Associations of Steroid Sex Hormones and Sex Hormone-Binding Globulin With the Risk of Type 2 Diabetes in Women: A Population-Based Cohort Study and Meta-analysis.
It remains unclear whether endogenous sex hormones (ESH) are associated with risk of type 2 diabetes (T2D) in women. Data of 3,117 postmenopausal women participants of the Rotterdam Study were analyzed to examine whether ESH and sex hormone-binding globulin (SHBG) were associated with the risk of incident T2D. Additionally, we performed a systematic review and meta-analysis of studies assessing the prospective association of ESH and SHBG with T2D in women. During a median follow-up of 11.1 years, we identified 384 incident cases of T2D in the Rotterdam Study. No association was observed between total testosterone (TT) or bioavailable testosterone (BT) with T2D. SHBG was inversely associated with the risk of T2D, whereas total estradiol (TE) was associated with increased risk of T2D. Similarly, in the meta-analysis of 13 population-based prospective studies involving more than 1,912 incident T2D cases, low levels of SHBG and high levels of TE were associated with increased risk of T2D, whereas no associations were found for other hormones. The association of SHBG with T2D did not change by menopause status, whereas the associations of ESH and T2D were based only in postmenopausal women. SHBG and TE are independent risk factors for the development of T2D in women.


Liposuction of the female breast: a histologic study of the aspirate.
Liposuction for female breast reduction is a new treatment modality that has many advantages over the generally accepted procedure of excision, which can damage glandular tissue and impair breastfeeding capacity. To assess any potential damage to glandular tissue caused by liposuction of the female breast. Specimens of the aspirate from 61 consecutive female patients who underwent liposuction of the breast using tumescent local anesthesia (TLA) and powered cannulae (PCs) were sent for histologic evaluation. In all cases, fat tissue was the main component observed in the breast aspirate specimens. In 58 cases, fragments of fibrotic tissue were found. In nine cases, minor fragments of the smallest glandular tissue ductuli were detected. In no case was there any sign of larger glandular structures. Histologic evaluation of 61 specimens of the aspirate obtained from breast liposuctions using TLA and PCs showed only minor signs of damage to glandular tissue in a small minority of patients. There was no indication that lactation might be impaired using this procedure. The authors have indicated no significant interest with commercial supporters.


Changes in presence of a segmental dysfunction pattern associated with hypertension: Part 1. A short-term longitudinal study.
A statistically significant pattern of segmental components of somatic dysfunction associated with a history of high blood pressure was investigated for change after an interval of 4 to 8 months. The volunteer subjects, from an inner-city ambulatory clinic, included normotensive, borderline hypertensive, and hypertensive persons. A standardized palpatory examination determined whether there were specific motion asymmetries centered at spinal segments C6, T2, and T6 and confirmed by mirror-image motion asymmetries in adjacent segments. Blood pressure measurements and diagnosis of hypertension followed American Heart Association standards. The repeated presence of the pattern in subjects with a history of hypertension was statistically significant. Presence of the pattern in normotensive subjects, however, appeared to be random. The subjects' histories during the study period revealed no influence of antihypertensive medications, major accidents, or illness on the patterns' continuing presence in subjects requiring medical control of their hypertension.


Characterization of mutations in the rpoB gene that confer rifampin resistance in Staphylococcus aureus.
Mutations in the rifampin resistance-determining (Rif) regions of the rpoB gene of Staphylococcus aureus mutants obtained during therapy or in vitro were analyzed by gene amplification and sequencing. Each of the resistant clinical isolates, including five nonrelated clones and two strains isolated from the same patient, and of the 10 in vitro mutants had a single base pair change that resulted in an amino acid substitution in the beta subunit of RNA polymerase. Eight mutational changes at seven positions were found in cluster I of the central Rif region. Certain substitutions (His481/Tyr and Asp471/Tyr [S. aureus coordinates]) were present in several mutants. Substitutions Gln468/Arg, His481/Tyr, and Arg484/His, which conferred high-level rifampin resistance, were identical or in the same codon as those described in other bacterial genera, whereas Asp550/Gly has not been reported previously. Substitutions at codon 477 conferred high- or low-level resistance, depending on the nature of the new amino acid. The levels of resistance of in vivo and one-step in vitro mutants carrying identical mutations were similar, suggesting that no other resistance mechanism was present in the clinical isolates. On the basis of these data and the population distribution of more than 4,000 clinical S. aureus isolates, we propose </=0.5 and >/=8 microg/ml as new breakpoints for the clinical categorization of this species relative to rifampin.


Direct two-dimensional measurements of the field-aligned current associated with plasma blobs.
In simple magnetized toroidal plasmas, field-aligned blobs originate from ideal interchange waves and propagate radially outward under the effect of ∇B and curvature induced E×B drifts. We report on the first experimental two-dimensional measurements of the field-aligned current associated with blobs, whose ends terminate on a conducting limiter. A dipolar structure of the current density is measured, which originates from ∇B and curvature induced polarization of the blob and is consistent with sheath boundary conditions. The dipole is strongly asymmetric due to the nonlinear dependence of the current density at the sheath edge upon the floating potential. Furthermore, we directly demonstrate the existence of two regimes, in which parallel currents to the sheath do or do not significantly damp charge separation and thus blob radial velocity.


Regulation of sialic acid O-acetylation in human colon mucosa.
The expression of O-acetylated sialic acids in human colonic mucins is developmentally regulated, and a reduction of O-acetylation has been found to be associated with the early stages of colorectal cancer. Despite this, however, little is known about the enzymatic process of sialic acid O-acetylation in human colonic mucosa. Recently, we have reported on a human colon sialate-7(9)-O-acetyltransferase capable of incorporating acetyl groups into sialic acids at the nucleotide-sugar level [Shen et al., Biol. Chem. 383 (2002), 307-317]. In this report, we show that the CMP-N-acetyl-neuraminic acid (CMP-Neu5Ac) and acetyl-CoA (AcCoA) transporters are critical components for the O-acetylation of CMP-Neu5Ac in Golgi lumen, with specific inhibition of either transporter leading to a reduction in the formation of CMP-5-N-acetyl-9-O-acetyl-neuraminic acid (CMP-Neu5,9Ac2). Moreover, the finding that 5-N-acetyl-9-O-acetyl-neuraminic acid (Neu5,9Ac2 could be transferred from neo-synthesised CMP-Neu5,9Ac2 to endogenous glycoproteins in the same Golgi vesicles, together with the observation that asialofetuin and asialo-human colon mucin are much better acceptors for Neu5,9Ac2 than asialo-bovine submandibular gland mucin, suggests that a sialyltransferase exists that preferentially utilises CMP-Neu5,9Ac2 as the donor substrate, transferring Neu5,9Ac2 to terminal Galbeta1,3(4)R- residues.


Experimental rayless goldenrod (Isocoma pluriflora) toxicosis in goats.
Rayless goldenrod (Isocoma pluriflora) sporadically poisons livestock in the southwestern United States. Similarities with white snakeroot (Ageratina altissima) poisoning and nearly identical chemical analyses led early researchers to conclude that tremetol, a mixture of benzofuran ketones, is the rayless goldenrod toxin. The toxicity of these ketone toxins have not been fully characterized nor are the pathogenesis and sequelae of poisoning completely understood. The objective of the current study was to characterize and describe the clinical and pathologic changes of rayless goldenrod toxicity in goats. Fifteen goats were gavaged with rayless goldenrod to obtain benzofuran ketone doses of 0, 10, 20, 40, and 60 mg/kg/day. After 7 treatment days, the goats were euthanized, necropsied, and tissues were processed for microscopic studies. After 5 or 6 days of treatment, the 40-mg/kg and 60-mg/kg goats were reluctant to move, stood with an erect stance, and became exercise intolerant. They had increased resting heart rate, prolonged recovery following exercise, and increased serum aspartate aminotransferase, alanine aminotransferase, lactate dehydrogenase, and creatinine kinase activities. All treated animals developed skeletal myopathy with dose-related distribution and severity. The goats dosed with 20 mg/kg and higher also developed myocardial degeneration and necrosis. Although skeletal myonecrosis was patchy and widely distributed, the quadriceps femoris was consistently damaged, even in low-dosed animals. Myocardial lesions were most severe in the papillary muscles of 60-mg/kg-dosed animals. This indicates that goats are highly susceptible to rayless goldenrod poisoning, and that the characteristic lesion of poisoning is skeletal and cardiac myonecrosis.


Inhibition of the aminopeptidase from Aeromonas proteolytica by L-leucinethiol: kinetic and spectroscopic characterization of a slow, tight-binding inhibitor-enzyme complex.
The peptide inhibitor L-leucinethiol (LeuSH) was found to be a potent, slow-binding inhibitor of the aminopeptidase from Aeromonas proteolytica (AAP). The overall potency (K(I)*) of LeuSH was 7 nM while the corresponding alcohol L-leucinol (LeuOH) was a simple competitive inhibitor of much lower potency (K(I) = 17 microM). These data suggest that the free thiol is likely involved in the formation of the E x I and E x I* complexes, presumably providing a metal ligand. In order to probe the nature of the interaction of LeuSH and LeuOH with the dinuclear active site of AAP, we have recorded both the electronic absorption and EPR spectra of [CoCo(AAP)], [CoZn(AAP)], and [ZnCo(AAP)] in the presence of both inhibitors. In the presence of LeuSH, all three Co(II)-substituted AAP enzymes exhibited an absorption band centered at 295 nm, characteristic of a S --> Co(II) ligand-metal charge-transfer band. In addition, absorption spectra recorded in the 450 to 700 nm region all showed changes characteristic of LeuSH and LeuOH interacting with both metal ions. EPR spectra recorded at high temperature (19 K) and low power (2.5 mW) indicated that, in a given enzyme molecule, LeuSH interacts weakly with one of the metal ions in the dinuclear site and that the crystallographically identified mu-OH(H) bridge, which has been shown to mediate electronic interaction of the Co(II) ions, is likely broken upon binding LeuSH. EPR spectra of [CoCo(AAP)]-LeuSH, [ZnCo(AAP)]-LeuSH, and [Co_(AAP)]-LeuSH were also recorded at lower temperature (3.5-4.0 K) and high microwave power (50-553 mW). These signals were unusual and appeared to contain, in addition to the incompletely saturated contributions from the signals characterized at 19 K, a very sharp feature at g(eff) approximately 6.5 that is characteristic of thiolate-Co(II) interactions. Combination of the electronic absorption and EPR data indicates that LeuSH perturbs the electronic structure of both metal ions in the dinuclear active site of AAP. Since the spin-spin interaction seen in resting [CoCo(AAP)] is abolished upon the addition of LeuSH, it is unlikely that a mu-S(R) bridge is established.


