively. Ice thickness correlates with ice extent, which reached a record minimum in August 1995 and was well above average in 1996. These differences are explained by the strength and location of a summer cyclonic atmospheric circulation pattern affecting both ice advection and surface melt. From drifting buoys deployed in 1995 and satellite radar backscatter data, first- and second-year ice regimes are delineated. Differences in first-year ice backscatter coefficients between 1993, 1995, and 1996 are explained by differences in level ice surface roughness. The Lagrangian evolution of ice thickness between 1995 and 1996 is studied. While the shape of the thickness distribution does not change significantly, the mean (modal) ice thickness of the ice field increases from 1.80 m (1.25 m) in 1995 to 2.86 m (2.25 m) in 1996. The thickness distribution of second-year ice in 1996 closely agrees with that of level multiyear ice downstream in the Transpolar Drift obtained in 1991. In 1996, mean level ice thickness increases at 0.23 and 0.16 m deg−1 with latitude in the Kara and Laptev Sea sectors of the Arctic Ocean, respectively.
Transcriptional and Translational Mechanisms Controlling Circadian Rhythms in Drosophila: A Dissertation

Circadian rhythms are self-sustained 24-hour period oscillations present in most organisms, from bacteria to human. They can be synchronized to external cues, thus allowing organisms to anticipate environmental variations and optimize their performance in nature. In Drosophila , the molecular pacemaker consists of two interlocked transcriptional feedback loops. CLOCK/CYCLE (CLK/CYC) sits in the center and drives rhythmic transcription of period ( per ), timeless ( tim ), vrille ( vri ) and PAR domain protein 1 ( Pdp1 ). PER and TIM negatively feedback on CLK/CYC transcriptional activity, forming one loop, while VRI and PDP1 form the other by regulating Clk transcription negatively and positively, respectively. Posttranscriptional and posttranslational regulations also contribute to circadian rhythms. Although much has been learned about these feedback loops, we are still far from understanding how stable 24-hour period rhythms are generated. My thesis work was to determine by which molecular mechanisms kayak-α (kay-α) and Ataxin-2 (Atx2) regulate Drosophila circadian behavior. Both genes are required for the precision of circadian rhythms since knocking down either gene in circadian pacemaker neurons results in long period phenotype. The work on kay-α constitutes the first half of my thesis. We found that the transcription factor KAY-α can bind to VRI and inhibit VRI’s repression on the Clk promoter. Interestingly, KAY-α can also repress CLK’s transcriptional activity on its target genes (e.g., per and tim ). Therefore, KAY-α is proposed to bring precision and stability to the molecular pacemaker by regulating both transcriptional loops. The second half of my thesis focuses on ATX2, an RNA binding protein whose mammalian homolog has been implicated in neurodegenerative diseases. We found that ATX2 is required for PER accumulation in circadian pacemaker neurons. It forms a complex with TWENTY-FOUR (TYF)—a crucial activator of PER translation—and promotes TYF’s interaction with Poly(A)-binding protein. This work reveals the role of ATX2 in the control of circadian rhythms as an activator of PER translation, in contrast to its well-established role as a repressor of translation. It also further demonstrates the importance of translational regulation on circadian rhythms. Finally, it may help understanding how ATX2 causes neuronal degeneration in human diseases.
Sex-Related Differences in the Outcomes of Endovascular Interventions for Chronic Limb-Threatening Ischemia: Results from the LIBERTY 360 Study

