Computed Tomography Imaging Features in Acute Uncomplicated Stanford Type-B Aortic Dissection Predict Late Adverse Events.
Medical treatment of initially uncomplicated acute Stanford type-B aortic dissection is associated with a high rate of late adverse events. Identification of individuals who potentially benefit from preventive endografting is highly desirable. The association of computed tomography imaging features with late adverse events was retrospectively assessed in 83 patients with acute uncomplicated Stanford type-B aortic dissection, followed over a median of 850 (interquartile range 247-1824) days. Adverse events were defined as fatal or nonfatal aortic rupture, rapid aortic growth (>10 mm/y), aneurysm formation (≥6 cm), organ or limb ischemia, or new uncontrollable hypertension or pain. Five significant predictors were identified using multivariable Cox regression analysis: connective tissue disease (hazard ratio [HR] 2.94, 95% confidence interval [CI]: 1.29-6.72; P=0.01), circumferential extent of false lumen in angular degrees (HR 1.03 per degree, 95% CI: 1.01-1.04, P=0.003), maximum aortic diameter (HR 1.10 per mm, 95% CI: 1.02-1.18, P=0.015), false lumen outflow (HR 0.999 per mL/min, 95% CI: 0.998-1.000; P=0.055), and number of intercostal arteries (HR 0.89 per n, 95% CI: 0.80-0.98; P=0.024). A prediction model was constructed to calculate patient specific risk at 1, 2, and 5 years and to stratify patients into high-, intermediate-, and low-risk groups. The model was internally validated by bootstrapping and showed good discriminatory ability with an optimism-corrected C statistic of 70.1%. Computed tomography imaging-based morphological features combined into a prediction model may be able to identify patients at high risk for late adverse events after an initially uncomplicated type-B aortic dissection.


Cytokine gene polymorphisms in preterm infants with necrotising enterocolitis: genetic association study.
The inflammatory cytokine cascade is implicated in the pathogenesis of necrotising enterocolitis (NEC). Genetic association studies of cytokine polymorphisms may help to detect molecular mechanisms that are causally related to the disease process. To examine associations between the common genetic variants in candidate inflammatory cytokine genes and NEC in preterm infants. Multi-centre case-control and genetic association study. DNA samples were collected from 50 preterm infants with NEC and 50 controls matched for gestational age and ethnic group recruited to a multi-centre case-control study. Ten candidate single-nucleotide polymorphisms in cytokines previously associated with infectious or inflammatory diseases were genotyped. The findings were included in random-effects meta-analyses with data from previous genetic association studies. All allele distributions were in Hardy-Weinberg equilibrium. None of the studied cytokine polymorphisms was significantly associated with NEC. Four previous genetic association studies of cytokine polymorphisms and NEC in preterm infants were found. Meta-analyses were possible for several single-nucleotide polymorphisms. These increased the precision of the estimates of effect size but did not reveal any significant associations. The available data are not consistent with more than modest associations between these candidate cytokine variant alleles and NEC in preterm infants. Data from future association studies of these polymorphisms may be added to the meta-analyses to obtain more precise estimates of effects sizes.


The Influence of α-Lipoic Acid and Garlic Administration on Biomarkers of Oxidative Stress and Inflammation in Rabbits Exposed to Oxidized Nutrition Oils.
We hypothesized that addition of substances with antioxidant activity could decrease the concentrations of biomarkers of oxidative stress and inflammatory process, thus inhibiting nonalcoholic steatohepatitis development. We investigated the influence of α-lipoic acid (ALA) and garlic administration on the development of adverse changes in rabbit liver and serum under oxidative stress conditions induced with HFD from oxidized oils. We determined 8-hydroxy-2'-deoxyguanosine (8 OHdG) and malondialdehyde (MDA) in liver homogenates, total oxidant status (TOS), lipid peroxides (LOO) and tumor necrosis factor alpha (TNFα) in blood serum, and TNFα and IL-1α genes expression in liver. The results indicate that the intake of dietary ALA and garlic was significantly associated with decreases of 8 OHdG and MDA levels in rabbits' liver tissue as well as TOS and LOO levels in rabbits' serum. Similarly, TNFα and IL-1α gene expressions were suppressed due to ALA and garlic supplementation. The histopathological analysis confirmed that HFD results in liver disorder leading to steatosis. This adverse effect of HFD was ameliorated by the supplementation of ALA and garlic. The obtained results indicate a beneficial effect of ALA and garlic administration by reducing the oxidative stress intensity and the levels of some proinflammatory cytokines in rabbits fed HFD.


Performance of the BD GeneOhm methicillin-resistant Staphylococcus aureus (MRSA) PCR assay for detecting MRSA nasal colonization in Taiwanese adults.
A rapid diagnostic method for methicillin-resistant Staphylococcus aureus (MRSA) has been implemented for surveillance of the at-risk population, but its performance in those without traditional risk factors is not clear. The objective of this study was to evaluate MRSA colonization status by comparing the performance of the BD GeneOhm MRSA polymerase chain reaction (PCR) assay with that of conventional culture during a 3-month active surveillance of Taiwanese adults in the community. From 1 October 2007 to 28 December 2007, adults (≥ 18 years old) attending a mandatory health examination arranged by their employers as a part of the workplace health promotion program at three medical centers in northern Taiwan were enrolled in the study. No healthcare workers were included. A total of 498 paired nasal swabs were prospectively obtained and used for both the BD GeneOhm MRSA PCR assay and conventional culture. Of the 498 paired nasal swabs, 14 (2.8%) were positive for MRSA by conventional culture and 34 (6.8%) were positive by the BD GeneOhm MRSA PCR assay (p < 0.005). Thirteen specimens were both culture- and PCR-positive, and 463 samples were both culture- and PCR-negative. There were two discordant results: 21 specimens were culture-negative/PCR-positive, and one was culture-positive/PCR-negative. The simple kappa coefficient for measuring the agreement between conventional culture and the MRSA PCR assay was 0.52. This study demonstrates the feasibility of using both the MRSA PCR assay and conventional culture as surveillance tools. Also, the MRSA-positive rate detected by MRSA PCR assay was significantly higher than that of conventional culture.


Photoinduced Bimolecular Electron Transfer from Cyano Anions in Ionic Liquids.
Ionic liquids with electron-donating anions are used to investigate rates and mechanisms of photoinduced bimolecular electron transfer to the photoexcited acceptor 9,10-dicyanoanthracene (9,10-DCNA). The set of five cyano anion ILs studied comprises the 1-ethyl-3-methylimidazolium cation paired with each of these five anions: selenocyanate, thiocyanate, dicyanamide, tricyanomethanide, and tetracyanoborate. Measurements with these anions dilute in acetonitrile and 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide show that the selenocyanate and tricyanomethanide anions are strong quenchers of the 9,10-DCNA fluorescence, thiocyanate is a moderately strong quencher, dicyanamide is a weak quencher, and no quenching is observed for tetracyanoborate. Quenching rates are obtained from both time-resolved fluorescence transients and time-integrated spectra. Application of a Smoluchowski diffusion-and-reaction model showed that the complex kinetics observed can be fit using only two adjustable parameters, D and V0, where D is the relative diffusion coefficient between donor and acceptor and V0 is the value of the electronic coupling at donor-acceptor contact.


Functional and structural changes resulting from strain differences in the rat model of oxygen-induced retinopathy.
Results of studies that compared the racial incidence of retinopathy of prematurity (ROP) suggested that ocular pigmentation might offer protection against the development of severe ROP. The structural and functional consequences of postnatal hyperoxia (oxygen-induced retinopathy; OIR) were compared in albino Sprague-Dawley (SD) and pigmented Long-Evans (LE) rats to verify this finding. Newborn rats were exposed to 80% O(2) during selected postnatal day intervals. The severity of the OIR was determined by examining retinal flatmounts (retinal vasculature assessment), protein level quantification and cellular localization of fibroblast growth factor (FGF)-2 and ciliary neurotrophic factor (CNTF; Western blot analysis and immunohistochemistry, respectively), retinal histology, and photopic and scotopic electroretinograms (ERGs). Irrespective of the parameter considered, structural and functional deficits resulting from postnatal hyperoxia were significantly more pronounced in LE rats. Although FGF-2 levels in LE rats had a tendency to increase after hyperoxia compared with normoxic littermates, it did not reach statistical significance. A similar finding was observed in SD rats. Of interest, however, baseline levels of FGF-2 were approximately four to five times higher in SD rats than in LE rats. There was a similar, hyperoxia-induced increase in CNTF levels between SD and LE rats. The findings suggest an increased susceptibility of newborn LE rats to postnatal hyperoxia in comparison with SD rats. Whether a pro-oxidant rather than antioxidant role of melanin or other genetic factors can explain these differences in oxygen susceptibility of the animal model of this retinopathy, remains to be determined.


In vivo expression of mRNA for the Ca++-binding protein SPARC (osteonectin) revealed by in situ hybridization.
In situ hybridization is used to survey the tissue-specific and developmental expression of the cloned mouse gene Sparc, coding for a protein homologous to the bovine Ca++-binding protein, osteonectin. High levels of SPARC RNA are found in osteoblasts and odontoblasts. In addition, high grain counts are associated with a variety of other cell types in the embryo and newborn mouse, including parietal endoderm, deciduum, whisker follicles (connective tissue sheath), peripheral nerve trunk, skin (dermis), and stomach (submucosa). Spatially restricted but high levels of SPARC mRNA are also seen in the adult adrenal glands, testis, and ovary. This pattern of differential gene expression demands a reassessment of the function originally proposed for osteonectin, and predicts a much wider role for the protein in a variety of biological processes.


Neo-lymphoid aggregates in the adult liver can initiate potent cell-mediated immunity.
Subcutaneous immunization delivers antigen (Ag) to local Ag-presenting cells that subsequently migrate into draining lymph nodes (LNs). There, they initiate the activation and expansion of lymphocytes specific for their cognate Ag. In mammals, the structural environment of secondary lymphoid tissues (SLTs) is considered essential for the initiation of adaptive immunity. Nevertheless, cold-blooded vertebrates can initiate potent systemic immune responses even though they lack conventional SLTs. The emergence of lymph nodes provided mammals with drastically improved affinity maturation of B cells. Here, we combine the use of different strains of alymphoplastic mice and T cell migration mutants with an experimental paradigm in which the site of Ag delivery is distant from the site of priming and inflammation. We demonstrate that in mammals, SLTs serve primarily B cell priming and affinity maturation, whereas the induction of T cell-driven immune responses can occur outside of SLTs. We found that mice lacking conventional SLTs generate productive systemic CD4- as well as CD8-mediated responses, even under conditions in which draining LNs are considered compulsory for the initiation of adaptive immunity. We describe an alternative pathway for the induction of cell-mediated immunity (CMI), in which Ag-presenting cells sample Ag and migrate into the liver where they induce neo-lymphoid aggregates. These structures are insufficient to support antibody affinity maturation and class switching, but provide a novel surrogate environment for the initiation of CMI.


