Nanofluidic tuning of photonic crystal circuits.
By integrating soft-lithography-based nanofluidics with silicon nanophotonics, we demonstrate dynamic, liquid-based addressing and high deltan/n (approximately 0.1) refractive index modulation of individual features within photonic structures at subwavelength length scales. We show ultracompact tunable spectral filtering through nanofluidic targeting of a single row of holes within a planar photonic crystal. We accomplished this with an optofluidic integration architecture comprising a nanophotonic layer, a nanofluidic delivery structure, and a microfluidic control engine. Variants of this technique could enable dynamic reconfiguration of photonic circuits, selective introduction of optical nonlinearities, or delivery of single molecules into resonant cavities for biodetection.


TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities.
We describe a general multiplatform exploratory tool called TreeQ-Vista, designed for presenting functional annotations in a phylogenetic context. Traits, such as phenotypic and genomic properties, are interactively queried from a user-provided relational database with a user-friendly interface which provides a set of tools for users with or without SQL knowledge. The query results are projected onto a phylogenetic tree and can be displayed in multiple color groups. A rich set of browsing, grouping and query tools are provided to facilitate trait exploration, comparison and analysis. The program, detailed tutorial and examples are available online (http:/genome.lbl.gov/vista/TreeQVista).


Endocannabinoids, related compounds and their metabolic routes.
Endocannabinoids are lipid mediators able to bind to and activate cannabinoid receptors, the primary molecular targets responsible for the pharmacological effects of the Δ9-tetrahydrocannabinol. These bioactive lipids belong mainly to two classes of compounds: N-acylethanolamines and acylesters, being N-arachidonoylethanolamine (AEA) and 2-arachidonoylglycerol (2-AG), respectively, their main representatives. During the last twenty years, an ever growing number of fatty acid derivatives (endocannabinoids and endocannabinoid-like compounds) have been discovered and their activities biological is the subject of intense investigations. Here, the most recent advances, from a therapeutic point of view, on endocannabinoids, related compounds, and their metabolic routes will be reviewed.


Structural determinants for the stereoselective hydrolysis of chiral substrates by phosphotriesterase.
Wild-type phosphotriesterase (PTE) preferentially hydrolyzes the R(P) enantiomers of the nerve agents sarin (GB) and cyclosarin (GF) and their chromophoric analogues. The active site of PTE can be subdivided into three binding pockets that have been denoted as the small, large, and leaving group pockets based on high-resolution crystal structures. The sizes and shapes of these pockets dictate the substrate specificity and stereoselectivity for catalysis. Mutants of PTE that exhibit substantial changes in substrate specificity and the ability to differentiate between chiral substrates have been prepared. For example, the G60A mutant is stereoselective for the hydrolysis of the R(P) enantiomer of the chromophoric analogues of sarin and cyclosarin, whereas the H254G/H257W/L303T (GWT) mutant reverses the stereoselectivity for the enantiomers of these two compounds. Molecular dynamics simulations and high-resolution X-ray structures identified the correlations between structural changes in the active site and the experimentally determined kinetic parameters for substrate hydrolysis. New high-resolution structures were determined for the H257Y/L303T (YT), I106G/F132G/H257Y (GGY), and H254Q/H257F (QF) mutants of PTE. Molecular dynamics calculations were conducted using the S(P) and R(P) enantiomers of the analogues for sarin and cyclosarin for the wild-type PTE and the G60A, YT, GGY, QF, and GWT mutants. The experimental stereoselectivity correlated nicely with the difference in the computed angle of attack for the nucleophilic hydroxide relative to the phenolic leaving group of the substrate.


FDG-PET/CT(A) imaging in large vessel vasculitis and polymyalgia rheumatica: joint procedural recommendation of the EANM, SNMMI, and the PET Interest Group (PIG), and endorsed by the ASNC.
Large vessel vasculitis (LVV) is defined as a disease mainly affecting the large arteries, with two major variants, Takayasu arteritis (TA) and giant cell arteritis (GCA). GCA often coexists with polymyalgia rheumatica (PMR) in the same patient, since both belong to the same disease spectrum. FDG-PET/CT is a functional imaging technique which is an established tool in oncology, and has also demonstrated a role in the field of inflammatory diseases. Functional FDG-PET combined with anatomical CT angiography, FDG-PET/CT(A), may be of synergistic value for optimal diagnosis, monitoring of disease activity, and evaluating damage progression in LVV. There are currently no guidelines regarding PET imaging acquisition for LVV and PMR, even though standardization is of the utmost importance in order to facilitate clinical studies and for daily clinical practice. This work constitutes a joint procedural recommendation on FDG-PET/CT(A) imaging in large vessel vasculitis (LVV) and PMR from the Cardiovascular and Inflammation & Infection Committees of the European Association of Nuclear Medicine (EANM), the Cardiovascular Council of the Society of Nuclear Medicine and Molecular Imaging (SNMMI), and the PET Interest Group (PIG), and endorsed by the American Society of Nuclear Cardiology (ASNC). The aim of this joint paper is to provide recommendations and statements, based on the available evidence in the literature and consensus of experts in the field, for patient preparation, and FDG-PET/CT(A) acquisition and interpretation for the diagnosis and follow-up of patients with suspected or diagnosed LVV and/or PMR. This position paper aims to set an internationally accepted standard for FDG-PET/CT(A) imaging and reporting of LVV and PMR.


Effect of recombinant hirudin, a specific inhibitor of thrombin, on endotoxin-induced intravascular coagulation and acute lung injury in pigs.
We hypothesized that thrombin activation may play a prominent role in endotoxin-induced secondary organ failure, such as acute lung injury. To test this hypothesis, we administered a thrombin-specific inhibitor, recombinant hirudin, in endotoxemic pigs. The pigs were anesthetized, mechanically ventilated, and prepared with Swan-Ganz and extravascular lung water (EVLW) catheters. A total of 18 randomly selected animals received a pretreatment of 1,000 U/kg of hirudin, followed by a continuous infusion over 6 h of 500 U/kg/h given simultaneously with the infusion of 10 micrograms/kg/h of Salmonella abortus equi endotoxin. Another 18 animals received a continuous infusion over 6 h of endotoxin but did not receive hirudin. All animals were fluid resuscitated with 17 ml/kg/h of saline for the duration of the experiment. Data are expressed as the mean (95% confidence interval). Hirudin reduced the endotoxin-induced consumption of plasma fibrinogen from -110 (-138 to -82) mg/100 ml to -39 (-67 to -12) mg/100 ml (p = 0.0001) and endotoxin-induced increases in the soluble fibrin in plasma from 434 (369 to 499) ng/ml to 236 (171 to 300) ng/ml (p = 0.0002). These data suggest an effective inhibition of the endotoxin-generated thrombin by hirudin. Furthermore, hirudin significantly reduced endotoxin-induced increases in pulmonary vascular resistance from 32 (27 to 37) kdyn x s x cm-5 x kg to 20 (15 to 25) kdyn x s x cm-5 x kg (p = 0.0015) and increases in EVLW from 15.4 (13.2 to 17.6) ml/kg to 12.2 (10.0 to 14.4) ml/kg (p = 0.0299).(ABSTRACT TRUNCATED AT 250 WORDS)


Novel role of mitochondrial manganese superoxide dismutase in STAT3 dependent pluripotency of mouse embryonic stem cells.
Leukemia Inhibitory Factor (LIF)/Signal transducer and activator of transcription 3 (STAT3) signaling pathway maintains the stemness and pluripotency of mouse embryonic stem cells (mESCs). Detailed knowledge on key intermediates in this pathway as well as any parallel pathways is largely missing. We initiated our study by investigating the effect of small molecule Curcumin on various signalling pathways essential for self-renewal. Curcumin sustained the LIF independent self-renewal of mESCs and induced pluripotent stem cells (miPSCs) in a STAT3 activity dependent manner. Gene expression analysis showed LIF/STAT3 and redox signaling components to be majorly modulated. Amongst ROS genes, expression of Manganese Superoxide Dismutase (MnSOD) specifically relied on STAT3 signaling as evidenced by STAT3 inhibition and reporter assay. The silencing of MnSOD, but not Cu-ZnSOD expression, resulted in the loss of mESC pluripotency in presence of LIF, and the overexpression of MnSOD is sufficient for maintaining the expression of pluripotent genes in the absence of STAT3 signaling. Finally, we demonstrate MnSOD to stabilize the turnover of pluripotent proteins at the post-translational level by modulating proteasomal activity. In conclusion, our findings unravel a novel role of STAT3 mediated MnSOD in the self-renewal of mESCs.


[Mutations of ras and p53 genes in human non-small cell lung cancer cell lines and their clinical significance].
We examined 77 non-small cell lung cancer (NSCLC) cell lines for mutations of 3 ras genes and p53 gene, and ras mutations were detected by designed RFLP assay generated by mismatched primers during the PCR step and p53 gene mutations were detected using SSCP analysis. The incidence of ras mutations were 27/77 (35%) while that of p53 gene mutations were 57/77 (74%). The incidence of ras mutations in cell lines with p53 mutations were not different from that without p53 mutations, suggesting that they occurred independently. Neither ras nor p53 mutations correlated with histologic subtype, disease extent, in vitro culture time nor prior therapy status. The patients whose cell lines had any ras mutations survived for shorter period of time not only among the patients who were treated with curative intent but among those treated with palliative treatment. The Cox proportional hazards model predicted the higher risk for patients with ras mutations but not those with p53 mutations. We conclude that ras and p53 mutations are frequent, apparently independent genetic alterations which play different roles in NSCLC and that this information should be utilized in surgical oncology in the near future.