Absolute diversification rates in angiosperm clades.
The extraordinary contemporary species richness and ecological predominance of flowering plants (angiosperms) are even more remarkable when considering the relatively recent onset of their evolutionary diversification. We examine the evolutionary diversification of angiosperms and the observed differential distribution of species in angiosperm clades by estimating the rate of diversification for angiosperms as a whole and for a large set of angiosperm clades. We also identify angiosperm clades with a standing diversity that is either much higher or lower than expected, given the estimated background diversification rate. Recognition of angiosperm clades, the phylogenetic relationships among them, and their taxonomic composition are based on an empirical compilation of primary phylogenetic studies. By making an integrative and critical use of the paleobotanical record, we obtain reasonably secure approximations for the age of a large set of angiosperm clades. Diversification was modeled as a stochastic, time-homogeneous birth-and-death process that depends on the diversification rate (r) and the relative extinction rate (epsilon). A statistical analysis of the birth and death process was then used to obtain 95% confidence intervals for the expected number of species through time in a clade that diversifies at a rate equal to that of angiosperms as a whole. Confidence intervals were obtained for stem group and for crown group ages in the absence of extinction (e = 0.0) and under a high relative extinction rate (epsilon = 0.9). The standing diversity of angiosperm clades was then compared to expected species diversity according to the background rate of diversification, and, depending on their placement with respect to the calculated confidence intervals, exceedingly species-rich or exceedingly species-poor clades were identified. The rate of diversification for angiosperms as a whole ranges from 0.077 (epsilon = 0.9) to 0.089 (epsilon = 0.0) net speciation events per million years. Ten clades fall above the confidence intervals of expected species diversity, and 13 clades were found to be unexpectedly species poor. The phylogenetic distribution of clades with an exceedingly high number of species suggests that traits that confer high rates of diversification evolved independently in different instances and do not characterize the angiosperms as a whole.


MnmA and IscS are required for in vitro 2-thiouridine biosynthesis in Escherichia coli.
Thionucleosides are uniquely present in tRNA. In many organisms, tRNA specific for Lys, Glu, and Gln contain hypermodified 2-thiouridine (s(2)U) derivatives at wobble position 34. The s(2) group of s(2)U34 stabilizes anticodon structure, confers ribosome binding ability to tRNA and improves reading frame maintenance. Earlier studies have mapped and later identified the mnmA gene (formerly asuE or trmU) as required for the s(2)U modification in Escherichia coli. We have prepared a nonpolar deletion of the mnmA gene and show that it is not required for viability in E. coli. We also cloned mnmA from E. coli, and overproduced and purified the protein. Using a gel mobility shift assay, we show that MnmA binds to unmodified E. coli tRNA(Lys) with affinity in the low micromolar range. MnmA does not bind observably to the nonsubstrate E. coli tRNA(Phe). Corroborating this, tRNA(Glu) protected MnmA from tryptic digestion. ATP also protected MnmA from trypsinolysis, suggesting the presence of an ATP binding site that is consistent with analysis of the amino acid sequence. We have reconstituted the in vitro biosynthesis of s(2)U using unmodified E. coli tRNA(Glu) as a substrate. The activity requires MnmA, Mg-ATP, l-cysteine, and the cysteine desulfurase IscS. HPLC analysis of thiolated tRNA digests using [(35)S]cysteine confirms that the product of the in vitro reaction is s(2)U. As in the case of 4-thiouridine synthesis, purified IscS-persulfide is able to provide sulfur for in vitro s(2)U synthesis in the absence of cysteine. Small RNAs that represent the anticodon stem loops for tRNA(Glu) and tRNA(Lys) are substrates of comparable activity to the full length tRNAs, indicating that the major determinants for substrate recognition are contained within this region.


A Role for OCT4 in Tumor Initiation of Drug-Resistant Prostate Cancer Cells.
Drug resistance remains a clinical challenge in cancer treatment due to poor understanding of underlying mechanisms. We have established several drug-resistant prostate cancer cell lines by long-term culture in medium containing chemotherapeutic drugs. These resistant lines displayed a significant increase in side population cells due to overexpression of drug efflux pumps including ABCG2/BCRP and MDR1/Pgp. To uncover potential mechanisms underlying drug resistance, we performed microarray analysis to identify differentially expressed genes in 2 drug-resistant lines. We observed that POU5F1/OCT4, a transcription factor key to regulating pluripotency in embryonic stem cells, was upregulated in drug-resistant lines and accompanied by transcriptional activation of a set of its known target genes. Upregulation of OCT4 in drug-resistant cells was validated by RT-PCR and sequencing of PCR products as well as confirmation by Western blot and specific shRNA knockdown. Analysis of the regulatory region of POU5F1/OCT4 revealed a reduction of methylation in drug-resistant cell lines. Furthermore, these drug-resistant cells exhibited a significant increase in tumorigenicity in vivo. Subcutaneous inoculation of as few as 10 drug-resistant cells could initiate tumor formation in SCID mice, whereas no detectable tumors were observed from the parental line under similar conditions, suggesting that these drug-resistant cells may be enriched for tumor-initiating cells. Knocking down OCT4 expression by specific shRNAs attenuated growth of drug-resistant cells. Our data suggest that OCT4 re-expression in cancer cells may play an important role in carcinogenesis and provide one possible mechanism by which cancer cells acquire/maintain a drug-resistant phenotype.


Age-stratified and blood-pressure-stratified effects of blood-pressure-lowering pharmacotherapy for the prevention of cardiovascular disease and death: an individual participant-level data meta-analysis.
The effects of pharmacological blood-pressure-lowering on cardiovascular outcomes in individuals aged 70 years and older, particularly when blood pressure is not substantially increased, is uncertain. We compared the effects of blood-pressure-lowering treatment on the risk of major cardiovascular events in groups of patients stratified by age and blood pressure at baseline. We did a meta-analysis using individual participant-level data from randomised controlled trials of pharmacological blood-pressure-lowering versus placebo or other classes of blood-pressure-lowering medications, or between more versus less intensive treatment strategies, which had at least 1000 persons-years of follow-up in each treatment group. Participants with previous history of heart failure were excluded. Data were obtained from the Blood Pressure Lowering Treatment Triallists' Collaboration. We pooled the data and categorised participants into baseline age groups (<55 years, 55-64 years, 65-74 years, 75-84 years, and ≥85 years) and blood pressure categories (in 10 mm Hg increments from <120 mm Hg to ≥170 mm Hg systolic blood pressure and from <70 mm Hg to ≥110 mm Hg diastolic). We used a fixed effects one-stage approach and applied Cox proportional hazard models, stratified by trial, to analyse the data. The primary outcome was defined as either a composite of fatal or non-fatal stroke, fatal or non-fatal myocardial infarction or ischaemic heart disease, or heart failure causing death or requiring hospital admission. We included data from 358 707 participants from 51 randomised clinical trials. The age of participants at randomisation ranged from 21 years to 105 years (median 65 years [IQR 59-75]), with 42 960 (12·0%) participants younger than 55 years, 128 437 (35·8%) aged 55-64 years, 128 506 (35·8%) 65-74 years, 54 016 (15·1%) 75-84 years, and 4788 (1·3%) 85 years and older. The hazard ratios for the risk of major cardiovascular events per 5 mm Hg reduction in systolic blood pressure for each age group were 0·82 (95% CI 0·76-0·88) in individuals younger than 55 years, 0·91 (0·88-0·95) in those aged 55-64 years, 0·91 (0·88-0·95) in those aged 65-74 years, 0·91 (0·87-0·96) in those aged 75-84 years, and 0·99 (0·87-1·12) in those aged 85 years and older (adjusted pinteraction=0·050). Similar patterns of proportional risk reductions were observed for a 3 mm Hg reduction in diastolic blood pressure. Absolute risk reductions for major cardiovascular events varied by age and were larger in older groups (adjusted pinteraction=0·024). We did not find evidence for any clinically meaningful heterogeneity of relative treatment effects across different baseline blood pressure categories in any age group. Pharmacological blood pressure reduction is effective into old age, with no evidence that relative risk reductions for prevention of major cardiovascular events vary by systolic or diastolic blood pressure levels at randomisation, down to less than 120/70 mm Hg. Pharmacological blood pressure reduction should, therefore, be considered an important treatment option regardless of age, with the removal of age-related blood-pressure thresholds from international guidelines. British Heart Foundation, National Institute of Health Research Oxford Biomedical Research Centre, Oxford Martin School.


Histopathological changes in rat pancreas and skeletal muscle associated with high fat diet induced insulin resistance.
The effects of a high fat diet on the development of diabetes mellitus, insulin resistance and secretion have been widely investigated. We investigated the effects of a high fat diet on the pancreas and skeletal muscle of normal rats to explore diet-induced insulin resistance mechanisms. Forty-four male Wistar rats were divided into six groups: a control group fed standard chow, a group fed a 45% fat diet and a group fed a 60% fat diet for 3 weeks to measure acute effects; an additional three groups were fed the same diet regimens for 8 weeks to measure chronic effects. The morphological effects of the two high fat diets were examined by light microscopy. Insulin in pancreatic islets was detected using immunohistochemistry. The homeostasis model assessment of insulin resistance index and insulin staining intensity in islets increased significantly with acute administration of high fat diets, whereas staining intensity decreased with chronic administration of the 45% fat diet. Islet areas increased significantly with chronic administration. High fat diet administration led to islet degeneration, interlobular adipocyte accumulation and vacuolization in the pancreatic tissue, as well as degeneration and lipid droplet accumulation in the skeletal muscle tissue. Vacuolization in the pancreas and lipid droplets in skeletal muscle tissue increased significantly with chronic high fat diet administration. We suggest that the glucolipotoxic effects of high fat diet administration depend on the ratio of saturated to unsaturated fatty acid content in the diet and to the total fat content of the diet.


