Effect of the Rho Kinase Inhibitor Y-27632 on Corneal Endothelial Wound Healing.
The purpose of this study was to investigate the feasibility of using Rho-associated kinase (ROCK) inhibitor eye drops for treating severe corneal endothelial damage due to surgical invasion. A rabbit corneal endothelial damage model was created by mechanically scraping half the area of the corneal endothelium of eighteen eyes of Japanese white rabbits. A selective ROCK inhibitor, Y-27632 (10 mM), was applied topically for 2 weeks, and then the anterior segment was evaluated by slitlamp microscopy. The corneal endothelium was evaluated by phalloidin staining and immunohistochemical analysis. We then conducted pilot clinical research and applied Y-27632 eye drops topically to three patients who exhibited severe corneal edema due to corneal endothelial damage. In the corneal endothelial damage rabbit model, more Ki67-positive cells were detected in Y-27632-treated eyes than in control eyes. Five of six corneas became transparent in Y-27632-treated eyes, whereas zero of six corneas became transparent in the control eyes (P < 0.01). Actin fibers were distributed at the cell cortex in the eyes treated with Y-27632, whereas actin distribution was partially disrupted, and stress fibers were observed in control eyes. N-cadherin and Na+/K+-ATPase were expressed in almost all cells in Y-27632-treated eyes, but expression decreased in control eyes. Preliminary human cases confirmed that ROCK inhibitor eye drops were considerably effective for treatment of corneal edema associated with cataract surgery. ROCK inhibitor may be developed as an eye drop for treating acute corneal endothelial damage to prevent progression of bullous keratopathy. (University Hospital Medical Information Network Clinical Trial Registry no. UMIN000003625; www.umin.ac.jp/ctr).


Prognostic value of aortic regurgitation after TAVI in patients with chronic kidney disease.
Aortic regurgitation (AR) after transcatheter aortic valve implantation (TAVI) for severe aortic valve stenosis results in major haemodynamic changes. Influence of post-implant AR and aortic valve calcification on outcome in patients with chronic kidney disease (CKD) is unclear. Short-term outcome was defined as a combined 30-day endpoint, long-term outcome as survival. Post-implant AR was classified as none/mild or moderate/severe using transthoracic echocardiography. Aortic valve calcification was calculated by computed tomography. Logistic regression analyses were performed in patients with none/mild (estimated glomerular filtration rate [eGFR]≥30ml/min/1.73m(2)) and advanced (eGFR<30ml/min/1.73m(2)) CKD to evaluate predictors of outcome and post-implant AR. TAVI was performed in 546 consecutive patients. Moderate/severe post-implant AR was the only independent predictor of the 30-day endpoint in patients with advanced (OR 7.091, 95% CI 1.144-43.962, p=0.035), but not in patients with none/mild CKD. Similarly, moderate/severe AR predicted impaired survival only in patients with advanced CKD (p<0.001). NT-proBNP (OR 1.023 per 500ng/l increase, 95% CI 1.003-1.043; p=0.026) before intervention was the only independent predictor of the 30-day endpoint in patients with none/mild CKD. Aortic valve calcification was comparable in patients with none/mild versus advanced CKD and was an independent predictor of moderate/severe post-implant AR in the overall population as well as in the subgroups with none/mild or advanced CKD. Moderate/severe AR after TAVI predicts outcome in patients with advanced CKD, but not in patients with none/mild CKD. Aortic valve calcification is an important predictor of post-implant AR independent of kidney function.


Clinical Trial Endpoints in Metastatic Cancer: Using Individual Participant Data to Inform Future Trials Methodology.
Meta-analysis based on individual participant data (IPD) is a powerful methodology for synthesizing evidence by combining information drawn from multiple trials. Hitherto, its principal application has been in questions of clinical management, but an increasingly important use is in clarifying trials methodology, for instance in the selection of endpoints, as discussed in this review. In oncology, the Aide et Recherche en Cancérologie Digestive (ARCAD) Metastatic Colorectal Cancer Database is a leader in the use of IPD-based meta-analysis in methodological research. The ARCAD database contains IPD from more than 38 000 patients enrolled in 46 studies and continues to collect phase III trial data. Here, we review the principal findings of the ARCAD project in respect of endpoint selection and examine their implications for cancer trials. Analysis of the database has confirmed that progression-free survival (PFS) is no longer a valid surrogate endpoint predictive of overall survival in the first-line treatment of colorectal cancer. Nonetheless, PFS remains an endpoint of choice for most first-line trials in metastatic colorectal cancer and other solid tumors. Only substantial PFS effects are likely to translate into clinically meaningful benefits, and accordingly, we advocate an oncology research model designed to identify highly effective treatments in carefully defined patient groups. We also review the use of the ARCAD database in assessing clinical response including novel response metrics and prognostic markers. These studies demonstrate the value of IPD as a tool for methodological studies and provide a reference point for the expansion of this approach within clinical cancer research.


Applications of confocal microscopy in refractive surgery.
To evaluate applications of the Confoscan 2.0, a computerized confocal optical microscopy system by Nidek, in refractive surgery. We used the Confoscan 2.0 to evaluate the tissue reparative response after PRK, LASEK, and LASIK in 60 eyes of 40 patients. Confoscan 2.0 provided highly detailed images of the corneal layers, up to the cellular level. Furthermore, it measured corneal thickness as well as precise positioning of each single recorded corneal layer. The Confoscan was also used to analyse the LASIK flap. Findings in the transition zone between epithelium and anterior stroma in PRK and LASEK eyes were divided into two groups: Group 1, with marked hyper-reflectivity, and Group 2, with less hyper-reflectivity, similar to normal eyes. Group 2 eyes belonged to patients that underwent smoothing with a masking solution after ablation. Group 1 eyes received no smoothing. In LASIK eyes, we evaluated the quality of the flap interface. Hyper-reflecting specks could be observed in the interface, showing a tendency to decrease over time. Depth of the LASIK flap was measured, and showed variable thickness with all microkeratomes tested. We hypothesize that a more regular corneal surface, obtained with smoothing in PRK and LASEK, allows a better reparative response after refractive surgery. In LASIK eyes, the Confoscan provided precise measurement of the residual stromal bed, information particularly valuable for the prevention of ectasia in retreatments.


Initial Whole-Genome Sequencing of Plasma Cell Neoplasms in First Responders and Recovery Workers Exposed to the World Trade Center Attack of September 11, 2001.
The World Trade Center (WTC) attack of September 11, 2001 created an unprecedented environmental exposure to known and suspected carcinogens. High incidence of multiple myeloma and precursor conditions has been reported among first responders to the WTC disaster. To expand on our prior screening studies, and to characterize the genomic impact of the exposure to known and potential carcinogens in the WTC debris, we were motivated to perform whole-genome sequencing (WGS) of WTC first responders and recovery workers who developed a plasma cell disorder after the attack. We performed WGS of nine CD138-positive bone marrow mononuclear samples from patients who were diagnosed with plasma cell disorders after the WTC disaster. No significant differences were observed in comparing the post-WTC driver and mutational signature landscapes with 110 previously published WGSs from 56 patients with multiple myeloma and the CoMMpass WGS cohort (n = 752). Leveraging constant activity of the single-base substitution mutational signatures 1 and 5 over time, we estimated that tumor-initiating chromosomal gains were windowed to both pre- and post-WTC exposure. Although limitations in sample size preclude any definitive conclusions, our findings suggest that the observed increased incidence of plasma cell neoplasms in this population is due to complex and heterogeneous effects of the WTC exposure that may have initiated or contributed to progression of malignancy.


Self-Reported Health and Patterns of Romantic Love in Adolescents from Eight European Countries and Regions.
Purpose: Sexual minority youth (SMY) are at increased risk of poor health, but it remains unclear whether this phenomenon is universal. In this study, nationally representative samples of 15-year olds from eight European countries and regions were investigated to test if adolescents who have been in love with same- or both-gender partners report poorer health than those exclusively in love with opposite-gender partners or who have never been in love. Methods: A subsample of 13,674 adolescents participating in the 2014 Health Behaviour in School-aged Children (HBSC) study was used. We conducted binary logistic regression, adjusted for gender, region, and relative family affluence, to analyze associations between self-reported romantic love, multiple psychosomatic symptoms, and poor self-rated health. Results: Adolescents reporting same-gender love (adjusted odds ratio [aOR] = 1.50, 95% confidence interval [CI]: 1.11-2.02) and both-gender love (aOR = 3.57, 95% CI: 2.65-4.83) had significantly higher odds for multiple psychosomatic symptoms than those who reported opposite-gender love. Similarly, both SMY groups had higher odds of poor self-rated health (aOR = 2.95, 95% CI: 1.64-5.31 and aOR = 3.08, 95% CI: 1.79-5.31, respectively). Those who reported that they have never been in love had significantly lower odds for multiple symptoms. Adjustment for sociodemographic variables and stratifying by gender did not substantially change the odds ratios. Conclusion: Adolescents in love with same- and both-gender partners reported poorer subjective health outcomes than those in love with opposite-gender partners or who reported never being in love, suggesting that SMY health inequalities are found across various European countries and regions.


Age and gender interactions in short distance triathlon performance.
This study investigated the participation and performance trends as well as the age and gender interaction at the Olympic distance 'Zürich Triathlon' (1.5 km swim, 40 km cycle and 10 km run) from 2000 to 2010 in 7,939 total finishers (1,666 females and 6,273 males). Female triathletes aged from 40 to 54 years significantly (P < 0.05) increased their participation while the participation of younger females and males remained stable. Males of 50-54 years of age and females of 45-49 years of age improved their total race time. For elite top five overall triathletes, mean gender differences in swimming, cycling, running and overall race time were 15.2 ± 4.6%, 13.4 ± 2.3%, 17.1 ± 2.5%, and 14.8 ± 1.8%, respectively. For both elite and age group athletes, the gender difference in cycling time was significantly (P <0.001) lower than for swimming and running. The gender difference in overall Olympic distance triathlon performance increased after the age of 35 years, which appeared earlier compared to long distance triathlon as suggested by previous studies. Future investigations should compare gender difference in performance for different endurance events across age to confirm a possible effect of exercise duration on gender difference with advancing age.


