Identification of a high risk subgroup of patients with silent ischaemia after myocardial infarction: a group for early therapeutic revascularisation?
Asymptomatic ("silent") ischaemia has been shown to be of prognostic significance in patients with stable and unstable angina and more recently in patients recovering after myocardial infarction. No therapeutic regimen has yet been shown to improve the prognosis of patients with silent ischaemia after infarction, which can be found in as many as a third of these patients. Attempts to achieve therapeutic revascularisation in all these patients may be undesirable, but early revascularisation could be especially beneficial in some selected high risk patients. Two hundred and fifty consecutive clinically stable survivors of myocardial infarction who had predischarge submaximal exercise tests were followed up for a year. Silent ischaemia was found in 27% of these patients; 15% had symptomatic ischaemia. Patients with a positive exercise test were prescribed a beta blocker before discharge. Mortality in patients with silent (9.4%) and symptomatic (5.4%) ischaemia in the first year after infarction was not significantly different. Patients with symptomatic ischaemia were more likely to have undergone coronary artery bypass grafting in the first year. Patients with silent ischaemia were, however, significantly more likely to die than patients with a negative exercise test (relative odds 12:1). Patients with silent ischaemia and an abnormal blood pressure response or who could not complete a submaximal exercise protocol were at particularly high risk, being 32 times more likely to die than those with a negative test (95% confidence interval from 3.3 to 307 times more likely). First year mortality in this group was 22%. The benefits of therapeutic revascularisation in this high risk group need to be studied.


Enzootic and epizootic rabies associated with vampire bats, peru.
During the past decade, incidence of human infection with rabies virus (RABV) spread by the common vampire bat (Desmodus rotundus) increased considerably in South America, especially in remote areas of the Amazon rainforest, where these bats commonly feed on humans. To better understand the epizootiology of rabies associated with vampire bats, we used complete sequences of the nucleoprotein gene to infer phylogenetic relationships among 157 RABV isolates collected from humans, domestic animals, and wildlife, including bats, in Peru during 2002-2007. This analysis revealed distinct geographic structuring that indicates that RABVs spread gradually and involve different vampire bat subpopulations with different transmission cycles. Three putative new RABV lineages were found in 3 non-vampire bat species that may represent new virus reservoirs. Detection of novel RABV variants and accurate identification of reservoir hosts are critically important for the prevention and control of potential virus transmission, especially to humans.


Physiological phenotype and vulnerability in Parkinson's disease.
This review will focus on the principles underlying the hypothesis that neuronal physiological phenotype-how a neuron generates and regulates action potentials-makes a significant contribution to its vulnerability in Parkinson's disease (PD) and aging. A cornerstone of this hypothesis is that the maintenance of ionic gradients underlying excitability can pose a significant energetic burden for neurons, particularly those that have sustained residence times at depolarized membrane potentials, broad action potentials, prominent Ca(2+) entry, and modest intrinsic Ca(2+) buffering capacity. This energetic burden is shouldered in neurons primarily by mitochondria, the sites of cellular respiration. Mitochondrial respiration increases the production of damaging superoxide and other reactive oxygen species (ROS) that have widely been postulated to contribute to cellular aging and PD. Many of the genetic mutations and toxins associated with PD compromise mitochondrial function, providing a mechanistic linkage between known risk factors and cellular physiology that could explain the pattern of pathology in PD. Because much of the mitochondrial burden created by this at-risk phenotype is created by Ca(2+) entry through L-type voltage-dependent channels for which there are antagonists approved for human use, a neuroprotective strategy to reduce this burden is feasible.


Reactivity of monolayer-protected gold nanoclusters at dye-sensitized liquid/liquid interfaces.
Hexanethiolate monolayer-protected gold nanoclusters (MPCs) were used as redox quenchers at the polarizable water/1,2-dichloroethane (DCE) interface. Photocurrent responses originating from the heterogeneous quenching of photoexcited water soluble porphyrin complexes by MPCs dissolved in the DCE phase were observed. As MPCs can function as both electron acceptors and donors, the photocurrent results from the superposition of two simultaneous processes, which correspond to the oxidation and reduction of MPCs. The magnitude of the net photocurrent is essentially determined by the balance of the kinetics of these two processes, which can be controlled by tuning the Galvani potential difference between the two phases. We show that, within the available potential window, the apparent electron-transfer rate constants follow classical Butler-Volmer dependence on the applied potential difference.


Characterization of Aphanomyces invadans isolates using pyrolysis mass spectrometry (PyMS).
Twenty-one isolates of Aphanomyces invadans, the fungal pathogen associated with the Asian fish disease epizootic ulcerative syndrome (EUS), were compared with other Oomycete fungi in terms of their pyrolysis mass spectrometry (PvMS) profiles. Canonical variate analysis (CVA) of the pyrolysis mass spectra distinguished the Aphanomyces species from a wide scatter of Achlya and Saprolegnia isolates. Further CVA and hierarchal cluster analysis (HCA) separated the Aphanomyces species into two main groups. The first group clustered A. invadans isolates from EUS outbreaks in Thailand, Bangladesh, Indonesia, Philippines, Australia and Japan together. However, HCA also included the crayfish plague fungus Aphanomyces astaci within this group. Non-pathogenic Aphanomyces strains isolated from ulcerative mycosis (UM)-affected fish were shown to be distinct from A. invadans, and instead clustered with saprophytic Aphanomyces strains to form the second group. Recently, an invasive Aphanomyces pathogen has been isolated from UNI-affected fish, but that was not tested here. This is the first report using PyMS in the study of Oomycete systematics. The technique was not sensitive enough to show any intraspecific differences, but it was considered a useful technique for the discrimination of species where taxonomic relationships are uncertain.


Fixed pelvic obliquity after poliomyelitis: classification and management.
We classified fixed pelvic obliquity in patients after poliomyelitis into two major types according to the level of the pelvis relative to the short leg. Each type was then divided into four subtypes according to the direction and severity of the scoliosis. In 46 patients with type-I deformity the pelvis was lower and in nine with type II it was higher on the short-leg side. Subtype-A deformity was a straight spine with a compensatory angulation at the lower lumbar level, mainly at L4-L5, subtype B was a mild scoliosis with the convexity to the short-leg side, subtype C was a mild scoliosis with the convexity opposite the short-leg side, and subtype D was a moderate to severe paralytic scoliosis with the convexity to the short-leg side in type I and to the opposite side in type II. A combination of surgical procedures improved the obliquity in most patients. These included lumbodorsal fasciotomy, abductor fasciotomy and stabilisation of the hip by triple innominate osteotomy with or without transiliac lengthening. In patients with type ID or type IID appropriate spinal fusion was usually necessary.


Attraction of the southern pine beetle, Dendroctonus frontalis, to pheromone components of the western pine beetle, Dendroctonus brevicomis (Coleoptera: Curculionidae: Scolytinae), in an allopatric zone.
Subtle differences in pheromone components of sympatric species should be attractive only to the producing species and unattractive or repellent to the nonproducing species, and thereby maintain reproductive isolation and reduce competition between species. Bark beetles Dendroctonus brevicomis and D. frontalis (Coleoptera: Curculionidae) are known to have common pheromone components, except for exo-brevicomin, which is produced by D. brevicomis. We predicted that D. frontalis would not respond to exo-brevicomin outside of the zone of sympatry with D. brevicomis. We conducted a field experiment to determine the effect of exo-brevicomin on attraction of D. frontalis and associated species in Mississippi. We determined whether D. frontalis pheromone production differed inside and outside the sympatric zone and compared the pheromone profiles with D. brevicomis within the sympatric zone. Trapping studies revealed that D. frontalis can perceive and respond positively to exo-brevicomin, an aggregation pheromone of a sympatric congener (D. brevicomis), at locations hundreds of kilometers outside the sympatric zone. Qualitative pheromone profiles showed that both species emit similar pheromone components: frontalin, endo-brevicomin, exo-brevicomin, trans-verbenol, verbenone, and myrtenol. Although not previously reported, D. frontalis males from Arizona produced exo-brevicomin. The predator Thanasimus dubius did not discriminate traps baited with exo-brevicomin and was most attracted to traps with frontalin. Hylastes beetles were significantly attracted to traps baited with exo-brevicomin in combination with other compounds. Our results raise new practical and evolutionary questions on the role of exo-brevicomin in the behavioral ecology of D. frontalis. The addition of exo-brevicomin to the current lure might increase the efficiency of trapping programs in the southeastern United States.


Closing the gap between ethics knowledge and practice through active engagement: an applied model of physical therapy ethics.
Physical therapist practice has a distinct focus that is holistic (ie, patient centered) and at the same time connected to a range of other providers within health care systems. Although there is a growing body of literature in physical therapy ethics knowledge, including clinical obligations and underlying philosophical principles, less is known about the unique ethical issues that physical therapists encounter, and how and why they make ethical decisions. As moral agents, physical therapists are required to make autonomous clinical and ethical decisions based on connections and relationships with their patients, other health care team members, and health institutions and policies. This article identifies specific ethical dimensions of physical therapist practice and highlights the development and focus of ethics knowledge in physical therapy over the last several decades. An applied ethics model, called the "active engagement model," is proposed to integrate clinical and ethical dimensions of practice with the theoretical knowledge and literature about ethics. The active engagement model has 3 practical steps: to listen actively, to think reflexively, and to reason critically. The model focuses on the underlying skills, attitudes, and actions that are required to build a sense of moral agency and purpose within physical therapist practice and to decrease gaps between the ethical dimensions of physical therapist practice and physical therapy ethics knowledge and scholarship. A clinical case study is provided to illustrate how the ethics engagement model might be used to analyze and provide insight into the ethical dimensions of physical therapist practice.


