Salvia officinalis extract in the treatment of patients with mild to moderate Alzheimer's disease: a double blind, randomized and placebo-controlled trial.
Alzheimer's disease is characterized by a slow, progressive decline in cognitive function and behaviour. Acetylcholine esterase inhibitors are the only agents approved by the Food and Drug Administration for the treatment of Alzheimer's disease. All other agents prescribed for the treatment of Alzheimer's disease are used on an off-label basis. Current research into new drugs is focused on agents that will prevent, slow down and/or halt the progress of the disease process. Salvia officinalis has been used in herbal medicine for many centuries. It has been suggested, on the basis of traditional medicine, its in vitro cholinergic binding properties and modulation of mood and cognitive performance in humans, that Salvia officinalis might potentially provide a novel natural treatment for Alzheimer's disease. The objective of this study was to assess the efficacy and safety of Salvia officinalis extract using a fixed dose (60 drops/day), in patients with mild to moderate Alzheimer's disease, over a 4-month period. This was a 4-month, parallel group, placebo-controlled trial undertaken in three centres in Tehran, Iran. Patients with mild to moderate Alzheimer's disease aged between 65 and 80 years (n = 42, 18 women) with a score of > or = 12 on the cognitive subscale of Alzheimer's Disease Assessment Scale (ADAS-cog) and < or = 2 on the Clinical Dementia Rating (CDR) were randomized to placebo or fixed dose of S. officinalis extract. Over the 16 weeks, the main efficacy measures were the change in the ADAS-cog and CDR-Sum of Boxes scores compared with baseline. In addition, side-effects were systematically recorded throughout the study using a checklist. At 4 months, S. officinalis extract produced a significant better outcome on cognitive functions than placebo (ADAS-cog: F = 4.77, d.f. = 1, P = 0.03) (CDR-SB: F = 10.84, d.f. = 1, P < 0.003). There were no significant differences in the two groups in terms of observed side-effects except agitation that appears to be more frequent in the placebo group (P = 0.09). The results of this study indicate the efficacy of S. officinalis extract in the management of mild to moderate Alzheimer's disease. Moreover, S. officinalis may well reduce agitation of patients but this needs to be confirmed.


Immunity against heterosubtypic influenza virus induced by adenovirus and MVA expressing nucleoprotein and matrix protein-1.
Alternate prime/boost vaccination regimens employing recombinant replication-deficient adenovirus or MVA, expressing Influenza A virus nucleoprotein and matrix protein 1, induced antigen-specific T cell responses in intradermally (ID) vaccinated mice; with the strongest responses resulting from Ad/MVA immunization. In BALB/C mice the immunodominant response was shifted from the previously identified immunodominant epitope to a novel epitope when the antigen was derived from A/Panama/2007/1999 rather than A/PR/8. Alternate immunization routes did not affect the magnitude of antigen-specific systemic IFN-γ response, but higher CD8(+) T-cell IFN-γ immune responses were seen in the bronchoalveolar lavage following intransal (IN) boosting after intramuscular (IM) priming, whilst higher splenic antigen-specific CD8(+) T cell IFN-γ was seen following IM boosting. Partial protection against heterologous influenza virus challenge was achieved following either IM/IM or IM/IN but not ID/ID immunization. These data may be of relevance for the design of optimal immunization regimens for human influenza vaccines, especially for influenza-naïve infants.


The National Right to Life Committee: its founding, its history, and the emergence of the pro-life movement prior to Roe v. Wade.
During the mid-1960s a few Catholic journals and individuals advised that a more active role should be taken in defeating abortion reform. In 1967 the National Conference of Catholic Bishops selected James Thomas McHugh, administrator of the United States Catholic Conference's Family Life Bureau, to guide its National Right to Life Committee (NRLC). Several pro-life organizations, including Minnesota Citizens Concerned for Life, emerged and affiliated with the NRLC national office. To appeal to a more broad-based, nonsectarian movement, key Minnesota leaders proposed an organizational model that would separate the NRLC from its founder. In early 1973 McHugh and his executive assistant, Michael Taylor, proposed a different plan, facilitating the NRLC's move to independence.


Low energy optical excitations as an indicator of structural changes initiated at the termini of amyloid proteins.
There is a growing body of experimental work showing that protein aggregates associated with amyloid fibrils feature intrinsic fluorescence. In order to understand the microscopic origin of this behavior observed in non-aromatic aggregates of peptides and proteins, we conducted a combined experimental and computational study on the optical properties of amyloid-derived oligopeptides in the near-UV region. We have focused on a few model systems having charged termini (zwitterionic) or acetylated termini. For the zwitterionic system, we were able to simulate the longer tail absorption in the near UV (250-350 nm), supporting the experimental results in terms of excitation spectra. We analyzed the optical excitations responsible for the low-energy absorption and found a large role played by charge-transfer states around the termini. These charge-transfer excitations are very sensitive to the conformation of the peptide and in realistic fibrils may involve inter and intra chain charge reorganization.


Quantification of Bordetella pertussis in clinical samples by colorimetric detection of competitive PCR products.
Quantification of microorganisms is an important part of the normal diagnostic work of a clinical microbiology laboratory. Traditionally the diagnosis of pertussis is subject to a yes or no approach with no quantitative dimension. This can, however, be of interest as a factor when judging the risk of a patient spreading the bacterium and as a research tool. The aim of the present study was to develop a PCR-based quantitative assay for Bordetella pertussis DNA in clinical nasopharyngeal aspirates by combining a quantitative PCR with a colorimetric detection principle, DIANA (detection of immobilised amplified nucleic acid). A competitor to the PCR target sequence in IS-481, containing a lac-operator, was constructed and calibrated, and a test protocol prepared. A total of 46 clinical nasopharyngeal aspirates, previously diagnosed using a standard nested PCR assay and quantified by culture, were analysed by the quantitative PCR. The method showed acceptable precision and accuracy considering that it estimates the total number of bacterial genomes while culture detects viable bacteria. Recognised advantages were the simple colorimetric detection, the inborn indication of a working PCR assay, and the possibility of obtaining results even when partial inhibition of the PCR assay was seen. In addition, the quantitative PCR result can be obtained within one day compared to 3-10 days for culture. The present results and the qualities of the quantitative PCR suggest that this assay will be a useful complement in routine diagnostics and in research.


Intratumor heterogeneity in hepatocellular carcinoma.
Morphologic intratumor heterogeneity is well known to exist in hepatocellular carcinoma (HCC), but very few systematic analyses of this phenomenon have been performed. The aim of this study was to comprehensively characterize morphologic intratumor heterogeneity in HCC. Also, taken into account were well-known immunohistochemical markers and molecular changes in liver cells that are considered in proposed classifications of liver cell neoplasms or discussed as molecular therapeutic targets. In HCC of 23 patients without medical pretreatment, a total of 120 tumor areas were defined. Analyzed were cell and tissue morphology, expression of the liver cell markers cytokeratin (CK)7, CD44, α-fetoprotein (AFP), epithelial cell adhesion molecule (EpCAM), and glutamine synthetase (GS) along with mutations of TP53 and CTNNB1, assayed by both Sanger and next-generation sequencing. Overall, intratumor heterogeneity was detectable in the majority of HCC cases (20 of 23, 87%). Heterogeneity solely on the level of morphology was found in 6 of 23 cases (26%), morphologic heterogeneity combined with immunohistochemical heterogeneity in 9 of 23 cases (39%), and heterogeneity with respect to morphologic, immunohistochemical, and mutational status of TP53 and CTNNB1 in 5 of 23 cases (22%). Our findings demonstrate that intratumor heterogeneity represents a challenge for the establishment of a robust HCC classification and may contribute to treatment failure and drug resistance in many cases of HCC.


A differential response of wild type and mutant promoters to TFIIIB70 overexpression in vivo and in vitro.
TFIIIB, the initiation factor for transcription by RNA polymerase III (pol III) is, in yeast, composed of three subunits: TBP, TFIIIB70/Brf1 and TFIIIB90. To determine the extent to which each of these subunits is limiting for pol III transcription, the effect of overexpressing each subunit was assessed on the expression of wild-type and promoter mutant pol III genes both in vivo and in vitro . In vivo , we find that the synthesis of wild-type pol III genes is not limited to a significant extent by the level of any TFIIIB subunit. There is, however, a two-fold increase in the synthesis of the promoter mutant gene, sup9-e A19-supS1 , in strains overexpressing TFIIIB70. The findings suggest that overexpression of TFIIIB70has a differential effect on the expression of pol III genes with strong versus weak promoters. In vitro transcription assays support this conclusion and reveal an inverse correlation between the transcriptional response to TFIIIB70overexpression and promoter strength. The individual TFIIIB subunits are nuclear by immunofluorescence and are calculated to have nuclear concentrations in the low micromolar range. In comparison, the factors are diluted 100-fold or more in whole cell extracts. This dilution accounts for the generally limiting nature of TFIIIB70in pol III gene transcription in vitro.


Relative impact of form-induced stress vs. uniaxial alignment on multipotent stem cell myogenesis.
Tissue engineering strategies based on multipotent stem cells (MSCs) hold significant promise for the repair or replacement of damaged smooth muscle tissue. To design scaffolds which specifically induce MSC smooth muscle lineage progression requires a deeper understanding of the relative influence of various microenvironmental signals on myogenesis. For instance, MSC myogenic differentiation has been shown to be promoted by increases in active RhoA and FAK, both of which can be induced via increased cell-substrate stress. Separate studies have demonstrated MSC myogenesis to be enhanced by uniaxial cell alignment. The goal of the present study was to compare the impact of increased peak cell-substrate stresses vs. increased uniaxial cell alignment on MSC myogenic differentiation. To this end, MSC fate decisions were compared within two distinct multicellular "forms". A "stripe" multicellular pattern was designed to induce uniaxial cell alignment. In contrast, a second multicellular pattern was designed with "loops" or curves, which altered cell directionality while simultaneously generating regional peak stresses significantly above that intrinsic to the "stripe" form. As anticipated, the higher peak stress levels of the "loop" pattern were associated with increased fractions of active RhoA and active FAK. In contrast, two markers of early smooth muscle lineage progression, myocardin and SM-α-actin, were significantly elevated in the "stripe" pattern relative to the "loop" pattern. These results indicate that scaffolds which promote uniaxial MSC alignment may be more inductive of myogenic differentiation than those associated with increased peak, cell-substrate stress but in which cell directionality varies.