Hi-BEHRT: Hierarchical Transformer-Based Model for Accurate Prediction of Clinical Events Using Multimodal Longitudinal Electronic Health Records.
Electronic health records (EHR) represent a holistic overview of patients' trajectories. Their increasing availability has fueled new hopes to leverage them and develop accurate risk prediction models for a wide range of diseases. Given the complex interrelationships of medical records and patient outcomes, deep learning models have shown clear merits in achieving this goal. However, a key limitation of current study remains their capacity in processing long sequences, and long sequence modelling and its application in the context of healthcare and EHR remains unexplored. Capturing the whole history of medical encounters is expected to lead to more accurate predictions, but the inclusion of records collected for decades and from multiple resources can inevitably exceed the receptive field of the most existing deep learning architectures. This can result in missing crucial, long-term dependencies. To address this gap, we present Hi-BEHRT, a hierarchical Transformer-based model that can significantly expand the receptive field of Transformers and extract associations from much longer sequences. Using a multimodal large-scale linked longitudinal EHR, the Hi-BEHRT exceeds the state-of-the-art deep learning models 1% to 5% for area under the receiver operating characteristic (AUROC) curve and 1% to 8% for area under the precision recall (AUPRC) curve on average, and 2% to 8% (AUROC) and 2% to 11% (AUPRC) for patients with long medical history for 5-year heart failure, diabetes, chronic kidney disease, and stroke risk prediction. Additionally, because pretraining for hierarchical Transformer is not well-established, we provide an effective end-to-end contrastive pre-training strategy for Hi-BEHRT using EHR, improving its transferability on predicting clinical events with relatively small training dataset.


Dental predictors of high caries increment in children.
A comprehensive set of dental variables was investigated to find the "best" combination of predictors for high caries increment in 7/8-year-old and 10/11-year-old children. Four populations with widely different caries prevalence were studied. Logistic regression analysis supplied multiple-input models by stepwise selection of predictors. A "low number of sound primary molars" was the best and most consistent predictor of high caries increment. The second best predictors were "high numbers of pre-cavity lesions on permanent first molars" (discolored pits and fissures in the younger age group and white spots on the smooth parts of buccolingual surfaces in the older age group). Inclusion of radiological variables did not substantially increase the quality of prediction. For practical application, models with various multiple inputs selected by stepwise procedures were compared with "fixed" three-input models. These three-input models resulted in predictive quality nearly equal to those of the multiple models. Traditional one-input models, containing DMFT or dmft, were inferior to the three-input models, particularly in the older age class. The lower the caries prevalence of the source data, the better was the prediction. As a summary measure characterizing the predictive performance of a model, we used the index "area under the receiver operating characteristic curve" A. For the 1984 data and the three-input models, the area was approximately 80%, and for the 1972 data, the area was 65-70%.


Case Report: Whole exome sequencing identifies a novel frameshift insertion c.1325dupT (p.F442fsX2) in the tyrosine kinase domain of BTK gene in a young Indian individual with X-linked agammaglobulinemia.
X-linked agammaglobulinemia (XLA) is an extremely rare inherited primary immunodeficiency characterized by recurrent bacterial infections, decrease in number of mature B cells and low serum immunoglobulins. XLA is caused by mutations in the gene encoding Bruton's tyrosine kinase. We report a case of a young Indian boy suspected to have XLA. Immunophenotyping was performed for the affected child using CD20, CD19 and CD3 antibodies. Whole exome sequencing was performed using trio-based approach. The variants were further analyzed using capillary sequencing in the trio as well as maternal grandmother. Initial immunophenotyping in the affected child showed decreased count of CD19+ B cells. To strengthen the clinical findings and confirm the diagnosis of XLA, we performed whole exome sequencing. Our analysis identified a novel frameshift insertion (c.1325dupT) in the BTK gene, which was further validated by Sanger sequencing. Our approach shows the potential in using whole exome sequencing to pinpoint the molecular lesion, enabling timely diagnosis and genetic counseling, and potentially offering prenatal genetic testing for the family.


Tear osteopontin level and its relationship with local Th1/Th2/Th17/Treg cytokines in children with allergic conjunctivitis.
Allergic conjunctivitis (AC) is one of the most common allergic ocular diseases worldwide. Osteopontin (OPN), as a recently described Th2 inflammation related protein, may play a role in the pathogenesis of AC. The aim of this study was to identify the expression of OPN in children with AC. Eighty AC children (seasonal and perennial AC) and twenty controls were enrolled in this study. Serum and tears of different time points (during and out of the pollen season) were collected and used for enzyme-linked immunosorbent assay (ELISA) of OPN and T-help cell related cytokines, respectively. The relationship between serum and tears OPN and Th1/2/17Treg related cytokines as well as disease severity were analysed. Our results showed that expression of tear OPN protein by perennial AC patients increased significantly compared with controls or seasonal AC patients out of the pollen season. Tear OPN expression was positively related to local Th2/17 cytokines and negatively related to IL-10 and TGF-β expression. The tear OPN expression was also significantly related to disease severity. Tear OPN reflects the local clinical status of ocular allergy and might play an important pathophysiological role in local Th2/17/Treg inflammation in children with AC.


Frequency and time to relapse after discontinuing 6-month therapy with IVIg or pulsed methylprednisolone in CIDP.
We reported that 6-month therapy with intravenous immunoglobulin (IVIg) was more frequently effective or tolerated than intravenous methylprednisolone (IVMP) in patients with chronic inflammatory demyelinating polyradiculoneuropathy (CIDP). We now retrospectively compared the proportion of patients who eventually worsened after discontinuing therapy and the median time to clinical worsening. By March 2013, data were available from 41 of the 45 patients completing the trial with a median follow-up after therapy discontinuation of 42 months (range 1-60). Three patients withdrew during the original study and one failed to respond to either of the therapies. No patient received a diagnosis alternative to CIDP during the follow-up. Twenty-eight of the 32 patients treated with IVIg (as primary or secondary therapy after failing to respond to IVMP) improved after therapy (87.5%) as compared with 13 of the 24 patients treated with IVMP as primary or secondary therapy (54.2%). After a median follow-up of 42 months (range 1-57), 24 out of 28 patients responsive to IVIg (85.7%) worsened after therapy discontinuation. The same occurred in 10 out of 13 patients (76.9%) responsive to IVMP (p=0.659) after a median follow-up of 43 months (range 7-60). Worsening occurred 1-24 months (median 4.5) after IVIg discontinuation and 1-31 months (median 14) after IVMP discontinuation (p=0.0126). A similarly high proportion of patients treated with IVIg or IVMP eventually relapse after therapy discontinuation but the median time to relapse was significantly longer after IVMP than IVIg. This difference may help to balance the more frequent response to IVIg than to IVMP in patients with CIDP.


Neurofilament depletion improves microtubule dynamics via modulation of Stat3/stathmin signaling.
In neurons, microtubules form a dense array within axons, and the stability and function of this microtubule network is modulated by neurofilaments. Accumulation of neurofilaments has been observed in several forms of neurodegenerative diseases, but the mechanisms how elevated neurofilament levels destabilize axons are unknown so far. Here, we show that increased neurofilament expression in motor nerves of pmn mutant mice, a model of motoneuron disease, causes disturbed microtubule dynamics. The disease is caused by a point mutation in the tubulin-specific chaperone E (Tbce) gene, leading to an exchange of the most C-terminal amino acid tryptophan to glycine. As a consequence, the TBCE protein becomes instable which then results in destabilization of axonal microtubules and defects in axonal transport, in particular in motoneurons. Depletion of neurofilament increases the number and regrowth of microtubules in pmn mutant motoneurons and restores axon elongation. This effect is mediated by interaction of neurofilament with the stathmin complex. Accumulating neurofilaments associate with stathmin in axons of pmn mutant motoneurons. Depletion of neurofilament by Nefl knockout increases Stat3-stathmin interaction and stabilizes the microtubules in pmn mutant motoneurons. Consequently, counteracting enhanced neurofilament expression improves axonal maintenance and prolongs survival of pmn mutant mice. We propose that this mechanism could also be relevant for other neurodegenerative diseases in which neurofilament accumulation and loss of microtubules are prominent features.


The influence of light wavelength on reproductive photorefractoriness in migratory blackheaded bunting (Emberiza melanocephala).
There are two effects of long day length on reproductive responses in birds, one is the photoinduction of gonadal growth and maturation and the other is the induction of gonadal regression and photorefractoriness. Although it is likely that the same photoreceptors are involved in the photoinduction of gonadal growth and the onset and maintenance of photorefractoriness. and so the influence of wavelength should be similar, this has not been investigated. Therefore, we investigated the influence of light wavelength on reproductive photorefractoriness in the migratory male blackheaded bunting held under long photoperiods. In mid May, when photoperiod was approximately 14L:10D (14 hours light:10 hours darkness), eight groups of sexually mature birds were moved indoors on an artificial photoperiod of 14L:10D (L - 450 lux. D - 0 lux). Then after 3 weeks, for six groups, a 4-h light period in the morning (zt 0-4; zt 0 [zeitgeber time 0] refers to the beginning of lights-on period) or in the evening (zt 10-14) was substituted with green (428 nm), red (654 nm) or white light at 16 +/- 2 lux intensity. Of the remaining two groups, one was maintained on 14L: 10D and the other transferred to 10L:14D: these served as controls. At the end of 4 weeks, all birds were found to have undergone testicular regression, irrespective of LD cycle they were exposed to. When these gonadally regressed birds were subjected to 16L:8D for another 4 weeks, to test their responsiveness to the stimulatory effects of long day lengths, only those exposed to 10L:14D and 14L:10D with a 4-h green light period showed testicular regrowth. On the other hand, birds exposed to 14L:10D with a 4-h white or red light period remained fully regressed, similar to 14L:10D controls. Except for some individual difference, there was no difference in response between the groups that received a 4-h light period in the morning and that received it in the evening. These results suggest that the wavelengths of light influence induction of buntings from the photosensitive state into the photorefractory state. Whereas the short light wavelengths facilitated recovery from the photorefractoriness, the long light wavelengths were more effective in maintaining the photorefractoriness.


