Cost effectiveness of duloxetine in the treatment of fibromyalgia in the United States.
To evaluate the cost effectiveness of duloxetine when considered as an alternative treatment for patients in the United States (US) being treated for fibromyalgia pain. A Markov model was used to evaluate the economic and clinical advantages of duloxetine in controlling fibromyalgia pain symptoms over a 2-year time horizon. A base-case treatment sequence was adopted from clinical guidelines, based on tricyclic antidepressants, serotonin-norepinephrine reuptake inhibitors, anticonvulsants, and opioids. Treatment response was modeled using changes from baseline in pain severity, and response thresholds: full response (at least a 50% change), response (30-49% change), and no response (less than a 30% change). Clinical efficacy and discontinuation data were taken from placebo- and active-controlled trials identified in a systematic literature review and mixed-treatment comparison. Utility data were based on EQ-5D data. Additional symptom-control months (SCMs), defined as the amount of time at a response level of 30% or less, and quality-adjusted life-years (QALYs) over a 2-year time horizon. For every 1000 patients, first-line duloxetine resulted in an additional 665 SCMs and 12.3 QALYs, at a cost of $582,911 (equivalent to incremental cost-effectiveness ratios [ICERs] of $877 per SCM and $47,560 per QALY). Second-line duloxetine resulted in an additional 460 SCMs and 8.7 QALYs, at a cost of $143,752 (equivalent to ICERs of $312 per SMC and $16,565 per QALY). Response data for TCAs are limited to 30% improvement levels, reported trials are small, and have low placebo response rates. The model necessarily assumes that response rates are independent of placement in the treatment sequence. The results suggest that the introduction of duloxetine into the standard treatment sequence for fibromyalgia not only provides additional patient benefits, reflected by time spent in pain control, but also is cost effective when compared with commonly adopted thresholds.


Epidermal elafin expression is an indicator of poor prognosis in cutaneous graft-versus-host disease.
Graft-versus-host disease (GVHD) remains a common and potentially life-threatening complication of allogeneic hematopoietic stem cell transplantation. In the skin, GVHD can present in an acute (aGVHD), chronic lichenoid (clGVHD), or chronic sclerotic form (csGVHD). Measuring peripheral blood levels of the keratinocyte-derived protease inhibitor elafin has recently emerged as a promising tool for the diagnosis of cutaneous aGVHD. We evaluated whether the analysis of elafin expression in skin would allow distinguishing aGVHD from drug hypersensitivity rashes (DHR) and whether cutaneous elafin expression would correlate with disease severity or altered prognosis of aGVHD and clGVHD/csGVHD. Skin biopsies from aGVHD (n=22), clGVHD (n=15), csGVHD (n=7), and DHR (n=10) patients were collected and epidermal elafin expression and its association with diverse clinical/histological parameters were analyzed. Acute GVHD and DHR displayed varying degrees of elafin expression. No elafin was detectable in csGVHD, whereas the molecule was increased in clGVHD as compared with aGVHD. Elafin-high aGVHD/clGVHD lesions presented with epidermal thickening and were associated with poor prognosis-i.e., decreased overall survival in aGVHD and corticosteroid resistance in clGVHD. Although cutaneous elafin does not seem to discriminate aGVHD from DHR lesions, our study strongly suggests an association between cutaneous elafin expression and poor prognosis for patients with cutaneous GVHD.


Passive energy recapture in jellyfish contributes to propulsive advantage over other metazoans.
Gelatinous zooplankton populations are well known for their ability to take over perturbed ecosystems. The ability of these animals to outcompete and functionally replace fish that exhibit an effective visual predatory mode is counterintuitive because jellyfish are described as inefficient swimmers that must rely on direct contact with prey to feed. We show that jellyfish exhibit a unique mechanism of passive energy recapture, which is exploited to allow them to travel 30% further each swimming cycle, thereby reducing metabolic energy demand by swimming muscles. By accounting for large interspecific differences in net metabolic rates, we demonstrate, contrary to prevailing views, that the jellyfish (Aurelia aurita) is one of the most energetically efficient propulsors on the planet, exhibiting a cost of transport (joules per kilogram per meter) lower than other metazoans. We estimate that reduced metabolic demand by passive energy recapture improves the cost of transport by 48%, allowing jellyfish to achieve the large sizes required for sufficient prey encounters. Pressure calculations, using both computational fluid dynamics and a newly developed method from empirical velocity field measurements, demonstrate that this extra thrust results from positive pressure created by a vortex ring underneath the bell during the refilling phase of swimming. These results demonstrate a physical basis for the ecological success of medusan swimmers despite their simple body plan. Results from this study also have implications for bioinspired design, where low-energy propulsion is required.


The use of sonicated lipid vesicles for mass spectrometry of membrane protein complexes.
Recent applications of mass spectrometry (MS) to study membrane protein complexes are yielding valuable insights into the binding of lipids and their structural and functional roles. To date, most native MS experiments with membrane proteins are based on detergent solubilization. Many insights into the structure and function of membrane proteins have been obtained using detergents; however, these can promote local lipid rearrangement and can cause fluctuations in the oligomeric state of protein complexes. To overcome these problems, we developed a method that does not use detergents or other chemicals. Here we report a detailed protocol that enables direct ejection of protein complexes from membranes for analysis by native MS. Briefly, lipid vesicles are prepared directly from membranes of different sources and subjected to sonication pulses. The resulting destabilized vesicles are concentrated, introduced into a mass spectrometer and ionized. The mass of the observed protein complexes is determined and this information, in conjunction with 'omics'-based strategies, is used to determine subunit stoichiometry as well as cofactor and lipid binding. Within this protocol, we expand the applications of the method to include peripheral membrane proteins of the S-layer and amyloid protein export machineries overexpressed in membranes from which the most abundant components have been removed. The described experimental procedure takes approximately 3 d from preparation to MS. The time required for data analysis depends on the complexity of the protein assemblies embedded in the membrane under investigation.


In vitro fermentation of grape seed flavan-3-ol fractions by human faecal microbiota: changes in microbial groups and phenolic metabolites.
With the aim of investigating the potential of flavan-3-ols to influence the growth of intestinal bacterial groups, we have carried out the in vitro fermentation, with human faecal microbiota, of two purified fractions from grape seed extract (GSE): GSE-M (70% monomers and 28% procyanidins) and GSE-O (21% monomers and 78% procyanidins). Samples were collected at 0, 5, 10, 24, 30 and 48 h of fermentation for bacterial enumeration by fluorescent in situ hybridization and for analysis of phenolic metabolites. Both GSE-M and GSE-O fractions promoted growth of Lactobacillus/Enterococcus and decrease in the Clostridium histolyticum group during fermentation, although the effects were only statistically significant with GSE-M for Lactobacillus/Enterococcus (at 5 and 10 h of fermentation) and GSE-O for C. histolyticum (at 10 h of fermentation). Main changes in polyphenol catabolism also occurred during the first 10 h of fermentation; however, no significant correlation coefficients (P > 0.05) were found between changes in microbial populations and precursor flavan-3-ols or microbial metabolites. Together, these data suggest that the flavan-3-ol profile of a particular food source could affect the microbiota composition and its catabolic activity, inducing changes that could in turn affect the bioavailability and potential bioactivity of these compounds.


Immunologic characterization and functional properties of murine antibodies raised against deleted mutants of human beta 2-glycoprotein I.
beta 2-Glycoprotein I (beta 2GPI) is a 50 kDa molecule proposed as a principal target of 'autoimmune' antiphospholipid antibodies (aPL). We have used deleted mutants (DM) representing different domains of beta 2GPI (I-IV, IV-V and V) for immunization of naive mice and studied the characteristics of the respective murine IgG preparations in comparison with affinity-purified IgG from two patients with primary antiphospholipid syndrome. Immunization with beta 2GPI and with the DM produced anti-beta 2GPI antibodies, part of which reacted with negatively charged phospholipids (PL), whereas reactivity with cardiolipin was evident only in the IgG from mice immunized with beta 2GPI. These results are consistent with the presumption that aPL are induced following the in vivo association of beta 2GPI (used for immunization) with resident negatively charged PL. Accordingly, DM which either lack the PL binding site or aPL attachment locus did not elicit, upon immunization, antibodies reactive with PL. Further, murine anti-beta 2GPI IgG and human 'autoimmune' aPL were similar, albeit not identical, in terms of DM requirement for PL binding and charge dependency. Murine antibodies and human aPL, regardless of their binding characteristics, were found to bind significantly to platelets upon their activation with thrombin and to promote platelet activation. The results of the current study emphasize the dissimilarities between human 'autoimmune' aPL and murine anti-beta 2GPI. Thus, anti-beta 2GPI antibodies to different DM as well as human aPL are capable of binding and activating human platelets provided beta 2GPI is present.


TGF-β-driven muscle degeneration and failed regeneration underlie disease onset in a DMD mouse model.
Duchenne muscular dystrophy (DMD) is a chronic muscle disease characterized by poor myogenesis and replacement of muscle by extracellular matrix. Despite the shared genetic basis, severity of these deficits varies among patients. One source of these variations is the genetic modifier that leads to increased TGF-β activity. While anti-TGF-β therapies are being developed to target muscle fibrosis, their effect on the myogenic deficit is underexplored. Our analysis of in vivo myogenesis in mild (C57BL/10ScSn-mdx/J and C57BL/6J-mdxΔ52) and severe DBA/2J-mdx (D2-mdx) dystrophic models reveals no defects in developmental myogenesis in these mice. However, muscle damage at the onset of disease pathology, or by experimental injury, drives up TGF-β activity in the severe, but not in the mild, dystrophic models. Increased TGF-β activity is accompanied by increased accumulation of fibroadipogenic progenitors (FAPs) leading to fibro-calcification of muscle, together with failure of regenerative myogenesis. Inhibition of TGF-β signaling reduces muscle degeneration by blocking FAP accumulation without rescuing regenerative myogenesis. These findings provide in vivo evidence of early-stage deficit in regenerative myogenesis in D2-mdx mice and implicates TGF-β as a major component of a pathogenic positive feedback loop in this model, identifying this feedback loop as a therapeutic target.