Loss of CHCHD2 and CHCHD10 activates OMA1 peptidase to disrupt mitochondrial cristae phenocopying patient mutations.
Dominant mutations in the mitochondrial paralogs coiled-helix-coiled-helix (CHCHD) domain 2 (C2) and CHCHD10 (C10) were recently identified as causing Parkinson's disease and amyotrophic lateral sclerosis/frontotemporal dementia/myopathy, respectively. The mechanism by which they disrupt mitochondrial cristae, however, has been uncertain. Using the first C2/C10 double knockout (DKO) mice, we report that C10 pathogenesis and the normal function of C2/C10 are intimately linked. Similar to patients with C10 mutations, we found that C2/C10 DKO mice have disrupted mitochondrial cristae, because of cleavage of the mitochondrial-shaping protein long form of OPA1 (L-OPA1) by the stress-induced peptidase OMA1. OMA1 was found to be activated similarly in affected tissues of mutant C10 knock-in (KI) mice, demonstrating that L-OPA1 cleavage is a novel mechanism for cristae abnormalities because of both C10 mutation and C2/C10 loss. Using OMA1 activation as a functional assay, we found that C2 and C10 are partially functionally redundant, and some but not all disease-causing mutations have retained activity. Finally, C2/C10 DKO mice partially phenocopied mutant C10 KI mice with the development of cardiomyopathy and activation of the integrated mitochondrial integrated stress response in affected tissues, tying mutant C10 pathogenesis to C2/C10 function.


Promicromonospora kermanensis sp. nov., an actinobacterium isolated from soil.
A novel strain belonging to the genus Promicromonospora, designated HM 533T, was isolated from soil in Kerman Province, Iran. It produced long and branched hyphae on ISP 2 medium that developed into a large number of irregular-shaped spores. It showed optimal growth at 25-30 °C and pH 5.0-8.0 with 0-4 % (w/v) NaCl. The peptidoglycan type of strain HM 533T was A4α l-Lys-l-Ala-d-Glu. Whole-cell hydrolysates of strain HM 533T contained the sugars ribose, glucose and galactose. The main phospholipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, two unknown glycolipids and an unknown phospholipid. MK-9(H4) and MK-9(H2) were the predominant menaquinones. The fatty acids pattern was mainly composed of the saturated branched-chain acids anteiso-C15 : 0 and iso-C15 : 0. The 16S rRNA gene sequence analysis showed the highest pairwise sequence identity (99.5-97.1 %) with the members of the genus Promicromonospora. Based on phenotypic and genotypic features, strain HM 533T is considered to represent a novel species of the genus Promicromonospora, for which the name Promicromonospora kermanensis is proposed with strain HM 533T (=DSM 45485T=UTMC 00533T=CECT 8709T) as the type strain.


Contract management in USA hospitals: service duplication and access within local markets.
This paper examines the extent to which hospitals that are under external contract management engage in service duplication, as well as the degree to which the various services they offer contribute to or detract from community access. The study incorporates all USA hospitals using data from the American Hospital Association Annual Survey Database, supplemented by county level measures obtained from the area resource file (ARF). Using data on the 3794 hospitals classified as acute care facilities in 2002, we performed a set of logistic regressions that analyzed whether a hospital offered each of 74 distinct services. For each service (regression), key independent variables measured the number of other hospitals in the local market area that also offered the service. Local area market definitions are the areas circumscribed by the hospital within distances of 10 and 20 miles. Results suggest that contract-managed (CM) hospitals display a more competitive pattern (service duplication) than hospitals in general, but CM hospitals that are the sole provider of services locally are less likely to offer services than traditionally managed sole hospital providers. Contract management does not appear to offer any particular advantages in improving access to hospital services.


Adaptation to astigmatic blur.
Adapting to blurred or sharpened images alters the perceived focus of subsequently viewed images. We examined whether these adaptation effects could arise from actual sphero-cylindrical refractive errors, by testing aftereffects in images simulating second-order astigmatism. Image blur was varied from negative (vertical) through isotropic to positive (horizontal) astigmatism while maintaining constant blur strength. A 2AFC staircase was used to estimate the stimulus that appeared isotropically blurred before or after adapting to images with astigmatism. Adaptation to horizontal blur caused isotropically blurred images to appear vertically biased and vice versa, shifting the perceived isotropic point toward the adapting level. Aftereffects were similar for different types of images and showed partial selectivity so that strongest effects generally occurred when testing and adapting images were the same. Further experiments explored whether the adaptation depended more strongly on the blurring or "fuzziness" in the images vs. the apparent "figural" changes introduced by the blur, by comparing how the aftereffects transfer across changes in size or orientation. Our results suggest that strong selective adaptation can occur for different lower order aberrations of the eye and that these may be at least partly driven by the apparent figural changes that blurring introduces into the retinal image.


Chronic fatigue syndrome: aetiology, diagnosis and treatment.
Chronic fatigue syndrome is characterised by intense fatigue, with duration of over six months and associated to other related symptoms. The latter include asthenia and easily induced tiredness that is not recovered after a night's sleep. The fatigue becomes so severe that it forces a 50% reduction in daily activities. Given its unknown aetiology, different hypotheses have been considered to explain the origin of the condition (from immunological disorders to the presence of post-traumatic oxidative stress), although there are no conclusive diagnostic tests. Diagnosis is established through the exclusion of other diseases causing fatigue. This syndrome is rare in childhood and adolescence, although the fatigue symptom per se is quite common in paediatric patients. Currently, no curative treatment exists for patients with chronic fatigue syndrome. The therapeutic approach to this syndrome requires a combination of different therapeutic modalities. The specific characteristics of the symptomatology of patients with chronic fatigue require a rapid adaptation of the educational, healthcare and social systems to prevent the problems derived from current systems. Such patients require multidisciplinary management due to the multiple and different issues affecting them. This document was realized by one of the Interdisciplinary Work Groups from the Institute for Rare Diseases, and its aim is to point out the main social and care needs for people affected with Chronic Fatigue Syndrome. For this, it includes not only the view of representatives for different scientific societies, but also the patient associations view, because they know the true history of their social and sanitary needs. In an interdisciplinary approach, this work also reviews the principal scientific, medical, socio-sanitary and psychological aspects of Chronic Fatigue Syndrome.


Electrokinetic characterization of poly(dimethylsiloxane) microchannels.
This paper characterizes the basic electrokinetic phenomena occurring within native poly(dimethylsiloxane) (PDMS) microchannels. Using simple buffers and current measurements, current density and electroosmosis data were determined in trapezoidal, reversibly sealed PDMS/PDMS and hybrid PDMS/glass channels with a cross-sectional area of 1035.5 microm(2) and about 6 cm length. This data was then compared to that obtained in an air-thermostated 50 microm inner diameter (1963.5 microm(2) cross-sectional area) fused-silica (FS) capillary of 70 cm length. Having a pH 7.8 buffer with an ionic strength (I) of 90 mM, Ohms's law was observed in the microchannels with electric field strengths of up to about 420 V/cm, which is about twice as high as for the FS capillary. The electroosmotic mobility (micro(EO)) in PDMS and FS is shown to exhibit the same general dependences on I and pH. For all configurations tested, the experimentally determined micro(EO) values were found to correlate well with the relationship micro(EO) = a + b log(I), where a and b are coefficients that are determined via nonlinear regression analysis. Electroosmotic fluid pumping in native PDMS also follows a pH dependence that can be estimated with a model based upon the ionization of silanol. Compared to FS, however, the magnitude of the electroosmotic flow in native PDMS is 50-70% smaller over the entire pH range and is difficult to maintain at acidic pH values. Thus, the origin of the negative charge at the inner wall of PDMS, glass, and FS appears to be similar but the density is lower for PDMS than for glass and FS.


High burden of homelessness among sexual-minority adolescents: findings from a representative Massachusetts high school sample.
We compared the prevalence of current homelessness among adolescents reporting a minority sexual orientation (lesbian/gay, bisexual, unsure, or heterosexual with same-sex sexual partners) with that among exclusively heterosexual adolescents. We combined data from the 2005 and 2007 Massachusetts Youth Risk Behavior Survey, a representative sample of public school students in grades 9 though 12 (n = 6317). Approximately 25% of lesbian/gay, 15% of bisexual, and 3% of exclusively heterosexual Massachusetts public high school students were homeless. Sexual-minority males and females had an odds of reporting current homelessness that was between 4 and 13 times that of their exclusively heterosexual peers. Sexual-minority youths' greater likelihood of being homeless was driven by their increased risk of living separately from their parents or guardians. Youth homelessness is linked with numerous threats such as violence, substance use, and mental health problems. Although discrimination and victimization related to minority sexual orientation status are believed to be important causal factors, research is needed to improve our understanding of the risks and protective factors for homelessness and to determine effective strategies to prevent homelessness in this population.


Synergistic inhibitory effects of free nitrous acid and imidazoline derivative on metal corrosion in a simulated water injection system.
To maintain the integrity of the internal surfaces of the pipelines in oil and gas industry, chemicals, including corrosion inhibitors and biocides, are commonly dosed to prevent corrosion. Imidazoline and its derivatives are widely used corrosion inhibitors for the protection of oil pipelines, which have been shown effective in reducing general corrosion. As an effective biocide, free nitrous acid (FNA) is suitable to inhibit microbially influenced corrosion, induced by for example sulfate-reducing bacteria. In this paper, we hypothesize that the continuous addition of imidazoline and intermittent dosing of FNA, when used in combination, would yield effective control of both general and pitting corrosions. As a typical imidazoline derivative, N-b-hydroxyethyl oleyl imidazoline (HEI-17) was applied in conjunction with intermittent dosing of FNA in the experimental system, with the results compared with two control systems, one receiving HEI-17 only, and one receiving no chemical dosing. The corrosion properties were monitored with open circuit potential, electrochemical impedance spectroscopy, linear polarization resistance, 3D optical profiling, and weight-loss measurement. Following a single dose of FNA, the general corrosion rates in the experimental reactor dropped up to 50% of that in the reactor receiving continuous HEI-17 dosing (0.27 ± 0.04 vs. 0.54 ± 0.08 mm/y), but gradually recovered to 93.4% of that in 2.5 months. After the FNA treatment, the pitting corrosion was decreased by 64.6% compared with continuous HEI-17 dosing reactor for a month from measuring the cumulative distribution of the pitting depth. HEI-17 treatment alone showed moderate pitting corrosion inhibition effect (approx. 27%), and the FNA treatment inhibited the formation of deep pits effectively. The combined application of HEI-17 and FNA has shown synergistic effects and high efficiency in mitigating MIC in the simulated water injection system. This treatment strategy has strong potential to be applied in the practical oilfield operations.