A human-curated annotation of the Candida albicans genome.
Recent sequencing and assembly of the genome for the fungal pathogen Candida albicans used simple automated procedures for the identification of putative genes. We have reviewed the entire assembly, both by hand and with additional bioinformatic resources, to accurately map and describe 6,354 genes and to identify 246 genes whose original database entries contained sequencing errors (or possibly mutations) that affect their reading frame. Comparison with other fungal genomes permitted the identification of numerous fungus-specific genes that might be targeted for antifungal therapy. We also observed that, compared to other fungi, the protein-coding sequences in the C. albicans genome are especially rich in short sequence repeats. Finally, our improved annotation permitted a detailed analysis of several multigene families, and comparative genomic studies showed that C. albicans has a far greater catabolic range, encoding respiratory Complex 1, several novel oxidoreductases and ketone body degrading enzymes, malonyl-CoA and enoyl-CoA carriers, several novel amino acid degrading enzymes, a variety of secreted catabolic lipases and proteases, and numerous transporters to assimilate the resulting nutrients. The results of these efforts will ensure that the Candida research community has uniform and comprehensive genomic information for medical research as well as for future diagnostic and therapeutic applications.


Form and metabolic scaling in colonial animals.
Benthic colonial organisms exhibit a wide variation in size and shape and provide excellent model systems for testing the predictions of models that describe the scaling of metabolic rate with organism size. We tested the hypothesis that colony form will influence metabolic scaling and its derivatives by characterising metabolic and propagule production rates in three species of freshwater bryozoans that vary in morphology and module organisation and which demonstrate two- and three-dimensional growth forms. The results were evaluated with respect to predictions from two models for metabolic scaling. Isometric metabolic scaling in two-dimensional colonies supported predictions of a model based on dynamic energy budget theory (DEB) and not those of a model based on fractally branching supply networks. This metabolic isometry appears to be achieved by equivalent energy budgets of edge and central modules, in one species (Cristatella mucedo) via linear growth and in a second species (Lophopus crystallinus) by colony fission. Allometric scaling characterised colonies of a three-dimensional species (Fredericella sultana), also providing support for the DEB model. Isometric scaling of propagule production rates for C. mucedo and F. sultana suggests that the number of propagules produced in colonies increases in direct proportion with the number of modules within colonies. Feeding currents generated by bryozoans function in both food capture and respiration, thus linking metabolic scaling with dynamics of self-shading and resource capture. Metabolic rates fundamentally dictate organismal performance (e.g. growth, reproduction) and, as we show here, are linked with colony form. Metabolic profiles and associated variation in colony form should therefore influence the outcome of biotic interactions in habitats dominated by colonial animals and may drive patterns of macroevolution.


Beyond maternal education: Socio-economic inequalities in children's diet in the ABCD cohort.
We examined whether the role of maternal education in children's unhealthy snacking diet is moderated by other socio-economic indicators. Participants were selected from the Amsterdam Born Children and their Development cohort, a large ongoing community-based birth cohort. Validated Food Frequency Questionnaires (FFQ) (n = 2782) were filled in by mothers of children aged 5.7±0.5yrs. Based on these FFQs, a snacking dietary pattern was derived using Principal Component Analysis. Socio-economic indicators were: maternal and paternal education (low, middle, high; based on the highest education completed) household finance (low, high; based on ability to save money) and neighbourhood SES (composite score including educational level, household income and employment status of residents per postal code). Cross-sectional multivariable linear regression analysis was used to assess the association and possible moderation of maternal education and other socio-economic indicators on the snacking pattern score. Analyses were adjusted for children's age, sex and ethnicity. Low maternal education (B 0.95, 95% CI 0.83;1.06), low paternal education (B 0.36, 95% CI 0.20;0.52), lower household finance (B 0.18, 95% CI 0.11;0.26) and neighbourhood SES (B -0.09, 95% CI -0.11;-0.06) were independently associated with higher snacking pattern scores (p<0.001). The association between maternal education and the snacking pattern score was somewhat moderated by household finance (p = 0.089) but remained strong. Children from middle-high educated mothers (B 0.44, 95% CI 0.35;0.52) had higher snacking pattern scores when household finance was low (B 0.49, 95% CI 0.33;0.65). All socio-economic indicators were associated with increased risk of unhealthy dietary patterns in young children, with low maternal education conferring the highest risk. Yet, within the group of middle-high educated mothers, lower household finance was an extra risk factor for unhealthy dietary patterns. Intervention strategies should therefore focus on lower educated mothers and middle-high educated mothers with insufficient levels of household finance.


Immuno-spin trapping of DNA radicals.
The detection of DNA radicals by immuno-spin trapping (IST) is based on the trapping of radicals with 5,5-dimethyl-1-pyrroline N-oxide (DMPO), forming stable nitrone adducts that are then detected using an anti-DMPO serum. DNA radicals are very reactive species, and because they are paramagnetic they have previously been detected only by electron spin resonance (ESR) with or without spin trapping, which is not available in most bioresearch laboratories. IST combines the simplicity, reliability, specificity and sensitivity of spin trapping with heterogeneous immunoassays for the detection of DNA radicals, and complements existing methods for the measurement of oxidatively generated DNA damage. Here we have used IST to demonstrate that DMPO traps Cu(II)-H(2)O(2)-induced DNA radicals in situ and in real time, forming DMPO-DNA nitrone adducts, but preventing both 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) formation and DNA fragmentation. We also applied IST to detect DNA radicals in rat hepatocytes exposed to Cu(II) and H(2)O(2) under nonlethal conditions.


Hypercytokinaemia accompanies HIV-tuberculosis immune reconstitution inflammatory syndrome.
Increased access to combination antiretroviral therapy in areas co-endemic for tuberculosis (TB) and HIV-1 infection is associated with an increased incidence of immune reconstitution inflammatory syndrome (TB-IRIS) whose cause is poorly understood. A case-control analysis of pro- and anti-inflammatory cytokines in TB-IRIS patients sampled at clinical presentation, and similar control patients with HIV-TB prescribed combined antiretroviral therapy who did not develop TB-IRIS. Peripheral blood mononuclear cells were cultured in the presence or absence of heat-killed Mycobacterium tuberculosis for 6 and 24 h. Stimulation with M. tuberculosis increased the abundance of many cytokine transcripts with interleukin (IL)-1β, IL-5, IL-6, IL-10, IL-13, IL-17A, interferon (IFN)-γ, granulocyte-macrophage colony-stimulating factor (GM-CSF) and tumour necrosis factor (TNF) being greater in stimulated TB-IRIS cultures. Analysis of the corresponding proteins in culture supernatants, revealed increased IL-1β, IL-2, IL-6, IL-8, IL-10, IL-12p40, IFN-γ, GM-CSF and TNF in TB-IRIS cultures. In serum, higher concentrations of TNF, IL-6, and IFN-γ were observed in TB-IRIS patients. Serum IL-6 and TNF decreased during prednisone therapy in TB-IRIS patients. These data suggest that cytokine release contributes to pathology in TB-IRIS. IL-6 and TNF were consistently elevated and decreased in serum during corticosteroid therapy. Specific blockade of these cytokines may be rational approach to immunomodulation in TB-IRIS.


Investigation of pathogenic mechanisms in multiple colorectal adenoma patients without germline APC or MYH/MUTYH mutations.
Patients with multiple (5-100) colorectal adenomas (MCRAs) often have no germline mutation in known predisposition genes, but probably have a genetic origin. We collected a set of 25 MCRA patients with no detectable germline mutation in APC, MYH/MUTYH or the mismatch repair genes. Extracolonic tumours were absent in these cases. No vertical transmission of the MCRA phenotype was found. Based on the precedent of MYH-associated polyposis (MAP), we searched for a mutational signature in 241 adenomatous polyps from our MCRA cases. Somatic mutation frequencies and spectra at APC, K-ras and BRAF were, however, similar to those in sporadic colorectal adenomas. Our data suggest that the genetic pathway of tumorigenesis in the MCRA patients' tumours is very similar to the classical pathway in sporadic adenomas. In sharp contrast to MAP tumours, we did not find evidence of a specific mutational signature in any individual patient or in the overall set of MCRA cases. These results suggest that hypermutation of APC does not cause our patients' disease and strongly suggests that MAP is not a paradigm for the remaining MCRA patients. Our MCRA patients' colons showed no evidence of microadenomas, unlike in MAP and familial adenomatous polyposis (FAP). However, nuclear beta-catenin expression was significantly greater in MCRA patients' tumours than in sporadic adenomas. We suggest that, at least in some cases, the MCRA phenotype results from germline variation that acts subsequent to tumour initiation, perhaps by causing more rapid or more likely progression from microadenoma to macroadenoma.


Geometric Deformations of the Thoracic Aorta and Supra-Aortic Arch Branch Vessels Following Thoracic Endovascular Aortic Repair.
To utilize 3-D modeling techniques to better characterize geometric deformations of the supra-aortic arch branch vessels and descending thoracic aorta after thoracic endovascular aortic repair. Eighteen patients underwent endovascular repair of either type B aortic dissection (n = 10) or thoracic aortic aneurysm (n = 8). Computed tomography angiography was obtained pre- and postprocedure, and 3-D geometric models of the aorta and supra-aortic branch vessels were constructed. Branch angle of the supra-aortic branch vessels and curvature metrics of the ascending aorta, aortic arch, and stented thoracic aortic lumen were calculated both at pre- and postintervention. The left common carotid artery branch angle was lower than the left subclavian artery angles preintervention ( P < .005) and lower than both the left subclavian and brachiocephalic branch angles postintervention ( P < .05). From pre- to postoperative, no significant change in branch angle was found in any of the great vessels. Maximum curvature change of the stented lumen from pre- to postprocedure was greater than those of the ascending aorta and aortic arch ( P < .05). Thoracic endovascular aortic repair results in relative straightening of the stented aortic region and also accentuates the native curvature of the ascending aorta when the endograft has a more proximal landing zone. Supra-aortic branch vessel angulation remains relatively static when proximal landing zones are distal to the left common carotid artery.