Gene expression analysis of PTEN positive glioblastoma stem cells identifies DUB3 and Wee1 modulation in a cell differentiation model.
The term astrocytoma defines a quite heterogeneous group of neoplastic diseases that collectively represent the most frequent brain tumors in humans. Among them, glioblastoma multiforme represents the most malignant form and its associated prognosis is one of the poorest among tumors of the central nervous system. It has been demonstrated that a small population of tumor cells, isolated from the brain neoplastic tissue, can reproduce the parental tumor when transplanted in immunodeficient mouse. These tumor initiating cells are supposed to be involved in cancer development and progression and possess stem cell-like features; like their normal counterpart, these cells remain quiescent until they are committed to differentiation. Many studies have shown that the role of the tumor suppressor protein PTEN in cell cycle progression is fundamental for tumor dynamics: in low grade gliomas, PTEN contributes to maintain cells in G1 while the loss of its activity is frequently observed in high grade gliomas. The mechanisms underlying the above described PTEN activity have been studied in many tumors, but those involved in the maintenance of tumor initiating cells quiescence remain to be investigated in more detail. The aim of the present study is to shed light on the role of PTEN pathway on cell cycle regulation in Glioblastoma stem cells, through a cell differentiation model. Our results suggest the existence of a molecular mechanism, that involves DUB3 and WEE1 gene products in the regulation of Cdc25a, as functional effector of the PTEN/Akt pathway.


Prognostic impact of CD168 expression in gastric cancer.
Interactions of stromal hyaluronic acid (HA) with its binding protein RHAMM (receptor for HA-mediated motility) (CD168) have been reported to affect tumor extension and the migration of crucial molecules to promote tumor progression and metastases. Cancerous CD168 expression is correlated with aggressive biological features in several cancers. However, the clinical implications of CD168 positivity in gastric cancer have remained unclear. We examined the CD168 expression of 196 consecutive gastric cancer patients by immunohistochemistry. According to CD168 positivity, the 196 gastric cancer patients were divided into two groups (57 CD168-positive and 139 CD168-negative patients). The correlation between CD168 expression and clinicopathological factors (age, sex, histology, tumor depth, lymph node status, and vessel invasion) was evaluated according to the Japanese Classification of Gastric Carcinoma. Cancerous CD168 expression was detectable in 57 of the 196 tumors (29%). CD168 positivity was significantly correlated with the depth of invasion, nodal involvement, and vessel invasion (p < 0.01). Survival analysis of the 196 gastric cancer patients showed that the CD168-positive group had a significantly higher mortality than the CD168-negative group (p < 0.01). In terms of a correlation with CD168 positivity at separate clinical stages, a significance difference was only found in stages II and III. Multivariate analysis revealed that CD168 expression was a significant independent prognostic marker (p = 0.013) after depth of invasion (p < 0.005) and nodal involvement (p < 0.01). Our results suggest that cancerous CD168 positivity is strongly related to the invasion and metastasis of gastric cancer tumors. These results suggest that cancerous CD168 expression can be used as a prognostic marker of gastric cancer owing to its interactions with stromal hyaluronic acid.


Design and demonstration of a small-animal up-conversion imager.
This first small-animal up-conversion imager (SAUCI) was developed and used for in-vivo imaging of up-converting nanoparticles (UCNs.) Unlike traditional fluorophores, UCNs absorb multiple lower-energy photons and emit a single higher-energy photon. This unique physical process makes it possible to image deeper into tissue with lower background signals. In vivo imaging of particle accumulation in the liver was demonstrated following intravenous injection of particles.


Different Mechanisms for Visual Attention at the Hand-movement Goal and Endogenous Visual Attention.
Visual perception is closely related to body movements and action, and it is known that processing visual stimuli is facilitated at the hand or at the hand-movement goal. Such facilitation suggests that there may be an attentional process associated with the hands or hand movements. To investigate the underlying mechanisms of visual attention at a hand-movement goal, we conducted two experiments to examine whether attention at the hand-movement goal is a process independent from endogenous attention. Endogenous attention is attention that is intentionally focused on a location, feature, or object. We controlled the hand-movement goal and endogenous attention separately to investigate the spatial profiles of the two types of attention. A visual target was presented either at the goal of hand movement (same condition) or at its opposite side (opposite condition) while steady-state visual-evoked potential (SSVEP) was used to estimate the spatial distributions of the facilitation effect from the 2 types of attention around the hand-movement goal and around the visual target through EEG. We estimated the spatial profile of attentional modulation for the hand-movement goal by taking the difference in SSVEP amplitude between conditions with and without hand movement, thereby obtaining the effect of visual endogenous attention alone. The results showed a peak at the hand-movement goal, independent of the location of the visual target where participants intentionally focused their attention (endogenous attention). We also found differences in the spatial extent of attentional modulation. Spatial tuning was narrow around the hand-movement goal (i.e., attentional facilitation only at the goal location) but was broadly tuned around the focus of endogenous attention (i.e., attentional facilitation spreading over adjacent stimulus locations), which was obtained from the condition without hand movement. These results suggest the existence of two separate mechanisms, one underlying the attention at the hand-movement goal and another underlying endogenous attention.


Systematic replication of smoking disease associations using survey responses and EHR data in the All of Us Research Program.
The All of Us Research Program (All of Us) aims to recruit over a million participants to further precision medicine. Essential to the verification of biobanks is a replication of known associations to establish validity. Here, we evaluated how well All of Us data replicated known cigarette smoking associations. We defined smoking exposure as follows: (1) an EHR Smoking exposure that used International Classification of Disease codes; (2) participant provided information (PPI) Ever Smoking; and, (3) PPI Current Smoking, both from the lifestyle survey. We performed a phenome-wide association study (PheWAS) for each smoking exposure measurement type. For each, we compared the effect sizes derived from the PheWAS to published meta-analyses that studied cigarette smoking from PubMed. We defined two levels of replication of meta-analyses: (1) nominally replicated: which required agreement of direction of effect size, and (2) fully replicated: which required overlap of confidence intervals. PheWASes with EHR Smoking, PPI Ever Smoking, and PPI Current Smoking revealed 736, 492, and 639 phenome-wide significant associations, respectively. We identified 165 meta-analyses representing 99 distinct phenotypes that could be matched to EHR phenotypes. At P < .05, 74 were nominally replicated and 55 were fully replicated. At P < 2.68 × 10-5 (Bonferroni threshold), 58 were nominally replicated and 40 were fully replicated. Most phenotypes found in published meta-analyses associated with smoking were nominally replicated in All of Us. Both survey and EHR definitions for smoking produced similar results. This study demonstrated the feasibility of studying common exposures using All of Us data.


Teachers' gaze over space and time in a real-world classroom.
Reading students' faces and their body language, checking their worksheets, and keeping eye contact is a key trait of teacher competence. The new technology of mobile eye-tracking provides researchers with possibilities to explore teaching from the viewpoint of teacher gaze, but also introduces many new method questions. This study had the primary aim to investigate teachers´ attention distribution over space: the number and durations of several types of their gazes, and how their gaze depends on the factors of students´ gender, achievement, and position in the classroom. Results show that teacher gaze was distributed unevenly across both space and time. Teachers looked at the most-watched students 3-8 times more often than at the least-watched ones. Students sitting in the first row and the middle section received significantly more gaze than those sitting outside this zone. All three teachers made more single gaze visits - looking at the students but making no eye contact - than mutual gazes or student material gazes. The three teachers' gaze distribution also varied substantially from lesson to lesson. Our results are important for understanding teacher behavior in real classrooms, but also point to the relevance of appropriate method design in future classroom studies with eye-tracking.


Removal and recovery of phosphate and fluoride from water with reusable mesoporous Fe3O4@mSiO2@mLDH composites as sorbents.
Three core/shell/shell MgAl-LDH composites using Fe3O4 microspheres as the core, a SiO2 matrix as the inner layer and a MgAl-LDH layer as the outer shell have been synthesized for the removal and recovery of phosphate and fluoride from water by a magnetic separation technique. The synthetic mesoporous MgAl-LDH composites show good magnetic separability, well-defined pore distributions, and have specific surface areas of 73 m2 g-1, 168 m2 g-1, and 137 m2 g-1 for Fe3O4@SiO2@LDH350, Fe3O4@SiO2@mLDH350, and Fe3O4@mSiO2@mLDH350, respectively. The adsorption isotherms of both phosphate and fluoride on these MgAl-LDH composites can be well fitted with the Langmuir model. The maximum adsorption capacities of 57.07 mg g-1 and 28.51 mg g-1 were obtained on Fe3O4@mSiO2@mLDH350 for phosphate and fluoride, respectively, much higher than those of other LDH-type materials. The adsorbed phosphate and fluoride could be successfully recovered by NaNO3-NaOH solution, and the regenerated MgAl-LDH composites could be reused for phosphate and fluoride removal. Owing to their high adsorption capacities of both phosphate and fluoride, easy magnetic separation from solution, and good reusability, the mesoporous MgAl-LDH composites are expected to have potential applications in removal or recovery of fluoride or phosphate from water.


Temporal trends in death causes in adults attending an urban HIV clinic in Uganda: a retrospective chart review.
To study temporal trends of mortality in HIV-infected adults who attended an HIV clinic in Kampala, Uganda, between 2002 and 2012. Descriptive retrospective study. Two doctors independently reviewed the clinic database that contained information derived from the clinic files and assigned one or more causes of death to each patient >18 years of age with a known date of death. Four cause-of-death categories were defined: 'communicable conditions and AIDS-defining malignancies', 'chronic non-communicable conditions', 'other non-communicable conditions' and 'unknown'. Trends in cause-of-death categories over time were evaluated using multinomial logistic regression with year of death as an independent continuous variable. 1028 deaths were included; 38% of these individuals were on antiretroviral therapy (ART). The estimated mortality rate dropped from 21.86 deaths/100 person years of follow-up (PYFU) in 2002 to 1.75/100 PYFU in 2012. There was a significant change in causes of death over time (p<0.01). Between 2002 and 2012, the proportion of deaths due to 'communicable conditions and AIDS-defining malignancies' decreased from 84% (95% CI 74% to 90%) to 64% (95% CI 53% to 74%) and the proportion of deaths due to 'chronic non-communicable conditions', 'other non-communicable conditions' and a combination of 'communicable and non-communicable conditions' increased. Tuberculosis (TB) was the main cause of death (34%). Death from TB decreased over time, from 43% (95% CI 32% to 53%) in 2002 to a steady proportion of approximately 25% from 2006 onwards (p<0.01). Mortality rate decreased over time. The proportion of deaths from communicable conditions and AIDS-defining malignancies decreased and from non-communicable diseases, both chronic and non-chronic, increased. Nevertheless, communicable conditions and AIDS-defining malignancies continued to cause the majority of deaths, with TB as the main cause. Ongoing monitoring of cause of death is warranted and strategies to decrease mortality from TB and other common opportunistic infections are essential.


