julilili42/papers huggingface dataset:
Tracer Tomography: Design Concepts and Field Experiments Using Heat as a Tracer
2014-11-13

Abstract Numerical and laboratory studies have provided evidence that combining hydraulic tomography with tomographic tracer tests could improve the estimation of hydraulic conductivity compared with using hydraulic data alone. Field demonstrations, however, have been lacking so far, which we attribute to experimental difficulties. In this study, we present a conceptual design and experimental applications of tracer tomography at the field scale using heat as a tracer. In our experimental design, we improve active heat tracer testing by minimizing possible effects of heat losses, buoyancy, viscosity, and changing boundary conditions. We also utilize a cost‐effective approach of measuring temperature changes in situ at high resolution. We apply the presented method to the 8 m thick heterogeneous, sandy gravel, alluvial aquifer at the Lauswiesen Hydrogeological Research Site in Tübingen, Germany. Results of our tomographic heat‐tracer experiments are in line with earlier work on characterizing the aquifer at the test site. We demonstrate from the experimental perspective that tracer tomography is applicable and suitable at the field scale using heat as a tracer. The experimental results also demonstrate the potential of heat‐tracer tomography as a cost‐effective means for characterizing aquifer heterogeneity.
Cluster Harvesting in the WBr6–P System
2014-11-13

A combined thermal scanning-X-ray diffraction (XRD) approach was performed for the WBr(6)-P system to detect and analyze phases in this system, including metal-rich phases generated with increasing amounts of elemental (red) phosphorus under partial PBr(3) release. Phases were characterized by powder XRD. A black crystalline powder of W(4)(PBr)Br(10) was obtained after reduction of WBr(6) with elemental phosphorus at 450 °C. The crystal structure of the new compound was found to be isotypic with the structure of W(4)(PCl)Cl(10) on the basis of powder XRD data. The structure of W(4)(PBr)Br(10) is represented by a cyclobutadiene-like tetranuclear tungsten cluster interconnected into a layered (W(4)(μ(4)-PBr)Br(6)(i))Br(8)/(2)(a-a) arrangement via outer bromide ligands. The μ(4)-capping bromophosphinidene ligand was verified by solid-state magic-angle spinning (31)P NMR spectroscopy.
REVOLUTA and WRKY53 connect early and late leaf development in Arabidopsis
2014-11-14

As sessile organisms, plants have to continuously adjust growth and development to ever-changing environmental conditions. At the end of the growing season, annual plants induce leaf senescence to reallocate nutrients and energy-rich substances from the leaves to the maturing seeds. Thus, leaf senescence is a means with which to increase reproductive success and is therefore tightly coupled to the developmental age of the plant. However, senescence can also be induced in response to sub-optimal growth conditions as an exit strategy, which is accompanied by severely reduced yield. Here, we show that class III homeodomain leucine zipper (HD-ZIPIII) transcription factors, which are known to be involved in basic pattern formation, have an additional role in controlling the onset of leaf senescence in Arabidopsis. Several potential direct downstream genes of the HD-ZIPIII protein REVOLUTA (REV) have known roles in environment-controlled physiological processes. We report that REV acts as a redox-sensitive transcription factor, and directly and positively regulates the expression of WRKY53, a master regulator of age-induced leaf senescence. HD-ZIPIII proteins are required for the full induction of WRKY53 in response to oxidative stress, and mutations in HD-ZIPIII genes strongly delay the onset of senescence. Thus, a crosstalk between early and late stages of leaf development appears to contribute to reproductive success.
Killing of Staphylococci by θ-Defensins Involves Membrane Impairment and Activation of Autolytic Enzymes
2014-11-14

θ-Defensins are cyclic antimicrobial peptides expressed in leukocytes of Old world monkeys. To get insight into their antibacterial mode of action, we studied the activity of RTDs (rhesus macaque θ-defensins) against staphylococci. We found that in contrast to other defensins, RTDs do not interfere with peptidoglycan biosynthesis, but rather induce bacterial lysis in staphylococci by interaction with the bacterial membrane and/or release of cell wall lytic enzymes. Potassium efflux experiments and membrane potential measurements revealed that the membrane impairment by RTDs strongly depends on the energization of the membrane. In addition, RTD treatment caused the release of Atl-derived cell wall lytic enzymes probably by interaction with membrane-bound lipoteichoic acid. Thus, the premature and uncontrolled activity of these enzymes contributes strongly to the overall killing by θ-defensins. Interestingly, a similar mode of action has been described for Pep5, an antimicrobial peptide of bacterial origin.
Strong Interaction of MnPc on Ni(111): Influence of Graphene Buffer Layer
2014-11-14