The adaptation of migrant children.
Alejandro Portes and Alejandro Rivas examine how young immigrants are adapting to life in the United States. They begin by noting the existence of two distinct pan-ethnic populations: Asian Americans, who tend to be the offspring of high-human-capital migrants, and Hispanics, many of whose parents are manual workers. Vast differences in each, both in human capital origins and in their reception in the United States, mean large disparities in resources available to the families and ethnic communities raising the new generation. Research on the assimilation of these children falls into two theoretical perspectives. Culturalist researchers emphasize the newcomers' place in the cultural and linguistic life of the host society; structuralists, their place in the socioeconomic hierarchy. Within each camp, views range from darkly pessimistic-that disadvantaged children of immigrants are simply not joining the American mainstream--to optimistic--that assimilation is taking place today just as it has in the past. A middle ground is that although poorly endowed immigrant families face distinct barriers to upward mobility, their children can overcome these obstacles through learning the language and culture of the host society while preserving their home country language, values, and customs. Empirical work shows that immigrants make much progress, on average, from the first to the second generation, both culturally and socioeconomically. The overall advancement of the immigrant population, however, is largely driven by the good performance and outcomes of youths from professional immigrant families, positively received in America. For immigrants at the other end of the spectrum, average socioeconomic outcomes are driven down by the poorer educational and economic performance of children from unskilled migrant families, who are often handicapped further by an unauthorized or insecure legal status. Racial stereotypes produce a positive self-identity for white and Asian students but a negative one for blacks and Latinos, and racialized self-perceptions among Mexican American students endure into the third and fourth generations. From a policy viewpoint, these children must be the population of greatest concern. The authors cite two important policy measures for immigrant youth. One is to legalize unauthorized migrants lest, barred from conventional mobility channels, they turn to unorthodox means of self-affirmation and survival. The other is to provide volunteer programs and other forms of outside assistance to guide the most disadvantaged members of this population and help them stay in school.


Self-identified Obese People Request Less Money: A Field Experiment.
Empirical evidence suggests that obese people are discriminated in different social environments, such as the work place. Yet, the degree to which obese people are internalizing and adjusting their own behavior as a result of this discriminatory behavior has not been thoroughly studied. We develop a proxy for measuring experimentally the "self-weight bias" by giving to both self-identified obese (n = 90) and non-obese (n = 180) individuals the opportunity to request a positive amount of money after having performed an identical task. Consistent with the System Justification Theory, we find that self-identified obese individuals, due to a preexisting false consciousness, request significantly lower amounts of money than non-obese ones. A within subject comparison between self-reports and external monitors' evaluations reveals that the excessive weight felt by the "self" but not reported by evaluators captures the self-weight bias not only for obese but also for non-obese individuals. Linking our experimental results to the supply side of the labor market, we argue that self-weight bias, as expressed by lower salary requests, enhances discriminatory behavior against individuals who feel, but may not actually be, obese and consequently exacerbates the wage gap across weight.


Eremogone ali-gulii (Caryophyllaceae), a new species from Turkey.
Eremogone ali-gulii (Caryophyllaceae) is described as a new species of Eremogone in Turkey. The specimens were collected from Kop Mountain (Erzurum). The new species is endemic of the Irano-Turanian region and is related to Eremogone scariosa and Eremogone armeniaca. The differences on sterile shoots, habit, sepals and capsules between these species are discussed. Description, distribution, illustration and conservation status of the new species are given.


Cassowary frugivory, seed defleshing and fruit fly infestation influence the transition from seed to seedling in the rare Australian rainforest tree, Ryparosa sp. nov. 1 (Achariaceae).
The rare Australian rainforest tree Ryparosa sp. nov. 1 aff. javanica (sensu Webber & Curtis, BW-017; Achariaceae) has large fleshy fruits that undergo a distinctive colour change during ripening. Fruit seem highly suited to frugivore interactions with large ground-dwelling avian or marsupial frugivores, a role primarily filled by the endangered cassowary. We found that fruits had chemical defence traits that closely paralleled morphological ripening signals. Young fruit seeds had amongst the highest concentrations of plant tissue cyanogens ever recorded (some in excess of 12 mg g-1 dw), yet the flesh of ripe fruits had negligible cyanogen defence. A seed treatment trial found that cassowary gut passage significantly improved germination from 4% to 92%, and we were not able to replicate this result with simulated treatments. While high levels of fruit fly larval infestation accounted for reduced seed viability, this predation was apparently reduced by cassowary gut passage. Post-germination seedling traits such as haustorial cryptocotylar cotyledons and epigeal germination may increase the chance of survival for establishing seedlings. We conclude that the range of traits seen in Ryparosa recruitment is particularly suited to interactions with frugivores and survival in a rainforest ecosystem.


Trust, trustworthiness and sharing patient data for research.
When it comes to using patient data from the National Health Service (NHS) for research, we are often told that it is a matter of trust: we need to trust, we need to build trust, we need to restore trust. Various policy papers and reports articulate and develop these ideas and make very important contributions to public dialogue on the trustworthiness of our research institutions. But these documents and policies are apparently constructed with little sustained reflection on the nature of trust and trustworthiness, and therefore are missing important features that matter for how we manage concerns related to trust. We suggest that what we mean by 'trust' and 'trustworthiness' matters and should affect the policies and guidance that govern data sharing in the NHS. We offer a number of initial, general reflections on the way in which some of these features might affect our approach to principles, policies and strategies that are related to sharing patient data for research. This paper is the outcome of a 'public ethics' coproduction activity which involved members of the public and two academic ethicists. Our task was to consider collectively the accounts of trust developed by philosophers as they applied in the context of the NHS and to coproduce an argumentative position relevant to this context.


The dual-bootstrap iterative closest point algorithm with application to retinal image registration.
Motivated by the problem of retinal image registration, this paper introduces and analyzes a new registration algorithm called Dual-Bootstrap Iterative Closest Point (Dual-Bootstrap ICP). The approach is to start from one or more initial, low-order estimates that are only accurate in small image regions, called bootstrap regions. In each bootstrap region, the algorithm iteratively: 1) refines the transformation estimate using constraints only from within the bootstrap region; 2) expands the bootstrap region; and 3) tests to see if a higher order transformation model can be used, stopping when the region expands to cover the overlap between images. Steps 1): and 3), the bootstrap steps, are governed by the covariance matrix of the estimated transformation. Estimation refinement [Step 2)] uses a novel robust version of the ICP algorithm. In registering retinal image pairs, Dual-Bootstrap ICP is initialized by automatically matching individual vascular landmarks, and it aligns images based on detected blood vessel centerlines. The resulting quadratic transformations are accurate to less than a pixel. On tests involving approximately 6000 image pairs, it successfully registered 99.5% of the pairs containing at least one common landmark, and 100% of the pairs containing at least one common landmark and at least 35% image overlap.


Absolute distance measurement by dual-comb nonlinear asynchronous optical sampling.
A dual-comb nonlinear asynchronous optical sampling method is proposed to simplify determination of the time interval and extend the non-ambiguity range in absolute length measurements. Type II second harmonic generation facilitates curve fitting in determining the time interval between adjacent pulses. Meanwhile, the non-ambiguity range is extended by adjusting the repetition rate of the signal laser. The performance of the proposed method is compared with a heterodyne interferometer. Results show that the system achieves a maximum residual of 100.6 nm and an uncertainty of 1.48 μm in a 0.5 ms acquisition time. With longer acquisition time, the uncertainty can be reduced to 166.6 nm for 50 ms and 82.9 nm for 500 ms. Moreover, the extension of the non-ambiguity range is demonstrated by measuring an absolute distance beyond the inherent range determined by the fixed repetition rate.


CD38 is required for the peripheral survival of immunotolerogenic CD4+ invariant NK T cells in nonobese diabetic mice.
T cell-mediated autoimmune type-1 diabetes (T1D) in NOD mice partly results from this strain's numerical and functional defects in invariant NK T (iNKT) cells. T1D is inhibited in NOD mice treated with the iNKT cell superagonist alpha-galactosylceramide through a process involving enhanced accumulation of immunotolerogenic dendritic cells in pancreatic lymph nodes. Conversely, T1D is accelerated in NOD mice lacking CD38 molecules that play a role in dendritic cell migration to inflamed tissues. Unlike in standard NOD mice, alpha-galactosylceramide pretreatment did not protect the CD38-deficient stock from T1D induced by an adoptively transferred pancreatic beta cell-autoreactive CD8 T cell clone (AI4). We found that in the absence of CD38, ADP-ribosyltransferase 2 preferentially activates apoptotic deletion of peripheral iNKT cells, especially the CD4+ subset. Therefore, this study documents a previously unrecognized role for CD38 in maintaining survival of an iNKT cell subset that preferentially contributes to the maintenance of immunological tolerance.


Sources of fine particulate matter in personal exposures and residential indoor, residential outdoor and workplace microenvironments in the Helsinki phase of the EXPOLIS study.
This study assessed the source contributions to the mass concentrations of fine particles (PM2.5) in personal exposures and in residential indoor, residential outdoor, and workplace indoor microenvironments of the nonsmoking adult population unexposed to environmental tobacco smoke in Helsinki, Finland. The elemental composition of 48-hour personal exposure and residential indoor, residential outdoor, and workplace indoor PM2.5 was analyzed by energy-dispersive X-ray fluorescence spectrometry for 76 participants not exposed to environmental tobacco smoke and 102 participating residences with no smoking in Helsinki as a part of the EXPOLIS study. Subsequently, a principal component analysis was used to identify the emission sources of PM2.5-bound elements and black smoke in each microenvironment, and this information was used to identify the corresponding sources in personal exposures. Finally, source reconstruction was done to determine the relative contributions of each source type to the total PM2.5 mass concentrations. Inorganic secondary particles, primary combustion, and soil were the dominant source types for the PM2.5 mass concentration in all the microenvironments and personal exposures. The ratio of the residential indoor-to-outdoor PM2.5 concentration was close to unity, but the corresponding elemental ratios and source contributions varied. Resuspension of soil dust tracked indoors was a much larger contributor to residential and workplace indoor PM2.5 than soil dust to residential outdoor PM2.5. Source contributions to personal PM2.5 exposures were best approximated by data from residential and workplace indoor microenvironments. Population exposure assessment of PM2.5, based on outdoor fixed-site monitoring, overestimates exposures to outdoor sources like traffic and long-range transport and does not account for the contribution of significant indoor sources.