Percutaneous Coronary Intervention Versus Medical Therapy for Chronic Total Occlusion of Coronary Arteries: A Systematic Review and Meta-Analysis.
Chronic total occlusion (CTO) of the coronary arteries is a significant clinical problem and has traditionally been treated by medical therapy or coronary artery bypass grafting. Recent studies have examined percutaneous coronary intervention (PCI) as an alternative option. This systematic review and meta-analysis compared medical therapy to PCI for treating CTOs. PubMed and Embase were searched from their inception to March 2019 for studies that compared medical therapy and PCI for clinical outcomes in patients with CTOs. Quality of the included studies was assessed by Newcastle-Ottawa scale. The results were pooled by DerSimonian and Laird random- or fixed-effect models as appropriate. Heterogeneity between studies and publication bias was evaluated by I2 index and Egger's regression, respectively. Of the 703 entries screened, 17 studies were included in the final analysis. This comprised 11,493 participants. Compared to PCI, medical therapy including randomized and observational studies was significantly associated with higher risk of all-cause mortality (risk ratio (RR) 1.99, 95% CI 1.38-2.86), cardiac mortality (RR 2.36 (1.97-2.84)), and major adverse cardiac event (RR 1.25 (1.03-1.51)). However, no difference in the rate of myocardial infarction and repeat revascularization procedures was observed between the two groups. Univariate meta-regression demonstrated multiple covariates as independent moderating factors for myocardial infarction and repeat revascularization but not cardiac death and all-cause mortality. However, when only randomized studies were included, there was no difference in overall mortality or cardiac death. In CTO, when considering randomized and observational studies, medical therapy might be associated with a higher risk of mortality and myocardial infarction compared to PCI treatment.


A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data.
A genetic network can be represented as a directed graph in which a node corresponds to a gene and a directed edge specifies the direction of influence of one gene on another. The reconstruction of such networks from transcript profiling data remains an important yet challenging endeavor. A transcript profile specifies the abundances of many genes in a biological sample of interest. Prevailing strategies for learning the structure of a genetic network from high-dimensional transcript profiling data assume sparsity and linearity. Many methods consider relatively small directed graphs, inferring graphs with up to a few hundred nodes. This work examines large undirected graphs representations of genetic networks, graphs with many thousands of nodes where an undirected edge between two nodes does not indicate the direction of influence, and the problem of estimating the structure of such a sparse linear genetic network (SLGN) from transcript profiling data. The structure learning task is cast as a sparse linear regression problem which is then posed as a LASSO (l1-constrained fitting) problem and solved finally by formulating a Linear Program (LP). A bound on the Generalization Error of this approach is given in terms of the Leave-One-Out Error. The accuracy and utility of LP-SLGNs is assessed quantitatively and qualitatively using simulated and real data. The Dialogue for Reverse Engineering Assessments and Methods (DREAM) initiative provides gold standard data sets and evaluation metrics that enable and facilitate the comparison of algorithms for deducing the structure of networks. The structures of LP-SLGNs estimated from the INSILICO1, INSILICO2 and INSILICO3 simulated DREAM2 data sets are comparable to those proposed by the first and/or second ranked teams in the DREAM2 competition. The structures of LP-SLGNs estimated from two published Saccharomyces cerevisae cell cycle transcript profiling data sets capture known regulatory associations. In each S. cerevisiae LP-SLGN, the number of nodes with a particular degree follows an approximate power law suggesting that its degree distributions is similar to that observed in real-world networks. Inspection of these LP-SLGNs suggests biological hypotheses amenable to experimental verification. A statistically robust and computationally efficient LP-based method for estimating the topology of a large sparse undirected graph from high-dimensional data yields representations of genetic networks that are biologically plausible and useful abstractions of the structures of real genetic networks. Analysis of the statistical and topological properties of learned LP-SLGNs may have practical value; for example, genes with high random walk betweenness, a measure of the centrality of a node in a graph, are good candidates for intervention studies and hence integrated computational - experimental investigations designed to infer more realistic and sophisticated probabilistic directed graphical model representations of genetic networks. The LP-based solutions of the sparse linear regression problem described here may provide a method for learning the structure of transcription factor networks from transcript profiling and transcription factor binding motif data.


Circulating amino acid signature in older people with Parkinson's disease: A metabolic complement to the EXosomes in PArkiNson Disease (EXPAND) study.
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder in old age. Neurotoxicity of dopaminergic neurons triggered by aggregation of misfolded α-synuclein is a major pathogenic trait of PD. However, growing evidence indicates that peripheral processes, including metabolic changes, may precede and contribute to neurodegeneration. The present study was undertaken to identify a metabolic signature of PD through the quantification of serum amino acids and derivatives. Twenty older adults with PD (11 men and 9 women; mean age 73.1 ± 10.2 years) and 30 age-matched controls (14 men and 16 women; mean age 74.6 ± 4.3 years) were enrolled. A panel of 37 serum amino acids and derivatives was assessed by ultra-performance liquid chromatography/mass spectrometry. Partial least squares - discriminant analysis (PLS-DA) followed by double cross-validation was used to characterize the relationship between amino acid profiles and PD. The optimal complexity of the PLS-DA model was found to be three latent variables. The proportion of correct classifications was 99.3 ± 2.5% for participants with PD and 94.7 ± 3.0% for non-PD controls. Higher levels of β-amino butyric acid, cystine, ornithine, phosphoethanolamine, and proline defined the circulating amino acid profile of older people with PD. Controls were characterized by higher concentrations of 3-methyl-histidine, citrulline, and serine. Our findings indicate the existence of a distinct metabotype in older persons with PD. Future studies will have to establish whether changes in amino acid metabolism are involved in the pathogenesis of PD. This knowledge may be harnessed to identify novel disease biomarkers as well as new targets for interventions.


Mitochondria targeted therapeutic approaches in Parkinson's and Huntington's diseases.
Substantial evidence from both genetic and toxin induced animal and cellular models and postmortem human brain tissue indicates that mitochondrial dysfunction plays a central role in pathophysiology of the neurodegenerative disorders including Parkinson's disease (PD), and Huntington's disease (HD). This review discusses the emerging understanding of the role of mitochondrial dysfunction including bioenergetics defects, mitochondrial DNA mutations, familial nuclear DNA mutations, altered mitochondrial fusion/fission and morphology, mitochondrial transport/trafficking, altered transcription and increased interaction of pathogenic proteins with mitochondria in the pathogenesis of PD and HD. This review recapitulates some of the key therapeutic strategies applied to surmount mitochondrial dysfunction in these debilitating disorders. We discuss the therapeutic role of mitochondrial bioenergetic agents such as creatine, Coenzyme-Q10, mitochondrial targeted antioxidants and peptides, the SIRT1 activator resveratrol, and the pan-PPAR agonist bezafibrate in toxin and genetic cellular and animal models of PD and HD. We also summarize the phase II-III clinical trials conducted using some of these agents. Lastly, we discuss PGC-1α, TORC and Sirtuins as potential therapeutic targets for mitochondrial dysfunction in neurodegenerative disorders. This article is part of a Special Issue entitled 'Mitochondrial function and dysfunction in neurodegeneration'.


Healthy Heart Africa-Kenya: A 12-Month Prospective Evaluation of Program Impact on Health Care Providers' Knowledge and Treatment of Hypertension.
Given the rising burden of hypertension in Africa, the Healthy Heart Africa program was developed to improve access to quality hypertension care in the primary care setting. The Healthy Heart Africa program provides a comprehensive, coordinated intervention directed at health care providers (HCPs) and the general public. The impact of Healthy Heart Africa on HCPs' knowledge of hypertension and facility-level services in Kenya was evaluated by a 12-month prospective study. Intervention facilities were selected by stratified random sampling and matched to similar control facilities. Intervention facilities received a hypertension treatment protocol, equipment, training and patient education materials, and improved medical supply chain, whereas control facilities did not. HCPs responsible for hypertension care were surveyed at baseline and 12 months later. Hypertension screening and treatment data were abstracted from service delivery registers. A differences-in-differences analysis estimated the impact of Healthy Heart Africa on HCPs' knowledge, hypertension services, and the number of patients diagnosed with and seeking treatment for hypertension. Sixty-six intervention and 66 control facilities were surveyed. Healthy Heart Africa improved HCPs' knowledge of ≥5 hypertension risk factors and ≥5 methods for reducing/managing hypertension but not hypertension consequences. At end line, more intervention than control facilities measured blood pressure more than once during the same visit to diagnose hypertension, dedicated days to hypertension care, used posters to increase hypertension awareness, and provided access to hypertension medications. The number of patients diagnosed with hypertension and those seeking treatment for hypertension increased with intervention, but the change was not significant relative to control subjects. HCP-directed hypertension education and provision of basic resources positively influenced hypertension care in Kenya in the first 12 months of implementation.


Minority stress and mechanisms of risk for depression and suicidal ideation among lesbian, gay, and bisexual youth.
The experience of minority stress is often named as a cause for mental health disparities among lesbian, gay, and bisexual (LGB) youth, including higher levels of depression and suicidal ideation. The processes or mechanisms through which these disparities occur are understudied. The interpersonal-psychological theory of suicide posits 2 key mechanisms for suicidal ideation: perceived burdensomeness and thwarted belongingness (Joiner et al., 2009). The aim of the current study is to assess the mental health and adjustment among LGB youth emphasizing the minority stress model (Meyer, 2003) and the interpersonal-psychological theory of suicide (Joiner et al., 2009). With a survey of 876 LGB self-identified youth, levels of coming-out stress, sexual orientation victimization, perceived burdensomeness, thwarted belongingness, depression, and suicidal ideation were examined. The results of a multigroup mediation model show that for all gender and sexual identity groups, the association of sexual orientation victimization with depression and suicidal ideation was mediated by perceived burdensomeness. For gay, lesbian, and bisexual girls coming-out stress was also found to be related to depression and suicidal ideation, mediated by perceived burdensomeness. The results suggest that feeling like a burden to "people in their lives" is a critical mechanism in explaining higher levels of depression and suicidal ideation among LGB youth. These results have implications for community and social support groups, many of which base their interventions on decreasing social isolation rather than addressing youths' beliefs of burdensomeness. Implications for future research, clinical and community settings are discussed.