Reticulate Evolution Helps Explain Apparent Homoplasy in Floral Biology and Pollination in Baobabs (Adansonia; Bombacoideae; Malvaceae).
Baobabs (Adansonia) are a cohesive group of tropical trees with a disjunct distribution in Australia, Madagascar, and continental Africa, and diverse flowers associated with two pollination modes. We used custom-targeted sequence capture in conjunction with new and existing phylogenetic comparative methods to explore the evolution of floral traits and pollination systems while allowing for reticulate evolution. Our analyses suggest that relationships in Adansonia are confounded by reticulation, with network inference methods supporting at least one reticulation event. The best supported hypothesis involves introgression between Adansonia rubrostipa and core Longitubae, both of which are hawkmoth pollinated with yellow/red flowers, but there is also some support for introgression between the African lineage and Malagasy Brevitubae, which are both mammal-pollinated with white flowers. New comparative methods for phylogenetic networks were developed that allow maximum-likelihood inference of ancestral states and were applied to study the apparent homoplasy in floral biology and pollination mode seen in Adansonia. This analysis supports a role for introgressive hybridization in morphological evolution even in a clade with highly divergent and geographically widespread species. Our new comparative methods for discrete traits on species networks are implemented in the software PhyloNetworks. [Comparative methods; Hyb-Seq; introgression; network inference; population trees; reticulate evolution; species tree inference; targeted sequence capture.].


Inhibition of thrombus formation in vivo by novel antiplatelet agent.
The antithrombotic and antihemostatic effects of the novel antiplatelet compound, alpha, alpha'-bis[3-(N,N-diethylcarbamoyl)piperidino]-p-xylene dihydrobromide (GT-12), were investigated in a baboon model of platelet-dependent thrombosis under high flow conditions. In this model, segments of collagen-coated tubing and Dacron vascular graft were placed as thrombus-inducing extension devices in exteriorized femoral arteriovenous shunts. The deposition of 111In-labeled platelets was measured for each thrombogenic segment throughout 1 hour by using gamma camera imaging. In addition, the 125I-fibrin retained in the forming thrombus was measured. Intravenous infusion of GT-12 (100 mumol/kg, 63.3 mg/kg) over a 15-minute period before the insertion of the test segments prolonged the bleeding time from a baseline value of 4.4 +/- 0.4 min to 7.6 +/- 1.0 min (p = 0.036) and inhibited platelet aggregation ex vivo induced by adenosine diphosphate (ED50 4.7 +/- 0.9 to 10.3 +/- 2.2 microM; p less than 0.02) and collagen (ED50 2.0 +/- 0.4 to 8.0 +/- 2.4 micrograms/ml; p less than 0.05). Deposition of platelets and fibrin was decreased in concert by 30% (p less than 0.05) for vascular grafts and possibly collagen segments at the end of the 60-minute observation period. We conclude that GT-12 is antithrombotic for Dacron graft-induced thrombus formation in vivo.


A biofilm growth protocol and the design of a magnetic field exposure setup to be used in the study of magnetic fields as a means of controlling bacterial biofilms.
The use of prosthetic implants is increasing both in the United States and around the world and there is a concomitant rise in cases of biofilm-based, persistent infections that are quite serious and virtually impervious to antibiotic treatment. The development of alternate therapies that do not involve long term use of high levels of antibiotics or surgical intervention is needed. Based on the success of using electric or magnetic fields to alter certain physiological processes, it is hypothesized that relatively low level magnetic fields, in conjunction with the appropriate antibiotic, may be able to help control and eventually clear bacterial biofilms on a prosthetic. In order to test this hypothesis, it is necessary to first develop a means of growing laboratory grade biofilms on specific materials in a way that is repeatable between experiments and that can be reproduced by other laboratories. Secondly, a means of applying controlled magnetic fields to the surfaces supporting the biofilms at a defined temperature must be developed. This article addresses both of these points.


Corpus callosum morphology across the lifespan in baboons (Papio anubis): A cross-sectional study of relative mid-sagittal surface area and thickness.
The corpus callosum enables integration and coordination of cognitive processing between the cerebral hemispheres. In the aging human brain, these functions are affected by progressive axon and myelin deteriorations, reflected as atrophy of the midsagittal corpus callosum in old age. In non-human primates, these degenerative processes are less pronounced as previous morphometric studies on capuchin monkey, rhesus monkeys, and chimpanzees do not find old-age callosal atrophy. In the present study, we extend these previous findings by studying callosal development of the olive baboon (Papio anubis) across the lifespan and compare it to chimpanzee and human data. For this purpose, total relative (to forebrain volume) midsagittal area, subsectional area, and regional thickness of the corpus callosum were assessed in 91 male and female baboons using non-invasive MRI-based morphometry. The studied age range was 2.5-26.6 years and lifespan trajectories were fitted using general additive modelling. Relative area of the total and anterior corpus callosum showed a positive linear trajectory. That is, both measures increased slowly but continuously from childhood into old age, and no decline was observed in old age. Thus, comparable with all other non-human primates studied to-date, baboons do not show callosal atrophy in old age. This observation lends supports to the notion that atrophy of the corpus callosum is a unique characteristic of human brain aging.


Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "Alchemical" path, and practical solutions.
Thermodynamic integration is a widely used method to calculate and analyze the effect of a chemical modification on the free energy of a chemical or biochemical process, for example, the impact of an amino acid substitution on protein association. Numerical fluctuations can introduce large uncertainties, limiting the domain of application of the method. The parametric energy function describing the chemical modification in the thermodynamic integration, the "Alchemical path," determines the amplitudes of the fluctuations. In the present work, I propose a measure of the fluctuations in the thermodynamic integration and an approach to search for a parametric energy path minimizing that measure. The optimal path derived with this approach is very close to the theoretical minimum of the measure, but produces nonergodic sampling. Nevertheless, this path is used to guide the design of a practical and efficient path producing correct sampling. The convergence with this practical path is evaluated on test cases, and compares favorably with that of other methods such as power or polynomial path, soft-core van der Waals, and some other approaches presented in the literature.


Optimization and Control of Cyber-Physical Vehicle Systems.
A cyber-physical system (CPS) is composed of tightly-integrated computation, communication and physical elements. Medical devices, buildings, mobile devices, robots, transportation and energy systems can benefit from CPS co-design and optimization techniques. Cyber-physical vehicle systems (CPVSs) are rapidly advancing due to progress in real-time computing, control and artificial intelligence. Multidisciplinary or multi-objective design optimization maximizes CPS efficiency, capability and safety, while online regulation enables the vehicle to be responsive to disturbances, modeling errors and uncertainties. CPVS optimization occurs at design-time and at run-time. This paper surveys the run-time cooperative optimization or co-optimization of cyber and physical systems, which have historically been considered separately. A run-time CPVS is also cooperatively regulated or co-regulated when cyber and physical resources are utilized in a manner that is responsive to both cyber and physical system requirements. This paper surveys research that considers both cyber and physical resources in co-optimization and co-regulation schemes with applications to mobile robotic and vehicle systems. Time-varying sampling patterns, sensor scheduling, anytime control, feedback scheduling, task and motion planning and resource sharing are examined.


Thermoelectric properties of the Zintl phases Yb5M2Sb6 (M = Al, Ga, In).
Zintl compounds with chemical formula Yb5M2Sb6 (M = Al, Ga, and In) form one of two known A5M2Pn6 structure types characterized by double chains of corner-linked MPn4 tetrahedra bridged by Pn2 dumbbells. High temperature electronic and thermal transport measurements were used to characterize the thermoelectric properties of Yb5M2Sb6 compounds. All samples were found to exhibit similar high p-type carrier concentrations, low resistivity and low Seebeck coefficients in agreement with the band structure calculations. These results, combined with previous studies, suggest that Yb5M2Sb6 compounds are semimetals (i.e., they lack an energy gap between the valence and conduction bands), in contrast to the semiconducting alkaline earth (Ca, Sr, Ba) and Eu based A5M2Sb6 compounds. Yb5M2Sb6 compounds have very low lattice thermal conductivity, comparable to other closely related A5M2Sb6 and A3MSb3 phases. However, due to the semimetallic behaviour, the figure of merit of investigated samples remains low (zT < 0.15).


Assessing the probability of acquisition of meticillin-resistant Staphylococcus aureus (MRSA) in a dog using a nested stochastic simulation model and logistic regression sensitivity analysis.
Meticillin-resistant Staphylococcus aureus (MRSA) is an important nosocomial and community-acquired pathogen with zoonotic potential. The relationship between MRSA in humans and companion animals is poorly understood. This study presents a quantitative exposure assessment, based on expert opinion and published data, in the form of a second order stochastic simulation model with accompanying logistic regression sensitivity analysis that aims to define the most important factors for MRSA acquisition in dogs. The simulation model was parameterised using expert opinion estimates, along with published and unpublished data. The outcome of the model was biologically plausible and found to be dominated by uncertainty over variability. The sensitivity analysis, in the form of four separate logistic regression models, found that both veterinary and non-veterinary routes of acquisition of MRSA are likely to be relevant for dogs. The effects of exposure to, and probability of, transmission of MRSA from the home environment were ranked as the most influential predictors in all sensitivity analyses, although it is unlikely that this environmental source of MRSA is independent of alternative sources of MRSA (human and/or animal). Exposure to and transmission from MRSA positive family members were also found to be influential for acquisition of MRSA in pet dogs, along with veterinary clinic attendance and, while exposure to and transmission from the veterinary clinic environment was also found to be influential, it was difficult to differentiate between the importance of independent sources of MRSA within the veterinary clinic. The implementation of logistic regression analyses directly to the input/output relationship within the simulation model presented in this paper represents the application of a variance based sensitivity analysis technique in the area of veterinary medicine and is a useful means of ranking the relative importance of input variables.


Contribution of the Portuguese Laboratory Network for the Diagnosis of Influenza A(H1N1)pdm09 infection during the 2009/10 and 2010/11 influenza seasons.
This article describes the data obtained by the Portuguese Laboratory Network, reactivated following the World Health Organization declaration of the 2009 influenza pandemic, on the diagnoses of influenza A(H1N1)pdm09 infection during the pandemic (2009/10) and post-pandemic (2010/11) influenza seasons. The laboratories analysed and reported cases of influenza-like illness (ILI) and severe acute respiratory infection (SARI) to the National Influenza Reference Laboratory, which performed more detailed antigenic and genetic characterisation of the virus isolates. In 2009/10, a total of 62,089 ILI cases, distributed in two peaks, were analysed, 25,985 of which were positive for influenza A(H1N1)pdm09. Children aged 5–14 years were the most affected. Viruses were both antigenically and genetically similar to the pandemic strain A/California/7/2009, included in the 2009/10 pandemic vaccine. During the post-pandemic season, 1,496 ILI cases were tested for influenza A(H1N1) pdm09, 572 of which were positive. Infection was mainly diagnosed in adolescent and adults. Although the 2010/11 viruses remained antigenically similar to A/California/7/2009, increased genetic variation was observed. During the two seasons, two viruses with the neuraminidase H275Y amino acid substitution, associated with oseltamivir resistance, were detected. The Laboratory Network made an important contribution to the description of the influenza activity in the two seasons.


