Multichannel blind separation and deconvolution of images for document analysis.
In this paper, we apply Bayesian blind source separation (BSS) from noisy convolutive mixtures to jointly separate and restore source images degraded through unknown blur operators, and then linearly mixed. We found that this problem arises in several image processing applications, among which there are some interesting instances of degraded document analysis. In particular, the convolutive mixture model is proposed for describing multiple views of documents affected by the overlapping of two or more text patterns. We consider two different models, the interchannel model, where the data represent multispectral views of a single-sided document, and the intrachannel model, where the data are given by two sets of multispectral views of the recto and verso side of a document page. In both cases, the aim of the analysis is to recover clean maps of the main foreground text, but also the enhancement and extraction of other document features, such as faint or masked patterns. We adopt Bayesian estimation for all the unknowns and describe the typical local correlation within the individual source images through the use of suitable Gibbs priors, accounting also for well-behaved edges in the images. This a priori information is particularly suitable for the kind of objects depicted in the images treated, i.e., homogeneous texts in homogeneous background, and, as such, is capable to stabilize the ill-posed, inverse problem considered. The method is validated through numerical and real experiments that are representative of various real scenarios.


Association of worker characteristics and early reimbursement for physical therapy, chiropractic and opioid prescriptions with workers' compensation claim duration, for cases of acute low back pain: an observational cohort study.
To assess the association between early reimbursement for physiotherapy, chiropractic and opioid prescriptions for acute low back pain (LBP) with disability claim duration. Observational cohort study. From a random sample of 6665 claims for acute, uncomplicated LBP approved by the Ontario Workplace Safety and Insurance Board (WSIB) in 2005, we analysed 1442 who remained on full benefits at 4 weeks after claim approval. Our primary outcome was WSIB claim duration. We had complete data for all but 3 variables, which had <15% missing data, and we included missing data as a category for these factors. Our time-to-event analysis was adjusted for demographic, workplace and treatment factors, but not injury severity, although we attempted to include a sample with very similar, less-severe injuries. Regarding significant factors and treatment variables in our adjusted analysis, older age (eg, HR for age ≥ 55 vs <25=0.52; 99% CI 0.36 to 0.74) and WSIB reimbursement for opioid prescription in the first 4 weeks of a claim (HR=0.68; 99% CI 0.53 to 0.88) were associated with longer claim duration. Higher predisability income was associated with longer claim duration, but only among persistent claims (eg, HR for active claims at 1 year with a predisability income >$920 vs ≤$480/week=0.34; 99% CI 0.17 to 0.68). Missing data for union membership (HR=1.27; 99% CI 1.01 to 1.59), and working for an employer with a return-to-work programme were associated with fewer days on claim (HR=1.78; 99% CI 1.45 to 2.18). Neither reimbursement for physiotherapy (HR=1.01; 99% CI 0.86 to 1.19) nor chiropractic care (HR for active claims at 60 days=1.15; 99% CI 0.94 to 1.41) within the first 4 weeks was associated with claim duration. Our meta-analysis of 3 studies (n=51,069 workers) confirmed a strong association between early opioid use and prolonged claim duration (HR=0.57, 95% CI 0.48 to 0.69; low certainty evidence). Our analysis found that early WSIB reimbursement for physiotherapy or chiropractic care, in claimants fully off work for more than 4 weeks, was not associated with claim duration, and that early reimbursement for opioids predicted prolonged claim duration. Well-designed randomised controlled trials are needed to verify our findings and establish causality between these variables and claim duration.


Pulmonary rehabilitation and severe exacerbations of COPD: solution or white elephant?
Hospitalisations for severe exacerbations of chronic obstructive pulmonary disease are associated with significant physical and psychological consequences including an increase in symptom severity, severe reductions in physical activity, a deleterious effect on skeletal muscle, impaired exercise tolerance/ability to self-care, decline in quality of life, and increased anxiety and depression. As these consequences are potentially amenable to exercise training, there is a clear rationale for pulmonary rehabilitation in the peri/post-exacerbation setting. Although a 2011 Cochrane review was overwhelmingly positive, subsequent trials have shown less benefit and real-life observational studies have revealed poor acceptability. Qualitative studies have demonstrated that the patient experience is a determining factor while the presence of comorbidities may influence referral, adherence and response to pulmonary rehabilitation. Systematic reviews of less supervised interventions, such as self-management, have shown limited benefits in the post-exacerbation setting. The recent update of the Cochrane review of peri-exacerbation pulmonary rehabilitation showed that benefits were associated with the "comprehensive" nature of the intervention (the number of sessions received, the intensity of exercise training and education delivered, and the degree of supervision) but implementation is demanding. The challenge is to develop interventions that are deliverable and acceptable around the time of an acute exacerbation but also deliver the desired clinical impact.


Global Heat Wave Hazard Considering Humidity Effects during the 21st Century.
Humidity is a significant factor contributing to heat stress, but without enough consideration in studies of quantifying heat hazard or heat risk assessment. Here, the simplified wet-bulb globe temperature (WBGT) considering joint effects of temperature and humidity was utilized as a heat index and the number of annual total heat wave days (HWDs) was employed to quantify heat hazard. In order to evaluate the humidity effects on heat waves, we quantified the difference in the number of HWDs over global land based on air temperature and WBGT. Spatial and temporal changes in surface air temperature, relative humidity, WBGT, and the difference in HWDs were analyzed using multi-model simulations for the reference period (1986-2005) and different greenhouse gas emission scenarios. Our analysis suggests that annual mean WBGT has been increasing since 1986, which is consistent with the rising trend in surface air temperature despite a slight decrease in relative humidity. Additionally, changes in annual mean WBGT are smaller and more spatially uniform than those in annual mean air temperature as a cancelation effect between temperature and water vapor. Results show that there is an underestimation of around 40-140 days in the number of HWDs per year in most regions within 15° latitude of the equator (the humid and warm tropics) during 2076-2095 without considering humidity effects. However, the estimation of HWDs has limited distinction between using WBGT and temperature alone in arid or cold regions.


Molecular Functions of Glycoconjugates in Autophagy.
Glycoconjugates, glycans, carbohydrates, and sugars: these terms encompass a class of biomolecules that are diverse in both form and function ranging from free oligosaccharides, glycoproteins, and proteoglycans, to glycolipids that make up a complex glycan code that impacts normal physiology and disease. Recent data suggest that one mechanism by which glycoconjugates impact physiology is through the regulation of the process of autophagy. Autophagy is a degradative pathway necessary for differentiation, organism development, and the maintenance of cell and tissue homeostasis. In this review, we will highlight what is known about the regulation of autophagy by glycoconjugates focusing on signaling mechanisms from the extracellular surface and the regulatory roles of intracellular glycans. Glycan signaling from the extracellular matrix converges on "master" regulators of autophagy including AMPK and mTORC1, thus impacting their localization, activity, and/or expression. Within the intracellular milieu, gangliosides are constituents of the autophagosome membrane, a subset of proteins composing the autophagic machinery are regulated by glycosylation, and oligosaccharide exposure in the cytosol triggers an autophagic response. The examples discussed provide some mechanistic insights into glycan regulation of autophagy and reveal areas for future investigation.


Endodontic re-treatment or implants: a contemporary conundrum.
In recent years, dental implants have become a common alternative in dental care. Of course, not all patients present with clear-cut treatment needs. Treatment planning an endodontically treated tooth that may require re-treatment vs extracting that same tooth and placing an implant may be one such conundrum. Given the disparity between the implant and endodontic re-treatment literature and the relative paucity of data-based results for indications and contraindications of endosseous root-form implants vs endodontic re-treatment, treatment planning can become a complex task. This article presents a few criteria to consider when treatment planning endodontic re-treatment vs extraction and subsequent implant placement. Because treatment planning can become such a complex issue, using all the varied resources of the dental team is imperative.


An in-plane nano-mechanics approach to achieve reversible resonance control of photonic crystal nanocavities.
Control of photonic crystal resonances in conjunction with large spectral shifting is critical in achieving reconfigurable photonic crystal devices. We propose a simple approach to achieve nano-mechanical control of photonic crystal resonances within a compact integrated on-chip approach. Three different tip designs utilizing an in-plane nano-mechanical tuning approach are shown to achieve reversible and low-loss resonance control on a one-dimensional photonic crystal nanocavity. The proposed nano-mechanical approach driven by a sub-micron micro-electromechanical system integrated on low loss suspended feeding nanowire waveguide, achieved relatively large resonance spectral shifts of up to 18 nm at a driving voltage of 25 V. Such designs may potentially be used as tunable optical filters or switches.


Efficacy of various plant hydrosols as natural food sanitizers in reducing Escherichia coli O157:H7 and Salmonella Typhimurium on fresh cut carrots and apples.
In the present study, inhibitory effects of the hydrosols of thyme, black cumin, sage, rosemary and bay leaf were investigated against Salmonella Typhimurium and Escherichia coli O157:H7 inoculated to apple and carrots (at the ratio of 5.81 and 5.81 log cfu/g for S. Typhimurium, and 5.90 and 5.70 log cfu/g for E. coli O157:H7 on to apple and carrot, respectively). After the inoculation of S. Typhimurium or E. coli O157:H7, shredded apple and carrot samples were washed with the hydrosols and sterile tap water (as control) for 0, 20, 40 and 60 min. While the sterile tap water was ineffective in reducing (P>0.05) S. Typhimurium and E. coli O157:H7, 20 min hydrosol treatment caused a significant (P<0.05) reduction compared to the control group. On the other hand, thyme and rosemary hydrosol treatments for 20 min produced a reduction of 1.42 and 1.33 log cfu/g respectively in the E. coli O157:H7 population on apples. Additional reductions were not always observed with increasing treatment time. Moreover, thyme hydrosol showed the highest antibacterial effect on both S. Typhimurium and E. coli O157:H7 counts. Inhibitory effect of thyme hydrosol on S. Typhimurium was higher than that for E. coli O157:H7. Bay leaf hydrosol treatments for 60 min reduced significantly (P<0.05) E. coli O157:H7 population on apple and carrot samples. In conclusion, it was shown that plant hydrosols, especially thyme hydrosol, could be used as a convenient sanitizing agent during the washing of fresh-cut fruits and vegetables.