The effects of isomaltulose ingestion on gastric parameters and cycling performance in young men.
Isomaltulose is a disaccharide with a low glycaemic index and plays a role in maintaining postprandial glucose. The maintenance of glucose availability during prolonged exercise has been shown to enhance exercise performance. The present study compared the effects of pre-exercise isomaltulose versus maltodextrin ingestion on gastric parameters and cycling performance in young men. Fourteen young men (mean ± S.D., age 23 ± 2 years) performed 60 min of continuous cycling at 75% of maximum heart rate followed by a 15-min exercise performance test while ingesting a 500-mL of water containing 100 mg of 13C-sodium acetate with either 50 g of isomaltulose or 50 g of maltodextrin. Gastrointestinal discomfort was assessed periodically using an 11-point visual analogue scale throughout the study. The gastric emptying rate was evaluated periodically with the 13C-sodium acetate breath test. For the exercise performance test, participants were instructed to pedal a cycle ergometer, exerting as much effort as possible at a self-selected pace. Plasma glucose and insulin concentrations measured at 30 min after ingestion were lower in the isomaltulose trial than in the maltodextrin trial. There were no differences in mean power output during the exercise performance test, gastric emptying rate or the subjective feelings of gastrointestinal discomfort between both trials. Under the current exercise protocol, pre-exercise ingestion of isomaltulose compared with maltodextrin provided no additional benefit relative to gastric emptying or aerobic exercise performance. Both isomaltulose and maltodextrin ingestion did not influence gastrointestinal distress during 60 min of cycling and performance test.


Origin and fate of A/H1N1 influenza in Scotland during 2009.
The spread of influenza has usually been described by a 'density' model, where the largest centres of population drive the epidemic within a country. An alternative model emphasizing the role of air travel has recently been developed. We have examined the relative importance of the two in the context of the 2009 H1N1 influenza epidemic in Scotland. We obtained genome sequences of 70 strains representative of the geographical and temporal distribution of H1N1 influenza during the summer and winter phases of the pandemic in 2009. We analysed these strains, together with another 128 from the rest of the UK and 292 globally distributed strains, using maximum-likelihood phylogenetic and bayesian phylogeographical methods. This revealed strikingly different epidemic patterns within Scotland in the early and late parts of 2009. The summer epidemic in Scotland was characterized by multiple independent introductions from both international and other UK sources, followed by major local expansion of a single clade that probably originated in Birmingham. The winter phase, in contrast, was more diverse genetically, with several clades of similar size in different locations, some of which had no particularly close phylogenetic affinity to strains sampled from either Scotland or England. Overall there was evidence to support both models, with significant links demonstrated between North American sequences and those from England, and between England and East Asia, indicating that major air-travel routes played an important role in the pattern of spread of the pandemic, both within the UK and globally.


In-line fiber-optic etalon formed by hollow-core photonic crystal fiber.
A novel fiber-optic in-line etalon formed by splicing a section of hollow-core photonic crystal fiber (HCPCF) in between two single-mode fibers is proposed and demonstrated, for the first time to our knowledge. Such a HCPCF-based etalon acts as an excellent optical waveguide to form a Fabry-Perot interferometer and hence allows the cavity length to be as long as several centimeters with good visibility as the transmission loss of the HCPCF is much smaller than that of a hollow core fiber; this offers great potential to generate a practical dense fiber-optic sensor network with spatial frequency division-multiplexing. This novel etalon is demonstrated for strain measurement, and the experimental results show that a good visibility of 0.3 and a strain accuracy of better than +/- 5 microepsilon are achieved.


Solid-state carbon-13 NMR and computational characterization of the N719 ruthenium sensitizer adsorbed on TiO₂ nanoparticles.
The ruthenium-containing sensitizing dye N719 grafted on TiO2 nanoparticles was investigated by solid-state NMR. The carbon resonances are assigned by means of (13)C cross-polarized dipolar dephasing experiments. DFT calculations of the carbon magnetic shielding tensors accurately describe the changes in chemical shifts observed upon grafting onto a titania surface via one or two carboxylic functions in the plane defined by the two isothiocyanate groups.


High HIV incidence in a cohort of male injection drug users in Delhi, India.
India has an estimated 177,000 injection drug users (IDU) with a national HIV prevalence of 7.14%. Reliable estimates of HIV incidence are not available for this population. We report HIV incidence in a cohort of male, HIV-negative IDUs recruited through peer-referral, targeted outreach and as walk-in clients in Delhi from May to October, 2011. Fourth-generation Antigen-Antibody tests were used to diagnose new infections and results were confirmed using Western blot tests. HIV incidence based on HIV seroconversion was calculated as number of events/person-years. Cox regression was used to identify significant (p<0.05) seroconversion predictors. A total of 2790 male HIV-negative IDUs were recruited at baseline; 67.4% (n=1880) returned for their first follow-up visit and 96% (n=1806) underwent HIV testing. Participants were followed for a median of 9.7 months. A total of 112 new HIV infections occurred over a cumulative 1398.5 person-years of follow-up resulting in an incidence rate of 8.01 new infections/100 person-years (95% CI: 6.65-9.64); 74% of these participants reported risky injection practices in the past month. In multivariate analysis, moderate-high risk injection behaviors (Adjusted Hazard Ratio [AHR] 2.59; 95% CI 1.45-4.62) were associated with a higher risk of new infections. Male IDUs in Delhi continue to practice unsafe injection practices leading to high sero-incidence despite the availability of HIV prevention services offered through targeted intervention programs.


A new GFP-tagged line reveals unexpected Otx2 protein localization in retinal photoreceptors.
Dynamic monitoring of protein expression and localization is fundamental to the understanding of biological processes. The paired-class homeodomain-containing transcription factor Otx2 is essential for normal head and brain development in vertebrates. Recent conditional knockout studies have pointed to multiple roles of this protein during late development and post-natal life. Yet, later expression and functions remain poorly characterized as specific reagents to detect the protein at any stage of development are still missing. We generated a new mouse line harbouring an insertion of the GFP gene within the Otx2 coding sequence to monitor the gene activity while preserving most of its functions. Our results demonstrate that this line represents a convenient tool to capture the dynamics of Otx2 gene expression from early embryonic stages to adulthood. In addition, we could visualize the intracellular location of Otx2 protein. In the retina, we reinterpret the former view of protein distribution and show a further level of regulation of intranuclear protein localization, which depends on the cell type. The GFP-tagged Otx2 mouse line fully recapitulates previously known expression patterns and brings additional accuracy and easiness of detection of Otx2 gene activity. This opens up the way to live imaging of a highly dynamic actor of brain development and can be adapted to any mutant background to probe for genetic interaction between Otx2 and the mutated gene.


Decision-makers' perspectives on the use of bioaccessibility for risk-based regulation of contaminated land.
Information on contaminant bioaccessibility has been recognized by researchers, legislators and regulators as a decision-support tool for contaminated land assessment and has been subject to interest and discussion at both national and international levels. A sustainable, proportionate and risk-based approach to contaminated land management has been adopted by contaminated land regimes throughout the world. While this approach guides national and international priorities, its practical implementation in many countries, including the United Kingdom, is reliant upon local authorities. Here, we present an investigation into the views of local authorities in England and Wales regarding the practical application of bioaccessibility and constraints associated with its implementation. The research involved an online survey followed by semi-structured interviews with selected respondents. A majority of survey respondents (70%) perceived bioaccessibility to be a useful tool that facilitates contaminated land management. However, 76% of participants indicated a need for more information regarding bioaccessibility as well as emphasising a need for more research into polycyclic aromatic hydrocarbons. Lack of statutory guidance was indicated by 78% of respondents as the main factor hampering the use of bioaccessibility data in regulatory decision-making. Divergence of policy-maker and local regulator perceptions of bioaccessibility was also indicated by the respondents. This research brings the voice of front-line regulators for contaminated land into the on-going discussion between policy-makers and scientists on the uses of bioaccessibility. This study concludes by proposing action priorities both for the research community and for policy-makers, which are transferable to risk-based regimes elsewhere.


Dietary Crude Lecithin Increases Systemic Availability of Dietary Docosahexaenoic Acid with Combined Intake in Rats.
Crude lecithin, a mixture of mainly phospholipids, potentially helps to increase the systemic availability of dietary omega-3 polyunsaturated fatty acids (n-3 PUFA), such as docosahexaenoic acid (DHA). Nevertheless, no clear data exist on the effects of prolonged combined dietary supplementation of DHA and lecithin on RBC and plasma PUFA levels. In the current experiments, levels of DHA and choline, two dietary ingredients that enhance neuronal membrane formation and function, were determined in plasma and red blood cells (RBC) from rats after dietary supplementation of DHA-containing oils with and without concomitant dietary supplementation of crude lecithin for 2-3 weeks. The aim was to provide experimental evidence for the hypothesized additive effects of dietary lecithin (not containing any DHA) on top of dietary DHA on PUFA levels in plasma and RBC. Dietary supplementation of DHA-containing oils, either as vegetable algae oil or as fish oil, increased DHA, eicosapentaenoic acid (EPA), and total n-3 PUFA, and decreased total omega-6 PUFA levels in plasma and RBC, while dietary lecithin supplementation alone did not affect these levels. However, combined dietary supplementation of DHA and lecithin increased the changes induced by DHA supplementation alone. Animals receiving a lecithin-containing diet also had a higher plasma free choline concentration as compared to controls. In conclusion, dietary DHA-containing oils and crude lecithin have synergistic effects on increasing plasma and RBC n-3 PUFA levels, including DHA and EPA. By increasing the systemic availability of dietary DHA, dietary lecithin may increase the efficacy of DHA supplementation when their intake is combined.


Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1(T), an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake.
Thioalkalivibrio paradoxus strain ARh 1(T) is a chemolithoautotrophic, non-motile, Gram-negative bacterium belonging to the Gammaproteobacteria that was isolated from samples of haloalkaline soda lakes. It derives energy from the oxidation of reduced sulfur compounds and is notable for its ability to grow on thiocyanate as its sole source of electrons, sulfur and nitrogen. The full genome consists of 3,756,729 bp and comprises 3,500 protein-coding and 57 RNA-coding genes. This organism was sequenced as part of the community science program at the DOE Joint Genome Institute.