Expression of the cell cycle in sperm of Arabidopsis: implications for understanding patterns of gametogenesis and fertilization in plants and other eukaryotes.
The relationship between developmental events and the cell cycle was examined in sperm of Arabidopsis thaliana. Sperm of Arabidopsis rapidly enter the S (synthesis) phase of the cell cycle after inception from mitosis of the generative cell. Sperm in pollen grains within anthers continue to synthesize DNA, and at the time of pollination, contain approximately 1.5C DNA. Following pollination, sperm continue through the S phase of the cell cycle during pollen tube growth. By the time pollen tubes reach the ovary, sperm nuclei contain approximately 1.75C DNA. Just prior to double fertilization, sperm nuclei within embryo sacs contain the 2C quantity of DNA. These data indicate that molecular programs associated with the G1-S transition and the S phase of the cell cycle are expressed in sperm cells of developing pollen grains and pollen tubes in Arabidopsis. This pattern of prefertilization S phase activity in the sperm of a flowering plant stands in marked contrast to all other non-plant eukaryotes (from ciliates to yeast to sea urchins to mammals) where sperm remain in G1 during development, prior to the initiation of gametic fusion. In addition, when patterns of cell cycle activity in sperm of Arabidopsis and other flowering plants are compared, developmental analysis reveals that heterochronic alterations (changes in the relative timing of ontogenetic events) in cell cycle activity are a central cause of the diversification of patterns of gametogenesis in higher plants. Finally, comparative analysis of the patterns of cell cycle activity in Arabidopsis and other angiosperms may be used to predict which flowering plants will be amenable to development of successful in vitro fertilization techniques.


A Chinese chan-based mind-body intervention improves sleep on patients with depression: a randomized controlled trial.
Sleep disturbance is a common problem associated with depression, and cognitive-behavioral therapy (CBT) is a more common behavioral intervention for sleep problems. The present study compares the effect of a newly developed Chinese Chan-based intervention, namely Dejian mind-body intervention (DMBI), with the CBT on improving sleep problems of patients with depression. Seventy-five participants diagnosed with major depressive disorder were randomly assigned to receive 10 weekly sessions of CBT or DMBI, or placed on a waitlist. Measurements included ratings by psychiatrists who were blinded to the experimental design, and a standardized questionnaire on sleep quantity and quality was obtained before and after the 10-week intervention. Results indicated that both the CBT and DMBI groups demonstrated significantly reduced sleep onset latency and wake time after sleep onset (effect size range = 0.46-1.0, P ≤ 0.05) as compared to nonsignificant changes in the waitlist group (P > 0.1). Furthermore, the DMBI group, but not the CBT or waitlist groups, demonstrated significantly reduced psychiatrist ratings on overall sleep problems (effect size = 1.0, P = 0.00) and improved total sleep time (effect size = 0.8, P = 0.05) after treatment. The present findings suggest that a Chinese Chan-based mind-body intervention has positive effects on improving sleep in individuals with depression.


Ultrastructural correlates of transmitter release in presynaptic areas of lamprey reticulospinal axons.
The ultrastructure of presynaptic areas of lamprey reticulospinal axons was studied before, during, and after periods of elevated transmitter release produced either by repetitive action potential activity or depolarization by elevated extracellular potassium. Controls for possible effects of these procedures per se were done by replacing extracellular Ca with Mg to block transmitter release. In some experiments the time course of ultrastructural changes during K depolarization and subsequent recovery were studied by fixing tissue samples at various times. Transmitter release produced by action potential activity (20/sec for 15 min) in the presence of extracellular Ca significantly and reversibly decreased the number of synaptic vesicles, the area occupied by the vesicles, and the density of synaptic vesicles. An unexpected finding was a reversible decrease in the length of the differentiated membrane during periods of increased transmitter release. Transmitter release significantly and reversibly increased the number of coated vesicles, expanded the presynaptic membrane, and increased the number of pleomorphic vesicles. K depolarization (50 mM K for 15 min) produced identical, reversible effects, except that the expansion of the presynaptic membrane, although significant, was relatively small and there was no change in the number of pleomorphic vesicles. Raising the temperature of the saline from 2 degrees C (K depolarization experiments) or 7 degrees C (action potential experiments) to 20 degrees C did not change the results qualitatively but did produce somewhat larger effects during stimulation and appeared to increase the speed of recovery. Action potential activity or K depolarization in control experiments with the Ca in the saline replaced by Mg had little or no effect on synaptic ultrastructure. Synaptic vesicles in lamprey reticulospinal axons never contacted the axonal membrane anywhere other than at the differentiated membrane. During periods of elevated transmitter release, although the absolute number of vesicles in contact with the differentiated membrane decreased, the percentage of total vesicles in contact with the differentiated membrane increased dramatically. This suggests that the differentiated membrane is the site of vesicle release and there is an active process of vesicle movement to this membrane. In the course of this work it was observed that presynaptic areas closer than approximately 2 mm to the site of axonal transection, regardless of the composition of the saline or the experimental conditions, showed ultrastructural changes typical of increased transmitter release.(ABSTRACT TRUNCATED AT 400 WORDS)


Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.
Genetically identical populations of cells grown in the same environmental condition show substantial variability in gene expression profiles. Although single-cell RNA-seq provides an opportunity to explore this phenomenon, statistical methods need to be developed to interpret the variability of gene expression counts. We develop a statistical framework for studying the kinetics of stochastic gene expression from single-cell RNA-seq data. By applying our model to a single-cell RNA-seq dataset generated by profiling mouse embryonic stem cells, we find that the inferred kinetic parameters are consistent with RNA polymerase II binding and chromatin modifications. Our results suggest that histone modifications affect transcriptional bursting by modulating both burst size and frequency. Furthermore, we show that our model can be used to identify genes with slow promoter kinetics, which are important for probabilistic differentiation of embryonic stem cells. We conclude that the proposed statistical model provides a flexible and efficient way to investigate the kinetics of transcription.


Using magnetic resonance imaging measurements for the determination of local wave speed and arrival time of reflected waves in human ascending aorta.
Wave speed is one of the key factors describing wave propagation in arteries [1]. Local wave speed is directly related to the arterial wall properties [2]. With aging, arterial wave speed increases due to the stiffening of arterial wall, and also related to arterial disease.


Rapid Reconstitution Packages (RRPs) implemented by integration of computational fluid dynamics (CFD) and 3D printed microfluidics.
Rapid Reconstitution Packages (RRPs) are portable platforms that integrate microfluidics for rapid reconstitution of lyophilized drugs. Rapid reconstitution of lyophilized drugs using standard vials and syringes is an error-prone process. RRPs were designed using computational fluid dynamics (CFD) techniques to optimize fluidic structures for rapid mixing and integrating physical properties of targeted drugs and diluents. Devices were manufactured using stereo lithography 3D printing for micrometer structural precision and rapid prototyping. Tissue plasminogen activator (tPA) was selected as the initial model drug to test the RRPs as it is unstable in solution. tPA is a thrombolytic drug, stored in lyophilized form, required in emergency settings for which rapid reconstitution is of critical importance. RRP performance and drug stability were evaluated by high-performance liquid chromatography (HPLC) to characterize release kinetics. In addition, enzyme-linked immunosorbent assays (ELISAs) were performed to test for drug activity after the RRPs were exposed to various controlled temperature conditions. Experimental results showed that RRPs provided effective reconstitution of tPA that strongly correlated with CFD results. Simulation and experimental results show that release kinetics can be adjusted by tuning the device structural dimensions and diluent drug physical parameters. The design of RRPs can be tailored for a number of applications by taking into account physical parameters of the active pharmaceutical ingredients (APIs), excipients, and diluents. RRPs are portable platforms that can be utilized for reconstitution of emergency drugs in time-critical therapies.


Structural comparison of the vacuolar and Golgi V-ATPases from Saccharomyces cerevisiae.
Proton-translocating vacuolar-type ATPases (V-ATPases) are necessary for numerous processes in eukaryotic cells, including receptor-mediated endocytosis, protein maturation, and lysosomal acidification. In mammals, V-ATPase subunit isoforms are differentially targeted to various intracellular compartments or tissues, but how these subunit isoforms influence enzyme activity is not clear. In the yeast Saccharomyces cerevisiae, isoform diversity is limited to two different versions of the proton-translocating subunit a: Vph1p, which is targeted to the vacuole, and Stv1p, which is targeted to the Golgi apparatus and endosomes. We show that purified V-ATPase complexes containing Vph1p have higher ATPase activity than complexes containing Stv1p and that the relative difference in activity depends on the presence of lipids. We also show that VO complexes containing Stv1p could be readily purified without attached V1 regions. We used this effect to determine structures of the membrane-embedded VO region with Stv1p at 3.1-Å resolution, which we compare with a structure of the VO region with Vph1p that we determine to 3.2-Å resolution. These maps reveal differences in the surface charge near the cytoplasmic proton half-channel. Both maps also show the presence of bound lipids, as well as regularly spaced densities that may correspond to ergosterol or bound detergent, around the c-ring.


Isotopic signals of summer denitrification in a northern hardwood forested catchment.
Despite decades of measurements, the nitrogen balance of temperate forest catchments remains poorly understood. Atmospheric nitrogen deposition often greatly exceeds streamwater nitrogen losses; the fate of the remaining nitrogen is highly uncertain. Gaseous losses of nitrogen to denitrification are especially poorly documented and are often ignored. Here, we provide isotopic evidence (δ(15)NNO3 and δ(18)ONO3) from shallow groundwater at the Hubbard Brook Experimental Forest indicating extensive denitrification during midsummer, when transient, perched patches of saturation developed in hillslopes, with poor hydrological connectivity to the stream, while streamwater showed no isotopic evidence of denitrification. During small rain events, precipitation directly contributed up to 34% of streamwater nitrate, which was otherwise produced by nitrification. Together, these measurements reveal the importance of denitrification in hydrologically disconnected patches of shallow groundwater during midsummer as largely overlooked control points for nitrogen loss from temperate forest catchments.