Virtual reality clinical-experimental tests of compassion treatment techniques to reduce paranoia.
Paranoia may build on negative beliefs held both about the self and others. Compassionate imagery may be one way of reducing such negative beliefs, and hence paranoia. Two studies tested this idea, one targeting compassion for the self and one targeting compassion for others. Two-hundred individuals from the general population scoring highly for paranoia were recruited. The studies used a randomised controlled experimental design, with embedded tests for mediation. Study one targeted self-compassion via creation of a compassionate coach (CC) image. Study two targeted compassion for others via loving kindness meditation (LKM). Individuals repeatedly entered neutral virtual reality social environments. Changes in compassion and paranoia were assessed. Compared to controls, the CC group increased in self-compassion (group difference = 2.12, C.I. = 1.57;2.67, p = <0.0001, d = 1.4) and decreased in paranoia (group difference = -1.73, C.I. = -2.48; -0.98, p = <0.0001, d = 0.8). Change in self-compassion explained 57% of change in paranoia. Compared to controls, the LKM group increased their compassion for others (group difference = 3.26, C.I. = 2.72;3.80, p = <0.0001, d = 1.7), and decreased in paranoia (group difference = -1.70, C.I. = -2.50; -0.89, p = <0.0001, d = 0.8). Change in compassion for others explained 67% of change in paranoia. Targeting negative beliefs about the self and others using compassionate imagery causes reductions in paranoia. Tests in clinical populations are indicated.


Deriving a mutation index of carcinogenicity using protein structure and protein interfaces.
With the advent of Next Generation Sequencing the identification of mutations in the genomes of healthy and diseased tissues has become commonplace. While much progress has been made to elucidate the aetiology of disease processes in cancer, the contributions to disease that many individual mutations make remain to be characterised and their downstream consequences on cancer phenotypes remain to be understood. Missense mutations commonly occur in cancers and their consequences remain challenging to predict. However, this knowledge is becoming more vital, for both assessing disease progression and for stratifying drug treatment regimes. Coupled with structural data, comprehensive genomic databases of mutations such as the 1000 Genomes project and COSMIC give an opportunity to investigate general principles of how cancer mutations disrupt proteins and their interactions at the molecular and network level. We describe a comprehensive comparison of cancer and neutral missense mutations; by combining features derived from structural and interface properties we have developed a carcinogenicity predictor, InCa (Index of Carcinogenicity). Upon comparison with other methods, we observe that InCa can predict mutations that might not be detected by other methods. We also discuss general limitations shared by all predictors that attempt to predict driver mutations and discuss how this could impact high-throughput predictions. A web interface to a server implementation is publicly available at http://inca.icr.ac.uk/.


Rgg coordinates virulence factor synthesis and metabolism in Streptococcus pyogenes.
Streptococcus pyogenes is a human-specific pathogen that relies on its host for metabolic substrates. Rgg-like proteins constitute a family of transcriptional regulators present in several gram-positive bacteria. In S. pyogenes, Rgg influences the expression of several virulence-associated proteins localized to the cell wall and extracellular environment. Secreted enzymes may degrade host macromolecules, thereby liberating metabolic substrates. To determine if Rgg regulation of exoprotein expression is associated with altered metabolism, the catabolic activities of S. pyogenes strain NZ131 (serotype M49) and an isogenic rgg mutant strain were analyzed during growth with complex and defined media. As expected, the wild-type strain preferentially used glucose and produced lactic acid during the exponential phase of growth. In contrast, the rgg mutant fermented arginine in the exponential phase of growth, even in the presence of glucose. Arginine degradation was associated with a neutral culture pH and excretion of NH(3) and ornithine. Arginine, serine, and asparagine were depleted from mutant cultures during growth. The addition of arginine and serine to culture media increased the growth yield and NH(3) production of mutant but not wild-type cultures. Addition of asparagine had no effect on the growth yield of either strain. Altered metabolism of arginine and serine in the mutant was associated with increased transcript levels of genes encoding arginine deiminase and a putative serine dehydratase. Thus, Rgg coordinates virulence factor synthesis and catabolic activity and may be important in the pathogen's adaptation to changes in the availability of metabolic substrates.


How I treat myelofibrosis.
It is currently assumed that myelofibrosis (MF) originates from acquired mutations that target the hematopoietic stem cell and induce dysregulation of kinase signaling, clonal myeloproliferation, and abnormal cytokine expression. These pathogenetic processes are interdependent and also individually contributory to disease phenotype-bone marrow stromal changes, extramedullary hematopoiesis, ineffective erythropoiesis, and constitutional symptoms. Molecular pathogenesis of MF is poorly understood despite a growing list of resident somatic mutations that are either functionally linked to Janus kinase (JAK)-signal transducer and activator of transcription hyperactivation (eg JAK2, MPL, and LNK mutations) or possibly involved in epigenetic dysregulation of transcription (TET2, ASXL1, or EZH2 mutations). Current prognostication in primary MF is based on the Dynamic International Prognostic Scoring System-plus model, which uses 8 independent predictors of inferior survival to classify patients into low, intermediate 1, intermediate 2, and high-risk disease groups; corresponding median survivals are estimated at 15.4, 6.5, 2.9, and 1.3 years. Such information is used to plan a risk-adapted treatment strategy for the individual patient, which might include observation alone, conventional or investigational (eg, JAK inhibitors, pomalidomide) drug therapy, allogenic stem cell transplantation with reduced- or conventional-intensity conditioning, splenectomy, or radiotherapy. I discuss these treatment approaches in the context of who should get what and when.


Comparison of metal accumulation in fish species from the southeastern Black sea.
In this study, it was aimed to determine accumulation of the metal concentrations in fish species in different regions which are Sürmene and Yomra bay at southeastern Black sea in Trabzon-Turkey. For this purpose, concentrations of metals (Cr, Co, Ni, Cu, Zn, As, Se, Cd, Sb, Hg, Pb) were measured by inductively coupled plasma mass spectrometry (ICP-MS) in muscle of red mullet (Mullus barbatus ponticus) and whiting (Merlangius merlangus euxinus). Metal concentrations were found for whiting ranged as follows; 0.35-1.64 (Cr), 0.01-0.09 (Co), 0.01-0.71 (Ni), 0.71-1.45 (Cu), 18.64-68.06 (Zn), 2.05-9.66 (As), 0.15-14.16 (Se), 0.01-0.22 (Cd), 0.01-0.01 (Sb), 0.01-0.15 (Hg), 0.01-0.25 (Pb) and for red mullet as 0.43-1.04 (Cr), 0.05-0.23 (Co), 0.02-0.67 (Ni), 0.74-2.32 (Cu), 19.89-43.50 (Zn), 6.04-24.82 (As), 0.02-9.83 (Se), 0.01-0.11 (Cd), 0.01-0.01 (Sb), 0.07-0.18 (Hg), 0.01-0.20 (Pb) μg g(-1) dry weight. Metal concentrations in samples were found to be lower than legal limits proposed by Turkish Food Codex (2008), Food and Agricultural Organization (1983), and European Commission (Off J Eur Union L364-5-L364-24, 2006) for human consumption.


Synthesis of metallo-supramolecular materials based on terpyridine functionalized double-decker silsesquioxane with improved complexation efficiency.
Silsesquioxane-based transition-metal complexes have come to the forefront due to the ability of silsesquioxane to control nanostructures and properties. However, some difficulties in complete complexation and purification limit the widespread use of transition-metal-based supramolecular coordination complexes comprising silsesquioxane. Herein, 2 different approaches have been proposed for the synthesis of metallo-supramolecular materials on the basis of ruthenium(II)-terpyridine functional double-layer silsesquioxane (DDSQ) (Tpy/Ru-DDSQ) (Routes 1 and 2). In Route 1, complexation was followed by functionalization of DDSQ with the ligand, whereas in Route 2, complexation was performed before the ligand was inserted into the DDSQ. Tpy/Ru-DDSQ obtained from both approaches was characterized by 1H NMR, X-ray photoelectron spectrometer, and FTIR and found in the same structure. Both methods were fully discussed and their merits were explored. The complexation yield of the routes was similar. However, the results based on NMR and UV-Vis spectroscopy demonstrated that the incorporation rate of DDSQ into the complex was quite high in Route 2. As far as is known, this is the first study based on the effects of complexing Tpy ligands before/after binding to the target compound, particularly to silsesquioxane-based materials.


Provenance in neuroimaging.
Provenance, the description of the history of a set of data, has grown more important with the proliferation of research consortia-related efforts in neuroimaging. Knowledge about the origin and history of an image is crucial for establishing data and results quality; detailed information about how it was processed, including the specific software routines and operating systems that were used, is necessary for proper interpretation, high fidelity replication and re-use. We have drafted a mechanism for describing provenance in a simple and easy to use environment, alleviating the burden of documentation from the user while still providing a rich description of an image's provenance. This combination of ease of use and highly descriptive metadata should greatly facilitate the collection of provenance and subsequent sharing of data.


Mobility and versatility of the liquid bismuth promoter in the working iron catalysts for light olefin synthesis from syngas.
Liquid metals are a new emerging and rapidly growing class of materials and can be considered as efficient promoters and active phases for heterogeneous catalysts for sustainable processes. Because of low cost, high selectivity and flexibility, iron-based catalysts are the catalysts of choice for light olefin synthesis via Fischer-Tropsch reaction. Promotion of iron catalysts supported by carbon nanotubes with bismuth, which is liquid under the reaction conditions, results in a several fold increase in the reaction rate and in a much higher light olefin selectivity. In order to elucidate the spectacular enhancement of the catalytic performance, we conducted extensive in-depth characterization of the bismuth-promoted iron catalysts under the reacting gas and reaction temperatures by a combination of cutting-edge in situ techniques: in situ scanning transmission electron microscopy, near-atmospheric pressure X-ray photoelectron spectroscopy and in situ X-ray adsorption near edge structure. In situ scanning transmission electron microscopy conducted under atmospheric pressure of carbon monoxide at the temperature of catalyst activation showed iron sintering proceeding via the particle migration and coalescence mechanism. Catalyst activation in carbon monoxide and in syngas leads to liquid bismuth metallic species, which readily migrate over the catalyst surface with the formation of larger spherical bismuth droplets and iron-bismuth core-shell structures. In the working catalysts, during Fischer-Tropsch synthesis, metallic bismuth located at the interface of iron species undergoes continuous oxidation and reduction cycles, which facilitate carbon monoxide dissociation and result in the substantial increase in the reaction rate.