Open source software to control Bioflo bioreactors.
Bioreactors are designed to support highly controlled environments for growth of tissues, cell cultures or microbial cultures. A variety of bioreactors are commercially available, often including sophisticated software to enhance the functionality of the bioreactor. However, experiments that the bioreactor hardware can support, but that were not envisioned during the software design cannot be performed without developing custom software. In addition, support for third party or custom designed auxiliary hardware is often sparse or absent. This work presents flexible open source freeware for the control of bioreactors of the Bioflo product family. The functionality of the software includes setpoint control, data logging, and protocol execution. Auxiliary hardware can be easily integrated and controlled through an integrated plugin interface without altering existing software. Simple experimental protocols can be entered as a CSV scripting file, and a Python-based protocol execution model is included for more demanding conditional experimental control. The software was designed to be a more flexible and free open source alternative to the commercially available solution. The source code and various auxiliary hardware plugins are publicly available for download from https://github.com/LibourelLab/BiofloSoftware. In addition to the source code, the software was compiled and packaged as a self-installing file for 32 and 64 bit windows operating systems. The compiled software will be able to control a Bioflo system, and will not require the installation of LabVIEW.


THE MULTIFACETED ROLE OF T CELL-MEDIATED IMMUNITY IN PATHOGENESIS AND RESISTANCE TO MYCOPLASMA RESPIRATORY DISEASE.
Mycoplasma respiratory diseases have a significant impact on the economy, health and wildlife. The hallmark of these diseases is the persistence of the mycoplasma infections and chronic inflammatory responses associated with the airways. There is still much that needs to be understood about the immune mechanisms involved in mycoplasma disease and resistance from infection. It is clear that immune responses can contribute to the generation of inflammatory lesions in mycoplasma respiratory disease, as well as provide protection from infection and extrapulmonary dissemination of the organisms. The evolution of this lung disease is under the control innate immune mechanisms and the contrasting effects of different T cell populations. The mechanisms of immunity involved in mycoplasma diseases are multifaceted, and a fascinating story of its complexity is being uncovered. Research in mycoplasma respiratory diseases have underscored the idea that immunity along the respiratory tract against infectious agents is a dynamic process and involves a network of cellular and cytokine signals that determine the type of responses generated, and ultimately, the outcome of infection. The aim of this article is to present on overview of our work on mycoplasma disease and immunity, focusing on the interactions and regulation of T cell responses that influence disease pathogenesis. We will first provide an overview of immune mechanisms involved in controlling infection and participate in the generation of T cell responses, and the role of T cell populations in generating protection and contributing to lesion development will be discussed.


Examining the influence of treatment preferences on attrition, adherence and outcomes: a protocol for a two-stage partially randomized trial.
Empirical evidence pertaining to the influence of treatment preferences on attrition, adherence and outcomes in intervention evaluation trials is inconsistent. The inconsistency can be explained by the method used for allocating treatment and measuring preferences. The current methodological study is designed to address these factors by implementing the two-stage partially randomized or preference trial design, and administering a validated measure to assess participants' preferences for the treatments under evaluation. It aims to compare attrition, adherence and outcomes for participants allocated randomly or by preference to treatment. The study is in its final stages of data collection; its protocol is presented in this paper. A partially randomized clinical or preference trial is used. Eligible participants are randomized to two trial arms. First is the random arm involving random assignment to treatments, and second is the preference arm involving allocation to the chosen treatment. Participants with chronic insomnia are targeted. Two behavioral treatments are offered, stimulus control therapy and sleep restriction therapy, in the same format (small group) and dose (two sessions given over a 4-week period). A participant log is used to collect data on attrition. Adherence is evaluated in terms of exposure and enactment of treatment. Sleep-related outcomes (sleep parameters and perceived insomnia severity) are measured at pretest, posttest, 6 and 12 month follow-up. Treatment preferences, adherence and outcomes are assessed with reliable and valid measures. The advantages and limitations of the preference trial design are highlighted. The challenges in implementing the trial are discussed relative to the distribution of participants in the groups defined by treatment received and method of treatment allocation. ClinicalTrials.gov Registry NCT02513017.


Children with severe malnutrition: can those at highest risk of death be identified with the WHO protocol?
With strict adherence to international recommended treatment guidelines, the case fatality for severe malnutrition ought to be less than 5%. In African hospitals, fatality rates of 20% are common and are often attributed to poor training and faulty case management. Improving outcome will depend upon the identification of those at greatest risk and targeting limited health resources. We retrospectively examined the major risk factors associated with early (<48 h) and late in-hospital death in children with severe malnutrition with the aim of identifying admission features that could distinguish a high-risk group in relation to the World Health Organization (WHO) guidelines. Of 920 children in the study, 176 (19%) died, with 59 (33%) deaths occurring within 48 h of admission. Bacteraemia complicated 27% of all deaths: 52% died before 48 h despite 85% in vitro antibiotic susceptibility of cultured organisms. The sensitivity, specificity, and likelihood ratio of the WHO-recommended "danger signs" (lethargy, hypothermia, or hypoglycaemia) to predict early mortality was 52%, 84%, and 3.4% (95% confidence interval [CI] = 2.2 to 5.1), respectively. In addition, four bedside features were associated with early case fatality: bradycardia, capillary refill time greater than 2 s, weak pulse volume, and impaired consciousness level; the presence of two or more features was associated with an odds ratio of 9.6 (95% CI = 4.8 to 19) for early fatality (p < 0.0001). Conversely, the group of children without any of these seven features, or signs of dehydration, severe acidosis, or electrolyte derangements, had a low fatality (7%). Formal assessment of these features as emergency signs to improve triage and to rationalize manpower resources toward the high-risk groups is required. In addition, basic clinical research is necessary to identify and test appropriate supportive treatments.


Effects of environmental enrichment and voluntary exercise on neurogenesis, learning and memory, and pattern separation: BDNF as a critical variable?
Adult-generated neurons in the dentate gyrus of the hippocampus have been the focus of many studies concerned with learning and memory (L&M). It has been shown that procedures like environmental enrichment (EE) or voluntary physical exercise (Vex) can increase neurogenesis (NG) and also enhance L&M. It is tempting to conclude that improvements in L&M are due to the increased NG; that is, a causal relationship exists between enhancement of NG and enhancement of L&M. However, it remains unclear whether the L&M enhancement observed after these treatments is causally dependent on the increase in newborn neurons in the dentate gyrus. It remains a possibility that some unspecified change--a "third variable"--brought about by EE and/or Vex could be a causal determinant of both NG and L&M. We suggest that this third variable could be neurotrophic and/or plasticity-related factors such as BDNF. Indeed, both EE and Vex can induce expression of such proteins, and BDNF in particular has long been linked with L&M. In addition, we argue that a very likely source of variation in previous experiments was the load on "pattern separation", a process that keeps similar memories distinct, and in which NG has been shown to be critically involved. To attempt to bring these ideas together, we present preliminary evidence that BDNF is also required for pattern separation, which strengthens the case for BDNF as a candidate third variable. Other ways in which BDNF might be involved are also discussed.


Rheumatoid arthritis susceptibility loci at chromosomes 10p15, 12q13 and 22q13.
The WTCCC study identified 49 SNPs putatively associated with rheumatoid arthritis at P = 1 x 10(-4) - 1 x 10(-5) (tier 3). Here we show that three of these SNPs, mapping to chromosome 10p15 (rs4750316), 12q13 (rs1678542) and 22q13 (rs3218253), are also associated (trend P = 4 x 10(-5), P = 4 x 10(-4) and P = 4 x 10(-4), respectively) in a validation study of 4,106 individuals with rheumatoid arthritis and an expanded reference group of 11,238 subjects, confirming them as true susceptibility loci in individuals of European ancestry.


Design of the Familial Hypercholesterolaemia Australasia Network Registry: Creating Opportunities for Greater International Collaboration.
Familial Hypercholesterolemia (FH) is the most common and serious monogenic disorder of lipoprotein metabolism that leads to premature coronary heart disease. There are over 65,000 people estimated to have FH in Australia, but many remain undiagnosed. Patients with FH are often under-treated, but with early detection, cascade family testing and adequate treatment, patient outcomes can improve. Patient registries are key tools for providing new information on FH and enhancing care worldwide. The development and design of the FH Australasia Network Registry is a crucial component in the comprehensive model of care for FH, which aims to provide a standardized, high-quality and cost-effective system of care that is likely to have the highest impact on patient outcomes. Informed by stakeholder engagement, the FH Australasia Network Registry was collaboratively developed by government, patient and clinical networks and research groups. The open-source, web-based Rare Disease Registry Framework was the architecture chosen for this registry owing to its open-source standards, modular design, interoperability, scalability and security features; all these are key components required to meet the ever changing clinical demands across regions. This paper provides a high level blueprint for other countries and jurisdictions to help inform and map out the critical features of an FH registry to meet their particular health system needs.


Surveillance for nervous necrosis virus-specific antibodies in barramundi Lates calcarifer in Australian hatcheries.
We conducted single point-in-time and repeated cross-sectional studies of the prevalence of antibodies against nervous necrosis virus (NNV) in populations of adult barramundi Lates calcarifer in Australia. Serum samples collected between 2002 and 2012 were analyzed with indirect ELISA (n = 468). Most of the samples were sourced from broodstock with unknown exposure history, and these were compared with reference populations with confirmed history of exposure to NNV. Non-lethally collected gonad fluid samples from economically valuable barramundi broodstock (n = 164) were tested for the presence of NNV using RT-quantitative PCR at the time of blood sampling to compare infectivity with serostatus, but no virus was detected. NNV-specific immunoreactivity in broodstock was significantly lower than that for immunized and persistently infected populations. Seroprevalence increased over time in broodstock sampled longitudinally, probably reflecting repeated exposure to NNV in a region where the virus was endemic. The seroprevalence for the broodstock was 23.8% over the entire sample period while a cross-sectional survey conducted in 2012 found a seroprevalence of 34.5% with no significant difference between populations based on the geographic region or the history of occurrence of viral nervous necrosis (VNN) disease in the progeny in the respective hatcheries. Although serological surveillance was useful for studying the history of exposure of barramundi to NNV, the lack of association between serostatus in broodstock and the subsequent occurrence of VNN disease in their progeny indicates that ELISA tests for anti-NNV antibodies are not suitable for the purpose of preventing vertical transmission of NNV in barramundi.