Estimating the extent of household contact misclassification with index cases of disease in longitudinal studies using a stochastic simulation model.
Household contact with an index case of an infectious disease is a known risk factor for infection transmission. However, such contact may be underestimated due to the dynamic nature of households, particularly in longitudinal studies. Such studies generally begin with contact defined at a single point in time ('snap-shot'), leading to contact misclassification for some individuals who actually experienced contact before and after the snapshot. To quantify contact misclassification with index cases of disease in households. Historical data of 112,026 individuals from 17,889 households from an epidemiological study on leprosy in northern Malawi were used. Individuals were interviewed in the early 1980s and followed up over 5 years. It was possible to trace whether individuals died, changed household within the area, or moved out of the area between the two surveys.Using a 10% sample of households as the starting population and parameters for demographic and household changes over 5 years, the extent of contact misclassification was estimated through a simulation model of household dynamics, which traced contact with index cases in households over time. The model thereafter compared initial contact status and 'true' contact status generated from simulations. The starting population had 11,401 individuals, 52% female, and 224 (2%) leprosy index cases. Eleven percent of the households had at least one index case resident and 10% (1, 177) of non-case individuals were initial contacts. Sensitivity of initial contact status ranged from 0.52 to 0.74 and varied by age and sex. Sensitivity was low in those aged 20-29 and under 5 years but high in 5- to 14-year-olds. By gender, there were no differences among those aged under 5; females had lower sensitivity among those aged under 20 and higher for those above 30, respectively. Sensitivity was also low in simulations of long incubation periods. This work demonstrates the implications of changes in households on household contact-associated disease spread, particularly for long durations of follow-up and infections with long incubation periods where earlier unobserved contact is critical.


Avida: a software platform for research in computational evolutionary biology.
Avida is a software platform for experiments with self-replicating and evolving computer programs. It provides detailed control over experimental settings and protocols, a large array of measurement tools, and sophisticated methods to analyze and post-process experimental data. We explain the general principles on which Avida is built, as well as its main components and their interactions. We also explain how experiments are set up, carried out, and analyzed.


Frequency and predictors for postpartum fecal incontinence.
The goal of this study was to describe the frequency of postpartum fecal incontinence and to examine associated delivery events in a group of women participating in a validation study of a postpartum fecal incontinence survey. A self-administered survey of fecal incontinence symptoms and delivery events was administered to 50 women seen for their 6-week postpartum appointments. An analysis of association between postpartum fecal incontinence and individual delivery characteristics was performed. The frequency of at least one fecal incontinence symptom post partum was 38%. Specifically, 24% of women reported incontinence to flatus and 10% incontinence to stool. Vaginal delivery and perineal laceration were associated with an increased risk of reporting at least one symptom. Neither infant birth weight nor parity was associated with an increased risk of postpartum fecal incontinence. Cesarean delivery was associated with a lower frequency of overall fecal incontinence symptoms. The frequency of postpartum fecal incontinence was higher than previously reported. Similar to other studies, perineal laceration, especially extension into the anal sphincter, was an important risk factor for postpartum fecal incontinence.


A single-cell assay for telomere DNA content shows increasing telomere length heterogeneity, as well as increasing mean telomere length in human spermatozoa with advancing age.
The effect of age on telomere length heterogeneity in men has not been studied previously. Our aims were to determine the relationship between variation in sperm telomere length (STL), men's age, and semen parameters in spermatozoa from men undergoing in vitro fertilization (IVF) treatment. To perform this prospective cross-sectional pilot study, telomere length was estimated in 200 individual spermatozoa from men undergoing IVF treatment at the NYU Fertility Center. A novel single-cell telomere content assay (SCT-pqPCR) measured telomere length in individual spermatozoa. Telomere length among individual spermatozoa within an ejaculate varies markedly and increases with age. Older men not only have longer STL but also have more variable STL compared to younger men. STL from samples with normal semen parameters was significantly longer than that from samples with abnormal parameters, but STL did not differ between spermatozoa with normal versus abnormal morphology. The marked increase in STL heterogeneity as men age is consistent with a role for ALT during spermatogenesis. No data have yet reported the effect of age on STL heterogeneity. Based on these results, future studies should expand this modest sample size to search for molecular evidence of ALT in human testes during spermatogenesis.


AUT3, a serine/threonine kinase gene, is essential for autophagocytosis in Saccharomyces cerevisiae.
Autophagocytosis is a starvation-induced process, carrying proteins destined for degradation to the lysosome. In the yeast Saccharomyces cerevisiae, the autophagic process is visualized by the appearance of autophagic vesicles in the vacuoles of proteinase yscB-deficient strains during starvation. aut3-1 mutant cells which exhibit a block in the autophagic process have been isolated previously. By using the drastically reduced sporulation frequency of homozygous aut3-1 diploid cells, the AUT3 gene was cloned by complementation. The Aut3 protein consists of 897 amino acids. The amino-terminal part of the protein shows significant homologies to serine/threonine kinases. aut3 null mutant cells are fully viable on rich media but show a reduced survival rate upon starvation. They are unable to accumulate autophagic vesicles in the vacuole during starvation. Starvation-induced vacuolar protein breakdown is almost completely impaired in aut3-deficient cells. Vacuolar morphology and acidification are not influenced in aut3-deficient cells. Also, secretion of invertase, endocytic uptake of Lucifer Yellow, and vacuolar protein sorting appear wild type like in aut3-deficient cells, suggesting autophagocytosis as a novel route for the transport of proteins from the cytosol to the vacuole. By using a fusion of Aut3p with green-fluorescent protein, Aut3p was localized to the cytosol.


Shining Light on an mGlu5 Photoswitchable NAM: A Theoretical Perspective.
Metabotropic glutamate receptors (mGluRs) are important drug targets because of their involvement in several neurological diseases. Among mGluRs, mGlu5 is a particularly high-profile target because its positive or negative allosteric modulation can potentially treat schizophrenia or anxiety and chronic pain, respectively. Here, we computationally and experimentally probe the functional binding of a novel photoswitchable mGlu5 NAM, termed alloswitch-1, which loses its NAM functionality under violet light. We show alloswitch-1 binds deep in the allosteric pocket in a similar fashion to mavoglurant, the co-crystallized NAM in the mGlu5 transmembrane domain crystal structure. Alloswitch-1, like NAM 2-Methyl-6-(phenylethynyl)pyridine (MPEP), is significantly affected by P655M mutation deep in the allosteric pocket, eradicating its functionality. In MD simulations, we show alloswitch-1 and MPEP stabilize the co-crystallized water molecule located at the bottom of the allosteric site that is seemingly characteristic of the inactive receptor state. Furthermore, both NAMs form H-bonds with S809 on helix 7, which may constitute an important stabilizing interaction for NAM-induced mGlu5 inactivation. Alloswitch-1, through isomerization of its amide group from trans to cis is able to form an additional interaction with N747 on helix 5. This may be an important interaction for amide-containing mGlu5 NAMs, helping to stabilize their binding in a potentially unusual cis-amide state. Simulated conformational switching of alloswitch-1 in silico suggests photoisomerization of its azo group from trans to cis may be possible within the allosteric pocket. However, photoexcited alloswitch-1 binds in an unstable fashion, breaking H-bonds with the protein and destabilizing the co-crystallized water molecule. This suggests photoswitching may have destabilizing effects on mGlu5 binding and functionality.


Actions of estradiol on discrete attributes of the luteinizing hormone pulse signal in man. Studies in postmenopausal women treated with pure estradiol.
We assessed the time-dependent impact of estradiol on properties of the luteinizing hormone (LH) pulse signal in 12 hypoestrogenemic postmenopausal volunteers studied basally and after 1, 5, 10, and 30 d of estradiol delivery via an intravaginal Silastic ring. Computerized analysis of the plasma LH time series revealed a significant decrease in LH pulse frequency within 24 h of estrogen treatment, followed by a secondary increase (days 5 and 10), and then a sustained decline (day 30) in LH pulsatility. Estradiol also significantly suppressed incremental and maximal (but not fractional) LH pulse amplitudes in a biphasic manner. In contrast, LH peak duration was invariant until day 30 of estradiol replacement. These observations indicate that the well recognized biphasic actions of estradiol on mean serum LH concentrations can be modeled in relation to specific and time-dependent alterations in LH pulse frequency and amplitude.


Thallium-201 scintigraphy after intravenous infusion of adenosine compared with exercise thallium testing in the diagnosis of coronary artery disease.
Adenosine is an endogenously produced compound that has significant effects as a coronary and systemic vasodilator. Previous studies suggest that intravenous infusion of adenosine, coupled with thallium-201 scintigraphy, may have specific value as a noninvasive means of evaluating coronary artery disease. The purpose of this study was to compare the diagnostic value of adenosine thallium testing with that of standard exercise thallium testing. One hundred subjects were studied with exercise thallium imaging and thallium imaging after adenosine infusion, including 47 with angiographically proved coronary artery disease and 53 control subjects. The overall sensitivity of the thallium procedures was 81% for the exercise study and 83% for the adenosine study (p = NS); the specificity was 74% for the exercise study and 75% for the adenosine study (p = NS). The diagnostic accuracy of the exercise study was 77% and that of the adenosine study was 79%. Ninety-four percent of subjects had an adverse effect due to the adenosine infusion; however, most of these effects were mild and well tolerated. All adverse effects abated within 30 to 45 s of the termination of the study, consistent with the very brief half-life of the agent. Thus, thallium-201 scintigraphy after intravenous infusion of adenosine has a diagnostic value similar to that of exercise thallium testing for evaluation of coronary artery disease. Adenosine thallium testing may be particularly useful in evaluating patients unable to perform treadmill exercise testing.


Expression of p190A during apoptosis in the regressing rat ventral prostate.
After hormonal ablation, 90% of the secretory epithelial cells of the prostate undergo apoptosis, and the remaining cells are reorganized as the tissue is remodeled. Using differential display RT-PCR of total RNA extracted from the rat ventral prostate before and 4 days after castration, we have cloned and sequenced a number of complementary DNAs whose cognate messenger RNAs (mRNAs) may be either up- or down-regulated during prostatic regression. One sequence of particular interest, 25.2, is up-regulated after castration and is homologous to p190, a protein associated with cytoskeletal reorganization. RT-PCR has confirmed that the steady state level of p190A mRNA is increased in the rat ventral prostate after castration, and Western blot analysis indicates that the protein levels for p190A also increase. The steady state level of p190B mRNA, the second isoform of p190, does not appear to change significantly after hormone ablation. Immunohistochemical analysis demonstrates that p190A is up-regulated primarily in the columnar epithelial cells that actively undergo cell death after hormone ablation. As Rho-GAP signaling had been shown to be influenced by p190 levels, leading to the disassembly of focal adhesion contacts and the loss of cytoskeletal architecture, we also measured the changes in Rho-GAP during prostate regression. Rho-GAP levels do not change significantly, suggesting that changes in stoichiometry of the interaction between p190A and Rho-GAP may be a prerequisite for the initiation of cytoplasmic condensation. These intracellular events coupled with the proteolytic degradation of the extracellular matrix appear to be integral to the apoptotic process in glandular epithelia.