Women's liberation and the rhetoric of "choice" in infant feeding debates.
This short essay examines infant formula marketing and information sources for their representation of "choice" in the infant feeding context, and finds that while providing information about breast and bottle feeding, infant formula manufacturers focus on mothers' feelings and intuition rather than knowledge in making decisions. In addition, the essay considers how "choice" operates in the history of reproductive rights, shifting the discourse from a rights-based set of arguments to one based on a consumerist mentality. Utilizing the work of historian Rickie Solinger and a 2007 paper for the National Bureau of Labor Statistics, I argue that the structure of market work, and not abstract maternal decision making, determine mothers' choices and practices concerning infant feeding. For true freedoms for mothers to be achieved, freedoms that would include greater social provisions for mothers, our culture will have to confront how structural constraints make breastfeeding difficult, as well as how the concept of choice divides mothers into those who make good choices and those who do not.


Factors and processes shaping the population structure and distribution of genetic variation across the species range of the freshwater snail radix balthica (Pulmonata, Basommatophora).
Factors and processes shaping the population structure and spatial distribution of genetic diversity across a species' distribution range are important in determining the range limits. We comprehensively analysed the influence of recurrent and historic factors and processes on the population genetic structure, mating system and the distribution of genetic variability of the pulmonate freshwater snail Radix balthica. This analysis was based on microsatellite variation and mitochondrial haplotypes using Generalised Linear Statistical Modelling in a Model Selection framework. Populations of R. balthica were found throughout North-Western Europe with range margins marked either by dispersal barriers or the presence of other Radix taxa. Overall, the population structure was characterised by distance independent passive dispersal mainly along a Southwest-Northeast axis, the absence of isolation-by-distance together with rather isolated and genetically depauperated populations compared to the variation present in the entire species due to strong local drift. A recent, climate driven range expansion explained most of the variance in genetic variation, reducing at least temporarily the genetic variability in this area. Other factors such as geographic marginality and dispersal barriers play only a minor role. To our knowledge, such a population structure has rarely been reported before. It might nevertheless be typical for passively dispersed, patchily distributed taxa (e.g. freshwater invertebrates). The strong local drift implied in such a structure is expected to erode genetic variation at both neutral and coding loci and thus probably diminish evolutionary potential. This study shows that the analysis of multiple factors is crucial for the inference of the processes shaping the distribution of genetic variation throughout species ranges.


PKCε promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria.
The transcription factor ATF2 elicits oncogenic activities in melanoma and tumor suppressor activities in nonmalignant skin cancer. Here, we identify that ATF2 tumor suppressor function is determined by its ability to localize at the mitochondria, where it alters membrane permeability following genotoxic stress. The ability of ATF2 to reach the mitochondria is determined by PKCε, which directs ATF2 nuclear localization. Genotoxic stress attenuates PKCε effect on ATF2; enables ATF2 nuclear export and localization at the mitochondria, where it perturbs the HK1-VDAC1 complex; increases mitochondrial permeability; and promotes apoptosis. Significantly, high levels of PKCε, as seen in melanoma cells, block ATF2 nuclear export and function at the mitochondria, thereby attenuating apoptosis following exposure to genotoxic stress. In melanoma tumor samples, high PKCε levels associate with poor prognosis. Overall, our findings provide the framework for understanding how subcellular localization enables ATF2 oncogenic or tumor suppressor functions.


I feel how you feel but not always: the empathic brain and its modulation.
The ability to share the other's feelings, known as empathy, has recently become the focus of social neuroscience studies. We review converging evidence that empathy with, for example, the pain of another person, activates part of the neural pain network of the empathizer, without first hand pain stimulation to the empathizer's body. The amplitude of empathic brain responses is modulated by the intensity of the displayed emotion, the appraisal of the situation, characteristics of the suffering person such as perceived fairness, and features of the empathizer such as gender or previous experience with pain-inflicting situations. Future studies in the field should address inter-individual differences in empathy, development and plasticity of the empathic brain over the life span, and the link between empathy, compassionate motivation, and prosocial behavior.


Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing of the rat beta-tropomyosin gene.
In the rat beta-tropomyosin (beta-TM) gene, exons 6 and 7 are spliced alternatively in a mutually exclusive manner. Exon 6 is included in mRNA encoding nonmuscle TM-1, whereas exon 7 is used in mRNA encoding skeletal muscle beta-TM. Previously, we demonstrated that a six nucleotide mutation at the 5' end of exon 7, designated as ex-1, activated exon 7 splicing in nonmuscle cells. In this study, we show that the activating effect of this mutation is not the result of creating an exonic splicing enhancer (ESE) or disrupting a putative secondary structure. The sequence in exon 7 acts as a bona fide exonic splicing silencer (ESS), which is bound specifically by a trans-acting factor. Isolation and peptide sequencing reveal that this factor is hnRNP H, a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. Binding of hnRNP H correlates with the ESS activity. Furthermore, addition of antibodies that specifically recognizes hnRNP H to the splicing reactions or partial depletion of hnRNP H from nuclear extract activates exon 7 splicing in vitro and this effect can be reversed by addition of purified recombinant hnRNP H. These results indicate that hnRNP H participates in exclusion of exon 7 in nonmuscle cells. The involvement of hnRNP H in the activity of an ESS may represent a prototype for the regulation of tissue- and developmental-specific alternative splicing.


Illness perceptions, coping strategies, and symptoms contribute to psychological distress in patients with recurrent symptomatic atrial fibrillation.
Atrial fibrillation (AF) is a prevalent, life-complicating illness associated with psychological distress. Interventions to manage the psychological challenges of living with AF are needed. Evidence suggests that illness perceptions, coping strategies, and symptoms that contribute to psychological distress may be modified by psychoeducational interventions to reduce psychological distress. However, little is known about how illness perceptions, coping strategies, and symptoms contribute to psychological distress in patients with AF. The aim of this correlational study guided by Levethal's Common Sense Model of Self-regulation was to identify the extent to which illness perceptions, coping strategies, symptom frequency, and symptom severity contributed to psychological distress in patients with recurrent symptomatic AF. The contribution of these factors was considered with respect to the effects of gender, age, type of AF, and time since AF diagnosis. Participants (n = 207; 56% male; 64.2 ± 12.3 years old) completed the Illness Perception Questionnaire-Revised, the COPE Inventory, the Symptom Checklist-Frequency and Severity, and the Profile of Mood States. Data were analyzed using Pearson correlation and hierarchical multiple regression. Illness perceptions contributed most to psychological distress, followed by coping strategies and symptom frequency. Illness perceptions explained the largest portion of the total variance for the following: Tension-Anxiety, 44/56%; Depression-Dejection, 38/50%; Fatigue-Inertia, 43/53%; Confusion-Bewilderment, 41/49%; Vigor-Activity, 24/35%; and Total Mood Disturbance, 47/63%. Illness perceptions of AF as having serious consequences, a psychological cause, and perceived poor understanding of AF together contributed more (.47) to Total Mood Disturbance than did coping by focusing on emotion (.08) or symptom frequency (.06). Illness perceptions are important contributors to psychological distress in patients with AF. Assessment of patients' illness perceptions may reveal those that increase the risk for psychological distress. Research is warranted to evaluate interventions to modify psychological cause and consequence beliefs and to promote understanding of AF.


Mesotrione control and pigment concentration of large crabgrass (Digitaria sanguinalis) under varying environmental conditions.
Mesotrione is a carotenoid biosynthesis-inhibiting herbicide currently labeled for crabgrass (Digitaria spp.) control. Mesotrione control of large crabgrass has been reported to vary with temperature and relative humidity; however, the effect of irradiance on mesotrione efficacy has not previously been reported. Likewise, little is known about pigment concentrations of Digitaria spp. The present research investigated the effects of mesotrione on large crabgrass, Digitaria sanguinalis (L.) Scop., control and pigment concentrations under varying irradiance at three temperatures. Mesotrione (0.28 kg ha(-1)) control of large crabgrass did not differ between temperature levels (18, 26 and 32 degrees C). Control was similar at tested irradiance levels (600, 1100 and 1600 micromol m(-2) s(-1)). Mesotrione reduced large crabgrass chlorophyll a, chlorophyll b and total carotenoid concentrations, as well as chlorophyll a to b ratios. Treated plant bleaching was highest 7 days after treatment (DAT) but decreased by 21 DAT. Treated plants were less than 10% necrotic 3 and 7 DAT but nearly 35% necrotic 21 DAT. Treated large crabgrass bleaching was highest and photochemical efficiency was lowest 7 DAT. These results indicate that some plant recovery occurs prior to 21 DAT. Although mesotrione efficacy has previously been reported to vary according to environmental factors, mesotrione control of large crabgrass did not vary with measured temperature and irradiance levels in this study. On account of crabgrass convalescence, secondary applications of mesotrione may control large crabgrass more effectively when applied prior to 21 DAT.


Risk assessment of microplastics in the ocean: Modelling approach and first conclusions.
We performed an environmental risk assessment for microplastics (<5 mm) in the marine environment by estimating the order of magnitude of the past, present and future concentrations based on global plastic production data. In 2100, from 9.6 to 48.8 particles m-3 are predicted to float around in the ocean, which is a 50-fold increase compared to the present-day concentrations. From a meta-analysis with effect data available in literature, we derived a safe concentration of 6650 buoyant particles m-3 below which adverse effects are not likely to occur. Our risk assessment (excluding the potential role of microplastics as chemical vectors) suggests that on average, no direct effects of free-floating microplastics in the marine environment are to be expected up to the year 2100. Yet, even today, the safe concentration can be exceeded in sites that are heavily polluted with buoyant microplastics. In the marine benthic compartment between 32 and 144 particles kg-1 dry sediment are predicted to be present in the beach deposition zone. Despite the scarcity of effect data, we expect adverse ecological effects along the coast as of the second half of the 21st century. From then ambient concentrations will start to outrange the safe concentration of sedimented microplastics (i.e. 540 particles kg-1 sediment). Additional ecotoxicological research in which marine species are chronically exposed to realistic environmental microplastic concentration series are urgently needed to verify our findings.