β-Glucosidase 2 (GBA2) activity and imino sugar pharmacology.
β-Glucosidase 2 (GBA2) is an enzyme that cleaves the membrane lipid glucosylceramide into glucose and ceramide. The GBA2 gene is mutated in genetic neurological diseases (hereditary spastic paraplegia and cerebellar ataxia). Pharmacologically, GBA2 is reversibly inhibited by alkylated imino sugars that are in clinical use or are being developed for this purpose. We have addressed the ambiguity surrounding one of the defining characteristics of GBA2, which is its sensitivity to inhibition by conduritol B epoxide (CBE). We found that CBE inhibited GBA2, in vitro and in live cells, in a time-dependent fashion, which is typical for mechanism-based enzyme inactivators. Compared with the well characterized impact of CBE on the lysosomal glucosylceramide-degrading enzyme (glucocerebrosidase, GBA), CBE inactivated GBA2 less efficiently, due to a lower affinity for this enzyme (higher KI) and a lower rate of enzyme inactivation (k(inact)). In contrast to CBE, N-butyldeoxygalactonojirimycin exclusively inhibited GBA2. Accordingly, we propose to redefine GBA2 activity as the β-glucosidase that is sensitive to inhibition by N-butyldeoxygalactonojirimycin. Revised as such, GBA2 activity 1) was optimal at pH 5.5-6.0; 2) accounted for a much higher proportion of detergent-independent membrane-associated β-glucosidase activity; 3) was more variable among mouse tissues and neuroblastoma and monocyte cell lines; and 4) was more sensitive to inhibition by N-butyldeoxynojirimycin (miglustat, Zavesca®), in comparison with earlier studies. Our evaluation of GBA2 makes it possible to assess its activity more accurately, which will be helpful in analyzing its physiological roles and involvement in disease and in the pharmacological profiling of monosaccharide mimetics.


Measuring Tijuana residents' choice of Mexican or U.S. health care services.
There is growing concern that the indigent health care burden in the southwestern United States may be caused partly by Mexican residents who cross the border to use U.S. health services. This article describes the first attempt to measure the extent of this use by border residents. It also compares factors associated with their use of health care services in both the United States and Mexico. Data were obtained from a household survey conducted in Tijuana, Mexico, near the California border, using a random, stratified analytic sample of 660 households that included a total of 2,954 persons. The dependent variables--extent and volume of contacts with health professionals--were examined according to sociodemographic characteristics, insurance coverage, payment modality, type of visit, and health care setting. The results indicate that 40.3 percent of the Tijuana population used health services exclusively in Mexico during a 6-month period, compared with only 2.5 percent who used services in the United States. Of the Mexican users of U.S. services, the largest proportion appeared to be older people, lawful permanent residents or citizens of the United States who are living in Mexico, and persons from high- or middle-income sectors. In addition to the low level of use of U.S. health services, the findings show that more than 84 percent of the visits were to providers in the private sector and, for 59 percent of the visits, a fee for services was implied. Overall, this border population does not seem to be a drain on the U.S. public health system. The findings must remain tentative, given some methodological constraints of the study; they point to the need for further assessments of the demand for specific services by distinct segments of the border population. Furthermore,since health care financing is a critical issue for Mexico as well, more studies are needed that examine the behavior of U.S. residents who use Mexican health services.


Risk of kidney cancer and chronic kidney disease in relation to hepatitis C virus infection: a nationwide register-based cohort study in Sweden.
Chronic hepatitis C virus (HCV) infection is an established cause of liver cancer, and recent studies have suggested a link with kidney cancer. The aim of this study was to evaluate risk of kidney cancer in relation to HCV infection in a nationwide registry-based study of Swedish residents diagnosed with HCV between 1990 and 2006. A total of 43 000 individuals with chronic HCV infection were included, and the mean follow-up time was 9.3 years. Observed kidney cancer incidence and mortality in the cohort were compared with expected values based on the age-adjusted and sex-adjusted rates in the general population. Risk of hospitalization for other chronic kidney disease was also evaluated using Cox proportional hazards regression. No association between HCV infection and risk of kidney cancer was observed [standardized incidence ratio with 1-year lag=1.2; 95% confidence interval (CI): 0.8-1.7]. Risk of hospitalization for noncancer kidney disease was significantly elevated in the HCV cohort, with significantly stronger associations observed among women than among men [hazard ratio=5.8 (95% CI: 4.2-7.9) and 3.9 (95% CI: 3.2-4.8) for women and men, respectively]. Results of this study do not support the hypothesis that chronic HCV infection confers an increased risk of kidney cancer. However, we did find an association between HCV infection and chronic kidney disease, particularly among women. Given inconsistent findings in the literature, it is premature to consider HCV infection to be a risk factor for kidney cancer.


Cumulative inequality in child health and academic achievement.
Our understanding of health and social stratification can be enriched by testing tenets of cumulative inequality theory that emphasize how the accumulation of inequality is dependent on the developmental stage being considered, the duration and stability of poor health, and the family resources available to children. I analyze longitudinal data from the British National Child Development Study (N = 9,252) to ask: (1) if child health is a source of cumulative inequality in academic achievement, (2) whether this relationship depends on the timing and duration of poor health, and (3) whether trajectories are sensitive to levels of family capital. The results suggest that the relationship between health and academic achievement emerges very early in life and persists and that whether we observe shrinking or widening inequality as children age depends on when we measure their health and whether children have access to compensatory resources.


Oxygen free radical scavenger enzyme polymorphisms in systemic sclerosis.
We performed a case-control study of polymorphisms of glutathione S-transferase (GST) isoenzymes and manganese superoxide dismutase (MnSOD) in black South Africans with systemic sclerosis (SSc). The frequency of the GSTM1*B phenotype was significantly decreased in the overall SSc group compared with controls (OR=0.19, p(corr)<.05), implying a possible protective effect against development of the disease. There was also a trend toward increased MnSODAla allele and phenotype frequencies in the diffuse cutaneous SSc subset compared with controls (OR=2.11 and 3.15, respectively, p(corr)<.1). Our findings provide new data on the distribution of GST and MnSOD polymorphisms in healthy Africans and further evidence that genetic factors may have a contributory role to play in predisposing to oxidative stress in SSc.


Quantifying the level of difficulty to treat major depressive disorder with antidepressants: Treatment Resistance to Antidepressants Evaluation Scale.
The present study aimed to develop a new scale to evaluate the level of difficulty in treating major depressive disorder with antidepressants based on the lifetime treatment profile. In addition to evaluating the difficulty of treatment with antidepressants (A subscale), the Treatment Resistance to Antidepressants Evaluation Scale (TRADES) is comprised of a subscale to account for the attributes that compromise the efficacy of treatment (B subscale). One hundred and six participants aged 18 to 65 years with remitted major depressive disorder were enrolled. Eligible cases were those with at least 2 years from disease onset until the scoring date of the TRADES (the index date), with a complete treatment record. Various psychosocial and clinical features, such as neuroticism, harm avoidance, and utilization of psychiatric services, were used to validate the TRADES. The mean duration of the course before and after the index date were 5.5 ± 3.5 and 3.1 ± 1.7 years, respectively. In a multiple regression analysis, the final total scores of the TRADES independently correlated with higher levels of neuroticism and harm avoidance. Total scores were also associated with a higher utilization of psychiatric outpatient and admission services before the index date. Furthermore, it is thought that total scores could predict a higher number of visits to psychiatric outpatient, emergency, and admission services following the index date. The TRADES has acceptable validity and could help to quantify the level of treatment difficulty with antidepressants in major depressive disorder.


Clustered cadherin genes: a sequence-ready contig for the desmosomal cadherin locus on human chromosome 18.
We describe the assembly of a cosmid and PAC contig of approximately 700 kb on human chromosome 18q12 spanning the DSC and DSG genes coding for the desmocollins and desmogleins. These are members of the cadherin superfamily of calcium-dependent cell adhesion proteins present in the desmosome type of cell junction found especially in epithelial cells. They provide the strong cell-cell adhesion generated by this type of cell junction for which expression of both a desmocollin and a desmoglein is required. In the autoimmune skin diseases pemphigus foliaceous and pemphigus vulgaris (PV), where the autoantigens are, respectively, encoded by the DSG1 and DSG3 genes, severe areas of acantholysis (cell separation), potentially life-threatening in the case of PV, are evident. Dominant mutations in the DSG1 gene causing striate palmoplantar keratoderma result in hyperkeratosis of the skin on the parts of the body where pressure and abrasion are greatest, viz., on the palms and soles. These genes are also candidate tumor suppressor genes in squamous cell carcinomas and other epithelial cancers. We have screened two chromosome 18-specific cosmid libraries by hybridization with previously isolated YAC clones and DSC and DSG cDNAs, and a whole genome PAC library, both by hybridization with the YACs and by screening by PCR using cDNA sequences and YAC end sequence. The contigs were extended by further PCR screens using STSs generated by vectorette walking from the ends of the cosmids and PACs, together with sequence from PAC ends. Despite screening of two libraries, the cosmid contig still had four gaps. The PAC contig filled these gaps and in fact covered the whole locus. The positions of 45 STSs covering the whole of this region are presented. The desmocollin and desmoglein genes, which are about 30-35 kb in size, are quite well separated at approximately 20-30 kb apart and are arranged in two clusters, one DSC cluster and one DSG cluster, which are transcribed outward from the interlocus region. The order of the genes is correlated with the spatial order of gene expression in the developing mouse embryo, and this, and previous transgenic experiments, suggests that long-range genetic elements that coordinate expression of these genes may be present. The complete bacterial clone contig described in this paper is thus a resource not only for future sequencing but also for investigations into the control of expression of these clustered genes.


