The initiation codon determines the efficiency but not the site of translation initiation in Chlamydomonas chloroplasts.
To study translation initiation in Chlamydomonas chloroplasts, we mutated the initiation codon AUG to AUU, ACG, ACC, ACU, and UUC in the chloroplast petA gene, which encodes cytochrome f of the cytochrome b6/f complex. Cytochrome f accumulated to detectable levels in all mutant strains except the one with a UUC codon, but only the mutant with an AUU codon grew well at 24 degrees C under conditions that require photosynthesis. Because no cytochrome f was detectable in the UUC mutant and because each mutant that accumulated cytochrome f did so at a different level, we concluded that any residual translation probably initiates at the mutant codon. As a further demonstration that alternative initiation sites are not used in vivo, we introduced in-frame UAA stop codons immediately downstream or upstream or in place of the initiation codon. Stop codons at or downstream of the initiation codon prevented accumulation of cytochrome f, whereas the one immediately upstream of the initiation codon had no effect on the accumulation of cytochrome f. These results suggest that an AUG codon is not required to specify the site of translation initiation in chloroplasts but that the efficiency of translation initiation depends on the identity of the initiation codon.


What do patients and family-caregivers value from hospice care? A systematic mixed studies review.
It is not known which attributes of care are valued the most by those who experience hospice services. Such knowledge is integral to service development as it facilitates opportunities for continuous improvement of hospice care provision. The objectives of this mixed-studies systematic review were to explore patients' and their family carer views and experiences, to determine what they valued about adult hospice care in the UK. ASSIA, PubMed, CINAHL and PsycINFO were searched from inception, up until March 2017 to identify qualitative, quantitative, and mixed-methods studies. Four additional searching techniques supplemented the main search and grey literature was included. A three-stage mixed-method systematic review was conducted with a sequential exploratory design. Thematic synthesis was used with qualitative data, followed by a narrative summary of the quantitative data. The qualitative and quantitative syntheses were then juxtaposed within a matrix to produce an overarching synthesis. Thirty-four studies highlighted that what patients and carers valued was generally context specific and stemmed from an amalgamation of hospice service components, which both individually and collectively contributed to improvements in quality of life. When the syntheses of qualitative and quantitative studies were viewed in isolation, the value placed on services remained relatively consistent, with some discrepancies evident in service availability. These were commonly associated with geographical variations, as well as differences in service models and timeframes. Through an overarching synthesis of the qualitative and quantitative evidence, however, notable variations and a more nuanced account of what people valued and why were more prominent, specifically in relation to a lack of social support for carers, disparate access to essential services, the underrepresentation of patients with a non-cancer diagnosis, and the dissatisfaction with the range of services provided. Review findings strengthen the existing evidence base and illuminates the underpinning elements of hospice care most valued by patients and their families. With large disparities in the availability of services, however, the underrepresentation of patients with non-malignant diseases and the limited evidence base demonstrating the adequate addressment of the social needs of carers, there continues to be considerable gaps that warrants further research.


Associations between white matter microstructure and infants' working memory.
Working memory emerges in infancy and plays a privileged role in subsequent adaptive cognitive development. The neural networks important for the development of working memory during infancy remain unknown. We used diffusion tensor imaging (DTI) and deterministic fiber tracking to characterize the microstructure of white matter fiber bundles hypothesized to support working memory in 12-month-old infants (n=73). Here we show robust associations between infants' visuospatial working memory performance and microstructural characteristics of widespread white matter. Significant associations were found for white matter tracts that connect brain regions known to support working memory in older children and adults (genu, anterior and superior thalamic radiations, anterior cingulum, arcuate fasciculus, and the temporal-parietal segment). Better working memory scores were associated with higher FA and lower RD values in these selected white matter tracts. These tract-specific brain-behavior relationships accounted for a significant amount of individual variation above and beyond infants' gestational age and developmental level, as measured with the Mullen Scales of Early Learning. Working memory was not associated with global measures of brain volume, as expected, and few associations were found between working memory and control white matter tracts. To our knowledge, this study is among the first demonstrations of brain-behavior associations in infants using quantitative tractography. The ability to characterize subtle individual differences in infant brain development associated with complex cognitive functions holds promise for improving our understanding of normative development, biomarkers of risk, experience-dependent learning and neuro-cognitive periods of developmental plasticity.


Improved 5-year prediction of all-cause mortality by coronary CT angiography applying the CONFIRM score.
To investigate the long-term performance of the CONFIRM score for prediction of all-cause mortality in a large patient cohort undergoing coronary computed tomography angiography (CCTA). Patients with a 5-year follow-up from the international multicentre CONFIRM registry were included. The primary endpoint was all-cause mortality. The predictive value of the CONFIRM score over clinical risk scores (Morise, Framingham, and NCEP ATP III score) was studied in the entire patient population as well as in subgroups. Improvement in risk prediction and patient reclassification were assessed using categorical net reclassification index (NRI) and integrated discrimination improvement (IDI). During a median follow-up period of 5.3 years, 982 (6.5%) of 15 219 patients died. The CONFIRM score outperformed the prognostic value of the studied three clinical risk scores (c-indices: CONFIRM score 0.696, NCEP ATP III score 0.675, Framingham score 0.610, Morise score 0.606; c-index for improvement CONFIRM score vs. NCEP ATP III score 0.650, P < 0.0001). Application of the CONFIRM score allowed reclassification of 34% of patients when compared with the NCEP ATP III score, which was the best clinical risk score. Reclassification was significant as revealed by categorical NRI (0.06 with 95% CI 0.02 and 0.10, P = 0.005) and IDI (0.013 with 95% CI 0.01 and 0.015, P < 0.001). Subgroup analysis revealed a comparable performance in a variety of patient subgroups. The CONFIRM score permits a significantly improved prediction of mortality over clinical risk scores for >5 years after CCTA. These findings are consistent in a large variety of patient subgroups.


Antimicrobial activity of commercial Olea europaea (olive) leaf extract.
The aim of this research was to investigate the activity of a commercial extract derived from the leaves of Olea europaea (olive) against a wide range of microorganisms (n=122). Using agar dilution and broth microdilution techniques, olive leaf extract was found to be most active against Campylobacter jejuni, Helicobacter pylori and Staphylococcus aureus [including meticillin-resistant S. aureus (MRSA)], with minimum inhibitory concentrations (MICs) as low as 0.31-0.78% (v/v). In contrast, the extract showed little activity against all other test organisms (n=79), with MICs for most ranging from 6.25% to 50% (v/v). In conclusion, olive leaf extract was not broad-spectrum in action, showing appreciable activity only against H. pylori, C. jejuni, S. aureus and MRSA. Given this specific activity, olive leaf extract may have a role in regulating the composition of the gastric flora by selectively reducing levels of H. pylori and C. jejuni.


Effect of Advanced Platelet-rich Fibrin on Wound Healing after Third Molar Extraction: A Split-mouth Randomized Double-blind Study.
To evaluate the potential of advanced platelet-rich fibrin (A-PRF) as a regenerative biomaterial for bone regeneration and postoperative sequelae after impacted third molar extractions. This was a split-mouth, randomized, double-blind clinical trial. A total of 10 female patients in King Abdulaziz University Dental Hospital with bilateral impacted third molars were recruited into the study. Surgical extractions were performed on both sides of the mandible. Randomization was done by a coin toss; A-PRF was placed on the one side while the other side did not receive any intervention. Each patient acted as their own control. Both the patients and the investigators were blinded about the A-PRF side. The outcome on periodontal regeneration was made measuring pocket depth (PD), gum recession (GR), and clinical attachment level (CAL) before and at 1- and 3-months postoperatively. Pain, swelling, and healing were assessed on the 7th postoperative day. p value less than 0.05 was considered statistically significant. An estimated 10 patients completed the study. There were no significant differences in PD, CAL, and GR between the two groups at any time point, although the data obtained were slightly favoring the A-PRF. However, a statistically significant reduction in pain and swelling was observed in the A-PRF group compared to the controls (p < 0.05). The findings of this study demonstrate A-PRF as a potential biomaterial for lessening the severity of pain and swelling after third molar surgery. Long-term trials with a larger sample size and more methodically sound assessment tools are needed to obtain more meaningful results on periodontal regeneration. Placement of A-PRF clot in the extraction socket could lessen postoperative pain and increase patient comfort after third molar extraction. NCT03703479. Registered 8 October 2018 How to cite this article: Zahid TM, Nadershah M. Effect of Advanced Platelet-rich Fibrin on Wound Healing after Third Molar Extraction: A Split-mouth Randomized Double-blind Study. J Contemp Dent Pract 2019;20(10):1164-1170.


Infrastructure, programs, and policies to increase bicycling: an international review.
To assess existing research on the effects of various interventions on levels of bicycling. Interventions include infrastructure (e.g., bike lanes and parking), integration with public transport, education and marketing programs, bicycle access programs, and legal issues. A comprehensive search of peer-reviewed and non-reviewed research identified 139 studies. Study methodologies varied considerably in type and quality, with few meeting rigorous standards. Secondary data were gathered for 14 case study cities that adopted multiple interventions. Many studies show positive associations between specific interventions and levels of bicycling. The 14 case studies show that almost all cities adopting comprehensive packages of interventions experienced large increases in the number of bicycle trips and share of people bicycling. Most of the evidence examined in this review supports the crucial role of public policy in encouraging bicycling. Substantial increases in bicycling require an integrated package of many different, complementary interventions, including infrastructure provision and pro-bicycle programs, supportive land use planning, and restrictions on car use.