Comparison of pulp response to mineral trioxide aggregate and a bioceramic paste in partial pulpotomy of sound human premolars: a randomized controlled trial.
This randomized clinical trial evaluated clinical sign/symptoms as well as histological pulp reactions in terms of inflammation and mineralized bridge formation after partial pulpotomy of sound human premolars and placement of a bioceramic paste (iRoot BP) or tooth-colored ProRoot MTA as pulp-covering biomaterials. Twenty-four human sound premolars were randomly allocated into two experimental groups (n = 12) treated either with iRoot BP or MTA subsequent to partial pulpotomy. Six weeks after treatment, clinical sign/symptoms and radiographic changes were evaluated. The teeth were then extracted and examined histologically for inflammatory status of the pulp, formation of hard tissue bridge and appearance of the bridge. In terms of pulp inflammation and dentinal bridge formation, the Mann-Whitney U, and for clinical signs, the chi-square test was used (α = 0.05). In terms of pulp inflammation, formation of hard tissue bridge and its appearance, the differences between the two experimental groups were not significant. However, clinical sensitivity to cold was significantly less for teeth treated with MTA (P < 0.05). All cases had formed a hard tissue bridge, and none of the specimens in either group had pulpal necrosis. When treating teeth with healthy pulps, the response to partial pulpotomy treatment with both MTA and iRoot BP was favourable. However, pulps covered with iRoot BP were more sensitive to cold stimuli.


MO-D-BRB-09: Treatment Delivery QA for Online Adaptive Radiation Therapy Based on Dynamic Machine Information (DMI): A Feasibility Study.
To implement a quality assurance (QA) system for the treatment delivery of online adaptive radiation therapy utilizing Dynamic Machine Information (DMI). DMI provides the expected/actual MLC leaf-positions, delivered MU, and beam-on status every 50ms during delivery. In this study a stream of DMI inputs is simulated by playing back Dynalog information recorded while delivering a test fluence map (FM). Based on these DMI inputs, the QA system performs three levels of monitoring/verification on the plan delivery process: (1) Following each input, actual and expected FMs delivered up to the current MLC position is dynamically updated using corresponding MLC positions in the DMI. The magnitude and frequency of pixel-by-pixel fluence differences between these two FMs are calculated and visualized in histograms.(2) At each control point, actual MLC positions are verified against the treatment plan for potential errors in data transfer between the treatment planning system (TPS) and the MLC controller.(3) Both (1) and (2) can signal beam-hold with a user-specified error tolerance.(4) After treatment, delivered dose is reconstructed in TPS based on DMI data during delivery, and compared to planned dose. (1) Efficiency: Average latency from DMI input to the completion of fluence difference calculation is <1ms.(2) Efficacy: For test FM, transient error in leaf positions is (-0.07±0.28)mm; cumulative errors in delivered fluence is (0.003±0.183)% of the maximal fluence. The system can also identify data transfer errors between TPS and MLC controller. Off-line dose reconstruction and evaluation show <0.5% dosimetric discrepancy from planned dose distribution for the test FM. This QA system is capable of identifying MLC position/fluence errors in near real-time, and assessing dosimetric impact of the treatment delivery process. It is thus a valuable tool for clinical implementation of online adaptive radiation therapy. (Research partially supported by Varian) Research partially supported by Varian Medical Systems.


Prognostic Performance of Kidney Volume Measurement for Polycystic Kidney Disease: A Comparative Study of Ellipsoid vs. Manual Segmentation.
Total kidney volume (TKV) is a validated prognostic biomarker for risk assessment in autosomal dominant polycystic kidney disease (ADPKD). TKV by manual segmentation (MS) is the "gold standard" but is time-consuming and requires expertise. The purpose of this study was to compare TKV-based prognostic performance by ellipsoid (EL) vs. MS in a large cohort of patients. Cross-sectional study of 308 patients seen at a tertiary referral center; all had a standardized MRI with typical imaging of ADPKD. An experienced radiologist blinded to patient clinical results performed all TKV measurements by EL and MS. We assessed the agreement of TKV measurements by intraclass correlation(ICC) and Bland-Altman plot and also how the disagreement of the two methods impact the prognostic performance of the Mayo Clinic Imaging Classification (MCIC). We found a high ICC of TKV measurements (0.991, p < 0.001) between EL vs. MS; however, 5.5% of the cases displayed disagreement of TKV measurements >20%. We also found a high degree of agreement of the individual MCIC risk classes (i.e. 1A to 1E) with a Cohen's weighted-kappa of 0.89; but 42 cases (13.6%) were misclassified by EL with no misclassification spanning more than one risk class. The sensitivity and specificity of EL in distinguishing low-risk (1A-B) from high-risk (1C-E) MCIC prognostic grouping were 96.6% and 96.1%, respectively. Overall, we found an excellent agreement of TKV-based risk assessment between EL and MS. However, caution is warranted for patients with MCIC 1B and 1C, as misclassification can have therapeutic consequence.


T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data.
Transposable elements (TEs) constitute the most active, diverse and ancient component in a broad range of genomes. Complete understanding of genome function and evolution cannot be achieved without a thorough understanding of TE impact and biology. However, in-depth analysis of TEs still represents a challenge due to the repetitive nature of these genomic entities. In this work, we present a broadly applicable and flexible tool: T-lex2. T-lex2 is the only available software that allows routine, automatic and accurate genotyping of individual TE insertions and estimation of their population frequencies both using individual strain and pooled next-generation sequencing data. Furthermore, T-lex2 also assesses the quality of the calls allowing the identification of miss-annotated TEs and providing the necessary information to re-annotate them. The flexible and customizable design of T-lex2 allows running it in any genome and for any type of TE insertion. Here, we tested the fidelity of T-lex2 using the fly and human genomes. Overall, T-lex2 represents a significant improvement in our ability to analyze the contribution of TEs to genome function and evolution as well as learning about the biology of TEs. T-lex2 is freely available online at http://sourceforge.net/projects/tlex.


Identification of three new cis-regulatory IRF5 polymorphisms: in vitro studies.
Polymorphisms in the interferon regulatory factor 5 (IRF5) gene are associated with susceptibility to systemic lupus erythematosus, rheumatoid arthritis and other diseases through independent risk and protective haplotypes. Several functional polymorphisms are already known, but they do not account for the protective haplotypes that are tagged by the minor allele of rs729302. Polymorphisms in linkage disequilibrium (LD) with rs729302 or particularly associated with IRF5 expression were selected for functional screening, which involved electrophoretic mobility shift assays (EMSAs) and reporter gene assays. A total of 54 single-nucleotide polymorphisms in the 5' region of IRF5 were genotyped. Twenty-four of them were selected for functional screening because of their high LD with rs729302 or protective haplotypes. In addition, two polymorphisms were selected for their prominent association with IRF5 expression. Seven of these twenty-six polymorphisms showed reproducible allele differences in EMSA. The seven were subsequently analyzed in gene reporter assays, and three of them showed significant differences between their two alleles: rs729302, rs13245639 and rs11269962. Haplotypes including the cis-regulatory polymorphisms correlated very well with IRF5 mRNA expression in an analysis based on previous data. We have found that three polymorphisms in LD with the protective haplotypes of IRF5 have differential allele effects in EMSA and in reporter gene assays. Identification of these cis-regulatory polymorphisms will allow more accurate analysis of transcriptional regulation of IRF5 expression, more powerful genetic association studies and deeper insight into the role of IRF5 in disease susceptibility.


High-throughput phenotyping with deep learning gives insight into the genetic architecture of flowering time in wheat.
Measurement of plant traits with precision and speed on large populations has emerged as a critical bottleneck in connecting genotype to phenotype in genetics and breeding. This bottleneck limits advancements in understanding plant genomes and the development of improved, high-yielding crop varieties. Here we demonstrate the application of deep learning on proximal imaging from a mobile field vehicle to directly estimate plant morphology and developmental stages in wheat under field conditions. We developed and trained a convolutional neural network with image datasets labeled from expert visual scores and used this "breeder-trained" network to classify wheat morphology and developmental stages. For both morphological (awned) and phenological (flowering time) traits, we demonstrate high heritability and very high accuracy against the "ground-truth" values from visual scoring. Using the traits predicted by the network, we tested genotype-to-phenotype association using the deep learning phenotypes and uncovered novel epistatic interactions for flowering time. Enabled by the time-series high-throughput phenotyping, we describe a new phenotype as the rate of flowering and show heritable genetic control for this trait. We demonstrated a field-based high-throughput phenotyping approach using deep learning that can directly measure morphological and developmental phenotypes in genetic populations from field-based imaging. The deep learning approach presented here gives a conceptual advancement in high-throughput plant phenotyping because it can potentially estimate any trait in any plant species for which the combination of breeder scores and high-resolution images can be obtained, capturing the expert knowledge from breeders, geneticists, pathologists, and physiologists to train the networks.


Low cleaved caspase-7 levels indicate unfavourable outcome across all breast cancers.
Elevated levels of the anti-apoptotic BCL2 protein associate with favourable outcome in breast cancer. We investigated whether executioner caspase activation downstream of mitochondrial apoptosis was associated with, or independent, of BCL2's prognostic signature in breast cancer. Levels of pro- and anti-apoptotic BCL2 family proteins were quantified in triple negative breast cancer (TNBC) samples and utilised to calculate BCL2 profiles of 845 breast cancer patients. Biomarkers including single apoptosis proteins and network-enriched apoptosis system signatures were evaluated using uni- and multi-variate Cox-models. In both TNBC and non-TNBC breast cancer, the anti-apoptotic BCL2 protein was particularly abundant when compared to other solid tumours. High BCL2 protein levels were prognostic of favourable outcome across all breast cancers (HR 0.4, 95% CI 0.2-0.6, Wald p < 0.0001). Although BCL2 and cleaved caspase-7 levels were negatively correlated, levels of cleaved caspase-7 were also associated with favourable outcome (HR 0.4, 95% CI 0.3-0.7, Wald p = 0.001). A combination of low BCL2 and low cleaved caspase-7 protein levels was highly prognostic of unfavourable outcome across all breast cancers (HR 11.29, 95% CI 2.20-58.23, Wald p = 0.01). A combination of BCL2 and cleaved caspase-7 levels is a promising prognostic biomarker in breast cancer patients. BCL2 levels are elevated in breast cancer where they are marker of good prognosis. BCL2 and active caspase levels correlate negatively; yet, active caspases indicate good outcome. Low BCL2 and low caspase-7 are highly prognostic of unfavourable outcome across all breast cancers. BCL2 levels indicate molecular subtype and tumour proliferation status in breast cancer.