Characteristics of malt liquor beer drinkers in a low-income, racial minority community sample.
The authors describe and compare drinking patterns among malt liquor beer (MLB), regular beer (RB), and hard liquor (HL) drinkers in a low-income, racial/ethnic minority community. Drinkers were recruited from randomly selected alcohol outlets in South Los Angeles. Respondents were assessed on sociodemographic characteristics, alcohol use history, drinking patterns, and drinking context among other items in a face-to-face interview with research staff. Three hundred twenty-nine drinkers were interviewed, of whom 297 reported drinking MLB, RB, or HL brands of alcohol most often in the past 90 days. This subsample was 88% African-American, 72% male, and 35% unemployed. As compared with RB and HL drinkers, MLB drinkers were more likely to be homeless, to receive public assistance for housing, and to be unemployed. MLB drinkers also reported significantly higher rates of daily or near-daily drinking (74%, as compared with 48% for RB and 29% for HL) of drinks per day on drinking days (5.2, as compared with 4.2 for RB and 3.1 for HL), and daily average ethanol consumption (6.97 oz, as compared with 2.13 oz for RB drinkers and 6.13 oz for HL drinkers). In multinomial regression analysis that controlled for potential confounders, the odds of preferring RB as compared with MLB were significantly increased among persons with blue-collar occupations and those who reported drinking in public settings and were reduced among persons who drank outdoors, those who combined drinking with tobacco smoking, and those who drank alcohol with members of the same sex. Average daily ethanol consumption odds were reduced for RB drinkers as compared with MLB drinkers. The odds of preferring HL as compared with MLB were significantly increased for persons with white-collar occupations and those who drank in public settings and were reduced for persons who drank outdoors and those who combined drinking and smoking. The authors observed substantial differences in sociodemographic characteristics, drinking patterns, and ethanol consumption by beverage type in this community sample. MLB drinkers seem to have distinctive drinking patterns that require additional study to determine whether this pattern is associated with increased individual or community risk.


Detection of residual tumor cells in bladder biopsy specimens: pitfalls in the interpretation of cytokeratin stains.
Some patients who have had prior bladder biopsies or transurethral resections undergo a repeat resection within several months for various reasons. The detection of a few residual tumor cells in bladder specimens with prior biopsy site changes can be challenging based on histology alone. Immunohistochemistry for cytokeratins may be used as an adjunct in this situation. We have noted several cases in which keratin stains were performed and positive cells were noted, raising the issue as to whether the cytokeratin positive cells were residual tumor cells or stromal cells. Immunohistochemistry for a panel of antibodies [AE1/AE3, CAM 5.2, high molecular weight cytokeratin, smooth muscle actin (SMA), desmin, and anaplastic lymphoma kinase (ALK)] was performed on 29 cases of bladder biopsies with prior biopsy site changes. Of 29 patients, 25 had a prior history of bladder tumor: 17 had invasive high-grade urothelial carcinoma (T1, 5 cases; T2, 11 cases; T3,1 case); 7 had noninvasive high-grade papillary urothelial carcinoma; 1 had noninvasive low-grade papillary urothelial carcinoma). One of the patients with noninvasive high-grade papillary urothelial carcinoma and one of the patents with invasive high-grade urothelial carcinoma had associated carcinoma in-situ. Four patients had prior benign bladder diagnoses: cystitis cystica et glandularis; polypoid cystitis; follicular cystitis; and neurogenic bladder with benign prostate hyperplasia. Of the 29 cases, 6 (21%) had cells with staining for at least 2 of the cytokeratin markers. Cytokeratin (CK) AE1/ AE3 was positive for cells in 8/29 cases (28%). In 6 of these cases, cells displayed a spindle cell and 2 cases a more epithelioid morphology. CAM 5.2 was positive in cells in 5/29 cases (17%); 3 of the cases had spindle cell and 2 cases epithelioid morphology. High molecular weight cytokeratin was expressed in cells in 2/29 cases (7%) with 1 case having spindle cell and 1 epithelioid morphology. SMA was positive in cells with a spindle cell morphology and negative in the more epitheloid cytokeratin positive cells. Desmin was positive in 3/6 keratin positive spindle cells and negative in keratin positive epithelioid cells. ALK was negative in all the cases. Three cases with spindle cell morphology and positivity for at least 1 of the keratins and SMA stains were interpreted as aberrant keratin expression in myofibroblastic cells based on the staining and the morphology of the spindle cells. Another 3 cases with concurrent staining for at least 1 of the keratins, SMA and desmin were consistent with smooth muscle cells on the basis of their cellular morphology. Another 2 cases had cells, which expressed at least 2 CK markers but did not express SMA, desmin, or ALK and a more epithelioid morphology. These cells were interpreted as residual tumors cells. When interpreting CK stains for the detection of residual tumor cells, one should pay attention to the nature of the cells and not assume all CK staining cells are residual tumor cells.


The use of rapid antigen testing and matrix-assisted laser desorption/ionization-time of flight mass spectrometry in the diagnosis of group A beta-hemolytic streptococci in throat swab samples
Background/aim: We aimed to evaluate the efficacy of a rapid antigen test in detecting group A beta-hemolytic streptococci (GAS) in throat samples in comparison with the culture method and to compare the efficiency of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and traditional methods in identifying GAS in cultures. Materials and methods: A total of 3668 throat samples from patients with a prediagnosis of tonsillopharyngitis were assessed by the QuickVue+Strep A antigen test and culture. For GAS identification from cultures, bacitracin sensitivity, PYR, and latex agglutination tests and MALDI-TOF MS were used. Results: A total of 567 (15.5%) and 536 (14.6%) of the samples were positive for GAS culture and rapid antigen testing, respectively. The sensitivity and specificity of the rapid antigen test compared to culture was 89.07% and 99%, respectively, while positive and negative predictive values were 94.22% and 98.02%. Traditional methods were in full concordance with MALDI-TOF-MS for all 567 isolates. In all densities of growth in culture, the time to diagnosis with MALDI-TOF MS was significantly lower than with traditional identification tests. Conclusion: This study shows that both the rapid antigen testing of samples and bacterial identification with MALDI-TOF MS contribute much to the rapid diagnosis of GAS tonsillopharyngitis.


Multiple myeloma, version 1.2013.
These NCCN Guidelines Insights highlight the important updates/changes specific to the management of relapsed or progressive disease in the 2013 version of the NCCN Clinical Practice Guidelines in Oncology for Multiple Myeloma. These changes include the addition of new regimens as options for salvage therapy and strategies to mitigate the adverse effects and risks associated with newer regimens for the treatment of multiple myeloma.


Factors enabling comprehensive maternal health services in the benefits package of emerging financing schemes: A cross-sectional analysis from 1990 to 2014.
Maternal delivery is the costliest event during pregnancy, especially if a complicated delivery occurs that requires emergency hospital services. A health financing scheme or program that covers comprehensive maternal services, including specialized hospital services in the benefits health package, enhances maternal survival and improves financial risk protection. The objective of this study is to identify factors that enable the inclusion of comprehensive maternal services in the benefits package of emerging health financing schemes in low and middle-income countries across selected world regions. Comprehensive care is presumed if, in addition to normal delivery, primary health care, and secondary or tertiary hospital care are included. Multilevel regression analysis is performed on 220 health financing schemes and programs initiated during the period 1990-2014, in 40 countries in Sub-Saharan Africa, Asia, and Latin America. About two-thirds of emerging health financing schemes explicitly include maternal care in the benefits package, and less-than-half cover comprehensive maternal services. Provision of any type of maternal services and comprehensive services is significantly associated with the presence of donors/philanthropies as funders, and beneficiaries possessing an ID card that links them to entitled services. Other enabling factors are prepayment and risk pooling. However, private and community insurances are negatively associated with covering comprehensive maternal services, because they are subject to market failures, such as adverse and risk selection. Emerging health financing schemes in low and upper-middle-income countries lag in coverage of maternal care. Advancing financial protection of these services in the health package needs policy attention, including government oversight and mandatory regulations. The enabling factors identified can enrich the ongoing discourse on Universal Health Coverage.


Insomnia symptoms as a cause of type 2 diabetes Incidence: a 20 year cohort study.
Insomnia symptoms are associated with type 2 diabetes incidence but are also associated with a range of potential time-varying covariates which may confound and/or mediate associations. We aimed to assess whether cumulative exposure to insomnia symptoms has a causal effect on type 2 diabetes incidence. A prospective cohort study in the West of Scotland, following respondents for 20 years from age 36. 996 respondents were free of diabetes at baseline and had valid data from up to four follow-up visits. Type 2 diabetes was assessed at the final visit by self-report, taking diabetic medication, or blood-test (HbA1c ≥ 6.5% or 48 mmol/mol). Effects of cumulative insomnia exposure on type 2 diabetes incidence were estimated with traditional regression and marginal structural models, adjusting for time-dependent confounding (smoking, diet, physical inactivity, obesity, heavy drinking, psychiatric distress) as well as for gender and baseline occupational class. Traditional regression yielded an odds ratio (OR) of 1.34 (95% CI: 1.06-1.70) for type 2 diabetes incidence for each additional survey wave in which insomnia was reported. Marginal structural models adjusted for prior covariates (assuming concurrently measured covariates were potential mediators), reduced this OR to 1.20 (95% CI: 0.98-1.46), and when concurrent covariates were also included (viewing them as potential confounders) this dropped further to 1.08 (95% CI: 0.85-1.37). The association between cumulative experience of insomnia and type 2 diabetes incidence appeared confounded. Evidence for a residual causal effect depended on assumptions as to whether concurrently measured covariates were confounders or mediators.


[Neuraminidase inhibitors oseltamivir and zanamivir: new means of defence against influenza].
Recently two new neuraminidase inhibitors zanamivir and oseltamivir have been marketed. They appear to considerably reduce morbidity and mortality from influenza. Their adverse effects are infrequent and mild and the chance of development of pathogenically significant resistant mutants appears to be small. During the first six months of a pandemic, neuraminidase inhibitors are the only defence against the virus. It is therefore important to stockpile in each country sufficient quantities of these drugs. During the usual influenza epidemics the main value of neuraminidase inhibitors lies in their use for therapy, prophylaxis and post-exposure prophylaxis in long-term care institutions for the elderly (for prophylaxis only oseltamivir is licensed). Although data on the effectiveness against complications of influenza and on the effect on people with an increased risk of (fatal) complications as a result of an influenza virus infection are limited, the available information on the effects of the neuraminidinase inhibitors indicates that these drugs will also protect against complications and that high-risk groups will benefit from the rapid deployment of these products. The cost-effectiveness of treatment and post-exposure prophylaxis with neuraminidinase inhibitors is probably not favourable for healthy children and adults but seems to be favourable for the high-risk groups (vaccinated or not) in winter.