Effect of disodium EDTA chelation regimen on cardiovascular events in patients with previous myocardial infarction: the TACT randomized trial.
Chelation therapy with disodium EDTA has been used for more than 50 years to treat atherosclerosis without proof of efficacy. To determine if an EDTA-based chelation regimen reduces cardiovascular events. Double-blind, placebo-controlled, 2 × 2 factorial randomized trial enrolling 1708 patients aged 50 years or older who had experienced a myocardial infarction (MI) at least 6 weeks prior and had serum creatinine levels of 2.0 mg/dL or less. Participants were recruited at 134 US and Canadian sites. Enrollment began in September 2003 and follow-up took place until October 2011 (median, 55 months). Two hundred eighty-nine patients (17% of total; n=115 in the EDTA group and n=174 in the placebo group) withdrew consent during the trial. Patients were randomized to receive 40 infusions of a 500-mL chelation solution (3 g of disodium EDTA, 7 g of ascorbate, B vitamins, electrolytes, procaine, and heparin) (n=839) vs placebo (n=869) and an oral vitamin-mineral regimen vs an oral placebo. Infusions were administered weekly for 30 weeks, followed by 10 infusions 2 to 8 weeks apart. Fifteen percent discontinued infusions (n=38 [16%] in the chelation group and n=41 [15%] in the placebo group) because of adverse events. The prespecified primary end point was a composite of total mortality, recurrent MI, stroke, coronary revascularization, or hospitalization for angina. This report describes the intention-to-treat comparison of EDTA chelation vs placebo. To account for multiple interim analyses, the significance threshold required at the final analysis was P = .036. Qualifying previous MIs occurred a median of 4.6 years before enrollment. Median age was 65 years, 18% were female, 9% were nonwhite, and 31% were diabetic. The primary end point occurred in 222 (26%) of the chelation group and 261 (30%) of the placebo group (hazard ratio [HR], 0.82 [95% CI, 0.69-0.99]; P = .035). There was no effect on total mortality (chelation: 87 deaths [10%]; placebo, 93 deaths [11%]; HR, 0.93 [95% CI, 0.70-1.25]; P = .64), but the study was not powered for this comparison. The effect of EDTA chelation on the components of the primary end point other than death was of similar magnitude as its overall effect (MI: chelation, 6%; placebo, 8%; HR, 0.77 [95% CI, 0.54-1.11]; stroke: chelation, 1.2%; placebo, 1.5%; HR, 0.77 [95% CI, 0.34-1.76]; coronary revascularization: chelation, 15%; placebo, 18%; HR, 0.81 [95% CI, 0.64-1.02]; hospitalization for angina: chelation, 1.6%; placebo, 2.1%; HR, 0.72 [95% CI, 0.35-1.47]). Sensitivity analyses examining the effect of patient dropout and treatment adherence did not alter the results. Among stable patients with a history of MI, use of an intravenous chelation regimen with disodium EDTA, compared with placebo, modestly reduced the risk of adverse cardiovascular outcomes, many of which were revascularization procedures. These results provide evidence to guide further research but are not sufficient to support the routine use of chelation therapy for treatment of patients who have had an MI. clinicaltrials.gov Identifier: NCT00044213.


Value in Oral and Maxillofacial Surgery: A Systematic Review of Economic Analyses.
The purpose of this study is to describe the state of economic analyses in the field of oral and maxillofacial surgery (OMS). A systematic search of published literature up to 2016 was performed. The inclusion criteria were as follows: English-language articles on economic analyses pertaining to OMS including anesthesia and pain management; dentoalveolar surgery; orthognathic, cleft, and/or obstructive sleep apnea treatment; pathology; reconstruction; temporomandibular disorders; trauma; and other. The exclusion criteria were as follows: opinion or perspective articles, studies unrelated to OMS, nonhuman research, and implant-related studies. Cost-effectiveness analyses (CEAs), cost-utility analyses, and cost-minimization analyses (CMAs) were evaluated with the original Consolidated Health Economic Evaluation Reporting Standards (CHEERS) checklist or a modified CHEERS checklist. The search yielded 798 articles, 77 of which met the inclusion criteria (published from 1980 to 2016, 48 from the United States). There were an increasing number of studies over time (P for trend < .01). There were 7 economic studies on anesthesia and pain management (9.1%); 16 studies on dentoalveolar surgery (20.7%); 15 studies on orthognathic, cleft, and/or obstructive sleep apnea treatment (19.4%); 1 study on pathology (1.3%); 6 studies on reconstruction (7.8%); no studies on temporomandibular joint disorders and/or facial pain (0%); 20 studies on trauma (25.9%); and 12 studies categorized as other (15.5%). CEAs made up 11.7% of studies, and CMAs comprised 58.4%. Of the 9 CEAs, 55.6% were published in 2010 or later. Of the 45 CMAs, 88.6% were published in 2000 or later and 61.4% in 2010 or later. CEAs met 56.0% (range, 29.2 to 87.5%) of the CHEERS criteria, whereas CMA studies met 45.1% (range, 23.9 to 76.1%) of the modified CHEERS criteria. Only 1 study succeeded in estimating costs and health outcomes (value) of an OMS procedure. There is an increasing trend in the number of economic studies in the field of OMS. More high-quality economic evaluations are needed to demonstrate the value of OMS procedures. To determine value, future studies should compare both costs and health-related outcomes.


Diffusion-weighted MRI derived apparent diffusion coefficient identifies prognostically distinct subgroups of pediatric diffuse intrinsic pontine glioma.
While pediatric diffuse intrinsic pontine gliomas (DIPG) remain fatal, recent data have shown subgroups with distinct molecular biology and clinical behavior. We hypothesized that diffusion-weighted MRI can be used as a prognostic marker to stratify DIPG subsets with distinct clinical behavior. Apparent diffusion coefficient (ADC) values derived from diffusion-weighted MRI were computed in 20 consecutive children with treatment-naïve DIPG tumors. The median ADC for the cohort was used to stratify the tumors into low and high ADC groups. Survival, gender, therapy, and potential steroid effects were compared between the ADC groups. Median age at diagnosis was 6.6 (range 2.3-13.2) years, with median follow-up seven (range 1-36) months. There were 14 boys and six girls. Seventeen patients received radiotherapy, five received chemotherapy, and six underwent cerebrospinal fluid diversion. The median ADC of 1,295 × 10(-6) mm(2)/s for the cohort partitioned tumors into low or high diffusion groups, which had distinct median survivals of 3 and 13 months, respectively (log-rank p < 0.001). Low ADC tumors were found only in boys, whereas high ADC tumors were found in both boys and girls. Available tissue specimens in three low ADC tumors demonstrated high-grade histology, whereas one high ADC tumor demonstrated low-grade histology with a histone H3.1 K27M mutation and high-grade metastatic lesion at autopsy. ADC derived from diffusion-weighted MRI may identify prognostically distinct subgroups of pediatric DIPG.


Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets.
A key question when analyzing high throughput data is whether the information provided by the measured biological entities (gene, metabolite expression for example) is related to the experimental conditions, or, rather, to some interfering signals, such as experimental bias or artefacts. Visualization tools are therefore useful to better understand the underlying structure of the data in a 'blind' (unsupervised) way. A well-established technique to do so is Principal Component Analysis (PCA). PCA is particularly powerful if the biological question is related to the highest variance. Independent Component Analysis (ICA) has been proposed as an alternative to PCA as it optimizes an independence condition to give more meaningful components. However, neither PCA nor ICA can overcome both the high dimensionality and noisy characteristics of biological data. We propose Independent Principal Component Analysis (IPCA) that combines the advantages of both PCA and ICA. It uses ICA as a denoising process of the loading vectors produced by PCA to better highlight the important biological entities and reveal insightful patterns in the data. The result is a better clustering of the biological samples on graphical representations. In addition, a sparse version is proposed that performs an internal variable selection to identify biologically relevant features (sIPCA). On simulation studies and real data sets, we showed that IPCA offers a better visualization of the data than ICA and with a smaller number of components than PCA. Furthermore, a preliminary investigation of the list of genes selected with sIPCA demonstrate that the approach is well able to highlight relevant genes in the data with respect to the biological experiment.IPCA and sIPCA are both implemented in the R package mixomics dedicated to the analysis and exploration of high dimensional biological data sets, and on mixomics' web-interface.


Fiber-optic OCT sensor guided "SMART" micro-forceps for microsurgery.
A handheld Smart Micromanipulation Aided Robotic-surgery Tool (SMART) micro-forceps guided by a fiber-optic common-path optical coherence tomography (CP-OCT) sensor is presented. A fiber-optic CP-OCT distance and motion sensor is integrated into the shaft of a micro-forceps. The tool tip position is manipulated longitudinally through a closed loop control using a piezoelectric motor. This novel forceps design could significantly enhance safety, efficiency and surgical outcomes. The basic grasping and peeling functions of the micro-forceps are evaluated in dry phantoms and in a biological tissue model. As compared to freehand use, targeted grasping and peeling performance assisted by active tremor compensation, significantly improves micro-forceps user performance.


Learning in the Machine: Random Backpropagation and the Deep Learning Channel.
Random backpropagation (RBP) is a variant of the backpropagation algorithm for training neural networks, where the transpose of the forward matrices are replaced by fixed random matrices in the calculation of the weight updates. It is remarkable both because of its effectiveness, in spite of using random matrices to communicate error information, and because it completely removes the taxing requirement of maintaining symmetric weights in a physical neural system. To better understand random backpropagation, we first connect it to the notions of local learning and learning channels. Through this connection, we derive several alternatives to RBP, including skipped RBP (SRPB), adaptive RBP (ARBP), sparse RBP, and their combinations (e.g. ASRBP) and analyze their computational complexity. We then study their behavior through simulations using the MNIST and CIFAR-10 bechnmark datasets. These simulations show that most of these variants work robustly, almost as well as backpropagation, and that multiplication by the derivatives of the activation functions is important. As a follow-up, we study also the low-end of the number of bits required to communicate error information over the learning channel. We then provide partial intuitive explanations for some of the remarkable properties of RBP and its variations. Finally, we prove several mathematical results, including the convergence to fixed points of linear chains of arbitrary length, the convergence to fixed points of linear autoencoders with decorrelated data, the long-term existence of solutions for linear systems with a single hidden layer and convergence in special cases, and the convergence to fixed points of non-linear chains, when the derivative of the activation functions is included.


