Sequences that adopt non-B-DNA conformation in form V DNA as probed by enzymic methylation

pBR322 form V DNA is a highly torsionally strained molecule with a linking number of zero. We have used sequence- specific DNA methylases as probes for B-DNA in this molecule, exploiting the inability of methylases to methylate single-stranded DNA and Z-DNA, both of which are known to occur in form V DNA. Some sequences in form V DNA were shown to be totally in the B-form, others were totally in an altered, unmethylatable conformation, while still other sites appeared to exist partly in altered and partly in normal B-conformation. Some potential Z-forming sequences (alternating pyrimidine/purine) of less than seven base-pairs were not in the Z conformation in form V DNA, whereas others did adopt an altered structure, indicating a modulating influence of flanking sequences. Furthermore, regions of imperfect alternating pyrimidine/purine structure were sometimes capable of adopting an altered structure. In addition, some regions of altered structure had no apparent Z-forming sequences, nor were they in polypurine stretches, which have also been proposed to form left-handed DNA. These non-B-DNA conformations may represent novel left-handed helical structures or sequences that become single stranded under torsional strain. Long regions of either altered (unmethylatable) DNA or B-DNA were not always observed. In fact, one region showed three transitions between B-like DNA and altered structure within 26 base-pairs.

Small Polaron Hopping And High-Temperature Dc Conductivity Of Chalcogenide Glasses

D.C. conductivity behaviour of a variety of chalcogenide glasses have been analysed using ln σ vs Image plots as suggested in the multiphonon assisted polaron hopping model of Triberis and Friedman. The agreement with the model is very satisfactory and further analysis of the model using c.

Independent replication and meta-analysis for endometriosis risk loci

Endometriosis is a complex disease that affects 6-10% of women in their reproductive years and 20-50% of women with infertility. Genome-wide and candidate-gene association studies for endometriosis have identified 10 independent risk loci, and of these, nine (rs7521902, rs13394619, rs4141819, rs6542095, rs1519761, rs7739264, rs12700667, rs1537377, and rs10859871) are polymorphic in European populations. Here we investigate the replication of nine SNP loci in 998 laparoscopically and histologically confirmed endometriosis cases and 783 disease-free controls from Belgium. SNPs rs7521902, rs13394619, and rs6542095 show nominally significant (p <.05) associations with endometriosis, while the directions of effect for seven SNPs are consistent with the original reports. Association of rs6542095 at the IL1A locus with 'All' (p =.066) and 'Grade-B' (p =.01) endometriosis is noteworthy because this is the first successful replication in an independent population. Meta-analysis with the published results yields genome-wide significant evidence for rs7521902, rs13394619, rs6542095, rs12700667, rs7739264, and rs1537377. Notably, three coding variants in GREB1 (near rs13394619) and CDKN2B-AS1 (near rs1537377) also showed nominally significant associations with endometriosis. Overall, this study provides important replication in a uniquely characterized independent population, and indicates that the majority of the original genome-wide association findings are not due to chance alone. © The Author(s) 2015.

An elementary approach to gap theorems

Using elementary comparison geometry, we prove: Let (M, g) be a simply-connected complete Riemannian manifold of dimension >= 3. Suppose that the sectional curvature K satisfies -1-s(r) <= K <= -1, where r denotes distance to a fixed point in M. If lim(r ->infinity) e(2r) s(r) = 0, then (M, g) has to be isometric to H-n.The same proof also yields that if K satisfies -s(r) <= K <= 0 where lim(r ->infinity) r(2) s(r) = 0, then (M, g) is isometric to R-n, a result due to Greene and Wu.Our second result is a local one: Let (M, g) be any Riemannian manifold. For a E R, if K < a on a geodesic ball Bp (R) in M and K = a on partial derivative B-p (R), then K = a on B-p (R).