The prevalence of weight loss during (chemo)radiotherapy treatment for lung cancer and associated patient- and treatment-related factors.
Thoracic radiotherapy is associated with toxicities that can adversely impact nutritional intake. This study aimed to investigate the prevalence and predictors of ≥5% weight loss and commencement of enteral nutrition in lung cancer patients receiving radiotherapy. A retrospective study of 96 patients treated with high dose palliative or radical radiotherapy for a primary diagnosis of small cell or non-small cell lung cancer. Weight loss was calculated between the start and up to 90 days from radiotherapy commencement. Associations between ≥5% weight loss and enteral feeding, and demographic and clinical factors (age, gender, nutritional status, total dose of radiotherapy, concurrent chemotherapy, disease stage, prior surgery, hyper-fractionation and performance status) were assessed. The prevalence of weight loss ≥5% was 31% (median weight loss 8%, range 5-19%). The prevalence of commencement of enteral nutrition was 12%. Patients receiving concurrent chemotherapy were more likely to have ≥5% weight loss (40 versus 0%, phi = 0.35, p < 0.001). The odds of a patient with late stage disease having ≥5% weight loss were 15 times greater than for a patient with earlier disease stage (95% CI 1.97, 122.8, p = 0.009). Only Patient Generated Subjective Global Assessment score was associated with starting enteral nutrition (r = 0.27, p = 0.03). Clinically significant weight loss is prevalent in lung cancer patients receiving radiotherapy and is associated with concurrent chemotherapy and late stage disease. Identification of factors associated with weight loss assists with early identification and intervention in patients at high nutritional risk.


GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data.
RNA-Seq is quickly becoming the preferred method for comprehensively characterizing whole transcriptome activity, and the analysis of count data from RNA-Seq requires new computational tools. We developed GSAASeqSP, a novel toolset for genome-wide gene set association analysis of sequence count data. This toolset offers a variety of statistical procedures via combinations of multiple gene-level and gene set-level statistics, each having their own strengths under different sample and experimental conditions. These methods can be employed independently, or results generated from multiple or all methods can be integrated to determine more robust profiles of significantly altered biological pathways. Using simulations, we demonstrate the ability of these methods to identify association signals and to measure the strength of the association. We show that GSAASeqSP analyses of RNA-Seq data from diverse tissue samples provide meaningful insights into the biological mechanisms that differentiate these samples. GSAASeqSP is a powerful platform for investigating molecular underpinnings of complex traits and diseases arising from differential activity within the biological pathways. GSAASeqSP is available at http://gsaa.unc.edu.


A primary care nurse-delivered walking intervention in older adults: PACE (pedometer accelerometer consultation evaluation)-Lift cluster randomised controlled trial.
Brisk walking in older people can increase step-counts and moderate to vigorous intensity physical activity (MVPA) in ≥10-minute bouts, as advised in World Health Organization guidelines. Previous interventions have reported step-count increases, but not change in objectively measured MVPA in older people. We assessed whether a primary care nurse-delivered complex intervention increased objectively measured step-counts and MVPA. A total of 988 60-75 year olds, able to increase walking and randomly selected from three UK family practices, were invited to participate in a parallel two-arm cluster randomised trial; randomisation was by household. Two-hundred-ninety-eight people from 250 households were randomised between 2011 and 2012; 150 individuals to the intervention group, 148 to the usual care control group. Intervention participants received four primary care nurse physical activity (PA) consultations over 3 months, incorporating behaviour change techniques, pedometer step-count and accelerometer PA intensity feedback, and an individual PA diary and plan. Assessors were not blinded to group status, but statistical analyses were conducted blind. The primary outcome was change in accelerometry assessed average daily step-counts between baseline and 3 months, with change at 12 months a secondary outcome. Other secondary outcomes were change from baseline in time in MVPA weekly in ≥10-minute bouts, accelerometer counts, and counts/minute at 3 months and 12 months. Other outcomes were adverse events, anthropometric measures, mood, and pain. Qualitative evaluations of intervention participants and practice nurses assessed the intervention's acceptability. At 3 months, eight participants had withdrawn or were lost to follow-up, 280 (94%) individuals provided primary outcome data. At 3 months changes in both average daily step-counts and weekly MVPA in ≥10-minute bouts were significantly higher in the intervention than control group: by 1,037 (95% CI 513-1,560) steps/day and 63 (95% CI 40-87) minutes/week, respectively. At 12 months corresponding differences were 609 (95% CI 104-1,115) steps/day and 40 (95% CI 17-63) minutes/week. Counts and counts/minute showed similar effects to steps and MVPA. Adverse events, anthropometry, mood, and pain were similar in the two groups. Participants and practice nurses found the intervention acceptable and enjoyable. The PACE-Lift trial increased both step-counts and objectively measured MVPA in ≥10-minute bouts in 60-75 year olds at 3 and 12 months, with no effect on adverse events. To our knowledge, this is the first trial in this age group to demonstrate objective MVPA increases and highlights the value of individualised support incorporating objective PA assessment in a primary care setting. Controlled-Trials.com ISRCTN42122561.


Low Plasma Level of Leucine-Rich Repeat-Containing 17 (LRRc17) Is an Independent and Additive Risk Factor for Osteoporotic Fractures in Postmenopausal Women.
A novel role of leucine-rich repeat-containing 17 (LRRc17), an LRR protein secreted by osteoblasts, as a negative regulator of receptor activator of NF-κB ligand-induced osteoclast differentiation was found. However, the clinical association between LRRc17 and osteoporotic fracture (OF) has not yet been investigated. We hypothesized that low circulating plasma level of LRRc17 might serve as an independent and additive risk factor for OF, including vertebral fractures (VF) and non-vertebral fractures (non-VF). In this case-control study, 102 OF cases and 102 age- and body mass index-matched controls (mean age, 63.2 years) were analyzed among 532 postmenopausal women. VF (n = 49) and non-VF (n = 60) participants were identified using lateral thoracolumbar radiographs and an interviewer-assisted questionnaire, respectively. Median LRRc17 levels were significantly lower in participants with any OF (117.5 versus 197.3 pg/mL, p < 0.001), VF (93.2 versus 172.4 pg/mL, p = 0.002), and non-VF (124.5 versus 206.9 pg/mL, p = 0.008) compared with the respective controls without fractures. The prevalence of OF increased from the highest LRRc17 tertile (≥228.5 pg/mL, 33.8%) to the lowest (<95.6 pg/mL, 63.2%). Each log unit decrease of LRRc17 was associated with greater risk of OF (odds ratio [OR] = 1.46; 95% confidence interval [CI] 1.10-1.96; p = 0.009) and VF (OR = 2.42; 95% CI 1.39-4.23; p = 0.002). Plasma LRRc17 significantly improved discrimination of OF, particularly VF, when added to models including clinical risk factors and bone mineral density according to the area under receiver operating characteristics curves (AUC 0.71 to 0.81, p = 0.036), category-free net reclassification improvement (0.79; 95% CI 0.37-1.21; p < 0.001), and integrated discrimination improvement (0.13; 95% CI 0.06-0.20; p < 0.001). Low plasma LRRc17 was an independent risk factor for OF, which improved risk stratification, particularly in the spines of postmenopausal women. © 2016 American Society for Bone and Mineral Research.


Reduced hypertrophy in vitro after chondrogenic differentiation of adult human mesenchymal stem cells following adenoviral SOX9 gene delivery.
Mesenchymal stem cell (MSC) based-treatments of cartilage injury are promising but impaired by high levels of hypertrophy after chondrogenic induction with several bone morphogenetic protein superfamily members (BMPs). As an alternative, this study investigates the chondrogenic induction of MSCs via adenoviral gene-delivery of the transcription factor SOX9 alone or in combination with other inducers, and comparatively explores the levels of hypertrophy and end stage differentiation in a pellet culture system in vitro. First generation adenoviral vectors encoding SOX9, TGFB1 or IGF1 were used alone or in combination to transduce human bone marrow-derived MSCs at 5 × 102 infectious particles/cell. Thereafter cells were placed in aggregates and maintained for three weeks in chondrogenic medium. Transgene expression was determined at the protein level (ELISA/Western blot), and aggregates were analysed histologically, immunohistochemically, biochemically and by RT-PCR for chondrogenesis and hypertrophy. SOX9 cDNA was superior to that encoding TGFB1, the typical gold standard, as an inducer of chondrogenesis in primary MSCs as evidenced by improved lacuna formation, proteoglycan and collagen type II staining, increased levels of GAG synthesis, and expression of mRNAs associated with chondrogenesis. Moreover, SOX9 modified aggregates showed a markedly lower tendency to progress towards hypertrophy, as judged by expression of the hypertrophy markers alkaline phosphatase, and collagen type X at the mRNA and protein levels. Adenoviral SOX9 gene transfer induces chondrogenic differentiation of human primary MSCs in pellet culture more effectively than TGFB1 gene transfer with lower levels of chondrocyte hypertrophy after 3 weeks of in vitro culture. Such technology might enable the formation of more stable hyaline cartilage repair tissues in vivo.


A randomized controlled trial protocol testing a decision support intervention for older patients with advanced kidney disease.
To assess the effectiveness of a decision support intervention using a pragmatic single blind Randomized Controlled Trial. Worldwide the proportion of older people (aged 65 years and over) is rising. This population is known to have a higher prevalence of chronic diseases including chronic kidney disease. The resultant effect of the changing health landscape is seen in the increase in older patients (aged ≥65 years) commencing on dialysis. Emerging evidence suggests that for some older patients dialysis may provide minimal benefit. In a majority of renal units non-dialysis management is offered as an alternative to undertaking dialysis. Research regarding decision-making support that is required to assist this population in choosing between dialysis or non-dialysis management is limited. A multisite single blinded pragmatic randomized controlled trial is proposed. Patients will be recruited from four Queensland public hospitals and randomizd into either the control or intervention group. The decision support intervention is multimodal and includes counselling provided by a trained nurse. The comparator is standard decision-making support. The primary outcomes are decisional regret and decisional conflict. Secondary outcomes are improved knowledge and quality of life. Ethics approval obtained November 2014. This is one of the first randomized controlled trials assessing a decision support intervention in older people with advance chronic kidney disease. The results may provide guidance for clinicians in future approaches to assist this population in decision-making to ensure reduced decisional regret and decisional conflict.


