Miracle-dz/UniFAR-FTUs huggingface dataset:
Ancient Martian aeolian processes and palaeomorphology reconstructed from the Stimson formation on the lower slope of Aeolis Mons, Gale crater, Mars

Reconstruction of the palaeoenvironmental context of Martian sedimentary rocks is central to studies of ancient Martian habitability and regional palaeoclimate history. This paper reports the analysis of a distinct aeolian deposit preserved in Gale crater, Mars, and evaluates its palaeomorphology, the processes responsible for its deposition, and its implications for Gale crater geological history and regional palaeoclimate. Whilst exploring the sedimentary succession cropping out on the northern flank of Aeolis Mons, Gale crater, the Mars Science Laboratory rover Curiosity encountered a decametre‐thick sandstone succession, named the Stimson formation, unconformably overlying lacustrine deposits of the Murray formation. The sandstone contains sand grains characterized by high roundness and sphericity, and cross‐bedding on the order of 1 m in thickness, separated by sub‐horizontal bounding surfaces traceable for tens of metres across outcrops. The cross‐beds are composed of uniform thickness cross‐laminations interpreted as wind‐ripple strata. Cross‐sets are separated by sub‐horizontal bounding surfaces traceable for tens of metres across outcrops that are interpreted as dune migration surfaces. Grain characteristics and presence of wind‐ripple strata indicate deposition of the Stimson formation by aeolian processes. The absence of features characteristic of damp or wet aeolian sediment accumulation indicate deposition in a dry aeolian system. Reconstruction of the palaeogeomorphology suggests that the Stimson dune field was composed largely of simple sinuous crescentic dunes with a height of ca 10 m, and wavelengths of ca 150 m, with local development of complex dunes. Analysis of cross‐strata dip azimuths indicates that the general dune migration direction and hence net sediment transport was towards the north‐east. The juxtaposition of a dry aeolian system unconformably above the lacustrine Murray formation represents starkly contrasting palaeoenvironmental and palaeoclimatic conditions. Stratigraphic relationships indicate that this transition records a significant break in time, with the Stimson formation being deposited after the Murray formation and stratigraphically higher Mount Sharp group rocks had been buried, lithified and subsequently eroded.
Minimality and symplectic sums

Let X1, X2 be symplectic 4-manifolds containing symplectic sur- faces F1, F2 of identical positive genus and opposite squares. Let Z denote the symplectic sum of X1 and X2 along the Fi. Using relative Gromov-Witten theory, we determine precisely when the symplectic 4-manifold Z is minimal (i.e., cannot be blown down); in particular, we prove that Z is minimal unless either: one of the Xi contains a ( 1)-sphere disjoint from Fi; or one of the Xi admits a ruling with Fi as a section. As special cases, this proves a conjecture of Stipsicz asserting the minimality of fiber sums of Lefschetz fibrations, and implies that the non-spin examples constructed by Gompf in his study of the geography problem are minimal. Let (X1,! 1), (X2,! 2) be symplectic 4-manifolds, and let F1 ⊂ X1, F2 ⊂ X2 be two-dimensional symplectic submanifolds with the same genus whose homology classes satisfy (F1) 2 + (F2) 2 = 0, with the ! i normalized to give equal area to the surfaces Fi. For i = 1,2, a neighborhood of Fi is symplectically identified by Weinstein's symplectic neighborhood theorem (19) with the disc normal bundlei of Fi in Xi. Choose a smooth isomorphismof the normal bundle to F1 in X1 (which is a complex line bundle) with the dual of the normal bundle to F2 in X2. According to (2) (and independently (11)), the symplectic sum
The epstein‐barr‐virus‐encoded membrane protein LMP but not the nuclear antigen EBNA‐1 induces rejection of transfected murine mammary carcinoma cells