Polypharmacy among inpatients aged 70 years or older in Australia

Objectives To investigate medication changes for older patients admitted to hospital and to explore associations between patient characteristics and polypharmacy. Design Prospective cohort study. Participants and setting Patients aged 70 years or older admitted to general medical units of 11 acute care hospitals in two Australian states between July 2005 and May 2010. All patients were assessed using the interRAI assessment system for acute care. Main outcome measures Measures of physical, cognitive and psychosocial functioning; and number of regular prescribed medications categorised into three groups: non-polypharmacy (0–4 drugs), polypharmacy (5–9 drugs) and hyperpolypharmacy (≥ 10 drugs). Results Of 1220 patients who were recruited for the study, medication records at admission were available for 1216. Mean age was 81.3 years (SD, 6.8 years), and 659 patients (54.2%) were women. For the 1187 patients with complete medication records on admission and discharge, there was a small but statistically significant increase in mean number of regular medications per day between admission and discharge (7.1 v 7.6), while the prevalence of medications such as statins (459 [38.7%] v 457 [38.5%] patients), opioid analgesics (155 [13.1%] v 166 [14.0%] patients), antipsychotics (59 [5.0%] v 65 [5.5%] patients) and benzodiazepines (122 [10.3%] v 135 [11.4%] patients) did not change significantly. Being in a higher polypharmacy category was significantly associated with increase in comorbidities (odds ratio [OR], 1.27; 95% CI, 1.20–1.34), presence of pain (OR, 1.31; 1.05–1.64), dyspnoea (OR, 1.64; 1.30–2.07) and dependence in terms of instrumental activities of daily living (OR, 1.70; 1.20–2.41). Hyperpolypharmacy was observed in 290/1216 patients (23.8%) at admission and 336/1187 patients (28.3%) on discharge, and the proportion of preventive medication in the hyperpolypharmacy category at both points in time remained high (1209/3371 [35.9%] at admission v 1508/4117 [36.6%] at discharge). Conclusions Polypharmacy is common among older people admitted to general medical units of Australian hospitals, with no clinically meaningful change to the number or classification (symptom control, prevention or both) of drugs made by treating physicians.

Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations

Elevated serum uric acid levels cause gout and are a risk factor for cardiovascular disease and diabetes. To investigate the polygenetic basis of serum uric acid levels, we conducted a meta-analysis of genome-wide association scans from 14 studies totalling 28,141 participants of European descent, resulting in identification of 954 SNPs distributed across nine loci that exceeded the threshold of genome-wide significance, five of which are novel. Overall, the common variants associated with serum uric acid levels fall in the following nine regions: SLC2A9 (p = 5.2x10(-201)), ABCG2 (p = 3.1x10(-26)), SLC17A1 (p = 3.0x10(-14)), SLC22A11 (p = 6.7x10(-14)), SLC22A12 (p = 2.0x10(-9)), SLC16A9 (p = 1.1x10(-8)), GCKR (p = 1.4x10(-9)), LRRC16A (p = 8.5x10(-9)), and near PDZK1 (p = 2.7x10(-9)). Identified variants were analyzed for gender differences. We found that the minor allele for rs734553 in SLC2A9 has greater influence in lowering uric acid levels in women and the minor allele of rs2231142 in ABCG2 elevates uric acid levels more strongly in men compared to women. To further characterize the identified variants, we analyzed their association with a panel of metabolites. rs12356193 within SLC16A9 was associated with DL-carnitine (p = 4.0x10(-26)) and propionyl-L-carnitine (p = 5.0x10(-8)) concentrations, which in turn were associated with serum UA levels (p = 1.4x10(-57) and p = 8.1x10(-54), respectively), forming a triangle between SNP, metabolites, and UA levels. Taken together, these associations highlight additional pathways that are important in the regulation of serum uric acid levels and point toward novel potential targets for pharmacological intervention to prevent or treat hyperuricemia. In addition, these findings strongly support the hypothesis that transport proteins are key in regulating serum uric acid levels.

