Miracle-dz/UniFAR-FTUs huggingface dataset:
Affect-Modulated Startle: Interactive Influence of Catechol-O-Methyltransferase Val158Met Genotype and Childhood Trauma

The etiology of emotion-related disorders such as anxiety or affective disorders is considered to be complex with an interaction of biological and environmental factors. Particular evidence has accumulated for alterations in the dopaminergic and noradrenergic system – partly conferred by catechol-O-methyltransferase (COMT) gene variation – for the adenosinergic system as well as for early life trauma to constitute risk factors for those conditions. Applying a multi-level approach, in a sample of 95 healthy adults, we investigated effects of the functional COMT Val158Met polymorphism, caffeine as an adenosine A2A receptor antagonist (300 mg in a placebo-controlled intervention design) and childhood maltreatment (CTQ) as well as their interaction on the affect-modulated startle response as a neurobiologically founded defensive reflex potentially related to fear- and distress-related disorders. COMT val/val genotype significantly increased startle magnitude in response to unpleasant stimuli, while met/met homozygotes showed a blunted startle response to aversive pictures. Furthermore, significant gene-environment interaction of COMT Val158Met genotype with CTQ was discerned with more maltreatment being associated with higher startle potentiation in val/val subjects but not in met carriers. No main effect of or interaction effects with caffeine were observed. Results indicate a main as well as a GxE effect of the COMT Val158Met variant and childhood maltreatment on the affect-modulated startle reflex, supporting a complex pathogenetic model of the affect-modulated startle reflex as a basic neurobiological defensive reflex potentially related to anxiety and affective disorders.
Solving high-order nonlinear Volterra-Fredholm integro-differential equations by differential transform method

In this paper, we apply the differential transformation method to high-order nonlinear Volterra- Fredholm integro-differential equations with se- parable kernels. Some different examples are considered the results of these examples indi-cated that the procedure of the differential transformation method is simple and effective, and could provide an accurate approximate solution or exact solution.
Cobalt ameliorates renal injury in an obese, hypertensive type 2 diabetes rat model.

BACKGROUND Chronic renal hypoxia is suspected to play a pathogenic role in the genesis of diabetic nephropathy (DN). Cobalt enhances the activity of the hypoxia-inducible factor (HIF), a key factor in the defence against hypoxia. Its long-term effect on DN is evaluated. METHODS Cobalt chloride was given to hypertensive, type 2 diabetic rats with nephropathy (SHR/NDmcr-cp). Treatment was initiated at the age of 13 weeks and continued for 26 weeks. RESULTS Cobalt did not correct hypertension and metabolic abnormalities (obesity, hyperglycaemia and hyperlipidaemia) but reduced proteinuria as well as histological kidney injury. Cobalt upregulated renal HIF-1alpha and HIF-2alpha expression and increased the expression of HIF-regulated genes, including erythropoietin, vascular endothelial growth factor and heme oxygenase-1. The renal expression of transforming growth factor (TGF)-beta and connective tissue growth factor (CTGF) was significantly reduced by cobalt. The renal expression of NADPH oxidase, a marker of oxidative stress, and the renal content of pentosidine, a marker of advanced glycation, were also significantly reduced by cobalt. CONCLUSIONS Cobalt achieved renal protection independently of metabolic status and blood pressure. Its effect was attributed to the upregulation of HIF and HIF-regulated genes and to a mitigated advanced glycation and oxidative stress.
Clostridium Perfringens Epsilon Toxin Binds to Membrane Lipids and Its Cytotoxic Action Depends on Sulfatide