Bombesin and [Leu8]phyllolitorin promote fetal mouse lung branching morphogenesis via a receptor-mediated mechanism.
Pulmonary neuroendocrine cells are localized predominantly at airway branchpoints. Previous work showed that gastrin-releasing peptide (GRP), a major pulmonary bombesin-like peptide, occurred in neuroendocrine cells exclusively in branching human fetal airways. We now demonstrate that GRP and GRP receptor genes are expressed in fetal mouse lung as early as embryonic day 12 (E12), when lung buds are beginning to branch. By in situ hybridization, GRP receptor transcripts were at highest levels in mesenchymal cells at cleft regions of branching airways and blood vessels. To explore the possibility that bombesin-like peptides might play a role in branching morphogenesis, E12 lung buds were cultured for 48 hr in serum-free medium. In the presence of 0.10-10 microM bombesin, branching was significantly augmented as compared with control cultures, with a peak of 94% above control values at 1 microM (P < 0.005). The bombesin receptor antagonist [Leu13- psi(CH2NH)Leu14]bombesin alone (100 nM) had no effect on baseline branching but completely abolished bombesin-induced branching. A bombesin-related peptide, [Leu8]phyllolitorin also increased branching (65% above control values at 10 nM, P < 0.005). [Leu8]Phyllolitorin also significantly augmented thymidine incorporation in cultured lung buds. Fibronectin, which is abundant at branchpoints, induces GRP gene expression in undifferentiated cell lines. These observations suggest that BLPs secreted by pulmonary neuroendocrine cells may contribute to lung branching morphogenesis. Furthermore, components of branchpoints may induce pulmonary neuroendocrine cell differentiation as part of a positive feedback loop, which could account in part for the high prevalence of these cells at branchpoints.


Theanaphthoquinone inhibits fatty acid synthase expression in EGF-stimulated human breast cancer cells via the regulation of EGFR/ErbB-2 signaling.
Fatty acid synthase (FAS) is a major lipogenic enzyme catalyzing the synthesis of long-chain saturated fatty acids. Most breast cancers require lipogenesis for growth. Here, we demonstrated the effects of theanaphthoquinone (TNQ), a member of the thearubigins generated by the oxidation of theaflavin (TF-1), on the expression of FAS in human breast cancer cells. TNQ was found to suppress the EGF-induced expression of FAS mRNA and FAS protein in MDA-MB-231 cells. Expression of FAS has previously been shown to be regulated by the SREBP family of transcription factors. In this study, we demonstrated that the EGF-induced nuclear translocation of SREBP-1 was blocked by TNQ. Moreover, TNQ also modulated EGF-induced ERK1/2 and Akt phosphorylation. Treatment of MDA-MB-231 cells with PI 3-kinase inhibitors, LY294002 and Wortmannin, inhibited the EGF-induced expression of FAS and nuclear translocation of SREBP-1. Treatment with TNQ inhibited EGF-induced EGFR/ErbB-2 phosphorylation and dimerization. Furthermore, treatment with kinase inhibitors of EGFR and ErbB-2 suggested that EGFR/ErbB-2 activation was involved in EGF-induced FAS expression. In constitutive FAS expression, TNQ inhibited FAS expression and Akt autophosphorylation in BT-474 cells. The PI 3-kinase inhibitors and tyrosine kinase inhibitors of EGFR and ErbB-2 also reduced constitutive FAS expression. In addition, pharmacological blockade of FAS by TNQ decreased cell viability and induced cell death in BT-474 cells. In summary, our findings suggest that TNQ modulates FAS expression by the regulation of EGFR/ErbB-2 pathways and induces cell death in breast cancer cells.


Between- and within-subject variance of motor variability metrics in females performing repetitive upper-extremity precision work.
Kinematic motor variability is extensively studied in occupational, clinical and sports biomechanics, but the consistency of most motor variability metrics have never been reported. In this study, fourteen subjects performed a repetitive pipetting task on three separate days. Movements of hand, arm and pipette tip were recorded in 3D and used to compute shoulder elevation, elbow flexion and shoulder-arm coordination angles, as well as pipette-tip endpoint precision. Cycle-to-cycle motor variability was quantified using linear dispersion measures of standard kinematics properties such as peak velocity, range of motion, and inter-segmental relative phase. Between- and within-subject consistencies of these variability metrics were quantified by variance components estimated using a nested random effects model. For most metrics, the variance between subjects was larger than that between days and cycles. Entering the variance components in statistical power equations showed that for most metrics, a total of 80-100 subjects will be required to detect a 20% difference between two groups with sufficient power, while this difference can typically be detected in repeated-measures (paired) designs using 25 subjects. The reported between and within-subject variance components can be used as a data base to facilitate efficient designs of future studies of kinematic motor variability.


A randomised controlled trial of a self-management plan for patients with newly diagnosed angina.
There are approximately 1.8 million patients with angina in the United Kingdom, many of whom report a poor quality of life, including raised levels of anxiety and depression. To evaluate the effect of a cognitive behavioural disease management programme, the Angina Plan, on psychological adjustment in patients newly diagnosed with angina pectoris. Randomised controlled trial. Patients from GP practices in a Northern UK city (York) between April 1999 and May 2000. Recruited patients were randomised to receive the Angina Plan or to a routine, practice nurse-led secondary prevention educational session. Twenty of the 25 practices invited to join the study supplied patients' names; 142 patients attended an assessment clinic and were randomised There were no significant differences in any baseline measures. At the six month post-treatment follow-up, 130 (91%) patients were reassessed. When compared with the educational session patients (using analysis of covariance adjusted for baseline scores in an intention-to-treat analysis) Angina Plan patients showed a greater reduction in anxiety (P = 0.05) and depression (P = 0.01), the frequency of angina (reduced by three episodes per week, versus a reduction of 0.4 per week, P = 0.016) the use of glyceryl trinitrate (reduced by 4.19 fewer doses per week versus a reduction of 0.59 per week, P = 0.018), and physical limitations (P<0.001: Seattle Angina Questionnaire). They were also more likely to report having changed their diet (41 versus 21, P<0.001) and increased their daily walking (30 versus 2, P<0.001). There was no significant difference between the groups on the other sub-scales of the Seattle Angina Questionnaire or in any of the medical variables measured. The Angina Plan appears to improve the psychological, symptomatic, and functional status of patients newly diagnosed with angina.


Pluralism as Outcome: The Ecology of Religious Resources, Suppliers, and Consumers.
A great deal of interest has surrounded the topic of religious pluralism and the effects of the frequently used pluralism index on outcomes such as religious participation rates. But surprisingly little work has tried to understand the sources of pluralism or what the pluralism index is actually measuring. In an attempt to reframe the debate, we treat pluralism as an outcome variable. Drawing on ideas in the organizational ecology literature and data from previous studies on pluralism and participation, we show that the pluralism of religious suppliers is a product of the pluralism of religious preferences and the number of potential adherents within an environment. This pluralism of suppliers, in turn, produces a pluralism of religious consumers. We then distinguish between expected pluralism and observed pluralism, and we argue that a relationship between pluralism and participation will be expected only when a meaningful gap between these two measures exists. We close by examining the previous research to show how this reframing of the pluralism and participation question sheds light on that literature.


Small bowel obstruction following restorative proctocolectomy: affected by a laparoscopic approach?
Total proctocolectomy with ileal pouch-anal anastomosis (IPAA) is the gold standard surgical treatment for chronic ulcerative colitis. More recently, this procedure is being performed laparoscopically assisted. Postoperatively, small bowel obstruction (SBO) is one of the more common associated complications. However, it is unknown whether the addition of a laparoscopic approach has changed this risk. This study aims to assess and compare the incidence of SBOs after both open and laparoscopic restorative proctocolectomy. All subjects who underwent restorative proctocolectomy from 1998-2008 were identified from a prospective Colorectal Surgery Database. Medical records were reviewed for all cases of SBO, confirmed by a combination of clinical symptoms and radiologic evidence. Comparisons were made between laparoscopic and open approaches. The incidence of SBO was also subdivided into pre-ileostomy takedown, early post-ileostomy takedown (30 d post), and late post-ileostomy takedown (30 d to 1 y post). Several potential risk factors were also evaluated. Statistical analysis was performed utilizing Fisher's exact (for incidence) or t-tests (for means). Significance was defined as P < 0.05 A total of 290 open cases and 100 laparoscopic cases were identified during this time period. The overall incidence of SBO at 1 y post-ileostomy takedown was 14% (n = 42) in the open group and 16% (n = 16) laparoscopic (P = NS). In the pre-ileostomy takedown period the incidence of SBO was 7% (n = 21) open and 13% (n = 13) laparoscopic (P = NS). While in the post-takedown period, the early incidence was 4% (n = 12) open and 1% (n = 1) laparoscopic and late incidence was 3% (n = 9) open and 2% (n = 2) laparoscopic (P = NS). Factors associated with an increased risk of SBO include coronary artery disease, prior appendectomy and W and J pouch configurations. The burden of postoperative small bowel obstruction after restorative proctocolectomy is not changed with a laparoscopic approach. Most cases occur in the early postoperative period, especially prior to ileostomy reversal.


Using e-mail recruitment and an online questionnaire to establish effect size: A worked example.
Sample size calculations require effect size estimations. Sometimes, effect size estimations and standard deviation may not be readily available, particularly if efficacy is unknown because the intervention is new or developing, or the trial targets a new population. In such cases, one way to estimate the effect size is to gather expert opinion. This paper reports the use of a simple strategy to gather expert opinion to estimate a suitable effect size to use in a sample size calculation. Researchers involved in the design and analysis of clinical trials were identified at the University of Birmingham and via the MRC Hubs for Trials Methodology Research. An email invited them to participate.An online questionnaire was developed using the free online tool 'Survey Monkey©'. The questionnaire described an intervention, an electronic participant information sheet (e-PIS), which may increase recruitment rates to a trial. Respondents were asked how much they would need to see recruitment rates increased by, based on 90%. 70%, 50% and 30% baseline rates, (in a hypothetical study) before they would consider using an e-PIS in their research.Analyses comprised simple descriptive statistics. The invitation to participate was sent to 122 people; 7 responded to say they were not involved in trial design and could not complete the questionnaire, 64 attempted it, 26 failed to complete it. Thirty-eight people completed the questionnaire and were included in the analysis (response rate 33%; 38/115). Of those who completed the questionnaire 44.7% (17/38) were at the academic grade of research fellow 26.3% (10/38) senior research fellow, and 28.9% (11/38) professor. Dependent upon the baseline recruitment rates presented in the questionnaire, participants wanted recruitment rate to increase from 6.9% to 28.9% before they would consider using the intervention. This paper has shown that in situations where effect size estimations cannot be collected from previous research, opinions from researchers and trialists can be quickly and easily collected by conducting a simple study using email recruitment and an online questionnaire. The results collected from the survey were successfully used in sample size calculations for a PhD research study protocol.


