julilili42/papers huggingface dataset:
Assessment of chlorinated ethenes biodegradation in an anaerobic aquifer by isotope analysis and microcosm studies
2011-12-01

This work focused on identification and quantification of natural attenuation of chlorinated ethenes in a contaminated aquifer beneath an industrial area using compound specific isotope analysis (CSIA). Presence of cis-1,2-dichloroethene (cis-DCE) and vinylchloride (VC), as well as in situ redox conditions indicated degradation of the primary contaminant trichloroethene (TCE) by reductive dechlorination. The potential for VC degradation was further corroborated by PCR-analysis on water samples which confirmed the presence of Dehalococcoides strains and VC reductases. In situ biodegradation was estimated by various approaches, including concentration measurements along the groundwater flow path, microcosm studies and by compound specific stable carbon isotope analysis. Using the Rayleigh model carbon isotope enrichment factors, e, were determined both in the field and in microcosm experiments for each dechlorination step. Estimates of biodegradation based on enrichment factors derived from microcosms (―8.6‰ (cis-DCE) and ―27.2‰ (VC)) were consistently lower (up to 40%) than those based on field data. Our results of the isotope study at field scale, microcosm experiments and molecular marker analysis provided conclusive information on natural attenuation processes and can be recommended as a general approach for site characterisation and risk assessment in NA studies.
TRANSCENDENTAL EXCHANGE: A MODEL TO LEGITIMIZE HUMAN RIGHTS?
2011-12-01

In view of the difficulty in achieving an appropriate model to legitimize human rights, this remains an unfinished task of contemporary philosophy. This article proposes a model of consensual legitimacy, which is called transcendental exchange. The conceptual basis of this exchange is constituted by the idea of an intercultural discourse and the impossibility to give up the protection of certain interests essential to the existence. Given their importance, these interests are called transcendental interests.
Evaluation in a continuous-flow column of different fermenting substrates for the reductive dehalogenation of trichloroethene
2011-12-01

A continuous-flow column study was conducted to analyse the reductive dehalogenation of trichloroethene (TCE) in aquifer material with a composition high in iron oxides. The column was bioaugmented with the Point Mugu (PM) culture, which is a mixed microbial enrichment culture capable of completely transforming TCE to ethene (ETH). Most of the metabolic reducing equivalents were channelled to sulfate, Fe(III), and Mn(IV) reduction. When equal electron-reducing equivalents were added, the most effective dehalogenation was achieved using formate as an electron donor, with 14% of the electron equivalents going towards dehalogenation reactions, compared to 6.7% for lactate and 9.6% for propionate. Lactate and propionate addition resulted in a significant increase in Geobacter, Spirochaetes, and Desulfovibrio phylotypes relative to Dehalococcides when compared to formate addition. Molecular results support chemical observations that a greater percentage of the electron donor addition was channeled to Fe(III) reduction when lactate and propionate were added compared to formate.
Enhanced natural attenuation - Determining the potential for reductive dechlorination in an oxic aquifer
2011-12-01

The aim of the study was to demonstrate the stimulation of reductive dehalogenation of chlorinated ethenes in an oxic aquifer. Microcosms with aquifer material were amended with different organic substrates as electron donors in order to stimulate microbial reductive dechlorination. Next to molasses and lactate a commercial product was applied, which has been described as controlled-release carbon zero valent iron particles (EHCTM). In addition, vitamins and bicarbonate buffer were added to the microcosms to further stimulate growth of halorespiring microorganisms. Reductive dechlorination was followed by measuring chlorinated ethene concentrations and their stable carbon isotope fractionation. The microbiological community was monitored by terminal restriction fragment length polymorphism (T-RFLP). The EHC amended microcosms showed only incomplete conversion of PCE, resulting in an accumulation of cis-DCE after incubation for 103 days. In the microcosms amended with molasses, complete reductive dechlorination of PCE to ethene was observed within 56 days. The degradation of the less chlorinated ethenes correlated with the appearance of Dehalococcoides microorganisms and carbon isotope fractionation. Also one of the parallel set-ups amended with lactate showed complete dechlorination. In this microcosm an isotopic overtaking of VC was observed, proving complete microbiological degradation to ethene. Control microcosms without substrate addition showed no dechlorination during the whole experiment. Our study demonstrates that the potential for microbial reductive dechlorination was present and can be stimulated in an oxic aquifer by establishing reducing conditions and supplementing fermentable substrates.
On the distribution of deciduous oak in the second half of the Holocene in northern Syria
2011-12-01

