The role and robustness of the Gini coefficient as an unbiased tool for the selection of Gini genes for normalising expression profiling data.
We recently introduced the Gini coefficient (GC) for assessing the expression variation of a particular gene in a dataset, as a means of selecting improved reference genes over the cohort ('housekeeping genes') typically used for normalisation in expression profiling studies. Those genes (transcripts) that we determined to be useable as reference genes differed greatly from previous suggestions based on hypothesis-driven approaches. A limitation of this initial study is that a single (albeit large) dataset was employed for both tissues and cell lines. We here extend this analysis to encompass seven other large datasets. Although their absolute values differ a little, the Gini values and median expression levels of the various genes are well correlated with each other between the various cell line datasets, implying that our original choice of the more ubiquitously expressed low-Gini-coefficient genes was indeed sound. In tissues, the Gini values and median expression levels of genes showed a greater variation, with the GC of genes changing with the number and types of tissues in the data sets. In all data sets, regardless of whether this was derived from tissues or cell lines, we also show that the GC is a robust measure of gene expression stability. Using the GC as a measure of expression stability we illustrate its utility to find tissue- and cell line-optimised housekeeping genes without any prior bias, that again include only a small number of previously reported housekeeping genes. We also independently confirmed this experimentally using RT-qPCR with 40 candidate GC genes in a panel of 10 cell lines. These were termed the Gini Genes. In many cases, the variation in the expression levels of classical reference genes is really quite huge (e.g. 44 fold for GAPDH in one data set), suggesting that the cure (of using them as normalising genes) may in some cases be worse than the disease (of not doing so). We recommend the present data-driven approach for the selection of reference genes by using the easy-to-calculate and robust GC.


The role of postoperative antibiotic duration on surgical site infection after lumbar surgery.
Despite a general consensus regarding the administration of preoperative antibiotics, poorly defined comparison groups and underpowered studies prevent clear guidelines for postoperative antibiotics. Utilizing a data set tailored specifically to spine surgery outcomes, in this clinical study the authors aimed to determine whether there is a role for postoperative antibiotics in the prevention of surgical site infection (SSI). The Michigan Spine Surgery Improvement Collaborative registry was queried for all lumbar operations performed for degenerative spinal pathologies over a 5-year period from 2014 to 2019. Preoperative prophylactic antibiotics were administered for all surgical procedures. The study population was divided into three cohorts: no postoperative antibiotics, postoperative antibiotics ≤ 24 hours, and postoperative antibiotics > 24 hours. This categorization was intended to determine 1) whether postoperative antibiotics are helpful and 2) the appropriate duration of postoperative antibiotics. First, multivariable analysis with generalized estimating equations (GEEs) was used to determine the association between antibiotic duration and all-type SSI with adjusted odds ratios; second, a three-tiered outcome-no SSI, superficial SSI, and deep SSI-was calculated with multivariable multinomial logistical GEE analysis. Among 37,161 patients, the postoperative antibiotics > 24 hours cohort had more men with older average age, greater body mass index, and greater comorbidity burden. The postoperative antibiotics > 24 hours cohort had a 3% rate of SSI, which was significantly higher than the 2% rate of SSI of the other two cohorts (p = 0.004). On multivariable GEE analysis, neither postoperative antibiotics > 24 hours nor postoperative antibiotics ≤ 24 hours, as compared with no postoperative antibiotics, was associated with a lower rate of all-type postoperative SSIs. On multivariable multinomial logistical GEE analysis, neither postoperative antibiotics ≤ 24 hours nor postoperative antibiotics > 24 hours was associated with rate of superficial SSI, as compared with no antibiotic use at all. The odds of deep SSI decreased by 45% with postoperative antibiotics ≤ 24 hours (p = 0.002) and by 40% with postoperative antibiotics > 24 hours (p = 0.008). Although the incidence of all-type SSI was highest in the antibiotics > 24 hours cohort, which also had the highest proportions of risk factors, duration of antibiotics failed to predict all-type SSI. On multinomial subanalysis, administration of postoperative antibiotics for both ≤ 24 hours and > 24 hours was associated with decreased risk of only deep SSI but not superficial SSI. Spine surgeons can safely consider antibiotics for 24 hours, which is equally as effective as long-term administration for prophylaxis against deep SSI.


A multilayered synthetic human elastin/polycaprolactone hybrid vascular graft with tailored mechanical properties.
Small-diameter synthetic vascular graft materials fail to match the patency of human tissue conduits used in vascular bypass surgery. The foreign surface retards endothelialization and is highly thrombogenic, while the mismatch in mechanical properties induces intimal hyperplasia. Using recombinant human tropoelastin, we have developed a synthetic vascular conduit for small-diameter applications. We show that tropoelastin enhances endothelial cell attachment (threefold vs. control) and proliferation by 54.7 ± 1.1% (3 days vs. control). Tropoelastin, when presented as a monomer and when cross-linked into synthetic elastin for biomaterials applications, had low thrombogenicity. Activation of the intrinsic pathway of coagulation, measured by plasma clotting time, was reduced for tropoelastin (60.4 ± 8.2% vs. control). Platelet attachment was also reduced compared to collagen. Reductions in platelet interactions were mirrored on cross-linked synthetic elastin scaffolds. Tropoelastin was subsequently incorporated into a synthetic elastin/polycaprolactone conduit with mechanical properties optimized to mimic the human internal mammary artery, including permeability, compliance, elastic modulus and burst pressure. Further, this multilayered conduit presented a synthetic elastin internal lamina to circulating blood and demonstrated suturability and mechanical durability in a small scale rabbit carotid interposition model.


Single-Walled Carbon Nanotubes Inhibit the Cytochrome P450 Enzyme, CYP3A4.
We report a detailed computational and experimental study of the interaction of single-walled carbon nanotubes (SWCNTs) with the drug-metabolizing cytochrome P450 enzyme, CYP3A4. Dose-dependent inhibition of CYP3A4-mediated conversion of the model compound, testosterone, to its major metabolite, 6β-hydroxy testosterone was noted. Evidence for a direct interaction between SWCNTs and CYP3A4 was also provided. The inhibition of enzyme activity was alleviated when SWCNTs were pre-coated with bovine serum albumin. Furthermore, covalent functionalization of SWCNTs with polyethylene glycol (PEG) chains mitigated the inhibition of CYP3A4 enzymatic activity. Molecular dynamics simulations suggested that inhibition of the catalytic activity of CYP3A4 is mainly due to blocking of the exit channel for substrates/products through a complex binding mechanism. This work suggests that SWCNTs could interfere with metabolism of drugs and other xenobiotics and provides a molecular mechanism for this toxicity. Our study also suggests means to reduce this toxicity, eg., by surface modification.


Upper-thoracic versus lower-thoracic upper instrumented vertebra in adult spinal deformity patients undergoing fusion to the pelvis: surgical decision-making and patient outcomes.
Optimal patient selection for upper-thoracic (UT) versus lower-thoracic (LT) fusion during adult spinal deformity (ASD) correction is challenging. Radiographic and clinical outcomes following UT versus LT fusion remain incompletely understood. The purposes of this study were: 1) to evaluate demographic, radiographic, and surgical characteristics associated with choice of UT versus LT fusion endpoint; and 2) to evaluate differences in radiographic, clinical, and health-related quality of life (HRQOL) outcomes following UT versus LT fusion for ASD. Retrospective review of a prospectively collected multicenter ASD database was performed. Patients with ASD who underwent fusion from the sacrum/ilium to the LT (T9-L1) or UT (T1-6) spine were compared for demographic, radiographic, and surgical characteristics. Outcomes including proximal junctional kyphosis (PJK), reoperation, rod fracture, pseudarthrosis, overall complications, 2-year change in alignment parameters, and 2-year HRQOL metrics (Lumbar Stiffness Disability Index, Scoliosis Research Society-22r questionnaire, Oswestry Disability Index) were compared after controlling for confounding factors via multivariate analysis. Three hundred three patients (169 LT, 134 UT) were evaluated. Independent predictors of UT fusion included greater thoracic kyphosis (odds ratio [OR] 0.97 per degree, p = 0.0098), greater coronal Cobb angle (OR 1.06 per degree, p < 0.0001), and performance of a 3-column osteotomy (3-CO; OR 2.39, p = 0.0351). While associated with longer operative times (ratio 1.13, p < 0.0001) and greater estimated blood loss (ratio 1.31, p = 0.0018), UT fusions resulted in greater sagittal vertical axis improvement (-59.5 vs -41.0 mm, p = 0.0035) and lower PJK rates (OR 0.49, p = 0.0457). No significant differences in postoperative HRQOL measures, reoperation, or overall complication rates were detected between groups (all p > 0.1). Greater deformity and need for 3-CO increased the likelihood of UT fusion. Despite longer operative times and greater blood loss, UT fusions resulted in better sagittal correction and lower 2-year PJK rates following surgery for ASD. While continued surveillance is necessary, this information may inform patient counseling and surgical decision-making.


The Active Inference Approach to Ecological Perception: General Information Dynamics for Natural and Artificial Embodied Cognition.
The emerging neurocomputational vision of humans as embodied, ecologically embedded, social agents-who shape and are shaped by their environment-offers a golden opportunity to revisit and revise ideas about the physical and information-theoretic underpinnings of life, mind, and consciousness itself. In particular, the active inference framework (AIF) makes it possible to bridge connections from computational neuroscience and robotics/AI to ecological psychology and phenomenology, revealing common underpinnings and overcoming key limitations. AIF opposes the mechanistic to the reductive, while staying fully grounded in a naturalistic and information-theoretic foundation, using the principle of free energy minimization. The latter provides a theoretical basis for a unified treatment of particles, organisms, and interactive machines, spanning from the inorganic to organic, non-life to life, and natural to artificial agents. We provide a brief introduction to AIF, then explore its implications for evolutionary theory, ecological psychology, embodied phenomenology, and robotics/AI research. We conclude the paper by considering implications for machine consciousness.