Structural characteristics of immunogenic liver-stage antigens derived from P. falciparum malarial proteins.
A fully effective antimalarial vaccine must contain multiple proteins from the different development stages of Plasmodium falciparum parasites involved in host-cell invasion or their biologically active fragments. It must therefore include sporozoite molecules able to induce protective immunity by blocking the parasite's access to hepatic cells, and/or proteins involved in the development of this stage, amongst which are included the Liver Stage Antigen-1 (LSA-1) and the Sporozoite and Liver Stage Antigen (SALSA). Our studies have focused on the search for an association between the structure of high activity binding peptides (HABPs), including both conserved native and their modified analogues, and their ability to bind to the MHC Class II HLA-DR molecules during formation of the MHCII-peptide-TCR complex leading to inducing the appropriate immune response. These studies are part of a logical and rational strategy for developing multi-stage, multi-component, minimal subunit-based vaccines, mainly against the P. falciparum malaria.


Excessive Treadmill Training Enhances Brain-Specific MicroRNA-34a in the Mouse Hippocampus.
Background: An imbalance between total training load and total recovery may cause overtraining (OT). The purpose of the present study was to verify the effects of OT on the expression of brain-derived neurotrophic factor (BDNF), its receptor tropomyosin receptor kinase B (TrkB) and p75 and the dynamic expression patterns of brain-specific miR-34a and miR-124 or inflammation-related miR-21 and miR-132 in the mouse hippocampus. Method: Eight weeks old C57BL/6J mice were randomly assigned to the control (CON), normal training (NT) and OT groups. An 8-week OT training protocol was applied to evaluate the phenotype of mice endurance (incremental load test, ILT) and cognitive capacity (Morris water maze test). We used qRT-PCR and immunoblotting to detect changes in the molecular level of hippocampal samples. Result: Compared with the CON, both NT and OT decreased bodyweight after 8-week training. After 8-week of training, NT increased the exhaustion velocity (EV) while the EV of OT was lower than NT. Mice in NT decreased the escape latency than CON. The percentage of time spent in the probe quadrant and the number of crossing platform times in NT were higher than CON and OT. The BDNF, p75 and TrkB mRNA levels were increased in NT than CON, only the p75 mRNA was increased in OT. The NT exhibited increased protein levels of BDNF and TrkB compared to CON. The protein expression of BDNF was decreased in OT than NT and CON. The protein level of p75 in the OT was higher than in NT and CON. In addition, the phosphorylation level of TrkB in OT was higher than CON and NT. Only the miR-34a level was increased in the OT. Moreover, the expression of miR-34a was found to be negatively correlated with the expression of BDNF, and the increase in miR-34a level was accompanied by a decrease in performance. Conclusion: In summary, the training-evoked increase in the BDNF level may help to improve performance, whereas this conditioning is lost after OT. Moreover, miR-34a potentially mediated changes in the expression of BDNF and may reflect the decrease in performance after OT.


Contingent adaptation in masking and surround suppression.
Adaptation is the process that changes a neuron's response based on recent inputs. In the traditional model, a neuron's state of adaptation depends on the recent input to that neuron alone, whereas in a recently introduced model (Hebbian normalization), adaptation depends on the structure of neural correlated firing. In particular, increased response products between pairs of neurons leads to increased mutual suppression. We test a psychophysical prediction of this model: adaptation should depend on 2nd-order statistics of input stimuli. That is, if two stimuli excite two distinct sub-populations of neurons, then presenting those stimuli simultaneously during adaptation should strengthen mutual suppression between those subpopulations. We confirm this prediction in two experiments. In the first, pairing two gratings synchronously during adaptation (i.e., a plaid) rather than asynchronously (interleaving the two gratings in time) leads to increased effectiveness of one pattern for masking the other. In the second, pairing the gratings in a center-surround configuration results in reduced apparent contrast for the central grating when paired with the same surround (as compared with a condition in which the central grating appears with a different surround at test than during adaptation). These results are consistent with the prediction that an increase in response covariance leads to greater mutual suppression between neurons. This effect is detectable both at threshold (masking) and well above threshold (apparent contrast).


Identification of Helicobacter spp. in bile and gallbladder tissue of patients with symptomatic gallbladder disease.
This experimental study was designed to determine if Helicobacter spp. contribute to benign gallbladder disease using polymerase chain reaction (PCR) methods. Patients with benign gallbladder disease scheduled for elective cholecystectomy at New York University Langone Medical Center were recruited from February to May 2008. Bile, gallbladder tissue and gallstones were collected. DNA was isolated from these specimens and amplified via PCR using C97F and C98R primers specific for Helicobacter spp. Appropriate positive and negative controls were used. Products were analysed with agarose gel electrophoresis, sequenced and results aligned using sequencher. Plasma was collected for detection of anti-Helicobacter pylori antibodies via enzyme-linked immunosorbent assay. Of 36 patients, 12 patients' bile and/or tissue were positive for Helicobacter spp. by PCR. Species were most homologous with H. pylori, although other Helicobacter spp. were suggested. Six of 12 patients demonstrated anti-Helicobacter antibodies in plasma, suggesting that the remaining six might have demonstrated other species besides H. pylori. Four of six plasma samples with anti-Helicobacter antibodies were anti-CagA (cytotoxin associated gene) negative. Helicobacter spp. can be detected in bile and gallbladder tissue of patients with benign gallbladder disease. The contribution of these bacteria to the pathophysiology of gallbladder disease and gallstone formation requires further study.


The impact of an electronic nursing documentation system on efficiency of documentation by caregivers in a residential aged care facility.
To examine the effect of the introduction of an electronic nursing documentation system on the efficiency of documentation in a residential aged care facility. Modern technology has the potential to free caregivers in residential aged care facilities from their burden of paper documentation and allow them more time to care for residents. To date, there is inadequate evidence to verify this assumption. Longitudinal cohort study with work sampling method for data collection. This study was conducted between 2009-2011; two months before and 3, 6, 12 and 23 months after implementation of an electronic documentation system. A work classification tool was used by an observer to record documentation activities being performed on paper or on a computer by the caregivers. When compared with the proportion of time caregivers spent on documentation in the preimplementation period, personal carers' proportion reduced at three months after implementation. The proportion increased from six months and then dropped at 23 months. Recreational activity officers' proportion increased at three months after implementation. It stabilised at six months and increased again at 12 months. At 23 months, the proportion returned to the preimplementation level. Less than half of the caregivers' time on documentation after implementation was associated with computer-related tasks. Introduction of an electronic documentation system may not necessarily lead to efficiency in documentation for the caregivers. Charting some information items on paper and others on a computer may hinder realization of documentation efficiency. To optimise the efficiency benefit of electronic documentation in a residential aged care facility, it is not only necessary to automate all nursing forms but also to ensure that the system is aligned with caregivers' documentation practice. Continuous education and mentor support is essential to ensure caregivers' effective usage of the electronic system.


Laser desorption single-conformation UV and IR spectroscopy of the sulfonamide drug sulfanilamide, the sulfanilamide-water complex, and the sulfanilamide dimer.
We have studied the conformational preferences of the sulfonamide drug sulfanilamide, its dimer, and its monohydrated complex through laser desorption single-conformation UV and IR spectroscopy in a molecular beam. Based on potential energy curves for the inversion of the anilinic and the sulfonamide NH2 groups calculated at DFT level, we suggest that the zero-point level wave function of the sulfanilamide monomer is appreciably delocalized over all four conformer wells. The sulfanilamide dimer, and the monohydrated complex each exhibit a single isomer in the molecular beam. The isomeric structures of the sulfanilamide dimer and the monohydrated sulfanilamide complex were assigned based on their conformer-specific IR spectra in the NH and OH stretch region. Quantum Theory of Atoms in Molecules (QTAIM) analysis of the calculated electron density in the water complex suggests that the water molecule is bound side-on in a hydrogen bonding pocket, donating one O-HO[double bond, length as m-dash]S hydrogen bond and accepting two hydrogen bonds, a NHO and a CHO hydrogen bond. QTAIM analysis of the dimer electron density suggests that the Ci symmetry dimer structure exhibits two dominating N-HO[double bond, length as m-dash]S hydrogen bonds, and three weaker types of interactions: two CHO bonds, two CHN bonds, and a chalcogen OO interaction. Most interestingly, the molecular beam dimer structure closely resembles the R dimer unit - the dimer unit with the greatest interaction energy - of the α, γ, and δ crystal polymorphs. Interacting Quantum Atoms analysis provides evidence that the total intermolecular interaction in the dimer is dominated by the short-range exchange-correlation contribution.


Abnormal lipid peroxidation in patients with sleep apnoea.
The prevalence of cardiovascular diseases is increased in patients with the obstructive sleep apnoea syndrome (OSAS). The fall and rise of arterial oxygenation that follows each apnoea may increase lipid peroxidation and contributes to explaining this association. In the present study, the authors determined lipid peroxidation in patients with OSAS and the effect of treatment with continuous positive airway pressure (CPAP). Fourteen male patients with severe OSAS (59+/-5 apnoea x h(-1)) (+/-SEM) and 13 healthy nonsmoking, male volunteers of similar age were studied. Patients were studied at diagnosis and after treatment with CPAP for more than 1 yr (>4 h x night(-1)). A venous blood sample was obtained early in the morning after fasting all night. In patients with OSAS, a sample before and during sleep was also obtained. Low density lipoprotein (LDL) particles were isolated by sequential ultracentrifugation. Their level of oxidation was determined by the thiobarbituric acid assay (TBARs), and their susceptibility to oxidation by the lag phase measurement. Patients with OSAS showed higher TBARs (28.1+/-2.8 versus 20.0+/-1.8 nmol x malondialdehyde x mgLDL protein(-1), p=0.02) and shorter lag phase values (83.8+/-3.4 versus 99.7+/-3.4 min, p=0.005) than controls. These differences were not due to the smoking status of the patient. Likewise, these values did not change significantly throughout the night yet, the lag phase value was significantly improved by treatment with CPAP (124.9+/-8.5 min; p<0.001). These results indicate that obstructive sleep apnoea syndrome is associated with abnormal lipid peroxidation and that this is improved by chronic use of Continuous positive airway pressure. These results can contribute towards explaining the high prevalence of cardiovascular diseases seen in Obstructive sleep apnoea syndrome.