Today oak park woodland is absent in northern Syria (Fig 1). However, recent charcoal analysis at the sites of Tell Mozan (3rd and early 2nd millennium BC), Tell Leilan (3rd millennium BC), Tell Hamoukar (4th millennium BC), Tell Halaf (first millennium BC till second millennium AD), Tell Jerablus (4th and 3rd millennium BC) and Tell Shioukh Tahtani (late 4th till second millennium BC) indicates a more southward distribution of deciduous oak through the second half of the Holocene in Northern Syria (see also partially in Deckers and Pessin, 2010).
Personality and Relationship Quality during the Transition from High School to Early Adulthood
2011-12-01

The post-high school transition period is believed to be associated with considerable changes in social networks, yet longitudinal studies documenting these changes are scarce.To address this gap, the current research explored 3 relevant issues.First, changes in participants' relationship characteristics during the transition from high school were examined.Second, the roles of personality traits as antecedents of these changes were studied.Third, the association between change in relationship characteristics and personality during the transition was explored.A sample of over 2,000 German emerging adults, surveyed before leaving school and then 2 years after the transition from high school, was assessed on personality traits and a multidimensional assessment of the quality of their relationships.Findings indicated that participants experienced mostly positive changes in relationship quality during the transition from high school and that antecedent personality at school was an important predictor of the nature of this change.Finally, change in relationship quality was found to be associated with personality change during the post-school transition.Findings indicated that personality traits may influence transition success and that change in relationships during this transition may influence personality development.The implications of the research for post-school transition success are discussed.The transition to post-high school life is a major developmental milestone marking the beginning of emerging adulthood and is associated with greater independence from parents and considerable change in established social networks (Arnett,
Decellularization of porcine corneas and repopulation with human corneal cells for tissue‐engineered xenografts
2011-12-02

Abstract. Purpose: To evaluate the potential use of decellularized porcine corneas (DPCs) as a carrier matrix for cultivating human corneal cells in tissue engineering. Methods: Corneal cells were isolated from human corneoscleral rims. Porcine corneas were decellularized using hypotonic tris buffer, ethylene diamine tetra‐acetic acid (EDTA, 0.1%), aprotinin (10 KIU/ml) and 0.3% sodium dodecyl sulphate. Haematoxylin–eosin (HE) and 4,6‐diamidino‐2‐phenylindole (DAPI) staining were performed to confirm removal of the corneal cells. Quantitative analysis was performed to determine levels of desoxyribonucleic acid (DNA) using DNA Purification Kit (Fermentas, St. Leon‐Rot, Germany). Alcian blue staining was carried out to analyse the structure of the extracellular matrix (ECM). Corneal stromal cells were injected into the DPCs; limbal corneal epithelial cells and corneal endothelial cells were seeded onto the anterior and posterior surfaces of the DPCs, respectively. Evaluation was undertaken at days 14 and 30. The phenotypical properties of the cultivated corneal cells were investigated using Immunolocalization of type I collagen, keratocan, lumican, cytokeratin 3 (AE5) and type VIII collagen. Results: Haematoxylin–eosin and DAPI staining showed efficient elimination of porcine corneal cells, whereas alcian blue confirmed gross preservation of the ECM. The quantitative analysis of the DNA content showed a significant reduction (mean before decellularization: 75.45 ± 13.71 ng/mg; mean after decellularization: 9.87 ± 2.04 ng/mg, p &lt; 0.001). All three types of corneal cells were efficiently cultured and expanded on the DPCs. Conclusions: Decellularized porcine corneas might serve as a potential scaffold for tissue engineering of the cornea, possibly providing xenogenic substrate for corneal transplantation.
Reconstruction of corneal stroma with decellularized porcine xenografts in a rabbit model
2011-12-02

