julilili42/papers huggingface dataset:
Comprehensive Metabolomic and Lipidomic Profiling of Human Kidney Tissue: A Platform Comparison
2016-12-19

Metabolite profiling of tissue samples is a promising approach for the characterization of cancer pathways and tumor classification based on metabolic features. Here, we present an analytical method for nontargeted metabolomics of kidney tissue. Capitalizing on different chemical properties of metabolites allowed us to extract a broad range of molecules covering small polar molecules and less polar lipid classes that were analyzed by LC-QTOF-MS after HILIC and RP chromatographic separation, respectively. More than 1000 features could be reproducibly extracted and analyzed (CV < 30%) in porcine and human kidney tissue, which were used as surrogate matrices for method development. To further assess assay performance, cross-validation of the nontargeted metabolomics platform to a targeted metabolomics approach was carried out. Strikingly, from 102 metabolites that could be detected on both platforms, the majority (>90%) revealed Spearman's correlation coefficients ≥0.3, indicating that quantitative results from the nontargeted assay are largely comparable to data derived from classical targeted assays. Finally, as proof of concept, the method was applied to human kidney tissue where a clear differentiation between kidney cancer and nontumorous material could be demonstrated on the basis of unsupervised statistical analysis.
Nonsense Mutation Inside Anthocyanidin Synthase Gene Controls Pigmentation in Yellow Raspberry (Rubus idaeus L.)
2016-12-19

Yellow raspberry fruits have reduced anthocyanin contents and offer unique possibility to study the genetics of pigment biosynthesis in this important soft fruit. Anthocyanidin synthase (<i>Ans</i>) catalyzes the conversion of leucoanthocyanidin to anthocyanidin, a key committed step in biosynthesis of anthocyanins. Molecular analysis of the <i>Ans</i> gene enabled to identify an inactive <i>ans</i> allele in a yellow fruit raspberry ("Anne"). A 5 bp insertion in the coding region was identified and designated as ans<sup>+5</sup>. The insertion creates a premature stop codon resulting in a truncated protein of 264 amino acids, compared to 414 amino acids wild-type ANS protein. This mutation leads to loss of function of the encoded protein that might also result in transcriptional downregulation of <i>Ans</i> gene as a secondary effect, i.e., nonsense-mediated mRNA decay. Further, this mutation results in loss of visible and detectable anthocyanin pigments. Functional characterization of raspberry <i>Ans</i>/<i>ans</i> alleles via complementation experiments in the <i>Arabidopsis thaliana ldox</i> mutant supports the inactivity of encoded protein through ans<sup>+5</sup> and explains the proposed block in the anthocyanin biosynthetic pathway in raspberry. Taken together, our data shows that the mutation inside <i>Ans</i> gene in raspberry is responsible for yellow fruit phenotypes.
Expression of CD68 positive macrophages in the use of different barrier materials to prevent peritoneal adhesions—an animal study
2016-12-19

In preventing postoperative adhesion formation the optimal barrier material has still not been found. It is therefore imperative to assess the biocompatibility of potential barrier devices. Macrophages play a decisive role in the regulation of wound healing, tissue regeneration and foreign body reaction. Since the number of CD68-positive macrophages represents an important parameter within biomaterial testing, in the present study it was analysed whether a correlation exists between the total number of CD68-positive macrophages and the extent of fibrosis or inflammation in peritoneal adhesion prevention using biomaterials. After standardized peritoneal wounding, Wistar rats were treated with five adhesion barriers or remained untreated as a control. After 14 days, animals were sacrificed and the treated areas were evaluated histomorphologically and immunohistologically. A heterogeneous pattern of macrophage count in relation to fibrosis or inflammation was found. While some groups described a moderate macrophage infiltration without fibrosis, others showed similar numbers of macrophages, but accompanied by moderate fibrosis. Moreover, a minimal number of macrophages was associated with minimal fibrosis. Mild inflammation was seen both with minimal and moderate macrophage infiltration. Altogether, no correlation could be established between the tissue response and the count of CD68-positive macrophages. With a view to macrophage heterogeneity further studies are required to determine the different macrophage subpopulations and clarify the role of these in the tissue responses to barrier materials.
Thermoelectric response of a correlated impurity in the nonequilibrium Kondo regime
2016-12-19