The EBV‐encoded membrane protein (LMP) and the nuclear antigen EBNA‐I were compared for their capacity to induce rejection of transfected murine mammary carcinoma cells in syngenelc hosts. The tumorigenic potential of stable LMP and EBNA‐I expressing sublines of the ACA (H‐2f)‐derived mammary carcinoma line S6C was tested in pre‐immunized syngeneic and semi‐syngeneic animals. LMP expressing S6C cells elicited a strong rejection response as demonstrated by the lower tumor take and slower growth in immunized vs. control mice. In contrast, EBNA‐I‐expressing cells were non‐immunogenic in syngeneic hosts and in one semi‐syngeneic F1‐hybrid. Rejection in 2 additional F1‐hybrids did not appear to be due to EBNA‐I‐specific immune responses. Our findings support the hypothesis that the escape of EBV carrying tumor cells from EBV‐specific immune surveillance may be facilitated by the fact that viral gene expression is limited to EBNA‐I.
Air Pollution and Mortality

We analyzed a national data base of air pollution and mortality for the 88 largest U.S. cities for the period 1987–1994, to estimate relative rates of mortality associated with airborne particulate matter smaller than 10 microns (PM10) and the form of the relationship between PM10 concentration and mortality. To estimate city-specific relative rates of mortality associated with PM10, we built log-linear models that included nonparametric adjustments for weather variables and longer term trends. To estimate PM10 mortality dose-response curves, we modeled the logarithm of the expected value of daily mortality as a function of PM10 using natural cubic splines with unknown numbers and locations of knots. We also developed spatial models to investigate the heterogeneity of relative mortality rates and of the shapes of PM10 mortality dose-response curves across cities and geographical regions. To determine whether variability in effect estimates can be explained by city-specific factors, we explored the dependence of relative mortality rates on mean pollution levels, demographic variables, reliability of the pollution data, and specific constituents of particulate matter. We implemented estimation with simulation-based methods, including data augmentation to impute the missing data of the city-specific covariates and the reversible jump Markov chain Monte Carlo (RJMCMC) to sample from the posterior distribution of the parameters in the hierarchical spline model. We found that previous-day PM10 concentrations were positively associated with total mortality in most the locations, with a . 5% increment for a 10 μg/m3 increase in PM10. The effect was strongest in the Northeast region, where the increase in the death rate was twice as high as the average for the other cities. Overall, we found that the pooled concentration-response relationship for the nation was linear.
Combining Knowledge- and Corpus-based Word-Sense-Disambiguation Methods

In this paper we concentrate on the resolution of the lexical ambiguity that arises when a given word has several different meanings. This specific task is commonly referred to as word sense disambiguation (WSD). The task of WSD consists of assigning the correct sense to words using an electronic dictionary as the source of word definitions. We present two WSD methods based on two main methodological approaches in this research area: a knowledge-based method and a corpus-based method. Our hypothesis is that word-sense disambiguation requires several knowledge sources in order to solve the semantic ambiguity of the words. These sources can be of different kinds--- for example, syntagmatic, paradigmatic or statistical information. Our approach combines various sources of knowledge, through combinations of the two WSD methods mentioned above. Mainly, the paper concentrates on how to combine these methods and sources of information in order to achieve good results in the disambiguation. Finally, this paper presents a comprehensive study and experimental work on evaluation of the methods and their combinations.
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

Cryo-EM has revealed many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions accurately positioning individual atoms remains challenging and may be error-prone. Manually refining thousands of amino acids – typical in a macromolecular assembly – is tedious and time-consuming. We present an automated method that can improve the atomic details in models manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining or improving the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.
Thioesterase Superfamily Member 2 (Them2) and Phosphatidylcholine Transfer Protein (PC-TP) Interact To Promote Fatty Acid Oxidation and Control Glucose Utilization