The influence of graphene as an buffer interlayer on the behavior of MnPc on a Ni(111) single crystal surface has been investigated by means of photoemission and X-ray absorption spectroscopy (XAS). MnPc suffers serious damage to its molecular structure on the Ni(111) surface as evident from photoemission signals, with large impact on the molecular orientation and the electronic structure. The insertion of a graphene buffer layer prevents the chemical reaction and enables highly oriented growth of unaltered molecules. The electronic situation at the interface, however, is different than the bulk: An interfacial charge transfer is observed involving both nitrogen and manganese atoms of MnPc.
Stimulation of Suicidal Erythrocyte Death by Ellipticine
2014-11-14

Abstract Ellipticine is a potent antineoplastic alkaloid effective in part by triggering apoptosis. Mechanisms involved in ellipticine‐induced apoptosis include mitochondrial depolarization and DNA damage. Erythrocytes lack mitochondria and nuclei but may nevertheless enter suicidal death or eryptosis, which is characterized by cell shrinkage and phosphatidylserine translocation to the erythrocyte surface. Stimulators of eryptosis include increase in cytosolic Ca 2+ activity ([Ca 2+ ] i ), ceramide formation and oxidative stress. This study tested whether ellipticine stimulates eryptosis. Phosphatidylserine exposure at the cell surface was estimated from annexin V binding, cell volume from forward scatter (FSC), [Ca 2+ ] i from Fluo‐3 fluorescence, ceramide abundance from binding of specific antibodies and reactive oxygen species from 2′,7′‐dichlorodihydrofluorescein diacetate fluorescence. A 24‐hr exposure of human erythrocytes to ellipticine (5 μg/ml) significantly increased the percentage of annexin V binding cells, ceramide abundance and oxidative stress. Ellipticine did not significantly modify [Ca 2+ ] i , and the stimulation of annexin V binding by ellipticine (5 μg/ml) did not require the presence of extracellular Ca 2+ . Ellipticine (5 μg/ml) did not significantly modify FSC. Ionomycin (1 μM, 1 hr) decreased FSC, an effect slightly but significantly blunted by ellipticine (5 μg/ml). Ellipticine thus stimulates phosphatidylserine translocation in the erythrocyte cell membrane, an effect at least partially due to stimulation of oxidative stress and ceramide formation.
Innovative diagnostic tools for early detection of Alzheimer's disease
2014-11-15

Abstract Current state‐of‐the‐art diagnostic measures of Alzheimer's disease (AD) are invasive (cerebrospinal fluid analysis), expensive (neuroimaging) and time‐consuming (neuropsychological assessment) and thus have limited accessibility as frontline screening and diagnostic tools for AD. Thus, there is an increasing need for additional noninvasive and/or cost‐effective tools, allowing identification of subjects in the preclinical or early clinical stages of AD who could be suitable for further cognitive evaluation and dementia diagnostics. Implementation of such tests may facilitate early and potentially more effective therapeutic and preventative strategies for AD. Before applying them in clinical practice, these tools should be examined in ongoing large clinical trials. This review will summarize and highlight the most promising screening tools including neuropsychometric, clinical, blood, and neurophysiological tests.
Can personality traits and intelligence compensate for background disadvantage? Predicting status attainment in adulthood.
2014-11-17

This study investigated the interplay of family background and individual differences, such as personality traits and intelligence (measured in a large U.S. representative sample of high school students; N = 81,000) in predicting educational attainment, annual income, and occupational prestige 11 years later. Specifically, we tested whether individual differences followed 1 of 3 patterns in relation to parental socioeconomic status (SES) when predicting attained status: (a) the independent effects hypothesis (i.e., individual differences predict attainments independent of parental SES level), (b) the resource substitution hypothesis (i.e., individual differences are stronger predictors of attainments at lower levels of parental SES), and (c) the Matthew effect hypothesis (i.e., "the rich get richer"; individual differences are stronger predictors of attainments at higher levels of parental SES). We found that personality traits and intelligence in adolescence predicted later attained status above and beyond parental SES. A standard deviation increase in individual differences translated to up to 8 additional months of education, $4,233 annually, and more prestigious occupations. Furthermore, although we did find some evidence for both the resource substitution and the Matthew effect hypotheses, the most robust pattern across all models supported the independent effects hypothesis. Intelligence was the exception, the interaction models being more robust. Finally, we found that although personality traits may help compensate for background disadvantage to a small extent, they do not usually lead to a "full catch-up" effect, unlike intelligence. This was the first longitudinal study of status attainment to test interactive models of individual differences and background factors.
Melanotic Tumors of the Nervous System are Characterized by Distinct Mutational, Chromosomal and Epigenomic Profiles
2014-11-17