Performance of the trim and fill method in the presence of publication bias and between-study heterogeneity.
The trim and fill method allows estimation of an adjusted meta-analysis estimate in the presence of publication bias. To date, the performance of the trim and fill method has had little assessment. In this paper, we provide a more comprehensive examination of different versions of the trim and fill method in a number of simulated meta-analysis scenarios, comparing results with those from usual unadjusted meta-analysis models and two simple alternatives, namely use of the estimate from: (i) the largest; or (ii) the most precise study in the meta-analysis. Findings suggest a great deal of variability in the performance of the different approaches. When there is large between-study heterogeneity the trim and fill method can underestimate the true positive effect when there is no publication bias. However, when publication bias is present the trim and fill method can give estimates that are less biased than the usual meta-analysis models. Although results suggest that the use of the estimate from the largest or most precise study seems a reasonable approach in the presence of publication bias, when between-study heterogeneity exists our simulations show that these estimates are quite biased. We conclude that in the presence of publication bias use of the trim and fill method can help to reduce the bias in pooled estimates, even though the performance of this method is not ideal. However, because we do not know whether funnel plot asymmetry is truly caused by publication bias, and because there is great variability in the performance of different trim and fill estimators and models in various meta-analysis scenarios, we recommend use of the trim and fill method as a form of sensitivity analysis as intended by the authors of the method.


NFL Physicians: Committed to Excellence in Patient-Player Care.
The National Football League Physicians Society read with disappointment the article "A Proposal to Address NFL Club Doctors' Conflicts of Interest and to Promote Player Trust." In spite of the authors' suggestions, NFL physicians are accomplished medical professionals who abide by the highest ethical standards in providing treatment to all of their patients, including those who play in the NFL. It defies logic for the authors not to have engaged experienced and active NFL physicians from the very start of their effort to explore, challenge, and recommend significant alterations to the delivery of health care to NFL players. As troubling as this article is from so many perspectives, it does represent an opportunity for the NFLPS to set the record straight and call attention to the excellent quality of care NFL players receive. In addition, it represents an opportunity to expose the extraordinarily weak evidence presented in the article and to refute the baseless allegations that challenge the high ethical standards of NFL physicians. Contrary to solid scientific research that starts with a hypothesis based on theory, in this case, it seems quite apparent that the authors started with a predetermined conclusion and set out to justify it. Their premise was flawed, and they failed in their execution.


Prebiotic, Immunomodulating, and Antifatigue Effects of Konjac Oligosaccharide.
Irregular and long time work schedules not only makes people feel fatigue, but also brings great risks of diseases, due to gastrointestinal disorder and immune dysfunction. Therefore, it has positive significance to help challenged people stay energetic and healthy with food supplement. Konjac oligosaccharide has shown various physiological benefits and been recommended in the fortification of functional foods. However, there have been few reports on its application aimed to simultaneously relieve physical fatigue and keep body healthy. In this paper, the potential prebiotic, immunoregulatory, and antifatigue activities of konjac oligosaccharide were evaluated in vitro and in vivo. The results showed that konjac oligosaccharide could promote probiotics growth and short chain fatty acids production in mice cecum. At the concentration of 50 to 200 μg/mL, konjac oligosaccharide could activate murine macrophage RAW 264.7 to secret NO and cytokines of IL-10 and IL-6. Moreover, this oligosaccharide could alleviate physical fatigue by prolonging exhaustive time, improving the level of superoxide dismutases and glutathione peroxidase, increasing the content of blood glucose, and decreasing the content of blood urea nitrogen. The results suggested that konjac oligosaccharide had prebiotic, immunoregulatory, and antifatigue effects, providing its application potential in functional food aimed at people with irregular and long time work.


The Duty to Look for Incidental Findings in Imaging Research.
Imaging research regularly yields incidental findings that may have personal medical or reproductive decision-making significance to study participants. It is widely assumed that researchers have a moral obligation to disclose at least some kinds of incidental findings to research participants. However, it is also a widely held view that researchers do not have a moral obligation to actively look for abnormalities irrelevant to the aims of their study. This paper challenges that assumption.


Timing and duration of incarceration and high-risk sexual partnerships among African Americans in North Carolina.
Incarceration may contribute to HIV transmission by disrupting stable partnerships and promoting high-risk partnerships. We investigated incarceration and high-risk partnerships among African Americans in North Carolina. We conducted a weighted analysis using the North Carolina Rural Health Project (N = 320), a population-based case-control study of HIV among African Americans. We measured associations between timing and duration of incarceration and high-risk partnerships (multiple partnerships or sex trade for money or drugs). Duration of incarceration appeared to be more important than how long ago incarceration occurred. After adjustment for sociodemographic indicators, high-risk partnerships were associated with short-term (<1 month) incarceration of the respondent versus no respondent incarceration (men: adjusted prevalence ratio (aPR) 1.9, 95% confidence interval (95% CI) 1.2-2.8; women: aPR 3.1, 95% CI 1.2-8.3). High-risk partnerships also were associated with incarceration of a partner versus no partner incarceration (men: aPR 1.8, 95% CI 1.1-3.0; women: aPR 2.0, 95% CI 1.1-3.8). Among men, associations remained when adjusting for substance use. Among women, adjustment for substance use weakened estimates due to the strong correlation between substance use and incarceration. HIV-prevention programs targeting currently and formerly incarcerated individuals and their partners may decrease HIV in African American communities with high incarceration rates.


Short-term variation in the subgingival microbiota in two groups of patients treated with clear aligners and vestibular fixed appliances: A longitudinal study.
To evaluate the subgingival microbiological changes during the first six months of therapy with clear aligners (CAs) and fixed appliances (FAs). The null hypothesis was that there would be no microbiological differences between the two. Two groups of patients to be treated, respectively, with CAs (14 patients; 9 females and 5 males; mean age 21 years ± 0.25) and FAs (13 patients; 8 females and 5 males; mean 14 years ± 0.75) were consecutively recruited. Subgingival microbiological samples were obtained at the right upper central incisor and right first molar at four different time points: before appliance fitting (T0), and at 1 month (T1), 3 months (T3) and 6 months (T6) thereafter. Total bacterial load (TBL) and counts of the bacteria Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Fusobacterium nucleatum, Campylobacter rectus, Treponema denticola and Tannerella forsythia were determined using real-time PCR. Total bacterial load did not vary in the CA group, while a significant increase was detected after 3 and 6 months of treatment in the FA group. Unlike red complex species, C rectus and F nucleatum were often detected: levels remained stable in the CA group but increased progressively in the FA group. The type of orthodontic appliance influences the subgingival microbiota. TBL increased in the FA group but not in the CA group, although the levels of the individual periodontal pathogenic bacteria species did not significantly increase during the observation period.


Cholesterol and coronary heart disease. Future directions.
The importance of high serum cholesterol levels as a risk factor for coronary heart disease and the benefit of lowering cholesterol levels for reducing risk are being increasingly accepted. A broad consensus to this effect has led to the establishment of the National Cholesterol Education Program. Although the available evidence fully justifies this program, its practical application to the American public has generated a series of new questions that must be explored. For example, it can be questioned whether reduction in coronary risk through lowering cholesterol levels extends to both sexes and all age groups. For people with high cholesterol levels, dietary modification is undoubtedly the first step of management, but the fraction of people responding adequately to dietary change remains to be determined. Finally, indications for drug therapy and choice of drugs need further exploration, particularly in the area of cost vs benefit. Thus, continuing research must be carried out in parallel with clinical and public health application of cholesterol education.


Microdamage generation by tapered and cylindrical mini-screw implants after pilot drilling.
To investigate the relationship between mini-screw implant (MSI) diameter (1.6 vs 2.0 mm) and shape (tapered vs cylindrical) and the amount of microdamage generated during insertion. Thirty-six cylindrical and 36 tapered MSIs, 6 mm long, were used in this study. Half of each shape was 1.6 mm in diameter, while the other half was 2.0 mm. After pilot drilling, four and five MSIs were inserted, respectively, into fresh cadaveric maxillae and mandibles of dogs. Bone blocks containing the MSIs were sectioned and ground parallel to the MSI axis. Epifluorescent microscopy was used to measure overall cortical thickness, crack length, and crack number adjacent to the MSI. Crack density and total microdamage burden per surface length were calculated. Three-way analysis of variance (ANOVA) was used to test the effects of jaw, and MSI shape and diameter. Pairwise comparisons were made to control the overall significance level at 5%. The larger (2.0 vs 1.6 mm) cylindrical MSIs increased the numbers, lengths, and densities of microcracks, and the total microdamage burden. The same diameter cylindrical and tapered MSIs generated a similar number of cracks and crack lengths. More total microdamage burden was created by the 2.0-mm cylindrical than the 2.0-mm tapered MSIs. Although higher crack densities were produced by the insertion of 1.6-mm tapered MSIs, there was no difference in total microdamage burden induced by 1.6-mm tapered and 1.6-mm cylindrical MSIs. Pilot drilling is effective in reducing microdamage during insertion of tapered MSIs. To prevent excessive microdamage, large diameter and cylindrical MSIs should be avoided.