Ethnic differences in risk of acute compulsory admission in Amsterdam, 1996-2005.
Several European studies have shown that migrants from non-western countries are at increased risk of psychotic disorders. This study examines how this is reflected in the risk of acute compulsory admission (ACA). Information on all patients with an ACA in Amsterdam from 1996 to 2005 was linked to the Amsterdam municipal register. The incidence of first ACA in Amsterdam was 4.5 per 10,000 person years. The incidence risk of ACA for any psychiatric disorders and for psychotic disorders in particular showed a 2- to 3-fold increase in almost all migrant groups from non-western countries, and especially for second-generation migrants. In addition, all non-western migrant groups were at increased risk of being assessed as posing a danger to others. The relative risk of ACA for psychotic disorders was similar to that for the incidence of psychotic disorders in most ethnic groups from other studies, suggesting that the increased risk of ACA in non-western migrants can mainly be explained by the increased incidence of psychotic disorders in these groups. However, the relative risk of ACA for psychotic disorders among Moroccan migrants was lower than expected on the basis of incidence studies, which suggests that additional factors are relevant, such as illness-related expression and access to and quality of care.


Staking a claim for claims: a case study of resource allocation in Australian Aboriginal health care.
There have been numerous ways in which the notion of equity has been put forward in the literature. This reflects the fact that equity is essentially driven by values and is therefore subject to individual interpretation and preferences. Deciding between these various value judgements is however outside the scope of economic analysis, as conventionally defined. This poses a problem for the examination of issues of resource allocation in Aboriginal health services in Australia, where equity, very clearly, has a role to play. One possibility for moving forward on this issue is the adoption of a 'claims' approach where the emphasis is on the explicit recognition of the values to be employed in the 'equitable' allocation of resources. This involves teasing out the principles by which, under various approaches, resources are allocated differentially across groups (e.g. under resource allocation formulae, the criterion of 'need' as measured by SMRs can be viewed to be a basis for a 'claim' over resources). The commonly cited 'basic needs approach' is then used in the paper as a case in point to illustrate how such underlying principles may be identified and then assessed. In relation to the issue of equity in Aboriginal health services, there are a number of possible standards for equity which seem to have a significant degree of community acceptance. The paper discusses ways in which they can be applied to the problem of deciding how to allocate resources in Aboriginal health.


Operative management of Cushing syndrome secondary to micronodular adrenal hyperplasia.
We reviewed our experience with micronodular adrenal hyperplasia (MAH), its pigmented variant primary pigmented nodular adrenocortical disease (PPNAD), and the association with Carney's complex (CNC) to better characterize these disorders. This retrospective study analyzes clinical data and operative reports of 34 patients identified with MAH and/or PPNAD who underwent resection between 1969 and 2006 at the Clinical Research Center, an inpatient research hospital at the National Institutes of Health. Symptoms and anthropometric and biochemical data were used to evaluate effect of resection. Fifteen patients (44%) presented as adults and 19 (56%) as children. Twenty-five patients (74%) presented with noncyclic Cushing syndrome and 9 patients (26%) presented with cyclic Cushing syndrome. Thirty-one patients underwent bilateral resection; this was curative biochemically in 30 patients. Fourteen operations were performed laparoscopically (41%), and 20 were performed as open resections (59%). There was 1 postoperative complication in the laparoscopic group (7%) and 6 complications in the open group (30%; P = .20). Follow-up was available for 25 patients (74%). Statistically significant improvements in anthropometrics were observed for both adults and children. The most frequent manifestation of CNC requiring additional operation was cardiac myxoma, which was associated strongly with an atypical (cyclic) presentation of Cushing syndrome (P = .009). Cushing syndrome due to MAH and PPNAD may be cured by bilateral adrenal resection. All patients should be screened for manifestations of CNC at the time of adrenal diagnosis with particular attention to cardiac disease.


Pulsed Electromagnetic Field (PEMF) Treatment Ameliorates Murine Model of Collagen-Induced Arthritis.
Rheumatoid arthritis (RA) is an autoimmune disease of the joint synovial membranes. RA is difficult to prevent or treat; however, blocking proinflammatory cytokines is a general therapeutic strategy. Pulsed electromagnetic field (PEMF) is reported to alleviate RA's inflammatory response and is being studied as a non-invasive physical therapy. In this current study, PEMF decreased paw inflammation in a collagen-induced arthritis (CIA) murine model. PEMF treatment at 10 Hz was more effective in ameliorating arthritis than at 75 Hz. In the PEMF-treated CIA group, the gross inflammation score and cartilage destruction were lower than in the untreated CIA group. The CIA group treated with PEMF also showed lower serum levels of IL-1β but not IL-6, IL-17, or TNF-α. Serum levels of total anti-type II collagen IgG and IgG subclasses (IgG1, IgG2a, and IgG2b) remained unchanged. In contrast, tissue protein levels of IL-1β, IL-6, TNF-α, receptor activator of nuclear factor kappa-Β (RANK), RANK ligand (RANKL), IL-6 receptor (IL-6R), and TNF-α receptor1 (TNFR1) were all lower in the ankle joints of the PEMF-treated CIA group compared with the CIA group. The results of this study suggest that PEMF treatment can preserve joint morphology cartilage and delay the occurrence of CIA. PEMF has potential as an effective adjuvant therapy that can suppress the progression of RA.


Posttransplant lymphoproliferative disorder following pancreas transplantation.
The incidence, risk factors and impact on patient and graft survival were evaluated for posttransplant lymphoproliferative disorder (PTLD) among 212 pancreas transplant recipients. Thirteen (6.1%) developed PTLD during 71 +/- 27 months follow-up. Cumulative incidences of PTLD at 1, 3, 5 and 10 years posttransplant were 4.2%, 5.3%, 6.0% and 7.0%, respectively. Incidence of PTLD was lower for recipients of simultaneous pancreas kidney compared to pancreas after kidney transplant or pancreas transplant alone, though not significantly so. Recipient Epstein-Barr virus (EBV) seronegativity and number of doses of depleting antibody therapy administered at transplant were associated with increased risk of PTLD, while recipient age, gender, transplant type, cytomegalovirus mismatch maintenance immunosuppression type and treated acute rejection were not. All 13 cases underwent immunosuppression reduction, and 10 received anti-CD20 monoclonal antibody. During follow-up, 10/13 (77%) responded to treatment with complete remission, while 3 (23%) died as a result of PTLD. Patient and graft survivals did not differ for recipients with and without PTLD. The strong association of PTLD with EBV-seronegativity requires considering this risk factor when evaluating and monitoring pancreas transplant recipients. With reduction of immunosuppression and anti-CD20 therapy, survival for pancreas transplant recipients with PTLD was substantially better than previously reported.


Mechanisms of vancomycin resistance in Staphylococcus aureus.
Vancomycin is a glycopeptide antibiotic used for the treatment of Gram-positive bacterial infections. Traditionally, it has been used as a drug of last resort; however, clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) strains with decreased susceptibility to vancomycin (vancomycin intermediate-resistant S. aureus [VISA]) and more recently with high-level vancomycin resistance (vancomycin-resistant S. aureus [VRSA]) have been described in the clinical literature. The rare VRSA strains carry transposon Tn1546, acquired from vancomycin-resistant Enterococcus faecalis, which is known to alter cell wall structure and metabolism, but the resistance mechanisms in VISA isolates are less well defined. Herein, we review selected mechanistic aspects of resistance in VISA and summarize biochemical studies on cell wall synthesis in a VRSA strain. Finally, we recapitulate a model that integrates common mechanistic features of VRSA and VISA strains and is consistent with the mode of action of vancomycin.


Chronic infection during placental malaria is associated with up-regulation of cycloxygenase-2.
Placental malaria (PM) is associated with poor foetal development, but the pathophysiological processes involved are poorly understood. Cyclooxygenase (COX) and lipoxygenase (LOX) which convert fatty acids to prostaglandins and leukotrienes, play important roles in pregnancy and foetal development. COX-2, currently targeted by specific drugs, plays a dual role as it associates with both pre-eclampsia pathology and recovery during infection. The role of COX during PM was questioned by quantifying at delivery COX-1, COX-2, 15-LOX, and IL-10 expression in two groups of malaria infected and uninfected placenta. Placental biopsies were collected at delivery for mRNA isolation and quantification, using real time PCR. COX-2 and IL-10 mRNAs increased mainly during chronic infections (nine- and five-times, respectively), whereas COX-1 transcripts remained constant. COX-2 over-expression was associated with a higher birth weight of the baby, but with a lower rate of haemoglobin of the mother. It was associated with a macrophage infiltration of the placenta and with a low haemozoin infiltration. In the opposite way, placental infection was associated with lower expression of 15-LOX mRNA. A high degree of haemozoin deposition correlates with low birth weight and decreased expression of COX-2. These data provide evidence that COX-2 and IL-10 are highly induced during chronic infection of the placenta, but were not associated with preterm delivery or low birth weight. The data support the involvement of COX-2 in the recovery phase of the placental infection.


[Self-role perception of nurse practitioners in northern Taiwan].
The Nurse Practitioners (NP) is a position title introduced into the Taiwanese nursing care system in 2006. NP perception of themselves is critical to successful development of the NP position as well as to good coordination with other healthcare team members. Understanding NP self-perception can help determine self- or policy deficiencies and facilitate necessary changes to ameliorate such in order to advance the NP system in Taiwan. This study investigated the self-role perception of NPs in northern Taiwan. Researchers used a qualitative research design. Participants comprised ten nurses recruited from a general hospital in northern Taiwan. Data were collected using a semi-structured interview format and analyzed using qualitative content analysis. Two themes that evolved from data analysis included negative and positive self-role perception. Negative self-role perception included feelings of regret, helplessness, frustration and volatility. Positive self-role perception included feelings of enjoying success, reflecting on the present, connecting with nursing, happiness, and self-improvement. Enhancing clinical, educational, and policy requirements for NPs can promote positive self-role perception. Based on the medical culture in Taiwan, NPs receive clearly defined roles and clear and specific job descriptions to expand their role functions. Continued self-growth and mutual respect among team members are essential to improving professional cooperation and medical care quality.