Abstract Melanotic tumors of the nervous system show overlapping histological characteristics but differ substantially in their biological behavior. In order to achieve a better delineation of such tumors, we performed an in‐depth molecular characterization. Eighteen melanocytomas, 12 melanomas, and 14 melanotic and 14 conventional schwannomas (control group) were investigated for methylome patterns (450k array), gene mutations associated with melanotic tumors and copy number variants ( CNV s). The methylome fingerprints assigned tumors to entity‐specific groups. Methylation groups also showed a substantial overlap with histology‐based diagnosis suggesting that they represent true biological entities. On the molecular level, melanotic schwannomas were characterized by a complex karyotype with recurrent monosomy of chromosome 22q and variable whole chromosomal gains and recurrent losses commonly involving chromosomes 1, 17p and 21. Melanocytomas carried GNAQ /11 mutations and presented with CNV involving chromosomes 3 and 6. Melanomas were frequently mutated in the TERT promoter, harbored additional oncogene mutations and showed recurrent chromosomal losses involving chromosomes 9, 10 and 6q, as well as gains of 22q. Together, melanotic nervous system tumors have several distinct mutational and chromosomal alterations and can reliably be distinguished by methylome profiling.
Investigating spinning test particles: Spin supplementary conditions and the Hamiltonian formalism
2014-11-17

In this paper we report the results of a thorough numerical study of the\\nmotion of spinning particles in Kerr spacetime with different prescriptions. We\\nfirst evaluate the Mathisson-Papapetrou equations with two different spin\\nsupplementary conditions, namely, the Tulczyjew and the Newton-Wigner, and make\\na comparison of these two cases. We then use the Hamiltonian formalism given by\\nBarausse, Racine, and Buonanno in [Phys. Rev. D, 80, 104025 (2009)] to evolve\\nthe orbits and compare them with the corresponding orbits provided by the\\nMathisson-Papapetrou equations. We include a full description of how to treat\\nthe issues arising in the numerical implementation.\\n
Hardware Architecture and Cutting-Edge Assembly Process of a Tiny Curved Compound Eye
2014-11-17

The demand for bendable sensors increases constantly in the challenging field of soft and micro-scale robotics. We present here, in more detail, the flexible, functional, insect-inspired curved artificial compound eye (CurvACE) that was previously introduced in the Proceedings of the National Academy of Sciences (PNAS, 2013). This cylindrically-bent sensor with a large panoramic field-of-view of composed of 630 artificial ommatidia weighs only 1.75 g, is extremely compact and power-lean (0.9 W), while it achieves unique visual motion sensing performance (1950 frames per second) in a five-decade range of illuminance. In particular, this paper details the innovative Very Large Scale Integration (VLSI) sensing layout, the accurate assembly fabrication process, the innovative, new fast read-out interface, as well as the auto-adaptive dynamic response of the CurvACE sensor. Starting from photodetectors and microoptics on wafer substrates and flexible printed circuit board, the complete assembly of CurvACE was performed in a planar configuration, ensuring high alignment accuracy and compatibility with state-of-the art assembling processes. The characteristics of the photodetector of one artificial ommatidium have been assessed in terms of their dynamic response to light steps. We also characterized the local auto-adaptability of CurvACE photodetectors in response to large illuminance changes: this feature will certainly be of great interest for future applications in real indoor and outdoor environments.
Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes
2014-11-17

NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3-0.6 ppm and correlation coefficients (r(2)) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization.
Zircon U-Pb ages and geochemical composition of gneisses from the Mesozoic foreland basin in the Yellow Sea, China
2014-11-17

AbstractThe South Yellow Sea basin in eastern China has experienced a multi-stage tectonic evolution history. The major structures were created when the basin was a foreland basin during the Mesozoic. However the geological evolution of the basin has not yet been corroborated by direct evidence from the underlying basement rocks. Qianliyan Island in the southern Yellow Sea provides an opportunity to study the formation and evolution of the basin by means of direct geochronological and geochemical evidence. On Qianliyan Island, basement rocks are exposed that consist of granitic gneiss, felsic gneiss and minor mylonite, and lenses of eclogite. Major and trace element characteristics of these four types of gneiss indicate that they originated from crustal material, varying in composition from pelite to greywacke. SHRIMP U-Pb zircon dating results of a felsic gneiss sample show that this rock crystallized between 659 and 796 Ma and underwent a metamorphic overprint at 229 ± 4 Ma. This age pattern resembles that of gneisses from the ultra-high-pressure terrain in the Dabie–Sulu belt. We conclude that the study area was part of the northern margin of the Yangtze Block during the Neoproterozoic. Neoproterozoic magmatic activity occurred along this margin and the basement sequence underwent Triassic metamorphic overprint during the northward subduction of the Yangtze Block beneath the North China Block. We further conclude that the deformation associated with this metamorphic event led to the formation of the southern Yellow Sea foreland basin.Keywords: Yangtze BlockYellow Sea basinSulu orogengneisszircon age AcknowledgementsE. Kolaray and an anonymous reviewer are sincerely acknowledged for constructive suggestions for the manuscript. We gratefully thank Lilin Du and Zhiqing Lai for technical support during SHRIMP analysis, and Anlong Li, Jinqing Liu, and Li Zhao for assistance during fieldwork.
Post-Cueing Deficits with Maintained Cueing Benefits in Patients with Parkinsonâ€™s Disease Dementia
2014-11-17