Serum p53 antibody detection in patients with impaired lung function.
TP53 gene mutations can lead to the expression of a dysfunctional protein that in turn may enable genetically unstable cells to survive and change into malignant cells. Mutant p53 accumulates early in cells and can precociously induce circulating anti-p53 antibodies (p53Abs); in fact, p53 overexpression has been observed in pre-neoplastic lesions, such as bronchial dysplasia, and p53Abs have been found in patients with chronic obstructive pulmonary disease, before the diagnosis of lung and other tobacco-related tumors. A large prospective study was carried out, enrolling non-smokers, ex-smokers and smokers with or without the impairment of lung function, to analyze the incidence of serum p53Abs and the correlation with clinicopathologic features, in particular smoking habits and impairment of lung function, in order to investigate their possible role as early markers of the onset of lung cancer or other cancers. The p53Ab levels were evaluated by a specific ELISA in 675 subjects. Data showed that significant levels of serum p53Abs were present in 35 subjects (5.2%); no difference was observed in the presence of p53Abs with regard to age and gender, while p53Abs correlated with the number of cigarettes smoked per day and packs-year. Furthermore, serum p53Abs were associated with the worst lung function impairment. The median p53Ab level in positive subjects was 3.5 units/ml (range 1.2 to 65.3 units/ml). Only fifteen positive subjects participated in the follow-up, again resulting positive for serum p53Abs, and no evidence of cancer was found in these patients. The presence of serum p53Abs was found to be associated with smoking level and lung function impairment, both risk factors of cancer development. However, in our study we have not observed the occurrence of lung cancer or other cancers in the follow-up of positive subjects, therefore we cannot directly correlate the presence of serum p53Abs with cancer risk.


STN vs. GPi Deep Brain Stimulation: Translating the Rematch into Clinical Practice.
When formulating a deep brain stimulation (DBS) treatment plan for a patient with Parkinson's disease (PD), two critical questions should be addressed: 1- Which brain target should be chosen to optimize this patient's outcome? and 2- Should this patient's DBS operation be unilateral or bilateral? Over the past two decades, two targets have emerged as leading contenders for PD DBS; the subthalamic nucleus (STN) and the globus pallidus internus (GPi). While the GPi target does have a following, most centers have uniformly employed bilateral STN DBS for all Parkinson's disease cases (Figure 1). This bilateral STN "one-size-fits-all" approach was challenged by an editorial entitled "STN vs. GPi: The Rematch," which appeared in the Archives of Neurology in 2005. Since 2005, a series of well designed clinical trials and follow-up studies have addressed the question as to whether a more tailored approach to DBS therapy might improve overall outcomes. Such a tailored approach would include the options of targeting the GPi, or choosing a unilateral operation. The results of the STN vs. GPi 'rematch' studies support the conclusion that bilateral STN DBS may not be the best option for every Parkinson's disease surgical patient. Off period motor symptoms and tremor improve in both targets, and with either unilateral or bilateral stimulation. Advantages of the STN target include more medication reduction, less frequent battery changes, and a more favorable economic profile. Advantages of GPi include more robust dyskinesia suppression, easier programming, and greater flexibility in adjusting medications. In cases where unilateral stimulation is anticipated, the data favor GPi DBS. This review summarizes the accumulated evidence regarding the use of bilateral vs. unilateral DBS and the selection of STN vs. GPi DBS, including definite and possible advantages of different targets and approaches. Based on this evidence, a more patient-tailored, symptom specific approach will be proposed to optimize outcomes of PD DBS therapy. Finally, the importance of an interdisciplinary care team for screening and effective management of DBS patients will be reaffirmed. Interdisciplinary teams can facilitate the proposed patient-specific DBS treatment planning and provide a more thorough analysis of the risk-benefit ratio for each patient.


Clinical holding: ethical guidance for children's nurses working in the UK.
This article explores ethical decision-making surrounding clinical holding of children and young people in healthcare environments with the aim of enhancing autonomy and engagement on their behalf. A considerable body of evidence, published over the last 20 years, suggests that this complex and challenging area of practice is not always well managed, with mixed messages about the nature of consent, choice and negotiated practice countered by best interests decisions taking precedence ahead of the child's wishes. An ethical framework is proposed comprising four levels of value-based interventions and how they may be applied in clinical practice, allowing for increased engagement, empowerment and support on behalf of children and young people in relation to clinical holding decisions.


Both host prion protein 131-188 subregion and prion strain characteristics regulate glycoform of PrP Sc.
Prion proteins (PrPs) contain 2 N-linked glycosylation sites and are present in cells in 3 different forms. An abnormal isoform of prion protein (PrP(Sc)) has different glycoform patterns for different prion strains. However, the molecular basis of the strain-specific glycoform variability in prions has remained elusive. To understand the molecular basis of these glycoform differences, we analyzed PrP(Sc) in 2 lines of transgenic mice (MHM2 and MH2M with PrP null background) that expressed a chimeric PrP. Our result indicated that PrP 131-188 (substitutions at I139M, Y155N, and S170N) contributed to both PrP(C) and PrP(Sc) glycoform ratios. Furthermore, the PrP(Sc) glycoform pattern within these transgenic mice showed a subtle difference depending on the inoculated prion. This study indicated that the PrP(Sc) glycoform ratio was influenced by both host PrP(C) and the prion strain.


Unusual causes of tubo-ovarian abscess: CT and MR imaging findings.
Actinomycosis, tuberculosis, and xanthogranulomatous inflammation are rare but specific causes of tubo-ovarian abscess (TOA). TOAs with these causes are frequently misdiagnosed as ovarian malignancies due to their unusual appearances at computed tomography (CT) and magnetic resonance (MR) imaging. Tubo-ovarian actinomycosis frequently has a predominantly solid appearance. A linear, solid, well-enhancing lesion extending directly from the mass is a characteristic CT and MR imaging finding. Small rim-enhancing lesions in the solid part of the mass are also suggestive of actinomycosis. Tuberculous TOAs usually mimic peritoneal carcinomatosis from ovarian cancers. The granulomatous and fibrotic nature of this infection may be reflected in the CT and MR imaging appearances, which can help in differentiation. TOAs from xanthogranulomatous inflammation demonstrate more nonspecific imaging findings than actinomycotic or tuberculous TOAs, although multiple xanthogranulomas in the mass may be seen on MR images. Knowledge of these characteristics can help one make the correct diagnosis and treat the patients appropriately.


Ex vivo gene transfer into hepatocytes.
Ex vivo gene transfer into hepatocytes could serve several purposes in the context of gene therapy or cell transplantation: (1) isolated hepatocytes can be transduced in culture with therapeutic genes and then transplanted into the recipient; (2) marker genes can be introduced for subsequent identification of transplanted cells and their progeny; (3) gene transfer can be used for conditional immortalization of hepatocytes for expansion in culture; (4) immunomodulatory genes can be transferred into hepatocytes to prevent allograft rejection. Gene transfer into cultured hepatocytes can be achieved using DNA that is not incorporated into recombinant viruses. In such systems, transgene integration into the host cell genome can be enhanced using transposon systems, such as "sleeping beauty." In addition to using the conventional reagents, such as cationic liposomes, DNA transfer into hepatocytes can be achieved by Nucleofection or special hepatocyte-targeted carriers such as proteoliposomes containing galactose-terminated glycoproteins (e.g. the F protein of the Sendai virus). Alternatively, genes can be transferred using recombinant viruses, such as adenoviral vectors that are episomal or retroviral vectors (including lentiviruses) that permit integration of the transgene into the host genome. Gene transfer using lentiviral vectors has been achieved in both attached and suspended hepatocytes. Transduction efficiency of lentiviral vectors can be enhanced using magnetic nanoparticles (Magnetofection).


EULAR recommendations for the management of knee osteoarthritis: report of a task force of the Standing Committee for International Clinical Studies Including Therapeutic Trials (ESCISIT).
Osteoarthritis (OA) is the most common joint disease encountered throughout Europe. A task force for the EULAR Standing Committee for Clinical Trials met in 1998 to determine the methodological and logistical approach required for the development of evidence based guidelines for treatment of knee OA. The guidelines were restricted to cover all currently available treatments for knee OA diagnosed either clinically and/or radiographically affecting any compartment of the knee. The first stage was the selection of treatment modalities to be considered. The second stage comprised a search of the electronic databases Medline and Embase using a combination of subject headings and keywords. All European language publications in the form of systematic reviews, meta-analyses, randomised controlled trials, controlled trials, and observational studies were included. During stage three all the relevant studies were quality scored. The summary statistics for validated outcome measures, when available, were recorded and, where practical, the numbers needed to treat and the effect size for each treatment were calculated. In the fourth stage key clinical propositions were determined by expert consensus employing a Delphi approach. The final stage ranked these propositions according to the available evidence. A second set of propositions relating to a future research agenda was determined by expert consensus using a Delphi approach. Over 2400 English language publications and 400 non-English language publications were identified. Seven hundred and forty four studies presented outcome data of the effects of specific treatments on knee OA. Quantitative analysis of treatment effect was possible in only 61 studies. Recommendations for the management of knee OA based on currently available data and expert opinion are presented. Proposals for a future research agenda are highlighted. These are the first clinical guidelines on knee OA to combine an evidence based approach and a consensus approach across a wide range of treatment modalities. It is apparent that certain clinical propositions are supported by substantial research based evidence, while others are not. There is thus an urgent need for future well designed trials to consider key clinical questions.


