julilili42/papers huggingface dataset:
Stable Isotope-Assisted Lipidomics Combined with Nontargeted Isotopomer Filtering, a Tool to Unravel the Complex Dynamics of Lipid Metabolism
2013-03-28

Investigations of complex metabolic mechanisms and networks have become a focus of research in the postgenomic area, thereby creating an increasing demand for sophisticated analytical approaches. One such tool is lipidomics analysis that provides, a detailed picture of the lipid composition of a system at a given time. Introducing stable isotopes into the studied system can additionally provide information on the synthesis, transformation and degradation of individual lipid species. However, capturing the entire dynamics of lipid networks is still a challenge. We developed and evaluated a novel strategy for the in-depth analysis of the dynamics of lipid metabolism with the capacity for high molecular specificity and network coverage. The general workflow consists of stable isotope-labeling experiments, ultrahigh-performance liquid chromatography (UHPLC)/high-resolution Orbitrap-mass spectrometry (MS) lipid profiling and data processing by a software tool for global isotopomer filtering and matching. As a proof of concept, this approach was applied to the network-wide mapping of dynamic lipid metabolism in primary human skeletal muscle cells cultured for 4, 12, and 24 h with [U-(13)C]-palmitate. In the myocellular lipid extracts, 692 isotopomers were detected that could be assigned to 203 labeled lipid species spanning 12 lipid (sub)classes. Interestingly, some lipid classes showed high turnover rates but stable total amounts while the amount of others increased in the course of palmitate treatment. The novel strategy presented here has the potential to open new detailed insights into the dynamics of lipid metabolism that may lead to a better understanding of physiological mechanisms and metabolic perturbations.
RX J0440.9 + 4431: a persistent Be/X-ray binary in outburst
2013-03-28

The persistent Be/X-ray binary RX J0440.9 + 4431 flared in 2010 and 2011 and has been followed by various X-ray facilities (Swift, RXTE, XMM-Newton, and INTEGRAL). We studied the source timing and spectral properties as a function of its X-ray luminosity to investigate the transition from normal to flaring activity and the dynamical properties of the system. We have determined the orbital period from the long-term Swift/BAT light curve, but our determinations of the spin-period are not precise enough to constrain any orbital solution. The source spectrum can always be described by a bulk-motion Comptonization model of black body seed photons attenuated by a moderate photoelectric absorption. At the highest luminosity, we measured a curvature of the spectrum, which we attribute to a significant contribution of the radiation pressure in the accretion process. This allows us to estimate that the transition from a bulk-motion-dominated flow to a radiatively dominated one happens at a luminosity of ~2 × 1036 erg s−1. The luminosity dependency of the size of the black body emission region is found to be rBB ∝ Lx 0.39±0.02 . This suggests that either matter accreting onto the neutron star hosted in RX J0440.9 + 4431 penetrates through closed magnetic field lines at the border of the compact object magnetosphere or that the structure of the neutron star magnetic field is more complicated than a simple dipole close to the surface.
Remobilization of U and REE and the formation of secondary minerals in oxidized U deposits
2013-03-28

The hydrothermal uranium vein-type deposits of Menzenschwand and Wittichen in the Schwarzwald in southwestern Germany have been investigated with regards to their primary and secondary mineralization. Primary magmatic uraninite I from the host granite of Menzenschwand, primary hydrothermal uraninite II and secondary (supergene) uranyl silicates (uranophane and cuprosklodowskite), uranyl phosphates (torbernite and uranocircite), and uranyl arsenates (zeunerite, heinrichite, nováčekite, walpurgite, and uranospinite) were analyzed for their REE contents by LA-ICP-MS together with uraninite II samples from other known Schwarzwald uraninite II occurrences for comparison. Water samples were taken from drillings and abandoned mines and were analyzed for their major and trace element composition including U and REE.
Synthesis of Tetra(2-hydroxyethoxy)-Substituted Dibenzocyclooctyne Derivatives as Novel, Highly Hydrophilic Tool Compounds for Strain-Promoted Alkyne-Azide Cycloaddition Applications
2013-03-28