to determine whether there are sex-related differences in of with derived from the LIBERTY 360 study Hazard ratios and the respective 95% con ﬁ dence intervals were synthesized to examine the association between sex and all-cause mortality, target vessel revascularization (TVR), major amputation, major adverse event (MAE) and major amputation/ death up to 3 years of follow-up. Results: A total of 689 patients with CLTI (female: N=252 vs male: N=437) treated with any FDA approved or cleared device were The mean lesion length was 126.9 ±117.3mm and 127.4±113.3mm for the female and male patients, respectively. Although a slightly higher incidence of in-hospital mortality was observed in the female group (1.2% vs 0.0%, p=0.049), there was no difference in female vs male survival rates during follow-up. However, the risk of major amputation at 18 months was higher for the male group (male vs female: HR: 2.36; 95% CI: 1.09 – 5.12; p=0.030). No difference between the two groups was detected in terms of TVR or MAE during follow-up. Discussion: Data regarding sex-related disparity in outcomes after endovascular therapy of patients with CLTI are con ﬂ icting. Gender-related characteristics rather than biological sex characteristics might be the cause of these con ﬂ icting ﬁ ndings. Further studies are needed to evaluate the role of sex in revascularization outcomes among this high-risk population.
Turbulent mixing and the chemical breakdown of isoprene in the atmospheric boundary layer

In this paper we study the effect of turbulence on the oxidation rate of isoprene and its reaction products in the atmospheric boundary layer. We use two models of different complexity: a simple model consisting of two well-mixed layers and a one-dimensional off-line second-order closure model. Both models include an extensive set of chemical reactions to describe the oxidation of isoprene. A 5-day simulation is performed to compare the simple model output with data from the Amazon Boundary Layer Experiment (ABLE-2A). The model is able to represent fairly the basic dynamics and chemistry during this experiment. Subsequently, the simple model provides boundary and initial conditions for a one-dimensional second-order closure model that is used to assess the impact of higher-order chemistry terms on turbulent mixing and chemical transformations. We focus on covariances of NO with (peroxy-) radicals and covariances of OH with stable intermediate products. We find only small effects on the effective reaction rates due to the OH covariances. A significant effect is found of the covariances of NO, inhibiting the effective reaction rates with the peroxy radicals by a maximum of 10% in the afternoon. The inclusion of covariance terms resulted in an increase of radical concentrations, but the NO concentration profiles remained unchanged. Higher-order chemistry terms do have an effect on NO and NO2 fluxes, which change by 5 to 30% in the middle of the boundary layer. Therefore these terms have to be taken into account when flux-gradient relationships or deposition velocities are derived from observations. The present results indicate that the incorporation of higher-order chemistry terms is not essential for a correct representation of the mean profiles of most stable species involved.
RED CELLS, IRON, AND ERYTHROPOIESIS MASL1 induces erythroid differentiation in human erythropoietin-dependent CD34 1 cells through the Raf/MEK/ERK pathway

Human erythropoiesis is a dynamic and complex multistep process involving differentiation of early erythroid progenitors into enucleated RBCs. The mechanisms underlying erythropoiesis still remain incompletely understood. We previously demonstrated that erythropoietin-stimulated clone-1, which is selectively expressed in normal human erythroid-lineage cells, shares 99.5% identity with malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1 (MASL1). In this study, we hypothesized that the MASL1 gene plays a role in erythroid differentiation, and used a humanerythroid cellculture systemtoexplore thisconcept. MASL1mRNA and proteinexpressionlevelswere significantly increased during the erythroid differentiation of CD34 1 cells following erythropoietin (EPO) treatment. Conversely, MASL1 knockdown reduced erythroid differentiation in EPO-treated CD34 1 cells. In addition, MASL1 knockdown interrupted the Raf/MEK/ERK signaling pathway in CD34 1 cells. MASL1 mutant-transfected CD34 1 cells also showed decreased erythroid differentiation. Furthermore, inhibition of the SH3 domain of Son of Sevenless, which is an upstream adapter protein in EPO-induced erythroid differentiation, also reduced MASL1 expression and phosphorylation of Raf/MEK/ERK kinases that consequently reduced erythroid differentiation of EPO-induced CD34 1 cells. Importantly,wealso demonstrated thatMASL1interactsphysicallywith Raf1. Taken together,ourdataprovidenovelinsightsinto MASL1 regulation of erythropoiesis through the Raf/MEK/ERK pathway. ( Blood . 2013;121(16):3216-3227)