Copy number polymorphisms and anticancer pharmacogenomics.
Recent studies have investigated the contribution of copy number variants (CNVs) to disease susceptibility in a multitude of complex disorders, including systemic lupus erythematosus, Crohn's disease, and various neurodevelopmental disorders. Relatively few CNV studies, however, have been conducted on pharmacologic phenotypes even though these structural variants are likely to play an important role. We developed a genome-wide method to identify CNVs that contribute to heterogeneity in drug response, focusing on drugs that are widely used in anticancer treatment regimens. We conducted a comprehensive genome-wide study of CNVs from population-scale array-based and sequencing-based surveys by analyzing their effect on cellular sensitivity to platinating agents and topoisomerase II inhibitors. We identified extensive CNV regions associated with cellular sensitivity to functionally diverse chemotherapeutics, supporting the hypothesis that variation in copy number contributes to variation in drug response. Interestingly, although single nucleotide polymorphisms (SNPs) tag some of the CNVs associated with drug sensitivity, several of the most significant CNV-drug associations are independent of SNPs; consequently, they represent genetic variations that have not been previously interrogated by SNP studies of pharmacologic phenotypes. Our findings demonstrate that pharmacogenomic studies may greatly benefit from the study of CNVs as expression quantitative trait loci, thus contributing broadly to our understanding of the complex traits genetics of CNVs. We also extend our PACdb resource, a database that makes available to the scientific community relationships between genetic variation, gene expression, and sensitivity to various drugs in cell-based models.


A review of nicotine-containing electronic cigarettes-Trends in use, effects, contents, labelling accuracy and detection methods.
Electronic cigarettes (ECs) are thought to be less harmful than traditional combustible cigarettes and were originally intended to help smokers quit. Over the past two decades, they have especially gained popularity with the younger generation. To date, there are over 7000 unique e-liquid flavours available and over 400 different e-cigarette brands. The accuracy of nicotine strength labelling in e-liquids was assessed in this work. Twenty-three studies from around the world were chosen to assess the level and frequency of nicotine mislabelling in 545 e-liquid products. Nicotine strengths were most commonly mislabelled by between 5% and 20%, with the majority testing lower than what the label indicated. Fifteen European e-liquids that were assessed were labelled as 20 mg/ml or less, yet when tested, they contained more than 20 mg/ml of nicotine. One e-liquid that was supposed to contain no nicotine in fact contained 23.91 mg/ml of nicotine. Furthermore, the difference between the medians of the available labelled and experimental nicotine concentrations was significant (p < 0.001, Wilcoxon signed rank test). Preliminary studies show that high nicotine levels delivered via aerosol increase the risk for nicotine poisoning and cause airway inflammation. Other EC ingredients, such as flavourings, contribute to EVALI and 'popcorn lung'. There is evidence that certain flavourings, such as menthol, reinforce the effects of nicotine and modify drug absorption and metabolism. There is a global need for better quality control in EC products in order to make these safe for consumers.


Fibrinogen nitrotyrosination after ischemic stroke impairs thrombolysis and promotes neuronal death.
Ischemic stroke is an acute vascular event that compromises neuronal viability, and identification of the pathophysiological mechanisms is critical for its correct management. Ischemia produces increased nitric oxide synthesis to recover blood flow but also induces a free radical burst. Nitric oxide and superoxide anion react to generate peroxynitrite that nitrates tyrosines. We found that fibrinogen nitrotyrosination was detected in plasma after the initiation of ischemic stroke in human patients. Electron microscopy and protein intrinsic fluorescence showed that in vitro nitrotyrosination of fibrinogen affected its structure. Thromboelastography showed that initially fibrinogen nitrotyrosination retarded clot formation but later made the clot more resistant to fibrinolysis. This result was independent of any effect on thrombin production. Immunofluorescence analysis of affected human brain areas also showed that both fibrinogen and nitrotyrosinated fibrinogen spread into the brain parenchyma after ischemic stroke. Therefore, we assayed the toxicity of fibrinogen and nitrotyrosinated fibrinogen in a human neuroblastoma cell line. For that purpose we measured the activity of caspase-3, a key enzyme in the apoptotic pathway, and cell survival. We found that nitrotyrosinated fibrinogen induced higher activation of caspase 3. Accordingly, cell survival assays showed a more neurotoxic effect of nitrotyrosinated fibrinogen at all concentrations tested. In summary, nitrotyrosinated fibrinogen would be of pathophysiological interest in ischemic stroke due to both its impact on hemostasis - it impairs thrombolysis, the main target in stroke treatments - and its neurotoxicity that would contribute to the death of the brain tissue surrounding the infarcted area.


Gene copy number change events at chromosome 20 and their association with recurrence in gastric cancer patients.
This study examined the gene copy number change events at chromosome 20 in gastric cancer, and their possible relationship with recurrence using cDNA microarray-based comparative genomic hybridization. Thirty pairs of gastric tumor and normal gastric tissues were used in the cDNA microarray-based comparative genomic hybridization. The cDNA microarrays containing 17,000 sequence-verified human gene probes were used in a direct comparison design, where genomic DNAs from the normal and tumor tissues were labeled with fluorescent dyes Cy3 and Cy5, respectively, and cohybridized. Genes with log(2) (Cy5/Cy3) > or = 0.58 in at least one case were selected as the amplified genes. In order to search for the association between gene copy number changes and the recurrence status, patients were grouped according to their recurrence status. Gene selection between the two groups was done, and each patient was given a score based on the sum of the selected genes' ratios. Logistic regression analysis was carried out in order to determine if the score of a group of patients was correlated with a recurrence. A group of genes including NCOA6, CYP24A1, PTPN1, and ZNF217 was amplified in gastric cancer. Another group of 39 genes, whose sum of copy number change levels was significantly associated with a poor prognosis for recurrence, was selected (P < 0.05). Ninety-six amplified genes at chromosome 20 of gastric cancer are reported. A scoring system based on gene copy changes at chromosome 20 can provide an independent patient grouping system that can distinguish patient recurrence status and survival.


Dynamic clustering of dynamin-amphiphysin helices regulates membrane constriction and fission coupled with GTP hydrolysis.
Dynamin is a mechanochemical GTPase essential for membrane fission during clathrin-mediated endocytosis. Dynamin forms helical complexes at the neck of clathrin-coated pits and their structural changes coupled with GTP hydrolysis drive membrane fission. Dynamin and its binding protein amphiphysin cooperatively regulate membrane remodeling during the fission, but its precise mechanism remains elusive. In this study, we analyzed structural changes of dynamin-amphiphysin complexes during the membrane fission using electron microscopy (EM) and high-speed atomic force microscopy (HS-AFM). Interestingly, HS-AFM analyses show that the dynamin-amphiphysin helices are rearranged to form clusters upon GTP hydrolysis and membrane constriction occurs at protein-uncoated regions flanking the clusters. We also show a novel function of amphiphysin in size control of the clusters to enhance biogenesis of endocytic vesicles. Our approaches using combination of EM and HS-AFM clearly demonstrate new mechanistic insights into the dynamics of dynamin-amphiphysin complexes during membrane fission.


How much do soil and water contribute to the composition of meat? A case study: meat from three areas of Argentina.
The main goal of this study was to propose a reliable method to verify the geographical origin of meat, establishing the influence of soil and water on its isotopic and elemental composition. Thus, beef meat, soil, and water samples were collected from three major cattle-producing regions of Argentina (Buenos Aires, Córdoba, and Entre Ríos). Multielemental composition was determined on these three matrices by inductively coupled plasma mass spectrometry (ICP-MS), δ(13)C and δ(15)N by isotope-ratio mass spectrometry (IRMS), and the (87)Sr/(86)Sr ratio by thermal ionization mass spectrometry (TIMS). Soil and drinking water samples could be characterized and clearly differentiated by combining the isotopic ratios and elements, demonstrating differences in geology and climatic conditions of three regions. Similarly, meat originating at each sampling area was characterized and differentiated using only five key variables (Rb, Ca/Sr, δ(13)C, δ(15)N, and (87)Sr/(86)Sr). Generalized procrustes analysis (GPA), using the three studied matrices (soil, water, and meat) shows consensus between them and clear differences between studied areas. Furthermore, canonical correlation analysis (CCA) demonstrates significant correlation between the chemical-isotopic profile of meat with those corresponding to both soil and water (r(2) = 0.93, p < 0.001; and r(2) = 0.83, p < 0.001, respectively). So far, there are clear coincidences between the meat fingerprint and those from soil/water where cattle grew, presenting a good method to establish beef provenance. To the authors' knowledge this is the first report linking the influence of soil and water all together on the composition of beef, presenting the basis for the authentication of Argentinean beef, which could be extended to meat from different provenances.


Fast and SNP-tolerant detection of complex variants and splicing in short reads.
Next-generation sequencing captures sequence differences in reads relative to a reference genome or transcriptome, including splicing events and complex variants involving multiple mismatches and long indels. We present computational methods for fast detection of complex variants and splicing in short reads, based on a successively constrained search process of merging and filtering position lists from a genomic index. Our methods are implemented in GSNAP (Genomic Short-read Nucleotide Alignment Program), which can align both single- and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for the study of methylation state. In comparison testing, GSNAP has speeds comparable to existing programs, especially in reads of > or=70 nt and is fastest in detecting complex variants with four or more mismatches or insertions of 1-9 nt and deletions of 1-30 nt. Although SNP tolerance does not increase alignment yield substantially, it affects alignment results in 7-8% of transcriptional reads, typically by revealing alternate genomic mappings for a read. Simulations of bisulfite-converted DNA show a decrease in identifying genomic positions uniquely in 6% of 36 nt reads and 3% of 70 nt reads. Source code in C and utility programs in Perl are freely available for download as part of the GMAP package at http://share.gene.com/gmap.