The experience of pregnancy in women with a history of anorexia nervosa: An interpretive phenomenological analysis.
To explore the experience of pregnancy for women who have a history of anorexia nervosa (AN), in relation to the impact of AN on pregnancy, and pregnancy on AN. Semi-structured interviews were conducted with six women with a history of AN. Data were analysed using Interpretive Phenomenological Analysis. Four super-ordinate themes emerged: 'Effortful resistance of AN'; 'The unvalued self, valued other dialectic'; 'In new territory'; and 'Feeling distanced'. Various factors motivated the women to try and change their AN behaviours. This was achieved with varying degrees of success. Attempts to manage AN cognitions and emotions were less successful, and this aspect of their illness persisted. Whilst the baby was viewed as worthy of nurturance, the self was not. Pregnancy represented an unfamiliar experience, and was a time of relative isolation and lack of psychological support. Findings are discussed in the context of theory, research and practice.


Clinical use of antimicrobial regional limb perfusion in horses: 174 cases (1999-2009).
To describe the clinical use of regional limb perfusion with antimicrobials (A-RLP), complications, and outcome in a large series of patients. Retrospective case series. 174 horses. Medical records of horses treated with A-RLP between 1999 and 2009 were reviewed. Signalment, primary complaint, horse use, etiology, duration of clinical signs, previous treatment, structures involved, concurrent conditions, A-RLP characteristics, additional treatments, complications, and outcome were recorded. At long-term follow-up, 2 outcomes were investigated: survival rate and return to previous use at the same or higher level. Univariate and multivariate logistic regression analyses were conducted. Group 1 (96 horses) included septic synovitis. Group 2 (50 horses) included extrasynovial lacerations (23 horses) and fresh, minimally contaminated intrasynovial lacerations without evidence of established synovial infection (27 horses). Group 3 (28 horses) included miscellaneous other conditions. Only minor complications were reported in 12.26% of horses that received IV (n = 155) and 33% of horses that received intraosseous (27) A-RLP. Horses with septic synovitis had a lower survival rate (53.43%) than did horses with lacerations (91.89%). Within group 2, no significant differences in short- or long-term outcomes were found between horses with extrasynovial and fresh, minimally contaminated intrasynovial lacerations. For the horses returning to previous use, 80% of horses with septic synovitis and 72.72% of horses with lacerations were performing at the same or higher level at the time of follow-up. The results of the present study indicated that A-RLP is a safe technique with minimal adverse effects. The IV route presented fewer complications than intraosseous injection. Horses with infection of synovial structures had a lower survival rate than did those with acute, minimally contaminated intrasynovial lacerations. The latter had a similar prognosis for horses with extrasynovial lacerations treated with A-RLP.


High-speed optical signal processing potential of grating-coupled waveguide filters.
The application of grating-coupled waveguides to spread spectrum fiber-optic communications systems is described. It is first shown that such a device can act as its own matched filter for impulsive excitation, which allows its use as an encoder and decoder of ultrashort pulses. This is true even in the case of strong coupling, although considerable pulse distortion occurs. A typical performance that might be expected from existing technology is then outlined, and a number of numerical examples are presented to illustrate typical signal processing operations.


Can constructed wetlands reduce the diffuse phosphorus loads to eutrophic water in cold temperate regions?
Construction of wetlands is a possible supplement to best management practices (BMP) at the field level to mitigate phosphorus (P) pollution from agricultural areas. In this paper, annual results from 17 intensively studied wetlands in the cold temperate or boreal climatic zone are reported and analyzed. Surface areas varied from 0.007 to 8.7% of the catchment area. The average total phosphorus (TP) retention varied from 1 to 88%, and the dissolved reactive phosphorus (DRP) retention from -19 to 89%. Retention varied substantially from site to site, indicating the existence of site-specific factors in the catchment and wetlands that influenced the P removal. Factors important for P retention in wetlands were evaluated through multiple statistical analyses by dividing P into two fractions: particulate phosphorus (PP) and DRP. Both relative (%) PP and DRP retention increased with wetland surface area. However, PP retention was not as sensitive as DRP in terms of wetland size and retention: specific PP retention (gram P retention per m(2) and year) decreased as wetland area (A(w)) increased, suggesting the existence of a site-specific optimal wetland to catchment area (A(c)) ratio. Particulate P retention decreased with increasing DRP to TP ratio, while the opposite was found for DRP. Dissolved reactive P retention was higher in new than in old wetlands, while increasing age did not influence PP retention negatively. Effective BMP in the catchment is important to keep the P loss low, because the outlet concentration of P from wetlands is often positively correlated to the input concentration. However, wetlands act as the last buffer in a catchment, since the retention often increases as the P concentration in streams increases.


Interactions of CO2 with various functional molecules.
The CO2 capturing and sequestration are of importance in environmental science. Understanding of the CO2-interactions with various functional molecules including multi-N-containing superbases and heteroaromatic ring systems is essential for designing novel materials to effectively capture the CO2 gas. These interactions are investigated using density functional theory (DFT) with dispersion correction and high level wave function theory (resolution-of-identity (RI) spin-component-scaling (scs) Möller-Plesset second-order perturbation theory (MP2) and coupled cluster with single, double and perturbative triple excitations (CCSD(T))). We found intriguing molecular systems of melamine, 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD), 7-azaindole and guanidine, which show much stronger CO2 interactions than the well-known functional systems such as amines. In particular, melamine could be exploited to design novel materials to capture the CO2 gas, since one CO2 molecule can be coordinated by four melamine molecules, which gives a binding energy (BE) of ∼85 kJ mol(-1), much larger than in other cases.


Effect of varying PCO2 on intracellular pH and lactate consumption in the isolated perfused rat liver.
1. The effects of varying PCO2 on lactate uptake and intracellular pH (pHi) were studied in the isolated rat liver perfused with differing concentration of lactate. 2. In general, pHi and lactate uptake are inversely related to PCO2, and pHi and lactate uptake are directly related to each other, but the quantitative aspects and significance of these relationships vary with the availability of lactate. A model of hepatic lactate metabolism is proposed which may account for the quantitative variation. 3. The metabolism of lactate within the hepatocyte exerts a destabilizing effect on hepatocyte cell pH, in contrast to the buffering effect seen in predominantly glycolytic tissues. 4. An attempt is made to relate the findings to the disturbances of lactate metabolism in clinical respiratory failure.


Pharmacologic preconditioning with berberine attenuating ischemia-induced apoptosis and promoting autophagy in neuron.
Pharmacologic preconditioning is an intriguing and emerging approach adopted to prevent injury of ischemia/reperfusion. Neuroprotection is the cardinal effect of these pleiotropic actions of berberine. Here we investigated that whether berberine could acts as a preconditioning stimuli contributing to attenuate hypoxia-induced neurons death as well. Male Sprague-Dawley rats of middle cerebral artery occlusion (MCAO) and rat primary cortical neurons undergoing oxygen and glucose deprivation (OGD) were preconditioned with berberine (40 mg/kg, for 24 h in vivo, and 10(-6) mol/L, for 2 h in vitro, respectively). The neurological deficits and cerebral water contents of MCAO rats were evaluated. The autophagy and apoptosis were further determined in primary neurons in vitro. Berberine preconditioning (BP) was then shown to ameliorate the neurological deficits, decrease cerebral water content and promote neurogenesis of MCAO rats. Decreased LDH release from OGD-treated neurons was observed via BP, which was blocked by LY294002 (20 µmol/L), GSK690693 (10 µmol/L), or YC-1 (25 µmol/L). Furthermore, BP stimulated autophagy and inhibited apoptosis via modulated the autophagy-associated proteins LC 3, Beclin-1 and p62, and apoptosis-modulating proteins caspase 3, caspase 8, caspase 9, PARP and BCL-2/Bax. In conclusion, berberine acts as a stimulus of preconditioning that exhibits neuroprotection via promoting autophagy and decreasing anoxia-induced apoptosis.


Formation of the killer Ig-like receptor repertoire on CD4+CD28null T cells.
Killer Ig-like receptors (KIRs) are expressed on CD4(+)CD28(null) T cells, a highly oligoclonal subset of T cells that is expanded in patients with rheumatoid arthritis. It is unclear at what stage of development these T cells acquire KIR expression. To determine whether KIR expression is a consequence of clonal expansion and replicative senescence, multiple CD4(+)CD28(null) T cell clones expressing the in vivo dominant TCR beta-chain sequences were identified in three patients and analyzed for their KIR gene expression pattern. Based on sharing of TCR sequences, the clones were grouped into five clone families. The repertoire of KIRs was diverse, even within each clone family; however, the gene expression was not random. Three particular receptors, KIR2DS2, KIR2DL2, and KIR3DL2, had significant differences in gene expression frequencies between the clone families. These data suggest that KIRs are successively acquired after TCR rearrangement, with each clone family developing a dominant expression pattern. The patterns did not segregate with the individual from whom the clones were derived, indicating that peripheral selection in the host environment was not a major shaping force. Several models were examined using a computer algorithm that was designed to simulate the expression of KIRs at various times during T cell proliferation. The computer simulations favored a model in which KIR gene expression is inducible for a limited time during the initial stages of clonal expansion.


Novel in situ self-assembly nanoparticles for formulating a poorly water-soluble drug in oral solid granules, improving stability, palatability, and bioavailability.
The purpose of this study was to develop a novel lipid-based nanotechnology to formulate poorly water-soluble drugs in oral solid granules to improve stability, palatability, and bioavailability. In one method, we prepared ritonavir (RTV) nanoparticles (NPs) by a microemulsion-precursor method and then converted the RTV NPs to solid granules by wet granulation to produce RTV NP-containing granules. In the other innovative method, we did not use water in the formulation preparation, and discovered novel in situ self-assembly nanoparticles (ISNPs). We prepared RTV ISNP granules that did not initially contain NPs, but spontaneously produced RTV ISNPs when the granules were introduced to water with gentle agitation. We fully characterized these RTV nanoformulations. We also used rats to test the bioavailability of RTV ISNP granules. Finally, an Astree electronic tongue was used to assess the taste of the RTV ISNP granules. RTV NP-containing granules only had about 1% drug loading of RTV in the solid granules. In contrast, RTV ISNP granules achieved over 16% drug loading and were stable at room temperature over 24 weeks. RTV ISNPs had particle size between 160 nm and 300 nm with narrow size distribution. RTV ISNPs were stable in simulated gastric fluid for 2 hours and in simulated intestinal fluid for another 6 hours. The data from the electronic tongue showed that the RTV ISNP granules were similar in taste to blank ISNP granules, but were much different from RTV solution. RTV ISNP granules increased RTV bioavailability over 2.5-fold compared to RTV solution. We successfully discovered and developed novel ISNPs to manufacture RTV ISNP granules that were reconstitutable, stable, and palatable, and improved RTV bioavailability. The novel ISNP nanotechnology is a platform to manufacture oral solid dosage forms for poorly water-soluble drugs, especially for pediatric formulation development.