Scent of danger: floc formation by a freshwater bacterium is induced by supernatants from a predator-prey coculture.
We investigated predator-prey interactions in a model system consisting of the bacterivorous flagellate Poterioochromonas sp. strain DS and the freshwater bacterium Sphingobium sp. strain Z007. This bacterial strain tends to form a subpopulation of grazing-resistant microscopic flocs, presumably by aggregation. Enhanced formation of such flocs could be demonstrated in static batch culture experiments in the presence of the predator. The ratio of aggregates to single cells reached >0.1 after 120 h of incubation in an oligotrophic growth medium. The inoculation of bacteria into supernatants from cocultures of bacteria and flagellates (grown in oligotrophic or in rich media) also resulted in a substantially higher level of floc formation than that in supernatants from bacterial monocultures only. After separation of supernatants on a C(18) cartridge, the aggregate-inducing activity could be assigned to the 50% aqueous methanolic fraction, and further separation of this bioactive fraction could be achieved by high-pressure liquid chromatography. These results strongly suggest the involvement of one or several chemical factors in the induction of floc formation by Sphingobium sp. strain Z007 that are possibly released into the surrounding medium by flagellate grazing.


DNA methylation analysis of bone marrow cells at diagnosis of acute lymphoblastic leukemia and at remission.
To detect genes with CpG sites that display methylation patterns that are characteristic of acute lymphoblastic leukemia (ALL) cells, we compared the methylation patterns of cells taken at diagnosis from 20 patients with pediatric ALL to the methylation patterns in mononuclear cells from bone marrow of the same patients during remission and in non-leukemic control cells from bone marrow or blood. Using a custom-designed assay, we measured the methylation levels of 1,320 CpG sites in regulatory regions of 413 genes that were analyzed because they display allele-specific gene expression (ASE) in ALL cells. The rationale for our selection of CpG sites was that ASE could be the result of allele-specific methylation in the promoter regions of the genes. We found that the ALL cells had methylation profiles that allowed distinction between ALL cells and control cells. Using stringent criteria for calling differential methylation, we identified 28 CpG sites in 24 genes with recurrent differences in their methylation levels between ALL cells and control cells. Twenty of the differentially methylated genes were hypermethylated in the ALL cells, and as many as nine of them (AMICA1, CPNE7, CR1, DBC1, EYA4, LGALS8, RYR3, UQCRFS1, WDR35) have functions in cell signaling and/or apoptosis. The methylation levels of a subset of the genes were consistent with an inverse relationship with the mRNA expression levels in a large number of ALL cells from published data sets, supporting a potential biological effect of the methylation signatures and their application for diagnostic purposes.


A comparison of the Pac-X trans-Pacific Wave Glider data and satellite data (MODIS, Aquarius, TRMM and VIIRS).
Four wave-propelled autonomous vehicles (Wave Gliders) instrumented with a variety of oceanographic and meteorological sensors were launched from San Francisco, CA in November 2011 for a trans-Pacific (Pac-X) voyage to test platform endurance. Two arrived in Australia, one in Dec 2012 and one in February 2013, while the two destined for Japan both ran into technical difficulties and did not arrive at their destination. The gliders were all equipped with sensors to measure temperature, salinity, turbidity, oxygen, and both chlorophyll and oil fluorescence. Here we conduct an initial assessment of the data set, noting necessary quality control steps and instrument utility. We conduct a validation of the Pac-X dataset by comparing the glider data to equivalent, or near-equivalent, satellite measurements. Sea surface temperature and salinity compared well to satellite measurements. Chl fluorescence from the gliders was more poorly correlated, with substantial between glider variability. Both turbidity and oil CDOM sensors were compromised to some degree by interfering processes. The well-known diel cycle in chlorophyll fluorescence was observed suggesting that mapping physiological data over large scales is possible. The gliders captured the Pacific Ocean's major oceanographic features including the increased chlorophyll biomass of the California Current and equatorial upwelling. A comparison of satellite sea surface salinity (Aquarius) and glider-measured salinity revealed thin low salinity lenses in the southwestern Pacific Ocean. One glider survived a direct passage through a tropical cyclone. Two gliders traversed an open ocean phytoplankton bloom; extensive spiking in the chlorophyll fluorescence data is consistent with aggregation and highlights another potential future use for the gliders. On long missions, redundant instrumentation would aid in interpreting unusual data streams, as well as a means to periodically image the sensor heads. Instrument placement is critical to minimize bubble-related problems in the data.


Lack of Marburg Virus Transmission From Experimentally Infected to Susceptible In-Contact Egyptian Fruit Bats.
Egyptian fruit bats (Rousettus aegyptiacus) were inoculated subcutaneously (n = 22) with Marburg virus (MARV). No deaths, overt signs of morbidity, or gross lesions was identified, but microscopic pathological changes were seen in the liver of infected bats. The virus was detected in 15 different tissues and plasma but only sporadically in mucosal swab samples, urine, and fecal samples. Neither seroconversion nor viremia could be demonstrated in any of the in-contact susceptible bats (n = 14) up to 42 days after exposure to infected bats. In bats rechallenged (n = 4) on day 48 after infection, there was no viremia, and the virus could not be isolated from any of the tissues tested. This study confirmed that infection profiles are consistent with MARV replication in a reservoir host but failed to demonstrate MARV transmission through direct physical contact or indirectly via air. Bats develop strong protective immunity after infection with MARV.


The histone chaperone sNASP binds a conserved peptide motif within the globular core of histone H3 through its TPR repeats.
Eukaryotic chromatin is a complex yet dynamic structure, which is regulated in part by the assembly and disassembly of nucleosomes. Key to this process is a group of proteins termed histone chaperones that guide the thermodynamic assembly of nucleosomes by interacting with soluble histones. Here we investigate the interaction between the histone chaperone sNASP and its histone H3 substrate. We find that sNASP binds with nanomolar affinity to a conserved heptapeptide motif in the globular domain of H3, close to the C-terminus. Through functional analysis of sNASP homologues we identified point mutations in surface residues within the TPR domain of sNASP that disrupt H3 peptide interaction, but do not completely disrupt binding to full length H3 in cells, suggesting that sNASP interacts with H3 through additional contacts. Furthermore, chemical shift perturbations from(1)H-(15)N HSQC experiments show that H3 peptide binding maps to the helical groove formed by the stacked TPR motifs of sNASP. Our findings reveal a new mode of interaction between a TPR repeat domain and an evolutionarily conserved peptide motif found in canonical H3 and in all histone H3 variants, including CenpA and have implications for the mechanism of histone chaperoning within the cell.


Serial monitoring of isavuconazole blood levels during prolonged antifungal therapy.
Isavuconazole is the newest triazole antifungal approved for the treatment of invasive aspergillosis (IA) and invasive mucormycosis in adult patients. To characterize the assessment of the blood levels of isavuconazole and their association with efficacy and toxicity. From January 2017 to May 2018, blood samples obtained from patients receiving isavuconazole were analysed for therapeutic drug monitoring. Factors influencing the blood concentrations of isavuconazole, such as weight, length of treatment, route of administration and results of selected liver function tests, were analysed in univariate and multivariate models. The receiver operating characteristic (ROC) curve was analysed to detect the best cut-off for isavuconazole toxicity. A total of 264 isavuconazole blood concentrations in 19 patients were analysed. The median value of isavuconazole concentration in all patients during the first 30 days of therapy was 3.69 mg/L (range 0.64-8.13 mg/L). A linear increase of 0.032 mg/L (range 0.023-0.041 mg/L) for each day of treatment (P = 0.002) was observed. In multivariate analysis the association between the length of treatment and higher levels of isavuconazole (P < 0.001) and higher serum GGT and lower isavuconazole levels (P = 0.001) was confirmed. Adverse events, mainly gastrointestinal, were reported in six patients (31.6%). Based on time-dependent and fixed-time ROC curve analysis, 4.87 mg/L and 5.13 mg/L, respectively, were the identified thresholds for toxicity. Isavuconazole was efficacious and well tolerated. Side effects, mainly gastrointestinal, were associated with prolonged administration and high serum levels.


The ability of synoviocytes to support terminal differentiation of activated B cells may explain plasma cell accumulation in rheumatoid synovium.
To understand the accumulation of plasma cells within RA synovium, the ability of rheumatoid synoviocytes to support the differentiation of B cells into plasma cells was explored. Tonsillar B lymphocytes cultured over confluent monolayers of synoviocytes, secreted threefold more Igs (mainly IgM) than B cells cultured directly on plastic well. More importantly, synoviocytes enhanced by 14-fold the production of Igs (mainly IgG) by B cells costimulated with Staphylococcus aureus Cowan (SAC) particles. IL-10 and, in a lower extent, IL-2 increased Ig secretion in cocultures, and their combination was synergistic. In the presence of SAC, IL-2, and IL-10, synoviocytes increased by 13-884-fold the production of IgG, which reached 0.19 ng/cell per day. RA as well as normal synoviocytes were more potent than other adherent cell lines to support terminal B cell differentiation. Synoviocyte activity involved both a support of B cell survival, and an induction of the terminal differentiation of B cells into mature plasma cells with typical morphology, high levels of intracytoplasmic Igs, and CD20- CD38high surface expression. The present observation should permit the identification of molecules involved in the maturation of B cells into plasma cells, and in their accumulation in rheumatoid synovium.


A different rhythm of life: sleep patterns in the first 4 years of life and associated sociodemographic characteristics in a large Brazilian birth cohort.
Sleep is an important marker of healthy development and has been associated with emotional, behavioral, and cognitive development. There is limited longitudinal data on children's sleep with only a few reports from low- and middle-income countries (LMICs). We investigate sleep parameters and associated sociodemographic characteristics in a population-based longitudinal study in Pelotas, Brazil. Data from the Pelotas 2004 Birth Cohort were used (N = 3842). Infant sleep was collected through maternal report at 3, 12, 24, and 48 months: sleep duration, bed and wake time, nighttime awakenings, co-sleeping and sleep disturbances (24 and 48 months). Compared to children in high-income countries (HICs), children in Brazil showed a substantial shift in rhythms with later bed and wake times by approximately 2 hours. These remain stable throughout the first 4 years of life. This population also shows high levels of co-sleeping which remain stable throughout (49.0-52.2%). Later bedtime was associated with higher maternal education and family income. Higher rates of co-sleeping were seen in families with lower income and maternal education and for children who were breastfed. All other sleep parameters were broadly similar to data previously reported from HICs. The shift in biological rhythms in this representative community sample of children in Brazil challenges our understanding of optimal sleep routine and recommendations.