Urine RAS components in mice and people with type 1 diabetes and chronic kidney disease.
The pathways implicated in diabetic kidney disease (DKD) are largely derived from animal models. To examine if alterations in renin-angiotensin system (RAS) in humans are concordant with those in rodent models, we measured concentration of angiotensinogen (AOG), cathepsin D (CTSD), angiotensin-converting enzyme (ACE), and ACE2 and enzymatic activities of ACE, ACE2, and aminopeptidase-A in FVB mice 13-20 wk after treatment with streptozotocin (n = 9) or vehicle (n = 15) and people with long-standing type 1 diabetes, with (n = 37) or without (n = 81) DKD. In streptozotocin-treated mice, urine AOG and CTSD were 10.4- and 3.0-fold higher than in controls, respectively (P < 0.001). Enzymatic activities of ACE, ACE2, and APA were 6.2-, 3.2-, and 18.8-fold higher, respectively, in diabetic animals (P < 0.001). Angiotensin II was 2.4-fold higher in diabetic animals (P = 0.017). Compared with people without DKD, those with DKD had higher urine AOG (170 vs. 15 μg/g) and CTSD (147 vs. 31 μg/g). In people with DKD, urine ACE concentration was 1.8-fold higher (1.4 vs. 0.8 μg/g in those without DKD), while its enzymatic activity was 0.6-fold lower (1.0 vs. 1.6 × 109 RFU/g in those without DKD). Lower ACE activity, but not ACE protein concentration, was associated with ACE inhibitor (ACEI) treatment. After adjustment for clinical covariates, AOG, CTSD, ACE concentration, and ACE activity remained associated with DKD. In conclusion, in mice with streptozotocin-induced diabetes and in humans with DKD, urine concentrations and enzymatic activities of several RAS components are concordantly increased, consistent with enhanced RAS activity and greater angiotensin II formation. ACEI use was associated with a specific reduction in urine ACE activity, not ACE protein concentration, suggesting that it may be a marker of exposure to this widely-used therapy.


Transcatheter arterial chemoembolization improves the resectability of malignant breast phyllodes tumor with angiosarcoma component: a case report.
A giant phyllodes tumor of the breast is a rare fibroepithelial lesion, and its treatment is controversial. Many case reports have reported performing skin graft reconstruction after tumor excision. Chest wall resection may be required if the tumor has invaded the chest muscle layer. We speculated that transcatheter arterial chemoembolization (TACE) can improve the resectability of malignant phyllodes tumor of the breast without requiring skin grafting. The English literature contains only one case report similar to our experience. We report a rare case of a 51-year-old woman who had a giant malignant phyllodes tumor with heterologous sarcomatous differentiation in her right breast. The tumor was 19.43 × 12.98 × 21.47 cm. Whole-body computed tomography (CT) and bone scan did not reveal distant metastasis. Chest magnetic resonance imaging showed chest wall tumor invasion. Considering that skin defects after mastectomy can be extensive, we administered four courses of chemoembolization in the 5 weeks before surgery (30 mg of epirubicin and embozene microspheres [400, 500, and 700 μm]/week). Each process was well tolerated, with no serious complications. Only fever and local pain at the tumor site were noted, and these symptoms resolved with time. The follow-up CT scan showed a 45% reduction in tumor volume. Therefore, simple mastectomy was performed without skin grafting reconstruction. Wound healing was satisfactory, and the patient was discharged 1 week after surgery. Pathological and immunohistochemistry (IHC) findings showed a malignant phyllodes tumor with an angiosarcoma component. Because of tumor invasion of the chest wall, we recommended the patient receive radiotherapy, but she refused. Two months after surgery, recurrence of the malignant phyllodes tumor with right axillary lymph node involvement and lung metastasis was confirmed. Initial surgical resection of giant phyllodes tumors is often challenging. For initial presentation with unresectable giant phyllodes tumor, we recommend to perform TACE prior to surgery. In our patient, preoperative TACE was effective and safe. If the tumor has invaded the chest wall, early radiotherapy after surgery may be recommended for preventing recurrence.


Evaluation of contact lens multipurpose solutions on bacterial biofilm development.
No sooner are contact lenses (CLs) inserted into the eyes than lipids, proteins, and glycoproteins rapidly accumulate on their surface, thus favoring the adhesion of commensal bacteria and biofilm formation. Infections may be caused by the proliferation of indigenous flora or other opportunistic pathogens. Our purpose was to evaluate the activity and the capacity of different CL solutions to interfere with the mechanisms of biofilm formation and stability and use of a system to study dynamically biofilm development. We evaluated the antibiofilm activity of three different multipurpose solutions (MPSs): Regard, Biotrue, and OPTI-FREE PureMoist on four bacterial species (Serratia marcescens, Pseudomonas aeruginosa, Staphylococcus epidermidis, and Staphylococcus aureus). Static biofilm assay was first performed to analyze the effect of MPSs. Dynamic assays were performed with the BioFlux system to analyze the effect of the OxyChlorite solution Regard on the biofilm formation. Our studies show that MPSs are able to completely inhibit biofilm formation of Staphylococcus species and of S. marcescens after only 4 hr of incubation. Moreover, a reduction of biofilm formation by Pseudomonas was noted. Best results on P. aeruginosa were obtained with Regard. Regard was also used for dynamic assay, revealing its ability to disaggregate the mature biofilm. Regard completely inhibited biofilm formation by S. epidermidis and slowed down biofilm development by P. aeruginosa. Our findings indicate that the CL solutions tested were all able to reduce biofilm formation. Furthermore, the BioFlux system was proven to be useful for the evaluation of the effectiveness of CL solutions against microbial biofilm formation.


Capacity of the national influenza surveillance system in Afghanistan, a chronic conflict setting.
Influenza surveillance is needed to monitor potential public health threats from the emergence of novel influenza viruses. This study assessed the capacity and performance of the national influenza surveillance system in Afghanistan from 2007 to 2014. Data were collected by review of hospital registers and the National Influenza Centre (NIC) database, interviews with influenza focal points at 9 influenza sentinel surveillance sites and the Centre staff, and observation of the sites. Out of 6900 specimens collected, influenza virus was detected in 253 (3.6%), predominantly H1N1 (63%); most of these cases were detected during the 2009 pandemic. The NIC had the capacity for virus isolation and PCR identification and performed reasonably until 2011 when support of the Naval American Medical Research Unit 3 was withdrawn. The limitations identified in the system indicated the need for: more complete data, improved technical competence and trained human resources, updating of the infrastructure/facilities, and the presence of standard operating procedures throughout surveillance.


Cu isotopes in marine black shales record the Great Oxidation Event.
The oxygenation of the atmosphere ∼2.45-2.32 billion years ago (Ga) is one of the most significant geological events to have affected Earth's redox history. Our understanding of the timing and processes surrounding this key transition is largely dependent on the development of redox-sensitive proxies, many of which remain unexplored. Here we report a shift from negative to positive copper isotopic compositions (δ(65)CuERM-AE633) in organic carbon-rich shales spanning the period 2.66-2.08 Ga. We suggest that, before 2.3 Ga, a muted oxidative supply of weathering-derived copper enriched in (65)Cu, along with the preferential removal of (65)Cu by iron oxides, left seawater and marine biomass depleted in (65)Cu but enriched in (63)Cu. As banded iron formation deposition waned and continentally sourced Cu became more important, biomass sampled a dissolved Cu reservoir that was progressively less fractionated relative to the continental pool. This evolution toward heavy δ(65)Cu values coincides with a shift to negative sedimentary δ(56)Fe values and increased marine sulfate after the Great Oxidation Event (GOE), and is traceable through Phanerozoic shales to modern marine settings, where marine dissolved and sedimentary δ(65)Cu values are universally positive. Our finding of an important shift in sedimentary Cu isotope compositions across the GOE provides new insights into the Precambrian marine cycling of this critical micronutrient, and demonstrates the proxy potential for sedimentary Cu isotope compositions in the study of biogeochemical cycles and oceanic redox balance in the past.


Organoid cultures of early-onset colorectal cancers reveal distinct and rare genetic profiles.
Sporadic early-onset colorectal cancer (EOCRC) has bad prognosis, yet is poorly represented by cell line models. We examine the key mutational and transcriptomic alterations in an organoid biobank enriched in EOCRCs. We established paired cancer (n=32) and normal organoids (n=18) from 20 patients enriched in microsatellite-stable EOCRC. Exome and transcriptome analysis was performed. We observed a striking diversity of molecular phenotypes, including PTPRK-RSPO3 fusions. Transcriptionally, RSPO fusion organoids resembled normal colon organoids and were distinct from APC mutant organoids, with high BMP2 and low PTK7 expression. Single cell transcriptome analysis confirmed the similarity between RSPO fusion organoids and normal organoids, with a propensity for maturation on Wnt withdrawal, whereas the APC mutant organoids were locked in progenitor stages. CRISPR/Cas9 engineered mutation of APC in normal human colon organoids led to upregulation of PTK7 protein and suppression of BMP2, but less so with an engineered RNF43 mutation. The frequent co-occurrence of RSPO fusions with SMAD4 or BMPR1A mutation was confirmed in TCGA database searches. RNF43 mutation was found in organoid from a leukaemia survivor with a novel mutational signature; and organoids with POLE proofreading mutation displayed ultramutation. The cancer organoid genomes were stable over long culture periods, while normal human colon organoids tended to be subject to clonal dominance over time. These organoid models enriched in EOCRCs with linked genomic data fill a gap in existing CRC models and reveal distinct genetic profiles and novel pathway cooperativity.