Effect of an optical negative index thin film on optical bistability.
We investigate nonlinear transmission in a layered structure consisting of a slab of positive index material with Kerr-type nonlinearity and a subwavelength layer of linear negative index material (NIM) sandwiched between semi-infinite linear dielectrics. We find that a thin layer of NIM leads to significant changes in the hysteresis width when the nonlinear slab is illuminated at an angle near that of total internal reflection. Unidirectional diodelike transmission with enhanced operational range is demonstrated. These results may be useful for NIMs characterization and for designing novel NIMs-based devices.


Computational search for potential COVID-19 drugs from FDAapproved drugs and small molecules of natural origin identifies several anti-virals and plant products.
The world is currently facing the COVID-19 pandemic, for which mild symptoms include fever and dry cough. In severe cases, it could lead to pneumonia and ultimately death in some instances. Moreover, the causative pathogen is highly contagious and there are no drugs or vaccines for it yet. The pathogen, SARS-CoV-2, is one of the human coronaviruses which was identified to infect humans first in December 2019. SARS-CoV-2 shares evolutionary relationship to other highly pathogenic viruses such as Severe Acute Respiratory Syndrome (SARS) and Middle East respiratory syndrome (MERS). We have exploited this similarity to model a target non-structural protein, NSP1, since it is implicated in the regulation of host gene expression by the virus and hijacking of host machinery. We next interrogated the capacity to repurpose around 2300 FDA-approved drugs and more than 3,00,000 small molecules of natural origin towards drug identification through virtual screening and molecular dynamics. Interestingly, we observed simple molecules like lactose, previously known anti-virals and few secondary metabolites of plants as promising hits. These herbal plants are already practiced in Ayurveda over centuries to treat respiratory problems and inflammation. Disclaimer: we would not like to recommend uptake of these small molecules for suspect COVID patients until it is approved by competent national or international authorities.


Mangos and their bioactive components: adding variety to the fruit plate for health.
The diet is an essential factor affecting the risk for development and progression of modern day chronic diseases, particularly those with pathophysiological roots in inflammation and oxidative stress-induced damage. The potential impact of certain foods and their bioactive compounds to reverse or prevent destructive dysregulated processes leading to disease has attracted intense research attention. The mango (Mangifera indica Linn.) is a tropical fruit with distinctive nutritional and phytochemical composition. Notably, the mango contains several essential water- and lipid-soluble micronutrients along with the distinguishing phytochemicals gallotannins and mangiferin. In vitro and in vivo studies reveal various mechanisms through which mangos or their associated compounds reduce risk or reverse metabolic- and inflammation-associated diseases. Health benefits of isolated individual mango compounds and extracts from mango by-products are well described in the literature with less attention devoted to the whole fruit. Here, we review and summarize the available literature assessing the health promoting potential of mango flesh, the edible portion contributing to dietary fruit intake, focusing specifically on modern day health issues of obesity and the risk factors and diseases it precipitates, including diabetes and cardiovascular disease. Additionally, this review explores new insights on the benefits of mango for brain, skin and intestinal health. Overall, the foundation of research supporting the potential role of mangos in reducing risk for inflammation- and metabolically-based chronic diseases is growing.


Association of protein tyrosine phosphatase non-receptor type 22 gene functional variant C1858T, HLA-DQ/DR genotypes and autoantibodies with susceptibility to type-1 diabetes mellitus in Kuwaiti Arabs.
The incidence of type-1 Diabetes Mellitus (T1DM) has increased steadily in Kuwait during recent years and it is now considered amongst the high-incidence countries. An interaction between susceptibility genes, immune system mediators and environmental factors predispose susceptible individuals to T1DM. We have determined the prevalence of protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene functional variant (C1858T; R620W, rs2476601), HLA-DQ and DR alleles and three autoantibodies in Kuwaiti children with T1DM to evaluate their impact on genetic predisposition of the disease. This study included 253 Kuwaiti children with T1DM and 214 ethnically matched controls. The genotypes of PTPN22 gene functional variant C1858T (R620W; rs2476601) were detected by PCR-RFLP method and confirmed by DNA sequencing. HLA-DQ and DR alleles were determined by sequence-specific PCR. Three autoantibodies were detected in the T1DM patients using radio-immunoassays. A significant association was detected between the variant genotype of the PTPN22 gene (C1858T, rs2476601) and T1DM in Kuwaiti Arabs. HLA-DQ2 and DQ8 alleles showed a strong association with T1DM. In T1DM patients which carried the variant TT-genotype of the PTPN22 gene, 93% had at least one DQ2 allele and 60% carried either a DQ2 or a DQ8 allele. Amongst the DR alleles, the DR3-DRB5, DR3-3, DR3-4 and DR4-4 showed a strong association with T1DM. Majority of T1DM patients who carried homozygous variant (TT) genotype of the PTPN22 gene had either DR3-DRB5 or DRB3-DRB4 genotypes. In T1DM patients who co-inherited the high risk HLA DQ, DR alleles with the variant genotype of PTPN22 gene, the majority were positive for three autoantibodies. Our data demonstrate that the variant T-allele of the PTPN22 gene along with HLA-DQ2 and DQ8 alleles constitute significant determinants of genetic predisposition of T1DM in Kuwaiti children.


Topology-guided design and syntheses of highly stable mesoporous porphyrinic zirconium metal-organic frameworks with high surface area.
Through a topology-guided strategy, a series of Zr6-containing isoreticular porphyrinic metal-organic frameworks (MOFs), PCN-228, PCN-229, and PCN-230, with ftw-a topology were synthesized using the extended porphyrinic linkers. The bulky porphyrin ring ligand effectively prevents the network interpenetration which often appears in MOFs with increased linker length. The pore apertures of the structures range from 2.5 to 3.8 nm, and PCN-229 demonstrates the highest porosity and BET surface area among the previously reported Zr-MOFs. Additionally, by changing the relative direction of the terminal phenyl rings, this series replaces a Zr8 cluster with a smaller Zr6 cluster in a topologically identical framework. The high connectivity of the Zr6 cluster yields frameworks with enhanced stability despite high porosity and ultralarge linker. As a representative example, PCN-230, constructed with the most extended porphyrinic linker, shows excellent stability in aqueous solutions with pH values ranging from 0 to 12 and demonstrates one of the highest pH tolerances among all porphyrinic MOFs. This work not only presents a successful example of rational design of MOFs with desired topology, but also provides a strategy for construction of stable mesoporous MOFs.


Genetic structure of human populations.
We studied human population structure using genotypes at 377 autosomal microsatellite loci in 1056 individuals from 52 populations. Within-population differences among individuals account for 93 to 95% of genetic variation; differences among major groups constitute only 3 to 5%. Nevertheless, without using prior information about the origins of individuals, we identified six main genetic clusters, five of which correspond to major geographic regions, and subclusters that often correspond to individual populations. General agreement of genetic and predefined populations suggests that self-reported ancestry can facilitate assessments of epidemiological risks but does not obviate the need to use genetic information in genetic association studies.


Characterization of an enantioselective odorant receptor in the yellow fever mosquito Aedes aegypti.
Enantiomers differ only in the left or right handedness (chirality) of their orientations and exhibit identical chemical and physical properties. In chemical communication systems, enantiomers can be differentially active at the physiological and behavioral levels. Only recently were enantioselective odorant receptors demonstrated in mammals while their existence in insects has remained hypothetical. Using the two-microelectrode voltage clamp of Xenopus oocytes, we show that the yellow fever mosquito, Aedes aegypti, odorant receptor 8 (AaOR8) acts as a chiral selective receptor for the (R)-(-)-enantiomer of 1-octen-3-ol, which in the presence of other kairomones is an attractant used by blood-sucking insects to locate their hosts. In addition to steric constraints, chain length and degree of unsaturation play important roles in this recognition process. This is the first characterization of an enantioselective odorant receptor in insects and the results demonstrate that an OR alone, without helper proteins, can account for chiral specificity exhibited by olfactory sensory neurons (OSNs).


Development of a Quantitative Immunoassay for Tear Lacritin Proteoforms.
Lacritin is a tear glycoprotein with pro-tearing and pro-ocular surface homeostasis activities that is selectively deficient in most dry eye tears. Proteoforms include an active monomer, inactive polymers, and a splice variant termed lacritin-c. Quantitation of the different proteoforms of tear lacritin may provide a diagnostic tool for ocular diseases. Here, we report the development of an immunoassay for the quantification of multiple lacritin proteoforms in human tear samples. Basal tears collected on Schirmer test strips with anesthesia were eluted by diffusion and centrifugation under optimized conditions. Tear protein concentrations were determined, and 2.56 µg of each sample was separated by SDS-PAGE followed by western blot analysis. Blots were challenged with anti-Pep Lac N-term antibodies. Detection was with fluorescent secondary antibodies visualized by the LI-COR Odyssey CLx imaging system and quantified with standard curves of recombinant lacritin. The percent total lacritin (ng lacritin/100 ng total protein) ranged from 1.8% to 14.8%. Monomer, lacritin-c, and polymer proteoform percent total protein ranged from 1.1% to 6.3%, 0.3% to 5.4%, and 0.7% to 5.7%, respectively. Monomer lacritin was detected at concentrations of 6 to 176 µM, with lacritin-c and polymer proteoforms at 2 to 46 µM and 1 to 23 µM, respectively. This assay greatly exceeds the power and sensitivity of our prior lacritin enzyme-linked immunosorbent assay that was not capable of distinguishing monomer from polymers and lacritin-c proteoforms. A new method has been developed to quantitate multiple proteoforms of tear lacritin in preparation for analyses of samples from clinical trials.


Salt doping to improve thermoelectric power factor of organic nanocomposite thin films.
Thermoelectric materials with a large Seebeck coefficient (S) and electrical conductivity (σ) are required to efficiently convert waste heat into electricity, but their interdependence makes simultaneously improving these variables immensely challenging. To address this problem, bilayers (BL) of poly(diallyldimethylammonium chloride) (PDDA) and double-walled carbon nanotubes (DWNT), stabilized by KBr-doped poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) were deposited using layer-by-layer (LbL) assembly. Doping PEDOT:PSS with KBr, prior to DWNT dispersion and LbL assembly, results in a six-fold improvement in electrical conductivity with little change in the Seebeck coefficient. A maximum power factor (PF = S 2 σ) of 626 ± 39 μW m-1 K-2 is obtained from a 20 BL PDDA/PEDOT:PSS-DWNT film (∼46 nm thick), where PEDOT:PSS was doped with 3 mmol KBr. This large PF is due to the formation of a denser film containing a greater proportion of DWNT, which was influenced by the charge-screening effects imparted by the salt dopant that separates PSS from PEDOT. This study demonstrates a relatively simple strategy to significantly increase the thermoelectric performance of fully organic nanocomposites that are useful for low temperature thermoelectric devices.