Epsilon toxin (Etx) is one of the major lethal toxins produced by Clostridium perfringens types B and D, being the causal agent of fatal enterotoxemia in animals, mainly sheep and goats. Etx is synthesized as a non-active prototoxin form (proEtx) that becomes active upon proteolytic activation. Etx exhibits a cytotoxic effect through the formation of a pore in the plasma membrane of selected cell targets where Etx specifically binds due to the presence of specific receptors. However, the identity and nature of host receptors of Etx remain a matter of controversy. In the present study, the interactions between Etx and membrane lipids from the synaptosome-enriched fraction from rat brain (P2 fraction) and MDCK cell plasma membrane preparations were analyzed. Our findings show that both Etx and proEtx bind to lipids extracted from lipid rafts from the two different models as assessed by protein-lipid overlay assay. Lipid rafts are membrane microdomains enriched in cholesterol and sphingolipids. Binding of proEtx to sulfatide, phosphatidylserine, phosphatidylinositol (3)-phosphate and phosphatidylinositol (5)-phosphate was detected. Removal of the sulphate groups via sulfatase treatment led to a dramatic decrease in Etx-induced cytotoxicity, but not in proEtx-GFP binding to MDCK cells or a significant shift in oligomer formation, pointing to a role of sulfatide in pore formation in rafts but not in toxin binding to the target cell membrane. These results show for the first time the interaction between Etx and membrane lipids from host tissue and point to a major role for sulfatides in C. perfringens epsilon toxin pathophysiology.
Forgetting in Managing Rules and Ontologies

The language of HEX-programs under the answer-set semantics is designed for interoperating with heterogeneous sources via external atoms and for meta-reasoning via higher-order literals in the context of the semantic Web. As an important technique in managing knowledge bases, the notion of forgetting has received increasing interest in the knowledge-representation area. In this paper, we introduce a semantics-based theory of forgetting for HEX-programs and, in turn, for a class of OWL/RDF(S) ontologies which allows to fully employ semantic information in managing ontologies like editing, merging, aligning, and redundancy removal
YabA and DnaD inhibit helix assembly of the DNA replication initiation protein DnaA

Control of DNA replication initiation is essential for cell growth. A unifying characteristic of DNA replication initiator proteins is their distinctive AAA+ nucleotide‐binding domains. The bacterial initiator DnaA assembles into a right‐handed helical oligomer built upon interactions between neighbouring AAA+ domains to form an active initiation complex. Recently we developed a unique cross‐linking assay that specifically detects ATP‐dependent DnaA helix assembly. Here we have utilized this assay to show that two DnaA regulatory proteins in Bacillus subtilis, YabA and DnaD, inhibit DnaA helix formation. These results, in combination with our previous finding that the regulatory factor Soj/ParA also targets DnaA filament formation, highlight the critical importance of regulating DnaA helix formation during the initiation reaction. Moreover, these observations lead us to suggest that DnaA oligomerization may be the main regulatory step of the initiator assembly pathway in B. subtilis, in contrast to the prevailing model of bacterial DNA replication based on Escherichia coli DnaA where ATP binding appears to be the targeted activity.
On the impact of central Pacific warming events on Atlantic tropical storm activity

A recent study by Kim et al. (2009) claim that central Pacific warming (CPW) events in 1969, 1991, 1994, 2002 and 2004 are associated with a greater‐than‐average frequency of tropical storms and increasing landfall potential along the Gulf of Mexico coast and Central America. Based on an independent data analysis of tropical cyclone activity in the five CPW years, it is shown here that only 1969, 2002 and 2004 were characterized with significantly greater‐than‐average cyclone activity in the Gulf of Mexico and Caribbean Sea, whereas 1991 and 1994 were characterized with significantly lower‐than‐average activity. Coincidently, the Atlantic warm pool (AWP) was significantly larger than average during 1969 and 2004, and significantly smaller than average during 1991 and 1994. By performing multiple sets of ensemble model experiments using the NCAR atmospheric general circulation model, it is shown here that the increased tropical storm frequency in 1969 and 2004 can be readily explained by a large AWP and the associated vertical wind shear reduction and enhanced moist convective instability in the main development region for Atlantic hurricanes, without invoking a remote influence from the tropical Pacific. Therefore, we conclude that it is premature to associate CPW events to an increasing frequency of cyclone activity in the Gulf of Mexico and Caribbean Sea.
Decreased glutathione peroxidase activity secondary to severe iron deficiency: a possible mechanism responsible for the shortened life span of the iron-deficient red cell.