An oxime-based glycocluster microarray.
Carbohydrate microarrays represent powerful tools to study and detect carbohydrate-binding proteins, pathogens or cells. In this paper, we report two original oxime-based methods to prepare surfaces displaying well-defined structures and valency in a given microspot with improved recognition potency with lectins. In a first "direct" approach, fully synthetic aminooxylated glycoclusters have been coated onto aldehyde-activated SiO2 (silicium substrate doped with 50 nm thermal oxide layer). To improve the preparation of the microarray in terms of rapidity and simplicity and to provide addressable surfaces on which sugars can be linked chemoselectively as clusters at defined plots, a second "indirect" strategy has been developed using successive oxime ligation steps. In both cases, binding assays with labelled lectins have revealed more potent and selective interaction due to the clustered presentation of sugars. The observed differences of interaction have been confirmed in solution by ITC.


The basic reproductive number of Ebola and the effects of public health measures: the cases of Congo and Uganda.
Despite improved control measures, Ebola remains a serious public health risk in African regions where recurrent outbreaks have been observed since the initial epidemic in 1976. Using epidemic modeling and data from two well-documented Ebola outbreaks (Congo 1995 and Uganda 2000), we estimate the number of secondary cases generated by an index case in the absence of control interventions R0. Our estimate of R0 is 1.83 (SD 0.06) for Congo (1995) and 1.34 (SD 0.03) for Uganda (2000). We model the course of the outbreaks via an SEIR (susceptible-exposed-infectious-removed) epidemic model that includes a smooth transition in the transmission rate after control interventions are put in place. We perform an uncertainty analysis of the basic reproductive number R0 to quantify its sensitivity to other disease-related parameters. We also analyse the sensitivity of the final epidemic size to the time interventions begin and provide a distribution for the final epidemic size. The control measures implemented during these two outbreaks (including education and contact tracing followed by quarantine) reduce the final epidemic size by a factor of 2 relative the final size with a 2-week delay in their implementation.


Relationship of Fuchs endothelial corneal dystrophy severity to central corneal thickness.
To define the relationship between Fuchs endothelial corneal dystrophy (FECD) severity and central corneal thickness (CCT). We examined 1610 eyes from a subset of index cases, family members, and unrelated control subjects with normal corneas from the FECD Genetics Multi-Center Study. To estimate the association between FECD severity grade (7-point severity scale based on guttae confluence) and CCT measured by ultrasonographic pachymetry, a multivariable model was used that adjusted for eye, age, race, sex, history of glaucoma or ocular hypertension, diabetes mellitus, contact lens wear, intraocular pressure, and familial relationship to the index case. An interaction between FECD severity grade and edema (stromal or epithelial) on slitlamp examination findings was used to investigate whether the effect of FECD severity grade on CCT differed between those with and without edema. Average CCT was thicker in index cases for all FECD grades compared with unaffected controls (P ≤ .003) and in affected family members with an FECD grade of 4 or greater compared with unaffected family members (P ≤ .04). Similar results were observed for subjects without edema. Average CCT of index cases was greater than that of affected family members with grades 4, 5, and 6 FECD (P ≤ .02). Intraocular pressure was also associated with CCT (P = .01). An increase in CCT occurs with increasing severity of FECD, including at lower FECD grades in which clinically observable edema is not present. Monitoring CCT changes serially could be a more sensitive measure of disease progression with surgical therapeutic implications.


Light-extraction enhancement and directional emission control of GaN-based LEDs by self-assembled monolayer of silica spheres.
The light extraction of 1 × 1 mm(2) GaN-based blue light-emitting diodes (LEDs) was enhanced by a self-assembled monolayer (SAM) of silica submicron spheres. The silica spheres were synthesized with various spherical sizes via the ammonia-catalyzed hydrolysis and condensation of tetraethyl orthosilicate in water/ethanol solutions. Hexagonal closely-packed (HCP) silica sphere monolayer was formed onto the indium tin oxide layer of the LED by a spin coating process. The size effect of silica spheres on the light-extraction efficiency (LEE) of GaN-based LEDs was theoretically studied and their optimum size was determined. The simulation results showed that the use of silica spheres can improve the LEE by 1.1-1.32 times compared to the conventional LEDs. The light output power of the LED with 650-nm-thick SAM of HCP silica spheres was experimentally enhanced by 1.28 and 1.23 times under the injection currents of 100 and 350 mA, respectively. By employing the SAM of HCP silica spheres, the directional emission pattern was relatively converged, indicating a reasonable consistency with the simulation result.


Resonance spectrum of a three-dimensional photonic quantum ring laser with an equilateral triangle microcavity.
We have fabricated three-dimensional (3D) photonic quantum ring lasers with an equilateral triangle microcavity. Their spectra were well explained by combining the off-normal resonance and hexagonally bounced in-plane whispering-gallery-mode condition. The angular distribution of the emission modes and their discrete wavelengths were shown to be in excellent agreement with a 3D Rayleigh Fabry-Perot model. We confirmed that the allowed modes in the equilateral triangle microcavity decrease by decreasing the length of equilateral triangle side, L, and the spectral mode spacing linearly increases with the mode index m and is inversely proportional to L2.


DRGraph: An Efficient Graph Layout Algorithm for Large-scale Graphs by Dimensionality Reduction.
Efficient layout of large-scale graphs remains a challenging problem: the force-directed and dimensionality reduction-based methods suffer from high overhead for graph distance and gradient computation. In this paper, we present a new graph layout algorithm, called DRGraph, that enhances the nonlinear dimensionality reduction process with three schemes: approximating graph distances by means of a sparse distance matrix, estimating the gradient by using the negative sampling technique, and accelerating the optimization process through a multi-level layout scheme. DRGraph achieves a linear complexity for the computation and memory consumption, and scales up to large-scale graphs with millions of nodes. Experimental results and comparisons with state-of-the-art graph layout methods demonstrate that DRGraph can generate visually comparable layouts with a faster running time and a lower memory requirement.


The efficacy of a 9-month treadmill walking program on the exercise capacity and weight reduction for adolescents with severe autism.
This study evaluated the efficacy of a 9-month treadmill walking (TW) program on exercise capacity and body mass index (BMI) for adolescents with severe autism. Ten youth residing in a residential/school treatment facility were assigned to either a supplemental treadmill walking (TW) or control group. Both groups continued to participate in their regular physical education curriculum. Monthly records were maintained for the following: (a) TW progression in frequency, duration, speed and elevation; (b) caloric expenditure; and (c) BMI. The TW program resulted in significant increases in mean monthly TW frequency, speed, elevation, and calories expended coupled with a reduction in BMI.


Cortical visual dysfunction in children: a clinical study.
Damage to the cerebral cortex was responsible for impairment in vision in 90 of 130 consecutive children referred to the Vision Assessment Clinic in Glasgow. Cortical blindness was seen in 16 children. Only 2 were mobile, but both showed evidence of navigational blind-sight. Cortical visual impairment, in which it was possible to estimate visual acuity but generalised severe brain damage precluded estimation of cognitive visual function, was observed in 9 children. Complex disorders of cognitive vision were seen in 20 children. These could be divided into five categories and involved impairment of: (1) recognition, (2) orientation, (3) depth perception, (4) perception of movement and (5) simultaneous perception. These disorders were observed in a variety of combinations. The remaining children showed evidence of reduced visual acuity and/ or visual field loss, but without detectable disorders of congnitive visual function. Early recognition of disorders of cognitive vision is required if active training and remediation are to be implemented.


Length-tension characteristics of bovine tracheobronchial lymphatic smooth muscle.
Current information regarding the physiology of lymphatic smooth muscle is derived from experiments on mesenteric and thoracic duct lymph trunks. We hypothesized that tracheobronchial lymphatics share many of the same properties possessed by the mesenteric lymphatics, and examined the passive and active length-tension characteristics of the two. Fresh isolated lymph vessel rings were prepared from bovine mesenteric and tracheobronchial lymphatic collectors, mounted in organ baths, and connected to force-displacement transducers. Isometric contractions were induced by exposure to 65mM KCl-substituted perfusate after intermittent ring length changes. Active tension was calculated. Optimal vessel length was greater in tracheobronchial vessel rings, averaging 4.9 +/- 0.4mm vs 2.8 +/- 0.3mm in mesenteric rings (p < 0.001). Optimal resting tension and ATmax were similar for both truncal types, measuring 738 +/- 95mg and 2379 +/- 289mg in tracheobronchial vessel rings, and 625 +/- 108mg and 2501 +/- 320mg in mesenteric vessel rings, respectively. Stress developed at L(o) (optimal length) was similar for tracheobronchial (35.4 +/- 4.3mN mm-2) and mesenteric (26 +/- 4.3mN mm-2) lymphatics (P = N.S.). The data demonstrate that tracheobronchial lymph vessels are similar to mesenteric lymph vessels in their ability to generate significant stress, and suggest that these lymphatics participate in the regulation of lymph flow.


Secretion of inorganic phosphate in the rat nephron.
1. The existence of tubular secretion of inorganic phosphate (Pi) in the mammalian kidney has been investigated by studying the renal response of rats infused with sodium phosphate by three different techniques. 2. Clearance studies indicate that, in anaesthetized rats, the net tubular reabsorption decreases markedly in response to Pi infusion. In conscious rats, the clearance of Pi slightly exceeded that of inulin at high plasma Pi concentration. 3. Free-flow micropuncture in control rats showed a net tubular reabsorption of Pi along the proximal tubule, and probably between the end of the distal tubule and the ureteral urine. In phosphate-loaded rats, whether receiving parathyroid hormone or not, an apparent net secretion of Pi was observed between the end of the distal tubule and the reteral urine. In the phosphate-loaded group receiving parthyroid hormone, net secretion was also observed very early in the proximal tubule followed by a predominant reabsorption along this segment. Thus the early proximal tubule and probably also the terminal nephron can be the site of either net reabsorption or net secretion. 4. Microperfusions of proximal tubules show a fall in the specific radioactivity of the perfused radioactive Pi solution, indicating entry of Pi into the lumen.