Actinomycosis of the larynx and pharynx.
This paper presents a case report of a 67-year-old man who was seen in the Otolaryngology Clinic, University of Wisconsin Medical Center with a seven-month history of dyspnea and laryngeal stridor. On examination there were several slightly tender firm submucosal nodules in the soft palate and left tonsilar area and a 1.5-cm polypoid subglottic mass arising from the body of the cricoid cartilage. Because of the marked airway obstruction, a tracheotomy was necessary. The laryngeal polypoid mass was removed and biopsies were obtained from the submucosal nodular masses of the palate. Microscopic examination of the tissue revealed the lesions to be caseating granulomas, and actinomycosis was identified on the cultures. The patient received long-term penicillin therapy and has remained asymptomatic. A discussion of the biologic and clinical aspects of actinomycosis is included. A review of the literature revealed only one other description of endolaryngeal actinomycosis.


RIG-I-like receptors: their regulation and roles in RNA sensing.
Retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) are key sensors of virus infection, mediating the transcriptional induction of type I interferons and other genes that collectively establish an antiviral host response. Recent studies have revealed that both viral and host-derived RNAs can trigger RLR activation; this can lead to an effective antiviral response but also immunopathology if RLR activities are uncontrolled. In this Review, we discuss recent advances in our understanding of the types of RNA sensed by RLRs in the contexts of viral infection, malignancies and autoimmune diseases. We further describe how the activity of RLRs is controlled by host regulatory mechanisms, including RLR-interacting proteins, post-translational modifications and non-coding RNAs. Finally, we discuss key outstanding questions in the RLR field, including how our knowledge of RLR biology could be translated into new therapeutics.


Ventricular hypertrophy and cavity dilatation in relation to body mass index in women with uncomplicated obesity.
The traditionally accepted mechanism for ventricular adaptation to obesity suggests that cavity dilatation in response to increased blood volume and elevated filling pressure results in ventricular hypertrophy as a compensatory mechanism. Our hypothesis was that, instead, initiation of ventricular hypertrophy in obesity may be explained by changes in hormonal milieu and not by cavity dilatation. 88 female subjects without identifiable cardiovascular risk factors, covering a wide range of body mass indices (BMI), from normal (21.2 ± 1.6 kg/m(2)) to severely obese (45.0 ± 4.6 kg/m(2)), underwent cardiovascular MRI to determine left ventricular (LV) and right ventricular (RV) mass and volumes. BMI correlated positively with LV and RV mass and end-diastolic volumes (EDV). However overweight is associated with a significant LV and RV hypertrophy (LV: 78 ± 11 g vs 103 ± 16 g, p<0.01; RV: 26 ± 7 g vs 40 ± 11 g, p<0.01) was observed in the absence of differences in LV and RV volumes (LV: EDV 119 ± 15 vs 121 ± 21 ml, p>0.99, RV: 131 ± 17 vs 130 ± 24 ml; p>0.99). Furthermore, significant increases of serum leptin occurred at this pre-obese stage (15.6 ± 19 vs 36.5 ± 22 ng/ml; p=0.013). In a cohort of healthy female subjects with a wide range of BMIs, ventricular hypertrophy occurs without associated cavity dilatation in overweight individuals, while in manifest obesity, both cavity dilatation and ventricular hypertrophy occur. Elevated leptin levels may have a role in this effect on ventricular mass.


Unilateral renal ischaemia in the rat: effect of contralateral nephrectomy and intrarenal flush with phosphate-buffered sucrose.
1. This study examined whether the severity of acute renal failure seen within 4 h of a 45 min period of unilateral occlusion of the renal pedicle could be reduced by removal of the contralateral healthy kidney and/or intrarenal flush with a phosphate-buffered sucrose (PBS50) solution. 2. After ischaemia, unflushed kidneys became oliguric and isosthenuric, with a fall in inulin clearance (Cin) to 0.1% of the pre-ischaemic value. Removal of the healthy contralateral kidney upon release of the occlusion caused no improvement in immediate post-ischaemic function. 3. Intrarenal flush with 1.5 ml of PBS50 resulted in a significantly improved post-ischaemic Cin, with increased urine flow rate and solute excretion; urine was also concentrated. 4. Protection of renal function against ischaemic damage was seen only when kidney tissue remained blood-free and exposed to PBS50 throughout the period of ischaemia, and when the speed of flush was similar to the expected renal blood flow (6 ml/min). Protection did not depend upon the presence or absence of the contralateral kidney. 5. The study also showed that functional removal of one kidney, either by pedicle occlusion or nephrectomy, caused an immediate rise in solution excretion from the contralateral kidney, but Cin remained unchanged. Unflushed severely damaged kidneys showed no compensatory response to unilateral nephrectomy, whereas kidneys flushed with PBS50 exhibited increases in solute excretion similar to those seen in healthy non-ischaemic kidneys.


Catalytic Activity of Peptide-Nanoparticle Conjugates Regulated by a Conformational Change.
Herein, we present the design and synthesis of a catalytically active peptide-nanoparticle conjugate whose activity is regulated by a defined conformational change in the self-assembled peptide monolayer. A catalytically active peptide, designed after the heterodimeric α-helical coiled-coil principle was immobilized onto gold nanoparticles, and kinetic studies were performed according to the Michaelis-Menten model. The formed peptide monolayer at the gold nanoparticle surface accelerated p-nitrophenylacetate (pNPA) hydrolysis by 1 order of magnitude compared to the soluble peptide while exhibiting no defined secondary structure as determined by infrared (IR) and circular dichroism (CD) spectroscopy. Addition of the complementary peptide-induced coiled-coil formation while significantly hindering the pNPA hydrolysis catalyzed by the peptide-nanoparticle conjugate. The heptad repeat sequence of a coiled-coil opens up the opportunity for regulation of conformation and thus catalytic activity of peptide-nanoparticle conjugates upon interaction with a complementary coiled-coil sequence. Strategies of regulation of catalytic activity by interaction with a complementary cofactor/ligand are well-established in nature and are introduced here into rationally designed peptide-nanoparticle conjugates.


Effect of acetazolamide and autoCPAP therapy on breathing disturbances among patients with obstructive sleep apnea syndrome who travel to altitude: a randomized controlled trial.
Many patients with obstructive sleep apnea syndrome (OSA) living near sea level travel to altitude, but this may expose them to hypoxemia and exacerbation of sleep apnea. The treatment in this setting is not established. To evaluate whether acetazolamide and autoadjusted continuous positive airway pressure (autoCPAP) control breathing disturbances in OSA patients at altitude. Randomized, placebo-controlled, double-blind, crossover trial involving 51 patients with OSA living below an altitude of 800 m and receiving CPAP therapy who underwent studies at a university hospital at 490 m and resorts in Swiss mountain villages at 1630 m and 2590 m in summer 2009. Patients were studied during 2 sojourns of 3 days each in mountain villages, 2 days at 1630 m, 1 day at 2590 m, separated by a 2-week washout period at less than 800 m. At altitude, patients either took acetazolamide (750 mg/d) or placebo in addition to autoCPAP. Primary outcomes were nocturnal oxygen saturation and the apnea/hypopnea index; secondary outcomes were sleep structure, vigilance, symptoms, adverse effects, and exercise performance. Acetazolamide and autoCPAP treatment was associated with higher nocturnal oxygen saturation at 1630 m and 2590 m than placebo and autoCPAP: medians, 94% (interquartile range [IQR], 93%-95%) and 91% (IQR, 90%-92%) vs 93% (IQR, 92%-94%) and 89% (IQR, 87%-91%), respectively. Median increases were 1.0% (95% CI, 0.3%-1.0%) and 2.0% (95% CI, 2.0%-2.0). Median night-time spent with oxygen saturation less than 90% at 2590 m was 13% (IQR, 2%-38%) vs 57% (IQR, 28%-82%; P < .001). Acetazolamide and autoCPAP resulted in better control of sleep apnea at 1630 m and 2590 m than placebo and autoCPAP: median apnea/hypopnea index was 5.8 events per hour (5.8/h) (IQR, 3.0/h-10.1/h) and 6.8/h (IQR, 3.5/h-10.1/h) vs 10.7/h (IQR, 5.1/h-17.7/h) and 19.3/h (IQR, 9.3/h-29.0/h), respectively; median reduction was 3.2/h (95% CI, 1.3/h-7.5/h) and 9.2 (95% CI, 5.1/h-14.6/h). Among patients with OSA spending 3 days at moderately elevated altitude, a combination of acetazolamide and autoCPAP therapy, compared with autoCPAP alone, resulted in improvement in nocturnal oxygen saturation and apnea/hypopnea index. clinicaltrials.gov Identifier: NCT00928655.


Sampling Error in Relation to Cyst Nematode Population Density Estimation in Small Field Plots.
Cyst nematodes are serious plant-parasitic pests which could cause severe yield losses and extensive damage. Since there is still very little information about error of population density estimation in small field plots, this study contributes to the broad issue of population density assessment. It was shown that there was no significant difference between cyst counts of five or seven bulk samples taken per each 1-m2 plot, if average cyst count per examined plot exceeds 75 cysts per 100 g of soil. Goodness of fit of data to probability distribution tested with χ2 test confirmed a negative binomial distribution of cyst counts for 21 out of 23 plots. The recommended measure of sampling precision of 17% expressed through coefficient of variation (cv) was achieved if the plots of 1 m2 contaminated with more than 90 cysts per 100 g of soil were sampled with 10-core bulk samples taken in five repetitions. If plots were contaminated with less than 75 cysts per 100 g of soil, 10-core bulk samples taken in seven repetitions gave cv higher than 23%. This study indicates that more attention should be paid on estimation of sampling error in experimental field plots to ensure more reliable estimation of population density of cyst nematodes.


Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury.
We have developed a novel plasma protein analysis platform with optimized sample preparation, chromatography, and MS analysis protocols. The workflow, which utilizes chemical isobaric mass tag labeling for relative quantification of plasma proteins, achieves far greater depth of proteome detection and quantification while simultaneously having increased sample throughput than prior methods. We applied the new workflow to a time series of plasma samples from patients undergoing a therapeutic, "planned" myocardial infarction for hypertrophic cardiomyopathy, a unique human model in which each person serves as their own biologic control. Over 5300 proteins were confidently identified in our experiments with an average of 4600 proteins identified per sample (with two or more distinct peptides identified per protein) using iTRAQ four-plex labeling. Nearly 3400 proteins were quantified in common across all 16 patient samples. Compared with a previously published label-free approach, the new method quantified almost fivefold more proteins/sample and provided a six- to nine-fold increase in sample analysis throughput. Moreover, this study provides the largest high-confidence plasma proteome dataset available to date. The reliability of relative quantification was also greatly improved relative to the label-free approach, with measured iTRAQ ratios and temporal trends correlating well with results from a 23-plex immunoMRM (iMRM) assay containing a subset of the candidate proteins applied to the same patient samples. The functional importance of improved detection and quantification was reflected in a markedly expanded list of significantly regulated proteins that provided many new candidate biomarker proteins. Preliminary evaluation of plasma sample labeling with TMT six-plex and ten-plex reagents suggests that even further increases in multiplexing of plasma analysis are practically achievable without significant losses in depth of detection relative to iTRAQ four-plex. These results obtained with our novel platform provide clear demonstration of the value of using isobaric mass tag reagents in plasma-based biomarker discovery experiments.


Analysis of immune responses induced by avian pathogenic Escherichia coli infection in turkeys and their association with resistance to homologous re-challenge.
Avian pathogenic Escherichia coli (APEC) cause severe respiratory and systemic disease in poultry yet the nature and consequences of host immune responses to infection are poorly understood. Here, we describe a turkey sub-acute respiratory challenge model and cytokine, cell-mediated and humoral responses associated with protection against homologous re-challenge. Intra-airsac inoculation of turkeys with 105 colony-forming units of APEC O78:H9 strain χ7122nalR induced transient and mild clinical signs of colibacillosis followed by clearance of the bacteria from the lungs and visceral organs. Upon re-challenge with 107 χ7122nalR, primed birds were solidly protected against clinical signs and exhibited negligible bacterial loads in visceral organs, whereas age-matched control birds exhibited high lesion scores and bacterial loads in the organs. Levels of mRNA for signature cytokines suggested induction of a Th1 response in the lung, whereas a distinct anti-inflammatory cytokine profile was detected in the liver. Proliferative responses of splenocytes to either Concanavalin A or soluble χ7122nalR antigens were negligible prior to clearance of bacteria, but APEC-specific responses were significantly elevated at later time intervals and at re-challenge relative to control birds. Primary infection also induced significantly elevated χ7122nalR-specific serum IgY and bile IgA responses which were bactericidal against χ7122nalR and an isogenic Δrfb mutant. Bactericidal activity was observed in the presence of immune, but not heat-inactivated immune serum, indicating that the antibodies can fix complement and are not directed solely at the lipopolysaccharide O-antigen. Such data inform the rational design of strategies to control a recalcitrant endemic disease of poultry.


Daily QA of linear accelerators using only EPID and OBI.
As treatment delivery becomes more complex, there is a pressing need for robust quality assurance (QA) tools to improve efficiency and comprehensiveness while simultaneously maintaining high accuracy and sensitivity. This work aims to present the hardware and software tools developed for comprehensive QA of linear accelerator (LINAC) using only electronic portal imaging devices (EPIDs) and kV flat panel detectors. A daily QA phantom, which includes two orthogonally positioned phantoms for QA of MV-beams and kV onboard imaging (OBI) is suspended from the gantry accessory holder to test both geometric and dosimetric components of a LINAC and an OBI. The MV component consists of a 0.5 cm water-equivalent plastic sheet incorporating 11 circular steel plugs for transmission measurements through multiple thicknesses and one resolution plug for MV-image quality testing. The kV-phantom consists of a Leeds phantom (TOR-18 FG phantom supplied by Varian) for testing low and high contrast resolutions. In the developed process, the existing LINAC tools were used to automate daily acquisition of MV and kV images and software tools were developed for simultaneous analysis of these images. A method was developed to derive and evaluate traditional QA parameters from these images [output, flatness, symmetry, uniformity, TPR20/10, and positional accuracy of the jaws and multileaf collimators (MLCs)]. The EPID-based daily QA tools were validated by performing measurements on a detuned 6 MV beam to test its effectiveness in detecting errors in output, symmetry, energy, and MLC positions. The developed QA process was clinically commissioned, implemented, and evaluated on a Varian TrueBeam LINAC (Varian Medical System, Palo Alto, CA) over a period of three months. Machine output constancy measured with an EPID (as compared against a calibrated ion-chamber) is shown to be within ±0.5%. Beam symmetry and flatness deviations measured using an EPID and a 2D ion-chamber array agree within ±0.5% and ±1.2% for crossline and inline profiles, respectively. MLC position errors of 0.5 mm can be detected using a picket fence test. The field size and phantom positioning accuracy can be determined within 0.5 mm. The entire daily QA process takes ∼15 min to perform tests for 5 photon beams, MLC tests, and imaging checks. The exclusive use of EPID-based QA tools, including a QA phantom and simultaneous analysis software tools, has been demonstrated as a viable, efficient, and comprehensive process for daily evaluation of LINAC performance.


Improving statistical power in severe malaria genetic association studies by augmenting phenotypic precision.
Severe falciparum malaria has substantially affected human evolution. Genetic association studies of patients with clinically defined severe malaria and matched population controls have helped characterise human genetic susceptibility to severe malaria, but phenotypic imprecision compromises discovered associations. In areas of high malaria transmission, the diagnosis of severe malaria in young children and, in particular, the distinction from bacterial sepsis are imprecise. We developed a probabilistic diagnostic model of severe malaria using platelet and white count data. Under this model, we re-analysed clinical and genetic data from 2220 Kenyan children with clinically defined severe malaria and 3940 population controls, adjusting for phenotype mis-labelling. Our model, validated by the distribution of sickle trait, estimated that approximately one-third of cases did not have severe malaria. We propose a data-tilting approach for case-control studies with phenotype mis-labelling and show that this reduces false discovery rates and improves statistical power in genome-wide association studies.


Tobacco cessation interventions by Swedish dental hygienists--a questionnaire study.
The aim of the study was to investigate tobacco cessation interventions by Swedish dental hygienists and their perception of the importance of tobacco cessation to oral health. A questionnaire was mailed to 400 randomly selected dental hygienists (DH) in Sweden. The questions covered such topics as tobacco cessation interventions, perceived barriers, and their perception of the importance of tobacco cessation in relation to caries, gingivitis, periodontitis and dental implants. The response rate was 57%. Tobacco habits were routinely recorded by 94% of the respondents. 52% of the dental hygienists reported time constraints, 50% reported insufficient competence and 43% answered that they had lack of experience to work with tobacco cessation. All respondents perceived tobacco cessation to be an important determinant of treatment outcomes in patients with dental implants and periodontitis. Bivariate analysis showed an association between training courses in tobacco cessation and tobacco cessation interventions (OR 3.25, CI 95% 1.80-5.85). A logistic multivariate regression model disclosed two other factors significantly correlated with tobacco cessation interventions: competence (OR 2.4, 95% CI 1.16-4.85), and experience (OR 2.1, 95% CI 1.06-4.28). The analyses were adjusted for age, length of undergraduate training course, and dental care organization. The dental hygienists considered tobacco cessation to be very important in patients with periodontitis and in those with dental implants. Most of the DH in this study undertook some tobacco cessation interventions, though not extensive; the main barriers reported were lack of time, competence and experience.


Inverse modeling of the 137Cs source term of the Fukushima Dai-ichi Nuclear Power Plant accident constrained by a deposition map monitored by aircraft.
The amount of 137Cs released by the Fukushima Dai-ichi Nuclear Power Plant accident of 11 March 2011 was inversely estimated by integrating an atmospheric dispersion model, an a priori source term, and map of deposition recorded by aircraft. An a posteriori source term refined finer (hourly) variations comparing with the a priori term, and estimated 137Cs released 11 March to 2 April to be 8.12 PBq. Although time series of the a posteriori source term was generally similar to those of the a priori source term, notable modifications were found in the periods when the a posteriori source term was well-constrained by the observations. Spatial pattern of 137Cs deposition with the a posteriori source term showed better agreement with the 137Cs deposition monitored by aircraft. The a posteriori source term increased 137Cs deposition in the Naka-dori region (the central part of Fukushima Prefecture) by 32.9%, and considerably improved the underestimated a priori 137Cs deposition. Observed values of deposition measured at 16 stations and surface atmospheric concentrations collected on a filter tape of suspended particulate matter were used for validation of the a posteriori results. A great improvement was found in surface atmospheric concentration on 15 March; the a posteriori source term reduced root mean square error, normalized mean error, and normalized mean bias by 13.4, 22.3, and 92.0% for the hourly values, respectively. However, limited improvements were observed in some periods and areas due to the difficulty in simulating accurate wind fields and the lack of the observational constraints.


Whole genome sequence of a Turkish individual.
Although whole human genome sequencing can be done with readily available technical and financial resources, the need for detailed analyses of genomes of certain populations still exists. Here we present, for the first time, sequencing and analysis of a Turkish human genome. We have performed 35x coverage using paired-end sequencing, where over 95% of sequencing reads are mapped to the reference genome covering more than 99% of the bases. The assembly of unmapped reads rendered 11,654 contigs, 2,168 of which did not reveal any homology to known sequences, resulting in ∼1 Mbp of unmapped sequence. Single nucleotide polymorphism (SNP) discovery resulted in 3,537,794 SNP calls with 29,184 SNPs identified in coding regions, where 106 were nonsense and 259 were categorized as having a high-impact effect. The homo/hetero zygosity (1,415,123∶2,122,671 or 1∶1.5) and transition/transversion ratios (2,383,204∶1,154,590 or 2.06∶1) were within expected limits. Of the identified SNPs, 480,396 were potentially novel with 2,925 in coding regions, including 48 nonsense and 95 high-impact SNPs. Functional analysis of novel high-impact SNPs revealed various interaction networks, notably involving hereditary and neurological disorders or diseases. Assembly results indicated 713,640 indels (1∶1.09 insertion/deletion ratio), ranging from -52 bp to 34 bp in length and causing about 180 codon insertion/deletions and 246 frame shifts. Using paired-end- and read-depth-based methods, we discovered 9,109 structural variants and compared our variant findings with other populations. Our results suggest that whole genome sequencing is a valuable tool for understanding variations in the human genome across different populations. Detailed analyses of genomes of diverse origins greatly benefits research in genetics and medicine and should be conducted on a larger scale.