Assessment of a cancer screening program.
Several Asian countries are implementing nationwide cancer screening programs. Assessment of the effectiveness of these programs is critical to their success as this is the only way to ensure that the benefits of screening outweigh the harms. In this paper we focus on colorectal cancer (CRC) screening to illustrate the principles of screening program assessment. The International Agency for Research on Cancer (IARC) has defined organized screening, distinguishing it from opportunistic screening. The key advantage of organized screening is that it provides greater protection against the possible harms of screening. Since screening is a process, not simply a test, the effectiveness of a program depends on the quality of each step in the cancer screening process. The evaluation of long-term screening program outcomes (CRC incidence and mortality) will not be observable for many years, given the time it takes to plan, pilot and implement a program. However, early performance indicators of the impact of screening should be monitored to give an early indication whether the program is on track. The European Union (EU) has recommended a minimum dataset to be collected and reported regularly by a screening program. Using information from these data tables, early performance indicators can be generated (e.g., participation rate, proportion of screen-detected cancers that are early-stage). Subsequently, modeling the natural history of the disease can be very helpful to estimate long-term outcomes, making use of these directly measured early performance indicators. Modeling can also be used to estimate the cost-effectiveness of a screening program and the potential impact of changes in policy, as illustrated by its recent use in the Netherlands to change the definition of a positive fecal immunochemical test (FIT) for the CRC screening program. Programs should consider modeling as an important component of screening program evaluation.


Design and synthesis of analogues of natural products.
In this article strategies for the design and synthesis of natural product analogues are summarized and illustrated with some selected examples. Proven strategies include diverted total synthesis (DTS), function-oriented synthesis (FOS), biology-oriented synthesis (BIOS), complexity to diversity (CtD), hybrid molecules, and biosynthesis inspired synthesis. The latter includes mutasynthesis, the synthesis of natural products encoded by silent genes, and propionate scanning. Most of the examples from our group fall in the quite general concept of DTS. Thus, in case an efficient strategy to a natural product is at hand, modifications are possible at almost any stage of a synthesis. However, even for compounds of moderate complexity, organic synthesis remains a bottle neck. Unless some method for predicting the biological activity of a designed molecule becomes available, the design and synthesis of natural product analogues will remain what it is now, namely it will largely rely on trial and error.


The role of hyperhomocysteinemia as well as folate, vitamin B(6) and B(12) deficiencies in osteoporosis: a systematic review.
Hyperhomocysteinemia (HHCY) has been suggested as a new risk factor for osteoporosis. Recent epidemiological, clinical and experimental studies provide a growing body of data, which is reviewed in this article. Epidemiological and (randomized) clinical trials suggest that HHCY increases fracture risk, but has minor effects on bone mineral density. Measurement of biochemical bone turnover markers indicates a shift of bone metabolism towards bone resorption. Animal studies confirm these observations showing a reduced bone quality and stimulation of bone resorption in hyperhomocysteinemic animals. Homocysteine (HCY) has been found to accumulate in bone by collagen binding. Cell culture studies demonstrate that high HCY levels stimulate osteoclasts but not osteoblasts, indicating again a shift of bone metabolism towards bone resorption. Regarding B-vitamins, only a few in vivo studies with equivocal results have been published. However, two large cell culture studies confirm the results obtained with exogenous HCY administration. In addition, HHCY seems to have adverse affects on extracellular bone matrix by disturbing collagen crosslinking. In conclusion, existing data suggest that HHCY (and possibly B-vitamin deficiencies) adversely affects bone quality by a stimulation of bone resorption and disturbance of collagen crosslinking.


Enrichment of immunoregulatory proteins in the biomolecular corona of nanoparticles within human respiratory tract lining fluid.
When inhaled nanoparticles deposit in the lungs, they transit through respiratory tract lining fluid (RTLF) acquiring a biomolecular corona reflecting the interaction of the RTLF with the nanomaterial surface. Label-free snapshot proteomics was used to generate semi-quantitative profiles of corona proteins formed around silica (SiO2) and poly(vinyl) acetate (PVAc) nanoparticles in RTLF, the latter employed as an archetype drug delivery vehicle. The evolved PVAc corona was significantly enriched compared to that observed on SiO2 nanoparticles (698 vs. 429 proteins identified); however both coronas contained a substantial contribution from innate immunity proteins, including surfactant protein A, napsin A and complement (C1q and C3) proteins. Functional protein classification supports the hypothesis that corona formation in RTLF constitutes opsonisation, preparing particles for phagocytosis and clearance from the lungs. These data highlight how an understanding of the evolved corona is necessary for the design of inhaled nanomedicines with acceptable safety and tailored clearance profiles. Inhaled nanoparticles often acquire a layer of protein corona while they go through the respiratory tract. Here, the authors investigated the identity of these proteins. The proper identification would improve the understanding of the use of inhaled nanoparticles in future therapeutics.


Microarray-based optimization to detect genomic deletion mutations.
We performed array comparative genome hybridization (aCGH) analyses of five Arabidopsis thaliana mutants with genomic deletions ranging in size from 4 bp to > 5 kb. We used the Roche NimbleGen Arabidopsis CGH 3 × 720 K whole genome custom tiling array to optimize deletion detection. Details of the microarray design and hybridization data have been deposited at the NCBI GEO repository with accession number GSE55327.


Electrospun Orodispersible Films of Isoniazid for Pediatric Tuberculosis Treatment.
Child-appropriate dosage forms are critical in promoting adherence and effective pharmacotherapy in pediatric patients, especially those undergoing long-term treatment in low-resource settings. The present study aimed to develop orodispersible films (ODFs) for isoniazid administration to children exposed to tuberculosis. The ODFs were produced from the aqueous solutions of natural and semi-synthetic polymer blends using electrospinning. The spinning solutions and the resulting fibers were physicochemically characterized, and the disintegration time and isoniazid release from the ODFs were assessed in simulated salivary fluid. The ODFs comprised of nanofibers with adequate thermal stability and possible drug amorphization. Film disintegration occurred instantly upon contact with simulated salivary fluid within less than 15 s, and isoniazid release from the ODFs in the same medium followed after the disintegration profiles, achieving rapid and total drug release within less than 60 s. The ease of administration and favorable drug loading and release properties of the ODFs may provide a dosage form able to facilitate proper adherence to treatment within the pediatric patient population.


Predicting dementia with routine care EMR data.
Our aim is to develop a machine learning (ML) model that can predict dementia in a general patient population from multiple health care institutions one year and three years prior to the onset of the disease without any additional monitoring or screening. The purpose of the model is to automate the cost-effective, non-invasive, digital pre-screening of patients at risk for dementia. Towards this purpose, routine care data, which is widely available through Electronic Medical Record (EMR) systems is used as a data source. These data embody a rich knowledge and make related medical applications easy to deploy at scale in a cost-effective manner. Specifically, the model is trained by using structured and unstructured data from three EMR data sets: diagnosis, prescriptions, and medical notes. Each of these three data sets is used to construct an individual model along with a combined model which is derived by using all three data sets. Human-interpretable data processing and ML techniques are selected in order to facilitate adoption of the proposed model by health care providers from multiple institutions. The results show that the combined model is generalizable across multiple institutions and is able to predict dementia within one year of its onset with an accuracy of nearly 80% despite the fact that it was trained using routine care data. Moreover, the analysis of the models identified important predictors for dementia. Some of these predictors (e.g., age and hypertensive disorders) are already confirmed by the literature while others, especially the ones derived from the unstructured medical notes, require further clinical analysis.


Role of the transcription factor sox4 in insulin secretion and impaired glucose tolerance.
To identify, map, clone, and functionally validate a novel mouse model for impaired glucose tolerance and insulin secretion. Haploinsufficiency of the insulin receptor and associated mild insulin resistance has been used to sensitize an N-ethyl-N-nitrosourea (ENU) screen to identify novel mutations resulting in impaired glucose tolerance and diabetes. The new impaired glucose tolerance 4 (IGT4) model was selected using an intraperitoneal glucose tolerance test and inheritance of the phenotype confirmed by generation of backcross progeny. Segregation of the phenotype was correlated with genotype information to map the location of the gene and candidates sequenced for mutations. The function of the SRY-related high mobility group (HMG)-box 4 (Sox4) gene in insulin secretion was tested using another ENU allele and by small interfering RNA silencing in insulinoma cells. We describe two allelic autosomal dominant mutations in the highly conserved HMG box of the transcription factor Sox4. Previously associated with pancreas development, Sox4 mutations in the adult mouse result in an insulin secretory defect, which exhibits impaired glucose tolerance in association with insulin receptor(+/-)-induced insulin resistance. Elimination of the Sox4 transcript in INS1 and Min6 cells resulted in the abolition of glucose-stimulated insulin release similar to that observed for silencing of the key metabolic enzyme glucokinase. Intracellular calcium measurements in treated cells indicate that this defect lies downstream of the ATP-sensitive K(+) channel (K(ATP) channel) and calcium influx. IGT4 represents a novel digenic model of insulin resistance coupled with an insulin secretory defect. The Sox4 gene has a role in insulin secretion in the adult beta-cell downstream of the K(ATP) channel.


Mechanically induced calcium waves in articular chondrocytes are inhibited by gadolinium and amiloride.
Chondrocytes in articular cartilage utilize mechanical signals from their environment to regulate their metabolic activity. However, the sequence of events involved in the transduction of mechanical signals to a biochemical signal is not fully understood. It has been proposed that an increase in the concentration of intracellular calcium ion ([Ca2+]i) is one of the earliest events in the process of cellular mechanical signal transduction. With use of fluorescent confocal microscopy, [Ca2+]i was monitored in isolated articular chondrocytes subjected to controlled deformation with the edge of a glass micropipette. Mechanical stimulation resulted in an immediate and transient increase in [Ca2+]i. The initiation of Ca2+ waves was abolished by removing Ca2+ from the extracellular media and was significantly inhibited by the presence of gadolinium ion (10 microM) or amiloride (1 mM), which have previously been reported to block mechanosensitive ion channels. Inhibitors of intracellular Ca2+ release (dantrolene and 8-diethylaminooctyl 3,4,5-trimethoxybenzoate hydrochloride) or cytoskeletal disrupting agents (cytochalasin D and colchicine) had no significant effect on the characteristics of the Ca2+ waves. These findings suggest that a possible mechanism of Ca2+ mobilization in this case is a self-reinforcing influx of Ca2+ from the extracellular media, initiated by a Ca2+-permeable mechanosensitive ion channel. Our results indicate that a transient increase in intracellular Ca2+ concentration may be one of the earliest events involved in the response of chondrocytes to mechanical stress and support the hypothesis that deformation-induced Ca2+ waves are initiated through mechanosensitive ion channels.