A phase IIa randomized controlled clinical and histological pilot study evaluating rhGDF-5/β-TCP for periodontal regeneration.
The primary objective of this study was to clinically and histologically evaluate periodontal wound healing/regeneration following surgical implantation of recombinant human growth/differentiation factor-5 (rhGDF-5) adsorbed onto a particulate β-tricalcium phosphate (β-TCP) carrier rhGDF-5/β-TCP into periodontal defects in man. Twenty chronic periodontitis patients, each with at least one tooth scheduled for extraction exhibiting a probing depth ≥6 mm and an associated intra-bony defect ≥4 mm participated in the study upon written informed consent. Subjects (one defect/patient) were randomized to receive open flap debridement (OFD) + rhGDF-5/β-TCP (n = 10) or OFD alone (control; n = 10). Block biopsies of the defect sites were collected at 6 months post-surgery and prepared for the histological evaluation. Two masked examiners evaluated the deepest aspect of each defect site relative to bone (height/area), periodontal ligament (PDL) and cementum regeneration, and residual β-TCP. Sites receiving rhGDF-5/β-TCP showed numerically greater PD reduction (3.7 ± 1.2 versus 3.1 ± 1.8 mm; p = 0.26), less gingival recession (0.5 ± 0.8 versus 1.4 ± 1.0 mm; p < 0.05) and greater clinical attachment level (CAL) gain (3.2 ± 1.7 versus 1.7 ± 2.2 mm; p = 0.14) at the deepest aspect of the defect compared with OFD alone. One biopsy in the rhGDF-5/β-TCP and four biopsies in the OFD group were deemed as not evaluable. Histologically, bone regeneration height was almost threefold greater for the rhGDF-5/β-TCP treatment compared with OFD alone (2.19 ± 1.59 versus 0.81 ± 1.02 mm; p = 0.08). Similarly an almost twofold increase was observed for PDL (2.16 ± 1.43 versus 1.23 ± 1.07 mm; p = 0.26), cementum (2.16 ± 1.43 versus 1.23 ± 1.07 mm; p = 0.26) and bone regeneration area (0.74 ± 0.69 versus 0.32 ± 0.47 mm(2) ; p = 0.14). Root resorption/ankylosis was not observed. Residual β-TCP occupied 8.4 ± 11.5% of the area of interest in biopsies of patients receiving rhGDF-5/β-TCP. Five biopsies (one rhGDF-5/β-TCP, four OFD) were deemed unsuitable to allow a meaningful histological or histometrical evaluation. Descriptive statistics showed greater PD reduction and CAL gain, and greater alveolar bone regeneration and periodontal regeneration at sites that received rhGDF-5/β-TCP compared to control. However, these differences were not statistically significant. Future studies with larger sample sizes will have to be conducted to verify these findings.


Vitamin D modulates the association of circulating insulin-like growth factor-1 with carotid artery intima-media thickness.
Experimental evidence indicates that circulating insulin-like growth factor-1 (IGF-1) counteracts vascular aging and atherosclerosis, for which increased carotid artery intima-media thickness (IMT) is a marker. Yet, IGF-1 concentrations have been inconsistently associated with carotid IMT in epidemiological studies. Since vitamin D is also implicated in vascular protection and affects IGF-1 biology, we hypothesized that it would influence the effect of IGF-1 on IMT. The relationship between carotid IMT and fasting serum IGF-1 was examined across strata of 25-hydroxyvitamin D [25(OH)D] in 472 participants in the Baltimore Longitudinal Study of Aging (BLSA) with well-controlled blood pressure and in 165 treatment-naive patients with essential hypertension from the Microalbuminuria: A Genoa Investigation on Complications (MAGIC) study. Moreover, the interplay between vitamin D and IGF-1 was preliminarily explored in EA.hy926 endothelial cells. After adjusting for age, sex, BMI, renal function, smoking, systolic blood pressure, LDL-cholesterol, glycemia, antihypertensive or lipid-lowering therapy, season, parathyroid hormone, and vitamin D supplementation, IGF-1 was significantly and negatively associated with carotid IMT only within the lowest 25(OH)D quartile (range 6.8-26 ng/mL) of the BLSA (β -0.095, p = 0.03). Similarly, a significant negative correlation between IGF-1 and carotid IMT was found after full adjustment only in MAGIC patients with 25(OH)D concentrations below either the deficiency cut-off of 20 ng/mL (β -0.214, p = 0.02) or 26 ng/mL (β -0.174, p = 0.03). Vitamin D dose-dependently decreased hydrogen peroxide-induced endothelial cell oxidative stress and apoptosis, which were further inhibited by IGF in the presence of low, but not high vitamin D concentration. Circulating IGF-1 is vasoprotective primarily when vitamin D levels are low. Future studies should address the mechanisms of vitamin D/IGF-1 interaction.


Will we cure cancer by sequencing thousands of genomes?
The promise to understand cancer and develop efficacious therapies by sequencing thousands of cancers has not occurred. Mutations in specific genes termed oncogenes and tumor suppressor genes are extremely heterogeneous amongst the same type of cancer as well as between cancers. They provide little selective advantage to the cancer and in functional tests have yet to be shown to be sufficient for transformation. Here I discuss the karyotyptic theory of cancer and ask if it is time for a new approach to understanding and ultimately treating cancer.


A mass spectrometry platform for a streamlined investigation of proteasome integrity, posttranslational modifications, and inhibitor binding.
The proteasome is responsible for the majority of protein degradation within eukaryotic cells and proteasome inhibitors have gained blockbuster status as anticancer drugs. Here, we introduce an analytical platform comprising reverse phase chromatography, intact protein mass spectrometry, and customized data analysis that allows a streamlined investigation of proteasome integrity and posttranslational modifications. We report the complete mass spectrometric assignment of all subunits of the yeast core particle, as well as of the human constitutive 20S proteasome and the human immunoproteasome, including phosphorylated isoforms of α7. Importantly, we found several batches of commercially available immunoproteasome to also contain constitutive catalytic subunits. Moreover, we applied the method to study the binding mechanisms of proteasome inhibitors, both validating the approach and providing a direct readout of subunit preferences complementary to biochemical methods. Collectively, our platform facilitates an easy, reliable and comprehensive detection of different types of covalent modifications on multisubunit protein complexes with high accuracy.


Synergistic third-party rewarding and punishment in the public goods game.
We study the evolution of cooperation in the spatial public goods game in the presence of third-party rewarding and punishment. The third party executes public intervention, punishing groups where cooperation is weak and rewarding groups where cooperation is strong. We consider four different scenarios to determine what works best for cooperation, in particular, neither rewarding nor punishment, only rewarding, only punishment or both rewarding and punishment. We observe strong synergistic effects when rewarding and punishment are simultaneously applied, which are absent if neither of the two incentives or just each individual incentive is applied by the third party. We find that public cooperation can be sustained at comparatively low third-party costs under adverse conditions, which is impossible if just positive or negative incentives are applied. We also examine the impact of defection tolerance and application frequency, showing that the higher the tolerance and the frequency of rewarding and punishment, the more cooperation thrives. Phase diagrams and characteristic spatial distributions of strategies are presented to corroborate these results, which will hopefully prove useful for more efficient public policies in support of cooperation in social dilemmas.


First Record of White Rust, Caused by Albugo occidentalis, on Spinach in Greece.
In early December 2012 and February 2013, severe symptoms of white rust were observed on several commercial crops of the spinach (Spinacia oleracea L.) cvs. Tahiti and Rembrandt in the Aghia Pelaghia and Elia areas, respectively, of Heraklio, Crete, Greece. Initially, small, chlorotic lesions developed on the upper side of the leaves. As disease progressed, small, glassy white pustules developed on the underside of each leaf, frequently in concentric rings. The pustules were blister-like and oval, irregularly oval, or elongated, ranging from 0.5 to 2.0 mm in diameter and up to 3 mm in length. Lesions often coalesced, and the pustules could cover the entire lower leaf surface, rendering them unmarketable. The dome-like epidermis of host tissue covering the white rust pustules ruptured and exposed a white, chalky 'dust' of numerous powdery spores in small, circular to elongate sori. The sporangia were arranged in basipetal chains, were globose to oval, with a smooth wall that was uniformly thick and measured 19.1 ± 1.93 (14.1 to 23.5) μm × 15.3 ± 1.49 (12.9 to 20.0) μm when hydrated. Oospores were absent from the leaves. The morphological characteristics closely resembled those reported for the white rust pathogen, Albugo occidentalis Wilson (4), as well as those of A. occidentalis measured from dried leaves of Chenopodium spp. and Monolepis nuttalliana (Schult.) Greene (Herb. IMI96980, IMI351202, and IMI26345, respectively), kindly loaned by the Royal Botanic Gardens, Kew, United Kingdom. Pathogenicity was confirmed by spraying a suspension of 105 sporangia/ml on 10 healthy 20-day-old potted spinach plants of cv. Tahiti. Inoculated plants were covered with polyethylene bags for 3 days and incubated in a growth chamber at 16 to 20°C with a 10-h photoperiod. White rust symptoms were observed on the lower surface of the leaves 10 days after inoculation. Ten control plants sprayed similarly with distilled water and maintained under the same conditions as inoculated plants showed no symptoms. The fungus present on the inoculated plants was morphologically identical to that originally observed on diseased plants, fulfilling Koch's postulates. Genomic DNA from spinach leaf sori was extracted, and the internal transcribed spacer (ITS) region of ribosomal DNA (rDNA), ITS1-5,8S-ITS2, as well as the cytochrome oxidase subunit II (COX2) mitochondrial gene, were amplified. PCR products were sequenced and deposited in GenBank (KC676794 and KC676795, respectively). In a BLAST search, the ITS1-5,8S-ITS2 and COX2 sequences showed 99% similarities to 684 bp (AJ553900.1) and 599 bp (AY286220.1) sequences of the corresponding A. occidentalis genes in GenBank, respectively. Based on morphological characteristics, pathogenicity tests, and molecular sequencing data, it was concluded that the pathogen on spinach in Crete is A. occidentalis. This is an economically important pathogen of spinach in the United States, that has also has been recorded in Iran (2) and India on a Chenopodium sp. (IMI351202), and in Canada on M. nuttalliana (IMI26345). To our knowledge, this is the first report of this pathogen in Greece, and the first record on spinach in Europe. A voucher specimen has been deposited at the Royal Botanic Gardens, Kew, United Kingdom (Accession No. K(M) 181610). References: (1) J. C. Correll et al. Eur. J. Plant Pathol. 129:193, 2011. (2) A. G. Ebrahimi and H. Afzali. Rostaniha 1:73, 2000. (3) D. F. Farr et al. Fungi on Plants and Plant Products in the United States. American Phytopathological Society, St. Paul, MN, 1989. (4) G. W. Wilson. Bull. Torrey Bot. Club 34:61, 1907.


