Scope and Predictive Genetic/Phenotypic Signatures of Bicarbonate (NaHCO3) Responsiveness and β-Lactam Sensitization in Methicillin-Resistant Staphylococcus aureus.

Addition of sodium bicarbonate (NaHCO3) to standard antimicrobial susceptibility testing medium reveals certain methicillin-resistant Staphylococcus aureus (MRSA) strains to be highly susceptible to β-lactams. We investigated the prevalence of this phenotype (NaHCO3 responsiveness) to two β-lactams among 58 clinical MRSA bloodstream isolates. Of note, ∼75% and ∼36% of isolates displayed the NaHCO3 responsiveness phenotype to cefazolin (CFZ) and oxacillin (OXA), respectively. Neither intrinsic β-lactam MICs in standard Mueller-Hinton broth (MHB) nor population analysis profiles were predictive of this phenotype. Several genotypic markers (clonal complex 8 [CC8]; agr I and spa t008) were associated with NaHCO3 responsiveness for OXA

Bicarbonate Resensitization of Methicillin-Resistant Staphylococcus aureus to β-Lactam Antibiotics.

Endovascular infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a major health care concern, especially infective endocarditis (IE). Standard antimicrobial susceptibility testing (AST) defines most MRSA strains as "resistant" to β-lactams, often leading to the use of costly and/or toxic treatment regimens. In this investigation, five prototype MRSA strains, representing the range of genotypes in current clinical circulation, were studied. We identified two distinct MRSA phenotypes upon AST using standard media, with or without sodium bicarbonate (NaHCO3) supplementation: one highly susceptible to the antistaphylococcal β-lactams oxacillin and cefazolin (NaHCO3 responsive) and one resistant to such agents (NaHCO3 nonresponsive). These phenotypes accurately predicted clearance profiles of MRSA from target tissues in experimental MRSA IE treated with each β-lactam. Mechanistically, NaHCO3 reduced the expression of two key genes involved in the MRSA phenotype, mecA and sarA, leading to decreased production of penicillin-binding protein 2a (that mediates methicillin resistance), in NaHCO3-responsive (but not in NaHCO3-nonresponsive) strains. Moreover, both cefazolin and oxacillin synergistically killed NaHCO3-responsive strains in the presence of the host defense antimicrobial peptide (LL-37) in NaHCO3-supplemented media. These findings suggest that AST of MRSA strains in NaHCO3-containing media may potentially identify infections caused by NaHCO3-responsive strains that are appropriate for β-lactam therapy

Role of defects and disorder in the half-metallic full-Heusler compounds

Half-metallic ferromagnets and especially the full-Heusler alloys containing Co are at the center of scientific research due to their potential applications in spintronics. For realistic devices it is important to control accurately the creation of defects in these alloys. We review some of our late results on the role of defects and impurities in these compounds. More precisely we present results for the following cases (i) doping and disorder in Co$_2$Cr(Mn)Al(Si) alloys, (ii) half-metallic ferrimagnetism appeared due to the creation of Cr(Mn) antisites in these alloys, (iii) Co-doping in Mn$_2$VAl(Si) alloys leading to half-metallic antiferromagnetism, and finally (iv) the occurrence of vacancies in the full-Heusler alloys containing Co and Mn. These results are susceptible of encouraging further theoretical and experimental research in the properties of these compounds.Comment: Chapter intended for a book with contributions of the invited speakers of the International Conference on Nanoscale Magnetism 2007. Revised version contains new figure

Sedimentary record of coseismic subsidence in Hersek coastal lagoon (Izmit Bay, Turkey) and the late Holocene activity of the North Anatolian Fault