Activating efficient room temperature phosphorescence of carbon dots by synergism of orderly non-noble metals and dual structural confinements.
Obtaining high efficiency room temperature phosphorescence (RTP) by employing non-noble metals poses two challenges: (1) strengthening spin-orbit coupling of excitons to improve the rate of intersystem crossing (ISC) by using non-noble metals with small-atomic-number; (2) employing structural confinement to enhance radiation relaxation because harsh conditions, including carefully selected matrices, rigid solid-state crystalline structure and low temperature, are commonly needed. Here, layered double hydroxides (LDHs) with orderly non-noble metal arrangements were used as an inorganic matrix to activate RTP of carbon dots (CDs). The Zn orderly arranged on the LDH layer contributes to the enhancement in spin-orbit coupling of excitons and the decrease in the energy gap for the singlet-triplet state. The structural confinements of the LDH layer and nano-interlayer testify that the phosphorescence of CDs-LDHs originates from the suppressed radiationless relaxation processes. Using the high tunability of metal species and ratios on the LDH layer, this method can be widely applied to optimize ISC and phosphorescence properties.


Timing and frequency of chlamydia and gonorrhoea testing in a cross-sectional study of HIV postexposure prophylaxis recipients.
Australian HIV postexposure prophylaxis (PEP) guidelines recommend Chlamydia trachomatis (CT) and Neisseria gonorrheae (NG) testing at both baseline and 2-week postexposure visits. We aimed to determine the diagnostic yield of testing at one or more visits, and predictors of infection. Data were collected from patients prescribed PEP at RPA Sexual Health over a 4-year period from January 2008 to December 2011. Predictors of CT/NG were assessed by logistic regression. 282 individuals presented for PEP on 319 occasions during the study period. The majority (94.3%) were male and over 90% of presentations followed unprotected anal sexual exposures. Most (279, 87.5%) had CT/NG testing at least once. Almost half (153, 48.0%) of baseline presentations, two-thirds (214, 67.1%) of 2-week presentations and over a quarter (88, 27.6%) of both presentations included CT/NG testing. CT/NG was diagnosed at baseline in eight (5.2%, 95% CI 2.3% to 10.0%) presentations. A new CT/NG diagnosis occurred at the 2-week visit in 18 (8.4%, 95% CI 5.1% to 13.0%) presentations, of whom 7 tested negative and 11 were not tested at baseline. Over one-quarter (28.1%) of PEP recipients reported sexual contact between baseline and 2-week visits. Independent predictors of CT/NG at baseline were recent sex work (OR 48.0, 95% CI 3.77 to 611.94); and at 2 weeks a known HIV-positive PEP exposure source (OR 3.54, 95% CI 1.04 to 12.06) and sex between baseline and 2-week visits (OR 3.63, 95% CI 1.10 to 11.96). Our findings suggest that screening PEP recipients for CT/NG at both baseline and 2 weeks may be warranted.


Fundamental chemistry of binary S,N and ternary S,N,O anions: analogues of sulfur oxides and N,O anions.
Binary S,N anions, e.g., NSN2- and SSNSS-, and related ternary S,N,O anions such as the structural isomers NSO-/SNO- and SSNO- are rarely mentioned in inorganic chemistry textbooks, despite the fact that their salts were synthesised and structurally characterised more than 30 years ago. These fundamentally important species and their conjugate acids, e.g. HNSO and HSNO, have been the focus of numerous investigations in recent years in view of their significance in disciplines as diverse as atmospheric chemistry and cell biology. This Tutorial Review provides a consolidated account of the fundamental chemistry including synthesis, spectroscopic characterisation, molecular and electronic structures, and properties of these intriguing species, and compares these aspects of their behaviour with those of isoelectronic sulfur oxides and N,O anions. A final section draws attention to the significance and applications of these simple S-N species in a broader context.


MultiRTA: a simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes.
The binding of peptide fragments of antigens to class II MHC is a crucial step in initiating a helper T cell immune response. The identification of such peptide epitopes has potential applications in vaccine design and in better understanding autoimmune diseases and allergies. However, comprehensive experimental determination of peptide-MHC binding affinities is infeasible due to MHC diversity and the large number of possible peptide sequences. Computational methods trained on the limited experimental binding data can address this challenge. We present the MultiRTA method, an extension of our previous single-type RTA prediction method, which allows the prediction of peptide binding affinities for multiple MHC allotypes not used to train the model. Thus predictions can be made for many MHC allotypes for which experimental binding data is unavailable. We fit MultiRTA models for both HLA-DR and HLA-DP using large experimental binding data sets. The performance in predicting binding affinities for novel MHC allotypes, not in the training set, was tested in two different ways. First, we performed leave-one-allele-out cross-validation, in which predictions are made for one allotype using a model fit to binding data for the remaining MHC allotypes. Comparison of the HLA-DR results with those of two other prediction methods applied to the same data sets showed that MultiRTA achieved performance comparable to NetMHCIIpan and better than the earlier TEPITOPE method. We also directly tested model transferability by making leave-one-allele-out predictions for additional experimentally characterized sets of overlapping peptide epitopes binding to multiple MHC allotypes. In addition, we determined the applicability of prediction methods like MultiRTA to other MHC allotypes by examining the degree of MHC variation accounted for in the training set. An examination of predictions for the promiscuous binding CLIP peptide revealed variations in binding affinity among alleles as well as potentially distinct binding registers for HLA-DR and HLA-DP. Finally, we analyzed the optimal MultiRTA parameters to discover the most important peptide residues for promiscuous and allele-specific binding to HLA-DR and HLA-DP allotypes. The MultiRTA method yields competitive performance but with a significantly simpler and physically interpretable model compared with previous prediction methods. A MultiRTA prediction webserver is available at http://bordnerlab.org/MultiRTA.


Systemic inflammation alters central 5-HT function as determined by pharmacological MRI.
Considerable evidence indicates a link between systemic inflammation and central 5-HT function. This study used pharmacological magnetic resonance imaging (phMRI) to study the effects of systemic inflammatory events on central 5-HT function. Changes in blood oxygenation level dependent (BOLD) contrast were detected in selected brain regions of anaesthetised rats in response to intravenous administration of the 5-HT-releasing agent, fenfluramine (10 mg/kg). Further groups of rats were pre-treated with the bacterial lipopolysaccharide (LPS; 0.5 mg/kg), to induce systemic inflammation, or the selective 5-HT2A receptor antagonist MDL100907 prior to fenfluramine. The resultant phMRI data were investigated further through measurements of cortical 5-HT release (microdialysis), and vascular responsivity, as well as a more thorough investigation of the role of the 5-HT2A receptor in sickness behaviour. Fenfluramine evoked a positive BOLD response in the motor cortex (+15.9±2%) and a negative BOLD response in the dorsal raphe nucleus (-9.9±4.2%) and nucleus accumbens (-7.7±5.3%). In all regions, BOLD responses to fenfluramine were significantly attenuated by pre-treatment with LPS (p<0.0001), but neurovascular coupling remained intact, and fenfluramine-evoked 5-HT release was not affected. However, increased expression of the 5-HT2A receptor mRNA and decreased 5-HT2A-dependent behaviour (wet-dog shakes) was a feature of the LPS treatment and may underpin the altered phMRI signal. MDL100907 (0.5 mg/kg), 5-HT2A antagonist, significantly reduced the BOLD responses to fenfluramine in all three regions (p<0.0001) in a similar manner to LPS. Together these results suggest that systemic inflammation decreases brain 5-HT activity as assessed by phMRI. However, these effects do not appear to be mediated by changes in 5-HT release, but are associated with changes in 5-HT2A-receptor-mediated downstream signalling pathways.


Integrated mate-pair and RNA sequencing identifies novel, targetable gene fusions in peripheral T-cell lymphoma.
Peripheral T-cell lymphomas (PTCLs) represent a heterogeneous group of T-cell malignancies that generally demonstrate aggressive clinical behavior, often are refractory to standard therapy, and remain significantly understudied. The most common World Health Organization subtype is PTCL, not otherwise specified (NOS), essentially a "wastebasket" category because of inadequate understanding to assign cases to a more specific diagnostic entity. Identification of novel fusion genes has contributed significantly to improving the classification, biologic understanding, and therapeutic targeting of PTCLs. Here, we integrated mate-pair DNA and RNA next-generation sequencing to identify chromosomal rearrangements encoding expressed fusion transcripts in PTCL, NOS. Two of 11 cases had novel fusions involving VAV1, encoding a truncated form of the VAV1 guanine nucleotide exchange factor important in T-cell receptor signaling. Fluorescence in situ hybridization studies identified VAV1 rearrangements in 10 of 148 PTCLs (7%). These were observed exclusively in PTCL, NOS (11%) and anaplastic large cell lymphoma (11%). In vitro, ectopic expression of a VAV1 fusion promoted cell growth and migration in a RAC1-dependent manner. This growth was inhibited by azathioprine, a clinically available RAC1 inhibitor. We also identified novel kinase gene fusions, ITK-FER and IKZF2-ERBB4, as candidate therapeutic targets that show similarities to known recurrent oncogenic ITK-SYK fusions and ERBB4 transcript variants in PTCLs, respectively. Additional novel and potentially clinically relevant fusions also were discovered. Together, these findings identify VAV1 fusions as recurrent and targetable events in PTCLs and highlight the potential for clinical sequencing to guide individualized therapy approaches for this group of aggressive malignancies.