Is adenosine involved in inhibition of forskolin-stimulated cyclic AMP accumulation by caffeine in rat brain?
Caffeine potently inhibited forskolin-stimulated cyclic AMP accumulation in slices of rat cerebral cortex, with an IC50 of 21 +/- 3 microM. Because caffeine competitively blocks adenosine receptors, we examined whether the action of forskolin involved endogenous adenosine or whether caffeine was acting through some novel mechanism. Inhibition by caffeine was observed at all forskolin concentrations examined, although the degree of inhibition decreased at higher concentrations of forskolin. The effect of caffeine was not blocked by the presence of a phosphodiesterase inhibitor but was mimicked by several other methylxanthines. The most potent of these was 8-(p-sulfophenyl)-theophylline, which does not readily cross cell membranes, arguing for an extracellular site of action. Addition of either adenosine or the adenosine uptake blocker dipyridamole potentiated the forskolin response, suggesting that forskolin and adenosine act synergistically in increasing cyclic AMP accumulation. The nonxanthine adenosine receptor antagonist CGS 15943 potently blocked cyclic AMP responses to forskolin, adenosine, and combinations. 3-Isobutyl-1-methylxanthine potently blocked the response to adenosine but caused little or no inhibition of the response to forskolin. Adenosine deaminase (ADA) was added to eliminate contributions of endogenous adenosine. ADA inhibited the response to both adenosine and forskolin; however, 200 times as much enzyme was necessary to inhibit the forskolin response. Inhibition of added ADA with 2'deoxycoformycin dramatically increased the concentration of ADA required to inhibit the adenosine response, without altering the concentration required to inhibit the forskolin response. These results suggest that forskolin-stimulated cyclic AMP accumulation may be partially dependent on endogenous adenosine but that the inhibition observed with caffeine is not solely due to blockade of adenosine receptors.


Effect of Conservative vs Conventional Oxygen Therapy on Mortality Among Patients in an Intensive Care Unit: The Oxygen-ICU Randomized Clinical Trial.
Despite suggestions of potential harm from unnecessary oxygen therapy, critically ill patients spend substantial periods in a hyperoxemic state. A strategy of controlled arterial oxygenation is thus rational but has not been validated in clinical practice. To assess whether a conservative protocol for oxygen supplementation could improve outcomes in patients admitted to intensive care units (ICUs). Oxygen-ICU was a single-center, open-label, randomized clinical trial conducted from March 2010 to October 2012 that included all adults admitted with an expected length of stay of 72 hours or longer to the medical-surgical ICU of Modena University Hospital, Italy. The originally planned sample size was 660 patients, but the study was stopped early due to difficulties in enrollment after inclusion of 480 patients. Patients were randomly assigned to receive oxygen therapy to maintain Pao2 between 70 and 100 mm Hg or arterial oxyhemoglobin saturation (Spo2) between 94% and 98% (conservative group) or, according to standard ICU practice, to allow Pao2 values up to 150 mm Hg or Spo2 values between 97% and 100% (conventional control group). The primary outcome was ICU mortality. Secondary outcomes included occurrence of new organ failure and infection 48 hours or more after ICU admission. A total of 434 patients (median age, 64 years; 188 [43.3%] women) received conventional (n = 218) or conservative (n = 216) oxygen therapy and were included in the modified intent-to-treat analysis. Daily time-weighted Pao2 averages during the ICU stay were significantly higher (P < .001) in the conventional group (median Pao2, 102 mm Hg [interquartile range, 88-116]) vs the conservative group (median Pao2, 87 mm Hg [interquartile range, 79-97]). Twenty-five patients in the conservative oxygen therapy group (11.6%) and 44 in the conventional oxygen therapy group (20.2%) died during their ICU stay (absolute risk reduction [ARR], 0.086 [95% CI, 0.017-0.150]; relative risk [RR], 0.57 [95% CI, 0.37-0.90]; P = .01). Occurrences were lower in the conservative oxygen therapy group for new shock episode (ARR, 0.068 [95% CI, 0.020-0.120]; RR, 0.35 [95% CI, 0.16-0.75]; P = .006) or liver failure (ARR, 0.046 [95% CI, 0.008-0.088]; RR, 0.29 [95% CI, 0.10-0.82]; P = .02) and new bloodstream infection (ARR, 0.05 [95% CI, 0.00-0.09]; RR, 0.50 [95% CI, 0.25-0.998; P = .049). Among critically ill patients with an ICU length of stay of 72 hours or longer, a conservative protocol for oxygen therapy vs conventional therapy resulted in lower ICU mortality. These preliminary findings were based on unplanned early termination of the trial, and a larger multicenter trial is needed to evaluate the potential benefit of this approach. clinicaltrials.gov Identifier: NCT01319643.


Cytotoxicity of halogenated graphenes.
Graphene and its family of derivatives possess unique and remarkable physicochemical properties which make them valuable materials for applications in many areas like electronics, energy storage and biomedicine. In response to the possibility of its large-scale manufacturing as commercial products in the future, an investigation was conducted to determine the cytotoxicity of one particular family of graphene derivatives, the halogenated graphenes, for the first time. Halogenated graphenes were prepared through thermal exfoliation of graphite oxide in gaseous chlorine, bromine or iodine atmospheres to yield chlorine- (TRGO-Cl), bromine- (TRGO-Br) and iodine-doped graphene (TRGO-I) respectively. 24 h exposure of human lung carcinoma epithelial cells (A549) to the three halogenated graphenes and subsequent cell viability assessments using methylthiazolyldiphenyl-tetrazolium bromide (MTT) and water-soluble tetrazolium salt (WST-8) assays revealed that all the halogenated graphenes examined are rather cytotoxic at the concentrations tested (3.125 μg mL(-1) to 200 μg mL(-1)) and the effects are dose-dependent, with TRGO-Cl reducing the cell viability to as low as 25.7% at the maximum concentration of 200 μg mL(-1). Their levels of cytotoxicity can be arranged in the order of TRGO-Cl > TRGO-Br > TRGO-I, and it is suggested that the amount of halogen present in the graphene material is the determining factor for the observed trend. Control experiments were carried out to test for possible nanomaterial-induced interference as a consequence of reaction between the halogenated graphenes and the viability markers (MTT/WST-8 reagent) or binding of the formazan products under cell-free conditions. The data obtained eliminate the probability of significant influence by these interferents as the change in the normalized percentage of formazan formed is relatively small and thorough washings were performed prior to the viability assessments to reduce the amount of halogenated graphenes that could eventually interact with the MTT/WST-8 assays. More studies need to be carried out in the future to complement the results obtained in this initial study in an attempt to develop a better understanding of the health hazards that the halogenated graphenes pose.


Preventing Childhood Caries: A Review of Recent Behavioral Research.
The etiology of dental caries reflects a complex interplay of biochemical, microbial, genetic, social and physical environmental, and health-influencing behavioral factors. This review updates the literature on the efficacy of behavioral approaches to caries prevention for children up to 18 y of age. Included were studies of behavioral interventions implemented at individual, family, and community levels that assessed results in terms of reductions in caries increments. Only those reports published since 2011 were considered. Outcomes were variable, although motivational interviewing, which involves individuals in decisions about oral health within the context of their respective life circumstances, proved effective in 3 of 4 reported studies, and more definitive trials are underway. Recommendations for future research include examinations of the cost-effectiveness of interventions, as well as work focused on understanding the mechanisms underlying oral health behavior change and variables that may mediate or moderate responses to interventions.


Loss-of-Function Mutations in the Cell-Cycle Control Gene CDKN2A Impact on Glucose Homeostasis in Humans.
At the CDKN2A/B locus, three independent signals for type 2 diabetes risk are located in a noncoding region near CDKN2A. The disease-associated alleles have been implicated in reduced β-cell function, but the underlying mechanism remains elusive. In mice, β-cell-specific loss of Cdkn2a causes hyperplasia, while overexpression leads to diabetes, highlighting CDKN2A as a candidate effector transcript. Rare CDKN2A loss-of-function mutations are a cause of familial melanoma and offer the opportunity to determine the impact of CDKN2A haploinsufficiency on glucose homeostasis in humans. To test the hypothesis that such individuals have improved β-cell function, we performed oral and intravenous glucose tolerance tests on mutation carriers and matched control subjects. Compared with control subjects, carriers displayed increased insulin secretion, impaired insulin sensitivity, and reduced hepatic insulin clearance. These results are consistent with a model whereby CDKN2A loss affects a range of different tissues, including pancreatic β-cells and liver. To test for direct effects of CDKN2A-loss on β-cell function, we performed knockdown in a human β-cell line, EndoC-bH1. This revealed increased insulin secretion independent of proliferation. Overall, we demonstrated that CDKN2A is an important regulator of glucose homeostasis in humans, thus supporting its candidacy as an effector transcript for type 2 diabetes-associated alleles in the region.


Palmitoylethanolamide prevents metabolic alterations and restores leptin sensitivity in ovariectomized rats.
It has been suggested a role of fatty acid ethanolamides in control of feeding behavior. Among these, palmitoylethanolamide (PEA) has not been directly implicated in appetite regulation and weight gain. The aim of this study was to investigate the effect of PEA on food intake and body weight and the interaction between PEA and hypothalamic leptin signaling in ovariectomized rats. Ovariectomy produced hyperphagia and increased weight gain, making it an useful model of mild obesity. Ovariectomized rats were treated with PEA (30 mg/kg sc) for 5 weeks. Then, blood was collected, and hypothalamus and adipose tissue were removed for histological, cellular, and molecular measurements. We showed that PEA caused a reduction of food intake, body weight, and fat mass. The mechanisms underlying PEA effects involved an improvement in hypothalamic leptin signaling, through a raise in signal transducer and activator of transcription 3 phosphorylation. We also reported that PEA reduced AMP-activated protein kinase-α phosphorylation and modulated transcription of anorectic and orexigenic neuropeptides in the hypothalamus. Moreover, PEA increased AMP-activated protein kinase-α phosphorylation and carnitine palmitoyltransferase 1 transcription in adipose tissue, suggesting an increase in ATP-producing catabolic pathway. PEA also polarized adipose tissue macrophages to M2 lean phenotype, associated to a reduction of inflammatory cytokines/adipokines. To demonstrate the direct effect of PEA on leptin sensitivity without interference of adiposity loss, we obtained consistent data in PEA-treated sham-operated animals and in vitro in SH-SY5Y neuroblastoma cell line. Therefore, our data provide a rationale for the therapeutic use of PEA in obese postmenopausal woman.