In Parkinson's disease (PD), internal cueing mechanisms are impaired leading to symptoms like hypokinesia. However, external cues can improve movement execution by using cortical resources. These cortical processes can be affected by cognitive decline in dementia. It is still unclear how dementia in PD influences external cueing. We investigated a group of 25 PD patients with dementia (PDD) and 25 non-demented PD patients (PDnD) matched by age, sex, and disease duration in a simple reaction time task using an additional acoustic cue. PDD patients benefited from the additional cue in similar magnitude as did PDnD patients. However, withdrawal of the cue led to a significantly increased reaction time in the PDD group compared to the PDnD patients. Our results indicate that even PDD patients can benefit from strategies using external cue presentation but the process of cognitive worsening can reduce the effect when cues are withdrawn.
Periodic Glacial Lake Outburst Floods threatening the oldest Buddhist monastery in north-west Nepal
2014-11-17

Abstract. Since 2004 Halji Village, home of the oldest Buddhist Monastery in north-west Nepal has suffered from recurrent Glacial Lake Outburst Floods (GLOFs). Studies of recent satellite images identified a supra-glacial lake, located at a distance of 6.5 km from the village, as a possible source of the flood. During a field survey in 2013, the finding was confirmed and several entrances to en-glacial conduits which are draining the lake were found. The topography of the lake basin was then mapped by combining Differential Global Positioning System (DGPS) measurements with a Structure From Motion (SFM) approach from terrestrial photographs. From this model the maximum filling capacity of the lake has been estimated as 1.06 × 106 m3 with a maximum discharge of 77.8 m3 s−1 calculated using an empirical relation. The flooded area in the valley has been estimated by employing a raster-based hydraulic model considering six scenarios of discharge volume and surface roughness. To understand the changes in glacier geometry in the last decade the thinning and retreat of Halji Glacier have been analysed by geodetic mass balance measurements and a time series of satellite images respectively. The GLOF occurrences have further been correlated with cumulative temperature and cumulative liquid precipitation calculated from the High Asia Reanalysis (HAR) dataset. Finally, effective mitigation measures and adaption strategies for Halji village have been discussed.
Body image and quality of life in patients with and without body contouring surgery following bariatric surgery: a comparison of pre- and post-surgery groups
2014-11-18

Our results support the results of longitudinal studies demonstrating significant improvements in different aspects of body image, quality of life, and general psychopathology after bariatric surgery. Also, we found better AE and physical functioning in patients after BCS following bariatric surgery compared to patients with MWL after bariatric surgery who did not undergo BCS. Overall, there appears to be an effect of BCS on certain aspects of body image and quality of life but not on psychological aspects on the whole.
Universal I-Q relations for rapidly rotating neutron and strange stars in scalar-tensor theories
2014-11-18

We study how rapid rotation influences the relation between the normalized\\nmoment of inertia and quadrupole moment for scalarized\\nneutron stars. The questions one has to answer are whether the EOS universality\\nis preserved in this regime and what are the deviations from general\\nrelativity. Our results show that the relation is nearly EOS\\nindependent for scalarized rapidly rotating stars, but the differences with\\npure Einstein's theory increase compared to the slowly rotating case. In\\ngeneral, smaller negative values of the scalar field coupling parameters\\n lead to larger deviations, but these deviations are below the expected\\naccuracy of the future astrophysical observations if one considers values of\\n in agreement with the current observational constraint. An important\\nremark is that although the normalized relation is quite\\nsimilar for scalar-tensor theories and general relativity, the unnormalized\\nmoment of inertia and quadrupole moment can be very different in the two\\ntheories. This demonstrates that although the relations are\\npotentially very useful for some purposes, they might not serve us well when\\ntrying to distinguish between different theories of gravity.\\n