ABSTRACT Thioesterase superfamily member 2 (Them2) is a mitochondrion-associated long-chain fatty acyl coenzyme A (CoA) thioesterase that is highly expressed in the liver and oxidative tissues. Them2 activity in vitro is increased when it interacts with phosphatidylcholine transfer protein (PC-TP), a cytosolic lipid binding protein. Them2−/− and Pctp−/− mice exhibit enhanced hepatic insulin sensitivity and increased adaptive thermogenesis, and Them2−/− mice are also resistant to diet-induced hepatic steatosis. Although we showed previously that a Them2–PC-TP complex suppresses insulin signaling, the enzymatic activity of Them2 suggests additional direct involvement in regulating hepatic nutrient homeostasis. Here we used cultured primary hepatocytes to elucidate biochemical and cellular mechanisms by which Them2 and PC-TP regulate lipid and glucose metabolism. Under conditions simulating fasting, Them2−/− and Pctp−/− hepatocytes each exhibited decreased rates of fatty acid oxidation and gluconeogenesis. In results indicative of Them2-dependent regulation by PC-TP, chemical inhibition of PC-TP failed to reproduce these changes in Them2−/− hepatocytes. In contrast, rates of glucose oxidation and lipogenesis in the presence of high glucose concentrations were decreased only in Them2−/− hepatocytes. These findings reveal a primary role for Them2 in promoting mitochondrial oxidation of fatty acids and glucose in the liver.
Grafting for Root-knot Nematode Control and Yield Improvement in Organic Heirloom Tomato Production

Organic heirloom tomatoes (Solanum lycopersicum L.) are difficult to grow in Florida as a result of root-knot nematodes (Meloidogyne spp.) (RKN) and hot, humid growing conditions. Although grafting with resistant rootstocks has been shown effective for RKN management in tomato production, little research has been conducted on grafted heirloom tomatoes under Florida conditions. In this 2-year study, two susceptible heirloom tomato scions, 'Brandywine' and 'Flamme', were grafted onto two hybrid rootstocks, i.e., interspecific tomato hybrid rootstock 'Multifort' (S. lycopersicum · S. habrochaites) and tomato hybrid rootstock 'Survivor' (S. lycopersicum). Non-grafted and self-grafted scions were used as controls. Three field trials were conducted in- cluding the 2010 and 2011 organic field trials as well as a transitional organic field trial in2011.Therewasalack of RKNpressurein theorganicfield in2010.In2011,theRKN population was higher in the transitional field than the organic field, whereas grafting with hybrid rootstocks significantly reduced root galling (P # 0.0001) in both fields. In the organic field, the hybrid rootstocks performed similarly and significantly reduced root galling compared with the non-grafted and self-grafted scions by '80.8%. In the transitional field, compared with non-grafted scions, the root galling reduction by 'Survivor' (97.1%) was significantly greater than that by 'Multifort' (57.6%). In general, tomato plants grafted onto 'Multifort' tended to be more vigorous than all other treatments. There was noclearrelationshipbetweenrootgallingandtomatoyields. Grafting did not significantly affect the total marketable yield for the scion 'Flamme' in both years. Total marketable yield was similar among treatments in 2010 but varied in 2011 for the scion'Brandywine'. In2011, the non-grafted'Brandywine' and 'Brandywine' grafted to 'Survivor' produced significantly higher (P < 0.05) yields than other treatments in the organic field. However, in the transitional field, 'Brandywine' grafted to 'Multifort' resulted in significantly higher (P < 0.05) yields than the non- and self-grafted 'Brandy- wine' treatments. Grafting with appropriate rootstocks may play an effective role in RKN management during the transition to organic production when high populations of nematodes are present.
Method of calibration of a fluorescence microscope for quantitative studies

Confocal microscopy is based on measurement of intensity of fluorescence originating from a limited volume in the imaged specimen. The intensity is quantized in absolute (albeit arbitrary) units, producing a digital 3D micrograph. Thus, one may obtain quantitative information on local concentration of biomolecules in cells and tissues. This approach requires estimation of precision of light measurement (limited by noise) and conversion of the digital intensity units to absolute values of concentration (or number) of molecules of interest. To meet the first prerequisite we propose a technique for measurement of signal and noise. This method involves registration of a time series of images of any stationary microscope specimen. The analysis is a multistep process, which separates monotonic, periodic and random components of pixel intensity change. This approach permits simultaneous determination of dark and photonic components of noise. Consequently, confidence interval (total noise estimation) is obtained for every level of signal. The algorithm can also be applied to detect mechanical instability of a microscope and instability of illumination source. The presented technique is combined with a simple intensity standard to provide conversion of relative intensity units into their absolute counterparts (the second prerequisite of quantitative imaging). Moreover, photobleaching kinetics of the standard is used to estimate the power of light delivered to a microscope specimen. Thus, the proposed method provides in one step an absolute intensity calibration, estimate of precision and sensitivity of a microscope system.
FxpNet : Training deep convolutional neural network in fixed-point representation