We study nonequilibrium thermoelectric transport properties of a correlated impurity connected to two leads for temperatures below the Kondo scale. At finite bias, for which a current flows across the leads, we investigate the differential response of the current to a temperature gradient. In particular, we compare the influence of a bias voltage and of a finite temperature on this thermoelectric response. This is of interest from a fundamental point of view to better understand the two different decoherence mechanisms produced by a bias voltage and by temperature. Our results show that in this respect the thermoelectric response behaves differently from the electric conductance. In particular, while the latter displays a similar qualitative behavior as a function of voltage and temperature, both in theoretical and experimental investigations, qualitative differences occur in the case of the thermoelectric response. In order to understand this effect, we analyze the different contributions in connection to the behavior of the impurity spectral function versus temperature. Especially in the regime of strong interactions and large enough bias voltages we obtain a simple picture based on the asymmetric suppression or enhancement of the split Kondo peaks as a function of the temperature gradient. Besides the academic interest, these studies could additionally provide valuable information to assess the applicability of quantum dot devices as responsive nanoscale temperature sensors.
Anemia tolerance during normo‐, hypo‐, and hypervolemia
2016-12-19

BACKGROUND Restrictive intraoperative fluid management has been demonstrated to improve outcome of visceral and lung surgery in several studies. However, subsequent hypovolemia (HOV) may be accompanied by a decrease of anemia tolerance, resulting in increased transfusion needs. We therefore investigated the effect of volume status on anemia tolerance. STUDY DESIGN AND METHODS Eighteen domestic pigs of either sex (mean weight, 23.5 ± 4.8 kg) were anesthetized, ventilated, and randomized into three experimental groups: normovolemia (no intervention), HOV (blood loss of 40% of blood volume), and hypervolemia (HEV; volume infusion of 40% of blood volume). The animals were then hemodiluted until their individual critical hemoglobin concentrations (Hb crit ) were reached by the exchange of whole blood for hydroxyethyl starch (HES; 130:0.4). Subsequently, organ‐specific hypoxia was assessed using pimonidazole tissue staining in relevant organs. Hemodynamic and metabolic variables were also investigated. RESULTS Despite significant differences in exchangeable blood volume, Hb crit was the same in all groups (2.3 g/dL, NS). During HOV, tissue hypoxia was aggravated in the myocardium, brain, and kidneys, whereas tissue oxygenation of the liver and intestine was not influenced by volume status. HEV increased tissue hypoxia in the lungs, but did not impact tissue oxygenation of other organs. CONCLUSIONS The combination of hemorrhagic HOV with subsequent anemia leads to accentuated tissue hypoxia, revealed by a significant increase in pimonidazole binding at Hb crit , in heart, lungs, brain, and kidney. The lungs were the only organ that showed increased tissue hypoxia after pretreatment of HES infusion and subsequent anemia by normovolemic hemodilution.
Higher order time discretizations with ALE finite elements for parabolic problems on evolving surfaces
2016-12-19

A linear evolving surface partial differential equation is first discretized in space by an arbitrary Lagrangian Eulerian (ALE) evolving surface finite element method, and then in time either by a Runge-Kutta method, or by a backward difference formula. The ALE technique allows to maintain the mesh regularity during the time integration, which is not possible in the original evolving surface finite element method. Unconditional stability and optimal order convergence of the full discretizations is shown, for algebraically stable and stiffly accurate Runge-Kutta methods, and for backward differentiation formulae of order less than 6. Numerical experiments are included, supporting the theoretical results.
Atlantic forcing of Western Mediterranean winter rain minima during the last 12,000 years
2016-12-19