Reversal of endocrine resistance in breast cancer: interrelationships among 14-3-3ζ, FOXM1, and a gene signature associated with mitosis.
Despite the benefits of estrogen receptor (ER)-targeted endocrine therapies in breast cancer, many tumors develop resistance. 14-3-3 ζ/YWHAZ, a member of the 14-3-3 family of conserved proteins, is over-expressed in several types of cancer, and our previous work showed that high expression of 14-3-3ζ in ER-positive breast cancers was associated with a poor clinical outcome for women on tamoxifen. Therefore, we now probe the role of 14-3-3ζ in endocrine resistance, and we examine the functional dimensions and molecular basis that underlie 14-3-3ζ activities. From analyses of four independent breast cancer microarray datasets from nearly 400 women, we characterized a gene signature that correlated strongly with high expression of 14-3-3ζ in breast tumors and examined its association with breast cancer molecular subtypes and clinical-pathological features. We investigated the effects of altering 14-3-3ζ levels in ER-positive, endocrine sensitive and resistant breast cancer cells on the regulation of 14-3-3ζ signature genes, and on cellular signaling pathways and cell phenotypic properties. The gene signature associated with high 14-3-3ζ levels in breast tumors encompassed many with functions in mitosis and cytokinesis, including aurora kinase-B, polo-like kinase-1, CDC25B, and BIRC5/survivin. The gene signature correlated with early recurrence and risk of metastasis, and was found predominantly in luminal B breast cancers, the more aggressive ER-positive molecular subtype. The expression of the signature genes was significantly decreased or increased upon reduction or overexpression of 14-3-3ζ in ER-positive breast cancer cells, indicating their coregulation. 14-3-3ζ also played a critical role in the regulation of FOXM1, with 14-3-3ζ acting upstream of FOXM1 to regulate cell division-signature genes. Depletion of 14-3-3ζ markedly increased apoptosis, reduced proliferation and receptor tyrosine kinase (HER2 and EGFR) signaling, and, importantly, reversed endocrine resistance. This study reveals that 14-3-3ζ is a key predictive marker for risk of failure on endocrine therapy and serves a pivotal role impacting growth factor signaling, and promoting cell survival and resistance to endocrine therapies. Targeting 14-3-3ζ and its coregulated proteins, such as FOXM1, should prove valuable in restoring endocrine sensitivity and reducing risk of breast cancer recurrence.


Prevention of venous thrombosis in long-haul flights with Flite Tabs: the LONFLIT-FLITE randomized, controlled trial.
The aim of this study was to evaluate the development of edema, and superficial and deep vein thrombosis (DVT) prophylaxis with an oral profibrinolytic agent (Flite Tabs, 150 mg pinokinase, Aidan, Tempe, AZ, USA) in long-haul flights (7-8 hours), in high-risk subjects. A group of 300 subjects was included; 76 were excluded for several problems including concomitant treatments; 204 were randomized into 2 groups (active treatment or placebo) to evaluate the effects of prophylaxis with Flite Tabs. An exercise program was used in both groups. The femoral, popliteal, tibial, and superficial veins were scanned with ultrasound before and within 90 minutes after flights. Of the included subjects, 92 of 103 controls and 94 of 101 treated subjects completed the study. Dropouts were due to connection problems. Age, gender, and risk distribution were comparable in the groups. In the treatment group, no DVT was observed. In the control group, 5 subjects (5.4%) had a DVT and there were 2 superficial thromboses (7 events in 92 subjects; 7.6%). At inclusion, edema was comparable in the 2 groups. After flights there was an increase in score in controls (+12%) in comparison with a decrease (-15%) in the Flite Tabs group (the difference in variation was statistically significant). Intention-to-treat analysis for thrombotic events shows 18 failures in controls (11 lost to follow-up + 7 thrombotic events) of 92 subjects (19.6%) in comparison with 7 failures (of 94 subjects, equivalent to 7.4%) in the treatment group (p < 0.05). Events were asymptomatic. In conclusion, Flite Tabs were effective in reducing thrombotic events and in controlling edema in high-risk subjects in long flights.


Tectonic control of Yarlung Tsangpo Gorge revealed by a buried canyon in Southern Tibet.
The Himalayan mountains are dissected by some of the deepest and most impressive gorges on Earth. Constraining the interplay between river incision and rock uplift is important for understanding tectonic deformation in this region. We report here the discovery of a deeply incised canyon of the Yarlung Tsangpo River, at the eastern end of the Himalaya, which is now buried under more than 500 meters of sediments. By reconstructing the former valley bottom and dating sediments at the base of the valley fill, we show that steepening of the Tsangpo Gorge started at about 2 million to 2.5 million years ago as a consequence of an increase in rock uplift rates. The high erosion rates within the gorge are therefore a direct consequence of rapid rock uplift.


The Next Quarter Century.
Immunity celebrates its 25th anniversary at an exciting time in immunology, marked by the advent of new, door-opening approaches and a deeper understanding of the centrality of the immune system to both health and disease. We asked 25 investigators to look forward and share a vision of the next quarter century of immunology research.


The abundance of invertebrate herbivores in relation to the availability of nitrogen in stressed food plants.
It has previously been postulated that when plants are stressed by certain changes in patterns of weather they become a better source of food for invertebrate herbivores because this stress causes an increase in the amount of nitrogen available in their tissues for young herbivores feeding on them. And this may cause outbreaks of such phytophagous invertebrates.Evidence is now presented that a similar physiological mechanism appears to operate when a wide variety of apparently unrelated environmental factors impinge on plants or parts of plants in such a way as to perturb their metabolism. A broken branch, lightning strike, fire, nutrient deficiencies or an otherwise adverse site; all may have this effect. With the advent of modern man the available agencies increase and diversify to include pesticides, irradiation and air pollutants.One common metabolic response by plants to all such agents impinging on them seems to be equivalent to that found in senescing plant tissues - the breakdown and mobilization of nitrogen in soluble form away from the senescing/stressed tissues. Young herbivores which chance to feed on such stressed/senescing tissues have a greater and more readily available supply of nitrogen in their food than they would have had if feeding on unstressed plants. As a result many more of them survive, and there is an increase in abundance of their kind. Such increases may be quite localised and short-lived or more widespread and persistent, depending on the extent and duration of the stress experienced by the plants. And in the face of this improved nutrition and survival of the very young, predators and parasites seem to have only a minor influence on subsequent changes in abundance of their herbivorous prey.Another effect of increased mobilization of nitrogen in stressed plants is an increase in the quantity of the seed that they set. This has led to the conclusion that increased abundance of some species of birds at such times is due to a greater supply of seeds as winter food for recent fledglings. But it may be that the increased abundance is due to the synchronous increase in phytophagous insects providing a richer source of protein food for laying hens and growing nestlings.


Malaria diagnostic capacity in health facilities in Ethiopia.
Accurate early diagnosis and prompt treatment is one of the key strategies to control and prevent malaria in Ethiopia where both Plasmodium falciparum and Plasmodium vivax are sympatric and require different treatment regimens. Microscopy is the standard for malaria diagnosis at the health centres and hospitals whereas rapid diagnostic tests are used at community-level health posts. The current study was designed to assess malaria microscopy capacity of health facilities in Oromia Regional State and Dire Dawa Administrative City, Ethiopia. A descriptive cross-sectional study was conducted from February to April 2011 in 122 health facilities, where health professionals were interviewed using a pre-tested, standardized assessment tool and facilities' laboratory practices were assessed by direct observation. Of the 122 assessed facilities, 104 (85%) were health centres and 18 (15%) were hospitals. Out of 94 health facilities reportedly performing blood films, only 34 (36%) used both thin and thick smears for malaria diagnosis. The quality of stained slides was graded in 66 health facilities as excellent, good and poor quality in 11(17%), 31 (47%) and 24 (36%) respectively. Quality assurance guidelines and malaria microscopy standard operating procedures were found in only 13 (11%) facilities and 12 (10%) had involved in external quality assessment activities, and 32 (26%) had supportive supervision within six months of the survey. Only seven (6%) facilities reported at least one staff's participation in malaria microscopy refresher training during the previous 12 months. Although most facilities, 96 (79%), had binocular microscopes, only eight (7%) had the necessary reagents and supplies to perform malaria microscopy. Treatment guidelines for malaria were available in only 38 (31%) of the surveyed facilities. Febrile patients with negative malaria laboratory test results were managed with artemether-lumefantrine or chloroquine in 51% (53/104) of assessed health facilities. The current study indicated that most of the health facilities had basic infrastructure and equipment to perform malaria laboratory diagnosis but with significant gaps in continuous laboratory supplies and reagents, and lack of training and supportive supervision. Overcoming these gaps will be critical to ensure that malaria laboratory diagnosis is of high-quality for better patient management.


Comparison of endoscopic papillary large balloon dilation with or without endoscopic sphincterotomy for the treatment of large bile duct stones.
Endoscopic papillary large balloon dilation (EPLBD) without prior endoscopic sphincterotomy (EST) produces excellent outcomes for the treatment of large common bile duct (CBD) stones. However, it remains unclear how the outcomes of EPLBD alone compare with those of EPLBD with EST. In this study, we assessed the safety and therapeutic outcomes of EPLBD with vs. without EST for the removal of large bile duct stones. This prospective, multicenter study was conducted on 200 patients with bile duct stones of ≥ 10 mm in diameter. Patients were randomly assigned to an EPLBD alone group (n = 100) or an EPLBD with EST group (n = 100). These two groups were compared with respect to overall procedure-related adverse events, overall stone removal success rate, number of endoscopic sessions required for complete stone removal, need for mechanical lithotripsy, and total procedure time. The incidence of adverse events was not significantly different between the groups (EPLBD alone vs. EPLBD with EST: overall adverse events 6 % vs. 4 %, P = 0.75; pancreatitis 1 % vs. 3 %, P = 0.62). Overall success (P = 0.35), initial success (P = 0.28), and the need for mechanical lithotripsy (P = 0.39) were also similar between groups. Median total procedure time tended to be greater in the EPLBD alone group (20.5 minutes) than in the EPLBD with EST group (18 minutes; P = 0.08). The therapeutic outcomes and adverse events of EPLBD alone for the removal of large bile duct stones were comparable to those of EPLBD with EST.


Responding to pandemic (H1N1) 2009 influenza in Aboriginal communities in NSW through collaboration between NSW Health and the Aboriginal community-controlled health sector.
As a vulnerable population, Aboriginal people in NSW were thought likely to be at more risk of serious illness from pandemic (H1N1) 2009 influenza than non-Aboriginal people. As such, the importance of consulting with Aboriginal people and communities was recognised early in the pandemic. This consultation was to enable key messages to be disseminated appropriately and to facilitate access to health care. Key stakeholders in the response were the NSW Department of Health, Area Health Services, the NSW Aboriginal Health and Medical Research Council, and Aboriginal Community Controlled Health Services. Regular teleconferences between the key stakeholders facilitated the flow of information and assisted with the identification of issues. A consultation process between Hunter New England Area Health Service and six Aboriginal communities helped inform the development of resources as well as the planning and delivery of pandemic-related services. Aboriginal people were four times more likely to be admitted to hospital with pandemic (H1N1) 2009 influenza than non-Aboriginal people.