Exploring benzimidazole resistance in Haemonchus contortus by next generation sequencing and droplet digital PCR.
Anthelmintic resistance in gastrointestinal nematode (GIN) parasites of grazing ruminants is on the rise in countries across the world. Haemonchus contortus is one of most frequently encountered drug-resistant GINs in small ruminants. This blood-sucking abomasal nematode contributes to massive treatment costs and poses a serious threat to farm animal health. To prevent the establishment of resistant strains of this parasite, up-to-date molecular techniques need to be proposed which would allow for quick, cheap and accurate identification of individuals infected with resistant worms. The effort has been made in the previous decade, with the development of the pyrosequencing method to detect resistance-predicting alleles. Here we propose a novel droplet digital PCR (ddPCR) assay for rapid and precise identification of H. contortus strains as being resistant or susceptible to benzimidazole drugs based on the presence or absence of the most common resistance-conferring mutation F200Y (TAC) in the β tubulin isotype 1 gene. The newly developed ddPCR assay was first optimized and validated utilizing DNA templates from single-worm samples, which were previously sequenced using the next generation PacBio RSII Sequencing (NGS) platform. Subsequent NGS results for faecal larval cultures were then used as a reference to compare the obtained values for fractional abundances of the resistance-determining mutant allele between ddPCR and NGS techniques in each sample. Both methods managed to produce highly similar results and ddPCR proved to be a reliable tool which, when utilized at full capacity, can be used to create a powerful mutation detection and quantification assay.


Treatment of nasopharyngeal carcinoma: stereotactic radiosurgical boost following fractionated radiotherapy.
Treatment of patients with nasopharyngeal carcinoma (NPC) using external beam radiation therapy (XRT) alone results in significant local recurrence. To improve local control, stereotactic radiosurgery (SRS) was used to boost radiation to the primary tumor site following XRT in 23 patients with NPC. SRS was delivered utilizing a frame-based linear accelerator as a boost (range 7-15 Gy, median 12 Gy) following XRT (range 64.8- 70 Gy, median 66 Gy). In all 23 patients (100%) receiving SRS following XRT local control was achieved at a mean follow-up of 21 months (range 2-64 months). There have been no complications of treatment caused by SRS. However, 8 patients (35%) have subsequently developed regional or distant metastases. SRS boost following XRT provides excellent local control in NPC and should be considered for patients with skull base involvement.


Nucleation mechanisms and speciation of metal oxide clusters.
The self-assembly mechanisms of polyoxometalates (POMs) are still a matter of discussion owing to the difficult task of identifying all the chemical species and reactions involved. We present a new computational methodology that identifies the reaction mechanism for the formation of metal-oxide clusters and provides a speciation model from first-principles and in an automated manner. As a first example, we apply our method to the formation of octamolybdate. In our model, we include variables such as pH, temperature and ionic force because they have a determining effect on driving the reaction to a specific product. Making use of graphs, we set up and solved 2.8 × 105 multi-species chemical equilibrium (MSCE) non-linear equations and found which set of reactions fitted best with the experimental data available. The agreement between computed and experimental speciation diagrams is excellent. Furthermore, we discovered a strong linear dependence between DFT and empirical formation constants, which opens the door for a systematic rescaling.


Right anterior temporal lobe dysfunction underlies theory of mind impairments in semantic dementia.
Semantic dementia is a progressive neurodegenerative disorder characterized by the amodal and profound loss of semantic knowledge attributable to the degeneration of the left anterior temporal lobe. Although traditionally conceptualized as a language disorder, patients with semantic dementia display significant alterations in behaviour and socioemotional functioning. Recent evidence points to an impaired capacity for theory of mind in predominantly left-lateralized cases of semantic dementia; however, it remains unclear to what extent semantic impairments contribute to these deficits. Further the neuroanatomical signature of such disturbance remains unknown. Here, we sought to determine the neural correlates of theory of mind performance in patients with left predominant semantic dementia (n=11), in contrast with disease-matched cases with behavioural-variant frontotemporal dementia (n=10) and Alzheimer's disease (n=10), and healthy older individuals (n=14) as control participants. Participants completed a simple cartoons task, in which they were required to describe physical and theory of mind scenarios. Irrespective of subscale, patients with semantic dementia exhibited marked impairments relative to control subjects; however, only theory of mind deficits persisted when we covaried for semantic comprehension. Voxel-based morphometry analyses revealed that atrophy in right anterior temporal lobe structures, including the right temporal fusiform cortex, right inferior temporal gyrus, bilateral temporal poles and amygdalae, correlated significantly with theory of mind impairments in the semantic dementia group. Our results point to the marked disruption of cognitive functions beyond the language domain in semantic dementia, not exclusively attributable to semantic processing impairments. The significant involvement of right anterior temporal structures suggests that with disease evolution, the encroachment of pathology into the contralateral hemisphere heralds the onset of social cognitive deficits in this syndrome.


Common variants at the CHEK2 gene locus and risk of epithelial ovarian cancer.
Genome-wide association studies have identified 20 genomic regions associated with risk of epithelial ovarian cancer (EOC), but many additional risk variants may exist. Here, we evaluated associations between common genetic variants [single nucleotide polymorphisms (SNPs) and indels] in DNA repair genes and EOC risk. We genotyped 2896 common variants at 143 gene loci in DNA samples from 15 397 patients with invasive EOC and controls. We found evidence of associations with EOC risk for variants at FANCA, EXO1, E2F4, E2F2, CREB5 and CHEK2 genes (P ≤ 0.001). The strongest risk association was for CHEK2 SNP rs17507066 with serous EOC (P = 4.74 x 10(-7)). Additional genotyping and imputation of genotypes from the 1000 genomes project identified a slightly more significant association for CHEK2 SNP rs6005807 (r (2) with rs17507066 = 0.84, odds ratio (OR) 1.17, 95% CI 1.11-1.24, P = 1.1×10(-7)). We identified 293 variants in the region with likelihood ratios of less than 1:100 for representing the causal variant. Functional annotation identified 25 candidate SNPs that alter transcription factor binding sites within regulatory elements active in EOC precursor tissues. In The Cancer Genome Atlas dataset, CHEK2 gene expression was significantly higher in primary EOCs compared to normal fallopian tube tissues (P = 3.72×10(-8)). We also identified an association between genotypes of the candidate causal SNP rs12166475 (r (2) = 0.99 with rs6005807) and CHEK2 expression (P = 2.70×10(-8)). These data suggest that common variants at 22q12.1 are associated with risk of serous EOC and CHEK2 as a plausible target susceptibility gene.


Incidence and mortality of acute renal failure in Medicare beneficiaries, 1992 to 2001.
This study's objective was to determine the incidence and mortality of acute renal failure (ARF) in Medicare beneficiaries. Data were from hospitalized Medicare beneficiaries (5,403,015 discharges) between 1992 and 2001 from the 5% sample of Medicare claims. For 1992 to 2001, the overall incidence rate of ARF was 23.8 cases per 1000 discharges, with rates increasing by approximately 11% per year. Older age, male gender, and black race were strongly associated (P < 0.0001) with ARF. The overall in-hospital death rate was 4.6% in discharges without ARF, 15.2% in discharges with ARF coded as the principal diagnosis, and 32.6% in discharges with ARF as a secondary diagnosis. In-hospital death rates were 32.9% in discharges with ARF that required renal dialysis and 27.5% in those with ARF that did not require dialysis. Death within 90 d after hospital admission was 13.1% in discharges without ARF, 34.5% in discharges with ARF coded as the principal diagnosis, and 48.6% in discharges with ARF as a secondary diagnosis. Discharges with ARF were more (P < 0.0001) likely to have intensive care and other acute organ dysfunction than those without ARF. For discharges both with and without ARF, rates for death within 90 d after hospital admission showed a declining trend. In conclusion, the incidence rate of ARF in Medicare beneficiaries has been increasing. Those of older age, male gender, and black race are more likely to have ARF. These data show ARF to be a major contributor to morbidity and mortality in hospitalized patients.


Molecular methods to study transcriptional regulation of Clostridium difficile toxin genes.
Toxin A (TcdA) and Toxin B (TcdB) are the major virulence factors that contribute to the pathogenesis of Clostridium difficile-associated diarrhoea (CDAD). These enterotoxins act by glucosylation of members of the Rho protein family of small GTP-binding proteins. This leads to the disorganization of the host cell actin cytoskeleton (cytopathic effect) and apoptosis (cytotoxic effect). Due to their glucosyltransferase activity, they are referred as "clostridial glucosylating toxins". The severe form of CDAD has been recently correlated to the levels of toxin production. This reinforces the idea that regulation of toxin production is an important part of the C. difficile infection. Genes encoding TcdA (tcdA) and TcdB (tcdB) are present in a pathogenicity locus (PaLoc) that also includes three accessory genes: tcdR, tcdE and tcdC. TcdR is an alternative RNA polymerase sigma factor that positively regulates toxin gene transcription as well as its own. TcdE has high homologies with bacteriophage holin proteins. TcdC negatively regulates toxin synthesis by interfering with the RNA polymerase formed with TcdR. Therefore, TcdR and TcdC constitute specific regulators of toxin gene transcription thereby tightly regulating toxin synthesis. In addition a variety of environmental signals, such as the presence of carbon sources or amino acids in the growth medium, and temperature also regulate toxin synthesis.


Mental disorders among college students in the World Health Organization World Mental Health Surveys.
Although mental disorders are significant predictors of educational attainment throughout the entire educational career, most research on mental disorders among students has focused on the primary and secondary school years. The World Health Organization World Mental Health Surveys were used to examine the associations of mental disorders with college entry and attrition by comparing college students (n = 1572) and non-students in the same age range (18-22 years; n = 4178), including non-students who recently left college without graduating (n = 702) based on surveys in 21 countries (four low/lower-middle income, five upper-middle-income, one lower-middle or upper-middle at the times of two different surveys, and 11 high income). Lifetime and 12-month prevalence and age-of-onset of DSM-IV anxiety, mood, behavioral and substance disorders were assessed with the Composite International Diagnostic Interview (CIDI). One-fifth (20.3%) of college students had 12-month DSM-IV/CIDI disorders; 83.1% of these cases had pre-matriculation onsets. Disorders with pre-matriculation onsets were more important than those with post-matriculation onsets in predicting subsequent college attrition, with substance disorders and, among women, major depression the most important such disorders. Only 16.4% of students with 12-month disorders received any 12-month healthcare treatment for their mental disorders. Mental disorders are common among college students, have onsets that mostly occur prior to college entry, in the case of pre-matriculation disorders are associated with college attrition, and are typically untreated. Detection and effective treatment of these disorders early in the college career might reduce attrition and improve educational and psychosocial functioning.