Risperidone versus other atypical antipsychotics for schizophrenia.
In many countries of the industrialised world second-generation ("atypical") antipsychotics (SGAs) have become the first line drug treatment for people with schizophrenia. The question as to whether and if so how much the effects of the various SGAs differ is a matter of debate. In this review we examined how the efficacy and tolerability of risperidone differs from that of other SGAs. To evaluate the effects of risperidone compared with other atypical antipsychotics for people with schizophrenia and schizophrenia-like psychosis. 1. Electronic searching We searched the Cochrane Schizophrenia Group Trials Register (April 2007) which is based on regular searches of BIOSIS, CENTRAL, CINAHL, EMBASE, MEDLINE and PsycINFO.2. Reference searching We inspected the references of all identified studies for more trials.3. Personal contact We contacted the first author of each included study for missing information.4. Drug companies We contacted the manufacturers of all atypical antipsychotics included for additional data. We included all randomised, blinded trials comparing oral risperidone with oral forms of amisulpride, aripiprazole, clozapine, olanzapine, quetiapine, sertindole, ziprasidone or zotepine in people with schizophrenia or schizophrenia-like psychosis. We extracted data independently. For dichotomous data we calculated risk ratio (RR) and their 95% confidence intervals (CI) on an intention-to-treat basis based on a random-effects model. We calculated numbers needed to treat/harm (NNT/NNH) where appropriate. For continuous data, we calculated mean differences (MD), again based on a random-effects model. The review currently includes 45 blinded RCTs with 7760 participants. The number of RCTs available for each comparison varied: four studies compared risperidone with amisulpride, two with aripiprazole, 11 with clozapine, 23 with olanzapine, eleven with quetiapine, two with sertindole, three with ziprasidone and none with zotepine. Attrition from these studies was high (46.9%), leaving the interpretation of results problematic. Furthermore, 60% were industry sponsored, which can be a source of bias.There were few significant differences in overall acceptability of treatment as measured by leaving the studies early. Risperidone was slightly less acceptable than olanzapine, and slightly more acceptable than ziprasidone in this regard.Risperidone improved the general mental state (PANSS total score) slightly less than olanzapine (15 RCTs, n = 2390, MD 1.94 CI 0.58 to 3.31), but slightly more than quetiapine (9 RCTs, n = 1953, MD -3.09 CI -5.16 to -1.01) and ziprasidone (3 RCTs, n = 1016, MD -3.91 CI -7.55 to -0.27). The comparisons with the other SGA drugs were equivocal. Risperidone was also less efficacious than olanzapine and clozapine in terms of leaving the studies early due to inefficacy, but more efficacious than ziprasidone in the same outcome.Risperidone produced somewhat more extrapyramidal side effects than a number of other SGAs (use of antiparkinson medication versus clozapine 6 RCTs, n = 304, RR 2.57 CI 1.47 to 4.48, NNH 6 CI 33 to 3; versus olanzapine 13 RCTs, n = 2599, RR 1.28 CI 1.06 to 1.55, NNH 17 CI 9 to 100; versus quetiapine 6 RCTs, n = 1715, RR 1.98 CI 1.16 to 3.39, NNH 20 CI 10 to 100; versus ziprasidone 2 RCTs, n = 822, RR 1.42 CI 1.03 to 1.96, NNH not estimable; parkinsonism versus sertindole 1 RCT, n = 321, RR 4.11 CI 1.44 to 11.73, NNH 14 CI 100 to 8). Risperidone also increased prolactin levels clearly more than all comparators, except for amisulpride and sertindole for which no data were available.Other adverse events were less consistently reported, but risperidone may well produce more weight gain and/or associated metabolic problems than amisulpride (weight gain: 3 RCTs, n = 585, MD 0.99 CI 0.37 to 1.61), aripiprazole (cholesterol increase: 1 RCT, n = 83, MD 22.30 CI 4.91 to 39.69) and ziprasidone (cholesterol increase 2 RCTs, n = 767, MD 8.58 CI 1.11 to 16.04) but less than clozapine (weight gain 3 RCTs n = 373, MD -3.30 CI -5.65 to -0.95), olanzapine (weight gain 13 RCTs, n = 2116, MD -2.61 CI -3.74 to -1.48), quetiapine (cholesterol increase: 5 RCTs, n = 1433, MD -8.49 CI -12. 23 to -4.75) and sertindole (weight gain: 2 RCTs, n = 328, MD -0.99 CI -1.86 to -0.12). It may be less sedating than clozapine and quetiapine, lengthen the QTc interval less than sertindole (QTc change: 2 RCTs, n = 495, MD -18.60 CI -22.37 to 14.83), produce fewer seizures than clozapine (2 RCTs, n = 354, RR 0.22 CI 0.07 to 0.70, NNT 14 CI 8 to 33) and less sexual dysfunction in men than sertindole (2 RCTs, n = 437, RR 0.34 CI 0.16 to 0.76, NNT 13 CI 8 to 33). Risperidone seems to produce somewhat more extrapyramidal side effects and clearly more prolactin increase than most other SGAs. It may also differ from other compounds in efficacy and in the occurrence of other adverse effects such as weight gain, metabolic problems, cardiac effects, sedation and seizures. Nevertheless, the large proportion of participants leaving studies early and incomplete reporting of outcomes makes it difficult to draw firm conclusions. Further large trials, especially comparing risperidone with those other new drugs for which only a few RCTs are available, are needed.


Chronic post-traumatic headache after mild head injury: a descriptive study.
The aetiology behind chronic post-traumatic headache (CPTH) after mild head injury is unclear and management is complicated. In order to optimize treatment strategies we aimed to characterize a CPTH population. Ninety patients with CPTH and 45 patients with chronic primary headaches were enrolled from the Danish Headache Center. All patients were interviewed about demographic and headache data. They completed the Harvard Trauma Questionnaire (HTQ), Rivermead Post Concussion Symptoms Questionnaire, SF-36 and a headache diary. The CPTH group experienced more cognitive ( P < 0.001) and somatic symptoms ( P = 0.048) and rated their self-perceived health as more affected in terms of physical function ( P = 0.036), physical role function ( P = 0.012) and social function ( P = 0.012) than the control group. Surprisingly, 31% of the CPTH group had a score equal to or above the cut-off score for having post-traumatic stress disorder (PTSD) according to the HTQ. In terms of demographics and headache, the groups were comparable except the CPTH group were more often without affiliation to the labour market ( P < 0.001). The loss of work capacity and high levels of disability for the CPTH patients suggests directions for further research into what important factors are embedded in the patients' PTSD symptoms and might explain their prolonged illness.


A Photoreceptor Contributes to the Natural Variation of Diapause Induction in Daphnia magna.
Diapause is an adaptation that allows organisms to survive harsh environmental conditions. In species occurring over broad habitat ranges, both the timing and the intensity of diapause induction can vary across populations, revealing patterns of local adaptation. Understanding the genetic architecture of this fitness-related trait would help clarify how populations adapt to their local environments. In the cyclical parthenogenetic crustacean Daphnia magna, diapause induction is a phenotypic plastic life history trait linked to sexual reproduction, as asexual females have the ability to switch to sexual reproduction and produce resting stages, their sole strategy for surviving habitat deterioration. We have previously shown that the induction of resting stage production correlates with changes in photoperiod that indicate the imminence of habitat deterioration and have identified a Quantitative Trait Locus (QTL) responsible for some of the variation in the induction of resting stages. Here, new data allows us to anchor the QTL to a large scaffold and then, using a combination of a new mapping panel, targeted association mapping and selection analysis in natural populations, to identify candidate genes within the QTL. Our results show that variation in a rhodopsin photoreceptor gene plays a significant role in the variation observed in resting stage induction. This finding provides a mechanistic explanation for the link between diapause and day-length perception that has been suggested in diverse arthropod taxa.


An increased risk of stroke among panic disorder patients: a 3-year follow-up study.
To explore whether panic disorder (PD) increases the risk for stroke, using a nationwide, population-based dataset. Our study used data from Taiwan's National Health Insurance Research Database. The study cohort included patients who received ambulatory psychiatric care for PD between 2002 and 2003, inclusive (n = 3891). We selected our comparison cohort by randomly recruiting enrollees (n = 19 455) matched with the study group by sex and age. Each patient was tracked for 3 years, from their index ambulatory care visit until the end of 2006, to identify whether or not a patient had a stroke during the follow-up period. Cox proportional hazard regressions were performed as a means of computing the 3-year survival rate, adjusting for potential confounding factors. Among the total sample, 2029 patients (8.7%) experienced a stroke during the 3-year follow-up period, including 647 from the study cohort (16.6% of the PD patients) and 1382 (7.1%) from the comparison cohort. After adjusting for the patients' sex, age, monthly income, level of urbanization, and comorbid medical disorders, the hazard of stroke occurring during the 3-year follow-up period was 2.37 (P < 0.001) times greater for patients with PD than for patients in the comparison cohort. In further analyses, stratified by medical diseases and age, the significant risk of PD on subsequent stroke persisted. We conclude that PD is an independent risk factor for stroke. For patients with PD, aggressive treatment of PD may be considered as part of stroke prevention.


Pathways to decoding the clinical potential of stress response FOXO-interaction networks for Huntington's disease: of gene prioritization and context dependence.
The FOXO family of transcription factors is central to the regulation of organismal longevity and cellular survival. Several studies have indicated that FOXO factors lie at the center of a complex network of upstream pathways, cofactors and downstream targets (FOXO-interaction networks), which may have developmental and post-developmental roles in the regulation of chronic-stress response in normal and diseased cells. Noticeably, FOXO factors are important for the regulation of proteotoxicity and neuron survival in several models of neurodegenerative disease, suggesting that FOXO-interaction networks may have therapeutic potential. However, the status of FOXO-interaction networks in neurodegenerative disease remains largely unknown. Systems modeling is anticipated to provide a comprehensive assessment of this question. In particular, interrogating the context-dependent variability of FOXO-interaction networks could predict the clinical potential of cellular-stress response genes and aging regulators for tackling brain and peripheral pathology in neurodegenerative disease. Using published transcriptomic data obtained from murine models of Huntington's disease (HD) and post-mortem brains, blood samples and induced-pluripotent-stem cells from HD carriers as a case example, this review briefly highlights how the biological status and clinical potential of FOXO-interaction networks for HD may be decoded by developing network and entropy based feature selection across heterogeneous datasets.