The synthesis of a novel, hydrophilic dibenzocyclooctyne derivative for strain-promoted alkyne-azide cycloaddition (SPAAC) is described. Starting from 2-(3,4-dimethoxyphenyl)acetaldehyde, the corresponding activated carbonate of 2,3,8,9-tetrakis(2-hydroxyethoxy)-5,6-dihydro-11,12-didehydrodibenzo[<i>a</i>,<i>e</i>][8]annulene, termed THE-DIBO, was prepared in seven steps and 24% overall yield. A water-soluble THE-DIBO analogue showed a <i>k<sub>2</sub> </i> value of (21.9 ± 0.2) × 10<sup>–2</sup> M<sup>–1</sup> s<sup>–1</sup> for SPAAC with 2-azidoethanol in water. The high hydrophilicity and steric bulk of THE-DIBO derivatives should to suppress nonspecific thiol-yne addition of proteins to strained alkynes observed for SPAAC labeling in complex proteomes.
Potent and Prolonged Hypoglycemic Activity of an Oral Insulin - Tat Mixture in Diabetic Mice
2013-03-28

Trans-activator of transcription (Tat) is a cell penetrating peptide which can translocate and carry macromolecular cargoes through cell membranes. This study investigated the hypoglycemic activity of orally delivered insulin - Tat mixture in alloxan-induced diabetic mice. The mixtures of insulin and Tat at 1:1, 1:3 and 1:6 molar ratios were given orally at the insulin doses ranging from 1-200 IU/kg. The fasting blood glucose (FBG) levels were measured at initial, 1, 2, 4, 6, and 12 h after administration. At 1:3 molar ratio of the mixture and after 12 h of administration, insulin at 200 IU/kg showed the highest with prolonged hypoglycemic activity of 74.0±10.3% FBG reduction (2.18 folds of subcutaneously injected (SC) insulin). Free insulin administered orally did not show any hypoglycemic activity. The mixtures at the insulin doses of 100 and 50 IU/kg also showed potent FBG reduction of 73.8±8.2 and 71.3±16.9% at 12 h after administration (2.18 and 2.10 folds of SC insulin, respectively). After incubation with Mono-Mac-6 cells, only the -mixtures but not the free insulin showed intra-cellular insulin uptake, indicating the insulin penetration through the cell membranes via Tat. In simulated gastric fluid, the insulin content in the mixture was not found, demonstrating the degradation of insulin in the gastric environments. Insulin may be absorbed at upper gastrointestinal tract facilitated by Tat. The potent and prolonged hypoglycemic activity of insulin co-administered orally with Tat can be further developed as an effective oral insulin delivery system.
Two fast temperature sensors for probing of the Atmospheric Boundary Layer using small Remotely Piloted Aircraft (RPA)
2013-03-28

Abstract. Two types of temperature sensors are designed and tested, a thermocouple and a fine wire resistance thermometer. The intention of this study is to figure out which kind of measurement principle is in general more suited for atmospheric boundary layer meteorology with small RPA. The sensors are calibrated in a NIST traceable climate chamber and validated in flight against tower measurements, radiosondes and remote sensing. The sensors have a measurement range of at least −10...50° C, an absolute RMS error of less than ±0.2 K which is stable over the lifetime of the sensors, and a resolution of about 0.01 K. Both devices are tested for typical errors like radiation error and adiabatic heating, as well as for their dynamic response. Spectral resolutions of up to approximately 10 Hz can be obtained with both sensors, which makes them suitable for turbulence measurements. Their low cost of less than 100 EUR in pure hardware is a major advantage for research with small RPA.
Another passive that isn’t one
2013-03-28

This article adresses the semantics of the so-called haben -passive, i.e. the stative reading of sentences like Er hat den Arm verbunden (‘He has his arm bandaged’). In line with recent research on haben -passives (Rothstein 2007; Businger this volume), I assume that these involve adjectivization of the participle. I will argue that participles in haben -passives share two main semantic properties with participles in German adjectival passives ( sein -passives): (i) the semantic underspecification of the property denoted by the participle (ii) the generic interpretation of the event introduced by the verbal baseI propose an adjectival zero-affix that accounts for these semantic properties. The conclusion will be that adjectivization of the participle, in adjectival sein -passives as well as in haben -passives, has a specific semantic impact: it serves to create a property – the property of belonging to a contextually mediated ad hoc category based on the verbal event kind.
“Imagine your neighbor mows the lawn”: a pilot study of psychological sequelae due to awake craniotomy
2013-03-29