Neutrophil CD11B expression and neutrophil activation in pre-eclampsia.
1. Neutrophil activation was examined in 22 women with pre-eclampsia and 22 age- and gestation-matched control subjects using whole-blood flow cytometry to assess basal and platelet-activating factor stimulated CD11b and CD18. 2. Basal neutrophil CD11b expression was significantly increased in women with pre-eclampsia compared with normal pregnancy before delivery. A similar non-significant trend for CD18 was also observed. 3. Before delivery, neutrophil CD11b expression increased in a dose-dependent fashion after platelet-activating factor stimulation, with the differences between the groups maintained. A similar dose-dependent increase in CD18 expression was observed after platelet-activating factor. 4. There were no between-group differences in expression of either CD11b or CD18 at either 6 weeks or 6 months post partum, either before or after platelet-activating factor stimulation. 5. Neutrophil CD11b was positively correlated with plasma uric acid (r = 0.44, P = 0.04) in women with pre-eclampsia, suggesting that the extent of neutrophil activation correlates with disease severity. 6. An increase in basal neutrophil CD11b expression in women with pre-eclampsia is likely to be an index of neutrophil activation in vivo. Neutrophil release of free radicals and proteases may then help perpetuate a vicious cycle of endothelial and vascular dysfunction in the placental and systemic circulations. The cause of this activation is not known but could involve platelet activation, increased production of endothelin-1 or release of cytokines. Further studies will be required to elucidate the consequences of neutrophil activation in pre-eclampsia.


Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs.
Most psychiatric disorders are moderately to highly heritable. The degree to which genetic variation is unique to individual disorders or shared across disorders is unclear. To examine shared genetic etiology, we use genome-wide genotype data from the Psychiatric Genomics Consortium (PGC) for cases and controls in schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorders (ASD) and attention-deficit/hyperactivity disorder (ADHD). We apply univariate and bivariate methods for the estimation of genetic variation within and covariation between disorders. SNPs explained 17-29% of the variance in liability. The genetic correlation calculated using common SNPs was high between schizophrenia and bipolar disorder (0.68 ± 0.04 s.e.), moderate between schizophrenia and major depressive disorder (0.43 ± 0.06 s.e.), bipolar disorder and major depressive disorder (0.47 ± 0.06 s.e.), and ADHD and major depressive disorder (0.32 ± 0.07 s.e.), low between schizophrenia and ASD (0.16 ± 0.06 s.e.) and non-significant for other pairs of disorders as well as between psychiatric disorders and the negative control of Crohn's disease. This empirical evidence of shared genetic etiology for psychiatric disorders can inform nosology and encourages the investigation of common pathophysiologies for related disorders.


Indium-111 labeled leukocytes in evaluation of active specific immunotherapy responses.
Active immunization of patients utilizing viral oncolysates (VO) has been studied in clinical trials. VO are extracts of cultured tumor cells that have been infected with certain types of viruses, particularly surface budding varieties. The objectives of the current studies were to examine the trafficking patterns of Indium (In)-111-labeled leukocytes or lymphocytes in two groups of patients with gynecologic malignancies to determine whether these cells migrate to sites of active immunization after VO. Eight patients with ovarian cancer received VO intraperitoneally followed by In-111-labeled leukocytes or lymphocytes (500 &mgr;Ci) intravenously. In a separate trial, three patients with cervical cancer received In-111-labeled lymphocytes after they had been treated with VO administered by the intralymphatic route. Gamma camera imaging was performed to evaluate the distribution patterns of the labeled cells at several time intervals after injection. Results indicate that metastatic tumor sites exposed to VO therapy show significant uptake of In-111 cells. These sites of malignancies were confirmed by computerized tomography and ultrasound scans. In patients with ovarian cancer no uptake of the radiolabeled cells was observed in metastatic tumors of the liver and lymph nodes. In patients with cervical cancer, lymph node metastases exposed to intralymphatic VO therapy were visualized very well. Other known tumor sites not exposed to VO therapy showed no uptake of radioactivity. These findings confirm that VO induces immune responses. This diagnostic nuclear medicine technique may prove to be a useful method for following-up responses to immunotherapy.


Ensemble Estimation of Information Divergence †.
Recent work has focused on the problem of nonparametric estimation of information divergence functionals between two continuous random variables. Many existing approaches require either restrictive assumptions about the density support set or difficult calculations at the support set boundary which must be known a priori. The mean squared error (MSE) convergence rate of a leave-one-out kernel density plug-in divergence functional estimator for general bounded density support sets is derived where knowledge of the support boundary, and therefore, the boundary correction is not required. The theory of optimally weighted ensemble estimation is generalized to derive a divergence estimator that achieves the parametric rate when the densities are sufficiently smooth. Guidelines for the tuning parameter selection and the asymptotic distribution of this estimator are provided. Based on the theory, an empirical estimator of Rényi-α divergence is proposed that greatly outperforms the standard kernel density plug-in estimator in terms of mean squared error, especially in high dimensions. The estimator is shown to be robust to the choice of tuning parameters. We show extensive simulation results that verify the theoretical results of our paper. Finally, we apply the proposed estimator to estimate the bounds on the Bayes error rate of a cell classification problem.


An integrated assessment model of carbon sequestration benefits: a case study of Liping county, China.
This research attempts to model the complexity of planting trees to increase China's CO(2) sequestration potential by using a GIS-based integrated assessment (IA) approach. We use the IA model to assess the impact of China's Grain for Green reforestation and afforestation program on farmer and state incomes as well as CO(2) sequestration in Liping County, Guizhou Province. The IA model consists of five sub-models for carbon sequestration, crop income, timber income, Grain for Green, and carbon credits. It also includes a complementary qualitative module for assessing program impacts by gender and ethnicity. Using four scenarios with various assumptions about types of trees planted, crop incomes by township, CO(2) credit prices, state subsidies, methods for estimating carbon sequestered, and harvesting of trees, we find great variation in the impact of the Grain for Green program on incomes and on carbon sequestered over a 48 year period at both the county and township levels.


Difference frequency generation in GaAs microdisks.
Semiconductor-based whispering-gallery-mode microcavities are very promising for nonlinear optics applications, thanks to the high optical quality factors attainable with today's technology. We propose to exploit this advantage to generate cw light through phase-matched difference frequency generation in a triply resonant GaAs microdisk. A proper choice of the microdisk radius and thickness allows one to select the generated wavelength in the band of 2.5-2.9 microm. Besides illustrating the design features, we numerically show that temperature can be effectively used to compensate for wavelength shifts induced on the generated field by fabrication errors.


A modular platform for one-step assembly of multi-component membrane systems by fusion of charged proteoliposomes.
An important goal in synthetic biology is the assembly of biomimetic cell-like structures, which combine multiple biological components in synthetic lipid vesicles. A key limiting assembly step is the incorporation of membrane proteins into the lipid bilayer of the vesicles. Here we present a simple method for delivery of membrane proteins into a lipid bilayer within 5 min. Fusogenic proteoliposomes, containing charged lipids and membrane proteins, fuse with oppositely charged bilayers, with no requirement for detergent or fusion-promoting proteins, and deliver large, fragile membrane protein complexes into the target bilayers. We demonstrate the feasibility of our method by assembling a minimal electron transport chain capable of adenosine triphosphate (ATP) synthesis, combining Escherichia coli F1Fo ATP-synthase and the primary proton pump bo3-oxidase, into synthetic lipid vesicles with sizes ranging from 100 nm to ∼10 μm. This provides a platform for the combination of multiple sets of membrane protein complexes into cell-like artificial structures.


Lessons from a seven-year experience of paediatric HIV in Pakistan: A single centre experience.
To describe demographic, clinical and immunologic features of children with human immunodeficiency virus. This descriptive study was conducted at the Shifa International Hospital, Islamabad, Pakistan, from 2005 to 2011, and comprised children with human immunodeficiency virus and acquired immune deficiency syndrome. Patients with detailed physical examination and appropriate investigations and those eligible for therapy were included. SPSS 21 was used for data analysis. Of the 43 patients, 27(62.8%) were boys and 16(37.2%) were girls. The overall median age was 5 years (interquartile range: 3-8.5 years). Moreover, 18(42%) children were aged equal to or below 5 years. Fathers of 5(12%) children and mothers of 6(14%) children had died. Siblings of 3(7%) patients, fathers of 20(47%) patients and mothers of 31(72%) patients had human immunodeficiency virus or acquired immune deficiency syndrome. The median duration of breastfeeding was 24 months (interquartile range: 15-24 months). Risk factors identified were foreign job by father in 12(28%) patients, birth by vaginal delivery in 20(47%), breastfeeding >6 months in 34(79%), fathers with human immunodeficiency virus or acquired immune deficiency syndrome in 20(47%), mothers with human immunodeficiency virus or acquired immune deficiency syndrome in 31(72%) and lack of maternal anti-retrovirals during pregnancy in all (100%). There were 27(63%) children being symptomatic and 29(67%) had advanced disease at diagnosis with World Health Organisation's classification stage 3 or 4. The pretreatment median CD4 count was 294.5 cells/mm3 (IQR, 208.5-808) and a follow-up CD4 of 757 cells/mm3 (IQR, 352-874) which was significant (p <0.005). The intial median HIV viral load was 83 RNA copiesx105/mm3 (IQR, 1.8-8.25). Anti-retroviral therapy (ARV) was initiated in 65% (28/43) with good compliance. The mean duration of follow-up was 12 months. There was clinical and immunologic improvement in 65% (18/28) in first 12 months. There were opportunistic infections in 20 children (46%), serious side effects in 5 (18%), progression of disease or poor response in 7 (16%) and discontinuation or switch of therapy in 2 (7%). Four children had suspected HIV drug resistance but confirmed in 2 (6.7%) requiring second-line therapy. Five children (12%) died, two within one week of diagnosis. Most human immunodeficiency virus-infected children had risk factors, present with severe immune suppression and had improved CD-4 after anti-retroviral therapy.