The topoisomerase II inhibitor VM-26 induces marked changes in histone H1 kinase activity, histones H1 and H3 phosphorylation, and chromosome condensation in G2 phase and mitotic BHK cells.
We have examined the effects of topoisomerase inhibitors on the phosphorylation of histones in chromatin during the G2 and the M phases of the cell cycle. Throughout the G2 phase of BHK cells, addition of the topoisomerase II inhibitor VM-26 prevented histone H1 phosphorylation, accompanied by the inhibition of intracellular histone H1 kinase activity. However, VM-26 had no inhibitory effect on the activity of the kinase in vitro, suggesting an indirect influence on histone H1 kinase activity. Entry into mitosis was also prevented, as monitored by the absence of nuclear lamina depolymerization, chromosome condensation, and histone H3 phosphorylation. In contrast, the topoisomerase I inhibitor, camptothecin, inhibited histone H1 phosphorylation and entry into mitosis only when applied at early G2. In cells that were arrested in mitosis, VM-26 induced dephosphorylation of histones H1 and H3, DNA breaks, and partial chromosome decondensation. These changes in chromatin parameters probably reverse the process of chromosome condensation, unfolding condensed regions to permit the repair of strand breaks in the DNA that were induced by VM-26. The involvement of growth-associated histone H1 kinase in these processes raises the possibility that the cell detects breaks in the DNA through their effects on the state of DNA supercoiling in constrained domains or loops. It would appear that histone H1 kinase and topoisomerase II work coordinately in both chromosome condensation and decondensation, and that this process participates in the VM-26-induced G2 arrest of the cell.


Longer-but Harder-Lives?: The Hispanic Health Paradox and the Social Determinants of Racial, Ethnic, and Immigrant-Native Health Disparities from Midlife through Late Life.
Though Hispanics live long lives, whether a "Hispanic paradox" extends to older-age health remains unclear, as do the social processes underlying racial-ethnic and immigrant-native health disparities. Using data from the Health and Retirement Study (2004-2012; N = 6,581), we assess the health of U.S.- and foreign-born Hispanics relative to U.S.-born whites and blacks and examine the socioeconomic, stress, and behavioral pathways contributing to health disparities. Findings indicate higher disability, depressive, metabolic, and inflammatory risk for Hispanics relative to whites and similar health profiles among Hispanics and blacks. We find limited evidence of a healthy immigrant pattern among foreign-born Hispanics. While socioeconomic factors account for Hispanic-white gaps in inflammation, disparities in other outcomes persist after adjustment for socioeconomic status, due in part to group differences in stress exposure. Hispanics may live long lives, but their lives are characterized by more socioeconomic hardship, stress, and health risk than whites and similar health risks as blacks.


Blocking beta-catenin binding to the ZBP1 promoter represses ZBP1 expression, leading to increased proliferation and migration of metastatic breast-cancer cells.
ZBP1 (zipcode-binding protein 1, also known as IMP-1) is an mRNA regulator, functioning in mRNA localization, stability and translational control. ZBP1 is actively expressed during embryogenesis and tumorigenesis, but its expression is repressed in metastatic breast-cancer cell lines and tumors. In this article, we show that downregulation of ZBP1 expression results from its promoter methylation, an epigenetic process that remodels the chromatin structure and frequently represses gene activity. Demethylation of the ZBP1 promoter in metastatic cells reactivated ZBP1 expression, owing to restoration of the interaction of the ZBP1 promoter with beta-catenin. Loss of ZBP1 function not only increased growth ability of metastatic cells, but also promoted cell migration. We identified a number of mRNAs that were selectively associated with ZBP1 in breast-cancer cells. Many of these are involved in cell motility and in cell-cycle regulation, and displayed altered expression patterns in the absence of ZBP1. These data suggest that repression of ZBP1 deregulates its associated mRNAs, leading to the phenotypic changes of breast cancers.


Protein kinase and Ca2+ modulation of myo-inositol transport in cultured retinal pigment epithelial cells.
The acute regulation of inwardly directed Na(+)-myo-inositol (MI) cotransporter activity and basal and volume-sensitive MI efflux by protein kinases C (PKC) and A (PKA), cytosolic Ca2+, and phosphoinositide (PI) turnover were characterized in cultured human retinal pigment epithelial cells using 2-[3H]MI and liquid scintillation spectrometry. Kinetic analysis revealed two distinct Na(+)-MI cotransporter components differing in apparent Michaelis constant and maximal velocity. Composite Na(+)-MI cotransport activity was stimulated by PKA activation, the muscarinic agonist carbachol, and the Ca2+ ionophore A-23187 and was inhibited by PKC activation. PKC activation also increased MI efflux, but only the volume-sensitive component, whereas PKA activation increased both basal and volume-sensitive MI efflux. These studies implicate PKC as a negative modulator of MI content through Na(+)-MI cotransport inhibition and potentiation of volume-sensitive MI efflux. PKA is a positive modulator of both Na(+)-MI cotransport and basal and volume-sensitive MI efflux. Cytosolic Ca2+ release through receptor-mediated PI hydrolysis may facilitate Na(+)-MI cotransport activity.


Coproduction of novel 16S rRNA methylase RmtD and metallo-beta-lactamase SPM-1 in a panresistant Pseudomonas aeruginosa isolate from Brazil.
Serious infections with Pseudomonas aeruginosa are frequently treated with the combination of a beta-lactam antimicrobial and an aminoglycoside. P. aeruginosa strain PA0905 was isolated in 2005 from an inpatient in Brazil. It showed a panresistant phenotype that included resistance to beta-lactams, aminoglycosides, and fluoroquinolones. The beta-lactam resistance was conferred by the production of the metallo-beta-lactamase SPM-1. No inhibitory zone was observed when a disk diffusion test was performed with the semisynthetic aminoglycoside arbekacin, raising suspicion of 16S rRNA methylase production. A cloning experiment subsequently revealed the presence of a novel 16S rRNA methylase, RmtD, which accounted for the high-level resistance to all 4,6-disubstituted deoxystreptamine aminoglycosides, such as amikacin, tobramycin, and gentamicin. RmtD shared a moderate degree of identity with RmtA, another 16S rRNA methylase that was initially reported to occur in P. aeruginosa in Japan in 2003. This is the first identification of aminoglycoside resistance mediated by a 16S rRNA methylase in South America. This is also the first report to document coproduction of a metallo-beta-lactamase and a 16S rRNA methylase, a combination that would severely compromise therapeutic options for the infected patients.


The retention and disruption of color information in human short-term visual memory.
Previous studies have demonstrated that the retention of information in short-term visual perceptual memory can be disrupted by the presentation of masking stimuli during interstimulus intervals (ISIs) in delayed discrimination tasks (S. Magnussen & W. W. Greenlee, 1999). We have exploited this effect in order to determine to what extent short-term perceptual memory is selective for stimulus color. We employed a delayed hue discrimination paradigm to measure the fidelity with which color information was retained in short-term memory. The task required 5 color normal observers to discriminate between spatially non-overlapping colored reference and test stimuli that were temporally separated by an ISI of 5 s. The points of subjective equality (PSEs) on the resultant psychometric matching functions provided an index of performance. Measurements were made in the presence and absence of mask stimuli presented during the ISI, which varied in hue around the equiluminant plane in DKL color space. For all reference stimuli, we found a consistent mask-induced, hue-dependent shift in PSE compared to the "no mask" conditions. These shifts were found to be tuned in color space, only occurring for a range of mask hues that fell within bandwidths of 29-37 deg. Outside this range, masking stimuli had little or no effect on measured PSEs. The results demonstrate that memory masking for color exhibits selectivity similar to that which has already been demonstrated for other visual attributes. The relatively narrow tuning of these interference effects suggests that short-term perceptual memory for color is based on higher order, non-linear color coding.


Acceptance of guidance to care at the emergency department following attempted suicide.
Research, aimed at improving the continuity of care after hospital discharge following attempted suicide focuses on the effectiveness of the interventions. Little attention has been paid to patients who immediately decline guidance to advised post-discharge care. We aimed to identify differences between accepters and decliners of guidance to care (GtC) in relation to the characteristics of patients who presented at the emergency department (ED) of an urban hospital in the Netherlands after attempted suicide. This cross-sectional study included all patients who presented at the ED of OLVG-West Amsterdam with a suicide attempt or intentional self-harm and were referred for psychiatric evaluation. Data were collected over a period of twenty months using a semi-structured questionnaire. Subgroups were described in relation the acceptance of GtC using univariate and multivariate logistic regression analyses. In total, 257 patients were included. GtC was accepted by 77%. Suicide attempters who reported loneliness as reason for the attempt showed a positive relation to acceptance. No indication was found that patients at higher risk for suicide are more reluctant to accept GtC. Suicide attempters with a non-Western ethnicity, especially patients with a Turkish/Moroccan ethnicity, declined contact by the GtC nurse significantly more often. In addition, patients who currently did not receive care were significantly more often of non-Western ethnicity and younger than 25. Acceptance of GtC is high among patients who presented at the ED after attempted suicide. The patients who were the most reluctant to accept GtC were young suicide attempters of non-Western ethnicity who were not in current care. As this study is the first to address the acceptance of GtC, we point out two lines of inquiry for further research. First, reasons to accept or decline need to be investigated further since only interventions that are accepted by patients have a chance to improve clinically relevant outcome. Second, follow-up research is warranted comparing the adherence to advised post-discharge care and attempted or completed suicide among accepters versus decliners of GtC in various ethnic and sociodemographic subgroups.


The New Demographic Transition: Most Gains in Life Expectancy Now Realized Late in Life.
The share of increases in life expectancy realized after age 65 was only about 20 percent at the beginning of the 20th century for the US and 16 other countries at comparable stages of development; but that share was close to 80 percent by the dawn of the 21st century, and is almost certainly approaching 100 percent asymptotically. This new demographic transition portends a diminished survival effect on working life. For high-income countries at the forefront of the longevity transition, expected lifetime labor force participation as a percent of life expectancy is declining. Innovative policies are needed if societies wish to preserve a positive relationship running from increasing longevity to greater prosperity.


SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species.
A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.