Red cell glutathione peroxidase activity decreased to 26% of initial activity following the induction of severe iron deficiency in rabbits. The fall in enzyme activity does not appear to be related to anemia per se, aging of the animals during the course of the experiment, or a generalized decrease in enzyme protein synthesis. With iron repletion, glutathione peroxidase activity did not return to initial values for 10 wk after the hemoglobin concentration had returned to normal. During this period of time, the young red cell population had a higher concentration of GSH-Px activity than the older cells. In contrast, there is no age differential in the concentration of this enzyme in normal red cells, and during the induction of iron deficiency young red cells have decreased enzyme activity as compared to older cells. Reduction in glutathione peroxidase activity may result in increased oxidative damage to the irondeficient red cell. This, in turn, may be responsible for the previously reported membrane abnormalities and shortened red cell survival of iron-deficient red cells. It remains to be shown if glutathione peroxidase is dependent on iron for its synthesis or if the function of the enzyme is dependent on an iron-containing protein serving as an electron carrier. ED CELL SURVIVAL is significantly decreased in severe iron deficiency. ’4 Recent work from our laboratory has shown that the iron-deficient red cell has increased membrane rigidity, increased susceptibility to hemolysis by inhibitors of membrane sulfhydryl groups, and increased autohemolysis.4 In addition other investigators have demonstrated that the iron-deficient red cell is more susceptible to hemolysis by hydrogen peroxide.5 These observations suggest that a metabolic defect may be present in the iron-deficient red cell that allows oxidative damage of the membrane to occur. Alteration in the membrane may in turn result in increased cellular rigidity, increased sequestration in the spleen and other organs, and ultimately premature cell destruction. It has been proposed that the
BonnPlace Legalization: Minimizing Movement by Iterative Augmentation

We describe BONNPLACELEGAL, an algorithm for VLSI placement legalization. Based on a minimum-cost flow algorithm that iteratively augments flows along paths, our approach ensures that only augmentations are considered that can be realized exactly by cell movements. Hence, this method avoids realization problems that are inherent to previous flow-based legalization algorithms. As a result, it combines the global perspective of minimum-cost flow approaches with the efficiency of local search algorithms. The tool is mainly designed to minimize total and maximum cell movement, but it is flexible enough to optimize other objective functions provided that the effect of single cell movements on them can be estimated efficiently. We compare our approach to legalization tools from industry and academia by experiments on dense recent real-world designs and public benchmarks. The results show that we are much faster and produce significantly better results in terms of average (linear and quadratic) and maximum movement than any other tool. The experiments also demonstrate that by minimizing squared movement we also produce a smaller increase in net length than the other tools.
Blue Luminescence and the Presence of Small PAHs in the ISM

Blue Luminescence (BL) was first discovered in a proto-planetary nebula, the Red Rectangle (RR) surrounding the post-AGB star HD 44179. BL has been attributed to fluorescence by small, 3-4 ringed neutral polycyclic aromatic hydrocarbon (PAH) molecules, and was thought to be unique to the RR environment where such small molecules are actively being produced and shielded from the harsh interstellar radiation by a dense circumstellar disk. In this paper we present the BL spectrum detected in several ordinary reflection nebulae illuminated by stars having temperatures between 10,000 -- 23,000 K. All these nebulae are known to also exhibit the infrared emission features called aromatic emission features (AEFs) attributed to large PAHs. We present the spatial distribution of the BL in these nebulae. In the case of Ced~112, the BL is spatially correlated with mid-IR emission structures attributed to AEFs. These observations provide evidence for grain processing and possibly for in-situ formation of small grains and large molecules from larger aggregates. Most importantly, the detection of BL in these ordinary reflection nebulae suggests that the BL carrier is an ubiquitous component of the ISM and is not restricted to the particular environment of the RR.
Halophilic Archaea Cultivated from Surface Sterilized Middle-Late Eocene Rock Salt Are Polyploid

