Protective effect of Coriandrum sativum extract against inflammation and apoptosis in liver ischaemia/reperfusion injury

Background: The aim of this study was to investigate the anti-inflammatory and antioxidant effects of Coriandrum sativum extract on liver ischaemia reperfusion injury at light microscopic and biochemical levels. Materials and methods: Sham, ischaemia/reperfusion injury (IRI), IRI + Coriandrum sativum extract and only Coriandrum sativum extract groups were formed. Sixty minutes of ischaemia and 60 minutes of reperfusion were performed. In the treatment group, 300 mg/kg/day Coriandrum sativum was given by gavage. Hepatic tissues were fixed in 4% paraformaldehyde. Serum alanine aminotransferase (ALT), aspartate aminotransferase (AST) and alkaline phosphatase (ALP) enzymes were measured. Nuclear factor-kappa beta (NF-κB), tumour necrosis factor-alpha (TNF-α) and caspase-3 immunohistochemistry staining was performed. Microscopic scoring was performed in terms of sinusoidal congestion, vacuolisation, and necrosis. Results: Sinusoidal enlargement and diffuse congestion, Kupffer cell increase, neutrophil increase in necrotic areas, vacuolisation in hepatocytes, and bile duct proliferation in the portal triad were observed in ischaemia/reperfusion hepatic tissue. Very rare, necrotic areas were observed in the Coriandrum sativum treatment group, while congestion and vacuolisation and bile duct proliferation were decreased compared to the ischaemic group. The AST and ALT levels were increased in the IRI and IRI + Coriandrum sativum groups. When compared to the IRI group, the AST and ALT levels of the Coriandrum sativum were considerably decreased. The IRI and IRI + Coriandrum sativum groups had statistically significant differences in ALP compared to that of the Coriandrum sativum and Sham groups. There was no significant difference between the ALP levels of the IRI and IRI + Coriandrum sativum groups TNF-α, NF-κB and caspase-3 immune positive stained hepatocytes were numerous and widely observed in the injury group. There were positive TNF-α immunohistochemical staining Kupffer cells in the IRI group. In the group treated with Coriandrum sativum, Kupffer cells were not stained, while TNF-α, NF κB and caspase-3 expressing hepatocytes were found to be decreased compared to the IRI group. When the expression values of the TNF-α, NF-κB and caspase-3 groups were evaluated statistically, it was seen that there was a significant decrease in the group treated with Coriandrum sativum. Conclusions: It was found that Coriandrum sativum extract decreased proinflammatory cytokine TNF-α and apoptotic cell death and liver enzymes in liver ischaemia/reperfusion injury

CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data.

MOTIVATION: Simple bioinformatic tools are frequently used to analyse time-series datasets regardless of their ability to deal with transient phenomena, limiting the meaningful information that may be extracted from them. This situation requires the development and exploitation of tailor-made, easy-to-use and flexible tools designed specifically for the analysis of time-series datasets. RESULTS: We present a novel statistical application called CLUSTERnGO, which uses a model-based clustering algorithm that fulfils this need. This algorithm involves two components of operation. Component 1 constructs a Bayesian non-parametric model (Infinite Mixture of Piecewise Linear Sequences) and Component 2, which applies a novel clustering methodology (Two-Stage Clustering). The software can also assign biological meaning to the identified clusters using an appropriate ontology. It applies multiple hypothesis testing to report the significance of these enrichments. The algorithm has a four-phase pipeline. The application can be executed using either command-line tools or a user-friendly Graphical User Interface. The latter has been developed to address the needs of both specialist and non-specialist users. We use three diverse test cases to demonstrate the flexibility of the proposed strategy. In all cases, CLUSTERnGO not only outperformed existing algorithms in assigning unique GO term enrichments to the identified clusters, but also revealed novel insights regarding the biological systems examined, which were not uncovered in the original publications. AVAILABILITY AND IMPLEMENTATION: The C++ and QT source codes, the GUI applications for Windows, OS X and Linux operating systems and user manual are freely available for download under the GNU GPL v3 license at http://www.cmpe.boun.edu.tr/content/CnG. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.This work was supported by the Turkish State Planning Organization [DPT09K120520 to B.K.]; the Bogazici University Research Fund [10A05D4 to B.K., 08A506 to B.K., 6882-12A01D5 to A.T.C.]; TUBITAK [106M444 to B.K., 110E292 to A.T.C.], Biotechnology and Biological Sciences Research Council [BRIC2.2 grant BB/K011138/1 to S.G.O.]; and EU 7th Framework Programme [BIOLEDGE Contract No: 289126 to S.G.O.].This is the final version of the article. It first appeared from Oxford University Press via http://dx.doi.org/10.1093/bioinformatics/btv53