Clinical Microbiology Is Growing Up: The Total Laboratory Automation Revolution.
Historically, culture-based microbiology laboratory testing has relied on manual methods, and automated methods (such as those that have revolutionized clinical chemistry and hematology over the past several decades) were largely absent from the clinical microbiology laboratory. However, an increased demand for microbiology testing and standardization of sample-collection devices for microbiology culture, as well as a dwindling supply of microbiology technologists, has driven the adoption of automated methods for culture-based laboratory testing in clinical microbiology. We describe systems currently enabling total laboratory automation (TLA) for culture-based microbiology testing. We describe the general components of a microbiology automation system and the various functions of these instruments. We then introduce the 2 most widely used systems currently on the market: Becton Dickinson's Kiestra TLA and Copan's WASPLab. We discuss the impact of TLA on metrics such as turnaround time and recovery of microorganisms, providing a review of the current literature and perspectives from laboratory directors, managers, and technical staff. Finally, we provide an outlook for future advances in TLA for microbiology with a focus on artificial intelligence for automated culture interpretation. TLA is playing an increasingly important role in clinical microbiology. Although challenges remain, TLA has great potential to affect laboratory efficiency, turnaround time, and the overall quality of culture-based microbiology testing.


Daily acyclovir to decrease herpes simplex virus type 2 (HSV-2) transmission from HSV-2/HIV-1 coinfected persons: a randomized controlled trial.
Daily suppressive therapy with valacyclovir reduces risk of sexual transmission of herpes simplex virus type 2 (HSV-2) in HSV-2-serodiscordant heterosexual couples by 48%. Whether suppressive therapy reduces HSV-2 transmission from persons coinfected with HSV-2 and human immunodeficiency virus type 1 (HIV-1) is unknown. Within a randomized trial of daily acyclovir 400 mg twice daily in African HIV-1 serodiscordant couples, in which the HIV-1-infected partner was HSV-2 seropositive, we identified partnerships in which HIV-1-susceptible partners were HSV-2 seronegative to estimate the effect of acyclovir on risk of HSV-2 transmission. We randomly assigned 911 HSV-2/HIV-1-serodiscordant couples to daily receipt of acyclovir or placebo. We observed 68 HSV-2 seroconversions, 40 and 28 in acyclovir and placebo groups, respectively (HSV-2 incidence, 5.1 cases per 100 person-years; hazard ratio [HR], 1.35 [95% confidence interval, .83-2.20]; P = .22). Among HSV-2-susceptible women, vaginal drying practices (adjusted HR, 44.35; P = .004) and unprotected sex (adjusted HR, 9.91; P = .002) were significant risk factors for HSV-2 acquisition; having more children was protective (adjusted HR, 0.47 per additional child; P = .012). Among HSV-2-susceptible men, only age ≤30 years was associated with increased risk of HSV-2 acquisition (P = .016). Treatment of African HSV-2/HIV-1-infected persons with daily suppressive acyclovir did not decrease risk of HSV-2 transmission to susceptible partners. More-effective prevention strategies to reduce HSV-2 transmission from HIV-1-infected persons are needed.


Fibromatosis: a potential sequela of neuromuscular choristoma.
Neuromuscular choristoma (NMC) is a rare peripheral nerve lesion in which mature skeletal muscle fibers lie within the nerve and its fascicles. Given limited follow-up, its natural history is poorly understood. The occurrence of aggressive fibromatosis in one of the authors' patients and its occurrence in reported cases suggests an etiological relationship between the 2 lesions. This study attempts to explain the association and its frequency. All cases of NMCs seen in consultation or treated at the Mayo Clinic were identified. Demographic and clinical data were reviewed in cases with coexistent aggressive fibromatosis. Pathology and neuroimaging studies were reexamined. In addition, an extensive literature review was performed to explore the association of NMC with aggressive fibromatosis, with special attention given to pathological and imaging characteristics and the development of aggressive fibromatosis. The authors identified 10 patients with a diagnosis of NMC who were treated at the Mayo Clinic between 1992 and 2010. Four of 5 with adequate follow-up had developed a definite or suspected aggressive fibromatosis. A review of the initial pathological specimens in these cases revealed no evidence of fibromatosis, but all of the lesions exhibited accompanying hypocellular collagenous tissue. On MR images, all cases showed areas of low signal intensity, which significantly differed from muscle, nerve, and NMC components. On available serial MR imaging studies, aggressive fibromatosis seemed to originate in such lower-intensity regions. In the 18 previously reported cases of NMC, 5 patients developed recurrent masses diagnosed as either definite (2 cases) or possible (3 cases) fibromatosis. Review of the published imaging studies in these cases suggests the presence of lower intensity areas similar to those observed in the 10 patients treated at the Mayo Clinic. This study confirms that the development of aggressive fibromatosis in patients with NMC has been underreported. A direct relationship between the NMC and the development of aggressive fibromatosis is suggested by pathological and neuroimaging evidence.


Projected Prevalence of Actionable Pharmacogenetic Variants and Level A Drugs Prescribed Among US Veterans Health Administration Pharmacy Users.
Implementation of pharmacogenetic testing to guide drug prescribing has potential to improve drug response and prevent adverse events. Robust data exist for more than 30 gene-drug pairs linking genotype to drug response phenotypes; however, it is unclear which pharmacogenetic tests, if implemented, would provide the greatest utility for a given patient population. To project the proportion of veterans in the US Veterans Health Administration (VHA) with actionable pharmacogenetic variants and evaluate how testing might be associated with prescribing decisions. This cross-sectional study included veterans who used national VHA pharmacy services from October 1, 2011, to September 30, 2017. Data analyses began April 26, 2018, and were completed February 6, 2019. Receipt of level A drugs based on VHA pharmacy dispensing records. Projected prevalence of actionable pharmacogenetic variants among VHA pharmacy users based on variant frequencies from the 1000 Genomes Project and veteran demographic characteristics; incident number of level A prescriptions, and proportion of new level A drug recipients projected to carry an actionable pharmacogenetic variant. During the study, 7 769 359 veterans (mean [SD] age, 58.1 [17.8] years; 7 021 504 [90.4%] men) used VHA pharmacy services. It was projected that 99% of VHA pharmacy users would carry at least 1 actionable pharmacogenetic variant. Among VHA pharmacy users, 4 259 153 (54.8%) received at least 1 level A drug with 1 188 124 (15.3%) receiving 2 drugs, and 912 189 (11.7%) receiving 3 or more drugs. The most common incident prescriptions during the study were tramadol (923 671 new recipients), simvastatin (533 928 new recipients), citalopram (266 952 new recipients), and warfarin (205 177 new recipients). Gene-drug interactions projected to have substantial clinical impacts in the VHA population include the interaction of SLCO1B1 with simvastatin (1 988 956 veterans [25.6%]), CYP2D6 with tramadol (318 544 veterans [4.1%]), and CYP2C9 or VKORC1 with warfarin (7 163 349 veterans [92.2%]). Clinically important pharmacogenetic variants are highly prevalent in the VHA population. Almost all veterans would carry an actionable variant, and more than half of the population had been exposed to a drug affected by these variants. These results suggest that pharmacogenetic testing has the potential to affect pharmacotherapy decisions for commonly prescribed outpatient medications for many veterans.


Evaluation of Parmotrema reticulatum Taylor for Antibacterial and Antiinflammatory Activities.
Lichens produce variety of secondary metabolites including depsides, depsidones and dibenzofurans having multifunctional activity in response to external environmental condition. Present study provides evidence for in vitro antibacterial and in vivo antiinflammatory activity of acetone and ethanol extracts of Parmotrema reticulatum. In vitro antibacterial activity was investigated against gram positive and gram negative bacteria. Cotton pellet-induced granuloma, xylene-induced ear swelling, carragennan-induced edema, histamine-induced and carboxymethylcellulose sodium-induced leukocyte emigration in mice models were used to quantify the antiinflammatory activity. Acetone and ethanol extracts were showed antibacterial activity against Bacillus subtilis (minimal inhibitory concentration: 100 and 150 μg/ml) and Staphylococcus aureus (minimal inhibitory concentration: 100 and 200 μg/ml), Escherichia coli (minimal inhibitory concentration: 200 and 250 μg/ml), and Pseudomonasa eruginosa (minimal inhibitory concentration: 200 and 300 μg/ml). Acetone extract was inhibited edema significantly at 200 mg/kg with xylene, cotton pellet, carragennan and histamine induced edema in vivo models. Ethanol extract was found effective at dose of 300 mg/kg with all in vivo antiinflammatory models. The results showed significant (P<0.01) antiinflammatory effects at 200 and 300 mg/kg dose of acetone and ethanol extracts, respectively, which can be concluded that significant activity may be due to presence of flavanoids in ethanol extract and usnic acid in acetone extract.


Linear chromosome-generating system of Agrobacterium tumefaciens C58: protelomerase generates and protects hairpin ends.
Agrobacterium tumefaciens C58, the pathogenic bacteria that causes crown gall disease in plants, harbors one circular and one linear chromosome and two circular plasmids. The telomeres of its unusual linear chromosome are covalently closed hairpins. The circular and linear chromosomes co-segregate and are stably maintained in the organism. We have determined the sequence of the two ends of the linear chromosome thus completing the previously published genome sequence of A. tumefaciens C58. We found that the telomeres carry nearly identical 25-bp sequences at the hairpin ends that are related by dyad symmetry. We further showed that its Atu2523 gene encodes a protelomerase (resolvase) and that the purified enzyme can generate the linear chromosomal closed hairpin ends in a sequence-specific manner. Agrobacterium protelomerase, whose presence is apparently limited to biovar 1 strains, acts via a cleavage-and-religation mechanism by making a pair of transient staggered nicks invariably at 6-bp spacing as the reaction intermediate. The enzyme can be significantly shortened at both the N and C termini and still maintain its enzymatic activity. Although the full-length enzyme can uniquely bind to its product telomeres, the N-terminal truncations cannot. The target site can also be shortened from the native 50-bp inverted repeat to 26 bp; thus, the Agrobacterium hairpin-generating system represents the most compact activity of all hairpin linear chromosome- and plasmid-generating systems to date. The biochemical analyses of the protelomerase reactions further revealed that the tip of the hairpin telomere may be unusually polymorphically capable of accommodating any nucleotide.