Controlling crystal polymorphism of isotactic poly(1-butene) by incorporating long chain branches.
Isotactic poly(1-butene) (iPB-1) is a high performance plastic with outstanding properties, such as flexibility, superior creep, environmental stress cracking and abrasive resistance. However, it exhibits a complex crystal polymorphism and polymorphic transformation behavior, which has limited its commercial development. In this paper, the incorporation of long chain branches (LCBs) causes coil contraction in the melt, which favors the direct melt-crystallization of form III that was generally crystallized from solutions and made of unconventional highly twined lamellae. Consequently, low-to-moderately branched iPB-1 samples as-crystallize from the melt into mixtures of form II and form III by compression-molding and fast cooling of the melt to room temperature, and the fraction of crystals of form III (fIII) increases with increasing concentration of LCBs, whereas highly branched samples can as-crystallize into pure form III with uniform crystal size distribution. The corresponding thermomechanical properties can be modified by controlling fIII.


Highly pathogenic avian influenza virus nucleoprotein interacts with TREX complex adaptor protein Aly/REF.
We constructed a novel chicken (Gallus gallus) lung cDNA library fused inside yeast acting domain vector (pGADT7). Using yeast two-hybrid screening with highly pathogenic avian influenza (HPAI) nucleoprotein (NP) from the strain (A/chicken/Malaysia/5858/2004(H5N1)) as bait, and the Gallus gallus lung cDNA library as prey, a novel interaction between the Gallus gallus cellular RNA export adaptor protein Aly/REF and the viral NP was identified. This interaction was confirmed and validated with mammalian two hybrid studies and co-immunoprecipitation assay. Cellular localization studies using confocal microscopy showed that NP and Aly/REF co-localize primarily in the nucleus. Further investigations by mammalian two hybrid studies into the binding of NP of other subtypes of influenza virus such as the swine A/New Jersey/1976/H1N1 and pandemic A/Malaysia/854/2009(H1N1) to human Aly/REF, also showed that the NP of these viruses interacts with human Aly/REF. Our findings are also supported by docking studies which showed tight and favorable binding between H5N1 NP and human Aly/REF, using crystal structures from Protein Data Bank. siRNA knockdown of Aly/REF had little effect on the export of HPAI NP and other viral RNA as it showed no significant reduction in virus titer. However, UAP56, another component of the TREX complex, which recruits Aly/REF to mRNA was found to interact even better with H5N1 NP through molecular docking studies. Both these proteins also co-localizes in the nucleus at early infection similar to Aly/REF. Intriguingly, knockdown of UAP56 in A549 infected cells shows significant reduction in viral titer (close to 10 fold reduction). Conclusively, our study have opened new avenues for research of other cellular RNA export adaptors crucial in aiding viral RNA export such as the SRSF3, 9G8 and ASF/SF2 that may play role in influenza virus RNA nucleocytoplasmic transport.


Temporal distribution of the annual nymphal stock of Ixodes ricinus ticks.
The human risk of contracting Lyme disease or other tick borne diseases transmitted by the tick species Ixodes ricinus is broadly linked to the tick nymph density. The study was performed in Rambouillet forest (Yvelines, France), a known focus of Lyme borreliosis, from January 1997 to December 1999. We used a nymph sampling methodology which permitted us to obtain a monthly nymph density index (from 0 to 5). Studying the seasonal nymph and larval activity patterns and estimating the larval developmental duration, we demonstrate the existence of an annual nymphal stock. Secondly, we elucidate how this stock is distributed throughout the year, month by month. Its distribution is principally dependent on two factors: the monthly mean ambient temperature and the proportion of active nymphs which find a host each month. Expected monthly nymph densities derived from a theoretical model describing the temperature-dependent stock distribution gave a good fit to the observed densities, accounting for between 76-86% of the monthly variation in observed nymph densities. Predicting the temporal distribution of nymph activity within a stable Lyme borreliosis focus enables more precise identification of risk periods.


Urinary Peptides As a Novel Source of T Cell Allergen Epitopes.
Mouse allergy in both laboratory workers and in inner-city children is associated with allergic rhinitis and asthma, posing a serious public health concern. Urine is a major source of mouse allergens, as mice spray urine onto their surroundings, where the proteins dry up and become airborne on dust particles. Here, we tested whether oligopeptides that are abundant in mouse urine may contribute to mouse allergic T cell response. Over 1,300 distinct oligopeptides were detected by mass spectrometry analysis of the low molecular weight filtrate fraction of mouse urine (LoMo). Posttranslationally modified peptides were common, accounting for almost half of total peptides. A pool consisting of 225 unique oligopeptides of 13 residues or more in size identified within was tested for its capacity to elicit T cell reactivity in mouse allergic donors. Following 14-day in vitro stimulation of PBMCs, we detected responses in about 95% of donors tested, directed against 116 distinct peptides, predominantly associated with Th2 cytokines (IL-5). Peptides from non-urine related proteins such as epidermal growth factor, collagen, and Beta-globin accounted for the highest response (15.9, 9.1, and 8.1% of the total response, respectively). Peptides derived from major urinary proteins (MUPs), kidney androgen-regulated protein (KAP), and uromodulin were the main T cell targets from kidney or urine related sources. Further ex vivo analysis of enrichment of 4-1BB expressing cells demonstrated that LoMo pool-specific T cell reactivity can be detected directly ex vivo in mouse allergic but not in non-allergic donors. Further cytometric analysis of responding cells revealed a bone fide memory T cell phenotype and confirmed their Th2 polarization. Overall, these data suggest that mouse urine-derived oligopeptides are a novel target for mouse allergy-associated T cell responses, which may contribute to immunopathological mechanisms in mouse allergy.


Bacteriophage T4 self-assembly: in vitro reconstitution of recombinant gp2 into infectious phage.
T4 gene 2 mutants have a pleiotropic phenotype: degradation of injected phage DNA by exonuclease V (ExoV) in the recBCD(+) host cell cytoplasm and a low burst size due, at least in part, to a decreased ability for head-to-tail (H-T) joining. The more N terminal the mutation, the more pronounced is the H-T joining defect. We have overexpressed and purified the recombinant gene 2 product (rgp2) to homogeneity in order to test its role in H-T joining, during in vitro reconstitution. When we mix extracts of heads from a gp2(+) phage infection (H(+)) with tails from a gp2(+) or gp2(-) phage infection (T(+) or T(-)), the H-T joining is fast and all of the reconstituted phage grow equally well on cells with or without ExoV activity. When heads from gene 2 amber mutants (H(-)) are used, addition of rgp2 is required for H-T joining. In this case, H-T joining is slow and only about 10% of the reconstituted phage can form plaques on ExoV(+) cells. When extracts of heads with different gene 2 amber mutations are mixed with extracts of tails (with a gene 2 amber mutation) in the presence of rgp2, we find that the size of the gp2 amber peptide of the head extract is inversely related to the fraction of reconstituted phage with a 2(+) phenotype. We conclude that free rgp2 is biologically active and has a direct role in H-T joining but that the process is different from H-T joining promoted by natural gp2 that is incorporated into the head in vivo. Furthermore, it seems that gp2 has a domain which binds it to the head. Thus, the presence of the longer gp2am mutants (with this domain) inhibits their replacement by full-length rgp2.


MicroRNA-223 Attenuates Hypoxia-induced Vascular Remodeling by Targeting RhoB/MLC2 in Pulmonary Arterial Smooth Muscle Cells.
There is growing evidence that microRNAs are implicated in pulmonary arterial hypertension (PAH), but underlying mechanisms remain elusive. Here, we identified that miR-223 was significantly downregulated in chronically hypoxic mouse and rat lungs, as well as in pulmonary artery and pulmonary artery smooth muscle cells (PASMC) exposed to hypoxia. Knockdown of miR-223 increased PASMC proliferation. In contrast, miR-223 overexpression abrogated cell proliferation, migration and stress fiber formation. Administering miR-223 agomir in vivo antagonized hypoxia-induced increase in pulmonary artery pressure and distal arteriole muscularization. RhoB, which was increased by hypoxia, was identified as one of the targets of miR-223. Overexpressed miR-223 suppressed RhoB and inhibited the consequent phosphorylation of myosin phosphatase target subunit (MYPT1) and the expression of myosin light chain of myosin II (MLC2), which was identified as another target of miR-223. Furthermore, serum miR-223 levels were decreased in female patients with PAH associated with congenital heart disease. Our study provides the first evidence that miR-223 can regulate PASMC proliferation, migration, and actomyosin reorganization through its novel targets, RhoB and MLC2, resulting in vascular remodeling and the development of PAH. It also highlights miR-223 as a potential circulating biomarker and a small molecule drug for diagnosis and treatment of PAH.


Effects of Antioxidant N-acetylcysteine Against Paraquat-Induced Oxidative Stress in Vital Tissues of Mice.
Paraquat (PQ) is a commonly used herbicide that induces oxidative stress via reactive oxygen species (ROS) generation. This study aimed to investigate the effects of the antioxidant N-acetylcysteine (NAC) against PQ-induced oxidative stress in mice. Male Balb/C mice (24) were randomly divided into 4 groups and treated for 3 weeks: 1) control (saline), 2) NAC (0.5% in diet), 3) PQ (20 mg/kg, IP) and 4) combination (PQ + NAC). Afterwards mice were sacrificed and oxidative stress markers were analyzed. Our data showed no significant change in serum antioxidant capacity. PQ enhanced lipid peroxidation (MDA) levels in liver tissue compared to control whereas NAC decreased MDA levels (p<0.05). NAC significantly increased MDA in brain tissue (p<0.05). PQ significantly depleted glutathione (GSH) levels in liver (p=0.001) and brain tissue (p<0.05) but non-significant GSH depletion in lung tissue. NAC counteracted PQ, showing a moderate increase GSH levels in liver and brain tissues. PQ significantly increased 8-oxodeoxyguanosine (8-OH-dG) levels (p<0.05) in liver tissue compared to control without a significant change in brain tissue. NAC treatment ameliorated PQ-induced oxidative DNA damage in the liver tissue. PQ significantly decreased the relative mtDNA amplification and increased the frequency of lesions in liver and brain tissue (p<0.0001), while NAC restored the DNA polymerase activity in liver tissue but not in brain tissue. In conclusion, PQ induced lipid peroxidation, oxidative nuclear DNA and mtDNA damage in liver tissues and depleted liver and brain GSH levels. NAC supplementation ameliorated the PQ-induced oxidative stress response in liver tissue of mice.