Observing and modelling the young solar analogue EK Draconis: starspot distribution, elemental abundances, and evolutionary status

Observations and modelling of stars with near-solar masses in their early phases of evolution is critical for a better understanding of how dynamos of solar-type stars evolve. We examine the chemical composition and the spot distribution of the pre-main-sequence solar analogue EK Dra. Using spectra from the HERMES Spectrograph (La Palma), we obtain the abundances of 23 elements with respect to the solar ones, which lead to a $[{\rm Fe/H}]=0.03$, with significant overabundance of Li and Ba. The s-process elements Sr, Y, and Ce are marginally overabundant, while Co, Ni, Cu, Zn are marginally deficient compared to solar abundances. The overabundance of Ba is most likely due to the assumption of depth-independent microturbulent velocity. Li abundance is consistent with the age and the other abundances may indicate distinct initial conditions of the pre-stellar nebula. We estimate a mass of 1.04 $M_\odot$ and an age of $27^{+11}_{-8}$\,Myr using various spectroscopic and photometric indicators. We study the surface distribution of dark spots, using 17 spectra collected during 15 nights using the CAFE Spectrograph (Calar Alto). We also conduct flux emergence and transport (FEAT) simulations for EK Dra's parameters and produce 15-day-averaged synoptic maps of the likely starspot distributions. Using Doppler imaging, we reconstruct the surface brightness distributions for the observed spectra and FEAT simulations, which show overall agreement for polar and mid-latitude spots, while in the simulations there is a lack of low-latitude spots compared to the observed image. We find indications that cross-equatorial extensions of mid-latitude spots can be artefacts of the less visible southern-hemisphere activity.Comment: 15 pages, 16 figures, accepted for publication in MNRAS; corrections in Abstract and Introductio

Enhanced topical delivery of dexamethasone by β-cyclodextrin decorated thermoresponsive nanogels

Highly hydrophilic, responsive nanogels are attractive as potential systems for the topical delivery of bioactives encapsulated in their three-dimensional polymeric scaffold. Yet, these drug carrier systems suffer from drawbacks for efficient delivery of hydrophobic drugs. Addressing this, β-cyclodextrin (βCD) could be successfully introduced into the drug carrier systems by exploiting its unique affinity toward dexamethasone (DXM) as well as its role as topical penetration enhancer. The properties of βCD could be combined with those of thermoresponsive nanogels (tNGs) based on dendritic polyglycerol (dPG) as a crosslinker and linear thermoresponsive polyglycerol (tPG) inducing responsiveness to temperature changes. Electron paramagnetic resonance (EPR) studies localized the drug within the hydrophobic cavity of βCD by differences in its mobility and environmental polarity. In fact, the fabricated carriers combining a particulate delivery system with a conventional penetration enhancer, resulted in an efficient delivery of DXM to the epidermis and the dermis of human skin ex vivo (enhancement compared to commercial DXM cream: ∼2.5 fold in epidermis, ∼30 fold in dermis). Furthermore, DXM encapsulated in βCD tNGs applied to skin equivalents downregulated the expression of proinflammatory thymic stromal lymphopoietin (TSLP) and outperformed a commercially available DXM cream