Live bacteria and archaea have been isolated from several rock salt deposits of up to hundreds of millions of years of age from all around the world. A key factor affecting their longevity is the ability to keep their genomic DNA intact, for which efficient repair mechanisms are needed. Polyploid microbes are known to have an increased resistance towards mutations and DNA damage, and it has been suggested that microbes from deeply buried rock salt would carry several copies of their genomes. Here, cultivable halophilic microbes were isolated from a surface sterilized middle-late Eocene (38–41 million years ago) rock salt sample, drilled from the depth of 800 m at Yunying salt mine, China. Eight unique isolates were obtained, which represented two haloarchaeal genera, Halobacterium and Halolamina. We used real-time PCR to show that our isolates are polyploid, with genome copy numbers of 11–14 genomes per cell in exponential growth phase. The ploidy level was slightly downregulated in stationary growth phase, but the cells still had an average genome copy number of 6–8. The polyploidy of halophilic archaea living in ancient rock salt might be a factor explaining how these organisms are able to overcome the challenge of prolonged survival during their entombment.
Membrane Trafficking of NADPH Oxidase p47phox in Paraventricular Hypothalamic Neurons Parallels Local Free Radical Production in Angiotensin II Slow-Pressor Hypertension

NADPH oxidase-generated reactive oxygen species (ROS) are highly implicated in the development of angiotensin II (AngII)-dependent hypertension mediated in part through the hypothalamic paraventricular nucleus (PVN). This region contains vasopressin and non-vasopressin neurons that are responsive to cardiovascular dysregulation, but it is not known whether ROS is generated by one or both cell types in response to “slow-pressor” infusion of AngII. We addressed this question using ROS imaging and electron microscopic dual labeling for vasopressin and p47phox, a cytoplasmic NADPH oxidase subunit requiring mobilization to membranes for the initiation of ROS production. C57BL/6 mice or vasopressin-enhanced green fluorescent protein (VP–eGFP) mice were infused systemically with saline or AngII (600 ng · kg−1 · min−1, s.c.) for 2 weeks, during which they slowly developed hypertension. Ultrastructural analysis of the PVN demonstrated p47phox immunolabeling in many glial and neuronal profiles, most of which were postsynaptic dendrites. Compared with saline, AngII recipient mice had a significant increase in p47phox immunolabeling on endomembranes just beneath the plasmalemmal surface (+42.1 ± 11.3%; p < 0.05) in non-vasopressin dendrites. In contrast, AngII infusion decreased p47phox immunolabeling on the plasma membrane (−35.5 ± 16.5%; p < 0.05) in vasopressin dendrites. Isolated non-VP–eGFP neurons from the PVN of AngII-infused mice also showed an increase in baseline ROS production not seen in VP–eGFP neurons. Our results suggest that chronic low-dose AngII may offset the homeostatic control of blood pressure by differentially affecting membrane assembly of NADPH oxidase and ROS production in vasopressin and non-vasopressin neurons located within the PVN.
Newfound Hantavirus in Chinese Mole Shrew, Vietnam

Sequence analysis of the full-length medium segment and the partial small and large segments of a hantavirus, detected by reverse transcription–PCR in lung tissues of the Chinese mole shrew (Anourosorex squamipes) captured in Cao Bang Province, Vietnam, in December 2006, indicated that it is genetically distinct from rodentborne hantaviruses.
Plasma enhanced chemical vapor deposition of nanocrystalline graphene and device fabrication development