Slow CCL2-dependent translocation of biopersistent particles from muscle to brain.
Long-term biodistribution of nanomaterials used in medicine is largely unknown. This is the case for alum, the most widely used vaccine adjuvant, which is a nanocrystalline compound spontaneously forming micron/submicron-sized agglomerates. Although generally well tolerated, alum is occasionally detected within monocyte-lineage cells long after immunization in presumably susceptible individuals with systemic/neurologic manifestations or autoimmune (inflammatory) syndrome induced by adjuvants (ASIA). On the grounds of preliminary investigations in 252 patients with alum-associated ASIA showing both a selective increase of circulating CCL2, the major monocyte chemoattractant, and a variation in the CCL2 gene, we designed mouse experiments to assess biodistribution of vaccine-derived aluminum and of alum-particle fluorescent surrogates injected in muscle. Aluminum was detected in tissues by Morin stain and particle induced X-ray emission) (PIXE) Both 500 nm fluorescent latex beads and vaccine alum agglomerates-sized nanohybrids (Al-Rho) were used. Intramuscular injection of alum-containing vaccine was associated with the appearance of aluminum deposits in distant organs, such as spleen and brain where they were still detected one year after injection. Both fluorescent materials injected into muscle translocated to draining lymph nodes (DLNs) and thereafter were detected associated with phagocytes in blood and spleen. Particles linearly accumulated in the brain up to the six-month endpoint; they were first found in perivascular CD11b+ cells and then in microglia and other neural cells. DLN ablation dramatically reduced the biodistribution. Cerebral translocation was not observed after direct intravenous injection, but significantly increased in mice with chronically altered blood-brain-barrier. Loss/gain-of-function experiments consistently implicated CCL2 in systemic diffusion of Al-Rho particles captured by monocyte-lineage cells and in their subsequent neurodelivery. Stereotactic particle injection pointed out brain retention as a factor of progressive particle accumulation. Nanomaterials can be transported by monocyte-lineage cells to DLNs, blood and spleen, and, similarly to HIV, may use CCL2-dependent mechanisms to penetrate the brain. This occurs at a very low rate in normal conditions explaining good overall tolerance of alum despite its strong neurotoxic potential. However, continuously escalating doses of this poorly biodegradable adjuvant in the population may become insidiously unsafe, especially in the case of overimmunization or immature/altered blood brain barrier or high constitutive CCL-2 production.


Optimum classification of correlation-plane data by Bayesian decision theory.
A multimodal model for correlation-plane distributions generated by composite filters is presented. From this model a statistical classifier referred to as a composite Bayesian classifier is developed. By exploiting the Gaussian behavior of correlation-plane data, this classifier concisely represents multimodal distributions as composite algebraic functions. These multimodal distributions, each of which is constructed by superposition of many normal distributions, are used to partition a vector signal space into optimum classification regions derived from Bayes's likelihood ratio test. For the purpose of validating the multimodal model, expected performance for the training images is derived from calibration data and compared with observed performance.


Evaluation of Antibody Biotinylation Approaches for Enhanced Sensitivity of Single Molecule Array (Simoa) Immunoassays.
In this study, we evaluated the performance of Single Molecule Array (Simoa) immunoassays based on various detection antibody biotinylation approaches. Simoa immunoassays, like other sandwich ELISAs, are highly dependent on the interaction of a biotinylated detection antibody with an enzyme conjugated to streptavidin. Thus, we sought to assess whether different biotinylation reagents can improve the performance and sensitivity of Simoa assays. We selected three proteins, GM-CSF, IFNγ, and IL-2, that are present at ultralow levels in many biological samples. We compared the performance of these Simoa assays by using five different biotinylation reagents and varying the amount of molar fold excess biotin during the biotinylation process. We found that the choice of biotinylation reagent and the molar fold excess biotin can highly affect the performance of the Simoa assays, with differences of up to an order of magnitude in sensitivity. We also tested the performance of bulk ELISAs using the different biotinylated detection antibodies and observe differences greater than an order of magnitude in sensitivity. We show that evaluating different strategies for detection antibody biotinylation is a simple approach for optimizing immunoassay performance for enhanced sensitivity.


Amorphous solid water: a neutron diffraction study.
The structure factor of amorphous solid D(2)O deposited from the vapor at 10 degrees K has been obtained by measuring the neutron diffraction spectrum in the wave vector transfer from 0.8 to 12.3 reciprocal angstroms. The results indicate that the phase investigated is amorphous and has a liquiid-like structure factor. The Fourier-transformed structure e factor yields a real space pair distribution function consistent with local tetrahedral coordination and hydrogen bonding, as in other condensed phases of water. The intramolecular OD separation is 1.00 angstrom; the lack of data for very large wave vector transfer and the expected near equality of the intramolecular DD separation and intermolecular O . . . D separation make it impossible to determine the intramolecular DOD angle with precision. The neutron scattering data presented are complementary to the x-ray diffraction studies of Venkatesh, Rice, antd Narten.


Can the Risk of Lymph Node Metastases Be Gauged in Endoscopically Resected Submucosal Esophageal Adenocarcinomas? A Multi-Center Study.
Endoscopic resection (ER) allows for local therapy of superficial esophageal cancers. Factors reported to be associated with an increased risk of lymph node metastases in patients with adenocarcinoma are poor differentiation, lymphovascular invasion (LVI), and submucosal invasion >500 μ. The aim of this study was to determine whether depth of invasion and tumor characteristics in an ER specimen can be used to gauge the risk of lymph node metastases in patients with superficial esophageal adenocarcinoma. Patients from seven US centers that had ER of an adenocarcinoma followed by an esophagectomy were identified. The ER pathology slides were rereviewed by three experienced GI pathologists for depth of invasion, presence of LVI, and tumor differentiation. The findings from the ER specimen were correlated with the presence and number of lymph node metastases in the final esophagectomy specimen. There were 19 T1a and 23 T1b tumors. A median of 24 nodes were resected per patient. None of the T1a tumors had involved lymph nodes despite the presence of LVI in 5% and poor differentiation in 21% of patients. In contrast, 26% of T1b tumors had involved nodes. None of the four patients with submucosal invasion ≤500 μ, no LVI, and no poor differentiation had involved nodes. However, with an increasing number of risk factors, the likelihood of involved lymph nodes increased, reaching 50% when all three factors were present. Endoscopic therapy appears appropriate for intramucosal tumors and may be an option for low-risk T1b tumors. Esophagectomy is preferred for patients with submucosal invasion and one or more risk factors.


The effect of a single 4CMenB vaccine booster in young people more than ten years after infant immunisation: protocol of an exploratory immunogenicity study.
The four-component capsular group B meningococcal vaccine (4CMenB) was introduced into the national immunisation schedule in the UK in September 2015 for infants in a 2 + 1 schedule at two, four and 12 months of age. A two-dose immunisation schedule for adolescents was also considered but was not found to be cost-effective in view of the relatively low rates of disease in this age group. Uncertainty about the longevity of protection induced by the vaccine and lack of certainty about an anamnestic response in primed individuals contributed to this decision. This study is an open-label, descriptive immunogenicity analysis. Up to 113 participants will be recruited, including up to 83 children who are now aged 11 years and took part in previous trials involving the administration of 4CMenB to infants, plus a group of 30 naïve age-matched controls. All previously immunised participants will receive one booster dose of 4CMenB. The 30 naïve participants will be randomised to receive two doses of 4CMenB either at 0 and 28 days or 0 and 365 days. Blood samples will be collected from all participants at 0, 28, 180 and 365 days. The primary endpoint will explore immunogenicity at day 0 and 180 in previously immunised and naïve participants. Secondary outcomes will include investigating the persistence of antibody protection in previously immunised participants at the beginning of the study, describing the characteristics of the memory B-cell responses in previously immunised participants, and measuring reactogenicity in all participants following 4CMenB doses. This study aims to describe whether or not a single booster dose of 4CMenB given to those who have received an infant course of 4CMenB induces a recall immune response, while concurrently describing immune responses in naïve children of the same age. If an anamnestic response is proven, a single dose adolescent booster could be envisaged as an addition to the current UK vaccination schedule. EudraCT, 2017-004732-11. ISRCTN, ISRCTN16774163. Registered on 10 May 2018 (retrospectively registered).


Protein Biomarkers for Insulin Resistance and Type 2 Diabetes Risk in Two Large Community Cohorts.
Insulin resistance (IR) is a precursor of type 2 diabetes (T2D), and improved risk prediction and understanding of the pathogenesis are needed. We used a novel high-throughput 92-protein assay to identify circulating biomarkers for HOMA of IR in two cohorts of community residents without diabetes (n = 1,367) (mean age 73 ± 3.6 years). Adjusted linear regression identified cathepsin D and confirmed six proteins (leptin, renin, interleukin-1 receptor antagonist [IL-1ra], hepatocyte growth factor, fatty acid-binding protein 4, and tissue plasminogen activator [t-PA]) as IR biomarkers. Mendelian randomization analysis indicated a positive causal effect of IR on t-PA concentrations. Two biomarkers, IL-1ra (hazard ratio [HR] 1.28, 95% CI 1.03-1.59) and t-PA (HR 1.30, 1.02-1.65) were associated with incident T2D, and t-PA predicted 5-year transition to hyperglycemia (odds ratio 1.30, 95% CI 1.02-1.65). Additional adjustment for fasting glucose rendered both coefficients insignificant and revealed an association between renin and T2D (HR 0.79, 0.62-0.99). LASSO regression suggested a risk model including IL-1ra, t-PA, and the Framingham Offspring Study T2D score, but prediction improvement was nonsignificant (difference in C-index 0.02, 95% CI -0.08 to 0.12) over the T2D score only. In conclusion, proteomic blood profiling indicated cathepsin D as a new IR biomarker and suggested a causal effect of IR on t-PA.


Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs.
Recent reports have highlighted instances of mRNAs that, in addition to coding for protein, regulate the abundance of related transcripts by altering microRNA availability. These two mRNA roles - one mediated by RNA and the other by protein - are inter-dependent and hence cannot easily be separated. Whether the RNA-mediated role of transcripts is important, per se, or whether it is a relatively innocuous consequence of competition by different transcripts for microRNA binding remains unknown. Here we took advantage of 48 loci that encoded proteins in the earliest eutherian ancestor, but whose protein-coding capability has since been lost specifically during rodent evolution. Sixty-five percent of such loci, which we term 'unitary pseudogenes', have retained their expression in mouse and their transcripts exhibit conserved tissue expression profiles. The maintenance of these unitary pseudogenes' spatial expression profiles is associated with conservation of their microRNA response elements and these appear to preserve the post-transcriptional roles of their protein-coding ancestor. We used mouse Pbcas4, an exemplar of these transcribed unitary pseudogenes, to experimentally test our genome-wide predictions. We demonstrate that the role of Pbcas4 as a competitive endogenous RNA has been conserved and has outlived its ancestral gene's loss of protein-coding potential. These results show that post-transcriptional regulation by bifunctional mRNAs can persist over long evolutionary time periods even after their protein coding ability has been lost.