Gas and seismicity within the Istanbul seismic gap

Understanding micro-seismicity is a critical question for earthquake hazard assessment. Since the devastating earthquakes of Izmit and Duzce in 1999, the seismicity along the submerged section of North Anatolian Fault within the Sea of Marmara (comprising the “Istanbul seismic gap”) has been extensively studied in order to infer its mechanical behaviour (creeping vs locked). So far, the seismicity has been interpreted only in terms of being tectonic-driven, although the Main Marmara Fault (MMF) is known to strike across multiple hydrocarbon gas sources. Here, we show that a large number of the aftershocks that followed the M 5.1 earthquake of July, 25th 2011 in the western Sea of Marmara, occurred within a zone of gas overpressuring in the 1.5–5 km depth range, from where pressurized gas is expected to migrate along the MMF, up to the surface sediment layers. Hence, gas-related processes should also be considered for a complete interpretation of the micro-seismicity (~M < 3) within the Istanbul offshore domain

The Elements, Lawrence University Flute Ensemble, January 30, 2017

Harper Hal

High-K volcanism in the Afyon region, western Turkey: from Si-oversaturated to Si-undersaturated volcanism

Volcanic rocks of the Afyon province (eastern part of western Anatolia) make up a multistage potassic and ultrapotassic alkaline series dated from 14 to 12 Ma. The early-stage Si-oversaturated volcanic rocks around the Afyon city and further southward are trachyandesitic volcanic activity (14.23 ± 0.09 Ma). Late-stage Si-undersaturated volcanism in the southernmost part of the Afyon volcanic province took place in three episodes inferred from their stratigraphic relationships and ages. Melilite– leucitites (11.50 ± 0.03 Ma), spotted rachyandesites, tephryphonolites and lamproites (11.91 ± 0.13 Ma) formed in the first episode; trachyandesites in the second episode and finally phonotephrites, phonolite, basaltic trachyandesites and nosean-bearing trachyandesites during the last episode. The parameter Q [normative q-(ne + lc + kls + ol)] of western Anatolia volcanism clearly decreased southward with time becoming zero in the time interval 10–15 Ma. The magmatism experienced a sudden change in the extent of Si saturation after 14 Ma, during late-stage volcanic activity of Afyon volcanic province at around 12 Ma, though there was some coexistence of Si-oversaturated and Si-undersaturated magmas during the whole life of Afyon volcanic province

Supply Chain Intelligence

This chapter provides on overall picture of business intelligence (BI) and supply chain analytics (SCA) as a means to support supply chain management (SCM) and decision-making. Based on the literature review, we clarify the needs of BI and performance measurement in the SCM sphere, and discuss its potential to enhance decision-making in strategic, tactical and operational levels. We also make a closer look in to SCA in different areas and functions of SCM. Our findings indicate that the main challenge for harnessing the full potential of SCA is the lack of holistic and integrated BI approaches that originates from the fact that each functional area is using its own IT applications without necessary integration in to the company’s overall BI system. Following this examination, we construct a holistic framework that illustrates how an integrated, managerially planned BI system can be developed. Finally, we discuss the main competency requirements, as well as the challenges still prohibiting the great majority of firms from building smart and comprehensive BI systems for SCM.fi=vertaisarvioitu|en=peerReviewed

Plot by plot: plotting urbanism as an ordinary process of urbanization

With this paper, we analyse an ordinary urban process, which has received little attention so far and propose a new concept to take account of it: plotting urbanism. It is usually subsumed under terms like “urban informality” or “incremental urbanism” and not studied as a distinct process. In comparing Lagos, Istanbul and Shenzhen we captured four defining features of plotting urbanism: first, it unfolds in a piecemeal fashion with limited comprehensive planning. Second, it emerges from conflicts between multiple overlapping modes of territorial regulation, land tenure and property rights, which result in specific territorial compromises. Third, plotting is based on commodification of housing and land, which might accentuate socio-economic differentiations between property-owners, who often live in the same area, and their tenants. The term “plotting” highlights the key role of the plot in the process. It also alludes to strategic acts of collaboration for individual and collaborative benefit