Impacts of climatic change and fishing on Pacific salmon abundance over the past 300 years.
The effects of climate variability on Pacific salmon abundance are uncertain because historical records are short and are complicated by commercial harvesting and habitat alteration. We use lake sediment records of delta15N and biological indicators to reconstruct sockeye salmon abundance in the Bristol Bay and Kodiak Island regions of Alaska over the past 300 years. Marked shifts in populations occurred over decades during this period, and some pronounced changes appear to be related to climatic change. Variations in salmon returns due to climate or harvesting can have strong impacts on sockeye nursery lake productivity in systems where adult salmon carcasses are important nutrient sources.


Differential gene expression in individual papilla-resistant and powdery mildew-infected barley epidermal cells.
Resistance and susceptibility in barley to the powdery mildew fungus (Blumeria graminis f. sp. hordei) is determined at the single-cell level. Even in genetically compatible interactions, attacked plant epidermal cells defend themselves against attempted fungal penetration by localized responses leading to papilla deposition and reinforcement of their cell wall. This conveys a race-nonspecific form of resistance. However, this defense is not complete, and a proportion of penetration attempts succeed in infection. The resultant mixture of infected and uninfected leaf cells makes it impossible to relate powdery mildew-induced gene expression in whole leaves or even dissected epidermal tissues to resistance or susceptibility. A method for generating transcript profiles from individual barley epidermal cells was established and proven useful for analyzing resistant and successfully infected cells separately. Contents of single epidermal cells (resistant, infected, and unattacked controls) were collected, and after cDNA synthesis and PCR amplification, the resulting sample was hybridized to dot-blots spotted with genes, including some previously reported to be induced upon pathogen attack. Transcripts of several genes, (e.g., PR1a, encoding a pathogenesis related protein, and GLP4, encoding a germin-like protein) accumulated specifically in resistant cells, while GRP94, encoding a molecular chaperone, accumulated in infected cells. Thus, the single-cell method allows discrimination of transcript profiles from resistant and infected cells. The method will be useful for microarray expression profiling for simultaneous analysis of many genes.


Expression pattern and regulation of genes differ between fibroblasts of adhesion and normal human peritoneum.
Injury to the peritoneum during surgery is followed by a healing process that frequently results in the attachment of adjacent organs by a fibrous mass, referred commonly as adhesions. Because injuries to the peritoneum during surgery are inevitable, it is imperative that we understand the mechanisms of adhesion formation to prevent its occurrence. This requires thorough understanding of the molecular sequence that results in the attachment of injured peritoneum and the development of fibrous tissue. Recent data show that fibroblasts from the injured peritoneum may play a critical role in the formation of adhesion tissues. Therefore, identifying changes in gene expression pattern in the peritoneal fibroblasts during the process may provide clues to the mechanisms by which adhesion develop. In this study, we compared expression patterns of larger number of genes in the fibroblasts isolated from adhesion and normal human peritoneum using gene filters. Contributions of TGF-beta1 and hypoxia in the altered expression of specific genes were also examined using a semiquantitative RT-PCR technique. Results show that several genes are differentially expressed between fibroblasts of normal and adhesion peritoneum and that the peritoneal fibroblast may acquire a different phenotype during adhesion formation. Genes that are differentially expressed between normal and adhesion fibroblasts encode molecules involved in cell adhesion, proliferation, differentiation, migration and factors regulating cytokines, transcription, translation and protein/vesicle trafficking. Our data substantiate that adhesion formation is a multigenic phenomenon and not all changes in gene expression pattern between normal and adhesion fibroblasts are the function of TGF-beta1 and hypoxia that are known to influence adhesion formation. Analysis of the gene expression data in the perspective of known functions of genes connote to additional targets that may be manipulated to inhibit adhesion development.


Impact of bladder cancer on health related quality of life in 1,476 older Americans: a cross-sectional study.
The impact of bladder cancer diagnosis on health related quality of life is poorly understood. We compared health related quality of life measures in patients before and after bladder cancer diagnosis. We performed a cross-sectional study in 1,476 patients 65 years old or older with bladder cancer in the SEER-MHOS linkage database between 1998 and 2007 to assess differences in physical and mental component summary scores in 620 and 856 who completed a survey before and after bladder cancer diagnosis, respectively. To determine differences in physical and mental scores in the prediagnosis and post-diagnosis cohorts, we used ANOVA adjusting for baseline covariates. There were statistically significant differences in physical and mental component summary scores between the prediagnosis and post-diagnosis groups (-2.7, 95% CI -3.8, -1.7 vs -1.4, 95% CI -2.6, -0.3). In patients with nonmuscle invasive bladder cancer the physical and mental score differences were -1.9 (p <0.01) and -1.4 (p = 0.01), respectively. In those with muscle invasive bladder cancer there was a statistically and clinically significant difference in the physical but not the mental score (-5.3, p <0.01 vs -2.7, p = 0.07). This difference in the physical domain persisted up to 10 years after the diagnosis of muscle invasive bladder cancer. Patients with bladder cancer who had 4 or more comorbid medical conditions and 1 or more deficits in daily living activity were most at risk for low physical component summary scores. Future research into interventions to improve health related quality of life and methods to incorporate health related quality of life into decision making models are critical to improve outcomes in older patients with bladder cancer.


The motor disorders of severe psychiatric illness: a conflict of paradigms.
The motor disorder of 100 patients with severe psychiatric illness is described and the contribution of previous treatment, hospitalization and possible neurological disorder is considered. The conflict of paradigms between the concept that this motor disorder has two distinct aetiologies, psychiatric and neurological, and the concept that both motor and mental disorder are an expression of underlying cerebral disorder is discussed. An attempt is made to resolve this conflict by description of motor disorder without reference to neurological or psychiatric diagnosis.


Acute care nurse practitioner curriculum: content and development process.
Curriculum development for preparation of acute care nurse practitioners requires a comprehensive process. To develop a program for their preparation at a large university, the faculty examined needs of the target patient population and care delivery system; scope of acute care nurse practitioner practice; current guidelines for the education of primary care nurse practitioners; evolving guidelines for the didactic and clinical education of acute care nurse practitioners; educational requirements of governing or licensing and certifying bodies; and placement of this new role within the existing healthcare team structure. A curriculum was then developed using a collaborative, multidisciplinary approach.


A method for radiation-force localized drug delivery using gas-filled lipospheres.
We have developed a method using ultrasound and acoustically active lipospheres (AALs) that might be used to deliver bioactive substances to the vascular endothelium. The AALs consist of a small gas bubble surrounded by a thick oil shell and enclosed by an outermost lipid layer. The AALs are similar to ultrasound contrast agents: they can be nondestructively deflected using ultrasound radiation force, and fragmented with high-intensity ultrasound pulses. The lipid-oil complex might be used to carry bioactive substances at high concentrations. An optimized sequence of ultrasound pulses can deflect the AALs toward a vessel wall then disrupt them, painting their contents across the vascular endothelium. This paper presents results from a series of in vitro and ex vivo experiments demonstrating localization of a fluorescent model drug. In experiments using a human melanoma cell (A2085) monolayer, a specific radiation force-fragmentation ultrasound pulse sequence increased cell fluorescence more than 10-fold over no ultrasound or fragmentation pulses alone, and by 50% over radiation force pulses alone. We observe that dye transfer is limited to cells that are in the region of ultrasonic focus, indicating that the application of radiation force pulses to bring the delivery vehicle into proximity with the cell is required for successful adhesion of the vehicle fragments to the cell membrane. We also demonstrate dye transfer from flowing AALs, both in a mimetic vessel and in excised rat cecum. We believe that this method could be successfully used for drug delivery in vivo.


Pharmacogenetics of asthma.
Pharmacogenetics offers the potential to optimize treatment for individual patients by using genetic information to improve efficacy or avoid side effects. While there are a number of examples in which the approach is already in routine clinical usage, exploitation of this approach in asthma is still under development. A number of examples of possible pharmacogenetic approaches that may prove of value in the management of asthma are discussed.


A nanocomplex of C60 fullerene with cisplatin: design, characterization and toxicity.
The self-organization of C60 fullerene and cisplatin in aqueous solution was investigated using the computer simulation, dynamic light scattering and atomic force microscopy techniques. The results evidence the complexation between the two compounds. The genotoxicity of С60 fullerene, Cis and their complex was evaluated in vitro with the comet assay using human resting lymphocytes and lymphocytes after blast transformation. The cytotoxicity of the mentioned compounds was estimated by Annexin V/PI double staining followed by flow cytometry. The results clearly demonstrate that water-soluble C60 fullerene nanoparticles (0.1 mg/mL) do not induce DNA strand breaks in normal and transformed cells. C60 fullerene in the mixture with Cis does not influence genotoxic Cis activity in vitro, affects the cell-death mode in treated resting human lymphocytes and reduces the fraction of necrotic cells.


A qualitative exploration of doctors and nurses experiences on the management of tuberculosis and HIV co-infection in a tuberculosis-HIV high burden community in northern KwaZulu-Natal, South Africa.
South Africa is faced with a huge challenge of addressing the high burden of tuberculosis-human immune virus (TBHIV) co-infection, and this challenge is more pronounced in the province of KwaZulu-Natal which has one of the highest burdens of TB-HIV co-infection in the world. The study explored the experiences of doctors and nurses with regard to the management of tuberculosis and HIV coinfection in a TB-HIV high burden community in northern KwaZulu-Natal, South Africa. The particular focus was to provide insight and to inform policy and programme development for effective management of TB-HIV co-infection in the TB-HIV high burden community of northern KwaZulu- Natal. An interpretivist exploratory qualitative approach was employed through individual semi-structured interviews of 16 participants comprising eight doctors and eight nurses, with a total interview time of 8.95 hours. Purposive sampling was used to select the doctors and nurses from the public and private sector of the TB-HIV high burden community of northern KwaZulu- Natal. Thematic analysis was used to analyse the data. Five key themes emerged from this study and these themes were discussed together with the sub-themes based on the various participant responses. The five key themes were practical experience about the management of TB-HIV co-infection; access to information and training on the management of TB-HIV co-infection; challenges and concerns about the management of TB-HIV co-infection; perception about local beliefs; and knowledge of policies and guidelines. Overall, this study highlights barriers that hamper the effective management of TB-HIV co-infection in northern KwaZulu-Natal. Recommendations of this study point towards an urgent need to scale up the management of TB-HIV co-infection through effective policies, improved capacity and infrastructure, stronger partnerships of all stakeholders, and further research.