Campylobacter Infections of Domestic Origin in Finland

Campylobacter jejuni and C. coli are the leading causes of human bacterial gastroenteritis in developed countries. Most human Campylobacter infections are sporadic and a seasonal peak in the distribution of infections can be seen in the summer months in several countries, including Finland. A variety of risk factors for Campylobacter infections have been identified; handling and eating poultry, drinking unpasteurized milk, contact with domestic animals, and travelling abroad. However, the relative importance of the different risk factors in sporadic cases of Campylobacter infection remains unknown. In most cases, the infection is self-limiting and no specific treatment is required. Campylobacter enteritis can cause a wide range of complications, including reactive arthritis (ReA) that is reported in 1-5% of the cases. Seven clinical microbiology laboratories serving different geographical areas of Finland, participated in this multi-centre study, conducted during a seasonal peak in 2002. In a matched case-control study, domestically-acquired sporadic Campylobacter infections from three geographical areas were collected. The final study comprised 100 cases and 137 controls. Risk factors for sporadic domestically-acquired Campylobacter infections were identified on the basis of a questionnaire; swimming in natural waters was found to be a novel risk factor for Campylobacter infection. Other independent risk factors were tasting or eating raw or undercooked meat and drinking untreated water from a dug well. The role of bacterial strain and host characteristics are not fully understood in Campylobacter infections. Exposure factors, demographical characteristics, and the serotype of the Campylobacter isolate may affect the severity of the enteritis. This cross-sectional study comprised 114 patients with C. jejuni enteritis, diagnosed in three clinical microbiology laboratories; most of the patients had participated in the previous case-control study. Swimming was associated with age ≤ 5 years and serotype Pen 6,7 was found significantly more often among patients reporting swimming. The geographical distribution among serotypes varied; serotype Pen 4-complex appeared more often in patients from urban areas and serotype Pen 21 among patients from more rural areas. Thus, risk factors and sources of infection for C. jejuni infection may vary among individuals depending on age and geographical location. The in vitro susceptibilities of C. jejuni and C. coli strains isolated from patients infected abroad (85 strains) or domestically (393 strains) revealed that susceptibility to erythromycin is still high, even among isolates of foreign origin. However, the novel antimicrobial agent telithromycin did not offer any advantage over erythromycin; isolates with high minimal inhibitory concentrations (MICs) for erythromycin also showed reduced susceptibility to telithromycin. Reduced susceptibility to fluoroquinolones was detected almost exclusively among isolates of foreign origin and half of these isolates with high MICs for fluoroquinolones also showed elevated MICs for doxycycline. Questionnaires concerning complications associated with C. jejuni enteritis were sent to patients two months after becoming ill; 201 patients from seven different geographical areas were included in the study. Musculoskeletal complications after C. jejuni infection were commonly reported by patients (39%). The incidence of classical ReA was 4% and that of Achilles enthesopathy and/or heel pain 9%. Other C. jejuni-associated reactive joint symptoms were commonly reported, however, due to their milder nature seldom seen and diagnosed by a physician. The severity of the enteritis may predict further complications; stomach ache during enteritis was connected to the development of later joint pain. Early antimicrobial treatment, within two days from the start of symptoms, shortened the duration of diarrhoea by two days but did not prevent later musculoskeletal complications. Campylobacter is an important human enteropathogen and causes a significant burden of illness. As the incidence of Campylobacter infections is high, the importance of the infection and the occurrence of complications will increase. This stresses the importance of understanding the risk factors for acquiring Campylobacter infection and how bacterial strain and host characteristics may affect the risk for infection. The role of antimicrobial treatment for acute Campylobacter enteritis seems to be marginal and should be used restrictively.

A laminated anisotropic curved beam and shell stiffening finite element

The details of development of the stiffness matrix of a laminated anisotropic curved beam finite element are reported. It is a 16 dof element which makes use of 1-D first order Hermite interpolation polynomials for expressing it's assumed displacement state. The performance of the element is evaluated considering various examples for which analytical or other solutions are available.

Fungal Planet description sheets: 128-153

Novel species of microfungi described in the present study include the following from Australia: Catenulostroma corymbiae from Corymbia, Devriesia stirlingiae from Stirlingia, Penidiella carpentariae from Carpentaria, Phaeococcomyces eucalypti from Eucalyptus, Phialophora livistonae from Livistona, Phyllosticta aristolochiicola from Aristolochia, Clitopilus austroprunulus on sclerophyll forest litter of Eucalyptus regnans and Toxicocladosporium posoqueriae from Posoqueria. Several species are also described from South Africa, namely: Ceramothyrium podocarpi from Podocarpus, Cercospora chrysanthemoides from Chrysanthemoides, Devriesia shakazului from Aloe, Penidiella drakensbergensis from Protea, Strelitziana cliviae from Clivia and Zasmidium syzygii from Syzygium. Other species include Bipolaris microstegii from Microstegium and Synchaetomella acerina from Acer (USA), Brunneiapiospora austropalmicola from Rhopalostylis (New Zealand), Calonectria pentaseptata from Eucalyptus and Macadamia (Vietnam), Ceramothyrium melastoma from Melastoma (Indonesia), Collembolispora aristata from stream foam (Czech Republic), Devriesia imbrexigena from glazed decorative tiles (Portugal), Microcyclospora rhoicola from Rhus (Canada), Seiridium phylicae from Phylica (Tristan de Cunha, Inaccessible Island), Passalora lobeliaefistulosis from Lobelia (Brazil) and Zymoseptoria verkleyi from Poa (The Netherlands). Valsalnicola represents a new ascomycete genus from Alnus (Austria) and Parapenidiella a new hyphomycete genus from Eucalyptus (Australia). Morphological and culture characteristics along with ITS DNA barcodes are also provided. © 2012 Nationaal Herbarium Nederland & Centraalbureau voor Schimmelcultures.

Genera of fungivorous Phlaeothripinae (Thysanoptera) from dead branches and leaf-litter in Australia

An illustrated key is provided for the identification of 39 genera of Thysanoptera-Phlaeothripinae with species that live in association with dead branches and leaf-litter in Australia and are considered to be fungus-feeding. Seven of these gen-era are not previously recorded from this continent, including un-named species of Deplorothrips, Malacothrips, Mystro-thrips, Preeriella and Tylothrips, together with Azaleothrips lepidus Okajima and Terthrothrips ananthakrishnani Kudo. A brief generic diagnosis is provided for each genus, together with comments on systematic problems and numbers of species. Copyright © 2013 Magnolia Press.