Object Although it has been reported that awake neurosurgical procedures are well tolerated, the long-term occurrence of general psychological sequelae has not yet been investigated. This study assessed the frequency and effects of psychological symptoms after an awake craniotomy on health-related quality of life (HRQOL). Methods Sixteen patients undergoing an awake surgery were surveyed with a self-developed questionnaire, the Posttraumatic Stress Disorder Inventory For Awake Surgery Patients, which adopts the core components of the Diagnostic and Statistical Manual of Mental Disorders (Fourth Edition) posttraumatic stress disorder (PTSD) criteria. The mean time between surgery and data collection was 97.3 ± 93.2 weeks. Health-related quality of life was assessed with the 36-Item Short Form Health Survey. Results Forty-four percent of the patients stated that they had experienced either repetitive distressing recollections or dreams related to the awake surgery, 18.8% stated persistent avoidance of stimuli associated with the awake surgery, and symptoms of increased arousal occurred in 62.5%. Two patients presented with postoperative psychological sequelae resembling PTSD symptoms. Younger age at surgery and female sex were risk factors for symptoms of increased arousal. The experience of intense anxiety during awake surgery appears to favor the development of postsurgical PTSD symptoms, while recurrent distressing recollections particularly affect HRQOL negatively. Conclusions In many cases awake craniotomy is necessary to preserve language and motor function. However, in some cases awake craniotomy can lead to postoperative psychological sequelae resembling PTSD symptoms. Therefore, possible long-term effects of an awake surgery should be considered and discussed with the patient when planning this type of surgery.
Night work and breast cancer estrogen receptor status – results from the German GENICA study
2013-03-29

Our case-control study suggests that long-term night-shift work is associated with an increased risk of ER-negative breast cancers. Further studies on histological subtypes and the analysis of other potentially relevant factors are crucial for discovering putative mechanisms.
THE ONTOLOGICAL EINSTEIN - FOUR CASES IN POINT
2013-03-31

The four points which are the message of this paper are as follows: (i) ontological clock slow-down, downstairs in gravity; (ii) ontological rest-mass decrease, downstairs in gravity; (iii) ontological size increase, downstairs in gravity; and (iv) ontological charge decrease, downstairs in gravity. The simplest proofs of these partially unfamiliar results are sketched and their far-reaching consequences pointed at.
Limitations on the developing preterm brain: impact of periventricular white matter lesions on brain connectivity and cognition
2013-04-01

Brain lesions to the white matter in peritrigonal regions, periventricular leukomalacia, in children who were born prematurely represent an important model for studying limitations on brain development. The lesional pattern is of early origin and bilateral, that constrains the compensatory potential of the brain. We suggest that (i) topography and severity of periventricular lesions may have a long-term predictive value for cognitive and social capabilities in preterm birth survivors; and (ii) periventricular lesions may impact cognitive and social functions by affecting brain connectivity, and thereby, the dissociable neural networks underpinning these functions. A further pathway to explore is the relationship between cerebral palsy and cognitive outcome. Restrictions caused by motor disability may affect active exploration of surrounding and social participation that may in turn differentially impinge on cognitive development and social cognition. As an outline for future research, we underscore sex differences, as the sex of a preterm newborn may shape the mechanisms by which the developing brain is affected.
Telltale Tails: A New Approach to Estimating Unique Market Information Shares
2013-04-01

Abstract The trading of securities on multiple markets raises the question of each market’s share in the discovery of the informationally efficient price. We exploit salient distributional features of multivariate financial price processes to uniquely determine these contributions, thereby resolving the main drawback of the widely used Hasbrouck (1995) methodology, which merely provides upper and lower bounds of a market’s information share. We show how tail dependence of price changes, which may emerge as a result of differences in market design, can be exploited to estimate unique information shares. Two empiricalapplications illustrate the practical use of the new methodology.
The histone deacetylase inhibitor trichostatin a promotes apoptosis and antitumor immunity in glioblastoma cells.
2013-04-01