The future of HIV microbicides: challenges and opportunities.
HIV microbicides are topical, self-administered products aimed at preventing or reducing HIV infection in women and may represent the most promising strategy for combating the HIV/AIDS epidemic at the present time. Although a safe and effective microbicide has yet to be identified, all products tested in Phase III trials to date have been vaginal gels containing non-specific compounds with modest potency that had to be applied close to the time of sexual intercourse. Issues regarding these early generation products were further complicated by widely publicized cases of halted efficacy trials. However, as a result of each of these challenges, new information and essential lessons have emerged for the field. These lessons have resulted in a meaningful increase in microbicide development efforts focusing on compounds with highly potent and HIV-specific mechanisms of action, combination products, novel formulations, and carefully designed pharmacokinetic and pharmacodynamic evaluations, all of which are reasons for renewed confidence that a safe and effective microbicide is achievable.


Characterization of ameboid microglia isolated from developing mammalian brain.
Ameboid microglia are isolated from the cerebral tissue of neonatal rat by selective cell adhesion to plastic. Histochemical markers show that the microglial preparations are homogeneous (95 +/- 3%) and represent a 10% yield from starting cultures. Isolated ameboid microglia contain nonspecific esterase activity, the macrophage surface antigens MAC-1 and MAC-3, and acetylated low-density lipoprotein receptors. Ameboid cells have functional properties similar to those of macrophages, including the ability to engulf 5 micron latex beads, to secrete Interleukin-1 (IL-1) and to release superoxide anion. Unlike monocytes and adherent spleen cells, ameboid microglia do not show peroxidase activity by histochemical stain. Unlike resident peritoneal macrophages, ameboid microglia proliferate in vitro. Scanning electron microscopy shows that ameboid cells have short, spinous processes that can be distinguished from the ruffled surfaces of body macrophages. Our observations suggest that ameboid microglia are a distinct class of mononuclear phagocytic cells. Retinoic acid and dimethyl sulfoxide, agents known to accelerate differentiation in vitro, stimulate ameboid cells to develop thin processes several hundred microns in length. These "process-bearing" microglia eventually lose the capacity to engulf latex beads and to proliferate. They also show reductions in nonspecific esterase activity and in the binding of acetylated low-density lipoprotein. We suggest that in vitro ameboid microglia differentiate into nonphagocytic cells similar to ramified microglia found in normal adult brain. The isolation techniques described here provide the opportunity to study the composition and function of different microglial subpopulations during the development of the CNS.


MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements.
Cell-specific patterns of gene expression are determined by combinatorial actions of sequence-specific transcription factors at cis-regulatory elements. Studies indicate that relatively simple combinations of lineage-determining transcription factors (LDTFs) play dominant roles in the selection of enhancers that establish cell identities and functions. LDTFs require collaborative interactions with additional transcription factors to mediate enhancer function, but the identities of these factors are often unknown. We have shown that natural genetic variation between individuals has great utility for discovering collaborative transcription factors. Here, we introduce MMARGE (Motif Mutation Analysis of Regulatory Genomic Elements), the first publicly available suite of software tools that integrates genome-wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. MMARGE is optimized to work with chromatin accessibility assays (such as ATAC-seq or DNase I hypersensitivity), as well as transcription factor binding data collected by ChIP-seq. Herein, we provide investigators with rationale for each step in the MMARGE pipeline and key differences for analysis of datasets with different experimental designs. We demonstrate the utility of MMARGE using mouse peritoneal macrophages, liver cells, and human lymphoblastoid cells. MMARGE provides a powerful tool to identify combinations of cell type-specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation.


Testosterone, sex hormone-binding globulin, calculated free testosterone, and oestradiol in male vegans and omnivores.
Total testosterone (T), total oestradiol (E2) and sex hormone-binding globulin (SHBG) concentrations were measured in plasma samples from fifty-one male vegans and fifty-seven omnivores of similar age. Free T concentration was estimated by calculation. In comparison with the omnivores, the vegans had 7% higher total T (P = 0.250), 23% higher SHBG (P = 0.001), 3% lower free T (P = 0.580), and 11% higher E2 (P = 0.194). In a subset of eighteen vegans and twenty-two omnivores for whom 4 d diet records were available, there were statistically significant correlations between T and polyunsaturated fatty acids (r 0.37), SHBG and fat (r 0.43 for total fat, 0.46 for saturated fatty acids and 0.33 for polyunsaturated fatty acids), and SHBG and alcohol (r-0.39). It is concluded that a vegan diet causes a substantial increase in SHBG but has little effect on total or free T or on E2.


Estimates of within-herd incidence rates of Mycobacterium bovis in Canadian cattle and cervids between 1985 and 1994.
We analysed the individual-animal data from six of the nine outbreaks of tuberculosis in Canadian cattle and cervids from 1985 to 1994. A "positive/reactor" animal was one which had either a positive culture or a positive or suspicious reaction on a mid-cervical, comparative cervical, or gross or histopathological test for tuberculosis. Individual-animal data were collected only for herds which had one or more positive/reactor animals. Data were collected from the outbreak records in the Regional or District offices of Agriculture and Agri-food Canada's Animal and Plant Health Directorate. The within-herd spread of Mycobacterium bovis was studied by determining the most-likely date at which the herd was first exposed to M. bovis and the number of reactions which had developed by the time the herd was investigated. The animal-time units at risk in the herd were probably overestimated, resulting in conservative estimates of the within-herd incidence rates. Negative-binomial regression was used to investigate factors which might have influenced the within-herd spread of tuberculosis. Increasing age appeared to be a risk factor for being a positive/reactor animal. When compared to animals 0-12 months old, animals 13-24 months old had an incidence rate ratio (IRR) of 7.6, while animals >24 months old had an IRR of 10.4 (p=0.009). Actual and predicted incidence rates for tuberculosis in mature (>24 months old) animals were calculated. Actual and predicted incidence rates were similar for cervids, within an outbreak. There was more variability between actual and predicted rates in the dairy and beef animals. In the one outbreak (Ontario) where there were positive/reactor cervid, dairy and beef herds, the actual incidence rate for cervids (IR=9.3 cases per 100 animal-years) was almost twice that of dairy cattle (IR=5.0) and three times that of beef cattle (IR=3.1).


Tumour-educated circulating monocytes are powerful candidate biomarkers for diagnosis and disease follow-up of colorectal cancer.
Cancer immunology is a growing field of research whose aim is to develop innovative therapies and diagnostic tests. Starting from the hypothesis that immune cells promptly respond to harmful stimuli, we used peripheral blood monocytes in order to characterise a distinct gene expression profile and to evaluate its potential as a candidate diagnostic biomarker in patients with colorectal cancer (CRC), a still unmet clinical need. We performed a case-control study including 360 peripheral blood monocyte samples from four European oncological centres and defined a gene expression profile specific to CRC. The robustness of the genetic profile and disease specificity were assessed in an independent setting. This screen returned 43 putative diagnostic markers, which we refined and validated in the confirmative multicentric analysis to 23 genes with outstanding diagnostic accuracy (area under the curve (AUC)=0.99 (0.99 to 1.00), Se=100.0% (100.0% to 100.0%), Sp=92.9% (78.6% to 100.0%) in multiple-gene receiver operating characteristic analysis). The diagnostic accuracy was robustly maintained in prospectively collected independent samples (AUC=0.95 (0.85 to 1.00), Se=92.6% (81.5% to 100.0%), Sp=92.3% (76.9% to 100.0%). This monocyte signature was expressed at early disease onset, remained robust over the course of disease progression, and was specific for the monocytic fraction of mononuclear cells. The gene modulation was induced specifically by soluble factors derived from transformed colon epithelium in comparison to normal colon or other cancer histotypes. Moreover, expression changes were plastic and reversible, as they were abrogated upon withdrawal of these tumour-released factors. Consistently, the modified set of genes reverted to normal expression upon curative treatment and was specific for CRC. Our study is the first to demonstrate monocyte plasticity in response to tumour-released soluble factors. The identified distinct signature in tumour-educated monocytes might be used as a candidate biomarker in CRC diagnosis and harbours the potential for disease follow-up and therapeutic monitoring.


Surgical and nonsurgical management of sciatica secondary to a lumbar disc herniation: five-year outcomes from the Maine Lumbar Spine Study.
A prospective cohort study. To assess 5-year outcomes for patients with sciatica caused by a lumbar disc herniation treated surgically or nonsurgically. There is limited knowledge about long-term treatment outcomes of sciatica caused by a lumbar disc herniation, particularly the relative benefits of surgical and conservative therapy in contemporary clinical practice. Eligible, consenting patients recruited from the practices of orthopedic surgeons, neurosurgeons, and occupational medicine physicians throughout Maine had baseline interviews with mailed follow-up questionnaires at 3, 6, and 12 months and annually thereafter. Clinical data were obtained at baseline from a physician questionnaire. Outcomes included patient-reported symptoms of leg and back pain, functional status, satisfaction, and employment and compensation status. Of 507 patients initially enrolled, 5-year outcomes were available for 402 (79.3%) patients: 220 (80%) treated surgically and 182 (78.4%) treated nonsurgically. Surgically treated patients had worse baseline symptoms and functional status than those initially treated nonsurgically. By 5 years 19% of surgical patients had undergone at least one additional lumbar spine operation, and 16% of nonsurgical patients had opted for at least one lumbar spine operation. Overall, patients treated initially with surgery reported better outcomes. At the 5-year follow-up, 70% of patients initially treated surgically reported improvement in their predominant symptom (back or leg pain) versus 56% of those initially treated nonsurgically (P < 0.001). Similarly, a larger proportion of surgical patients reported satisfaction with their current status (63% vs. 46%, P < 0.001). These differences persisted after adjustment for other determinants of outcome. The relative advantage of surgery was greatest early in follow-up and narrowed over 5 years. There was no difference in the proportion of patients receiving disability compensation at the 5-year follow-up. The least symptomatic patients at baseline did well regardless of initial treatment, although function improved more in the surgical group. For patients with moderate or severe sciatica, surgical treatment was associated with greater improvement than nonsurgical treatment at 5 years. However, patients treated surgically were as likely to be receiving disability compensation, and the relative benefit of surgery decreased over time.