Large area growth of high quality graphene remains a challenge, and is currently dominated by chemical vapor deposition (CVD) on metal catalyst films. This method requires a transfer of the graphene onto an insulating substrate for electronic applications, and the graphene film quality and performance can vary with the transfer. A more attractive approach is plasma enhanced chemical vapor deposition (PECVD) of graphene and nanocrystalline graphene (NCG) directly on insulating substrates. The aim of this project was to explore the deposition process and microfabrication processes based on these NCG films. A deposition process for nanocrystalline graphene was developed in this work based on parallel-plate PECVD. NCG with thicknesses between 3 and 35nm were deposited directly on wet thermal oxidized silicon wafers with diameter of 150 mm, quartz glass and sapphire glass. High NCG thickness uniformities of 87% over full wafer were achieved. Surface roughness was measured by atomic force microscopy and shows root mean square (RMS) values of less than 0.23nm for 3nm thin films. NCG films deposited on quartz and sapphire show promising performance as transparent conductor with 13kΩ/X sheet resistance at 85% transparency. Furthermore, the suitability of the developed PECVD NCG films for microfabrication was demonstrated. Microfabrication process development was focused on four device types. NCG membranes were fabricated based on through-wafer inductively coupled plasma etching from the back, and consecutive membrane release by HF vapor etching. The fabrication of suspended NCG strips, based on HF vapor release, shows promising results, but was not entirely successful due to insufficient thickness of the sacrificial oxide. Top gated NCG strips are successfully fabricated, and the increased modulation by the top gate is demonstrated. Finally, NCG nanowire fabrication is performed on 150mm wafers. Experiments yielded an increased back gate modulation effect by a reduced NCG thickness, although no nanowire formation was observed. A highly accurate focused ion beam (FIB) prototyping technique was developed and applied to exfoliated graphene in this work. This technique systematically avoids any exposure of the graphene to Ga+-ions through the use of an alignment marker system, achieving alignment accuracies better than 250 nm. Contacts were deposited by FIB- or e-beam-assisted tungsten deposition, and FIB trench milling was used to confine conduction to a narrow channel. A channel passivation method based on e-beam-assisted insulator deposition has been demonstrated, and showed a reduction of ion damage to the graphene. Three fabricated transistor structures were electrically characterized.
By-product of Tropical Vermicelli Waste as a Novel Alternative Feedstuff in Broiler Diets

Two experiments were conducted to determine physical and chemical properties of vermicelli waste (VW) and effect of VW inclusion levels on growth performance of broilers. In experiment 1, VW samples were randomly collected from vermicelli industry in Thailand to analyze nutritional composition. Vermicelli waste contained 9.96% moisture, 12.06% CP, 32.30% crude fiber (CF), and 0.57% ether extract (EE), as DM basis. The ratio of insoluble:soluble non-starch polysaccharide (NSP) was 43.4:8.9. A total of 120 chicks (6 pens per treatment and 10 chicks per pen) were fed a corn-soybean meal-based diet or 20% VW substituted diet to determine the apparent metabolizable energy corrected for nitrogen retention (AMEn) of VW. The AMEn of VW was 1,844.7±130.71 kcal/kg. In experiment 2, a total of 1,200 chicks were randomly allotted to 1 of 4 dietary treatments for 42-d growth assay. There were 300 chicks with 6 pens per treatment and 50 chicks per pen. The dietary treatments contained 0%, 5%, 10%, or 15% VW, respectively. All diets were formulated to be isocaloric and isonitrogenous. From 0 to 18 d of age chicks fed VW diets had higher (p<0.001) feed conversion ratio (FCR) compared with those fed the control diet. No difference was observed during grower and finisher phase (19 to 42 d). Chicks fed VW diets had lower relative weight of abdominal fat (p<0.001) but higher relative weight of gizzard (p<0.05) than those of chicks fed the control diet. Increasing VW inclusion levels increased ileal digesta viscosity (p<0.05) and intestinal villus height of chicks (p< 0.001). For apparent total tract digestibility assay, there were 4 metabolic cages of 6 chicks that were fed experimental treatment diets (the same as in the growth assay) in a 10-d total excreta collection. Increasing VW inclusion levels linearly decreased (p<0.05) apparent total tract digestibility of DM and CF.