Fire forbids fifty-fifty forest.
Recent studies have interpreted patterns of remotely sensed tree cover as evidence that forest with intermediate tree cover might be unstable in the tropics, as it will tip into either a closed forest or a more open savanna state. Here we show that across all continents the frequency of wildfires rises sharply as tree cover falls below ~40%. Using a simple empirical model, we hypothesize that the steepness of this pattern causes intermediate tree cover (30‒60%) to be unstable for a broad range of assumptions on tree growth and fire-driven mortality. We show that across all continents, observed frequency distributions of tropical tree cover are consistent with this hypothesis. We argue that percolation of fire through an open landscape may explain the remarkably universal rise of fire frequency around a critical tree cover, but we show that simple percolation models cannot predict the actual threshold quantitatively. The fire-driven instability of intermediate states implies that tree cover will not change smoothly with climate or other stressors and shifts between closed forest and a state of low tree cover will likely tend to be relatively sharp and difficult to reverse.


The changes of individual carotid artery wall layer by aging and carotid intima-media thickness value for high risk.
It is still unclear which layer (intima or media) is mainly involved in increased carotid intima-media thickness (CIMT) by aging and also unclear regarding CIMT value suggesting high cardiovascular risk, although 75th percentile value of CIMT is known as a high risk in asymptomatic adults. We sought to find the changes of carotid intima thickness (CIT) and carotid media thickness (CMT) by aging and the 75th percentile value of CIMT in asymptomatic Korean adults. This is an observational cohort study. Carotid ultrasound findings (n=2204 from 12 hospitals) were prospectively collected. The carotid images were sent to Korea Research Institute of Standards and Science for analysis using specialized software which can measure intima and media wall also. Mean age was 58.1±13.5 years old (52% of men). Pearson's correlation coefficient between age and right CIMT (r=.489, P<.001) and right CMT (r=.482, P<.001) was higher than that between age and right CIT (r=.284, P<.001). Mean right CIMT in male and female was 0.696±0.163 and 0.686±0.167 mm (P=.180), and the 75 percentile value was 0.778 and 0.771 mm, respectively. Mean right CIT was 0.311±0.069 and 0.303±0.064 mm (P=.009), and mean right CMT was 0.391±0.124 and 0.388±0.131 mm (P=.694) in male and female, respectively. Left carotid ultrasound findings showed similar to the right one. An increased CIMT by aging was mainly due to increased CMT rather than CIT in asymptomatic adults. The 75th percentile values of right CIMT were 0.778 and 0.771 mm in asymptomatic Korean male and female adults, respectively.


Phytochemical profile, antioxidant, antiproliferative, and enzyme inhibition-docking analyses of Salvia ekimiana Celep & Doğan.
Salvia ekimiana Celep & Doğan is an endemic species of Turkey. To our knowledge, the number of studies on biological activities and phytochemical profiling of this plant is quite limited. Therefore, this study aimed to analyze its activities and phytochemical content in detail. The qualitative-quantitative compositions were determined via spectrophotometric and chromatographic (LC-MS/MS and HPLC) techniques. 1,1-Diphenyl-2-picrylhydrazyl radical (DPPH•) and 2,2'-Azino-bis 3-ethylbenzothiazoline-6-sulfonic acid (ABTS•+) radical scavenging and ascorbate-iron (III)-catalyzed phospholipid peroxidation experiments were performed to measure antioxidant capacity. Hyaluronidase, collagenase, and elastase enzyme inhibition tests were determined in vitro using a spectrophotometer. Antiproliferative activity was evaluated in human lung cancer (A549) and human breast cancer (MCF7) cells. The murine fibroblast (L929) cell line was used as a normal control cell. While the subextract rich in phenolic compounds was n-butanol extract, rosmarinic acid was defined as the main secondary metabolite. The highest antioxidant activity observed for the n-butanol subextract included the following: DPPH• EC50: 0.08±0.00 mg/mL, TEAC/ABTS: 2.19±0.09 mmol/L Trolox, MDA EC50: 0.42±0.03 mg/mL. The methanolic extract, the ethyl acetate, and n-butanol subextracts displayed significant inhibitory activity on collagenase, while the other subextracts did not show any inhibitory activity on hyaluronidase and elastase. Due to strong interactions with their active sites, molecular docking showed luteolin 7-glucuronide, apigenin 7-glucuronide, and luteolin 5-glucoside had the highest binding affinity with target enzymes. The chloroform subextract showed significant cytotoxicity in all cell lines. These novel results revealed that S. ekimiana has strong antioxidant, collagenase enzyme inhibitory, and cytotoxic potential.


Educational and homeownership inequalities in stroke incidence: a population-based longitudinal study of mid-aged women.
We aimed to determine which socioeconomic status measures are associated with stroke risk in mid-aged women and assess the contribution of lifestyle, biological and psychosocial factors to observed associations. We included women born in 1946-51 from the Australian Longitudinal Study on Women's Health, who were surveyed every 3 years. Using generalized estimating equation analysis, we determined the association between socioeconomic status and stroke at the subsequent survey, adjusting for time-varying covariates. For significant associations, we calculated the contribution of individual mediating factors in explaining these associations. Among 11 468 women aged 47-52 years, 177 strokes occurred during a 12-year follow-up. Education (odds ratio lowest vs. highest 2.45, 95% confidence interval: 1.40-4.30) and homeownership, but not occupation or managing on income, were significantly associated with stroke. After full adjustment, the overall association between education and stroke was non-significant. Lifestyle (smoking, exercise, alcohol and body mass index), biological (hypertension, diabetes, heart disease and hysterectomy/oophorectomy) and psychosocial (depression and marital status) factors explained 38% of the association in the lowest versus highest education groups. Lifestyle and biological factors together accounted for 34%. Mediators accounted for 29% of the association between homeownership and stroke, with lifestyle and psychosocial factors responsible for most of this attenuation. However, a significant association remained in fully adjusted models (odds ratio non-homeowner vs. homeowner 1.63, 95% confidence interval: 1.12-2.38). Lower education level is associated with increased stroke risk in mid-aged women, and is partially mediated by known risk factors, particularly lifestyle and biological factors. Non-homeownership is associated with increased stroke risk, but the underlying mechanism is unclear.


Saliva, an easily accessible fluid as diagnostic tool and potent stem cell source for Alzheimer's Disease: Present and future applications.
Alzheimer's disease (AD) is a progressive and multifactorial disease. Many scientific advances have advanced our understanding of the pathogenesis of AD. However, the clinical diagnosis of AD remains difficult, with only post-mortem assays confirming its definitive diagnosis. There is a crucial need for an early and accurate detection of AD related symptoms. To date, current diagnosis techniques are costly or invasive. Finding a peripheral biomarker that could provide a sensitive, reproducible, and accurate detection prior to the onset of the AD clinical symptoms will allow identification of "at risk" individuals, thereby facilitating early initiation of treatments that may prove more effective. Salivary glands contain stem cells, which are affected by aging, suggesting that tissue samples from these glands may reveal a stem cell biomarker of AD, but also stem cells may be harvested from these glands, with proper timing and isolation technique, for cell-based regenerative medicine. Alternatively, instead of the salivary glands, saliva may represent an attractive source for biomarkers due to minimal discomfort to the patient, non-invasive collection, and the possibility of cost-effective screening large populations, encouraging greater compliance in clinical trials and frequent testing. In addition, salivary glands contain stem cells, which are likely also present in the saliva, making these cells as potentially sensitive cellular biomarker of and a therapeutic agent for AD. The aim of this review is to critically analyze the use of saliva for the identification of circulating biological markers to help the diagnosis of early cognitive impairment associated with AD and to generate insights into the potential application of stem cells derived from salivary glands or saliva as therapeutics (i.e., stem cell transplantation) for the disease.


Fibroblast EXT1-levels influence tumor cell proliferation and migration in composite spheroids.
Stromal fibroblasts are important determinants of tumor cell behavior. They act to condition the tumor microenvironment, influence tumor growth, support tumor angiogenesis and affect tumor metastasis. Heparan sulfate proteoglycans, present both on tumor and stromal cells, interact with a large number of ligands including growth factors, their receptors, and structural components of the extracellular matrix. Being ubiquitously expressed in the tumor microenvironment heparan sulfate proteoglycans are candidates for playing central roles in tumor-stroma interactions. The objective of this work was to investigate the role of heparan sulfate expressed by stromal fibroblasts in modulating the growth of tumor cells and in controlling the interstitial fluid pressure in a 3-D model. We generated spheroids composed of fibroblasts alone, or composite spheroids, composed of fibroblasts and tumor cells. Here we show that stromal fibroblasts with a mutation in the heparan sulfate elongating enzyme Ext1 and thus a low heparan sulfate content, formed composite fibroblast/tumor cell spheroids with a significant lower interstitial fluid pressure than corresponding wild-type fibroblast/tumor cell composite spheroids. Furthermore, immunohistochemistry of composite spheroids revealed that the cells segregated, so that after 6 days in culture, the wild-type fibroblasts formed an inner core and the tumor cells an outer layer of cells. For composite spheroids containing Ext1-mutated fibroblasts this segregation was less obvious, indicating impaired cell migration. Analysis of tumor cells expressing the firefly luciferase gene revealed that the changes in tumor cell migration in mutant fibroblast/tumor cell composite spheroids coincided with a lower proliferation rate. This is the first demonstration that stromal Ext1-levels modulate tumor cell proliferation and affect the interstitial fluid pressure in a 3-D spheroid model. Learning how structural changes in stromal heparan sulfate influence tumor cells is essential for our understanding how non-malignant cells of the tumor microenvironment influence tumor cell progression.


Crosstalk between the Ras2p-controlled mitogen-activated protein kinase and cAMP pathways during invasive growth of Saccharomyces cerevisiae.
The two highly conserved RAS genes of the budding yeast Saccharomyces cerevisiae are redundant for viability. Here we show that haploid invasive growth development depends on RAS2 but not RAS1. Ras1p is not sufficiently expressed to induce invasive growth. Ras2p activates invasive growth using either of two downstream signaling pathways, the filamentation MAPK (Cdc42p/Ste20p/MAPK) cascade or the cAMP-dependent protein kinase (Cyr1p/cAMP/PKA) pathway. This signal branch point can be uncoupled in cells expressing Ras2p mutant proteins that carry amino acid substitutions in the adenylyl cyclase interaction domain and therefore activate invasive growth solely dependent on the MAPK cascade. Both Ras2p-controlled signaling pathways stimulate expression of the filamentation response element-driven reporter gene depending on the transcription factors Ste12p and Tec1p, indicating a crosstalk between the MAPK and the cAMP signaling pathways in haploid cells during invasive growth.