Acoustic consequences of articulatory variability during productions of /t/ and /k/ and its implications for speech error research.
An increasing number of studies has linked certain types of articulatory or acoustic variability with speech errors, but no study has yet examined the relationship between such articulatory variability and acoustics. The present study aims to evaluate the acoustic properties of articulatorily errorful /k/ and /t/ stimuli to determine whether these errors are consistently reflected in the acoustics. The most frequent error observed in the articulatory data is the production of /k/ and /t/ with simultaneous tongue tip and tongue dorsum constrictions. Spectral analysis of these stimuli's bursts shows that /k/ and /t/ are differently affected by such co-production errors: co-production of tongue tip and tongue dorsum during intended /k/ results in typical /k/ spectra (and hence in tokens robustly classified as /k/), while co-productions during intended /t/ result in spectra with roughly equal prominence at both the mid-frequency (/k/-like) and high-frequency (/t/-like) ranges (and hence in tokens ambiguous between /k/ and /t/). This outcome is not due to an articulatory timing difference, but to tongue dorsum constriction having an overall greater effect on the acoustic than a tongue tip constriction when the two are co-produced.


The effect of intracarotid nonionic contrast media on the blood-brain barrier in acute hypertension.
To determine whether acute hypertension (HT) is a risk factor for damage to the blood-brain barrier in carotid angiography with nonionic contrast media. Anesthetized rats received intravenous injections of technetium-99m-pertechnetate and horseradish peroxidase. Two groups of rats received metaraminol to raise their blood pressure to between 165 and 190 mmHg peak systolic and then received intracarotid injections of saline or iopamidol. Two other groups remained normotensive and received intracarotid injections of saline or iopamidol. Animals were perfused with a fixative solution and their brains removed. Activity of extravasated Tc-99m-pertechnetate was determined to assess blood-brain barrier breakdown. Brains were then sectioned, treated histochemically to visualize extravasated horseradish peroxidase, and ranked visually according to horseradish peroxidase staining. Extravasation of both tracers was significantly greater in the hypertensive group that received contrast media than in the other three groups. Acute hypertension potentiates the blood-brain barrier-damaging effects of nonionic contrast media during carotid angiography in rats.


In vivo validation of the unified BARGE method to assess the bioaccessibility of arsenic, antimony, cadmium, and lead in soils.
The relative bioavailability of arsenic, antimony, cadmium, and lead for the ingestion pathway was measured in 16 soils contaminated by either smelting or mining activities using a juvenile swine model. The soils contained 18 to 25,000 mg kg(-1) As, 18 to 60,000 mg kg(-1) Sb, 20 to 184 mg kg(-1) Cd, and 1460 to 40,214 mg kg(-1) Pb. The bioavailability in the soils was measured in kidney, liver, bone, and urine relative to soluble salts of the four elements. The variety of soil types, the total concentrations of the elements, and the range of bioavailabilities found were considered to be suitable for calibrating the in vitro Unified BARGE bioaccessibility method. The bioaccessibility test has been developed by the BioAccessibility Research Group of Europe (BARGE) and is known as the Unified BARGE Method (UBM). The study looked at four end points from the in vivo measurements and two compartments in the in vitro study ("stomach" and "stomach and intestine"). Using benchmark criteria for assessing the "fitness for purpose" of the UBM bioaccessibility data to act as an analogue for bioavailability in risk assessment, the study shows that the UBM met criteria on repeatability (median relative standard deviation value <10%) and the regression statistics (slope 0.8 to 1.2 and r-square > 0.6) for As, Cd, and Pb. The data suggest a small bias in the UBM relative bioaccessibility of As and Pb compared to the relative bioavailability measurements of 3% and 5% respectively. Sb did not meet the criteria due to the small range of bioaccessibility values found in the samples.


Food-borne radiolytic compounds (2-alkylcyclobutanones)may promote experimental colon carcinogenesis.
Food irradiation is acknowledged as a safe process to improve food quality by reducing microbial contamination. Information on the toxicological potential of 2-alkylcyclobutanones (2-ACBs), radiolytic derivatives of triglycerides found exclusively in irradiated food, is scarce. Wistar rats received daily a solution of highly pure 2-tetradecylcyclobutanone (2-tDCB) or 2-(tetradec-5-enyl)-cyclobutanone (2-tDeCB) at a concentration of 0.005% in 1% ethanol as drinking fluid, while control animals received 1% ethanol. All animals received a single intraperitoneal injection of the chemical carcinogen azoxymethane (AOM) at Weeks 3 and 4. At 3 mo after AOM injection, no significant changes were observed in the total number of preneoplastic lesions in the colon of AOM controls and 2-ACB-treated animals. After 6 mo, the total number of tumors in the colon was threefold higher in the 2-ACB-treated animals than in the AOM controls. The colon of four of six AOM control rats exhibited only one small tumor ( &6 mm3). Multiple tumors were observed in four and three of six animals treated with 2-tDCB or 2-tDeCB, respectively. Medium (6 < S < 25 mm3) and larger (>25 mm3) tumors were detected only in 2-ACB-treated animals. This is the first demonstration that a compound found exclusively in irradiated dietary fats may promote colon carcinogenesis in animals treated with a chemical carcinogen.


Repositioning drugs for traumatic brain injury - N-acetyl cysteine and Phenserine.
Traumatic brain injury (TBI) is one of the most common causes of morbidity and mortality of both young adults of less than 45 years of age and the elderly, and contributes to about 30% of all injury deaths in the United States of America. Whereas there has been a significant improvement in our understanding of the mechanism that underpin the primary and secondary stages of damage associated with a TBI incident, to date however, this knowledge has not translated into the development of effective new pharmacological TBI treatment strategies. Prior experimental and clinical studies of drugs working via a single mechanism only may have failed to address the full range of pathologies that lead to the neuronal loss and cognitive impairment evident in TBI and other disorders. The present review focuses on two drugs with the potential to benefit multiple pathways considered important in TBI. Notably, both agents have already been developed into human studies for other conditions, and thus have the potential to be rapidly repositioned as TBI therapies. The first is N-acetyl cysteine (NAC) that is currently used in over the counter medications for its anti-inflammatory properties. The second is (-)-phenserine ((-)-Phen) that was originally developed as an experimental Alzheimer's disease (AD) drug. We briefly review background information about TBI and subsequently review literature suggesting that NAC and (-)-Phen may be useful therapeutic approaches for TBI, for which there are no currently approved drugs.


Vascularization and odontode structure of a dorsal ridge spine of Romundina stellina Ørvig 1975.
There are two types of dermal skeletons in jawed vertebrates: placoderms and osteichthyans carry large bony plates (macromery), whereas chondrichthyans and acanthodians are covered by small scales (micromery). Fin spines are one of the last large dermal structures found on micromeric taxa and offer a potential source of histology and morphology that can be compared to those found on macromeric groups. Dermal fin spines offer a variety of morphology but aspects of their growth modes and homology are unclear. Here, we provide detailed descriptions of the microstructure and growth of a dorsal ridge spine from the acanthothoracid placoderm, Romundina stellina, using virtual three-dimensional paleohistological datasets. From these data we identify several layers of dentine ornamentation covering the lateral surfaces of the spine and reconstructed their growth pattern. We show that this spine likely grew posteriorly and proximally from a narrow portion of bone located along the leading edge of the spine. The spine is similarly constructed to the scales with a few exceptions, including the absence of polarized fibers distributed throughout the bone and the presence of a thin layer of perichondral bone. The composition of the spine (semidentine odontodes, dermal bone, perichondral bone) is identical to that of the Romundina dermal plates. These results illustrate the similarities and differences between the dermal tissues in Romundina and indicate that the spine grew differently from the dentinous fin spines from extant and fossil chondrichthyans. The morphology and histology of Romundina is most similar to the fin spine of the probable stem osteichthyan Lophosteus, with a well-developed inner cellular bony base and star-shaped odontodes on the surface. Results from these studies will undoubtedly have impact on our understanding of fossil fin spine histology and evolution, contributing to the on-going revision of early gnathostome phylogeny.


Mechanism of apoptotic cell death of human gastric carcinoma cells mediated by transforming growth factor beta.
Human gastric carcinoma cell line HSC-39 has been shown to undergo apoptotic cell death in response to treatment with transforming growth factor beta1 (TGF-beta1). To understand better the cell death mechanism in this TGF-beta1-mediated apoptosis, we investigated the effect of the expression of TGF-beta-stimulated clone 22 (TSC-22) on cell death events. TGF-beta1 induced TSC-22 gene expression in HSC-39 cells only when the cells had previously been adapted to the serum-free culture conditions required to undergo TGF-beta1-mediated apoptosis. HSC-39 cells transfected with a TSC-22 expression vector showed a significant decrease in cell viability compared with those transfected with a control vector. The cellular events characteristic of apoptosis, chromatin condensation and DNA fragmentation were observed only in cells transfected with a TSC-22 expression vector. On immunostaining of the transfected cells, almost every cell that expressed TSC-22 tagged with influenza virus haemagglutinin exhibited the morphology of an apoptotic cell. Partial protection from the cell death effect of TGF-beta1 on HSC-39 cells was observed when cells were treated with acetyl-L-aspartyl-L-glutamyl-L-valyl-L-aspart-1-al (Ac-DEVD-CHO, an inhibitor specific for CPP32-type protease). Protection against cell death by the transfection of a TSC-22 expression vector was also offered by Ac-DEVD-CHO addition. These results suggest that TSC-22 elicits the apoptotic cell death of human gastric carcinoma cells through the activation of CPP32-like protease and mediates the TGF-beta1 signalling pathway to apoptosis.