Soft-Pillared@Magadiite: influence of the interlayer space and amine type on CO2 adsorption.
Layered silicates are versatile materials that can be grafted with different organosilanes for several applications. Despite this, there are few studies on the use of layered silicate-based materials in CO2 adsorption. In this regard, the present study describes the synthesis of organo-magadiite followed by simultaneous grafting with two organosilanes ((3-glycidyloxypropyl)trimethoxysilane (GPTS) and N1-(3-trimethoxysilylpropyl)diethylenetriamine (TMSPETA)) to prepare an adsorbent labeled Soft-Pillared@Magadiite. The adsorbents were characterized through XRD, 13C- and 29Si-NMR, TGA/DTG, and elemental analyses of carbon, hydrogen, and nitrogen (CHN). The results suggest that this adsorbent has an expanded interlayer space (3.05 nm) that is larger than the interlayer space when the layered material is grafted with the organosilanes separately, and it may display improved CO2 adsorption. The CO2 adsorption was evaluated by TGA, CO2-TPD, and DSC. Moreover, the adsorption isotherms were fitted using a pseudo-second order, a fractional order, and Avrami models. The optimum adsorption temperature of Soft-Pillared@Magadiite was 25 °C, and the adsorption capacity and efficiency were 0.36 mmol g-1 and 0.15, respectively, obtained using 5 vol% CO2 in He for 3 h. The CO2-TPD shows that the desorption of CO2 occurs below 90 °C, and from DSC, it is found that thermodynamic parameters, specifically sensible heat and heat of regeneration, are low as compared to those of aqueous MEA solution; the current technology indicates that Soft-Pillared@Magadiite has a good potential for CO2 adsorption.


Lentiviral Vpx accessory factor targets VprBP/DCAF1 substrate adaptor for cullin 4 E3 ubiquitin ligase to enable macrophage infection.
Vpx is a small virion-associated adaptor protein encoded by viruses of the HIV-2/SIVsm lineage of primate lentiviruses that enables these viruses to transduce monocyte-derived cells. This probably reflects the ability of Vpx to overcome an as yet uncharacterized block to an early event in the virus life cycle in these cells, but the underlying mechanism has remained elusive. Using biochemical and proteomic approaches, we have found that Vpx protein of the pathogenic SIVmac 239 strain associates with a ternary protein complex comprising DDB1 and VprBP subunits of Cullin 4-based E3 ubiquitin ligase, and DDA1, which has been implicated in the regulation of E3 catalytic activity, and that Vpx participates in the Cullin 4 E3 complex comprising VprBP. We further demonstrate that the ability of SIVmac as well as HIV-2 Vpx to interact with VprBP and its associated Cullin 4 complex is required for efficient reverse transcription of SIVmac RNA genome in primary macrophages. Strikingly, macrophages in which VprBP levels are depleted by RNA interference resist SIVmac infection. Thus, our observations reveal that Vpx interacts with both catalytic and regulatory components of the ubiquitin proteasome system and demonstrate that these interactions are critical for Vpx ability to enable efficient SIVmac replication in primary macrophages. Furthermore, they identify VprBP/DCAF1 substrate receptor for Cullin 4 E3 ubiquitin ligase and its associated protein complex as immediate downstream effector of Vpx for this function. Together, our findings suggest a model in which Vpx usurps VprBP-associated Cullin 4 ubiquitin ligase to enable efficient reverse transcription and thereby overcome a block to lentivirus replication in monocyte-derived cells, and thus provide novel insights into the underlying molecular mechanism.


Sildenafil therapy in thalassemia patients with Doppler-defined risk of pulmonary hypertension.
Pulmonary hypertension is a common but often overlooked complication associated with thalassemia syndromes. There are limited data on the safety and efficacy of selective pulmonary vasodilators in this at-risk population. We, therefore, designed a 12-week, open-label, phase 1/2, pilot-scale, proof-of-principle trial of sildenafil therapy in 10 patients with β-thalassemia and at increased risk of pulmonary hypertension based on an elevated tricuspid regurgitant jet velocity >2.5 m/s on Doppler-echocardiography. Variables compared at baseline and after 12 weeks of sildenafil treatment included Doppler-echocardiographic parameters, 6-minute walked distance, Borg Dyspnea Score, New York Heart Association functional class, pulmonary function, and laboratory parameters. Treatment with sildenafil resulted in a significant decrease in tricuspid regurgitant jet velocity by 13.3% (3.0±0.7 versus 2.6±0.5 m/s, P=0.04), improved left ventricular end systolic/diastolic volume, and a trend towards a improved New York Heart Association functional class. No significant change in 6-minute walked distance was noted. Sildenafil was well tolerated, although minor expected adverse events were commonly reported. The total dose of sildenafil (mg) was strongly correlated with percent change in nitric oxide metabolite concentration in the plasma (ρ=0.80, P=0.01). There were also significant increases in plasma and erythrocyte arginine concentrations. Our study suggests that sildenafil is safe and may improve pulmonary hemodynamics in patients at risk of pulmonary hypertension; however, it was not demonstrated to improve the distance walked in 6 minutes. Clinical trials are needed to identify the best treatment strategy for pulmonary hypertension in patients with β-thalassemia. (clinicaltrials.gov identifier: NCT00872170).


Effect of warfarin on the induction and course of experimental Staphylococcus epidermidis endocarditis.
The effect of warfarin treatment on an experimental Staphylococcus epidermidis endocarditis was studied. Warfarin was found to affect both the induction and course of the infection of catheter-induced endocardial vegetations. In warfarin-treated rabbits, larger bacterial inocula were needed to induce an infection, and the degree of infection of the vegetations was also significantly lower, eventually resulting in the total elimination of the bacteria from the vegetations. Thus, warfarin treatment seems to have an inhibitory effect on the induction and development of an S. epidermidis infection of the endocardium. The results differ from previous findings in studies done with Streptococcus anguis, where warfarin was found to have no effect on the induction or course of the infection of endocardial vegetations, which suggests that different mechanisms are involved in the pathogenesis of endocarditis caused by these two species of bacteria.


Transcriptome sequencing for SNP discovery across Cucumis melo.
Melon (Cucumis melo L.) is a highly diverse species that is cultivated worldwide. Recent advances in massively parallel sequencing have begun to allow the study of nucleotide diversity in this species. The Sanger method combined with medium-throughput 454 technology were used in a previous study to analyze the genetic diversity of germplasm representing 3 botanical varieties, yielding a collection of about 40,000 SNPs distributed in 14,000 unigenes. However, the usefulness of this resource is limited as the sequenced genotypes do not represent the whole diversity of the species, which is divided into two subspecies with many botanical varieties variable in plant, flowering, and fruit traits, as well as in stress response. As a first step to extensively document levels and patterns of nucleotide variability across the species, we used the high-throughput SOLiD™ system to resequence the transcriptomes of a set of 67 genotypes that had previously been selected from a core collection representing the extant variation of the entire species. The deep transcriptome resequencing of all of the genotypes, grouped into 8 pools (wild African agrestis, Asian agrestis and acidulus, exotic Far Eastern conomon, Indian momordica and Asian dudaim and flexuosus, commercial cantalupensis, subsp. melo Asian and European landraces, Spanish inodorus landraces, and Piel de Sapo breeding lines) yielded about 300 M reads. Short reads were mapped to the recently generated draft genome assembly of the DHL line Piel de Sapo (inodorus) x Songwhan Charmi (conomon) and to a new version of melon transcriptome. Regions with at least 6X coverage were used in SNV calling, generating a melon collection with 303,883 variants. These SNVs were dispersed across the entire C. melo genome, and distributed in 15,064 annotated genes. The number and variability of in silico SNVs differed considerably between pools. Our finding of higher genomic diversity in wild and exotic agrestis melons from India and Africa as compared to commercial cultivars, cultigens and landraces from Eastern Europe, Western Asia and the Mediterranean basin is consistent with the evolutionary history proposed for the species. Group-specific SNVs that will be useful in introgression programs were also detected. In a sample of 143 selected putative SNPs, we verified 93% of the polymorphisms in a panel of 78 genotypes. This study provides the first comprehensive resequencing data for wild, exotic, and cultivated (landraces and commercial) melon transcriptomes, yielding the largest melon SNP collection available to date and representing a notable sample of the species diversity. This data provides a valuable resource for creating a catalog of allelic variants of melon genes and it will aid in future in-depth studies of population genetics, marker-assisted breeding, and gene identification aimed at developing improved varieties.


Structural basis of recognition of farnesylated and methylated KRAS4b by PDEδ.
Farnesylation and carboxymethylation of KRAS4b (Kirsten rat sarcoma isoform 4b) are essential for its interaction with the plasma membrane where KRAS-mediated signaling events occur. Phosphodiesterase-δ (PDEδ) binds to KRAS4b and plays an important role in targeting it to cellular membranes. We solved structures of human farnesylated-methylated KRAS4b in complex with PDEδ in two different crystal forms. In these structures, the interaction is driven by the C-terminal amino acids together with the farnesylated and methylated C185 of KRAS4b that binds tightly in the central hydrophobic pocket present in PDEδ. In crystal form II, we see the full-length structure of farnesylated-methylated KRAS4b, including the hypervariable region. Crystal form I reveals structural details of farnesylated-methylated KRAS4b binding to PDEδ, and crystal form II suggests the potential binding mode of geranylgeranylated-methylated KRAS4b to PDEδ. We identified a 5-aa-long sequence motif (Lys-Ser-Lys-Thr-Lys) in KRAS4b that may enable PDEδ to bind both forms of prenylated KRAS4b. Structure and sequence analysis of various prenylated proteins that have been previously tested for binding to PDEδ provides a rationale for why some prenylated proteins, such as KRAS4a, RalA, RalB, and Rac1, do not bind to PDEδ. Comparison of all four available structures of PDEδ complexed with various prenylated proteins/peptides shows the presence of additional interactions due to a larger protein-protein interaction interface in KRAS4b-PDEδ complex. This interface might be exploited for designing an inhibitor with minimal off-target effects.