Adverse drug reactions: types and treatment options.
Drug hypersensitivity results from interactions between a pharmacologic agent and the human immune system. These types of reactions constitute only a small subset of all adverse drug reactions. Allergic reactions to medications represent a specific class of drug hypersensitivity reactions mediated by IgE. Immune-mediated drug reactions may be discussed generally in the Gell and Coombs classification system, a widely accepted conceptual framework for understanding complex immune reactions. However, some reactions involve additional, poorly understood mechanisms that are not easily classified. Identifiable risk factors for drug hypersensitivity reactions include age, female gender, concurrent illnesses, and previous hypersensitivity to related drugs. Drug hypersensitivity is a clinical diagnosis based on available data. Laboratory testing may be useful, with skin testing providing the greatest specificity. Treatment is largely supportive and includes discontinuation of the offending medication, symptomatic treatment, and patient education. Patients with penicillin allergy should avoid carbapenems, and caution should be used in prescribing cephalosporins in these patients. Reactions to radiocontrast media can be limited by pretreatment with prednisone, diphenhydramine, and either ephedrine or a histamine H2-receptor antagonist.


Self-assembly of supramolecular light-harvesting arrays from covalent multi-chromophore perylene-3,4:9,10-bis(dicarboximide) building blocks.
We report on two multi-chromophore building blocks that self-assemble in solution and on surfaces into supramolecular light-harvesting arrays. Each building block is based on perylene-3,4:9,10-bis(dicarboximide) (PDI) chromophores. In one building block, N-phenyl PDI chromophores are attached at their para positions to both nitrogens and the 3 and 6 carbons of pyromellitimide to form a cross-shaped molecule (PI-PDI(4)). In the second building block, N-phenyl PDI chromophores are attached at their para positions to both nitrogens and the 1 and 7 carbons of a fifth PDI to produce a saddle-shaped molecule (PDI(5)). These molecules self-assemble into partially ordered dimeric structures (PI-PDI(4))(2) and (PDI(5))(2) in toluene and 2-methyltetrahydrofuran solutions with the PDI molecules approximately parallel to one another primarily due to pi-pi interactions between adjacent PDI chromophores. On hydrophobic surfaces, PDI(5) grows into rod-shaped nanostructures of average length 130 nm as revealed by atomic force microscopy. Photoexcitation of these supramolecular dimers in solution gives direct evidence of strong pi-pi interactions between the excited PDI chromophore and other PDI molecules nearby based on the observed formation of an excimer-like state in <130 fs with a lifetime of about 20 ns. Multiple photoexcitations of the supramolecular dimers lead to fast singlet-singlet annihilation of the excimer-like state, which occurs with exciton hopping times of about 5 ps, which are comparable to those observed in photosynthetic light-harvesting proteins from green plants.


Restoration of fast inactivation in an inactivation-defective human heart sodium channel by the cysteine modifying reagent benzyl-MTS: analysis of IFM-ICM mutation.
It has been suggested that the region linking domain III and IV of voltage-gated sodium channels forms the inactivation gate. A combination of site-directed mutagenesis, cysteine covalent modification, and electrophysiological recording techniques was used to identify the role of the Phe1486, a conserved phenylalanine residue located in the III-IV linker of Na+ channels. This Phe1486 is part of a hydrophobic amino acid cluster (IFM) that was proposed to play an essential role in the fast inactivation of voltage-gated sodium channels. Expression in tsA201 cells of an altered human heart 1 Na+ channel (hH1/F1486C) in which Phe1486 was replaced by a cysteine is associated with the appearance of a residual current, a loss of voltage-dependence of the time constants of inactivation, a shift of the steady-state inactivation to more depolarized voltages, and a recovery from inactivation that is faster than the wild-type hH1. Exposure of the cytoplasmic surface of mutant F1486C to the methanthiosulfonate reagents, MTSEA, MTSET, and MTSES, further disrupted macroscopic inactivation, but exposure to MTSBN completely restores fast inactivation and the voltage-dependence of fast inactivation. These findings support the formulation that the IFM motif of the III-IV-linker of voltage-gated sodium channels serves as an essential component of the inactivation particle and that the phenyl group of Phe1486 may play a crucial role in inactivation gate closure.


Cardiolipin mediates membrane and channel interactions of the mitochondrial TIM23 protein import complex receptor Tim50.
The phospholipid cardiolipin mediates the functional interactions of proteins that reside within energy-conserving biological membranes. However, the molecular basis by which this lipid performs this essential cellular role is not well understood. We address this role of cardiolipin using the multisubunit mitochondrial TIM23 protein transport complex as a model system. The early stages of protein import by this complex require specific interactions between the polypeptide substrate receptor, Tim50, and the membrane-bound channel-forming subunit, Tim23. Using analyses performed in vivo, in isolated mitochondria, and in reductionist nanoscale model membrane systems, we show that the soluble receptor domain of Tim50 interacts with membranes and with specific sites on the Tim23 channel in a manner that is directly modulated by cardiolipin. To obtain structural insights into the nature of these interactions, we obtained the first small-angle x-ray scattering-based structure of the soluble Tim50 receptor in its entirety. Using these structural insights, molecular dynamics simulations combined with a range of biophysical measurements confirmed the role of cardiolipin in driving the association of the Tim50 receptor with lipid bilayers with concomitant structural changes, highlighting the role of key structural elements in mediating this interaction. Together, these results show that cardiolipin is required to mediate specific receptor-channel associations in the TIM23 complex. Our results support a new working model for the dynamic structural changes that occur within the complex during transport. More broadly, this work strongly advances our understanding of how cardiolipin mediates interactions among membrane-associated proteins.


Facilitating uptake of Aboriginal Adult Health Checks through community engagement and health promotion.
Adult Health Checks (AHCs) for Aboriginal and Torres Strait Islander people (MBS Item 710) promote comprehensive physical and psychosocial health assessments. Despite the poor uptake of health assessments in Aboriginal and Torres Strait Islander people, a small number of successful implementation initiatives have been reported. In order to ensure uptake of these screening initiatives, there remains a need to demonstrate the feasibility of models of implementing AHCs. The aim of this paper is to address the process issues and overarching outcomes of a two-day targeted screening and assessment programme to increase the uptake of AHCs at an Aboriginal Community Controlled Medical Service. Clients of an urban Aboriginal Medical Service (AMS) were invited to undertake an AHC during a two-day screening initiative. On-site general practitioners (GPs), nurses, and Aboriginal Health Workers (AHWs) worked within a team to facilitate screenings at an AMS. Barriers and facilitators to the initiative and strategies for quality improvement were discussed by the team. A review of medical notes was undertaken six months following the screening days to document uptake of recommendations. Forty clients undertook AHCs as part of the initiative. In total, 113 diagnostic tests, interventions, specialist referrals and medication initiatives had been enacted within the following six months as a result of screening day visits. Benefits to individual clients, the community, the AMS and staff were identified. The screening day demonstrated feasibility and acceptability of this approach and provides support for its implementation in other health facilities. Importantly, this service was provided in a culturally sensitive framework and within an interdisciplinary teamwork model. This targeted approach increased uptake of assessment items and provided opportunities for health advice and risk factor modification.


Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates.
RNA-cleaving deoxyribozyme 8-17 has been increasingly used in nanotechnology and biosensing applications. Conventional methods to equip 8-17 with fluorescent signaling property usually involve covalent attachment of two dyes at nucleotide positions that are far away from the catalytic core, such that the bulky dye structures would not affect the deoxyribozyme activity. However, the maximum fluorescent enhancement associated with these 8-17 constructs is typically < or =10-fold, due to a high fluorescent background. To find an optimal balance between signal enhancement and signaling speed, we have conducted a comprehensive study on the effects of the nature of dyes (Alexa Fluor 488, 546 and 647; QSY 9 and 21) as well as their attaching positions along the substrate strand on the catalytic and signaling performance of 8-17. Our results have indicated that 8-17 is able to cleave almost every modified substrate, including those that have chromophores only 1 nt away from the cleavage site. Most importantly, almost all of these substrates are able to generate 15- to 85-fold signal enhancement within 10 min. We have also provided guidelines for selecting substrates that could offer the best signal enhancement, the fastest signaling speed, or the best balance between signal enhancement and signaling speed.


Elementary structural motifs in a random network of cytosine adsorbed on a gold(111) surface.
Nonsymmetrical organic molecules adsorbed on solid surfaces may assemble into random networks, thereby providing model systems for organic glasses that can be directly observed by scanning tunneling microscopy (STM). We investigated the structure of a disordered cytosine network on a gold(111) surface created by thermal quenching, to temperatures below 150 K, of the two-dimensional fluid present on the surface at room temperature. Comparison of STM images to density functional theory calculations allowed us to identify three elementary structural motifs (zigzag filaments and five- and six-membered rings) that underlie the whole supramolecular random network. The identification of elementary structural motifs may provide a new framework for understanding medium-range order in amorphous and glassy systems.


Importance and usefulness of evaluating self-esteem in children.
Self-esteem is the "feeling of self-appreciation" and is an indispensable emotion for people to adapt to society and live their lives. For children, in particular, the environment in which they are raised contributes profoundly to the development of their self-esteem, which in turn helps them to adapt better to society. Various psychologists have provided definitions of self-esteem, and examined methods of objectively evaluating self-esteem. Questionnaire-style assessment methods for adult include Rosenberg Self-Esteem Scale and Janis-Field Feeling of Inadequacy Scale, and these for children include Coopersmith Self-Esteem Inventory, Pope's 5-Scale Test of Self-Esteem for children, and Kid- KINDL®. Other methods include Ziller Social Self-Esteem Scale and Implicit Association Test. The development of children's self-esteem is heavily influenced by their environment, that is, their homes, neighborhoods, and schools. Children with damaged self-esteem are at risk of developing psychological and social problems, which hinders recovery from low self-esteem. Thus, to recover low self-esteem, it is important for children to accumulate a series of successful experiences to create a positive concept of self. Evaluating children's self-esteem can be an effective method for understanding their past and present circumstances, and useful to treat for children with psychosomatic disorders.