We introduce FxpNet, a framework to train deep convolutional neural networks with low bit-width arithmetics in both forward pass and backward pass. During training procedure, FxpNet further reduces the bit-width of stored parameters (also known as primal parameters) by adaptively updating their fixed-point formats. These primal parameters are ususally represented in full resolution of floating-point values in previous binarzied and quantized neural networks. In FxpNet, during forward pass fixed-point primal weights and activations will first be binarized before computation, while in backward pass all gradients are represented as low resolution fixed-point values and then accumulated to corresponding fixed-point primal parameters. To have highly efficient implementations in FPGAs, ASICs and other dedicated devices, FxpNet introduces Integer Batch Normalization (IBN) and Fixed-point ADAM (FxpADAM) methods to further reduce the required floating-point operations, which will save considerable power and chip area. The evaluation on CIFAR-10 dataset indicates the effectiveness that FxpNet with 12-bit primal parameters and 12-bit gradients achieves comparable prediction accuracy with state-of-art binarized and quantized neural networks. The corresponding training code implemented in TensorFlow is available online.
Synaptic contacts between physiologically identified neurons in the visual system of the barnacle

Neurons in the median visual system of the barnacle were injected with horseradish peroxidase (HRP) and their processes traced in serial thick (3 micrometers) and thin (100 nm) sections with light and electron microscopy. The anatomy confirms that the I-cells identified by Oertel and Stuart (Oertel, D., and A. E. Stuart (1981) J. Physiol. (Lond.) 311: 127–146) are second-order neurons in the median visual pathway. The terminal branches of the photoreceptor axons are associated in each half of the supraesophageal ganglion with a region of neuropil that extends for 30 to 40 micrometers along the commissure; this photoreceptor-associated neuropil is continuous with but much simpler than the main mass of neuropil in the core of each hemiganglion. The photoreceptor-associated neuropil consists of a small number of different neuronal elements, each with distinctive cytological features. The photoreceptor terminal processes dominate the neuropil; in addition, one finds there the most medial processes of the arborizations of the ipsilateral and contralateral I-cells and the processes of an axon or class of axons of unknown origin referred to as the “RL” fibers. These RL processes associate and branch with the receptor axons and constitute the only major neuronal element in this region of neuropil besides the median photoreceptors and the I-cells. In preparations with an HRP-filled I-cell, the photoreceptors were shown to be presynaptic to I-cell processes at synapses which are characterized by a pair of closely apposed postsynaptic profiles referred to as a dyad. The filled I-cell constituted only one element of the dyad. Receptor endings were also presynaptic to dyads where both postsynaptic elements were unfilled. The RL processes were presynaptic to the photoreceptor terminals at nondyadic synapses, and the receptor endings made specialized junctions, possibly synaptic, with the RL processes. Lateral to the region occupied by the photoreceptor arborization, varicosities of the I-cell are juxtaposed to processes of the A-cell; thus, these sites of the I-cell, where it is most likely to be presynaptic to the A-cell, are segregated from the sites at which it is postsynaptic to the photoreceptors. The I-cell is postsynaptic to photoreceptors and has varicosities juxtaposed to A-cell processes in both hemiganglia.
The impact of saturation on seismic dispersion in shales — Laboratory measurements

Previous studies found a significant increase of acoustic velocities between seismic and ultrasonic frequencies (seismic dispersion) for shales, which would have to be taken into account when comparing seismic or sonic field data with ultrasonic measurements in the laboratory. We report on a series of experiments performed with partially saturated Mancos shale and Pierre shale I in which the influence of water saturation on acoustic velocities and seismic dispersion was investigated. The experiments were carried out in a triaxial set-up allowing for combined measurements of quasi-static rock deformation, ultrasonic velocities, and dynamic elastic stiffness at seismic frequencies under deviatoric stresses. Prior to testing, the rock samples were preconditioned in desiccators at different relative humidities. For both shale types, we present and discuss experimental results that demonstrate strong saturation and frequency dependence of dynamic Young's moduli, Poisson’s ratios and Thomsen’s anisotropy parame.
Immunosuppression‐induced leukoencephalopathy from tacrolimus (FK506)