Carotenoids and apocarotenoids in cellular signaling related to cancer: a review.
The basis for the vivid color of carotenoids and their antioxidant activity is the multiple conjugated double bonds, which are characteristic for these phytonutrients. Moreover, the cleavage of these oxidation-prone double bonds leads to the formation of apocarotenoids. A large number of carbonyl-containing oxidation products are expected to be produced as a result of carotenoid oxidation and these can be further metabolized into the corresponding acids and alcohols. As discussed in this review, many, but not all, of these potential products have been detected and identified in plants as well as in human and animal plasma and tissues. Some of these compounds were found to be biologically active as anticancer agents. In addition to the inhibition of cancer cell proliferation, several carotenoid metabolites were shown to modulate the activity of various transcription systems. These include ligand-activated nuclear receptors, such as the retinoic acid receptor, retinoid X receptor, peroxisome proliferator-activated receptor and estrogen receptor, as well as other transcription systems that have an important role in cancer, such as the electrophile/antioxidant response element pathway and nuclear factor-κB. Therefore, apocarotenoids can be considered as natural compounds with multifunctional, rather than monofunctional, activity and, thus, can be useful in the prevention of cancer and other degenerative diseases.


Microbial contamination in the operating theatre: a study in a hospital in Baghdad.
Contamination of the operating theatre is a major cause of nosocomial infection. This study aimed to evaluate the incidence of bacterial contamination of operating theatres in Al Imam Ali Hospital in Baghdad, and the source of contamination. From 1216 swabs collected from surfaces, equipment and antiseptic solutions from different operating theatres in 2001 and 2002, the rates of positive cultures were 3.7% in 2001 and 4.0% in 2002. Staphylococcus epidermidis was the most common isolate in 2001 followed by Pseudomonas aeruginosa, whereas in 2002 coliform bacteria were the highest, followed by P. aeruginosa. No clear pattern of isolates was found in different types of operating theatres, although coliforms and P. aeruginosa were mostly found in the delivery theatre.


Measurement of absolute cell volume, osmotic membrane water permeability, and refractive index of transmembrane water and solute flux by digital holographic microscopy.
A dual-wavelength digital holographic microscope to measure absolute volume of living cells is proposed. The optical setup allows us to reconstruct two quantitative phase contrast images at two different wavelengths from a single hologram acquisition. When adding the absorbing dye fast green FCF as a dispersive agent to the extracellular medium, cellular thickness can be univocally determined in the full field of view. In addition to the absolute cell volume, the method can be applied to derive important biophysical parameters of living cells including osmotic membrane water permeability coefficient and the integral intracellular refractive index (RI). Further, the RI of transmembrane flux can be determined giving an indication about the nature of transported solutes. The proposed method is applied to cultured human embryonic kidney cells, Chinese hamster ovary cells, human red blood cells, mouse cortical astrocytes, and neurons.


Dynamic microRNA expression programs during cardiac differentiation of human embryonic stem cells: role for miR-499.
MicroRNAs (miRNAs) are a newly discovered endogenous class of small, noncoding RNAs that play important posttranscriptional regulatory roles by targeting messenger RNAs for cleavage or translational repression. Human embryonic stem cells are known to express miRNAs that are often undetectable in adult organs, and a growing body of evidence has implicated miRNAs as important arbiters of heart development and disease. To better understand the transition between the human embryonic and cardiac "miRNA-omes," we report here the first miRNA profiling study of cardiomyocytes derived from human embryonic stem cells. Analyzing 711 unique miRNAs, we have identified several interesting miRNAs, including miR-1, -133, and -208, that have been previously reported to be involved in cardiac development and disease and that show surprising patterns of expression across our samples. We also identified novel miRNAs, such as miR-499, that are strongly associated with cardiac differentiation and that share many predicted targets with miR-208. Overexpression of miR-499 and -1 resulted in upregulation of important cardiac myosin heavy-chain genes in embryoid bodies; miR-499 overexpression also caused upregulation of the cardiac transcription factor MEF2C. Taken together, our data give significant insight into the regulatory networks that govern human embryonic stem cell differentiation and highlight the ability of miRNAs to perturb, and even control, the genes that are involved in cardiac specification of human embryonic stem cells.


Effects of hydrogen rich water on prolonged intermittent exercise.
Recent studies showed a positive effect of hydrogen rich water (HRW) intake on acid-base homeostasis at rest. We investigated 2-weeks of HRW intake on repeated sprint performance and acid-base status during prolonged intermittent cycling exercise. In a cross over single-blind protocol, 8 trained male cyclists (age [mean±SD] 41±7 years, body mass 72.3±4.4 kg, height 1.77±0.04 m, maximal oxygen uptake [V̇O2max] 52.6±4.4 mL·kg-1·min-1) were provided daily with 2 liters of placebo normal water (PLA, pH 7.6, oxidation/reduction potential [ORP] +230 mV, free hydrogen content 0 ppb) or HRW (pH 9.8, ORP -180 mV, free Hydrogen 450 ppb). Tests were performed at baseline and after each period of 2 weeks of treatment. The treatments were counter-balanced and the sequence randomized. The 30-minute intermittent cycling trial consisted in 10 3-minute blocks, each one composed by 90 seconds at 40% V̇O2max, 60 seconds at 60% V̇O2max, 16 seconds all out sprint, and 14 seconds active recovery. Oxygen uptake (V̇O2), heart rate and power output were measured during the whole test, while mean and peak power output (PPO), time to peak power and Fatigue Index (FI) were determined during all the 16 seconds sprints. Lactate, pH and bicarbonate (HCO3-) concentrations were determined at rest and after each sprint on blood obtained by an antecubital vein indwelling catheter. In the PLA group, PPO in absolute values decreased significantly at the 8th and 9th of 10 sprints and in relative values, ΔPPO, decreased significantly at 6th, 8th and 9th of 10 sprints (by mean: -12±5%, P<0.006), while it remained unchanged in HRW group. Mean power, FI, time to peak power and total work showed no differences between groups. In both conditions lactate levels increased while pH and HCO3- decreased progressively as a function of the number of sprints. Two weeks of HRW intake may help to maintain PPO in repetitive sprints to exhaustion over 30 minutes.


Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico.
Genome-scale metabolic networks and flux models are an effective platform for linking an organism genotype to its phenotype. However, few modeling approaches offer predictive capabilities to evaluate potential metabolic engineering strategies in silico. A new method called "flux balance analysis with flux ratios (FBrAtio)" was developed in this research and applied to a new genome-scale model of Clostridium acetobutylicum ATCC 824 (iCAC490) that contains 707 metabolites and 794 reactions. FBrAtio was used to model wild-type metabolism and metabolically engineered strains of C. acetobutylicum where only flux ratio constraints and thermodynamic reversibility of reactions were required. The FBrAtio approach allowed solutions to be found through standard linear programming. Five flux ratio constraints were required to achieve a qualitative picture of wild-type metabolism for C. acetobutylicum for the production of: (i) acetate, (ii) lactate, (iii) butyrate, (iv) acetone, (v) butanol, (vi) ethanol, (vii) CO2 and (viii) H2. Results of this simulation study coincide with published experimental results and show the knockdown of the acetoacetyl-CoA transferase increases butanol to acetone selectivity, while the simultaneous over-expression of the aldehyde/alcohol dehydrogenase greatly increases ethanol production. FBrAtio is a promising new method for constraining genome-scale models using internal flux ratios. The method was effective for modeling wild-type and engineered strains of C. acetobutylicum.


Coral reefs for coastal protection: A new methodological approach and engineering case study in Grenada.
Coastal communities in tropical environments are at increasing risk from both environmental degradation and climate change and require urgent local adaptation action. Evidences show coral reefs play a critical role in wave attenuation but relatively little direct connection has been drawn between these effects and impacts on shorelines. Reefs are rarely assessed for their coastal protection service and thus not managed for their infrastructure benefits, while widespread damage and degradation continues. This paper presents a systematic approach to assess the protective role of coral reefs and to examine solutions based on the reef's influence on wave propagation patterns. Portions of the shoreline of Grenville Bay, Grenada, have seen acute shoreline erosion and coastal flooding. This paper (i) analyzes the historical changes in the shoreline and the local marine, (ii) assess the role of coral reefs in shoreline positioning through a shoreline equilibrium model first applied to coral reef environments, and (iii) design and begin implementation of a reef-based solution to reduce erosion and flooding. Coastline changes in the bay over the past 6 decades are analyzed from bathymetry and benthic surveys, historical imagery, historical wave and sea level data and modeling of wave dynamics. The analysis shows that, at present, the healthy and well-developed coral reefs system in the southern bay keeps the shoreline in equilibrium and stable, whereas reef degradation in the northern bay is linked with severe coastal erosion. A comparison of wave energy modeling for past bathymetry indicates that degradation of the coral reefs better explains erosion than changes in climate and historical sea level rise. Using this knowledge on how reefs affect the hydrodynamics, a reef restoration solution is designed and studied to ameliorate the coastal erosion and flooding. A characteristic design provides a modular design that can meet specific engineering, ecological and implementation criteria. Four pilot units were implemented in 2015 and are currently being field-tested. This paper presents one of the few existing examples available to date of a reef restoration project designed and engineered to deliver risk reduction benefits. The case study shows how engineering and ecology can work together in community-based adaptation. Our findings are particularly important for Small Island States on the front lines of climate change, who have the most to gain from protecting and managing coral reefs as coastal infrastructure.