Abstract. Purpose: To evaluate the potential use of decellularized porcine stromal matrix (PSM) for reconstruction of corneal stroma in a rabbit model. Methods: Ten chinchilla bastard rabbit corneas were exposed to a circular half‐thickness keratotomy with a 3.0 mm diameter at the central cornea. Porcine corneas were decellularized using hypotonic tris buffer, ethylene diamine tetra‐acetic acid (EDTA, 0.1%), aprotinin (10 K IU/ml) and 0.3% sodium dodecyl sulphate (SDS). The 3.0 mm in diameter decellularized corneal stromal xenograft was inserted into the pocket, and the incision was closed with four 10.0 nylon sutures. Clinical photographs were taken at day 1, day 7, day 30 and on a monthly basis for up to 6 months after transplantation. Six months after surgery, the rabbits were killed and eyes were enucleated. Haematoxylin–eosin (HE) and 4,6‐diamidino‐2‐phenylindole (DAPI) staining were performed to confirm the complete removal of the corneal cells after decellularization of porcine corneas and repopulation with rabbit cells. Alcian blue staining was performed for analysing the structure of the extracellular matrix (ECM). Results: Efficient elimination of porcine cells was achieved by our decellularization protocol and confirmed via HE and DAPI stainings. Moreover, the major histoarchitectural ECM structure had been maintained as visualized by the alcian blue stain. Finally, the PSM was biocompatible with the host’s epithelium evidenced as a regrowth covering the exposed xenograft. Conclusions: This novel technique of tissue engineering may provide one of many solutions to addressing anterior corneal pathological conditions in the face of a shortage of human corneal material.
Pharmacophore-based discovery of a novel cytosolic phospholipase A2α inhibitor
2011-12-04

The release of arachidonic acid, a precursor in the production of prostaglandins and leukotrienes, is achieved by activity of the cytosolic phospholipase A(2)α (cPLA(2)α). Signaling mediated by this class of bioactive lipids, which are collectively referred to as eicosanoids, has numerous effects in physiological and pathological processes. Herein, we report the development of a ligand-based pharmacophore model and pharmacophore-based virtual screening of the National Cancer Institute (NCI) database, leading to the identification of 4-(hexadecyloxy)-3-(2-(hydroxyimino)-3-oxobutanamido)benzoic acid (NSC 119957) as cPLA(2)α inhibitor in cell-free and cell-based in vitro assays.
Static detection of malicious JavaScript-bearing PDF documents
2011-12-05

Despite the recent security improvements in Adobe's PDF viewer, its underlying code base remains vulnerable to novel exploits. A steady flow of rapidly evolving PDF malware observed in the wild substantiates the need for novel protection instruments beyond the classical signature-based scanners. In this contribution we present a technique for detection of JavaScript-bearing malicious PDF documents based on static analysis of extracted JavaScript code. Compared to previous work, mostly based on dynamic analysis, our method incurs an order of magnitude lower run-time overhead and does not require special instrumentation. Due to its efficiency we were able to evaluate it on an extremely large real-life dataset obtained from the VirusTotal malware upload portal. Our method has proved to be effective against both known and unknown malware and suitable for large-scale batch processing.
Topical interventions for genital lichen sclerosus
2011-12-05

The current limited evidence demonstrates the efficacy of clobetasol propionate, mometasone furoate, and pimecrolimus in treating genital lichen sclerosus. Further RCTs are needed to determine the optimal potency and regimen of topical corticosteroids, examine other topical interventions, assess the duration of remission or prevention of flares, evaluate the reduction in the risk of genital squamous cell carcinoma or genital intraepithelial neoplasia, and examine the efficacy in improving the quality of the sex lives of people with this condition.
Gamma‐glutamyltransferase, cardiovascular disease and mortality in individuals with diabetes mellitus
2011-12-05