Identification and outcomes of clinical phenotypes in amyotrophic lateral sclerosis/motor neuron disease: Australian National Motor Neuron Disease observational cohort.
To capture the clinical patterns, timing of key milestones and survival of patients presenting with amyotrophic lateral sclerosis/motor neuron disease (ALS/MND) within Australia. Data were prospectively collected and were timed to normal clinical assessments. An initial registration clinical report form (CRF) and subsequent ongoing assessment CRFs were submitted with a completion CRF at the time of death. Prospective observational cohort study. 1834 patients with a diagnosis of ALS/MND were registered and followed in ALS/MND clinics between 2005 and 2015. 5 major clinical phenotypes were determined and included ALS bulbar onset, ALS cervical onset and ALS lumbar onset, flail arm and leg and primary lateral sclerosis (PLS). Of the 1834 registered patients, 1677 (90%) could be allocated a clinical phenotype. ALS bulbar onset had a significantly lower length of survival when compared with all other clinical phenotypes (p<0.004). There were delays in the median time to diagnosis of up to 12 months for the ALS phenotypes, 18 months for the flail limb phenotypes and 19 months for PLS. Riluzole treatment was started in 78-85% of cases. The median delays in initiating riluzole therapy, from symptom onset, varied from 10 to 12 months in the ALS phenotypes and 15-18 months in the flail limb phenotypes. Percutaneous endoscopic gastrostomy was implemented in 8-36% of ALS phenotypes and 2-9% of the flail phenotypes. Non-invasive ventilation was started in 16-22% of ALS phenotypes and 21-29% of flail phenotypes. The establishment of a cohort registry for ALS/MND is able to determine clinical phenotypes, survival and monitor time to key milestones in disease progression. It is intended to expand the cohort to a more population-based registry using opt-out methodology and facilitate data linkage to other national registries.


Investigation of downstream target genes of PAX3c, PAX3e and PAX3g isoforms in melanocytes by microarray analysis.
PAX3 encodes a transcription factor, which with Zic1 is necessary for induction of the neural crest during early embryonic development. There are 7 human PAX3 isoforms (a-h). PAX3e is the full length isoform comprising 10 exons. PAX3c comprises 8 exons plus 5 codons of intron 8, while PAX3g has a truncated transactivation domain. Previous studies by us indicated that these isoforms have different activities in melanocytes in vitro. In this study, a mouse gene oligo array ( approximately 7.5 k oligos), from the Human Genome Mapping Project (HGMP) Resource Centre, was used to screen for alterations in downstream gene expression in PAX3c, PAX3e and PAX3g melanocyte transfectants, compared with empty vector controls. The data analyses identified 109 genes up or downregulated, at least 2-fold, and involved in cell differentiation, proliferation, migration, adhesion, apoptosis and angiogenesis. Semi-quantitative RT-PCR and Western blotting confirmed the changes identified by microarrays for several putative targets of PAX3, including Met, MyoD and Muc18, and previously undescribed targets, including Dhh, Fgf17, Kitl and Rac1. Thus, our data reveal that PAX3 isoforms regulate distinct but overlapping sets of genes in melanocytes in vitro.


Intraorbital training munition.
To present a case report of an intraorbital training munition during combat simulation. A 36-year-old National Guardsman presented to our hospital after being struck in the right orbit with a training munition during combat exercises at Fort Carson, Colorado. The clinical findings, treatment course, and outcome of the case are discussed with review of the literature. An anterior orbitotomy and retinal detachment repair was performed on the patient. The training munition was recovered through the entrance wound in the upper eyelid. At 1 month postoperative, the patient?s vision was 20/20 with correction. No complications were noted. This case report is serves as an example of the ocular morbidity associated with training munitions as well as a reminder of the importance of compliance with protective eyewear during training exercises. While surgical excision is this case was straightforward, intraorbital foreign bodies can pose a significant surgical challenge.


Career plans of primary care midwives in the Netherlands and their intentions to leave the current job.
In labour market policy and planning, it is important to understand the motivations of people to continue in their current job or to seek other employment. Over the last decade, besides the increasingly medical approach to pregnancy and childbirth and decreasing home births, there were additional dramatic changes and pressures on primary care midwives and midwifery care. Therefore, it is important to re-evaluate the career plans of primary care midwives and their intentions to leave their current job. All 108 primary care midwives of 20 selected midwifery care practices in the Netherlands were invited to fill out a written questionnaire with questions regarding career plans and intentions to leave. Bivariate analyses were carried out to compare career plans and work-related and personal characteristics and attitudes towards work among the group of midwives who indicated that they intended to leave their current job (ITL group) and those who indicated they had no intention to leave (NITL group). Significant predictors of ITL were included in the multiple binary logistic regression with 'intention to leave' as the dependent variable. In 2010, 32.7% of the 98 participating primary care midwives surveyed had considered an intention to leave their current type of job in the past year. Fewer ITL midwives wanted to be a self-employed practitioner with the full range of primary care tasks and work full-time. Significant predictors of the primary care midwives' intention to leave included a lower overall score on the job satisfaction scale (OR = 0.18; 95% CI = 0.06-0.58; p = 0.004) and being between 30 and 45 years old (OR = 2.69; 95% CI = 1.04-7.0; p = 0.041). Our study shows that, despite significant changes in the reproductive, maternal and newborn health service delivery that impact on independent midwifery practice, the majority of primary care midwives intended to stay in primary care. The absence of job satisfaction, and being in the age group between 30 and 45 years old, is associated with primary care midwives' intention to leave their current job. Ongoing monitoring will be important in the future.


Subunit structure of aldolase.
A new crystal form of rabbit muscle aldolase shows that the molecule has 222 symmetry to at least 4-angstrom resolution, and hence that the gross conformation of the four subunits is the same. Comparison of the new form with a previously reported form establishes the number of molecules per unit cell, n, in the older form. For an independent check, the "crystal-volume and protein-content method" was developed to determine n without directly measuring the water content of the crystals.


Real-world and natural history data for drug evaluation in Duchenne muscular dystrophy: suitability of the North Star Ambulatory Assessment for comparisons with external controls.
Using external controls based on real-world or natural history data (RWD/NHD) for drug evaluations in Duchenne muscular dystrophy (DMD) is appealing given the challenges of enrolling placebo-controlled trials, especially for multi-year trials. Comparisons to external controls, however, face risks of bias due to differences in outcomes between trial and RWD/NHD settings. To assess this bias empirically, we conducted a multi-institution study comparing mean 48-week changes in North Star Ambulatory Assessment (NSAA) total score between trial placebo arms and RWD/NHD sources, with and without adjustment for baseline prognostic factors. Analyses used data from three placebo arms (235 48-week intervals, N = 235 patients) and three RWD/NHD sources (348 intervals, N = 202 patients). Differences in mean ΔNSAA between placebo arms and RWD/NHD sources were small before adjustment (-1.2 units, 95% CI: [-2.0 -0.5]) and were attenuated and no longer statistically significant after adjustment (0.1 units (95% CI: [-0.6, 0.8]). Results were similar whether adjusting using multivariable regression or propensity score matching. This consistency in ΔNSAA between trial placebo arms and RWD/NHD sources accords with prior findings for the six-minute walk distance, provides a well-validated framework for baseline adjustment of prognostic factors, and supports the suitability of RWD/NHD external controls for drug evaluations in ambulatory DMD.


Identification and High-Resolution Imaging of α-Tocopherol from Human Cells to Whole Animals by TOF-SIMS Tandem Mass Spectrometry.
A unique method for identification of biomolecular components in different biological specimens, while preserving the capability for high speed 2D and 3D molecular imaging, is employed to investigate cellular response to oxidative stress. The employed method enables observing the distribution of the antioxidant α-tocopherol and other molecules in cellular structures via time-of-flight secondary ion mass spectrometry (TOF-SIMS (MS1)) imaging in parallel with tandem mass spectrometry (MS2) imaging, collected simultaneously. The described method is employed to examine a network formed by neuronal cells differentiated from human induced pluripotent stem cells (iPSCs), a model for investigating human neurons in vitro. The antioxidant α-tocopherol is identified in situ within different cellular layers utilizing a 3D TOF-SIMS tandem MS imaging analysis. As oxidative stress also plays an important role in mediating inflammation, the study was expanded to whole body tissue sections of M. marinum-infected zebrafish, a model organism for tuberculosis. The TOF-SIMS tandem MS imaging results reveal an increased presence of α-tocopherol in response to the pathogen. Graphical Abstract .


Absence of Helicobacter pylori high tetracycline resistant 16S rDNA AGA926-928TTC genotype in gastric biopsy specimens from dyspeptic patients of a city in the interior of São Paulo, Brazil.
Treatment effectiveness of Helicobacter pylori varies regionally and is decreasing worldwide, principally as a result of antibiotic resistant bacterium. Tetracycline is generally included in second line H. pylori eradication regimens. In Brazil, a high level of tetracycline resistance (TetR) is mainly associated with AGA926-928TTC 16 S rDNA nucleotide substitutions. As H. pylori culture is fastidious, we investigated the primary occurrence of H. pylori 16 S rDNA high level TetR genotype using a molecular approach directly on gastric biopsies of dyspeptic patients attending consecutively at Hospital das Clinicas of Marilia, São Paulo, Brazil. Gastric biopsy specimens of 68 peptic ulcer disease (PUD) and 327 chronic gastritis (CG) patients with a positive histological diagnosis of H. pylori were investigated for TetR 16 S rDNA genotype through a molecular assay based on amplification of a 16 S rDNA 545 bp fragment by polymerase chain reaction and HinfI restriction fragment length polymorphism (PCR/RFLP). Through this assay, AGA926-928TTC 16 S rDNA TetR genotype resulted in a three DNA fragment restriction pattern (281, 227 and 37 bp) and its absence originated two DNA fragments (264 and 281 bp) due to a 16 S rDNA conserved Hinf I restriction site. The 545 bp 16 S rDNA PCR fragment was amplified from 90% of gastric biopsies from histological H. pylori positive patients. HinfI RFLP revealed absence of the AGA926-928TTC H. pylori genotype and PCR products of two patients showed absence of the conserved 16 S rDNA HinfI restriction site. BLASTN sequence analysis of four amplicons (two conserved and two with an unpredicted HinfI restriction pattern) revealed a 99% homology to H. pylori 16 S rDNA from African, North and South American bacterial isolates. A nucleotide substitution abolished the conserved HinfI restriction site in the two PCR fragments with unpredicted HinfI RFLP, resulting in an EcoRI restriction site. H. pylori AGA926-928TTC 16 S rDNA gene substitutions were not found in our population. More research is required to investigate if H. pylori TetR has a different genetic background in our region and if the nucleotide substitutions of the uncultured H. pylori 16 S rRNA partial sequences have biological significance.