The effects of add-on zafirlukast treatment to budesonide on bronchial hyperresponsiveness and serum levels of eosinophilic cationic protein and total antioxidant capacity in asthmatic patients.
Mild persistent asthma is most effectively controlled with inhaled corticosteroids. Leukotriene receptor antagonists have complementary effects to corticosteroids on inflammation control. The additional effect of a leukotriene receptor antagonist, zafirlukast, was investigated in stable asthma patients under control with inhaled budesonide. We conducted a randomised, double-blind, placebo-controlled, single center trial to investigate the effects of add-on zafirlukast treatment to budesonide, on symptom score, pulmonary function, bronchial responsiveness, and serum levels of eosinophilic cationic protein (ECP) and antioxidant capacity in stable asthmatic patients under control with inhaled budesonide. The present study included 21 mild or moderate asthmatic patients (8 males and 13 females), who were stable at least for 6 weeks with inhaled budesonide (400 microg/day). Serum total antioxidant capacity (TAC) and ECP levels were measured, and symptom scoring, spirometry, and bronchial provocation with methacholine were performed. Then, the patients were randomised to use either placebo or oral zafirlukast (40 mg/day) in addition to budesonide for 6 weeks. At the 6th week, symptom scoring, spirometry, and bronchial provocation tests were repeated and serum TAC and ECP levels were measured again. After add-on zafirlukast treatment to budesonide, forced expiratory volume in 1 second (FEV(1)), TAC and ECP values did not change significantly (p > 0.05) but bronchial hyperresponsiveness and symptom score decreased significantly (p = 0.022) compared to baseline. Thus, in stable asthmatic patients, add-on zafirlukast treatment to budesonide improves symptoms and decreases bronchial hyperresponsiveness.


The effects of combined x-axis translations and y-axis rotations on projected lamina junction offset.
To quantify the projection errors caused by the combining of selected x-axis translations with selected y-axis rotations as seen on plain film anteroposterior (AP) radiographs. A computer was used to model the projection of the lamina junction and points on the lateral body margins of a 2-dimensional vertebral model onto an AP radiograph. This simulation was done in the neutral position and in a number of combinations of x-axis translations and y-axis rotations. Some combinations of x-axis translation and y-axis rotation can increase or decrease the projected horizontal lamina offset as compared with what would be found with rotation alone. The projection of some combinations may lead the viewer to believe that rotation of the vertebral model is in the opposite direction of its true rotation. The projections of combined movements of x-axis translations and y-axis rotations can lead to confusion when the clinician attempts to discern quantity and direction of y-axis vertebral rotation from the AP radiograph.


Towards systematic discovery of signaling networks in budding yeast filamentous growth stress response using interventional phosphorylation data.
Reversible phosphorylation is one of the major mechanisms of signal transduction, and signaling networks are critical regulators of cell growth and development. However, few of these networks have been delineated completely. Towards this end, quantitative phosphoproteomics is emerging as a useful tool enabling large-scale determination of relative phosphorylation levels. However, phosphoproteomics differs from classical proteomics by a more extensive sampling limitation due to the limited number of detectable sites per protein. Here, we propose a comprehensive quantitative analysis pipeline customized for phosphoproteome data from interventional experiments for identifying key proteins in specific pathways, discovering the protein-protein interactions and inferring the signaling network. We also made an effort to partially compensate for the missing value problem, a chronic issue for proteomics studies. The dataset used for this study was generated using SILAC (Stable Isotope Labeling with Amino acids in Cell culture) technique with interventional experiments (kinase-dead mutations). The major components of the pipeline include phosphopeptide meta-analysis, correlation network analysis and causal relationship discovery. We have successfully applied our pipeline to interventional experiments identifying phosphorylation events underlying the transition to a filamentous growth form in Saccharomyces cerevisiae. We identified 5 high-confidence proteins from meta-analysis, and 19 hub proteins from correlation analysis (Pbi2p and Hsp42p were identified by both analyses). All these proteins are involved in stress responses. Nine of them have direct or indirect evidence of involvement in filamentous growth. In addition, we tested four of our predicted proteins, Nth1p, Pbi2p, Pdr12p and Rcn2p, by interventional phenotypic experiments and all of them present differential invasive growth, providing prospective validation of our approach. This comprehensive pipeline presents a systematic way for discovering signaling networks using interventional phosphoproteome data and can suggest candidate proteins for further investigation. We anticipate the methodology to be applicable as well to other interventional studies via different experimental platforms.


Proteomic Analysis of Irradiation with Millimeter Waves on Soybean Growth under Flooding Conditions.
Improving soybean growth and tolerance under environmental stress is crucial for sustainable development. Millimeter waves are a radio-frequency band with a wavelength range of 1-10 mm that has dynamic effects on organisms. To investigate the potential effects of millimeter-waves irradiation on soybean seedlings, morphological and proteomic analyses were performed. Millimeter-waves irradiation improved the growth of roots/hypocotyl and the tolerance of soybean to flooding stress. Proteomic analysis indicated that the irradiated soybean seedlings recovered under oxidative stress during growth, whereas proteins related to glycolysis and ascorbate/glutathione metabolism were not affected. Immunoblot analysis confirmed the promotive effect of millimeter waves to glycolysis- and redox-related pathways under flooding conditions. Sugar metabolism was suppressed under flooding in unirradiated soybean seedlings, whereas it was activated in the irradiated ones, especially trehalose synthesis. These results suggest that millimeter-waves irradiation on soybean seeds promotes the recovery of soybean seedlings under oxidative stress, which positively regulates soybean growth through the regulation of glycolysis and redox related pathways.


Induction of HIV-1-specific mucosal immune responses following intramuscular recombinant adenovirus serotype 26 HIV-1 vaccination of humans.
Defining mucosal immune responses and inflammation to candidate human immunodeficiency virus type 1 (HIV-1) vaccines represents a current research priority for the HIV-1 vaccine field. In particular, it is unclear whether intramuscular immunization can elicit immune responses at mucosal surfaces in humans. In this double-blind, randomized, placebo-controlled clinical trial, we evaluated systemic and mucosal immune responses to a candidate adenovirus serotype 26 (Ad26) vectored HIV-1 envelop (Env) vaccine in baseline Ad26-seronegative and Ad26-seropositive healthy volunteers. Systematic mucosal sampling with rectal Weck-Cel sponges and rectal biopsies were performed. Intramuscular immunization elicited both systemic and mucosal Env-specific humoral and cellular immune responses in the majority of subjects. Individuals with preexisting Ad26-specific neutralizing antibodies had vaccine-elicited immune responses comparable to those of subjects who were Ad26 seronegative. We also observed no increase in activated total or vector-specific mucosal CD4+ T lymphocytes following vaccination by either histopathology or flow cytometry. These data demonstrate that a single intramuscular administration of this Ad26-vectored HIV-1 Env vaccine elicited both systemic and mucosal immune responses in humans. Induction of antigen-specific humoral and cellular mucosal immunity was not accompanied by a detectable increase in mucosal inflammation. NCT01103687.


Altered Anterior Segment Biometric Parameters in Mice Deficient in SPARC.
Secreted protein acidic and rich in cysteine (SPARC) and Hevin are structurally related matricellular proteins involved in extracellular matrix assembly. In this study, we compared the anterior chamber biometric parameters and iris collagen properties in SPARC-, Hevin- and SPARC-/Hevin-null with wild-type (WT) mice. The right eyes of 53 WT, 35 SPARC-, 56 Hevin-, and 63 SPARC-/Hevin-null mice were imaged using the RTVue-100 Fourier-domain optical coherence tomography system. The parameters measured were anterior chamber depth (ACD), trabecular-iris space area (TISA), angle opening distance (AOD), and pupil diameter. Biometric data were analyzed using analysis of covariance and adjusted for age, sex, and pupil diameter. Expression of Col1a1, Col8a1, and Col8a2 transcripts in the irises was measured by quantitative polymerase chain reaction. Collagen fibril thickness was evaluated by transmission electron microscopy. Mice that were SPARC- and SPARC-/Hevin-null had 1.28- and 1.25-fold deeper ACD, 1.45- and 1.53-fold larger TISA, as well as 1.42- and 1.51-fold wider AOD than WT, respectively. These measurements were not significantly different between SPARC- and SPARC-/Hevin-null mice. The SPARC-null iris expressed lower Col1a1, but higher Col8a1 and Col8a2 transcripts compared with WT. Collagen fibrils in the SPARC- and SPARC-/Hevin-null irises were 1.5- and 1.7-fold thinner than WT, respectively. The Hevin-null iris did not differ from WT in these collagen properties. SPARC-null mice have deeper anterior chamber as well as wider drainage angles compared with WT. Therefore, SPARC plays a key role in influencing the spatial organization of the anterior segment, potentially via modulation of collagen properties, while Hevin is not likely to be involved.


Complex Economies Have a Lateral Escape from the Poverty Trap.
We analyze the decisive role played by the complexity of economic systems at the onset of the industrialization process of countries over the past 50 years. Our analysis of the input growth dynamics, considering a further dimension through a recently introduced measure of economic complexity, reveals that more differentiated and more complex economies face a lower barrier (in terms of GDP per capita) when starting the transition towards industrialization. As a consequence, we can extend the classical concept of a one-dimensional poverty trap, by introducing a two-dimensional poverty trap: a country will start the industrialization process if it is rich enough (as in neo-classical economic theories), complex enough (using this new dimension and laterally escaping from the poverty trap), or a linear combination of the two. This naturally leads to the proposal of a Complex Index of Relative Development (CIRD) which shows, when analyzed as a function of the growth due to input, a shape of an upside down parabola similar to that expected from the standard economic theories when considering only the GDP per capita dimension.


Genetic analysis of the human tumor necrosis factor alpha/cachectin promoter region in a macrophage cell line.
The 615-bp 5' flanking region of the human TNF-alpha/cachectin gene was isolated and ligated to the luciferase reporter gene. In addition, a series of truncated promoter constructs was generated by exonuclease III digestion. The promoter activity of these constructs was studied in a transient transfection system using the TNF-alpha-producing U937 cell line. Full-length and truncated TNF promoter constructions extending from -615 to -95 bp relative to the transcription start site (TSS) could be induced by phorbol esters. A construct truncated to within 36 bp of the TSS (and within 11 bp of the TATAA box) was inactive. Therefore, the phorbol ester responsive is localized in the TNF/cachectin promoter to a relatively short region proximal to the TATAA box.