Abstract Background Increased plasma activity of gamma‐glutamyltransferase (GGT) is associated with cardiovascular diseases (CVD) and mortality in the general population. We investigated the association between GGT, CVD and mortality in individuals with diabetes mellitus. Methods Data used were from 1280 participants, aged 35–70 years, with a confirmed diagnosis of diabetes mellitus in the European Prospective Investigation into Cancer and Nutrition in Potsdam (Germany), Bilthoven and Utrecht (the Netherlands). Multivariate hazard ratios (HR) and 95% confidence intervals (CI) for CVD (non‐fatal and fatal events) and overall mortality were estimated using sex‐specific quartiles of GGT. Results After 8.2 years follow‐up, 108 incident CVD cases and 84 deaths were observed. Participants with high GGT activity had an increased mortality risk: HR in the highest quartile was 3.96 (95% CI 1.74, 9.00). This association was in particular present in former and current smokers, younger persons and those with a higher waist–height ratio and alcohol consumption. No associations were observed for non‐fatal CVD and non‐fatal and fatal CVD events combined. Conclusions Higher GGT plasma activity is associated with increased all‐cause mortality in individuals with diabetes. Copyright © 2011 John Wiley &amp; Sons, Ltd.
4‐1BB ligand modulates direct and Rituximab‐induced NK‐cell reactivity in chronic lymphocytic leukemia
2011-12-05

Abstract NK cells play an important role in tumor immunosurveillance and largely contribute to the therapeutic success of anti‐tumor antibodies like Rituximab. Here, we studied the role of the TNF family member 4‐1BB ligand (4‐1BBL) during the interaction of NK cells with chronic lymphocytic leukemia (CLL) cells. 4‐1BBL was highly expressed on patient B‐CLL cells in all 56 investigated cases. Signaling via 4‐1BBL following interaction with 4‐1BB, which was detected on NK cells of CLL patients but not healthy individuals, led to the release of immunoregulatory cytokines including TNF by CLL cells. CLL patient sera contained elevated levels of TNF and induced 4‐1BB upregulation on NK cells, which in turn impaired direct and Rituximab‐induced NK‐cell reactivity against 4‐1BBL‐expressing targets. NK‐cell reactivity was not only enhanced by blocking the interaction of NK cell‐expressed 4‐1BB with 4‐1BBL expressed by CLL cells, but also by preventing 4‐1BB upregulation on NK cells via neutralization of TNF in patient serum with Infliximab. Our data indicate that 4‐1BBL mediates NK‐cell immunosubversion in CLL, and thus might contribute to the reportedly compromised efficacy of Rituximab to induce NK‐cell reactivity in the disease, and that TNF neutralization may serve to enhance the efficacy of Rituximab treatment in CLL.
Polioviral receptor binding ligand: A novel and safe peptide drug carrier from polioviral capsid
2011-12-05

Cellular uptake enhancement of green fluorescent protein (GFP) into human colon adenocarcinoma (HT-29) and human mouth epidermal carcinoma (KB) cells by a segment of VP1-BC loop polioviral capsid (V), a polioviral receptor binding peptide and HIV-I transactivator of transcription (Tat) was evaluated. HT-29 and KB cells were incubated with various molar concentrations of GFP, V, and Tat mixtures. Both V and Tat showed potent enhancement of GFP uptake into HT-29 and KB cells. In HT-29 cells, the V-GFP, Tat-GFP, and V-Tat-GFP mixtures enhanced the GFP cellular uptake efficiency with the maximum of 3.98-, 4.59-, and 4.08-folds of GFP at 1:3, 1:1/6, and 1/6:1:1/6 molar ratios, respectively. For KB cells, the V-GFP, Tat-GFP, and V-Tat-GFP mixtures enhanced the GFP cellular uptake efficiency with the maximum of 4.05-, 5.09-, and 4.91-folds of GFP at 1:1/6, 1:1, and 1:1:1 molar ratios, respectively. Both V and V-GFP mixtures showed a lower cytotoxicity effect than Tat and Tat-GFP mixture. These studies demonstrated the potential of polioviral capsid, a polioviral receptor binding peptide as a novel, low cytotoxicity carrier for the development of peptide drugs delivery system.
3D-QSPR Method of Computational Technique Applied on Red Reactive Dyes by Using CoMFA Strategy
2011-12-05