Histone deacetylase inhibitors (HDACi) have been described as multifunctional anticancer agents. The failure of conventional therapy for glioblastoma (GBM) renders this tumor an attractive target for immunotherapy. Innate immune cells, such as natural killer (NK) cells, play a crucial role in antitumor immune responses. Here, we describe how the HDACi trichostatin A (TSA) promotes apoptosis of tumor cells, as well as augments anti-GBM innate immune responses. In vitro treatment of GBM cells with TSA results in an up-regulation of the natural killer group-2 member-D (NKG2D) ligands major histocompatibility complex class I-related chain (MIC)-A and UL16 binding protein (ULBP)-2 at both mRNA and protein levels, rendering them susceptible to NK cell-mediated lysis. In vivo, TSA delays tumor growth of GBM xenografts. Both the in vitro and in vivo antitumor effect of TSA was significantly reduced by blocking NK cell activity. Our data suggest that HDACi, especially in combination with other clinical immunotherapeutical approaches, may be considered in a combined therapeutic approach for GBM.
Within‐lesion differences in quantitative MRI parameters predict contrast enhancement in multiple sclerosis
2013-04-01

Purpose To investigate the relationship between quantitative magnetic resonance imaging (qMRI) and contrast enhancement in multiple sclerosis (MS) lesions. We compared maps of T1 relaxation time, proton density (PD), and magnetization transfer ratio (MTR) between lesions with and without contrast enhancement as quantified by the amount of T1 shortening postcontrast agent (CA). Materials and Methods In 17 patients with relapsing‐remitting MS (RRMS), 15 with progressive MS (PMS), and 17 healthy controls, T1, PD, and MTR were measured at 3T and T1‐mapping was repeated after CA administration. Manually drawn MS‐lesions (3D‐FLAIR) were labeled as enhancing if post‐CA T1‐shortening exceeded mean T1‐shortening in normal‐appearing white matter (NAWM) by at least 2 standard deviations. Precontrast T1, PD, and MTR were compared in enhancing lesions, nonenhancing lesions, NAWM, and gray matter. Results Precontrast T1, PD, and MTR differed significantly between enhancing and nonenhancing lesions in RRMS and PMS patients (all P &lt; 0.01). In PMS patients, PD of NAWM, enhancing, and nonenhancing lesions and MTR and T1 of gray matter differed significantly from RRMS and controls. Only MTR of gray matter differed between RRMS and controls. Conclusion Contrast enhancement in MS quantified by relative T1 shortening may be predicted by precontrast abnormalities of T1, PD, and MTR and likely represents blood–brain barrier damage. J. Magn. Reson. Imaging 2013;38:1454–1461. © 2013 Wiley Periodicals, Inc.
Tinderet volcano, Kenya: an altered natrocarbonatite locality?
2013-04-01

Abstract The Tinderet volcano (19.9 to 5.5 Ma), located within the Kavirondo rift in Kenya, contains blocks of carbonatite lavas with calcite, minor apatite, fluorite, spinel-group minerals, accessory perovskite and 'plumbopyrochlore'; nyerereite is present as inclusions in the perovskite. At least four types of calcite are present in the carbonatite lavas; they differ in morphology, composition and origin. The dominant variety is secondary type-II calcite, which is enriched in sodium (up to 1.1 wt.% Na 2 O) and strontium (up to 1.3 wt.% SrO). The spinel-group minerals are manganese-bearing and include Mn-rich magnetite, magnesioferrite and jacobsite. Oxygen isotope data for bulk carbonatite samples (δ 18 O = +16.2 % to +22.6 % VSMOW) support a low crystallization temperature for the secondary calcite. Petrographic, mineralogical and isotopic data indicate that the Tinderet carbonatites are similar to natrocarbonatites from the Oldoinyo Lengai and Kerimasi volcanoes that have altered and recrystallized to form calcite carbonatites. These data support the hypothesis that some of the Tinderet carbonatites were originally alkali-rich rocks which contained primary nyerereite.
Observing SQL queries in their natural habitat
2013-04-01

We describe H abitat , a declarative observational debugger for SQL. H abitat facilitates true language-level (not: plan-level) debugging of, probably flawed, SQL queries that yield unexpected results. Users mark SQL subexpressions of arbitrary size and then observe whether these evaluate as expected. H abitat understands query nesting and free row variables in correlated subqueries, and generally aims to not constrain users while suspect subexpressions are marked for observation. From the marked SQL text, H abitat 's algebraic compiler derives a new query whose result represents the values of the desired observations. These observations are generated by the target SQL database host itself and are derived from the original data: H abitat does not require prior data extraction or extra debugging middleware. Experiments with TPC-H database instances indicate that observations impose a runtime overhead sufficiently low to allow for interactive debugging sessions.
A Fast and Accurate FPGA-Based Fault Injection System
2013-04-01