Enhancement of disease resistance, growth potential, and photosynthesis in tomato (Solanum lycopersicum) by inoculation with an endophytic actinobacterium, Streptomyces thermocarboxydus strain BPSAC147.
Biotic stresses in plants have a significant impact on agricultural productivity. In the present study, in vivo experiments were conducted to determine the physiological responses of tomato (Solanum lycopersicum L.) seedlings by inoculation with an endophytic actinobacterium, Streptomyces thermocarboxydus isolate BPSAC147 under greenhouse conditions. Further, photochemical quantum yield of photosystem II (PSII) (Fv/Fm), photochemical quenching (qP) and non-photochemical (NPQ) were calculated in seedlings inoculated with S. thermocarboxydus (T1) and were compared with control (T0) plants. Furthermore, the electron transport rate (ETR) of PSII exhibited a significant increase in T1 plants, relative to T0 plants. These results indicate that inoculation of tomato seedlings with S. thermocarboxydus had a positive effect on the process of photosynthesis, resulting in enhanced chlorophyll fluorescence parameters due to increased ETR in the thylakoid membrane. GC-MS analysis showed significant differences in the volatile compounds in the different treatments performed under greenhouse conditions. The present study suggests that S. thermocarboxydus can be used as new biocontrol agent to control Fusarium wilt in tomato crops and enhance productivity by enhancing photosynthesis.


Phase velocity nonuniformity-resulted beam patterns in difference frequency generation.
The evolution of the difference frequency generation between a planar pump wave and a focused signal wave has been numerically investigated in this paper. We show that, at the difference frequency wave, various beam patterns such as ring and moon-like, are resulted due to the nonuniform distribution of phase velocity in the focused signal wave. The subluminal and superluminal regions can be identified by the intersection of two generated beam profiles that correspond to a pair of phase-mismatches with equal value but opposite signs.


Elevated Circulating Activin A Levels in Patients With Malignant Pleural Mesothelioma Are Related to Cancer Cachexia and Reduced Response to Platinum-based Chemotherapy.
Previous preclinical studies have shown that activin A is overexpressed in malignant pleural mesothelioma (MPM), associates with cancer cachexia, and is observed in in vitro resistance to platinum-based chemotherapy. We evaluated circulating activin levels and their endogenous antagonists' follistatin/follistatin-like 3 in intrathoracic tumors. Patients suspected of thoracic malignancy were recruited prior to surgery. Serum samples were collected from 21 patients with MPM, 59 patients with non-small-cell lung cancer (NSCLC), and 22 patients with benign lung lesions. Circulating activin/follistatin levels were measured using enzyme-linked immunosorbent assay and compared with clinicopathologic parameters. Circulating activin A levels were elevated in patients with MPM when compared with patients with NSCLC or benign lung lesion samples (P < .0001). Also, follistatin and follistatin-like 3 levels were the highest in MPM, although with less difference compared with activin A. Receiver operating characteristic analysis for activin A for separating NSCLC from benign lung lesion showed an area under the curve of 0.856 (95% confidence interval, 0.77-0.94). Activin A levels were higher in patients with cachexia (P < .001). In patients with MPM, activin A levels correlated positively with computed tomography-based baseline tumor size (R = 0.549; P = .010) and the change in tumor size after chemotherapy (R = 0.743; P = .0006). Patients with partial response or stable disease had lower circulating activin A levels than the ones with progressive disease (P = .028). Activin A serum level could be used as a biomarker in differentiating malignant and benign lung tumors. Circulating activin A levels were elevated in MPM and associates with cancer cachexia and reduced chemotherapy response.


The persistence of bacterial and methanogenic archaeal communities residing in the rumen of young lambs.
The aim of this experiment was to study the persistence in time of bacterial and methanogenic archaeal communities that establish in the rumen of lambs fed two different diets at weaning. Twenty ewes with single lambs were used in two phases. In phase I, 10 lambs had access only to grass hay (H group). The other 10 lambs had free access to concentrate and grass hay (C group). After 20 weeks, five lambs from each group were slaughtered and rumen samples were kept for analysis. In phase II, the remaining lambs were grouped together and fed grass plus concentrate for 4 months and then slaughtered, and rumen samples were collected for analysis. Terminal restriction fragment length polymorphism analysis showed a different bacterial and methanogen population established in the rumen of H and C lambs in phase I. These differences disappeared for methanogens after both groups were fed the same diet for 4 months; however, the total bacterial community remained different for the H and C samples. Our results suggest that some of the differences in the microbial populations that establish in animals fed different diets at weaning persist in the long term, which provides the possibility of programming the microbial populations in the adult animal.


Recruitment and retention of women in a large randomized control trial to reduce repeat preterm births: the Philadelphia Collaborative Preterm Prevention Project.
Recruitment and retention of patients for randomized control trial (RCT) studies can provide formidable challenges, particularly with minority and underserved populations. Data are reported for the Philadelphia Collaborative Preterm Prevention Project (PCPPP), a large RCT targeting risk factors for repeat preterm births among women who previously delivered premature (< 35 weeks gestation) infants. Design of the PCPPP incorporated strategies to maximize recruitment and retention. These included an advanced database system tracking follow-up status and assessment completion rates; cultural sensitivity training for staff; communication to the community and eligible women of the benefits of participation; financial incentives; assistance with transportation and supervised childcare services; and reminder calls for convenient, flexibly scheduled appointments. Analyses reported here: 1) compare recruitment projections to actual enrollment 2) explore recruitment bias; 3) validate the randomization process 4) document the extent to which contact was maintained and complete assessments achieved 5) determine if follow-up was conditioned upon socio-economic status, race/ethnicity, or other factors. Of eligible women approached, 1,126 (77.7%) agreed to participate fully. Of the 324 not agreeing, 118 (36.4%) completed a short survey. Consenting women were disproportionately from minority and low SES backgrounds: 71.5% consenting were African American, versus 38.8% not consenting. Consenting women were also more likely to report homelessness during their lifetime (14.6% vs. 0.87%) and to be unmarried at the time of delivery (81.6% versus 47.9%). First one-month postpartum assessment was completed for 83.5% (n = 472) of the intervention group (n = 565) and 76% (426) of the control group. Higher assessment completion rates were observed for the intervention group throughout the follow-up. Second, third, fourth and fifth postpartum assessments were 67.6% vs. 57.5%, 60.0% vs. 48.9%, 54.2% vs. 46.3% and 47.3% vs. 40.8%, for the intervention and control group women, respectively. There were no differences in follow-up rates according to race/ethnicity, SES or other factors. Greater retention of the intervention group may reflect the highly-valued nature of the medical and behavior services constituting the intervention arms of the Project. Findings challenge beliefs that low income and minority women are averse to enrolling and continuing in clinical trials or community studies.


Time-dependent association between metabolic syndrome and risk of CKD in Korean men without hypertension or diabetes.
The time-dependent association between metabolic syndrome and risk of chronic kidney disease (CKD) is not clear. Prospective cohort study. The study cohort was composed of 10,685 healthy men without CKD, hypertension, or diabetes who participated in a health-checkup program at a large work site. Metabolic syndrome. CKD was defined as an estimated glomerular filtration rate (GFR) less than 60 mL/min/1.73 m(2). A standard Cox proportional hazards model and a time-dependent Cox model were used to calculate adjusted hazard ratios (HRs) in the CKD model. During 40,616.8 person-years of follow-up, 291 incident cases of CKD developed; 787 patients (7.4%) had metabolic syndrome at baseline and 1,444 (14.4%) developed incident metabolic syndrome during follow-up. After adjustment for age, baseline GFR, gamma-glutamyltransferase level, and uric acid level, metabolic syndrome at baseline was associated with a significantly increased risk of CKD (HR, 1.99; 95% confidence interval, 1.46 to 2.73). Metabolic syndrome over time as a time-dependent variable also predicted the development of CKD (HR, 1.83; [corrected] 95% confidence interval, 1.34 to 2.49) [corrected] The relationship between metabolic syndrome and incident CKD remained significant, even after further adjustment for the homeostasis model assessment of insulin resistance, high-sensitivity C-reactive protein level, current smoking, alcohol consumption, or regular exercise. In addition, there were graded relationships between number of metabolic syndrome traits or quintile of homeostasis model assessment of insulin resistance over time as a time-dependent variable and risk of CKD. Both increased triglyceride and low high-density lipoprotein cholesterol levels among metabolic syndrome traits were associated with significantly increased risk of CKD. These results were effectively unchanged, even after additional adjustment for incident hypertension and incident diabetes. Estimated GFR was used instead of a directly measured GFR to define CKD. Metabolic syndrome is an independent risk factor for the development of CKD in Korean men without hypertension or diabetes, even with changes in status of metabolic syndrome over time.


Large scale Brownian dynamics of confined suspensions of rigid particles.
We introduce methods for large-scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method [F. Balboa Usabiaga et al., Commun. Appl. Math. Comput. Sci. 11(2), 217-296 (2016)] at a cost comparable to the cost of deterministic simulations. We demonstrate that we can efficiently generate deterministic and random displacements for many particles using preconditioned Krylov iterative methods, if kernel methods to efficiently compute the action of the Rotne-Prager-Yamakawa (RPY) mobility matrix and its "square" root are available for the given boundary conditions. These kernel operations can be computed with near linear scaling for periodic domains using the positively split Ewald method. Here we study particles partially confined by gravity above a no-slip bottom wall using a graphical processing unit implementation of the mobility matrix-vector product, combined with a preconditioned Lanczos iteration for generating Brownian displacements. We address a major challenge in large-scale BD simulations, capturing the stochastic drift term that arises because of the configuration-dependent mobility. Unlike the widely used Fixman midpoint scheme, our methods utilize random finite differences and do not require the solution of resistance problems or the computation of the action of the inverse square root of the RPY mobility matrix. We construct two temporal schemes which are viable for large-scale simulations, an Euler-Maruyama traction scheme and a trapezoidal slip scheme, which minimize the number of mobility problems to be solved per time step while capturing the required stochastic drift terms. We validate and compare these schemes numerically by modeling suspensions of boomerang-shaped particles sedimented near a bottom wall. Using the trapezoidal scheme, we investigate the steady-state active motion in dense suspensions of confined microrollers, whose height above the wall is set by a combination of thermal noise and active flows. We find the existence of two populations of active particles, slower ones closer to the bottom and faster ones above them, and demonstrate that our method provides quantitative accuracy even with relatively coarse resolutions of the particle geometry.