Modelling schizophrenia using human induced pluripotent stem cells.
Schizophrenia (SCZD) is a debilitating neurological disorder with a world-wide prevalence of 1%; there is a strong genetic component, with an estimated heritability of 80-85%. Although post-mortem studies have revealed reduced brain volume, cell size, spine density and abnormal neural distribution in the prefrontal cortex and hippocampus of SCZD brain tissue and neuropharmacological studies have implicated dopaminergic, glutamatergic and GABAergic activity in SCZD, the cell types affected in SCZD and the molecular mechanisms underlying the disease state remain unclear. To elucidate the cellular and molecular defects of SCZD, we directly reprogrammed fibroblasts from SCZD patients into human induced pluripotent stem cells (hiPSCs) and subsequently differentiated these disorder-specific hiPSCs into neurons (Supplementary Fig. 1). SCZD hiPSC neurons showed diminished neuronal connectivity in conjunction with decreased neurite number, PSD95-protein levels and glutamate receptor expression. Gene expression profiles of SCZD hiPSC neurons identified altered expression of many components of the cyclic AMP and WNT signalling pathways. Key cellular and molecular elements of the SCZD phenotype were ameliorated following treatment of SCZD hiPSC neurons with the antipsychotic loxapine. To date, hiPSC neuronal pathology has only been demonstrated in diseases characterized by both the loss of function of a single gene product and rapid disease progression in early childhood. We now report hiPSC neuronal phenotypes and gene expression changes associated with SCZD, a complex genetic psychiatric disorder.


Anti-gluten immune response following Toxoplasma gondii infection in mice.
Gluten sensitivity may affect disease pathogenesis in a subset of individuals who have schizophrenia, bipolar disorder or autism. Exposure to Toxoplasma gondii is a known risk factor for the development of schizophrenia, presumably through a direct pathological effect of the parasite on brain and behavior. A co-association of antibodies to wheat gluten and to T. gondii in individuals with schizophrenia was recently uncovered, suggesting a coordinated gastrointestinal means by which T. gondii and dietary gluten might generate an immune response. Here, we evaluated the connection between these infectious- and food-based antigens in mouse models. BALB/c mice receiving a standard wheat-based rodent chow were infected with T. gondii via intraperitoneal, peroral and prenatal exposure methods. Significant increases in the levels of anti-gluten IgG were documented in all infected mice and in offspring from chronically infected dams compared to uninfected controls (repetitive measures ANOVAs, two-tailed t-tests, all p≤0.00001). Activation of the complement system accompanied this immune response (p≤0.002-0.00001). Perorally-infected females showed higher levels of anti-gluten IgG than males (p≤0.009) indicating that T. gondii-generated gastrointestinal infection led to a significant anti-gluten immune response in a sex-dependent manner. These findings support a gastrointestinal basis by which two risk factors for schizophrenia, T. gondii infection and sensitivity to dietary gluten, might be connected to produce the immune activation that is becoming an increasingly recognized pathology of psychiatric disorders.


Evaluation of the activity of P450 enzymes in rats: use of the single marker or combined drug administration.
A "cocktail" of several substrates is frequently used to assess metabolic activity of multiple cytochrome P450 enzymes in one session. Some interactions among substrates can appear and may influence the rate of biotransformation of other ones. Our current work was aimed on the influence of tolbutamide on cytochrome P450-mediated metabolism of phenacetin and vice versa. In the presented work, the biotransformation rates of phenacetin and tolbutamide (markers of rat CYP1A2 and CYP2C6/11 metabolic activities, respectively) administered either separately or both simultaneously were compared. The model of isolated perfused rat liver was used. Phenacetin had no significant effect on tolbutamide hydroxylation. Tolbutamide addition to the perfusion medium significantly increased the rate of O-deethylation of phenacetin. Some differences in the rate of P450-mediated metabolism can be observed when comparing assessment using combination of two model substrates with the common way (single marker administration). Due to these differences, results obtained by the mentioned methodologies might not be fully comparable.


Internet Disruptions in the Doctor-Patient Relationship.
The ubiquitous access by patients to online information about health issues is disrupting the traditional doctor-patient relationship in fundamental ways. The knowledge imbalance has shifted and the last nails are being hammered into the coffin of medical paternalism. Ready access to Dr Google has many positive aspects but the risk of undiscerning acceptance by patients of unscientific, out-of-date or biased information for their decision-making remains. In turn this may feed into the content of the legal duty of care for doctors and contribute to a need for them to inquire sensitively into the sources of information that may be generating surprising or apparently illogical patient treatment choices. In addition, patients, those related to patients, and others have the potential to publish on the Internet incorrect and harmful information about doctors. A number of influential decisions by courts have now established the legitimacy of medical practitioners taking legal proceedings for defamation and injunctive relief to stop vituperative and vindictive online publications that are harming them personally, reputationally and commercially. Furthermore, disciplinary accountability has been imposed on doctors for intemperate, disrespectful online postings. All of these factors are contributing to a disruptive recalibration of the dynamics between doctors and their patients.


Poxviral Strategies to Overcome Host Cell Apoptosis.
Apoptosis is a form of cellular suicide initiated either via extracellular (extrinsic apoptosis) or intracellular (intrinsic apoptosis) cues. This form of programmed cell death plays a crucial role in development and tissue homeostasis in multicellular organisms and its dysregulation is an underlying cause for many diseases. Intrinsic apoptosis is regulated by members of the evolutionarily conserved B-cell lymphoma-2 (Bcl-2) family, a family that consists of pro- and anti-apoptotic members. Bcl-2 genes have also been assimilated by numerous viruses including pox viruses, in particular the sub-family of chordopoxviridae, a group of viruses known to infect almost all vertebrates. The viral Bcl-2 proteins are virulence factors and aid the evasion of host immune defenses by mimicking the activity of their cellular counterparts. Viral Bcl-2 genes have proved essential for the survival of virus infected cells and structural studies have shown that though they often share very little sequence identity with their cellular counterparts, they have near-identical 3D structures. However, their mechanisms of action are varied. In this review, we examine the structural biology, molecular interactions, and detailed mechanism of action of poxvirus encoded apoptosis inhibitors and how they impact on host-virus interactions to ultimately enable successful infection and propagation of viral infections.


Correlation between clot density and recanalization success or stroke etiology in acute ischemic stroke patients.
Background Predicting recanalization success for patients undergoing endovascular treatment for acute ischemic stroke is of significant interest. Studies have previously correlated the success of recanalization with the density of the clot. We evaluated clot density and its relationship to revascularization success and stroke etiology. Methods We conducted a retrospective review of 118 patients undergoing intra-arterial therapy for acute ischemic stroke. Mean and maximum thrombus density was measured by drawing a circular region of interest on an axial slice of a non-contrast computed tomography scan. T-tests were used to compare clot density to recanalization success or to stroke etiology, namely large artery atherosclerosis and cardioembolism. Recanalization success was compared in four device groups: aspiration, stent retriever, aspiration and stent retriever, and all other. Results There was no significant difference in the mean clot density in patients with successful ( n = 80) versus unsuccessful recanalization ( n = 38, 50.1 ± 7.4 Hounsfield unit (HU) vs. 53 ± 12.7 HU; P = 0.17). Comparing the large artery thromboembolism ( n = 35) to the cardioembolic etiology group ( n = 56), there was no significant difference in mean clot density (51.5 ± 7.7 HU vs. 49.7 ± 8.5 HU; P = 0.31). A subgroup analysis of middle cerebral artery occlusions ( n = 65) showed similar, non-statistically significant differences between groups. There was no difference in the rate of recanalization success in patients with a mean clot density greater than 50 HU or less than 50 HU in each of the four device groups. Conclusions There was no relationship between clot density and revascularization success or stroke etiology in our study. More research is needed to determine if clot density can predict recanalization rates or indicate etiology.


Predicting prostate cancer many years before diagnosis: how and why?
Evidence of reduced prostate cancer mortality from randomized trials in Europe supports early detection of prostate cancer with prostate-specific antigen (PSA). Yet PSA screening has generated considerable controversy: it is far from clear that the benefits outweigh risks, in terms of overdiagnosis and overtreatment. One way to shift the ratio of benefits to harm is to focus on men at highest risk, who have more to benefit than average. Neither family history nor any of the currently identified genomic markers offer sufficient risk stratification for practical use. However, there is considerable evidence that the levels of PSA in blood are strongly prognostic of the long-term risk of aggressive prostate cancer. Specifically, it is difficult to justify continuing to screen men aged 60 or older if they have a PSA less than 1 or 2 ng/ml; for men 45-60, intervals between PSA tests can be based on PSA levels, with 2-4-year retesting interval for men with PSA of 1 ng/ml or higher, and tests every 6-8 years for men with PSA <1 ng/ml. Men with the top 10% of PSAs at a young age (PSA ~1.5 ng/ml or higher below 50) are at particularly high risk and should be subject to intensive monitoring.


Computational fractal-based analysis of brain arteriovenous malformation angioarchitecture.
Neuroimaging is the gold standard for diagnosis and follow-up of brain arteriovenous malformations (bAVMs), but no objective parameter has been validated for the assessment of the nidus angioarchitecture and for prognostication following treatment. The fractal dimension (FD), which is a mathematical parameter able to quantify the space-filling properties and roughness of natural objects, may be useful in quantifying the geometrical complexity of bAVMs nidus. To propose FD as a neuroimaging biomarker of the nidus angioarchitecture, which might be related to radiosurgical outcome. We retrospectively analyzed 54 patients who had undergone stereotactic radiosurgery for the treatment of bAVMs. The quantification of the geometric complexity of the vessels forming the nidus, imaged in magnetic resonance imaging, was assessed by means of the box-counting method to obtain the fractal dimension. FD was found to be significantly associated with the size (P = .03) and volume (P < .001) of the nidus, in addition to several angioarchitectural parameters. A nonsignificant association between clinical outcome and FD was observed (area under the curve, 0.637 [95% confidence interval, 0.49-0.79]), indicative of a potential inverse relationship between FD and bAVM obliteration. In our exploratory methodological research, we showed that the FD is an objective computer-aided parameter for quantifying the geometrical complexity and roughness of the bAVM nidus. The results suggest that more complex bAVM angioarchitecture, having higher FD values, might be related to decreased response to radiosurgery and that the FD of the bAVM nidus could be used as a morphometric neuroimaging biomarker.