Apitherapy products enhance the recovery of CCL4-induced hepatic damages in rats.
Our objective was to identify the antioxidant properties of honeybee products from Turkey, chestnut honey, pollen, propolis, and royal jelly, and their hepatoprotective activity against CCl4-induced hepatic damage in rats. Animals were fed with honeybee products for 7 days following CCl4 injection. Development of liver damage and oxidative stress were monitored by measuring the activities of the enzymes alanine transaminase, aspartate transaminase, malondialdehyde, superoxide dismutase, and catalase. Antioxidant capacities of the bee products were identified using FRAP and DPPH assays, as well as by measuring total phenolic and flavonoid contents. The antioxidant activities of the honeybee products were highest in propolis, followed, in order, by pollen, honey, and royal jelly. Despite their different levels of antioxidant capacity, their roles in the prevention of liver damage induced by CCl4 were very similar, which can be explained through their bioavailability to the treated animals. Our results suggest that honey, propolis, pollen, and royal jelly significantly enhanced the healing of CCl4-induced liver damage, partially due to their antioxidant properties and bioavailability.


Major facilitator superfamily.
The major facilitator superfamily (MFS) is one of the two largest families of membrane transporters found on Earth. It is present ubiquitously in bacteria, archaea, and eukarya and includes members that can function by solute uniport, solute/cation symport, solute/cation antiport and/or solute/solute antiport with inwardly and/or outwardly directed polarity. All homologous MFS protein sequences in the public databases as of January 1997 were identified on the basis of sequence similarity and shown to be homologous. Phylogenetic analyses revealed the occurrence of 17 distinct families within the MFS, each of which generally transports a single class of compounds. Compounds transported by MFS permeases include simple sugars, oligosaccharides, inositols, drugs, amino acids, nucleosides, organophosphate esters, Krebs cycle metabolites, and a large variety of organic and inorganic anions and cations. Protein members of some MFS families are found exclusively in bacteria or in eukaryotes, but others are found in bacteria, archaea, and eukaryotes. All permeases of the MFS possess either 12 or 14 putative or established transmembrane alpha-helical spanners, and evidence is presented substantiating the proposal that an internal tandem gene duplication event gave rise to a primordial MFS protein prior to divergence of the family members. All 17 families are shown to exhibit the common feature of a well-conserved motif present between transmembrane spanners 2 and 3. The analyses reported serve to characterize one of the largest and most diverse families of transport proteins found in living organisms.


Determination of the packing model of a supramolecular nanofiber via mass-per-length measurement and de novo simulation.
Herein, we report an example of using scanning transmission electron microscopy to determine the mass-per-length of supramolecular nanofibers. Together with the measurement of the diameter of nanofibers via transmission electron microscopy, we could estimate the packing density of assembling molecules along the nanofibers. A parallel unbiased de novo simulation screens and reveals the most plausible molecular packing pattern of small molecules along the supramolecular nanofibers. Remarkably, the simulated packing patterns and density correlate well with the experimental measurements. Unexpectedly, the naphthalene groups are likely facing outward, creating a hydrophobic surface, which is driven by the geometry of the hydrogelator molecule. Overall, this study establishes a complementary method to determine molecular arrangement along the supramolecular nanofibers, which is potentially useful for the guidance of rational design of biomaterials based on self-assembly.


Reproductive life-history strategies in a species-rich assemblage of Amazonian electric fishes.
The reproductive biology of only a small fraction of Neotropical freshwater fishes has been described, and detailed comparative studies of reproductive life-history variation in the Neotropical ichthyofauna are lacking. Here we describe interspecific variation in reproductive life history for a multi-species assemblage of the electric knifefish genus Brachyhypopomus (Hypopomidae: Gymnotiformes: Ostariophysi) from Amazonian floodplain and terra firme stream systems. During a year-round quantitative sampling program, we collected and measured key life-history traits from 3,410 individuals. Based on oocyte size distributions, and on circannual variation in gonadosomatic indices, hepatosomatic indices, and capture-per-unit-effort abundance of reproductive adults, we concluded that all species exhibit a single protracted annual breeding season during which females spawn fractionally. We found small clusters of post-larval individuals in one floodplain species and one terra firme stream species, but no signs of parental care. From analyses of body size-frequency distributions and otolith growth increments, we concluded that five species in our study area have approximately one-year (annual) semelparous life history with a single reproductive period followed by death, while two species have a two-year iteroparous life history, with breeding in both year-groups. Despite predictions from life-history theory we found no salient correlations between life history strategy (semelparity or iteroparity) and habitat occupancy (floodplain or terra firme stream). In the iteroparous species B. beebei, we documented evidence for reproductive restraint in the first breeding season relative to the second breeding season and argue that this is consistent with age-regulated terminal investment.


Eliminating fast reactions in stochastic simulations of biochemical networks: a bistable genetic switch.
In many stochastic simulations of biochemical reaction networks, it is desirable to "coarse grain" the reaction set, removing fast reactions while retaining the correct system dynamics. Various coarse-graining methods have been proposed, but it remains unclear which methods are reliable and which reactions can safely be eliminated. We address these issues for a model gene regulatory network that is particularly sensitive to dynamical fluctuations: a bistable genetic switch. We remove protein-DNA and/or protein-protein association-dissociation reactions from the reaction set using various coarse-graining strategies. We determine the effects on the steady-state probability distribution function and on the rate of fluctuation-driven switch flipping transitions. We find that protein-protein interactions may be safely eliminated from the reaction set, but protein-DNA interactions may not. We also find that it is important to use the chemical master equation rather than macroscopic rate equations to compute effective propensity functions for the coarse-grained reactions.


The PhenX Toolkit: get the most from your measures.
The potential for genome-wide association studies to relate phenotypes to specific genetic variation is greatly increased when data can be combined or compared across multiple studies. To facilitate replication and validation across studies, RTI International (Research Triangle Park, North Carolina) and the National Human Genome Research Institute (Bethesda, Maryland) are collaborating on the consensus measures for Phenotypes and eXposures (PhenX) project. The goal of PhenX is to identify 15 high-priority, well-established, and broadly applicable measures for each of 21 research domains. PhenX measures are selected by working groups of domain experts using a consensus process that includes input from the scientific community. The selected measures are then made freely available to the scientific community via the PhenX Toolkit. Thus, the PhenX Toolkit provides the research community with a core set of high-quality, well-established, low-burden measures intended for use in large-scale genomic studies. PhenX measures will have the most impact when included at the experimental design stage. The PhenX Toolkit also includes links to standards and resources in an effort to facilitate data harmonization to legacy data. Broad acceptance and use of PhenX measures will promote cross-study comparisons to increase statistical power for identifying and replicating variants associated with complex diseases and with gene-gene and gene-environment interactions.


Teneurin transmembrane protein 4 is not a cause for essential tremor in a Canadian population.
Mutations in teneurin transmembrane protein 4 were reported to be a risk factor for essential tremor, but the relevance of this across different population remains to be examined. The aim of this study was to determine the frequency and spectrum of variations in teneurin transmembrane protein 4 in a cohort of Canadian essential tremor cases. The coding portion of teneurin transmembrane protein 4 was sequenced in 269 unrelated essential tremor cases and 288 matched control individuals using a targeted and high-throughput sequencing approach. A total of 157 single nucleotide variations were identified, and from these 99 were a missense or nonsense mutation. A total of 68 cases were carriers of ≥1 rare missense or nonsense mutations, and 39 control individuals were carriers of the same types of variations. Gene-based association tests were used to jointly analyze the single nucleotide variations. Our results do not support a positive association between teneurin transmembrane protein 4 and the Canadian population. © 2017 International Parkinson and Movement Disorder Society.


How do SNP ascertainment schemes and population demographics affect inferences about population history?
The selection of variable sites for inclusion in genomic analyses can influence results, especially when exemplar populations are used to determine polymorphic sites. We tested the impact of ascertainment bias on the inference of population genetic parameters using empirical and simulated data representing the three major continental groups of cattle: European, African, and Indian. We simulated data under three demographic models. Each simulated data set was subjected to three ascertainment schemes: (I) random selection; (II) geographically biased selection; and (III) selection biased toward loci polymorphic in multiple groups. Empirical data comprised samples of 25 individuals representing each continental group. These cattle were genotyped for 47,506 loci from the bovine 50 K SNP panel. We compared the inference of population histories for the empirical and simulated data sets across different ascertainment conditions using F ST and principal components analysis (PCA). Bias toward shared polymorphism across continental groups is apparent in the empirical SNP data. Bias toward uneven levels of within-group polymorphism decreases estimates of F ST between groups. Subpopulation-biased selection of SNPs changes the weighting of principal component axes and can affect inferences about proportions of admixture and population histories using PCA. PCA-based inferences of population relationships are largely congruent across types of ascertainment bias, even when ascertainment bias is strong. Analyses of ascertainment bias in genomic data have largely been conducted on human data. As genomic analyses are being applied to non-model organisms, and across taxa with deeper divergences, care must be taken to consider the potential for bias in ascertainment of variation to affect inferences. Estimates of F ST , time of separation, and population divergence as estimated by principal components analysis can be misleading if this bias is not taken into account.


Number-processing skills in adults with dyslexia.
The present study investigated basic numerical skills and arithmetic in adults with developmental dyslexia. Participants performed exact and approximate calculation, basic numerical tasks (e.g., counting; symbolic number comparison; spatial-numerical association of response codes, SNARC), and visuospatial tasks (mental rotation and visual search tasks). The group with dyslexia showed a marginal impairment in counting compared to age- and IQ-matched controls, and they were impaired in exact addition, in particular with respect to speed. They were also significantly slower in multiplication. In basic number processing, however, there was no significant difference in performance between those with dyslexia and controls. Both groups performed similarly on subtraction and approximate addition tasks. These findings indicate that basic number processing in adults with dyslexia is intact. Their difficulties are restricted to the verbal code and are not associated with deficits in nonverbal magnitude representation, visual Arabic number form, or spatial cognition.


Sleep Habits and Nighttime Texting Among Adolescents.
The aim of this study was to examine sleep habits (i.e., bedtimes and rising times) and their association with nighttime text messaging in 15- to 17-year-old adolescents. This cross-sectional study analyzed data from a web-based survey of adolescent students attending secondary schools in southern Sweden ( N = 278, 50% female). Less than 8 hr of time in bed during school nights was significantly associated with more sleep difficulties, wake time variability on school days and weekends, daytime tiredness, and less enjoyment at school (all ps < .05). Sending and/or receiving text messages (Short Message Service [SMS]) at night was significantly associated with later bedtimes, shorter time in bed, daytime tiredness during school, and irregular sleep habits ( p < .05). These findings highlight the importance of regular, consistent sleep habits and the problems associated with sleeping with a cell phone in the bedroom.