The limited availability of high-resolution continuous archives, insufficient chronological control, and complex hydro-climatic forcing mechanisms lead to many uncertainties in palaeo-hydrological reconstructions for the Western Mediterranean. In this study we present a newly recovered 19.63 m long core from Lake Sidi Ali in the North African Middle Atlas, a transition zone of Atlantic, Western Mediterranean and Saharan air mass trajectories. With a multi-proxy approach based on magnetic susceptibility, carbonate and total organic C content, core-scanning and quantitative XRF, stable isotopes of ostracod shells, charcoal counts, Cedrus pollen abundance, and a first set of diatom data, we reconstruct Western Mediterranean hydro-climatic variability, seasonality and forcing mechanisms during the last 12,000 yr. A robust chronological model based on AMS 14C dated pollen concentrates supports our high-resolution multi-proxy study. Long-term trends reveal low lake levels at the end of the Younger Dryas, during the mid-Holocene interval 6.6 to 5.4 cal ka BP, and during the last 3000 years. In contrast, lake levels are mostly high during the Early and Mid-Holocene. The record also shows sub-millennial- to centennial-scale decreases in Western Mediterranean winter rain at 11.4, 10.3, 9.2, 8.2, 7.2, 6.6, 6.0, 5.4, 5.0, 4.4, 3.5, 2.9, 2.2, 1.9, 1.7, 1.5, 1.0, 0.7, and 0.2 cal ka BP. Early Holocene winter rain minima are in phase with cooling events and millennial-scale meltwater discharges in the sub-polar North Atlantic. Our proxy parameters do not show so far a clear impact of Saharan air masses on Mediterranean hydro-climate in North Africa. However, a significant hydro-climatic shift at the end of the African Humid Period (∼5 ka) indicates a change in climate forcing mechanisms. The Late Holocene climate variability in the Middle Atlas features a multi-centennial-scale NAO-type pattern, with Atlantic cooling and Western Mediterranean winter rain maxima generally associated with solar minima.
Cholestasis is associated with induction of antimicrobial active reduced human β-defensin 1
2016-12-19

Background & Aims: Despite a multitude of microbial challenges, knowledge about innate antimicrobial defense of the liver is limited. We systematically investigated expression and regulation of hepatic antibacterial peptides and post-translational modification of human beta defensin-1 (hBD-1).
Current sights for mechanisms of deoxynivalenol‐induced hepatotoxicity and prospective views for future scientific research: A mini review
2016-12-20

Abstract Deoxynivalenol (DON) belongs to the group B trichothecenes, which are the most common mycotoxins in cereal commodities. It is very stable within the temperature range 170–350 °C, showing no reduction in its concentration after 30 min at 170 °C. This chemical property is a very dangerous factor for human and animal health. Liver is also responsible for the detoxification and formation of DON‐glucuronide in both human and animals. Some studies already demonstrated that DON could induce liver damage remarkably through DON altering expressions of p53, caspase‐3, caspase‐7, caspase‐8 and Bax in different cell lines. At the same time, other publications illustrated some opposite results. At present, a full and systematic discussion of the hepatic toxicity of DON is still lacking. Therefore, the aim of the present review is to summarize and update the prominent evidence, regarding DON effects on liver tissues and cell lines. Moreover, based on the current studies we outline some of the identified molecule targets or pathways involved in DON‐induced hepatotoxicity, and put forward our opinions and suggest an hypothesis for future research. Copyright © 2016 John Wiley &amp; Sons, Ltd.
Pentamethylcyclopentadienyl‐Supported Cerocene(III) Complexes
2016-12-20

The trivalent ate complex [Cp* 2 CeCl 2 K(thf)] (Cp* = C 5 Me 5 ) was used in a diverse set of salt metathesis reactions. Equimolar reactions with LiN i Pr 2 , LiN(SiHMe 2 ) 2 , KN(SiMe 3 ) 2 , and LiCH 2 C 6 H 4 ‐ o ‐NMe 2 gave the alkali metal‐free complexes [Cp* 2 Ce(N i Pr 2 )], [Cp* 2 Ce{N(SiHMe 2 ) 2 }], [Cp* 2 Ce{N(SiMe 3 ) 2 }], and [Cp* 2 Ce(CH 2 C 6 H 4 ‐ o ‐NMe 2 )]. Employing [Cp* 2 CeCl 2 K(thf)] and KC≡C t Bu in a 1:2 ratio produced a mixture of [Cp* 2 Ce(C≡C t Bu) 2 Li(thf)] and [Cp* 2 Ce(C≡C t Bu)] 2 (LiCl) that was difficult to separate. The reaction of [Cp* 2 CeCl 2 Li(Et 2 O)] with 2 equiv. of LiC≡CPh involved Cp* displacement and formation of the tetrametallic half‐sandwich complex [Cp*Ce(C≡CPh) 2 ] 4 (LiCl). All complexes were characterized by single‐crystal X‐ray structure analysis. The distinct terminal bonding behavior of the similarly sized N i Pr 2 and N(SiHMe 2 ) 2 , of which the latter revealed a strong Ce ··· HSi β‐diagostic interaction, is supported by distinct paramagnetic shifts of the amido substituents in the 1 H NMR spectra. As examples, [Cp* 2 Ce{N(SiHMe 2 ) 2 }] and [Cp* 2 Ce(C≡C t Bu) 2 Li(thf)] were tested for oxidation reactions with 1,4‐benzoquinone and Ph 3 CCl, respectively.
Longitudinal Computed Tomography Monitoring of Pelvic Bones in Patients With Breast Cancer Using Automated Bone Subtraction Software
2016-12-20