Tacrolimus (FK506) has recently been approved for immunosuppressionin organ transplantation, although its use is accompanied by a wide spectrum ofneurotoxic side effects. We describe the clinical, radiological, and pathological features of 3 cases of tacrolimus‐related leukoencephalopathy. The syndrome of immunosuppression‐related leukoencephalopathy is proposed as an uncommon neurological syndrome occurring in patintw with organ transplants involving demyelination, in particular in the parieto‐occipital region and centrum semiovale. Although the syndrome is not associated with a particular (absolute) serum level of tacrolimus, it resolves spontaneously upon decreasing the dose. The tacrolimus‐related syndrome has a similar radiographic and pathologic appearance as the analogous syndrome that occurs in patients taking cyclosporine.
Molecular subtyping of Blastocystis spp. using a new rDNA marker from the mitochondria-like organelle genome

SUMMARY Blastocystis spp. are common anaerobic intestinal protozoa found in both human and animals. They are characterized by a high genetic diversity with at least 17 subtypes (STs) that have been described on the basis of a 600 bp ‘barcoding region’ from the 18S rDNA gene. However, analysis of the recently sequenced genome of a Blastocystis ST7 isolate (strain B) revealed the presence of multiple variable copies of the 18S rDNA gene, with 17 completely assembled copies. Comparison of the barcoding region from these 17 copies allowed us to classify the 18S rDNA sequences into 6 clusters, each cluster containing identical sequences. Surprisingly, 4 of these clusters had the highest homology with 18S rDNA sequences from 2 other Blastocystis ST7 isolates referred as QQ98-4 and H. These results suggest that the 18S rDNA gene is not the marker of choice to discriminate between strains within STs. In the present study, we identified a single-copy subtyping rDNA marker in the genome of the mitochondria-like organelles (MLOs). Using a partial sequence of the MLO rDNA, we successfully subtyped 66 isolates from both human and animals belonging to Blastocystis ST1 to ST10. Our results also indicate that this mitochondrial marker could be useful to detect co-infections by different isolates of a same ST.
Mechanism of clathrin basket dissociation: separate functions of protein domains of the DnaJ homologue auxilin

Auxilin was recently identified as cofactor for hsc70 in the uncoating of clathrin-coated vesicles (Ungewickell, E., H. Ungewickell, S.E. Holstein, R. Lindner, K. Prasad, W. Barouch, B. Martin, L.E. Greene, and E. Eisenberg. 1995. Nature (Lond.). 378: 632-635). By constructing different glutathione-S-transferase (GST)-auxilin fragments, we show here that cooperation of auxilin's J domain (segment 813-910) with an adjoining clathrin binding domain (segment 547-814) suffices to dissociate clathrin baskets in the presence of hsc70 and ATP. When the two domains are expressed as separate GST fusion proteins, the cofactor activity is lost, even though both retain their respective functions. The clathrin binding domain binds to triskelia like intact auxilin with a maximum stoichiometry of 3 and concomitantly promotes their assembly into regular baskets. A fragment containing auxilin's J domain associates in an ATP-dependent reaction with hsc70 to form a complex with a half-life of 8 min at 25 degrees C. When the clathrin binding domain and the J domain are recombined via dimerization of their GST moieties, cofactor activity is partially recovered. The interaction between auxilin's J domain and hsc70 causes rapid hydrolysis of bound ATP. Release of inorganic phosphate appears to be correlated with the disintegration of the complex between auxilin's J domain and hsc70. We infer that the metastable complex composed of auxilin, hsc70, ADP, and P(i) contains an activated form of hsc70, primed to engage clathrin that is brought into apposition with it by the DnaJ homologue auxilin.