Cellulose fiber is a tremendous natural resource that has broad application in various productions including the textile industry. The dyes, which are commonly used for cellulose printing, are “reactive dyes” because of their high wet fastness and brilliant colors. The interaction of various dyes with the cellulose fiber depends upon the physiochemical properties that are governed by specific features of the dye molecule. The binding pattern of the reactive dye with cellulose fiber is called the ligand-receptor concept. In the current study, the three dimensional quantitative structure property relationship (3D-QSPR) technique was applied to understand the red reactive dyes interactions with the cellulose by the Comparative Molecular Field Analysis (CoMFA) method. This method was successfully utilized to predict a reliable model. The predicted model gives satisfactory statistical results and in the light of these, it was further analyzed. Additionally, the graphical outcomes (contour maps) help us to understand the modification pattern and to correlate the structural changes with respect to the absorptivity. Furthermore, the final selected model has potential to assist in understanding the charachteristics of the external test set. The study could be helpful to design new reactive dyes with better affinity and selectivity for the cellulose fiber.
Engrailed homeoprotein recruits the adenosine A1 receptor to potentiate ephrin A5 function in retinal growth cones
2011-12-06

Engrailed 1 and engrailed 2 homeoprotein transcription factors (collectively Engrailed) display graded expression in the chick optic tectum where they participate in retino-tectal patterning. In vitro, extracellular Engrailed guides retinal ganglion cell (RGC) axons and synergises with ephrin A5 to provoke the collapse of temporal growth cones. In vivo disruption of endogenous extracellular Engrailed leads to misrouting of RGC axons. Here we characterise the signalling pathway of extracellular Engrailed. Our results show that Engrailed/ephrin A5 synergy in growth cone collapse involves adenosine A1 receptor activation after Engrailed-dependent ATP synthesis, followed by ATP secretion and hydrolysis to adenosine. This is, to our knowledge, the first evidence for a role of the adenosine A1 receptor in axon guidance. Based on these results, together with higher expression of the adenosine A1 receptor in temporal than nasal growth cones, we propose a computational model that illustrates how the interaction between Engrailed, ephrin A5 and adenosine could increase the precision of the retinal projection map.
Metabolic Switches and Adaptations Deduced from the Proteomes of Streptomyces coelicolor Wild Type and phoP Mutant Grown in Batch Culture
2011-12-06

Bacteria in the genus Streptomyces are soil-dwelling oligotrophs and important producers of secondary metabolites. Previously, we showed that global messenger RNA expression was subject to a series of metabolic and regulatory switches during the lifetime of a fermentor batch culture of Streptomyces coelicolor M145. Here we analyze the proteome from eight time points from the same fermentor culture and, because phosphate availability is an important regulator of secondary metabolite production, compare this to the proteome of a similar time course from an S. coelicolor mutant, INB201 (ΔphoP), defective in the control of phosphate utilization. The proteomes provide a detailed view of enzymes involved in central carbon and nitrogen metabolism. Trends in protein expression over the time courses were deduced from a protein abundance index, which also revealed the importance of stress pathway proteins in both cultures. As expected, the ΔphoP mutant was deficient in expression of PhoP-dependent genes, and several putatively compensatory metabolic and regulatory pathways for phosphate scavenging were detected. Notably there is a succession of switches that coordinately induce the production of enzymes for five different secondary metabolite biosynthesis pathways over the course of the batch cultures.
Exometabolome Analysis Identifies Pyruvate Dehydrogenase as a Target for the Antibiotic Triphenylbismuthdichloride in Multiresistant Bacterial Pathogens
2011-12-06

The desperate need for new therapeutics against notoriously antibiotic-resistant bacteria has led to a quest for novel antibacterial target structures and compounds. Moreover, defining targets and modes of action of new antimicrobial compounds remains a major challenge with standard technologies. Here we characterize the antibacterial properties of triphenylbismuthdichloride (TPBC), which has recently been successfully used against device-associated infections. We demonstrate that TPBC has potent antimicrobial activity against many bacterial pathogens. Using an exometabolome profiling approach, a unique TPBC-mediated change in the metabolites of Staphylococcus aureus was identified, indicating that TPBC blocks bacterial pyruvate catabolism. Enzymatic studies showed that TPBC is a highly efficient, uncompetitive inhibitor of the bacterial pyruvate dehydrogenase complex. Our study demonstrates that metabolomics approaches can offer new avenues for studying the modes of action of antimicrobial compounds, and it indicates that inhibition of the bacterial pyruvate dehydrogenase complex may represent a promising strategy for combating multidrug-resistant bacteria.