CK1α suppresses lung tumour growth by stabilizing PTEN and inducing autophagy.
The contribution of autophagy to cancer development remains controversial, largely owing to the fact that autophagy can be tumour suppressive or oncogenic in different biological contexts. Here, we show that in non-small-cell lung cancer (NSCLC), casein kinase 1 alpha 1 (CK1α) suppresses tumour growth by functioning as an autophagy inducer to activate an autophagy-regulating, tumour-suppressive PTEN/AKT/FOXO3a/Atg7 axis. Specifically, CK1α bound the C-terminal tail of PTEN and enhanced both PTEN stability and activity by competitively antagonizing NEDD4-1-induced PTEN polyubiquitination and abrogating PTEN phosphorylation, thereby inhibiting AKT activity and activating FOXO3a-induced transcription of Atg7. Notably, blocking CK1α-induced Atg7-dependent autophagy cooperates with oncogenic HRasV12 to initiate tumorigenesis of lung epithelial cells. An association of a CK1α-modulated autophagic program with the anti-neoplastic activities of the CK1α/PTEN/FOXO3a/Atg7 axis was demonstrated in xenografted tumour models and human NSCLC specimens. This provides insights into the biological and potentially clinical significance of autophagy in NSCLC.


Seasonal changes in 24-h patterns of suicide rates: a study on train suicides in The Netherlands.
Annual patterns in suicide rates, peaking near the summer solstice, are well documented. It has been suggested that day length or total hours of sunshine has an impact on suicide rates. If these environmental factors are involved, we would expect changes in the daily pattern of suicide rates to occur over the year. To test this hypothesis, the 24-h patterns of suicide rate were investigated as a function of time of year. Detailed information about the exact time of suicides in The Netherlands is only available for train suicides. Therefore, information concerning age, sex, time and place of occurrence of all verified train suicides over 15 years in The Netherlands (n=2830) was obtained from The Netherlands Railways archives. Daily patterns in train suicides show systematic variations of two kinds. First, independently of time of year, suicide rates at night drop to about 10% of their daytime values. Second, there are two daily peaks in the patterns which shift their timing over the year, with one peak occurring shortly after sunset, and the other one consistently occurring 9-10 h earlier. Both peaks shift with the 5.5-h shift in sunset time. Train suicidal behaviour may not represent fatal suicidal behaviour in general. There are pronounced and systematic daily variations in train suicide rates in The Netherlands. One of these is related to clock time, the others are related to the light-dark cycle. The consistency of the patterns suggests a strong environmental influence on train suicidal behaviour. Research on 24-h patterns of suicide rates should control for time of year.


High density O-glycosylation of the MUC2 tandem repeat unit by N-acetylgalactosaminyltransferase-3 in colonic adenocarcinoma extracts.
A synthetic peptide corresponding to the human MUC2 tandem repeat unit was glycosylated in vitro using UDP-GalNAc and extracts of colonic adenocarcinoma and paired normal mucosa, followed by fractionation of the products by reverse phase high-performance liquid chromatography. Several peaks of glycopeptides with different numbers of GalNAc residues attached were detected. It is notable that the adenocarcinoma extract was capable of glycosylating peptides to a much greater extent than was normal mucosa. The levels of mRNA for N-acetylgalactosaminyltransferases-1, -2, and -3 were determined by reverse transcription-PCR. Only N-acetylgalactosaminyltransferase-3 mRNA was expressed at a higher level in the adenocarcinoma than in the normal tissue. When the MUC2 tandem repeat peptide was glycosylated with a mixture of the normal mucosa extract and recombinant N-acetylgalactosaminyltransferase-3, larger amounts of glycopeptides with higher contents of GalNAc residues were produced. The MUC2 tandem repeat peptides glycosylated extensively by recombinant N-acetylgalactosaminyltransferase-1, -2, or -3 were prepared and characterized. Substitution at each Thr residue, as revealed by Edman degradation sequencing, in conjunction with evidence obtained on mass spectrometry indicated a heterogeneous pattern of site-specific glycosylation within the MUC2 tandem repeat. It was found that maximum numbers of 6, 8, and 11 GalNAc residues were incorporated by N-acetylgalactosaminyltransferases-1, -2, and -3, respectively, and that only N-acetylgalactosaminyltransferase-3 could completely glycosylate both consecutive sequences composed of three and five Thr residues in the MUC2 tandem repeat unit. These results suggest that O-glycosylation of the clustered Thr residues is a selective process controlled by N-acetylgalactosaminyltransferase-3 in the synthesis of clustered carbohydrate antigens.


Linking seasonal inorganic nitrogen shift to the dynamics of microbial communities in the Chesapeake Bay.
Seasonal shifts of dissolved inorganic nitrogen (DIN) and the dynamics of microbial communities for nitrogen transformation were investigated in the water column of Chesapeake Bay. The relative abundance of nitrogen over phosphorus (N) showed a strong seasonal and spatial pattern: gradually decreased from upstream to downstream; high in winter and low in summer. Because the phosphorus concentration remained relatively stable, the spatiotemporal pattern of N implied that a substantial fraction of DIN was removed in the bay, especially in summer. Correlation analyses indicated the functional microbial communities and environmental variables, such as temperature, dissolved oxygen, salinity, played important roles for connecting the seasonal variation of N. Among them, temperature was the trigger factor. High temperature in the summer induced the growth of functional microbes, which subsequently consumed a large portion of DIN inputted from the tributaries and reduced the N. The current study provided the relative importance of microbial communities and environmental variables in driving the DIN loss in the bay.


A real-time optimal inverse planning for Gamma Knife radiosurgery by convex optimization: description of the system and first dosimetry data.
OBJECTIVEThe authors developed a new, real-time interactive inverse planning approach, based on a fully convex framework, to be used for Gamma Knife radiosurgery.METHODSThe convex framework is based on the precomputation of a dictionary composed of the individual dose distributions of all possible shots, considering all their possible locations, sizes, and shapes inside the target volume. The convex problem is solved to determine the plan, i.e., which shots and with which weights, that will actually be used, considering a sparsity constraint on the shots to fulfill the constraints while minimizing the beam-on time. The system is called IntuitivePlan and allows data to be transferred from generated dose plans into the Gamma Knife treatment planning software for further dosimetry evaluation.RESULTSThe system has been very efficiently implemented, and an optimal plan is usually obtained in less than 1 to 2 minutes, depending on the complexity of the problem, on a desktop computer or in only a few minutes on a high-end laptop. Dosimetry data from 5 cases, 2 meningiomas and 3 vestibular schwannomas, were generated with IntuitivePlan. Results of evaluation of the dosimetry characteristics are very satisfactory and adequate in terms of conformity, selectivity, gradient, protection of organs at risk, and treatment time.CONCLUSIONSThe possibility of using optimal, interactive real-time inverse planning in conjunction with the Leksell Gamma Knife opens new perspectives in radiosurgery, especially considering the potential use of the full capabilities of the latest generations of the Leksell Gamma Knife. This approach gives new users the possibility of using the system for easier and quicker access to good-quality plans with a shorter technical training period and opens avenues for new planning strategies for expert users. The use of a convex optimization approach allows an optimal plan to be provided in a very short processing time. This way, innovative graphical user interfaces can be developed, allowing the user to interact directly with the planning system to graphically define the desired dose map and to modify on-the-fly the dose map by moving, in a very user-friendly manner, the isodose surfaces of an initial plan. Further independent quantitative prospective evaluation comparing inverse planned and forward planned cases is warranted to validate this novel and promising treatment planning approach.


Clinical implication of natural killer cells and reproduction.
The regulation of natural killer (NK) cells in the peripheral blood and endometrial layers has been associated with reproductive immunopathology such as recurrent spontaneous abortions (RSA), infertility of implantation failures, or pre-eclampsia. The placenta has a complex anatomical structure and different subsets of NK cells with various functional roles can directly interact with trophoblasts. NK cell subpopulations and their functions, putative roles of NK cells in peripheral blood and endometrium are reviewed in relation to RSA and infertility. An increase in NK cell numbers and /or activity in pre- or post-conceptional period in women with RSA or infertility with multiple implantation failures are a significant clinical concern. In addition, immuno-phenotypic characteristics of NK cells in these women support the changes for their increased activity status. Further studies are needed to explore underlying mechanism of NK cells in RSA, infertility, and other reproductive immunopathologies. Possible neurological and hormonal control of NK cells and NK cell interaction with various leukocyte populations need further investigation in women with reproductive failures.


Integrated primary care in Germany: the road ahead.
Health care delivery in Germany is highly fragmented, resulting in poor vertical and horizontal integration and a system that is focused on curing acute illness or single diseases instead of managing patients with more complex or chronic conditions, or managing the health of determined populations. While it is now widely accepted that a strong primary care system can help improve coordination and responsiveness in health care, primary care has so far not played this role in the German system. Primary care physicians traditionally do not have a gatekeeper function; patients can freely choose and directly access both primary and secondary care providers, making coordination and cooperation within and across sectors difficult. Since 2000, driven by the political leadership and initiative of the Federal Ministry of Health, the German Bundestag has passed several laws enabling new forms of care aimed to improve care coordination and to strengthen primary care as a key function in the German health care system. These include on the contractual side integrated care contracts, and on the delivery side disease management programmes, medical care centres, gatekeeping and 'community medicine nurses'. Recent policy reforms improved framework conditions for new forms of care. There is a clear commitment by the government and the introduction of selective contracting and financial incentives for stronger cooperation constitute major drivers for change. First evaluations, especially of disease management programmes, indicate that the new forms of care improve coordination and outcomes. Yet the process of strengthening primary care as a lever for better care coordination has only just begun. Future reforms need to address other structural barriers for change such as fragmented funding streams, inadequate payment systems, the lack of standardized IT systems and trans-sectoral education and training of providers.