The YTA10-12 complex, an AAA protease with chaperone-like activity in the inner membrane of mitochondria.
The mitochondrial members of the highly conserved AAA family, Yta10p and Yta12p, constitute a membrane-embedded complex of about 850 kDa. As an ATP dependent metallopeptidase (AAA protease), the YTA10-12 complex mediates the degradation of nonassembled inner membrane proteins. In contrast to nucleotide-dependent complex formation and substrate binding, proteolysis of bound polypeptides depends on the hydrolysis of ATP and the metallopeptidase activity of both subunits. Independent of its proteolytic function, the chaperone-like activity of the YTA10-12 complex is required for assembly of the membrane-associated ATP synthase. We propose that proteolytic and chaperone-like activities in the YTA10-12 complex mediate assembly and degradation processes of membrane protein complexes and thereby exert key functions in the maintenance of membrane integrity.


Questionable validity of the catheter-associated urinary tract infection metric used for value-based purchasing.
Catheter-associated urinary tract infections (CAUTIs) occur in 290,000 US hospital patients annually, with an estimated cost of $290 million. Two different measurement systems are being used to track the US health care system's performance in lowering the rate of CAUTIs. Since 2010, the Agency for Healthcare Research and Quality (AHRQ) metric has shown a 28.2% decrease in CAUTI, whereas the Centers for Disease Control and Prevention metric has shown a 3%-6% increase in CAUTI since 2009. Differences in data acquisition and the definition of the denominator may explain this discrepancy. The AHRQ metric analyzes chart-audited data and reflects both catheter use and care. The Centers for Disease Control and Prevention metric analyzes self-reported data and primarily reflects catheter care. Because analysis of the AHRQ metric showed a progressive change in performance over time and the scientific literature supports the importance of catheter use in the prevention of CAUTI, it is suggested that risk-adjusted catheter-use data be incorporated into metrics that are used for determining facility performance and for value-based purchasing initiatives.


Squeeze bottle versus syringe nasal saline irrigation for persistent allergic rhinitis - a randomized controlled trial.
Nasal irrigation is widely used as an adjunctive treatment for allergic rhinitis. There is little evidence regarding the efficacy of the devices used in this procedure. The objective of this study was to evaluate the efficacy of the squeeze bottle nasal saline irrigation in persistent allergic rhinitis patients compared with a syringe. We included patients between 18- and 60-years old presenting with persistent allergic rhinitis. All patients were instructed to perform nasal irrigation twice daily for four weeks. The patients were randomly assigned to use either the squeeze bottle nasal irrigation or a syringe for nasal irrigation. Symptoms score, physical examination results, satisfaction scores and adverse events were collected. There were 116 patients enrolled in the study, 58 of whom used the squeeze bottle nasal irrigation system and 58 of whom used a syringe. During a four-week follow-up, improvements in patients' nasal symptom scores for rhinitis symptoms were significantly greater in the group treated with the squeeze bottle. However, the physical examination score was no statistically significant difference. No adverse events were reported. The overall satisfaction scores for both devices were excellent. This study supports the regular use of nasal irrigation with a positive-pressure device, particularly a squeeze bottle, as an effective adjunctive treatment for allergic rhinitis. It is effective for reducing allergic rhinitis symptoms and can be used by patients with good compliance and minimal side effects.


Improved Anti-Inflammatory Effects of Liposomal Astaxanthin on a Phthalic Anhydride-Induced Atopic Dermatitis Model.
Previously, we found that astaxanthin (AST) elicited an anti-inflammatory response in an experimental atopic dermatitis (AD) model. However, the use of AST was limited because of low bioavailability and solubility. We hypothesized that liposome formulation of AST could improve this. In this study, we compared the anti-inflammatory and anti-dermatotic effects of liposomal AST (L-AST) and free AST. We evaluated the effect of L-AST on a phthalic anhydride (PA)-induced animal model of AD by analyzing morphological and histopathological changes. We measured the mRNA levels of AD-related cytokines in skin tissue and immunoglobulin E concentrations in the serum. Oxidative stress and transcriptional activities of signal transducer and activator of transcription 3 (STAT3) and nuclear factor (NF)-κB were analyzed via western blotting and enzyme-linked immunosorbent assay. PA-induced dermatitis severity, epidermal thickening, and infiltration of mast cells in skin tissues were ameliorated by L-AST treatment. L-AST suppressed AD-related inflammatory mediators and the inflammation markers, inducible nitric oxide synthase (iNOS) and cyclooxygenase (COX)-2 in PA-induced skin conditions. Oxidative stress and expression of antioxidant proteins, glutathione peroxidase-1 (GPx-1) and heme oxygenase-1 (HO-1), were recovered by L-AST treatment in skin tissues from PA-induced mice. L-AST treatment reduced transcriptional activity of STAT3 and NF-κB in PA-induced skin tissues. Our results indicate that L-AST could be more effective than free AST for AD therapy.


Investigating the global genomic diversity of Escherichia coli using a multi-genome DNA microarray platform with novel gene prediction strategies.
The gene content of a diverse group of 183 unique Escherichia coli and Shigella isolates was determined using the Affymetrix GeneChip® E. coli Genome 2.0 Array, originally designed for transcriptome analysis, as a genotyping tool. The probe set design utilized by this array provided the opportunity to determine the gene content of each strain very accurately and reliably. This array constitutes 10,112 independent genes representing four individual E. coli genomes, therefore providing the ability to survey genes of several different pathogen types. The entire ECOR collection, 80 EHEC-like isolates, and a diverse set of isolates from our FDA strain repository were included in our analysis. From this study we were able to define sets of genes that correspond to, and therefore define, the EHEC pathogen type. Furthermore, our sampling of 63 unique strains of O157:H7 showed the ability of this array to discriminate between closely related strains. We found that individual strains of O157:H7 differed, on average, by 197 probe sets. Finally, we describe an analysis method that utilizes the power of the probe sets to determine accurately the presence/absence of each gene represented on this array. These elements provide insights into understanding the microbial diversity that exists within extant E. coli populations. Moreover, these data demonstrate that this novel microarray-based analysis is a powerful tool in the field of molecular epidemiology and the newly emerging field of microbial forensics.


Ecological correlates of group integrity among dispersing cliff swallows.
Breeding colonies of birds represent groups of individuals that associate during one breeding season, at least partially dissociate for the non-breeding season, and may re-associate the next year through collective settlement at another breeding site. Little is known about the extent to which colonial birds maintain group integrity when occupying different sites in different years or the benefits of long-term associations among colonial individuals. For cliff swallows (Petrochelidon pyrrhonota) in western Nebraska, USA, we examined ecological correlates and potential benefits associated with group integrity. Using a dataset of over 25,000 individuals, we found that associations between dispersing cliff swallows were greater than would be predicted by purely random settlement among colony sites. The extent of group integrity varied widely among sites, with birds seeming to settle together more often at sites with fewer ectoparasites and at colonies similar in size and closer in physical proximity to the one they had previously occupied. Some associations of birds lasted three years in which they used a different site each year. Successful colonies had higher levels of group integrity among their settlers than did colonies that failed completely. Cliff swallows that were known to have settled with at least one conspecific from the previous year's site had a higher survival the next year than those not known to have settled with past residents. The results are consistent with cliff swallows choosing colonies based in part on parasite load and with sorting among colonies based on the birds' preferences for colonies of certain sizes.


Identification of two distinct populations of dendritic cells in afferent lymph that vary in their ability to stimulate T cells.
Immunofluorescent staining and flow cytometric analysis of dendritic cells from cattle afferent lymph has established that within the afferent lymph veiled cells (ALVC) there are two phenotypically distinct, major populations. One is CD11a+, CD5+, CD21- and expresses the bovine WC10 (workshop cluster 10) molecule and the Ag recognized by mAb CC81 but is not recognized by mAbs CC149 and IL-A24. The second ALVC subpopulation is CD11a-, CD5-, CD21+/-, workshop cluster 10- and is not recognized by mAb CC81 but is recognized by mAb CC149. Thus, the two populations, which can be identified by staining for CD11a, are defined by the differential expression of a number of Ag. The ALVC populations had differing capacities to stimulate T cells. CD11a- ALVC were more effective at stimulating proliferative responses in allogeneic CD4+ T cells and CD8+ T cells. This was not related to binding of CTLA4Ig or CD40L fusion proteins, implying similar levels of expression of their ligands, CD80 and CD86 or CD40. Both subsets were able to present OVA to resting memory CD4+ T cells, indicating that both were able to take up and process soluble native protein. In contrast, the CD11a- ALVC were more effective in presenting respiratory syncytial virus Ag to resting CD4+ T cells. Considering the central role of dendritic cells in the initiation of immune responses in naive animals, the two cell types may have different roles in the induction of primary responses induced following infection or immunization.


Facilitating Engaging Journal Clubs in Online Upper-Level Undergraduate Courses.
STEM curricula often prepare students with fundamental knowledge, allowing students to have strong backgrounds in technical concepts. However, upper-level students may lack the ability to critically analyze primary research articles, which is important for understanding the current state of the field. Journal clubs can be used within the classroom to facilitate discussion of recent work and teach students to critically analyze research and data. Traditional journal clubs (JCs) are conducted in face-to-face classrooms and consist of presentations and discussions. It is possible to adapt these techniques to form virtual Journal Clubs (vJCs) when courses are taught fully online; however, student engagement is often lacking and can lead to less knowledge gained in vJCs. In this article, we summarize several key teaching tips and best practices which we used to increase student engagement in vJCs. We found that vJCs, compared to JCs, equally increased student perceptions of their skills in reading, analyzing, and critiquing scientific literature and decreased their perceived levels of stress and frustration.