Transfusion-transmitted infections in haemophilia patients.
One of the largest therapeutic problem during the continuous treatment of the patients with Hemophilia A and B, are viral infections as Hepatitis B and C, and HIV, and the other infective diseases, which can be transmitted by the transfusion of blood products. The aim of this study is to analyze the complications of the hemophiliacs in Kosovo which have been treated with fresh frozen plasma, cryoprecipitate and concentrated products of FVIII and FIX. We have tested 75 patients with hemophilia A or B and there were used enzyme immunoassay test-Elisa method for the following: anti-HCV, HBsAg, HIV and TPHA.The serological data showed that HCV infection was positive in 29 cases or 38,7%, whereas infection with HBV and HIV were present in a smaller percentage of the patients (2,7% HBV and 1,4% for HIV). HCV infection was present only in 9,5% of the cases of the age group under 18 years. Infected hemophiliacs with one or two infective agents were found in 34,7%, respectively 4%. Infection with T. pallidum was present at none of the examined patients with hemophilia. HCV infection was higher in severe forms of hemophilia B (44,4%), compared with severe form of hemophilia A (30%).Based on our results, despite the infrequent application of FVIII and FIX concentrates, and other anti hemophilic preparations used in treating hemophilia patients, the number of infected hemophiliacs with blood-transmittable infectious agents was substantially high, especially with hepatitis C virus.


Data-driven normalization strategies for high-throughput quantitative RT-PCR.
High-throughput real-time quantitative reverse transcriptase polymerase chain reaction (qPCR) is a widely used technique in experiments where expression patterns of genes are to be profiled. Current stage technology allows the acquisition of profiles for a moderate number of genes (50 to a few thousand), and this number continues to grow. The use of appropriate normalization algorithms for qPCR-based data is therefore a highly important aspect of the data preprocessing pipeline. We present and evaluate two data-driven normalization methods that directly correct for technical variation and represent robust alternatives to standard housekeeping gene-based approaches. We evaluated the performance of these methods against a single gene housekeeping gene method and our results suggest that quantile normalization performs best. These methods are implemented in freely-available software as an R package qpcrNorm distributed through the Bioconductor project. The utility of the approaches that we describe can be demonstrated most clearly in situations where standard housekeeping genes are regulated by some experimental condition. For large qPCR-based data sets, our approaches represent robust, data-driven strategies for normalization.


The Wnt pathway, epithelial-stromal interactions, and malignant progression in phyllodes tumours.
In a previous study of phyllodes tumours, it has been shown that both the stroma and the epithelium can exhibit distinct molecular changes, suggesting that both are part of the neoplastic process. In view of this finding, it was decided to study stromal-epithelial interactions in these tumours by examining the Wnt-APC-beta-catenin pathway. Beta-catenin and cyclin D1 immunohistochemistry was performed on 119 phyllodes tumours. Eighty-six (72%) showed stromal nuclear beta-catenin localization and in 57% the staining was moderate or strong; however, of the eight malignant tumours in the series, seven showed absent or weak nuclear staining (p<0.025). In no tumour was nuclear beta-catenin staining seen in the epithelial component. Moderate or strong stromal cyclin D1 staining correlated with nuclear stromal beta-catenin staining (p<0.05). Forty-five of the tumours, including two malignant lesions, were screened for beta-catenin exon 3 mutations using SSCP and sequencing, but none was found. Loss of heterozygosity (LOH) of the marker D5S346 was used to infer APC mutation, but only one (benign) tumour showed LOH. Wnt2 and Wnt5a mRNA was localized by in situ hybridization in 13 cases (three malignant) chosen to reflect the different beta-catenin staining patterns. There was an association between strong nuclear beta-catenin staining of stromal cells and epithelial Wnt5a expression (p<0.0015). These data suggest that stromal proliferation in benign phyllodes tumours relies on abnormalities in the Wnt pathway which result not from mutation, but from Wnt5a expression in the epithelium. In the progression to malignancy, the stromal proliferation appears to become independent of the Wnt pathway and, presumably, of the epithelial component of these tumours.


Long-term monitoring of hippocampus-dependent behavior in naturalistic settings: mutant mice lacking neurotrophin receptor TrkB in the forebrain show spatial learning but impaired behavioral flexibility.
Previous behavioral studies (Minichiello et al., Neuron 1999;24:401-414) showed that mice deficient for the TrkB receptor in the forebrain were unable to learn a swimming navigation task with an invisible platform and were severely impaired in finding a visible platform in the same setup. Likewise, additional behavioral deficits suggested a malfunction of the hippocampus and proximally connected forebrain structures. In order to discriminate whether the behavioral impairment was caused either by deficits in spatial memory and learning, or alternatively by loss of behavioral flexibility, 8 trkB mutant, 13 wild-type, and 22 heterozygous mice were implanted with transponders and released for 21 days into a large outdoor pen (10 x 10 m). The enclosure contained 2 shelters and 8 computer-controlled feeder boxes, delivering food portions for every mouse only during their first visit. Every third day, mice received food ad libitum inside the shelters. All mice learned to patrol the boxes correctly within a few days. However, significant differences emerged during those days with free food available. Wild-type mice remained inside the shelters, while all homozygous mutants continued to patrol the boxes in their habitual way, the heterozygous mutants showing intermediate scores. These and previous data suggest that one of the natural functions of the mouse hippocampus is to comediate behavioral flexibility, and that TrkB receptors might play an essential role in maintaining the neuronal short-term plasticity necessary for this capacity.


Effectiveness of a School-Based 'Tobacco Free' Intervention on Adolescents' Knowledge and Exposure to Second Hand Tobacco Smoke - A Multiphase Study.
There is no safe level of exposure to second hand tobacco smoke (SHS). The World Health Organization has stressed that 100% smoke-free environments are the only effective way to protect the population from the harmful effects of exposure to SHS. A multiphase study with a descriptive cross-sectional questionnaire phase 1 and a phase 2 cluster randomized controlled trial (RCT), conceptualized to determine the effectiveness of a school-based 'tobacco free' health education intervention on adolescents' knowledge and attitude towards SHS. Baseline assessment will include a questionnaire followed by estimation of salivary cotinine levels. The experimental arm will receive the 'tobacco free' intervention, which includes 40 min health education session delivered once a week for 3 consecutive weeks. Participants will also be given 'take home brochures' every week containing messages on the effects of tobacco and how to make their homes smoke-free. The sample of 250 participants, for the Phase 2 RCT, with salivary cotinine levels of > 0.1 ng/mL will be selected from the participants of the Phase 1 study. The effect of the intervention will be quantitatively assessed by estimating the salivary cotinine levels after the intervention. Participants in the control arm will receive conventional standard health education once. This research will help in assessing if there is any change in the salivary cotinine levels and the knowledge, attitude and behaviour scores after the health educational intervention and help in developing an effective school-based 'tobacco free' intervention program which could be incorporated into the school curriculum. This study has received the Public Health Research Initiative (PHRI) Research Grant of Rs. 18,99,205 and is registered with the Clinical Trial Registry of India (CTRI) with number CTRI/2018/09/015706 (Registered on 13/09/2018). Ethical approval has been obtained from The Institutional Ethics Committee (No.17021 dated 13 march 2017).


Long-term effectiveness and costs of a brief self-management intervention in women with pregnancy-related low back pain after delivery.
Pregnancy-related low back pain is considered an important health problem and potentially leads to long-lasting pain and disability. Investigators draw particular attention to biomedical factors but there is growing evidence that psychosocial and social factors might be important. It prompted us to start a large cohort study (n = 7526) during pregnancy until one year after delivery and a nested randomized controlled intervention study in the Netherlands. A randomized controlled trial (n = 126) nested within a cohort study, of brief self-management techniques versus usual care for treatment of women with persisting non-specific pregnancy-related low back pain three weeks after delivery. Women in the intervention group were referred to a participating physiotherapist. Women in the usual care group were free to choose physiotherapy, guidance by a general practitioner or no treatment. Follow up took place at 3 months, 6 months and one year after delivery.Outcomes included change in limitations in activities (RDQ), pain (VAS), severity of main complaints (MC), global feeling of recovery (GPE), impact on participation and autonomy (IPA), pain-related fear (TSK), SF-36, EuroQol and a cost diary. For the outcome measures, series of mixed models were considered. For the outcome variable global perceived effect (GPE) a logistic regression analysis is performed. Intention-to-treat outcomes showed a statistical significant better estimated regression coefficient RDQ -1.6 {-2.9;-0.5} associated with treatment, as well as better IPA subscale autonomy in self-care -1.0 {-1.9;-0.03} and TSK -2.4 {-3.8;-1.1} but were not clinical relevant over time. Average total costs in the intervention group were much lower than in usual care, primarily due to differences in utilization of sick leave but not statistically significant. Brief self-management techniques applied in the first 3 months after delivery may be a more viable first-line approach but further research is needed to draw inference on costs and to determine whether no care is a better option in the long term. [ISRCTN08477490].


Optical upper atmospheric investigations at the University of Saskatchewan.
The history and philosophy of optical instrumentation for auroral and airglow studies, as developed at the University of Saskatchewan, is reviewed. Some details are given of the applications of grating spectroscopic systems, Fabry-Perot monochromators, Michelson interferometers, and birefringent and filter photometers with both photographic, photomultiplier, and photoconductive detectors. Finally, examples are given of the applications of these techniques to upper atmosphere temperature determinations, auroral excitation theory, auroral hydrogen arc studies, atmospheric alkali metals, and dayglow molecular oxygen emissions.