This paper introduces an FPGA-based fault injection system. To realize this system a library was developed, which implements a static mapping between a circuit described at RTL or gate-level and its corresponding placed and routed FPGA design. The aim of this mapping is to preserve module and port structure of the placed and routed FPGA design to the RT/gate-level circuit description. To demonstrate the accuracy of this mapping the ISCAS'89 benchmark circuits and the VHDL netlist of the LEON3 system are used. The results show that about 99% of the ports in the RT/gate-level circuit description can be located in the placed and routed FPGA design. Based on this library a fault injection tool was developed to accelerate the fault injection experiment time by bypassing some stages (synthesis, placement and routing) of a re-compilation process. In these experiments a 12 × speedup was achieved when compared to fault injections based on serial fault emulation.
Penetration of Light into Multiple Scattering Media: Model Calculations and Reflectance Experiments. Part II: The Radial Transfer
2013-04-01

In continuation of our contribution to “The Axial Transfer” ( Appl. Spectr. 2012. 66(8): 934–943), this paper describes the distribution of localized incident radiation in multiple scattering layers of arbitrary thickness and analyzes the lateral intensity profiles of radiation leaving the sample from its illuminated and non-illuminated surfaces. The theoretical profiles are calculated with different approximations of the equation of transfer. We derive for both non-absorbing and absorbing layers simple analytical expressions and verify their accuracy and range of applicability by comparison with Monte Carlo simulations. Particular emphasis is given to the analysis of the radial absorption, an under-theorized and under-investigated feature that can help to identify weak or hidden absorbers. In addition, we contribute to the description of how the radial reflectance is affected by anisotropy or by error sources like multiple surface reflection for samples in glass cells or deflectance (sideway loss) of radiation in small samples. Finally, the theoretical results are compared with experimental data of radial reflectance for quasi non-absorbing and absorbing powder layers.
The link between the foreign policy of states and escalating political violence: Turkey and the PKK
2013-04-01

In this article, I analyse the escalation of ongoing violence between the Turkish state and the Kurdistan Workers' Party (Partiya Karkaren Kurdistan, PKK) through a new perspective. More specifically, I concentrate on the full-blown political violence in the period between 1992 and 1995, in which the Turkish state's power (and authority) was genuinely threatened in one part of the country. The central political authority employed violent measures, whereas some of the Kurds supported the violent acts of the PKK rebels in order to attain certain political goals, in the case at hand, autonomy and/or secession. I argue that the explanatory power of conventional approaches to the PKK conflict does not offer a sufficiently broad perspective with which to analyse the micro-dynamics of violence in the ongoing conflict. I offer a new causal explanation that employs a process-based perspective that considers how the ongoing violent conflict produces new opportunity structures for the PKK in a transnational conflict landscape. This approach reveals the causal link between the foreign policy decisions of the Turkish state at the beginning of the 1990s and its influence on the radical escalation of political violence.
Parasitism and evolution: opposing versus balancing strategies
2013-04-01

Parasitism refers to a particular symbiosis (deBary 1879) of organisms that live at the cost of their hosts. Virulent microbes (viruses and bacteria) proliferate unlimited causing toxic infections that end either by the host's death or its protective immunity. By this opposing survival strategy, via the population density, i.e. the contact rate, finally results a sequence of epidemic and endemic periods. The host population is kept at a reasonable level to resources, but host and pathogenic agent are wasted in the evolutionary arms race. Sparing such losses, eukaryotic proto- and metazoan parasites induce in natural hosts a delayed infection course by self-controlled propagation and avoid protective immunity. Hosts are ‘immunized but not immune’ and parasites propagate simultaneously with them. Metazoic and some protozoic parasitoses end with the parasite's natural death, pathogenic effects remain irrelevant. Nevertheless, the host's fitness becomes reduced by multiple re-infections and/or by increasing parasite loads. This balancing survival strategy controls host populations at lower costs. A network of parasitoses offers considerable selection advantages and explains the polyphyletic origin of eukaryotic parasites. Parasitism and other kinds of symbioses contribute to the stability of ecosystems and to stasis in long-term evolution but are invisible in the fossil record.