Predictors of aided speech recognition, with and without frequency compression, in older adults.
The aim was to investigate whether cognitive and/or audiological measures predict aided speech recognition, both with and without frequency compression (FC). Participants wore hearing aids, with and without FC for a total of 12 weeks (six weeks in each signal processing condition, ABA design). Performance on a sentence-in-noise recognition test was assessed at the end of each six-week period. Audiological (severity of high frequency hearing loss, presence of dead regions) and cognitive (reading span and trail making test scores) measures were obtained and assessed as predictors of sentence-in-noise recognition with and without FC enabled. Twelve experienced hearing-aid users (aged 65-84 years old) with moderate-to-severe high-frequency hearing loss took part in the study. The results suggest that both auditory and cognitive factors can be predictive of sentence-in-noise recognition with conventional amplification. However, only auditory factors were significantly correlated with the degree of benefit obtained from FC. The strongest predictor of aided speech recognition, both with and without FC, was high frequency hearing loss. Cognitive performance was also a predictor of benefit from conventional amplification, but not of additional benefit from the use of FC.


Brain systems underlying encounter expectancy bias in spider phobia.
Spider-phobic individuals are characterized by exaggerated expectancies to be faced with spiders (so-called encounter expectancy bias). Whereas phobic responses have been linked to brain systems mediating fear, little is known about how the recruitment of these systems relates to exaggerated expectancies of threat. We used fMRI to examine spider-phobic and control participants while they imagined visiting different locations in a forest after having received background information about the likelihood of encountering different animals (spiders, snakes, and birds) at these locations. Critically, imagined encounter expectancies modulated brain responses differently in phobics as compared with controls. Phobics displayed stronger negative modulation of activity in the lateral prefrontal cortex, precuneus, and visual cortex by encounter expectancies for spiders, relative to snakes or birds (within-participants analysis); these effects were not seen in controls. Between-participants correlation analyses within the phobic group further corroborated the hypothesis that these phobia-specific modulations may underlie irrationality in encounter expectancies (deviations of encounter expectancies from objective background information) in spider phobia; the greater the negative modulation a phobic participant displayed in the lateral prefrontal cortex, precuneus, and visual cortex, the stronger was her bias in encounter expectancies for spiders. Interestingly, irrationality in expectancies reflected in frontal areas relied on right rather than left hemispheric deactivations. Our data accord with the idea that expectancy biases in spider phobia may reflect deficiencies in cognitive control and contextual integration that are mediated by right frontal and parietal areas.


RNAi-based glyconanoparticles trigger apoptotic pathways for in vitro and in vivo enhanced cancer-cell killing.
Gold glyconanoparticles (GlycoNPs) are full of promise in areas like biomedicine, biotechnology and materials science due to their amazing physical, chemical and biological properties. Here, siRNA GlycoNPs (AuNP@PEG@Glucose@siRNA) in comparison with PEGylated GlycoNPs (AuNP@PEG@Glucose) were applied in vitro to a luciferase-CMT/167 adenocarcinoma cancer cell line and in vivo via intratracheal instillation directly into the lungs of B6 albino mice grafted with luciferase-CMT/167 adenocarcinoma cells. siRNA GlycoNPs but not PEGylated GlycoNPs induced the expression of pro-apoptotic proteins such as Fas/CD95 and caspases 3 and 9 in CMT/167 adenocarcinoma cells in a dose dependent manner, independent of the inflammatory response, evaluated by bronchoalveolar lavage cell counting. Moreover, in vivo pulmonary delivered siRNA GlycoNPs were capable of targeting c-Myc gene expression (a crucial regulator of cell proliferation and apoptosis) via in vivo RNAi in tumour tissue, leading to an ∼80% reduction in tumour size without associated inflammation.


Refractive error blindness.
Recent data suggest that a large number of people are blind in different parts of the world due to high refractive error because they are not using appropriate refractive correction. Refractive error as a cause of blindness has been recognized only recently with the increasing use of presenting visual acuity for defining blindness. In addition to blindness due to naturally occurring high refractive error, inadequate refractive correction of aphakia after cataract surgery is also a significant cause of blindness in developing countries. Blindness due to refractive error in any population suggests that eye care services in general in that population are inadequate since treatment of refractive error is perhaps the simplest and most effective form of eye care. Strategies such as vision screening programmes need to be implemented on a large scale to detect individuals suffering from refractive error blindness. Sufficient numbers of personnel to perform reasonable quality refraction need to be trained in developing countries. Also adequate infrastructure has to be developed in underserved areas of the world to facilitate the logistics of providing affordable reasonable-quality spectacles to individuals suffering from refractive error blindness. Long-term success in reducing refractive error blindness worldwide will require attention to these issues within the context of comprehensive approaches to reduce all causes of avoidable blindness.


A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition.
Patient-specific analysis of molecular networks is a promising strategy for making individual risk predictions and treatment decisions in cancer therapy. Although systems biology allows the gene network of a cell to be reconstructed from clinical gene expression data, traditional methods, such as bayesian networks, only provide an averaged network for all samples. Therefore, these methods cannot reveal patient-specific differences in molecular networks during cancer progression. In this study, we developed a novel statistical method called NetworkProfiler, which infers patient-specific gene regulatory networks for a specific clinical characteristic, such as cancer progression, from gene expression data of cancer patients. We applied NetworkProfiler to microarray gene expression data from 762 cancer cell lines and extracted the system changes that were related to the epithelial-mesenchymal transition (EMT). Out of 1732 possible regulators of E-cadherin, a cell adhesion molecule that modulates the EMT, NetworkProfiler, identified 25 candidate regulators, of which about half have been experimentally verified in the literature. In addition, we used NetworkProfiler to predict EMT-dependent master regulators that enhanced cell adhesion, migration, invasion, and metastasis. In order to further evaluate the performance of NetworkProfiler, we selected Krueppel-like factor 5 (KLF5) from a list of the remaining candidate regulators of E-cadherin and conducted in vitro validation experiments. As a result, we found that knockdown of KLF5 by siRNA significantly decreased E-cadherin expression and induced morphological changes characteristic of EMT. In addition, in vitro experiments of a novel candidate EMT-related microRNA, miR-100, confirmed the involvement of miR-100 in several EMT-related aspects, which was consistent with the predictions obtained by NetworkProfiler.


Wave coupling theory of Quasi-Phase-Matched linear electro-optic effect.
Starting from Maxwell's equations and taking the nonlinearity of linear electro-optic effect as a perturbation, we derive general wave coupling equations of quasi-phase-matched (QPM) linear electro-optic effect. And then we use the equations to study the electro-optic effect in PPLN. The numerical results indicate that the QPM condition plays an important role in electro-optic coupling. In addition, the coupling is very sensitive to the temperature and incident light wavelength, but it has a large tolerance to the direction of incident light.


In-depth characterization of viral isolates from plasma and cells compared with plasma circulating quasispecies in early HIV-1 infection.
The use of in vitro models to unravel the phenotypic characteristics of circulating viral variants is key to understanding HIV-1 pathogenesis but limited by the availability of primary viral isolates from biological samples. However, overall in vivo genetic variability of HIV-1 within a subject may not be reflected in the viable viral population obtained after isolation. Although several studies have tried to determine whether viral populations expanded in vitro are representative of in vivo findings, the answer remains unclear due to the reduced number of clonal sequences analyzed or samples compared. In order to overcome previous experimental limitations, here we applied Deep Pyrosequencing (DPS) technology in combination with phenotypic experiments to analyze and compare with unprecedented detail the composition of viral isolates and in vivo quasispecies. We amplified by DPS HIV-1 genomic regions covering gag, protease, integrase and env-V3 to characterize paired isolates from plasma and peripheral blood mononuclear cells and compare them with total plasma viral RNA in four recently HIV-1 infected subjects. Our study demonstrated the presence of unique haplotypes scattered between sample types with conservation of major variants. In addition, no differences in intra- and inter-population encoded protein variability were found between the different types of isolates or when these were compared to plasma viral RNA within subjects. Additionally, in vitro experiments demonstrated phenotypic similarities in terms of replicative capacity and co-receptor usage between viral isolates and plasma viral RNA. This study is the first in-depth comparison and characterization of viral isolates from different sources and plasma circulating quasispecies using DPS in recently HIV-1 infected subjects. Our data supports the use of primary isolates regardless of their plasma or cellular origin to define genetic variability and biological traits of circulating HIV-1 quasispecies.


Enlarged Perivascular Spaces and Dementia: A Systematic Review.
Perivascular compartments surrounding the penetrating arteries in the brain are part of a physiologic system, which facilitates fluids exchange and clearance of solutes from the brain. The perivascular compartments become visible on MRI when enlarged and are commonly referred to as perivascular spaces (ePVS). Previous studies on the association between ePVS and dementia have been inconsistent due to varying methods of measuring ePVS. As a frame of reference for future MRI studies on ePVS, we systematically review the literature on ePVS as a marker of vascular brain injury related to dementia from population-based as well as hospital-based settings. We identified three longitudinal and ten cross-sectional studies involving 7,581 persons. Potential outcomes were all-cause dementia, Alzheimer's disease, and vascular dementia. There was considerable heterogeneity in ePVS assessment: with studies using either visual inspection or segmentation, examining different brain locations and implementing different grading scales. Moreover, out of the total of 13 studies, all five studies on vascular dementia reported an association with presence of basal ganglia ePVS after adjustment for age, gender, and white matter hyperintensities. For seven studies on Alzheimer's disease and all-cause dementia, the results were ambiguous. This review did not identify an independent association of ePVS with prevalent or incident dementia. Harmonized methods for ePVS assessment, tested across different populations, may benefit future MRI studies on ePVS and dementia.


Comparative study of serum amyloid A protein and C-reactive protein in disease.
On the basis of results from 3000 parallel measurements of serum amyloid A protein (SAA) and C-reactive protein (CRP) in various clinical and experimental conditions, the relationship between these proteins was examined and the question of whether measurements of SAA can provide clinically useful information beyond that from CRP assays was evaluated. The concentrations of SAA and CRP showed a close relationship in a wide range of clinical conditions and the general clinical impact of an elevated SAA or CRP level is similar. SAA was, however, more sensitive than CRP in reflecting inflammatory activity, and in some conditions characterized by normal or only slightly elevated CRP concentrations, measurements of SAA concentrations could be used for monitoring disease activity and response to treatment. Marked variation in the ratios of SAA to CRP concentration occurred in response to different stimuli (e.g. surgical trauma/immunological tissue injury), suggesting the existence of independent, disease-specific pathways of regulation for the serum concentrations of SAA and CRP.