Construction of a high-density composite map and comparative mapping of segregation distortion regions in barley.
Segregation distortion can negatively impact on gains expected using selection. In order to increase our understanding of genetic factors that may influence the extent and direction of segregation distortion, segregation distortion analyses were conducted in four different doubled haploid (DH) populations. A high-density composite map of barley was then constructed by integrating information from the four populations. The composite map contained 2,111 unique loci, comprising RFLP, SSR and DArT markers and spanned 1,136 cM. In the four populations investigated, the proportion of markers with segregation distortion ranged from 15 to 38%, depending on the population. The highest distortion was observed in populations derived by the microspore culture technique. Distorted loci tended to be clustered, which allowed definition of segregation distortion regions (SDRs). A total of 14 SDRs were identified in the 4 populations. Using the high-density composite map, several SDRs were shown to have consistent map locations in two or more populations; one SDR on chromosome 1H was present in all four populations. The analysis of haplotypes underlying seven SDRs indicated that in three cases the under-represented haplotypes were common across populations, but for four SDRs the under-represented haplotypes varied across populations. Six of the seven centromeric regions harboured SDRs suggesting that genetic processes related to position near a centromere caused the segregation distortion in these SDRs. Other SDRs were most likely due to the methods used to produce the DH populations. The association of the SDRs identified in this study and some of the genes involved in the process of haploid production described in other studies were compared. The composite map constructed in this study provides an additional resource for the barley community via increased genome coverage and the provision of additional marker options. It has also enabled further insights into mechanisms that underpin segregation distortion.


Hot flushes and reproductive hormone levels during the menopausal transition.
Evidence suggests that hot flushes are associated with fluctuating levels of oestradiol (E2) during menopause, as well as changes in the levels of follicle-stimulating hormone (FSH) and inhibin B. The relationship between hot flushes and anti-Müllerian hormone (AMH) is unknown. To examine specific hormone levels and ethnic differences in relation to hot flushes. Data were drawn from 108 women aged 40-59 years. There were three groups of participants: European women in London, UK; Bangladeshi women in Sylhet, Bangladesh; and Bangladeshi women who had migrated to London as adults. Symptom information was collected via questionnaires. Serum blood samples were collected to detect inhibin B, AMH, FSH, and E2. AMH and FSH were significantly associated with the experience of hot flushes in the past 2 weeks. Inhibin B and E2 were not associated with hot flushes. Body mass index (BMI), ethnicity, and education level were associated with both the occurrence and the frequency hot flushes. Menopausal status was also associated with the frequency of hot flushes. Relationships between AMH, FSH and symptoms are indicative of women's progress through the menopausal transition. The influence of BMI and education suggest that lifestyle changes may contribute to the management of symptoms. This merits further research.


Over-optimism in bioinformatics: an illustration.
In statistical bioinformatics research, different optimization mechanisms potentially lead to 'over-optimism' in published papers. So far, however, a systematic critical study concerning the various sources underlying this over-optimism is lacking. We present an empirical study on over-optimism using high-dimensional classification as example. Specifically, we consider a 'promising' new classification algorithm, namely linear discriminant analysis incorporating prior knowledge on gene functional groups through an appropriate shrinkage of the within-group covariance matrix. While this approach yields poor results in terms of error rate, we quantitatively demonstrate that it can artificially seem superior to existing approaches if we 'fish for significance'. The investigated sources of over-optimism include the optimization of datasets, of settings, of competing methods and, most importantly, of the method's characteristics. We conclude that, if the improvement of a quantitative criterion such as the error rate is the main contribution of a paper, the superiority of new algorithms should always be demonstrated on independent validation data. The R codes and relevant data can be downloaded from http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/020_professuren/boulesteix/overoptimism/, such that the study is completely reproducible.


Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life.
The assembly of the tree of life has seen significant progress in recent years but algae and protists have been largely overlooked in this effort. Many groups of algae and protists have ancient roots and it is unclear how much data will be required to resolve their phylogenetic relationships for incorporation in the tree of life. The red algae, a group of primary photosynthetic eukaryotes of more than a billion years old, provide the earliest fossil evidence for eukaryotic multicellularity and sexual reproduction. Despite this evolutionary significance, their phylogenetic relationships are understudied. This study aims to infer a comprehensive red algal tree of life at the family level from a supermatrix containing data mined from GenBank. We aim to locate remaining regions of low support in the topology, evaluate their causes and estimate the amount of data required to resolve them. Phylogenetic analysis of a supermatrix of 14 loci and 98 red algal families yielded the most complete red algal tree of life to date. Visualization of statistical support showed the presence of five poorly supported regions. Causes for low support were identified with statistics about the age of the region, data availability and node density, showing that poor support has different origins in different parts of the tree. Parametric simulation experiments yielded optimistic estimates of how much data will be needed to resolve the poorly supported regions (ca. 103 to ca. 104 nucleotides for the different regions). Nonparametric simulations gave a markedly more pessimistic image, some regions requiring more than 2.8 105 nucleotides or not achieving the desired level of support at all. The discrepancies between parametric and nonparametric simulations are discussed in light of our dataset and known attributes of both approaches. Our study takes the red algae one step closer to meaningful inclusion in the tree of life. In addition to the recovery of stable relationships, the recognition of five regions in need of further study is a significant outcome of this work. Based on our analyses of current availability and future requirements of data, we make clear recommendations for forthcoming research.


Socio-economic resources, young child feeding practices, consumption of highly processed snacks and sugar-sweetened beverages: a population-based survey in rural northwestern Nicaragua.
Socio-economic resources may be associated with infant feeding in complex patterns in societies undergoing a nutrition transition. This study evaluates associations of housing quality, food security and maternal education to the World Health Organization (WHO) feeding recommendations and to consumption of highly processed snacks (HP snacks) and sugar-sweetened beverages (SSBs) in rural Nicaragua. Data were collected from May to November 2009, with mothers of 0- to 35-month-olds being asked about young child feeding using a food frequency questionnaire. A validated questionnaire was used to assess household food insecurity and data were collected on maternal education and housing quality. Pearson's chi-squared test was used to compare proportions and determine associations between the resources and young child feeding. The three socio-economic resources and other confounders were introduced to multivariate logistic regression analyses to assess the independent contribution of the resources to the feeding practices and consumption of HP snacks and SSBs. Mothers with the lowest education level were more likely to be exclusively breastfeeding (EBF) their infants (OR not EBF: 0.19; 95% CI: 0.07, 0.51), whilst mothers of 6- to 35-month-olds in the lowest education category had more inadequate dietary diversity (DD) (OR for not meet DD: 2.04; 95% CI: 1.36, 3.08), were less likely to consume HP snacks (OR for HP snacks: 0.47; 95% CI: 0.32, 0.68) and SSBs (OR for SSBs: 0.68; 95% CI: 0.46, 0.98), compared to mothers with the highest level of education. Similarly, children residing in households with the highest food insecurity were also more prone to have inadequate dietary diversity (OR for not meet DD: 1.47; 95% CI: 1.05, 2.05). The odds for double burden of suboptimal feeding (concurrent inadequate diet and consumption of HP snacks/SSBs) were significantly lower in children of least educated mothers (OR: 0.64; 95% CI: 0.44, 0.92). Higher level of education was associated with both more and less adherence to the WHO recommended feeding practices as well as with more consumption of HP snacks and SSBs. Regardless of educational strata, the children in the community were exposed to suboptimal feeding practices conducive to both under- as well as overnutrition.


Infection of barramundi Lates calcarifer with Streptococcus iniae: effects of different routes of exposure.
The use of various challenge techniques has allowed the formation of a hypothesis for the mode of infection of Streptococcus iniae in barramundi. A bacterial dose of 1 x 10(3) colony forming units (cfu), corresponding to the LD50, delivered orally to barramundi could initiate the sub-acute form of the disease observed at the farms. The acute form of the disease could be initiated through bath exposure to the pathogen. S. iniae was equally as infective in freshwater, saltwater or when fish were subject to skin trauma prior to exposure, with LD50 values of 3.2 x 10(4), 2.0 x 10(4), 3.2 x 10(4) cfu, respectively, when observed over a 10 d period. It is suggested that sub-acute infection occurs orally, with mass mortalities occurring through the increased presence of the bacterium in the environment.


Relationship Between Care Burden and Religious Beliefs Among Family Caregivers of Mentally Ill Patients.
Families are considered as primary sources of care for individuals suffering from mental disorders. However, one of the major stresses in families is the infliction of a family member with mental illnesses causing dysfunction in health dimensions or generally their quality of life. Currently, most experts believe that religion can affect physical health and other aspects of human life. So, the aim of this study was to investigate "the relationship between care burden and religious beliefs among family caregivers of mentally ill patients." This cross-sectional study was carried out in Iran on 152 families with mentally ill patients who were hospitalized in psychiatric wards. The sampling method was nonprobability and consecutive sampling method. The data collection instruments included a demographic characteristic questionnaire, Religious Beliefs, and Zarit Care Burden Questionnaires. The mean score for care burden was 30.99 (SD = 16.45). 5.9% of the participants reported a low level, and 39.5% experienced a moderate level of care burden. Moreover, the mean score for religious beliefs was 115.5 (SD = 13.49), and majority of the participants (70.4%) were endowed with strong religious beliefs. There were no significant associations between care burden and intensity of religious beliefs among the study samples (P = 0.483). Considering the results of this study indicating experience of moderate-to-high levels of care burden in families with mentally ill patients, it is recommended to consider such families and their religious beliefs as contributing factors in coping with challenges of mental disorders.


Development of a new perfusion system for pharmacological study on rabbit basilar arteries.
We developed a constant-flow perfusion system to measure vascular responses to vasoactive agents applied intraluminally or extraluminally. The intraluminal and extraluminal sides of a cylindrical section of rabbit basilar artery were isolated completely. By loading with 0.75 g of tension, the resting condition of each preparation was made constant. The intraluminal side was perfused at a constant flow of 8 ml/min and under an intraluminal pressure of 8 mm Hg. When 30 mM KCl was administered intraluminally the preparation showed marked contraction, whereas only slight contraction was observed with extraluminal administration. When 2 x 10(-7) M 5-hydroxytryptamine was administered, no significant differences in contraction could be detected between the intraluminal and extraluminal routes. Application of 10(-6) to 10(-4) M acetylcholine after precontraction with 30 mM KCl resulted in much stronger dilatation upon intraluminal application. Thus, it was demonstrated that under certain conditions significant differences exist in the responses of rabbit basilar arteries to vasoactive agents applied intraluminally or extraluminally. This system can detect the effects of vasoactive agents administered intraluminally and extraluminally at a high level of sensitivity and shows good reproducibility as a means of analyzing vascular functions and characteristics.