An analysis of the dynamic range and linearity of an infrared DNA sequencer.
We are currently developing genotyping software and protocols for use on the Li-Cor model 4000(L) infrared fluorescence DNA sequencers. During the development of the genotyping software it became apparent that the potential dynamic range of the instrument was not being realized when the data collection parameters were optimized to produce a high-contrast image on the computer screen. In particular, we were unable to obtain peaks with signal to noise (S/N) greater than about 30:1 and the stronger peaks often saturated the detector. Because the numerical dynamic range available in 16-bit data collection mode exceeds 65000, our limited dynamic range of about 30 in actual data was somewhat puzzling. Hence, we undertook a study to explore the dynamic range and linearity of the Li-Cor DNA sequencer in order to minimize background fluorescence and noise as well as maximize the available S/N. Data is presented on the background and noise using different polyacrylamide gel mixes with various signal gain and offset values, and the relative contribution of the glass, gel and instrumentation to the background fluorescence is discussed. Based on these results, optimum gain and offset values were determined that maintain the background fluorescence at approximately 1-2% of the maximum dynamic range with a minimum amount of noise. Using these optimized values, we determined the detection system is linear over three orders of magnitude by titrating known quantities of an infrared fluorophore-labeled primer. In addition, we were able to detect approximately 15.2 amoles of labeled primer. The results provided by this study establish a set of guidelines for evaluating how to set the signal gain and offset in order to minimize the background and maximize the S/N and dynamic range of the Li-Cor sequencer.


The use of drotrecogin alfa (activated) in severe sepsis during acute pancreatitis - two case studies.
Twenty-five percent of patients with diagnosed acute pancreatitis (AP) present a severe form of it. One of the most widespread complications of such a form is severe sepsis or septic shock, in which mortality can reach 80%. A complication of this state is multiple organ failure, which requires multi-directional treatment in an intensive care unit (ICU). Among the standard therapies are: control of the source of infection, supportive treatment of failed organ function, and others (e.g. dietary therapy, pain management, and physiotherapy). It is also now possible to use recombinant human activated protein C [drotrecogin alfa (activated); Xigris, Eli Lilly, USA] in the treatment of severe sepsis. In this study, the cases of two patients in whom severe sepsis was found during the course of acute pancreatitis are presented. In both cases it was established clinically (by laparotomy) and bacteriologically that necrosis-altered fragments of the pancreas were the sources of infection. Both the cases presented indicate that drotrecogin alfa (activated) interrupts the developmental cascade of severe sepsis. Proofs of the efficacy of the treatment were improvements in the functions of organs previously insufficient during the course of sepsis. The rapid elimination of the drug allowed planning therapy strategies (the possibility of conducting surgical operations and smaller therapeutic interventions) without the risk of increased bleeding. The decision to use Xigris in severe sepsis during AP should always include consideration of the risk of bleeding in connection with the local status within the pancreas.


Inflammation in Post-Traumatic Stress Disorder (PTSD): A Review of Potential Correlates of PTSD with a Neurological Perspective.
Post-traumatic stress disorder (PTSD) is a chronic condition characterized by symptoms of physiological and psychosocial burden. While growing research demonstrated signs of inflammation in PTSD, specific biomarkers that may be representative of PTSD such as the detailed neural correlates underlying the inflammatory responses in relation to trauma exposure are seldom discussed. Here, we review recent studies that explored alterations in key inflammatory markers in PTSD, as well as neuroimaging-based studies that further investigated signs of inflammation within the brain in PTSD, as to provide a comprehensive summary of recent literature with a neurological perspective. A search was conducted on studies published from 2009 through 2019 in PubMed and Web of Science. Fifty original articles were selected. Major findings included elevated levels of serum proinflammatory cytokines in individuals with PTSD across various trauma types, as compared with those without PTSD. Furthermore, neuroimaging-based studies demonstrated that altered inflammatory markers are associated with structural and functional alterations in brain regions that are responsible for the regulation of stress and emotion, including the amygdala, hippocampus, and frontal cortex. Future studies that utilize both central and peripheral inflammatory markers are warranted to elucidate the underlying neurological pathway of the pathophysiology of PTSD.


Systemic prostaglandin E2 increases cancellous bone formation and mass in aging rats and stimulates their bone marrow osteogenic capacity in vivo and in vitro.
Prostaglandin E(2) (PGE(2)) has been shown to exert a bone anabolic effect in young and adult rats. In this study we tested whether it possesses a similar effect on bone formation and bone mass in aging rats. Fifteen-month-old rats were injected daily with either PGE(2) at 5 mg/kg or vehicle for 14 days. PGE(2) treatment stimulated the rate of cancellous bone formation (a approximately 5.5-fold increase in bone formation rate), measured by the incorporation of calcein into bone-forming surfaces at the tibial proximal metaphysis. This effect resulted in increased cancellous bone area (+54%) at the same site. Since PGE(2) treatment resulted in a much higher proportion of bone surface undergoing bone formation and thus lined with osteoblasts, we tested the hypothesis that PGE(2) stimulates osteoblast differentiation from bone marrow precursor cells both in vivo and in vitro. We found that ex vivo cultures of bone marrow stromal cells from rats injected for 2 weeks with PGE(2) at 5 mg/kg per day yielded more ( approximately 4-fold) mineralized nodules and exhibited a greater (by 30-40%) alkaline phosphatase activity compared with cultures from vehicle-injected rats, attesting to a stimulation of osteoblastic differentiation by PGE(2). We also compared the osteogenic capacity of bone marrow from aging (15-month-old) versus young (5-week-old) rats and its regulation by PGE(2) in vitro. Bone marrow stromal cell cultures from aging rats exhibited a greatly diminished osteogenic capacity, reflected in reduced nodule formation ( approximately 6% of young animals) and lower alkaline phosphatase activity ( approximately 60% of young animals). However, these parameters could be stimulated in both groups of animals by incubation with 10-100 nM PGE(2). The magnitude of this stimulation was greater in cultures from aging rats (+550% vs +70% in nodule formation of aging compared with young rats). In conclusion, we demonstrate here that PGE(2) exerts a bone anabolic effect in aging rats, similar to the effect we and others have reported in young, growing rats. The PGE(2)-stimulated bone formation, which augments bone mass, most likely results from recruitment of osteoblasts from their bone marrow stromal precursors.


The focal adhesion targeting domain of p130Cas confers a mechanosensing function.
Members of the Cas family of focal adhesion proteins contain a highly conserved C-terminal focal adhesion targeting (FAT) domain. To determine the role of the FAT domain in these proteins, we compared wild-type exogenous NEDD9 with a hybrid construct in which the NEDD9 FAT domain had been exchanged for the p130Cas (also known as BCAR1) FAT domain. Fluorescence recovery after photobleaching (FRAP) revealed significantly slowed exchange of the fusion protein at focal adhesions and significantly slower two-dimensional migration. No differences were detected in cell stiffness as measured using atomic force microscopy (AFM) and in cell adhesion forces measured with a magnetic tweezer device. Thus, the slowed migration was not due to changes in cell stiffness or adhesion strength. Analysis of cell migration on surfaces of increasing rigidity revealed a striking reduction of cell motility in cells expressing the p130Cas FAT domain. The p130Cas FAT domain induced rigidity-dependent phosphorylation of tyrosine residues within NEDD9. This in turn reduced post-translational cleavage of NEDD9, which we show inhibits NEDD9-induced migration. Collectively, our data therefore suggest that the p130Cas FAT domain uniquely confers a mechanosensing function.


Role of corneal elasticity in damping of intraocular pressure.
To determine corneal elasticity and its contribution in damping acute intraocular pressure spikes. Twenty corneas with intact scleral rims were excised from human donor eyes and mounted on an artificial anterior chamber. A watertight seal was obtained with 17 corneas. Saline was infused into the chamber at a rate of 10 mL/h, and subsequent changes in pressure were measured to generate a pressure-volume relationship. Real-time anterior segment OCT was used to measure the change in radius of curvature and corneal thickness in nine eyes. The pressure-versus-volume curves of all corneal-scleral buttons were concave-up asymptotes, demonstrating elasticity. The range of the slope was 0.34 to 1.6 +/- 0.29 mm Hg/microL. The mean change in the radius of curvature in the nine eyes that were visualized by optical coherence tomography (OCT) was 247 +/- 106 microm (range, 168-412 microm). The OCT image was centered on the epithelial surface. In two eyes, the entire cornea was visible by OCT throughout the course of the experiment, and corneal thickness was measured and found to decrease by 116 +/- 4 microm. Human eye bank corneas demonstrate elasticity ex vivo, with expansion and thinning in response to increases in anterior chamber pressure. These elastic properties may serve as a buffering mechanism for microvolumetric changes in the eye, thus protecting the eye from intraocular pressure surges in vivo.


Bortezomib and endocannabinoid/endovanilloid system: a synergism in osteosarcoma.
Osteosarcoma is the most common primary malignant tumor of bone in children and adolescents. Bortezomib (BTZ) is an approved anticancer drug, classified as a selective reversible inhibitor of the ubiquitin-dependent proteasome system, that leads to cancer cell cycle arrest and apoptosis reducing the invasion ability of Osteosarcoma cells in vitro. It also regulates the RANK/RANKL/OPG system, involved in the pathogenesis of bone tumors and in cell migration. A side effect of BTZ is to induce painful sensory peripheral neuropathy which lead to cessation of therapy or dose reduction. Recently BTZ has been evaluated in combination with Cannabinoids targeting CB1 receptor, demonstrating a promising synergic effect. The Endocannabinoid/Endovanilloid (EC/EV) system includes two G protein-coupled receptors (CB1 and CB2), the Transient Potential Vanilloid 1 (TRPV1) channel and their endogenous ligands and enzymes. CB1 and CB2 are expressed mainly in Central Nervous System and Immune Peripheral cells respectively. TRPV1 is also expressed in primary sensory neurons and is involved in pain modulation. EC/EV system induces apoptosis, reduces invasion and cell proliferation in Osteosarcoma cell lines and is involved in bone metabolism. We analyzed the effects of BTZ, alone and in combination with selective agonists at CB2 (JWH-133) and TRPV1 (RTX) receptors, in the Osteosarcoma cell line (HOS) on Apoptosis, Cell Cycle progression, migration and bone balance. We observed that the stimulation of CB2 and TRPV1 receptors increase the efficacy of BTZ in inducing apoptosis and reducing invasion, cell cycle progression and by modulating bone balance. These data suggest the possibility to use BTZ, in combination with EC/EV agonists, in Osteosarcoma therapy reducing its dose and its side effects.