Influence of brain-derived neurotrophic factor-tyrosine receptor kinase B signalling in the nucleus tractus solitarius on baroreflex sensitivity in rats with chronic heart failure.
Impairment of baroreflex function is associated with the progression of chronic heart failure (CHF) and a poor prognosis. The baroreflex desensitization in CHF is at least partly the result of central neuronal network dysfunction. The dorsal medial nucleus tractus solitarius (dmNTS) has long been appreciated as a primary site of baroreceptor afferent termination in the central nervous system. However, the influence of neurotransmitters and neuromodulators in the dmNTS on baroreflex function both in normal and CHF states is not fully understood. The present study provides the first evidence showing a tonic sympatho-inhibitory role for brain-derived neurotrophic factor (BDNF) neurotransmission in the dmNTS. Most importantly, BDNF- tyrosine receptor kinase B (TrkB) signalling in the dmNTS is integral for normal baroreflex function as indicated by the blunting of baroreflex sensitivity (BRS) following the antagonization of TrkB, which inhibited baroreflex gain and range. Furthermore, we found that the tonic sympatho-inhibition of BDNF was withdrawn in the CHF state, thus contributing to the increased sympathetic tone associated with CHF. Consistent with this finding, BDNF/TrkB antagonism had little effect on reducing BRS in CHF animals, which is corroborated by the observation of decreased TrkB expression in the dmNTS during CHF. Taken together, these results implicate a reduction in BDNF-TrkB signalling in the dmNTS during CHF that contributes to sympatho-excitation and baroreflex desensitization. The observation that the BDNF/TrkB pathway is impaired in the dmNTS during CHF provides a novel mechanism for understanding the central alterations that contribute to baroreflex desensitization during CHF. Chronic heart failure (CHF) results in blunting of arterial baroreflex sensitivity (BRS), which arises from alterations to both peripheral baroreceptors and central autonomic nuclei such as the nucleus tractus solitarius (NTS). Although glutamate is known to be an important neurotransmitter released from baroreceptor afferent synapses in the NTS, the influence of other neurotransmitters and neuromodulators remains unclear. Alterations to NTS signalling in CHF remain particularly undefined. The present study aimed to evaluate the role of brain-derived neurotrophic factor (BDNF) and tyrosine receptor kinase B (TrkB) receptor signalling in the NTS on baroreflex control both in healthy and CHF rats. To this end, we microinjected BDNF or the highly selective TrkB receptor antagonist [N2-2-2-oxoazepan-3-yl amino] carbonyl phenyl benzo (b)thiophene-2-carboxamide (ANA-12) into the dorsal medial NTS (dmNTS) of male Sprague-Dawley rats with coronary artery ligation-induced CHF and sham operated controls and recorded blood pressure and renal sympathetic nerve activity responses. We subsequently measured BRS before and after bilateral dmNTS microinjections of ANA-12. In sham rats, BDNF evoked a dose-dependent depressor and sympatho-inhibitory effect and ANA-12 produced the opposite response. Both of these responses were significantly blunted in CHF rats. Furthermore, bilateral microinjection of ANA-12 into the dmNTS greatly diminished baroreflex sensitivity in sham rats, whereas it had less of an effect in CHF rats. We observed decreased levels of TrkB protein and mRNA in the dmNTS of CHF rats. These data indicate that endogenous BDNF signalling in the NTS is integral for the maintenance of BRS and that BDNF/TrkB signalling is impaired in the NTS in the CHF state.


Association between vitamin D levels and alopecia areata.
Alopecia areata (AA) is an autoimmune disease, based on the response to local and/or systemic corticosteroid treatment. The role of vitamin D in the pathogenesis of immune/autoimmune mediated diseases has been widely studied. To investigate a possible association between serum 25-hydroxyvitamin D levels and alopecia areata. The study included 23 patients diagnosed with AA followed at our outpatient clinic during the period March 2010 to May 2011, as well as a control group matched for age and gender. All subjects underwent a complete work-up and medical examination, anthropometric measurements and laboratory tests. Laboratory tests included complete blood count, C-reactive protein (CRP), and vitamin D levels. Mean CRP values were significantly higher in the AA group than the control group (1.1 +/- 0.7 mg/dl vs. 0.4 +/- 0.8 mg/ dl, P < 0.05). Vitamin D levels were significantly decreased in the AA group (11.32 +/- 10.18 ng/ml vs. 21.55 +/- 13.62 ng/ml in the control group, P < 0.05). Multivariate analysis showed that CRP (odds ratio 3.1, 95% confidence interval 2.6-4.2, P = 0.04) and serum vitamin D levels < 30 ng/ml (OR 2.3, 95% CI 2.2-3.1, P = 0.02) were associated with AA. We found a significant correlation between AA and vitamin D deficiency. Vitamin D deficiency can be a significant risk factor for AA occurrence.


Metachronal waves for deterministic switching two-state oscillators with hydrodynamic interaction.
We employ a model system, called rowers, as a generic physical framework to define the problem of the coordinated motion of cilia (the metachronal wave) as a far from equilibrium process. Rowers are active (two-state) oscillators in a low Reynolds number fluid, and interact solely through the forces of hydrodynamic origin. In this work, we consider the case of fully deterministic dynamics, find analytical solutions of the equation of motion in the long-wavelength (continuum) limit, and investigate numerically the short-wavelength limit. We prove the existence of metachronal waves below a characteristic wavelength. Such waves are unstable and become stable only if the sign of the coupling is reversed. We also find that with normal hydrodynamic interaction, the metachronal pattern has the form of stable trains of traveling wave packets sustained by the onset of anti-coordinated beating of consecutive rowers.


Interplay of early-life nutritional programming on obesity, inflammation and epigenetic outcomes.
The huge health burden accompanying obesity is not only attributable to inadequate dietary and sedentary lifestyle habits, since a predisposing genetic make-up and other putative determinants concerning easier weight gain and fat deposition have been reported. Thus, several investigations aiming to understand energy metabolism and body composition maintenance have been performed considering the participation of perinatal nutritional programming and epigenetic processes as well as inflammation phenomena. The Developmental Origins of Health and Disease hypothesis and inheritance-oriented investigations concerning gene-nutrient interactions on energy homoeostasis and metabolic functions have suggested that inflammation could be not only a comorbidity of obesity but also a cause. There are several examples about the role of nutritional interventions in pregnancy and lactation, such as energetic deprivation, protein restriction and excess fat, which determine a cluster of disorders affecting energy efficiency in the offspring as well as different metabolic pathways, which are mediated by epigenetics encompassing the chromatin information encrypted by DNA methylation patterns, histone covalent modifications and non-coding RNA or microRNA. Epigenetic mechanisms may be boosted or impaired by dietary and environmental factors in the mother, intergenerationally or transiently transmitted, and could be involved in the obesity and inflammation susceptibility in the offspring. The aims currently pursued are the early identification of epigenetic biomarkers concerned in individual's disease susceptibility and the description of protocols for tailored dietary treatments/advice to counterbalance adverse epigenomic events. These approaches will allow diagnosis and prognosis implementation and facilitate therapeutic strategies in a personalised 'epigenomically modelled' manner to combat obesity and inflammation.


Comparison of two methods of eliciting time preference for future health states.
Mean estimates of time preference rates for health vary widely in the literature. If these studies are to inform discounting practice and analyses of health-affecting behaviour, it is crucial to understand why this is the case. One reason for the variation in time preference rates is the use of different elicitation methods. The influence of elicitation method has received little attention in the time preference literature. This study compares directly an open-ended and a closed-ended method. Both private and social time preferences for health are elicited. The closed-ended method produced much lower mean rates than the open-ended method. This is in contrast to the contingent valuation literature which shows that closed-ended methods produce higher estimates of willingness to pay than open-ended methods. That the elicitation methods produce different mean estimates is clearly worrying if the interest is in estimating the true time preference rate. However, the results of this study suggest that if the interest is in testing different types of time preferences or investigating the relationship between time preference and individual characteristics then the choice of elicitation method is less important.


Measuring the effectiveness of protected area networks in reducing deforestation.
Global efforts to reduce tropical deforestation rely heavily on the establishment of protected areas. Measuring the effectiveness of these areas is difficult because the amount of deforestation that would have occurred in the absence of legal protection cannot be directly observed. Conventional methods of evaluating the effectiveness of protected areas can be biased because protection is not randomly assigned and because protection can induce deforestation spillovers (displacement) to neighboring forests. We demonstrate that estimates of effectiveness can be substantially improved by controlling for biases along dimensions that are observable, measuring spatial spillovers, and testing the sensitivity of estimates to potential hidden biases. We apply matching methods to evaluate the impact on deforestation of Costa Rica's renowned protected-area system between 1960 and 1997. We find that protection reduced deforestation: approximately 10% of the protected forests would have been deforested had they not been protected. Conventional approaches to evaluating conservation impact, which fail to control for observable covariates correlated with both protection and deforestation, substantially overestimate avoided deforestation (by over 65%, based on our estimates). We also find that deforestation spillovers from protected to unprotected forests are negligible. Our conclusions are robust to potential hidden bias, as well as to changes in modeling assumptions. Our results show that, with appropriate empirical methods, conservation scientists and policy makers can better understand the relationships between human and natural systems and can use this to guide their attempts to protect critical ecosystem services.


Big pharma: a story of success in a market economy.
In this paper, I will argue that the current discussions about regulating certain activities concerning the pharmaceutical industry do miss a crucial point. The Pharmaceutical Industry is a story of success, providing a wealth of new discoveries and applied technologies, which have greatly enhanced our lives. The current call for strict regulation of the Pharmaceutical Industry makes the unwarranted assumption that such regulation will not disturb the mechanisms of the Industry's success. I will claim that a centralised regulation profoundly transforms the direction of travel. I will also claim that the role of the executive in bypassing regulations creates a parallel industry of subsidiary regulations to counter such bypassing. The predictable consequence is the increasing role of central regulatory control and the progressive slowing down of the success of the Pharmaceutical Industry leading towards an undesirable mediocrity. The conclusion I wish to advance is that our choices are not limited to 'a wild open market' and 'a regulated open market' scenarios, and the strategy to avoid a robustly regulated but mediocre Pharmaceutical Industry may involve 'non-open market scenarios' which have so far been absent from the alternatives discussed.


Inferring recent historic abundance from current genetic diversity.
Recent historic abundance is an elusive parameter of great importance for conserving endangered species and understanding the pre-anthropogenic state of the biosphere. The number of studies that have used population genetic theory to estimate recent historic abundance from contemporary levels of genetic diversity has grown rapidly over the last two decades. Such assessments often yield unexpectedly large estimates of historic abundance. We review the underlying theory and common practices of estimating recent historic abundance from contemporary genetic diversity, and critically evaluate the potential issues at various estimation steps. A general issue of mismatched spatio-temporal scales between the estimation itself and the objective of the estimation emerged from our assessment; genetic diversity-based estimates of recent historic abundance represent long-term averages, whereas the objective typically is an estimate of recent abundance for a specific population. Currently, the most promising approach to estimate the difference between recent historic and contemporary abundance requires that genetic data be collected from samples of similar spatial and temporal duration. Novel genome-enabled inference methods may be able to utilize additional information of dense genome-wide distributions of markers, such as of identity-by-descent tracts, to infer recent historic abundance from contemporary samples only.