Self-thermophoretic motion of controlled assembled micro-/nanomotors.
As artificial active colloids, micro-/nanomotors (MNMs) can convert energy from the environment into mechanical motion in different fluids, showing potential applications in diverse fields such as targeted drug delivery and photothermal therapy. However, chemical fuels for typical catalytic MNMs, e.g., hydrogen peroxide, are highly toxic to organisms, and thus fuel-free MNMs are required. Recently, we have developed near-infrared light (NIR) propelled MNMs through integrating plasmonic gold nanoshells into nanoparticles or layer-by-layer assemblies in an asymmetric manner. In this perspective, we give an account of self-thermophoresis motion of these NIR-powered MNMs. The design of the motor architectures, as well as the theoretical study on the propulsion mechanism, is highlighted. We believe that the insights into self-thermophoretic motion would pave the way to access powerful MNMs for future applications and to explore interesting collective behaviors of active matter.


Shear stress-induced release of nitric oxide from endothelial cells grown on beads.
An in vitro bioassay system was developed to study endothelium-mediated, shear stress-induced, or flow-dependent generation of endothelium-derived relaxing factor (EDRF). Monolayers of aortic endothelial cells were grown on a rigid and large surface area of microcarrier beads and were packed in a small column perfused with Krebs bicarbonate solution. The perfusate was allowed to superfuse three endothelium-denuded target pulmonary arterial strips arranged in a cascade. Fluid shear stress caused a flow-dependent release of EDRF from the endothelial cells. The action of EDRF was abolished by oxyhemoglobin and methylene blue, and the generation of EDRF in response to shear stress was markedly inhibited or abolished by NG-nitro-L-arginine, by NG-amino-L-arginine, by calcium-free extracellular medium, and by depleting endothelial cells of endogenous L-arginine. Addition of L-arginine to arginine-deficient but not arginine-containing endothelial cells rapidly restored the capacity of shear stress and bradykinin to generate EDRF. These observations indicate that fluid shear stress causes the generation of EDRF with properties of nitric oxide from aortic endothelial cells and that the bioassay system described may be useful for studying the mechanism of mechanochemical coupling that leads to nitric oxide generation.


Bleomycin and X-ray-hypersensitive Chinese hamster ovary cell mutants: genetic analysis and cross-resistance to neocarzinostatin.
We have previously reported the isolation of 3 mutants of Chinese hamster ovary cells which exhibit hypersensitivity to bleomycin. 2 mutants were isolated on the basis of bleomycin-sensitivity [designated BLM-1 and BLM-2, Robson et al., Cancer Res., 45 (1985) 5304-5309] and 1 as adriamycin-sensitive [ADR-1, Robson et al., Cancer Res., 47 (1987) 1560-1565]. Because bleomycin generates DNA-strand breaks via a free-radical mechanism, we have studied the survival response of these mutants to a range of drugs which also generate free radicals and consequently DNA-strand breaks. The mutants are all hypersensitive to phleomycin, which differs from bleomycin in being unable to intercalate due to a modified bithiazole moiety. However, BLM-2 cells alone are hypersensitive to pepleomycin, a semi-synthetic bleomycin analogue. In contrast, BLM-1 cells are more sensitive than BLM-2 to streptonigrin (which operates via a hydroquinone intermediate). ADR-1 cells show wild-type resistance to streptonigrin. The results obtained with neocarzinostatin, an antibiotic requiring thiol activation, are unusual in that both BLM-1 and BLM-2 are approximately 3-fold more resistant than parental cells. However, the steady-state intracellular level of the major non-protein thiol, glutathione, is not altered in BLM-1 or BLM-2 cells. ADR-1 cells show essentially wild-type resistance to neocarzinostatin. Analysis of cell hybrids shows that BLM-1 and BLM-2 cells are phenotypically recessive in combination with parental CHO-K1 cells and represent different genetic complementation groups not only from one another, but also from the bleomycin-sensitive mutant xrs-6, isolated on the basis of X-ray sensitivity by Jeggo and Kemp [Mutation Res., 112 (1983) 313-319]. These results indicate that at least 3 gene products are involved in cellular protection against bleomycin toxicity in mammalian cells.


New Insights Into CRASP-Mediated Complement Evasion in the Lyme Disease Enzootic Cycle.
Lyme disease (LD), which is caused by genospecies of the Borrelia burgdorferi sensu lato complex, is the most common vector-borne disease in the Northern hemisphere. Spirochetes are transmitted by Ixodes ticks and maintained in diverse vertebrate animal hosts. Following tick bite, spirochetes initially establish a localized infection in the skin. However, they may also disseminate hematogenously to several distal sites, including heart, joints, or the CNS. Because they need to survive in diverse microenvironments, from tick vector to mammalian hosts, spirochetes have developed multiple strategies to combat the numerous host defense mechanisms. One of these strategies includes the production of a number of complement-regulator acquiring surface proteins (CRASPs) which encompass CspA, CspZ, and OspE paralogs to blunt the complement pathway. These proteins are capable of preventing complement activation on the spirochete surface by binding to complement regulator Factor H. The genes encoding these CRASPs differ in their expression patterns during the tick-to-host infection cycle, implying that these proteins may exhibit different functions during infection. This review summarizes the recent published reports which investigated the roles that each of these molecules plays in conferring tick-borne transmission and dissemination in vertebrate hosts. These findings offer novel mechanistic insights into LD pathobiology and may facilitate the identification of new targets for preventive strategies against Lyme borreliosis.


L2 kernel classification.
Nonparametric kernel methods are widely used and proven to be successful in many statistical learning problems. Well-known examples include the kernel density estimate (KDE) for density estimation and the support vector machine (SVM) for classification. We propose a kernel classifier that optimizes the L2 or integrated squared error (ISE) of a "difference of densities." We focus on the Gaussian kernel, although the method applies to other kernels suitable for density estimation. Like a support vector machine (SVM), the classifier is sparse and results from solving a quadratic program. We provide statistical performance guarantees for the proposed L2 kernel classifier in the form of a finite sample oracle inequality and strong consistency in the sense of both ISE and probability of error. A special case of our analysis applies to a previously introduced ISE-based method for kernel density estimation. For dimensionality greater than 15, the basic L2 kernel classifier performs poorly in practice. Thus, we extend the method through the introduction of a natural regularization parameter, which allows it to remain competitive with the SVM in high dimensions. Simulation results for both synthetic and real-world data are presented.


Tracer diffusion in a polymer gel: simulations of static and dynamic 3D networks using spherical boundary conditions.
We have investigated an alternative to the standard periodic boundary conditions for simulating the diffusion of tracer particles in a polymer gel by performing Brownian dynamics simulations using spherical boundary conditions. The gel network is constructed by randomly distributing tetravalent cross-linking nodes and connecting nearest pairs. The final gel structure is characterised by the radial distribution functions, chain lengths and end-to-end distances, and the pore size distribution. We have looked at the diffusion of tracer particles with a wide range of sizes, diffusing in both static and dynamic networks of two different volume fractions. It is quantitatively shown that the dynamical effect of the network becomes more important in facilitating the diffusional transport for larger particle sizes, and that one obtains a finite diffusion also for particle sizes well above the maximum in the pore size distribution.


Genome-wide association studies of cancer: principles and potential utility.
Genome-wide association studies (GWAS) have emerged as a new approach for investigating the genetic basis of complex diseases. In oncology, genome-wide studies of nearly all common malignancies have been performed and more than 100 genetic variants associated with increased risks have been identified. GWAS approaches are powerful research tools that are revealing novel pathways important in carcinogenesis and promise to further enhance our understanding of the basis of inherited cancer susceptibility. However, "personal genomic tests" based on cancer GWAS results that are currently being offered by for-profit commercial companies for cancer risk prediction have unproven clinical utility and may risk false conveyance of reassurance or alarm.


Non-local polymerization driven diffusion based model: general dependence of the polymerization rate to the exposure intensity.
The nonlocal diffusion model proposed by Sheridan and coworkers has provided a useful interpretation of the nature of grating formation inside photopolymer materials. This model accounts for some important experimental facts, such as the cut-off of diffraction efficiency for high spatial frequencies. In this article we examine the predictions of the model in the case of a general dependence of the polymerisation rate with respect to the intensity pattern. The effects of this dependence on the different harmonic components of the polymerisation concentration will be investigated. The influence of the visibility on the different harmonic components will also be studied. These effects are compared to the effects of varying RD and sigmaD.


Helicobacter pylori infection and circulating ghrelin levels - a systematic review.
The nature of the association between ghrelin, an orexigenic hormone produced mainly in the stomach, and Helicobacter pylori (H pylori), a bacterium that colonises the stomach, is still controversial. We examined available evidence to determine whether an association exists between the two; and if one exists, in what direction. We reviewed original English language studies on humans reporting circulating ghrelin levels in H pylori infected and un-infected participants; and circulating ghrelin levels before and after H pylori eradication. Meta-analyses were conducted for eligible studies by combining study specific estimates using the inverse variance method with weighted average for continuous outcomes in a random effects model. Seventeen out of 27 papers that reported ghrelin levels in H pylori positive and negative subjects found lower circulating ghrelin levels in H pylori positive subjects; while 10 found no difference. A meta-analysis of 19 studies with a total of 1801 participants showed a significantly higher circulating ghrelin concentration in H pylori negative participants than in H pylori positive participants (Effect estimate (95%CI) = -0.48 (-0.60, -0.36)). However, eradicating H pylori did not have any significant effect on circulating ghrelin levels (Effect estimate (95% CI) = 0.08 (-0.33, 0.16); Test for overall effect: Z = 0.67 (P = 0.5)). We conclude that circulating ghrelin levels are lower in H pylori infected people compared to those not infected; but the relationship between circulating ghrelin and eradication of H pylori is more complex.