Development and testing of the questionnaire CEC-61: Knowledge about cervical cancer in Chilean adolescents.
Despite a clear association between human papillomavirus and cervical cancer, knowledge in adolescent populations regarding the disease and methods for its detection and prevention is deficient. The aim of this study was to develop and test a new questionnaire concerning knowledge on cervical cancer. An instrument was developed and validated to measure knowledge in 226 Chilean adolescents between April and June 2011. Content validity, construct validity, and reliability analysis of the instrument were performed. The new, validated instrument, called CEC-61 (Conocimientos en Cancer Cérvicouterino-61 items/Knowledge in Cervical Cancer-61 items), contains nine factors and 61 items. The new questionnaire explained 81% of the variance with a reliability of 0.96. The assessment of knowledge with a valid and reliable instrument is the first step in creating interventions for a population and to encourage appropriate preventive behavior. CEC-61 is highly reliable and has a clear factorial structure to evaluate knowledge in nine domains related to cervical cancer disease, cervical cancer risk, papilloma virus infection, the Papanicolaou test, and the papilloma virus vaccine.


STIM1 regulates platelet-derived growth factor-induced migration and Ca2+ influx in human airway smooth muscle cells.
It is suggested that migration of airway smooth muscle (ASM) cells plays an important role in the pathogenesis of airway remodeling in asthma. Increases in intracellular Ca(2+) concentrations ([Ca(2+)](i)) regulate most ASM cell functions related to asthma, such as contraction and proliferation. Recently, STIM1 was identified as a sarcoplasmic reticulum (SR) Ca(2+) sensor that activates Orai1, the Ca(2+) channel responsible for store-operated Ca(2+) entry (SOCE). We investigated the role of STIM1 in [Ca(2+)](i) and cell migration induced by platelet-derived growth factor (PDGF)-BB in human ASM cells. Cell migration was assessed by a chemotaxis chamber assay. Human ASM cells express STIM1, STIM2, and Orai1 mRNAs. SOCE activated by thapsigargin, an inhibitor of SR Ca(2+)-ATPase, was significantly blocked by STIM1 siRNA and Orai1 siRNA but not by STIM2 siRNA. PDGF-BB induced a transient increase in [Ca(2+)](i) followed by sustained [Ca(2+)](i) elevation. Sustained increases in [Ca(2+)](i) due to PDGF-BB were significantly inhibited by a Ca(2+) chelating agent EGTA or by siRNA for STIM1 or Orai1. The numbers of migrating cells were significantly increased by PDGF-BB treatment for 6 h. Knockdown of STIM1 and Orai1 by siRNA transfection inhibited PDGF-induced cell migration. Similarly, EGTA significantly inhibited PDGF-induced cell migration. In contrast, transfection with siRNA for STIM2 did not inhibit the sustained elevation of [Ca(2+)](i) or cell migration induced by PDGF-BB. These results demonstrate that STIM1 and Orai1 are essential for PDGF-induced cell migration and Ca(2+) influx in human ASM cells. STIM1 could be an important molecule responsible for airway remodeling.


Variation of excited-state dynamics in trifluoromethyl functionalized C60 fullerenes.
We report on electronically excited-state dynamics of three different trifluoromethyl C60 fullerenes (TMFs, C60(CF3)n: C60/4-1, C60/6-2, and C60/10-1, featuring four, six, and ten trifluoromethyl groups, respectively) using steady-state and time-resolved optical spectroscopy as well as ultrafast pump/probe transient absorption spectroscopy. C60/4-1 and C60/6-2 dissolved in toluene solvent show near-unity S1 → T1 intersystem crossing quantum yield (ΦISC), ca. 1 ns S1-state lifetimes, and microsecond-timescale T1-state lifetimes, which are typical of the fullerene class. On the other hand, C60/10-1 exhibits a dominant sub-nanosecond nonradiative S1 → S0 relaxation mechanism and negligible ΦISC, therefore decreasing the average excited-state lifetime (τavg) by about 5 orders of magnitude compared to that of C60/4-1 and C60/6-2 (τavg ≈ 17 μs and 54 μs for C60/4-1 and C60/6-2, respectively, whereas τavg ≈ 100 ps for C60/10-1). These excited-state characteristics of C60/4-1 and C60/6-2 are preserved in polymer matrix, suggesting that fullerene/polymer interactions do not modulate intrinsic photophysics of trifluoromethyl-substituted fullerenes. The contrasting excited-state study results of C60/4-1 and C60/6-2 to that of C60/10-1 infer that intrinsic optical properties and excited-state dynamics can be affected by the substitution on the fullerene.


One-year MRI scan predicts clinical response to interferon beta in multiple sclerosis.
To define the predictive value of clinical and magnetic resonance imaging (MRI) characteristics in identifying relapsing-remitting multiple sclerosis (RR-MS) patients with sustained disability progression during interferon beta (IFNB) treatment. All patients receiving treatment with one of the available IFNB formulations for at least 1 year were included in this single-centre, prospective and post-marketing study. Demographic, clinical and MRI data were collected at IFNB start and at 1 year of therapy; patients were followed-up at least yearly. Poor clinical response was defined as the occurrence of a sustained disability progression of > or =1 point in the Expanded Disability Status Scale (EDSS) during the follow-up period. Out of 454 RR-MS patients starting IFNB therapy, data coming from 394 patients with a mean follow-up of 4.8 (2.4) years were analysed. Sixty patients were excluded because of too short follow-up. Less than 1/3 (30.4%) of the patients satisfied the criterion of 'poor responders'. Patients presenting new lesions on T2-weighted MRI scan after 1 year of therapy (compared with baseline) had a higher risk of being poor responder to treatment with IFNB during the follow-up period (HR 16.8, 95% CI 7.6-37.1, P < 0.001). An augmented risk increasing the number of lesions was observed, with a 10-fold increase for each new lesion. Developing new T2-hyperintense lesions during IFNB treatment was the best predictor of long-term poor response to therapy. MRI scans performed after 1 year of IFNB treatment may be useful in contributing to early identification of poor responders.


Clinical, morphological, and hemodynamic independent characteristic factors for rupture of posterior communicating artery aneurysms.
To identify clinical, morphological, and hemodynamic independent characteristic factors that discriminate posterior communicating artery (PCoA) aneurysm rupture status. 173 patients with single PCoA aneurysms (108 ruptured, 65 unruptured) between January 2012 and June 2014 were retrospectively collected. Patient-specific models based on their three-dimensional digital subtraction angiography images were constructed and analyzed by a computational fluid dynamic method. All variables were analyzed by univariate analysis and multivariate logistic regression analysis. Two clinical factors (younger age and atherosclerosis), three morphological factors (higher aspect ratio, bifurcation type, and irregular shape), and six hemodynamic factors (lower mean and minimum wall shear stress, higher oscillatory shear index, a greater portion of area under low wall shear stress, unstable and complex flow pattern) were significantly associated with PCoA aneurysm rupture. Independent factors characterizing the rupture status were identified as age (OR 0.956, p=0.015), irregular shape (OR 6.709, p<0.001), and minimum wall shear stress (OR 0.001, p=0.038). We combined clinical, morphological, and hemodynamic characteristics analysis and found the three strongest independent factors for PCoA aneurysm rupture were younger age, irregular shape, and low minimum wall shear stress. This may be useful for guiding risk assessments and subsequent treatment decisions for PCoA aneurysms.


Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities.
The assessment of microbial diversity and distribution is a major concern in environmental microbiology. There are two general approaches for measuring community diversity: quantitative measures, which use the abundance of each taxon, and qualitative measures, which use only the presence/absence of data. Quantitative measures are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present. We illustrate these principles using two 16S rRNA-based surveys of microbial populations and two phylogenetic measures of community beta diversity: unweighted UniFrac, a qualitative measure, and weighted UniFrac, a new quantitative measure, which we have added to the UniFrac website (http://bmf.colorado.edu/unifrac). These studies considered the relative influences of mineral chemistry, temperature, and geography on microbial community composition in acidic thermal springs in Yellowstone National Park and the influences of obesity and kinship on microbial community composition in the mouse gut. We show that applying qualitative and quantitative measures to the same data set can lead to dramatically different conclusions about the main factors that structure microbial diversity and can provide insight into the nature of community differences. We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny.


Electrocorticographic representations of segmental features in continuous speech.
Acoustic speech output results from coordinated articulation of dozens of muscles, bones and cartilages of the vocal mechanism. While we commonly take the fluency and speed of our speech productions for granted, the neural mechanisms facilitating the requisite muscular control are not completely understood. Previous neuroimaging and electrophysiology studies of speech sensorimotor control has typically concentrated on speech sounds (i.e., phonemes, syllables and words) in isolation; sentence-length investigations have largely been used to inform coincident linguistic processing. In this study, we examined the neural representations of segmental features (place and manner of articulation, and voicing status) in the context of fluent, continuous speech production. We used recordings from the cortical surface [electrocorticography (ECoG)] to simultaneously evaluate the spatial topography and temporal dynamics of the neural correlates of speech articulation that may mediate the generation of hypothesized gestural or articulatory scores. We found that the representation of place of articulation involved broad networks of brain regions during all phases of speech production: preparation, execution and monitoring. In contrast, manner of articulation and voicing status were dominated by auditory cortical responses after speech had been initiated. These results provide a new insight into the articulatory and auditory processes underlying speech production in terms of their motor requirements and acoustic correlates.