A Genome-Wide Linkage Study for Chronic Obstructive Pulmonary Disease in a Dutch Genetic Isolate Identifies Novel Rare Candidate Variants.
Chronic obstructive pulmonary disease (COPD) is a complex and heritable disease, associated with multiple genetic variants. Specific familial types of COPD may be explained by rare variants, which have not been widely studied. We aimed to discover rare genetic variants underlying COPD through a genome-wide linkage scan. Affected-only analysis was performed using the 6K Illumina Linkage IV Panel in 142 cases clustered in 27 families from a genetic isolate, the Erasmus Rucphen Family (ERF) study. Potential causal variants were identified by searching for shared rare variants in the exome-sequence data of the affected members of the families contributing most to the linkage peak. The identified rare variants were then tested for association with COPD in a large meta-analysis of several cohorts. Significant evidence for linkage was observed on chromosomes 15q14-15q25 [logarithm of the odds (LOD) score = 5.52], 11p15.4-11q14.1 (LOD = 3.71) and 5q14.3-5q33.2 (LOD = 3.49). In the chromosome 15 peak, that harbors the known COPD locus for nicotinic receptors, and in the chromosome 5 peak we could not identify shared variants. In the chromosome 11 locus, we identified four rare (minor allele frequency (MAF) <0.02), predicted pathogenic, missense variants. These were shared among the affected family members. The identified variants localize to genes including neuroblast differentiation-associated protein (AHNAK), previously associated with blood biomarkers in COPD, phospholipase C Beta 3 (PLCB3), shown to increase airway hyper-responsiveness, solute carrier family 22-A11 (SLC22A11), involved in amino acid metabolism and ion transport, and metallothionein-like protein 5 (MTL5), involved in nicotinate and nicotinamide metabolism. Association of SLC22A11 and MTL5 variants were confirmed in the meta-analysis of 9,888 cases and 27,060 controls. In conclusion, we have identified novel rare variants in plausible genes related to COPD. Further studies utilizing large sample whole-genome sequencing should further confirm the associations at chromosome 11 and investigate the chromosome 15 and 5 linked regions.


Structural variation and its potential impact on genome instability: Novel discoveries in the EGFR landscape by long-read sequencing.
Structural variation (SV) is typically defined as variation within the human genome that exceeds 50 base pairs (bp). SV may be copy number neutral or it may involve duplications, deletions, and complex rearrangements. Recent studies have shown SV to be associated with many human diseases. However, studies of SV have been challenging due to technological constraints. With the advent of third generation (long-read) sequencing technology, exploration of longer stretches of DNA not easily examined previously has been made possible. In the present study, we utilized third generation (long-read) sequencing techniques to examine SV in the EGFR landscape of four haplotypes derived from two human samples. We analyzed the EGFR gene and its landscape (+/- 500,000 base pairs) using this approach and were able to identify a region of non-coding DNA with over 90% similarity to the most common activating EGFR mutation in non-small cell lung cancer. Based on previously published Alu-element genome instability algorithms, we propose a molecular mechanism to explain how this non-coding region of DNA may be interacting with and impacting the stability of the EGFR gene and potentially generating this cancer-driver gene. By these techniques, we were also able to identify previously hidden structural variation in the four haplotypes and in the human reference genome (hg38). We applied previously published algorithms to compare the relative stabilities of these five different EGFR gene landscape haplotypes to estimate their relative potentials to generate the EGFR exon 19, 15 bp canonical deletion. To our knowledge, the present study is the first to use the differences in genomic architecture between targeted cancer-linked phased haplotypes to estimate their relative potentials to form a common cancer-linked driver mutation.


Plasma 1-deoxysphingolipids are predictive biomarkers for type 2 diabetes mellitus.
Serine palmitoyltransferase (SPT) catalyzes the condensation of serine and palmitoyl coenzyme A, the first step in the de novo sphingolipid synthesis. Apart from these canonical substrates, SPT can also metabolize alanine and other acyl coenzyme As. This forms a spectrum of atypical sphingoid bases which are altered in the context of the metabolic syndrome (MetS) and type 2 diabetes mellitus (T2DM). We investigated whether atypical sphingolipids can be used as prospective markers to predict the incidence of T2DM. Using liquid chromatography/mass spectrometry, we analyzed the sphingoid base profile in a prospective cohort with 339 individuals. All individuals were followed up for a period of 8 years. Confirming earlier results, we found 1-deoxysphingolipids (1-deoxySLs) to be significantly elevated in patients with MetS, impaired fasting glucose, and T2DM. Patients who developed T2DM during the follow-up period (n=32) showed significantly higher 1-deoxySL levels at baseline compared with those who did not develop T2DM until the end of the study (n=70). 1-Deoxysphingosine levels were independent predictors for T2DM even after adjusting for glycated hemoglobin (standardized adjusted OR=2.1, CI 95% (1.19 to 3.71); p=0.010), MetS (standardized adjusted OR=1.97, CI 95% (1.13 to 3.43); p=0.017), and other risk factors such as age, sex, BMI, and lipid-lowering drugs. Similar results were observed for the 1-deoxysphinganine levels. Our results support a novel role for 1-deoxySL as predictive biomarkers for the development of T2DM in risk patients and warrants further larger prospective trials in lower risk cohorts.


Secular trends of physical fitness in Swedish adults.
The aim of the present study was to study differences in fitness (maximal aerobic power (VO(2max)), balance control, abdominal strength and endurance) and anthropometric data in Swedish women and men (20-65 years of age) between two national cross-sectional samples, studied in 1990/1991 and 2000/2001, respectively. The absolute and relative VO(2max) (aerobic fitness), estimated from a submaximal test, declined with increasing age in both genders. The submaximal test was validated against running VO(2max). Furthermore, the relative aerobic fitness (mL/min/kg) was lower in the 2000/2001 sample in men but not in women. Overall physical activity level was unchanged in both genders. An unexpected finding was that in both samples there were no major differences in relative VO(2max) between men and women of the same age. Combined overweight and obesity (body mass index> or =25) is becoming more prevalent in men, but not in women with prevalence in 2000/2001 of 61% and 38% for men and women, respectively. Balance control and abdominal strength and endurance decrease with increasing age with no differences between the two samples. Thus, the near future health situation for men may be worse, while for women it may be less or no differences compared with today.


MAD2 Combined with Mitotic Spindle Apparatus (MSA) and Anticentromere Antibody (ACA) for Diagnosis of Small Cell Lung Cancer (SCLC).
BACKGROUND MAD2 is the gene controlling mitosis. Many studies have assessed MAD2 in various types of carcinoma. Antinuclear mitotic spindle apparatus antibody (MSA) and anticentromere antibody (ACA) are related mitotic antibodies, playing roles in autoimmune diseases and carcinomas, but the expression of MAD2, MSA, and ACA in SCLC is unclear. MATERIAL AND METHODS We enrolled 70 SCLC patients, 72 non-small cell lung cancer (NSCLC) patients, and 65 pulmonary nodule (PN) patients. MAD2 expression was measured through agarose electrophoresis and qt-PCR. Antinuclear mitotic spindle apparatus antibody (MSA) and anticentromere antibody (ACA) were detected by indirect immunofluorescence (IIF). RESULTS MAD2 was found both in SCLC and NSCLC. Interestingly, there was a significant difference found between SCLC and NSCLC using qt-PCR (P<0.05). The area under the ROC curve of MAD2 expression was 0.799, with medium diagnostic value. MAD2 expression was related to age, lymphatic metastasis, and survival time, but not with sex. The positivity for MSA and ACA by IIF assay were 37.20% and 34.00%, respectively, in the SCLC group, which were higher than in the NSCLC and pulmonary nodule groups (P<0.05). The kappa values of MSA and ACA with MAD2 expression were 0.73 and 0.65, respectively, with moderate consistency. Combining MAD2 with MSA and ACA enhanced the sensitivity and specificity for diagnosing SCLC. CONCLUSIONS MAD2 expression was found to be involved in carcinogenesis and prognosis of SCLC. The combination of MAD2 with MSA and ACA is useful for early diagnosis and shows promise in treatment of SCLC.


A comparison of the ability of rilpivirine (TMC278) and selected analogues to inhibit clinically relevant HIV-1 reverse transcriptase mutants.
The recently approved anti-AIDS drug rilpivirine (TMC278, Edurant) is a nonnucleoside inhibitor (NNRTI) that binds to reverse transcriptase (RT) and allosterically blocks the chemical step of DNA synthesis. In contrast to earlier NNRTIs, rilpivirine retains potency against well-characterized, clinically relevant RT mutants. Many structural analogues of rilpivirine are described in the patent literature, but detailed analyses of their antiviral activities have not been published. This work addresses the ability of several of these analogues to inhibit the replication of wild-type (WT) and drug-resistant HIV-1. We used a combination of structure activity relationships and X-ray crystallography to examine NNRTIs that are structurally related to rilpivirine to determine their ability to inhibit WT RT and several clinically relevant RT mutants. Several analogues showed broad activity with only modest losses of potency when challenged with drug-resistant viruses. Structural analyses (crystallography or modeling) of several analogues whose potencies were reduced by RT mutations provide insight into why these compounds were less effective. Subtle variations between compounds can lead to profound differences in their activities and resistance profiles. Compounds with larger substitutions replacing the pyrimidine and benzonitrile groups of rilpivirine, which reorient pocket residues, tend to lose more activity against the mutants we tested. These results provide a deeper understanding of how rilpivirine and related compounds interact with the NNRTI binding pocket and should facilitate development of novel inhibitors.


Molecular docking for substrate identification: the short-chain dehydrogenases/reductases.
Protein ligand docking has recently been investigated as a tool for protein function identification, with some success in identifying both known and unknown substrates of proteins. However, identifying a protein's substrate when cross-docking a large number of enzymes and their cognate ligands remains a challenge. To explore a more limited yet practically important and timely problem in more detail, we have used docking for identifying the substrates of a single protein family with remarkable substrate diversity, the short-chain dehydrogenases/reductases. We examine different protocols for identifying candidate substrates for 27 short-chain dehydrogenase/reductase proteins of known catalytic function. We present the results of docking >900 metabolites from the human metabolome to each of these proteins together with their known cognate substrates and products, and we investigate the ability of docking to (a) reproduce a viable binding mode for the substrate and (b) to rank the substrate highly amongst the dataset of other metabolites. In addition, we examine whether our docking results provide information about the nature of the substrate, based on the best-scoring metabolites in the dataset. We compare two different docking methods and two alternative scoring functions for one of the docking methods, and we attempt to rationalise both successes and failures. Finally, we introduce a new protocol, whereby we dock only a set of representative structures (medoids) to each of the proteins, in the hope of characterising each binding site in terms of its ligand preferences, with a reduced computational cost. We compare the results from this protocol with our original docking experiments, and we find that although the rank of the representatives correlates well with the mean rank of the clusters to which they belong, a simple structure-based clustering is too naive for the purpose of substrate identification. Many clusters comprise ligands with widely varying affinities for the same protein; hence important candidates can be missed if a single representative is used.