Objective The aim of this study was to optimize computed tomography (CT) surveillance of skeletal metastases in patients with breast cancer through the use of osseous subtraction maps between baseline and follow-up examinations created by a novel software algorithm. The new postprocessing algorithm segments the original bone followed by image intensity-based rigid alignment creating gray-shaded maps that highlight focal or diffuse loss or increase in bone attenuation. Materials and Methods Institutional review board was obtained for this retrospective data evaluation. A total of 33 consecutive patients (31 female; 2 male; mean age, 59.13 ± 12.68 years; range, 32–81 years) with breast cancer were included, who underwent 143 standardized baseline and follow-up CT examinations between February 2014 and June 2016. We classified bone metastases into lytic, sclerotic, and mixed osseous lesions. Any new osteolysis inside a known sclerotic lesion and enlargement of pre-existing sclerotic lesions were considered to represent progressive disease (PD), whereas no change was classified as stable disease (SD). Results were compared additionally with the course of the disease considering the entire skeleton and other involved organs. Software-created automated bone subtraction maps were compared with conventional CT interpretations of axial 5-mm and coronal 1-mm reformatted images. Region of interest measurements were used to quantify new lesions. Results were validated by clinical and CT follow-up. Reading time was evaluated. Results Skeletal metastases were present in 17/33 (51%) patients (9 sclerotic, 2 lytic, 6 mixed) at baseline. The use of bone subtraction maps resulted in an overall change of response classification into PD in 9/33 (8.1%) patients. Compared with conventional CT evaluation, the bone subtraction maps disclosed 123 new or enlarging sclerotic and 32 new lytic metastases in 23/33 (30.9%) examinations. Mean attenuation of new bone lesions (sclerotic or lytic) significantly increased or decreased ( P &lt; 0.01) in all patients. Bone attenuation in pelvic areas without evident metastatic disease significantly increased in patients with PD ( P = 0.019), whereas there was no change in SD ( P = 0.076). Lesion-based sensitivity, specificity, accuracy, positive predictive values, and negative predictive values were 98.7%, 79.5%, 94.5%, 95.1%, and 94.5%, respectively. Interobserver agreement was good (κ = 0.80; P = 0.077). Reading time was significantly faster for the bone subtraction maps versus 5-mm axial images ( P &lt; 0.001). Conclusions Longitudinal bone subtraction maps increase the accuracy and efficiency of CT diagnosis of skeletal metastases in patients with breast cancer.
Review on Superconducting Materials
2016-12-20

The article contains sections titled: Introduction Cuprate High‐Temperature Superconductors Other Oxide Superconductors Iron‐Based Superconductors Other Chalcogenide Superconductors Heavy Fermion Superconductors Nitride Superconductors Organic and Other Carbon‐ and Silicon‐Based Superconductors Borides and Borocarbides
Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline forCYP2D6genotype and use of ondansetron and tropisetron
2016-12-21

5-hydroxytryptamine type 3 (5-HT3) receptor antagonists are used in the prevention of chemotherapy- induced, radiation-induced and postoperative nausea and vomiting. CYP2D6 polymorphisms can influence the metabolism of some of these drugs (i.e. ondansetron and tropisetron) thereby affecting drug efficacy. We summarize evidence from the published literature supporting these associations and provide therapeutic recommendations for ondansetron and tropisetron based on CYP2D6 genotype (updates at www.pharmgkb.org).
Late Jurassic Magmatism and Stratigraphy in the Eastern Sakarya Zone, Turkey: Evidence for the Slab Breakoff of Paleotethyan Oceanic Lithosphere
2016-12-21