Development and preliminary validation of the Drinking Expectancy Sexual Vulnerabilities Questionnaire (DESV-Q): A purpose-specific instrument for rape-perception research

Background Alcohol expectancies likely play a role in people’s perceptions of alcohol-involved sexual violence. However, no appropriate measure exists to examine this link comprehensively. Objective The aim of this research was to develop an alcohol expectancy measure which captures young adults’ beliefs about alcohol’s role in sexual aggression and victimization. Method Two cross-sectional samples of young Australian adults (18–25 years) were recruited for scale development (Phase 1) and scale validation (Phase 2). In Phase 1, participants (N = 201; 38.3% males) completed an online survey with an initial pool of alcohol expectancy items stated in terms of three targets (self, men, women) to identify the scale’s factor structure and most effective items. A revised alcohol expectancy scale was then administered online to 322 young adults (39.6% males) in Phase 2. To assess the predictive, convergent, and discriminant validity of the scale, participants also completed established measures of personality, social desirability, alcohol use, general and context-specific alcohol expectancies, and impulsiveness. Results Principal axis factoring (Phase 1) and confirmatory factor analysis (Phase 2) resulted in a target-equivalent five-factor structure for the final 66-item Drinking Expectancy Sexual Vulnerabilities Questionnaire (DESV-Q). The factors were labeled: - (1) Sexual Coercion - (2) Sexual Vulnerability - (3) Confidence - (4) Self-Centeredness - (5) Negative Cognitive and Behavioral Changes The measure demonstrated effective items, high internal consistency, and satisfactory predictive, convergent, and discriminant validity. Conclusions The DESV-Q is a purpose-specific instrument that could be used in future research to elucidate people’s attributions for alcohol-involved sexual aggression and victimization.

Crinkles in connectivity: combining genetics and other types of biological data to estimate movement and interbreeding between populations

Marine species generally have large population sizes, continuous distributions and high dispersal capacity. Despite this, they are often subdivided into separate populations, which are the basic units of fisheries management. For example, populations of some fisheries species across the deep water of the Timor Trench are genetically different, inferring minimal movement and interbreeding. When connectivity is higher than the Timor Trench example, but not so high that the populations become one, connectivity between populations is crinkled. Crinkled connectivity occurs when migration is above the threshold required to link populations genetically, but below the threshold for demographic links. In future, genetic estimates of connectivity over crinkled links could be uniquely combined with other data, such as estimates of population size and tagging and tracking data, to quantify demographic connectedness between these types of populations. Elasmobranch species may be ideal targets for this research because connectivity between populations is more likely to be crinkled than for finfish species. Fisheries stock-assessment models could be strengthened with estimates of connectivity to improve the strategic and sustainable harvesting of biological resources.

Emotional climate of a pre-service science teacher education class in Bhutan

This study explored pre-service secondary science teachers’ perceptions of classroom emotional climate in the context of the Bhutanese macro-social policy of Gross National Happiness. Drawing upon sociological perspectives of human emotions and using Interaction Ritual Theory this study investigated how pre-service science teachers may be supported in their professional development. It was a multi-method study involving video and audio recordings of teaching episodes supported by interviews and the researcher’s diary. Students also registered their perceptions of the emotional climate of their classroom at 3-minute intervals using audience response technology. In this way, emotional events were identified for video analysis. The findings of this study highlighted that the activities pre-service teachers engaged in matter to them. Positive emotional climate was identified in activities involving students’ presentations using video clips and models, coteaching, and interactive whole class discussions. Decreases in emotional climate were identified during formal lectures and when unprepared presenters led presentations. Emotions such as frustration and disappointment characterized classes with negative emotional climate. The enabling conditions to sustain a positive emotional climate are identified. Implications for sustaining macro-social policy about Gross National Happiness are considered in light of the climate that develops in science teacher education classes.

Some empirical evidence on offender time discount rates

The conventional wisdom is that offenders have very high discount rates not only with respect to income and fines but also with respect to time incarcerated. These rates are difficult to measure objectively and the usual approach is to ask subjects hypothetical questions and infer time preference from their answers. In this article, we propose estimating rates at which offenders discount time incarcerated by specifying their equilibrium plea, defined as the discount rate, which equates the time and expected time spent in jail following a guilty plea and a trial. Offenders are assumed to exhibit positive time preference and discount time spent in jail at a constant rate. Our choice of sample is interesting because the offenders are not on bail, punishment is not delayed and the offences are planned therefore conforming to Becker’s model of the decision to commit a crime. Contrary to the discussion in the literature, we do not find evidence of consistently high time discount rates, and therefore cannot unequivocally infer that the prison experience always results in low levels of specific deterrence.