This research was funded by the European Union in the framework of the REL.I.E.F. (Reliable Information on Earthquake Faulting) project (EVG1‐CT‐2002‐00069). Copyright @ 2011 American Geophysical Union.The late Holocene activity of a restraining bend of the northern strand of the North Anatolian Fault in Izmit Bay was investigated by a sedimentological, geochemical, and paleoecological analysis of sediment cores from Hersek coastal lagoon, NW Turkey. The sediment cores show a succession of sedimentary sequences composed of three units separated by gradual transitions. The first unit is composed of a thin layer of shell debris-rich sediment in abrupt contact with the underlying organic-rich deposits. This unit is over-lain by a thick foraminifera-rich mud deposit, and the sequences are capped by an organic-rich mud unit. These sequences are interpreted as silting up, shallowing upward deposits, typical of a lagoon becoming isolated from the sea. We suggest that they represent the sedimentary signature of coseismic subsidence, which was caused by reverse slip at the Hersek bend, and tsunamis in Izmit Bay. Our radiocarbon-dated paleoseismological record indicates (1) the atypical collapse of the hanging wall during the 740 earthquake and (2) subsidence of the footwall during the 987, 1509, and 1719 earthquakes. This study contributes to the understanding of the dynamics of restraining bends, and it highlights the potential of coastal sediments for reconstructing past earthquakes and tsunamis in regions dominated by strike-slip deformations.This article is available through the Brunel Open Access Publishing Fun

Turkey

published or submitted for publicatio

Assessment of Institutional Thickness in the Turkish Context

Peer reviewedPublisher PD

Predicting risk of malignancy in patients with indeterminate thyroid nodules

Thyroid cancer is the most prevalent endocrine cancer (1). The prevalence of palpable thyroid nodules in the general adult population is 4% to 7% (2). Ultrasound imaging detects thyroid nodules in 19%-68% of randomly selected individuals (3). The rate of thyroid cancer in nodules found on US is 4% to 15% (4). In order to evaluate thyroid nodules patients undergo thyroid ultrasonography and, if needed, a fine-needle aspiration biopsy. Of all fine-needle aspiration biopsies, 15-30% are indeterminate on cytology (5). While only 3% of these nodules are malignant on average, a much higher percentage of nodules are surgically removed in order to rule out malignancy after indeterminate FNA results. Our goal is to identify clinical and ultrasound predictors of benign results in indeterminate nodules, to assist physicians in selecting nodules for surgical removal versus monitoring with ultrasound imaging. Between October 2010 and November 2017 there were 129 patients with 134 thyroid nodules from Temple University Hospital, Jeanes Hospital, and Fox Chase Cancer Center who had a total or partial thyroidectomy after a cytology report of at least one AUS or FLUS thyroid nodule. These patients were evaluated for age, sex, BMI, TSH, fT4, tT3, nodule size, and ultrasonography features to determine if any features were predictive of a benign or malignant thyroid nodule. Additionally, we looked at whether any of these features were more likely to occur in an AUS nodule or a FLUS nodule. We found that none of the demographic factors, thyroid function tests, or ultrasound features were good predictors of malignancy in AUS or FLUS thyroid nodules. We found that AUS nodules are more likely to be malignant than FLUS nodules, and this held true when we accounted for age, sex, smoking history, and BMI. We concluded that demographic factors and thyroid function tests are unable to predict increased risk of malignancy in Bethesda category III nodules, AUS nodules are more likely to be malignant that FLUS nodules, and nodules with at least one suspicious ultrasound feature are more likely to be AUS nodules than FLUS nodules due to AUS nodules having nuclear atypia and FLUS nodules having architectural atypia

A kinetic scheme for transient mixed flows in non uniform closed pipes: a global manner to upwind all the source terms

We present a numerical kinetic scheme for an unsteady mixed pressurised and free surface model. This model has a source term depending on both the space variable and the unknown, U, of the system. The source term is composed by a topography, a section variation, a curvature (also called corrective) and a friction term. Using the Finite Volume and Kinetic (FVK) framework, we propose an approximation of the source terms following the principle of interfacial upwind with a kinetic interpretation: the source term is not treated as a volumic term, but included in the numerical fluxes. Then, several numerical tests are presented