MCM-22: A Molecular Sieve with Two Independent Multidimensional Channel Systems.
The molecular sieve MCM-22 contains structural features previously unobserved in this class of materials. Its framework topology, derived from high-resolution electron micrographs and refined with synchrotron x-ray diffraction powder data, contains two independent pore systems, both of which are accessed through rings composed of ten tetrahedral (T) atoms (such as Si, Al, and B). One of these pore systems is defined by two-dimensional, sinusoidal channels. The other consists of large supercages whose inner free diameter, 7.1 angstroms, is defined by 12 T-O species (12-rings) and whose inner height is 18.2 angstroms. These coexisting pore systems may provide opportunities for a wide variety of catalytic applications in the petrochemical and refining industries. Another structural feature is an unusual -T-O-T- chain that passes through the center of a modified dodecasil-1H [4(3)5(6)6(3)] cage.


Antigenic characterization and cytolocalization of P35, the major Mycoplasma penetrans antigen.
Mycoplasma penetrans is a mycoplasma with unique morphology, recently identified in urine samples collected from HIV-infected patients. This mycoplasma has been found to be statistically associated with HIV infection, and to be cytopathic in vitro. The dominant antigen recognized during natural and experimental infections is an abundant lipoprotein, P35, which, upon extraction, segregates in the Triton X-114 detergent phase. It is used as the basis of M. penetrans-specific serological assays. Although mycoplasma lipoproteins, including M. penetrans P35, are the main antigens recognized by the host humoral immune response, very little is known about the nature of the epitopes involved. Immunoelectron microscopy revealed that all P35 is exposed at the cell surface and is distributed all over the membrane. P35 linear B-epitopes were mapped by an ELISA approach based on a set of overlapping peptides covering the entire mature polypeptide. The immunoreactivity of the peptides was first tested with sera from immunized animals. The dominant B-epitopes were found at the C- and N-terminal regions, in partial agreement with algorithmic predictions. Patient sera were evaluated with the same assay. Only some reacted with linear epitopes whereas others did not, indicating the importance of P35 nonsequential epitopes. Statistical analysis of the results allowed the definition of a set of peptides which were clearly immunodominant. Finally, the P35-encoding gene was modified by in vitro mutagenesis to allow the production and purification of a recombinant protein (rP35delta0) in Escherichia coil. The antigenicity of rP35delta0 was tested by Western blotting and compared to that of another recombinant product, rP35delta3, a truncated P35 polypeptide. Although rP35delta0 reacted with the M. penetrans-seropositive patient sera tested, rP35delta3 was only immunoreactive with one of six sera. This result confirmed that P35-nonsequential epitopes dominate during M. penetrans infection. Our results have important implications for the understanding of lipoprotein antigenicity during mycoplasma infections. In addition, the P35-derived immunodominant synthetic peptides defined in this study, as well as the purified rP35delta0, provide the antigenic material for the necessary improvement of M. penetrans serological assays.


Melatonin secretion in the Mashona mole-rat, Cryptomys darlingi--influence of light on rhythmicity.
The hormone melatonin is synthesised and secreted from the pineal gland in darkness and triggers the daily and seasonal timing of various physiological and behavioural processes. The Mashona mole-rat, Cryptomys darlingi, lives in subterranean burrows that are completely sealed and is therefore rarely, if ever, exposed to light under natural conditions. Hence, this species is of particular interest for studies on rhythms of melatonin secretion. We investigated how plasma melatonin concentrations of the Mashona mole-rat responded to exposure to a long-term standard photoperiod of 12 h light, 12 h dark (12:12 LD), constant light (LL) and constant dark (DD). In addition, we examined whether plasma melatonin concentration was coupled to locomotor activity. Mashona mole-rats displayed rhythms of plasma melatonin concentration that appeared entrained to the standard LD photoperiod, suggesting that the mole-rat is capable of perceiving and entraining to this photic zeitgeber. Furthermore, under chronic constant lighting conditions (DD, LL), circadian rhythms in plasma melatonin concentration were observed, suggesting the possible existence of an endogenous rhythm. Light suppressed melatonin secretion, but constant light did not abolish the rhythm of plasma melatonin concentration. Between active and non-active animals, no difference in plasma melatonin concentration was found for any of the sequential photoperiods (LD1 DD, LD2, LL), tentatively suggesting that the rhythm of melatonin secretion is uncoupled from that of locomotor activity.


HLA-DRB1*0402 (DW10) transgene protects collagen-induced arthritis-susceptible H2Aq and DRB1*0401 (DW4) transgenic mice from arthritis.
To investigate the role of HLA-DR4 in predisposition to arthritis, we generated transgenic mice carrying DRB1*0401 and DRB1*0402 genes. We have previously shown that DRB1*0401 molecule renders B10.RQB3 (H2A(q)) mice susceptible to porcine and human type II collagen-induced arthritis. We report that the introduction of DRB1*0402 transgene does not lead to development of arthritis in mice when they are immunized with porcine and human type II collagen. In addition, DRB1*0402 protects B10.RQB3 mice against developing arthritis with bovine type II collagen. These data show that DRB1 can modulate the disease mediated by A(q). In vivo depletion of DRB1*0402 did not lead to induction of collagen-induced arthritis in transgenic mice. In vitro cytokine analysis shows that mice protected from collagen-induced arthritis produce lower amounts of Th1 and higher levels of Th2 type cytokines upon immunization with type II collagen. Protection of mice was also related to higher apoptosis in DW10 mice as indicated by higher amounts of BclII in response to type II collagen. On the basis of our observations in HLA transgenic mice, we hypothesize that DRB1 polymorphism can modulate disease by shaping the T cell repertoire in thymus and select autoreactive T cells.


Annular pancreas in children: a decade of experience.
Annular pancreas is an uncommon cause of duodenal obstruction in children. In this study, the clinical, radiological, and prognostic findings related to this disorder over a 12-year review period were analyzed. A retrospective review of 22 patients with annular pancreas who were treated with surgical repair between April 1998 and February 2010 was performed at two different pediatric surgical units. Presenting symptoms, associated anomalies, radiological findings, the type of surgery performed, postoperative outcomes, and complications were analyzed. Twenty-two patients were identified. Thirteen of the 22 patients (59.1%) were born prematurely, 11 patients (50%) had low birth weight, 2 patients (9.1%) had very low birth weight and 1 patient (4.5%) had extremely low birth weight. The mean birth weight was 2285.23±675.12 g. (970-3300). All patients presented with vomiting, which was bilious in nine (40.9%). Nine patients (40.9%) had chromosomal anomalies. Corrective surgery consisted of duodenoduodenostomy in 9 patients (40.9 %), duodenojejunostomy in 9 patients (40.9%), and gastrojejunostomy in 4 patients (18.1%). Fourteen of the 22 patients have survived (63.6%). The causes of death were combinations of sepsis, pneumonia, brain hemorrhage, and cardiac anomaly. Infants with annular pancreas associated with duodenal obstruction were often born prematurely and/or had low birth weights; many had cardiovascular anomalies. Annular pancreas associated with duodenal obstruction correlated strongly with the trisomy 21 karyotype among the chromosomal anomalies, as did duodenal atresia. The oral feeding tolerance time was nearly the same for all patients regardless of the surgical procedure used.


Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d.
Aromatic amino acids play a critical role in protein-glycan interactions. Clusters of surface aromatic residues and their features may therefore be useful in distinguishing glycan-binding sites as well as predicting novel glycan-binding proteins. In this work, a structural bioinformatics approach was used to screen the Protein Data Bank (PDB) for coplanar aromatic motifs similar to those found in known glycan-binding proteins. The proteins identified in the screen were significantly associated with carbohydrate-related functions according to gene ontology (GO) enrichment analysis, and predicted motifs were found frequently within novel folds and glycan-binding sites not included in the training set. In addition to numerous binding sites predicted in structural genomics proteins of unknown function, one novel prediction was a surface motif (W34/W36/W192) in the tobacco pathogenesis-related protein, PR-5d. Phylogenetic analysis revealed that the surface motif is exclusive to a subfamily of PR-5 proteins from the Solanaceae family of plants, and is absent completely in more distant homologs. To confirm PR-5d's insoluble-polysaccharide binding activity, a cellulose-pulldown assay of tobacco proteins was performed and PR-5d was identified in the cellulose-binding fraction by mass spectrometry. Based on the combined results, we propose that the putative binding site in PR-5d may be an evolutionary adaptation of Solanaceae plants including potato, tomato, and tobacco, towards defense against cellulose-containing pathogens such as species of the deadly oomycete genus, Phytophthora. More generally, the results demonstrate that coplanar aromatic clusters on protein surfaces are a structural signature of glycan-binding proteins, and can be used to computationally predict novel glycan-binding proteins from 3 D structure.


Setting research priorities to achieve long-term health targets in Iran.
In 2015, it was estimated that the burden of disease in Iran comprised of 19 million disability-adjusted life years (DALYs), 74% of which were due to non-communicable diseases (NCDs). The observed leading causes of death were cardiovascular diseases (41.9%), neoplasms (14.9%), and road traffic injuries (7.4%). Even so, the health research investment in Iran continues to remain limited. This study aims to identify national health research priorities in Iran for the next five years to assist the efficient use of resources towards achieving the long-term health targets. Adapting the Child Health and Nutrition Research Initiative (CHNRI) method, this study engaged 48 prominent Iranian academic leaders in the areas related to Iran's long-term health targets, a group of research funders and policy makers, and 68 stakeholders from the wider society. 128 proposed research questions were scored independently using a set of five criteria: feasibility, impact on health, impact on economy, capacity building, and equity. The top-10 priorities were focused on the research questions relating to: health insurance system reforms to improve equity; integration of NCDs prevention strategy into primary health care; cost-effective population-level interventions for NCDs and road traffic injury prevention; tailoring medical qualifications; epidemiological assessment of NCDs by geographic areas; equality in the distribution of health resources and services; current and future common health problems in Iran's elderly and strategies to reduce their economic burden; the status of antibiotic resistance in Iran and strategies to promote rational use of antibiotics; the health impacts of water crisis; and research to replace the physician-centered health system with a team-based one. These findings highlight consensus amongst various prominent Iranian researchers and stakeholders over the research priorities that require investment to generate information and knowledge relevant to the national health targets and policies. The exercise should assist in addressing the knowledge gaps to support both the National General Health Policies by 2025 and the health targets of the United Nations' Sustainable Development Goals by 2030.