Trans-heterozygous Pkd1 and Pkd2 mutations modify expression of polycystic kidney disease.
Autosomal dominant polycystic kidney disease (ADPKD) occurs by germline mutation in PKD1 or PKD2. Evidence of homozygous inactivation of either gene in human cyst lining cells as well as in mouse knockout models strongly supports a two-hit mechanism for cyst formation. Discovery of trans-heterozygous mutations in PKD1 and PKD2 in a minority of human renal cysts has led to the proposal that such mutations also can play a role in cyst formation. In the current study, we investigated the role of trans-heterozygous mutations in mouse models of polycystic kidney disease. In Pkd1(+/-), Pkd2 (+/-) and Pkd1(+/-) : Pkd2 (+/-) mice, the renal cystic lesion was mild and variable with no adverse effect on survival at 1 year. In keeping with the two-hit mechanism of cyst formation, approximately 70% of kidney cysts in Pkd2 (+/-) mice exhibited uniform loss of polycystin-2 expression. Cystic disease in trans-heterozygous Pkd1(+/-) : Pkd2 (+/-) mice, however, was notable for severity in excess of that predicted by a simple additive effect based on cyst formation in singly heterozygous mice. The data suggest a modifier role for the 'trans' polycystin gene in cystic kidney disease, and support a contribution from threshold effects to cyst formation and growth.


Heterologous biosynthesis of a fungal macrocyclic polylactone requires only two iterative polyketide synthases.
Menisporopsin A is a bioactive macrocyclic polylactone produced by the fungus Menisporopsis theobromae BCC 4162. A scheme for the biosynthesis of this compound has been proposed, in which reducing (R) and non-reducing (NR) polyketide synthases (PKSs) would catalyze the formation of each menisporopsin A subunit, while an additional non-ribosomal peptide synthetase (NRPS)-like enzyme would be required to perform multiple esterification and cyclolactonization reactions. Transcriptome analysis of M. theobromae identified an R-PKS gene, men1, and an NR-PKS gene, men2, which both exhibited highest expression levels during the menisporopsin A production phase. These were cloned into separate vectors for heterologous expression in Aspergillus oryzae NSAR1. Unexpectedly, coexpression of the two PKSs alone was sufficient to catalyze the formation of the macrocyclic polylactone, ascotrichalactone A, a structural derivative of menisporopsin A. The unanticipated esterification and cyclolactonization activities could reside in the unusual thioesterase domain of the NR-PKS, which is similar to that of the NRPS catalyzing elongation and cyclization of trilactone in enterobactin biosynthesis and that of modular PKSs catalyzing macrodiolide formation in elaiophylin and conglobatin biosyntheses.


Patterns of substance use before and after hospitalization among patients seen by an inpatient addiction consult service: A latent transition analysis.
Polysubstance use is common and contributes to morbidity and mortality of hospitalized patients, and yet little is known about patterns of substance use among hospitalized patients, or how an addiction consult service (ACS) might impact polysubstance use after discharge. The objective of this study was to identify patterns of substance use at admission and after discharge among hospitalized patients with substance use disorders who saw an ACS. Prospective cohort study. We used latent transition analysis of substance use scores at the time of hospital admission and 30 to 90 days posthospitalization. Single, academic health center with an ACS in Portland, Oregon, from 2015 to 2018. Patients were eligible if they received a consult to the inpatient ACS. We used Addiction Severity Index-Lite scores to capture self-reported substance use at baseline and follow-up for heroin, other opioid, alcohol, amphetamine, and cocaine. From 2015 to 2018, 486 individuals consented to participate. More than half of patients used more than one substance at baseline. Of those reporting any baseline opioid use, nearly three-quarters (n=187, 69.5%) had polysubstance use in the previous 30 days, including alcohol (n=80, 29.7%), cocaine (n=25, 9.3%), or amphetamine use (n=142, 52.8%). We identified three patterns of substance use at baseline: 1) alcohol use dominant, 2) polysubstance use dominant, and 3) heroin and other opioid use dominant. Patients transitioned along five trajectories to three different follow-up profiles that showed lower endorsement of all substances used. Slightly more than 40% (40.1%) of patients newly endorsed abstinence of at least one substance at follow-up. Polysubstance use is common in hospitalized patients with substance use disorders and identifying patterns of polysubstance use can guide clinical management. Hospital providers should prepare to manage polysubstance use during hospitalization and hospitals should broaden care beyond interventions for opioid use disorder.


Increasing fecal butyrate in ulcerative colitis patients by diet: controlled pilot study.
Topical butyrate has been shown to be effective in the treatment of ulcerative colitis (UC). Butyrate is derived from colonic fermentation of dietary fiber, and our aim was to study whether UC patients could safely increase the fecal butyrate level by dietary means. We enrolled 22 patients with quiescent UC (mean age, 44 years; 45% women; median time from last relapse, 1 year) in a controlled pilot trial lasting 3 months. The patients were instructed to add 60 g oat bran (corresponding to 20 g dietary fiber) to the daily diet, mainly as bread slices. Fecal short-chain fatty acids (SCFAs) including butyrate, disease activity, and gastrointestinal symptoms were recorded every 4 weeks. During the oat bran intervention the fecal butyrate concentration increased by 36% at 4 weeks (from 11 +/- 2 (mean +/- SEM) to 15 +/- 2 micromol/g feces) (p < 0.01). The mean butyrate concentration over the entire test period was 14 +/- 1 micromol/g feces (p < 0.05). Remaining fecal SCFA levels were unchanged. No patient showed signs of colitis relapse. Unlike controls, the patients showed no increase in gastrointestinal complaints during the trial. Yet patients reporting abdominal pain and reflux complaints at entry showed significant improvement at 12 weeks that returned to baseline 3 months later. This pilot study shows that patients with quiescent UC can safely take a diet rich in oat bran specifically to increase the fecal butyrate level. This may have clinical implications and warrants studies of the long-term benefits of using oat bran in the maintenance therapy in UC.


The positive circadian regulators CLOCK and BMAL1 control G2/M cell cycle transition through Cyclin B1.
We previously identified a tight bidirectional phase coupling between the circadian clock and the cell cycle. To understand the role of the CLOCK/BMAL1 complex, representing the main positive regulator of the circadian oscillator, we knocked down Bmal1 or Clock in NIH3T33C mouse fibroblasts (carrying fluorescent reporters for clock and cell cycle phase) and analyzed timing of cell division in individual cells and cell populations. Inactivation of Bmal1 resulted in a loss of circadian rhythmicity and a lengthening of the cell cycle, originating from delayed G2/M transition. Subsequent molecular analysis revealed reduced levels of Cyclin B1, an important G2/M regulator, upon suppression of Bmal1 gene expression. In complete agreement with these experimental observations, simulation of Bmal1 knockdown in a computational model for coupled mammalian circadian clock and cell cycle oscillators (now incorporating Cyclin B1 induction by BMAL1) revealed a lengthening of the cell cycle. Similar data were obtained upon knockdown of Clock gene expression. In conclusion, the CLOCK/BMAL1 complex controls cell cycle progression at the level of G2/M transition through regulation of Cyclin B1 expression.


Comparative transcriptomics analyses reveal the conservation of an ancestral infectious strategy in two bacteriophage genera.
Although the evolution of tailed bacteriophages has increasingly been better understood through comparisons of their DNA sequences, the functional consequences of this evolution on phage infectious strategies have remained unresolved. In this study, we comprehensively compared the transcriptional strategies of two related myoviruses, PAK_P3 and PAK_P4, infecting the same Pseudomonas aeruginosa host strain. Outside of the conservation of their structural clusters, their highly syntenic genomes display only limited DNA similarity. Despite this apparent divergence, we found that both viruses follow a similar infection scheme, relying on a temporal regulation of their gene expression, likely involving the use of antisense transcripts, as well as a rapid degradation of 90% of the host non-ribosomal mRNA, as previously reported for PAK_P3. However, the kinetics of the mRNA degradation is remarkably faster during PAK_P4 infection. Moreover, we found that each virus has evolved specific adaptations, as exemplified by the distinct patterns of their core genes expression as well as the specific manipulation of the expression of iron-related host genes by PAK_P4. This study enhances our understanding of the evolutionary process of virulent phages, which relies on adjusting globally conserved ancestral infection mechanisms.


Light, photoreceptors, and circadian clocks.
Research over the past decade has focused increasingly on the photoreceptor mechanisms that regulate the circadian system in all forms of life. Some of the results to emerge are surprising. For example, the rods and cones within the mammalian eye are not required for the alignment (entrainment) of circadian rhythms to the dawn-dusk cycle. There exists a population of directly light-sensitive ganglion cells within the eye that act as brightness detectors; these regulate both circadian rhythms and melatonin synthesis. An understanding of these "circadian photoreceptor" pathways, and the features of the light environment used for entrainment, have been and will continue to be heavily dependent on the appropriate use and measurement of light stimuli. Furthermore, if results from different laboratories, or species, are to be compared in any meaningful sense, standardized methods for light measurement and manipulation need to be adopted by circadian biologists. To this end, we describe light measurement in terms of both radiometric and photometric units and consider the appropriate use of light as a stimulus in circadian experiments. In addition, the construction of action spectra has been very helpful in associating photopigments with particular responses in a broad range of photobiological systems. Because the identity of the photopigments mediating circadian responses to light are often not known, we have also taken this opportunity to provide a step-by-step approach to conducting action spectra, including the construction of irradiance response curves, the calculation of relative spectral sensitivities, photopigment template fitting, and the underlying assumptions behind this approach. The aims of this chapter are to provide an accessible introduction to photobiological methods and explain why these approaches need to be applied to the study of circadian systems.


Altered Hippocampal White Matter Connectivity in Type 2 Diabetes Mellitus and Memory Decrements.
Type 2 diabetes mellitus is associated with cognitive decrements. Specifically affected cognitive domains are learning and memory, for which the hippocampus plays an essential role. The pathophysiological mechanism remains to be revealed. The present study examined whether local hippocampal microstructure and white matter connectivity are related to type 2 diabetes and memory performance. Forty participants with type 2 diabetes and 38 participants without type 2 diabetes underwent detailed cognitive assessment and 3-Tesla diffusion magnetic resonance imaging (MRI). Diffusion MRI was performed to assess microstructure (fractional anisotropy and mean diffusivity) and white matter connectivity (tract volume) of the hippocampus, which were compared between participants with and without type 2 diabetes. No differences in hippocampal microstructure were observed. Participants with type 2 diabetes had fewer white matter connections between the hippocampus and frontal lobe (P = 0.017). Participants who scored lower on memory function, regardless of type 2 diabetes, had fewer white matter connections between the hippocampus and temporal lobe (P = 0.017). Taken together, type 2 diabetes and memory decrements appear to be associated with altered hippocampal white matter connectivity.