Middle-Late Jurassic Cimmerian events in Turkey have been actively discussed in the past three decades, but proposed tectonic models associated with magmatism, metamorphism, and stratigraphic features remain controversial. To address this issue, Upper Jurassic mafic lavas are investigated at three locations (Alucra, Gümüşhane, and Olur) in the eastern Sakarya Zone, northeastern Turkey. These lavas are submarine and form planar flows parallel with the bedding plane in the Upper Jurassic carbonate sequence near the base or just below in the clastic sedimentary rocks. The basaltic lavas show calc-alkaline features and possess Nb-Ta values and Nb/U, Nb/La, and Ce/Pb ratios that are greater than those of island arc basalts. Multielement patterns are almost hump shaped, similar to ocean island basalts, which experience Pb depletion and weak negative Nb-Ta, Zr-Hf, and Ti anomalies. The low initial (87Sr/86Sr) ratios (0.70372–0.70554), positive initial εNd values (+2.7 to +4.4), and initial Pb isotope ratios that plot between mid-ocean-ridge and ocean island basalts are consistent with a melt derived from subcontinental lithospheric mantle, metasomatized by earlier fluids from subducted sediments and plume materials from the asthenosphere. Moderate Dy/Yb ratios with an average value of 1.8 imply partial melting in the spinel-garnet transition zone at depths of ∼70–100 km. Slab breakoff is suggested as a geodynamic mechanism that accounts for these geochemical signatures. This inference is also favored by stratigraphic and sedimentologic evidence from the Upper Jurassic–Lower Cretaceous sedimentary rocks, which is consistent with short-lived vertical (epirogenic) movements in the region. Lower-Middle Jurassic sequences are transgressive, suggesting that subduction-related extension opened a backarc basin (Neotethys) in the south of the Sakarya Zone. Upper Jurassic–Lower Cretaceous carbonates point tectonically to tranquility during carbonate deposition in the Neotethys Ocean, which seems to have been achieved by complete closure of the Paleotethys in the north. About 15–20 m.yr. later (Kimmeridgian), after first carbonate deposition, intraplate-type mafic lavas ascended up to the shelf surface of the Neotethys. This was followed by formation of disconformity surfaces and then accumulation of coarse clastic sediments. All this points to a short-lived epirogenic movement that we ascribe to the breakoff of the southward-subducting Paleotethyan oceanic lithosphere in the Late Jurassic.
Low-Dose Effects: Nonmonotonic Responses for the Toxicity of a Bacillus thuringiensis Biocide to Daphnia magna
2016-12-21

Currently, there is a trend toward an increasing use of biopesticides assumed to be environmentally friendly, such as Bacillus thuringiensis (Bt). Studies of the Bt toxicity to nontarget organisms have reported low effects at high exposure levels, which is interpreted as indicating negligible risk to nontarget organisms. We investigated the response of the nontarget organism Daphnia magna to waterborne DiPel ES, a globally used Bt formulation. Neonates and adults were exposed for 48 h to a wide range of concentrations, and immobilization and mortality were monitored. Whole body biomarkers (body weight, protein, chitobiase, catalase, xenobiotic metabolism, and acetylcholinesterase) were measured in the adults. The immobilization and mortality of the neonates were affected in a nonmonotonic and inverted U-shaped pattern with EC<sub>50</sub>s that were ∼10<sup>5</sup>-fold lower than those reported by the manufacturer. The immobilization of adults demonstrated a similar pattern, but significant mortality was not observed. The biomarker results revealed multiphasic dose-response curves, which suggested toxicity mechanisms that affected various physiological pathways. The main particle size in exposure media was in the size range of bacterial spores and crystal toxins. However, the chemical heterogeneity was nonmonotonic, with a change in the phase at the maximum of toxicity (∼5 μL L<sup>-1</sup>), which might explain the observed nonmonotonic effects. These results demonstrate the vulnerability of a nontarget organism to a biopesticide that is considered to be safe, while challenging the universal applicability of the central ecotoxicological assumption of monotonicity.
Strain localization and dynamic recrystallization in the ice–air aggregate: a numerical study
2016-12-21

Abstract. We performed numerical simulations on the microdynamics of ice with air inclusions as a second phase. Our aim was to investigate the rheological effects of air inclusions and explain the onset of dynamic recrystallization in the permeable firn. The simulations employ a full-field theory crystal plasticity code coupled to codes simulating dynamic recrystallization processes and predict time-resolved microstructure evolution in terms of lattice orientations, strain distribution, grain sizes and grain-boundary network. Results show heterogeneous deformation throughout the simulations and indicate the importance of strain localization controlled by air inclusions. This strain localization gives rise to locally increased energies that drive dynamic recrystallization and induce heterogeneous microstructures that are coherent with natural firn microstructures from EPICA Dronning Maud Land ice coring site in Antarctica. We conclude that although overall strains and stresses in firn are low, strain localization associated with locally increased strain energies can explain the occurrence of dynamic recrystallization.