How well do covariates perform when adjusting for sampling bias in online COVID-19 research? Insights from multiverse analyses.
COVID-19 research has relied heavily on convenience-based samples, which-though often necessary-are susceptible to important sampling biases. We begin with a theoretical overview and introduction to the dynamics that underlie sampling bias. We then empirically examine sampling bias in online COVID-19 surveys and evaluate the degree to which common statistical adjustments for demographic covariates successfully attenuate such bias. This registered study analysed responses to identical questions from three convenience and three largely representative samples (total N = 13,731) collected online in Canada within the International COVID-19 Awareness and Responses Evaluation Study ( www.icarestudy.com ). We compared samples on 11 behavioural and psychological outcomes (e.g., adherence to COVID-19 prevention measures, vaccine intentions) across three time points and employed multiverse-style analyses to examine how 512 combinations of demographic covariates (e.g., sex, age, education, income, ethnicity) impacted sampling discrepancies on these outcomes. Significant discrepancies emerged between samples on 73% of outcomes. Participants in the convenience samples held more positive thoughts towards and engaged in more COVID-19 prevention behaviours. Covariates attenuated sampling differences in only 55% of cases and increased differences in 45%. No covariate performed reliably well. Our results suggest that online convenience samples may display more positive dispositions towards COVID-19 prevention behaviours being studied than would samples drawn using more representative means. Adjusting results for demographic covariates frequently increased rather than decreased bias, suggesting that researchers should be cautious when interpreting adjusted findings. Using multiverse-style analyses as extended sensitivity analyses is recommended.


Artery of Percheron: an unusual stroke presentation.
An 86-year-old woman was admitted with multiple episodes of transient loss of consciousness. She was initially treated for seizures, and stroke was not considered likely. MRI on the same day of admission showed acute bilateral medial thalamic infarcts in keeping with the Artery of Percheron (AOP) territory infarcts. Investigation for polycythaemia and thrombocytosis showed JAK2 positive myeloproliferative neoplasm.A diagnosis of AOP infarction is often missed or delayed because it is rare and presents with variable neurological symptoms. Initial imaging in the form of CT is often negative, and some report that initial MRI findings may also be normal.An awareness of a wide range of differential diagnoses alongside a multi-modality imaging approach is required to reach a diagnosis.Although there are several other case reports of AOP infarction in the literature, this is the first to present with transient symptoms initially mistaken for seizure activity.


A Monte Carlo Evaluation of Weighted Community Detection Algorithms.
The past decade has been marked with a proliferation of community detection algorithms that aim to organize nodes (e.g., individuals, brain regions, variables) into modular structures that indicate subgroups, clusters, or communities. Motivated by the emergence of big data across many fields of inquiry, these methodological developments have primarily focused on the detection of communities of nodes from matrices that are very large. However, it remains unknown if the algorithms can reliably detect communities in smaller graph sizes (i.e., 1000 nodes and fewer) which are commonly used in brain research. More importantly, these algorithms have predominantly been tested only on binary or sparse count matrices and it remains unclear the degree to which the algorithms can recover community structure for different types of matrices, such as the often used cross-correlation matrices representing functional connectivity across predefined brain regions. Of the publicly available approaches for weighted graphs that can detect communities in graph sizes of at least 1000, prior research has demonstrated that Newman's spectral approach (i.e., Leading Eigenvalue), Walktrap, Fast Modularity, the Louvain method (i.e., multilevel community method), Label Propagation, and Infomap all recover communities exceptionally well in certain circumstances. The purpose of the present Monte Carlo simulation study is to test these methods across a large number of conditions, including varied graph sizes and types of matrix (sparse count, correlation, and reflected Euclidean distance), to identify which algorithm is optimal for specific types of data matrices. The results indicate that when the data are in the form of sparse count networks (such as those seen in diffusion tensor imaging), Label Propagation and Walktrap surfaced as the most reliable methods for community detection. For dense, weighted networks such as correlation matrices capturing functional connectivity, Walktrap consistently outperformed the other approaches for recovering communities.


Modeling and measurement of signaling outcomes affecting decision making in noisy intracellular networks using machine learning methods.
Characterization of decision-making in cells in response to received signals is of importance for understanding how cell fate is determined. The problem becomes multi-faceted and complex when we consider cellular heterogeneity and dynamics of biochemical processes. In this paper, we present a unified set of decision-theoretic, machine learning and statistical signal processing methods and metrics to model the precision of signaling decisions, in the presence of uncertainty, using single cell data. First, we introduce erroneous decisions that may result from signaling processes and identify false alarms and miss events associated with such decisions. Then, we present an optimal decision strategy which minimizes the total decision error probability. Additionally, we demonstrate how graphing receiver operating characteristic curves conveniently reveals the trade-off between false alarm and miss probabilities associated with different cell responses. Furthermore, we extend the introduced framework to incorporate the dynamics of biochemical processes and reactions in a cell, using multi-time point measurements and multi-dimensional outcome analysis and decision-making algorithms. The introduced multivariate signaling outcome modeling framework can be used to analyze several molecular species measured at the same or different time instants. We also show how the developed binary outcome analysis and decision-making approach can be extended to more than two possible outcomes. As an example and to show how the introduced methods can be used in practice, we apply them to single cell data of PTEN, an important intracellular regulatory molecule in a p53 system, in wild-type and abnormal cells. The unified signaling outcome modeling framework presented here can be applied to various organisms ranging from viruses, bacteria, yeast and lower metazoans to more complex organisms such as mammalian cells. Ultimately, this signaling outcome modeling approach can be utilized to better understand the transition from physiological to pathological conditions such as inflammation, various cancers and autoimmune diseases.


US Practice Patterns and Impact of Monitoring for Mucosal Inflammation After Biologic Initiation in Inflammatory Bowel Disease.
We assessed practice patterns for monitoring mucosal inflammation after biologic initiation and the association between monitoring approaches and development of disease-related complications for Crohn's disease (CD) and ulcerative colitis (UC). This study used a Truven Health MarketScan (2007-2016) query for CD and UC patients initiating biologic therapy. Cumulative 24-month disease-related complications (corticosteroids, change of biologic, hospitalization, surgery) in patients undergoing proactive disease monitoring with lower endoscopy, fecal calprotectin, or cross-sectional radiographic enterography (computed tomography enterography or magnetic resonance enterography) within 6 months of biologic initiation vs no early monitoring after biologic initiation were compared. Cox proportional hazard ratios (HRs with 95% confidence intervals [CIs]) adjusted for propensity score were used. Within the first 24 months after biologic initiation, monitoring (proactive or reactive) was performed in 56.4% of CD patients and 67.8% of UC patients, with considerable geographic variability. Early (within 6 months) proactive monitoring was endoscopy-based (87.9%), performed in 11% of CD (n = 2195/19,899) and 12.8% of UC (n = 925/7247) patients. Compared with no early monitoring, early proactive monitoring was associated with a reduction in disease-related complications for CD (adjusted HR [aHR], 0.90; 95% CI, 0.84-0.96) and UC (aHR, 0.87; 95% CI, 0.78-0.97) and predominately driven by a reduction in corticosteroid use (CD: aHR, 0.83; 95% CI, 0.77-0.90; UC: aHR, 0.77; 95% CI, 0.69-0.87). Results were consistent across multiple sensitivity analyses. Early proactive monitoring of mucosal inflammation in CD and UC within 6 months of biologic initiation was associated with reduction in disease-related complications over 24 months, primarily related to reduced steroid utilization. Wide variation exists in practice patterns for monitoring of mucosal inflammation after biologic initiation.


Effects of a flaxseed-derived lignan supplement on C-reactive protein, IL-6 and retinol-binding protein 4 in type 2 diabetic patients.
Elevated C-reactive protein (CRP), IL-6 and retinol-binding protein 4 (RBP4) levels are associated with insulin resistance and diabetes mellitus. Phytoestrogens (including lignans and isoflavones) may enhance the management of diabetes and are hypothesized to act through inflammation pathways. The present study explored the effects of flaxseed-derived lignan on inflammatory factors and RBP4 concentrations in type 2 diabetics, who have higher levels of these biomarkers. Seventy community-dwelling diabetic patients (twenty-six men and forty-four post-menopausal women) with mild hypercholesterolaemia completed a randomized, double-blind, placebo-controlled, cross-over trial of supplementation with flaxseed-derived lignan capsules (360 mg/d) or placebo for 12 weeks, separated by an 8-week wash-out period. The participants maintained their habitual diets and levels of physical activity. Baseline to follow-up concentrations of CRP increased significantly within the placebo group (1.42 (sem 0.19) v. 1.96 (sem 0.22) mg/l, P < 0.001), but were comparatively unchanged in the lignan-supplemented group (1.67 (sem 0.19) v. 1.90 (sem 0.26) mg/l, P = 0.94); a significant difference was observed between treatments ( - 0.45 (95 % CI - 0.76, - 0.08) mg/l, P = 0.021). This effect was confined to women (P = 0.016), but not observed in men (P = 0.49). No between-treatment differences were found with regard to IL-6 or RBP4; though IL-6 concentrations increased significantly from baseline to follow-up in both groups (P = 0.004 and P < 0.001 following lignan and placebo treatments, respectively). The study suggests that lignan might modulate CRP levels in type 2 diabetics. These results need to be confirmed by further large clinical trials of longer duration.


Gambling in Two Regional Australian Aboriginal Communities: A Social Practice Analysis.
Reflecting international patterns, Aboriginal people in Victoria are more likely to gamble and to experience gambling harm than non-Indigenous Victorians. This paper describes experiences of gambling reported by 50 Aboriginal people interviewed in regional Victoria in 2016 and 2017 as part of studies initiated by two Aboriginal community-controlled organisations. Data were analysed using social practice theory (SPT) and coded to the elements of 'meaning', 'material', 'competence', and 'temporality'. Across each element we identified highly contradictory experiences. Gambling held meaning as an opportunity for community gatherings but was also regarded as a cause of domestic violence, conflict, isolation and shame. Materially, the venues that offered gambling were experienced by many Aboriginal people as safe and welcoming, but at the same time gambling produced a damaging affective sense of addiction for some. Gambling was a competency that some people valued and taught to children, but it was also seen as undermining cultural practices. While Aboriginal people were historically denied access to licensed venues offering commercial gambling, many participants now found opportunities to gamble inescapable. The intermingling of benefits and harms described above supports the need for a multi-faceted response to gambling in Aboriginal communities, which includes harm reduction as well as supply restriction and treatment. Some experiences of gambling related by our participants reflected those reported also by non-Indigenous Australians, while others were differently nuanced. Because SPT is used to understand collectively-shared practices, it facilitates the identification of gambling interventions at the level of the community, as recommended by our research participants.