Specific citrullination causes assembly of a globular S100A3 homotetramer: a putative Ca2+ modulator matures human hair cuticle.
S100A3 is a unique member of the Ca2+-binding S100 protein family with the highest cysteine content and affinity for Zn2+. This protein is highly expressed in the differentiating cuticular cells within the hair follicle and organized into mature hair cuticles. Previous studies suggest a close association of S100A3 with epithelial differentiation, leading to hair shaft formation, but its molecular function is still unknown. By two-dimensional PAGE-Western blot analyses using a modified citrulline antibody, we discovered that more than half of the arginine residues of native S100A3 are progressively converted to citrullines by Ca2+-dependent peptidylarginine deiminases. Confocal immunofluorescent microscopy showed that the cytoplasmic S100A3 within the cuticular layer is mostly co-localized with the type III isoform of peptidylarginine deiminase (PAD3) but not with PAD1. Recombinant PAD1 and PAD2 are capable of converting all 4 arginines in recombinant S100A3, whereas PAD3 specifically converts only Arg-51 into citrulline. Gel filtration analyses showed that either enzymatic conversion of Arg-51 in S100A3 to citrulline or its mutational substitution with alanine (R51A) promotes a homotetramer assembly. Fluorescent titration of R51A suggested that its potential Ca2+ binding property increased during tetramerization. A prototype structural model of the globular Ca2+-bound S100A3 tetramer with citrulline residues is presented. High concentrations of S100A3 homotetramer might provide the millimolar level of Ca2+ required for hair cuticular barrier formation.


Y-chromosome variability in four Native American populations from Panama.
The allele and haplotype frequencies for 13 Y-chromosome short tandem repeats (STRs) [nine STR loci of the minimal Y-chromosome haplotype (DYS19 - DYS385a - DYS385b - DYS389I - DYS389II - DYS390 - DYS391- DYS392 - DYS393) plus four additional loci (DYS388, DYS426, DYS439, DXYS156)] were determined in 99 males from 4 Panamanian native American populations, including the Chibcha-speaking Ngöbé and Kuna and the Chocó-speaking Emberá and Wounan. Fifty haplotypes were identified, of which 48 (96%) were specific to a single population and 29 (63%) were found in only a single individual. Gene diversity per locus per population ranged from 0 to 0.814, with the highest gene diversity present at the DYS389II locus in the Emberá. The haplotypic discrimination capacity was low, ranging from 42.3% in the Kuna to 63.1% in the Wounan. The four tribes showed a high degree of differentiation both at the Y chromosome and in the mitochondrial genome, highlighting the importance of genetic structure even in geographically proximate and linguistically related populations.


Chromatin Conformation Links Putative Enhancers in Intracranial Aneurysm-Associated Regions to Potential Candidate Genes.
Background We previously showed that intracranial aneurysm ( IA )-associated single-nucleotide polymorphisms are enriched in promoters and putative enhancers identified in the human circle of Willis, on which IA s develop, suggesting a role for promoters and enhancers in IAs . We further investigated the role of putative enhancers in the pathogenesis of IA by identifying their potential target genes and validating their regulatory activity. Methods and Results Using our previously published circle of Willis chromatin immunoprecipitation and sequencing data, we selected 34 putative enhancers in IA -associated regions from genome-wide association studies. We then used a chromatin conformation capture technique to prioritize target genes and found that 15 putative enhancers interact with the promoters of 6 target genes: SOX 17, CDKN 2B, MTAP , CNNM 2, RPEL 1, and GATA 6. Subsequently, we assessed the activity of these putative enhancers in vivo in zebrafish embryos and confirmed activity for 8 putative enhancers. Last, we found that all 6 target genes are expressed in the circle of Willis, on the basis of RNA sequencing data and in situ hybridization. Furthermore, in situ hybridization showed that these genes are expressed in multiple cell types in the circle of Willis. Conclusions In 4 of 6 IA -associated genome-wide association study regions, we identified 8 putative enhancers that are active in vivo and interact with 6 nearby genes, suggesting that these genes are regulated by the identified putative enhancers. These genes, SOX 17, CDKN 2B, MTAP , CNNM 2, RPEL 1, and GATA 6, are therefore potential candidate genes involved in IA pathogenesis and should be studied using animal models in the future.


Cutting edge: merocytic dendritic cells break T cell tolerance to beta cell antigens in nonobese diabetic mouse diabetes.
In type 1 diabetes, the breach of central and peripheral tolerance results in autoreactive T cells that destroy insulin-producing, pancreatic beta cells. In this study, we identify a critical subpopulation of dendritic cells responsible for mediating both the cross-presentation of islet Ags to CD8(+) T cells and the direct presentation of beta cell Ags to CD4(+) T cells. These cells, termed merocytic dendritic cells (mcDCs), are more numerous in the NOD mouse and, when Ag-loaded, rescue CD8(+) T cells from peripheral anergy and deletion while stimulating islet-reactive CD4(+) T cells. When purified from the pancreatic lymph nodes of overtly diabetic NOD mice, mcDCs break peripheral T cell tolerance to beta cells in vivo and induce rapid onset type 1 diabetes in the young NOD mouse. Thus, the mcDC subset appears to represent the long-sought APC responsible for breaking peripheral tolerance to beta cell Ags in vivo.


Sequence and Evolutionary Features for the Alternatively Spliced Exons of Eukaryotic Genes.
Alternative splicing of pre-mRNAs is a crucial mechanism for maintaining protein diversity in eukaryotes without requiring a considerable increase of genes in the number. Due to rapid advances in high-throughput sequencing technologies and computational algorithms, it is anticipated that alternative splicing events will be more intensively studied to address different kinds of biological questions. The occurrences of alternative splicing mean that all exons could be classified to be either constitutively or alternatively spliced depending on whether they are virtually included into all mature mRNAs. From an evolutionary point of view, therefore, the alternatively spliced exons would have been associated with distinctive biological characteristics in comparison with constitutively spliced exons. In this paper, we first outline the representative types of alternative splicing events and exon classification, and then review sequence and evolutionary features for the alternatively spliced exons. The main purpose is to facilitate understanding of the biological implications of alternative splicing in eukaryotes. This knowledge is also helpful to establish computational approaches for predicting the splicing pattern of exons.


Atomic-level structure characterization of an ultrafast folding mini-protein denatured state.
Atomic-level analyses of non-native protein ensembles constitute an important aspect of protein folding studies to reach a more complete understanding of how proteins attain their native form exhibiting biological activity. Previously, formation of hydrophobic clusters in the 6 M urea-denatured state of an ultrafast folding mini-protein known as TC5b from both photo-CIDNP NOE transfer studies and FCS measurements was observed. Here, we elucidate the structural properties of this mini-protein denatured in 6 M urea performing (15)N NMR relaxation studies together with a thorough NOE analysis. Even though our results demonstrate that no elements of secondary structure persist in the denatured state, the heterogeneous distribution of R(2) rate constants together with observing pronounced heteronuclear NOEs along the peptide backbone reveals specific regions of urea-denatured TC5b exhibiting a high degree of structural rigidity more frequently observed for native proteins. The data are complemented with studies on two TC5b point mutants to verify the importance of hydrophobic interactions for fast folding. Our results corroborate earlier findings of a hydrophobic cluster present in urea-denatured TC5b comprising both native and non-native contacts underscoring their importance for ultra rapid folding. The data assist in finding ways of interpreting the effects of pre-existing native and/or non-native interactions on the ultrafast folding of proteins; a fact, which might have to be considered when defining the starting conditions for molecular dynamics simulation studies of protein folding.


Incidence of metachronous contralateral breast cancer in the Canton of Zurich: a population-based study of the cancer registry.
To examine the incidence and characteristics of metachronous contralateral breast cancer (CBC) among women in the Canton of Zurich, Switzerland. For 1980-2006, patients with unilateral invasive breast cancer (UBC) were analysed for metachronous CBC. Poisson's regression was used to estimate incidence rates of metachronous CBC according to age, year of diagnosis, follow-up period since first breast cancer and morphology. Of 16,323 patients with UBC, 700 (4.3%) developed a second malignant tumour of the opposite breast. Median age at first breast cancer was lower in the CBC group than in the full cohort. Median interval time between first and second breast cancer was 5.5 (interquartile range 2.6-10.1) years. Incidence rate at age 20-29 was 1006 (95% confidence interval, CI, 452-2238) cases per 100,000 person-years and decreased to 299 (199-450) at 80-84. Age-adjusted incidence rates according to period of diagnosis decreased from 618 (530-721) for 1980-1984 to 329 (217-500) cases per 100,000 person-years for 2005-2006. Incidence rate ratio of CBC for lobular carcinoma was 1.28 (95% CI 0.99-1.67) adjusted by age group and period of diagnosis compared to ductal carcinoma. In our study, incidence rates for CBC are comparable with findings from the literature. A reduction in the incidence of metachronous CBC, thought to be due to adjuvant therapies, is seen in our data. In our cohort, younger age and lobular carcinoma were associated with an increased risk of CBC.


Cancellation of simple optical anisotropies without use of a Faraday mirror.
We first derive the round-trip Jones matrix for double passage through a reciprocal optical medium by means of reflection off a plane mirror that could be optically anisotropic. We then show that if a medium with only linear birefringence and linear dichroism is placed between a pair of orthogonal quarter-wave plates with principal axes at 45 degrees to that of the medium and the sandwich is placed in front of an isotropic mirror it behaves, under double passage, like an isotropic medium. We describe a simple liquid crystal device that behaves, in reflection, as an isotropic medium whose refractive index can be varied by application of an electric field, thus acting as a phase only modulator for light in any polarization state.


Effects of ischemia-like conditions on cultured neurons: protection by low Na+, low Ca2+ solutions.
An in vitro system was used to mimic several aspects of ischemia, including low oxygen pressure, low nutrient levels, and the accumulation of cellular products thought to contribute to damage during ischemia. We replaced normal culture medium from 3-week-old basal ganglia cultures with oxygen-depleted, nutrient-deficient medium. After incubation in an atmosphere of 94% N2, 6% CO2 for 5 hr at 37 degrees C, the cultures were returned to normal medium. After a 24 hr recovery period, cell viability was assessed in terms of cell number, electrophysiological properties, and immunohistochemical markers. When the medium used during the ischemic period was a normal balanced salt solution, more than 70% of the cells were damaged by the low-oxygen, low-glucose stress. Loss of cell processes and cell swelling were the most evident signs of damage. The majority of the cells remaining viable were astrocytes. Neuronal damage was observed only when both glucose and oxygen were deficient. Some damage was evident even at oxygen tensions of 60 mm Hg when glucose was absent from the medium; much more extensive damage was observed at tensions below 1.0 mm Hg. Lowering both extracellular sodium and calcium resulted in more than a 2-fold increase in survival (70 vs 28%). These results indicate that damage to neurons during conditions of extreme energy deprivation such as ischemia may be mediated by the influx of calcium and/or sodium.